title: PBMC_d4_CD56loCD16+  [000008514669_B05]


title: pTSA1-mCherry-tTSA1, modNAA, 2

status: Public on Apr 09 2022

type: SRA

city: Edinburgh

first: Edward

last: Wallace

address: Waddington 2.18, Max Born Crescent, King’s Buildings

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

description:
QS_processed_polyAconstructs.tsv
QS_processed_polyAcontrols.tsv
QS_all_sample_gene_counts.tsv

library_source: transcriptomic

data_processing:
Read quality was checked with fastqc=0.11.9
Adapters were removed with cutadapt=1.18 (Options = --trim-n -O 1 -m 20)
Alignment was completed with hisat2=2.1.0 (Options = --no-spliced-alignment --no-unal --maxins 1500 -k 2)
Reads per gene were counted with featureCounts=2.00 (Options = -p -s 2 -R BAM)
Bed files were created with bedtools=2.30.0
Alignment quality was checked with multiQC=1.9
Bam files were create with samtools=1.11
Analysis was conducted using the Nextflow pipeline available here: https://github.com/DimmestP/nextflow_paired_reads_pipeline
The custom 3’UTR gff file used in this analysis was created by the code available here: https://github.com/ewallace/yeastutrgff
Assembly: sacCer3 (R64-2)
Supplementary files format and content: Format: tsv, Content: quantified reads ending in 3'-UTR region of reporter constructs, per construct
Supplementary files format and content: Format: tsv, Content: raw read counts mapped to each gene across the genome, one file per sample.
Supplementary files format and content: Format: tsv, Content: quantified reads ending in 3'-UTR region of control gene, per construct

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae expressing plasmid with reporter gene pTsa1-mCherry-tTsa1_modNAA

growth_protocol: Yeast cultures were grown for 4h at 30degC, 200rpm, in liquid SC-Ura medium up to OD600=0.7

extract_protocol:
RNA extraction protocol: dx.doi.org/10.17504/protocols.io.beetjben
QuantSeq REV (Lexogen)
3'-end sequencing

tag: parent strain

tag: plasmid

value: pTSA1-mCherry-tTSA1_modNAA (pJA0091)


title: pTSA1-mCherry-tTSA1, modNAA, 1


title: PBMC_d5_CD56hiCD16- [000008514669_G05]

city: Maynooth

first: Mark

last: Robinson

state: Co. Kildare

address: Department of Biology, Maynooth University

department: Department of Biology

country: Ireland

institute: Maynooth University

data_processing:
Sequencing data quality was assessed using FastQC
Reads were aligned to the hg38 human genome build using the HISAT2 with parameters --score-min L,0,-2 --no-mixed --no-discordant --no-unal
Multimapping reads were removed and BAM files were generated using samtools view with parameters -h -q 50 -b
BAM file alignments were loaded into Qlucore Omics Explorer 3.2 using the UCSC hg38 genome gtf file. The BAM files were loaded with a minimum of one read count across all samples was required for inclusion of each specific variable. Expression values were calculated using the "TMM" approach. Differential expression was assessed using t-test and ANOVA, controlling for the false discovery rate using the Benjamini-Hochberg method.
Assembly: hg38
Supplementary files format and content: CSV text file containing expression values calculated using the TMM approach. Differential expression was assessed using ANOVA, controlling for the false discovery rate using the Benjamini-Hochberg method.

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
NK cell subpopulations cells were stained with the following antibodies: CD56, clone NCAM16.2; CD16, clone 3G8; CD3, clone UCHT1; CD45, clone HI30 (all BD Biosciences); CD127, clone REA614 (Miltenyi Biotec); with propidium iodide (ThermoFischer Scientific, Massachusetts, USA) for live/dead discrimination. NK cell subpopulations were then sorted to >98% purity using either a FACS Aria or a FACS Melody (BD Biosciences). A total of 1,500 cells of each sub-population of interest was FACS sorted into 1x TCL buffer (Qiagen, Manchester, UK) with 1% b-mercaptoethanol (molecular biology grade, v/v; Sigma-Aldrich, Missouri, USA). Sorted samples were frozen on dry-ice and stored at -80°C until library preparation.
Libraries were constructed using a modified version of the SMART-Seq2 protocol (as described in Picelli et. al., 2013 and Picelli et. al., 2014). Polyadenylated transcripts were captured, reverse transcribed, then template switching was performed and pre-amplification used to increase both yield and length of cDNA inserts generated. The generated libraries were sequenced on an Illumina NextSeq 500using a High Output kit to generate 2 x 25 bp indexed reads.

tag: cell type

tag: tissue

value: PBMC

tag: donor id


title: PBMC_d4_CD56hiCD16- [000008514669_C05]


title: PBMC_d2_CD56loCD16+  [000008514669_H03]


title: Panc10.05 cells, Parental indisulam, rep 2

city: Amsterdam

first: Rodrigo

last: Leite de Oliveira

address: De Boelelaan 1118

country: Netherlands

institute: Amsterdam UMC / location VUmc

data_processing:
Reads were aligned to the prebuilt reference GRCh38 genome_snp_tran using HiSAT2 version 2.2.1
PCR duplcates were marked using a UMI barcode sequence using Picard version UmiAwareMarkDuplicatesWithMateCigar
Genecounts were generated by counting non PCR duplicated mapped reads overlapping genes defined in Ensembl GTF release 100 using a Htseq-count union strategy
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files with genecounts for Ensembl gene id's

growth_protocol: A549 cells were grown in RPMI (Gibco) supplemented with 10% FBS

extract_protocol:
Total RNA was extracted with RNeasy mini kit (Qiagen, cat# 74106) including a column DNase digestion (Qiagen, cat#79254).
polyA+ stranded RNA library prep

treatment_protocol: A549 cells were treated with 2µM Indisulam for 18 hours.

value: pancreatic cancer

tag: cell line

tag: phenotype

value: parental

tag: treatment

value: indisulam


title: Panc10.05 cells, Resistant untreated, rep 1

value: indisulam-resistant

value: untreated


title: pTSA1-mCherry-tTSA1, modNNN, 1

source_name: S.cerevisiae expressing plasmid with reporter gene pTsa1-mCherry-tTsa1_modNNN

value: pTSA1-mCherry-tTSA1_modNNN (pJA0089)


title: PBMC_d1_CD56loCD16+  [000008514669_H02]


title: PBMC_d1_CD56hiCD16- [000008514669_A03]


title: Panc10.05 cells, Parental untreated, rep 2


title: Overexpression-WalR-D54E_biol rep1

city: Iowa City

first: Craig

last: Ellermeier

state: IA

address: 431 Newton Road

department: Microbiology and Immunology

country: USA

institute: University of Iowa

description: High Output 75cyc

data_processing:
Fastq files were trimmed and filtered using a combination of Trimmomatic and FastQC
Alignment, normalization and differential expression were analyzed with SeqMan NGen® Version 17.2. DNASTAR, Madison, WI.
Annotation was imported from NCBI with additional information obtained from proGenomes v2.1.
All subsequent analysis was performed in Excel.
Assembly: AM180355
Supplementary files format and content: Comma separated values (csv) file contains linear rlog reads, log2 fold change and adjusted P-value

organism: Clostridioides difficile

source_name: Bacterial

growth_protocol: All cultures were grown in tryptone-yeast exract broth at 37C under anaerobic conditions

extract_protocol:
Cultures were fixed by mixing with an equal volume of cells with ice-cold 1:1 ethanol:acetone. Cells were lysed with a FastPrep-24 homogenizer and RNA was extracted with the Qiagen RNeasy kit. All samples had a RIN of 9.4 or higher (Agilent Bioanalyzer).
Illumina Stranded RNA library preparation paired with RiboZero Plus  was prepared per manufacturer's specifications.

treatment_protocol:
Overexpression: strains were subcultured to OD600=0.05, grown to 0.2, induced with 3% xylose, grown for an additional 3h and fixed.
No xylose: strains were subcultured to OD600=0.03 and grown to 0.7 (~5-6h) and fixed.
Low xylose: strains were subcultured to OD600=0.03, grown to 0.3, back-diluted to 0.1 and induced with 0.1% xylose. They were then grown for an additional 2.5h and fixed.

value: Bacterial

tag: genotype

value: Overexpression (3% xylose, 3h)


title: M38

city: Kunming

first: Kai

last: Qian

address: Jinbi Road, 157#, Xishan District

country: China

institute: The First People’s Hospital of Yunnan Province

library_source: genomic

data_processing:
Paired-end reads   were merged using FLASH v1.2.7, and tags with more than six mismatches were   discarded. The merged tags with an average quality score <20 in a 50 bp sliding window   were determined using Trimmomatic and those shorter than 350 bps were removed.
Possible chimeras were further removed and the denoised sequences were clustered into   operational taxonomic units (OTUs) with 97% similarity using USEARCH (version 10.0).
Taxonomy was assigned to all OTUs by searching against the Silva databases   (Release128) using QIIME software.
Assembly: silva

molecule: genomic DNA

organism: human lung metagenome

source_name: bacteria DNA

extract_protocol:
The bacterial DNA was extracted from human airway samples with a QIAamp Fast DNA stool Mini Kit   (Qiagen, Cat# 51604) and PCR amplification was conducted with barcoded specific bacterial   primers targeting the variable region 3–4 (V3–V4) of the 16S rRNA gene: forward primer 338F:   5'- ACTCCTACGGGAGGCAGCA-3' and reverse primer 806R: 5'-  GGACTACHVGGGTWTCTAAT-3'.
Construction of sequencing libraries and paired-end sequencing was performed on an Illumina NovaSeq6000 platform at Biomarker   Technologies Co, Ltd. (Beijing, China) according to standard protocols.

value: BLAF


title: M37


title: M36


title: M39


title: M35


title: Engineered Cardiomyocytes, MOI5 S3

city: Milwaukee

first: Ulrich

last: Broeckel

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description:
SARSCoV2 CM
MOI5_redo_2

data_processing:
The raw reads in FASTQ format were aligned to the human hg19 reference genome using bwa mem with default parameters: bwa mem -M -t 8 -R "@RG\tID:SampleName\tPL:ILLUMINA\tSM:SampleName" -L 5
Gene quantification was done using HTSeq using the default parameters: htseq-count -f bam -r pos -s no Sorted.bam Transcriptome.rna_manifest.20190313.geneExpression.targets.gtf
reads with median count less than 10 removed
raw counts vst normalized and differential gene expression was analyzed using the DESeq2 (v.1.26.0) R/Bioconductor package
Genome_build: hg19, custom annotation GTF file for targeted transcripts (Transcriptome.rna_manifest.20190313.geneExpression.targets.gtf) received from the manufacturer
Supplementary_files_format_and_content: Matrix table with raw gene counts (rows) for all AmpliSeq targets and sample names (columns)

source_name: Engineered Cardiomyocytes, MOI5

growth_protocol: Cardiac tissues were created by a combination of human induced pluripotent stem cell (BJ1D, hiPSC) cardiomyocytes and human ventricular cardiac fibroblasts with collagen-based hydrogel. After one week of cell-gel compaction to stabilize the tissue size and additional one week of electrical stimulation to promote maturation.

extract_protocol:
Bulk mRNA of cardiac tissue was extracted by PicoPure™ RNA Isolation Kit (Thermofisher Scientific) following cell pellet RNA extraction protocol
Targeted whole transcriptome sequencing was done using the AmpliSeq for Illumina Transcriptome Human Gene Expression Panel (Illumina, Inc) following manufacturer’s recommendations.
Targeted whole transcriptome sequencing
AmpliSeq Targeted RNA

treatment_protocol: Cardiac tisuses and the cardiomyopathy model with one week  agiotensin II treatment were exposed to SAR-CoV-2. During the first week post infection, the cardiac tissues were treated with extracellular vesicles derived from hiPSC (BJ1D). RNA sequencing was performed two weeks after infection.

value: Engineered Cardiomyocytes

tag: alias

value: MOI5 redo_2


title: pTSA1-mCherry-tTSA1, WT, 1

source_name: S.cerevisiae expressing plasmid with reporter gene pTsa1-mCherry-tTsa1_WT

value: pTSA1-mCherry-tTSA1_WT (pJA0088)


title: pTSA1-mCherry-tTSA1, WT, 2


title: FM_AEV_GR_siRNA.MPA

city: Durham

first: Sarah

middle: Jean

last: Cunningham

state: NC

address: 101 Science Dr, IGSP Box 3382

institute: Duke University

data_processing:
Illumina adapters were removed using Trimmomatric v0.32
Reads less than 20 nucleatides were filtered out from further analysis
Seqeunces were aligned to the GRCh38 human referende genome using the alignment too STARv2.4.2a with the default parameter except for "--outFilterMultimapNmax1' to remove multimapping reads.
Reads per Killobase Mapped and Transcripts per Million were computed for each mapped gene using RSEM v1.2.25
Assembly: human NCBI genome build 38
Supplementary files format and content: Gene counts for each library

source_name: Patient 10 amnion GR siRNA MPA

growth_protocol: Amnion epithelial cells from healthy cesearean section patients were harvested and isolated.

extract_protocol:
Cells were lyzed with Trizol reagent and the RNA was isolated with Qiagen Rneasy kit with optional on column Dnase
Libraries were seqeunced using Illumina's TruSeq stranded mRNA-seq kit. They were then sequenced on an Illumina Illumina NextSeq using 50 base pair dual end sequencing

treatment_protocol: Cells were treated with 10-6M medroxyprogesterone acetate. A portion of cells were treated with 10 ng/mL TNFa.

value: Amnion epithelial cells

tag: patient

value: Patient 10

tag: sirna

value: glucocorticoid receptor knockdown

tag: tnfa challenge

value: No


title: FM_AEV_GR_siRNA.MPA_TNF

source_name: Patient 10 amnion GR siRNA MPA+TNF

value: Yes


title: pRPS3-mCherry-tRPS3, modHTH, 2

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_modHTH

value: pRPS3-mCherry-tRPS3_modHTH (pJA0073)


title: Engineered Cardiomyocytes, Control S3

description:
SARSCoV2 CM
Control1_9

source_name: Engineered Cardiomyocytes, Control

value: Control


title: Panc10.05 cells, Parental indisulam, rep 1

value: pancreatic cancer

value: parental

value: indisulam


title: FM_AEV_Control_siRNA.MPA

source_name: Patient 10 amnion Control siRNA MPA

value: control siRNA


title: M34


title: pRPS3-mCherry-tRPS3, modHTH, 1


title: Engineered Cardiomyocytes, MOI5 EV S4

description:
SARSCoV2 CM
MOI5_EV_8

source_name: Engineered Cardiomyocytes, MOI5 EV

value: MOI5 EV

value: MOI5 EV_8


title: pRPS3-mCherry-tRPS3, modNAA, 2

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_modNAA

value: pRPS3-mCherry-tRPS3_modNAA (pJA0070)


title: FM_AEV_Control_siRNA.MPA_TNF

source_name: Patient 10 amnion Control siRNA MPA+TNF


title: Panc10.05 cells, Parental untreated, rep 1

value: untreated


title: pRPS3-mCherry-tRPS3, modNAA, 1


title: M31

value: BLAF


title: FM_AES_GR_siRNA.MPA

source_name: Patient 9 amnion GR siRNA MPA

value: Patient 9


title: pRPS3-mCherry-tRPS3, modNNN, 2

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_modNNN

value: pRPS3-mCherry-tRPS3_modNNN (pJA0068)


title: M32

value: PSB


title: Engineered Cardiomyocytes, MOI5 EV S3

description:
SARSCoV2 CM
MOI5_EV_7

value: Engineered Cardiomyocytes

value: MOI5 EV_7


title: pRPS3-mCherry-tRPS3, modNNN, 1


title: Engineered Cardiomyocytes, MOI5 EV S2

description:
SARSCoV2 CM
MOI5_EV_10

value: MOI5 EV_10


title: M29


title: M30


title: FM_AES_Control_siRNA.MPA_TNF

source_name: Patient 9 amnion Control siRNA MPA+TNF

value: Amnion epithelial cells

value: Yes


title: Engineered Cardiomyocytes, MOI5 S2

description:
SARSCoV2 CM
MOI5_1


title: M33


title: Engineered Cardiomyocytes, MOI5 S1

description:
SARSCoV2 CM
MOI5_11


title: FM_AES_Control_siRNA.MPA

source_name: Patient 9 amnion Control siRNA MPA

value: No


title: pRPS3-mCherry-tRPS3, WT, 1

source_name: S.cerevisiae expressing plasmid with reporter gene pRps3-mCherry-tRps3_WT

value: pRPS3-mCherry-tRPS3_WT (pJA0066)


title: M28


title: Engineered Cardiomyocytes, Control S2

description:
SARSCoV2 CM
Control5_S11

value: Control


title: FM_AEO_GR_siRNA.MPA_TNF

source_name: Patient 8 amnion GR siRNA MPA+TNF

value: Patient 8

value: glucocorticoid receptor knockdown


title: FM_AES_GR_siRNA.MPA_TNF

source_name: Patient 9 amnion GR siRNA MPA+TNF


title: M27

source_name: bacteria DNA


title: Choroid - PAPA-NONOate (control) [L8]

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

data_processing:
Quality trim to a minimum of Q15
gsnap -D ./ -d Chicken_GRCg6a --use-splicing=chicken.splicesites --max-mismatches=0.06 -i2 -n2 -Q --gunzip --force-xs-dir --nofails -B5 -t${num_processors} --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam $outfile_R1 $outfile_R2 | samtools view -bS -@ ${num_processors} - | samtools sort -@ ${num_processors} -o ./Illumina_data/${j}.sorted.bam -; samtools index ./Illumina_data/${j}.sorted.bam
split forward and reverse reads using SAMTOOLS
call FPKM using CUFFLINKS, applying anti-sense reads to sense genes, and sense reads to anti-sense genes
Assembly: GRCg6a
Supplementary files format and content: Excel file containing FPKM values

organism: Gallus gallus

source_name: Choroid - PAPA-NONOate (control)

growth_protocol: Chicks were maintained in standard animal housing with a 12-hour light/dark cycle

extract_protocol:
Choroids were removed, snap frozen in liquid nitrogen, and RNA was extracted using TRIzol reagent. Illumina NEBNext poly(A) mRNA isolation kit and SWIFT RNA Library kit were used with 100ng of total RNA for the construction of sequencing libraries
Swift directional mRNA prep

treatment_protocol: Choroids were incubated with 1.5 mM PAPA-NONOate for 24 hours at 37 °C with 5% CO2

value: Whole tissue homogenate

tag: strain

value: Domesticus

tag: age

value: Post hatch day 15


title: M26


title: Engineered Cardiomyocytes, Control S1

description:
SARSCoV2 CM
Control3_S9


title: FM_AEO_GR_siRNA.MPA

source_name: Patient 8 amnion GR siRNA MPA


title: FM_AEO_Control_siRNA.MPA_TNF

source_name: Patient 8 amnion Control siRNA MPA+TNF

value: control siRNA


title: Engineered Cardiomyocytes, MOI5 EV S1

description:
SARSCoV2 CM
MOI5_EV_S13

value: MOI5 EV

value: MOI5 EV_S13


title: Choroid - PAPA-NONOate (control) [L5]


title: M25

value: BLAF


title: FM_AEO_Control_siRNA.MPA

source_name: Patient 8 amnion Control siRNA MPA


title: Choroid - PAPA-NONOate (control) [L4]


title: FM_AEJ_GR_siRNA.MPA_TNF

source_name: Patient 7 amnion GR siRNA MPA+TNF

value: Patient 7


title: pRPS3-mCherry-tRPS3, WT, 2


title: Engineered Cardiomyocytes, Ang II MOI5 S2

description:
SARSCoV2 CM
AngII_MOI5_4

source_name: Engineered Cardiomyocytes, Ang II MOI5

value: Engineered Cardiomyocytes

value: Ang II MOI5

value: Ang II MOI5_4


title: M24

value: PSB


title: Choroid - PAPA-NONOate (control) [L2]


title: Choroid + PAPA-NONOate [R8]

source_name: Choroid + PAPA-NONOate


title: M22


title: Engineered Cardiomyocytes, Ang II MOI5 S1

description:
SARSCoV2 CM
AngII_MOI5_3

value: Ang II MOI5_3


title: FM_AEJ_GR_siRNA.MPA

source_name: Patient 7 amnion GR siRNA MPA

value: Amnion epithelial cells

value: No


title: Engineered Cardiomyocytes, Ang II S4

description:
SARSCoV2 CM
AngII_4

source_name: Engineered Cardiomyocytes, Ang II

value: Ang II

value: Ang II_4


title: Choroid + PAPA-NONOate [R5]

value: Whole tissue homogenate


title: M21


title: Choroid + PAPA-NONOate [R4]

value: Domesticus


title: M20


title: FM_AEJ_Control_siRNA.MPA

source_name: Patient 7 amnion Control siRNA MPA


title: Engineered Cardiomyocytes, Ang II S3

description:
SARSCoV2 CM
AngII_3

value: Ang II_3


title: Engineered Cardiomyocytes, Ang II S2

description:
SARSCoV2 CM
AngII_2

value: Ang II_2


title: Choroid - PAPA-NONOate (control) [L3]

value: Post hatch day 15


title: Choroid + PAPA-NONOate [R3]


title: FM_AEG_GR_siRNA.MPA_TNF

source_name: Patient 6 amnion GR siRNA MPA+TNF

value: Patient 6

value: glucocorticoid receptor knockdown

value: Yes


title: Choroid + PAPA-NONOate [R2]


title: M19

value: BLAF


title: Engineered Cardiomyocytes, Ang II S1

description:
SARSCoV2 CM
AngII_1

value: Engineered Cardiomyocytes

value: Ang II_1


title: FM_AEG_GR_siRNA.MPA

source_name: Patient 6 amnion GR siRNA MPA


title: Engineered Cardiomyocytes, Ang II MOI5 S3

description:
SARSCoV2 CM
AngII_MOI5_5

value: Ang II MOI5

value: Ang II MOI5_5


title: FM_AEG_Control_siRNA.MPA_TNF

source_name: Patient 6 amnion Control siRNA MPA+TNF

value: Amnion epithelial cells

value: control siRNA


title: M23


title: M17


title: M18

value: PSB


title: FM_AEG_Control_siRNA.MPA

source_name: Patient 6 amnion Control siRNA MPA

value: No


title: LCFA + GSK0660 rep 3

city: New York

first: Nadeera

middle: Madhavi

last: Wickramasinghe

state: NY

address: 3227 Broadway

institute: Columbia University

description: Sample 18

data_processing:
Adapters were trimmed from the raw fastq data with cutadapt, and the raw data was aligned to hg38 with bwa mem.
PCR duplicates were removed with Picard, in addition to reads mapping to mitochondrial sequences or known problematic genomic regions in the ENCODE blacklist. Macs2 was used to call peaks with the bampe parameter.
To reduce false positives, peaks were used when overlapping with consensus regions mapped in at least two samples. Featurecounts was used to count reads associated with known promoter regions or candidate regulatory elements listed in the SCREEN (Search Candidate cis-Regulatory Elements by ENCODE) database.
DESeq2 was used to identify differential peaks with p<0.05, and peaks were annotated with the closest genes.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated text file containing gene-level counts for each ATAC-Seq sample.

source_name: cardiomyocyte

growth_protocol: Standard EB-differentiation protocols were used to generate PSC-derived cardiomyocytes, which were either cultured as Ebs, dissociated and plated as monolayers or dissociated and constructed into EHTs. A subset of cells were also subjected to lactate selection.

extract_protocol:
PSC-derived cardiomyocytes were dissociated using Collagenase Type II and FACS-isolated through SIRPA+ CD90- gating.
Lysed cells were incubated with 25 μL TD buffer, 2.5 μL Tn5 transposase (Illumina; Cat No: #20034198) and 22.5 μL nuclease-free H20 at 37°C for 30 min with gentle agitation. After purification (Qiagen; Cat No: #28004), transposed DNA fragments were amplified with custom PCR primers (Buenrostro et al., 2013) for a total of 9 cycles. The final PCR cycle number needed to minimally amplify libraries was determined by a separate qPCR reaction as described in Buenrostro et al., 2015 to minimize GC and size bias.

treatment_protocol: PSC-derived cardiomyocytes were treated with either GW0742 (5µM) orGSK0660 (2.5µM), and with or without LCFAs (12.5µM; palmitic acid, oleic acid, linoleic acid).

value: hPSC-derived cardiomyocyte

value: LCFA + GSK0660

tag: treatment duration

value: 28 days


title: M16


title: GSK0660 rep 3

description: Sample 17


title: FM_AEJ_Control_siRNA.MPA_TNF

source_name: Patient 7 amnion Control siRNA MPA+TNF

value: Patient 7


title: LCFA + GW0742 rep 3

description: Sample 16

value: LCFA + GW0742


title: M15

source_name: bacteria DNA


title: FM_AEF_GR_siRNA.MPA

source_name: Patient 5 amnion GR siRNA MPA

value: Patient 5


title: GW0742 rep 3

description: Sample 15


title: LCFA rep 3

description: Sample 14

value: LCFA


title: Control rep 3

description: Sample 13

value: Control


title: M13

value: BLAF


title: FM_AEF_Control_siRNA.MPA

source_name: Patient 5 amnion Control siRNA MPA


title: LCFA + GSK0660 rep 2

description: Sample 12


title: M12


title: M11


title: FM_AED_GR_siRNA.MPA_TNF

source_name: Patient 4 amnion GR siRNA MPA+TNF

value: Patient 4

value: glucocorticoid receptor knockdown

value: Yes


title: M10


title: FM_AED_Control_siRNA.MPA_TNF

source_name: Patient 4 amnion Control siRNA MPA+TNF


title: FM_AED_GR_siRNA.MPA

source_name: Patient 4 amnion GR siRNA MPA


title: LCFA + GW0742 rep 2

description: Sample 10


title: GW0742 rep 2

description: Sample 9


title: FM_AED_Control_siRNA.MPA

source_name: Patient 4 amnion Control siRNA MPA


title: FM_AEF_GR_siRNA.MPA_TNF

source_name: Patient 5 amnion GR siRNA MPA+TNF


title: M9


title: M8


title: M7


title: Control rep 2

description: Sample 7


title: M14


title: Sox17eKO-2

city: Bronx

first: Deyou

last: Zheng

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm10) using TopHat2. Based on GENCODE database (vM6), the number of RNA-seq fragments mapped to each gene was determined by HTSeq. Unnormalized count numbers are provided as processed data files.
Genome_build: mm10

organism: Mus musculus

source_name: outflow tract part of heart

growth_protocol: Mice of wildtype (n=20) and Sox17 gene knockout (n=20) at embryonic 12.5 days were isolated form anaesthetized littles.

extract_protocol:
Total RNA isolated according TRIZOL Reagent (ambion, lot:123906) protocol. Detail steps could be find at the link of: https://tools.thermofisher.com/content/sfs/manuals/trizol_reagent.pdf
RNA libraries were prepared for sequencing using standard Illumina strand-specific protocols. Detail steps could be find at the link of: http://wasp.einstein.yu.edu/index.php/Protocol:directional_WholeTranscript_seq

treatment_protocol: Outflow tract part of hearts were isolated from mice body at ice bed and collected in 1ml of Trizol. 10 pooled hearts as one biological repeat.

value: Embryonic 12.5 day

value: Sox17 gene knockout at aortic root endothelium by Nfatc1 enhancer Cre

value: heart outflow tract


title: Sox17eKO-1


title: LCFA rep 2

description: Sample 8


title: LCFA + GSK0660 rep 1

description: Sample 6


title: M5


title: WT-2

value: wild type


title: WT-1


title: M6

value: PSB


title: FM_AEF_Control_siRNA.MPA_TNF

source_name: Patient 5 amnion Control siRNA MPA+TNF

value: Amnion epithelial cells

value: control siRNA


title: GSK0660 rep 1

description: Sample 5

value: hPSC-derived cardiomyocyte

value: 28 days


title: M4


title: LCFA + GW0742 rep 1

description: Sample 4

value: LCFA + GW0742


title: GSK0660 rep 2

description: Sample 11


title: M3


title: GW0742 rep 1

description: Sample 3


title: 6 hours after LPS activation

city: New Haven

first: Zhuo

last: Chen

state: CT

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

library_source: transcriptomic single cell

data_processing:
Using DropSeq Tools to derive digital expression matrix from raw Fastq files
Filter out low-quality cells expressing fewer than 500 genes
Downstream data analysis and visualization using R package "Seurat" using default settings
Marker gene lists and p value output from "Seurat" was taken as input for gene ontology and pathway analysis using R packages "Gage" and "Pathview"
Assembly: hg19
Supplementary files format and content: Digital gene expression matrix with raw gene counts of each cell and gene

source_name: U937-derived macrophages

growth_protocol: Human U937 cell line was purchased from American Type Culture Collection (ATCC) and cultured in RPMI medium 1640 (Gibco; Invitrogen) supplemented with 10% fetal bovine serum (ATCC). The U937 cells were differentiated with 50 ng mL−1 phorbol 12-myristate 13-acetate (PMA) (Fisher) for 48 h, followed by culture in fresh standard medium for 24 h. The cells were harvested with trypsin for single-cell experiments.

extract_protocol: Standard DropSeq protocol was performed using custom built device. Then library were constructed using Illumina Nextera XT kit following standard protocol.

treatment_protocol: Cells were challenged with 100ng/mL LPS (Sigma)

value: U937-derived macrophages

value: LPS

tag: time

value: 6 hours after LPS activation


title: M2

value: protected specimen brushing(PSB)


title: 4 hours after LPS activation

value: 4 hours after LPS activation


title: LCFA rep 1

description: Sample 2

value: LCFA


title: M1

value: bronchoalveolar lavage fluid(BLAF)


title: Control rep 1

description: Sample 1

value: Control


title: Basal condition before LPS activation

value: No treatment

value: Basal condition before LPS activation


title: 2 hours after LPS activation

value: 2 hours after LPS activation


title: bulk_rnaseq_lag3_ko_islet_7

status: Public on Apr 08 2022

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

data_processing:
Demultiplexing was performed using bcl2fastq (v2.20.0).
For bulk RNAseq, STAR (v2.5.2a) was used for alignment. Unique mapped reads were normalized using PORT and counts were converted to log2 counts per million. Quantile normalization and precision weighting was performed using limma. For scRNAseq, cellranger (v3.1.0) was used for alignment and to create feature barcode matrices. For scTCRseq, cellranger vdj (v3.1.0) was used to build T cell receptor sequences from single cells. For CITEseq, cite-seq-count (v1.2) was used for alignment and to build feature barcode matrices. For scATACseq, cellranger-arc (v2.0.0) was used for peak calling and counting ATAC molecules and creation of Bigwig files and peak barcode matrices.
Assembly: GRCm38/mm10
Supplementary files format and content: bulk RNAseq: gzipped tar text-delimited file of gene counts per sample; scRNAseq: gzipped tar directory containing filtered feature barcode matrices; CITEseq: gzipped tar directory containing filtered feature barcode matrices; TCRseq: gzipped tar text-dellimited file of TCR reconstruction; multiome_scATACseq: gzipped tar file of bigwig file from cellranger arc; multiome_scRNAseq: gzipped tar directory containing filtered feature barcode matrices

source_name: pancreatic islet

growth_protocol: Female mice used for experiments were aged 30 weeks. Different groups of mice were co-housed.

extract_protocol:
CD8+ T cells were FACS sorted from lymph node and islet preparations. Islets were isolated by injecting collagenese solution in the clamped pandcreatic duct. Pancreata were then excised and incubated in collagenase for 30 mins at 37 degrees C and then washed and spun down twice ti distrupt the pancreas. Islets where then picled under a dissecting microscope and incubated for 15 mins at 37 degrees C in dissociation buffer (Life Technologies). CD8+ T cells were then sorted from these single cell suspensions.
For bulk RNAseq, libraries were generated using Smart-seq2. For scRNAseq, 10X Genomics 5' v1 kit was used in conjunction with Total-SeqC antibodies as per the manufacturer's instructions. Libraries were generated from scRNAseq, scATACseq, and CITEseq. For scATACseq, 10X Genomics Multiome ATAC + Gene Expression kit was used as per the manufactuerer's instructions.

value: NOD

value: Lag3L/L-yfp x E8I-CRE/CRE-gfp (LAG3 KO)

tag: Sex

value: female

value: 8 weeks

value: CD8+ T cells


title: bulk_rnaseq_lag3_ko_islet_4


title: bulk_rnaseq_wt_ln_1

source_name: non-draining lymph node

value: Lag3L/L-yfp  (WT)


title: bulk_rnaseq_wt_islet_3


title: bulk_rnaseq_wt_islet_7


title: multiome_scATACseq_islet

source_name: pancreatic lymph node


title: bulk_rnaseq_lag3_ko_islet_8


title: multiome_scATACseq_ln


title: bulk_rnaseq_wt_ln_2


title: bulk_rnaseq_lag3_ko_islet_3


title: bulk_rnaseq_lag3_ko_ln_2


title: bulk_rnaseq_lag3_ko_ln_1


title: bulk_rnaseq_lag3_ko_ln_5


title: bulk_rnaseq_wt_islet_8


title: bulk_rnaseq_wt_ln_6


title: multiome_scRNAseq_islet


title: bulk_rnaseq_lag3_ko_ln_6


title: multiome_scRNAseq_ln


title: bulk_rnaseq_wt_ln_5


title: GM-CSF-cultured bone marrow derived cells_LPS_3

city: Dusseldorf

first: Xiaoli

last: Yang

address: Moorenstr. 5

country: Germany

institute: Heinrich Heine University

data_processing:
Illumina bcl2fastq v2.20.0 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Illumina Adapter: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA)
Counts were calculated using featureCounts with standard parameters. Group comparison was calculated using DESeq2 after grouping of samples (four biological replicates each) according to their respective experimental condition.The resulting p values were corrected for multiple testing by FDR. A p value of < 0.05 was considered significant.
Genome_build: mm 39

source_name: bone marrow

growth_protocol: GM-CSF cultured bone marrow derived cells were generated as previously described (Richter L et al, Bioorg Med Chem 2019).

extract_protocol:
For RNA-Seq, GM-CSF-cultured bone marrow derived cells (CD3-CD19-CD11c+MHCIIhigh) were FACS purified using FACS Aria III (BD).
Library preparation was performed according to the manufacturers'protocol using the ‘VAHTS Stranded mRNA-Seq Library Prep Kit’ for Illumina®. Briefly, 500 ng total RNA were used for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification. Bead purified libraries were normalized and finally sequenced on the NextSeq550 system (Illumina Inc. San Diego, USA) with a read setup of 1x76 bp.

treatment_protocol: The GM-CSF-cultured bone marrow derived cells were left untreated or stimulated with 5 µM Beauvericin (Cayman Chemical), 1 μg/ml LPS(Escherichia coli O127:B8, Sigma)  for 4 hours. RNA was isolated by using NucleoSpin II RNA mini kit (Macherey- Nagel) and subjected to RNA-Seq.

tag: condition

value: LPS 4h


title: GM-CSF-cultured bone marrow derived cells_Beauvericin with LPS_3

tag: cell type

value: Beauvericin+LPS 4h


title: GM-CSF-cultured bone marrow derived cells_LPS_4


title: GM-CSF-cultured bone marrow derived cells_Beauvericin with LPS_2


title: GM-CSF-cultured bone marrow derived cells_Beauvericin with LPS_1


title: GM-CSF-cultured bone marrow derived cells_Beauvericin with LPS_4


title: GM-CSF-cultured bone marrow derived cells_LPS_2


title: bulk_rnaseq_wt_islet_4


title: GM-CSF-cultured bone marrow derived cells_LPS_1


title: GM-CSF-cultured bone marrow derived cells_Beauvericin_4

value: Beauvericin 4h


title: GM-CSF-cultured bone marrow derived cells_Beauvericin_3


title: GM-CSF-cultured bone marrow derived cells_Beauvericin_1


title: GM-CSF-cultured bone marrow derived cells_untreated control_2

value: untreated


title: GM-CSF-cultured bone marrow derived cells_untreated control_4


title: Valproate treated rep2

city: Highton

first: Trang

last: Truong

state: Victoria

address: 75 Pigdons Rd, Waurn Ponds VIC 3216, Waurn Ponds Campus

department: Department of Health

country: Australia

institute: Deakin University

data_processing:
Illumina Casava 1.8.2 software used for basecalling
The raw data yielded in FASTQ format were aligned to reference genomes using the Deakin Genomics Centre RNA-Seq alignment and expression quantification pipeline (https://github.com/m-richardson/RNASeq_pipe). Briefly, the pipeline included raw read quality filtering and adapter trimming (ILLUMINACLIP:2:30:10:4, SLIDINGWINDOW:5:20, AVGQUAL:20 MINLEN:36) with Trimmomatic v35, and alignment to the reference genome using STAR v2.5 in 2-pass mode (Human genome version GRCh38)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Teratocarcinoma-derived Ntera2/D1 neuron-like cells (NT2-N)

growth_protocol: NT2 cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM; Life Technologies, Melbourne, Australia), 10% fetal bovine serum (FBS; Thermo Fisher Scientific, Melbourne, Australia) and 1% antibiotic-antimycotic solution (Life Technologies). NT2-N cells were induced from NT2 cell cultures by treating with 10-5 M retinoic acid (Sigma-Aldrich, Sydney, Australia) for 28 days with media refreshed every 2–3 days.

extract_protocol:
Total RNA was extracted from cells post- treatment using RNeasy® mini kits (Qiagen, Melbourne, Australia), then checked for quality and quantity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Melbourne, Australia) and NanoDrop 1000 (Thermo Fisher Scientific), respectively.
RNA-seq libraries were prepared for all samples from 1 µg total RNA using a TruSeq RNA Sample Preparation Kit (Illumina, Victoria, Australia) as per the manufacturer’s instructions.

treatment_protocol: NT2-N cells were treated with lamotrigine (50 µM), lithium (2.5 mM), quetiapine (50 µM), or valproate (0.5 mM) for 24 hours (4 replicates for each group). All drugs were purchased from Sigma-Aldrich (Sydney, Australia). Vehicle control cells were treated with an equal volume of Milli-Q water for lithium or valproate controls, and 0.2% DMSO for lamotrigine or quetiapine controls.

value: Post-mitotic neurons

value: 0.5mM valproate in Milli-Q water for 24h


title: Lamotrigine treated rep4

value: 50uM lamotrigine in 0.2% DMSO for 24h


title: GM-CSF-cultured bone marrow derived cells_Beauvericin_2


title: H2O vehicle treated rep4

value: Milli-Q water for 24h


title: H2O vehicle treated rep1


title: Lamotrigine treated rep3


title: Lamotrigine treated rep1


title: Lithium treated rep4

value: 2.5mM lithium in Milli-Q water for 24h


title: GM-CSF-cultured bone marrow derived cells_untreated control_1


title: Valproate treated rep1


title: DMSO vehicle treated rep3

value: 0.2% DMSO for 24h


title: Quetiapine treated rep1

value: 50uM quetiapine in 0.2% DMSO for 24h


title: H2O vehicle treated rep3


title: DMSO vehicle treated rep2


title: DMSO vehicle treated rep1


title: Lithium treated rep3


title: Valproate treated rep3


title: Lithium treated rep2


title: Quetiapine treated rep2


title: Lamotrigine treated rep2


title: DMSO vehicle treated rep4


title: GM-CSF-cultured bone marrow derived cells_untreated control_3


title: Lithium treated rep1


title: H2O vehicle treated rep2


title: Quetiapine treated rep3


title: Valproate treated rep4


title: Quetiapine treated rep4


title: 123-D2

city: Seattle

first: Benjamin

last: Freedman

state: WA

address: 850 Republican St

department: Medicine/Nephrology

institute: University of Washington

description: mutant for KIF3B gRNA 1

data_processing:
Base calling with Hiseq
Alignment with STAR
Filtered out low quality libraries (< 1M reads, < 80 % alignment,or  >1 median CV of coverage)
Workflow - GenerateFastq; Application - HiSeq Fastq; Assay - Nextera XT
Output list of genes with the number of counts detected in each library
Genome_build: Hg38.91

source_name: pluripotent stem cells

growth_protocol: feeder free grown in mTeSR1 maintenance media replaced daily until confluent

extract_protocol:
cells lysed directly in SMARTseq lysis buffer, reverse transcribed in a thermocycler, and amplified by PCR (Benaroya Institute Genomics Core)
Libraries were prepared from small populations of cells (100-1000 cells), using a combination of the  Clontech SMARTseq chemistry and Illumina Nextera XT (Half Volume index set D ) kits.

treatment_protocol: untreated

value: iPS

tag: cell state

value: undifferentiated


title: 86-G2

description: mutant for KIF3A gRNA 1

value: ES


title: 124-D3

description: isogenic control for KIF3B gRNA 2

value: control


title: 123-F2

description: isogenic control for KIF3B gRNA 1


title: 86-E2

description: isogenic control for KIF3A gRNA 1


title: 124-C3

description: mutant for KIF3B gRNA 2


title: 86-E4

description: isogenic control for KIF3A gRNA 1


title: 123-A2

description: mutant for KIF3B gRNA 1


title: wt_Hop1-Chip_SpikeIn_rep1

first: Andreas

last: Hochwagen

address: 1009 Silver Center 100 Washington Square East

institute: New York University

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq and MNase-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009). Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis. The RNA-seq reads were mapped to the SK1 genome using Tophat2 with first strand library type, no novel junctions, and otherwise default options.
For ChIP-seq, 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. For MNase-seq, 3' ends were extended to a final length of 146 and bandwidth was set to 350 using MACS2 2.1.1. For RNA-seq, mapped reads were counted using featureCounts and statistical analysis was performed using a count-based workflow with the edgeR Bioconductor package
For ChIP-seq, the input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses. For MNase-seq, the pileup was SPMR-normalized and used for further analyses. For RNA-seq, gene counts were normalized to counts per million and were then gene length-corrected for transcripts per million (tpm).
Axis sites (Red1 summits in wild type conditions) were identified using MACS2 narrow and -log10 qvalue of 20
Peaks were identified using MACS broad flag.
Genome_build: Genome_build: SK1 (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph

source_name: meiotic nucleus

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C, except for H7606 which was innoculated at OD600 = 0.8 in BYTA medium and grown for 20 hours at room temperature. H7797 was also grown in BYTA medium at room temperature for the 34C experiments. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 1.9 or 2.0 at 30°C (details are described in (Blitzblau et al., 2012)). Rapamycin was added at 0h where indicated.

extract_protocol:
For ChIP-seq samples, 25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. For MNase-seq samples, 50 ml of the meiotic cells were collected at the 3-hr time point and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched with 125 mM glycine. ChIP-seq samples were processed as described in (Blitzblau et al., 2012). MNase-seq samples were processed as described in (Pan et al., 2011). A second sonication step was added just before library prep where indicated using a Bioruptor Pico (Diagenode, NJ, USA) with the following settings: 30 secs ON and 30 secs OFF for 5 cycles.
 libraries were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). For RNA-seq, libraries were prepared according to the Illumina TruSeq Stranded mRNA sample preparation kit, and sequencing libraries were prepared by PCR from the cDNA samples after ligation of adapters. Quality of all libraries was checked on 2200 Tapestation or Agilent 2100 Bioanalyzer. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads or 100 bp single-end reads.

treatment_protocol:
For 34C experiments, strains were shaken in SPO medium at room temperature for 1 hour and shifted to 34 degrees Celsius for the remaining time.
The spike in samples were spiked in with 20% SK288C yeast in order to normalize SK1 reads between genotypes.

tag: meitoic timepoint

value: meiosis Hr3

value: wild type

tag: antibody


title: hop1PHDrec8_Hop1-input_SpikeIn_rep2


title: hop1PHDrec8_Hop1-input_SpikeIn_rep1


title: hop1PHD_Red1-ChIP_Spikein_rep1


title: hop1PHDrec8_Hop1-Chip_SpikeIn_rep2


title: hop1PHD_Hop1-Chip_SpikeIn_rep1


title: rec8D_Red1-Chip_SpikeIn_rep1


title: wt_Hop1-input_SpikeIn_rep1


title: hop1PHDrec8_Red1-input_rep2

description: 10517-antiRed1-20211108-20210226--Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz


title: hop1PHD_Hop1-input_SpikeIn_rep1


title: hop1PHDrec8_Red1-Chip_rep1


title: hop1PHD_Red1-input_Spikein_rep1


title: rec8D_Red1-Input_SpikeIn_rep1


title: wt_Red1-input_SpikeIn_rep1


title: wt_Red1-ChIP_SpikeIn_rep1


title: hop1PHDrec8_Hop1-Chip_SpikeIn_rep1


title: hop1PHD_Hop1-input_rep1

description: AH9251-NHhop1-782021-912021-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz


title: hop1PHD_Hop1-Input_rep2


title: hop1PHD_Hop1-Chip-rep2


title: hop1PHDrec8_Red1-Chip_rep2


title: hop1PHD_Hop1-Chip-rep1


title: hop1PHDrec8_Red1-input_rep1


title: hop1PHDrec8_Hop1-input_Rep2

description: AH10517-NHhop1-782021-912021-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz


title: hop1PHDrec8_Hop1-Chip_rep2


title: hop1PHDrec8_Hop1-input_rep1


title: hop1PHDrec8_Hop1-Chip_rep1


title: hop1PHD_Red1-input_rep4

description: 9251-antiRed1-20211108-20171207-20171115-20170817-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz


title: hop1PHD_Red1-Chip_rep4


title: hop1PHD_Red1-input_rep2


title: hop1D chip for Red1 rep 2

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq and MNase-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009).  Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis. The RNA-seq reads were mapped to the SK1 genome using Tophat2 with first strand library type, no novel junctions, and otherwise default options.
For ChIP-seq, 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. For MNase-seq, 3' ends were extended to a final length of 146 and bandwidth was set to 350 using MACS2 2.1.1. For RNA-seq, mapped reads were counted using featureCounts and statistical analysis was performed using a count-based workflow with the edgeR Bioconductor package.
For ChIP-seq, the input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses. For MNase-seq, the pileup was SPMR-normalized and used for further analyses. For RNA-seq, gene counts were normalized to counts per million and were then gene length-corrected for transcripts per million (tpm).
Axis sites (Red1 summits in wild type conditions) were identified using MACS2 narrow and -log10 qvalue of 20.
Peaks were identified using MACS broad flag.
Genome_build: SK1 (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: csv (count of mRNAs in tmp)

source_name: hop1D chip for Red1 rep 2

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C, except for H7606  which was innoculated at OD600 = 0.8 in BYTA medium and grown for 20 hours at room temperature. H7797 was also grown in BYTA medium at room temperature for the 34C experiments. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 1.9 or 2.0 at 30°C (details are described in (Blitzblau et al., 2012)). Rapamycin was added at 0h where indicated.

extract_protocol:
For ChIP-seq samples, 25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. For MNase-seq samples, 50 ml of the meiotic cells were collected at the 3-hr time point and fixed for 30 min in 1% formaldehyde.  The formaldehyde was quenched with 125 mM glycine. ChIP-seq samples were processed as described in (Blitzblau et al., 2012). MNase-seq samples were processed as described in (Pan et al., 2011). A second sonication step was added just before library prep where indicated using a Bioruptor Pico (Diagenode, NJ, USA) with the following settings: 30 secs ON and 30 secs OFF for 5 cycles. For RNA-seq, 1.5 ml meiotic culture was taken at the 3-hr time point and RNA was extracted from mechanically lysed cells using the Qiagen RNeasy RNA isolation Kit and mRNA was extracted using Sera-Mag oligo-dT beads and fragmented.
For MNase-seq and ChIP-seq, libraries were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). For RNA-seq, libraries were prepared according to the Illumina TruSeq Stranded mRNA sample preparation kit, and sequencing libraries were prepared by PCR from the cDNA samples after ligation of adapters. Quality of all libraries was checked on 2200 Tapestation or Agilent 2100 Bioanalyzer. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads or 100 bp single-end reads.

treatment_protocol: For 34C experiments, strains were shaken in SPO medium at room temperature for 1 hour and shifted to 34 degrees Celsius for the remaining time.

tag: meiotic time point


title: hop1PHD_Red1-ChIP_rep1


title: hop1D chip for Red1 rep 1

source_name: hop1D chip for Red1 rep 1


title: SMC4-PK9 asynchronous resonicated input for PK9 rep 2

description: reanalysis of: GSM2829779

value: asynchronous


title: SMC4-PK9 asynchronous resonicated chip for PK9 rep 2

description: reanalysis of: GSM2829780


title: rtf1Δ input for Red1

source_name: rtf1Δ input for Red1


title: hop1PHD_Red1-input_rep1


title: anchor away no tag control  + rapa chip for Red1 rep 2

source_name: anchor away no tag control chip for Red1 rep 2


title: wild type 3h Mnase rep 2

description: reanalysis of: GSM3834086

source_name: wild type 3h Mnase rep 2


title: hop1D input for Red1 rep 1

source_name: hop1D input for Red1 rep 1


title: rtf1 3h Mnase

source_name: rtf1 3h Mnase


title: SCC2-3HA chip for HA rep 2

description: reanalysis of: GSM4677835

source_name: SCC2-3HA chip for HA rep 2

value: anti-HA


title: SMC4-PK9 asynchronous resonicated chip for PK9 rep 1

description: reanalysis of: GSM2829778


title: rtf1Δ chip for Red1

source_name: rtf1Δ chip for Red1


title: Brn1-FRB + rapa input for Red1 rep 2

source_name: Brn1-FRB input for Red1 rep 2


title: anchor away no tag control  + rapa input for Red1 rep 2

source_name: anchor away no tag control input for Red1 rep 2


title: hop1PHD_Red1-Chip_rep3


title: wild type 0h Mnase

source_name: wild type 0h Mnase


title: hop1PHD_Red1-input_rep3


title: hop1PHD_Red1-Chip_rep2


title: hop1D input for Red1 rep 2

source_name: hop1D input for Red1 rep 2


title: SMC4-PK9 asynchronous resonicated input for PK9 rep 1

description: reanalysis of: GSM2829777


title: wild type (ndt80Δ) chip for pH2A rep 1

description: reanalysis of: GSM2818458

source_name: wild type (ndt80Δ) chip for pH2A rep 1


title: Brn1-FRB + rapa chip for Red1 rep 2

source_name: Brn1-FRB chip for Red1 rep 2


title: wild type (ndt80Δ) chip for pH2A rep 2

description: reanalysis of: GSM2818462

source_name: wild type (ndt80Δ) chip for pH2A rep 2


title: set1Δ dot1Δ chip for Red1 rep 3

source_name: set1Δ dot1Δ chip for Red1 rep 3


title: set1Δ dot1Δ chip for Red1 rep 2

source_name: set1Δ dot1Δ chip for Red1 rep 2


title: wild type (ndt80Δ) input for pH2A rep 2

description: reanalysis of: GSM2818461

source_name: wild type (ndt80Δ) input for pH2A rep 2


title: set1Δ dot1Δ input for Red1 rep 2

source_name: set1Δ dot1Δ input for Red1 rep 2


title: set1Δ dot1Δ input for Red1 rep 3

source_name: set1Δ dot1Δ input for Red1 rep 3


title: SCC2-3HA input for HA rep 2

description: reanalysis of: GSM4677834

source_name: SCC2-3HA input for HA rep 2


title: set1Δ dot1Δ input for Red1 rep 1

source_name: set1Δ dot1Δ input for Red1 rep 1


title: set1Δ chip for Red1 rep 3

source_name: set1Δ chip for Red1 rep 3


title: set1Δ input for Red1 rep 2

source_name: set1Δ input for Red1 rep 2


title: set1Δ dot1Δ chip for Red1 rep 1

source_name: set1Δ dot1Δ chip for Red1 rep 1


title: set1Δ chip for Red1 rep 1

source_name: set1Δ chip for Red1 rep 1


title: set1Δ chip for Red1 rep 2

source_name: set1Δ chip for Red1 rep 2


title: set1Δ input for Red1 rep 3

source_name: set1Δ input for Red1 rep 3


title: wild type input for H3 rep 1

source_name: wild type input for H3 rep 1


title: set1Δ input for Red1 rep 1

source_name: set1Δ input for Red1 rep 1


title: wild type chip for H3 rep 1

source_name: wild type chip for H3 rep 1


title: wild type chip for Hop1 rep 3

source_name: wild type chip for Hop1 rep 3


title: top2-1 chip for Hop1 3h rep 2

source_name: top2-1 chip for Hop1 3h rep 2


title: top2-1 chip for Hop1 3h rep 1

source_name: top2-1 chip for Hop1 3h rep 1


title: wild type chip for Hop1 rep 2

source_name: wild type chip for Hop1 rep 2


title: wild type input for Hop1 rep 2

source_name: wild type input for Hop1 rep 2


title: wild type input for Hop1 rep 3

source_name: wild type input for Hop1 rep 3


title: wild type (ndt80Δ) input for pH2A rep 1

description: reanalysis of: GSM2818457

source_name: wild type (ndt80Δ) input for pH2A rep 1


title: wild type chip for Hop1 34C rep 2

source_name: wild type chip for Hop1 34C rep 2


title: wild type chip for Hop1 34C rep 1

source_name: wild type chip for Hop1 34C rep 1


title: wild type chip for Red1 34C rep 2

description: reanalysis of: GSM3834074

source_name: wild type chip for Red1 34C rep 2


title: wild type input for Hop1 34C rep 1

description: reanalysis of: GSM3834066

source_name: wild type input for Hop1 34C rep 1


title: wild type chip for Red1 34C rep 1

description: reanalysis of: GSM3834073

source_name: wild type chip for Red1 34C rep 1


title: wild type input for Red1 34C rep 1

description: reanalysis of: GSM3834064

source_name: wild type input for Red1 34C rep 1


title: top2-1 chip for Red1 3h rep 3

description: reanalysis of: GSM4087897

source_name: top2-1 chip for Red1 3h rep 3


title: top2-1 input for Red1 and Hop1 3h rep 3

description: reanalysis of: GSM3834070

source_name: top2-1 input for Red1 and Hop1 3h rep 3


title: top2-1 input for Red1 and Hop1 3h rep 2

description: reanalysis of: GSM3834068

source_name: top2-1 input for Red1 and Hop1 3h rep 2


title: top2-1 chip for Red1 3h rep 2

description: reanalysis of: GSM4087896

source_name: top2-1 chip for Red1 3h rep 2


title: top2-1 chip for Red1 3h rep 1

description: reanalysis of: GSM4087895

source_name: top2-1 chip for Red1 3h rep 1


title: spo11Δ input for Top2 rep 3

source_name: spo11Δ input for Top2 rep 3


title: spo11Δ chip for Top2 rep 2

source_name: spo11Δ chip for Top2 rep 2


title: spo11Δ input for Top2 rep 2

source_name: spo11Δ input for Top2 rep 2


title: top2-1 input for Red1 3h rep 1

description: reanalysis of: GSM4087894

source_name: top2-1 input for Red1 3h rep 1


title: spo11YF input for Top2 rep 2

source_name: spo11YF input for Top2 rep 2


title: spo11YF input for Top2 rep 1

source_name: spo11YF input for Top2 rep 1


title: TOP1-13MYC chip for MYC rep 2

description: reanalysis of: GSM3834059

source_name: TOP1-13MYC chip for MYC rep 2

value: anti-Myc


title: TOP1-13MYC input for MYC rep 2

description: reanalysis of: GSM3834058

source_name: TOP1-13MYC input for MYC rep 2


title: spo11YF chip for Top2 rep 1

source_name: spo11YF chip for Top2 rep 1


title: TOP1-13MYC chip for MYC rep 1

description: reanalysis of: GSM3834057

source_name: TOP1-13MYC chip for MYC rep 1


title: wild type 0h chip for Top2 rep 2

source_name: wild type 0h chip for Top2 rep 2


title: wild type 0h input for Top2 rep 3

source_name: wild type 0h input for Top2 rep 3


title: TOP1-13MYC input for MYC rep 1

description: reanalysis of: GSM3834056

source_name: TOP1-13MYC input for MYC rep 1


title: wild type 0h chip for Top2 rep 3

source_name: wild type 0h chip for Top2 rep 3


title: wild type 0h input for Top2 rep 2

source_name: wild type 0h input for Top2 rep 2


title: wild type input for Red1 and Hop1 34C rep 2

description: reanalysis of: GSM3834072


title: wild type 3h chip for Top2 3h rep 2

description: reanalysis of: GSM3834063

source_name: wild type 3h chip for Top2 3h rep 2


title: Top1-13myc chip for Myc at 0h rep 2

source_name: Top1-13myc chip for Myc at 0h rep 2


title: spo11Δ chip for Top2 rep 3

source_name: spo11Δ chip for Top2 rep 3


title: Top1-13myc input for Myc at 0h rep 2

source_name: Top1-13myc input for Myc at 0h rep 2


title: Top1-13myc chip for Myc at 0h rep 1

source_name: Top1-13myc chip for Myc at 0h rep 1


title: Top1-13myc input for Myc at 0h rep 1

source_name: Top1-13myc input for Myc at 0h rep 1


title: spo11YF chip for Top2 rep 2

source_name: spo11YF chip for Top2 rep 2


title: Naïve_C5

city: Farmington

last: Vella

state: Connecticut

address: 263 Farmington Ave

institute: UConn Health

description:
poly(A) RNA from naïve CD8+ T cells
CTCTCTAC-TATCCTCT-s_3_1_sequence.txt.gz

data_processing:
Base-calling was done using Offline Base Caller (Illumina) v. 1.9.4
alignment was done using HISAT2 v 2.1.0 under default specfications
BAM files were generated and indexed using Samtools v 1.9 under default specifications
Peak-calling was done using Stringtie v 2.1.0 under parameter -B to first generate a usable list of ballgown files to prep for DESeq2 analysis. A separate python script (prepDE.py) was then used to convert the ballgown list (sample_list.txt) to gene and transcript counts as well as FPKM values for each sample as a list of gtf files (using python2.7 - python 3.7.4 does not work).
Analysis of counts was performed using R v 4.0.5, Rstudio v 1.2.1, DESeq2 v 1.30.1 using the filtering parameters of FDR<.05
Assembly: mm10
Supplementary files format and content: tab delimited file of counts on a per gene basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of counts on a transcript basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of FPKM values on a transcript basis (generated from Stringtie)

source_name: Purified CD8+ T cells from spleen and lymph nodes

extract_protocol:
QIAGEN miRNEasy Micro Kit
Clonetech SMART-Seq v4 Ultra-low w/Nextera XT, 1x50bp reads

treatment_protocol: CD8+ T cells from OT-I Tg mice were adoptively transferred into C57BL6/J mice. Recipients were stimulated with antigen-only or antigen+costimulatory agonist antibodies (anti-OX40, anti-41BB). Spleen and lymph nodes were collected after 4 days and sorted for pure CD8+ T cells and RNA was extracted. CD8+ T cells from naive OT-I Tg (non transferred) mice were purified as naive control.

value: OT-1 Tg C57BL/6J

value: CD8+ T cell

tag: treatment

value: naive


title: Costim_B5

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen and costimulatory antibodies
CGTACTAG-TATCCTCT-s_3_1_sequence.txt.gz


title: Costim_B4

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen and costimulatory antibodies
TAAGGCGA-TATCCTCT-s_3_1_sequence.txt.gz


title: Naïve_C2

description:
poly(A) RNA from naïve CD8+ T cells
TCCTGAGC-TATCCTCT-s_3_1_sequence.txt.gz


title: Naïve_C4

description:
poly(A) RNA from naïve CD8+ T cells
TAGGCATG-TATCCTCT-s_3_1_sequence.txt.gz


title: Costim_B1

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen and costimulatory antibodies
TAGGCATG-CTCTCTAT-s_2_1_sequence.txt.gz


title: Naïve_C1

description:
poly(A) RNA from naïve CD8+ T cells
AGGCAGAA-TATCCTCT-s_3_1_sequence.txt.gz


title: Antigen_A5

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen-alone
GGACTCCT-CTCTCTAT-s_2_1_sequence.txt.gz

value: antigen-only


title: Costim_B3

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen and costimulatory antibodies
CGAGGCTG-CTCTCTAT-s_2_1_sequence.txt.gz


title: Antigen_A3

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen-alone
AGGCAGAA-CTCTCTAT-s_2_1_sequence.txt.gz


title: Naïve_C3

description:
poly(A) RNA from naïve CD8+ T cells
GGACTCCT-TATCCTCT-s_3_1_sequence.txt.gz


title: wild type 3h input for Top2 3h rep 2

description: reanalysis of: GSM3834062

source_name: wild type 3h input for Top2 3h rep 2

tag: genotype


title: Antigen_A1

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen-alone
TAAGGCGA-CTCTCTAT-s_2_1_sequence.txt.gz


title: gRNA library of BM derived T cells from pooled CRISPR/Cas9 KO

city: Pasadena

first: Wen

last: Zhou

state: California

address: 1200 E California Blvd, Mail Code 250-86

department: BBE

institute: California Institute of Technology

description:
sgRNA captured by capture sequence 1 and 2
single cell droplet performed with 10x Chromium v3
ft_count_cap1_gd1.txt for guide RNA1 raw UMI count, ft_count_cap2_gd2.txt for guide RNA2 raw UMI count, ft_count_cap1_gd1_bin.txt for gRNA1 binarized assignment, and ft_count_cap2_gd2_bin.txt for gRNA2 binarized assignment,

data_processing: Read 1 includes cell barcode, UMI, and capture sequence 1 or capture sequence 2; read 2 includes gRNA sequences. Valid cell barcodes identified in Cellranger pipeline from cDNA library data were used as cell IDs, and the gRNA sequences were mapped to a 20 bases reference gRNA list based on capture sequence identity, using in house pipeline. The count was quantified by UMI. The UMI counts were binarized for gRNA assignment using the Gaussian mixture model.

source_name: Bone Marrow

extract_protocol: Purified LSK precursors were transduced with retro-virus deliverying gRNA sequences, cultured on OP9-DL1 stromal cells for 5 days. Samples from different batches were stained for surface markers and barcoded cell hashing antibodies separately, sorted through FACS, and pooled for scRNA-seq

tag: tissue

value: Bone Marrow

value: CD45+ Lin- 7AAD- CFP+ cKit+


title: Antigen_A2

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen-alone
CGTACTAG-CTCTCTAT-s_2_1_sequence.txt.gz


title: Antibody sample tag library for demultilexing biological replicates from BM derived T cells from pooled CRISPR/Cas9 KO

description:
polyA HTO DNA
single cell droplet performed with 10x Chromium v3
ft_count_perturb.txt for raw UMI counts of hashtags and ft_count_perturb_binary.txt for binarized cell hash assignment

data_processing: Read 1 includes cell barcode and UMI; read 2 includes HTO (cell hashing) sequences. Valid cell barcodes identified in CellRanger pipeline from cDNA library data were used as cell IDs, and the HTO sequences were mapped to a 15 bases reference HTO list from in house pipeline v2, count was quantified by UMI. The UMI counts were binarized for identity assignment using the Gaussian mixture model.


title: Antibody sample tag library for demultilexing individual WT and Bcl11b KO animals run2

description:
polyA HTO
single cell droplet performed with 10x Chromium v3
ft_count_bcl11b_run2.txt for raw UMI counts of hashtags and ft_count_binary_bcl11b_run2.txt for binarized cell hash assignment

extract_protocol: Purified LSK precursors from different animals were cultured in mouse artificial thymic organoids with MS5-mDLL4 stromal cells for 10-13 days. Samples from different animal origins and time points were stained for surface markers and barcoded cell hashing antibodies separately, sorted through FACS, and pooled for scRNA-seq

value: Vav1-iCre/+, Bcl11b wt/wt and Bcl11b flx/flx.

value: CD45+ Lin- 7AAD- CD25+


title: Antibody sample tag library for demultilexing individual WT and Bcl11b KO animals run1

description:
polyA HTO
single cell droplet performed with 10x Chromium v3
ft_count_bcl11b_run1.txt for raw UMI counts of hashtags and ft_count_binary_bcl11b_run1.txt for binarized cell hash assignment

data_processing: Read 1 includes cell barcode and UMI; read 2 includes HTO (cell hashing) sequences. Valid cell barcodes identified in CellRanger pipeline from cDNA library data were used as cell IDs, and the HTO sequences were mapped to a 15 bases reference HTO list from in house pipeline v1, count was quantified by UMI. The UMI counts were binarized for identity assignment with the Otsu threshold.

extract_protocol: Purified LSK precursors from different animals were cultured in mouse artificial thymic organoids with MS5-mDLL4 stromal cells for 10 days. Samples from different animal origins were stained for surface markers and barcoded cell hashing antibodies separately, sorted through FACS, and pooled for scRNA-seq

value: Vav1-iCre/+ or +/+ ,and Bcl11b wt/wt or Bcl11b flx/flx.


title: scRNA-seq library of BM derived T cells from pooled CRISPR/Cas9 KO

description:
polyA RNA
single cell droplet performed with 10x Chromium v3
scRNA_perturb.h5

data_processing: Single-cell RNA-seq data were processed using 10X Cellranger 3.0.0 software. Standard cellranger-mm10-3.0.0 reference annotations were loaded to the pipeline for read mapping and gene quantification.

value: Vav-Cre/+, Bcl11b wt/wt and Bcl11b flx/flx.


title: EpCAM neg 3

city: London

first: Linxiang

last: Lan

address: 237 Fulham Rd

institute: The Institute of Cancer Research

data_processing:
The RSEM package (version 1.3,0) (Li and Dewey, 2011) was used in conjunction with the STAR alignment algorithm (version 2.5.2) (Dobin et al., 2013) for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl mouse GRCm38 release 86  transcriptome
Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.24.0)  within the R programming environment (version 3.6.1)
Genome_build: GRCm38 release 86
Supplementary_files_format_and_content: rlog log2 normalised expression values. Rows = genes; Columns = samples.

source_name: EpCAM-

growth_protocol: KPCY mice in C57BL/6 background were bred and maintained in the BRF unit at the Francis Crick Institute; mice at 5-7 weeks of age were used for experiments.

extract_protocol:
RNA from FACS-sorted cells was extracted using the MagMAX-96 Total RNA Isolation Kit (Thermo Fisher) according to the manufacturer’s instructions.
Samples were prepared with KAPA mRNA HyperPrep Kit (Roche) and sequenced using Illumina HiSeq 4000 platform

tag: strain background

value: 5-7 weeks

value: Sorted primary pancreatic cancer cells from KPCY tumours

tag: cell markers

value: EpCAM-


title: EpCAM pos 3

source_name: EpCAM+

value: EpCAM+


title: scRNA-seq library of BM derived T cells from WT and Bcl11b KO animals run2

description:
polyA RNA
single cell droplet performed with 10x Chromium v3
scRNA_Bcl11b_run2.h5


title: EpCAM neg 2


title: EpCAM pos 2


title: EpCAM neg 1


title: EpCAM pos 1


title: Antigen_A4

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen-alone
TCCTGAGC-CTCTCTAT-s_2_1_sequence.txt.gz


title: HT1080 cells, Mock, 24 h

city: Tianjin

first: Junshi

last: Zhang

address: No. 94, Weijin Road

institute: Nankai University

data_processing:
Illumina Casava software used for basecalling. Adaptors of RNA-seq were trimmed using FASTX Toolkit . The tRNA and rRNA reads were removed by Bowtie.
The reads were mapped to both the human genome ( UCSC ,hg18). Clean reads were quantified by HISAT.
Raw counts of the genes were combined and FPKMs (Fragments per kilobase of transcript per million reads) were calculated by edgeR.
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: connective tissue

growth_protocol: High glucose DMEM with 10% FBS and 4mM L-Gln

extract_protocol:
Cells were harvested and RNA was extracted as TruSeq Ribo Profile (Mammalian) Kit (Illumina) manual.
RNA libraries were prepared for sequencing using TruSeq Ribo Profile (Mammalian) Kit (Illumina)

value: connective tissue

tag: cell line

value: fibrosarcoma cell

tag: infection

value: mock

tag: virus strain

value: not applicable


title: HT1080 cells, Infect, 12 h

value: prototype foamy virus (PFV)


title: Costim_B2

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen and costimulatory antibodies
CTCTCTAC-CTCTCTAT-s_2_1_sequence.txt.gz

tag: strain

value: OT-1 Tg C57BL/6J

value: CD8+ T cell


title: HT1080 cells, Infect, 24 h

tag: time


title: HT1080 cells, Infect, 6 h

value: 6 h


title: Non-treated plant Rep 4

city: Girona

first: Luis

middle: Alejandro

last: Moll Dos Santos

state: Catalonia

address: Pic de Peguera 15, Edifici Jaume Casademont

department: Department of Chemical and Agricultural Engineering and Agrifood Technology

country: Spain

institute: University of Girona

data_processing:
Illumina CASAVA v1.8.2 was used for base-calling
Raw sequence files were subjected to quality control analysisis using FastQC v0.10.1
Raw sequence files were trimmed and adapters were removed with BBDuk (minimum base quality of 25 and a minimum read length of 35 bp)
Reads were mapped against the Prunus dulcis genome with STAR v2.6
Raw expression counts were obtained with FeatureCounts v1.6.1 for each annotated gene using only uniquely mapping reads (MAPQ ≥ 30).
Genome_build: PRJDB7547
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Prunus dulcis

source_name: Finely grounded frozen leaves

growth_protocol: All plants were maintained in 0.8 liter pots (sphagnum peat with wood fiber (10%), calcium carbonate (9 g/liter), NPK fertilizer (1 Kg/m3) and microelements) in an environmentally controlled greenhouse at 25±2ºC (day) and 18±2ºC (night), with a minimum relative humidity of 60%, and with a photoperiod of 16 h light and 8 h dark. Prior and during the experiments, plants were watered to saturation every three days, and fertilized with a 200 ppm solution of NPK (20:10:20) once a week.

extract_protocol:
Sampling was carried out 1 dpt and for each replicate 20 leaves were pooled (4 leaves/plant) and they were immediately frozen in liquid nitrogen. The material was finely grounded and homogenized with a Tissue Lyser II. RNA was extracted from 100 mg of the grounded leaf material coming from each replicate using the PureLink™ Plant RNA Reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) following the manufacturer’s instructions. The remaining DNA was digested with the TURBO DNA-freeTM Kit (Invitrogen Life Technologies, Carlsbad, CA, USA).
RNA “TruSeq Stranded mRNA Sample Prep kit” (Illumina, San Diego, CA) was used for library preparation following the manufacturer’s instructions, starting with 1-2 µg of good quality RNA (RIN > 7) as input. The RNA was fragmented 3 min at 94°C and every purification step was performed using 0.81X Agencourt AMPure XP beads. Both RNA samples and final libraries were quantified using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and quality tested by Agilent 2100 Bioanalyzer RNA Nano assay (Agilent technologies, Santa Clara, CA, USA). Libraries were then processed with Illumina cBot for cluster generation on the flowcell, following the manufacturer’s instructions and sequenced on paired-end (2x150 bp, 30M reads per sample) at the multiplexing level requested on NovaSeq6000 (Illumina, San Diego, CA, USA).

treatment_protocol: The effect of the peptide BP178 on P. dulcis cv. Avijor transcriptome response was assessed by applying the peptide by two application systems, by spray and microinjection. Each plant was injected with 10 µL of BP178 at 20 mM , and subsequently sprayed with 2 mL of the peptide at 125 µM using an airbrush. The experimental design consisted of four replicates of five plants per treatment. Plants treated with water were used as untreated controls.

tag: organ

value: leaf

tag: agent

tag: variety

value: Avijor


title: BP178 treated plant Rep 1


title: BP178 treated plant Rep 3


title: Non-treated plant Rep 3


title: BP178 treated plant Rep 4


title: BP178 treated plant Rep 2


title: Non-treated plant Rep 2


title: Human Dermal Microvascular Endothelial Cells 6.3

type: RNA

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

institute: University of Cologne

hyb_protocol: 2.3 µg fragmented biotin-labeled ds cDNA were hybridized to Clariom™ S arrays using the Fluidics Station 450 Arrays were scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

scan_protocol: After hybridization and stainning  arrays were scanned using the and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

data_processing: The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA) and  QC passed CEL files were further analyzed using the Affymetrix Transcriptome Analysis Console (TAC) 4.0 Software. . All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.

label: biotin

label_protocol: 250 ng total RNA   were labelled using the GeneChip™ WT PLUS Reagent Kit

extract_protocol: Total RNA from cells was isolated by PureLink RNA Mini Kit (Life technologies, # 12183018A)

tag: sample type

value: commercial RNA from Dermal Microvascular Endothelial Cells


title: Human Dermal Microvascular Endothelial Cells 6.1


title: Human Dermal Microvascular Endothelial Cells 6.2


title: Human Umbilical Vein Endothelial Cells 4.3

description: Human Umbilical Vein Endothelial Cells

source_name: Human Umbilical Vein Endothelial Cells

value: commercial RNA from Human Umbilical Vein Endothelial Cells


title: Human Pulmonary Microvasculature Endothelial cell 7.1

value: commercial RNA from Human Pulmonary Microvasculature Endothelial Cells


title: Human Umbilical Vein Endothelial Cells 4.2

description: Human Umbilical Vein Endothelial Cells


title: Human Saphenous Vein Endothelial Cells 5.1

description: Human Saphenous Vein Endothelial Cells

source_name: Human Saphenous Vein Endothelial Cells

value: commercial RNA from Human Saphenous Vein Endothelial Cells


title: Human Cardiac Microvasculatur Endothelial cell 3.1

value: commercial RNA from Human Cardiac Microvasculatur Endothelial Cells


title: Human Umbilical Vein Endothelial Cells 4.1

description: Human Umbilical Vein Endothelial Cells


title: Human Saphenous Vein Endothelial Cells 5.3

description: Human Saphenous Vein Endothelial Cells


title: Human Pulmonary Microvasculature Endothelial cell 7.3


title: Non-treated plant Rep 1


title: Human Cardiac Microvasculatur Endothelial cell 3.3


title: hiPSC-ECs 1.3

description: hiPSC-ECs

source_name: hiPSC-ECs

value: RNA from differented endothelial-like cells from human iPSCs (hiPSCs)


title: Human Pulmonary Microvasculature Endothelial cell 7.2


title: Human Saphenous Vein Endothelial Cells 5.2

description: Human Saphenous Vein Endothelial Cells


title: Human Cardiac Microvasculatur Endothelial cell 3.2


title: Cord Blood_STORE-162

city: Philadelphia

first: Zubair

last: Aghai

address: 833 Chestnut Street East, Suite 1210,

department: Pediatrics

institute: Jefferson/Nemours Children's Health

description:
SST-RMA expression value derived from Expression Console software; gene level analysis
At the time of delivery, the umbilical cord blood was collected in PAXgene blood RNA tube (BD Catalog # 762165) and then processed and stored as per manufacturer’s guidelines.

hyb_protocol: Human Clariom S gene chips were hybridized with 2.5 µg of fragmented biotin-labeled cDNA in 100 µl hybridization cocktail, followed by target denaturation at 99°C for 5 min and then 45°C for 5 min. Hybridization was performed for 16 hours at 45°C with a rotation of 60 rpm.

scan_protocol: Chips were scanned on GeneChip Scanner 3000 using Command Console Software (Thermo Fisher Scientific, Waltham, MA)

data_processing: The data were processed and analyzed using Transcriptome Analysis Console software 4.0 (TAC 4.0, Thermo Fisher Scientific, Waltham, MA). SST-RMA normalization was performed on the cel files generated from the samples.

source_name: Mother with Covid exposure during pregnancy

label_protocol: Fragmented biotin-labeled cDNA by GeneChip WT PLUS reagent kit (Affymetrix, Santa Clara, CA)

extract_protocol: Total RNA was isolated using PAXgene Blood RNA Kit (PreAnalytiX, A Qiagen/BD Company, Switzerland) following manufacturer’s protocol. RNA was quantified on a Nanodrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and quality was assessed by an Agilent 2200 TapeStation (Agilent Technologies, Palo Alto, CA).

tag: blood

value: Umbilical Cord Blood


title: Cord Blood_STORE-262


title: hiPSC-ECs 1.1

description: hiPSC-ECs


title: Cord Blood_STORE-246


title: Human Coranary Artery Endothelial cell 2.3

description: Human Coranary Artery Endothelial cell

source_name: Human Coranary Artery Endothelial cell

value: commercial  RNA from Human Coranary Artery Endothelial Cells


title: hiPSC-ECs 1.2

description: hiPSC-ECs


title: Cord Blood_STORE-313


title: Cord Blood_STORE-028


title: Human Coranary Artery Endothelial cell 2.1

description: Human Coranary Artery Endothelial cell


title: Human Coranary Artery Endothelial cell 2.2

description: Human Coranary Artery Endothelial cell


title: Cord Blood_STORE-224


title: Cord Blood_JCRA-007

source_name: Healthy mother - no Covid exposure during pregnancy


title: Cord Blood_STORE-196


title: Cord Blood_STORE-152


title: Cord Blood_JCRA-005


title: Cord Blood_JCRA-004


title: Cord Blood_JCRA-002


title: Cord Blood_JCRA-010


title: ES8-KO_2Gy_24h_rep3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Five micrograms of biotin-labeled cDNA was hybridized for 16h at 45C on a Clariom S Human GeneChip array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: Ewings sarcoma ES8-SLFN11-ko cells, irradiated, 24h post-treatment

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Affymetrix GeneChip WT Plus (Applied Biosystems P/N 902281). cDNA was fragmented and biotin-labeled using the GeneChip™ WT Terminal Labeling Kit (Applied Biosystems P/N 900670).

growth_protocol: Cells were maintained in DMEM/F12 growth media, supplemented with glutamine plus 10% fetal bovine serum

extract_protocol: Total mRNA was extracted using the Maxwell RSC simplyRNA Tissue kit (Promega PN AS1340)

treatment_protocol: ES8 and ES8-SLFN11-ko cells were treated with either 0 Gy or 2 Gy gamma radiation, and cultured for an additional 4h or 24h before RNA collection


title: Cord Blood_JCRA-006


title: Cord Blood_STORE-210


title: ES8-KO_0Gy_4h_rep3

source_name: Ewings sarcoma ES8-SLFN11-ko cells, non-irradiated, 4h post-treatment


title: ES8-KO_2Gy_24h_rep2


title: ES8-KO_2Gy_4h_rep2

source_name: Ewings sarcoma ES8-SLFN11-ko cells, irradiated, 4h post-treatment


title: ES8-KO_2Gy_24h_rep1


title: ES8-KO_0Gy_24h_rep3

source_name: Ewings sarcoma ES8-SLFN11-ko cells, non-irradiated, 24h post-treatment


title: ES8-KO_2Gy_4h_rep3


title: ES8-KO_2Gy_4h_rep1


title: Cord Blood_STORE-032


title: Blood sample from individual 920_2

type: genomic

city: Darlinghurst

first: Joseph

middle: E

last: Powell

state: NSW

address: 384 Victoria Street

institute: Garvan Institute of Medical Research

description: Sample ID: 920_2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Genomic DNA extracted from blood was genotyped using the Infinium Global Screening Array-24 v1.0 BeadChip (Illumina).
Primary assessment and SNP call rate quality control of SNP intensity output files were performed using GenomeStudio software (Illumina).
Genotype: AA,AB,BB,or NC (no call)
Processed data file onek1k_genotype_matrix.txt.gz is linked as supplementary file at the foot of the Series record.

label: C-Bio and A-DNP

source_name: Blood sample

label_protocol: Standard Illumina label protocol

extract_protocol: DNA was extracted from blood stored in EDTA tubes using the QIAamp Blood Mini kit.

value: Blood

tag: disease state

value: No active inflammatory disease


title: Blood sample from individual 926_2

description: Sample ID: 926_2


title: Blood sample from individual 914_2

description: Sample ID: 914_2


title: Blood sample from individual 506_2

description: Sample ID: 506_2


title: ES8_2Gy_4h_rep3

source_name: Ewings sarcoma ES8 cells, irradiated, 4h post-treatment


title: Blood sample from individual 255_2

description: Sample ID: 255_2


title: Blood sample from individual 256_2

description: Sample ID: 256_2


title: ES8-KO_0Gy_24h_rep2


title: ES8-KO_0Gy_4h_rep1


title: ES8_2Gy_24h_rep1

source_name: Ewings sarcoma ES8 cells, irradiated, 24h post-treatment


title: ES8-KO_0Gy_24h_rep1


title: ES8-KO_0Gy_4h_rep2


title: ES8_0Gy_24h_rep1

source_name: Ewings sarcoma ES8 cells, non-irradiated, 24h post-treatment


title: ES8_0Gy_24h_rep3


title: ES8_2Gy_4h_rep2


title: ES8_2Gy_24h_rep2


title: ES8_2Gy_24h_rep3


title: ES8_2Gy_4h_rep1


title: ES8_0Gy_4h_rep2

source_name: Ewings sarcoma ES8 cells, non-irradiated, 4h post-treatment


title: Blood sample from individual 847_2

description: Sample ID: 847_2


title: Blood sample from individual 242_2

description: Sample ID: 242_2


title: Blood sample from individual 254_2

description: Sample ID: 254_2


title: Blood sample from individual 157_2

description: Sample ID: 157_2


title: Blood sample from individual 155_2

description: Sample ID: 155_2


title: Blood sample from individual 848_2

description: Sample ID: 848_2


title: Blood sample from individual 156_2

description: Sample ID: 156_2


title: Blood sample from individual 932_2

description: Sample ID: 932_2


title: Blood sample from individual 845_2

description: Sample ID: 845_2


title: Blood sample from individual 846_2

description: Sample ID: 846_2


title: Blood sample from individual 554_2

description: Sample ID: 554_2


title: Blood sample from individual 1084

description: Sample ID: 1084

tag: individual id

tag: gender

value: Female


title: Blood sample from individual 566_2

description: Sample ID: 566_2


title: ES8_0Gy_24h_rep2


title: Blood sample from individual 1083

description: Sample ID: 1083

value: Male


title: Blood sample from individual 1077

description: Sample ID: 1077


title: Blood sample from individual 1081

description: Sample ID: 1081


title: Blood sample from individual 1076

description: Sample ID: 1076


title: ES8_0Gy_4h_rep1


title: Blood sample from individual 1075

description: Sample ID: 1075


title: ES8_0Gy_4h_rep3


title: Blood sample from individual 915_2

description: Sample ID: 915_2


title: Blood sample from individual 1086

description: Sample ID: 1086


title: Blood sample from individual 1070

description: Sample ID: 1070


title: Blood sample from individual 1085

description: Sample ID: 1085


title: Blood sample from individual 1082

description: Sample ID: 1082


title: Blood sample from individual 1068

description: Sample ID: 1068


title: Blood sample from individual 1067

description: Sample ID: 1067


title: Blood sample from individual 1065

description: Sample ID: 1065


title: Blood sample from individual 1079

description: Sample ID: 1079


title: Blood sample from individual 1080

description: Sample ID: 1080


title: Blood sample from individual 1063

description: Sample ID: 1063


title: Blood sample from individual 1062

description: Sample ID: 1062


title: Blood sample from individual 1058

description: Sample ID: 1058


title: Blood sample from individual 1074

description: Sample ID: 1074


title: Blood sample from individual 1057

description: Sample ID: 1057


title: Blood sample from individual 1056

description: Sample ID: 1056


title: Blood sample from individual 1078

description: Sample ID: 1078


title: Blood sample from individual 1053

description: Sample ID: 1053


title: Blood sample from individual 1073

description: Sample ID: 1073


title: Blood sample from individual 1072

description: Sample ID: 1072


title: Blood sample from individual 1071

description: Sample ID: 1071


title: Blood sample from individual 1069

description: Sample ID: 1069


title: Blood sample from individual 1066

description: Sample ID: 1066


title: Blood sample from individual 1050

description: Sample ID: 1050


title: Blood sample from individual 1064

description: Sample ID: 1064


title: Blood sample from individual 1061

description: Sample ID: 1061


title: Blood sample from individual 1059

description: Sample ID: 1059


title: Blood sample from individual 1042

description: Sample ID: 1042


title: Blood sample from individual 1060

description: Sample ID: 1060


title: Blood sample from individual 1044

description: Sample ID: 1044


title: Blood sample from individual 1055

description: Sample ID: 1055


title: Blood sample from individual 1051

description: Sample ID: 1051


title: Blood sample from individual 1054

description: Sample ID: 1054


title: Blood sample from individual 1043

description: Sample ID: 1043


title: Blood sample from individual 1048

description: Sample ID: 1048


title: Blood sample from individual 1039

description: Sample ID: 1039


title: Blood sample from individual 1036

description: Sample ID: 1036


title: Blood sample from individual 1038

description: Sample ID: 1038


title: Blood sample from individual 1047

description: Sample ID: 1047


title: Blood sample from individual 1032

description: Sample ID: 1032


title: Blood sample from individual 1046

description: Sample ID: 1046


title: Blood sample from individual 1045

description: Sample ID: 1045


title: Blood sample from individual 1041

description: Sample ID: 1041


title: Blood sample from individual 1035

description: Sample ID: 1035


title: Blood sample from individual 1040

description: Sample ID: 1040


title: Blood sample from individual 1027

description: Sample ID: 1027


title: Blood sample from individual 1033

description: Sample ID: 1033


title: Blood sample from individual 1052

description: Sample ID: 1052


title: Blood sample from individual 1037

description: Sample ID: 1037


title: Blood sample from individual 1049

description: Sample ID: 1049


title: Blood sample from individual 1034

description: Sample ID: 1034


title: Blood sample from individual 1021

description: Sample ID: 1021


title: Blood sample from individual 1031

description: Sample ID: 1031


title: Blood sample from individual 1024

description: Sample ID: 1024


title: Blood sample from individual 1029

description: Sample ID: 1029


title: Blood sample from individual 1019

description: Sample ID: 1019


title: Blood sample from individual 1023

description: Sample ID: 1023


title: Blood sample from individual 1017

description: Sample ID: 1017


title: Blood sample from individual 1028

description: Sample ID: 1028


title: Blood sample from individual 1026

description: Sample ID: 1026


title: Blood sample from individual 1020

description: Sample ID: 1020


title: Blood sample from individual 1015

description: Sample ID: 1015


title: Blood sample from individual 1018

description: Sample ID: 1018


title: Blood sample from individual 1016

description: Sample ID: 1016


title: Blood sample from individual 1030

description: Sample ID: 1030


title: Blood sample from individual 1014

description: Sample ID: 1014


title: Blood sample from individual 1009

description: Sample ID: 1009


title: Blood sample from individual 1008

description: Sample ID: 1008


title: Blood sample from individual 1005

description: Sample ID: 1005


title: Blood sample from individual 1012

description: Sample ID: 1012


title: Blood sample from individual 1001

description: Sample ID: 1001


title: Blood sample from individual 1011

description: Sample ID: 1011


title: Blood sample from individual 1013

description: Sample ID: 1013


title: Blood sample from individual 994

description: Sample ID: 994


title: Blood sample from individual 1010

description: Sample ID: 1010


title: Blood sample from individual 1025

description: Sample ID: 1025


title: Blood sample from individual 1007

description: Sample ID: 1007


title: Blood sample from individual 1004

description: Sample ID: 1004


title: Blood sample from individual 1006

description: Sample ID: 1006


title: Blood sample from individual 992

description: Sample ID: 992


title: Blood sample from individual 991

description: Sample ID: 991


title: Blood sample from individual 990

description: Sample ID: 990


title: Blood sample from individual 1002

description: Sample ID: 1002


title: Blood sample from individual 987

description: Sample ID: 987


title: Blood sample from individual 1003

description: Sample ID: 1003


title: Blood sample from individual 1022

description: Sample ID: 1022


title: Blood sample from individual 1000

description: Sample ID: 1000


title: Blood sample from individual 999

description: Sample ID: 999


title: Blood sample from individual 985

description: Sample ID: 985


title: Blood sample from individual 998

description: Sample ID: 998


title: Blood sample from individual 997

description: Sample ID: 997


title: Blood sample from individual 983

description: Sample ID: 983


title: Blood sample from individual 981

description: Sample ID: 981


title: Blood sample from individual 980

description: Sample ID: 980


title: Blood sample from individual 995

description: Sample ID: 995


title: Blood sample from individual 993

description: Sample ID: 993


title: Blood sample from individual 989

description: Sample ID: 989


title: Blood sample from individual 988

description: Sample ID: 988


title: Blood sample from individual 986

description: Sample ID: 986


title: Blood sample from individual 974

description: Sample ID: 974


title: Blood sample from individual 976

description: Sample ID: 976


title: Blood sample from individual 975

description: Sample ID: 975


title: Blood sample from individual 984

description: Sample ID: 984


title: Blood sample from individual 996

description: Sample ID: 996


title: Blood sample from individual 982

description: Sample ID: 982


title: Blood sample from individual 968

description: Sample ID: 968


title: Blood sample from individual 979

description: Sample ID: 979


title: Blood sample from individual 977

description: Sample ID: 977


title: Blood sample from individual 978

description: Sample ID: 978


title: Blood sample from individual 973

description: Sample ID: 973


title: Blood sample from individual 962

description: Sample ID: 962


title: Blood sample from individual 961

description: Sample ID: 961


title: Blood sample from individual 970

description: Sample ID: 970


title: Blood sample from individual 957

description: Sample ID: 957


title: Blood sample from individual 972

description: Sample ID: 972


title: Blood sample from individual 959

description: Sample ID: 959


title: Blood sample from individual 967

description: Sample ID: 967


title: Blood sample from individual 971

description: Sample ID: 971


title: Blood sample from individual 965

description: Sample ID: 965


title: Blood sample from individual 969

description: Sample ID: 969


title: Blood sample from individual 966

description: Sample ID: 966


title: Blood sample from individual 956

description: Sample ID: 956


title: Blood sample from individual 960

description: Sample ID: 960


title: Blood sample from individual 952

description: Sample ID: 952


title: Blood sample from individual 955

description: Sample ID: 955


title: Blood sample from individual 951

description: Sample ID: 951


title: Blood sample from individual 958

description: Sample ID: 958


title: Blood sample from individual 947

description: Sample ID: 947


title: Blood sample from individual 948

description: Sample ID: 948


title: Blood sample from individual 945

description: Sample ID: 945


title: Blood sample from individual 963

description: Sample ID: 963


title: Blood sample from individual 953

description: Sample ID: 953


title: Blood sample from individual 949

description: Sample ID: 949


title: Blood sample from individual 964

description: Sample ID: 964


title: Blood sample from individual 950

description: Sample ID: 950


title: Blood sample from individual 946

description: Sample ID: 946


title: Blood sample from individual 943

description: Sample ID: 943


title: Blood sample from individual 941

description: Sample ID: 941


title: Blood sample from individual 944

description: Sample ID: 944


title: Blood sample from individual 940

description: Sample ID: 940


title: Blood sample from individual 936

description: Sample ID: 936


title: Blood sample from individual 935

description: Sample ID: 935


title: Blood sample from individual 938

description: Sample ID: 938


title: Blood sample from individual 939

description: Sample ID: 939


title: Blood sample from individual 934

description: Sample ID: 934


title: Blood sample from individual 931

description: Sample ID: 931


title: Blood sample from individual 932

description: Sample ID: 932

value: Unknown


title: Blood sample from individual 954

description: Sample ID: 954


title: Blood sample from individual 926

description: Sample ID: 926


title: Blood sample from individual 927

description: Sample ID: 927


title: Blood sample from individual 929

description: Sample ID: 929


title: Blood sample from individual 928

description: Sample ID: 928


title: Blood sample from individual 924

description: Sample ID: 924


title: Blood sample from individual 922

description: Sample ID: 922


title: Blood sample from individual 925

description: Sample ID: 925


title: Blood sample from individual 920

description: Sample ID: 920


title: Blood sample from individual 942

description: Sample ID: 942


title: Blood sample from individual 921

description: Sample ID: 921


title: Blood sample from individual 923

description: Sample ID: 923


title: Blood sample from individual 918

description: Sample ID: 918


title: Blood sample from individual 919

description: Sample ID: 919


title: Blood sample from individual 917

description: Sample ID: 917


title: Blood sample from individual 916

description: Sample ID: 916


title: Blood sample from individual 914

description: Sample ID: 914


title: Blood sample from individual 933

description: Sample ID: 933


title: Blood sample from individual 937

description: Sample ID: 937


title: Blood sample from individual 913

description: Sample ID: 913


title: Blood sample from individual 911

description: Sample ID: 911


title: Blood sample from individual 912

description: Sample ID: 912


title: Blood sample from individual 909

description: Sample ID: 909


title: Blood sample from individual 910

description: Sample ID: 910


title: Blood sample from individual 930

description: Sample ID: 930


title: Blood sample from individual 906

description: Sample ID: 906


title: Blood sample from individual 905

description: Sample ID: 905


title: Blood sample from individual 907

description: Sample ID: 907


title: Blood sample from individual 904

description: Sample ID: 904


title: Blood sample from individual 903

description: Sample ID: 903


title: Blood sample from individual 901

description: Sample ID: 901


title: Blood sample from individual 897

description: Sample ID: 897


title: Blood sample from individual 898

description: Sample ID: 898


title: Blood sample from individual 896

description: Sample ID: 896


title: Blood sample from individual 900

description: Sample ID: 900


title: Blood sample from individual 915

description: Sample ID: 915


title: Blood sample from individual 895

description: Sample ID: 895


title: Blood sample from individual 893

description: Sample ID: 893


title: Blood sample from individual 892

description: Sample ID: 892


title: Blood sample from individual 891

description: Sample ID: 891


title: Blood sample from individual 899

description: Sample ID: 899


title: Blood sample from individual 889

description: Sample ID: 889


title: Blood sample from individual 890

description: Sample ID: 890


title: Blood sample from individual 908

description: Sample ID: 908


title: Blood sample from individual 888

description: Sample ID: 888


title: Blood sample from individual 894

description: Sample ID: 894


title: Blood sample from individual 885

description: Sample ID: 885


title: Blood sample from individual 887

description: Sample ID: 887


title: Blood sample from individual 884

description: Sample ID: 884


title: Blood sample from individual 883

description: Sample ID: 883


title: Blood sample from individual 886

description: Sample ID: 886


title: Blood sample from individual 881

description: Sample ID: 881


title: Blood sample from individual 880

description: Sample ID: 880


title: Blood sample from individual 902

description: Sample ID: 902


title: Blood sample from individual 882

description: Sample ID: 882


title: Blood sample from individual 879

description: Sample ID: 879


title: Blood sample from individual 876

description: Sample ID: 876


title: Blood sample from individual 877

description: Sample ID: 877


title: Blood sample from individual 878

description: Sample ID: 878


title: Blood sample from individual 875

description: Sample ID: 875


title: Blood sample from individual 874

description: Sample ID: 874


title: Blood sample from individual 873

description: Sample ID: 873


title: Blood sample from individual 871

description: Sample ID: 871


title: Blood sample from individual 872

description: Sample ID: 872


title: Blood sample from individual 870

description: Sample ID: 870


title: Blood sample from individual 868

description: Sample ID: 868


title: Blood sample from individual 869

description: Sample ID: 869


title: Blood sample from individual 865

description: Sample ID: 865


title: Blood sample from individual 866

description: Sample ID: 866


title: Blood sample from individual 867

description: Sample ID: 867


title: Blood sample from individual 857

description: Sample ID: 857


title: Blood sample from individual 861

description: Sample ID: 861


title: Blood sample from individual 863

description: Sample ID: 863


title: Blood sample from individual 864

description: Sample ID: 864


title: Blood sample from individual 858

description: Sample ID: 858


title: Blood sample from individual 860

description: Sample ID: 860


title: Blood sample from individual 856

description: Sample ID: 856


title: Blood sample from individual 852

description: Sample ID: 852


title: Blood sample from individual 859

description: Sample ID: 859


title: Blood sample from individual 851

description: Sample ID: 851


title: Blood sample from individual 854

description: Sample ID: 854


title: Blood sample from individual 847

description: Sample ID: 847


title: Blood sample from individual 848

description: Sample ID: 848


title: Blood sample from individual 849

description: Sample ID: 849


title: Blood sample from individual 850

description: Sample ID: 850


title: Blood sample from individual 846

description: Sample ID: 846


title: Blood sample from individual 844

description: Sample ID: 844


title: Blood sample from individual 845

description: Sample ID: 845