title: 212: Orbitofrontal (OFC; BA11)


title: 222: Orbitofrontal (OFC; BA11)

status: Public on Aug 12 2017

type: SRA

city: New York

first: Eddie

last: Loh

address: 1425 Madison Avenue

department: Department of Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
FASTQ and FASTX-toolkit were used to examine the sequencing quality and trim reads. Paired-end reads for the human data were aligned to the HG19 and GENCODE 2014 version of the human genome and annotation using TopHat, using the comprehensive gene annotation on the reference chromosome only.
Reads were counted using HTSeq. A gene was considered the union of all its exons in any known isoforms. Any reads that fell in multiple genes were excluded from the analysis. Threshold for filtering out low expressed genes was set to >5 reads in at least 80% of the samples.
Differentially expressed genes (DEGs) between groups of samples were determined using linear models implemented in the ‘limma’ package of Bioconductor.
Genome_build: hg19
Supplementary_files_format_and_content: text file of fpkm matrix

molecule: total RNA

organism: Homo sapiens

source_name: postmortem brain

extract_protocol:
RNA was extracted using Trizol Reagents from human postmortem flash-frozen samples. 2.5ug of RNA for human samples was used, every samples got spike-in ERCC control 1. Libraries were created using the Epicenter (Illumina) Gold Kit with ribosomal depletion
Libraries for RNAseq were created using the Epicenter (Illumina) Gold Kit with a ribosomal depletion.

tag: tissue

value: Orbitofrontal (OFC; BA11)

tag: gender

value: Female

tag: Cause of death

value: Suicide

tag: age

tag: pmi

tag: ph

tag: phenotype

value: MDD

tag: alcool

value: No

tag: drugs

tag: drug type

value: no

tag: medication

value: yes

tag: medication type

value: Lithium

tag: smoking

value: yes(moderate)

tag: rin


title: 201: Orbitofrontal (OFC; BA11)

value: CTRL

value: AD


title: 199: Orbitofrontal (OFC; BA11)

value: Male


title: 198: Orbitofrontal (OFC; BA11)

value: yes (heavy)


title: 189: Orbitofrontal (OFC; BA11)

value: Natural


title: 162: Orbitofrontal (OFC; BA11)

value: Accident


title: 150: Orbitofrontal (OFC; BA11)


title: 124: Orbitofrontal (OFC; BA11)


title: 153: Orbitofrontal (OFC; BA11)


title: 120: Orbitofrontal (OFC; BA11)


title: 129: Orbitofrontal (OFC; BA11)


title: 117: Orbitofrontal (OFC; BA11)


title: 114: Orbitofrontal (OFC; BA11)

value: AP


title: 113: Orbitofrontal (OFC; BA11)


title: 111: Orbitofrontal (OFC; BA11)


title: 105: Orbitofrontal (OFC; BA11)


title: 84: Orbitofrontal (OFC; BA11)


title: Input B

city: Stanford

first: Ashby

last: Morrison

state: CA

address: 371 Serra Mall

department: Biology

institute: Stanford University

description: Barcode: CTTGTA

library_source: genomic

data_processing:
Library strategy: CPD-seq
Sequencing quality assess with FastQC and strand correlation analysis.
AQUAS TF and Histone ChIP-seq pipeline with default parameters was used to map raw reads(BWA), deduplicate aligned reads, perform strand cross correlation, pool replicates, and generate signal tracks with MACS2.
DAK_CPD100vInput.fc.signal.bw was generated by MACS2 using all 4 original raw files.
Genome_build: Human genome Hg19
Supplementary_files_format_and_content: bw

molecule: genomic DNA

source_name: Input, IMR90

growth_protocol: IMR-90 human embryo lung fibroblasts, obtained from the Coriell Institute, were maintained in DMEM/15% FBS and passaged 1:2 every two days

extract_protocol:
Cells were lysed immediately after treatment (<5 seconds) with 1% SDS and DNA was subsequently purified by exhaustive ethanol precipitations.
Libraries were prepared for single-end, single-index sequencing on an Illumina HiSeq platform using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (E6240, New England Biolabs), following manufacturer's instructions. Library samples were barcoded and amplified using NEBNext® Multiplex Oligos for Illumina® [Index Primers Set 1] (E7335, New England Biolabs).

treatment_protocol: 100J/m2 UVC treatments of confluent cells were performed at passage number 10 using a UV Stratalinker 1800.

tag: cell line

tag: cell type

value: Lung fibroblasts (healthy tissue)

tag: passages

tag: ip antibody

tag: treatment

value: Input was prepped for sequencing right after sonication


title: 205: Orbitofrontal (OFC; BA11)

tag: tissue

value: Orbitofrontal (OFC; BA11)

tag: gender

value: Female

tag: Cause of death


title: 100 J/m2 UVC – Replicate A

description: Barcode: ACAGTG

source_name: 100 J/m2 UVC, IMR90

value: Cyclobutane Pyrimidine Dimers (COSMBIO cat#  CAC-NM-DND-001)

value: IP was followed by repair of DNA lesions (both CPDs and 6-4 PPs)


title: 72: Orbitofrontal (OFC; BA11)

value: Suicide

tag: age

tag: pmi

tag: ph

value: MDD

value: No

value: no


title: 68: Orbitofrontal (OFC; BA11)

tag: phenotype

tag: alcool

tag: drugs


title: UUO

city: Beijing

first: Jiazeng

last: Sun

state: None Selected

address: National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China

country: China

data_processing:
Quality control: Raw data of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website  (ftp://ussd-ftp.illumina.com/Rattus_norvegicus/UCSC/rn5/Rattus_norvegicus_UCSC_rn5.tar.gz ) directly. Index of the reference genome was built using Bowtie v2.0.6 and  paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Transcriptome assembly: The mapped reads of each sample were assembled by both Scripture (beta2)  and Cufflinks (v2.1.1) in a reference-based approach. Both  methods use spliced reads to determine exons connectivity, but with two different approaches.  Scripture uses a statistical segmentation model to distinguish expressed loci from  experimental noise and uses spliced reads to assemble expressed segments. It reports all  statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to  simultaneously assemble and quantify the expression level of a minimal set of isoforms that  provides a maximum likelihood explanation of the expression data in a given locus . Scripture was run with default parameters, Cufflinks was run with  ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Coding potential analysis.  CNCI: CNCI (Coding-Non-Coding-Index) (v2) profiles adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. We use CNCI with default parameters.  CPC: CPC (Coding Potential Calculator) (0.9-r2) mainly through assess the extent and quality of the ORF in a transcript and search the sequences with known protein sequence database to clarify the coding and non-coding transcripts. We used the NCBI eukaryotes' protein database and set the e-value ‘1e-10’ in our analysis.  Pfam-scan We translated each transcript in all three possible frames and used Pfam Scan (v1.3) to identify occurrence of any of the known protein family domains documented in the Pfam database (release 27; used both Pfam A and Pfam B). Any transcript with a Pfam hit would be excluded in following steps. Pfam searches use default parameters of -E 0.001 --domE 0.001.  phyloCSF PhyloCSF (phylogenetic codon substitution frequency) (v20121028) examines evolutionary signatures characteristic to alignments of conserved coding regions, such as the high frequencies of synonymous codon substitutions and conservative amino acid substitutions, and the low frequencies of other missense and non-sense substitutions to distinguish protein-coding and non-coding transcripts. We build multi-species genome sequence alignments and run phyloCSF with default parameters. Transcripts predicted with coding potential by either/all of the four tools above were filtered out, and those without coding potential were our candidate set of lncRNAs.
Conservative analysis: Phast (v1.3) is a software package contains much of statistical programs, most used in phylogenetic analysis, and phastCons is a conservation scoring and identificating program of conserved elements. We used phyloFit to compute phylogenetic models for conserved and non-conserved regions among species and then gave the model and HMM transition parameters to phastCons to compute a set of conservation scores of lncRNA and coding genes.
Quantification of gene expression level: Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample. Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Differential expression analysis: Cuffdiff provides statistical routines for determining differential expression in digital transcript  or gene expression data using a model based on the negative binomial distribution. For biological replicates, transcripts or genes with an P-adjust <0.05 were  assigned as differentially expressed. For non-biological replicates, P-adjust < 0.05 and the  absolute value of log2(Fold change) < 1 were set as the threshold for significantly differential  expression.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Rattus norvegicus

source_name: urine

extract_protocol:
Put flash frozen urine sample on dry ice. RNA was harvested using Trizol reagent. RNA was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The experiments use all rats with 8 weeks of age. The rats were divided into two groups, including one undergoing ligation of the right ureter as UUO rat model, the other just under the same surgery but not ligation the ureters as shamed rat model. After 2 weeks, we collected the kidneys and stored in liquid nitrogen for further analysis.

tag: strain

value: Sprague Dawley

value: urine

value: post natal day 56


title: Plasma cells +GSKLSD1 rep3

first: Steven

last: Lipkin

address: 1300 York Avenue

institute: Weill Cornell Medical College

description:
Sample_LSD_PC3
LSD_PC3_GCCAAT

data_processing:
Reads were first trimmed of adapter with Flexbar.
Alignment to the mouse genome (mm10) was performed with STAR aligner.
Only uniquely mapped reads were used for transcript read count.
Raw read counts were input to DESeq2 for gene differential expression calculation.
Data were analyzed by gene set enrichment analysis (GSEA)using best practices and default conditions.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw read count for each Sample

organism: Mus musculus

source_name: Plasma cells

extract_protocol:
Mononuclear cells isolated from splenocytes suspensions were stained and B and plasma cells sorted as B220+ and CD138+, respectively.  Cell pellets were flash-frozen on dry ice, and RNA was harvested using Trizol reagent followed by purification with RNeasy micro columns. 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: GSK-LSD1 0.5 mg/kg x 45 days i.p. in 10-11 week old C57BL/6 male mice

value: Plasma cells

value: GSK-LSD1 0.5 mg/kg x 45 days


title: Plasma cells +GSKLSD1 rep2

description:
Sample_LSD_PC2
LSD_PC2_ACAGTG


title: Input A

description: Barcode: CAGATC


title: WT

institute: Chinese Academy of Medical Sciences & Peking Union Medical College


title: 69: Orbitofrontal (OFC; BA11)

tag: drug type

tag: medication

value: yes

tag: medication type

tag: smoking


title: Plasma cells +GSKLSD1 rep1

description:
Sample_LSD_PC1
LSD_PC1_TGACCA

tag: cell type


title: 128: Orbitofrontal (OFC; BA11)

value: Male

value: CTRL

tag: rin


title: 67: Orbitofrontal (OFC; BA11)

value: anticonvulsivant

value: yes (heavy)


title: 63: Orbitofrontal (OFC; BA11)

value: Orbitofrontal (OFC; BA11)

value: Female


title: 183: Orbitofrontal (OFC; BA11)

value: AD


title: 61: Orbitofrontal (OFC; BA11)

value: Suicide


title: Plasma cells rep3

description:
Sample_ct_PC3
ct_PC3_TTAGGC

tag: treatment

value: PBS 100 μL x 45 days


title: Plasma cells rep2

description:
Sample_ct_PC2
ct_PC2_CGATGT


title: Plasma cells rep1

description:
Sample_ct_PC1
ct_PC1_ATCACG


title: B cells +GSKLSD1 rep3

description:
Sample_LSD_B3
LSD_B3_CTTGTA

source_name: B cells

value: B cells


title: 93: Orbitofrontal (OFC; BA11)

tag: tissue

value: MDD

value: no


title: 51: Orbitofrontal (OFC; BA11)

tag: gender


title: 45: Orbitofrontal (OFC; BA11)

tag: Cause of death


title: B cells +GSKLSD1 rep2

description:
Sample_LSD_B2
LSD_B2_GGCTAC


title: 100 J/m2 UVC – Replicate B

description: Barcode: GCCAAT

tag: cell line

value: Lung fibroblasts (healthy tissue)

tag: passages

tag: ip antibody

value: Cyclobutane Pyrimidine Dimers (COSMBIO cat#  CAC-NM-DND-001)

value: IP was followed by repair of DNA lesions (both CPDs and 6-4 PPs)


title: 74: Orbitofrontal (OFC; BA11)

tag: age

tag: pmi

tag: ph

tag: phenotype


title: B cells +GSKLSD1 rep1

description:
Sample_LSD_B1
LSD_B1_2bis_TAGCTT

tag: strain

value: GSK-LSD1 0.5 mg/kg x 45 days


title: 43: Orbitofrontal (OFC; BA11)

tag: alcool

tag: drugs

value: yes

tag: drug type

value: cannabis

tag: medication


title: B cells rep3

description:
Sample_ct_B3
ct_B3_GATCAG

tag: cell type


title: B cells rep2

description:
Sample_ct_B2
ct_B2_ACTTGA

tag: treatment


title: 40: Orbitofrontal (OFC; BA11)

tag: tissue

value: Male

tag: medication type

tag: smoking

tag: rin


title: B cells rep1

description:
Sample_ct_B1
ct_B1_2bis_CAGATC


title: 28: Orbitofrontal (OFC; BA11)

tag: gender

tag: Cause of death

value: Natural

value: CTRL


title: 32: Orbitofrontal (OFC; BA11)

value: Orbitofrontal (OFC; BA11)

tag: age


title: 20: Orbitofrontal (OFC; BA11)

value: Accident

tag: pmi

value: yes (heavy)


title: 23: Orbitofrontal (OFC; BA11)

value: Suicide

tag: ph


title: 57: Orbitofrontal (OFC; BA11)

tag: phenotype


title: 14: Orbitofrontal (OFC; BA11)


title: 17: Orbitofrontal (OFC; BA11)


title: Flox3YFP-B_G08

city: Cambridge

first: Erin

last: Janssen

state: MA

address: 15 Chalk St

department: Medicine

institute: Boston Children's Hospital

data_processing:
Alignment to mm10 with STAR.
Transcript level per-transcript quantification was performed with Salmon.
Differential expression was called between treatments at the gene level using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited file containing the transcripts per million for each gene in the sample. The first column is the ensembl id and the second one, the tpm value.

source_name: mouse Treg cells

growth_protocol: CD3+CD25+CD39+YFP+ and CD3+CD25+CD39+YFP- Treg cells were isolated by FACS sorting from Foxp3YFP-Cre/+/Dock8flox/flox female mice. Cells were cultured overnight in supplemented RPMI media with 10% fetal calf serum.

extract_protocol:
Cells were frozen in Qiagen RLT buffer.  Frozen cells were then processed used a Qiagen RNeasy Micro Kit according to the manufacturer's instructions.
Smart-Seq2 libraries were generated and sequenced using a Broad Genomics Platform

treatment_protocol: Bead treated samples were cultured overnight with anti-CD3+CD28 beads at a ratio of 1 bead:1 Treg cells.

tag: strain

value: regulatory T cell

tag: genotype

value: WT

value: anti-CD3+CD28 beads


title: Flox1YFP-B_G07


title: Flox4YFPB_G06

value: DOCK8 deficient


title: Flox5YFPB_C07


title: Flox5YFP0_B07

value: unstimulated


title: 56: Orbitofrontal (OFC; BA11)

value: MDD

tag: alcool

value: no

tag: drugs

value: AD


title: Flox4YFP0_F06


title: Flox2YFP0_H05


title: Flox2YFP-B_C08


title: Flox3YFP-0_F08


title: Flox2YFP-0_B08


title: Flox3YFP0_C06


title: FloxYFP0_D01


title: Flox1YFP-0_F07


title: FloxYFP-0_G12


title: Flox1YFP0_E05


title: ChIPseq_Input_tf_NIPBL

first: Nezar

last: Abdennur

address: 77 Massachusetts Ave

institute: MIT

data_processing:
Hi-C. Alignment: Hi-C reads were mapped using bowtie 2.2.8 and the iterative mapping strategy (Imakaev et al, 2011) implemented in the hiclib package. Filtering: PCR duplicates and reads mapped to multiple or zero locations were removed. After binning, low-coverage bins were removed using a maximum allowed median absolute deviation (MAD) filter on log genomic coverage, set to five MADs. To remove the short-range Hi-C artifacts we also filter contacts mapping to the same or adjacent genomic bins (i.e., first two diagonals). Binning: the filtered reads pairs were binned into 20kb and 100kb contact matrices using the cooler library and stored as binary cool HDF5 files. Normalization: the filtered 20kb and 100kb contacts matrices were then normalized using the iterative correction procedure (IC), such that the genome-wide sum of contact probability for each row/column equals 1.0.
ChIP-seq. We processed ChIP-seq data following the steps of the ENCODE pipeline [https://github.com/ENCODE-DCC/chip-seq-pipeline]. Alignment: we used bwa 0.7.12 (program bwa aln with parameters: -q 5 -l 32 -k 2). Filtering: PCR duplicates were marked using picardtools 2.7.1. Unmapped reads, non-primary alignments, and low quality alignments (mapQ < 30) were removed using samtools 1.3. Cross-correlation analysis was performed using phantompeakqualtools. Peaks and signal tracks were generated using MACS2. For Rad21, Smc3 and CTCF ChIP-seq, we followed the same steps with the following variations: reads from pooled mouse hepatocyte chromatin and HEK human chromatin (internal control and calibration) were mapped to the combined mm9 and hg19 assemblies using the bwa mem program. After filtering, reads were divided into those that mapped uniquely to either mm9 or hg19. A database of CTCF motif instances was produced by performing a PWM scan of the canonical mouse CTCF motif against the mm9 genome using the fimo tool from the MEME suite with default parameters. Peak files with motif annotations were generated by intersecting the peak files against the motif database using bedtools 2.26.0.
RNA-seq. We mapped the RNA-seq data to mm9 reference mouse genome assembly and GENCODE vM1 transcriptome using STAR v.2.5.0a and adapted scripts from the ENCODE RNA-Seq pipeline [https://www.encodeproject.org/pipelines/ENCPL002LSE/]. To obtain the tracks of local transcription, we aggregated the uniquely mapped reads into RPKM-normalized bigWig files using the built-in STAR functionality. To find differentially expressed genes, we aggregated the read counts at the gene level using HTSeq with the “union” option and called DE genes with DESeq2. Alignment with STAR v2.5.0.a was done using parameters: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMunmapped Within --outFilterType BySJout --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1. Signal tracks were generated using STAR with parameters: --runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Stranded  --outWigReferencesPrefix chr.
Compartment eigenvectors. The compartment structure of Hi-C maps was detected using a modified procedure from (Imakaev et al, 2012). In short, compartments were quantified as the dominant eigenvector of the observed/expected 20kb and 100kb cis contacts maps upon subtraction of 1.0, as implemented in hiclib.
Domain detection. To identify contact domains, we used a segmentation that divides the genome into domains in such a way as to maximize a global domain scoring function. We used two different scoring functions: one was the corner score function from (Rao et al, 2014) and the other was based on network modularity, which is a metric widely used to detect communities in networks. The implementation of these and related algorithms is provided in the lavaburst package. To robustly call insulating boundaries across different conditions, we exploit the multi-resolution nature of the modularity score and compute the average marginal boundary scores on 20kb WT and ΔNipbl contact matrices sweeping over a range of gamma values to obtain a 1D boundary (i.e., insulation) track. Short intervals representing insulating loci were called by thresholding on the boundary score, and the common and unique loci to each condition were determined by interval intersection.
Genome_build: mm9
Supplementary_files_format_and_content: Cooler HDF5 files (extension .cool) contain contact matrices and were generated using the cooler Python package; ChIP-seq signal track bigWigs were generated using MACS2, in units of SPMR; RNA-seq bigWig files were generated using STAR in units of RPM; Eigenvector text files are fixed step bedGraph-like files covering the whole genome with a column for the eigenvector in each condition (U=WT, T=TAM, N=NIPBL); TAD call text files are BED-like files where each row corresponds to a detected domain; the TAD boundary probabilities file is a bedGraph-like file covering the whole genome at 20kb with columns for the insulation tracks in conditions U=WT and N=NIPBL; The deseq2 CSV file contains estimated transcript abundances and differential expression statistics across the three conditions

source_name: Liver

extract_protocol:
Liver was dissected and the left lateral lobe was prepped for a two-step perfusion adapted from (Li et al 2010 & Goncalves et al 2007): First, the liver was perfused with an EDTA-containing buffer to remove Ca2+ from the tissue in order to weaken the integrity of the desmosomes, which were subsequently digested using a Ca2+ rich buffer containing collagenase. The freed hepatocytes were rinsed through a cell strainer and washed four times with ice-cold Ca2+ rich buffer without collagenase. For each wash, the cells were spun at low centrifugal force (60g for 1min) to enrich intact hepatocytes and reduce non-mesenchymal debris. Part of each sample was fixed with 1% PFA for 10 minutes at room temperature. Fixed and unfixed hepatocytes were aliquoted and frozen in liN2 for later use.
Hi-C: Roughly 100 million fixed hepatocytes per sample were processed according to (Kalhor et al, 2012) using HindIII. TCC libraries were PCR-amplified (12 cycles) and size selected. Equimolar pools of libraries were sequenced; ChIP-seq: Fixed aliquots of hepatocytes were hypotonically lysed and sonicated in 1% SDS/TE. An aliquot of each sample was reverse cross-linked in order to determine chromatin concentration and sonication efficiency. 20μg chromatin per sample was diluted in RIPA and incubated with 1.5μg of either αH3k4me3 antibody (C15410003-50, Diagenode) or αH3K27Ac antibody (ab4729, Abcam) at 4°C, overnight. The antibodies were retrieved with Dynabeads (IgA, Invitrogen) and bound chromatin was washed and eluted. After reverse cross-linking, the amount of ChIPped and input DNA was determined with Qubit (Thermo Fisher).  The libraries were prepared with NEBNext® ChIP-Seq Library Prep Kit for Illumina®. After amplification and size selection with E-Gel® SizeSelect™ (Thermo Fisher) their size-distributions were determined with Bioanalyzer. Equimolar pools of libraries were sequenced with Illumina HiSeq2000 (50bp, single end). RNA-seq: RNA integrity was tested with Bioanalyzer (Agilent RNA Nano Kit) and ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit (Illumina) prior to library preparation.  Strand-specific libraries were prepared with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®. After amplification and size selection with Agencourt AMPure XP beads (Beckmann Coulter) their size-distributions were determined with Bioanalyzer. Equimolar pools of libraries were sequenced with Illumina HiSeq2000 (50bp, single end).

treatment_protocol: Treated 12 week old mice were injected with 1mg Tamoxifen (100μl of 10mg/ml Tamoxifen in corn oil) on 5 consecutive days. After keeping these mice for another 5 days without injection, they were sacrificed and the hepatocytes were harvested.

value: tamoxifen

value: 12 weeks

value: liver

tag: chip antibody


title: ChIPseq_CTCF_TAM

value: CTCF (Millipore 07-729)


title: 9-1434

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilian University

data_processing:
BaseCaller, Illumina bcl2fastq-1.8.4, default parameters
adaptor clipping, read length after clipping must be 20 nt, custom code
clip poly-A sequences, Poly-A reads were clipped if at least 6 poly-A sequences where found and the read length after clipping is > 20 , custom code
tophat-2.0.13, with provided gene annotations (GTF) from BosTau7 reference genome (-G)
Genome_build: BosTau7
Supplementary_files_format_and_content: rlog values produced by DESeq2

organism: Bos taurus

source_name: conceptus tissue

growth_protocol: Not applicable

extract_protocol:
Total RNA was harvested after grinding using Trizol reagent. NuGEN Encore RNA Seq Complete Kit (Cat# 0333 & 0334) was used with 150 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard NuGEN protocol

treatment_protocol: At approximately 65-75 days post-partum (dpp) the estrous cycles of non-lactating (n=12) and lactating (n=13) cows were synchronized with a controlled intravaginal drug-releasing device (CIDR) and one day prior to CIDR removal each animal received a 2 ml i.m. injection of a prostaglandin F2α analogue. Thirty-six hours after CIDR removal, each animal received a 2.5 ml i.m. injection of Receptal (equivelent to 0.012 mg buserelin) to ensure ovulation. On Day 7 following estrus, all cows were palpated rectally to determine the presence of a CL and suitability for embryo transfer. Eleven maiden heifers were synchronized for embryo donation as follows. The estrous cycle was synchronized using an eight day CIDR protocol and a 2 ml i.m. injection of PG one day prior to CIDR removal. On Day 10 following estrus detection (Day 0) each heifer received an i.m. injection of descending concentrations of Folltrophin (Bioniche Animal Health, Ontario, Canada) 12 h apart (2.5 ml, 2.0 ml, 1.0 ml and 0.5 ml) for four days. Animals also received a 2.0 ml i.m. injection of PG with the 6th injection of Folltrophin. All donors were monitored for estrus and were inseminated twice following the AM:PM rule with semen from a proven sire (French Holstein bull [VOLADI MAN FR4947788082]). All donors were non-surgically flushed 7 days after AI to recover embryos. Single grade 1 late morula/early blastocysts were transferred into recipients. As a control, a group of maiden heifers (n=8) were synchronized as above, inseminated to a standing heat and slaughtered on the same day as non-lactating and lactating recipients.

tag: embryo stage

value: day 19

tag: sample processing

value: embryonal disc removed

tag: treatment group

value: heifer


title: 9-2820

value: lactating cow


title: ChIPseq_Smc3_NIPBL

tag: treatment

tag: tissue

value: Smc3 (Abcam ab9263)


title: 9-0913

value: dry cow


title: UUO rep3

description: UUO3_vs_NC3.Differential_analysis_results.xls

source_name: kidney tissue

extract_protocol:
Put flash frozen rat tissue sample on dry ice. RNA was harvested using Trizol reagent. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

value: kidney

value: post natal day 56


title: ChIPseq_Smc3_TAM


title: ChIPseq_CTCF_NIPBL


title: ChIPseq_Rad21_NIPBL

value: Rad21 (Abcam ab992)


title: UUO rep2

description: UUO2_vs_NC2.Differential_analysis_results.xls


title: ChIPseq_Rad21_TAM


title: 7-1551


title: UUO rep1

description: UUO1_vs_NC1.Differential_analysis_results.xls


title: WT rep3


title: 7-2711


title: 3-2724


title: 6-1542


title: WT rep1


title: 3-1515


title: Wt 337

city: St. Louis

first: Michael

last: Rauchman

state: MO

address: 1100 S. Grand Ave.

department: Internal Medicine- Nephrology

institute: Saint Louis University

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using the default settings
Alignment to mus musculus genome mm10 sequence was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
The total sequencing base pair coverage in all exons was summed for all annotated genes in each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics 11:e1005655.
Average expression values of three wild type replicates were compared to the average of three mutant replicates.
Genome_build: mus musculus mm10
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated expressed genes and statistical comparison of expression in wild type kidney to mutant kidney.

source_name: kidney

growth_protocol: In utero mouse kidney growth to E17.

extract_protocol:
Total RNA was isolated from three E17.5 kidneys for each genotype using an RNeasy Mini Kit (Qiagen) with on the column DNAse I treatment.  Polyadenylated mRNA was purified from 4-5 µg total RNA using Dynabeads mRNA Direct (Life Technologies).
Construction of barcoded sequencing libraries from poy(A) selected RNA was performed using the Ion Total RNA-seq v2 kits (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: Fresh kidney tissue harvested.

value: Sall1 wild type

tag: developmental stage


title: Wt 331


title: 3-1507


title: Wt 330


title: ChIPseq_Input_tf_TAM


title: 3-1135


title: 3-0866


title: Mut 336

value: SRM deletion mutant


title: Mut 342


title: 2-2839


title: IgG

city: Stockholm

first: Christos

last: Samakovlis

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences

country: Sweden

institute: Stockholm University

data_processing:
Alignement: Bowtie, with parameters –v 2 –m 1
Peak calling: Quest with the following parameters: bandwidth, 30; region size, 300; ChIP enrichment, 5; ChIP to background enrichment, 2; and ChIP extension enrichment, 2.
Genome_build: dm3
Supplementary_files_format_and_content: bed file with called peaks

organism: Drosophila melanogaster

source_name: 13-16h embryos

growth_protocol: Embryos were aged to 13-16h

extract_protocol:
Embryos were homogenized and fixed in 1.8% formaldehyde at room temperature. After several washes, chromatin in lysis buffer was sonicated to a length range of 0.1kb-0.5kb. For each immunoprecipitation, sheared chromatin was precleared with Gammabind G agarose coated with BSA and incubated with pre-absorbed rabbit anti-Grh antibody, mouse anti-Grh antibody or rabbit IgG. Precipitated complexes were washed, eluted, and cross-links were reversed at 65°C. After Proteinase K treatment, DNA was purified using QIAprep Spin columns and recovered in 50 μl of elution buffer containing RNase A.
DNA libraries were made using the Illumina ChIP-seq library kit

value: 13-16h embryos

value: rabbit IgG


title: Grh_rabbit_ab_ChIP

value: rabbit anti-Grh antibody


title: WT rep2


title: 1-1587


title: 1-1505


title: RHG1556_hg19_accepted_hits

status: Public on Aug 11 2017

city: Singapore

first: Rajkumar

last: Dorajoo

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description:
PolyA RNA
scRNA-seq
Processed data file: 293alphaandbetacells.txt
The paired-end raw data files are loaded at SRA as single-end files.

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality control in Trimmomatic.
Read quality was checked for each sample using FastQC.
High-quality reads were then imported into TopHat v2.0.8 for alignment into BAM files.
BAM files were imported into the RNA-Seq pipeline of Partek Genomics Suite, version 6.6, and RPKM counts were calculated (RefSeq release 2016-8-1). Inclusion included a minimum RPKM value of 50.0 in at least 25% of cells. RPKM values were quantile normalized.
Genome_build: hg19
Supplementary_files_format_and_content: 293alphaandbetacells.txt: Tab-delimited text file includes normalized RPKM values for each sample.

source_name: Pancreatic islet, beta cell

extract_protocol:
Single cells were processed for RNA-seq using Nextera XT kits (Illumina). Cell lysis, reverse transcription (SMARTer Ultra Low RNA kit, Clontech) and PCR amplification (Advantage® 2 kit, Clontech) were performed on the C1™ Auto-prep module.
Approximately 0.15 ng of cDNA from each cell was processed for RNA-seq using Nextera XT DNA library preparation kits (Illumina).

tag: patient

tag: population

value: East-Asian

tag: disease status

value: Non-diabetic

value: Pancreatic islet

tag: endocrine cell-type

value: Beta


title: 3-1756

value: day 19

value: embryonal disc removed

value: heifer


title: Mut 328


title: 2-2748

value: lactating cow


title: RHG1550_hg19_accepted_hits


title: RHG1549_hg19_accepted_hits


title: RHG1554_hg19_accepted_hits

source_name: Pancreatic islet, alpha cell

value: Alpha


title: RHG1561_hg19_accepted_hits


title: RHG1551_hg19_accepted_hits


title: RHG1542_hg19_accepted_hits


title: RHG1558_hg19_accepted_hits


title: RHG1544_hg19_accepted_hits


title: RHG1563_hg19_accepted_hits


title: RHG1537_hg19_accepted_hits


title: RHG1526_hg19_accepted_hits


title: RHG1522_hg19_accepted_hits


title: RHG1539_hg19_accepted_hits


title: RHG1528_hg19_accepted_hits


title: RHG1527_hg19_accepted_hits


title: RHG1521_hg19_accepted_hits


title: RHG1524_hg19_accepted_hits


title: RHG1520_hg19_accepted_hits


title: RHG1515_hg19_accepted_hits


title: RHG1519_hg19_accepted_hits


title: RHG1513_hg19_accepted_hits


title: RHG1499_hg19_accepted_hits


title: RHG1497_hg19_accepted_hits


title: RHG1490_hg19_accepted_hits


title: RHG1475_hg19_accepted_hits


title: RHG1470_hg19_accepted_hits


title: RHG1462_hg19_accepted_hits


title: RHG1459_hg19_accepted_hits


title: RHG1487_hg19_accepted_hits


title: RHG1461_hg19_accepted_hits


title: RHG1488_hg19_accepted_hits


title: RHG1482_hg19_accepted_hits


title: RHG1471_hg19_accepted_hits


title: RHG1472_hg19_accepted_hits


title: RHG1454_hg19_accepted_hits


title: RHG1456_hg19_accepted_hits


title: RHG1452_hg19_accepted_hits


title: RHG1446_hg19_accepted_hits


title: RHG1457_hg19_accepted_hits


title: RHG1478_hg19_accepted_hits


title: RHG1485_hg19_accepted_hits


title: RHG1453_hg19_accepted_hits


title: RHG1438_hg19_accepted_hits


title: RHG1449_hg19_accepted_hits


title: RHG1451_hg19_accepted_hits


title: RHG1474_hg19_accepted_hits


title: RHG1436_hg19_accepted_hits


title: RHG1433_hg19_accepted_hits


title: RHG1437_hg19_accepted_hits


title: RHG1432_hg19_accepted_hits


title: RHG1476_hg19_accepted_hits


title: RHG1430_hg19_accepted_hits


title: RHG1431_hg19_accepted_hits


title: RHG1428_hg19_accepted_hits


title: RHG1417_hg19_accepted_hits


title: RHG1429_hg19_accepted_hits


title: RHG1421_hg19_accepted_hits


title: RHG1423_hg19_accepted_hits


title: RHG1420_hg19_accepted_hits


title: RHG1424_hg19_accepted_hits


title: RHG1416_hg19_accepted_hits


title: RHG1415_hg19_accepted_hits


title: RHG1405_hg19_accepted_hits


title: RHG1409_hg19_accepted_hits


title: RHG1410_hg19_accepted_hits


title: RHG1413_hg19_accepted_hits


title: RHG1414_hg19_accepted_hits


title: RHG1398_hg19_accepted_hits


title: RHG1401_hg19_accepted_hits


title: RHG1393_hg19_accepted_hits


title: RHG1396_hg19_accepted_hits


title: RHG1395_hg19_accepted_hits


title: RHG1394_hg19_accepted_hits


title: RHG1402_hg19_accepted_hits


title: RHG1389_hg19_accepted_hits


title: RHG1404_hg19_accepted_hits


title: RHG1391_hg19_accepted_hits


title: RHG1388_hg19_accepted_hits


title: RHG1387_hg19_accepted_hits


title: RHG1419_hg19_accepted_hits


title: RHG1384_hg19_accepted_hits


title: RHG1412_hg19_accepted_hits


title: RHG1381_hg19_accepted_hits


title: RHG1373_hg19_accepted_hits


title: RHG1371_hg19_accepted_hits


title: RHG1370_hg19_accepted_hits


title: RHG1369_hg19_accepted_hits


title: RHG1367_hg19_accepted_hits


title: RHG1365_hg19_accepted_hits


title: RHG1358_hg19_accepted_hits


title: RHG1356_hg19_accepted_hits


title: RHG1354_hg19_accepted_hits


title: RHG1342_hg19_accepted_hits


title: RHG1346_hg19_accepted_hits


title: RHG1341_hg19_accepted_hits


title: RHG1353_hg19_accepted_hits


title: RHG1366_hg19_accepted_hits


title: RHG1361_hg19_accepted_hits


title: RHG1374_hg19_accepted_hits


title: RHG1372_hg19_accepted_hits


title: RHG1337_hg19_accepted_hits


title: RHG1385_hg19_accepted_hits


title: RHG1386_hg19_accepted_hits


title: RHG1336_hg19_accepted_hits


title: RHG1335_hg19_accepted_hits


title: RHG1344_hg19_accepted_hits


title: RHG1333_hg19_accepted_hits

description:
PolyA RNA
scRNA-seq
Processed data file: 293alphaandbetacells.txt


title: RHG1331_hg19_accepted_hits


title: RHG1325_hg19_accepted_hits


title: RHG1323_hg19_accepted_hits


title: RHG1320_hg19_accepted_hits


title: RHG1321_hg19_accepted_hits


title: RHG1362_hg19_accepted_hits


title: RHG1316_hg19_accepted_hits


title: RHG1350_hg19_accepted_hits


title: RHG1315_hg19_accepted_hits


title: RHG1351_hg19_accepted_hits


title: RHG1310_hg19_accepted_hits


title: RHG1306_hg19_accepted_hits


title: RHG1303_hg19_accepted_hits


title: RHG1307_hg19_accepted_hits


title: RHG1309_hg19_accepted_hits


title: RHG1295_hg19_accepted_hits


title: RHG1297_hg19_accepted_hits


title: RHG1293_hg19_accepted_hits


title: RHG1296_hg19_accepted_hits


title: RHG1288_hg19_accepted_hits


title: RHG1289_hg19_accepted_hits


title: RHG1284_hg19_accepted_hits


title: RHG1291_hg19_accepted_hits


title: RHG1285_hg19_accepted_hits


title: RHG1283_hg19_accepted_hits


title: RHG1280_hg19_accepted_hits


title: RHG1282_hg19_accepted_hits


title: RHG1319_hg19_accepted_hits


title: RHG1273_hg19_accepted_hits


title: RHG1277_hg19_accepted_hits


title: RHG1276_hg19_accepted_hits


title: RHG1278_hg19_accepted_hits


title: RHG1271_hg19_accepted_hits


title: RHG1314_hg19_accepted_hits


title: RHG1268_hg19_accepted_hits


title: RHG1269_hg19_accepted_hits


title: RHG1266_hg19_accepted_hits


title: RHG1292_hg19_accepted_hits


title: RHG1260_hg19_accepted_hits


title: RHG1261_hg19_accepted_hits


title: RHG1262_hg19_accepted_hits


title: RHG1265_hg19_accepted_hits


title: RHG1257_hg19_accepted_hits


title: RHG1264_hg19_accepted_hits


title: RHG1259_hg19_accepted_hits


title: RHG1251_hg19_accepted_hits


title: RHG1258_hg19_accepted_hits


title: RHG1244_hg19_accepted_hits


title: RHG1247_hg19_accepted_hits


title: RHG1246_hg19_accepted_hits


title: RHG1220_hg19_accepted_hits


title: RHG1226_hg19_accepted_hits


title: RHG1230_hg19_accepted_hits


title: RHG1222_hg19_accepted_hits


title: RHG1267_hg19_accepted_hits


title: RHG1224_hg19_accepted_hits


title: RHG1221_hg19_accepted_hits


title: RHG1217_hg19_accepted_hits


title: RHG1215_hg19_accepted_hits


title: RHG1213_hg19_accepted_hits


title: RHG1209_hg19_accepted_hits


title: RHG1208_hg19_accepted_hits


title: RHG1205_hg19_accepted_hits


title: RHG1206_hg19_accepted_hits


title: RHG1256_hg19_accepted_hits


title: RHG1197_hg19_accepted_hits


title: RHG1202_hg19_accepted_hits


title: RHG1194_hg19_accepted_hits


title: RHG1201_hg19_accepted_hits


title: RHG1185_hg19_accepted_hits


title: RHG1199_hg19_accepted_hits


title: RHG1238_hg19_accepted_hits


title: RHG1181_hg19_accepted_hits


title: RHG1236_hg19_accepted_hits


title: RHG1178_hg19_accepted_hits


title: RHG1302_hg19_accepted_hits


title: RHG1177_hg19_accepted_hits


title: RHG1175_hg19_accepted_hits


title: RHG1165_hg19_accepted_hits


title: RHG1168_hg19_accepted_hits


title: RHG1162_hg19_accepted_hits


title: RHG1164_hg19_accepted_hits


title: RHG1149_hg19_accepted_hits


title: RHG1158_hg19_accepted_hits


title: RHG1161_hg19_accepted_hits


title: RHG1150_hg19_accepted_hits


title: RHG1157_hg19_accepted_hits


title: RHG1148_hg19_accepted_hits


title: RHG1146_hg19_accepted_hits


title: RHG1147_hg19_accepted_hits


title: RHG1189_hg19_accepted_hits


title: RHG1145_hg19_accepted_hits


title: RHG1143_hg19_accepted_hits


title: RHG1142_hg19_accepted_hits


title: RHG1190_hg19_accepted_hits


title: RHG1133_hg19_accepted_hits


title: RHG1127_hg19_accepted_hits


title: RHG1139_hg19_accepted_hits


title: RHG1135_hg19_accepted_hits


title: RHG1131_hg19_accepted_hits


title: RHG1125_hg19_accepted_hits


title: RHG1123_hg19_accepted_hits


title: RHG1144_hg19_accepted_hits


title: RHG1119_hg19_accepted_hits


title: RHG1118_hg19_accepted_hits


title: RHG1129_hg19_accepted_hits


title: RHG1115_hg19_accepted_hits


title: RHG1117_hg19_accepted_hits


title: RHG1113_hg19_accepted_hits


title: RHG1111_hg19_accepted_hits


title: RHG1112_hg19_accepted_hits


title: ein2_ethylene_IgG_control

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

institute: The University of Texas at Austin

description:
16_TGACCA
ethylene treated for 4 hours
C34_C36vs16_peaks.txt
C34_C36vs16_treat_pileup.bedgraph
C34_C36vs16_control_lambda.bedgraph

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 TAIR10 whole genome using bowtie (1.1.2) with default parameters
Duplicate reads were removed using SAMtools
For each histone modification in each condition,mapped reads were pooled across ChIP-seq replicates as described (Gjoneska, Pfenning et al.Nature, 2015)
Peaks significantly enriched in ChIP-seq tags were identified by Model-based Analysis for ChIP-Seq (MACS2, version 2.1.0.20150603; parameters: --nomodel, -p 0.01, -B). Use MACS2 "callpeak" comparing histone ChIP to IgG to produce a histone-ChIP treated file (_treat_pileup.bedgraph) and a control file (_control_lamba.bedgraph) which can be used for further data analysis, e.g. generate the signal file (*.bw) for genome browser.
Genome_build: tair10
Supplementary_files_format_and_content: the peaks.txt and bedgraph files are generated using MACS2 (version 2.1.0.20150603; parameters: --nomodel, -p 0.01, -B) software.

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis seeds were  dark-grown at 24 ºC for 3 days

extract_protocol:
Histone proteins were extracted from seedlings and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB instructions of the ChIP-seq Library Kit (NEB #E6240S/L)

treatment_protocol: Treated with air (hydrocarbon-free air (Zero grade air, AirGas)) or ethylene (hydrocarbon-free air with 10 parts per million  (ppm) ethylene) for 4 hours

value: whole seedling

value: ethylene treated for 4 hours

value: Magnetic Protein G Beads (Promega, G747A)


title: ein2_air_IgG_control

description:
19_CAGATC
air treated for 4 hours
C33_C35vs19_peaks.txt
C33_C35vs19_treat_pileup.bedgraph
C33_C35vs19_control_lambda.bedgraph

value: air treated for 4 hours


title: LTBI rep1

first: Fei

last: Chen

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for  low-quality sequence, then mapped to hg38 whole genome using TopHat v2.0.13 with parameter --library-type fr-unstranded
Counting the reads to each gene to the GENCODE (version 25) gtf gene annotation file  was done using Cufflinks (v2.2.1) .
Differentially expressed genes were computed via the Cuffdiff (v2.2.1) with parameters –M maskfile -u --library-type fr-unstranded.
Unsupervised hierarchical clustering of genome-wide expression proﬁles was performed using the pheatmap (R software).
Genome_build: hg38
Supplementary_files_format_and_content: txt files include FPKM, fold change and Pvalue for each gene and each pair of samples in the related statistical test.

source_name: serum exosomes

extract_protocol:
Pooled serum samples were conducted exosome isolation as previously described. Briefly, the cell debris were removed by differential centrifugation at 1000 g for 10min at 4℃, and 16,500 g for 30 min at 4℃, followed by ultrafiltration (0.22μm filter; Millipore, Billicera, MA, USA). Then the exosome pellet was obtained by ultracentrifugation at 120,000 g for 2 hrs) and washed with PBS.Isolated exosomes were immediately used for RNA extraction by phenol-chloroform method.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: serum exosomes

tag: disease stage

value: latent tuberculosis infection


title: ein2_H3K9Ac_C2H4_ChIPseq_rep1

description:
C34
ethylene treated for 4 hours
C34_C36vs16_peaks.txt
C34_C36vs16_treat_pileup.bedgraph
C34_C36vs16_control_lambda.bedgraph

value: AntiH3K9aC (Millipore; 07-352)


title: LTBI rep2


title: THAP1_sample2

first: Chengguo

last: Wei

state: NY

address: 1428 Madison Ave1468 Madison Ave

data_processing:
Data were filtered using the following specifications fastq_quality_filter -Q 64 -q 20 -p 80
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2
peaks were called using macs2 with the specifications: -f SAM -g mm -n GGACTC-s_2_2 -B -q 0.01
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph files

source_name: wild type mouse ES cells derived from C57Bl/6 blastocysts

growth_protocol: ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: strain

value: Embryonic stem cells derived from blastocysts


title: THAP1_sample1


title: RHG1130_hg19_accepted_hits

value: East-Asian


title: ein2_H3K9Ac_air_ChIPseq_rep1

description:
C33
air treated for 4 hours
C33_C35vs19_peaks.txt
C33_C35vs19_treat_pileup.bedgraph
C33_C35vs19_control_lambda.bedgraph

tag: genotype


title: 18H RVFV Mock Replicate 3

city: Manassas

first: Catherine

middle: Elizabeth

last: Campbell

state: VA

address: 10650 Pyramid Place, MS 1J5

department: National Center for Biodefense and Infectious Diseases

institute: George Mason University

data_processing:
Illumina Casava 1.8.4 software used for basecalling.
Cutadapt was used to trim off adapter sequences
BRB-DGE v0.1 was used for mapping and read counting to align reads to the human genome
DeSeq2 (R package) was used to normalize read counts with variance stabilizing transformation
Genome_build: Homo sapiens GRCh38 build 37.2
Supplementary_files_format_and_content: Excel spreadsheet file

source_name: HSAEC

growth_protocol: Human small airway epithelial cells (HSAECs) were acquired from Cambrex Inc., Walkersville, MD (now Lonza) and maintained in Ham’s F12 medium supplemented with 10% Fetal Bovine Serum (FBS), 1% L-glutamine, 1% penicillin/streptomycin, 1% nonessential amino acids, 1% sodium pyruvate, 0.001% of 55 mM β-mercaptoethanol. Vero cells (ATCC, CCL-81) were maintained in Dulbecco’s modified minimum essential medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, and 1% penicillin/streptomycin. All cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
HSAEC samples infected with RVFV MP12 or ZH548 were collected at 3, 9, and 18 hours post infection in TRIzol LS (Ambion, 10296010). RNA was extracted per the manufacturer’s instructions and quantified using the LabChipGX (Perkin Elmer).
RNA libraries were created using the TruSeq Stranded Total RNA Library Prep kit using 750 ng of input total RNA according to manufacturer’s protocol. The library preparation was automated using the Sciclone Workstation (Perkin Elmer). Prior to sequencing, ribosomal RNA was removed to enrich for mRNA. The completed libraries were quality checked with the LabChipGX and pooled, then the pools were quantified with qPCR. Sequencing was performed using the Illumina platform.

treatment_protocol: Recombinant (r) MP12 and ZH548 virus was rescued and titered as previously described (Benedict et al, 2015, Front Microbiol).  All experiments with RVFV ZH548 were performed under biosafety level 3 (BSL-3) conditions. All work involving select agents is registered with the Centers for Disease Control and Prevention and was conducted at George Mason University's Biomedical Research Laboratory, which is registered in accordance with federal select agent regulations. For viral infections, cells were plated and left to incubate overnight.  The next day, cells were infected with the appropriate virus at the specified multiplicity of infection (MOI). Cells were incubated for 1 hour at 37°C and 5% CO2.  Infectious media was removed, washed twice with phosphate buffered saline (PBS) without Ca2+ and Mg2+, and complete media was added. The cells were left to incubate and collected using the appropriate method for downstream applications at the specified time points.

value: human small airway epithelial cells, primary cells

tag: cell source

value: Lonza

tag: infection strain

value: Mock Infection

tag: strain source

tag: time

value: 18 hours

tag: moi


title: ein2_H3K9Ac_C2H4_ChIPseq_rep2

description:
C36
ethylene treated for 4 hours
C34_C36vs16_peaks.txt
C34_C36vs16_treat_pileup.bedgraph
C34_C36vs16_control_lambda.bedgraph

tag: chip antibody


title: RHG1116_hg19_accepted_hits

value: Non-diabetic

value: Pancreatic islet


title: 9H RVFV Mock Replicate 2

value: 9 hours


title: 9H RVFV Mock Replicate 3


title: 9H RVFV Mock Replicate 1


title: RHG1114_hg19_accepted_hits

value: Beta


title: 3H RVFV Mock Replicate 2

value: 3 hours


title: 3H RVFV Mock Replicate 1


title: 18H RVFV ZH548 Replicate 3

value: RVFV ZH548

value: reverse genetics system; Friedemann Weber (Justus Liebig-University Giessen, Germany)


title: 9H RVFV ZH548 Replicate 3


title: 18H RVFV ZH548 Replicate 2


title: 3H RVFV ZH548 Replicate 3


title: RHG1121_hg19_accepted_hits


title: ein2_H3K9Ac_air_ChIPseq_rep2

description:
C35
air treated for 4 hours
C33_C35vs19_peaks.txt
C33_C35vs19_treat_pileup.bedgraph
C33_C35vs19_control_lambda.bedgraph

value: whole seedling

tag: treatment

value: air treated for 4 hours


title: 9H RVFV ZH548 Replicate 2


title: 9H RVFV ZH548 Replicate 1


title: 3H RVFV ZH548 Replicate 1


title: 18H RVFV MP12 Replicate 2

value: RVFV MP12

value: reverse genetics system; Shinji Makano (UTMB)


title: 3H RVFV ZH548 Replicate 2


title: 3H RVFV MP12 Replicate 2


title: 18H RVFV MP12 Replicate 1


title: 9H RVFV MP12 Replicate 2


title: 18H RVFV Mock Replicate 2


title: 3H RVFV MP12 Replicate 3


title: 9H RVFV MP12 Replicate 1


title: 18H RVFV Mock Replicate 1


title: 9H RVFV MP12 Replicate 3


title: 3H RVFV MP12 Replicate 1


title: 3H RVFV Mock Replicate 3


title: 18H RVFV ZH548 Replicate 1


title: random6-48hr-TGFb

first: Suzanne

last: Szak

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

data_processing:
Paired-end reads were aligned to the hg19 human reference genome using STAR aligner, v2.4.0; approximately 90% of all reads aligned uniquely to the reference genome. RNASeq analysis was performed with Bioconductor, using DESeq2 (Ver. 1.12.3). DEG criterion: normalized counts >4, |fold change| > 1.5, and adjusted p-value < 0.05, Benjamin Hochberg (BH) correction. A total of 78 unique DEGs were identified following this criterion. Pathway analysis was performed using GOStats package (Ver. 2.38.0) in Bioconductor.
Supplementary_files_format_and_content: DESEQ2 normalized counts for genes.

source_name: fibroblast

growth_protocol: Human dermal fibroblasts were obtained from ATCC (Manassas, VA). Cells were grown in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% FBS and 1% Antibiotic-Antimycotic (ThermoFisher, Waltham MA). For in vitro assays on aligned versus random ECM fibers, cells were seeded at 500,000 cells/well into 60mm dishes with electrospun PCL nanofibers (Nanofiber Solutions Inc, Columbus OH) with adsorbed purified type I collagen (10ug/mL) overnight at 4°C, prior to cell seeding. Cells were cultured for 48 hours in a 37°C incubator, followed by total RNA extraction and whole genome transcriptomic analysis by RNASeq.

extract_protocol:
Total RNA was isolated from cells, using GenElute mammalian total RNA kit (Sigma, St Louis, MO).
500 ng RNA was used as starting input to Illumina TruSeq mRNA stranded library construction according to the manufacturers recommendation. High quality libraries were then pooled and sequenced on an Illumina HiSeq 2500

tag: tissue

value: fibroblast


title: random2-48hr-TGFb


title: random4-48hr-TGFb


title: random5-48hr-TGFb


title: align5-48hr-TGFb


title: random3-48hr-TGFb


title: align6-48hr-TGFb


title: random1-48hr-TGFb


title: align4-48hr-TGFb


title: 18H RVFV MP12 Replicate 3


title: random4-48hr


title: align2-48hr-TGFb


title: random5-48hr


title: random3-48hr


title: random6-48hr


title: align1-48hr-TGFb


title: align2-48hr


title: align4-48hr


title: random2-48hr


title: random5-12hr-TGFb


title: align1-48hr


title: align3-48hr


title: align5-48hr


title: random3-12hr-TGFb


title: random6-12hr-TGFb


title: random1-48hr


title: random4-12hr-TGFb


title: align1-12hr-TGFb


title: random2-12hr-TGFb


title: random6-12hr


title: random1-12hr-TGFb


title: align4-12hr-TGFb


title: align5-12hr-TGFb


title: align3-12hr-TGFb


title: align6-12hr-TGFb


title: random3-12hr


title: random5-12hr


title: random2-12hr


title: align2-12hr-TGFb


title: random4-12hr


title: align6-12hr


title: align4-12hr


title: align6-48hr


title: ATB rep2

value: serum exosomes

value: active tuberculosis patients


title: ATB rep1


title: align5-12hr


title: HC rep2

value: healthy control


title: align3-12hr


title: random1-12hr


title: align1-12hr


title: NVS-SM1-10

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

description:
TGACCA
NVS-SM1-10

data_processing:
Real time image analysis and base calling was performed on the HiSeq 2500 with the HiSeq Control Software v2.2.37
CASAVA software version 1.8.2 was used for demultiplexing and production of FASTQ sequence files
Reads were mapped onto hg19 with gsnap version 2014-10-22 using the following parameters -s rsnhum.fa.iit --ordered --novelsplicing=1 --format=sam --nthreads=12 --batch=4 --gunzip
Mapped reads per gene were determined by using human RefSeq mRNA annotations
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated.
Reads were mapped onto RefSeq human transcripts using gsnap version 2014-10-22 with default parameters and the option ‘sam-multiple-primaries’ in order to account for reads that map multiple times to different splice variants.
The numbers of reads mapped to exons, exon junctions, and to exons excluding junction reads was determined by applying the samtools mpileup software with default parameters for each transcript. Reads were excluded from the analysis if their start or end coordinate mapped exactly onto the splice-site.
Genome_build: hg19
Supplementary_files_format_and_content: NVS-SM1_counts.gct / NVS-SM1_rpkms.gct: text files in gct format containing raw read counts per gene and normalized read counts (rpkms) per gene, column 1: EntrezGene Index, column 2: Official gene symbol from EntrezGene
Supplementary_files_format_and_content: NVS-SM1_read_counts.txt.gz: Text file in tabular format containing counts of all mapped reads per exon including junction and non-junction reads, 1 exon per line, column 1: RefSeq mRNA accession identifier (ITEM), column 2: Official gene symbol from EntrezGene (GENE), column 3: Gene index from EntrezGene (GID), column 4: Exon number (EXONS)  Caution: this numbering is relative and might be different to other reference sources/literature, column 5: Exon coordinates of the transcript (SITE), column 6: Exon coordinates of the genome hg19 (GENOMIC) +/- denote the strand, columns 7-12: Number of all reads mapped to the exon
Supplementary_files_format_and_content: NVS-SM1_junction_read_counts.txt.gz: Text file in tabular format containing mapped read counts per exon-exon junction, 1 exon-exon junction per line, column 1: RefSeq mRNA accession identifier (ITEM), column 2: Official gene symbol from EntrezGene (GENE), column 3: Gene index from EntrezGene (GID), column 4: Exon numbers (EXONS) Caution: this numbering is relative and might be different to other reference sources/literature, column 5: Exon-exon junction coordinates of the mRNA (SITE), column 6: Exon-exon junction coordinates of the genome hg19 (GENOMIC) +/- denote the strand, columns 7-12: Number of reads mapped to the exon-exon junction
Supplementary_files_format_and_content: NVS-SM1_nojunction_read_counts.txt.gz: Text file in tabular format containing counts of reads mapped entirely to an exon, excluding all junction reads, 1 exon per line, column 1: RefSeq mRNA accession identifier (ITEM), column 2: Official gene symbol from EntrezGene (GENE), column 3: Gene index from EntrezGene (GID), column 4: Exon number (EXONS)  Caution: this numbering is relative and might be different to other reference sources/literature, column 5: Exon coordinates of the transcript (SITE), column 6: Exon coordinates of the genome gh19 (GENOMIC) +/- denote the strand, columns 7-12: Number of reads mapped entirely to the exon

source_name: type I SMA fibroblasts

extract_protocol:
PNN 1-46 cells derived from a type 1 SMA patient were treated with NVS-SM1 at 24 nM and 120 nM for 24 hours. RNA was extracted with the RNeasy Mini Kit (Qiagen Inc., USA).
Template DNA molecules suitable for sequencing were prepared from 400 ng of total RNA using the TruSeq Stranded mRNA Library Preparation Kit (lllumina Inc., San Diego, CA) according to manufacturer's instructions. After 14 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated by electrophoresis on Agilent High Sensitivity Bioanalyzer microfluidic chips. Minimum sizes of amplified libraries were determined as >200 nucleotides and average sizes of ~300 nucleotides. Libraries were quantified using the KAPA Library Quantification Kit (Kapa Biosystems, Boston, MA). Libraries were pooled at equimolar concentrations, spiked with 1% PhiX control library, and diluted to 20 pM prior to loading onto the flow cell of an Illumina HiSeq 2500 instrument (lllumina Inc., San Diego, CA) for both clustering and sequencing. Libraries were extended and bridge amplified to create single sequence clusters using the HiSeq PE Cluster Kit v4 cBot HS (lllumina Inc., San Diego, CA).

tag: concentration

value: 24 nM


title: drug-treated_Rep5

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

institute: University of Wuerzburg

data_processing:
reads were aligned to the mouse reference sequence GENCODE vM8 using STAR version 2.5.2b
Genes quantification using bedtools
differentially expressed genes were identified using DESeq
Genome_build: GENCODE vM8

source_name: Murine B cells from the spleen

extract_protocol:
RNA was extracted with a commercially available Qiagen kit.
RNA was extracted using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) and subjected to integrity checks using a Bioanalyzer 2100 (Agilent, Santa Clara, CA, U.S.A.).

treatment_protocol: The mice were immunized at the age of 8 weeks with the MP4 fusion protein (consisting of MBP and the hydrophilic loops of PLP) in complete Freund's adjuvant. Pertussis toxin was given on the day of immunization and 48 h later. Once mice established experimental autoimmune encephalomyelitis, they were orally treated with 1 mg/kg BW FTY720 for about 30 days. B cells were isolated from mouse spleen using a mouse B cell enrichment kit from Miltenyi.

value: B Cells


title: NVS-SM1-11

description:
GTCCGC
NVS-SM1-11


title: NVS-SM1-19

description:
CCGTCC
NVS-SM1-19


title: drug-treated_Rep4


title: NVS-SM1-21

description:
GAGTGG
NVS-SM1-21


title: NVS-SM1-12

description:
ACTTGA
NVS-SM1-12


title: HC rep1


title: NVS-SM1-20

description:
AGTCAA
NVS-SM1-20


title: align3-48hr-TGFb


title: drug-treated_Rep1


title: vehicle-treated_Rep4


title: drug-treated_Rep3


title: vehicle-treated_Rep3


title: vehicle-treated_Rep2


title: olfactory bulb, WT rep3, rRNA-depleted

city: Berlin

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

institute: Max Delbrück Center for Molecular Medicine

description: dissected olfactory bulb

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion with bcl2fastq v2.17.1.14
alignment to mm9 genome reference using STAR 2.5.1b
reads counted on Ensembl release 67 gene models with htseq-count 0.6.1p1.
Genome_build: mm9
Supplementary_files_format_and_content: htseq-count output, two-column text file with Ensembl gene identifier and read count columns

source_name: C57BL/6 mouse

extract_protocol:
TRIZOL
Rnase H-based rRNA depletion followed by TruSeq Stranded Total LT Sample Prep Kit

value: brain

value: wild type


title: align2-12hr


title: cortex, WT rep3, rRNA-depleted

description: dissected cortex


title: vehicle-treated_Rep1


title: hippocampus, WT rep3, rRNA-depleted

description: dissected hippocampus


title: cerebellum, WT rep3, rRNA-depleted

description: dissected cerebellum


title: hippocampus, WT rep1, rRNA-depleted

description: dissected hippocampus


title: olfactory bulb, WT rep1, rRNA-depleted

description: dissected olfactory bulb


title: cortex, WT rep1, rRNA-depleted

description: dissected cortex


title: hippocampus, WT rep2, rRNA-depleted

description: dissected hippocampus


title: olfactory bulb, WT rep2, rRNA-depleted

description: dissected olfactory bulb


title: cortex, WT rep2, rRNA-depleted

description: dissected cortex


title: cerebellum, WT rep2, rRNA-depleted

description: dissected cerebellum


title: cerebellum, WT rep1, rRNA-depleted

description: dissected cerebellum


title: olfactory bulb, KO rep3, rRNA-depleted

description: dissected olfactory bulb

value: Cdr1as knockout


title: hippocampus, KO rep3, rRNA-depleted

description: dissected hippocampus


title: cortex, KO rep3, rRNA-depleted

description: dissected cortex


title: cerebellum, KO rep3, rRNA-depleted

description: dissected cerebellum


title: cerebellum, KO rep2, rRNA-depleted

description: dissected cerebellum


title: drug-treated_Rep2


title: cortex, KO rep2, rRNA-depleted

description: dissected cortex


title: olfactory bulb, KO rep2, rRNA-depleted

description: dissected olfactory bulb


title: olfactory bulb, KO rep1, rRNA-depleted

description: dissected olfactory bulb


title: hippocampus, KO rep2, rRNA-depleted

description: dissected hippocampus


title: hippocampus, KO rep1, rRNA-depleted

description: dissected hippocampus


title: olfactory bulb, KO rep2

data_processing:
3' adapters were trimmed from the raw reads using flexbar (version 2.5) [--adapter-relaxed --adapter-trim-end RIGHT --adapter-gap -3 --pre-trim-phred 20 --min-read-length 17]
Using the trimmed reads, the expression levels of mature miRNAs (miRBase version 21) were estimated with miRDeep2 (version 2.0.0.7). For each library the read counts from identical mature miRNAs of different precursors were summed up.
Genome_build: mm9
Supplementary_files_format_and_content: two-column text file with miRNA identifier and read count columns

extract_protocol:
TRIZOL
TruSeq Small RNA Library Prep Kit

tag: sample type

value: dissected olfactory bulb


title: olfactory bulb, WT rep3


title: olfactory bulb, KO rep1


title: cerebellum, KO rep1, rRNA-depleted

description: dissected cerebellum


title: olfactory bulb, KO rep3


title: olfactory bulb, WT rep1


title: hippocampus, WT rep1

value: dissected hippocampus


title: hippocampus, WT rep2


title: cortex, KO rep3

value: dissected cortex


title: hippocampus, KO rep2


title: olfactory bulb, WT rep2


title: cortex, KO rep1


title: cortex, KO rep2


title: cortex, WT rep3


title: hippocampus, KO rep3


title: cortex, WT rep1


title: hippocampus, WT rep3


title: cortex, WT rep2


title: cerebellum, KO rep2

value: dissected cerebellum


title: cerebellum, KO rep1


title: cerebellum, WT rep2


title: cerebellum, WT rep3


title: olfactory bulb, KO rep3

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion with bcl2fastq v2.17.1.14
alignment to mm9 genome reference using STAR_2.5.1b
reads counted on Ensembl release 67 gene models with htseq-count 0.6.1p1.
Genome_build: mm9
Supplementary_files_format_and_content: htseq-count output, two-column text file with Ensembl gene identifier and read count columns

molecule: polyA RNA

extract_protocol:
TRIZOL
TruSeq Stranded mRNA LT Sample Prep Kit


title: cortex, KO rep1, rRNA-depleted

description: dissected cortex


title: cerebellum, KO rep3


title: olfactory bulb, KO rep1


title: olfactory bulb, WT rep3


title: olfactory bulb, KO rep2


title: olfactory bulb, WT rep2


title: cerebellum, WT rep1


title: hippocampus, KO rep3


title: hippocampus, KO rep1


title: hippocampus, WT rep3


title: hippocampus, WT rep2


title: olfactory bulb, WT rep1


title: cortex, WT rep3


title: cortex, KO rep2


title: cerebellum, KO rep3


title: cortex, WT rep1


title: cortex, WT rep2


title: cerebellum, WT rep3


title: hippocampus, WT rep1


title: cerebellum, KO rep2


title: cortex, KO rep1


title: cerebellum, WT rep2


title: cerebellum, KO rep1


title: p53KO_mBMSCs_clone8_cFos

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

data_processing:
Base calling: RTA 1.12.4.2 (performed at the Next Generation Sequencing Facility at the Center for Cancer Research at the National Cancer Institute)
Demultiplexing: Casava 1.8.2 allowing 1 mismatch
Alignment and filtering: tophat -G mm9.gtf -o ./ -r 10 --mate-std-dev 200 -p 16 read1.fastq read2.fastq
To generate FPKM files: Cufflinks using a gtf file of mm9 downloaded on 2013_05_07 from UCSC browser.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM files were generated using Cufflinks

growth_protocol: mBMSCs were grown in MesenCult® Proliferation Kit (Mouse) (Stem Cell Technologies, Cat:05512)  and split every three days.

extract_protocol:
RNAs were extracted using the GenElute Mammalian total RNA Miniprep kit (Sigma, Cat: RTN350-1kt).
Illumina TruSeq RNA, Protocol RS-930-2001 withIllumina TruSeq V3.0

treatment_protocol: Untreated

tag: genotype/variation

value: p53 knockout

value: mouse bone marrow-derived stem cells (mBMSCs)

tag: passage

value: less than 20 passages

tag: transduced with

value: retroviruses expressing cFos cDNAs

tag: repeat


title: p53KO_mBMSCs_clone8_Luc

tag: cell type

value: retroviruses expressing luciferase (Luc)


title: p53KO_mBMSCs_clone4_Luc


title: p53KO_mBMSCs_clone2_cFos


title: p53KO_mBMSCs_clone2_Luc


title: cerebellum, WT rep1


title: su-pcgbm2-nlgn3.2

first: Michelle

last: Monje

address: 265 Campus Drive, SIM1 G3035

institute: Stanford University

data_processing:
Mapping: tophat2, default parameters were used against hg19 reference genome
Gene expression: quantified using featureCounts against an RefSeq hg19 GTF
Normalization: FPKM values were calculated using length of exons and total number of assigned reads
Genome_build: hg19

source_name: patient-derived cell culture

growth_protocol: Cells are grown in Tumor Stem Media (TSM), consisting of Neurobasal (-A), DMEM F12, B27 (-A), bFGF, EGF, PDGF-AB, and heparin. See Grasso et al 2015.

extract_protocol:
RNA-seq samples were pelleted and lysed in Trizol reagent then subsequently precipitated.
After extraction from Trizol, RNA-seq samples were poly(A) selected using Dynabeads mRNA Purification Kit (Life Tech) before fragmentation using Thermo AM8740 and Second Strand Synthesis. Libraries were end-repaired using T4 DNA Polymerase, E. coli Klenow fragment, and T4 polynucleotide kinase. DNA was then A-tailed using exo(-) Klenow fragment and ligated to adaptors from NEBNext MultiPlex Oligos using New England BioLabs Quick Ligase.
Libraries were sequenced at 1x75 on an Illumina NextSeq 500

treatment_protocol: SU-pcGBM2 NLGN3 cells were treated with 100nM recombinant NLGN3 for 16 hours in growth media and SU-pcGBM2 DMSO cells were treated with ~1% DMSO as a vehicle control. Both were treated in biological duplicate.

tag: diagnosis

value: pediatric glioblastoma


title: p53KO_mBMSCs_clone4_cFos


title: su-pcgbm2-nlgn3.1

description: poly(A)+ RNA-seq


title: hippocampus, KO rep2

tag: genotype


title: Input

description: Input DNA

data_processing:
Base calling: RTA 1.12.4.2 and sequencing chemistry: Illumina TruSeq 3.0. All raw files were generated using this method.
Alignment: Illumina Casava 1.8.2. All processed data files were generated using this method.
Processed files are peak files. Peak calling was performed using MACS (version 1.4.1 2011_06_27; band width = 300; model fold = 10,30; pvalue cutoff = 1.00e-05)
Genome_build: mm9
Supplementary_files_format_and_content: bed file with called peaks

extract_protocol:
ChIP DNA was extracted by standard phenol approach.
NEB ChIP-seq prep kit

tag: antibody

value: none (input)

tag: passage number

value: mesenchymal stem cells

value: p53KO expressing cFos


title: cFos ChIP

description: ChIP DNA

value: anti-cFos antibody (Santa Cruz, Cat:sc-253)


title: su-pcgbm2-dmso.2


title: RUNX1_dMQ1 CTCF

city: HOUSTON

first: Jianzhong

last: Su

address: 1 Baylor Plaza

institute: Baylor college of Medicine

data_processing:
ChIP-seq reads were aligned to the hg19 human genome assembly using Bowtie2 version 2.1.0 with 2 mismatch in seed allowed. Peak calling was performed on uniquely aligned reads  with Macs2 version 2.0, command=macs2 callpeak -B -f BAMPE --keep-dup 2 -q 0.01.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were created from the Macs2 bedgraph files were normailized into 20 Millions reads by  the quantile normalization of software DANPOS 2.2.2.

source_name: K562 cell

growth_protocol: ATCC-formulated Iscove's Modified Dulbecco's Medium and 10% fetal bovine serum.

extract_protocol:
K562 cells were sorted and crosslinked with 1% formaldehyde at room temperature (RT) for 10 min, and the reaction was stopped by 0.125M glycine at RT for 5 min. Cross-linked cells were lysed and sonicated to 200-500 bp fragments (Bioruptor, Diagenode). ChIP-qualified antibodies (anti-CTCF) were added to the sonicated chromatin and incubated at 4°C overnight. Following this, 10 μl of protein A magnetic beads (Dynal, Invitrogen) previously washed in RIPA buffer were  added  and incubated for an additional 2 hours at 4°C. The bead: protein complexes were washed three times with RIPA buffer and twice with TE buffer. Following transfer into new 1.5 ml collection tube, genomic DNA was eluted for 2 hours at 68°C in 100 µl Complete Elution Buffer (20 mM Tris pH 7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, 50 µg/ml proteinase K), and combined with a second elution of 100 µl Elution Buffer (20 mM Tris pH 7.5, 5 mM EDTA, 50 mM NaCl) for 10 min at 68°C. ChIPed DNA was purified by MinElute Purification Kit (Qiagen) and eluted in 12 µl elution buffer.
Chip-Seq libraries was constructed using Rubicon Genomics ThruPLEX® DNA-seq Kit

treatment_protocol: Plasmids were delivered into K562 cells via Electroporation. Cells were further cultured additional 48 hours.

value: Wild type K562 lymphoblast cells


title: HOXA11_MQ1Q147L CTCF


title: RUNX1_MQ1Q147L CTCF


title: HOXA13_MQ1Q147L CTCF


title: HOXA11_dMQ1 CTCF


title: p53KO_mBMSCs_clone12_cFos


title: p53KO_mBMSCs_clone12_Luc


title: MCF-7 cell line Anti-miR-29a transfected replicate 2

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Illumina FASTQ Generation version 1.0.0 used for basecalling
Quality control (QC) of the raw sequence data was performed using FastQC. The FastQC results indicated that all sequences were of high quality.
Sequences were directly aligned to the Homo sapiens reference genome assembly hs_ref_GRCh37 downloaded from NCBI. The annotation file Homo_sapiens.GRCh37.73.gtf Downloaded from Ensembl August 26, 2015 was used with all records annotated as mitochondrial or ribosomal RNA removed.
The analysis was performed using The Illumina Basesapce RNA-Seq Alignment App version 1.0.0 with Tophat2 and Bowtie2, generating alignment files in bam format.
Differentially expressed genes (DEGS) were identified  using Cuffdiff (v2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] tab-delimited cuffnorm normalized FPKM file

growth_protocol: MCF-7 and LCC9 cells were grown in triplicates in phenol red IMEM supplemented with 5% dextran-coated charcoal-stripped fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S).

extract_protocol:
RNA was isolated using the Exiqon miRCURYTM RNA Isolation kit and its concentration and quality assessed using a NanoDrop spectrophotometer. Quantitative real-time PCR confirmed overexpression of miR-29b-1, miR-29a, or knockdown of miR-29b-1 and miR-29a in respective samples.
The Truseq Stranded mRNA kit was used to prepare mRNA libraries from 2ug total RNA.  Libraries were confirmed on the Agilent 2100 Bioanalyzer and quantitated using the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems and the ABI7900HT real-time PCR instrument.  75-76 cycle single read sequencing was performed with the 500 High-output v2 (75 cycle) sequencing kit on the Illumina NextSeq500 instrument.

treatment_protocol: Cells were transfected with anti-miR-29a (Anti-miRTMs, Ambion), pre-miR-29a and pre-miR-29b-1 (Pre-miRTMs, Ambion), using Lipofectamine RNAiMAX (Invitrogen) for 48 h.

tag: cell line

tag: transfection


title: LCC9 cell line Pre-miR-29a transfected replicate 3

source_name: LCC9 cell line Pre-miR-29a transfected


title: MCF-7 cell line Pre-miR-29a transfected replicate 2

source_name: MCF-7 cell line Pre-miR-29a transfected


title: MCF-7 cell line Anti-miR-29a transfected replicate 1


title: MCF-7 cell line Pre-miR-29a transfected replicate 3


title: MCF-7 cell line pre-miR-29b-1 transfected replicate 1


title: LCC9 cell line Pre-miR-29a transfected replicate 2


title: LCC9 cell line pre-miR-29b-1 transfected replicate 2


title: LCC9 cell line Anti-miR-29a transfected replicate 1

source_name: LCC9 cell line Anti-miR-29a transfected


title: LCC9 cell line pre-miR-29b-1 transfected replicate 3


title: LCC9 cell line Anti-miR-29a transfected replicate 2


title: MCF-7 cell line Pre-miR-29a transfected replicate 1


title: LCC9 cell line Pre-miR-29a transfected replicate 1


title: MCF-7 cell line Anti-miR-29a transfected replicate 3


title: MCF-7 cell line pre-miR-29b-1 transfected replicate 3


title: su-pcgbm2-dmso.1

description: poly(A)+ RNA-seq


title: HOXA13_dMQ1 CTCF


title: LCC9 cell line pre-miR-29b-1 transfected replicate 1


title: RNA-seq treatment replicate 3

city: Colchester

first: Vladimir

middle: B

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

description:
RNA-seq treated 226LDM cells
RNA-seq treated 226LDM cells
deseq_Pavlaki_differential_expression.tab

data_processing:
For ChIP-seq analysis uniquely mappable reads were aligned to the human hg19 genome with the help of Bowtie allowing up to 1 mismatch. Peak calling was done with MACS using standard parameters, and taking into account the corresponding Input. Replicate experiments were analysed separately, and then merged. Aggregate profiles were calculated using NucTools and visualised using OriginPro (Origin Lab). Sequence motif analysis was performed using HOMER.
RNA-seq reads were aligned using Novoalign 3.2 to the reference genome (hg19) and the raw counts were normalized to RPKM values using the Bam2rpkm tool from Galaxy. Differential expression was determined using DeSeq. Genes whose expression change was less than 1.5-fold were included in the “unchanged” gene expression category. Gene Ontology (GO) analysis was performed using DAVID.
Genome_build: hg19
Supplementary_files_format_and_content: peak and count

source_name: 226LDM cells treatment

growth_protocol: 226LDM cells, derived from human luminal breast cells, were seeded in flasks and grown in DMEM/F-12 (PAA) supplemented with 5 μg / ml insulin, 1 μg / ml hydrocortisone, 20 ng / ml epidermal growth factor, 20 ng / ml cholera toxin (all from Sigma), 10 % fetal bovine serum (FBS) (Biosera), and 50 μg / ml gentamicin (Life Technologies-Invitrogen) at 37oC and 5 % CO2.

extract_protocol: Total RNA from 226LDM cells (three independent samples from the control and three from the treated population) was extracted using the TRIsure reagent (Bioline) according to the manufacturer’s guidelines. Briefly, cells grown in a T75 flask were washed twice with PBS, then scraped off and pelleted at 300 g for 5 min. Following incubation with TRIsure for 5 min at RT, chloroform was added and the sample was incubated for 15 min at RT. After centrifugation at 9,500 g for 15 min at 4oC, the top aqueous layer was carefully extracted and the genetic material was precipitated with isopropanol for 20 min on ice. After centrifugation (9.500 g / 15 min / 4oC) the pellet was washed twice in 75 % ethanol before air-drying the obtained RNA pellet. The RNA was solubilized in sterile water (40-50 μl) and heated for 10 min at 55oC. The pellet was stored at -80oC. ChIP was performed using the ZymoSpin kit (Zymo Research USA) following the manufacturer’s instructions. In brief, 5 x 106 of 226LDM cells from the control and the treated populations were cross-linked with formaldehyde. The cross-linking was quenched with glycine and the cells were washed twice with PBS with the addition of a protease inhibitor cocktail before pelleting at 1000 g for 1 min at 4oC. The pellet was lysed in Chromatin Shearing Buffer and sonicated using Bioruptor Plus (Diagenode) on high power to obtain fragments of 250-300 bp. ChIP reaction mixes containing sheared chromatin, Chromatin Dilution Buffer, anti-CTCF antibody (Millipore, 07-729, lot # JBC1903613 or no-antibody for negative control) and protease inhibitor cocktail were incubated rotating overnight at 4oC. The next day, ZymoMag Protein A beads were added to the mix and incubated for 1 h at 4oC. The complexes were washed with Washing Buffers I, II and III and then the beads were re-suspended in DNA Elution Buffer. Following de-crosslinking with Proteinase K at 65oC, the ChIP DNA was purified using the ZymoSpin IC columns. The samples were stored at -80oC. The concentration of DNA in the ChIP samples was measured using the NanoDrop 3300 fluorospectrophotometer (Thermo Scientific) along with the Quant-iT™ PicoGreen ds DNA assay kit according to the manufacturer’s instructions.

treatment_protocol: To induce cell cycle arrest cells were treated with 100 mM hydroxyurea for 24 h followed by 1 h of complete medium and a further 24 h with 500 ng / ml nocodazole (SIGMA), and cells in suspension were then harvested for further analyses. Untreated adherent proliferating 226LDM cells were used as control.

value: treated with hydroxyurea and nocodazole


title: RNA-seq treatment replicate 2


title: RNA-seq treatment replicate 1


title: RNA-seq control replicate 2

description:
RNA-seq untreated 226LDM cells
RNA-seq untreated 226LDM cells
deseq_Pavlaki_differential_expression.tab

source_name: 226LDM cells

value: untreated


title: RNA-seq control replicate 3


title: RNA-seq control replicate 1


title: Input control replicate 3

description:
Input (no antibody) ChIP-seq treated 226LDM
Input treated 226LDM


title: H3K9me3 treatment replicate 2

description:
H3K9me3 ChIP-seq treated 226LDM
H3K9me3 ChIP-seq treated 226LDM
IP13andIP14_control_IP15andIP16_MACS_peaks.bed


title: MCF-7 cell line pre-miR-29b-1 transfected replicate 2


title: LCC9 cell line Anti-miR-29a transfected replicate 3


title: CTCF treatment replicate 1

description:
CTCF ChIP-seq treated 226LDM
CTCF ChIP-seq treated 226LDM
IP09andIP10_control_IP15andIP16_MACS_peaks.bed


title: CTCF treatment replicate 2


title: CTCF control replicate 2

description:
CTCF ChIP-seq untreated 226LDM
CTCF ChIP-seq untreated 226LDM
IP01andIP02_control_IP07andIP08_MACS_peaks.bed


title: CTCF control replicate 1


title: UC_D4 RRBS

data_processing:
Fastq files aligned with bsmap 2.90 in RRBS mode using the following parameters: -g 1 -w 5 -D C-CGG -p 8 -R -s 12 -S 42 -u; methylation ratios were calculated with the bsmap utility script methratio.py using the following parameters: -z --ct-snp=no-action
Genome_build: mm9
Supplementary_files_format_and_content: text output of bsmap utility methratio.py; chromosome, coordinate start, end, methylation ratio, number of effective total C+T counts on this locus, number of methylated C counts on this locus, strand, sequence context

source_name: HEK 293T

growth_protocol: ATCC-formulated Dulbecco's Modified Eagle's Medium and 10% fetal bovine serum

extract_protocol:
Extract DNA using Qiagen Allprep Micro kit.
Tru-Seq DNA sample prep kit

treatment_protocol: Plasmids were delivered into K562 cells via Lipo3000 transfection (invitrogen). Cells were further cultured additional 24 or 48 hours.

value: Human epithelial HEK 293T cells


title: H3K9me3 treatment replicate 1


title: MQ1_147_D2 RRBS


title: MQ1_147_D4 RRBS


title: MQ1147+sgRNA_D1 RRBS


title: Input control replicate 1

description:
Input (no antibody) ChIP-seq untreated 226LDM
Input untreated 226LDM


title: Input control replicate 2


title: MQ1_147_D1 RRBS


title: dMQ1+sgRNA_D1 RRBS


title: UC_D1 RRBS


title: MQ1_141_D4 RRBS


title: Input control replicate 4


title: OCILY10_C_R2

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

country: Spain

institute: CIMA

description: DLBCL cell line

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control was performed with FastQC version 0.11.3. The alignment of reads to the human genome (hg19) was performed using Tophat2 (release 2.1.0) mapper to generate BAM files.
The transcript assembly  and quantification using FPKM of transcripts was carried out using Cufflinks2.
Annotation of the gene locus obtained was performed using Cuffmerge with Gencode v19 as reference.
Genome_build: hg19
tab-delimited text files with raw counts for each sample using GENCODE v19 as reference

growth_protocol: CEMO-1 cell line was maintained in culture in RPMI 1640 medium supplemented with fetal bovine serum at 37 °C in a humid atmosphere containing 5% CO2. OCILY10 was maintained in culture in IMDM supplemented with 20% human serum and 55 µM of β-mercaptoethanol. All cell lines were tested for mycoplasma.

extract_protocol:
The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany). Before cDNA synthesis, RNA integrity from each sample was confirmed on Agilent RNA Nano LabChips (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell lines were treated with CM-272 inhibitor at GI50 concentrations, respectively

value: OCILY10 Diffuse large B-cell lymphoma (DLBCL) cell line

tag: treatment protocol

value: a dual inhibitor against G9a and DNMTs


title: MQ1_141_D2 RRBS


title: OCILY10_CM272_R1

description: DLBCL cell line

value: without treatment


title: H3K9me3 control replicate 1

description:
H3K9me3 ChIP-seq untreated 226LDM
H3K9me3 ChIP-seq untreated 226LDM
IP05andIP06_control_IP07andIP08_MACS_peaks.bed


title: MQ1_141_D1 RRBS


title: CEMO1_CM272_R2

description: ALL cell line

value: CEMO-1 Acute Lymphoblastic Leukemia (ALL) cell line


title: OCILY10_C_R1

description: DLBCL cell line


title: CEMO1_CM272_R1

description: ALL cell line


title: CEMO1_C_R2

description: ALL cell line


title: H3K9me3 control replicate 2


title: OCILY10_CM272_R2

description: DLBCL cell line


title: AdCMV+AdVammin_48h_rep1

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

description: AdCMV+AdVammin 48h

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation and poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
Reads were aligned to the hg19 genome using Tophat.
Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://homer.salk.edu/homer/
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values (RPKM) and UCSC Bedgraphs are provided

source_name: human umbilical vein endothelial cells

growth_protocol: HUVECs were cultured in Endothelial Cell Growth medium (EGM; Thermo Scientific) on fibronectin-gelatin coated surfaces (10 µg/ml, 0.05%; Sigma-Aldrich).

extract_protocol:
RNA was purified using Rneasy Plus Mini Kit and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit.
The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 10 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: Confluent cultures of HUVECs were washed with PBS, followed by transduction with AdCMV, AdVEGF-A109, AdVEGF-A165, AdVammin or AdCMV+AdVammin. After 24 hrs, starvation of cells was started with EGM medium supplemented with 0.5 % FBS and continued for 24 hrs .

tag: cell collection details

value: Sample from 1 individual

value: passage 5

tag: replicate

value: biological replicate #1

tag: experiment


title: AdVEGF-A165_48h_rep3

description: AdVEGF-A165 48h

value: biological replicate #3


title: AdVammin_48h_rep1

description: AdVammin 48h


title: AdVEGF-A109_48h_rep3

description: AdVEGF-A109 48h


title: AdCMV_48h_rep3

description: AdCMV 48h


title: AdVEGF-A165_48h_rep2

description: AdVEGF-A165 48h

value: biological replicate #2


title: AdVEGF-A165_48h_rep1

description: AdVEGF-A165 48h


title: AdVammin 48h_rep3

description: AdVammin 48h


title: AdVEGF-A109_48h_rep2_tech

description: AdVEGF-A109 48h

value: technical replicate #2 of biological replicate #2


title: CEMO1_C_R1

description: ALL cell line


title: AdCMV+AdVammin_48h_rep2

description: AdCMV+AdVammin 48h


title: 10weeks recovery-5

description: processed data file column: ATMT0137

data_processing:
Sequencing of 50bp paired-end reads was performed using an illumina HiSeq-2500, with an average coverage of 25 million reads/sample. Paired-end reads were aligned to the mm10 mouse reference genome using the STAR aligner, version 2.4.0; approximately 83% of all reads aligned uniquely to the genome. RNASeq analysis was performed with Bioconductor, using DESeq2 (Ver. 1.12.3). Criterion for assessing differentially expressed genes (DEG) was determined as follows: normalized counts > 3, |fold change| > 1.5, and adjusted p-value < 0.05, Benjamin Hochberg (BH) correction. A total of 4376 unique DEGs were identified following this criterion. Normalized counts of each expressed gene were correlated to each histopathological metric of skin fibrosis. Genes that met a threshold for correlation (r2 > 0.7, 0.4, 0.4 for dermis thickness, total collagen, and collagen bundle alignment, respectively) were then intersected with DEGs to identify gene signatures that captured each respective aspect of skin fibrosis. Pathway analysis was performed using GOStats package (Ver. 2.38.0)  in Bioconductor.
Supplementary_files_format_and_content: DESEQ2 normalized counts for genes.

source_name: Skin

growth_protocol: The bleomycin model was with daily subcutaneous injections of bleomycin (100uL at 1U/mL) into the back skin of 8 week old C57Bl/6 female mice, (N = 46 mice) (Jackson Labs, Bar Harbor, ME). At experimental endpoints, mice were euthanized with carbon dioxide, and back skin was harvested, with preservation of the anterior to posterior tissue orientation during tissue harvest. The biopsy was cut in half, with one half used for histopathology analysis, and the other half for RNASeq analysis.

extract_protocol:
Total RNA was isolated from skin biopsies, using GenElute mammalian total RNA kit (Sigma, St Louis, MO).
500 ng RNA was used as starting input to Illumina TruSeq mRNA stranded library construction according to the manufacturers recommendation. High quality libraries were then pooled and sequenced on an Illumina HiSeq 2500

tag: strain

value: WT

tag: treatment

value: 10weeks recovery


title: 10weeks recovery-2

description: processed data file column: ATMT0134

tag: genotype/variation


title: 10weeks recovery-4

description: processed data file column: ATMT0136


title: 10weeks recovery-3

description: processed data file column: ATMT0135


title: AdCMV_48h_rep2

description: AdCMV 48h

tag: passage


title: AdVEGF-A109_48h_rep1

description: AdVEGF-A109 48h


title: AdCMV_48h_rep1

description: AdCMV 48h


title: 10weeks recovery-8

description: processed data file column: ATMT0140


title: MQ1_D1 RRBS


title: AdVammin 48h_rep3_tech

description: AdVammin 48h

value: technical replicate #2 of biological replicate #3


title: 10weeks recovery-7

description: processed data file column: ATMT0139


title: 10weeks recovery-1

description: processed data file column: ATMT0133


title: 6weeks_recovery-5

description: processed data file column: ATMT0131


title: 6weeks_recovery-6

description: processed data file column: ATMT0132


title: AdVEGF-A109_48h_rep2

description: AdVEGF-A109 48h


title: 6weeks_recovery-4

description: processed data file column: ATMT0130


title: AdVammin_48h_rep2

description: AdVammin 48h


title: 10weeks recovery-6

description: processed data file column: ATMT0138


title: 6weeks_recovery-3

description: processed data file column: ATMT0129


title: 4weeks_bleo-7

description: processed data file column: ATMT0123


title: 4weeks_bleo-9

description: processed data file column: ATMT0125


title: 6weeks_recovery-2

description: processed data file column: ATMT0128


title: 6weeks_recovery-1

description: processed data file column: ATMT0127


title: 4weeks_bleo-3

description: processed data file column: ATMT0119


title: 4weeks_bleo-4

description: processed data file column: ATMT0120


title: 2week_bleo-10

description: processed data file column: ATMT0116

value: 2weeks bleomycin


title: 4weeks_bleo-2

description: processed data file column: ATMT0118


title: 4weeks_bleo-1

description: processed data file column: ATMT0117


title: 4weeks_bleo-6

description: processed data file column: ATMT0122


title: 4weeks_bleo-5

description: processed data file column: ATMT0121


title: 4weeks_bleo-8

description: processed data file column: ATMT0124


title: 4weeks_bleo-10

description: processed data file column: ATMT0126


title: 2week_bleo-4

description: processed data file column: ATMT0110


title: 2week_bleo-3

description: processed data file column: ATMT0109


title: 2week_bleo-9

description: processed data file column: ATMT0115


title: 2week_bleo-1

description: processed data file column: ATMT0107


title: 2week_bleo-7

description: processed data file column: ATMT0113


title: 2week_bleo-8

description: processed data file column: ATMT0114


title: 2week_bleo-6

description: processed data file column: ATMT0112


title: 2week_bleo-2

description: processed data file column: ATMT0108


title: saline-10

description: processed data file column: ATMT0106

value: saline


title: saline-9

description: processed data file column: ATMT0105


title: saline-8

description: processed data file column: ATMT0104


title: saline-7

description: processed data file column: ATMT0103


title: saline-6

description: processed data file column: ATMT0102


title: saline-3

description: processed data file column: ATMT0099


title: saline-5

description: processed data file column: ATMT0101


title: 2week_bleo-5

description: processed data file column: ATMT0111


title: saline-4

description: processed data file column: ATMT0100


title: saline-1

description: processed data file column: ATMT0097


title: saline-2

description: processed data file column: ATMT0098


title: Input CTL ventricle

city: Dallas

first: Kedryn

middle: K

last: Baskin

state: TX

address: 6000 Harry Hines

department: Molecular Biology

institute: UT Southwestern

description: IP with IgG antibody, used as control

data_processing:
Quality filtered raw reads were mapped using Bowtie2 and aligned to the mouse reference genome GRCm38 (mm10).
Peak calling was performed by MACS/MACS2
The resulting output files included the peak list in BED format, ChIP signal in bedgraph format, and mapped reads in BAM format. All files were subjected to integrative in-depth analysis with published data and data generated by the Encode project using the Bioconductor software project site. De novo motif discovery in MEF2 and RNA Polymerase II ChIP-seq peak regions were identified using Regulatory Sequence Analysis Tools (RSAT). ChIP-seq data tracks for MEF2 and RNA Poll II were visualized using Integrative Genomics Viewer available online from the Broad Institute.
Genome_build: GRCm38 (mm10)

source_name: heart ventricles from 8 week old mouse

extract_protocol:
Chromatin was isolated, immunoprecipitated using antibodies against MEF2 or RNA Polymerase II, and DNA was isolated.
Kapa Hyper Prep Kit (KK8500, Roche) according to the manufacturer’s instructions

tag: age

value: 8 week

tag: tissue

value: Heart ventricles

value: IGG


title: MEF2_KO58

description: Med12cKO ventricle 1


title: cortex, KO rep3

value: brain

value: Cdr1as knockout

tag: sample type

value: dissected cortex


title: MEF2_WT70

description: CTL ventricle 2


title: PolII_WT70

description: CTL ventricle 2

value: PolII


title: PolII_KO58

description: Med12cKO ventricle 1


title: MEF2_KO60

description: Med12cKO ventricle 2


title: PolII_KO60

description: Med12cKO ventricle 2


title: PolII_WT3

description: CTL ventricle 1


title: MEF2_WT3

description: CTL ventricle 1