title: NF90_ChIPSeq

city: Stanford

first: Mark

last: Nicolls

state: California

address: 300 Pasteur Drive

department: Pulmonary and Critical Care Medicine

institute: Stanford University School of Medicine

data_processing:
Paired end reads were mapped using bwa aln from Burrows-Wheeler Alignment tool (BWA) 0.7.7
Sorted BAM files were generated using bwa samse from BWA 0.7.7 and samtools 0.1.19
Raw bam file of mapped reads were filtered by removing unmapped reads, non-primary alignments, reads failing platform, duplicates, multi-mapping reads, and PCR duplicates. Unpaired reads were removed
Fold-over-control signal tracks for each replicates was generated, and pooled with Model-based Analysis of ChIP-Seq (MACS2)
For Irreproducibility Discovery Rate (IDR) analysis, the peaks were called using SPP, then thresholded with IDR using the reproducibility test.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak BED files contain called peaks of signal enrichement based on pooled, normalized (interpreted) data; BIGWIG file contains the continuous signal trak of fold enrichment over input DNA.

source_name: K562 erythroleukemia cells

growth_protocol: K562 erythroleukemia cells were grown in RPMI1640 media supplemented with 10% fetal bovine serum and Antibiotic-Antimycolic 100X (Life Technologies).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Bravo automatic library preparation. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: chip antibody

value: NF90 (mAb DRBP76; BD)


title: H2AX replicate 1

status: Public on Mar 01 2018

type: SRA

city: Bronx

first: Kami

last: Kim

state: New York

address: 1300 Morris Park Avenue

department: Medicine

country: USA

institute: Albert Einstein College of Medicine

description: Mnase-digested DNA

library_source: genomic

data_processing:
Adapter sequences were trimmed using cutadapt (https://cutadapt.readthedocs.io/en/stable/) and aligned to the T. gondii ME49 genome (release 26, ToxoDB.org) using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Aligned BAM files were normalised by library size and converted to bigwig format using deeptools bamCoverage(http://deeptools.readthedocs.io/en/latest/content/tools/bamCoverage.html)
Peaks were called using either HOMER (H2AX, H3.3 samples), MACS2 Callpeak (H3K4me3) or MACS2 Broadpeak (H2AZ, H2BV,CenH3 )
Genome_build: Toxoplasma gondii ME49 release 26
Supplementary_files_format_and_content: bigwig of read coverage, BED files containing called peak regions

molecule: genomic DNA

organism: Toxoplasma gondii RH

source_name: Intracellular tachyzoites

growth_protocol: Confluent human foreskin fibroblast cells were infected with tachyzoite forms of Toxoplasma gondii (RH_hxgprt) at a ratio of 3-5 parasites per cell.  After around 40hs of infection, cells were harvested and lysed sequentially with 20G/23G/25G needles.

extract_protocol:
Parasites were lysed in lysis buffer to release nuclei. Nuclei were digested with micrococcal nuclease and centrifuged to remove cell debris and harvest digested DNA. Histone-DNA complexes were immunoprecipitated with protein A-conjugated magnetic beads and digested with proteinase K before DNA purification.
Adapters were ligated to DNA using a TruSeq ChIP-seq kit (Illumina). Libraries were sequenced using a Hiseq2500 sequencing machine (Illumina). This involves a first step of cluster generation in situ on the flow cell followed by massively-parallel sequencing using fluorescently-labeled reversible terminator nucleotides. Clustered templates were sequenced base-by- base during each read. Images generated by the Hiseq2500 were processed by Hiseq Sequence Control Software (HCS V2 or latest with RTA v1.17 or latest and CASAVA 1.8 or latest software packages). These software components perform the functions of image analysis (Firecrest) and base-calling (Bustard).

tag: chip antibody name

tag: chip antibody source

value: Angel laboratory

tag: Stage

value: Intracellular tachyzoites


title: H3.3 replicate 2

description: Mnase-digested DNA

value: HA epitope tag

value: miltenyibiotec

tag: chip antobody catalogue number


title: H2BV replicate 2

description: Mnase-digested DNA


title: H2BV replicate 1 Input DNA

description: Mnase-digested DNA


title: H2AX replicate 2 Input DNA

description: Mnase-digested DNA


title: H2AX replicate 2

description: Mnase-digested DNA

value: myc


title: WT Lgr6 replicate 3

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

library_source: transcriptomic

data_processing:
Fastq files were processed using Galaxy and aligned using RNA STAR with default options
BAM files were processed in R using “rnaseqGene” workflow
The data was analysed using the edgeR package.
Genome_build: GRCm38/Mm10
Supplementary_files_format_and_content: single csv file with count data for all samples

molecule: total RNA

organism: Mus musculus

source_name: Epidermis

growth_protocol: Primary epidermal cell suspension was prepared from 4-OHT treated Pelofl/+; Lrig1EGFP-CreERT2, Pelofl/+; Lgr5EGFP-CreERT2, Pelofl/+; Lgr6EGFP-CreERT2 control mice and Pelofl/fl; Lrig1EGFP-CreERT2, Pelofl/fl; Lgr5EGFP-CreERT2, Pelofl/fl; Lgr6EGFP-CreERT2 Pelo mut mice.

extract_protocol:
Total epidermal population was FACS sorted for GFP+ cells and 1000 GFP+ cells collected from each population for RNA-seq.
Library construction and the strategy for RNA-seq was performed as reported previously (Picelli et al. Nature Protocol 2014).

tag: strain

tag: tissue

value: Epidermis

tag: age

tag: genotype

value: WT


title: WT Lgr6 replicate 2


title: H3.3 replicate 1

description: Mnase-digested DNA


title: Pelo -/- Lrig1 replicate 3

value: Pelo -/-


title: Pelo -/- Lgr6 replicate 3


title: H3K4me3 replicate 1

description: Mnase-digested DNA

value: Upstate


title: plus replicate 3

city: Exeter

first: Darren

middle: Mark

last: Soanes

address: RILD Building, RD&E Hospital Wonford, Barrack Road

department: College of Medicine and Health

country: United Kingdom

institute: University of Exeter

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were filtered using the fastq-mcf program from the eautils package (http://code.google.com/p/ea-utils/) applying –x 0.01, –q 20, –p 10, and –u.
Filtered reads were mapped to M. oryzae genome (70-15) using Tophat v 2.1.0
Cufflinks suite of programs was used to calculate FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values and to check for differential expression.
Genome_build: 70-15
Supplementary_files_format_and_content: "cds_exp.diff.txt" shows coding sequence differential expression output from Cufflinks. Gene identifiers are those used in M. oryzae genome database at Ensembl (http://fungi.ensembl.org/Magnaporthe_oryzae/Info/Index).

organism: Pyricularia oryzae

source_name: rice sheath infected with M. oryzae

growth_protocol: Rice leaf sheaths (CO39) were inoculated with pmk1AS mutant of Magnaporthe oryzae.

extract_protocol:
At 32 hpi, infected rice sheaths were trimmed manually and total RNA was extracted using QIAGEN RNeasy Plant Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1NA-PP1 added at 26 hpi. Control left untreated.

value: infected rice sheath

value: 32 hours post infection (hpi)

tag: treatment

value: 1NA-PP1 added at 26 hpi

value: Guy11 pmk1AS


title: H2AZ replicate 1

description: Mnase-digested DNA


title: WT Lrig1 replicate 1


title: WT_3d_4

city: New York

first: Robert

last: Darnell

address: 1230 York Ave

institute: Rockefeller University

data_processing:
base calling/Casava 1.8.2
quality filtering --minimum quality filter applied for barcode and insert, fastq_filter.pl, -if sanger -f min:7-10:20, mean:11-30:20 -maxN -1 -v -of fasta, http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download
collapse exact sequences --exact duplicate sequences removed, fasta2collapse.pl
remove 3' adapter sequene --3' adapter GTGTCAGTCACTTCCAGCGG clipped, fastx Clipper, -l 20 -a GTGTCAGTCACTTCCAGCGG -n, http://hannonlab.cshl.edu/fastx_toolkit/
strip 5' degenerate linker and barcode --7 nucleotide degenerate nucleotides followed by 4 nucleotide barcode (NNNNNNNXXXX) stripped and appended to read IDs, stripBarcode.pl, -linker 11 --linker-start-with --linker-end-with XXXX,
alignment against transcriptome reference --Bowtie 2, default settings
collapse PCR duplicates, mapped reads with same 5' end and same degenerate barcode consolidated --tag2collapse.pl, keep-tag-name --keep-max-score --random-linker -EM 30 --seq-error-model em-local --weight --weight-in-name
peak finding --tag2peak.pl, -ss -v -gap 25 -p 0.01 --multi-test
cross-link-induced truncations (CITS), step 1 , identification of read 3' ends, bedExt.pl, -n up -l "-1" -r "-1" -v
cross-link-induced truncations (CITS), step 2 , identification of truncation sites enriched over background --tag2peak.pl, -ss -v -gap 25 -p 0.01 --multi-test
Genome_build: mm10
Supplementary_files_format_and_content: Excel Spreadsheet with ZFP36 CLIP peak coordinates and annotation for each biological condition

source_name: CD4+ T-cells

growth_protocol: CD4+ T-cells were FACS-sorted from pooled spleen and lymph nodes of WT or ZFP36 KO mice activated with anti-CD3 antibody in the presence of formalin-fixed WT bone-marrow-derived dendritic cells, under Th1 polarizing conditions (10U/ml hIL-2 and 5 ng/ml mIL-12).  Cells were harvested 4 hours or 3 days after activation, and irradiated with UV light for cross-linking.

extract_protocol:
HITS-CLIP
Cross-linked RNA was ligated to 3' adapter, then purified by SDS-PAGE, transferred to nitrocellulose, and extracted with protease treatrment. RNA was reverse transcribed to cDNA with indexed RT primers in the presence of bromodeoxyuirdine. cDNA wasthen  captured on beads with anti-Br-dU antibody and circularized with CircLigase to position adapter sequences on the 5' end. Libraries were then PCR-amplified using primers with Illumina adapters.  Please see accompanying protocol for details.

tag: condition

tag: time point

value: 3 days

tag: biol. rep


title: ZFP36_KO_3d_1

treatment_protocol: CD4+ T-cells were FACS-sorted from pooled spleen and lymph nodes of WT or ZFP36 KO mice activated with anti-CD3 antibody in the presence of formalin-fixed WT bone-marrow-derived dendritic cells, under Th1 polarizing conditions (10U/ml hIL-2 and 5 ng/ml mIL-12).  Cells were harvested 4 hours or 3 days after activation, and irradiated with UV light for cross-linking.


title: WT_3d_2


title: WT_3d_1


title: ZFP36_KO_4h_3

value: ZFP36 KO

value: 4 hours


title: WT Lgr6 replicate 1


title: Pelo -/- Lgr6 replicate 1


title: ZFP36_KO_4h_2


title: ZFP36_KO_4h_1


title: WT_4h_5


title: WT_3d_3


title: Pelo -/- Lgr5 replicate 3


title: WT Lgr5 replicate 3


title: WT_4h_3


title: WT_4h_2


title: WT_4h_4


title: Pelo -/- Lrig1 replicate 1


title: Pelo -/- Lgr5 replicate 2


title: Pelo -/- Lgr6 replicate 2


title: WT Lrig1 replicate 2


title: WT_4h_1

data_processing:
base calling --Casava 1.8.2
quality filtering --minimum quality filter applied for barcode and insert, fastq_filter.pl, -if sanger -f min:7-10:20, mean:11-30:20 -maxN -1 -v -of fasta, http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download
collapse exact sequences --exact duplicate sequences removed, fasta2collapse.pl
remove 3' adapter sequene --3' adapter GTGTCAGTCACTTCCAGCGG clipped, fastx Clipper, -l 20 -a GTGTCAGTCACTTCCAGCGG -n, http://hannonlab.cshl.edu/fastx_toolkit/
strip 5' degenerate linker and barcode --7 nucleotide degenerate nucleotides followed by 4 nucleotide barcode (NNNNNNNXXXX) stripped and appended to read IDs, stripBarcode.pl, -linker 11 --linker-start-with --linker-end-with XXXX,
alignment against transcriptome reference --Bowtie 2, default settings
collapse PCR duplicates, mapped reads with same 5' end and same degenerate barcode consolidated --tag2collapse.pl, keep-tag-name --keep-max-score --random-linker -EM 30 --seq-error-model em-local --weight --weight-in-name
peak finding --tag2peak.pl, -ss -v -gap 25 -p 0.01 --multi-test
cross-link-induced truncations (CITS), step 1 , identification of read 3' ends, bedExt.pl, -n up -l "-1" -r "-1" -v
cross-link-induced truncations (CITS), step 2 , identification of truncation sites enriched over background --tag2peak.pl, -ss -v -gap 25 -p 0.01 --multi-test
Genome_build: mm10
Supplementary_files_format_and_content: Excel Spreadsheet with ZFP36 CLIP peak coordinates and annotation for each biological condition


title: Pelo -/- Lgr5 replicate 1


title: rib_KO_Th1_4h_4

data_processing:
Library strategy: ribo-seq
base calling, Casava 1.8.2
quality filtering --minimum quality filter applied for barcode and insert, fastq_filter.pl, -if sanger -f min:7-10:20,mean:11-30:20 -maxN -1 -v -of fasta
collapse exact sequences --exact duplicate sequences removed, fasta2collapse.pl
remove 3' adapter sequene --3' adapter GTGTCAGTCACTTCCAGCGG clipped, fastx Clipper, -l 20 -a GTGTCAGTCACTTCCAGCGG -n
strip 5' degenerate linker and barcode --7 nucleotide degenerate nucleotides followed by 4 nucleotide barcode (NNNNNNNXXXX) stripped and appended to read IDs, stripBarcode.pl, -linker 11 --linker-start-with --linker-end-with XXXX
alignment against transcriptome reference --Bowtie 2
collapse PCR duplicates --mapped reads with same 5' end and same degenerate barcode consolidated, tag2collapse.pl, keep-tag-name --keep-max-score --random-linker -EM 30 --seq-error-model em-local --weight --weight-in-name
counts per gene --HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: read counts in tabular format with ensembl gene ID and counts per biological replicate

extract_protocol:
ribosome profiling
Ribosome protected fragment RNA was ligated to 3' adapter, then size-selected by urea PAGE.. RNA was reverse transcribed to cDNA with indexed RT primers in the presence of bromodeoxyuirdine. cDNA was then  captured on beads with anti-Br-dU antibody and circularized with CircLigase to position adapter sequences on the 5' end. Libraries were then PCR-amplified using primers with Illumina adapters.  Please see accompanying protocol for details.

treatment_protocol: CD4+ T-cells were isolated from pooled spleen and lymph nodes of WT or  ZFP36 KO mice with the CD4+CD62L+ kit (Miltenyi) and activated with anti-CD3 antibody in the presence of formalin-fixed WT bone-marrow-derived dendritic cells, under Th1 polarizing conditions (10U/ml hIL-2 and 5 ng/ml mIL-12).  Cells were harvested at 4 hours after activation, and ribosome associated RNA was isolated on sucorse gradients.

tag: biol. rep.


title: WT Lgr5 replicate 1


title: Pelo -/- Lrig1 replicate 2


title: rib_KO_Th1_4h_3


title: WT Lgr5 replicate 2


title: rib_KO_Th1_4h_2


title: Sox9E13E16 mutant 2

city: Houston

first: Edwin

middle: Justin

last: Ostrin

state: Texas

address: 1515 Holcombe Blvd, Unit 1465

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

description: TRAP mRNA

data_processing:
Library strategy: TRAP-seq
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat2 v2.0.14
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a cufflinks v2.2.1 and bowtie2 v2.2.3 pipeline according to standard methods
Samples were normalized and summaries generated through use of a cuffquant and cuffnorm pipeline as part of the cufflinks suite
Genome_build: mm10
Supplementary_files_format_and_content: text file with abundance measurements

source_name: mouse embryonic lung

extract_protocol:
L10 immunoprecipitation of translating ribosomes
NEBNext Ultra with size selection and barcoding; 300 bp size selection

treatment_protocol: tamoxifen induced TRAP labeling

tag: sample source

value: TRAP-seq

value: embryonic lung

tag: developmental stage


title: rib_KO_Th1_4h_1


title: rib_WT_Th1_4h_4


title: Sox9E13E16 wild type 2

description: TRAP mRNA

value: wildtype


title: Sox9E13E16 mutant 1

description: TRAP mRNA


title: rib_WT_Th1_4h_3


title: Sox9E17 whole lung

description: total mRNA

value: whole lung homogenate


title: rib_WT_Th1_4h_2


title: Sox9E13E16 wild type 1

description: TRAP mRNA


title: Sox9E14 whole lung

description: total mRNA


title: rib_WT_Th1_4h_1


title: Sox9E17 TRAP-seq

description: TRAP mRNA


title: WGBS_380-3

city: Los Angeles

first: Eric

middle: Alva

last: Webb

address: 3616 Trousdale Parkway

institute: University of Southern California

data_processing:
Raw read files were downloaded from the USC Epigenome server upon completion
Reads were quality processed, filtered, and mapped onto the respective reference genomes using the MethPipe pipeline with default settings (http://smithlabresearch.org/software/methpipe/)
Bisulfite conversion rates were estimated using MethPipe
Samples 380-1, 380-2, 380-3, 380-750-1, 380-750-2, and 380-750-3 are of the same strain of Trichodesmium erythraeum (strain IMS101) and were used for IMS101 methylation characterization and a CO2 experiment. Hence, these libraries were mapped to the Trichodesmium erythraeum IMS101 genome. The "WGBS_380_and_380-750_proportions.txt" file contains one row for every cytosine in the IMS101 genome. The first column contains colon-delimited information including (from left to right): the IMS101 accession #, genome coordinate, strand, and sequence context. Each library (e.g. 380-1, 380-2, etc.) has two columns assigned to it in which the left column is the total number of reads mapping to that cytosine and right column is the number of reads showing that cytosine to be methylated per library. The processed files for the remaining libraries are different since they were meant for a different aspect of the study and thus contain no replicates. These processed files have a file ending as follows: *.meth. The format of those files going from left to right is as follows: Genome id, genome coordinate, strand, sequence context, methylation level (i.e. # of reads showing that cytosine to be methylated / # of total reads mapping to that cytosine), and total read coverage. IMSB is another sample of IMS101 cultured in a separate location, and so it was mapped to the Trichodesmium erythraeum IMS101 genome. 2175 is of the same species as the above samples (Trichodesmium erythraeum) except of a different strain (strain 2175). The genome for 2175 is a draft genome made up of different contigs. In order to map the WGBS_2175 library to the 2175 genome, we concatenated all of the 2175 contigs of the draft genome in order to obtain pseudo-coordinates of methylated cytosines. We then annotated genomic regions surrounding these methylated cytosines as genes or intergenic regions. Hence, in order to get reproducible data, we have included the concatenated 2175 genome as a processed data file (21-75.fa). Note that the coordinates in the processed 2175 file (2175_filtered.meth) are not true genome coordinates as we arbitrarily concatenated contigs. The concatenation was solely meant for mapping purposes to derive pseudo-coordinates for downstream analysis. The remaining libraries (VI-1, St-06, St-08) derive from Trichodesmium populations of either a different genus (Trichodesmium theibautii; VI-1) or from mixed populations of Trichodesmium collected at sea (St-06, St-08). These libraries were mapped onto the Trichodesmium erythraeum (strain IMS101) genome to identify putatively methylated cytosines in situ within the IMS101 genome. Detailed methods are outlined in the forthcoming paper.
A cytosine was deemed methylated if the residue had a combined coverage of at least 5 reads with at least 20% of total reads being methylated. For samples used in IMS101 characterization (380-1, 380-2, 380-3) and for the CO2 assays (380-750-1, 380-750-2, 380-750-3), methylation had to be detected in all biological replicates to be deemed methylated
Supplementary_files_format_and_content: The "WGBS_380_and_380-750_proportions.txt" file contains one row for every cytosine in the IMS101 genome. The first column contains colon-delimited information including (from left to right): the IMS101 accession #, genome coordinate, strand, and sequence context. Each library (e.g. 380-1, 380-2, etc.) has two columns assigned to it in which the left column is the total number of reads mapping to that cytosine and right column is the number of reads showing that cytosine to be methylated per library.
Supplementary_files_format_and_content: This row is to describe the processed files that have a file ending as follows: *.meth. The format of those files going from left to right is as follows: Genome id, genome coordinate, strand, sequence context, methylation level (i.e. # of reads showing that cytosine to be methylated / # of total reads mapping to that cytosine), and total read coverage.
Supplementary_files_format_and_content: The genome for 2175 is a draft genome made up of different contigs. In order to map the WGBS_2175 library to the 2175 genome, we concatenated all of the 2175 contigs of the draft genome in order to obtain pseudo-coordinates of methylated cytosines. We then annotated genomic regions surrounding these methylated cytosines as genes or intergenic regions. Hence, in order to get reproducible data, we have included the concatenated 2175 genome as a processed data file (21-75.fa). Note that the coordinates in the processed 2175 file (2175_filtered.meth) are not true genome coordinates as we arbitrarily concatenated contigs. The concatenation was solely meant for mapping purposes to derive pseudo-coordinates for downstream analysis.

organism: Trichodesmium erythraeum IMS101

source_name: cell population

growth_protocol: Cells were grown semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)

extract_protocol:
Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction.
DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol.
Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina).

tag: environment

value: cell culture

tag: co2 concentration

value: 380 microatm

tag: medium

value: Aquil medium w/o fixed nitrogen

tag: location

value: University of Southern California


title: WGBS_380-750-2

growth_protocol: Cells growing semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2 were transferred to the same medium but now under 750 µatm CO2. Cells were allowed to acclimate for 2 weeks (~5 generations) before sampling. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)

value: 750 microatm


title: WGBS_380-1


title: WGBS_380-2


title: WGBS_380-750-1


title: WGBS_380-750-3


title: WGBS_IMSB

growth_protocol: Cells were grown in batch culture in YBC medium devoid of fixed nitrogen. Cells were sampled during the middle of the photoperiod (i.e. midday)

value: YBC medium w/o fixed nitrogen


title: Sox9E14 TRAP-seq

description: TRAP mRNA


title: WGBS_St-08

organism: Trichodesmium

source_name: Trichodesmium mixed cell population sampled directly from ocean

growth_protocol: Natural populations of Trichodesmium isolated in situ on a cruise transect in the western South Atlantic that were collected on a 130 µm net, handpicked, and frozen. See Webb et al. 2007 for complete growth_protocol.

value: in situ cell population from ocean

value: western South Atlantic seawater

value: See description


title: WGBS_St-06


title: WGBS_VI-1

organism: Trichodesmium thiebautii VI-1

growth_protocol: Cells were grown in batch culture in RMP medium devoid of fixed nitrogen. Cells were sampled during the middle of the photoperiod (i.e. midday). See Hynes et al. 2012 for complete growth_protocol

value: Woods Hole Oceanographic Institution


title: Poplar 2

city: Santa Barbara

first: John

last: Henske

address: Engineering II Building

department: Department of Chemical Engineering

institute: University of California, Santa Barbara

description:
mRNA
Processed data file: pyc_expressiondata_expectedcounts.txt
Processed data file: pyc_substrate_tpm.txt

data_processing:
Assembled transcriptome using reads obtained from growth on each substrate and the Trinity algorithm.
Aligned reads from all conditions to transcriptome to get count data.
Genome_build: de novo
Supplementary_files_format_and_content: pyc_expressiondata_expectedcounts.txt: Tab-delimited text file contains the expected counts produced by RSEM analysis.
Supplementary_files_format_and_content: pyc_substrate_tpm.txt: Tab-delimited text file contains the transcripts per million counts produced by the RSEM analysis.
Supplementary_files_format_and_content: Pycnoporus_denovo.fasta: FASTA file contains all transcripts assembled by Trinity; de novo transcript assembly.

organism: Trametes cinnabarina

source_name: Whole organism, poplar

growth_protocol: Cultures were grown on semi-minimal media and inoculated with a 5mm agar cube overgrown with P. cinnabarinus. Cultures were grown for at least 5 days before harvesting RNA.

extract_protocol:
Qiagen RNeasy Mini Kit (Plant/Fungi Protocol).
Illumina TruSeq Stranded mRNA library standard protocol for Soluble substrate and control, Ribozero (yeast) kit used to remove rRNA from Poplar and Switchgrass samples.

treatment_protocol: Fungal cultures were grown on glucose, maltose, cellobiose, poplar, switchgrass, or no energy substrate (control).

tag: strain/background

value: Whole organism

tag: energy substrate

value: Poplar


title: Switchgrass 1

source_name: Whole organism, switchgrass

value: Switchgrass


title: Switchgrass 2


title: Poplar 3


title: RNASEQ_380-750-2

data_processing:
Raw read files were downloaded from the UC San Diego Genomics Core server upon completion
Raw Fastq files were quality trimmed using the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) with minimum quality 20 and minimum read length set to 35 bp.
Quality processed reads were mapped onto Trichodesmium IMS101 genes (per Integrated Microbial Genomes (JGI) annotation) using Bowtie2 v2.2.6 with default settings. Counts per gene were enumerated using the sam2counts.py script (https://github.com/vsbuffalo/sam2counts). Genes containing an average of less than 10 counts across libraries were removed.
Genome_build: Trichodesmium erythraeum IMS101 (https://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=637000329)
Supplementary_files_format_and_content: Tab-delimited file with raw counts per gene as rows and individual biological replicates as columns

growth_protocol: Cells were growing semi-continuously in Aquil medium with replete nutrients in 380 µatm CO2 were transferred to the same medium but now under 750 µatm CO2. Cells were allowed to acclimate for 2 weeks (~5 generations) before sampling. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)

extract_protocol:
Cultures were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until RNA extraction.
RNA was extracted using the Ambion MirVana miRNA Isolation Kit (Thermo Fisher Scientific) in an RNAse free environment according to the manufacturer’s instructions followed by two incubations with Ambion’s Turbo DNA-free kit to degrade trace amounts of DNA.
Extracted RNA was sent to the UC San Diego IGM Genomics Center for library construction and Illumina sequencing. Briefly, rRNA was removed from total RNA using the Ribo-Zero rRNA Removal Kit (Illumina), and libraries were constructed with the TruSeq Stranded mRNA Library Prep Kit (Illumina) followed by 50 base pair, single end sequencing with the Illumina HiSeq4000.

value: University of Southern California, Los Angeles


title: RNASEQ_380-750-1


title: RNASEQ_380-2


title: Maltose 2

source_name: Whole organism, maltose

value: Maltose


title: Maltose 3


title: Poplar 1


title: RNASEQ_380-1


title: Glucose 1

source_name: Whole organism, glucose

value: Glucose


title: Maltose 1


title: Cellobiose 2

source_name: Whole organism, cellobiose

value: Cellobiose


title: ibm1-3_HL48_r2

city: ChongQing

first: Di

last: Fan

address: NO.2 Tiansheng Road

country: China

institute: Southwest University

description: WT_HL_r2 vs ibm1_HL_r2.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to tair10 whole genome using bowtie2 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010.
Differentially expressed genes were analyzed with DEGseq
Genome_build: Arabidopsis thaliana tair10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: All Arabidopsis were planted in green house in long day condition

extract_protocol:
rosset leaves were removed, and RNA was havested using biospin plant total RNA extraction kit
RNA libraries were prepared for RNA sequencing using standard Illumina protocols and BGI protocols separately

treatment_protocol: 30 days old WT and ibm1-3 Arabidopsis were treated with high light for 48 hours

value: rosset leaf

value: 30 days

tag: background ecotype

value: Columbia

tag: genotype/variation

tag: protocol

value: high light for 48 hours


title: Cellobiose 1

tag: tissue


title: Cellobiose 3


title: ibm1-3_HL48_r1

description: WT_HL_r2 vs ibm1_HL_r2.txt

tag: age


title: Switchgrass 3


title: WGBS_2175

organism: Trichodesmium erythraeum 21-75

value: cell culture

value: 380 microatm

value: University of Southern California


title: WT_HL48_r2

description: WT_HL_r1 vs ibm1_HL_r1.txt

value: WT


title: Control 2

source_name: Whole organism, control


title: SC13F

status: Public on Feb 28 2018

city: Madrid

first: Jesus

last: del Mazo Martinez

address: C/ Ramiro de Maeztu 9

country: Spain

institute: Centro de Investigaciones Biologicas (CIB) - CSIC

description:
E13.5 Female gonadal somatic cells
Total RNA < 100 bp length
Processed data file: All_samples_NormalizedCounts_DESeq.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
To assess the quality of the raw and trimming sequence libraries the FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) program was used. Then, adapters and low quality bases were trimmed using the wrapper script Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The quality Phred threshold considered was 28 and the minimum sequence length of 16 nucleotides was established. Clean reads were collapsed using Fastx-toolkit suit (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
Assignment of reads to different miRNAs was performed by mapping to the pre-miRNA database miRBase21 using bowtie 1.1.2. Mismatches in sequence comparison should be required due potential miRNA editing and 3' nucleotide non-template additions. Bowtie parameters were: -v 3 -m 20 --strata --best -y --chunkmbs 256 --norc -S. Reads that mapped to multiple loci were divided by the total number of multi-mapped hits to avoid over-counting them.
Genome_build: miRBase21 (GRCm38)
Supplementary_files_format_and_content: *NormalizedCounts_DESeq.txt: Tab-delimited text files containing normalized expression of miRNAs by DESeq calculated with sequences without mismatches and with the same seed sequence than the canonical miRNA annotated at miRBase v21.

source_name: Gonadal somatic cell, Female, E13.5

growth_protocol: Pathogen-free (SPF), temperature (22°C ± 1°C), humidity (50%-55%). All animals were housed on a 12 h light/dark cycles with ad libitum access to food and water.

extract_protocol:
Mus musculus CD1 strain was used as animal model. PGCs and somatic gonadal cells were isolated from embryos obtained from pregnant females at E11.5, E12.5 and E13.5. At E11.5 and E12.5, male and female gonads are morphologically indistinguishable at early stages of development. To sex embryos at E11.5 and E12.5, we isolated and stored individually each set of gonads in PBS at 4ºC. Sex was identified in each single embryo by PCR of DNA, obtained from the heads, using primers to identify the presence of Sry gene and Jarid1d (a single band for XX and a double band for XY). After sexing the embryos, the mesonephros was removed before the purification of germ and somatic cells. PGCs and somatic cells were purified using a paramagnetic technology according to Brieño-Enriquez et al. 2015. Briefly, groups of about 80 gonads were incubated in 0.25% trypsin-EDTA during 15 minutes at 37ºC, washed followed by incubation with PGC-specific antibodies (anti-CD15) bound to paramagnetic-microbeads. Finally, PGCs were isolated from somatic stromal cells by a magnetic column (miniMAcs) and stained both separated fractions with the naphtol AS-MX/ FAST-RED (Sigma-Aldrich) (PGC specific) to determine the level of enrichment of cell populations. In all cases, the enrichment of the PGCs was 93-96%. Similarly, the purity of somatic cells was over 90% in all samples.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Gonad

tag: cell type

value: Gonadal somatic cell

value: Embryonic day 13.5

tag: gender

value: Female


title: WT_HL48_r1

description: WT_HL_r1 vs ibm1_HL_r1.txt


title: Control 3

value: Whole organism


title: SC12F

description:
E12.5 Female gonadal somatic cells
Total RNA < 100 bp length
Processed data file: All_samples_NormalizedCounts_DESeq.txt

source_name: Gonadal somatic cell, Female, E12.5

value: Embryonic day 12.5


title: Control 1


title: SC11M

description:
E11.5 Male gonadal somatic cells
Total RNA < 100 bp length
Processed data file: All_samples_NormalizedCounts_DESeq.txt

source_name: Gonadal somatic cell, Male, E11.5

value: Embryonic day 11.5

value: Male


title: PGC13M

description:
E13.5 Male PGCs
Total RNA < 100 bp length
Processed data file: All_samples_NormalizedCounts_DESeq.txt

source_name: Primordial Germ Cell, Male, E13.5

value: Primordial germ cell


title: SC11F

description:
E11.5 Female gonadal somatic cells
Total RNA < 100 bp length
Processed data file: All_samples_NormalizedCounts_DESeq.txt

source_name: Gonadal somatic cell, Female, E11.5


title: PGC11M

description:
E11.5 Male PGCs
Total RNA < 100 bp length
Processed data file: All_samples_NormalizedCounts_DESeq.txt

source_name: Primordial Germ Cell, Male, E11.5


title: PGC11F

description:
E11.5 Female PGCs
Total RNA < 100 bp length
Processed data file: All_samples_NormalizedCounts_DESeq.txt

source_name: Primordial Germ Cell, Female, E11.5


title: PGC12M

description:
E12.5 Male PGCs
Total RNA < 100 bp length
Processed data file: All_samples_NormalizedCounts_DESeq.txt

source_name: Primordial Germ Cell, Male, E12.5


title: PGC12F

description:
E12.5 Female PGCs
Total RNA < 100 bp length
Processed data file: All_samples_NormalizedCounts_DESeq.txt

source_name: Primordial Germ Cell, Female, E12.5


title: PGC13F

description:
E13.5 Female PGCs
Total RNA < 100 bp length
Processed data file: All_samples_NormalizedCounts_DESeq.txt

source_name: Primordial Germ Cell, Female, E13.5


title: Myeloma 3

city: Ferrara

first: Stefano

last: Volinia

address: Via Fossato di Mortara 64

country: Italy

institute: University of Ferrara

data_processing:
novalign was used to count miRNA occurrence using miRbase release 21
RPM were computed for normalization (reads per million of aligned miRNA reads)
Genome_build: miRBase 21
Supplementary_files_format_and_content: log2 RPM tab delimited text file

organism: Homo sapiens

source_name: Plasma cells

extract_protocol:
CD138+ plasma cells (PCs) were purified from the bone marrow of patients by Human Whole Blood CD138+ Selection Kit (Cat#18387, Stem Cell Technologies) as per the manufacturer’s instructions. Yield and purity of CD138+ cells was evaluated by flow cytometry using anti-CD138 antibody (Cat#347193 Becton Dickinson). The RNA from bone marrow cells was extracted by TRIZOL reagent (Invitrogen). CD138+ plasma cells obtained from newly diagnosed MM patients were obtained from the Tissue Bank of The University of Turin, Italy and from The OSU Leukemia Tissue Bank.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: myeloma

value: Plasma cells


title: Myeloma 2


title: Myeloma 1


title: Healthy 3

value: healthy


title: Healthy 2


title: siPrep1_S6

city: Milan

first: Dmitry

last: Penkov

address: Via Adamello 16

institute: IFOM

data_processing:
Library strategy: Repli-Seq
Reads were aligned to the hg19 genome using Bowtie v.0.12.8 (3)
Duplicate reads were removed using Samtool rmdup v 0.1.18
The reference genome was binned in 100bp intervals, and the signal from the sequencing data underlying these regions was calculated
TMM (trimmed mean of M values) normalization from the edgeR was applied to the six S-phase cells subpopulations, and for each genomic 100bp interval, the signal was scaled in values ranging from 0 to 1 among all S-phase fractions
Scaled signals were subtracted from an accordingly scaled signal derived from sequencing data from unsorted siPREP1 and siLUC cells
Negative values where converted to zero values and a quantile normalizazion was applied between the same data from S1-S6 sub-populations of cells.
Human genome was divided in 50-Kb intervals and S50 value was measured for each of them. S50 is a replication timing estimator that measures the fraction of the S phase at which 50% of a given genomic region has been replicated; it ranges from zero to 1
Genome_build: hg19
Supplementary_files_format_and_content: .txt files report S50 values

source_name: siPrep1, HeLa

growth_protocol: HeLa cells were grown in a complete DMEM medium containing FBS serum. The cells were splitted every 3 days

extract_protocol:
Sorted cells were lysed, DNA extracted by phenol-chloroform and immunoprecipitated using anti-BrdU antibody
Libraries were prepared according to Ion_torrent's instructions

treatment_protocol: 10nM ds siRNA  (Prep1 and Luc) were transfected using RNAi Max lipofectamine. Cells were FACS-sorted in six sub-phases of the S phase (S1-S6) according to increasing DNA content.

tag: cell line

value: HeLa

value: epithelial adenocarcinoma cells

value: Prep1 knockdown

tag: s-phase fraction


title: SC13M

description:
E13.5 Male gonadal somatic cells
Total RNA < 100 bp length
Processed data file: All_samples_NormalizedCounts_DESeq.txt

source_name: Gonadal somatic cell, Male, E13.5


title: siPrep1_S5


title: Healthy 1


title: siPrep1_S3


title: SC12M

description:
E12.5 Male gonadal somatic cells
Total RNA < 100 bp length
Processed data file: All_samples_NormalizedCounts_DESeq.txt

source_name: Gonadal somatic cell, Male, E12.5


title: siPrep1_S4


title: siLuc_S2

source_name: siLuc, HeLa

value: control


title: siLuc_S5


title: siPrep1_S1


title: siLuc_S4


title: siPrep1_S2


title: siLuc_S6


title: siLuc_S3


title: siPrep1 replicate 3

description: NormalizedCount.txt

data_processing:
Artifacts eliminated with FASTX-Toolkit v.0.0.13.2
Reads were aligned to the hg19 reference using  Tophat v2.0.9
GenomicFeatures, GenomicRanges and GenomicAligments R libraries were used to count the number of reads with respect to the annotation reference (UCSC, genome='hg19', tablename='refGene’).
Differentially expressed genes between different conditions were retrieved using DESEQ R library
Genome_build: hg19
Supplementary_files_format_and_content: .txt file represents a read count table

extract_protocol:
Total RNA was extracted using trizol 48 hours after transfection and then purified using RNAesy kit
RNA libraries were prepared for sequencing using standard Ion-Torrent protocols

treatment_protocol: 10nM ds siRNA  (Prep1 and Luc) were transfected using RNAi Max lipofectamine


title: siPrep1 replicate 2

description: NormalizedCount.txt


title: siPrep1 replicate 1

description: NormalizedCount.txt


title: siLuc replicate 3

description: NormalizedCount.txt


title: siLuc replicate 2

description: NormalizedCount.txt


title: siLuc replicate 1

description: NormalizedCount.txt


title: HeLa cells ChIP

data_processing:
Artifacts were eliminated with FASTX-Toolkit v.0.0.13.2
Reads were aligned to the hg19 genome using Bowtie v.0.12.8 (3)
Duplicate reads were removed using Samtool rmdup v 0.1.18
Enriched domains were identified using MACS version 2.0.10.20131028 with default parameters and p-value threshold (10e-5)
Genome_build: hg19
Supplementary_files_format_and_content: .narrowPeak reports PREP1 DNA binding domains

source_name: ChIP, HeLa

extract_protocol:
Cells were lysed and nuclei sonicated. The chromatin-Prep1 complexes were obtained using Prep1 Ab.
Libraries were prepared according to Ion_torrent's instructions

tag: chip antibody

value: Prep1 Santa-Cruz N15 (sc-6245)


title: C2C12 input

city: Rome

first: Viviana

last: M

address: Via A. Scarpa 16

department: SAIMLAL

institute: La Sapienza University of Rome

data_processing:
The CASAVA 1.8.2 version of the Illumina pipeline was used to processed raw data for both format conversion and de-multiplexing
Trimming - removing low quality bases and adapters using ERNE and Cutadapt.
Alignment - reads alignment on reference genome with Bowtie2 (with default parameters). Uniquely mapping read selection was performed on alignments.
Peak detection – peaks are detected with macs2 using default parameters
Peak annotation – identification of potential association of ChIP regions with functionally important genomic regions by CEAS. Analysis provides statistics on ChIP enrichment at important genome features such as specific chromosome, promoters, gene bodies, or exons, and infers genes most likely to be regulated by a binding factor
Genome_build: mm10
Supplementary_files_format_and_content: IP1_vs_input_peaks.xlsx is a tabular file which contains information about called peaks. Information include: chromosome name, start position of peak, end position of peak, length of peak region, absolute peak summit position, pileup height at peak summit, -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then this value should be 10), fold enrichment for this peak summit against random Poisson distribution with local lambda, -log10(qvalue) at peak summit. Coordinates in XLS is 1-based which is different with BED format, which is 0-based (i.e. 1 base shift).
Supplementary_files_format_and_content: IP1_vs_input_peaks_annotated.xlsx includes the name of the gene closest to each peak

source_name: Skeletal muscle cells

growth_protocol: C2C12 cells were grown in Dulbecco’s modified Eagle medium supplemented with 20% fetal bovine serum (Sigma-Aldrich), 2mM glutamine (Sigma-Aldrich), 50 μg/ml gentamicin (Sigma-Aldrich) (GM).

extract_protocol:
Chromatin from 30 X 106 C2C12 cells was cross-linked with 1% formaldehyde (Sigma-Aldrich) for 12 minutes at room temperature.  Glycine was then added to a final concentration of 0.125 M for 5 minutes. After washing, samples were centrifuged and suspended in cell lysis buffer (10mM Tris pH 8.0, 10mM NaCl, 0.2% NP40), incubated on ice for 30 minutes and centrifuged at 4000 rpm for 5 min. Nuclei were then suspended in nuclei lysis buffer (50 mM Tris-HCl pH 8.1, 1% SDS, 10 mM EDTA) and incubated on ice for 30 minutes. To obtain chromatin fragments of around 200–300 bp, sonication was performed using a Bioruptor UCD-200 sonicator (Diagenode). Chromatin extracts were incubated overnight on a rotating platform at 4 °C with 7.5 μg anti-HDAC4 (Santa Cruz, sc-11418) for immunoprecipitation. Rabbit IgG was used as negative control. Immunoprecipitated chromatin was conjugated with G-protein magnetic Beads (Invitrogen). After washing, bound DNA fragments were eluted by adding elution buffer (1% SDS, 1mM EDTA, 10mM Tris). Purified DNA and input DNA were sequenced at the NextGen Sequencing facility (IGA Technologies Service, Udine).
‘Ovation Ultralow Library System v2’ kit (NuGEN, San Carlos, CA) has been used for library preparation following the manufacturer’s instructions. Both input and immunoprecipitated samples as well as final libraries were quantified by using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and quality tested by Agilent 2100 Bioanalyzer High Sensitivity DNA assay (Agilent technologies, Santa Clara, CA) and Real Time Stratagen Mx3000P  (Agilent technologies, Santa Clara, CA).

treatment_protocol: Cells were grown 24h in growth conditions

value: Skeletal muscle

value: Immortalized mouse myoblast cell line

tag: passages

tag: strain


title: HeLa cells input

source_name: Input, HeLa


title: C2C12 GM1 IP

value: Santa Cruz, sc-11418


title: HDAC4 KO4 sat

description: Satellite cells were isolated from skeletal muscles of 4-week-old mice by FACS, after enzymatic dissociation

data_processing:
CASAVA 1.8.2 version of the Illumina pipeline was used to process raw data for both format conversion and de-multiplexing
Trimming - removing low quality bases and adapters were performed using ERNE and Cutadapt, respectively.
Reads were aligned on reference genome/transcriptome using TopHat with default parameters.
Transcripts count - Cufflinks was used with default parameters.
Pair-wise differential expression analysis. Cuffdiff tool was used to perform comparisons between expression levels of genes and transcripts using default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, tab-delimited text file including log2fold change, p- and q-values for all genes.

source_name: Satellite cells

growth_protocol: Satellite cells were plated on 0,01% collagen (Sigma-Aldrich)-coated dishes with Dulbecco’s modified Eagle medium supplemented with 20% horse serum (Sigma-Aldrich),100 U/ml penicillin (Sigma-Aldrich), 100μg/ml streptomycin (Sigma- Aldrich), 50 μg/ml gentamicin (Sigma-Aldrich), 3% of chicken embryo extract as growing medium (GM).

extract_protocol:
Total RNA collected from satellite cells, after 24 hours in growing conditions, was purified by using RNeasy MinElute Cleanup Kit (Qiagen). About 0,8 mg of RNA from duplicates was subjected to transcriptome analysis at the NextGen Sequencing facility (IGA Technologies Service, Udine).
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Prep kit (illumina) following the manufacturer’s instructions

treatment_protocol: Satellite cells were collected after 24h in growth medium

value: Satellite cells

value: 4 weeks

tag: genotype

value: HDAC4fl/fl Pax7CE/+ Cre treated with TMX


title: HDAC4 ctr3 sat

value: HDAC4fl/fl Pax7CE/+ Cre treated with vehicle


title: iTE rep5

city: Bethesda

first: Li

last: Jia

state: MD

address: 10 Clinic center

institute: NCI/NIH

data_processing:
Illumina RTA v1.18.66.3 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using star v2.4.2a with parameters as default
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using R. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The raw read counts were generated using subread v.1.4.6
The normalization was used TMM and differential expression analysis was used edgeR, R package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalization values for each Sample ...

source_name: iTE

growth_protocol: iPSC established from Pmel-mice were differentiated into T cell lineage on OP9/DLL1 for 16 days. Additional 7 days of culture were perfomed in either OP9/DLL1 or a 3D organ culture.

extract_protocol:
Qiagen RNeasy micro kit (following manufacturer instructions)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Non-adherent cells were harvested on OP9 co-cultures at day 23 of differentiation from iPSC stage. Naïve T cells were used as controls.

value: iPSC-derived Thymic Emigrants (iTE) generated after 7 days of 3D organ culture

tag: sorted phenotype

value: Cells sorted on Live CD45.1+CD4-CD8+CD25-NK1.1-TCRgd-CD62L+CD44-

tag: background strain

value: C57BL/6J pmel-1 Tg. Mice


title: iTE rep3


title: iTE rep2


title: HDAC4 ctr4 sat


title: iTE rep4


title: siLuc_S1


title: Extrathymic rep3

source_name: Extrathymic

value: iPSC-derived CD8 single positive T cells on OP9/DLL1 at day 23


title: Extrathymic rep1


title: iTE rep1


title: Extrathymic rep5


title: DP rep2

source_name: DP

value: iPSC-derived CD4+CD8+ double positive T cells on OP9/DLL1 at day 23

value: Cells sorted on Live CD45.1+CD4+CD8+CD25-NK1.1-TCRgd-CD62L+CD44-


title: DP rep3


title: Extrathymic rep4


title: Extrathymic rep2


title: Naïve rep5

source_name: Naïve

value: Naive T cells sorted from Pmel-mice


title: DP rep1


title: Naïve rep4


title: Naïve rep3


title: Naïve rep1


title: HDAC4 KO3 sat


title: EOGT siRNA D4 3

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

institute: University of Warwick

data_processing:
Transcriptomic maps of paired-end reads were generated using bowtie-2.2.3, samtools-0.1.19, and tophat-2.0.12 against the hg19 reference genome (2014)
Transcript counts were assessed by HTSeq-0.6.1 using the reverse strand setting and intersection-non-empty mode and counts were assigned to gene ids.
Genome_build: hg19
Supplementary_files_format_and_content: Count and TPM data in .XLS format

source_name: Endometrial stromal cells

growth_protocol: Human Endometrial Stromal Cells were prepared and maintained in culture as described (Brosens 1999).

extract_protocol:
RNA was purified using RNA STAT-60 (AMS Bio) according to manufacturer's instructions and treated using Amplification Grade DNase I (Invitrogen) followed by ethanol precipitation and clean-up.  RNA quality was examined using the Agilent Bioanalyser 2100 and all samples had a RIN >8.1
Library preparation was performed using Illumina TruSeq Stranded mRNA sample prep kit according to manufacturer's instructions.  The libraries were validated on the Agilent BioAnalyser 2100 to check the size distribution of the libraries and on the Qubit High Sensitivity to check the concentration of the samples.  Samples were pooled and pools were loaded onto 1 lane of an Illumina HiSeq4000 flow cell.

treatment_protocol: HESCs were transfected with 50nM small interfering siRNA (EOGT-siGENOME SMARTpool or siGENOME Non-Targeting siRNA Pool1 (Thermo Fisher Scientific, Waltham, MA, USA)) by jetPRIME Polyplus transfection kit (VWR Internation, Radnor, PA, USA)

value: Endometrial stromal cells

value: EOGT siRNA

tag: decidualization status

value: decidualized

tag: passage

tag: patient id

value: Patient 3


title: EOGT siRNA D0 3

tag: genotype/variation

value: undifferentiated


title: Non Targeting Control D0 3

value: non-targeting siRNA


title: Non Targeting Control D4 3


title: 5d_20D_PB

city: RTP

first: Susan

last: Hester

state: NC

address: 109 TW Alexander Dr

institute: US EPA

data_processing:
After sequencing, basecall files were converted into FASTQ output files using Illumina CASAVA software and other tools developed at EA (available at https://github.com/ExpressionAnalysis/ ea-utils/). FASTQ data were demultiplexed, and sequencing adapters and other low quality bases were clipped to prepare reads for alignment using fastq-mcf --max-ns 4 --qual-mean 25 -H -p 5 -q 7 -l 25 -l 25
Filtered reads were aligned using STAR v2.5 (parameters '--clip5pNbases 10','-sjdbGTFfile Mus_musculus.GRCm38.84.gtf', '--quantMode TranscriptomeSAM GeneCounts') to the mouse genome using Ensembl gene annotation GRCm38 v84
BAM files resulting from Star 2.5 were used as input for edgeR
Raw reads were assigned to Ensembl IDs for each sample using R. Ensembl IDs representing rRNA were removed from further analyses. The quantified, mapped reads were transformed to counts per million (CPM), and normalized using Trimmed Mean of M-values in edgeR
Genome_build: MM10
Supplementary_files_format_and_content: tab-delimited files with estimated counts for all genes and TMM normalized counts for all genes

growth_protocol: Male B6C3F1 ice were reared to 10-11 weeks of age under standard conditions within an AAALAC-accredited animal facility located in Research Triangle Park, NC, as previously described (Lake et al., 2016). All procedures involving animals were approved by the U.S. Environmental Protection Agency (U.S. EPA) Institutional Animal Care and Use Committee.

extract_protocol:
At the time of collection, liver lobes were systematically trimmed, and portions of left lateral, caudate, and right medial lobes were mixed, flash frozen in liquid nitrogen, and stored at -80°C. Frozen mouse liver samples were arbitrarily selected from control (Con) and PB groups (n=6/group), divided on dry ice into four portions (~20-30 mg each), and then preserved according to the following methods: stored at -80°C as frozen (FR); fixed in 70% ethanol for 3 months (OH); preserved in 10% buffered formalin for 18 hours followed by 70% ethanol for 3 months (18F); and fixed in 10% buffered formalin for 3 months (3F). Samples from OH, 18F, and 3F groups were kept at 4°C for 3 months, and then processed into paraffin blocks by standard histological methods: 80% ethanol for 30 minutes, twice; followed by 95% ethanol for 45 minutes each, twice; three changes of 100% ethanol for 45 minutes each; and three changes of xylenes (ThermoFisher Scientific, Fairlawn, NJ) for 30 minutes each; two changes of Paraplast™ Tissue Embedding Media (ThermoFisher Scientific, Fairlawn, NJ) for 30 minutes each and finally two changes of paraplast under vacuum for 1 hour each. The FR samples served as high-quality RNA controls. The 18-hour fixation time (18F) was selected to recapitulate a standard protocol for clinical and experimental samples, in particular those that may be used for immunohistochemical analyses (Fox et al., 1985). The 3-month formalin fixation (3F) was selected as an arbitrary long-term fixation scenario expected to have more severe formalin-induced RNA degradation. FFPE blocks were then stored at room temperature for up to 4 months until sectioning for RNA isolation. Total RNA was isolated from frozen (FR) liver samples following homogenization in RNAzolRT (Molecular Research Center, Cincinnati, OH) and then purified by RNeasy MinElute column according to manufacturer recommendations (Qiagen GmbH, Hilden, Germany). For FFPE samples (OH, 18F, and 3F), total RNA was isolated from two to four 10 µm-thick paraffin sections, which were collected with a Historange or Leica microtome under RNase-free conditions, deparaffinized (Qiagen Deparaffinization Solution, cat. #19093), and digested with proteinase K prior to RNA purification using the Qiagen AllPrep® DNA/RNA kit (Qiagen, cat. #80234), as described in Hester et al. (2016). To assess whether we could improve FFPE RNA quality for sequencing, additional sections from 3F were divided into demodification subgroups (DTAE, DQ, DP, and NoD). Total RNA was isolated from these samples using similar but slightly modified procedures to the protocol used for OH, 18F and 3F groups. DTAE RNA was isolated using the Qiagen AllPrep® DNA/RNA kit; however, after isolation, equal volumes of purified DTAE RNA and 2X TRIS-acetate-EDTA (TAE, final concentration 1X, pH 9.0; Sigma, St. Louis, MO) were combined and incubated for 30 minutes at 70°C. DQ RNA was isolated and purified using the Qiagen AllPrep® DNA/RNA kit according to the manufacturer’s protocol, except the 15-minute 80°C incubation following proteinase K digestion and RNA supernatant transfer was replaced by an incubation for ~18-hour at 55°C with 40 mM NaOH-buffered 2-amino-5-methylphenyl phosphonic acid (organocatalyst, final concentration 20 mM, pH 7.0; Evans Analytical Group, Maryland Heights, MO), which catalyzes the breakage of formaldehyde-induced aminal crosslinks and hemiaminal adducts on nucleic acids (Karmakar et al., 2015). DP RNA isolation was performed using the PureLink™ FFPE Total RNA Isolation Kit (Invitrogen, Carlsbad, CA; 92008, #K1560-02). FFPE sections were placed in paraffin melting buffer, digested in proteinase K, and incubated for ~18 hours at 55°C with 40 mM organocatalyst (final concentration 20 mM, pH 7.0). Following incubation, DP RNA purification proceeded as described in the manufacturer’s protocol. As a control for organocatalyst treatment, FFPE microtome sections for NoD were isolated exactly as for DQ, except that an equal volume of nuclease-free water (Ambion, Waltham, MA; cat. #AM9938) replaced the organocatalyst during the 18-hour incubation at 55°C. The concentration of RNA obtained from all samples was measured using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Qubit fluorometer (ThermoFisher Scientific, Waltham, MA). RNA integrity was evaluated by an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany) prior to sequencing.
Total RNA was converted into cDNA libraries using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Prep Kit (#RS-122-2303, Illumina, San Diego, CA). Briefly, ribosomal RNA (rRNA) was removed from 100 ng of total RNA by hybridization to a biotinylated probe selective for rRNA species, followed by streptavidin bead binding, purification, and fragmentation by heat in the presence of divalent cations. Double-stranded cDNA was generated by removing the RNA template and synthesizing the second strand with dUTP in place of dTTP. A single ‘A’ base was added to the 3’ end to facilitate ligation of sequencing adapters, which contained a single ‘T’ base overhang. Adapter-ligated cDNA was amplified by polymerase chain reaction (PCR) to increase the amount of sequence-ready library. During this amplification the polymerase stalls when it encounters a ‘U’ base, rendering the second strand a poor template. The first strand thus serves as template for amplified sequence, preserving strand information. Final cDNA libraries were analyzed for size distribution and integrity using an Agilent Bioanalyzer (DNA 1000 kit #5067-1504), quantitated by qPCR (KAPA Library Quant Kit #KK4824, KAPA Biosystems, Wilmington, MA), and normalized to 2 nM in preparation for sequencing.Samples were sequenced at EA Genomics (Q2 Solutions, Durham, NC) using the Illumina HiSeq platform

treatment_protocol: Phenobarbital (PB; 99.8% purity, lot number SLBF7347V) from Sigma-Aldrich (St. Louis, MO) was administered at 0 (Con) or 600 ppm via drinking water to 10-11 week-old mice for seven days.

tag: tissue

value: liver

value: 10-11 weeks

tag: Sex

value: male

tag: chemical treatment

value: Phenobarbital

tag: dose

value: 600 ppm

tag: experimental tissue preservation treatment

value: formalin-fixed 3 months and then paraffin-embedded (from frozen liver mixed lobes), 18 hr., 55C, incubation during RNA isolation using Qiagen AllPrep Kit


title: 5d_20B_PB

source_name: formalin-fixed 3 months and then paraffin-embedded (from frozen liver mixed lobes)

tag: age


title: 5d_75C_PB


title: EOGT siRNA D0 2

tag: cell type

value: Patient 2


title: 5d_80B_PB


title: 5d_18B_PB


title: 5d_18D_PB


title: Non Targeting Control D4 2


title: 5d_90C_Con

value: Control

value: 0 ppm


title: EOGT siRNA D4 2


title: Non Targeting Control D0 2


title: 5d_82B_Con


title: EOGT siRNA D0 1

value: Patient 1


title: Non Targeting Control D4 1


title: 5c_80B_PB

value: formalin-fixed 3 months and then paraffin-embedded (from frozen liver mixed lobes), 18 hr., 55C, organocatalyst incubation during RNA isolation using Invitrogen PureLink kit


title: 5d_21C_Con


title: 5d_8C_Con


title: Non Targeting Control D0 1

value: Endometrial stromal cells


title: 5d_8A_Con


title: Naïve rep2

value: Naive T cells sorted from Pmel-mice

value: Cells sorted on Live CD45.1+CD4-CD8+CD25-NK1.1-TCRgd-CD62L+CD44-

value: C57BL/6J pmel-1 Tg. Mice


title: EOGT siRNA D4 1

value: EOGT siRNA

value: decidualized


title: 5c_75C_PB

value: liver


title: 5c_20D_PB

value: 10-11 weeks


title: 5c_18D_PB

value: male


title: 5c_20B_PB

value: Phenobarbital


title: 5c_18B_PB

value: 600 ppm


title: 5c_82B_Con


title: 5c_8D_Con


title: 5c_90C_Con


title: 5c_21C_Con


title: 5c_8A_Con


title: 5b_80B_PB

value: formalin-fixed 3 months and then paraffin-embedded (from frozen liver mixed lobes), 18 hr., 55C, organocatalyst incubation during RNA isolation using Qiagen AllPrep kit


title: 5c_8C_Con


title: 5d_8D_Con

value: formalin-fixed 3 months and then paraffin-embedded (from frozen liver mixed lobes), 18 hr., 55C, incubation during RNA isolation using Qiagen AllPrep Kit


title: 5b_20D_PB


title: 5b_18B_PB


title: 5b_82B_Con

value: Control


title: 5b_21C_Con

value: 0 ppm


title: 5b_90C_Con


title: 5b_18D_PB


title: 5b_20B_PB


title: 5b_8D_Con


title: 5a_20D_PB

value: formalin-fixed 3 months and then paraffin-embedded (from frozen liver mixed lobes), 30 min, 70C, 1X tris-acetate EDTA incubation of isolated RNA


title: 5a_75C_PB


title: 5b_8A_Con


title: 5a_18D_PB


title: 5a_20B_PB


title: 5b_8C_Con


title: 5a_82B_Con


title: 5a_18B_PB


title: 5a_8C_Con


title: 5a_8D_Con


title: 5b_75C_PB


title: 5a_8A_Con


title: 4a_80B_PB

value: formalin-fixed 3 months and then paraffin-embedded (from frozen liver mixed lobes)


title: 5a_21C_Con


title: 4a_20D_PB


title: 4a_18D_PB


title: 4a_82B_Con


title: 5a_80B_PB


title: 4a_90C_Con


title: 4a_20B_PB


title: 4a_21C_Con


title: 4a_8D_Con


title: 4a_8C_Con


title: 5a_90C_Con


title: 4a_8A_Con


title: 3_20D_PB

source_name: 18 hour formalin-fixed, followed by 70% ethanol to 3 month and then paraffin-embedded (from frozen liver mixed lobes)


title: ATAC_Decidualized sample 3

data_processing:
ATAC-seq libraries were sequenced with 100 base pair (bp) paired-ends on a HiSeq 2500 (Illumina), and mapped to the hg19 human genome assembly using bowtie2-2.2.6 and samtools-1.2.0.
Peaks were called on a merged mapped file using MACS-2.1.0, leading to the identification of 202,169 peaks. 185,087 of these peaks were deemed high confidence (q-value < 1  10-4) and were used for further analysis.
To determine differential chromatin opening, HTSeq-0.6.1 was used to assign reads to peaks and DESeq2 was used to identify differential peaks. Peaks were then ranked according to their p-value, taking into account the direction of the fold-change, such that lower rank values represent peaks that open upon decidualization whereas high rank values represent closing regions of chromatin.
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq peak coordinates and change upon decidualization in .XLSX format

growth_protocol: Endometrial biopsies were collected in DMEM-F12 media supplemented with 10 % dextran coated charcoal-stripped FBS (DCC) and processed for primary EnSC culture as described (Brosens 1999).

extract_protocol: ATAC-seq was performed as described (Buenrostro et al 2013), although with some modifications. Briefly, EnSCs were grown in 35 mm diameter tissue culture dishes. Confluent monolayers were washed with cold Dulbecco's Phosphate Buffered Saline (PBS) and then lysed using cold EZ lysis buffer (Sigma-Aldrich, UK). The cells were scraped and then transferred to chilled pre-labelled nuclease-free 1.5 ml micro-centrifuge tubes. Samples were vortexed, left on ice for 5 minutes, then pelleted in a fixed-angle refrigerated benchtop centrifuge. Supernatant was carefully removed and the pellet was washed once in EZ lysis buffer. The nuclear pellet was re-suspended in the transposase reaction mix, containing 25 μl Tagment DNA (TD) Buffer, 5 μl Tagment DNA Enzyme and 20 μl nuclease free water (Nextera DNA sample preparation kit, Illumina, UK).  The transposition reaction was carried out for either 45 or 90 min at 37 °C. Samples were purified using a Zymo DNA Clean and Concentrator-5 Purification kit, according to the manufacturer’s instructions. Briefly, DNA binding buffer was added to the 50 μl sample which was then mixed and transferred to the column. Samples were centrifuged at 17,000 × g for 30 secs at room temperature (RT). Flow-through was discarded and 200 μl DNA wash buffer added, and columns centrifuged as described above. The wash and centrifugation steps were repeated twice. After removing the residual liquid, 23 μl pre-warmed elution buffer was added to the columns. Samples were incubated for 2 min at RT, then centrifuged for 2 min to elute DNA. Following purification, 20 μl sample was added to a 0.2 mL PCR tube containing the following reagents (Nextera DNA sample preparation kit and Nextera index kit, Illumina): 5 μl index 1, 5 μl index 2, 15 μl Master mix (NPM), 5 μl Primer Cocktail (PPC). Amplification was performed in a Veriti 96 Well Thermal Cycler (Applied Biosystems, USA) using the following PCR conditions: 72 °C for 3 min, 98 °C for 30 secs then 15 cycles of 98 °C for 10 secs, 63 °C for 30 secs, 72 °C for 1 min. The libraries were purified using AMPure XP beads according to the Illumina Nextera kit recommended protocol. The amplified libraries were quantified by using Qubit HS DNA Assay on a Qubit 2.0 Fluorometer according to the manufacturer’s instructions. Library sizes were assessed on an Agilent Technologies 2100 Bioanalyzer using the High Sensitivity DNA chip.

treatment_protocol: For decidualization studies, confluent monolayers of human endometrial stromal cells (EnSCs) were incubated overnight at 37 °C with 5 % CO2 in phenol red-free DMEM/F-12 containing 2 % DCC, containing antibiotic/antimycotic and L-glutamine (2 % media). To induce differentiation, cells were treated in 2 % DCC with 0.5 mM 8-bromo-cAMP (Sigma-Aldrich, Poole, UK) and 1 μM medroxyprogesterone acetate (MPA; Sigma-Aldrich, UK) for 4 days. Control cultures were incubated in media supplemented with 2 % DCC. The primary cultures were subjected to ATAC-seq at passage 2.

value: Endometrial stromal cells


title: 3_75C_PB

value: 18 hour formalin-fixed, followed by 70% ethanol to 3 month and then paraffin-embedded (from frozen liver mixed lobes)


title: 3_80B_PB


title: 3_18D_PB


title: 3_90C_Con


title: 3_18B_PB


title: ATAC_Undecidualized sample 2


title: ATAC_Decidualized sample 2


title: ATAC_Decidualized sample 1


title: 3_82B_Con


title: ATAC_Undecidualized sample 1


title: 4a_75C_PB


title: 4a_18B_PB


title: 3_8D_Con


title: HD_mobPB_Filgrastim_2

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

institute: University of Padova

data_processing:
Reads quality was checked using FastQC. Adapter removal and quality trimming was performed using BBDuk (v37.02).
Reads were mapped to the human reference genome (hg38 build) using STAR (v2.5.3a).
Raw gene counts were obtained using the featureCounts function of the Rsubread R package (v1.22.3) and the GENCODE basic gene annotation (GRCh38, Release 25).
The edgeR R package (v3.14) was employed to obtain counts per million (CPM) values.
Genome_build: hg38
Supplementary_files_format_and_content: CPM obtained using edgeR

source_name: healthy donor G-CSF-mobilized CD34+ cells

extract_protocol:
Total RNA was extracted from 0.1-1x10^6 CD34+ cells using RNeasy Micro kit (QIAGEN).
RNA-seq libraries were prepared starting from ~10 ng of total RNA using the Ovation Human FFPE RNA-Seq Multiplex System kit (Nugen) after DNase treatment (HL-dsDNase, ArcticZymes).

tag: disease state

value: healthy

value: peripheral blood

value: CD34+ cells

tag: drug

value: Filgrastim

tag: replicate


title: HD_mobPB_Filgrastim_3


title: HD_mobPB_Filgrastim_1


title: 3_21C_Con

value: liver

tag: strain


title: HD_mobPB_Plerixafor_2

source_name: healthy donor plerixafor-mobilized CD34+ cells

value: Plerixafor


title: 2_75C_PB

source_name: 70% ethanol fixed for 3 months then paraffin-embedded (from frozen liver mixed lobes)

value: 10-11 weeks

value: male


title: 3_8C_Con


title: SCD_BM_2

source_name: SCD patient bone marrow CD34+ cells

value: SCD

value: bone marrow


title: 2_20D_PB

value: Phenobarbital

value: 600 ppm

value: 70% ethanol fixed for 3 months then paraffin-embedded (from frozen liver mixed lobes)


title: 3_20B_PB


title: 2_80B_PB


title: SCD_BM_1


title: 2_20B_PB


title: 2_18D_PB


title: SCD_mobPB_Plerixafor_1

source_name: SCD patient plerixafor-mobilized CD34+ cells


title: 2_18B_PB


title: 2_90C_Con

value: Control

value: 0 ppm


title: SCD_mobPB_Plerixafor_3


title: SCD_mobPB_Plerixafor_2


title: 2_82B_Con


title: 2_8C_Con


title: 3_8A_Con


title: 2_8A_Con


title: 1_80B_PB

source_name: frozen liver (mixed lobes)

value: Flash frozen


title: HD_mobPB_Plerixafor_1


title: F3_012_V4_T0

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Illumina Real Time Analysis software (RTA) 1.18.61 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.9.1. Reads were aligned to human genome build hg19 using STAR aligner (v 2.5.0c).
Raw counts per gene were calculated with featureCounts, v1.4.4 and alignment confirmed by FASTQC (v 0.11.4)
Non protein-coding genes and genes with no assigned counts were removed before normalisation.
Normalisation factors for the scaling of the library were calculated by the 'TMM' method (Edge R, v. 3.12.1). These factors were then applied by the voom function (Limma, v 3.26.9) in a two-step process of normalisation. Firstly, all genes with a mean expression of <0 after the normalisation were removed. Secondly, the raw counts were normalised for the dataset with all low count genes removed.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID

source_name: Whole blood (PAXGENE)

extract_protocol:
Total RNA was extracted using miRNA whole blood purification kit (Qiagen EmbH, Germany) in accordance with the manufacturer’s recommendations.Total RNA was purified and concentrated with a standard ethanol purification protocol .
TruSeq stranded total RNA library prep kit (Illumina) with ribo-zero globin set A and B (Illumina) were used to prepare sequencing libraries according to the manufacturer's recommendations..

value: Whole blood

tag: subject id

tag: condition

tag: test day (visits 1-5

tag: time point (h)


title: 1_20D_PB


title: 1_75C_PB


title: HD_BM_2

source_name: healthy donor bone marrow CD34+ cells

value: healthy


title: HD_BM_1


title: F3_017_V2_T240


title: F3_009_V4_T120


title: F3_021_V2_T360


title: F3_005_V4_T240


title: F3_017_V2_T120


title: F3_021_V2_T240


title: F3_002_V4_T360


title: F3_014_V2_T360


title: 1_18D_PB


title: 2_8D_Con


title: F3_012_V3_T0


title: 1_82B_Con


title: F3_009_V4_T0


title: F3_014_V3_T0


title: 2_21C_Con


title: 1_21C_Con


title: F3_005_V4_T120


title: 1_8C_Con


title: F3_002_V4_T240


title: 1_8D_Con


title: F3_017_V2_T0


title: F3_021_V2_T120


title: F3_014_V2_T240


title: 1_8A_Con


title: MeDIP shKAP1 rep2

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

institute: EPFL

description: replicate 2

data_processing:
Illumina pipeline Casava 1.82
For ChIP-seq: Reads were mapped to the mouse genome (mm9) using Bowtie2 (v2.2.1) in sensitive mode (bowtie2 -p 6 --sensitive-local -x $index -U $reads); For RNA-seq: reads were aligned to the mm9 genome assembly using HISAT 2 v.2.0.1 with default parameters (--rna-strandness R was added when it applied)
For ChIP-seqs: Peaks were called using MACS v1.4 or SICER v1.1 for H3K27me3
For RNA-seq; only reads uniquely mapped (NH:i:1 flag) were selected for further processing
For RNA-seq, read summarization for genes were performed using featureCounts v1.5.1. For ERE, bedtools 2.25 multicov was used. For MeDIP counts on genes, htseq-count 0.6 was used. For all other MeDIP counts, bedtools multicov was used.
Genome_build: mm9
Supplementary_files_format_and_content: Count table: read counts [RNA-seq or ChIP-seq] for each feature of interest – either ensembl gene name or genome coordinates [last column is read counts]. Bed: peaks as called by MACS or SICER peak caller

source_name: MeDIP shKAP1

growth_protocol: Naive murine embryonic stem cells were cultured in N2B27 medium with 1x MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1x penicillin/streptomycin, 25µg/mL Bovine serum albumin, leukaemia inhibitory factor (LIF), and 2i containing 1µM MEK inhibitor  PD 0325901 (Axon 1408) and 3µM GSK3 inhibitor CHIR 99021 (Axon 1386). Cells were grown on 0.1% gelatin-coated plates and split every two days. Cells were transduced, selected with 4μg/mL puromycin and collected after 5 days.

extract_protocol:
Genomic DNA was extracted by lysing the cells (20 mM Tris-HCl pH 8.0, 4mM EDTA, 20mM NaCl, 1% SDS), purification of nucleic acids by phenol-chloroform extraction followed by precipitation with Na Acetate, resuspension in TrisEDTA and RNase A treatment. DNA was sonicated with Covaris (Peak Incident power 140, Duty factor 10%, cycles per burst 200, treatment time 100s) to obtain 200-500bp fragments. Sonicated DNA was then subjected to end repairing, A-tailing and adapter ligation, denatured and immunoprecipitated with antibodies against 5hmC (Active Motif, #39769) overnight at 4°C in IP buffer (100nM Na-Phosphate buffer pH 7.0, 1.4M NaCl, 0.5 % Triton X-100). DNA was purified for library size-selection and amplification.
Single-end libraries were prepared and sequenced in 100bp reads runs according to Illumina instructions. The steps of end repairing, A-tailing and adapter ligation were performed before denaturation and immunoprecipitation while size selection and library amplification were performed after

tag: cell line

value: Embryonic stem cells

value: wild type

tag: antibody

value: 5hmC (Active Motif, #39769)


title: F3_012_V2_T360

tag: tissue


title: F3_009_V3_T0


title: 1_18B_PB

value: liver

tag: Sex


title: F3_002_V4_T120


title: MeDIP shEmpty rep1

description: replicate 1

source_name: MeDIP shEmpty

tag: genotype/variation


title: MeDIP Input shKAP1 rep2

description: replicate 2

source_name: MeDIP Input shKAP1

value: input


title: MeDIP shKAP1 rep1

description: replicate 1


title: MeDIP shEmpty rep2

description: replicate 2


title: F3_017_V5_T0


title: 1_90C_Con

value: 10-11 weeks

tag: chemical treatment

tag: dose


title: MeDIP Input shEmpty rep2

description: replicate 2

source_name: MeDIP Input shEmpty


title: F3_021_V2_T0


title: 1_20B_PB

tag: age

value: male

tag: experimental tissue preservation treatment


title: F3_017_V1_T0

value: Baseline


title: MeDIP Input shKAP1 rep1

description: replicate 1

tag: cell type


title: RNAseq TET KO shEmpty rep2

description: replicate 2

source_name: RNAseq TET KO shEmpty

extract_protocol:
Total RNA was extracted and DNAse-I treated using a spin column-based RNA purification kit (Macherey-Nagel).
Single-end 100bp RNA-seq libraries were prepared using 200ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina).

value: Tet1, Tet2, Tet3 knockout


title: RNAseq TET KO shKAP1 rep1

description: replicate 1

source_name: RNAseq TET KO shKAP1


title: RNAseq TET KO shKAP1 rep2

description: replicate 2


title: F3_009_V2_T360


title: MeDIP Input shEmpty rep1

description: replicate 1


title: F3_014_V2_T120


title: F3_005_V3_T0


title: F3_012_V2_T240


title: RNAseq TET KO shEmpty rep1

description: replicate 1


title: RNAseq WT shKAP1 rep3

description: replicate 3

source_name: RNAseq WT shKAP1


title: F3_005_V4_T0


title: F3_017_V4_T360


title: RNAseq WT shKAP1 rep2

description: replicate 2


title: F3_021_V1_T0


title: F3_014_V2_T0


title: F3_021_V5_T0


title: RNAseq WT shEmpty rep2

description: replicate 2

source_name: RNAseq WT shEmpty


title: RNAseq WT shEmpty rep3

description: replicate 3


title: RNAseq DNMT KO shKAP1 rep3

description: replicate 3

source_name: RNAseq DNMT KO shKAP1

value: Dnmt1, Dnmt3a, Dnmt3b knockout


title: F3_012_V2_T120


title: F3_009_V2_T240


title: F3_005_V2_T360


title: RNAseq DNMT KO shKAP1 rep2

description: replicate 2


title: RNAseq DNMT KO shEmpty rep2

description: replicate 2

source_name: RNAseq DNMT KO shEmpty


title: F3_021_V4_T360


title: RNAseq DNMT KO shEmpty rep1

description: replicate 1


title: F3_017_V4_T240


title: F3_014_V5_T0


title: RNAseq DNMT KO shEmpty rep3

description: replicate 3


title: F3_012_V2_T0


title: F3_002_V4_T0


title: F3_005_V2_T240


title: F3_009_V2_T120


title: F3_002_V2_T360


title: F3_017_V4_T120


title: F3_021_V4_T240


title: RNAseq WT shKAP1 rep1

description: replicate 1


title: F3_012_V5_T0


title: RNAseq WT shEmpty rep1

description: replicate 1


title: F3_012_V1_T0


title: RNAseq DNMT KO shKAP1 rep1

description: replicate 1


title: s80_cherry

city: Boston

first: Ignacio S.

last: Caballero

state: MA

address: 620 Albany St., NEIDL 401V

department: NEIDL/Microbiology

institute: Boston University School of Medicine

data_processing:
Reads were aligned to the human genome (GRCh38) and quantified using the STAR aligner
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts matrix

source_name: CherryPicker Day 27 human Pluripotent Stem Cell-derived airway cells

extract_protocol:
Day 27 hPSC-derived airway spheres were dissociated to single cells and sorted for viability (calcein blue+) and SCGB3A2CherryPicker expression as described above. CherryPicker- cells were stained with CellTracker Green CMFDA (ThermoFisher) and re-sorted for dye uptake into CherryPicker+ sorted cells at a ratio of 1:2. Fluidigm C1 machine and a 96-well C1 integrated fluidics circuit (IFC) were used to capture cells from this preparation. Post-capture, 70 cells were captured (out of 96 possible wells) and each captured cell was identified as CherryPicker+ (CellTracker Green-) or CherryPicker- (CellTracker Green+) for later analysis. These cells were then lysed and RNA was converted to cDNA and amplified according to the detailed Fluidigm protocol (“Using C1 to Generate Single-Cell cDNA Libraries for mRNA Sequencing”, Fluidigm, PN 100-7168).
Cells were barcoded and a sequencing library prepared using the Illumina Nextera XT DNA kit and preparation protocol from Fluidigm. cDNA concentration was evaluated using Quant-iT PicoGreen dsDNA Assay (Life Technologies) on a Tecan Infinite M1000 Microplate Reader. Sequencing was performed on one pooled, barcoded sample with 75 base pair paired-end reads (150 cycles) with 130 million total reads in one lane of a flow cell using an Illumina NextSeq 500.

tag: reporter

value: Cherry


title: F3_005_V2_T120


title: s79_cherry

value: Day 27 human Pluripotent Stem Cell-derived airway cells


title: F3_014_V4_T360


title: F3_002_V3_T0


title: s78_cherry


title: F3_017_V4_T0


title: F3_009_V2_T0


title: s76_cherry


title: F3_014_V1_T0


title: F3_021_V4_T120


title: F3_002_V2_T240


title: s73_green

source_name: CellTracker Green CMFDA Day 27 human Pluripotent Stem Cell-derived airway cells

value: Green


title: F3_012_V4_T360


title: s74_cherry


title: F3_009_V5_T0


title: F3_014_V4_T240


title: s72_green


title: F3_009_V1_T0


title: F3_005_V2_T0


title: s68_cherry


title: s70_cherry


title: s67_green


title: F3_017_V3_T0


title: F3_002_V2_T120


title: s66_cherry


title: s65_cherry


title: F3_021_V4_T0


title: F3_012_V4_T240


title: s63_cherry


title: s71_cherry


title: F3_014_V4_T120


title: s61_cherry


title: s64_cherry


title: s62_cherry


title: F3_002_V2_T0


title: F3_009_V4_T360


title: F3_005_V5_T0


title: s60_cherry


title: F3_017_V2_T360


title: F3_005_V1_T0


title: F3_021_V3_T0


title: F3_014_V4_T0


title: s56_cherry


title: s59_green


title: F3_012_V4_T120


title: s55_cherry


title: F3_009_V4_T240


title: s54_green


title: F3_005_V4_T360


title: s53_cherry


title: F3_002_V5_T0


title: F3_002_V1_T0


title: s51_green


title: s50_green


title: D218_C3_83

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

description:
single cell RNA-seq
processed data file:
D218_QC_Pass_Samples_TPM.txt.gz

data_processing:
FASTQ files were generated by CASAVA (v1.8.2).
Reads were mapped to the human transcriptome using Bowtie 0.12.8 (Langmead et al. 2009).
The gene expected read counts and TPMs were estimated by RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: text file with gene expression values (TPM)

source_name: Human Retina

growth_protocol: hESC WA09 (WiCell) cells were harvested for transfection 2 days post-passaging and resuspended in OptiMEM (Life Technologies) at 5 x 10^6 cells/mL. 500 μl of cells was added to a cuvette containing 30 μg of linearized CRX reporter construct and 10 μg mRNA encoding a pair of zinc finger proteins (5 μg each) specific to CRX (Sigma) in 300 μl PBS.

extract_protocol:
All procedures of cell loading, capture, and library preparations were performed following the Fluidigm user manual and as previously described (Chu et al., 2016).
Full-length, single-cell cDNA libraries were harvested from the C1 chip and diluted to 0.1–0.3 ng/μl, fragmented, and amplified using the Nextera XT DNA Sample Preparation and Index Kits (Illumina). Libraries were multiplexed at 24-48 libraries per lane and single-end reads were sequenced (Illumina HiSeq 2500 system).

treatment_protocol: CRX+/tdTomato OVs and adult retinas were dissociated using papain.

tag: cell source

value: hPSC-derived retina


title: D218_C3_82


title: D218_C3_81


title: s49_cherry


title: s58_cherry


title: s47_cherry


title: s57_green


title: D218_C3_80


title: D218_C3_79


title: s46_green


title: D218_C3_78


title: D218_C3_76


title: s45_cherry


title: D218_C3_77


title: s44_cherry


title: s43_cherry


title: D218_C3_75


title: s42_green


title: D218_C3_74


title: D218_C3_73


title: s41_green


title: s52_cherry


title: s40_green


title: D218_C3_72


title: s39_green


title: s38_green


title: D218_C3_71


title: D218_C3_70


title: s48_cherry


title: s37_green


title: s36_cherry


title: s35_cherry


title: D218_C3_69


title: D218_C3_66


title: D218_C3_67


title: s34_cherry


title: s33_green


title: s32_cherry


title: D218_C3_65


title: s31_cherry


title: D218_C3_64


title: D218_C3_63


title: s30_cherry


title: D218_C3_61


title: s28_cherry


title: s29_cherry


title: s27_green


title: s26_green


title: D218_C3_59


title: D218_C3_58


title: D218_C3_57


title: s25_cherry


title: s24_cherry


title: s22_cherry


title: D218_C3_56


title: D218_C3_55


title: D218_C3_54


title: s21_cherry


title: D218_C3_53


title: s19_cherry


title: D218_C3_52


title: s20_cherry


title: D218_C3_50


title: D218_C3_60


title: D218_C3_49


title: D218_C3_51


title: D218_C3_62


title: s15_green


title: s17_cherry


title: s16_cherry


title: s18_cherry


title: s14_green


title: D218_C3_48


title: D218_C3_47


title: D218_C3_46


title: s13_cherry


title: s12_cherry


title: s11_green


title: D218_C3_45


title: D218_C3_44


title: D218_C3_43


title: D218_C3_42


title: D218_C3_68


title: s8_cherry


title: s9_cherry


title: D218_C3_41


title: s7_cherry


title: D218_C3_40


title: s6_green


title: s5_cherry


title: D218_C3_39


title: s4_green


title: D218_C3_37


title: D218_C3_38


title: s3_cherry


title: D218_C3_36


title: s2_green


title: distal

description: Total RNA

data_processing:
Reads were aligned to the human genome (hg19) and quantified using the STAR aligner via the Cell Ranger Single-Cell Software Suite
Genome_build: hg19
Supplementary_files_format_and_content: raw UMI counts sparse matrix
Supplementary_files_format_and_content: genes file
Supplementary_files_format_and_content: barcodes file (one for each cell)
Supplementary_files_format_and_content: mapping between barcodes (cells) and samples (distal or proximal)

source_name: NKX2-1 GFP + lung progenitors in distal media

extract_protocol:
BU3 NGST was differentiated to NKX2-1GFP+ lung progenitors, and replated to form spheres in airway or alveolar conditions, as described above. Airway and alveolar spheres were passaged on day 29 and day 26, respectively. For passaging, spheres were dissociated with 2 mg/mL dispase for 1 hour at 37°C, then dissociated to single cells with 0.05% Trypsin for 10 minutes at 37°C. Trypsin was stopped by addition of media containing 10% FBS and cells were washed two times with DMEM by spinning at 300xg for 5 minutes at 4°C. Cell pellets were resuspended in growth factor reduced Matrigel at a concentration of 500-1000 cells/μL. Pellets were solidified for 15-30 minutes at 37°C and re-fed with airway or alveolar culture medium, based on initial condition. Cells were further differentiated to day 41 and dissociated for sorting as described previously. DAPI was used for live/dead exclusion. Cells were sorted as described previously for viability (DAPI-) and resuspended in sort buffer at a concentration of 200 to 700 cells/μL.
Single-cell RNA-seq libraries were prepared per the Single Cell 3′ v2 Reagent Kits User Guide (10x Genomics, Pleasanton, California). Cellular suspensions were loaded on a Chromium Controller instrument (10X Genomics) to generate single-cell Gel Bead-In- EMulsions (GEMs). GEM-RT were performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA). After RT, GEMs were harvested and the cDNAs were amplified, cleaned up with SPRIselect Reagent Kit. Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA). Sequencing libraries were loaded on a NextSeq500 (Illumina, San Diego, CA) with a custom sequencing setting (26bp for Read 1 and 98bp for Read 2), to obtain a sequencing depth of ~200K reads per cell.

tag: media

value: distal

value: NKX2-1 GFP + lung progenitors


title: D218_C3_32


title: D218_C3_33


title: D218_C3_34


title: D218_C3_35


title: proximal

description: Total RNA

source_name: NKX2-1 GFP + lung progenitors in proximal media

value: proximal


title: D218_C3_31


title: D218_C3_30


title: s10_cherry


title: D218_C3_28


title: DMSO_K27_D2

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v 1.1.2
Peak calling was performed using MACS v1.4.2 or SICER v1.1
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig

source_name: Natural Killer cell

extract_protocol:
For ChIP-seq, NEBNext Ultra DNA library prep kit for illumina (Cat #:  E7420L) was used to prepare libraries. For ATAC-seq, transposed DNA was amplified using PCR
ChIP and ATAC libraries were prepared for sequencing using standard NEB protocols designed for Illumina sequencing.  Libraries were sequenced on the Illumina Nextseq following the manufacturer's protocols.

value: Natural Killer cell

tag: origin

value: Peripheral blood

tag: treatment

value: DMSO


title: D218_C3_27


title: J4_K27_D1


title: J4_K27_D2


title: DMSO_K27_D1


title: J4_K4_D3


title: D218_C3_25


title: DMSO_K4_D3


title: J4_K4_D1


title: DMSO_K4_D2


title: s1_cherry


title: D218_C3_23


title: DMSO_K4_D1


title: D218_C3_24


title: ATAC_D2_J4


title: D218_C3_21


title: ATAC_D1_DMSO


title: ATAC_D1_J4


title: D218_C3_19


title: ATAC_D2_DMSO


title: D218_C3_29


title: D218_C3_22


title: D218_C3_17


title: J4_K4_D2


title: D218_C3_16


title: D218_C3_15


title: GSK-J4_DONOR_2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat v0.1.6 with the parameters --score-min L,0.0,-0.2
Counts tables were generated using FeatureCounts v1.4.6
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file

molecule: polyA RNA

extract_protocol:
RNA was harvested using Direct-zol Zymo RNA isolation kit (Cat #: R2070). NEBNext Ultra RNA library prep kit for illumina (Cat #:  E7420L) was used to prepare libraries.
RNA libraries were prepared for sequencing using standard NEB protocols designed for Illumina sequencing


title: D218_C3_14


title: GSK-J4_DONOR_3


title: GSK-J4_DONOR_1


title: DMSO_DONOR_3


title: D218_C3_26


title: DMSO_DONOR_2


title: D218_C3_18


title: DMSO_DONOR_1


title: D218_C3_13


title: D218_C3_12


title: D218_C3_10


title: D218_C3_11


title: D218_C3_09


title: D218_C3_20


title: D218_C3_07


title: D218_C3_06


title: D218_C3_05


title: D218_C3_03


title: D218_C3_01


title: D218_C3_02


title: D218_C2_72


title: D218_C2_71


title: D218_C2_70


title: D218_C2_67


title: D218_C2_68


title: D218_C2_69


title: D218_C2_65


title: D218_C2_63


title: D218_C2_58


title: D218_C2_64


title: D218_C2_59


title: D218_C2_62


title: D218_C2_60


title: D218_C3_08


title: D218_C2_57


title: D218_C2_53


title: D218_C2_54


title: D218_C2_56


title: D218_C2_55


title: D218_C2_52


title: D218_C2_50


title: D218_C2_51


title: D218_C2_49


title: D218_C3_04


title: D218_C2_43


title: D218_C2_48


title: D218_C2_46


title: D218_C2_61


title: D218_C2_66


title: D218_C2_41


title: D218_C2_36


title: D218_C2_34


title: D218_C2_40


title: D218_C2_38


title: D218_C2_37


title: D218_C2_39


title: D218_C2_33


title: D218_C2_32


title: D218_C2_30


title: D218_C2_29


title: D218_C2_27


title: D218_C2_31


title: D218_C2_47


title: D218_C2_44


title: D218_C2_25


title: D218_C2_28


title: D218_C2_21


title: D218_C2_22


title: D218_C2_23


title: D218_C2_20


title: D218_C2_19


title: D218_C2_42


title: D218_C2_24


title: D218_C2_17


title: D218_C2_45


title: D218_C2_35


title: D218_C2_15


title: D218_C2_10


title: D218_C2_09


title: D218_C2_12


title: D218_C2_11


title: D218_C2_13


title: D218_C2_26


title: D218_C2_07


title: D218_C2_05


title: D218_C2_06


title: D218_C2_04


title: D218_C2_03


title: D218_C2_02


title: D218_C1_66


title: D218_C2_01


title: D218_C1_65


title: D218_C1_64


title: D218_C1_67


title: D218_C1_63


title: D218_C1_60


title: D218_C2_16


title: D218_C1_57


title: D218_C1_61


title: D218_C1_58


title: D218_C1_62


title: D218_C1_56


title: D218_C1_59


title: D218_C1_55


title: D218_C1_54


title: D218_C1_52


title: D218_C1_51


title: D218_C1_49


title: D218_C2_08


title: D218_C2_14


title: D218_C1_48


title: D218_C1_46


title: D218_C1_45


title: D218_C1_44


title: D218_C2_18


title: D218_C1_43


title: D218_C1_39


title: D218_C1_40


title: D218_C1_41


title: D218_C1_42


title: D218_C1_38


title: D218_C1_36


title: D218_C1_34


title: D218_C1_33


title: D218_C1_32


title: D218_C1_35


title: D218_C1_53


title: D218_C1_30


title: D218_C1_50


title: D218_C1_31


title: D218_C1_27


title: D218_C1_47


title: D218_C1_28


title: D218_C1_26


title: D218_C1_25


title: D218_C1_22


title: D218_C1_21


title: D218_C1_23


title: D218_C1_24


title: D218_C1_20


title: D218_C1_19


title: D218_C1_18


title: D218_C1_17


title: D218_C1_16


title: D218_C1_15


title: D218_C1_14


title: D218_C1_12


title: D218_C1_13


title: D218_C1_11


title: D218_C1_10


title: D218_C1_29


title: D218_C1_02


title: D218_C1_03


title: D218_C1_08


title: D070_R3_52

description:
single cell RNA-seq
processed data file:
D070_QC_Pass_Samples_TPM.txt.gz


title: D218_C1_07


title: D218_C1_05


title: D218_C1_09


title: D218_C1_04


title: D218_C1_06


title: D070_R3_50


title: D218_C1_37


title: D218_C1_01


title: D070_R3_49


title: D070_R3_48


title: D070_R3_47


title: D070_R3_46


title: D070_R3_45


title: D070_R3_43


title: D070_R3_40


title: D070_R3_38


title: D070_R3_42


title: D070_R3_37


title: D070_R3_36


title: D070_R3_35


title: D070_R3_34


title: D070_R3_33


title: D070_R3_51


title: D070_R3_24


title: D070_R3_25


title: D070_R3_30


title: D070_R3_31


title: D070_R3_28


title: D070_R3_32


title: D070_R3_26


title: D070_R3_23


title: D070_R3_16


title: D070_R3_29


title: D070_R3_20


title: D070_R3_19


title: D070_R3_27


title: D070_R3_17


title: D070_R3_22


title: D070_R3_18


title: D070_R3_41


title: D070_R3_44


title: D070_R3_39


title: D070_R3_13


title: D070_R3_11


title: D070_R3_14


title: D070_R3_12


title: D070_R3_10


title: D070_R3_21


title: D070_R3_09


title: D070_R3_06


title: D070_R3_07


title: D070_R3_08


title: D070_R3_03


title: D070_R3_02


title: D070_R3_15


title: D070_R3_05


title: D070_R3_04


title: D070_R2_55


title: D070_R2_56


title: D070_R2_53


title: D070_R2_51


title: D070_R3_01


title: D070_R2_48


title: D070_R2_58


title: D070_R2_57


title: D070_R2_52


title: D070_R2_50


title: D070_R2_54


title: D070_R2_44


title: D070_R2_49


title: D070_R2_47


title: D070_R2_39


title: D070_R2_46


title: D070_R2_37


title: D070_R2_36


title: D070_R2_42


title: D070_R2_45


title: D070_R2_32


title: D070_R2_41


title: D070_R2_38


title: D070_R2_31


title: D070_R2_27


title: D070_R2_30


title: D070_R2_35


title: D070_R2_26


title: D070_R2_33


title: D070_R2_29


title: D070_R2_28


title: D070_R2_40


title: D070_R2_43


title: D070_R2_24


title: D070_R2_25


title: D070_R2_23


title: D070_R2_22


title: D070_R2_21


title: D070_R2_15


title: D070_R2_14


title: D070_R2_16


title: D070_R2_34


title: D070_R2_12


title: D070_R2_20


title: D070_R2_19


title: D070_R2_11


title: D070_R2_17


title: D070_R2_18


title: D070_R2_04


title: D070_R2_07


title: D070_R2_08


title: D070_R2_10


title: D070_R2_13


title: D070_R2_09


title: D070_R2_02


title: D070_R2_03


title: D070_R2_01


title: D070_R1_068


title: D070_R1_071


title: D070_R1_065


title: D070_R1_064


title: D070_R2_06


title: D070_R1_072


title: D070_R1_066


title: D070_R1_070


title: D070_R1_063


title: D070_R1_069


title: D070_R1_067


title: D070_R1_062


title: D070_R1_060


title: D070_R1_061


title: D070_R1_059


title: D070_R1_054


title: D070_R1_049


title: D070_R1_058


title: D070_R1_047


title: D070_R1_057


title: D070_R2_05


title: D070_R1_056


title: D070_R1_053


title: D070_R1_055


title: D070_R1_051


title: D070_R1_050


title: D070_R1_048


title: D070_R1_046


title: D070_R1_042


title: D070_R1_040


title: D070_R1_037


title: D070_R1_034


title: D070_R1_035


title: D070_R1_033


title: D070_R1_045


title: D070_R1_030


title: D070_R1_039


title: D070_R1_041


title: D070_R1_052


title: D070_R1_032


title: D070_R1_031


title: D070_R1_029


title: D070_R1_036


title: D070_R1_027


title: D070_R1_028


title: D070_R1_026


title: D070_R1_023


title: D070_R1_025


title: D070_R1_044


title: D070_R1_022


title: D070_R1_024


title: D070_R1_043


title: D070_R1_038


title: D070_R1_020


title: D070_R1_017


title: D070_R1_016


title: D070_R1_021


title: D070_R1_019


title: D070_R1_018


title: D070_R1_015


title: D070_R1_014


title: D070_R1_013


title: D070_R1_012


title: D070_R1_011


title: D070_R1_010


title: D070_R1_008


title: D070_R1_007


title: D070_R1_009


title: D070_R1_005


title: D070_R1_004


title: D070_R1_006


title: D070_R1_002


title: Adult_64Y_C3_045

description:
single cell RNA-seq
processed data file:
Adult_QC_Pass_Samples_TPM.txt.gz

value: Adult

value: retina


title: Adult_64Y_C3_047


title: D070_R1_001


title: Adult_64Y_C3_046


title: Adult_64Y_C3_042


title: Adult_64Y_C3_044


title: Adult_64Y_C3_043