title: scRNA-seq - germ cell AR2778 [HHHNYBBXY_3_IDT-DUI-NXT-133]

description: scRNA-seq - germ cell AR2778


title: Volunteer G3CGE Sample D40G

status: Public on Apr 04 2022

type: protein

city: Irvine

first: Rafael

last: de Assis

state: CA

address: 3800 PARKVIEW LN APT 38A, Irvine, CA 92612

country: USA

institute: University of California Irvine

hyb_protocol: Antibodies were detected using Qdot (Q800) -conjugated anti-human IgG

scan_protocol: Slides were imaged using the ArrayCam system (https://gracebio.com/) for 300ms and images processed using ScanArray Express.

data_processing:
Raw data was normalized by re-scaling based on the positive control spots as descibed by Duarte J. 2013; Causton 2004 and Bolstad 2003
processed.xls: Normalized signal Intensity

molecule: protein

organism: Homo sapiens

source_name: Sera

label_protocol: No labeling

extract_protocol: Sera samples were extracted from finger pricks using a lancet and collected by capilary. Sera was then separated from the blood cells by centrifugation.

tag: volunteer id

tag: age

tag: gender

value: Female

tag: ethnicity

value: White

tag: job/role

value: Nurse

tag: first vaccination

tag: second vaccination

tag: vaccine

value: Pfizer

tag: days since vaccine


title: Volunteer B33GB Sample D34D

value: Other


title: scRNA-seq - germ cell AR2857 [HHHNYBBXY_3_IDT-DUI-NXT-131]

type: SRA

city: Barcelona

first: Moritz

last: Bauer

address: C/ Dr. Aiguader, 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Centre for Genomic Regulation

description: scRNA-seq - germ cell AR2857

library_source: transcriptomic

data_processing:
For bulk RNA-seq, fastQ files that passed quality control were aligned to the mm10 reference genome containing CAST/EiJ and 129S1/SvImJ SNPs positions masked. The positions of all 36 mouse strains SNPs were downloaded from ftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi.  From here, we generated a VCF file containing only the SNPs information for the strains of interest, CAST/EiJ and 29S1/SvImJ. Reads were then aligned using STAR (Dobin et al. 2013) implementing the WASP method (van de Geijn et al. 2015) for filtering of allele specific alignments. The generated bam files were used for counting reads using the HTseq tool (v0.6.1) (Anders, Pyl, and Huber 2015). All of the steps above were performed using a customized Nextflow pipeline (Di Tommaso et al. 2017). We obtained between 50*106 and 75*106 reads. Coherence between samples, time points and replicates was verified by principal component analysis (PCA). Batch effects in principal component analysis (PCA) were corrected using the R package limma (Ritchie et al. 2015). Differential expression analysis was performed using the R package DESeq2 (v1.16) (Love, Huber, and Anders 2014). Briefly, differentially expressed genes were called by comparing XGFP+ PGCLCs and XGFP- PGCLCs or XGFP+ PGCLCs to ESCs. The DESeqDataSet (dds) was generated considering the dataset in its entirety while the DEseq analysis was conducted on dataset filtered as follows: Read counts were normalized by library size using estimateSizeFactors, were filtered for having a mean across the samples >10 (a more stringent cut off than the sum across the samples >10 ) and poorly annotated genes on chromosomal patches were removed. The resulting 17089 genes were kept for downstream analysis. Log2 fold change was shrinked using the “normal” parameter.
For single-cell RNA-Seq, reads were disambiguated and mapped as explained above. Reads were log-normalized using the R package Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of non-allelic normalized expression counts of bulk and single-cell data
Supplementary_files_format_and_content: tab-delimited text file of allelic-ratio of bulk and single-cell data from chromosome X

molecule: total RNA

organism: Mus musculus

source_name: germ cell

growth_protocol: Embryonic Stem Cells (ESCs) were maintained and expanded on 0.2% gelatin-coated dishes in DMEM (Thermo Fisher Scientific, 31966021) supplemented with 10% Fetal Bovine Serum (FBS) (ES-qualified, Thermo Fisher Scientific, 16141079), 1,000 U/ml LIF (ORF Genetics, 01-A1140-0100), 1 mM Sodium Pyruvate (Thermo Fisher Scientific, 11360070), 1x MEM Non-Essential Amino Acids Solution (Thermo Fisher Scientific, 11140050), 50 U/ml penicillin/streptomycin (Ibian Tech, P06-07100) and 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific, 31350010). Cells were cultured at 37°C with 5% CO2. Medium was changed every day and cells were passaged using 0.05% Trypsin-EDTA (Thermo Fisher Scientific, 25300054) and quenched 1:5 in DMEM supplemented with 10% FBS (Life Technologies, 10270106). Cells were monthly tested for mycoplasma contamination by PCR.

extract_protocol:
Cells were dissociated using 0.05% Trypsin-EDTA (Thermo Fisher Scientific, 25300054) and then for PGCLCs additionally stained with SSEA-1 eFluor 660 (Thermo Fisher Scientific, 50-8813-42) and CD61-PE-Vio770 (Miltenyi Biotec, 130-102-627) for 1h at 4°C. Cells were washed once with 0.5% BSA in PBS and then FACS sorted using a BD FACSAria II SORP or a BD Influx using a 100 um nozzle.  RNA was extracted using phenol-chloroform (Sigma Aldrich, P2069) followed by ethanol precipitation or directly lysed in SMART-seq2 buffer for single-cell sequencing.
Bulk total RNA-Seq libraries were prepared using the TruSeq Stranded Total RNA Library Preparation Kit (Illumina, 20020597) followed by paired-end sequencing (2 x 125 bp) on an Illumina HiSeq 2500. Single-cell RNA-seq libraries were prepared using an updated SMART-seq2 protocol with paired-end sequencing (2 x 100 bp) on an Illumina HiSeq 2500.
Bulk libraries were sequence in paired-end (2 x 125 nt) on an Illumina HiSeq 2500. Single-cell libraries in paired-end (2 x 100 nt) on an Illumina HiSeq 2500.

treatment_protocol: Epiblast-like cell and primordial germ cell-like cell induction: ESCs were induced into primordial germ cell-like cells (PGCLCs) as described previously (Katsuhiko Hayashi and Saitou 2013) with the following modifications: ESCs were thawed on 0.2% gelatin in serum/LIF and after 24h seeded at a density of 0.6 x105 cells/cm2 in 2i/LIF medium on a dish coated with 0.01% poly-L-ornithine (Sigma-Aldrich, P3655) and 500 ng/ml laminin (Corning, 354232). 24h later, ESCs were dissociated with TrypLE Express for 5 mins at 37°C and induced into EpiLCs. After 48h, EpiLCs were split using TrypLE Express (Life Technologies 12604013) and re-seeded at 0.2 x 105 cells/cm2 on 16.7 µg/ml human plasma fibronectin coated plates (Merck Millipore, FC010). After an additional 48h, EpiLCs were aggregated in U-bottom 96-well Lipidure-Coat plate (Thermo Fisher Scientific, 81100525) at 2,000 cells per aggregate in GK15 medium (GMEM (Life Technologies, 11710035), 15% KnockOut Serum Replacement (KSR) (Thermo Fisher, 10828028), 0.1 mM nonessential amino acids (NEAA) (Thermo Fisher Scientific, 11140050), 1 mM sodium pyruvate (Thermo Fisher Scientific, 11360), 2 mM GLutamax (Life Technologies, 35050061), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific, 21985-023), and 100 U/ml penicillin and 0.1 mg/ml streptomycin (Thermo Fisher Scientific, 15140) with 1.5 µg/ml doxycycline (Tocris, 4090/50) for 5 days. Reconstituted ovaries (rOvaries) usd for scRNAseq were generated as follows: 5,000 sorted SSEA1+/CD61+ PGCLCs XGFP- or XGFP+ were mixed with 75,000 freshly thawed E13.5 female somatic gonadal cells (SSEA1- /CD31-) and cultured in Lipidure-Coat plate at 37°C in a 5% CO2 incubator for 6 days.

tag: strain

value: hybrid 129S1/SvImJ, CAST/EiJ

tag: cell type

value: germ cell

tag: cell population

value: from PGCLC d5 XGFP-; XGFP-, Xtomato+


title: scRNA-seq - germ cell AR2536 [HHHNYBBXY_3_IDT-DUI-NXT-13]

description: scRNA-seq - germ cell AR2536

value: from PGCLC d5 XGFP-; XGFP+, Xtomato+


title: scRNA-seq - germ cell AR2841 [HHHNYBBXY_3_IDT-DUI-NXT-129]

description: scRNA-seq - germ cell AR2841


title: scRNA-seq - germ cell AR2833 [HHHNYBBXY_3_IDT-DUI-NXT-128]

description: scRNA-seq - germ cell AR2833

value: from PGCLC d5 XGFP-; XGFPint., Xtomato+


title: Volunteer A4A0B Sample D333

value: Physician


title: Volunteer ECFFA Sample D33F

value: ECFFA

value: Latino

value: Food/EVS


title: Volunteer A4EA0 Sample D330

value: Asian


title: Volunteer GFD3E Sample DDC4

value: Not reported

value: Student


title: Volunteer ABC3F Sample D3EB

value: Female

value: Clinical staff


title: scRNA-seq - germ cell AR2801 [HHHNYBBXY_3_IDT-DUI-NXT-124]

description: scRNA-seq - germ cell AR2801


title: scRNA-seq - germ cell AR2809 [HHHNYBBXY_3_IDT-DUI-NXT-125]

description: scRNA-seq - germ cell AR2809


title: Volunteer EC4B0 Sample D30G

value: Male


title: Volunteer GE0EF Sample DCBB

value: Administrative


title: scRNA-seq - germ cell AR2825 [HHHNYBBXY_3_IDT-DUI-NXT-127]

description: scRNA-seq - germ cell AR2825


title: Volunteer GF4B4 Sample DD0C

value: Other


title: scRNA-seq - germ cell AR2793 [HHHNYBBXY_3_IDT-DUI-NXT-123]

description: scRNA-seq - germ cell AR2793

value: hybrid 129S1/SvImJ, CAST/EiJ


title: scRNA-seq - germ cell AR2785 [HHHNYBBXY_3_IDT-DUI-NXT-122]

description: scRNA-seq - germ cell AR2785

value: germ cell


title: Volunteer A4GB0 Sample D3GD

value: Nurse


title: Volunteer FECDB Sample DC3F

value: FECDB

value: White


title: Volunteer EAF3F Sample DCA4

value: Moderna


title: scRNA-seq - germ cell AR2615 [HHHNYBBXY_3_IDT-DUI-NXT-11]

description: scRNA-seq - germ cell AR2615

value: from PGCLC d5 XGFP-; XGFP-, Xtomato+


title: Volunteer GCAAG Sample DCEB

value: GCAAG


title: scRNA-seq - germ cell AR2817 [HHHNYBBXY_3_IDT-DUI-NXT-126]

description: scRNA-seq - germ cell AR2817

value: from PGCLC d5 XGFP-; XGFPint., Xtomato+


title: Volunteer A3GA4 Sample 3CB0

value: Asian


title: scRNA-seq - germ cell AR2777 [HHHNYBBXY_3_IDT-DUI-NXT-121]

description: scRNA-seq - germ cell AR2777

value: from PGCLC d5 XGFP-; XGFP+, Xtomato+


title: scRNA-seq - germ cell AR2864 [HHHNYBBXY_3_IDT-DUI-NXT-120]

description: scRNA-seq - germ cell AR2864


title: Volunteer BGDCE Sample DBGA

value: BGDCE


title: Volunteer AGFBA Sample DB4C

value: AGFBA


title: scRNA-seq - germ cell AR2848 [HHHNYBBXY_3_IDT-DUI-NXT-118]

description: scRNA-seq - germ cell AR2848


title: Volunteer ACFA3 Sample DB4D


title: scRNA-seq - germ cell AR2856 [HHHNYBBXY_3_IDT-DUI-NXT-119]

description: scRNA-seq - germ cell AR2856


title: scRNA-seq - germ cell AR2840 [HHHNYBBXY_3_IDT-DUI-NXT-117]

description: scRNA-seq - germ cell AR2840


title: scRNA-seq - germ cell AR2832 [HHHNYBBXY_3_IDT-DUI-NXT-116]

description: scRNA-seq - germ cell AR2832


title: Volunteer AEF43 Sample DB3A

value: Pfizer


title: scRNA-seq - germ cell AR2816 [HHHNYBBXY_3_IDT-DUI-NXT-114]

description: scRNA-seq - germ cell AR2816


title: scRNA-seq - germ cell AR2824 [HHHNYBBXY_3_IDT-DUI-NXT-115]

description: scRNA-seq - germ cell AR2824


title: Volunteer BECC3 Sample DB3B


title: Volunteer AEFC0 Sample DEBE


title: scRNA-seq - germ cell AR2792 [HHHNYBBXY_3_IDT-DUI-NXT-111]

description: scRNA-seq - germ cell AR2792


title: scRNA-seq - germ cell AR2808 [HHHNYBBXY_3_IDT-DUI-NXT-113]

description: scRNA-seq - germ cell AR2808


title: Volunteer EAG4F Sample DEGA

value: Female


title: scRNA-seq - germ cell AR2607 [HHHNYBBXY_3_IDT-DUI-NXT-10]

description: scRNA-seq - germ cell AR2607


title: Volunteer EBG3C Sample DED3

value: Male

value: Administrative


title: scRNA-seq - germ cell AR2800 [HHHNYBBXY_3_IDT-DUI-NXT-112]

description: scRNA-seq - germ cell AR2800

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Volunteer BB43A Sample DEFD


title: Volunteer BABGF Sample DBCB

value: BABGF


title: Volunteer AE04A Sample DE4D

value: Other


title: D5

city: Chengdu

first: Junli

last: Hao

address: No. 783, Xindu Avenue

country: China

institute: Chengdu Medical College

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
The clean reads were compared to the miRbase21 and Rfam database  to identify known miRNA and other non-coding RNAs.
The raw count for known miRNAs  were summarized and then normalized using reads per million mapped reads (RPM).
Total clean reads were  also mapped to the human reference genome using the bwa aligner.The mapped reads were further annotated to the repeats and exon regions based on the genome annotation.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: serum microvesicles

extract_protocol:
The serum was collected from the whole fresh blood and frozen to -80℃.The serum microvesicles of five acute ischemic stroke (AIS) and healthy controls was purified using RiboTM Exosome Isolation Reagent (for plasma or serum) and analyzed by flow cytometry and nanoparticle tracking analysis (NTA).The RNA from serum microvesicles were extracted using MagZolTM Reagent for quality inspection using Keo K5500/Qubit 2.0 and Agilent 2200 TapeStation. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext® Multiplex Small RNA Library Prep Set for Illumina®

tag: subject status

value: AIS patients

value: 18~80 years old

tag: tissue

value: serum

tag: molecule subtype

value: miRNA


title: D3


title: scRNA-seq - germ cell AR2784 [HHHNYBBXY_3_IDT-DUI-NXT-110]

description: scRNA-seq - germ cell AR2784

value: germ cell


title: Volunteer BDFEE Sample DEF4

value: BDFEE

value: Clinical staff


title: Volunteer BG443 Sample DEBA

value: Asian

value: Student


title: Volunteer FGEEC Sample DEDD

value: FGEEC

value: Nurse


title: N5

value: healthy control


title: Volunteer AE3B4 Sample DFA3

value: Moderna


title: Volunteer AE3D4 Sample DFED

value: Female

value: White

value: Administrative


title: D1


title: D4


title: Volunteer AFFC4 Sample DECG


title: N4


title: Volunteer AE4GD Sample DFEC


title: D2


title: Volunteer ECD0D Sample DFF3

value: Pfizer


title: scRNA-seq - germ cell AR2847 [HHHNYBBXY_3_IDT-DUI-NXT-106]

description: scRNA-seq - germ cell AR2847

value: hybrid 129S1/SvImJ, CAST/EiJ

value: from PGCLC d5 XGFP-; XGFP-, Xtomato+


title: scRNA-seq - germ cell AR2776 [HHHNYBBXY_3_IDT-DUI-NXT-109]

description: scRNA-seq - germ cell AR2776

value: from PGCLC d5 XGFP-; XGFP+, Xtomato+


title: Volunteer BG300 Sample DF3C

value: Physician


title: N3

value: 18~80 years old

value: serum

value: miRNA


title: scRNA-seq - germ cell AR2863 [HHHNYBBXY_3_IDT-DUI-NXT-108]

description: scRNA-seq - germ cell AR2863

value: germ cell


title: N1


title: N2


title: Volunteer FGA30 Sample DFFD


title: Volunteer EADEA Sample DFD4

value: EADEA

value: Male

value: Other


title: scRNA-seq - germ cell AR2855 [HHHNYBBXY_3_IDT-DUI-NXT-107]

description: scRNA-seq - germ cell AR2855


title: scRNA-seq - germ cell AR2839 [HHHNYBBXY_3_IDT-DUI-NXT-105]

description: scRNA-seq - germ cell AR2839


title: scRNA-seq - germ cell AR2815 [HHHNYBBXY_3_IDT-DUI-NXT-102]

description: scRNA-seq - germ cell AR2815

value: from PGCLC d5 XGFP-; XGFPint., Xtomato+


title: Volunteer BAA3F Sample DGAD


title: Volunteer A3AGE Sample DGBC


title: Volunteer BA3D3 Sample DE00


title: Volunteer BFG0B Sample DGBA

value: Latino


title: Volunteer EC43A Sample DF3B

value: Female

value: Nurse


title: Volunteer B3BAA Sample DFCG

value: Asian


title: Volunteer A3DGD Sample DGFC


title: Volunteer EGFFF Sample DFD0

value: EGFFF

value: Pfizer


title: Volunteer EB4G3 Sample DGEA


title: scRNA-seq - germ cell AR2831 [HHHNYBBXY_3_IDT-DUI-NXT-104]

description: scRNA-seq - germ cell AR2831

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Volunteer GACBE Sample DF0B

value: GACBE


title: scRNA-seq - germ cell AR2518 [HHHNYBBXY_2_IDT-DUI-NXT-382]

description: scRNA-seq - germ cell AR2518

value: from PGCLC d5 XGFP+; XGFP+, Xtomato+


title: Volunteer A4GFC Sample DGGA

value: Administrative


title: scRNA-seq - germ cell AR2799 [HHHNYBBXY_3_IDT-DUI-NXT-100]

description: scRNA-seq - germ cell AR2799

value: from PGCLC d5 XGFP-; XGFP+, Xtomato+


title: Volunteer AEDD0 Sample DGAC

value: White

value: Physician


title: scRNA-seq - germ cell AR2823 [HHHNYBBXY_3_IDT-DUI-NXT-103]

description: scRNA-seq - germ cell AR2823

value: germ cell


title: Volunteer ACA34 Sample DFCE


title: scRNA-seq - germ cell AR2510 [HHHNYBBXY_2_IDT-DUI-NXT-381]

description: scRNA-seq - germ cell AR2510


title: scRNA-seq - germ cell AR2534 [HHHNYBBXY_2_IDT-DUI-NXT-384]

description: scRNA-seq - germ cell AR2534

value: empty


title: Volunteer ABCFF Sample DG0C

value: ABCFF


title: Volunteer FCEDA Sample D4AF

value: FCEDA


title: scRNA-seq - germ cell AR2807 [HHHNYBBXY_3_IDT-DUI-NXT-101]

description: scRNA-seq - germ cell AR2807

value: from PGCLC d5 XGFP-; XGFPint., Xtomato+


title: Volunteer E43AD Sample DG0F

value: Male


title: Volunteer ABEFA Sample DG3D

value: ABEFA

value: Female

value: Clinical staff

value: Moderna


title: scRNA-seq - germ cell AR2526 [HHHNYBBXY_2_IDT-DUI-NXT-383]

description: scRNA-seq - germ cell AR2526

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Volunteer BE0G4 Sample DGCA


title: Volunteer BC400 Sample D4GC


title: Volunteer BGF00 Sample D4GG

value: Nurse


title: Volunteer A00CF Sample DFD3

value: Asian


title: Volunteer AC3FG Sample DG03

value: Student


title: scRNA-seq - germ cell AR2478 [HHHNYBBXY_2_IDT-DUI-NXT-377]

description: scRNA-seq - germ cell AR2478

value: from PGCLC d5 XGFP+; XGFP+, Xtomato+


title: Volunteer AGECG Sample D4DG

value: AGECG

value: Latino

value: Administrative


title: scRNA-seq - germ cell AR2502 [HHHNYBBXY_2_IDT-DUI-NXT-380]

description: scRNA-seq - germ cell AR2502

value: germ cell


title: Volunteer AADBA Sample D4BA

value: AADBA

value: Pfizer


title: scRNA-seq - germ cell AR2486 [HHHNYBBXY_2_IDT-DUI-NXT-378]

description: scRNA-seq - germ cell AR2486


title: Volunteer BFBF0 Sample D40B


title: Volunteer G4B4E Sample D4B0

value: Other


title: scRNA-seq - germ cell AR2454 [HHHNYBBXY_2_IDT-DUI-NXT-374]

description: scRNA-seq - germ cell AR2454


title: scRNA-seq - germ cell AR2494 [HHHNYBBXY_2_IDT-DUI-NXT-379]

description: scRNA-seq - germ cell AR2494


title: Volunteer G30DA Sample D3AC


title: Volunteer BGDCE Sample D3BF

value: BGDCE


title: Volunteer BFEE0 Sample D4FC


title: scRNA-seq - germ cell AR2470 [HHHNYBBXY_2_IDT-DUI-NXT-376]

description: scRNA-seq - germ cell AR2470


title: scRNA-seq - germ cell AR2446 [HHHNYBBXY_2_IDT-DUI-NXT-373]

description: scRNA-seq - germ cell AR2446


title: Volunteer AFA3G Sample D3FE

value: White


title: Volunteer GC4A4 Sample DGC0


title: scRNA-seq - germ cell AR2525 [HHHNYBBXY_2_IDT-DUI-NXT-371]

description: scRNA-seq - germ cell AR2525


title: Volunteer AF0E0 Sample D3F3

value: Female

value: moderna


title: Volunteer ABDF3 Sample D3AE


title: Volunteer AEC0B Sample D3F0


title: Volunteer BCBFE Sample D4EF

value: BCBFE


title: Volunteer GD3FA Sample D40D

value: Moderna


title: Volunteer AF0BA Sample D3GG


title: Volunteer BGCGE Sample DG04

value: BGCGE


title: scRNA-seq - germ cell AR2462 [HHHNYBBXY_2_IDT-DUI-NXT-375]

description: scRNA-seq - germ cell AR2462

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Volunteer FB4EC Sample D3G0

value: Asian

value: Nurse


title: Volunteer AC3EE Sample D3EC

value: Student


title: Volunteer AC3EC Sample D3ED


title: scRNA-seq - germ cell AR2517 [HHHNYBBXY_2_IDT-DUI-NXT-370]

description: scRNA-seq - germ cell AR2517

value: from PGCLC d5 XGFP+; XGFP+, Xtomato+


title: scRNA-seq - germ cell AR2533 [HHHNYBBXY_2_IDT-DUI-NXT-372]

description: scRNA-seq - germ cell AR2533


title: Volunteer A0C0D Sample D403

value: Clinical staff


title: Volunteer BG44A Sample D34G


title: Volunteer AFG33 Sample D3EG


title: scRNA-seq - germ cell AR2469 [HHHNYBBXY_2_IDT-DUI-NXT-364]

description: scRNA-seq - germ cell AR2469

value: germ cell


title: Volunteer AC34E Sample D3GF

value: Male


title: Volunteer AG4CF Sample D33B

value: Pfizer-BioNTech


title: Volunteer ECBA4 Sample D3G4

value: Latino


title: scRNA-seq - germ cell AR2509 [HHHNYBBXY_2_IDT-DUI-NXT-369]

description: scRNA-seq - germ cell AR2509


title: Volunteer AG03D Sample D3CE

value: Physician


title: Volunteer AC40D Sample D3GB

value: Other


title: scRNA-seq - germ cell AR2501 [HHHNYBBXY_2_IDT-DUI-NXT-368]

description: scRNA-seq - germ cell AR2501


title: Volunteer AE00F Sample D3D3


title: Volunteer BAAFC Sample D3CG

value: BAAFC

value: Female


title: Volunteer AF4FD Sample D3G3


title: Volunteer AF40F Sample D34F

value: White


title: scRNA-seq - germ cell AR2445 [HHHNYBBXY_2_IDT-DUI-NXT-361]

description: scRNA-seq - germ cell AR2445


title: Volunteer ECABF Sample D304

value: ECABF


title: Volunteer AD4E3 Sample D3GC

value: Food/EVS


title: Volunteer AB4B3 Sample D33A


title: scRNA-seq - germ cell AR2477 [HHHNYBBXY_2_IDT-DUI-NXT-365]

description: scRNA-seq - germ cell AR2477

value: hybrid 129S1/SvImJ, CAST/EiJ


title: scRNA-seq - germ cell AR2516 [HHHNYBBXY_2_IDT-DUI-NXT-358]

description: scRNA-seq - germ cell AR2516


title: scRNA-seq - germ cell AR2524 [HHHNYBBXY_2_IDT-DUI-NXT-359]

description: scRNA-seq - germ cell AR2524


title: Volunteer G4CBF Sample DDBA

value: Asian


title: scRNA-seq - germ cell AR2461 [HHHNYBBXY_2_IDT-DUI-NXT-363]

description: scRNA-seq - germ cell AR2461


title: Volunteer A4CDE Sample D30E

value: Nurse


title: Volunteer BDA4F Sample D34E


title: scRNA-seq - germ cell AR2485 [HHHNYBBXY_2_IDT-DUI-NXT-366]

description: scRNA-seq - germ cell AR2485


title: scRNA-seq - germ cell AR2500 [HHHNYBBXY_2_IDT-DUI-NXT-356]

description: scRNA-seq - germ cell AR2500


title: scRNA-seq - germ cell AR2508 [HHHNYBBXY_2_IDT-DUI-NXT-357]

description: scRNA-seq - germ cell AR2508


title: scRNA-seq - germ cell AR2493 [HHHNYBBXY_2_IDT-DUI-NXT-367]

description: scRNA-seq - germ cell AR2493


title: scRNA-seq - germ cell AR2492 [HHHNYBBXY_2_IDT-DUI-NXT-355]

description: scRNA-seq - germ cell AR2492


title: Volunteer B3E03 Sample D33C


title: Volunteer EFCCC Sample D3C3

value: EFCCC


title: Volunteer B0A03 Sample DDEF


title: scRNA-seq - germ cell AR2532 [HHHNYBBXY_2_IDT-DUI-NXT-360]

description: scRNA-seq - germ cell AR2532

value: from PGCLC d5 XGFP+; XGFP+, Xtomato+


title: Volunteer G4CA4 Sample DDE0


title: Volunteer ADACF Sample DDAD

value: ADACF


title: Volunteer AGFCA Sample DDBC

value: AGFCA


title: scRNA-seq - germ cell AR2453 [HHHNYBBXY_2_IDT-DUI-NXT-362]

description: scRNA-seq - germ cell AR2453

value: germ cell


title: scRNA-seq - germ cell AR2484 [HHHNYBBXY_2_IDT-DUI-NXT-354]

description: scRNA-seq - germ cell AR2484


title: Volunteer E43AD Sample DDBB

value: Male


title: Volunteer GBGBB Sample DDAB

value: GBGBB

value: Pfizer


title: Volunteer AD3F0 Sample D303


title: Volunteer F00C4 Sample DDBF

value: Clinical staff

value: Moderna


title: Volunteer AG0FG Sample DD4E

value: Physician


title: scRNA-seq - germ cell AR2468 [HHHNYBBXY_2_IDT-DUI-NXT-352]

description: scRNA-seq - germ cell AR2468


title: Volunteer AGCEF Sample DDA3

value: AGCEF

value: Other

value: Pfizer-BioNTech


title: Volunteer AGCEE Sample DDDE

value: AGCEE

value: Female

value: White


title: Volunteer EAFB0 Sample DDB0

value: Asian


title: Volunteer AEA0B Sample DCAA

value: Administrative


title: Volunteer EBCCD Sample D3CC

value: EBCCD


title: Volunteer A3C34 Sample DDFF

value: Nurse


title: Volunteer A3A30 Sample DDGD


title: Volunteer ECCDF Sample DDF0

value: ECCDF

value: Latino

value: Student


title: Volunteer AFAEC Sample DDDG

value: AFAEC


title: Volunteer GADGF Sample DCBF

value: GADGF


title: Volunteer FABG3 Sample DDGF

value: Clinical staff


title: Volunteer AFDBD Sample DCA0

value: AFDBD


title: scRNA-seq - germ cell AR2476 [HHHNYBBXY_2_IDT-DUI-NXT-353]

description: scRNA-seq - germ cell AR2476

value: hybrid 129S1/SvImJ, CAST/EiJ

value: germ cell

value: from PGCLC d5 XGFP+; XGFP+, Xtomato+


title: scRNA-seq - germ cell AR2452 [HHHNYBBXY_2_IDT-DUI-NXT-350]

description: scRNA-seq - germ cell AR2452


title: Volunteer GFFA0 Sample DCB3


title: scRNA-seq - germ cell AR2444 [HHHNYBBXY_2_IDT-DUI-NXT-349]

description: scRNA-seq - germ cell AR2444


title: Volunteer ADD4D Sample DCBD


title: Volunteer ECEG0 Sample DCEF

value: Other


title: scRNA-seq - germ cell AR2515 [HHHNYBBXY_2_IDT-DUI-NXT-346]

description: scRNA-seq - germ cell AR2515


title: scRNA-seq - germ cell AR2460 [HHHNYBBXY_2_IDT-DUI-NXT-351]

description: scRNA-seq - germ cell AR2460


title: Volunteer B4A0C Sample DCAF

value: Female


title: scRNA-seq - germ cell AR2523 [HHHNYBBXY_2_IDT-DUI-NXT-347]

description: scRNA-seq - germ cell AR2523


title: Volunteer BDFCG Sample DCE4

value: BDFCG

value: Pfizer


title: scRNA-seq - germ cell AR2507 [HHHNYBBXY_2_IDT-DUI-NXT-345]

description: scRNA-seq - germ cell AR2507


title: Volunteer BBAAB Sample DCB0

value: BBAAB

value: Asian

value: Moderna


title: Volunteer BE3F0 Sample DCFF

value: Nurse


title: scRNA-seq - germ cell AR2499 [HHHNYBBXY_2_IDT-DUI-NXT-344]

description: scRNA-seq - germ cell AR2499


title: Volunteer AFG0F Sample DCFE

value: Male


title: Volunteer B403B Sample DDDF

value: Physician


title: Volunteer BG044 Sample DCGE

value: White


title: Volunteer A3F3D Sample DC4D


title: Volunteer EACFC Sample DC3C

value: EACFC


title: scRNA-seq - germ cell AR2483 [HHHNYBBXY_2_IDT-DUI-NXT-342]

description: scRNA-seq - germ cell AR2483


title: scRNA-seq - germ cell AR2475 [HHHNYBBXY_2_IDT-DUI-NXT-341]

description: scRNA-seq - germ cell AR2475


title: Volunteer A30FE Sample DCBG

value: Clinical staff


title: Volunteer G30C0 Sample DC30


title: Volunteer A03DE Sample DCDD


title: scRNA-seq - germ cell AR2451 [HHHNYBBXY_2_IDT-DUI-NXT-338]

description: scRNA-seq - germ cell AR2451


title: Volunteer ADEC4 Sample DCDA


title: Volunteer AFD30 Sample DCCE


title: scRNA-seq - germ cell AR2491 [HHHNYBBXY_2_IDT-DUI-NXT-343]

description: scRNA-seq - germ cell AR2491


title: scRNA-seq - germ cell AR2467 [HHHNYBBXY_2_IDT-DUI-NXT-340]

description: scRNA-seq - germ cell AR2467


title: Volunteer B3ED4 Sample DC4B

value: Latino


title: Volunteer A4BAE Sample DCCD


title: Volunteer FB0E0 Sample DCFC


title: scRNA-seq - germ cell AR2443 [HHHNYBBXY_2_IDT-DUI-NXT-337]

description: scRNA-seq - germ cell AR2443

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Volunteer GCFGA Sample DC00

value: GCFGA


title: Volunteer A3GG0 Sample DCFG


title: Volunteer AB4D4 Sample DCCA


title: Volunteer BCGB0 Sample DC0B


title: Volunteer A04AF Sample DCD0


title: Volunteer AGCEA Sample D0G4

value: AGCEA


title: scRNA-seq - germ cell AR2530 [HHHNYBBXY_2_IDT-DUI-NXT-336]

description: scRNA-seq - germ cell AR2530

value: germ cell

value: from PGCLC d5 XGFP+; XGFP+, Xtomato+


title: Volunteer G3C3D Sample D0GD

value: Female


title: Volunteer AFFGB Sample DC3D

value: AFFGB

value: Other


title: Volunteer G3CDC Sample D0G3


title: scRNA-seq - germ cell AR2522 [HHHNYBBXY_2_IDT-DUI-NXT-335]

description: scRNA-seq - germ cell AR2522


title: scRNA-seq - germ cell AR2459 [HHHNYBBXY_2_IDT-DUI-NXT-339]

description: scRNA-seq - germ cell AR2459


title: scRNA-seq - germ cell AR2514 [HHHNYBBXY_2_IDT-DUI-NXT-334]

description: scRNA-seq - germ cell AR2514


title: Volunteer BGB40 Sample DC0F

value: Asian


title: Volunteer ADECF Sample DCD3

value: ADECF


title: Volunteer AEBGC Sample D04D

value: AEBGC

value: Nurse


title: Volunteer AE0FA Sample D03E

value: Pfizer


title: scRNA-seq - germ cell AR2506 [HHHNYBBXY_2_IDT-DUI-NXT-333]

description: scRNA-seq - germ cell AR2506


title: Volunteer E30BB Sample D04C


title: Volunteer EDC0C Sample D034


title: Volunteer GC3AC Sample D040


title: Volunteer ABF3A Sample D03C


title: Volunteer A3CFD Sample DCC0


title: scRNA-seq - germ cell AR2498 [HHHNYBBXY_2_IDT-DUI-NXT-332]

description: scRNA-seq - germ cell AR2498


title: Volunteer ACEFD Sample D033

value: ACEFD


title: Volunteer AEB3A Sample D03F

value: Male


title: scRNA-seq - germ cell AR2490 [HHHNYBBXY_2_IDT-DUI-NXT-331]

description: scRNA-seq - germ cell AR2490


title: scRNA-seq - germ cell AR2482 [HHHNYBBXY_2_IDT-DUI-NXT-330]

description: scRNA-seq - germ cell AR2482


title: Volunteer GBABE Sample DB03

value: GBABE

value: Moderna


title: Volunteer BFA3F Sample DA4B


title: Volunteer B0DF0 Sample DEEG

value: Student


title: scRNA-seq - germ cell AR2458 [HHHNYBBXY_2_IDT-DUI-NXT-327]

description: scRNA-seq - germ cell AR2458

value: hybrid 129S1/SvImJ, CAST/EiJ


title: scRNA-seq - germ cell AR2474 [HHHNYBBXY_2_IDT-DUI-NXT-329]

description: scRNA-seq - germ cell AR2474


title: scRNA-seq - germ cell AR2531 [HHHNYBBXY_2_IDT-DUI-NXT-348]

description: scRNA-seq - germ cell AR2531


title: scRNA-seq - germ cell AR2450 [HHHNYBBXY_2_IDT-DUI-NXT-326]

description: scRNA-seq - germ cell AR2450


title: Volunteer AE440 Sample D03A

value: White


title: Volunteer AE3G3 Sample DEGC


title: scRNA-seq - germ cell AR2466 [HHHNYBBXY_2_IDT-DUI-NXT-328]

description: scRNA-seq - germ cell AR2466

value: germ cell


title: scRNA-seq - germ cell AR2442 [HHHNYBBXY_2_IDT-DUI-NXT-325]

description: scRNA-seq - germ cell AR2442

value: from PGCLC d5 XGFP+; XGFP+, Xtomato+


title: Volunteer AFC4G Sample DFGA


title: Volunteer AG0CA Sample DFFE

value: Physician


title: Volunteer B0D3D Sample DFFA

value: Female


title: scRNA-seq - germ cell AR2521 [HHHNYBBXY_2_IDT-DUI-NXT-323]

description: scRNA-seq - germ cell AR2521


title: Volunteer EG03B Sample DECA

value: Other


title: scRNA-seq - germ cell AR2513 [HHHNYBBXY_2_IDT-DUI-NXT-322]

description: scRNA-seq - germ cell AR2513


title: Volunteer BGGDF Sample DEEE

value: BGGDF


title: Volunteer BA04D Sample DBGE


title: Volunteer AGFCC Sample DF3D

value: AGFCC


title: scRNA-seq - germ cell AR2529 [HHHNYBBXY_2_IDT-DUI-NXT-324]

description: scRNA-seq - germ cell AR2529


title: Volunteer A3DDC Sample DF3F

value: Asian


title: Volunteer BG3GG Sample DED0

value: Nurse


title: Volunteer AECD0 Sample DFGB

value: Pfizer


title: Volunteer BB4GG Sample DFGC


title: Volunteer AA0FD Sample DF0G

value: Latino


title: Volunteer BCDBC Sample DGEC

value: BCDBC

value: Male


title: scRNA-seq - germ cell AR2505 [HHHNYBBXY_2_IDT-DUI-NXT-321]

description: scRNA-seq - germ cell AR2505


title: Volunteer AF4F3 Sample DF34


title: Volunteer A44AB Sample DGB4


title: Volunteer AED0A Sample DGG3

value: Administrative


title: scRNA-seq - germ cell AR2497 [HHHNYBBXY_2_IDT-DUI-NXT-320]

description: scRNA-seq - germ cell AR2497


title: scRNA-seq - germ cell AR2473 [HHHNYBBXY_2_IDT-DUI-NXT-317]

description: scRNA-seq - germ cell AR2473


title: Volunteer F0FFD Sample DG4D


title: scRNA-seq - germ cell AR2465 [HHHNYBBXY_2_IDT-DUI-NXT-316]

description: scRNA-seq - germ cell AR2465


title: scRNA-seq - germ cell AR2481 [HHHNYBBXY_2_IDT-DUI-NXT-318]

description: scRNA-seq - germ cell AR2481


title: Volunteer GD4BC Sample DGFA


title: scRNA-seq - germ cell AR2489 [HHHNYBBXY_2_IDT-DUI-NXT-319]

description: scRNA-seq - germ cell AR2489


title: scRNA-seq - germ cell AR2457 [HHHNYBBXY_2_IDT-DUI-NXT-315]

description: scRNA-seq - germ cell AR2457


title: Volunteer BG3FG Sample DGCD


title: Volunteer AF400 Sample DGGD


title: Volunteer AE40E Sample DGFE


title: Volunteer EEEEC Sample DG3B

value: EEEEC


title: Volunteer AB0BG Sample DFGE

value: Moderna


title: scRNA-seq - germ cell AR2449 [HHHNYBBXY_2_IDT-DUI-NXT-314]

description: scRNA-seq - germ cell AR2449

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Volunteer BAD3D Sample DG0D


title: Volunteer AD4F3 Sample D4BF

value: White


title: Volunteer BB43A Sample DGDA


title: Volunteer E443D Sample D4F3


title: scRNA-seq - germ cell AR2441 [HHHNYBBXY_2_IDT-DUI-NXT-313]

description: scRNA-seq - germ cell AR2441

value: germ cell

value: from PGCLC d5 XGFP+; XGFP+, Xtomato+


title: Volunteer AE4DG Sample D444

value: Female


title: Volunteer A3D3G Sample DGE4


title: Volunteer AEDF0 Sample D4G3

value: Other


title: scRNA-seq - germ cell AR2528 [HHHNYBBXY_2_IDT-DUI-NXT-312]

description: scRNA-seq - germ cell AR2528


title: Volunteer BCFCG Sample D43F

value: BCFCG


title: Volunteer B30DF Sample D4FG


title: scRNA-seq - germ cell AR2520 [HHHNYBBXY_2_IDT-DUI-NXT-311]

description: scRNA-seq - germ cell AR2520


title: Volunteer EG4G4 Sample D4DA


title: Volunteer EAF0C Sample D430

value: Physician


title: scRNA-seq - germ cell AR2512 [HHHNYBBXY_2_IDT-DUI-NXT-310]

description: scRNA-seq - germ cell AR2512


title: Volunteer EDEDA Sample D4CF

value: EDEDA


title: Volunteer BB043 Sample D4DB

value: Nurse


title: Volunteer EE404 Sample D4C0

value: Asian

value: Pfizer


title: scRNA-seq - germ cell AR2504 [HHHNYBBXY_2_IDT-DUI-NXT-309]

description: scRNA-seq - germ cell AR2504


title: scRNA-seq - germ cell AR2496 [HHHNYBBXY_2_IDT-DUI-NXT-308]

description: scRNA-seq - germ cell AR2496


title: Volunteer GDF0F Sample D3BE


title: Volunteer BGGD3 Sample D3AA


title: Volunteer AF04D Sample D3EF

value: Latino


title: Volunteer AFAB4 Sample D3E4


title: Volunteer AF0G0 Sample D3FA

value: Male

value: Student


title: scRNA-seq - germ cell AR2488 [HHHNYBBXY_2_IDT-DUI-NXT-307]

description: scRNA-seq - germ cell AR2488


title: scRNA-seq - germ cell AR2480 [HHHNYBBXY_2_IDT-DUI-NXT-306]

description: scRNA-seq - germ cell AR2480


title: Volunteer E0A4E Sample D3DB


title: Volunteer G4CBD Sample D3DG


title: Volunteer A4GBD Sample D3D4


title: scRNA-seq - germ cell AR2464 [HHHNYBBXY_2_IDT-DUI-NXT-304]

description: scRNA-seq - germ cell AR2464


title: scRNA-seq - germ cell AR2472 [HHHNYBBXY_2_IDT-DUI-NXT-305]

description: scRNA-seq - germ cell AR2472


title: Volunteer AD03G Sample D3CF


title: Volunteer EF4FG Sample D30C


title: Volunteer BAADC Sample D3CD

value: BAADC


title: Volunteer ADEEG Sample D30D

value: ADEEG


title: scRNA-seq - germ cell AR2456 [HHHNYBBXY_2_IDT-DUI-NXT-303]

description: scRNA-seq - germ cell AR2456

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Volunteer AF0GF Sample DDAA

value: Moderna


title: Volunteer B04GC Sample DDEE

value: Clinical staff

value: Pfizer-BioNTech


title: scRNA-seq - germ cell AR2440 [HHHNYBBXY_2_IDT-DUI-NXT-301]

description: scRNA-seq - germ cell AR2440

value: germ cell

value: from PGCLC d5 XGFP+; XGFP+, Xtomato+


title: scRNA-seq - germ cell AR2527 [HHHNYBBXY_2_IDT-DUI-NXT-300]

description: scRNA-seq - germ cell AR2527


title: scRNA-seq - germ cell AR2519 [HHHNYBBXY_2_IDT-DUI-NXT-299]

description: scRNA-seq - germ cell AR2519


title: Volunteer A04FG Sample DDE3

value: Other


title: Volunteer BAAEC Sample D3C4

value: BAAEC

value: Female

value: Physician


title: Volunteer FCD30 Sample DDFA

value: Nurse


title: Volunteer FBECF Sample DDED

value: FBECF

value: Asian


title: Volunteer AE344 Sample D3DE


title: scRNA-seq - germ cell AR2511 [HHHNYBBXY_2_IDT-DUI-NXT-298]

description: scRNA-seq - germ cell AR2511


title: Volunteer AFE04 Sample DDFE

value: Male

value: Not reported


title: Volunteer F0FBF Sample DDFG

value: Food/EVS


title: Volunteer GCDAC Sample DDG4

value: GCDAC


title: scRNA-seq - germ cell AR2448 [HHHNYBBXY_2_IDT-DUI-NXT-302]

description: scRNA-seq - germ cell AR2448

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Volunteer B0CAD Sample DDD4

value: Student

value: Pfizer


title: Volunteer EBF3F Sample DDEB


title: Volunteer B0DCG Sample DDD3


title: Volunteer BG4F4 Sample DDD0

value: White


title: scRNA-seq - germ cell AR2503 [HHHNYBBXY_2_IDT-DUI-NXT-297]

description: scRNA-seq - germ cell AR2503

value: germ cell


title: scRNA-seq - germ cell AR2495 [HHHNYBBXY_2_IDT-DUI-NXT-296]

description: scRNA-seq - germ cell AR2495

value: from PGCLC d5 XGFP+; XGFP+, Xtomato+


title: Volunteer GEC4E Sample DDC3

value: Administrative


title: Volunteer B0FFG Sample DDCF


title: scRNA-seq - germ cell AR2487 [HHHNYBBXY_2_IDT-DUI-NXT-295]

description: scRNA-seq - germ cell AR2487


title: Volunteer B0D0B Sample DDCG

value: Other


title: scRNA-seq - germ cell AR2479 [HHHNYBBXY_2_IDT-DUI-NXT-294]

description: scRNA-seq - germ cell AR2479


title: Volunteer B0DEC Sample DDCD

value: Female


title: Volunteer A4003 Sample DD0A


title: Volunteer AFDDE Sample DCEC

value: AFDDE


title: Volunteer BGG4E Sample DD0E


title: Volunteer AECGD Sample DCFA

value: AECGD

value: Nurse


title: Volunteer B0D40 Sample DD0B


title: Volunteer E44DA Sample DCF3


title: Volunteer BC30A Sample DD03

value: Asian

value: Moderna


title: scRNA-seq - germ cell AR2471 [HHHNYBBXY_2_IDT-DUI-NXT-293]

description: scRNA-seq - germ cell AR2471


title: mPanc96 WT H3K27ac Rep2

city: Chicago

first: Meric

last: Kinali

address: Robert Lurie Biomedical research Building 303 E Superior St

department: Ob/gyn

institute: Northwestern University

description: H3K27ac_ISL2-oe_Rep2_mPanc_trimmed_qfiltered_dedup.bw

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie2
peaks were called using Homer
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files generated using Deeptools
Supplementary_files_format_and_content: Bed files

molecule: genomic DNA

source_name: Pancreas

extract_protocol:
Samples were sonicated and CHIP grade Flag Ab ( Cell signaling cat #: 14793s) and H3K27ac ab (Abcam cat#:ab4729) were used for CHIP and genomic DNA was isolated.
NebNext Library prep kit was used (Cat#:E7645S) accorging to manual. For library, Illumina (Cat#:E7335S) were used.

tag: cell line

value: PDAC cell line

value: Pancreas

tag: tag

value: 3X Flag

tag: expression

tag: chip antibody

value: H3K27ac ab (Abcam cat#:ab4729)


title: Volunteer A40F3 Sample DCGG

tag: volunteer id

tag: age

tag: gender


title: scRNA-seq - germ cell AR2463 [HHHNYBBXY_2_IDT-DUI-NXT-292]

description: scRNA-seq - germ cell AR2463

value: hybrid 129S1/SvImJ, CAST/EiJ


title: scRNA-seq - germ cell AR2439 [HHHNYBBXY_2_IDT-DUI-NXT-289]

description: scRNA-seq - germ cell AR2439


title: mPanc96 WT H3K27ac Rep1

description: H3K27ac_ISL2-oe_Rep1_mPanc_trimmed_qfiltered_dedup.bw


title: Volunteer FB0FA Sample DC4E

tag: ethnicity

tag: job/role

tag: first vaccination


title: Volunteer AA3FA Sample DC4G

tag: second vaccination

tag: vaccine

value: Pfizer-BioNTech

tag: days since vaccine


title: scRNA-seq - germ cell AR2455 [HHHNYBBXY_2_IDT-DUI-NXT-291]

description: scRNA-seq - germ cell AR2455

tag: strain

tag: cell type

tag: cell population


title: scRNA-seq - germ cell AR2674 [HHHNYBBXY_2_IDT-DUI-NXT-239]

description: scRNA-seq - germ cell AR2674

value: from PGCLC d5 XGFP-; XGFP-, Xtomato+


title: mPanc96 Flag ISL2 Rep2

description:
Flag_ISL2_CHIP-seq_merged_mPanc_trimmed_qfiltered_dedup.bw
Flag_ISL2_CHIP-seq_merged_mPanc.rmblacklist.bed

tag: tissue

value: Flag Ab ( Cell signaling cat #:14793s)


title: Volunteer EAFG0 Sample DC4C

value: White


title: scRNA-seq - germ cell AR2447 [HHHNYBBXY_2_IDT-DUI-NXT-290]

description: scRNA-seq - germ cell AR2447

value: germ cell

value: from PGCLC d5 XGFP+; XGFP+, Xtomato+


title: siSAM68_3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2016_1 were also provide

source_name: cell line

growth_protocol: MDA-MB-231 breast cancer cells were cultured in Dulbecco's Modified Eagle Medium, high-glucose, 25mM Hepes, containing 10% FBS and 1%Penicillin/streptomycin.

extract_protocol:
RNA was extracted and DNAse treated using the miRNeasy Mini Kit (Qiagen).
Libraries were prepared using the TruSeq Stranded mRNA kit protocol (Illumina technology) with an input total RNA of 1µg

treatment_protocol: MDA-MB-231 cells were transfected twice with control or SAM68-targeting siRNA, using  Lipofectamine RNA iMAX (Thermofisher) according to manufacturer's protocol, and harvested 24h after the second round of transfection.

tag: cell line

value: breast cancer cell line

tag: treatment

value: transfected with SAM68 targeting  siRNA


title: Volunteer A3BCD Sample DC40

value: Male

value: Latino


title: scRNA-seq - germ cell AR2670 [HHHNYBBXY_2_IDT-DUI-NXT-238]

description: scRNA-seq - germ cell AR2670


title: Volunteer BD30B Sample DC4F

value: Female

value: Asian

value: Nurse


title: Volunteer A40F4 Sample DCGD


title: Volunteer AGFG3 Sample DC44


title: mPanc96 Flag ISL2 Rep1

value: PDAC cell line

value: Pancreas

tag: tag

tag: expression


title: Volunteer ADA3D Sample DCC3

tag: volunteer id

value: Physician


title: Volunteer B0D34 Sample DC0A

tag: age

value: Student


title: siSAM68_2


title: siSAM68_1


title: Volunteer G4CE4 Sample DCC4

tag: gender

value: Pfizer


title: scRNA-seq - germ cell AR2666 [HHHNYBBXY_2_IDT-DUI-NXT-237]

description: scRNA-seq - germ cell AR2666

value: hybrid 129S1/SvImJ, CAST/EiJ

value: from PGCLC d5 XGFP-; XGFP-, Xtomato+


title: scRNA-seq - germ cell AR2662 [HHHNYBBXY_2_IDT-DUI-NXT-236]

description: scRNA-seq - germ cell AR2662

value: from PGCLC d5 XGFP-; XGFPint., Xtomato+


title: Volunteer EFCC0 Sample DCDB

tag: ethnicity


title: Volunteer EFCA4 Sample D0AG

value: Other

tag: job/role


title: Volunteer A3GE4 Sample DC0C

value: White

tag: first vaccination


title: siCTRL_2

value: breast cancer cell line

value: transfected with no-targeting control siRNA


title: scRNA-seq - germ cell AR2654 [HHHNYBBXY_2_IDT-DUI-NXT-234]

description: scRNA-seq - germ cell AR2654

value: germ cell


title: siCTRL_3


title: Volunteer A4EB3 Sample D0BA

tag: second vaccination


title: scRNA-seq - germ cell AR2658 [HHHNYBBXY_2_IDT-DUI-NXT-235]

description: scRNA-seq - germ cell AR2658


title: Volunteer AG3BF Sample D0AB

value: Clinical staff


title: scRNA-seq - germ cell AR2650 [HHHNYBBXY_2_IDT-DUI-NXT-233]

description: scRNA-seq - germ cell AR2650


title: Volunteer E3FA4 Sample D0FD

value: Male


title: Volunteer ADBCE Sample D044

value: ADBCE

value: Female

value: Asian


title: siCTRL_1


title: Volunteer ACFDD Sample CA4F

value: ACFDD

value: Nurse


title: scRNA-seq - germ cell AR2678 [HHHNYBBXY_2_IDT-DUI-NXT-240]

description: scRNA-seq - germ cell AR2678


title: scRNA-seq - germ cell AR2642 [HHHNYBBXY_2_IDT-DUI-NXT-231]

description: scRNA-seq - germ cell AR2642

value: from PGCLC d5 XGFP-; XGFP+, Xtomato+


title: scRNA-seq - germ cell AR2638 [HHHNYBBXY_2_IDT-DUI-NXT-230]

description: scRNA-seq - germ cell AR2638


title: scRNA-seq - germ cell AR2646 [HHHNYBBXY_2_IDT-DUI-NXT-232]

description: scRNA-seq - germ cell AR2646


title: Volunteer EGG3C Sample D0GG


title: Volunteer AC44A Sample CABG

value: Student


title: Volunteer BA3E4 Sample CBBG


title: Volunteer AGD0G Sample D0FG


title: MEF-Gs-12hr-1

city: Dongjak-Gu

first: Junil

last: Kim

state: Seoul

address: 369 Sangdo-Ro

department: Department of Bioinformatics

country: South Korea

institute: SOONGSIL UNIVERSITY

data_processing:
Sequences were mapped to mouse GRCm39 genome using STAR and quantified using multicov function implemented in bedtools.
Assembly: GRCm39
Supplementary files format and content: Gene count

source_name: Embryonic fibroblasts

extract_protocol:
For library construction, DNA/RNA is extracted from a sample. After performing quality control (QC), qualified samples proceed to library construction.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

value: MEF cells

tag: agent

value: glucose

tag: time point


title: MEF-Gs-6hr-2


title: scRNA-seq - germ cell AR2634 [HHHNYBBXY_2_IDT-DUI-NXT-229]

description: scRNA-seq - germ cell AR2634

tag: strain

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Volunteer E4CA3 Sample CADE

tag: days since vaccine


title: Volunteer AEE00 Sample CAAF


title: MEF-Gs-12hr-2

tag: cell type


title: MEF-Gs-3hr-2


title: Volunteer AB4CE Sample DB3C

tag: vaccine

value: Pfizer


title: Volunteer ABBG3 Sample CA4D

value: Latino

value: Administrative

value: Moderna


title: MEF-Gs-3hr-1


title: scRNA-seq - germ cell AR2677 [HHHNYBBXY_2_IDT-DUI-NXT-228]

description: scRNA-seq - germ cell AR2677

value: germ cell

tag: cell population

value: from PGCLC d5 XGFP-; XGFP-, Xtomato+


title: MEF-Gs-6hr-1


title: Volunteer AEF0C Sample DEAE


title: MEF-AAs-12hr-2

value: amino acid starvation


title: Volunteer AFC43 Sample CAEE

value: Other


title: Volunteer FBE44 Sample DE4C


title: scRNA-seq - germ cell AR2673 [HHHNYBBXY_2_IDT-DUI-NXT-227]

description: scRNA-seq - germ cell AR2673


title: Volunteer A4EE0 Sample DEG3

value: Female


title: MEF-AAs-12hr-1


title: Volunteer A44GG Sample CA43

value: Asian

value: Pfizer-BioNTech


title: Volunteer ECFB4 Sample DE3D

value: Food/EVS


title: Volunteer AE0AB Sample DECE

value: Male

value: White

value: Nurse


title: MEF-AAs-6hr-2

value: MEF cells


title: Volunteer BE3G3 Sample DECF


title: scRNA-seq - germ cell AR2665 [HHHNYBBXY_2_IDT-DUI-NXT-225]

description: scRNA-seq - germ cell AR2665

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Volunteer ADBAC Sample DFE4

value: ADBAC


title: scRNA-seq - germ cell AR2661 [HHHNYBBXY_2_IDT-DUI-NXT-224]

description: scRNA-seq - germ cell AR2661

value: from PGCLC d5 XGFP-; XGFPint., Xtomato+


title: Volunteer A3BCC Sample DFGG


title: MEF-AAs-6hr-1


title: MEF-AAs-3hr-1


title: Volunteer A4EGG Sample DF3G

value: Latino


title: MEF-AAs-3hr-2


title: scRNA-seq - germ cell AR2669 [HHHNYBBXY_2_IDT-DUI-NXT-226]

description: scRNA-seq - germ cell AR2669


title: scRNA-seq - germ cell AR2653 [HHHNYBBXY_2_IDT-DUI-NXT-222]

description: scRNA-seq - germ cell AR2653


title: scRNA-seq - germ cell AR2657 [HHHNYBBXY_2_IDT-DUI-NXT-223]

description: scRNA-seq - germ cell AR2657


title: MEF-0hr-2


title: Volunteer A33DB Sample DGGE


title: Volunteer ACBBA Sample DGBB

value: ACBBA

value: Clinical staff


title: Volunteer B30CE Sample DG0G

value: Pfizer


title: Volunteer ACAE4 Sample D4A3

value: Moderna


title: Volunteer AECFD Sample D4ED

value: AECFD

value: Physician


title: Volunteer A0E0E Sample D4A0


title: scRNA-seq - germ cell AR2649 [HHHNYBBXY_2_IDT-DUI-NXT-221]

description: scRNA-seq - germ cell AR2649

value: germ cell


title: scRNA-seq - germ cell AR2645 [HHHNYBBXY_2_IDT-DUI-NXT-220]

description: scRNA-seq - germ cell AR2645

value: from PGCLC d5 XGFP-; XGFP+, Xtomato+


title: MEF-0hr-1


title: Volunteer AECFB Sample DE30

value: AECFB

value: Female

value: Other


title: Volunteer ADEE3 Sample D4G4

value: White

value: Nurse


title: scRNA-seq - germ cell AR2637 [HHHNYBBXY_2_IDT-DUI-NXT-218]

description: scRNA-seq - germ cell AR2637

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Volunteer ADCCA Sample D4GD

value: ADCCA


title: Volunteer BFFED Sample DF33

value: BFFED

value: Male


title: scRNA-seq - germ cell AR2633 [HHHNYBBXY_2_IDT-DUI-NXT-217]

description: scRNA-seq - germ cell AR2633


title: Volunteer GDGAD Sample D44C

value: GDGAD

value: Latino


title: scRNA-seq - germ cell AR2676 [HHHNYBBXY_2_IDT-DUI-NXT-216]

description: scRNA-seq - germ cell AR2676

value: from PGCLC d5 XGFP-; XGFP-, Xtomato+


title: Volunteer AFCG4 Sample D3FC

value: Student

value: Pfizer


title: Volunteer AC40B Sample D3GE


title: Volunteer AFAGB Sample D3GA

value: AFAGB


title: Volunteer GCDBF Sample D33E

value: GCDBF

value: Not reported


title: AAV8-STAT5ca-treated Male-4 [G186_M8]

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: poly-A selected RNA, stranded library

data_processing:
RNA-seq data was processed using a custom pipeline, as described in Connerney et al., 2017 (PMID: 28323953)
Sequence reads were mapped to the mouse genome (mm9) using STAR aligner.
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene.
Differential expression analysis was performed with edgeR as described in Robinson et al., 2010 (PMID: 19910308)
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file containing normalized read counts and differential expression results for a set of 75,798 mouse mm9 genes comprised of the following: n = 20,884 RefSeq protein coding genes, n=48,360 mouse liver-expressed lncRNAs genes, n=2,061 RefSeq non-coding genes (NR accession numbers) that do not overlap with the set of 48,360 lncRNAs, n =4,490 Ensembl non-coding lncRNAs that do not overlap either the RefSeq NR gene set or the 48,360 lncRNA gene set, and n=3 other lncRNAs with interesting liver functions (lnc-LFAR1, LeXis, Lnclgr). Further details about these genes are provided in the annotation fields of the processed data file.

molecule: polyA RNA

source_name: liver tissue

extract_protocol:
Nuclei were isolated from frozen liver tissue using methods detailed in Goldfarb CN, Waxman DJ. BMC Genomics. 2021;22(1):212. Trizol was used to isolate RNA from the purified liver nuclei.
Polyadenylated mRNA was isolated from 1 μg of liver nuclear RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (cat. #E7490, New England Biolabs) and used for lllumina RNA-seq library preparation using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (cat. #E7420L, New England Biolabs), NEBNext® Multiplex Oligos for Illumina® Dual Index Primers (cat. #E7600, New England Biolabs), and AMPure® XP Beads (cat. #A63881, Beckman Coulter Inc., Indianapolis, IN) per the manufacturer’s instructions.

treatment_protocol: Male CD1 mice [Crl:CD(ICR); strain code 022], 7-8 wk of age, were purchased from Charles River Laboratories. Mice were housed in a temperature and humidity-controlled environment with a 12-h light, 12-h dark cycle, fed standard rodent chow, and supplied with tap water. AAV8-STAT5ca was administered to male mice by tail vein injection at 2 x E11 genome copies per mouse, or vehicle control. Virus was diluted into PBS + 35 mM NaCl + 5% glycerol (stabilizer) to give a total injection volume of 150 uL. Mice were euthanized by cervical dislocation at 11 AM (lights on 7:30 AM- 7:30 PM) to minimize the impact of circadian variations of gene expression. 'AAV8', adeno-associated virus, serotype 8, which has high specificity for hepatocytes.

value: CD1 mouse [Crl:CD(ICR); strain code 022]

tag: treatment

value: AAV8-STAT5ca, 2 x E11 genome copies/mouse, 6 weeks

tag: Sex

value: 13-14 weeks


title: AAV8-STAT5ca-treated Male-3 [G186_M7]

description: poly-A selected RNA, stranded library


title: scRNA-seq - germ cell AR2672 [HHHNYBBXY_2_IDT-DUI-NXT-215]

description: scRNA-seq - germ cell AR2672

value: germ cell


title: scRNA-seq - germ cell AR2668 [HHHNYBBXY_2_IDT-DUI-NXT-214]

description: scRNA-seq - germ cell AR2668


title: scRNA-seq - germ cell AR2641 [HHHNYBBXY_2_IDT-DUI-NXT-219]

description: scRNA-seq - germ cell AR2641

value: from PGCLC d5 XGFP-; XGFP+, Xtomato+


title: Volunteer BBB4A Sample D3DA

value: Female

value: White

value: Nurse


title: Volunteer BF44A Sample D3C0

value: Male

value: Asian


title: AAV8-STAT5ca-treated Male-5 [G186_M9]

description: poly-A selected RNA, stranded library


title: scRNA-seq - germ cell AR2664 [HHHNYBBXY_2_IDT-DUI-NXT-213]

description: scRNA-seq - germ cell AR2664

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Control Male_3 [G186_M3]

description: poly-A selected RNA, stranded library

value: Control, 6 weeks


title: AAV8-STAT5ca-treated Male-1 [G186_M5]

description: poly-A selected RNA, stranded library

value: AAV8-STAT5ca, 2 x E11 genome copies/mouse, 4 weeks

value: 11-12 weeks


title: Control Male_4 [G186_M4]

description: poly-A selected RNA, stranded library


title: scRNA-seq - germ cell AR2660 [HHHNYBBXY_2_IDT-DUI-NXT-212]

description: scRNA-seq - germ cell AR2660

value: from PGCLC d5 XGFP-; XGFPint., Xtomato+


title: Volunteer EACGB Sample D300

value: EACGB

value: Physician


title: Volunteer ABC4C Sample DDB3

value: Other

value: Administrative

value: Moderna


title: scRNA-seq - germ cell AR2656 [HHHNYBBXY_2_IDT-DUI-NXT-211]

description: scRNA-seq - germ cell AR2656

value: germ cell


title: Volunteer AF0BE Sample D3FF

value: Student


title: Control Male_2 [G186_M2]

description: poly-A selected RNA, stranded library

value: CD1 mouse [Crl:CD(ICR); strain code 022]

value: Control, 4 weeks


title: AAV8-STAT5ca-treated Male-2 [G186_M6]

description: poly-A selected RNA, stranded library


title: Volunteer BAA3B Sample DDEG


title: Control Male_1 [G186_M1]

description: poly-A selected RNA, stranded library


title: scRNA-seq - germ cell AR2652 [HHHNYBBXY_2_IDT-DUI-NXT-210]

description: scRNA-seq - germ cell AR2652


title: Volunteer AEGCG Sample DDGC

value: AEGCG

value: Female

value: Latino

value: Clinical staff


title: AAV8-STAT5ca-treated Male-2 [G169_M30]

description: poly-A selected RNA, stranded library

extract_protocol:
Trizol was ued to isolate total liver RNA from flash fozen mouse liver tissue.
Polyadenylated mRNA was isolated from 1 μg of liver nuclear RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (cat. #E7490, New England Biolabs) and used for lllumina RNA-seq library preparation using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (cat. #E7420L, New England Biolabs), NEBNext® Multiplex Oligos for Illumina® Dual Index Primers Set 1 (cat. #E7600, New England Biolabs), and AMPure® XP Beads (cat. #A63881, Beckman Coulter Inc., Indianapolis, IN) per the manufacturer’s instructions.

treatment_protocol: Male C57Bl/6 mice 10-12 wk of age were given AAV8-STAT5ca, or AAV8-Null by tail vein injection at 0.75 x E11 genome copies per mouse. 'AAV8', adeno-associated virus, serotype 8, which has high specificity for hepatocytes.

value: AAV8-STAT5ca, 0.75 x E11 genome copies/mouse, 2 weeks

value: Male

value: 12-14 weeks

tag: tissue

value: Liver


title: Volunteer A3000 Sample DDG3

tag: volunteer id

value: Nurse


title: Volunteer BGB43 Sample DCAG

tag: age

value: Asian


title: Volunteer BBE0C Sample DCFB

tag: gender

value: Other


title: scRNA-seq - germ cell AR2648 [HHHNYBBXY_2_IDT-DUI-NXT-209]

description: scRNA-seq - germ cell AR2648

value: hybrid 129S1/SvImJ, CAST/EiJ

value: from PGCLC d5 XGFP-; XGFPint., Xtomato+


title: Volunteer BDE40 Sample DCEA

tag: ethnicity


title: scRNA-seq - germ cell AR2640 [HHHNYBBXY_2_IDT-DUI-NXT-207]

description: scRNA-seq - germ cell AR2640

value: germ cell

value: from PGCLC d5 XGFP-; XGFP+, Xtomato+


title: scRNA-seq - germ cell AR2644 [HHHNYBBXY_2_IDT-DUI-NXT-208]

description: scRNA-seq - germ cell AR2644


title: AAV8-Null-treated Male-2 [G169_M28]

description: poly-A selected RNA, stranded library

value: AAV8-Null, 0.75 x E11 genome copies/mouse, 2 weeks


title: AAV8-STAT5ca-treated Male-1 [G169_M29]

description: poly-A selected RNA, stranded library


title: Volunteer B3CCF Sample DCF4

tag: job/role


title: Volunteer GA3CF Sample DDG0

value: White

tag: first vaccination

value: Moderna


title: Volunteer A40EE Sample DD43

tag: second vaccination


title: Volunteer G30DA Sample DC3E

value: Female


title: scRNA-seq - germ cell AR2636 [HHHNYBBXY_2_IDT-DUI-NXT-206]

description: scRNA-seq - germ cell AR2636


title: scRNA-seq - germ cell AR2632 [HHHNYBBXY_2_IDT-DUI-NXT-205]

description: scRNA-seq - germ cell AR2632


title: K002000234_87976_DKO 4

city: Stockholm

first: Christian

last: Oertlin

address: Tomtebodavägen 23A

country: Sweden

institute: Karolinska Institutet

data_processing:
Processing pipeline: Nf-core/RNAseq V1.4.2, Default settings
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: text file raw read counts

source_name: heart

extract_protocol:
RNA isolation for RNAseq was performed using the 'Direct-zol RNA MiniPrep Kit' (Zymo Research) according to the manufacturer’s instruction.
Libraries were prepared using the 'TruSeq mRNA Stranded Sample Preparation Kit' (Illumina) and validated on a tape station (Agilent). Equimolar amounts of libraries were pooled, quantified (Peqlab KAPA Library Quantification Kit, Applied Biosystems 7900HT Sequence Detection System) and finally sequenced on a 'HiSeq4000 sequencer' (Illumina).

value: heart

tag: ear tag

value: female

tag: genotype

value: Chop ko/ko; Ckmm_Cre tg/wt; Dars2 fl/fl

value: 2 weeks


title: Volunteer AFDCF Sample D0A4

value: AFDCF

value: Male


title: Volunteer EGBF0 Sample DC0E

value: Latino

value: Nurse


title: K002000234_87974_DKO 3


title: scRNA-seq - germ cell AR2671 [HHHNYBBXY_2_IDT-DUI-NXT-203]

description: scRNA-seq - germ cell AR2671

tag: strain

value: from PGCLC d5 XGFP-; XGFP-, Xtomato+


title: Volunteer BFB0B Sample DCDG

value: Asian

tag: days since vaccine


title: Volunteer A0CGB Sample D4F0


title: Volunteer GC3FA Sample D04G


title: scRNA-seq - germ cell AR2667 [HHHNYBBXY_2_IDT-DUI-NXT-202]

description: scRNA-seq - germ cell AR2667

value: hybrid 129S1/SvImJ, CAST/EiJ

tag: cell type


title: Volunteer E343B Sample D0F4

value: Other


title: AAV8-Null-treated Male-1 [G169_M27]

description: poly-A selected RNA, stranded library

value: 12-14 weeks

value: Liver


title: Volunteer EDG3E Sample DD4B

value: White


title: Volunteer AF0F0 Sample D00A

value: Student


title: scRNA-seq - germ cell AR2675 [HHHNYBBXY_2_IDT-DUI-NXT-204]

description: scRNA-seq - germ cell AR2675

value: germ cell


title: Volunteer AF0E0 Sample D00E

value: Female

tag: vaccine

value: moderna


title: Volunteer BFGAG Sample D0A3

value: BFGAG


title: scRNA-seq - germ cell AR2663 [HHHNYBBXY_2_IDT-DUI-NXT-201]

description: scRNA-seq - germ cell AR2663

tag: cell population


title: Volunteer A40FD Sample DCG4

value: Moderna


title: K002000234_87970_DKO 1

value: heart

value: male

value: Chop ko/ko; Ckmm_Cre tg/wt; Dars2 fl/fl

value: 2 weeks


title: K002000234_87966_Dars2 KO 3

value: female

value: Ckmm_Cre tg/wt; Dars2 fl/fl


title: Volunteer AF0GD Sample D000


title: scRNA-seq - germ cell AR2659 [HHHNYBBXY_2_IDT-DUI-NXT-200]

description: scRNA-seq - germ cell AR2659

value: hybrid 129S1/SvImJ, CAST/EiJ

value: from PGCLC d5 XGFP-; XGFPint., Xtomato+


title: Volunteer AC3B0 Sample D004

value: Male


title: scRNA-seq - germ cell AR2655 [HHHNYBBXY_2_IDT-DUI-NXT-199]

description: scRNA-seq - germ cell AR2655


title: K002000234_87968_Dars2 KO 4


title: Volunteer EB4AC Sample D0GC

value: Nurse


title: K002000234_87972_DKO 2


title: K002000234_87962_Dars2 KO 1


title: scRNA-seq - germ cell AR2651 [HHHNYBBXY_2_IDT-DUI-NXT-198]

description: scRNA-seq - germ cell AR2651


title: Volunteer AEC04 Sample CAA4

value: Other


title: K002000234_87960_Chop KO 4

value: Chop ko/ko ; Ckmm_Cre wt/wt; Dars2 fl/wt


title: Volunteer AF0G3 Sample CAAD

value: Latino

value: Student

value: Pfizer


title: Volunteer AFCG3 Sample CAA0

value: Female

value: Asian


title: K002000234_87958_Chop KO 3

value: heart

value: Chop ko/ko; Ckmm_Cre wt/wt ; Dars2 fl/fl


title: Volunteer BG4GF Sample CAAC

value: White


title: scRNA-seq - germ cell AR2643 [HHHNYBBXY_2_IDT-DUI-NXT-196]

description: scRNA-seq - germ cell AR2643

value: germ cell

value: from PGCLC d5 XGFP-; XGFP+, Xtomato+


title: K002000234_87964_Dars2 KO 2

value: female

value: Ckmm_Cre tg/wt; Dars2 fl/fl

value: 2 weeks


title: K002000234_87956_Chop KO 2


title: Volunteer AFCC0 Sample D0C0

value: Male


title: Volunteer AC4CC Sample CAAG


title: Volunteer AC3FE Sample D003


title: Volunteer AF0BA Sample CAB3


title: Volunteer AFCGD Sample CABA

value: AFCGD


title: K002000234_87954_Chop KO 1

value: male


title: Volunteer BGG3C Sample CABD


title: Volunteer AG003 Sample CAED

value: Physician


title: Volunteer BG4BD Sample CAE3


title: Volunteer AG0C3 Sample CAE0


title: Volunteer AG00E Sample CAFA


title: Volunteer AC440 Sample CABC


title: scRNA-seq - germ cell AR2647 [HHHNYBBXY_2_IDT-DUI-NXT-197]

description: scRNA-seq - germ cell AR2647

value: hybrid 129S1/SvImJ, CAST/EiJ

value: from PGCLC d5 XGFP-; XGFPint., Xtomato+


title: scRNA-seq - germ cell AR2639 [HHHNYBBXY_2_IDT-DUI-NXT-195]

description: scRNA-seq - germ cell AR2639


title: Volunteer B3BB0 Sample CAFE

value: Other


title: RNA-seq – ESC rep 3

description: RNA-seq – ESC rep 3

source_name: embryonic stem cell

value: embryonic stem cell

value: not FACS sorted


title: RNA-seq – ESC rep 2

description: RNA-seq – ESC rep 2


title: K002000234_87950_WT 3

value: heart

value: Ckmm_Cre wt/wt;  Dars2 fl/fl


title: Volunteer AC34A Sample CAA3

value: Female

value: White

value: Student

value: Pfizer


title: Volunteer BEGCD Sample CA44

value: BEGCD

value: Nurse


title: K002000234_87948_WT 2

value: female

value: Ckmm_Cre wt/wt; Dars2 fl/wt

value: 2 weeks


title: Volunteer GB4FF Sample CAF3

value: Asian

value: Clinical staff


title: Volunteer BBACB Sample CA40

value: BBACB


title: RNA-seq – ESC rep 4

description: RNA-seq – ESC rep 4

value: hybrid 129S1/SvImJ, CAST/EiJ


title: K002000234_87946_WT 1

value: male


title: K002000128_62241_DKO 2

value: Chop ko/ko ; Ckmm_Cre tg/wt ; Dars2 fl/fl

value: 1 week


title: Volunteer GGAFD Sample CAGE

value: GGAFD

value: Moderna


title: scRNA-seq - germ cell AR2631 [HHHNYBBXY_2_IDT-DUI-NXT-193]

description: scRNA-seq - germ cell AR2631

value: germ cell

value: from PGCLC d5 XGFP-; XGFP+, Xtomato+


title: Volunteer E3GF0 Sample CA3C

value: Female

value: White


title: K002000234_87952_WT 4

value: heart

value: Ckmm_Cre wt/wt;  Dars2 fl/fl


title: scRNA-seq - germ cell AR2635 [HHHNYBBXY_2_IDT-DUI-NXT-194]

description: scRNA-seq - germ cell AR2635


title: Volunteer B33EG Sample CA30

value: Latino

value: Nurse


title: RNA-seq – ESC rep 1

description: RNA-seq – ESC rep 1

value: embryonic stem cell

value: not FACS sorted


title: Volunteer ECDGD Sample CAGB

value: ECDGD

value: Asian


title: K002000128_62245_DKO 4

value: male

value: Chop ko/ko ; Ckmm_Cre tg/wt; Dars2 fl/fl


title: Volunteer AGFEC Sample CA34

value: AGFEC

value: Male


title: Volunteer B0GAA Sample CA33


title: RNA-seq – EpiLC rep 3

description: RNA-seq – EpiLC rep 3

source_name: epiblast-like cell

value: hybrid 129S1/SvImJ, CAST/EiJ

value: epiblast-like cell


title: Volunteer A443G Sample CA0E

value: Pfizer


title: Volunteer A0GE0 Sample CACE

value: Female

value: Other


title: Volunteer A4EAB Sample CAD0


title: K002000128_62235_Dars2 KO 3

value: heart

value: female

value: Ckmm_Cre tg/wt; Dars2 fl/fl

value: 1 week


title: K002000128_62239_DKO 1

value: Chop ko/ko; Ckmm_Cre tg/wt; Dars2 fl/fl


title: RNA-seq – EpiLC rep 2

description: RNA-seq – EpiLC rep 2

value: not FACS sorted


title: Volunteer BEAG0 Sample CADF

value: White

value: Nurse


title: Volunteer A3ACC Sample CA3D

value: Asian


title: Volunteer ACEFG Sample CA03

value: ACEFG

value: Latino

value: Pfizer-BioNTech


title: Volunteer BFGAE Sample CA0D

value: BFGAE


title: Volunteer EEBA4 Sample D33G


title: Volunteer ABG43 Sample CBAG

value: Male

value: Clinical staff

value: Moderna


title: RNA-seq – PGCLC day 5 XGFP- rep 3

description: RNA-seq – PGCLC day 5 XGFP- rep 3

source_name: primordial germ cell-like cell

value: hybrid 129S1/SvImJ, CAST/EiJ

value: primordial germ cell-like cell

value: CD61+, SSEA1+, XGFP-, XTomato+


title: K002000128_62237_Dars2 KO 4

value: heart

value: male

value: Ckmm_Cre tg/wt; Dars2 fl/fl


title: Volunteer A3FCC Sample CBBE

value: Female


title: RNA-seq – EpiLC rep 1

description: RNA-seq – EpiLC rep 1

value: epiblast-like cell

value: not FACS sorted


title: RNA-seq – PGCLC day 5 XGFP- rep 2

description: RNA-seq – PGCLC day 5 XGFP- rep 2


title: K002000128_62227_Chop KO 3

value: female

value: Chop ko/ko; Ckmm_Cre wt/wt;  Dars2 fl/fl

value: 1 week


title: Volunteer BE33G Sample CBE0

value: White

value: Nurse


title: RNA-seq – PGCLC day 5 XGFP- rep 4

description: RNA-seq – PGCLC day 5 XGFP- rep 4


title: K002000128_62231_Dars2 KO 1


title: RNA-seq – EpiLC rep 4

description: RNA-seq – EpiLC rep 4


title: K002000128_62243_DKO 3

value: Chop ko/ko; Ckmm_Cre tg/wt; Dars2 fl/fl


title: Volunteer E0AGA Sample CBE3

value: Male

value: Pfizer


title: Volunteer EBD0B Sample CBFD

value: Asian

value: Pfizer-BioNTech


title: K002000128_62233_Dars2 KO 2


title: Volunteer B0FGF Sample CBFG

value: Latino

value: Student


title: Volunteer A03GD Sample CBFC

value: Physician


title: K002000128_62223_Chop KO 1

value: heart

value: Chop ko/ko ; Ckmm_Cre wt/wt ; Dars2 fl/wt


title: Volunteer BBDCF Sample CA0F

value: BBDCF


title: K002000128_62229_Chop KO 4

value: Chop ko/ko; Ckmm_Cre wt/wt; Dars2 fl/fl


title: Volunteer EBDA3 Sample CA00

value: Female


title: RNA-seq – PGCLC day 5 XGFP- rep 1

description: RNA-seq – PGCLC day 5 XGFP- rep 1

value: hybrid 129S1/SvImJ, CAST/EiJ

value: primordial germ cell-like cell

value: CD61+, SSEA1+, XGFP-, XTomato+


title: Volunteer AF0EA Sample D3E0

value: Other


title: Volunteer AF0E4 Sample D00G


title: RNA-seq – PGCLC day 5 XGFP+ rep 4

description: RNA-seq – PGCLC day 5 XGFP+ rep 4

value: CD61+, SSEA1+, XGFP+, XTomato+


title: Volunteer A03DB Sample CBFF

value: White


title: K002000128_62219_WT 3

value: female

value: Ckmm_Cre wt/wt; Dars2 fl/wt

value: 1 week


title: RNA-seq – PGCLC day 5 XGFP+ rep 3

description: RNA-seq – PGCLC day 5 XGFP+ rep 3


title: K002000128_62225_Chop KO 2

value: male

value: Chop ko/ko ; Ckmm_Cre wt/wt ; Dars2 fl/fl


title: K002000128_62221_WT 4

value: Ckmm_Cre wt/wt;  Dars2 fl/fl


title: Volunteer FCG0E Sample CBF0

value: Administrative


title: RNA-seq – PGCLC day 5 XGFP+ rep 2

description: RNA-seq – PGCLC day 5 XGFP+ rep 2


title: RNA-seq – PGCLC day 5 XGFP+ rep 1

description: RNA-seq – PGCLC day 5 XGFP+ rep 1


title: Volunteer AA0FF Sample DBB4

value: Latino

value: Food/EVS

value: Pfizer


title: Volunteer AEDA4 Sample D3DC

value: Female

value: Asian

value: Nurse


title: Volunteer BDCF4 Sample DF0C


title: Volunteer A3CCC Sample DEDA

value: Male


title: Volunteer EAADB Sample DBBC

value: EAADB


title: Volunteer B33EF Sample DFEF


title: Volunteer AC3G3 Sample DE0A

value: Student


title: H3K4me3_2

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

institute: Inserm

description:
ChIP-seq in OCI-AML3 cells using specified antibody.
Hematopoietic cells

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie2 v2.2.6.
Peaks were called using MACS2.
RPKM normalized bigwig files were generated using Deeptools 3.1.2, reads were elongated to 250bp.
Assembly: hg19 (GRCh37)
Supplementary files format and content: *.bigWig: RPKM normalized bigWig files.

source_name: ChIPseq libraries

extract_protocol:
Cells were fixed in 1% formaldehyde, chromatin was sonicated using a Bioruptor Pico.
Libraries were constructed using a custom protocol and NEXTFLEX adapters and barcodes.

tag: cell line

value: Acute myeloid leukemia cell line

tag: chip antibody

value: anti-H3K4me3 antibody


title: Input

description:
Input material used for ChIP-seq in OCI-AML3 cells.
Sonicated Input chromatin
Hematopoietic cells


title: Volunteer BB4DE Sample DB4F


title: K002000128_62217_WT 2

tag: tissue

value: heart

tag: Sex

value: Ckmm_Cre wt/wt; Dars2 fl/wt


title: Volunteer BCBC3 Sample DFGD

tag: volunteer id

tag: age

value: Moderna


title: Volunteer G4CBA Sample DEBB


title: H3K4me3_1


title: K002000128_62215_WT 1

value: female

value: 1 week


title: Volunteer AEG33 Sample DEAA


title: Volunteer ACCGE Sample DG44

value: ACCGE

tag: gender

tag: ethnicity


title: Volunteer GCCA0 Sample DG43

value: Latino

tag: job/role

value: Other

tag: first vaccination


title: Volunteer B3GCB Sample D4B4

tag: second vaccination

value: Pfizer


title: Volunteer ADA3E Sample DG3G


title: NIH3T3 EGFR L858R_SB12 (Replicate_3)

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

data_processing:
The base calling was performed using RTA 1.18.64.0
Reads were aligned to mm10 genome index and mm10 annotations using tophat version 2.1.0  with parameters -T -G mm10.gtf
Aligned read counts are estimated from alignment file and mm10 gtf using Htseq-count  version 0.6.0.
Genome_build: mm10
Supplementary_files_format_and_content: Raw read counts in .txt format

source_name: Mouse NIH3T3 cells

growth_protocol: NIH3T3 cells stably expressing either vector, EGFR WT and different EGFR mutants were grown in DMEM medium with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: NIH3T3 cells that expressed either vector, EGFR WT and EGFR mutants were used for preparing the total RNA and to perform RNA-sequencing.

tag: transfected with

value: EGFR L858R Mutation


title: NIH3T3 EGFR L858R_SB10 (Replicate_1)


title: NIH3T3 EGFR L858R_SB11 (Replicate_2)


title: NIH3T3 EGFR L861Q_SB13 (Replicate_1)

value: EGFR L861Q Mutation


title: NIH3T3 EGFR L861Q_SB14 (Replicate_2)


title: NIH3T3 EGFR L861Q_SB15 (Replicate_3)


title: Volunteer EAD3G Sample D440

value: White

value: Physician


title: H3K9ac_2

value: anti-H3K9ac antibody


title: H3K9ac_1


title: H3K4me1_2

value: anti-H3K4me1 antibody


title: NIH3T3 EGFR Del1_SB8 (Replicate_2)

value: EGFR Del1


title: Volunteer A04F3 Sample D4DC

value: Female

value: Administrative


title: Volunteer BFE04 Sample D344

value: Male

value: Food/EVS


title: NIH3T3 EGFR Del1_SB7 (Replicate_1)


title: NIH3T3 EGFR Wild Type_SB6 (Replicate_3)

value: EGFR Wildtype


title: Volunteer AF0FB Sample D3FD

value: Student


title: H3K4me1_1

value: Acute myeloid leukemia cell line


title: H3K27ac_2

value: anti-H3K27ac antibody


title: Volunteer AG04E Sample D3CB

value: Asian


title: Volunteer A4AFD Sample D343

value: Pfizer-BioNTech


title: NIH3T3 EGFR Wild Type_SB5 (Replicate_2)


title: NIH3T3 EGFR Del1_SB9 (Replicate_3)


title: NIH3T3 EGFR Wild Type_SB4 (Replicate_1)


title: Volunteer B0D30 Sample DDBD


title: H3K27ac_1


title: NIH3T3 Vector (pBABEpuro)_SB3 (Replicate_3)

value: Empty Vector


title: Volunteer BFBCC Sample DDEC

value: BFBCC


title: Volunteer A44GA Sample DDFD


title: Volunteer ABGFC Sample D44B

value: ABGFC

value: Nurse

value: Moderna


title: Seedlings, fer Aradopside rep 4

city: Ames

first: Natalie

middle: M

last: Clark

state: IA

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

data_processing:
Libraries were run across two lanes on an Illumina HiSeq 3500. Prior to data processing, reads for the two runs were merged for each sample.
Adapters were trimmed using the bbduk function in BBTools.
Reads were mapped to the TAIR10 genome using the STAR aligner.
Alignment files were sorted and indexed using samtools.
Counts were obtained using htseq-count.
Genome_build: TAIR10
Supplementary_files_format_and_content: Read counts for each gene in the TAIR10 genome in each sample.

organism: Arabidopsis thaliana

source_name: 10-day-old seedlings

growth_protocol: 10-day-old seedlings of col and fer-4 grown on 1/2MS plates were transferred to 1/2MS liquid medium and incubated for 2 hours to minimize any effects due to the transfer.

extract_protocol:
Seedlings were collected, dabbed dry and flash frozen in liquid nitrogen. Total RNA was extracted using the Zymo Direct-zol RNA Miniprep kit.
Libraries were constructed using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit.

treatment_protocol: Arabidopside A (Hansen, et al. The Plant Journal 2019) was added to a final concentration of 12.5uM for 2 hours.

tag: genotype

value: fer

tag: treatment

value: Aradopside

value: seedling


title: Volunteer AE4GD Sample DD44

value: Female

value: White

value: Administrative

tag: days since vaccine


title: Seedlings, fer Aradopside rep 2


title: Seedlings, fer Aradopside rep 1


title: NIH3T3 Vector (pBABEpuro) _SB2 (Replicate_2)


title: NIH3T3 Vector (pBABEpuro)_SB1 (Replicate_1)


title: Volunteer AGA4D Sample DD4F


title: Volunteer AE3D4 Sample DDGE

tag: vaccine


title: Volunteer EF33G Sample D3DF


title: Volunteer BGGDE Sample DDCE

value: BGGDE

value: Male


title: Volunteer EC0F3 Sample DDCB

value: Other

value: Student


title: Seedlings, fer control rep 4

value: control


title: Volunteer AD30C Sample DDA4


title: K-EBS-1

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

description:
Replicate 1
K-EBS_EB1_9991

data_processing:
Library strategy: Ampli-seq
RNAseq libraries were sequenced on a  Ion Proton.
Filtering with PrinSeq (0.20.4)
Reads were mapped to the Amplicons sequence reference using bowtie2 local (v2.3.4.1) .Reads below a mapping score of 10 or multi-mapped were filtered using samtools (v0.1.19)
The differential gene expression (DEG) between conditions was calculated with DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: excel files containing raw counts ( genes expression ) and DEG.

source_name: Keratinocyte EBS replicate 1

growth_protocol: WT and EBS keratinocytes were amplified in keratinocyte medium (CnT07; CELLnTEC) on collagen type I coated flasks at 15 000 cells/cm2 until 80% confluency.

extract_protocol:
For each of the 6 samples, 50 ng of total RNA was reverse transcribed using the Ion AmpliSeq Transcriptome Human Gene Expression kit following the protocol of the manufacturer (Thermofisher Scientific).
The cDNA libraries were amplified and barcoded using Ion AmpliSeq Transcriptome Human Gene Expression core panel and Ion Xpress Barcode Adapter (Thermofisher Scientific). The amplicons were quantified using Agilent High Sensitivity DNA kit  before the samples were pooled in sets of eight. Emulsion PCR and Enrichment was performed on the Ion OT2 system Instrument using the Ion PI Hi-Q OT2 200 kit (Thermofisher Scientific). Samples were loaded on an Ion PI v3 Chip and sequenced on the Ion Proton System using Ion PI Hi-Q sequencing  200 kit chemistry (200 bp read length; Thermofisher Scientifif).

value: Keratinocytes

value: EBS


title: Volunteer A4D3G Sample DDAG


title: Seedlings, fer control rep 3


title: Volunteer EC0FD Sample DDCC

value: Asian


title: Volunteer BGG4C Sample DD0G


title: K-WT-2

description:
Replicate 2
K-WT_PC1432

source_name: Keratinocyte WT replicate2

value: WT


title: K-WT-3

description:
Replicate 3
K-WT_PC15

source_name: Keratinocyte WT replicate3


title: Seedlings, fer Aradopside rep 3


title: Volunteer EAG4F Sample DCBA

source_name: Sera


title: Volunteer EG44D Sample DC3A

value: Nurse


title: Seedlings, fer control rep 2


title: Volunteer AD4FC Sample DCED

value: Latino


title: Volunteer A4BEF Sample DCDE

value: Food/EVS

value: Moderna


title: K-EBS-3

description:
Replicate 3
K-EBS_EB3_NAMAD

source_name: Keratinocyte EBS replicate 3


title: K-WT-1

description:
Replicate 1
K-WT_PC085

source_name: Keratinocyte WT replicate1


title: Volunteer AFCCA Sample CABB

value: AFCCA


title: Seedlings, fer control rep 1

value: fer

value: seedling


title: Volunteer FAGF0 Sample D043

value: Female


title: Volunteer AFAFG Sample CABE

value: AFAFG


title: Seedlings, WT Aradopside rep 4

value: Aradopside


title: K-EBS-2

description:
Replicate 2
K-EBS_EB2_10295

source_name: Keratinocyte EBS replicate 2


title: Volunteer BG4FD Sample CAEA

value: Male


title: Volunteer AGF3C Sample CAEC

value: White


title: Volunteer A043E Sample CAF4

value: Physician


title: Seedlings, WT Aradopside rep 3


title: Volunteer DAE3 Sample CAFG

value: Pfizer


title: Seedlings, WT Aradopside rep 1


title: Volunteer 3GC3 Sample CAFC


title: Seedlings, WT Aradopside rep 2


title: Volunteer BBA0E Sample CAD3


title: Volunteer AE04A Sample DC0D

value: Other


title: Volunteer A3BC3 Sample CACA

value: Asian


title: Volunteer ED3FE Sample CADC


title: AB9363

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Well-barcode-RMT are extracted from the 9 first base pairs in the R2 fastq sequences. Unique-molecular-identifier are extracted from the subsequent 8 base pairs in the R2 sequences. R1 contains the genomic sequences.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Peripheral blood

extract_protocol:
human sample collection: skin samples were obtained through punch biopsy (4 mm), 10 cm distal to the elbow and placed in saline containing tubes on ice and then transferred to cold FACS buffer (EDTA pH8.0 2mM, BSA 0.5% in PBS). Whole blood samples were collected at the time of skin biopsy, were placed in EDTA-containing tubes (Beckton Dickenson) on ice and diluted 1:1 with ice cold FACS buffer. Skin and blood samples immediately transported to the lab.
Skin cell suspension and blood mononuclear cells were stained with the following antibodies: CD45 (PerCp/Cyanine, 3040285.5, Biolegend), CD90 (PE 328144, Biolegend), LGR5 (PE, 373803, Biolegend), CD55 (FITC, 311306, Biolegend). All FACS antibodies were used with a 1:100 dilution. Samples were filtered through a 40μm strainer before commencing sorting. Single cell sorting was performed using FACSAria Fusion cell sorter (BD Biosciences, San Jose, CA). After doublets exclusion, isolated live cells were single-cell sorted into 384-well cell capture plates containing 2μL of lysis solution and barcoded poly(T) reverse-transcription (RT) primers for single-cell RNA-seq. Four empty wells were kept in each 384-well plate as a no-cell control for data analysis. Immediately after sorting, each plate was spun down to ensure cell immersion into the lysis solution, snap frozen on dry ice, and stored at –80°C until processed. Cells were analyzed using BD FACSDiva software (BD Bioscience) and FlowJo software (FlowJo, LLC).
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

treatment_protocol:
treatment protocol (1): To generate gentle and efficient single-cell suspensions from human skin tissue, we used Miltenyi human whole skin dissociation kit (catalog num. 130-101-540), which combines mechanical dissociation with enzymatic degradation of the extracellular adhesion proteins. In short, first we cut the skin biopsy into small pieces (< 1mm) and transferred them into gentleMACS C Tube containing 435µL of Buffer and 65 µL of enzyme mix. Next, samples were incubated in a water bath at 37 °C for 1h. After incubation we diluted the samples by adding 0.5 mL of cold cell culture medium, tightly closed C Tube and attached it upside down onto the sleeve of the gentleMACS dissociator, and run the gentleMACS Program h_skin_01. After a short centrifugation step to collect the sample material at the tube bottom, we applied the cell suspension to a 70 µm pre-separation filter, placed on a 15 mL tube, and washed with ice cold FACS buffer. Then, we centrifuged the cell suspension at 300×g for 10 minutes at 4°C and aspirated the supernatant completely. Finally, after red blood cell lysis (Sigma) for 5min at 4°C, centrifugation at 300×g for 10 minutes at 4°C, and washing, we resuspended the cells for FACS staining and sorting.
treatment protocol (2): Blood mononuclear cell separation was performed by density centrifugation media (Ficol-paque, GE Life Sciences) in a 1:1 ratio with blood cells. Centrifugation (460g, 25min) was performed at 10°C, and the mononuclear cells were carefully aspirated and washed with ice cold FACS buffer. After red blood cell lysis (Sigma) for 5 minutes at 4°C, centrifugation at 300×g for 10 minutes at 4°C, and washing, we resuspended the cells for FACS staining and sorting.

value: Blood

tag: selection marker

tag: patient id


title: Seedlings, WT control rep 4

value: WT

value: control


title: AB9360


title: AB9362

source_name: Forearm skin

value: Skin


title: Seedlings, WT control rep 3


title: AB9361


title: Volunteer AEFFD Sample CACF

value: AEFFD

value: Clinical staff


title: AB9359


title: Volunteer FB4BE Sample CACB

value: Nurse


title: Volunteer ACC34 Sample CBAF


title: Seedlings, WT control rep 2

value: seedling


title: AB9358


title: Volunteer A40AC Sample CBBB

value: Female


title: Volunteer B0C0D Sample CBBF


title: Volunteer FAEA4 Sample CBA0


title: Volunteer EBCBE Sample CBB4

value: EBCBE


title: AB9357


title: AB9356


title: Seedlings, WT control rep 1


title: Volunteer E3CG4 Sample CBE4

value: Latino


title: AB9355


title: Volunteer E0FCC Sample CBEA


title: Volunteer BE33F Sample CBEC


title: AB9354


title: Volunteer ADG04 Sample CBBD


title: Volunteer B3043 Sample CBBC

value: Male


title: Volunteer GE0FE Sample CBGB

value: White

value: Administrative


title: Volunteer EBD0A Sample CBF4


title: AB9353


title: Volunteer E0F00 Sample CBGE

value: Pfizer-BioNTech


title: Has2+/- KO mice 24 after OVA stimulation 3

city: Tsukuba

first: Takumi

last: Kiwamoto

address: 1-1-1 Tennoudai

department: Pulmonary Medicine

country: Japan

institute: University of Tsukuba

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 10.1.1; Qiagen, Redwood City, CA).
Genome_build: mm10

source_name: Lung tissue

extract_protocol:
Lung tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 500 ng total RNA was used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420). Poly-A purification: Poly-T column kit (NEB, E7490), followed by NEB kit (E7420). Illumina NextSeq500 was used for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype/variation

value: Has2+/- KO

value: sensitized and interanasaly stimulated with ovalbumin


title: Volunteer AGB03 Sample DB3F

value: Moderna


title: Volunteer B0CA3 Sample CBGF

value: Asian

value: Student


title: AB9352

tag: tissue

value: Skin


title: Has2+/- KO mice 24 after OVA stimulation 2


title: Has2+/- KO mice 24 after OVA stimulation 1


title: N#3 induced

type: RNA

city: Tokorozawa

first: Yuko

last: Seko

state: Saitama

address: 4-1 Namiki

institute: NRCD

description: Gene expression profiles in induced healthy fibroblasts

hyb_protocol: Reaction was hybridized to SurePrint G3 Human GE v2 8x60K Microarray.

scan_protocol: Slides were scanned on the Agilent SureScan G4900DA.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent).

source_name: induced healthy fibroblasts

label_protocol: 0.1 ug total RNA was labeled using the RNA Spike in kit (Agilent) according to the manufacurer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer, Qubit® 2.0 Fluorometer and Bioanalyzer.

growth_protocol: The dermal fibroblasts were cultured DMEM containing 10%FBS.

extract_protocol: Total RNA was isolated with PicoPureTM RNA Isolation Kit (Arcturus Bioscience, CA, USA) according to the manufacturer's instructions.

treatment_protocol: The fibroblasts cells were seeded in laminin-coated 6-well. The cells were infected with media containing retroviral vector particles as a mixture of the four transcription factors i.e., CRX, RAX, OTX2 and NeuroD. After the retroviral infection, the media was replaced with the differentiation media; DMEM/F12/B27 medium supplemented with  bFGF, EGF, fibronectin, 1% FBS.

tag: cell type

value: healty fibroblasts

value: induced


title: Volunteer FGFAE Sample DE3G

tag: volunteer id

value: FGFAE

tag: age


title: Volunteer GBABE Sample DE0D

value: GBABE

tag: gender

tag: ethnicity

value: Other

value: Nurse


title: AB9350


title: AB9351


title: WT mice 24 after OVA stimulation 3

value: WT


title: Volunteer ABCBD Sample DG33

value: ABCBD

tag: first vaccination

value: Pfizer


title: WT mice 24 after OVA stimulation 2


title: Volunteer EDBBC Sample D4FA

value: EDBBC

value: Male

tag: job/role

tag: second vaccination


title: Pt#1 induced

description: Gene expression profiles in induced patient-derived fibroblasts

source_name: induced patient-derived fibroblasts

value: patient-derived fibroblasts


title: AB9348


title: AB9349


title: Volunteer A0AC3 Sample DDAC


title: Volunteer AFFGA Sample D3BB

value: AFFGA


title: Volunteer AE3CG Sample DEBD


title: WT mice 24 after OVA stimulation 1

value: sensitized and interanasaly stimulated with ovalbumin


title: Pt#1 non-induced

description: Gene expression profiles in non-induced patient-derived fibroblasts

source_name: non-induced patient-derived fibroblasts

value: non-induced


title: Has2+/- KO mice control 3

value: Has2+/- KO

value: saline


title: Volunteer AD30A Sample DDB4

value: Female

value: Asian

value: Student


title: N#3 non-induced

description: Gene expression profiles in non-induced healty fibroblasts

source_name: non-induced healty fibroblasts

value: healty fibroblasts


title: Volunteer E4EGB Sample DCFD


title: Volunteer ACD00 Sample DG4B

value: Latino

value: Other


title: Volunteer BDFEE Sample DCD4

value: BDFEE

value: Clinical staff


title: AB9345

value: Skin


title: Has2+/- KO mice control 2


title: Volunteer BADAC Sample DCCB

value: BADAC

value: White

value: Nurse


title: Volunteer AEEC4 Sample DC4A

value: Administrative


title: AB9346


title: Volunteer A0A00 Sample D0AE


title: WT mice control 3

value: WT


title: Has2+/- KO mice control 1


title: AB9344


title: Volunteer AEG4G Sample D0F0

value: Male


title: Volunteer BAADG Sample DCDC

value: BAADG

value: Physician


title: WT mice control 1

value: saline


title: AB9347


title: WT mice control 2


title: Volunteer EBE3C Sample D0G0

value: Asian


title: Volunteer AF0BE Sample D00D

value: Female

value: Student

value: Moderna


title: Volunteer AF0G0 Sample D00B


title: Volunteer BG4FG Sample DDDD


title: AB8497


title: Volunteer BG44B Sample DD0F


title: Volunteer AEC0D Sample CAAA


title: AB8496


title: AB8494

value: Blood


title: Volunteer AC3EF Sample CAAE


title: Volunteer AE03B Sample CAAB


title: AB8495


title: Skin Af rep1 [A370]

city: Shanghai

first: Shiyi

last: Zhang

address: 800 Dongchuan Rd

institute: Shanghai Jiao Tong University

data_processing:
Raw sequences were mapped to the rat reference sequence by Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.16.1).
P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: Ensemble 96; http://ftp.ensembl.org/pub/release-105/fasta/rattus_norvegicus/cdna/
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Back skin

extract_protocol:
Back skins were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague-Dawley

value: Administer 30mg/kg Afatinib p.o. once daily until rash occurrence


title: Skin Af rep2 [A420]

value: Skin


title: Volunteer AECC0 Sample CABF

extract_protocol: Sera samples were extracted from finger pricks using a lancet and collected by capilary. Sera was then separated from the blood cells by centrifugation.

value: Latino


title: Skin Ge rep2 [G407]

value: Administer 80mg/kg Gefitinib p.o. once daily until rash occurrence


title: AB8492


title: Volunteer AC3G4 Sample CAB4

value: White


title: AB8493


title: Volunteer AC44B Sample CAEB


title: Skin WT rep2 [C413]

value: Untreated


title: Skin Ge rep1 [G401]


title: Volunteer AFAGB Sample CAEF

value: AFAGB


title: AB8491


title: Volunteer AC4C0 Sample CAEG


title: AB8490


title: Volunteer EEE3D Sample CAF0

value: Food/EVS


title: Skin WT rep1 [C412]


title: Volunteer AGF30 Sample CA4A

value: Nurse


title: AB8489


title: Volunteer AGGCD Sample CA3B

value: AGGCD

value: Male

value: Clinical staff


title: Volunteer FA343 Sample CA4G

value: Female

value: Asian


title: Volunteer B0D3G Sample CBFB

value: Student


title: Volunteer BDCDE Sample CBEB

value: BDCDE

value: Administrative


title: Volunteer AB4E3 Sample CBG3

value: Moderna


title: AB8488

value: Skin


title: AB8487


title: Volunteer AEC3D Sample CBGD

value: Latino

value: Pfizer


title: Volunteer AFAGG Sample CAB0

value: AFAGG

value: Other


title: AB8486

value: Blood


title: Volunteer B3FFE Sample CBEG


title: AB8485


title: Volunteer AC403 Sample CB44


title: Volunteer ADDEF Sample 34C0

value: ADDEF


title: Control leaf, Botrytis inoculated, t=12 h; replicate 3

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

hyb_protocol: Labelling, hybridisation and scanning were outsourced to a commercial provider (Nottingham Arabidopsis Stock Centre Affymetrix Service - http://arabidopsis.info/affy). Biotin Labelled cRNA using Affymetrix GeneChip Hybridization, Wash and Stain Kit, according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Labelling, hybridisation and scanning were outsourced to a commercial provider (Nottingham Arabidopsis Stock Centre Affymetrix Service - http://arabidopsis.info/affy). Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Normalisation performed using RMA algorithm in the R Bioconductor Suite

label: biotin

organism: Solanum lycopersicum

label_protocol: Labelling, hybridisation and scanning were outsourced to a commercial provider (Nottingham Arabidopsis Stock Centre Affymetrix Service - http://arabidopsis.info/affy). Labelled using protocol described in Affymetrix manual 3' IVT Express Kit User Manual

growth_protocol: Plants were grown in a peat-based compost mixture (Levingtons M3) and cultivated in a heated, passively ventilated glasshouse (min 18 °C+/- 2  max 25 °C+/- 3) with supplementary lighting (Osram Greenpower 600 W high pressure sodium lamps) to a minimum 250±25 μmol m-2s-1 PAR at the canopy. A minimum 16-hour photoperiod was maintained.

extract_protocol: RNA was extracted essentially as described by Verwoerd et. al. (Verwoerd TC, Dekker BMM, Hoekema A (1989) Nucleic Acids Research 17: 2362), scaled up accordingly and then purified using Qiagen RNeasy spin columns (Qiagen.com).

treatment_protocol: Seven-day-old seedlings were root-drenched with a volume of 5 mM BABA equivalent to one tenth of the volume of the compost growing medium to achieve a final concentration of 0.5 mM BABA around the root system. One week later, seedlings were gently removed from the compost, their root systems rinsed in water and then re-potted to new compost. Control plants were similarly treated but given a water root drench rather than BABA. Inoculations of tomato leaves with Botrytis cinerea were performed as previously described (Worrall et al., (2012) New Phytol 193: 770-778. doi: 10.1111/j.1469-8137.2011.03987.x).

value: leaf

tag: cultivar

value: Money Maker

value: Botrytis inoculated, t=12 h


title: AB8482


title: Control leaf, Botrytis inoculated, t=12 h; replicate 2

tag: treatment


title: Volunteer BFGAE Sample 33AD

first: Rafael

last: de Assis

address: 3800 PARKVIEW LN APT 38A, Irvine, CA 92612

institute: University of California Irvine

data_processing:
Raw data was normalized by re-scaling based on the positive control spots as descibed by Duarte J. 2013; Causton 2004 and Bolstad 2003
processed.xls: Normalized signal Intensity

value: BFGAE

value: Nurse

tag: days since vaccine


title: Volunteer BEAAB Sample 33AA

value: BEAAB

value: Female


title: AB8481


title: Volunteer AD0CE Sample 33BF

tag: vaccine


title: Control leaf, Botrytis inoculated, t=12 h; replicate 1


title: Volunteer AGCEF Sample 33A3

value: AGCEF

value: Male

value: Pfizer-BioNTech


title: Volunteer AA0CC Sample 33B4


title: Control leaf, mock inoculated, t= 12 h; replicate 2

source_name: Control leaf, mock inoculated, t= 12 h

value: mock inoculated, t= 12 h


title: Volunteer F00C4 Sample 33B3

value: Asian

value: Clinical staff

value: Moderna


title: Control leaf, mock inoculated, t= 12 h; replicate 3


title: Volunteer AGA4F Sample 33BD

value: Physician

value: Pfizer


title: Control leaf, mock inoculated, t= 12 h; replicate 1


title: Control leaf, Botrytis inoculated, t=9 h; replicate 3

value: Botrytis inoculated, t=9 h


title: Control leaf, Botrytis inoculated, t=9 h; replicate 1

value: leaf


title: Control leaf, mock inoculated, t= 9 h; replicate 3

source_name: Control leaf, mock inoculated, t= 9 h

value: Money Maker

value: mock inoculated, t= 9 h


title: Volunteer ADECG Sample 33A0

value: ADECG


title: Volunteer AC3EG Sample CB4A

value: White

value: Student


title: Volunteer A34BG Sample 3404


title: Volunteer AF0GE Sample CBGC

value: Female


title: AB8480

value: Blood

tag: selection marker


title: AB8478

tag: patient id


title: Volunteer AA3G4 Sample 33AB


title: AB8477


title: Control leaf, Botrytis inoculated, t=9 h; replicate 2


title: Volunteer EDED3 Sample 3403

value: Nurse


title: AB8484


title: AB8483

value: Skin


title: Volunteer ACBA3 Sample CB4G


title: Volunteer G3CAC Sample 33E3


title: Volunteer BAEA4 Sample 33ED

value: Male


title: AB8479


title: Volunteer BBG3E Sample 33E4


title: Volunteer ABCFC Sample 340B

value: ABCFC

value: Asian


title: AB8475


title: Volunteer A3D4F Sample DFCD

value: Latino

value: Food/EVS


title: Volunteer ABF4E Sample 33GC

value: Pfizer


title: Volunteer A0CA3 Sample D30B

value: Physician


title: AB8474


title: Volunteer EED43 Sample 3DEG

value: Moderna


title: Volunteer BG443 Sample DDC0


title: Volunteer AEF4F Sample DCAC

value: Administrative


title: Volunteer ADACE Sample DCE0

value: ADACE


title: Volunteer AFDF3 Sample D3DD


title: Control leaf, Botrytis inoculated, t=6 h; replicate 2

value: leaf

value: Money Maker

value: Botrytis inoculated, t=6 h


title: Volunteer GAD3E Sample DC03

value: Other


title: Control leaf, mock inoculated, t= 9 h; replicate 2

value: mock inoculated, t= 9 h


title: Volunteer B0D3D Sample DDCA

value: Female


title: AB8476

value: Blood


title: Control leaf, mock inoculated, t= 6 h; replicate 2

source_name: Control leaf, mock inoculated, t= 6 h

value: mock inoculated, t= 6 h


title: AB8469

value: Skin


title: Volunteer AEF3C Sample DCGF

value: Male

value: Asian

value: Nurse


title: AB8473


title: AB8471


title: AB8472


title: AB8468


title: Control leaf, Botrytis inoculated, t=6 h; replicate 3


title: Control leaf, Botrytis inoculated, t=0 h; replicate 2

value: Botrytis inoculated, t=0 h


title: Control leaf, Botrytis inoculated, t=6 h; replicate 1


title: Control leaf, mock inoculated, t= 6 h; replicate 1


title: Control leaf, mock inoculated, t= 9 h; replicate 1


title: Volunteer AF0FB Sample D00F

value: White

value: Student

value: Pfizer


title: AB8470


title: Volunteer BG3GG Sample CBB0


title: AB8466


title: Volunteer AE4AD Sample D0AA


title: Volunteer B30CE Sample CA3G


title: Control leaf, Botrytis inoculated, t=0 h; replicate 1


title: Control leaf, mock inoculated, t= 6 h; replicate 3


title: Volunteer EBGBD Sample DC04

value: EBGBD


title: AB8465


title: Volunteer EF40F Sample CA4E


title: Volunteer EG03B Sample 33BB


title: Volunteer G3B04 Sample CBB3

value: Latino

value: Clinical staff

value: Moderna


title: Volunteer EB3CA Sample CBAA


title: Volunteer A3ABF Sample 33BG

value: Other


title: Control leaf, Botrytis inoculated, t=0 h; replicate 3

value: leaf

value: Money Maker


title: Control leaf, mock inoculated, t= 0 h; replicate 2

source_name: Control leaf, mock inoculated, t= 0 h

value: mock inoculated, t= 0 h


title: Volunteer A0C0D Sample 33EE

value: Female


title: Volunteer AE44E Sample 33EF


title: Volunteer AG3B0 Sample 334A


title: AB8467

value: Blood


title: Volunteer A4EC3 Sample CBF3

value: Male


title: Volunteer ABGDD Sample 3340

value: ABGDD


title: AB8464


title: Control leaf, mock inoculated, t= 0 h; replicate 3