Single-cell transcriptomes of the entire adult Drosophila

During 2020 and 2021, the FCA consortium ran a collaborative effort with CZ Biohub, Genentech, and NIH, to sequence all cells of the adult fly. Driven by Hongjie Li and Liqun Luo, along with dozens of Drosophila labs in the Bay area, 15 tissues were dissected for single-nucleus RNA-seq, alongside the whole head and body. Data analysis teams in Leuven (Aerts) and EPFL (Deplancke) analyzed all data, and through >20 online jamborees with >40 Drosophila labs around the world, more than 250 single-cell clusters were annotated with FlyBase FBbt terms. The data is now available via two portals, namely SCope and ASAP, and can be downloaded as loomX and h5ad files to be further analyzed in R or Python.

Paper

Publication is available on:
Preprint is available on:

Data Portals

Tissues

Hereunder are the main tissue datasets used for the Fly Cell Atlas paper

Head

Head
Data
Platforms

Body

Body
Data
Platforms

Antenna

Antenna
Data
Platforms

Body wall

Body wall
Data
Platforms

Fatbody

Fatbody
Data
Platforms

Gut

Gut
Data
Platforms

Haltere

Haltere
Data
Platforms

Heart

Heart
Data
Platforms

Leg

Leg
Data
Platforms

Male reproductive glands

Male reproductive glands
Data
Platforms

Malpighian tubule

Malpighian tubule
Data
Platforms

Oenocyte

Oenocyte
Data
Platforms

Ovary

Ovary
Data
Platforms

Proboscis

Proboscis
Data
Platforms

Testis

Testis
Data
Platforms

Trachea

Trachea
Data
Platforms

Wing

Wing
Data
Platforms

Data

Table hereunder contains all the different analyses performed. This includes:

  • The datasets from different technologies (10x Genomics and SMART-seq2) integrated by tissue
  • The 2 versions (relaxed and stringent) of the datasets generated from the 10x data.
  • The datasets from different technologies (10x and SMART-seq2) analyzed seperately (by technology and tissue)
  • The broad annotations (i.e. cross-tissue) datasets generated from the 10x data (stringent version)


Analysis Technology Tissue(s) Age (d) Sex Num. Samples Version Loom H5AD SCope ASAP
10x VSN All (Stringent) 10x Genomics All 5 Mix (50:50) 61 Stringent Loom H5AD SCope ASAP
10x VSN Body (Stringent) 10x Genomics Body 5 Mix (50:50) 13 Stringent Loom H5AD SCope ASAP
10x VSN Head (Stringent) 10x Genomics Head 5 Mix (50:50) 13 Stringent Loom H5AD SCope ASAP
10x VSN Antenna (Stringent) 10x Genomics Antenna 5 Mix (50:50) 5 Stringent Loom H5AD SCope ASAP
10x VSN Body Wall (Stringent) 10x Genomics Body Wall 5 Mix (50:50) 2 Stringent Loom H5AD SCope ASAP
10x VSN Fat Body (Stringent) 10x Genomics Fat Body 3 Mix (50:50) 2 Stringent Loom H5AD SCope ASAP
10x VSN Gut (Stringent) 10x Genomics Gut 5 Mix (50:50) 2 Stringent Loom H5AD SCope ASAP
10x VSN Haltere (Stringent) 10x Genomics Haltere 5 Mix (50:50) 2 Stringent Loom H5AD SCope ASAP
10x VSN Heart (Stringent) 10x Genomics Heart 5 Mix (50:50) 2 Stringent Loom H5AD SCope ASAP
10x VSN Leg (Stringent) 10x Genomics Leg 5 Mix (50:50) 2 Stringent Loom H5AD SCope ASAP
10x VSN Male Reproductive Glands (Stringent) 10x Genomics Male Reproductive Glands 2 Male 1 Stringent Loom H5AD SCope ASAP
10x VSN Malpighian Tubule (Stringent) 10x Genomics Malpighian Tubule 5 Mix (50:50) 2 Stringent Loom H5AD SCope ASAP
10x VSN Oenocyte (Stringent) 10x Genomics Oenocyte 5 Mix (50:50) 2 Stringent Loom H5AD SCope ASAP
10x VSN Ovary (Stringent) 10x Genomics Ovary 5 Female 2 Stringent Loom H5AD SCope ASAP
10x VSN Proboscis and Maxillary Palps (Stringent) 10x Genomics Proboscis and Maxillary Palps 5 Mix (50:50) 4 Stringent Loom H5AD SCope ASAP
10x VSN Testis (Stringent) 10x Genomics Testis 1 Male 3 Stringent Loom H5AD SCope ASAP
10x VSN Trachea (Stringent) 10x Genomics Trachea 5 Mix (50:50) 2 Stringent Loom H5AD SCope ASAP
10x VSN Wing (Stringent) 10x Genomics Wing 5 Mix (50:50) 2 Stringent Loom H5AD SCope ASAP
10x VSN All (Relaxed) 10x Genomics All 5 Mix (50:50) 61 Relaxed Loom H5AD SCope ASAP
10x VSN Body (Relaxed) 10x Genomics Body 5 Mix (50:50) 13 Relaxed Loom H5AD SCope ASAP
10x VSN Head (Relaxed) 10x Genomics Head 5 Mix (50:50) 13 Relaxed Loom H5AD SCope ASAP
10x VSN Antenna (Relaxed) 10x Genomics Antenna 5 Mix (50:50) 5 Relaxed Loom H5AD SCope ASAP
10x VSN Body Wall (Relaxed) 10x Genomics Body Wall 5 Mix (50:50) 2 Relaxed Loom H5AD SCope ASAP
10x VSN Fat Body (Relaxed) 10x Genomics Fat Body 3 Mix (50:50) 2 Relaxed Loom H5AD SCope ASAP
10x VSN Gut (Relaxed) 10x Genomics Gut 5 Mix (50:50) 2 Relaxed Loom H5AD SCope ASAP
10x VSN Haltere (Relaxed) 10x Genomics Haltere 5 Mix (50:50) 2 Relaxed Loom H5AD SCope ASAP
10x VSN Heart (Relaxed) 10x Genomics Heart 5 Mix (50:50) 2 Relaxed Loom H5AD SCope ASAP
10x VSN Leg (Relaxed) 10x Genomics Leg 5 Mix (50:50) 2 Relaxed Loom H5AD SCope ASAP
10x VSN Male Reproductive Glands (Relaxed) 10x Genomics Male Reproductive Glands 2 Male 1 Relaxed Loom H5AD SCope ASAP
10x VSN Malpighian Tubule (Relaxed) 10x Genomics Malpighian Tubule 5 Mix (50:50) 2 Relaxed Loom H5AD SCope ASAP
10x VSN Oenocyte (Relaxed) 10x Genomics Oenocyte 5 Mix (50:50) 2 Relaxed Loom H5AD SCope ASAP
10x VSN Ovary (Relaxed) 10x Genomics Ovary 5 Female 2 Relaxed Loom H5AD SCope ASAP
10x VSN Proboscis and Maxillary Palps (Relaxed) 10x Genomics Proboscis and Maxillary Palps 5 Mix (50:50) 4 Relaxed Loom H5AD SCope ASAP
10x VSN Testis (Relaxed) 10x Genomics Testis 1 Male 3 Relaxed Loom H5AD SCope ASAP
10x VSN Trachea (Relaxed) 10x Genomics Trachea 5 Mix (50:50) 2 Relaxed Loom H5AD SCope ASAP
10x VSN Wing (Relaxed) 10x Genomics Wing 5 Mix (50:50) 2 Relaxed Loom H5AD SCope ASAP
SMART-seq2 Scanpy Antenna SMART-seq2 Antenna 5 Mix (50:50) 2 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Body Wall SMART-seq2 Body Wall 5 Mix (50:50) 2 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Fat Body SMART-seq2 Fat Body 3 Mix (50:50) 4 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Gut SMART-seq2 Gut 5 Mix (50:50) 2 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Haltere SMART-seq2 Haltere 5 Mix (50:50) 2 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Heart SMART-seq2 Heart 5 Mix (50:50) 2 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Leg SMART-seq2 Leg 5 Mix (50:50) 2 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Male Reproductive Glands SMART-seq2 Male Reproductive Glands 2 Male 1 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Malpighian Tubule SMART-seq2 Malpighian Tubule 5 Mix (50:50) 2 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Oenocyte SMART-seq2 Oenocyte 5 Mix (50:50) 2 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Ovary SMART-seq2 Ovary 5 Female 2 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Proboscis and Maxillary Palps SMART-seq2 Proboscis and Maxillary Palps 5 Mix (50:50) 2 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Testis SMART-seq2 Testis 1 Male 1 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Trachea SMART-seq2 Trachea 5 Mix (50:50) 2 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy Wing SMART-seq2 Wing 5 Mix (50:50) 2 n.a. Loom H5AD SCope ASAP
SMART-seq2 Scanpy dilp2IPC SMART-seq2 dilp2IPC 5 Mix (50:50) 2 n.a. n.a. H5AD n.a. n.a.
SMART-seq2 Scanpy akhCC SMART-seq2 akhCC 5 Mix (50:50) 2 n.a. n.a. H5AD n.a. n.a.
10x and SMART-seq2 Integrated Antenna 10x Genomics and SMART-seq2 Antenna 5 Mix (50:50) 5+2 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Body Wall 10x Genomics and SMART-seq2 Body Wall 5 Mix (50:50) 2+2 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Fat Body 10x Genomics and SMART-seq2 Fat Body 3 Mix (50:50) 2+4 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Gut 10x Genomics and SMART-seq2 Gut 5 Mix (50:50) 2+2 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Haltere 10x Genomics and SMART-seq2 Haltere 5 Mix (50:50) 2+2 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Heart 10x Genomics and SMART-seq2 Heart 5 Mix (50:50) 2+2 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Leg 10x Genomics and SMART-seq2 Leg 5 Mix (50:50) 2+2 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Male Reproductive Glands 10x Genomics and SMART-seq2 Male Reproductive Glands 2 Male 1+1 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Malpighian Tubule 10x Genomics and SMART-seq2 Malpighian Tubule 5 Mix (50:50) 2+2 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Oenocyte 10x Genomics and SMART-seq2 Oenocyte 5 Mix (50:50) 2+2 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Ovary 10x Genomics and SMART-seq2 Ovary 5 Female 2+2 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Proboscis and Maxillary Palps 10x Genomics and SMART-seq2 Proboscis and Maxillary Palps 5 Mix (50:50) 2+2 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Testis 10x Genomics and SMART-seq2 Testis 1 Male 3+1 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Trachea 10x Genomics and SMART-seq2 Trachea 5 Mix (50:50) 2+2 n.a. Loom H5AD SCope n.a.
10x and SMART-seq2 Integrated Wing 10x Genomics and SMART-seq2 Wing 5 Mix (50:50) 2+2 n.a. Loom H5AD SCope n.a.
10x Adipose System (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Cardial Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Epithelial Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Excretory System (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Female Germline Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Female Reproductive System (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Germline Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Gland (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Glial Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Gut Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Hemocyte (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Male Germline Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Male Reproductive System (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Muscle Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Neuron (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Neuron and Sensory Organ Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Oenocyte (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Pigment Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Sensory Organ Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Stem Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.
10x Tracheal Cell (Stringent) 10x Genomics Cross-tissue n.a. Mix n.a. Stringent Loom H5AD SCope n.a.

Raw Data

  • The 10x Genomics raw data is available at ArrayExpress: E-MTAB-10519
  • The SMART-seq2 raw data is available at ArrayExpress: E-MTAB-10628

Code & Software

Code for processing the 10x Genomics data are available at FlyCellAtlas data_processing GitHub repository. Code is available as Nextflow config files since VSN-Pipelines was used to process the data from raw FASTQ files to Loom/h5ad files. Data processing has been divided into 3 parts:
  • Part 1: where index hopping filter and the mapping were performed
  • Part 2: Ambient RNA contamination removal (only in stringent version) and doublet removal
  • Part 3: Classical single RNA pipeline processing steps: gene/cell filtering, normalization, feature selection, dimensionality reduction, clustering.
10x Genomics data was powered by the VSN-Pipelines (processing based on Scanpy)
SMART-seq2 data analysis was powered by the Scanpy Python package.

Submitting new cell type annotations

To annotate new clusters in the FCA, or update any existing annotation, researchers can follow the steps below:
  • From the FlyCellAtlas SCope session, download the loom file of the tissue under study.
  • Re-upload the same file to a new SCope session (to create a new session, just click on the "Get new session" button at the top right corner of SCope.
  • Next, the user can follow the annotation tutorial to annotate new cell types.
  • These annotations can then be extracted from the loom file and sent to FlyBase along with some additional information like the tissue and the loom file name. This requires the user to download the loom file and generate the cell-based annotations table using the get_all_clustering_annotationsfunction from the SCopeLoomR (>= v0.13.0) R package (tutorial is available here, see section Get all newly added annotations by ORCID).
Alternatively, until the new SCope-v2 is in production, the ID (URL) of the user's session and the loom file with new annotations can currently be sent to fca@flycellatlas.org, and we can extract the new annotations to be sent to FlyBase.

Meetings

Follow us on Twitter to stay up-to-date on upcoming meetings.

  • Single-cell Research in Drosophila: The Fly Cell Atlas and Beyond

    March 31. 2021

    A workshop in conjunction with the 62th annual US Drosophila Research Conference.

    Organizers: Hongjie Li (Baylor), Lucy Erin O'Brien (Stanford), Brian Oliver (NIH), Norbert Perrimon (Harvard).

    FCA workshop March 2021 program.

  • Fly Cell Atlas meeting 2021

    April. 2021 FCA3 meeting

    FCA3 meeting on 29-30 April 2021, MDC Berlin.

  • Fly Cell Atlas workshop 2019

    Sep. 2019 EDRC meeting

    FCA organized a workshop on Single cell approaches in Drosophila research at the EDRC in Lausanne, on Thursday, September 5th.

  • Biohub meeting 2019

    Aug. 2019 Biohub meeting

    CZ Biohub meeting 2019 organised by Liqun Luo to discuss collaboritive data generation. The meeting took place on Thursday, August 29th (8-11am (Pacific time)).

  • Fly Cell Atlas 2019

    Mar. 2019 FCA meeting

    The second Fly Cell Atlas meeting was held at Janelia Farm, March 24-26 2019.

    Download Fly Cell Atlas meeting 2019 progam.

  • Fly Cell Atlas 2017

    Dec. 2017 FCA meeting

    The first Fly Cell Atlas meeting was held at the Gasthuisberg campus of the University of Leuven (Belgium) on December 8th 2017.

    Download Fly Cell Atlas meeting 2017 progam.

Fly Cell Atlas Consortium

Contributors

FCA Consortium

Founders

  • Stein Aerts
  • Bart Deplancke
  • Robert Zinzen

Steering Committee 2020-2021

Bart Deplancke

Bart Deplancke

Website

Norbert Perrimon

Norbert Perrimon

Website

Stephen Quake

Stephen Quake

Website

Liqun Luo

Liqun Luo

Website

Stein Aerts

Stein Aerts

Website