title: Primate fetal hepatic response to maternal obesity [mnr_miRNA_seq_71]

first: Sobha

last: Puppala

state: TX

department: Genetics

institute: Texas Biomedical Research Institute

description:
miRNA
MO 5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, reads less than 18 bp were discarded, and reads were mapped to hg18 whole genome using miRDeep2 mapper.pl with parameters -j -k TGGAATTCTCGGGTGCCAAGG -l 18 -q
Detection and quantification of known human miRbase 18 and novel miRNA species was performed using miRDeep2.pl
Raw read counts were normalized to reads per million (RPM)
Genome_build: hg18
Supplementary_files_format_and_content: Excel file with raw and normalized expression values and statistics. FASTA files with the hairpin and mature miRNA sequences for novel miRNAs are available on the series record.

organism: Papio hamadryas

source_name: Baboon fetal liver_obese mother

extract_protocol:
Qiagen miRNeasy Mini Kit according to manufacturer's protocol
Illumina Truseq Small RNA Sample Prep Kit according to manufacturer's protocol; 12 multiplexed samples pooled per lane with cBot v2 and GAIIX Truseq v5 36 SR flowcell

tag: gender

tag: condition

value: obese mother

value: fetal liver

tag: developmental stage

value: near term fetus (0.9 gestation)


title: PkcdRed-4

status: Public on Dec 26 2018

type: SRA

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

library_source: transcriptomic

data_processing:
Bascalling performed using RTA 1.18.64.0
The strand specific reads were screened for ribosomal RNA by aligning with BWA (0.7.12) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were subjected to single-end transcript abundance quantification with Kallisto (0.43.0) with an estimated fragment length of 200 and standard deviation of 20. Transcript sequences are derived via UCSC refFlat (downloaded on 2015_02_20) and the mm10 genome.
Genome_build: mm10
Supplementary_files_format_and_content: Standard output file of Kallisto (abundance.txt) as tab separated text files

molecule: polyA RNA

organism: Mus musculus

source_name: CEA (both sides) punched out of acute brain slice (mouse 4)

growth_protocol: PKCδ::Cre or SST::Cre mice were crossed to Cre-dependent Rosa::td-Tomato lines, and the offspring used for neural population sequencing.

extract_protocol:
Mice were decapitated, brains extracted on ice and 1mm thick brain section cut in ice-cold Hibernate A Low Fluorescence solution (BrainBits). The central amygdala was extracted using biopsy punchers (1mm diameter; Integra Miltex) and enzymatically dissociated (Papain Dissociation System, Worthington Biochem). Approximately 1000 td-Tomato+ cells were retrieved with subsequent FACS sorting.
Libraries were prepared with the SMARTer® smRNA-Seq Kit for Illumina® (Clontech, 78100 Saint-Germain-en-Laye, France) and submitted to deep sequencing on a HiSeq 2500 system (Illumina, San Diego, USA).

tag: strain/genotype

value: PKC delta-type::Cre (mmrrc #11559) X Rosa::loxP-STOP-loxP-td-Tomato (Jackson #007905)

tag: age

value: 18-week old

tag: Sex

value: male

tag: tissue

value: central amygdala


title: CON_1

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

country: USA

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b.
Gene count measurements were obtained using HTSeq-count.
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contains the read counts of the gene using htseq-count.

molecule: total RNA

organism: Homo sapiens

source_name: MDA-MB-231, control siRNA

growth_protocol: Human breast cancer cell line MDA-MB-231 was purchased from American Type Culture Collection (ATCC) and cultured in standard growth medium according to their guidelines. The cell lines were authenticated annually by using PCR for short tandem repeats.

extract_protocol:
Qiagen miRNeasy kit following manufacturer's protocol.
Total RNA samples about 1-2 g were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was barcoded and then pooled for cluster generation and sequencing run with 100bp single-end (SE) sequencing protocol.

treatment_protocol: METTL14-siRNA (siRNA ID: SASI_Hs01_00179440, Sigma_Aldrich, St. Louis, MO) and transfection by using ThermoFisher Lipofectamine RNAi MAX following manufacturer's protocol.

tag: cell line

tag: cell type

value: human breast cancer cell line

tag: treatment

value: Scrambled siRNA


title: PkcdRed-3

source_name: CEA (both sides) punched out of acute brain slice (mouse 3)


title: Primate fetal hepatic response to maternal obesity [mnr_miRNA_seq_68]

description:
miRNA
MO 2

value: female


title: SUM1315_DN_Rep2

city: Philadelphia

first: Rumela

last: Chakrabarti

state: PA

address: 380 S University Ave, 411 Hill Pavilion

department: Department of Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

data_processing:
Reads were mapped to the Homo Sapiens genome (GRCH37 build) with TopHat2 (v2.1.1),using Bowtie2 (v2.2.6) as the underlying aligner.
Reads aligning to the Ensembl GRCH37 build were quantified with featureCounts (v1.5.0) and subsequently converted Transcripts per Million (TPM) values location.
Genome_build: GRCH37
Supplementary_files_format_and_content: TPM

extract_protocol:
Total RNA was isolated from the cell lines using the Invitrogen RNA extraction kit in accordance with the manufacturer’s instructions.
RNA-Sequencing libraries were prepared using the Kapa Stranded mRNA-Seq Kit Illumina Librabry Prep Kit, multiplexed and sequenced on the Illumina NextSeq 500.

tag: shRNA


title: HCC1806RR_Vec_Rep1

value: Vector


title: Primate fetal hepatic response to maternal obesity [mnr_miRNA_seq_67]

description:
miRNA
MO 1


title: HCC1806RR_Vec_Rep2


title: Primate fetal hepatic response to maternal obesity [mnr_miRNA_seq_60]

description:
miRNA
CON 6

source_name: Baboon fetal liver_control mother

value: control mother


title: Primate fetal hepatic response to maternal obesity [mnr_miRNA_seq_56]

description:
miRNA
CON 2


title: Primate fetal hepatic response to maternal obesity [mnr_miRNA_seq_55]

description:
miRNA
CON 1


title: Primate fetal hepatic response to maternal obesity [mnr_miRNA_seq_58]

description:
miRNA
CON 4


title: Primate fetal hepatic response to maternal obesity [mnr_miRNA_seq_57]

description:
miRNA
CON 3


title: siCPSF73 (rep 2)

city: Oxford

first: Nicholas

last: Proudfoot

address: South Parks Road

country: United Kingdom

institute: Sir William Dunn School of Pathology,  University of Oxford

description: Chromatin RNA

data_processing:
RNA-sequencing reads were trimmed using Cutadapt and then mapped to the human reference genome with Tophat 2.0.13.
Aligned reads were processed to only include properly paired, properly mapped reads with no more than 2 mismatches using SAMtools.
Data were scaled to library size (genomeCoverageBed) using Bedtools.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig file containing read densities from RNA-seq experiments.

source_name: cervix

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, and 2 mM L-glutamine, at 37°C in a humidified incubator (5% CO2).

extract_protocol:
Approximately 3x106 cells were resuspended in 500 µL of ice-cold RLB buffer, (10 mM Tris-Hcl, pH 7.5, 140 mM NaCl, 0.5% NP40, 1.5 mM MgCl2), and lysed by adding an equal volume of RLB buffer with 24% (m/v)  sucrose. Nuclei were collected by centrifugation (14,000 x g) at 4°C for 10 min. Isolated nuclei were resuspended in 120 µl of NUN1 buffer, (20 mM Tri-HCl, pH 7.9, 75mM NaCl, 0.5 mM EDTA, 50% Glycerol, 0.125 mM PMSF, 1mM DTT), followed by addition of 1.2 ml NUN2 buffer, (20 mM HEPES-KOH pH 7.6, 7.5mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M urea, 1 % NP40, 1 mM DTT). Nuclei were incubated for 15 minute on ice with mixing by vortexing for 5 seconds every 5 min. Chromatin pellets were precipitated by centrifugation (14,000 x g) at 4°C for 10 min and then resuspended in 200 ml HSB buffer, (10 mM Tris-HCl, pH 7.5, 500 mM NaCl, 10 mM MgCl2), in presence of  4 U TURBO DNase (Ambion) and incubated at 37°C for 20 minutes. Followed a 20 minutes proteinase K treatment (Roche) at 37°C, chromatin RNA (chrRNA) was phenol-chloroform extracted and ethanol precipitated. RNA was resuspended in 200 µL of 1x TURBO DNAse buffer in presence of 4 U TURBO DNase and incubated at 37°C for 30 minutes. The entire procedure of extraction, precipitation and DNase treatment was repeated twice. RNA was then extracted and precipitated again, prior to solubilisation in 75 µL of RNase free water.   Prior to RNA libraries preparation, rRNAs were depleted using Ribo-Zero Magnetic kit (Illumina) from 2.5 µg of ChrRNA.
Libraries were prepared starting from chromatin RNA using the NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB) following the manufacturer’s instructions

treatment_protocol: About 50 % confluent HeLa cells were transfected with a SMARTpool of siRNA for HSE or CPSF73 (GE Dharmacon), or with a negative control siRNA (Luciferase), using the Lipofectamine™ RNAiMAX transfection reagent (Invitrogen) following the manufacturer’s instructions. Cells were transfected with a final concentration of 10 nM siRNA and knockdown efficiency was assessed 48 hours post transfection by western blot analysis. Transfected HeLa cells were synchronized using the double thymidine block method

value: HeLa

value: epithelial

tag: sirna treatment

value: 48h siCPSF73 (Dharmacon)

tag: chemical treatment

value: Double thymidine block

tag: cell cycle stage

value: Early S-phase


title: siCPSF73 (rep 1)

description: Chromatin RNA


title: siHSE (rep 2)

description: Chromatin RNA

value: 48h siHSE (Dharmacon)


title: siHSE (rep 1)

description: Chromatin RNA


title: Primate fetal hepatic response to maternal obesity [mnr_miRNA_seq_70]

description:
miRNA
MO 4

value: obese mother

value: fetal liver


title: Primate fetal hepatic response to maternal obesity [mnr_miRNA_seq_69]

description:
miRNA
MO 3

value: near term fetus (0.9 gestation)


title: siLuc (rep 2)

description: Chromatin RNA

value: 48h siLuciferase (Sigma-Aldrich)


title: siLuc (rep 1)

description: Chromatin RNA


title: ZT21 LDR

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California Irvine

description: ZT21 LDR

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads in sff format were converted from into fastq format using sequence processing kit seq_crumbs (https://bioinf.comav.upv.es/seq_crumbs/) and the adapters and low quality reads were clipped. Reads were then subjected to quality control using FastQCv0.10 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) with passing score threshold Q >30.
Prior to assembly, majority of ribosomal RNA (rRNA) sequences were eliminated using the short sequence alignment algorithm Bowtie 2 (version 2.0.2). Initial assembly was done using rna-STAR and used the latest zebra finch (Taeniopygia guttata) genome (taeGut build 3.2.4). Then, T. guttata genome guided de novo transcript assembly and FPKM quantification were done using Cufflinks (v2.2.1)
Finally, we annotated the draft assembly using BLASTX with e-value ≤ E-10 with zebra finch protein database as the reference, which is an accessible analytical tool and is a phylogenetically closer Passeriformes species (Fudikar et al., 2016). Genes with FPKM > 0.1 in 80% of samples were considered as “expressed” and were used for all downstream analyses
Genome_build: taeGut build 3.2.4
Supplementary_files_format_and_content: tab-delimited text files include Normalized log2 FPKM values for each Sample.

organism: Emberiza melanocephala

source_name: Liver

extract_protocol:
The total RNA was extracted from liver using Trizol Plus RNA Purification Kit and included DNase treatment with Ambion RNase-Free DNase Set and column cleanup with Purlink RNA Mini Kit (Invitrogen), as per manufacturers’ recommended protocol. Ribogreen assay (Invitrogen, xxxx) determined the sample’s RNA concentration and RNA Integrity Number (RIN; Schroeder: 2006ga) on the Agilent 2100 Bioanalyzer. 1μg of total RNA was used to generate poly-A selected mRNAs, which were isolated using oligo-dT attached magnetic beads, and the complimentary DNA (cDNA, 150 – 500 bp with mean size of 250 bp) libraries were generated with TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA). The quantified (Quant-iT PicoGreen assay; Life Technologies) and validated (Agilent 2200 TapeStation system) libraries were sequenced as 100-base single-end reads on the Illumina HiSeq 2500 at the Salk Institute (San Diego, La Jolla, CA).
TruSeq mRNA Sample preparation kit, v2, Illumina

value: Liver

tag: state

value: LDR

tag: time-point


title: ZT1 LDR

description: ZT1 LDR


title: ZT9 LDR

description: ZT9 LDR


title: ZT17 LDR

description: ZT17 LDR


title: Primate fetal hepatic response to maternal obesity [mnr_miRNA_seq_59]

description:
miRNA
CON 5

value: male


title: ZT13 LDR

description: ZT13 LDR


title: ZT21 LDM

description: ZT21 LDM

value: LDM


title: ZT9 LDM

description: ZT9 LDM


title: right colon primary tumor 4_NM

status: Public on Dec 25 2018

city: Shanghai

first: DA

last: FU

state: Shanghai

address: Middle 301 Yanchang Road

country: China

institute: Shanghai Tenth People's Hospital

data_processing:
Illumina Casava1.82 software used for basecalling.
Clean reads were mapped to reference Homo sapiens transcriptome sequences from the UCSC website (hg19) using Bowtie2 and Tophat 2.0.1 software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads per kilobase per million (RPKM) for each gene

source_name: right colon

growth_protocol: CRC patients

extract_protocol:
RNA was prepared with QIAGEN ALLPrep DNA/RNA Micro Kit (Qiagen, CA,US)
The mRNA libraries were separately generated from total RNA and constructed according to the standard Illumina mRNA library preparation (Illumina Inc, USA). Sequencing was done on the Illumina Nextseq 500 platform according to the manufacturer’s instructions
Illumina Nextseq 500 platform according to the manufacturer’s instructions.

treatment_protocol: clinical samples

tag: age (yr)

tag: staging

value: right colon primary tumor

tag: disease state

value: colorectal cancer patient


title: ZT1 LDM

description: ZT1 LDM


title: right colon primary tumor 6_NM

tag: gender


title: right colon primary tumor 5_NM


title: ZT5 LDM

description: ZT5 LDM


title: ZT17 LDM

description: ZT17 LDM


title: liver metastasis 3_LM

source_name: liver

value: liver metastasis


title: ZT13 LDM

description: ZT13 LDM


title: right colon primary tumor 2_PN


title: right colon primary tumor 2_MT


title: right colon primary tumor 3_PN


title: liver metastasis 2_LM


title: right colon primary tumor 3_MT


title: right colon primary tumor 1_MT

value: female


title: right colon adjacent normal 1_PN

value: right colon adjacent normal


title: Untreated C

city: New York

first: Dafna

last: Bar-Sagi

state: NY

address: 550 First Avenue, SML 206

department: Biochemistry and Molecular Phamacology

institute: NYU Langone Medical Center

description: Untreated

data_processing:
To generate differential expression values, sequencing results were demultiplexed and converted to FASTQ format using Illumina Bcl2FastQ software
Paired-end reads were aligned to the mouse genome (build mm10/ GRCm38) using the splice-aware STAR aligner
PCR duplicates were removed using the Picard toolkit
The HTSeq package was utilized to generate counts for each gene based on how many aligned reads overlap its exons.
These counts were then normalized and used to test for differential expression using negative binomial generalized linear models implemented by the DESeq2 R package
P values were corrected for multiple hypothesis testing using the Benjamini-Hochberg method
Genome_build: mm10/ GRCm38
Supplementary_files_format_and_content: One file contains normalized counts for each sample and a second contains average fold changes for each gene between the untreated and tgfb groups with associated p values

source_name: Pancreas

extract_protocol:
RNA was isolated using an RNeasy mini kit (QIAGEN; Venlo, Netherlands). Genomic DNA was then removed using an RNase-free DNase kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genetic background

value: KC (Pdx1-cre;LSL-KRASG12D) mouse


title: Untreated B

description: Untreated


title: TGF-b B

description: Exposed to human recombinant TGF-b1 (500 pg/mL) for 48 hours and then cultured for an additional 4 weeks


title: TGF-b C


title: TGF-b A


title: WT-1 Adenoma

city: Munich

first: Markus

last: Kaller

address: Thalkirchner Strasse 36

department: Institute of Pathology

country: Germany

institute: Ludwig-Maximilians-University Munich

data_processing:
alignment: CLC Genomics Workbench (QIAGEN) using default settings
expression levels: CLC Genomics Workbench (QIAGEN) using default settings
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts (RPKM) for each gene

source_name: Adenoma

extract_protocol:
Adenomas were isolated from small intestine, flash frozen into liquid nitrogen, and RNA was harvested using RNeasy  Mini Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: ApcMin/+; AP4fl/fl

tag: strain

tag: age

value: 16 weeks


title: KO-3 Small intestinal organoid

source_name: Small intestinal organoid

extract_protocol:
Crypts were isolated from small intestine, grown in matrigel in crypt culture medium including all needed growth factors. 7 days after conditional knockout of AP4 by 4-OHT treatment, RNA was harvested using RNeasy  Mini Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Vil-Cre-ERT2; AP4deltaIEC

value: mouse:20 weeks / 7 days after 4-OHT treatment


title: KO-3 Adenoma

value: ApcMin/+; AP4deltaIEC


title: WT-2 Adenoma


title: KO-1 Adenoma


title: KO-2 Adenoma


title: WT-1 Small intestinal organoid


title: WT-3 Adenoma


title: ZT5 LDR

description: ZT5 LDR

tag: tissue


title: Control rep2

city: Heraklion, Crete

first: KONSTANTINA

last: CHANOUMIDOU

address: Nikolaou Plastira 100

department: Institute of Molecular Biology and Biotechnology (IMBB)

country: Greece

institute: Foundation for research and technology - HELLAS (FORTH)

data_processing:
Basecalling performed with the Ion torrent platform.
For base quality purposes, raw reads were trimmed with Trimmomatic. In brief, reads that were 30nt long or less were cut out. The rest were trimmed at their 5' end by 30 bases. Reads that were longer than 200nts were further truncated by trimming their 3' end. Overall quality control of the raw reads was checked with FASTQC.
Quantification of reads was performed with FeatureCounts. The counting was performed on the level of exons and all the exons of a gene were attributed to a single meta-transcript.
Differential gene expression analysis was conducted with the aid of an R package, Deseq2. LogFCs and p-values were calculated for each gene with the aid of a negative binomial distribution model.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data include two tsv (tab separated values) files. The Total of genes.tsv file contains the total of genes that were expressed in both conditions along with the log2FC values and the p-values. Positive log2FC values indicate genes overexpressed in KD Grg5 ESCs. The normalized mean counts, for both conditions, of each gene are also included together with a normalized value to allow between-genes comparison (Average normalized mean counts divided by the effective length of each gene. The effective length was provided by FeatureCounts).  The Filtered genes.tsv file presents the differentially expressed genes with the cutoff of absolute log2FV values ≥0.65 and p-values≤0.05.

source_name: CGR8 Embryonic stem cells

growth_protocol: Silencing of Grg5 was established using a Grg5 specific shRNA-Plko.1 lentiviral vector. As control an empty Plko.1 lentiviral vector was used. Embryonic stem cells were infected with the lentiviruses and pools of infected cells were selected based on puromycin resistance. The silencing efficiency was validated in both mRNA and protein level. Cells were cultured in the presence of LIF to maintain pluripotency, they were expanded and used for RNA-Seq analysis.

extract_protocol:
Total RNA was extracted from cells using the TRIzol reagent (Invitrogen) according to the manufacturer's instructions. The integrity of the extracted RNA was assesed with Bioanalyzer.
RNA  libraries were prepared for sequencing using standard Ion Torrent protocols. Ion Total RNA-Seq Kit v2 for Whole Transcriptome Libraries (Catalog numbers 4475936,4479789) was used with 100ng of poly(A)RNA for the construction of sequencing libraries.Poly(a)RNA was purified from 1ug of Total RNA using Ambion's Dynabeads mRNA DIRECT Micro Kit (Catalog Number 61021).

tag: cell line

tag: passages

value: 6 and 7

tag: background strain

tag: knockdown

value: control


title: 50131: PCI-13 Wildtype

city: Houston

first: Yu

middle: Leo

last: Lei

address: 1901 East Rd

department: Head and Neck Surgery

institute: The University of Texas M.D. Anderson Cancer Center

data_processing:
 Fastq generation was performed using Illuminas bcl2fastq software version 1.8.4.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Head and Neck Squamous Cell Carcinoma

growth_protocol: Cell lines were maintained in complete DMEM high glucose medium, supplemented with 10% heat-inactivated FBS, penicillin (100U/ml) and streptomycin (100mg/ml). Cells were split when they reached about 80% confluence.

extract_protocol:
Total RNA from parental and immune cell-resistant HNSCC cells was isolated using the RNeasy plus mini kit (Cat. 74134, Qiagen, Germantown, MD).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate immune-resistant HNSCC cells, wildtype PCI-13 cells were repetitively co-cultured with primary human natural killer (NK) cells in the presence of 5µg/ml cetuximab, an EGFR-targeted antibody that activates antibody-dependent cytotoxicity. This dose of cetuximab alone does not show any cytotoxic effects. Dead tumor cells and NK were gently washed off every week, and fresh NK cells were replenished. After HNSCC-NK co-culture was repeated 12 times, we noticed that these HNSCC cells become resistant when challenged with NK cells at different target:effector (T:E) ratios (Figure 1A). We separated CD8+ T-cells from an HLA-matched donor, and generated EGFR-specific CTL. We then incubated the CTLs with HNSCC cells, and found that the NK-resistant tumor cells are also resistant to CD8+ CTL (Figure 1B).

tag: genotype/variation

value: wild type

tag: cell type

value: Squamous Cell Carcinoma Cells

tag: Sex

value: Male

tag: location

value: Oral Cavity

tag: tnm stage

tag: patient age (years)

tag: hpv

value: Negative


title: Grg5 KD rep1


title: 50132: PCI-13 Wildtype


title: 50133: Immune-resistant PCI-13

value: Immune-resistant


title: 50134: Immune-resistant PCI-13


title: jai1_systemic_w2_2

city: Taipei

first: Ming-Jung

last: Liu

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Academia sinica

data_processing:
Adaptor sequences were trimmed from the sequence reads. Adaptor sequences is for TrueSeq-3.
The RNA-seq reads to the genome through TopHat with the options (-I 500 -g 1; otherwise with default). Transcript levels of annotated genes were determined and shown as FPKM (Fragments Per Kilobase per Million fragments mapped) calculated with Cufflinks
Genome_build: The reference genome sequences and gene annotation of Solanum lycopersicum (ITAG2.4) and Solanum pennellii (Spenn_v2.0) were retrieved from Sol Genomics Network
Supplementary_files_format_and_content: The "Processed data_RNA-expression" contains the RNA expression (FPKM value) of annotated genes in the samples listed above.

organism: Solanum lycopersicum

source_name: leaves

growth_protocol: Tomato was grown on Jiffy-7 peat pot (Hummert International, Earth City, MO) in a growth chamber under 16 h light (6:00 to 22:00, 200 μmol m-2 s-1)/ 8 h dark cycle at 28ºC.

extract_protocol:
Total RNA from the leaf tissues were extracted with RNeasy Plant Mini Kit (Qiagen, Germantown, MD, USA).
The purified total RNA was used to construct a library for 100-bp paired-end sequencing following the Illumina protocol.
TruSeq Stranded Total RNA Library Prep Kit was used for library preparation.

treatment_protocol: Three to four weeks old plants with 3-4 true leaves were used for wound treatment. For the wound-elicitation, the lower 1st and 2nd true leaves were crushed with a hemostat to cross the midrib of all leaflets.

tag: replicate

value: 2h wounded leaves

tag: cultivar

value: Castlemart

value: jai1 mutant


title: Untreated A

description: Untreated

tag: genetic background

value: KC (Pdx1-cre;LSL-KRASG12D) mouse


title: GFP_3150

city: Beijing

first: Xiaoyu

last: Li

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

description: GFP labeled SSCs were used for transplantation.  Then fluorescent tubes were collected based on light absorption pattern and fluorescent property three months after transplantation when offsprings had been born.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for  low-quality sequence, then mapped to Mus_musculus.GRCm38.83.ensembl genome using TopHat v2.0.12 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Genome_build: Mus_musculus.GRCm38.83.ensembl
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: seminiferous tubule

extract_protocol:
RNA was extracted using RNAprep pure Micro Kit (TIANGEN, Beijing, China) according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We enriched fluorescent SSCs from GFP labeled mice and used these cells for transplantation.  Then we separated different tubules based on light absorption pattern and fluorescent property in the fifth week after transplantation when SSCs had differentiated into spermatocytes and round spermatids, or three months after transplantation when offsprings had been born.

tag: strain

value: KitW/KitWV mice

tag: group

value: sperm

tag: developmental stage

value: complete spermatogenesis


title: jai1_systemic_w0.5_3

tag: tissue

value: 0.5h wounded leaves


title: jai1_systemic_w0.5_2


title: KO-2 Small intestinal organoid

tag: genotype

value: Vil-Cre-ERT2; AP4deltaIEC

tag: age

value: mouse:20 weeks / 7 days after 4-OHT treatment


title: WT-3 Small intestinal organoid


title: jai1_systemic_w0.5_1


title: jai1_systemic_w2_1


title: WT-2 Small intestinal organoid


title: Grg5 KD rep2

tag: cell line

tag: passages

value: 6 and 7

tag: background strain

tag: knockdown


title: GFP_3409


title: GFP_6973


title: jai1_systemic_w2_3

tag: genotype/variation


title: jai1_local_w2_2


title: jai1_local_w2_1


title: GFP_6650

description: GFP labeled SSCs were used for transplantation.  Then fluorescent tubes were collected based on light absorption pattern and fluorescent property in the fifth week after transplantation when SSCs had differentiated into spermatocytes and round spermatids

value: spermatocytes and round spermatids


title: jai1_local_w0.5_2


title: jai1_local_w2_3


title: CON_7271

description: GFP labeled SSCs were used for transplantation.  Then empty tubes without fluorescence were collected based on light absorption pattern and fluorescent property in the fifth week after transplantation

value: EmptAtrans

value: no germ cells


title: jai1_uw_3

value: unwounded leaves


title: jai1_local_w0.5_1


title: CON_6974


title: jai1_local_w0.5_3


title: liver metastasis 1_LM

tag: gender

value: female

tag: age (yr)

tag: staging

value: liver metastasis

tag: disease state

value: colorectal cancer patient


title: jai1_uw_2

tag: replicate

tag: cultivar

value: Castlemart


title: CON_8345

tag: strain


title: Empty_tube_7543

description: seminiferous tubes collected from adult KitW/KitWV mice

tag: group

value: EmptBtrans


title: Empty_tube_7542

tag: developmental stage


title: sl_systemic_w2_3

tag: tissue

value: 2h wounded leaves


title: sl_systemic_w2_1


title: Empty_tube_7541

value: KitW/KitWV mice


title: sl_systemic_w2_2


title: jai1_uw_1

value: jai1 mutant


title: sl_systemic_w0.5_3


title: GFP_8345


title: sl_systemic_w0.5_2


title: GFP_7271


title: sl_local_w2_3


title: sl_local_w0.5_2


title: sl_local_w0.5_1


title: sl_local_w0.5_3


title: sl_systemic_w0.5_1


title: sl_local_w2_2


title: sl_uw_3


title: sl_local_w2_1


title: sl_uw_2


title: KO-1 Small intestinal organoid

tag: genotype


title: Pi sufficient leaf-rep1

city: Hangzhou

first: Houqing

last: Zeng

address: NO.2318, Yuhangtang Rd, Yuhang District

institute: Hangzhou Normal University

data_processing:
The initial base calling and quality filtering of the reads generated with the Illumina analysis pipeline (Fastq format) were performed using a custom Perl script and the default parameters of the Illumina pipeline (http://www.illumina.com). Additional filtering for poor-quality bases was performed using the FASTX-toolkit available in the FastQC software package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)..
To facilitate the read mapping, the Glycine max reference genome (Gmax2.0 version) was indexed by Bowtie2 (http://www.phytozome.net). The read mapping was performed using the Tophat software package.
Tophat allows multiple alignments per read (up to 40) and a maximum of two mismatches when mapping the reads to the reference genome.
The reads were first mapped directly to the genome using indexing and then the unmapped reads were used to identify novel splicing events. The aligned read files were processed by Cufflinks to measure the relative abundances of the transcripts by using the normalized RNA-seq fragement counts.
The estimated gene abundance was measured in terms of the fragments per kilobase of transcript per million mapped reads (FPKM). The differentially expressed genes (DEGs) between the two sets of samples were identified using Cuffdiff. Only the genes with a log2 fold change ≥1 or ≤−1, and a p-value ≤0.05 were considered as significantly DEGs.
Genome_build: the Glycine max reference genome (Gmax2.0 version)
Supplementary_files_format_and_content: one excel file includes FPKM values for each sample

organism: Glycine max

source_name: Leaf

growth_protocol: Soybean (Glycine max var. Williams 82) seeds were soaked in sterilized water for 4 hours, and then incubated at room temperature in the dark between two layers of moistened filter paper. Four days later, seedlings were grown hydroponically in a 10 L tank filled with half-strength modified Hoagland nutrient solution containing 2.5 mM Ca(NO3)2, 2.5 mM KNO3, 0.5 mM KH2PO4, 1.25 mM MgSO4, 10.0 μM Fe-EDTA, 3.4 μM MnSO4, 0.16 μM CuSO4, 0.38 μM ZnSO4, 23.0 μM H3BO3, 0.25 μM Na2MoO4, with pH adjusted to 5.6. Nutrient solution was changed every two days. Plants were grown in a growth chamber with a photoperiod set at 16-h-light/8-h-dark at 26/22 ◦C and light intensity set at 150 μmol m-2 s-1.

extract_protocol:
Roots and leaves of soybean seedlings were separately sampled after treatment of Pi-deficiency for 24 hours, frozen in liquid nitrogen and stored at -80°C until RNA preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 18 days of cultivation, soybean seedlings with the first trifoliate true leaves fully expanded were transferred into Pi-sufficient (500 μM KH2PO4) or Pi-deficient (0 μM KH2PO4, K2SO4 was substituted for KH2PO4) nutrient solutions.

value: Williams 82

value: first trifoliate true leaf

value: 18 days after germination


title: Pi sufficient leaf-rep2


title: Pi deficient leaf-rep2


title: Pi deficient leaf-rep1


title: Liver from C57 mice number 4 with BDL and anti-miR-873 treated

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

description:
NO_BDL_vs_anti873.tsv
miR_Ctrl_vs_anti873.tsv
anti_873_4

data_processing:
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and  their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and  only are retained those  with at least 20 phred quality score.
Reads were mapped to mm10 (Mus musculus) reference genome using Tophat (https://ccb.jhu.edu/software/tophat/index.shtml) toaccount for spliced reads alignments, allowing two  mismatches (n = 2).
Resulting BAM aligment files were used in as input for a Differential Expression Analysis pipeline based on DESeq2 BioconductoR package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: mm10
Supplementary_files_format_and_content: Tables of raw counts, obtained from the SAM files of the samples in each comparative. These tables are in tab separated plain text format.

growth_protocol: Mice were breed and housed at the Animal Facility of CIC bioGUNE under controled conditions according to the animal care international gidelines.

extract_protocol:
RNA was extracted from the livers using TRIZOL reagent (Invitrogen)
TruSeq® RNA Sample Preparation v2 (Illumina Inc.)

tag: age

value: 3 month

tag: treatment

value: anti-miR-873 treated


title: Liver from C57 mice number 2 with BDL and anti-miR-873 treated

description:
NO_BDL_vs_anti873.tsv
miR_Ctrl_vs_anti873.tsv
anti_873_2


title: Liver from C57 mice number 3 with BDL and anti-miR-873 treated

description:
NO_BDL_vs_anti873.tsv
miR_Ctrl_vs_anti873.tsv
anti_873_3


title: Liver from C57 mice number 1 with BDL and anti-miR-873 treated

description:
NO_BDL_vs_anti873.tsv
miR_Ctrl_vs_anti873.tsv
anti_873_1


title: Liver from C57 mice number 3 with BDL and miR Control treated

description:
NO_BDL_vs_miR_Ctrl.tsv
miR_Ctrl_vs_anti873.tsv
miR_Ctrl_3

value: miR Control treated


title: Liver from C57 mice number 3 without BDL

description:
NO_BDL_vs_miR_Ctrl.tsv
NO_BDL_vs_anti873.tsv
NO_BDL_3

value: Non treated


title: Liver from C57 mice number 1 with BDL and miR Control treated

description:
NO_BDL_vs_miR_Ctrl.tsv
miR_Ctrl_vs_anti873.tsv
miR_Ctrl_1


title: Liver from C57 mice number 4 with BDL and miR Control treated

description:
NO_BDL_vs_miR_Ctrl.tsv
miR_Ctrl_vs_anti873.tsv
miR_Ctrl_4


title: Liver from C57 mice number 2 with BDL and miR Control treated

description:
NO_BDL_vs_miR_Ctrl.tsv
miR_Ctrl_vs_anti873.tsv
miR_Ctrl_2


title: Liver from C57 mice number 2 without BDL

description:
NO_BDL_vs_miR_Ctrl.tsv
NO_BDL_vs_anti873.tsv
NO_BDL_2


title: Liver from C57 mice number 5 without BDL

description:
NO_BDL_vs_miR_Ctrl.tsv
NO_BDL_vs_anti873.tsv
NO_BDL_5


title: Liver from C57 mice number 4 without BDL

description:
NO_BDL_vs_miR_Ctrl.tsv
NO_BDL_vs_anti873.tsv
NO_BDL_4


title: Inducible_HIF1a_1

city: Hachioji

first: Yoshihiro

last: Hayashi

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: raw counts with genes in rows and samples in columns

source_name: Inducible_HIF1a_BM HSPCs

extract_protocol:
Bone marrow cells were harvested from WT control and inducible HIF-1a mice. HSPCs were purified using anti-mouse CD117 microBeads and autoMACS Pro Separator. The total RNA was isorated using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: inducible HIF-1a

tag: cell type

value: Bone marrow cells

tag: cell subtype

value: hematopoietic stem and progenitor cells (HSPC)


title: Wild_type_Control_2

source_name: WT_BM HSPCs

tag: genotype/variation

value: wild type


title: sl_uw_1

value: unwounded leaves


title: Inducible_HIF1a_2


title: Ko2Rep3

city: Jinan

first: Guangshan

last: Yao

address: No 27 ShanDa nan road

department: School of life science

institute: Shandong university

data_processing:
Base-calling using Illumina Casava 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence.
Reads were mapped to Aspergillus flavus NRRL 3357 genome
FPKM(expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs  sequenced) were calculated.
Genome_build: Aspergillus flavus NRRL 3357 genome sequences
Supplementary_files_format_and_content: One matrix table in Excel .xlsx format includes unique reads numbers, coverage and FPKM values for each genes. Samples were named according to the names of two raw files.

organism: Aspergillus flavus

source_name: Fungal mycelia

growth_protocol: A. flavus strains were inoculated into YES liquid media and pre-cultured for 24 h, and then transferred into fresh YES  and YEP media for stationary culture at 29°C for 48 h.

extract_protocol:
RNA extraction was performed using a RNA reagent Kit (TRIzol reagent, Biomarker Technologies, China) and following the protocols of the manufacture. The quality and integrity of RNA samples was determined using Nanodrop and Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA), respectively, while the quantity was determined with a Qubit RNA assay kit (Life Invitrogen, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no

value: AfRafA deletion

tag: medium

value: YEP media

tag: culture time

value: 48 h after transferring washed mycelia to the new medium


title: Wild_type_Control_1


title: Ko2Rep2


title: Ko4Rep1

value: AfStuA deletion


title: Ko4Rep2


title: Ko4Rep3


title: WTRep3

value: WT


title: Ko2Rep1


title: Control rep1

tag: cell line

tag: passages

value: 6 and 7

tag: background strain

tag: knockdown

value: control


title: WTRep2

tag: strain


title: WTNRep1


title: sp_systemic_w2_2

organism: Solanum pennellii

tag: replicate

value: 2h wounded leaves

tag: cultivar


title: Liver from C57 mice number 1 without BDL

description:
NO_BDL_vs_miR_Ctrl.tsv
NO_BDL_vs_anti873.tsv
NO_BDL_1

value: 3 month


title: sp_systemic_w0.5_3

tag: tissue

value: 0.5h wounded leaves


title: WTNRep3


title: WTRep1


title: WTNRep2


title: sp_local_w2_3


title: sp_local_w2_2


title: sp_systemic_w0.5_1


title: sp_systemic_w2_1


title: sp_local_w2_1


title: sp_local_w0.5_3


title: sp_local_w0.5_2


title: sp_systemic_w0.5_2


title: sp_uw_2


title: sp_uw_1


title: sp_local_w0.5_1


title: 48h_-LIF+RA_2(ATAC-Seq)

status: Public on Dec 24 2018

city: Stanford

first: Kevin

last: Wang

state: CA

address: 269 Campus Dr, CCSR 2115a

department: Dermatology

institute: Stanford University

description: Illumina HiSeq 2500 for 2 x 50 cycles.

library_source: genomic

data_processing:
RNASeq analysis was performed to mouse genome build mm9 using Tophat. Differential expression analysis for RNASeq was performed using DESeq.
ATACSeq samples were also aligned to mm9 using Bowtie
Genome_build: mm9
Supplementary_files_format_and_content: RNASeq normalized counts
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: embryonic stem cells

growth_protocol: Cells were grown in mESC growth media on 0.2% gelatin-coated 24-well plates.

extract_protocol:
nulei were isolated with NP-40.
Libraries were constructed as described in Buenrostro et al, Nature Methods 2013, (10.1038/nmeth.2688).

treatment_protocol: mESC culture conditions were either unmodified (+LIF), without LIF (-LIF), or without LIF and with 0.5mg/ml purified royalactin (-LIF+RA). Cells were grown in triplicate and harvested at the times indicated.

value: J1 cell line

tag: passage number


title: 48h_-LIF+RA_1(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 12h_-LIF+RA_2(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 12h_-LIF+RA_1(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 48h_-LIF+RA_3(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 12h_-LIF+RA_3(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 24h_-LIF+RA_2(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 24h_-LIF+RA_1(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 24h_-LIF+RA_3(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 6h_-LIF+RA_3(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 6h_-LIF+RA_1(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 6h_-LIF+RA_2(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 48h_-LIF_3(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 24h_-LIF_2(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 48h_-LIF_1(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 48h_-LIF_2(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 24h_-LIF_3(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: sp_systemic_w2_3


title: 12h_-LIF_3(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 12h_-LIF_1(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 24h_-LIF_1(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 6h_-LIF_3(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: sp_uw_3


title: 12h_-LIF_2(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 6h_-LIF_2(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 72h_-LIF+RA_1(ATAC-Seq)

description: Illumina Nextseq 500 High Output for 2 x 75 cycles.


title: 72h_-LIF+RA_2(ATAC-Seq)


title: 72h_+LIF1(ATAC-Seq)


title: 6h_-LIF_1(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: 72h_-LIF_1(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.


title: -LIF+RA_2(RNA-Seq)

description:
ribosomal RNA depleted RNA
Illumina NextSeq 500 High Output for 1 x 75 cycles

extract_protocol:
RNA was extracted using TRIzol and purified on column with the RNeasy Mini Kit (Qiagen).
Ribosomal RNA was depleted with the Ribo-Zero Gold rRNA Removal Kit (Illumina). RNA was lyophilized, suspended in 10 μL of water and fragmented to an average size of 200 base pairs by adding 5μL 1N NaOH (TEKnova) on ice for 30 minutes. The reaction was quenched with 25μL Tris HCl pH 7.0, brought up to 100 μL with water, and purified using the RNeasy Mini Kit (Qiagen). 3’ Phosphorylation, biotin-blocked adapter ligation, reverse transcription, immunoprecipitation, circularization, amplification, and PAGE separation were performed using the FAST-iCLIP library construction method as previously described (Flynn et. al 2014).


title: -LIF_2(RNA-Seq)


title: -LIF+RA_1(RNA-Seq)


title: GH23_MllPTD_Runx1null_Hif1anull

status: Public on Dec 23 2018

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
FASTQ files were processed in AltAnalyze 2.0.9 (Emig et al., 2010; Salomonis et al., 2009; Salomonis et al., 2010) with Kallisto using the Ensembl 72 AltAnalyze database (mm10). To identify differentially expressed genes using default parameters moderated t-test, raw p-value cut-off of 0.05, and an expression cut-off of 2-fold.
For all RNAseq experiments pathways, gene set and ontology enrichment analyses were performed with GO-Elite (Zambon et al., 2012). All heatmaps from AltAnalyze were created using the HOPACH package via a connection to R (Salomonis et al., 2005).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files

source_name: BM HSPCs

extract_protocol:
Bones were flushed and HSPCs were purified using anti-mouse CD117 microBeads and autoMACS Pro Separator (Miltenyi, San Diego, CA). The total RNA was isorated using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cKit+ bone marrow (BM) cells

value: hematopoietic stem and progenitor (HSPC) cells


title: 72h_+LIF2(ATAC-Seq)


title: -LIF_1(RNA-Seq)


title: GH22_MllPTD_Runx1null


title: GH24_MllPTD_Runx1null_Hif1anull


title: GH21_MllPTD_Runx1null


title: CpG sample 1

status: Public on Dec 22 2018

city: Basseterre

first: Felix

last: Toka

address: West Farm

department: Biomedical Sciences

country: Dominica

institute: Ross University School of Veterinary Medicine

description:
CpG sample 1
Cow

data_processing:
The 9 libraries were quantitated by qPCR, pooled in equimolar amounts and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina), which trims off adaptors and removes sequences less than 35 nt
All bases across the reads showed quality scores greater than Q30 (FASTQC v 0.11.2) so quality trimming was not performed
Alignment was done to NCBI's Bos Taurus UMD 3.1.1 genome and Annotation release 105 gene models using STAR (version 2.5.2b) [30] using parameters --sjdbGTFfeatureExon exon, --sjdbGTFtagExonParentGene gene_id and --sjdbOverhang 99.
Read counts per gene were generated using featureCounts3 from the subread package4 (v 1.5.0)
Genome_build: NCBI Bos Taurus UMD 3.1.1
Supplementary_files_format_and_content: tab-delimited text files of raw counts per gene per sample were used directly in edgeR 3.18.1 for statistical analysis and thus are the "normalized" data.

organism: Bos taurus

source_name: bovine macrophage cell line

growth_protocol: BoMac cells were routinely cultured in IMDM medium supplemented with fetal bovine serum, antibiotic-antimycotic, non-essential amino acids, vitamins and beta 2 mercaptoethanol. Cells were subcultured every 3 days.

extract_protocol:
RNA was extracted with the Qiagen miRNeasy kit according to the manufacturers' instructions.
Ribosomal RNA was removed with the Ribozero Human/mouse/rat kit (Illumina). Strand-specific single-end libraries were prepared using the TruSeq Stranded mRNAseq Sample Prep kit (Illumina).

treatment_protocol: BoMac cells were plated into 6-well plates at least 24 h before treatment. CpG or pI:C was later added at 50 ug/ml and 10 ug/ml, respectively. Cells were then incubated for 6 h and thereafter harvested for RNA isolation.

value: BoMac

tag: Sex

value: female

value: peripheral blood monocyte

value: CpG


title: CpG sample 3

description:
CpG sample 3
Cow

tag: treatment


title: CpG sample 2

description:
CpG sample 2
Cow


title: CPP injected GFP(-) 48 hpi rep3

first: Caghan

last: Kizil

institute: Columbia University Irving Medical Center

data_processing:
The FastQ files from sequencing were aligned to zebrafish genome (GRCz10/danRer10) using bwa (bwa-0.7.12) with default options. The read counts for each gene were calculated using featureCounts and GTF file from ensemble genome browser (Danio_rerio.GRCz10.82.gtf).
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: The processed data files contain read counts calculated by featureCounts. The first 6 columns is information about the gene (ensembl gene id, chromosome, start, end, strand, length), and the remaining columns contain read counts of each gene in the corresponding sample.

organism: Danio rerio

source_name: CPP injected, 48 hpi, zebrafish brain

growth_protocol: Fish were cultured at 28 °C at a 14:10 h light:dark cycle in a recirculating tank system.

extract_protocol:
Zebrafish brains from Tg(her4.1:EGFP) were dissected after control or TR-Aβ42 injections at 48 hpi. Cells were dissociated with Miltenyi Neural Tissue Dissociation Kit as described (Kyritsis et al., 2012). Cells were sorted with BD Aria II FACS machine, RNA was isolated using Norgen Total RNA Purification Kit.
Complete cDNA was synthesized from the obtained mRNA with SmartScribe reverse transcriptase using a universally tailed poly-dT primer and template switching oligo. This was followed by amplification of the purified cDNA with the Advantage 2 DNA Polymerase. After ultrasonic shearing of the amplified cDNA (Covaris S2) samples were subjected to standard Illumina fragment library preparation using the NEBnext chemistries (New England Biolabs). Libraries were purified using XP beads (Beckman Coulter), quantified by qPCR (KAPA Biosysytems) and subjected to Illumina 75bp single-end sequencing on the Illumina HiSeq2000 platform providing on average 31 million reads per sample.

treatment_protocol: Fish brains were injected with CPP or AB-42 peptides.

value: brain

tag: age

value: 6 mpf


title: AB42 injected GFP(-) 48 hpi rep2

source_name: AB42 injected, 48 hpi, zebrafish brain


title: AB42 injected GFP(-) 48 hpi rep3


title: CPP injected GFP(+) 48 hpi rep1


title: CPP injected GFP(-) 48 hpi rep2


title: AB42 injected GFP(-) 48 hpi rep1


title: LFS-1

first: Seungyeul

last: Yoo

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
HUVEC in LFS conditioned media for 16 hours
LFS_1_298

data_processing:
Sequence reads were aligned to human transcript reference (RefSeq Genes, hg19) for the expression analysis at gene levels using TopHat (Trapnell et al., 2009) and HTSeq softwares (Anders et al., 2015). The rawcount of reads aligned to each gene was further normalized by Reads Per Kilobase of transcript per Million (RPKM) as gene expression abundance measurement.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including RPKM values of each gene
Supplementary_files_format_and_content: log2 transformed RPKM

source_name: HUVEC in LFS conditioned media

extract_protocol:
Total RNA (1-3μg/sample) extracted from MSCs or pre-osteoblasts in vitro culture were submitted to Novogene for quality control analysis. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, and double stranded cDNA synthesized using random hexamers
cDNA was synthesized using random hexamers, M-MuLV Reverse Transcriptase (RNase H), and DNA Polymerase I. NEBNext Adaptor with hairpin loop structure were ligated to the cDNA in preparation for hybridization. The library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA)

tag: group

value: Angiogenic tube formation


title: CPP injected GFP(+) 48 hpi rep2


title: LFS-2

description:
HUVEC in LFS conditioned media for 16 hours
LFS_2_318


title: sFRP2OE-3

description:
HUVEC in SFRP2OE conditioned media for 16 hours
sFRP2_3

source_name: HUVEC in SFRP2OE conditioned media


title: CPP injected GFP(-) 48 hpi rep1


title: AB42 injected GFP(+) 48 hpi rep1


title: LFS-3

description:
HUVEC in LFS conditioned media for 16 hours
LFS_3_334


title: AB42 injected GFP(+) 48 hpi rep3


title: AB42 injected GFP(+) 48 hpi rep2


title: sFRP2OE-2

description:
HUVEC in SFRP2OE conditioned media for 16 hours
sFRP2_2


title: pl_C sample 2

description:
pl_C sample 2
Cow

tag: cell type


title: sFRP2OE-1

description:
HUVEC in SFRP2OE conditioned media for 16 hours
sFRP2_1


title: WT-2

description:
HUVEC in WT conditioned media for 16 hours
WT_2

source_name: HUVEC in WT conditioned media

value: No tube formation


title: pl_C sample 3

description:
pl_C sample 3
Cow


title: Control sample 3

description:
Control sample 3
Cow

value: Control


title: CPP injected GFP(+) 48 hpi rep3


title: WT-1

description:
HUVEC in WT conditioned media for 16 hours
WT_1


title: Control sample 2

description:
Control sample 2
Cow


title: Control sample 1

description:
Control sample 1
Cow


title: WT-3

description:
HUVEC in WT conditioned media for 16 hours
WT_3


title: pl_C sample 1

description:
pl_C sample 1
Cow


title: Microglia_H3K4me3_ChIP-seq

status: Public on Dec 21 2018

city: Ikoma

first: Taito

last: Matsuda

institute: Nara Institute of Science and Technology

data_processing:
ChIP-seq was performed with 50-bp single-end sequencing by an Illumina Hiseq 2500. Obtained reads were processed with FASTX tool kit to remove short (<20bp) and low quality (quality score<20) reads, followed by trimming of the adaptor sequence.
Processed reads were aligned to the mouse genome (UCSC mm10) using Bowtie v2.2.4. All redundant reads were removed from further analysis. SAM files were converted to the BAM format using SAMtools (v0.1.19).
Peak calling for ND1 was performed using MACS version 1.4.1 with default parameters and the input library as control.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files indicating alignment of each sample

source_name: Microglial cells

growth_protocol: We prepared primary microglia from mouse cortexies at postnatal day 1. To induce neuronal conversion, primary cultured microglia were infected with ND1-expressing lentivirus constructs together with an M2rtta-expressing lentivirus construct in microglia medium containing polybrene (8 µg/ml). After 16–20 h in medium containing lentivirus, the medium was replaced with iN medium, which consists of Neurobasal Medium (Gibco), B27 (Gibco), BDNF, GDNF, NT3 (10 ng/ml each, Peprotech) and penicillin/streptomycin/fungizone (HyClone). Doxycycline (2 mg/ml) was added only once to this medium to activate expression of the transduced genes. The medium was changed every 2–3 days for the duration of the culture period. Neuronal cultures were prepared from P1 mouse cortex and cultured with neuronal medium (Neurobasal Medium supplemented with B27).

extract_protocol:
Cells grown on 10-cm dishes were fixed with 1% formaldehyde-containing medium for 10 min and were quenched by glycine. Collected samples were then subjected to ChIP assay using anti-H3K4me1 (MBL, MABI0302),  anti-H3K4me3 (MBL, MABI0304), anti-H3K27me3 (MBL, MABI0323), anti-H3K27ac (MBL, MABI0309S) antibodies.
Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina

value: Cortex

value: Microglial cells

value: postnatal day 1

tag: genotype

value: WT

tag: chip antibody

value: anti-H3K4me3 antibody (MBL, MABI0304)


title: Microglia_H3K27ac_ChIP-seq

value: anti-H3K27ac antibody (MBL, MABI0309S)


title: Microglia_H3K27me3_ChIP-seq

value: anti-H3K27me3 antibody (MBL, MABI0323)


title: Input_ChIP-seq


title: iN_H3K4me3_ChIP-seq

source_name: ND1-transduced microglial cells


title: ND1_ChIP-seq

value: anti-FLAG antibody (Sigma, F1804)


title: Microglia_H3K4me1_ChIP-seq

value: anti-H3K4me1 antibody (MBL, MABI0302)


title: Cortical_Neuron_rep1_RNA-seq

data_processing:
RNA-seq was performed with 50-bp single-end sequencing by an Illumina Hiseq 2500. Obtained reads were processed with FASTX tool kit to remove short (<20bp) and low quality (quality score<20) reads, followed by trimming of the adaptor sequence.
Processed reads were mapped to the mouse genome mm10 genome using TopHat/Bowtie2.
Cuffdiff, a program in the Cufflinks software was used for differential gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: TXT files indicating FPKM values of each sample

source_name: Neurons

extract_protocol:
mRNAs were isolated from the cells for the construction of sequencing libraries using Dynabeads mRNA DIRECT Micro Kit (Invitrogen) following the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neurons


title: Microglial_ND1_day7_rep2_RNA-seq

tag: time


title: Microglia_day7_rep2_RNA-seq


title: Cortical_Neuron_rep2_RNA-seq


title: Microglia_day7_rep1_RNA-seq


title: Microglial_ND1_day2_rep2_RNA-seq


title: Neuron_H3K27me3_ChIP-seq


title: Neuron_H3K4me3_ChIP-seq


title: 72h_-LIF_2(ATAC-Seq)

description: Illumina HiSeq 2500 for 2 x 50 cycles.

value: J1 cell line


title: Microglial_ND1_day7_rep1_RNA-seq


title: Microglia_day7_rep3_RNA-seq


title: Cortical_Neuron_rep3_RNA-seq


title: Microglial_ND1_day7_rep3_RNA-seq


title: iN_Bisulfite-seq

data_processing:
Bisulfite-seq was performed with 100-bp single-end sequencing by an Illumina Hiseq 2500. Obtained reads were processed with FASTX tool kit to remove short and low quality reads, followed by trimming of the adaptor sequence.
Processed reads were mapped to the mouse mm10 reference genome using BMap software with default parameter settings.
We utilized WGBS data composed of more than 0.98 billion reads, with 72% of CpG sites in the mouse genome covered by at least five reads.
Genome_build: mm10
Supplementary_files_format_and_content: TXT files indicating methylation levels in CpG sites

growth_protocol: We prepared primary microglia from mouse cortexies at postnatal day 1. To induce neuronal conversion, primary cultured microglia were infected with ND1-expressing lentivirus constructs together with an M2rtta-expressing lentivirus construct in microglia medium containing polybrene (8 µg/ml). After 16–20 h in medium containing lentivirus, the medium was replaced with iN medium, which consists of Neurobasal Medium (Gibco), B27 (Gibco), BDNF, GDNF, NT3 (10 ng/ml each, Peprotech) and penicillin/streptomycin/fungizone (HyClone). Doxycycline (2 mg/ml) was added only once to this medium to activate expression of the transduced genes. The medium was changed every 2–3 days for the duration of the culture period.

extract_protocol:
Genomic DNA isolated from control and ND1-transduced microglia was subjected to bisulfite treatment with the Imprint DNA Modification Kit (Sigma) according to the manufacturer’s instructions.
We adopted a strategy termed post-bisulfite adaptor tagging (PBAT), which provides an unbiased methylome analysis (Miura et al., 2012). The multiplex PBAT method is described in detail on the CREST/IHEC Japan webpage (http://crest-ihec.jp/english/epigenome/index.html).


title: Microglial_ND1_day2_rep1_RNA-seq


title: Microglia_day2_rep2_RNA-seq


title: Microglia_day2_rep3_RNA-seq


title: Microglia_Bisulfite-seq


title: iN_H3K27me3_ChIP-seq


title: Microglial_ND1_day2_rep3_RNA-seq


title: Microglia_day2_rep1_RNA-seq


title: KPCL-PCC_391_GA

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the mm10 genome was performed using the STAR aligner version 2.4.0k using the --outFilterIntronMotifs RemoveNoncanonical parameter
Gene expression was quantified using the HOMER analysis suite and differential gene expression was carried out using the edgeR package v3.6.8. FDR < 0.05 and log2 fold change greater than 0.5
Genome_build: mm10
Supplementary_files_format_and_content: raw counts (text file) and fpkm normalized table (text file)

source_name: pancreatic tumor developed in KrasLSL-G12D;Tp53f/f;Rosa26LSL-Luc;Pdx1-Cre mice treated with gemcitabine and anti-LIF antibody

growth_protocol: primary cells isolated directly from fresh pancreatic tumor without culture in dish

extract_protocol:
Clontech NucleoSpin® RNA II kit per manufacture protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The KrasLSL-G12D;Tp53f/f;Rosa26LSL-Luc;Pdx1-Cre mice at 42~43 days of age were treated with either gemcitabine plus control IgG or gemcitabine plus anti-LIF antibody for five days (50mg/kg BW gemcitabine on day 1 and day4, 25 mg/kg BW control IgG or anti-LIF mAb on day 1,3,5), and whole tumors from each treated mice were individually dissected out on day 6, dissociated into single cell suspension by enzyme digestion, and EpCAM+ pancreatic cancer cells were purified by FACS

value: FVB/NJ

value: pancreas

value: around 48 days of age


title: KPCL-PCC_354_GA


title: KPCL-PCC_310_GA


title: KPCL-PCC_227_GA


title: KPCL-PCC_203_G

source_name: pancreatic tumor developed in KrasLSL-G12D;Tp53f/f;Rosa26LSL-Luc;Pdx1-Cre mice treated with gemcitabine and control IgG


title: MRUnotCD200pCD200R1p mouse 3

city: Rehovot

first: Dan

last: Ben-Avraham

address: Herzl 234

department: G-INCPM

country: Israel

institute: Weizmann Institute of Science

description: Mammary epithelial cells sorted by MRU (CD24medCD49fhigh) not CD200-positive not CD200R1-positive, mouse 3

data_processing:
Illumina adapters, polyA and polyT sequences were trimmed using cutadapt
Redas mapped to GRCm38 genome using STAR 2.4.2a
Counting over genes annotated in Ensembl release 82 using htseq-count (mode: intersection-strict)
Normalization performed using DESeq2
Differential expression statistics performed using DESeq2 with the betaPrior, cooksCutoff and independentFiltering parameters set to False
Genome_build: GRCm38
Supplementary_files_format_and_content: A single Excel file with raw counts of all sample, normalized counts and differential expression statistics

source_name: mammary gland

growth_protocol: 6- to 8-week-old FVB/N virgin females

extract_protocol:
Mouse mammary cells were dissociated from the fourth inguinal mammary glands. Lin- cell suspension was prepared using the EasySep mouse mammary enrichment kit (StemCell Technologies, Vancouver, Canada).  Epithelial cells were resuspended in HF containing Hank’s balanced salt solution (HBSS, Biological Industries) supplemented with 0.1% (v/v) Hepes (Biological Industries) and 2% (v/v) fetal bovine serum (FBS, Biological Industries) at a concentration of 107 cell/ml and incubated for 90 min on ice with fluorescent conjugated antibodies. Cell viability was tested by staining with propidium iodide (PI) (Sigma St. Louis, MO) or BD Horizon Fixable Viability Stain 450 (FVS450, BD Biosciences) according to the manufacturers' protocol. Dispersed mouse mammary cells were sorted using FACSAria II. 1000 cells 9.5µl of RNAsin-containing lysis buffer, incubated for 5 min at room temperature and kept at -80°C.
SMART-Seq V4 Ultra Low Input RNA kit

value: epithelial cell

value: mammary gland

tag: cell markers

value: FVB/N

tag: gender

value: female

value: 6-8 week-old


title: MRUnotCD200pCD200R1p mouse 2

description: Mammary epithelial cells sorted by MRU (CD24medCD49fhigh) not CD200-positive not CD200R1-positive, mouse 2


title: MRUnotCD200pCD200R1p mouse 6

description: Mammary epithelial cells sorted by MRU (CD24medCD49fhigh) not CD200-positive not CD200R1-positive, mouse 6


title: CD200pCD200R1n mouse 2

description: Mammary epithelial cells sorted by not MRU (not CD24medCD49fhigh) CD200 positive CD200R1 negative mouse 2


title: MRUnotCD200pCD200R1p mouse 5

description: Mammary epithelial cells sorted by MRU (CD24medCD49fhigh) not CD200-positive not CD200R1-positive, mouse 5


title: MRUCD200pCD200R1p mouse 6

description: Mammary epithelial cells sorted by MRU (CD24medCD49fhigh) CD200-positive CD200R1-positive, mouse 6


title: KPCL-PCC_343_G


title: CD200pCD200R1n mouse 6

description: Mammary epithelial cells sorted by not MRU (not CD24medCD49fhigh) CD200 positive CD200R1 negative mouse 6


title: KPCL-PCC_345_G


title: CD200pCD200R1n mouse 4

description: Mammary epithelial cells sorted by not MRU (not CD24medCD49fhigh) CD200 positive CD200R1 negative mouse 4


title: MRUCD200pCD200R1p mouse 4

description: Mammary epithelial cells sorted by MRU (CD24medCD49fhigh) CD200-positive CD200R1-positive, mouse 4


title: CD200nCD200R1p mouse 5

description: Mammary epithelial cells sorted by not MRU (not CD24medCD49fhigh) CD200 negative CD200R1 positive, mouse 5


title: MRUnotCD200pCD200R1p mouse 4

description: Mammary epithelial cells sorted by MRU (CD24medCD49fhigh) not CD200-positive not CD200R1-positive, mouse 4


title: CD200pCD200R1n mouse 5

description: Mammary epithelial cells sorted by not MRU (not CD24medCD49fhigh) CD200 positive CD200R1 negative mouse 5


title: MRUCD200pCD200R1p mouse 2

description: Mammary epithelial cells sorted by MRU (CD24medCD49fhigh) CD200-positive CD200R1-positive, mouse 2


title: MRUCD200pCD200R1p mouse 3

description: Mammary epithelial cells sorted by MRU (CD24medCD49fhigh) CD200-positive CD200R1-positive, mouse 3


title: CD200nCD200R1p mouse 4

description: Mammary epithelial cells sorted by not MRU (not CD24medCD49fhigh) CD200 negative CD200R1 positive, mouse 4 (added ~10% of cells from mouse 3)


title: CD200pCD200R1n mouse 3

description: Mammary epithelial cells sorted by not MRU (not CD24medCD49fhigh) CD200 positive CD200R1 negative mouse 3


title: CD200nCD200R1p mouse 3

description: Mammary epithelial cells sorted by not MRU (not CD24medCD49fhigh) CD200 negative CD200R1 positive, mouse 3


title: CD200nCD200R1p mouse 2

description: Mammary epithelial cells sorted by not MRU (not CD24medCD49fhigh) CD200 negative CD200R1 positive, mouse 2


title: KPCL-PCC_393_G


title: MRUCD200pCD200R1p mouse 5

description: Mammary epithelial cells sorted by MRU (CD24medCD49fhigh) CD200-positive CD200R1-positive, mouse 5


title: CD200nCD200R1p mouse 6

description: Mammary epithelial cells sorted by not MRU (not CD24medCD49fhigh) CD200 negative CD200R1 positive, mouse 6


title: IMP1 1

city: Oxford

first: Claus

last: Nerlov

address: WIMM

institute: University of Oxford

data_processing:
Alignment to mm9 tophat2 (2.0.10)
Filtering of non-unique aligments
Read counting with Rsamtools
Genome_build: mm9
Supplementary_files_format_and_content: CSV, read counts

source_name: adult Hematopoietic stem cells

extract_protocol:
LT-HSCs, were FACS sorted from primary recipients, 8 weeks after last PolyIC injection, directly into lysis buffer supplemented with RNase Inhibitor (Clontech). 3 biological replicates were generated from each genotype.
Samples were prepared using the SMARTer™ Ultra Low RNA kit for Illumina Sequencing (Clontech) as previously described (Ramskold et al., 2012).

value: Rosa26 I/+;Mx1-Cre tg/+

tag: Stage

value: 8 weeks after PolyIC injection for the  Imp1 re-expression


title: Control 3

value: Rosa26 +/+;Mx1-Cre tg/+


title: Control 1


title: IMP1 2


title: IMP1 3


title: Control 2


title: hnRNP K RIP 2

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

description: Immunoprecipitated RNAs

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to Rn6 using STAR2.4.0
Count read using HT-seq0.6.1 using Rn6 RefSeq as reference
Normalization (TMM) and differential expression analysis using EdgeR. Genes with 10 counts or more for at least one condition (all 3 reps) were used
Genome_build: Rn6
Supplementary_files_format_and_content: excel file with FPKM, raw and normalized counts for each sample and logFC, pVal and FDR for each comparison

organism: Rattus norvegicus

source_name: hnRNP K RIP, Sciatic nerve

extract_protocol: mRNA-RBP complex was immunoprecipitated from axoplasm using specific antibodies

value: SD

value: Sciatic nerve

tag: rip antibody

value: hnRNP K antibody


title: Input 2

description: input RNAs

source_name: Input, Sciatic nerve

tag: strain


title: Input 1

description: input RNAs


title: hnRNP K RIP 1

description: Immunoprecipitated RNAs


title: BY4730_4

city: New York

data_processing:
Sequence reads were aligned to yeast genome assembly using Tophat. Total 6,932 yeast transcripts were quantified using Cufflinks, and 5,542 of them overlap with transcripts on Yeast Genome 2.0 Arrays from Affymatrix, which was used for generating the yeast F2 time course data.  The 5,542 transcripts were used in further analysis.  Differentially expressed genes were defined by CuffDiff.
Genome_build: Yeast Genome 2.0 Array from Affymetrix
Supplementary_files_format_and_content: tab-delimited text file including FPKM values of each gene for each Sample.

organism: Saccharomyces cerevisiae

source_name: Wild type with Rapamycin treatment

growth_protocol: Yeast was grown in YPD medium to log-phase in shaken flasks at 30°C

extract_protocol:
After culture for 50 minutes, total RNA was extracted the same as above.  All experiments were repeated 3 times on three different days.
Approximately 250 ng of total RNA per sample were used for library construction by the TruSeq RNA Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2500 instrument with 100nt single read setting according to the manufacturer's instructions.

treatment_protocol: For rapamycin treatment, 100nM rapamycin (Cayman Chemical, Ann Arbor, MI) was added to the medium after yeast grew to log-phase.

value: wildtype


title: RRD1_4

source_name: RRD1 KO with Rapamycin treatment

value: RRD1 KO


title: La/SSB RIP 1

description: Immunoprecipitated RNAs

source_name: La/SSB RIP, Sciatic nerve

value: La/SSB antibody


title: BY4730_3

source_name: Wild type without Rapamycin treatment


title: RRD1_5

source_name: RRD1 KO without Rapamycin treatment


title: BY4730_6


title: BY4730_2


title: BY4730_5


title: RRD1_2


title: La/SSB RIP 2

description: Immunoprecipitated RNAs


title: hnRNP K RIP 3

description: Immunoprecipitated RNAs


title: RRD1_1


title: Input 3

description: input RNAs


title: hnRNP H1 RIP 3

description: Immunoprecipitated RNAs

source_name: hnRNP H1 RIP, Sciatic nerve

value: hnRNP H1 antibody


title: hnRNP H1 RIP 2

description: Immunoprecipitated RNAs


title: RRD1_6


title: hnRNP H1 RIP 1

description: Immunoprecipitated RNAs


title: hnRNP F RIP 2

description: Immunoprecipitated RNAs

source_name: hnRNP F RIP, Sciatic nerve

value: hnRNP F antibody


title: hnRNP F RIP 1

description: Immunoprecipitated RNAs


title: FLAG RIP 3

description: Immunoprecipitated RNAs

source_name: FLAG RIP, Sciatic nerve

value: FLAG antibody


title: La/SSB RIP 3

description: Immunoprecipitated RNAs


title: FLAG RIP 2

description: Immunoprecipitated RNAs


title: FLAG RIP 1

description: Immunoprecipitated RNAs


title: RRD1_3


title: hnRNP F RIP 3

description: Immunoprecipitated RNAs


title: BY4730_1


title: Kidney1

status: Public on Dec 20 2018

city: Utrecht

first: Frans

last: Schutgens

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute / UMC Utrecht

description: Primary kidney epithelial cells

data_processing:
Paired-end reads from Illumina sequencing were aligned to the human transcriptome with BWA. RaceID and RACEID2 analysis were performed as described.
Genome_build: hg10
Supplementary_files_format_and_content: coutt files contain UMI barcode normalised abundance counts

source_name: Human kidney tissue

growth_protocol: From cortical kidney tissue, tubular fragments were isolated by collagenase digestion (C9407, Sigma) for 45 minutes at 1 mg/ml. Fragments were seeded in growth factor-reduced Matrigel (Corning) or Basement Membrane Extract (BME - R&D Systems) and cultured in medium (ADMEM / F12 supplemented with 1% penicillin / streptomycin, HEPES, Glutamax, N-acetylcysteine (1 mM, Sigma) and 1.5% B27 supplement (Gibco)), supplemented with 10% Rspo1-conditioned medium or 1% Rspo3-conditioned medium, the latter produced via the r-PEX protein expression platform (U-Protein Express), EGF (50 ng/ml, Peprotech), FGF-10 (100 ng/ml, Preprotech), Rho-kinase inhibitor Y-27632 (10 µM, Abmole) A8301 (5 µM, Tocris Bioscience), primocine (0.1 mg/ml, Invivogen).

extract_protocol:
Samples were prepared according to the Sort-seq method as described previousy.Briefly, Epcam+ primary kidney cells, FACSsorted (Facsjazz, BD) with Alexa-fluor 488 anti-human CD326 (Epcam, clone9C4; Biolegend), and the single cell suspension from passage 4 tubuloids (derived from the same tissue as the Epcam+ primary kidney cells) were single cell sorted into 384 well plates (Biorad) containing 5 µl vapor lock (Qiagen) 100-200 nl of RT primers, dNTPs and synthetic mRNA spike-ins.
Live single cells were selected on the basis of DAPI and forward/side scatter properties. After the sort, plates were spun down and frozen to -80 degrees until further processing.
RNA samples were processed into cDNA libraries as described previously and on the basis of the CEL-seq2 technique. Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and sequenced paired-end at 75 bp read length the Illumina NextSeq. Primary cells and tubuloid cells were processed and sequenced in parallel.

value: wild-type

value: Cortical kidney tissue


title: Org2

description: Kidney organoids

source_name: Human kidney  organoids

value: Cultured kidney organoids


title: A thaliana, RecJ, rep2

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

institute: University of East Anglia

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters and HD signatures, for the HD samples, were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genomes (host and virus), allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: TAIR 10
Supplementary_files_format_and_content: csv, raw abundances

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: the plants were grown in Panasonic Plant Growth Chambers set at 25 and 18°C ( day and night, respectively) with 16 hours of light

extract_protocol:
total RNA was extracted using Tri-reagent while sRNA fraction was purifed using mirVana kit.
Illumina compatible method using high definition (HD) adapters [Sorefan et al 2012, Xu et al 2015]

treatment_protocol: no  treatment

tag: enzyme

value: RecJ


title: A thaliana, RecJ, rep1


title: A thaliana, SS, rep1

value: SS


title: Tbp ZT22

city: Wuhan

first: Xiaodong

last: Li

state: Hubei Province

address: Luojia Hill, Wuchang District

department: College of Life Sciences

institute: Wuhan University

data_processing:
Illumina Genome Analyzer software was used for basecalling. The fastq files are in the Illumina v1.5+ format (i.e. Phred64 quality score).
Sequenced reads were processed by the IlluQC script for quality control. They were then mapped to mm9  genome using bowtie v1.1.2 under -n mode with default settings (the --phred64-quals option was selected), allowing only one mapping location within the genome. The SAM files of alignment results were converted to BAM format, sorted, and duplicates were removed with SAMtools (rmdup -s)
MACS (v1.4.2) was used for peak calling. Tag shifting was fixed at 68 bp for all samples. IgG ChIP-seq was used as the control. MACS results for samples were scaled to that of IgG control. The peaks identified were not further selected by FDR.
Tag pileup was also obtained with the SPP package and traveling ration script in R. A fixed read extension of 136 bp was performed without tag shifting.
Genome_build: mm9
Supplementary_files_format_and_content: wig files containing MACS results of Pol II and Nelf-A ChIP-seq in the mouse liver. Can be viewed in IGV.

source_name: Liver

extract_protocol:
Livers were removed and flash frozen in liquid nitrogen. They were later homogenized in 1% PFA and the nuclei were isolated via sucrose density centrifugation. They were resuspended in SDS buffer and sonicated. The sonicated chromatin (major DNA fragment size ~150-400 bp) was aliquoted and used for ChIP. For Pol II ChIP, rabbit IgG was used as the control. For Nelf-A ChIP, goat IgG was used as the control.
ChIP-seq SE50 libraries were prepared for sequencing using standard Illumina protocols

value: wild type

value: 3-4 month old

value: Liver

tag: timepoint

value: Mouse anti-Tbp (Abcam ab51841)


title: Tbp ZT18

tag: tissue


title: Tbp ZT6


title: A thaliana, SS, rep2


title: Tbp ZT10


title: Tbp ZT2


title: Goat IgG control for Nelf-A

description: chromatin DNA

data_processing:
Illumina Genome Analyzer software was used for basecalling. The fastq files are in the Illumina v1.5+ format (i.e. Phred64 quality score).
Sequenced reads were processed by the IlluQC script for quality control. They were then mapped to mm9  genome using bowtie v1.1.2 under -n mode with default settings (the --phred64-quals option was selected), allowing only one mapping location within the genome. The SAM files of alignment results were converted to BAM format, sorted, and duplicates were removed with SAMtools (rmdup -s).
MACS (v1.4.2, python 2.7.9) was used for peak calling. Tag shifting was fixed at 68 bp for all samples. IgG ChIP-seq was used as the control. MACS results for samples were scaled to that of IgG control. The peaks identified were not further selected by FDR.
Tag pileup was also obtained with the SPP package and traveling ration script in R. A fixed read extension of 136 bp was performed without tag shifting.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files containing MACS results of Pol II and Nelf-A ChIP-seq in the mouse liver. Can be viewed in IGV.

value: Goat IgG (Jackson Immuno Res)


title: Nelf-A ZT22

description: chromatin DNA

value: Goat anti-Nelf-A, A-20 (sc-23599, Santa Cruz)


title: Nelf-A ZT14

description: chromatin DNA


title: Nelf-A ZT6

description: chromatin DNA


title: Nelf-A ZT10

description: chromatin DNA


title: Nelf-A ZT18

description: chromatin DNA


title: Pol II ZT14

description: chromatin DNA

value: Rabbit anti-Pol II, N-20 (sc-899, Santa Cruz)


title: Pol II ZT10

description: chromatin DNA


title: Pol II ZT6

description: chromatin DNA


title: Pol II ZT22

description: chromatin DNA


title: Pol II ZT2

description: chromatin DNA


title: Pol II ZT18

description: chromatin DNA


title: Rabbit IgG control for Pol II

description: chromatin DNA

value: Rabbit IgG (Jackson Immuno Res)


title: Nelf-A ZT2

description: chromatin DNA


title: Org1

description: Kidney organoids

source_name: Human kidney organoids


title: Kidney3

description: Primary kidney epithelial cells


title: Tbp ZT14


title: mouse IgG control for Tbp ChIP-seq

value: Mouse IgG (Jackson Immuno Res)


title: Antibiotic rep3

city: Nanjing

first: Kan

last: Gao

address: No.1 Weigang Road

institute: Nanjing Agricultural University

description: pigs fitted with T cannula in distal ileum

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Genome_build: susScr3
Supplementary_files_format_and_content: RPKM expression data of differential genes

organism: Sus scrofa

growth_protocol: Piglets were housed individually in metabolic cages under a comfortable environment with temperature maintained at 26 ± 2 °C.

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

treatment_protocol: Twelve piglets were randomly assigned to 1 of 2 groups using a randomized complete block design: infused 10 mL solution of saline (0.9% NaCl) through T-cannula in the distal ileum as the control group or infused 10 mL saline with the antibiotic combination (ampicillin, 150 mg/kg/day; gentamicin, 4 mg/kg/day; and metronidazole, 30 mg/kg/day) as the antibiotic group.

value: Duroc x Landrace x Large White

value: post natal day 45

tag: treated with

value: antibiotic combination

value: hypothalamus


title: Antibiotic rep1


title: Antibiotic rep2


title: Control rep4

value: saline (0.9% NaCl) solution


title: Control rep1


title: Control rep2


title: HL3

city: GUANGZHOU

first: Wuqiang

last: Ma

state: GUANGDONG

address: 483 WUSHAN ROAD , TIANHE DISTRICT

department: College of Horticulture

institute: South China Agricultural University

description: Strand-specific RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Fastx toolkit was used for data pre-processing. Original .fastq files were converted to .fasta files using fastq_to_fasta command (fastq_to_fasta -v -r -i INPUT_FILE.fastq -o OUTPUT_FILE.fasta -Q 33);
Adaptor was trimmed using the fastx_clipper (fastx_clipper -a "Adapter_seq" -c -v -i INPUT_FILE.fasta -o OUTPUT_FILE -l 15);  Trimmed read file was collapsed into tag_count file using fastx_collapser (fastx_collapser -i INPUT_FILE -o OUTPUT_FILE);
Collapsed reads were mapped to reference genome by bowtie 1.0(Small RNA) and STAR(ss-RNA-seq)
miRNA annotation, target identification and PHAS annotation were conducted with customized pipelines.
Genome_build: Litchi_genome_edit
Supplementary_files_format_and_content: Trimmed and collapsed read file in a tag_count formate. In the .txt file, each row has two columns. The first column is a small RNA sequence, and the second column the read count of the sequence. The HL2 and HL3 are strand-specific RNAseq data, which are different from small RNA data. It doesn't have adpator sequence and many duplicates. We simply use the raw fastq file for mapping to the reference genome without any further processing (like adapror trimming, reads collapse).

organism: Litchi chinensis

source_name: Flower

growth_protocol: Nine ‘Huaizhi’ litchi trees with similar growth condition, located in an orchard located at ShenZhen, China

extract_protocol:
Total RNA was extracted using Trizol (Ambion) plus Fruit-mate (Takara) method
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A total of six different tissues, including fruit pedicel, fruitlet, leaf, root,  flower,stem, were randomly collected from all directions of the tree, each set of three trees were considered as a biological replicate

value: Flower


title: WH1508007112_1_YG

description: PARE or degradome

source_name: Fruitlet

value: Fruitlet


title: WH1508007114_1_HL

description: PARE or degradome


title: WH1508007113_1_LQ

description: PARE or degradome

source_name: Carpopodium

value: Pedicel


title: HL2

description: Strand-specific RNA-seq


title: LQ1A_6tissues_mix

description: PARE or degradome

value: Equal amounts of RNA from 6 tissues(Pedicel,Flower,Fruitlet,Leaf,Root and shoot)


title: Fruitlet

description: small RNA

source_name: Fruit


title: Root

description: small RNA

source_name: Root

value: Root


title: Stem

description: small RNA

source_name: Stem

value: Stem


title: Flower

description: small RNA


title: Pedicel

description: small RNA


title: lung_wild_jr1435

status: Public on Dec 19 2018

city: Santa Cruz

first: Susan

last: Carpenter

address: 1156 High Street

department: Molecular Cell and Developmental Biology

institute: University of California Santa Cruz

data_processing:
RNAseq 1: the 50x50bp pairedEnd reads were not trimmed
RNAseq 2: reads mapping (by bowtie2) to mouse repeatMasker elements were discarded
RNAseq 3: reads were mapped to mm10 by STAR (2.5.1b), aided by a gtf file based on Gencode VM9basic with 100bp overlap
RNAseq 4: duplicate read mappings of the same start and end position were discarded using samtools rmdup.
RNAseq 5: bam files were converted to mm10 genomic coverage using bedtools genomeCoverageBed
RNAseq 6: the dup-removed coverage was used to extract coverage of all exonic positions for each gene in UCSC KnownGenes for mm10.
RNAseq 7: the exonic coverage (from paired-end 50x50bp reads) for each gene was divided by 100 to get read counts per gene for input to DESeq2
RNAseq 8: DESeq2 was run using the read counts for UCSC KnownGenes, from 3 wild-type replicates against 3 cox2 knockout replicates.
Genome_build: mm10
Supplementary_files_format_and_content: space separated text file of all genes from DESeq2 processing, with header line.

source_name: Wild type lung

growth_protocol: 4 months old WT and lincRNA-COX2 KO mice, male

extract_protocol:
Lungs were isolated after euthanasia by CO2 and cervical neck dissection. The tissue was snap frozen and homogenized in liquid nitrogen and resuspended in Trizol. Total RNA was extracted, quantified (Nanodrop) and the integrity was analyzed by bioanalyzer. The average RIN score of all samples was 9.45 (range: 9.0-10.0)
TruSeq RNA Sample Preparation Kit v2 (Illumina) according to manufacturers instructions with an input of 500 ng total RNA
50 bp  paired end sequencing (Illumina HighSeq2500)

treatment_protocol: No treatment

value: Wild type

value: Lung


title: Leaf

description: small RNA

source_name: Leaf

value: Leaf


title: lung_cox2_jr1436

source_name: lincRNA-Cox2 knockout lung

value: lincRNA-Cox2 KO


title: lung_wild_jr1433


title: lung_cox2_jr1434


title: lung_cox2_jr1438


title: Fibroblast STEN sample 25 from patient 13

city: Amsterdam

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

institute: Academic Medical Center Amsterdam

data_processing:
Sequenced checked for quality using FastQC (v1.10.1) after which reads were mapped to hg19 whole genome using STAR v2.5 at default settings and converted into binary files using SAMtools (v1.2)
Binary files were imported in R (v3.3.2) after which the reads were counted and annotated according to the Ensembl Gene ID using GenomicAlignments (v1.10)
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated text files including raw counts per sample

source_name: patient 13

growth_protocol: After 24 hours of culturing, fibroblast cells were adhered to the culture plates and the RPMI medium was refreshed to wash away debris, dead cells and non-adherent cells. After cells reached a minimum of 80% confluency, they were washed with HBSS (Lonza BioWhittaker, Switzerland) and then detached from the culture plates through a ten-minute trypsin wash (10x diluted in HBSS) at 37°C. The fibroblasts were then first plated in T25 flasks after which samples in later passages were transferred to T75 flasks (VWR, Pennsylvania, USA; Tissue Culture Flasks 25 cm2 & 75 cm2) to allow for further expansion. During passages 1 through 5, cells have been harvested for downstream DNA and RNA analysis. For RNA isolation were stored in RNAlater (Thermo Fisher Scientific, Waltham, Massachusetts, USA) at 4°C overnight after which the samples were transferred to -80°C as per manufacturer’s protocol.

extract_protocol:
RNA was isolated from the fibroblasts using the RNAeasy mini kit (Qiagen)
The NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs) was used for mRNA isolation, cDNA generation and sequencing adapter ligation.  Performed on an Illumina NextSeq500 at a coverage of 10M reads per sample. The preparation and sequencing of the RNA was performed at GenomeScan B.V. in Leiden, the Netherlands.

treatment_protocol: Mucosal samples were thoroughly washed in repeated cycles of ice-cold phosphate buffered saline (PBS) supplemented with 1% penicillin/streptomycin and 40 μg/mlL G418 (PGA). The mucosa was then finely cut and placed in full-grown RMPI 1640 culture medium (Invitrogen) supplemented with 1.5 mg/mL collagenase A (Roche, Germany) and minced using the Gentlemacs Dissociator (Miltenyi Biotec, Leiden, the Netherlands). After 60 minutes of incubation at 37 °C, the Gentlemacs Dissociator was used a second time for further dissociation. Cells were transferred to tubes and washed extensively with PGA after which the cells were plated and cultured at 37°C in RMPI 1640 with 10% FCS, 1% penicillin/streptomycin, 1% L-glutamin, G418 (40 μg/mlL; Lonza, Leusden, the Netherlands) and amphotericin B (0.025 μg/mL; Gibco, Rockford, IL).

value: M

tag: disease state

value: Crohn’s disease

tag: disease stage

value: stenotic

tag: montreal score

tag: passage

tag: sampleID

tag: thiopurine usage

value: No

tag: atnf usage

value: ileal fibroblast


title: Fibroblast STEN sample 26 from patient 14

source_name: patient 14

value: F

tag: age

value: Yes

tag: cell type


title: Fibroblast STEN sample 24 from patient 12

source_name: patient 12

tag: gender


title: Fibroblast INF sample 8 from patient 6

source_name: patient 6

value: inflamed


title: Fibroblast STEN sample 12 from patient 7

source_name: patient 7


title: Fibroblast STEN sample 27 from patient 14


title: Fibroblast INF sample 11 from patient 7


title: Fibroblast INF sample 20 from patient 11

source_name: patient 11


title: lung_wild_jr1437

tag: genotype


title: Fibroblast NINF sample 14 from patient 8

source_name: patient 8

value: non-inflamed


title: Control rep3

value: Duroc x Landrace x Large White

value: post natal day 45

value: saline (0.9% NaCl) solution

value: hypothalamus


title: Fibroblast NINF sample 9 from patient 7


title: Fibroblast NINF sample 16 from patient 9

source_name: patient 9


title: Fibroblast Non_CD sample 18 from patient 10

source_name: patient 10

value: Non_Crohn’s disease


title: Fibroblast Non_CD sample 7 from patient 5

source_name: patient 5


title: Fibroblast NINF sample 1 from patient 1

source_name: patient 1


title: Fibroblast Non_CD sample 4 from patient 3

source_name: patient 3


title: Fibroblast Non_CD sample 30 from patient 15

source_name: patient 15


title: Fibroblast Non_CD sample 28 from patient 15


title: S495KO3Spl

status: Public on Dec 18 2018

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped read pairs (fragments) were retained.
Genewise counts were obtained using featureCounts. Fragments overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped fragments) value of 1 or greater in at least two libraries. The Ig genes, pseudo genes, gene models, genes not on the primary assemblies of the chromosomes, genes not having official symbols and ribosomal RNA genes were also removed from the analysis.
Counts were converted to log2 counts per thousand bases per million fragments (log2 FPKM), quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.1 (adjusted globally) or less and had an expression change of two folds or greater.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file 'Supp_Raw_Counts.txt' includes raw read counts for genes in each library.

source_name: KO_Spleen Rep3

growth_protocol: Treg cells were sorted as CD4+ TCRb+ YFP+ cells from gut or spleen

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

value: spleen

value: Treg

value: Maf-KO (Maffl/fl x Foxp3Cre-YFP)


title: S495KO3Gut

source_name: KO_Gut Rep3

value: gut (colon plus small intestine)


title: S453KO2Spl

source_name: KO_Spleen Rep2


title: S453KO2Gut

source_name: KO_Gut Rep2


title: S433WT3Spl

source_name: WT_Spleen Rep3

value: WT (Foxp3Cre-YFP)


title: S371WT1Spl

source_name: WT_Spleen Rep1


title: S398WT2Spl

source_name: WT_Spleen Rep2


title: S366KO1Spl

source_name: KO_Spleen Rep1


title: S371WT1Gut

source_name: WT_Gut Rep1


title: Fibroblast INF sample 15 from patient 8

value: Crohn’s disease


title: Fibroblast NINF sample 2 from patient 2

source_name: patient 2

value: M

value: No