GSE237204 - RetinaEvolutionHumanHahn

[arschat]

part of Retina Atlas v1.0

Project short name:

RetinaEvolutionHumanHahn

Primary Wrangler:

Ida

Secondary Wrangler:

Arsenios

Associated files

• Google Drive: folder
• ingest: c3dd819d-abab-4957-b209-88f1e0900368

Published study links

• Paper: Evolution of neuronal cell classes and types in the vertebrate retina
• Accessioned data: GSE237204 - human data

Key Events

• Convert published metadata to HCA spreadsheet
• Manually curate dataset to meet HCA metadata standard
• Collect any matrix and cell-type annotation files
• Are the analysis files suitable for CellxGene? If something is missing get in touch with the authors to request it
• Upload sheet to validate metadata
• Transfer raw files to ingest to validate data files
• Check linking using ingest graph validator
• Ask the Secondary Wrangler for an end-to-end review of the project. Ask the Expertise Wrangler to review specific tabs if needed
• Submit dataset to Production
• Complete the Export SOP
• Convert project data to SCEA format following the SCEA conversion SOP if appropriate

[idazucchi]

Donor
I didn't find any donor metadata, the only metadata available is about samples here
The paper says there are 18 donors so I grouped the samples based on their names

We also profiled around 185,000 nuclei from 18 human donors, thereby allowing us to identify over 30 more cell types than had been detected in the dataset analysed previously

for developmental stage no information is available so I've used human life cycle - if you have better suggestions I'm happy to hear them

Sample
About sample Hu218OSmAll - the sample key says it's mac_neun-_218 but this sample is absent in extended data Fig1 - instead there is mac_all_218
I think mac_neun-_218 is a mistake and the sample is not enriched

[arschat]

Hi Ida! There were very limited metadata available but you've done a nice job.
I only have two suggestions and one comment.

Project

• abstract you can remove the reference numbers

Analysis protocol

• intron_inclusion you could fill yes here

  To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding.bam files. This generated two separate gene expression matrices (GEMs) (genes × cells) for each sample, corresponding to ‘spliced’ and ‘unspliced’ reads.

Analysis file

• input biomaterials Each of the 4 files, should have different input. If you open the count matrices the cell index includes the sample_ID. I've removed the UMI and the duplicates

sample_id extraction

for file in GSE237204*; do echo $file; zcat < $file | head -1 | sed 's/\,/\n/g' | sed 's/.\{18\}$//' | sort | uniq; done

GSE237204_Human_count_mat_1.csv.gz

Hu032616OD_macula_NeuNPos.possorted_genome_bam_PNH7N
Hu035516OS_macula_NeuNPosS1.possorted_genome_bam_TXN7J
Hu035516OS_macula_NeuNPosS2.possorted_genome_bam_D2QGV
Hu035516OS_macula_NeuNPosS2.possorted_genome_bam_PNH7N
Hu056316OD_macula_NeuNPos.possorted_genome_bam_M7UFG
Hu056416OS_macula_NeuNPos.possorted_genome_bam_RCC8P
Hu082219_macular_All.possorted_genome_bam_M28FQ
Hu086916OD_macula_NeuNPos.possorted_genome_bam_VL2TA

GSE237204_Human_count_mat_2.csv.gz

Hu086916OD_macula_NeuNPos.possorted_genome_bam_VL2TA
Hu088716OS_macula_NeuNPos.possorted_genome_bam_2L1A9
Hu105916OD_macula_NeuNPos.possorted_genome_bam_C9Z7N
Hu218OSPeriRetina.possorted_genome_bam_WYD8B
Hu218OSmAll.possorted_genome_bam_DGNOI
Hu218OSmRGC.possorted_genome_bam_Q49J3

GSE237204_Human_count_mat_3.csv.gz

Hu218OSPeriRetina.possorted_genome_bam_WYD8B
Hu220235OSmAll.possorted_genome_bam_V6O4A
Hu220OSPeriRetina.possorted_genome_bam_L340L
Hu220OSmRGC.possorted_genome_bam_Z9VX3
Hu235OSPeriRetina.possorted_genome_bam_3URIL
Hu235OSmRGC.possorted_genome_bam_W3LJK
HuCMixS1.possorted_genome_bam_B7X1A

GSE237204_Human_count_mat_4.csv.gz

HuCMixS1.possorted_genome_bam_B7X1A
HuCMixS2.possorted_genome_bam_HGXY1
HuPRet1059fc564mc.possorted_genome_bam_56BDZ
HuPRet326mc355fc.possorted_genome_bam_RJJ6M
HuPRet563mc.possorted_genome_bam_PYRF4
HuPRet887mc869fc.possorted_genome_bam_CHBYN

CS assignment

GSE237204_Human_count_mat_1.csv.gz -> Hu032616OD_macula_NeuNPos||Hu035516OS_macula_NeuNPosS1||Hu035516OS_macula_NeuNPosS2||Hu056316OD_macula_NeuNPos||Hu056416OS_macula_NeuNPos||Hu082219_macular_All||Hu086916OD_macula_NeuNPos

GSE237204_Human_count_mat_2.csv.gz -> Hu086916OD_macula_NeuNPos||Hu088716OS_macula_NeuNPos||Hu105916OD_macula_NeuNPos||Hu218OSPeriRetina||Hu218OSmAll||Hu218OSmRGC

GSE237204_Human_count_mat_3.csv.gz -> Hu218OSPeriRetina||Hu220235OSmAll||Hu220OSPeriRetina||Hu220OSmRGC||Hu235OSPeriRetina||Hu235OSmRGC||HuCMixS1

GSE237204_Human_count_mat_4.csv.gz -> HuCMixS1||HuCMixS2||HuPRet1059fc564mc||HuPRet326mc355fc||HuPRet563mc||HuPRet887mc869fc

[idazucchi]

fixed the issues and tried to export but the dataset is stuck on export

[idazucchi]

Enrique restarted the export and it worked - I've filled in the import form