title: H3K27ac_GemR_siSTIM1_Veh_rep1

value: Gemcitabine resistant L3.6pl

value: H3K27ac (Diagenode #C15410196)


title: whole blood, DU18-02S0011616

status: Public on Jan 14 2021

type: SRA

city: Durham

first: Florica

last: Constantine

state: NC

address: 304 Research Drive

country: USA

institute: Duke University

description:
counts_key.csv
counts.csv
key.csv
xpr_nlcpm.csv
xpr_tpm_geo.txt

library_source: transcriptomic

data_processing:
Generating genome indexes files using STAR v2.7.1a with parameters in the command line: runMode: genomeGenerate; runThreadN: 16;  genomeDir: path/index; genomeFastaFiles: path/Homo_sapiens.GRCh38.dna.primary_assembly.fa; sjdbGTFfile: path/Homo_sapiens.GRCh38.83.gtf
Mapping reads to the genome using STAR v2.7.1a with parameters in the command line: twopassMode: Basic; quantMode: GeneCounts; genomeDir: path/index; runThreadN: 16; readFilesIn: path/sampleid_R1.fastq.gz path/sampleid_R2.fastq.gz; outFileNamePrefix: path/sampleid; readFilesCommand: zcat.
Genes with counts per million greater than 1 in fewer than 20% of samples were dropped along with three samples that had a high proportion of lowly expressed reads.
Data was normalized using the TMM function from the Bioconductor package edgeR.
Data was log2 transformed
To get the gene length for calculating TPM, we first extracted transcript information from Homo_sapiens.GRCh38.83.gtf (same reference as STAR) by using the makeTxDbFromGFF function, then collect the exons per gene id using the exonsBy function and for each gene, reduce all the exons to a set of non-overlapping exons, calculate their lengths (widths) and sum them up. Use the median gene length if there are any duplicates.  Take the TMM normalized counts matrix from previous processing step, use the rpkm function from the to Bioconductor package edgeR v3.28.0 to calculate the RPKM and calculate TPM from RPKM based on the definition. Save the TPM counts matrix for CIBERSORTx analysis.
Genome_build: Homo_sapiens.GRCh38.83 (Homo_sapiens.GRCh38.83.gtf and Homo_sapiens.GRCh38.dna.primary_assembly.fa); Reference Download: http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/Old/ENSEMBL/homo_sapiens/ENSEMBL.homo_sapiens.release-83/
Supplementary_files_format_and_content: counts_key.csv: csv file with demographic information for all samples
counts.csv: csv file with gene counts for all samples
key.csv: csv file with demographic information for all samples used in analyses
xpr_nlcpm.csv: csv file with the TMM normalized expression values on the log2 scale (analysis ready data)
xpr_tpm_geo.txt: tab-delimited text file with TPM calculated from TMM normalized data

molecule: polyA RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Total RNA was extracted from peripheral blood preserved in PAXgene Blood RNA tubes using QIAGEN PAXgene miRNA Extraction Kit according to manufacturer's instructions.
Libraries were prepared using NUGEN Universal Plus mRNA-seq with AnyDeplete Globin Kit according to manufacturer's instructions.

tag: age

tag: gender

value: Female

tag: race

value: White

tag: cohort

value: late

tag: hospitalized

value: No

tag: tissue

value: whole blood

tag: batch


title: dge1_D04 RNA-seq of ReNcell VM treated with 1 uM fccp

city: Boston

first: Clemens

last: Hug

state: MA

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

institute: Harvard Medical School

description:
RNA-seq of ReNcell VM treated with 1 uM fccp
barcode: ATCTTA batch: dge1

data_processing:
Raw RNA reads were aligned against the reference genome and quantified using the bcbio-nextgen single cell/DGE RNA-seq analysis pipeline (https://bcbio-nextgen.readthedocs.io/). The pipeline consists of the following steps:
Well barcodes and unique molecular identifiers (UMIs) were extracted from the first read. All reads not within the edit distance of a single nucleotide from a predefined well barcode were discarded.
Each extant read was quasialigned to the human transcriptome (version GRCh38) using RapMap.
Reads per well were counted using the UMIs, discarding reads originating from the same original RNA molecule with duplicate UMI, weighting multi-mapped reads by the number of transcripts they aligned to and collapsing transcript counts to gene level by summing. across all transcripts of a gene.
Counts were normalized using the size factor method in DESeq2. Replicates with fewer than 30k total counts were excluded.
Genome_build: GRCh38
Supplementary_files_format_and_content: deduplicated_counts.csv.gz: CSV file of UMI-deduplicated counts of all 765 samples with Ensembl gene IDs.
Supplementary_files_format_and_content: normalized_counts.csv.gz: CSV file of UMI-deduplicated and normalized counts of all 765 samples with HUGO gene symbols.

source_name: in-vitro differentiated neural and glial cells

growth_protocol: A multiwell cell dispenser (catalog# 5840300, Thermo Scientific,Waltham, MA) with standard tubing (catalog# 24072670, Thermo Scientific,Waltham, MA) was used to plate 2500 neural stem cells (ReNcell VM, catalog# SCC008, Millipore, Billerica, MA) into each well of a 384-well cell culture plate (Perkin Elmer, Waltham, MA). Neural stem cells where differentiated into mature neural cells for one week.

extract_protocol:
For RNA extraction, the cell lysate plate was thawed and centrifuged for 1 min at 1000 rpm. Using a BRAVO (Agilent, Santa Clara, CA) liquid handler, the lysate was mixed thoroughly before transferring 10 ul to a 384 well PCR plate. 28 ul of home-made Serapure SPRI beads (GE Healthcare Life Sciences, Marlborough, MA) were added directly to the lysate, mixed and incubated for 5 min. The plate was transferred to a magnetic rack and incubated for 5 min prior to removing the liquid to aggregate the beads. The beads were washed with 80% ethanol twice, allowed to dry for 1 min, 20 ul of nuclease free water was added per well, the plate was removed from the magnetic rack and the beads were thoroughly resuspended. Following a 5 min incubation, the plate was returned to the magnetic rack and incubated an additional 5 min before transferring the supernatant to a fresh PCR plate.
5 ul of the RNA was transferred to a separate plate containing RT master mix and 3’ and 5’ adapters for reverse transcription and template switching, and incubated for 90 min at 42°C. The cDNA was pooled and purified with a QIAquick PCR purification kit according to the manufacturer’s directions with the final elution in 21 ul of nuclease free water. This was followed by exonuclease I treatment for 30 min at 37°C that was stopped with a 20 min incubation at 80°C. The cDNA was then amplified using the Advantage 2 PCR Enzyme System (Takara, Fremont, CA) for 6 cycles, and purified using AMPure XP magnetic beads (Beckman Coulter Genomics, Chaska, MN). Library preparation was performed using a Nextera XT DNA kit (Illumina, San Diego, CA) on 5 reactions per sample following the manufacturer’s instructions, amplified 12 cycles, and purified with AMPure XP magnetic beads (Beckman Coulter Genomics, Chaska, MN). The sample was then quantified by qPCR and sequenced on a single Illumina NextSeq run with 75bp paired end reads at the Harvard University Bauer Core Facility.

treatment_protocol: Differentiated cells were treated with compounds (Table 1) or DMSO using a D300 Digital Dispenser (Hewlett-Packard, Palo Alto, CA). D300 software was used to randomize dispensation of compounds. After 24 hours, the cells were washed once with PBS using an EL405x plate washer (BioTek, Winooski, VT) leaving 5-10 ul of PBS behind in each well. 10 ul of 1X TCL lysis buffer (catalog# 1070498, Qiagen, Hilden, Germany) with 1% (v/v) ß-mercaptoethanol was added per well, and the plates were stored at -80°C until the RNA extraction was performed.

tag: treatment

value: 1 uM fccp

value: ReNcell VM

value: fccp


title: dge1_C23 RNA-seq of ReNcell VM treated with 3 uM barasertib

description:
RNA-seq of ReNcell VM treated with 3 uM barasertib
barcode: GTAATA batch: dge1

value: in-vitro differentiated neural and glial cells

value: 3 uM barasertib

value: barasertib


title: H3K27ac_GemR_siCont_Thap_rep2

city: Rochester

first: Steven

middle: A

last: Johnsen

state: MN

address: 200 First Street SW

department: Gastroenterology Research

institute: Mayo Clinic

library_source: genomic

data_processing:
Bowtie2 (version 2.3.4.1) with a very sensitive read alignment setting was used to map fastq files to the human genome (hg38). Bam files for each condition were merged and their PCR duplicates removed using Samtools (version 1.9). Bamcoverage from deeptools (version 3.0.1) was used to normalize the ChIPseq signal to RPKM.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files were generated using bamcoverage from deeptools (version 3.0.1) and represent the ChIPseq signal normalized to RPKM. H3K27ac bigwigs were scaled to an equal background intensity. The scaling factor of each condition was individually defined as the the ratio of the median signal intensity of control (vehicle treated Par) across all TSSs +/- 1kb divided by the median signal intensity of each individual condition across all TSSs +/- 1kb.

molecule: genomic DNA

source_name: Pancreatic cancer

growth_protocol: The cells were cultured in Minimum Essential Medium Eagle (MEM) supplemented with 10% FBS, 1% Penicillin and Streptomycin and 1% L-Glutamine. GemR cells were maintained in 64nM gemcitabine.

extract_protocol:
The ChIP was performed by crosslinking protein to DNA using 1% formaldehyde in PBS for 20min followed by chromatin shearing and immunoprecipitation overnight with 1µg of antibody. The immunocomplexes were captured by protein A sepharose for 2h and washed. Crosslinking was reversed and the DNA extracted using phenol-chloroform-isoamyl.
ChIP-Seq libraries were prepared using the KAPA HyperPrep kit and 2.5ng DNA.

treatment_protocol: Gene knockdowns were performed for 48h using RNAiMax (Invitrogen) and following manufacturer's instructions. 3h prior to harvesting, the cells were submitted to vehicle (DMSO) or 500nM thapsigargin treatment.

tag: cell line

value: siCont. (48h), 500nM thapsigargin (3h)

tag: chip antibody


title: whole blood, DU18-02S0011671

value: Male

value: middle


title: dge1_C22 RNA-seq of ReNcell VM treated with 1 uM mg-132

description:
RNA-seq of ReNcell VM treated with 1 uM mg-132
barcode: GATATA batch: dge1


title: whole blood, DU18-02S0011672


title: whole blood, DU18-02S0011628

value: early


title: whole blood, DU18-02S0011605


title: whole blood, DU18-02S0011627


title: dge1_C21 RNA-seq of ReNcell VM treated with 1 uM r 59-022

description:
RNA-seq of ReNcell VM treated with 1 uM r 59-022
barcode: GATAAT batch: dge1


title: H3K27ac_GemR_siCont_Veh_rep2

value: Gemcitabine resistant L3.6pl

value: siCont. (48h), Veh. (3h)


title: whole blood, DU18-02S0011623


title: whole blood, DU18-02S0011603


title: H3K27ac_GemR_siCont_Veh_rep1

value: H3K27ac (Diagenode #C15410196)


title: whole blood, DU18-02S0011624

value: White


title: dge1_C19 RNA-seq of ReNcell VM treated with 1 uM r 59949

description:
RNA-seq of ReNcell VM treated with 1 uM r 59949
barcode: CTTTAA batch: dge1


title: whole blood, DU18-02S0011625

value: late


title: dge1_C20 RNA-seq of ReNcell VM treated with 3 uM brivanib

description:
RNA-seq of ReNcell VM treated with 3 uM brivanib
barcode: GAAATT batch: dge1

value: 3 uM brivanib

value: brivanib


title: H3K27ac_Par_siCont_Thap_rep2


title: whole blood, DU18-02S0011626

value: No

value: whole blood


title: whole blood, DU18-02S0011622


title: dge1_C17 RNA-seq of ReNcell VM treated with 1 uM ldn-193189

description:
RNA-seq of ReNcell VM treated with 1 uM ldn-193189
barcode: CTATAT batch: dge1

value: ReNcell VM


title: whole blood, DU18-02S0011621


title: whole blood, DU18-02S0011620


title: whole blood, DU18-02S0011619


title: H3K27ac_Par_siCont_Thap_rep1


title: whole blood, DU14-03S0000889

value: Female

value: Black/African American

value: CoV other


title: H3K27ac_GemR_siCont_Thap_rep1

value: siCont. (48h), 500nM thapsigargin (3h)


title: H3K27ac_Par_siCont_Veh_rep2


title: dge1_C15 RNA-seq of ReNcell VM treated with 10 uM r 59949

description:
RNA-seq of ReNcell VM treated with 10 uM r 59949
barcode: CATTAT batch: dge1

value: in-vitro differentiated neural and glial cells


title: Input_GemR_rep2

data_processing:
Bowtie2 (version 2.3.4.1) with a very sensitive read alignment setting was used to map fastq files to the human genome (hg38). Bam files for each condition were merged and their PCR duplicates removed using Samtools (version 1.9). Bamcoverage from deeptools (version 3.0.1) was used to normalize the ChIPseq signal to RPKM.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files were generated using bamcoverage from deeptools (version 3.0.1) and represent the ChIPseq signal normalized to RPKM.

growth_protocol: The cells were cultured in Minimum Essential Medium Eagle (MEM) supplemented with 10% FBS, 1% Penicillin and Streptomycin and 1% L-Glutamine and maintained in 64nM gemcitabine.

extract_protocol:
The ChIP was performed by crosslinking protein to DNA using 1% formaldehyde in PBS for 20min followed by chromatin shearing and immunoprecipitation overnight with 1µg of antibody. The immunocomplexes were captured by protein A sepharose for 2h and washed. Crosslinking was reversed and the DNA extracted using phenol-chloroform-isoamyl.
ChIP-Seq libraries were prepared using the Microplex Library Preparation V2 kit and 0.5ng DNA.


title: dge1_C16 RNA-seq of ReNcell VM treated with 10 uM pf04217903

description:
RNA-seq of ReNcell VM treated with 10 uM pf04217903
barcode: CATTTA batch: dge1


title: whole blood, DU14-03S0000878

value: Male


title: whole blood, DU09-03S0000775

value: Influenza


title: whole blood, DU09-03S19478


title: H3K27ac_Par_siCont_Veh_rep1


title: whole blood, DU09-03S0000774


title: dge1_C14 RNA-seq of ReNcell VM treated with 10 uM r 59949

description:
RNA-seq of ReNcell VM treated with 10 uM r 59949
barcode: CAATAA batch: dge1


title: whole blood, 105920


title: dge1_C13 RNA-seq of ReNcell VM treated with 0.3 uM r 59949

description:
RNA-seq of ReNcell VM treated with 0.3 uM r 59949
barcode: CAAATA batch: dge1


title: whole blood, DU09-03S0000611


title: whole blood, DU09-03S0000604


title: H3K27ac_GemR_rep2

value: Gemcitabine resistant L3.6pl


title: dge1_C18 RNA-seq of ReNcell VM treated with lipopolysaccharide

description:
RNA-seq of ReNcell VM treated with lipopolysaccharide
barcode: CTATTA batch: dge1

value: lipopolysaccharide

tag: stimulant


title: H1-LP-TK-58I-BS01566

city: New York

first: Mathew

middle: T

last: Maurano

state: NY

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Langone Health

description: genomic DNA

data_processing:
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics or NovaSeq 6000 operated by the NYU Langone Health Genome Technology Center. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences. All WGS and Capture-Seq data were processed using a uniform mapping and peak calling pipeline. Illumina sequencing adapters were trimmed with Trimmomatic v0.39{Bolger, 2014 #3524}. Sequencing reads were aligned using BWA v0.7.17{Li, 2009 #3526} to a genome reference (GRCh38/hg38 or GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24{Faust, 2014 #3527}. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35{Neph, 2012 #3540}. Data were visualized using the UCSC Genome Browser. The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: coverage depth track (bigwig)

growth_protocol: hESCs were grown on Geltrex-coated plates with StemFlex medium supplemented with 1% Pen-Strep and passaged in clumps using Versene. mESCs were cultured on gelatin-coated plates coated in 80/20 medium comprising 80% 2i medium and 20% mESC medium and with 1% Pen-strep.

extract_protocol:
Cells were dissociated using TryPE-Select, spun-down and media aspirate. Pellets were either processed immediately or stored at -80 deg. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN 69506).
Double-stranded DNA libraries were prepared from sheared genomic DNA. DNA fragments were end-repaired, A-tailed, and Illumina-compatible adapters were ligated to DNA ends.
Other - DNA Capture-seq

treatment_protocol: Cells were selected combinatorially with puromycin, blasticidin, proaerolysin and ganciclovir as described in the manuscript

tag: strain

tag: genotype

value: WT


title: whole blood, 94189

value: Bacterial


title: H3K27ac_GemR_rep1

value: H3K27ac (Diagenode #C15410196)


title: pSox2-143kb-BS07689A

description: Captured genomic DNA

organism: synthetic construct


title: dge1_C11 RNA-seq of ReNcell VM treated with 3 uM ruxolitinib

description:
RNA-seq of ReNcell VM treated with 3 uM ruxolitinib
barcode: ATTTCA batch: dge1

value: 3 uM ruxolitinib

value: ruxolitinib


title: week12_035

city: Vienna

first: Artem

middle: V

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

data_processing:
Sequenced bcl files were converted to fastq files with cellranger 3.0.1
The sequenced 10X libraries from 9 samples were mapped to GRCh38 human genome (bundle 3.0.0) and assigned to droplets with Cell Ranger software (version 3.0.1) with default parameters
The obtained read count matrices were analyzed with Seurat
Genome_build: GRCh38
Supplementary_files_format_and_content: h5datasets with raw gene expression counts

source_name: adrenal gland region

extract_protocol:
Human pre-natal tissue was retrieved from clinical routine abortions with oral and written consent from the patient. All procedures regarding the acquisition of human pre-natal tissue for research was approved by the Swedish Ethical Research Authority and the National Board of Health and Welfare. Post-conception age was determined using measurement of crown-rump-length (CRL) and anatomical landmarks. After identifying the adrenal glands, this tissue was retrieved and placed in ice-cold PBS pending dissociation. Tissue was chopped into 1 mm pieces and placed in 500 ul 0.05% Trypsin/0.02% EDTA (Sigma, 59417-C) and incubated at 37°C for 15 min with careful mix every 5 min. Following this, the tissue was triturated slowly and carefully with a P-1000, then P-200 pipette until complete dissociation. 500 ul 10% FBS in PBS was added to cell suspension for trypsin inactivation. Cell suspension was centrifuged at 500 rcf for 5 min at 4°C, followed by two washes with 1000 uL PBS. Cell suspension was pass though the 35 um cell strainer (Falcon, 352235 ) and spin down at 500 rcf for 5 min at 4°C. Cell pellet was resuspended in 100 ul 0.04% BSA in PBS and 400 ul of ice cold methanol was added for methanol fixation of the cells for storage. Cells suspension in cryotubes were placed in Mister Frosty (Thermo Scientific) and at -80°C for controlled cooling.
On the day of 10x Chromium library preparation the cells were brought to +4°C and centrifuged at 1000 rcf for 10 min at 4°C. Supernatant was carefully removed and 500 uL of rehydration buffer (1X DPBS (Gibco 14190144) containing 1.0% BSA (Sigma, B4287) and 0.5U/?l RNAse Out (ThermoFisher Scientific, 10777019) was added to cell pellet, re-suspended and centrifuged at 1000 rcf for 10 min at 4°C. The wash with rehydration buffer was repeated one more time, after which cells were counted. If a lot of debris was observed during cell count the cell suspension was subjected for FACS to remove debris. After cell count or FACS cells were pelleted again and re-suspended in rehydration buffer to get 700-1200 cells/ul but no less than 50 uL. Library preparation was done in accordance with 10x Genomics Chromium Single Cell 3’ (v3) aiming at recovering 5000-8000 cells at Illumina Novaseq with the help of Eukaryotic Single Cell Genomic Facility, SciLifeLab, Stockholm, Sweden.

tag: developmental stage, weeks


title: week8_016


title: pSox2-46kb-MC-BS03435A

description: Captured genomic DNA


title: LSC_scRNAseq_2

city: Houston

first: sangbae

last: Kim

address: 1 baylor plaza

institute: Baylor College of Medicine

description: The tissue was obtained from the Lions Eye Bank of Texas (LEBT, Houston, TX)

data_processing:
Illumina Casava software used for basecalling. Individual FASTQ files obtained were demultiplexed using the well-specific barcode identifiers for downstream data processing and analysis.
Cell Ranger software v2.1 (https://www.10xgenomics.com) with default settings was used for alignment, barcode assignment and UMI counting of the raw sequencing data with genome reference hg19.
After generating UMI count profile, we applied Seurat 3.0 for quality control and downstream analysis.
Read count profile were analyzed for the differential expression analysis using Seurat package (https://satijalab.org/seurat/, version 2.3.4) for data analysis including quality control, normalization, dimensional reduction, clustering, and visualization. Cells with less than 15% of total expressed genes, and genes that were detected in less than 3% of total cells in each dataset were discarded forom all further analyses. In addition, cells with over 20% mitochondrial gene percentage were excluded for filtering of dead or poor-quality cells
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each sample condition.

molecule: total RNA

source_name: Corneoscleral tissues-2

extract_protocol:
The loose limbal epithelial sheet will be peeled gently and digested with 1 ml of 0.05% trypsin/1 mM EDTA at 37oC for 10 min. The trypan blue will be used to test viability of single cells.
Single cell cDNA library preparation and sequencing were performed following manufacturer's protocols (https://www.10xgenomics.com). Single cell suspension at 1000 cells/µl in PBS will be loaded on a Chromium controller to generate single cell GEMS (Gel Beads-In-Emulsions). The scRNA-Seq library is prepared with chromium single cell 3’ reagent kit v2 (10x Genomics). ). In brief, single cells are partitioned to GEMS where cDNA is synthesized and barcoded. Subsequently, the GEMS are broken and cDNA are pooled and amplified. Library is made by fragmentation, end-repair, A-tailing, and adaptor ligation. Finally, the product is amplified by PCR and sequenced on Illumina Novaseq 6000 (https://www.illumina.com).

treatment_protocol: After superficial layers scraped, the remaining limbal tissue with basal cells will be incubated in dispase II (10 mg/ml) at 4oC for 16 hours.

value: Corneoscleral tissues


title: LSC_scRNAseq_1

source_name: Corneoscleral tissues-1


title: Input_GemR_rep1


title: week9_007

extract_protocol:
Human pre-natal tissue was retrieved from clinical routine abortions with oral and written consent from the patient. All procedures regarding the acquisition of human pre-natal tissue for research was approved by the Swedish Ethical Research Authority and the National Board of Health and Welfare. Post-conception age was determined using measurement of crown-rump-length (CRL) and anatomical landmarks. After identifying the adrenal glands, this tissue was retrieved and placed in ice-cold PBS pending dissociation. Tissue was chopped into 1 mm pieces and placed in 500 ul 0.05% Trypsin/0.02% EDTA (Sigma, 59417-C) and incubated at 37°C for 15 min with careful mix every 5 min. Following this, the tissue was triturated slowly and carefully with a P-1000, then P-200 pipette until complete dissociation. 500 ul 10% FBS in PBS was added to cell suspension for trypsin inactivation. Cell suspension was centrifuged at 500 rcf for 5 min at 4°C, followed by two washes with 1000 uL PBS. Cell suspension was pass though the 35 um cell strainer (Falcon, 352235 ) and spin down at 500 rcf for 5 min at 4°C. Cell pellet was resuspended in 100 ul 0.04% BSA in PBS and 400 ul of ice cold methanol was added for methanol fixation of the cells for storage. Cells suspension in cryotubes were placed in Mister Frosty (Thermo Scientific) and at -80°C for controlled cooling.
On the day of 10x Chromium library preparation the cells were brought to +4°C and centrifuged at 1000 rcf for 10 min at 4°C. Supernatant was carefully removed and 500 uL of rehydration buffer (1X DPBS (Gibco 14190144) containing 1.0% BSA (Sigma, B4287) and 0.5U/μl RNAse Out (ThermoFisher Scientific, 10777019) was added to cell pellet, re-suspended and centrifuged at 1000 rcf for 10 min at 4°C. The wash with rehydration buffer was repeated one more time, after which cells were counted. If a lot of debris was observed during cell count the cell suspension was subjected for FACS to remove debris. After cell count or FACS cells were pelleted again and re-suspended in rehydration buffer to get 700-1200 cells/ul but no less than 50 uL. Library preparation was done in accordance with 10x Genomics Chromium Single Cell 3’ (v3) aiming at recovering 5000-8000 cells at Illumina Novaseq with the help of Eukaryotic Single Cell Genomic Facility, SciLifeLab, Stockholm, Sweden.

tag: developmental stage (weeks)


title: week12_036_extraadrenal

source_name: tissue outside of the adrenal gland


title: week11_006


title: dge1_C10 RNA-seq of ReNcell VM treated with 10 uM mg-132

description:
RNA-seq of ReNcell VM treated with 10 uM mg-132
barcode: ATTGAA batch: dge1


title: pPL1-BS04321A

description: BAC


title: week9_031_paraganglia

source_name: paraganglia and Zuckerkandl organ


title: week8_125


title: dge1_C12 RNA-seq of ReNcell VM treated with 3 uM sb202190

description:
RNA-seq of ReNcell VM treated with 3 uM sb202190
barcode: ATTTGT batch: dge1


title: dge1_C06 RNA-seq of ReNcell VM treated with 10 uM barasertib

description:
RNA-seq of ReNcell VM treated with 10 uM barasertib
barcode: ATGATA batch: dge1

value: 10 uM barasertib

value: barasertib


title: ZM_fusion_GFP_ChIP

city: Chapel Hill

first: Gang (Greg)

last: Wang

address: 450 West Drive, Lineberger Cancer Center

institute: UNC-Chapel Hill

data_processing:
ChIP-seq reads were aligned to mouse genome build NCBI37/mm9 using STAR version 2.7.1a after quality trimming. Non-primary alignment and PCR duplicates were then removed by samtools.
Alignment files in the bam format were transformed into read coverage files (bigWig format) using DeepTools. Genomic binding profiles were generated using the deepTools “bamCompare” functions with options [--operation ratio ---pseudocount 1 -binSize 10 --extendReads 250] and normalized to the matched input.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

organism: Mus musculus

source_name: ZM-immortalized murine hematopoietic progenitor cells

growth_protocol: ZM-transformed murine AML cells were grown in the Opti-MEM base medium supplemented with 15% FBS (Invitrogen, 16000-044), 1% antibiotics, 50 μM β-mercaptoethanol, murine SCF (5% supernatant from murine SCF-producer cells) and murine Flt3 ligand (5% supernatant from murine Flt3 ligand-producing cells).

extract_protocol:
Cells were fixed in PBS containing 1% formaldehyde and then subject to lysis, sonication, IP, wash, elution, reverse crosslink, Rnase and Proteinase K digestion, and DNA recover by Qiagen PCR purification kit.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) following the manufacture’s protocol.

tag: cell type

value: anti-GFP (Abcam, ab290)


title: dge1_C09 RNA-seq of ReNcell VM treated with 1 uM r 59949

description:
RNA-seq of ReNcell VM treated with 1 uM r 59949
barcode: ATTCTA batch: dge1

value: ReNcell VM


title: dge1_C05 RNA-seq of ReNcell VM treated with lipopolysaccharide

description:
RNA-seq of ReNcell VM treated with lipopolysaccharide
barcode: ATGAAT batch: dge1


title: week14_123


title: week9_063


title: week6_088


title: ZM_fusion_HA_ChIP

value: ZM-immortalized murine hematopoietic progenitor cells

value: anti-HA (Abcam, ab9110)


title: ZM_fusion_HA_ChIP_input

value: n/a (input)


title: week8_001


title: pSox2-46kb-MC-BBTK-BS04322A

description: BAC


title: dge1_C03 RNA-seq of ReNcell VM treated with 1 uM torin1

description:
RNA-seq of ReNcell VM treated with 1 uM torin1
barcode: ATCAAA batch: dge1

value: in-vitro differentiated neural and glial cells

value: 1 uM torin1


title: week9_005


title: dge1_C04 RNA-seq of ReNcell VM treated with 1 uM pf04217903

description:
RNA-seq of ReNcell VM treated with 1 uM pf04217903
barcode: ATCATT batch: dge1


title: dge1_C08 RNA-seq of ReNcell VM treated with 3 uM hg-9-91-01

description:
RNA-seq of ReNcell VM treated with 3 uM hg-9-91-01
barcode: ATTAGA batch: dge1


title: dge1_C02 RNA-seq of ReNcell VM treated with 0.3 uM gsk1059615

description:
RNA-seq of ReNcell VM treated with 0.3 uM gsk1059615
barcode: ATATCT batch: dge1


title: Input PAMH

city: Illkirch

first: Damien

last: PLASSARD

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Preprocessing: Adapter dimer reads were removed using DimerRemover. Data were preprocessed with Cutadapt v1.13 (Martin, 2011) to remove the first 9 nucleotides and to remove sequences with a trailing polyT of at least 10 Ts. Cutadapt was used with the following parameters ‘-u 9 -a T{10} --discard-trimmed’.
Alignment: Reads were mapped to the mouse genome (mm10) using Bowtie  v1.0.0 (Langmead et al., 2009) with default parameters except for “-p 3 –m 1 --strata --best”.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized BigWig files were generated using Homer (Heinz et al. 2010) makeUCSCfile v4.9.1 with the following parameter ’-norm 1e7’.

source_name: IPed DNA from ovaries from Mice

extract_protocol:
Genomic DNA was extracted with Diagenode kit (MagMeDIP kit; Cat nr: C15200081), sonicated with the Bioruptor, and precipitated with 5meC-Ab (Diagenode; Cat nr: C15200081; Lot nr: RD004) or with control IgG (Diagenode; Cat nr: C15400001; Lot nr: MIG002S).
MeDIP-seq libraries were generated from 1 to 4 ng of single-stranded or double-stranded IP-DNA samples using the DNA SMART ChIP-Seq (634866, Takara Bio USA, Inc., Mountain View, CA, USA) according to manufacturer's instructions. Briefly, the differents steps of the library prep were: 1) denaturation of the DNA, 2) T-tailing of the 3' end of the single-stranded DNA by the terminal transferase 3), annealing of DNA SMART poly(dA) primer to the 3’ T-tail, 4) primer extension by the reverse transcriptase (RT), 5) template switching and extension by RT using SMART oligo, 6) addition of Illumina indexed adapters through a PCR amplification (12 cycles) using primers compatible with regions on the DNA SMART Poly(dA) primer and the SMART oligo, 7) purification and size-selection of amplified library using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: Pregnant F0 dams were injected subcutaneously with PBS (Control; CNTR) or with human recombinant bioactive AMH (R&D Systems, 0.12 mg/Kg/d; prenatal AMH-treated, PAMH) from embryonic day E16.5 to E18.5, to generate PAMH F1 male and female mice, that were successively bred to produce the second (F2) and third (F3) PAMH generations. F2 and F3 lineages did not receive any further AMH treatment during pregnancy. Control ovaries and ovaries from PAMH F3 adult mice (P60) were dissected and snap-frozen in liquid nitrogen and strored at -80 °C until further treatment.

value: Ovaries

tag: agent

value: PAMH


title: Input CNTR

value: PBS


title: ZM_fusion_GFP_ChIP_input


title: dge1_C01 RNA-seq of ReNcell VM treated with 10 uM plx-4720

description:
RNA-seq of ReNcell VM treated with 10 uM plx-4720
barcode: ATATAG batch: dge1


title: IgG PAMH

value: IgG (Diagenode; Cat nr:C15400001; Lot nr:MIG002S)


title: dge1_C07 RNA-seq of ReNcell VM treated with 0.3 uM alisertib

description:
RNA-seq of ReNcell VM treated with 0.3 uM alisertib
barcode: ATTACT batch: dge1

value: 0.3 uM alisertib

value: alisertib


title: IgG CNTR


title: dge1_B23 RNA-seq of ReNcell VM treated with 0.3 uM (+)-jq1

description:
RNA-seq of ReNcell VM treated with 0.3 uM (+)-jq1
barcode: ATAGAT batch: dge1


title: PAE 2wk Male 51

type: RNA

city: Bryan

first: Amanda

last: Mahnke

state: TX

address: 8447 Riverside Parkway

department: Neuroscience and Experimental Therapeutics

institute: Texas A&M University Health Science Center

description: PAE

data_processing: miRNAs expressed in >80% of samples (either PAE or cont) were normalized to average miRNA expression for each sample, with undetermined values replaced with 1+highest CT for each miRNA

label: SYBR Green

source_name: Plasma

label_protocol: Exiqon miRCURY LNA Universal RT cDNA synthesis kit, ExiLENT SYBR green master mix

extract_protocol: Qiagen miRNeasy Mini Kit with 1.2ug MS2 carrier RNA per sample

value: Male

tag: age

tag: participant number

tag: analysis inclusion

value: Included


title: PAE 2wk Female 49

description: PAE

tag: gender

value: Female


title: PAE 6.5mo Male 51

description: PAE


title: PAE 2wk Female 68

description: PAE


title: PAE 6.5mo Female 68

description: PAE


title: PAE 6.5mo Female 42

description: PAE


title: PAE 2wk Female 42

description: PAE


title: dge1_B24 RNA-seq of ReNcell VM treated with 3 uM gsk1059615

description:
RNA-seq of ReNcell VM treated with 3 uM gsk1059615
barcode: ATAGTA batch: dge1


title: Cont 2wk Female 27

description: Cont


title: week12_124


title: Cont 6.5mo Female 16

description: Cont


title: Cont 6.5mo Female 27

description: Cont


title: PAE 6.5mo Female 49

description: PAE


title: PAMH 4  [MeDIP-seq]

value: 5meC (Diagenode; Cat nr:C15200081; Lot nr:RD004)


title: dge1_B22 RNA-seq of ReNcell VM treated with 0.3 uM nvp-tae684

description:
RNA-seq of ReNcell VM treated with 0.3 uM nvp-tae684
barcode: ATAATG batch: dge1

value: 0.3 uM nvp-tae684


title: PAMH 3 [MeDIP-seq]


title: dge1_B21 RNA-seq of ReNcell VM treated with 3 uM gsk1070916

description:
RNA-seq of ReNcell VM treated with 3 uM gsk1070916
barcode: ATAAGT batch: dge1

value: ReNcell VM


title: Cont 2wk Female 16

description: Cont


title: Cont 2wk Female 53

description: Cont


title: Cont 2wk Male 58

description: Cont


title: PAMH 2 [MeDIP-seq]


title: PAE 2wk Female 59

description: PAE


title: dge1_B20 RNA-seq of ReNcell VM treated with 10 uM bortezomib

description:
RNA-seq of ReNcell VM treated with 10 uM bortezomib
barcode: AGTTAA batch: dge1

value: 10 uM bortezomib

value: bortezomib


title: PAMH 1 [MeDIP-seq]


title: dge1_B19 RNA-seq of ReNcell VM treated with 3 uM cabozantinib

description:
RNA-seq of ReNcell VM treated with 3 uM cabozantinib
barcode: AGTATA batch: dge1

value: 3 uM cabozantinib

value: cabozantinib


title: PAE 2wk Female 55

description: PAE


title: Cont 2wk Male 54

description: Cont


title: CNTR 2 [MeDIP-seq]


title: CNTR 3 [MeDIP-seq]


title: Cont 2wk Male 57

description: Cont

value: Excluded Hemolysis


title: dge1_B18 RNA-seq of ReNcell VM treated with 3 uM barasertib

description:
RNA-seq of ReNcell VM treated with 3 uM barasertib
barcode: AGATAT batch: dge1

value: in-vitro differentiated neural and glial cells

value: 3 uM barasertib

value: barasertib


title: PAE 2wk Male 44

description: PAE


title: CNTR 1 [MeDIP-seq]

value: Ovaries

value: PBS


title: dge1_B16 RNA-seq of ReNcell VM treated with 1 uM alisertib

description:
RNA-seq of ReNcell VM treated with 1 uM alisertib
barcode: ACTATT batch: dge1

value: 1 uM alisertib

value: alisertib


title: PAMH 4

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using STAR v.2.5.3a
Quantification : Gene Expression was quantified using HTSeq v.0.6.1p1 (union mode) and Ensembl release 97 annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Tabulated text file containing raw read counts in each sample.

source_name: PAMH F3_third generation (F3) after ancestral prenatal exposure to AMH (F0)

extract_protocol:
Total RNA was isolated from mice ovaries using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer instructions.
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Pregnant F0 dams were injected subcutaneously with PBS (Control; CNTR) or with human recombinant bioactive AMH (R&D Systems, 0.12 mg/Kg/d; prenatal AMH-treated, PAMH) from embryonic day E16.5 to E18.5, to generate PAMH F1 male and female mice, that were successively bred to produce the second (F2) and third (F3) PAMH generations. F2 and F3 lineages did not receive any further AMH treatment during pregnancy. Control ovaries and ovaries from PAMH F3 adult mice (P60) were dissected and snap-frozen in liquid nitrogen and strored at -80 °C until RNA extraction.

value: ovaries

value: AMH

tag: group

value: third generation of PCOS-like mice (PAMH F3)


title: Cont 6.5mo Female 62

description: Cont

value: Female

value: Included


title: PAE 2wk Male 64

description: PAE

value: Male


title: dge1_B17 RNA-seq of ReNcell VM treated with 10 uM plx-4720

description:
RNA-seq of ReNcell VM treated with 10 uM plx-4720
barcode: AGAATT batch: dge1

value: ReNcell VM


title: PAE 2wk Female 63

description: PAE


title: PAE 2wk Male 26

description: PAE


title: PAE 2wk Female 45

description: PAE

value: Excluded Panel 1


title: PAE 2wk Male 67

description: PAE


title: Cont 2wk Male 60

description: Cont


title: PAMH 3

tag: tissue


title: dge1_B14 RNA-seq of ReNcell VM treated with 1 uM tofacitinib

description:
RNA-seq of ReNcell VM treated with 1 uM tofacitinib
barcode: ACAAAT batch: dge1

value: 1 uM tofacitinib

value: tofacitinib


title: PAE 2wk Male 48

description: PAE


title: PAMH 2


title: dge1_B13 RNA-seq of ReNcell VM treated with 0.3 uM plx-4720

description:
RNA-seq of ReNcell VM treated with 0.3 uM plx-4720
barcode: AATTTC batch: dge1

value: in-vitro differentiated neural and glial cells


title: Cont 2wk Female 40

description: Cont


title: Cont 2wk Male 46

description: Cont


title: dge1_B12 RNA-seq of ReNcell VM treated with 10 uM ruxolitinib

description:
RNA-seq of ReNcell VM treated with 10 uM ruxolitinib
barcode: AATTAG batch: dge1

value: 10 uM ruxolitinib

value: ruxolitinib


title: PAMH 1


title: Cont 2wk Male 33

description: Cont


title: Cont 2wk Male 32

description: Cont


title: PAE 2wk Male 19

description: PAE


title: CNTR 3

source_name: Control_offspring of mothers treated with PBS during gestation

value: control


title: dge1_B11 RNA-seq of ReNcell VM treated with 1 uM ruxolitinib

description:
RNA-seq of ReNcell VM treated with 1 uM ruxolitinib
barcode: AATGTA batch: dge1

value: 1 uM ruxolitinib


title: dge1_B15 RNA-seq of ReNcell VM treated with 1 uM pazopanib

description:
RNA-seq of ReNcell VM treated with 1 uM pazopanib
barcode: ACTAAA batch: dge1

value: 1 uM pazopanib

value: pazopanib


title: CNTR 2

value: ovaries

value: PBS


title: CNTR 1


title: PAE 2wk Male 20

description: PAE


title: dge1_B09 RNA-seq of ReNcell VM treated with 10 uM sb202190

description:
RNA-seq of ReNcell VM treated with 10 uM sb202190
barcode: AATATG batch: dge1


title: PY-60 treated – Biological replicate 3

city: San Diego

first: Lara

last: Ibrahim

state: California

address: 10550 N Torrey Pines Rd

institute: Scripps Research

data_processing:
Basecalling was performed by the sequencing core at the Scripps Research Institute
Transcript abundance was estimated using Kallisto
Genome_build: GRCh37.p13 human genome reference assembly
Supplementary_files_format_and_content: PY-60.v.DMSO.293A.RNA-seq.TPM

source_name: 293A_PY-60 treatment

growth_protocol: 293A cells were maintained in standard DMEM supplemented with 10%FBS and 1%PenStrep at 37C and 5% CO2

extract_protocol:
After 24-hour treatment with compound, cells were washed once with PBS and then trypsinized with 500 µL of TrypLE Express dissociation reagent (Gibco) and neutralized with the addition of 500 µL of growth medium. After pelleting cells with centrifugation (300g) for 3 minutes in 1.5 mL microfuge tubes, total RNA was isolated using a RNeasy kit (Qiagen).
Three biological replicates were submitted for library preparation and sequencing on an Illumina HiSeq Platform (~58 million paired end reads per sample)

treatment_protocol: Cells were treated with DMSO or PY-60 for 24 hr.

value: human embryonic kidney cells

value: PY-60 treatment


title: dge1_B10 RNA-seq of ReNcell VM treated with 10 uM pf04217903

description:
RNA-seq of ReNcell VM treated with 10 uM pf04217903
barcode: AATCAA batch: dge1


title: PY-60 treated – Biological replicate 2


title: PY-60 treated – Biological replicate 1


title: PlacentaMvirusB1

first: Nicholas

last: Heaton

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
The reads were mapped to the mouse transcriptome (mm10) using STAR and the samples were run on Basespace (Illumina).
Mapped reads were normalized and averaged; fold change then calculated by comparing the indicated groups to one another ( vehicle infect. vs vehicle uninfect or G15 infect. vs vehicle infect.)
Supplementary_files_format_and_content: Raw ReadCounts

source_name: mouse placentas

extract_protocol:
Whole lungs or placentas were homogenized in PBS before being extracted via standard Trizol extraction protocol
mRNA was prepped for sequencing using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490), NEBNext Ultra II RNA Library Prep Kit (NEB #E7770), and NEBNext Multiplex Oligos for Illumina (NEB #E7335, #E7500).

treatment_protocol: pregnant females were given daily subcutaneous injections of vehicle (DMSO/PBS) or G15 (selective GPER1 antagonist) starting at E5. They were then infected with A/Puerto Rico/8/1934 at E10 and continually treated/monitored before collecting tissues at E17 (7 days post-infection).

value: Vehicle treatment

tag: infection

value: IAV Infected


title: PlacentaMvirusB2


title: Cont 6.5mo Female 66

description: Cont

value: Female

value: Included


title: dge1_B08 RNA-seq of ReNcell VM treated with 0.3 uM tofacitinib

description:
RNA-seq of ReNcell VM treated with 0.3 uM tofacitinib
barcode: AATAAC batch: dge1

tag: treatment

value: 0.3 uM tofacitinib

value: ReNcell VM


title: PAE 6.5mo Male 64

description: PAE

value: Male


title: PAE 6.5mo Male 67

description: PAE


title: dge1_B07 RNA-seq of ReNcell VM treated with 10 uM gsk1059615

description:
RNA-seq of ReNcell VM treated with 10 uM gsk1059615
barcode: AAGTTA batch: dge1

value: in-vitro differentiated neural and glial cells


title: PlacentaMvirusA2


title: PAE 6.5mo Female 63

description: PAE


title: DMSO treated control – Biological replicate 3

source_name: 293A_DMSO treatment

tag: cell line

value: DMSO treatment


title: PAE 6.5mo Female 61

description: PAE


title: PlacentaMnoVirusC3

value: Uninfected


title: PlacentaMvirusA1


title: DMSO treated control – Biological replicate 2


title: Cont 6.5mo Male 60

description: Cont


title: dge1_B05 RNA-seq of ReNcell VM treated with 3 uM brivanib

description:
RNA-seq of ReNcell VM treated with 3 uM brivanib
barcode: AACATA batch: dge1

value: 3 uM brivanib

value: brivanib


title: DMSO treated control – Biological replicate 1


title: Cont 6.5mo Male 25

description: Cont


title: Cont 6.5mo Female 65

description: Cont


title: dge1_B03 RNA-seq of ReNcell VM treated with 1 uM fccp

description:
RNA-seq of ReNcell VM treated with 1 uM fccp
barcode: AAATCA batch: dge1

value: 1 uM fccp

value: fccp


title: dge1_B04 RNA-seq of ReNcell VM treated with 1 uM cabozantinib

description:
RNA-seq of ReNcell VM treated with 1 uM cabozantinib
barcode: AAATGT batch: dge1

value: 1 uM cabozantinib

value: cabozantinib


title: PAE 6.5mo Female 59

description: PAE


title: IL-IFN_rep2

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

data_processing:
The RNAsik pipeline (version 1.5.3.) was used to process the data
Raw fastq files were aligned to the Ensembl Human GRCh38 (release 95)
Quality control checks were performed using Picard, samtools, qualimap 2
FeatureCounts was used to count reads to the annotated features in the genome
The count matrix was uploaded to Degust for differential gene expression
Genome_build: Ensembl Human GRCh38 (release 95)
Supplementary_files_format_and_content: Count matrix (tab separate format)

source_name: PBMC

extract_protocol:
Cells were sorted and RNA extracted using RNAqueous™-Micro Total RNA Isolation Kit according to the manufacturer’s instructions. DNase treatment of RNA was performed using TURBO DNA-free™ Kit (Invitrogen). Samples were quantified and quality checked on an Agilent Bioanalyzer 2100
library prepared using Ovation® SoLo RNA-Seq System (Human) (NuGEN)

value: PBMC

tag: stimulation

tag: cytokine

value: IFNg+


title: Cont 2wk Female 66

description: Cont


title: PAE 2wk Male 28

description: PAE

value: Excluded Panel 1


title: IL-IFN_rep1


title: dge1_B02 RNA-seq of ReNcell VM treated with 10 uM tofacitinib

description:
RNA-seq of ReNcell VM treated with 10 uM tofacitinib
barcode: AAACTA batch: dge1

value: 10 uM tofacitinib

value: tofacitinib


title: dge1_B06 RNA-seq of ReNcell VM treated with 0.3 uM metformin

description:
RNA-seq of ReNcell VM treated with 0.3 uM metformin
barcode: AACTAA batch: dge1

value: 0.3 uM metformin

value: metformin


title: dge1_B01 RNA-seq of ReNcell VM treated with 1 uM gsk1059615

description:
RNA-seq of ReNcell VM treated with 1 uM gsk1059615
barcode: AAACAT batch: dge1

value: ReNcell VM


title: PlacentaGvirusB2

value: G15 treatment

value: IAV Infected


title: PlacentaGvirusB1


title: dge1_A24 RNA-seq of ReNcell VM treated with 1 uM rotenone

description:
RNA-seq of ReNcell VM treated with 1 uM rotenone
barcode: ATACTT batch: dge1

value: in-vitro differentiated neural and glial cells

value: 1 uM rotenone

value: rotenone


title: IL-DN_rep2

value: negative


title: PAE 6.5mo Female 43

description: PAE

value: Female

value: Included


title: Cont 6.5mo Male 41

description: Cont

value: Male


title: IL-DN_rep1

value: PBMC


title: PAE 6.5mo Male 22

description: PAE


title: PlacentaGvirusA2


title: 5OP-TNF_rep3

value: 5-OP-RU 1 nM

value: TNF+


title: PlacentaMnoVirusC2

value: Vehicle treatment

value: Uninfected


title: PlacentaGvirusA1


title: PlacentaGnovirusB2


title: dge1_A22 RNA-seq of ReNcell VM treated with dsRNA + lipofectamine

description:
RNA-seq of ReNcell VM treated with dsRNA + lipofectamine
barcode: ATAACA batch: dge1

value: dsRNA + lipofectamine

tag: stimulant


title: PAE 6.5mo Female 55

description: PAE


title: dge1_A21 RNA-seq of ReNcell VM treated with 10 uM pha-665752

description:
RNA-seq of ReNcell VM treated with 10 uM pha-665752
barcode: ATAAAC batch: dge1


title: Cont 6.5mo Male 54

description: Cont


title: PlacentaGnovirusB1


title: 5OP-DN_rep3


title: PlacentaGnovirusA2


title: dge1_A20 RNA-seq of ReNcell VM treated with 0.3 uM r 59-022

description:
RNA-seq of ReNcell VM treated with 0.3 uM r 59-022
barcode: AGTAAT batch: dge1


title: 5OP-TNF_rep1


title: dge1_A18 RNA-seq of ReNcell VM treated with 3 uM kw2449

description:
RNA-seq of ReNcell VM treated with 3 uM kw2449
barcode: ACTTTA batch: dge1


title: Cont 6.5mo Male 58

description: Cont


title: LungsMVirusC

source_name: mouse lungs


title: Cont 6.5mo Male 57

description: Cont


title: 5OP-DN_rep2


title: PAE 6.5mo Male 24

description: PAE


title: dge1_A23 RNA-seq of ReNcell VM treated with dsRNA + lipofectamine

description:
RNA-seq of ReNcell VM treated with dsRNA + lipofectamine
barcode: ATACAA batch: dge1

source_name: in-vitro differentiated neural and glial cells


title: dge1_A19 RNA-seq of ReNcell VM treated with 10 uM a443654

description:
RNA-seq of ReNcell VM treated with 10 uM a443654
barcode: AGATTA batch: dge1


title: Cont 6.5mo Female 53

description: Cont


title: NS_rep4


title: dge1_A17 RNA-seq of ReNcell VM treated with 10 uM zm-447439

description:
RNA-seq of ReNcell VM treated with 10 uM zm-447439
barcode: ACTTAT batch: dge1


title: PlacentaMnoVirusC1


title: PAE 6.5mo Female 50

description: PAE


title: 5OP-TNF_rep2


title: dge1_A16 RNA-seq of ReNcell VM treated with 10 uM ldn-193189

description:
RNA-seq of ReNcell VM treated with 10 uM ldn-193189
barcode: ACATAA batch: dge1


title: NS_rep3


title: LungsMVirusA


title: PlacentaGnovirusA1


title: LungsMVirusB


title: Cont 6.5mo Male 46

description: Cont


title: NS_rep2


title: dge1_A15 RNA-seq of ReNcell VM treated with 1 uM (+)-jq1

description:
RNA-seq of ReNcell VM treated with 1 uM (+)-jq1
barcode: ACAATA batch: dge1


title: PAE 6.5mo Female 56

description: PAE


title: LungsMnoVirusC


title: NS_rep1


title: Cont 6.5mo Male 52

description: Cont


title: 5OP-DN_rep1


title: dge1_A13 RNA-seq of ReNcell VM treated with 10 uM kw2449

description:
RNA-seq of ReNcell VM treated with 10 uM kw2449
barcode: AATTCT batch: dge1


title: dge1_A14 RNA-seq of ReNcell VM treated with 0.3 uM sb202190

description:
RNA-seq of ReNcell VM treated with 0.3 uM sb202190
barcode: AATTGA batch: dge1


title: PAE 6.5mo Female 47

description: PAE


title: dge1_A12 RNA-seq of ReNcell VM treated with 1 uM fedratinib

description:
RNA-seq of ReNcell VM treated with 1 uM fedratinib
barcode: AATGAT batch: dge1

value: 1 uM fedratinib

value: fedratinib


title: LungsMnoVirusA


title: Cont 2wk Female 62

description: Cont


title: dge1_A11 RNA-seq of ReNcell VM treated with 10 uM tofacitinib

description:
RNA-seq of ReNcell VM treated with 10 uM tofacitinib
barcode: AATCTT batch: dge1

value: 10 uM tofacitinib

value: ReNcell VM

value: tofacitinib


title: LungsGVirusC

value: G15 treatment

value: IAV Infected


title: Mdmx-Tg/Pu.1-URE-/- 2

city: Bronx

first: Ulrich

last: Steidl

address: 1300 Morris Park Ave.

institute: Albert Einstein College of Medicine

data_processing:
Cleaned and trimmed reads were analyzed by FastQC for base sequence quality, GC content, N content, and sequence duplication levels.
Sequencing reads passing quality control criteria were aligned to the Mus musculus (mm10/GRCm38) transcriptome and quantified using Salmon.
Raw counts were normalized and analyzed for differential expression in R using the Bioconductor package DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.quant.sf: Salmon quantification files include TPMs.

source_name: Bone marrow

extract_protocol:
Flk2- Lin-Sca-1+Kit+ cells were FACS-sorted from murine bone marrow aspirates and subject to total RNA extraction using RNeasy micro kit.
Total RNA was subjected to mRNA enrichment, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification for library construction, with incorporation of the DNA nanoball technology (DNB-Seq). RNA-seq was performed by BGI Americas using the BGISEQ-500 platform, paired-end 100-bp read length.

tag: genotype/variation

value: Flk2- Lin-Sca-1+Kit+ hematopoietic stem cells


title: Mdmx-Tg/Pu.1-URE-/- 1


title: PAE 2wk Female 56

description: PAE

value: Female


title: LungsGVirusB


title: Pu.1-URE-/- 3


title: LungsGVirusA


title: LungsGnoVirusC


title: Pu.1-URE-/- 2


title: dge1_A09 RNA-seq of ReNcell VM treated with 0.3 uM torin1

description:
RNA-seq of ReNcell VM treated with 0.3 uM torin1
barcode: AATACA batch: dge1

value: in-vitro differentiated neural and glial cells

value: 0.3 uM torin1


title: LungsGnoVirusB


title: LungsMnoVirusB


title: dge1_A08 RNA-seq of ReNcell VM treated with 10 uM mg-132

description:
RNA-seq of ReNcell VM treated with 10 uM mg-132
barcode: AAGTAT batch: dge1


title: PAE 6.5mo Female 45

description: PAE

value: Included


title: dge1_A07 RNA-seq of ReNcell VM treated with 1 uM brivanib

description:
RNA-seq of ReNcell VM treated with 1 uM brivanib
barcode: AAGATT batch: dge1

value: 1 uM brivanib

value: brivanib


title: Mdmx-Tg/Pu.1-URE-/- 3


title: LungsGnoVirusA


title: Mdmx-Tg 3

value: Mdmx-Tg


title: PAE 6.5mo Male 48

description: PAE

value: Male


title: dge1_A06 RNA-seq of ReNcell VM treated with 0.3 uM (+)-jq1

description:
RNA-seq of ReNcell VM treated with 0.3 uM (+)-jq1
barcode: AACAAT batch: dge1


title: Mdmx-Tg 2


title: PAE 2wk Female 61

description: PAE


title: dge1_A10 RNA-seq of ReNcell VM treated with 1 uM bx-912

description:
RNA-seq of ReNcell VM treated with 1 uM bx-912
barcode: AATAGT batch: dge1


title: ATAC_seq_Meristems_rep5

city: Cold Spring Harbor

first: Zachary

last: Lippman

state: New York

address: 1 Bungtown Rd

department: Plant Biology

institute: Cold Spring Harbor Laboratory

data_processing:
ATAC-seq reads were trimmed with trimmomatic and aligned to Heinz SL4.0 reference genome with BWA mem. Reads that mapped to either chloroplast or mitochondria were filtered out together with PCR duplicate reads (picard MarkDuplicates) and multiple position aligned reads. Finally, only high quality properly paired reads were retained for the analysis (samtools view -b -h -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 30).
For Jbrowse visualization of the ATAC-seq, all six BAM files were merged anf coverage was calculated with genomeCoverageBed followed by bedGraphToBigWig command.
ATAC-seq peak calling was done by Genrich V0.6 (https://github.com/jsh58/Genrich) using all six libraries with the following parameters: -j -r -v -q 0.5 -g 30.
Genome_build: Tomato SL4.0 ITAG4.0
Supplementary_files_format_and_content: ATAC_seq_Meristem_Genrich_Rep_q_0.5_g30_Final.narrowPeak_sorted.bed - This file contain the ATAC-seq peaks called by Genrichusing all six libraries to calculate q-value. ATAC_seq_meristem_HQ_merged_final.bw - ATAC-seq reads genome coverage (merged).

organism: Solanum lycopersicum

source_name: anantha inflorescences

growth_protocol: Tomato anantha-e1546 (Solyc02g081670) in M82 background seeds were directly sown into soil in 96-cell plastic flats and grown in a greenhouse under long-day conditions (16-hr light/8-hr dark) supplemented with artificial light from high-pressure sodium bulbs (∼250 μmol m−2 s−1). The temperature ranged between 26-28°C during the day to 18-20°C during the night, with a relative humidity of 40-60%. One-month old seedlings were transplanted to a 4L pot and grown in the greenhouse at the same conditions.

extract_protocol:
Six biological replicates of 1g of freshly collected anantha inflorescences (meristematic enriched tissue) were ground in ice-cold isolation buffer (300 mM sucrose, 20 mM Tris pH 8.0, 5 mM MgCl2, 5 mM KCl, 5 mM beta-mercaptoethanol, 35% glycerol, 0.2% Triton X-100). After grinding, the suspension was filtered through a series of cell strainers (the smallest being 70 mm). Samples were further disrupted using a Dounce homogenizer, and then were washed four times with ice-cold isolation buffer. The enriched nuclei samples were resuspended in Resuspension Buffer (50 mM Tris pH 8.0, 5 mM MgCl2, 5 mM beta-mercaptoethanol, 20% glycerol).
For the transposase reaction 100,000 nuclei were resuspended  in 22.5 ml freezing buffer (5 mM MgCl2, 0.1 mM EDTA, 50 mM TRIS pH 8.0, 40% glycerol), and were mixed with  2X DMF Buffer (66 mM Tris-acetate (pH 7.8), 132 K-Acetate, 20 mM Mg-Acetate, 32% DMF) and 2.5ul Transposase enzyme from Illumina Nextera Kit (Catalog No. FC-121-1031), and incubated at 37°C for 30 min. Tagmented DNA was isolated using NEB Monarch PCR Purification kit (Catalog No. NEB #T1030).  Next-generation sequencing (NGS) libraries were amplified in two steps (Buenrostro et al., 2015) using KAPA HiFi HotStart ReadyMix PCR kit (Catalog No. KK2601). NGS libraries were PE50 sequenced on an Illumina MiSeq SY-410-1003 instrument.

tag: genotype

value: anantha-e1546 mutant in M82 background

value: inflorescences


title: dge1_A04 RNA-seq of ReNcell VM treated with 1 uM chitosan

description:
RNA-seq of ReNcell VM treated with 1 uM chitosan
barcode: AAATAC batch: dge1

value: 1 uM chitosan

value: chitosan


title: Cont 6.5mo Female 40

description: Cont


title: dge1_A05 RNA-seq of ReNcell VM treated with 1 uM bortezomib

description:
RNA-seq of ReNcell VM treated with 1 uM bortezomib
barcode: AAATTG batch: dge1

value: 1 uM bortezomib

value: ReNcell VM

value: bortezomib


title: ATAC_seq_Meristems_rep6


title: PAE 6.5mo Male 28

description: PAE


title: ATAC_seq_Meristems_rep4


title: Wild-type 3

value: Wild-type


title: Pu.1-URE-/- 1

value: Flk2- Lin-Sca-1+Kit+ hematopoietic stem cells


title: PAE 6.5mo Male 44

description: PAE


title: dge1_A03 RNA-seq of ReNcell VM treated with 0.3 uM pha-665752

description:
RNA-seq of ReNcell VM treated with 0.3 uM pha-665752
barcode: AAAGTT batch: dge1


title: PAE 6.5mo Male 26

description: PAE


title: PAE 2wk Female 50

description: PAE

value: Female


title: Wild-type 2


title: dge1_A02 RNA-seq of ReNcell VM treated with 10 uM hg-9-91-01

description:
RNA-seq of ReNcell VM treated with 10 uM hg-9-91-01
barcode: AAAATC batch: dge1

value: in-vitro differentiated neural and glial cells


title: PAE 2wk Female 30

description: PAE


title: PAE 6.5mo Female 30

description: PAE


title: ATAC_seq_Meristems_rep2


title: dge1_A01 RNA-seq of ReNcell VM treated with 0.3 uM bx-912

description:
RNA-seq of ReNcell VM treated with 0.3 uM bx-912
barcode: AAAACT batch: dge1


title: ATAC_seq_Meristems_rep1


title: AGM10_Medialstinal Lymph Node

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

description: 10X Genomics single-cell RNA Sequencing

data_processing:
reads demultiplexed and bcl to fastq conversion using cellranger mkfastq v3.0.2
reads aligned and counted using cellranger count v3.0.2
Genome_build: GCF_000409795.2 & NC_045512.2
Supplementary_files_format_and_content: features.tsv, barcodes.tsv, and matrix.mtx (set of 3 files)

organism: Chlorocebus aethiops

source_name: Medialstinal Lymph Node

growth_protocol: Samples were extracted and process directly from African Green Monkeys during necropsy

extract_protocol:
Tissues were manually disaccociated, digested with liberase, filtered, and treated with ACK lysis before being processed on the 10X genomics NextGEM instrument
Libraries were prepped according to the 10X genomics V3.0 library prep kits

treatment_protocol: 8 animals received  active SARS-CoV-2 and 2 received irradiated SARS-CoV-2

tag: virus

tag: virus subtype

value: Active

value: Medialstinal Lymph Node


title: Islet 3 snATAC (CB)

city: La Jolla

first: Kyle

last: Gaulton

state: CA

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California, San Diego

data_processing:
Note: Barcodes for combinatorial barcoding snATAC-seq experiments are integrated into the original read names.
Alignment: Trimmed Nextera adapter sequences using trim_galore v.0.4.4 and aligned reads to hg19 using bwa mem v.0.7.17-r1188.
Filtering: Low mapping quality (MAPQ<30), mitochondrial reads, duplicate reads on a per-barcode basis with MarkDuplicates from picard.
Clustering: Custom code for processing snATAC-seq datasets is available at https://github.com/kjgaulton/pipelines/tree/master/islet_snATAC_pipeline
Peak calling: MACS2 (v.2.1.2) with --nomodel --keep-dup all on aggregate chromatin accessibility profiles for each cluster.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: islet_snATAC.merged_sites.bed: Merged peaks.
Supplementary_files_format_and_content: islet_snATAC.cluster_labels.txt: Single cell cluster labels.

source_name: pancreatic islets

extract_protocol:
Nuclei were isolated from fresh pancreatic islets using a glass dounce homogenizer with a tight-fitting pestle or frozen whole pancreas using a mortar and pestle.
(CB; combinatorial barcoding) Permeabilized nuclei were distributed to 96 wells and tagmentation was carried out to introduce a first barcode combination. After pooling, 20 nuclei were sorted into each well of a 96 well plate and a second barcode was introduced by PCR. Libraries were purified according to the MinElute PCR Purification Kit manual using a vacuum manifold and size selection was performed with SPRI Beads.
(10X; 10X Genomics) Libraries were generated using the 10X Genomics Chromium Chip E Single Cell ATAC kit following the manufacturer's instructions.

value: pancreatic islets

tag: Sex

value: male

tag: bmi

tag: donor id


title: HCT-116 shSHP2CPT11-2

city: Nanjing

first: Bin

last: Wei

state: Jiangsu

address: 101 Longmian Avenue

country: China

institute: Nanjing medical university

data_processing:
Hisat2 v2.0.5 was used as the mapping  tool for the reference genome.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.16.1).
Genome_build: Hg19

source_name: colon cancer cell

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: WT, SHP2-silenced, and lovastatin-pretreated HCT-116 cells that all underwent CPT-11 treatment.

tag: cell type

value: colon cancer

value: lovastatin-pretreated for 4h,and CPT-11 for 24h


title: Cont 6.5mo Male 33

description: Cont

tag: gender

value: Male

tag: age

tag: participant number

tag: analysis inclusion

value: Included


title: AGM9_Medialstinal Lymph Node

description: 10X Genomics single-cell RNA Sequencing

tag: tissue


title: AGM8_Medialstinal Lymph Node

description: 10X Genomics single-cell RNA Sequencing


title: Cont 6.5mo Male 32

description: Cont


title: Islet 2 snATAC (CB)


title: Mdmx-Tg 1

value: Mdmx-Tg


title: HCT-116 shSHP2CPT11-3

tag: cell line

tag: treatment


title: AGM7_Medialstinal Lymph Node

description: 10X Genomics single-cell RNA Sequencing


title: HCT-116 LovaCPT11-3

value: wild type


title: RS0042

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
Reference Genome was indexed from RSem (Li B et al. 2011) and sequence reads were aligned using RSem.
RNA-Seq data for the sense strand were normalized using Transcripts Per Million (TPM) Trimmed Mean of M values (Robinson MD and A Oshlack 2010).
Genome_build: Human sequenced genome GRCh38 v91
Supplementary_files_format_and_content: Tab-delimited text files include raw, TPM and RPKM (Reads Per Kilobase Million) values for each sample.

source_name: Blood

extract_protocol:
A blood sample was collected in PAXgene Blood RNA tubes (PreAnalytiX, Hombrechtikon, Switzerland) before the administration of the anti-TNF agent (week 0) and after 2 weeks of treatment (week 2). Total whole blood RNA was extracted using PAXgene Blood RNA kits (PreAnalitiX) according to the manufacturer’s instructions. RNA concentrations were measured using the Quawell Q5000 Spectrophotometer (Quawell Technology Inc, San Jose, CA, USA). RNA integrity was verified using the Agilent RNA 6000 Nano Kit in a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Extracted RNA was stored at −80 °C until further processing. All RNA samples fulfilled the following criteria: RNA integrity ˃7.
200 ng of total RNA were used with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) to construct index-tagged cDNA libraries. Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis single reads of 60 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 or the HiSeq 4000 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

value: Blood

tag: primary response

value: Non-responder

tag: weeks fron start of treatment

tag: anti-tnf

value: Adalimumab

tag: disease state

value: pediatric inflammatory bowel disease


title: HCT-116 shSHP2CPT11-1

tag: genotype


title: AGM6_Medialstinal Lymph Node

description: 10X Genomics single-cell RNA Sequencing

tag: virus

tag: virus subtype


title: ATAC_seq_Meristems_rep3

value: anantha-e1546 mutant in M82 background

value: inflorescences


title: Cont 6.5mo Female 34

description: Cont

value: Female


title: AGM5_Medialstinal Lymph Node

description: 10X Genomics single-cell RNA Sequencing

value: Active


title: HCT-116 LovaCPT11-2


title: Cont 2wk Female 34

description: Cont


title: PAE 6.5mo Male 21

description: PAE


title: Wild-type 1

tag: genotype/variation

value: Wild-type

value: Flk2- Lin-Sca-1+Kit+ hematopoietic stem cells


title: D0052


title: AGM4_Medialstinal Lymph Node

description: 10X Genomics single-cell RNA Sequencing

value: Medialstinal Lymph Node


title: AGM3_Medialstinal Lymph Node

description: 10X Genomics single-cell RNA Sequencing


title: HCT-116 CPT11-2

value: colon cancer

value: CPT-11 for 24h


title: Islet 1 snATAC (CB)

value: pancreatic islets

tag: Sex

value: male

tag: bmi

tag: donor id


title: RM0162

value: Infliximab


title: HCT-116 CPT11-1

tag: cell type

value: wild type


title: AGM2_Medialstinal Lymph Node

description: 10X Genomics single-cell RNA Sequencing

value: Irradiated


title: PAE 6.5mo Male 19

description: PAE

tag: gender

value: Male

tag: age

tag: participant number

value: Included


title: AGM1_Medialstinal Lymph Node

description: 10X Genomics single-cell RNA Sequencing

tag: tissue


title: HCT-116 C-3

tag: cell line

tag: treatment

value: untreated


title: HCT-116 LovaCPT11-1

value: lovastatin-pretreated for 4h,and CPT-11 for 24h


title: VR0132

value: Blood

tag: primary response

value: Non-responder

tag: weeks fron start of treatment

value: pediatric inflammatory bowel disease


title: HCT-116 C-2


title: HCT-116 C-1


title: Cont 6.5mo Male 38

description: Cont

tag: analysis inclusion


title: Cont 2wk Male 38

description: Cont


title: AGM9_Lung

description: 10X Genomics single-cell RNA Sequencing

source_name: Lung

value: Active

value: Lung


title: AGM8_Lung

description: 10X Genomics single-cell RNA Sequencing


title: PM0052

tag: anti-tnf

tag: disease state


title: PAE 6.5mo Female 23

description: PAE

value: Female


title: AGM10_Lung

description: 10X Genomics single-cell RNA Sequencing

tag: virus

tag: virus subtype


title: Cont 6.5mo Female 18

description: Cont


title: AGM7_Lung

description: 10X Genomics single-cell RNA Sequencing


title: PAE 2wk Female 23

description: PAE


title: single-cell RNAseq of SW480 tumors at 4dpi (library 10)

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used for identification of the Illumina library barcode, cell barcode and Unique Molecular Identifiers (UMI) (van den Brink et al. 2017, PMID: 28960196).
R2 was assigned 60 base pairs and used to map to the Human reference transcriptome with BWA
Data was demultiplexed as described in Grün et al. 2014 (PMID: 24747814)
Mapping and generation of count tables was automated using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo)
Single-cell transcriptomics analysis was done using the RaceID3 algorithm, following an adapted version of the RaceID manual (https://cran.r-project.org/web/packages/RaceID/vignettes/RaceID.html).
Genome_build: hg38
Supplementary_files_format_and_content: BarcodeCounts.tsv

source_name: SW480 tumors from zebrafish xenografts

growth_protocol: SW480 were grown in Dulbecco’s Modified Eagle Medium (DMEM) High Glucose (Biowest), supplemented with 10% Fetal Bovine Serum (FBS) (Sigma-Aldrich) and antibiotics (100U ml-1 penicillin and 100ug ml-1 streptomycin, Hyclone) in a humidified 5% CO2 atmosphere at 37ºC. Cells were splitted twice a week not exceeding 70% of confluence. SW480 were transfected with GFP lentiviral vectors and sorted with 99% of purity. Cells were tested for mycoplasma contamination prior experiments.

extract_protocol:
Single-cell mRNA sequencing was performed at Single Cell Discoveries (single-cell sequencing provider, the Netherlands) according to an adapted version of the SORT-seq protocol (Muraro et al. 2016 with primers described in van den Brink et al. 2017). In short, single cells were FACS sorted into 384-well plates containing 384 primers and Mineral oil (Sigma). After sorting, plates were snap-frozen on dry ice and stored at -80° C. For amplification cells were heat-lysed at 65° C followed by cDNA synthesis using the CEL-Seq2 protocol (Hashimshony et al. 2016) and robotic liquid handling platforms. After second strand cDNA synthesis, the barcoded material was pooled into libraries of 384 cells and amplified using IVT.
Following amplification, the rest of the CEL-seq2 protocol was followed for preparation of the amplified cDNA library, using TruSeq small RNA primers (Illumina).
The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles)

tag: time

value: SW480 tumors from zebrafish xenografts


title: single-cell RNAseq of SW480 tumors at 4dpi (library 11)


title: PAE 6.5mo Male 20

description: PAE

source_name: Plasma


title: PAZ0162


title: AGM6_Lung

description: 10X Genomics single-cell RNA Sequencing


title: PAE 2wk Male 21

description: PAE


title: Cont 6.5mo Male 17

description: Cont


title: single-cell RNAseq of SW480 tumors at 1dpi (library 8)


title: AGM5_Lung

description: 10X Genomics single-cell RNA Sequencing


title: PAE 6.5mo Male 31

description: PAE


title: single-cell RNAseq of SW480 tumors at 1dpi (library 7)


title: AGM4_Lung

description: 10X Genomics single-cell RNA Sequencing


title: PAE 6.5mo Female 37

description: PAE


title: VR0162

value: Responder


title: bulk RNA-seq of SW620 tumors (replicate O_SW620_7)

data_processing:
Data quality was assessed with the FastQC quality-control tool ad low quality reads were filtered out with Trimmomatic..
RNA-seq reads were mapped to the human reference transcriptome with Salmon software (v 0.13.1) and reads counts were estimated for human Ensembl annotation (Hg38).
The output of the Salmon was compressed and is provided as processed data.
Genome_build: hg38
Supplementary_files_format_and_content: Salmon output tar archive

source_name: SW620 tumors from zebrafish xenografts

growth_protocol: SW480 and SW620 were grown in Dulbecco’s Modified Eagle Medium (DMEM) High Glucose (Biowest), supplemented with 10% Fetal Bovine Serum (FBS) (Sigma-Aldrich) and antibiotics (100U ml-1 penicillin and 100ug ml-1 streptomycin, Hyclone) in a humidified 5% CO2 atmosphere at 37ºC. Cells were splitted twice a week not exceeding 70% of confluence and were used for experiments between passage number 2 and 11. SW480 and SW620 were authenticated through short tandem repeat (STR) profile analysis and tested routinely for mycoplasma contamination.

extract_protocol:
Total RNA was extracted from the dissected tumors using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) and further purified with RNeasy Plus Micro Kit (Qiagen) in accordance with the manufacturer’s instructions.
mRNA-libraries were prepared using the Smart-seq2 protocol (Illumina, USA).
Samples were sequenced by Next-Seq 500 Illumina sequencer and unstranded single-end mRNA-seq libraries of 76bp  were obtained. An average of approximately 38 millions of reads per sample.

value: SW620 tumors from zebrafish xenografts


title: AGM2_Lung

description: 10X Genomics single-cell RNA Sequencing


title: RM0102

value: Adalimumab


title: single-cell RNAseq of SW480 tumors at 1dpi (library 6)


title: PAE 6.5mo Female 29

description: PAE


title: bulk RNA-seq of SW620 tumors (replicate I_SW620_5)


title: Cont 6.5mo Female 13

description: Cont


title: PAE 2wk Male 31

description: PAE


title: bulk RNA-seq of SW620 tumors (replicate L_SW620_1)


title: HCT-116 CPT11-3

value: colon cancer

tag: genotype

value: CPT-11 for 24h


title: bulk RNA-seq of SW620 tumors (replicate C_SW620_2)


title: AGM1_Lung

description: 10X Genomics single-cell RNA Sequencing

value: Irradiated


title: Cont 6.5mo Male 14

description: Cont

value: Male


title: PAE 2wk Female 37

description: PAE

value: Included


title: JC0122

value: Infliximab


title: W_M_001

city: Kansas City

first: Venkatesh

last: Sampath

state: MO

address: 2401 Gillham Road

department: Neonatology

institute: Children's Mercy Hospital

data_processing:
The raw base calling (.bcl) files were converted to demultiplexed compressed FASTQ files using CASAVA
Novogene's STAR was used to  map RNA-seq reads against the mouse reference genome
Transcript assembly and abundance estimation and comparing expression were conducted and  reported in Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text file of a matrix table generated and reported in Fragments Per Kilobase of exon per Million fragments mapped (FPKM).

source_name: lung

growth_protocol: Post natal day 6 (P6)

extract_protocol:
Total RNA isolation from lung
NEB Library
Whole transcriptome paired end sequencing ( 2 X 150 cycles)

treatment_protocol: heterozygous compared with wildtype

tag: strain

value: M

value: whole Lung


title: W_M_003


title: W_M_006


title: Cont 6.5mo Male 15

description: Cont


title: bulk RNA-seq of SW480 tumors (replicate B_SW480_B)


title: bulk RNA-seq of SW480 tumors (replicate N_SW480_7)


title: Cont 2wk Male 14

description: Cont


title: W_F_004

value: F


title: bulk RNA-seq of SW480 tumors (replicate P_SW480_A)


title: GM0032

value: Blood

value: pediatric inflammatory bowel disease


title: AGM3_Lung

description: 10X Genomics single-cell RNA Sequencing

value: Active

value: Lung


title: PAE 2wk Female 29

description: PAE

value: Female


title: ES-derived beta cells, high glucose (Hi-C)

data_processing:
Analysis: We analyzed Hi-C data using the Juicer tool set with default settings and visualized results with HiGlass. All Hi-C interaction frequencies shown in the paper were normalized using iterative matrix balancing as implemented in cooler.
Genome_build: hg19
Supplementary_files_format_and_content: Juicer contact matrices

source_name: ES-derived beta cells

growth_protocol: hESC lines were differentiated in a suspension-based format using rotational culture with some modifications to a published protocol. Undifferentiated hESCs were aggregated by preparing a single cell suspension in mTeSR media and overnight culture in six-well ultra-low attachment plates with 5.5ml per well on an orbital rotator at 100 rpm. The following day, undifferentiated aggregates were washed in DMEM/F12 and differentiated using a multistep protocol with daily media changes and continued orbital rotation at either 100 rpm or at 108 rpm from days 8 to 28. In addition to 1% GlutaMAX and 15 mM (days 0-10) or 20 mM (days 11-28) glucose, MCDB 131 media was supplemented with 0.5% (days 0-5) or 2% (days 6-14) fatty acid-free BSA, 1.5 g/L (days 0-5 and days 11-28) or 2.5 g/L (days 6-10) NaHCO3, and 0.25 mM (days 3-10) ascorbic acid.

extract_protocol:
Hi-C as previously described using MboI on two batches of hESC-derived beta cells.
Each sample was sequenced three times (twice on an Illumina NextSeq 500 and once on an Illumina NovaSeq 6000). The sequencing runs are technical replicates and were combined prior to analysis.

treatment_protocol: Cells were cultured in either high glucose (20mM mg/mL; rep 1) or low glucose (5mM mg/mL; rep 2), respectively, to capture a range of potential physiological conditions

tag: cell type

value: ES-derived beta cells

tag: Sex

value: male

value: 20mM mg/mL glucose


title: W_F_002

tag: gender


title: RM0172

value: Responder


title: H_M_004

description: H_M_004_Dll4 +/-


title: ES-derived beta cells, low glucose (Hi-C)

value: 5mM mg/mL glucose


title: VV0012


title: H_M_001

description: H_M_001_Dll4 +/-


title: H_F_003

description: H_F_003_Dll4 +/-


title: H_F_002

description: H_F_002_Dll4 +/-


title: ZM∆M_CR_HA

data_processing:
Library strategy: CUT&RUN
Raw sequencing reads were first trimmed by Trim Galore to remove low-quality and adapter bases, then aligned to hg19 using STAR.
After mapping reads to the genome, only primary alignments were extracted followed by removal of duplicate reads using the Picard MarkDuplicates tool.
The bigwig coverage file was generated from BAM alignment file using the deeptools bamCoverage function and the number of reads per bin was normalized to 1x depth (reads per genome coverage, RPGC).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: HEK293T cell line

growth_protocol: HEK293T cells were cultured in the DMEM base medium supplemented with 10% FBS and 1% antibiotics.

extract_protocol:
Cells were immobilized to ConA beads and then subject to permeabilization, antibody binding, pAG-Mnase binding and activation, targeted chromatin digestion and release, and DNA recovery by NEB Monarch DNA Cleanup Kit according to the EpiCypher CUT&RUN Protocol.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) following the manufacture’s protocol.

treatment_protocol: HEK293T cells were retrovirally transduced with 3HA-3Flag-tagged ZM, ZM∆M or ZM∆Z for their stable expression.

tag: transduced with

value: 3HA-3Flag-tagged ZM deltaM

tag: chip antibody

value: anti-HA (Abcam, ab9110)


title: ZM∆Z_CR_HA

value: 3HA-3Flag-tagged ZM deltaZ

tag: cell line


title: ZM∆Z_CR_Flag

value: anti-Flag (Sigma, F1804)


title: ZM∆M_CR_Flag


title: Cont 6.5mo Male 12

description: Cont

value: Male

tag: age

tag: participant number

value: Included


title: Cont 6.5mo Female 39

description: Cont


title: 17942X16 knockout HC800-A8-1 AG#2 rep2

city: Salt Lake City

first: Soledad

last: Camolotto

address: 201 Presidents' Cir

institute: University of Utah

description: Single cell clon#12 from murine PDAC HC800-A8-1 cell line transduced with lentivirus coexpressing Cas9 and sgRNA-A (targeting mouse Six1) and sgRNA-G (targeting mouse Six4)

data_processing:
The human GRCh38 FASTA and GTF files were downloaded from Ensembl release 92.
The reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.26.0.
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).

growth_protocol: Cell were grown in DMEM + 10% FBS.

extract_protocol:
TRIzol extraction followed by PureLink RNA Mini Kit purification
TruSeq Stranded mRNA Library Prep (Illumina)

tag: tissue

value: pancreas

value: mixed 129/B6

tag: hnf4a status

value: Negative

tag: six1 and six4 status

value: Both negative


title: 17942X15 knockout HC800-A8-1 AG#15 rep2

description: Single cell clon#3 from murine PDAC HC800-A8-1 cell line transduced with lentivirus coexpressing Cas9 and sgRNA-A (targeting mouse Six1) and sgRNA-H (targeting mouse Six4)


title: ZM_CR_HA

value: 3HA-3Flag-tagged ZM


title: PAE 2wk Male 35

description: PAE

data_processing: miRNAs expressed in >80% of samples (either PAE or cont) were normalized to average miRNA expression for each sample, with undetermined values replaced with 1+highest CT for each miRNA

extract_protocol: Qiagen miRNeasy Mini Kit with 1.2ug MS2 carrier RNA per sample

tag: analysis inclusion


title: Cont 6.5mo Male 11

description: Cont


title: ZM_CR_Flag


title: 17942X14 knockout HC800-A8-1 AH#24 rep2

description: Single cell clon#15 from murine PDAC HC800-A8-1 cell line transduced with lentivirus coexpressing Cas9 and sgRNA-A (targeting mouse Six1) and sgRNA-G (targeting mouse Six4)


title: W_F_005

value: F

value: whole Lung


title: Pancreas 1 snATAC (10X)

source_name: whole pancreas

value: whole pancreas

value: male

tag: bmi

tag: donor id


title: Cont 2wk Male 15

description: Cont


title: Pancreas 1 snATAC (CB)


title: 17942X12 control HC800-A8-1-NT rep3

description: 2D cultures of murine PDAC HC800-A8-1 cell line transduced with lentivirus coexpressing Cas9 and control sgRNA

value: Both positive


title: 17653X8 knockout HC800-A8-1 AG#2

description: Single cell clon#2 from murine PDAC HC800-A8-1 cell line transduced with lentivirus coexpressing Cas9 and sgRNA-A (targeting mouse Six1) and sgRNA-G (targeting mouse Six4)


title: 17653X7 knockout HC800-A8-1 AH#24

description: Single cell clon#24 from murine PDAC HC800-A8-1 cell line transduced with lentivirus coexpressing Cas9 and sgRNA-A (targeting mouse Six1) and sgRNA-H (targeting mouse Six4)


title: PAE 6.5mo Male 35

description: PAE


title: Cont 2wk Female 13

description: Cont

value: Female


title: PAE 6.5mo Female 8

description: PAE


title: H1-transfected-with-pLP-with-gRNA-sites-BS02732A

city: New York

first: Mathew

last: Maurano

address: 435 E 30th St

institute: NYU Langone Health

description: Captured genomic DNA

data_processing:
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics or NovaSeq 6000 operated by the NYU Langone Health Genome Technology Center. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences. All WGS and Capture-Seq data were processed using a uniform mapping and peak calling pipeline. Illumina sequencing adapters were trimmed with Trimmomatic v0.39{Bolger, 2014 #3524}. Sequencing reads were aligned using BWA v0.7.17{Li, 2009 #3526} to a genome reference (GRCh38/hg38 or GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24{Faust, 2014 #3527}. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35{Neph, 2012 #3540}. Data were visualized using the UCSC Genome Browser. The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: coverage depth track (bigwig)

extract_protocol:
Cells were dissociated using TryPE-Select, spun-down and media aspirate. Pellets were either processed immediately or stored at -80 deg. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN 69506).
Double-stranded DNA libraries were prepared from sheared genomic DNA. DNA fragments were end-repaired, A-tailed, and Illumina-compatible adapters were ligated to DNA ends.
Other - DNA Capture-seq

tag: treatment


title: H1-transfected-with-pLP-w/o-gRNA-sites-BS02731A

description: Captured genomic DNA

tag: genotype


title: H1-Parental-BS01564

description: genomic DNA

tag: strain


title: Cont 2wk Male 11

description: Cont


title: 17653X5 knockout HC800-A8-1 AH#3


title: PAE 2wk Female 7

description: PAE


title: Cont 2wk Male 12

description: Cont


title: Cont 2wk Female 39

description: Cont


title: PAE 2wk Female 8

description: PAE


title: 17653X6 knockout HC800-A8-1 AG#12


title: H1-PL1-C6-BS06875A

description: Captured genomic DNA


title: PAE 6.5mo Female 7

description: PAE


title: 17653X2 control HC800-A8-1-NT rep2


title: H1-PL1-C5-BS06874A

description: Captured genomic DNA


title: Lamina propria cells mock infected 2

city: Boston

first: Matthew

middle: K

last: Waldor

address: 181 Longwood Avenue

department: Microbiology

institute: Harvard Medical School

data_processing:
Reads were trimmed using TrimGalore! (Galaxy tool version 0.4.3.1) using automatic adapter sequence detection
Reads were mapped to rabbit genome OryCun2.0 GCA_000003625.1 using RNA STAR (Galaxy tool version 2.6.0b-1)
Read count matrix was created from mapped reads using featureCounts (Galaxy tool 1.6.4+galaxy1) using OryCun2.0 Ensembl Annotation from May 2019
Genome_build: OryCun2.0 GCA_000003625.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryctolagus cuniculus

source_name: Infant rabbit colonic lamina propria cells

extract_protocol:
Colonic epithelial and lamina propria cells were harvested and preserved using Trizol reagent. Total RNA was extracted using the Direct-Zol RNA MiniPrep Plus (Zymo)
mRNA libraries were prepared using KAPA mRNA HyperPrep kit (Roche)

tag: agent

value: PBS

tag: cell type

value: Lamina propria cells


title: Lamina propria cells mock infected 3


title: 17653X1 control HC800-A8-1-NT rep1


title: PAE 6.5mo Female 36

description: PAE

tag: gender


title: 17653X4 knockout HC800-A8-1 AG#15


title: H1-PL1-C2-BS06873A

description: Captured genomic DNA


title: Lamina propria cells ∆∆stx infected 3

description:
∆∆stx EHEC

raw_counts_matrix_lp.txt

value: deltadeltastx EHEC


title: H1-PL1-B6-BS06872A

description: Captured genomic DNA


title: Lamina propria cells mock infected 1


title: Lamina propria cells ∆∆stx infected 2

description:
∆∆stx EHEC

raw_counts_matrix_lp.txt


title: Cont 6.5mo Female 10

description: Cont


title: Cont 6.5mo Female 9

description: Cont


title: ETV2 ECs day10 replicate 2

city: Leuven

first: Jonathan

last: De Smedt

address: ON4 - Herestraat 49 PB804

department: Development and Regeneration

country: Belgium

institute: Stem Cell Institute Leuven

data_processing:
Cutadapt version 1.9.1 was used to trim adapter sequences, to trim low-quality bases (i.e. bases with Phred score<20), to remove ambiguous bases (--max-n=0.1), and to trim poly-A tails (A{10}).
STAR version 020201 was used to align reads to the human genome (GRCh38) with parameters (twopassMode=Basic, alignIntronMax=1000000, alignIntronMin=20).
The featureCounts function of the Rsubread R package was used to create the count matrix.
Genome_build: hg38.92
Supplementary_files_format_and_content: Raw counts are provided in count_matrix.txt, as generated by featureCounts (Rsubread). Columns contain samples, rows contain Ensembl identifiers. Counts are raw, i.e. not normalised in any manner. To compare with primary LSECs, LSEC expression data from E-GEOD-43984 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43984/) was processed with the same pipeline and same settings and raw counts are also given in count_matrix.txt. Reads from the same sample but from different lanes were summated.

source_name: Endothelial cells

growth_protocol: H9 embryonic stem cells are grown in E8 Flex medium (cat. A2858501, ThermoFisher Scientific) until a confluency of about 40% was reached. As of day 0 of differentiation, the medium was supplemented with 5µg/ml of docycycline. As of day 2 of differentiation, the medium was supplemented with 2% FBS. Medium composition is described in: Boon R, Kumar M, Tricot T, Elia I, Ordovas L, Jacobs F, et al. Amino acid levels determine metabolism and CYP450 function of hepatocytes and hepatoma cell lines. Nat Commun. 2020 Dec 1;11(1):1–16.

extract_protocol:
RNA was extracted with Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols. Sequence-libraries of each sample were sequenced on an Illumina NextSeq 500 instrument (high output, 75bp, single reads, v2.5)"
RNA libraries were prepared for sequencing using standard Illumina protocols

value: H9 embryonic stem cell-derived endothelial cells

tag: overexpressed transcription factor

tag: differentiation day


title: Cont 6.5mo Male 6

description: Cont

value: Male


title: ETV2 ECs day10 replicate 3


title: Lamina propria cells ∆∆stx infected 1

description:
∆∆stx EHEC

raw_counts_matrix_lp.txt


title: Lamina propria cells WT infected 2

value: WT EHEC


title: PAE 6.5mo Male 3

description: PAE

value: Excluded Hemolysis


title: Cont 2wk Female 10

description: Cont

value: Included


title: Lamina propria cells WT infected 1


title: Cavin-1PC3_Exo3

city: Herston

first: Harley

middle: Rose

last: Robinson

state: QLD

address: 300 Herston Road

institute: QIMRBerghofer

description:
miRNA
Cavin-1-PC3 extracellular vesicles

data_processing:
Base calls were generated using the Illumina NextSeq500 software, RTA (v2.1.3).
Trimming of adaptor sequences was completed using cutadapt (v1.9) for the following adaptors: >TruSeq1  AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  >TruSight1  GCGAATTTCGACGATCGTTGCATTAACTCGCGA  Trimmed reads shorter than 1 base were discarded if any.
Alignment to the whole known human miRNAome (miRbase v21) using STAR (v2.5.2a) and the following non-default parameters: --outFilterMismatchNoverLmax 0.05  --outFilterMatchNmin 16  --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0  --alignIntronMax 1
Using samtools (v1.3), we merged and coordinate sorted the alignments
Data was filtered using the following cut off: rowSums(row>20) >=2, where rowSums is the sum of all counts for miRNA across all replicates and test conditions.
miRNAs were normalised using empirical normalization method from the RUVseq package and DESeq2 (default parameters)
Genome_build: human mature sequences miRBase v21
Supplementary_files_format_and_content: tab-delimited text file contains raw counts for identified miRNAs, pre- and post- filter, and normalised counts.

source_name: Advanced prostate cancer

growth_protocol: Cells maintained in 37°C, 5% CO2, in 5%FBS/RPMI-1640. Stable cell lines were maintained in 0.1 mg/ml G418 (Gibco).

extract_protocol:
Extracellular vesicles were extracted using ultracentrifugation. Subsequent total RNA extraction from both EVs and cells completed using Trizol reagent. Small RNA were selected for sequencing using the NEBNext Small RNA library Prep Kit.
Small RNA were selected for sequencing using the NEBNext Small RNA library Prep Kit. Libraries were size selected using a Perkin Elmer Labchip XT

value: Epithelial cell line

tag: ectopic expression

value: GFP tagged cavin-1

tag: cell line


title: Cavin-1PC3_Exo2


title: Lamina propria cells WT infected 3


title: Epithelial cells mock infected 3

source_name: Infant rabbit colonic epithelial cells

value: Epithelial cells


title: Cavin-1PC3_Exo1


title: PAE 6.5mo Male 5

first: Amanda

last: Mahnke

address: 8447 Riverside Parkway

institute: Texas A&M University Health Science Center

description: PAE

tag: age

tag: participant number


title: GFPPC3_Exo3

description:
miRNA
GFP-PC3 extracellular vesicles

value: GFP


title: Epithelial cells mock infected 1


title: Cont 2wk Female 9

description: Cont


title: PAE 2wk Male 3

description: PAE


title: Cont 2wk Male 6

description: Cont


title: Epithelial cells ∆∆stx infected 3

description:
∆∆stx EHEC

raw_counts_matrix_epithelial.txt


title: Cavin-1PC3_Pellet3

description:
miRNA
Cavin-1-PC3 cell lysate


title: GFPPC3_Exo2

description:
miRNA
GFP-PC3 extracellular vesicles


title: PAE 2wk Male 5

description: PAE


title: Epithelial cells ∆∆stx infected 2


title: Epithelial cells mock infected 2


title: ETV2 ECs day10 replicate 1


title: PAE 2wk Female 36

description: PAE


title: Cont 6.5mo Female 4

description: Cont


title: Cavin-1PC3_Pellet2

description:
miRNA
Cavin-1-PC3 cell lysate


title: PAE 6.5mo Male 1

description: PAE


title: Epithelial cells ∆∆stx infected 1


title: Epithelial cells WT infected 3


title: Epithelial cells WT infected 2


title: Mouse5_blood_CD8Tcells_CITE

status: Public on Jan 13 2021

first: Osmaan

last: Shahid

address: 77 Avenue Louis Pasteur

department: Department of Immunology

description:
Sorted CD8+ CD44+ T cells from the peripheral blood of Mouse 5 for the same time point that the MC38 tumor was extracted. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE seq was also used to detect Feature Barcodes for CD39, NKG2D, and CX3CR1 proteins. These files contain the CITE seq data to detect protein expression using Feature Barcodes.
M5_Blood.rds

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and csv files of TCR clonality were performed using the Cell Ranger analysis pipeline (v3.0.2)
Data normalization, dimension reduction, and differential expression analysis were performed using R version 3.6.1 and the Seurat R package (version 3)
When applicable, samples were integrated using the SCTransform Method (Hafemeister and Satija, 2019, Genome Biol 20:196)
Genome_build: mm10
Supplementary_files_format_and_content: .rds files contain Seurat objects with the count matrix as an RNA assay, and the TCR data, matching status, and other data in the @meta.data field.

source_name: Mouse 5

growth_protocol: C57BL/6 mice received 100,000 MC38 tumor cells subcutaneously in the flank on day 0. Peripheral blood was isolated using retroorbital collection prior to euthanasia, and then tumors were collected from the same mice after euthanasia. Leukocytes were enriched from peripheral blood using histopaque gradients. Tumor-infiltrating lymphocytes were enriched from tumor samples by performing digestion with collagenase I followed by discontinous percoll gradient. CD8+ CD44+ T cells from blood and CD8+ T cells from tumors were sorted using a BD Aria sorter prior to performing 10X.

extract_protocol:
Sorted CD8+ CD44+ T cells from peripheral blood and sorted CD8+ T cells from tumors were loaded into the 10X Chromium Controller using the Chromium Single Cell 5' Library and Gel Bead Kit (10X Genomics)
For samples with gene expression and T cell receptor sequencing only, protocol number CG000086 Rev G from 10X Genomics (User Guide, Chromium Single Cell V(D)J Reagent Kits) was used. For samples with had gene expression, T cell receptor sequencing, and CITE seq to detect Feature Barcodes, protocol number CG000208 RevD from 10X Genomics (User Guide, Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 with Feature Barcoding technology for Cell Surface Protein) was used
10X Chromium Single Cell V(D)J kits (5' gene expression with paired T cell receptor sequencing, and for some samples Feature Barcode detection)

treatment_protocol: Mice did not receive any treatments.

tag: tissue

value: peripheral blood

value: CD8+ CD44+ T cells

tag: mouse strain


title: Mouse5_blood_CD8Tcells_GEX

description:
Sorted CD8+ CD44+ T cells from the peripheral blood of Mouse 5 for the same time point that the MC38 tumor was extracted. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE seq was also used to detect Feature Barcodes for CD39, NKG2D, and CX3CR1 proteins. These files contain the gene expression data.
M5_Blood.rds


title: Cavin-1PC3_Pellet1

description:
miRNA
Cavin-1-PC3 cell lysate


title: Mouse5_blood_CD8Tcells_VDJ

description:
Sorted CD8+ CD44+ T cells from the peripheral blood of Mouse 5 for the same time point that the MC38 tumor was extracted. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE seq was also used to detect Feature Barcodes for CD39, NKG2D, and CX3CR1 proteins
M5_Blood.rds


title: GFPPC3_Pellet2

description:
miRNA
GFP-PC3 cell lysate


title: Mouse5_MC38_tumor_CD8Tcells_GEX

description:
Sorted CD8+ T cells from the MC38 tumor extracted from Mouse 5. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE seq was also used to detect Feature Barcodes for CD39, NKG2D, and CX3CR1 proteins. These files contain the gene expression data.
M5_Tumor.rds

value: MC38 tumor

value: CD8+ T cells


title: Mouse5_MC38_tumor_CD8Tcells_VDJ

description:
Sorted CD8+ T cells from the MC38 tumor extracted from Mouse 5. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE seq was also used to detect Feature Barcodes for CD39, NKG2D, and CX3CR1 proteins. These files contain the TCR sequencing data.
M5_Tumor.rds


title: PAE 6.5mo Female 2

description: PAE

value: Female

tag: analysis inclusion


title: Cont 2wk Female 4

description: Cont


title: GFPPC3_Pellet1

description:
miRNA
GFP-PC3 cell lysate


title: GFPPC3_Pellet3

description:
miRNA
GFP-PC3 cell lysate