title: DARPA_20_GTGGCC_L005_R1


title: DARPA_16_CCGTCC_L005_R1

status: Public on Jan 08 2015

type: SRA

city: new york

first: Bojan

last: Losic

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomics

country: USA

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

library_source: transcriptomic

data_processing:
Raw 100 bp cDNA reads were aligned to the Ensembl NCBIM37 mouse reference genome via the popular wrapper tophat (Trapnell et al., 2009), which uses bowtie1 (Langmead et al., 2009) and a spliced junction mapper to treat the problem of spliced gap alignment. Nearly default settings were used with the exception of disabling coverage-based junction detection, which artificially constricts candidate splice junctions to GT-AG (thus losing e.g. GCAG and ATAC) and is only useful for relatively short (<= 75 bp) reads.
Raw read count values were deduced from quantitation against the NCBIM37 annotation features using the package htseq with a strict intersection criterion (reads must be completely enclosed within genic feature, i.e. zero overhang), and these raw values in turn were normalized for median coverage across all samples on a genewise basis.
Based on the distribution of count values, the entire mode of low count values was deleted since it likely corresponds to mapping or other technical errors. The resulting data contain a total of 26,927 genes.
This expression dataset was then investigated for influences from potential covariates, including testing cohorts and process variables of RNA preparation and sequencing. The identification of covariates with significant effects was the same as described for phenotypic measurements. Animal cohorts, RNA preparation batches, and sequencing runs were subsequently identified as significant covariates, and expression data of all genes were then adjusted for these selected covariates by fitting them in a robust linear model and taking the intercept + residuals as the adjusted expression values. Additionally, principal components were extracted from the covariate-adjusted expression data, as they can capture additional unknown factors that influenced gene expression. The first few principal components that were not driven by genetic factors (i.e., did not yield QTL) were selected to further adjust expression data by fitting with a robust linear model. For this expression dataset, the first three principal components were used. Finally, adjusted expression data were inverse normal-transformed and were then for downstream analyses.
Genome_build: MGSCv37 (mm9, NCBIM37)
Supplementary_files_format_and_content: raw_count_matrix.txt file: Count quantitation, constructed as an N x M matrix, where N is the number of genes and M is the number of samples.
Supplementary_files_format_and_content: processed_normalized_expression_matrix.txt file: Normalized, covariate-adjusted, transformed count matrix, as described above.

molecule: total RNA

organism: Mus musculus

source_name: striatum

extract_protocol:
RNA samples were extracted using TRIzol® reagent (Life Technologies, Grand Island, NY) from the striatum of a random subset of 100 F2 mice, and were then shipped to the Genomics Core Facility at the Icahn School of Medicine at Mount Sinai. Sample integrity was assessed using either an Agilent 2100 Bioanalyzer with the RNA 6000 Nano assay or an Agilent 2200 TapeStation with the R6K ScreenTape (Agilent, Santa Clara, CA). The average RIN values were above 9 for all processed total RNA samples.
The standard TruSeq RNA Sample Prep Kit v2 protocol (Illumina, San Diego, CA) was used to prepare the sequencing library. Briefly, the cDNA was synthesized from poly-A-selected and then fragmented total RNA using random hexamers, followed by end-repair and ligation with appropriate sequencing adaptors. The libraries were then subject to size selection and was purified using AMPure XP beads (Beckman Coulter, Brea, CA). Barcode bases (6 bp) were introduced at one end of the adaptors during PCR amplification steps. The size and concentration of the cDNA libraries was measured by Bioanalyzer and Qubit fluorometry (Life Technologies, Grand Island, NY) before sequencing. The cDNA libraries were sequenced on the Illumina HiSeq 2500 System with 100 nucleotide single-end reads, according to the standard manufacturer's protocol (Illumina, San Diego, CA).

tag: strain/background

tag: tissue

value: striatum

tag: animal id


title: DARPA_14_AGTTCC_L004_R1


title: DARPA_15_ATGTCA_L004_R1


title: DARPA_31_ATCACG_L001_R1


title: DARPA_11_GGCTAC_L004_R1


title: DARPA_9_GATCAG_L003_R1


title: DARPA_5_ACAGTG_L002_R1


title: DARPA_2_CGATGT_L002_R1


title: Kai-2 tech rep1

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

data_processing:
Adapters were trimed by FASTX and also the first and last bases were selectively removed based on quality.
Then the reads were mapped onto the human genome (hg19) using bowtie with at most two mismatches allowed.
PARalyzer was used for peak calling using default parameters except using read depth cutoff 50.
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains the m6A sites

organism: Homo sapiens

source_name: HeLa

growth_protocol: HeLa cell was grown in Gibco DMEM media supplemented with 10% FBS and 1% pen-strep (Life Technologies).

extract_protocol:
Total RNA was extracted by TRIzol and mRNA was isolated by FastTrack MAG mRNA isolation kit.
Libraries were constructed by Illumina TruSeq Small RNA Sample Prep Kit.

treatment_protocol: 4-thiouridine was added to growth media to a final concentration of 200 mM and treated for 16 hrs.

tag: cell line

value: HeLa

tag: cell type

value: Cervical cancer cells

tag: passages

tag: ip antibody

value: Anti-m6A antibody


title: F. bidentis juvenil

city: shanghai

first: Ming

middle: Ju

last: Lu

state: shanghai

address: 320 Yueyang Road, Xuhui Area, Shanghai, China

department: Partner Institute for Computational Biology, Shanghai Institutes for Biologic Sciences, CAS

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

data_processing:
raw reads were mapping to CDS of Arabidopsis thanliana using Blat  version v. 34x12 with parameter [-t=dnax -q=dnax -repMatch=100 -trim
calculate RPM of gene for each samples
calingl consensus sequence and construct phylgenetic data matrix are using in-home perl program
extimate proper DNA mutation model using PartitionFinder version V1.1.1
infer phylogentic tree using Bayesian version 3.2.1 and RAxMLboth  apply applying GTR+GAMMA+I model
visual phylogentic tree using Figtree
Genome_build: Arabidopsis thaliana coding sequence, TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for 17 Flaveria sample

organism: Flaveria bidentis

source_name: F. bidentis juvenil

growth_protocol: plant were grown in green house at the University of Toronto

extract_protocol:
This RNA isolation method is a multi-component method involving an initial extraction by hot acid phenol and then a purification and DNase treatment using the RNeasy Mini Kit by Qiagen
RNA libraries were prepared for sequencing using an in-house service by BGI using 20 µg total RNA and the standard Illumina protocol

treatment_protocol: Leaves of multiple plants were sampled to make up 0.1 to 1.0 grams of tissue. For mature leaves, the newest fully expanded leaf was chosen. For juvenile leaves, the leaves most recently starting to expand from the main stem were chosen (0.1 to 0.5 mm depending on species).

value: leaves

tag: developmental stage

value: juvenile


title: F. bidentis mature

source_name: F. bidentis mature

value: mature


title: DARPA_7_CAGATC_L003_R1


title: Tanacetum parthenium

organism: Tanacetum parthenium

source_name: Tanacetum parthenium


title: F. palmeri juvenil

organism: Flaveria palmeri

source_name: F. palmeri juvenil


title: DARPA_13_AGTCAA_L004_R1


title: DARPA_8_ACTTGA_L003_R1


title: F. vaginata juvenil

organism: Flaveria vaginata

source_name: F. vaginata juvenil


title: F. cronquistii juvenil

organism: Flaveria cronquistii

source_name: F. cronquistii juvenil


title: F. cronquistii mature

source_name: F. cronquistii mature


title: DARPA_3_TTAGGC_L002_R1


title: DARPA_12_CTTGTA_L004_R1


title: Footprint_c14_1

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was removed from the reads using the function preprocessReads from within the bioconductor package QuasR (default parameters). The short fragments (about 30bp length) were mapped to the c.elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included aligner bowtie allowing only for uniquely mapping reads. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6")". Gene expression was quantified by counting the number of reads that started within any of the exons beloning to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons,orientation="same"). To compensate for differences in the read depths of the various libraries, each library was normalized to a total of 22.3M reads which represents the smallest library size considering RNA-seq as well as matching RPF samples. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts.
Genome_build: ce6
Supplementary_files_format_and_content: counts

organism: Caenorhabditis elegans

source_name: Whole-worm

growth_protocol: C. elegans eggs were allowed to hatch overnight, hatched L1s were plated on NG 2% plates seeded with OP50, grown to young adult stage and harvested.

extract_protocol:
Worms were lysed, monosomes purified and RNA was isolated using Trizol Reagent (Life Technologies)
The RNA from the monosomal fraction was separated using a 15% TBE-Urea Gel (Invitrogen) and the region around 28-30 nucleotides excised to isolate Ribosome protected fragments (RPFs). The gel piece was forced through a pierced small tube inside an eppendorf tube by centrifugation and RNA from the gel debris was eluted by overnight incubation in 600 µl cracking buffer (20 mM Tris-HCl (pH 7.9), 1 mM EDTA, 400 mM NH4Acetate, 0.5 % SDS). RNA was precipitated with isopropanol at -80 °C for at least 4 hours (isopropanol precipitation). RPFs were 3’ dephosphorylated with 10 Units of T4 polynucleotide kinase (NEB) in T4 PNK buffer with 40 Units of RNasin for 1 hour at 37 °C. Following isopropanol precipitation, the RNA samples were ligated to 3’ adapters according to the Illumina® TruSeq™ Small RNA Sample Preparation protocol and using the reagents of the kit, then again precipitated with isopropanol. Ligation products were 5’ phosphorylated for 30 minutes at 37 °C with 15 Units of T4 polynucleotide kinase (NEB) in T4 PNK buffer, 1 mM ATP and 40 Units of RNasin. Following heat-inactivation of the enzyme for 10 minutes at 70 °C, the RNA was precipitated by isopropanol. Ligation to 5’ adapters, reverse transcription, PCR amplification with barcoded primers and gel-purification of the PCR products were performed using the Illumina® TruSeq™ Small RNA Sample Prep kit. Four different barcodes (RPIX 2, 4, 5, 6) were used.

treatment_protocol: Worms were washed of the plates, washed three times with M9 and frozen in liquid nitrogen

tag: time in development

value: young adults

tag: strain

value: cey-1 (rrr12), cey-4 (ok858) mutant


title: Footprint_c14_2


title: RNASeq_N2_2

data_processing:
The RNA-seq data (50bp read length) were mapped to the c.elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6",splicedAlignment=TRUE)". Gene expression was quantified by counting the number of reads that started within any of the exons beloning to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons,orientation="same"). To compensate for differences in the read depths of the various libraries, each library was normalized to a total of 22.3M reads which represents the smallest library size considering RNA-seq as well as matching RPF samples. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts.
Genome_build: ce6
Supplementary_files_format_and_content: counts

extract_protocol:
Total RNA isolation was performed using Trizol Reagent (Life Technologies). Important: Total RNA was extracted from the same lysate used subsequently for the corresponding ribosome profiling experiment.
Library preparation was performed using the ScriptSeq v2 RNA-Seq library preparation kit (Epicentre) according to the manufacturer's protocol


title: Footprint_N2_1


title: Footprint_N2_2


title: RNASeq_c14_2


title: RNASeq_c14_1


title: RNASeq_N2_1


title: DARPA_6_GCCAAT_L003_R1


title: DARPA_4_TGACCA_L002_R1


title: DARPA_10_TAGCTT_L003_R1


title: Kai-1 tech rep1


title: FLAG-CEY4_MYC_IP_1

data_processing:
The RNA-seq data (50bp read length) were mapped to the c.elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6",splicedAlignment=TRUE)". Gene expression was quantified by counting the number of reads that started within any of the exons beloning to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons,orientation="same"). To compensate for differences in the read depths of the various libraries, we divided each sample by the total number of reads and multiplied by the average library size of all MYC controls. The MYC controls were chosen as a reference for sequence depth because they had substantially fewer reads than the FLAG-IPs. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts.
Genome_build: ce6
Supplementary_files_format_and_content: counts

extract_protocol:
RNA was dissociated from beads by adding Trizol Reagent (Life Technologies) directly to the beads, followed by the normal extraction protocol
Library preparation was performed using the ScriptSeq v2 RNA-Seq library preparation kit (Epicentre) according to the manufacturer's protocol

value: rrrSi307 [dpy-30pro::FLAG(1x)::cey-4ORF::cey-4 3’-UTR::operon linker::PEST:GFPH2B::tbb-2 3'UTR; unc-119(+)] I


title: FLAG-CEY4_MYC_IP_2


title: FLAG-CEY2_MYC_IP_2

value: rrrSi233 [cey-2pro::FLAG(1x)::cey-2ORF::cey-2 3’-UTR::operon linker::PEST:GFPH2B::tbb-2 3'UTR; unc-119(+)] I


title: FLAG-CEY2_MYC_IP_1


title: FLAG-CEY1_MYC_IP_2

value: rrrSi300 [cey-1pro::FLAG(1x)::cey-1ORF::cey-1 3’-UTR::operon linker::PEST:GFPH2B::tbb-2 3'UTR; unc-119(+)] I


title: FLAG-CEY1_MYC_IP_1


title: FLAG-CEY2_FLAG_IP_1


title: FLAG-CEY1_FLAG_IP_2


title: FLAG-CEY4_FLAG_IP_1


title: FLAG-CEY4_FLAG_IP_2


title: FLAG-CEY1_FLAG_IP_1


title: F. angustifolia mature

organism: Flaveria angustifolia

source_name: F. angustifolia mature


title: FLAG-CEY2_FLAG_IP_2


title: F. angustifolia juvenil

source_name: F. angustifolia juvenil


title: DARPA_1_ATCACG_L002_R1


title: BMDC_IFNB_6hr

city: St. Louis

first: Michael

last: Diamond

state: MO

address: McDonnell Pediatric Research Building, Room 7264

department: Division of Infectious Diseases

institute: Washington University in St. Louis

description:
Sample name: DC_IFNB(02_03_L1.D704)
BMDC treated with IFNB for 6 hours

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were clipped for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2-2.2.4 , tophat 2.013 (parameters: tophat --library-type=fr-firststrand -p 8 -r 250 --segment-length 18 -G )
Expression quantification was done with CuffDiff of the Cufflinks package (v.2.20) comparing IFNB-treated to Mock and IFNL-treated to Mock
Genome_build: mm10
Supplementary_files_format_and_content: Output files are generated from CuffDiff of the Cufflinks package: gene_exp_DC_mock_vs_IFNB_6hr (txt file with FPKM values from Mock and IFNB treatment) and gene_exp_DC_mock_vs_IFNL_6hr (txt file with FPKM values from Mock and IFNB treatment)
Supplementary_files_format_and_content: IFN_DC_expression (summary file with larger than 3 fold expression differences relative to mock)

source_name: Bone Marrow Derived Dendritic Cells

growth_protocol: BM-DCs were cultured in RPMI medium supplemented with 10% defined fetal calf serum (HyClone), 20 ng/ml granulocyte-macrophage colony-stimulating factor, sodium pyruvate, kanamycin, sulfate, nonessential amino acids, and glutamine for 6 days.

extract_protocol:
Total RNA was harvested using Qiagen Rneasy Mini Kit.
IlluminaTruSeq Stranded Total RNA with Ribo-Zero Gold  was used for the construction of sequencing libraries.

treatment_protocol: BMDCs are treated with either Serum Free Media(Mock), interferon beta(20ng/ml), or interferon lambda(10ng/ml) for 6 hours.

value: BMDC

tag: treatment

value: IFNB (6 hours)


title: glp-4_2

data_processing:
The RNA-seq data (50bp read length) were mapped to the c.elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6",splicedAlignment=TRUE)". Gene expression was quantified by counting the number of reads that started within any of the exons beloning to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons) which counts the reads irrespective of the strand (unstranded protocol). To compensate for differences in the read depths of the various libraries, we divided each sample by the total number of reads and multiplied by the average library size. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts.
Genome_build: ce6
Supplementary_files_format_and_content: counts

growth_protocol: C. elegans eggs were allowed to hatch overnight, hatched L1s were plated on NG 2% plates seeded with OP50 and grown to the young adult stage.

extract_protocol:
Total RNA isolation was performed using the PicoPure extraction kit following the manufacturer’s instructions. All RNA samples were eluted from columns with 11 µl DEPC treated water. Then all samples were processed with the RIBO-ZERO magnetic gold kit (Epicentre) according to the manufacturer’s protocol to remove rRNA. The resultant rRNA-free supernatant was concentrated using the RNA clean and concentrator kit (Zymo research).
Library preparation was performed using the Ovation® RNA-Seq System V2 kit (Nugen) according to the manufacturer's protocol

treatment_protocol: Around 50 whole glp-4 worms or dissected gonads were transferred to extraction buffer (PicoPure Kit, Life Technologies)

value: glp-4 (bn2) mutant

value: whole worm


title: BMDC_Mock_6hr

description:
Sample name: DC_Mock(02_01_L1.D702)
BMDC treated with serum free media for 6 hours

value: Mock


title: gonad_2

source_name: Gonad only

value: N2 (gonads only)

value: gonad


title: TGEV

city: Ya’an

first: Xiao

last: Liu

state: Sichuan Province

address: 46# Xinkang Road

department: College of Veterinary Medicine

institute: Sichuan Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
After sequencing, the total raw sequencing reads were filtered using Solexa CHASTITY quality control filter. The clean reads which passed quality filtering were then filtered by searching for reads, whose 3’-ends aligned to at least 6 nt of the 3’-adapter.
The adapter sequences were trimmed and the adapter-trimmed-reads (>= 15nt) were aligned to the known Sus scrofa pre-miRNA sequences in the miRBase 19 (miRNA) using Novoalign program (v2.07.11) with at most one mismatch. The unmapped reads were discarded as unusable reads.Any sequence that matched the mature miRNA region ±4nt within a known pre-miRNA hairpin were grouped and the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin were also indicated.
To correct for the difference in tag counts between samples, the tag counts were scaled to tpm (the copy number of transcripts per million) based on the total number of tag aligned to known Sus scrofa pre-miRNAs in miRBase 19. When comparing the differentially expressed miRNA profiles between two samples, fold change was calculated.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Sus scrofa

source_name: Porcine testicular cells (ST cell)

growth_protocol: TGEV Sichuan strain and the ST cell line (Provided by Animal Biotechnology Center of Sichuan Agricultural University) were used in this study. Cell cultures were performed at 106 cells/175 cm2 dishes and were maintained under standard conditions of 37°C and 5% CO2 in modified RPMI-1640 nutrient solution (Thermo Fisher Scientific, Waltham, UK), supplemented with 10% heat-inactivated fetal bovine serum and 50 mg/ml penicillin/streptomycin antibiotic solution (GIBCO, Beijing, China).   The experiment consisted of pooled samples, samples were performed in triplicates. When the cells were 70% confluent in the culture dishes, they were infected with TGEV at 10 PFU per cell. The infected and control cells groups were harvested at 72 post infection (hpi), and resuspended in Trizol (Invitrogen, Shanghai, China) and stored at -70°C. All infected and control samples were combined into a single control group and a single infected group, respectively.

extract_protocol:
RNA was harvested using Trizol reagent. The purity and concentration of total RNA samples were determined with NanoDrop ND-1000.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TGEV infected porcine testicular cells (ST cell)

value: Porcine testicular


title: glp-4_1


title: BMDC_IFNL_6hr

description:
Sample name: DC_IFNL(02_04_L1.D705)
BMDC treated with IFNL media for 6 hours

value: IFNL (6 hours)


title: CM+HFC

city: Hangzhou

first: zhaowei

last: cai

state: Zhejiang

address: Binwen road 548

department: Laboratory Animal Research Center

institute: zhejiang chinese medical university

description: B

data_processing:
Raw sequencing data were evaluated by FAST-QC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), an online bioinformatics program used to characterize quality distributions of nucleotides, position-specific sequencing qualities, GC contents, the proportions of PCR duplication, and k-mer frequencies
Raw reads after quality control testing were then mapped to the reference pig genome version 10.2 (Sscrofa 10.2), using TopHat software
The normalized expression level of each gene was measured by Fragments Per Kilobase of exon per Million Reads (FPKM).
Genome_build: Sscrofa 10.2

source_name: three castrated individuals pooled

extract_protocol:
Liver tissues from pigs were subjected to total RNA extraction using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Total RNA from pigs of the same group was pooled together in equal amounts to generate a mixed sample. Sequencing libraries were prepared using a TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: three groups of pigs were fed a high-fat and high-cholesterol diet

value: Chinese Wuzhishan Pigs

value: liver

tag: age

value: 6–7 months old


title: CM+HFC+T

description: C

source_name: three castrated and testosterone treatment inividuals pooled


title: gonad_1

value: young adults


title: IM+HFC

description: A

source_name: three intact individuals pooled


title: cDC_PU.1

status: Public on Jan 07 2015

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie (version 0.12.8) with the following parameter settings: -m 1 -a - - best - - strata
H3K4me3, H3K27me3 and H3K9me3 peaks were identified using SICER, a spatial clustering approach for the identification of ChIP-enriched regions. H3K4me1 and PU.1 peaks were identified by MACS software (version 1.4.2).
Genome_build: mm9
Supplementary_files_format_and_content: wig files of histone modification and PU.1 profiles were generated by IGVTools (version 2.1.7).

molecule: genomic DNA

source_name: Classical dendritic cell (cDC)

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as described before (Dahl and Collas, 2008) with minor modifications. Briefly, sorted cells were cross-linked at a concentration of 2 million cells/ml with 1% formaldehyde for 6 min at room temperature. Cross-linking was stopped with 0.125 M glycine. Chromatin sonification into fragments of 200-400 bp in size was done by Diagenode Bioruptor with cooling device at 4°C for 10 min with 30 s pulse/pause cycles. Sheared lysates were clarified by centrifugation at 12,000g (10 mins, 4°C). 10 µl Dynabeads Protein A (Life Technologies) were preincubated with either 1 µg IgG control (Santa Cruz) or specific antibodies for H3K4me1, H3K4me3, H3K9me3, H3K27me3 or PU.1. For immunoprecipitation sheared chromatin of 1 million cells was added to the preincubated beads over night at 4°C. Chromatin complexes were isolated by magnetic bead selection and washed with RIPA and TE buffer. Chromatin complexes were digested with 50 µg/ml RNase (Roche) at 37°C for 30 min. Immunoprecipitated DNA was purified using QIAquick PCR Purification Kit according to the manufacturer's protocol (Qiagen). DNA concentration of immunoprecipitated DNA was determined by using Qubit dsDNA HS Assay kit (Life Technologies).
Libraries were prepared and subjected to deep-sequencing on the Illunima platform according to then manufacturer's protocols.

value: Classical dendritic cell (cDC)

tag: chip antibody

value: PU.1 ( Santa Cruz, sc-352)


title: pDC_PU.1

source_name: Plasmacytoid dendritic cell (pDC)

value: Plasmacytoid dendritic cell (pDC)


title: pDC_H3K4me1

value: H3K4me1 (Abcam, ab8895)


title: CDP_PU.1

source_name: Common dendritic cell progenitor (CDP)

value: Common dendritic cell progenitor (CDP)


title: MPP_PU.1

source_name: Multipotent progenitor (MPP)

value: Multipotent progenitor (MPP)


title: CDP_H3K4me1


title: MPP_H3K4me1


title: veh_rep1

city: Gainesville

first: Xiefan

last: Fang

state: Florida

address: 1200 Newell Drive, ARB R1-148

department: Pediatrics

institute: University of Florida

description: Processed data files: counts_gene_refseq.txt; counts_gene_ensembl.txt; counts_transcript_refseq.txt; counts_transcript_ensembl.txt.

data_processing:
RNA-seq reads were uploaded to the galaxy platform (https://main.g2.bx.psu.edu/). 5' or 3' ends with low scores were trimmed, and RNA-seq reads were mapped to the mouse genome (mm10) with the Tophat for Illumina tool. The resulting Binary Sequence Alignment/Map (BAM) files were analyzed with Partek Genomics Suite (GS) version 6.11 (Partek, St. Louis, MO). mRNA quantification and alternative splicing were performed with Partek GS. Refseq Transcripts (2013-05-10) and Ensembl Transcripts release 71 databases were used for gene and transcript annotation.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each gene or transcript annotated to the UCSC RefSeq Transcripts (2013-05-10) or Ensembl Transcripts release 71 databases. Each file contains data for all of the samples.
Supplementary_files_format_and_content: counts_gene_refseq.txt: abundance measurements (raw counts mapped to UCSC RefSeq transcript database).
Supplementary_files_format_and_content: counts_gene_ensembl.txt: abundance measurements (raw counts mapped to Ensembl transcript database).
Supplementary_files_format_and_content: counts_transcript_refseq.txt: abundance measurements (raw counts mapped to UCSC RefSeq transcript database).
Supplementary_files_format_and_content: counts_transcript_ensembl.txt: abundance measurements (raw counts mapped to Ensembl transcript database).

source_name: heart ventricle, vehicle

extract_protocol:
Heart ventricles of embryos from the same dams were dissected and pooled (this represents as N of 1) for total RNA isolation with RNeasy Plus Mini Kit (Qiagen).
TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Pregnant CD-1 mice were injected with 20 mg/kg of caffeine or vehicle control daily from embryonic day (E) 6.5-9.5. On E10.5, total RNA was isolated from embryonic ventricles.

value: heart ventricle

value: embryonic day 10.5

value: vehicle (0.9% NaCl)


title: veh_rep2


title: caff_rep2

source_name: heart ventricle, caffeine

value: caffeine (20 mg/kg)


title: caff_rep1


title: ctrl NPCs RNA-seq 1

city: Lausanne

first: Adamandia

last: Kapopoulou

address: Station 15

department: Sciences de la Vie

institute: EPFL

data_processing:
Raw reads were mapped to the RepBase consensus sequences using bowtie v0.12.7 with parameters -n 3 --best --strata -a
Reads Per Kilobase of consensus sequence per Megabase of library size (RPKM) were calculated using R libraries ShortRead, biomaRt and DESeq
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RPKM values

source_name: ctrl NPCs

growth_protocol: Embryonic forebrain (E13.5) was dissected, dissociated and cultured as neurospheres (500 000 cells/T25 flask) in mouse DMEM/F12 supplemented with EGF (20ng/ml, R&D) and bFGF (10ng/ml, R&D)

extract_protocol:
Total RNA extraction was performed using the RNeasy Mini Kit
RNA (5ug) was subjected to fragmentation using Covaris device, cDNA synthesis and library preparation using an IlluminaTruSeq DNA sample preparation kit as recommended by the manufacturer with a 250-350bp size selection.

value: E13.5 derived neurospheres

tag: passage

value: ´5


title: ctrl NPCs RNA-seq 3


title: ctrl NPCs RNA-seq 2


title: Trim28-deficent NPCs RNA-seq 3

source_name: Trim28-deficent NPCs


title: caff_rep3


title: Trim28-deficent NPCs RNA-seq 1


title: Restricted 6 tp2

city: Dunsany

first: Anthony

middle: Gerard

last: Doran

state: Co Meath

address: Grange

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc

description:
Experimental: day 131 (32 days post restricted diet) with ad libitum following 99 days of restricted diet.
00976_tp2_rest
mRNA

data_processing:
Basecalls performed using CASAVA version 1.4.
Paired fastq files were quality trimmed (q<29) using the fastq-mcf trimming tool. Read pairs with at least one mate read length less than 19 bps were discarded.
RNA-seq reads were aligned to UMD3.1 genome using Bowtie (--very-senstive setting, --solexa1.3-quals), sorted and possible PCR duplicates were removed using Samtools.
Raw counts were enumerated using HTSEQ-count (settings: mode = union).
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: Tab-delimited txt files; First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene.

organism: Bos taurus

source_name: Muscle, energy restricted diet followed by realimentation period, day 131

extract_protocol:
Total RNA was extracted from frozen muscle tissue by homogenisation in Trizol. RNA was then DNase treated and purified using QIAquick PCR spin columns.
Standard Illumina paired-end mRNA-seq libraries were constructed from cDNA which was made from mRNA which had been purified from total RNA by two rounds of polyA tail selection using oligo dT beads.

treatment_protocol: Crossbred Aberdeen Angus x Holstein Friesian (n = 24) steers were assigned to one of two feeding treatments. Over a 99 d period, 1 group (n=12) was offered a high energy control diet consisting of concentrates ad libitum and 7 kg of grass silage per head daily. The second group (n=12) was offered an energy restricted diet consisting of grass silage ad libitum plus 0.5 kg of concentrate per head per day. From the end of the differential feeding period (99 d), both groups of animals were offered a total mixed ration (grass silage:concentrate ratio of 80:20). This period, which lasted 200 d, was known as the realimentation period. All animals were slaughtered on d 299 of the study.

tag: breed

value: crossbred Aberdeen Angus x Holstein Friesian

tag: gender

value: male

value: muscle

tag: diet

value: mixed ration of grass silage:concentrates with ratio of 80:20

tag: restriction model

value: undergoing compensatory growth

tag: biopsy day

value: day 131 of study period

tag: feeding period

value: realimentation period


title: Trim28-deficent NPCs RNA-seq 2


title: Restricted 4 tp1

description:
Experimental: day 99 with restricted diet.
00921_tp1_rest
mRNA

source_name: Muscle, energy restricted diet, day 99

tag: tissue

value: energy restricted diet of grass silage ad libitum plus 0.5 kg of concentrates

value: undergoing restricted feed intake

value: day 99 of study period

value: differential feeding


title: Restricted 6 tp1

description:
Experimental: day 99 with restricted diet.
00976_tp1_rest
mRNA


title: Restricted 4 tp2

description:
Experimental: day 131 (32 days post restricted diet) with ad libitum following 99 days of restricted diet.
00921_tp2_rest
mRNA


title: ST

tag: cell type

value: Normal porcine testicular cells (ST cell)

value: Porcine testicular


title: Restricted 5 tp2

description:
Experimental: day 131 (32 days post restricted diet) with ad libitum following 99 days of restricted diet.
00926_tp2_rest
mRNA


title: cDC_H3K4me1

value: Classical dendritic cell (cDC)

value: H3K4me1 (Abcam, ab8895)


title: Restricted 2 tp2

description:
Experimental: day 131 (32 days post restricted diet) with ad libitum following 99 days of restricted diet.
00553_tp2_rest
mRNA


title: Restricted 3 tp1

description:
Experimental: day 99 with restricted diet.
00587_tp1_rest
mRNA


title: Restricted 3 tp2

description:
Experimental: day 131 (32 days post restricted diet) with ad libitum following 99 days of restricted diet.
00587_tp2_rest
mRNA


title: Restricted 5 tp1

description:
Experimental: day 99 with restricted diet.
00926_tp1_rest
mRNA


title: Restricted 2 tp1, rep1

description:
Experimental: day 99 with restricted diet.
00553_tp1_rest_r1
mRNA


title: Restricted 2 tp1, rep2

description:
Experimental: day 99 with restricted diet.
00553_tp1_rest_r2
mRNA


title: Foreskin fibroblasts

city: Cambridge

first: Nataly

middle: Moran

last: Cabili

state: MA

address: 7  Cambridge Center

institute: Broad Institute ;  Harvard University

description:
Foreskin
Reanalysis of GSM759893.
polyA RNA

data_processing:
All reads aligned with TopHat version 1.4.0 using the following options: "-a 5" against hg19 and annotated UCSC coding transcripts.
Alignments were processed with Cuffdiff version 2.0.0 using default options in the 'non-diff' mode.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: genes.fpkm_tracking: Cuffdiff expression tracking.
Supplementary_files_format_and_content: refAnnotation.UcscAndCabiliEtAl2011lncRNA.hg19.gtf: GTF file including UCSC coding genes and long non-coding RNA from Cabili et al. Genes and Development 2011 (PMID 21890647); Cuffdiff was applied on this reference GTF.

source_name: Cultured human foreskin fibroblast

extract_protocol:
RNA was extracted from in-house cultured cell lines using TRIzol (Invitrogen) following the manufacturer instructions. After extraction a DNAse treatment was applied using Turbo DNAse (Ambion) and a second RNA extraction with TRIzol was performed.
The standard mRNA-seq library preparations was done using the “Illumina mRNA-Seq Sample Prep Kit” (Part #RS-100-0801). Briefly, poly A+ RNA is purified from 100ng of total RNA with oligo-dT beads. Purified mRNA or RiboMinus RNA (200 ng)  is then fragmented with divalent cations under elevated temperature. First strand cDNA synthesis is performed with random hexamers and reverse transcriptase. Second strand cDNA synthesis is performed using RNAseH and DNA PolI.  Following cDNA synthesis, double stranded products are end repaired, a single “A” base is added, and then the Illumina PE adaptors are ligated onto the cDNA products. For this study ligation products were purified using gel electrophoresis.  The target size range for these libraries was ~350-500 bp on the gel such that the final library for sequencing would have cDNA inserts with sizes of ~160-380 bp long.  Following gel purification the adapter ligated cDNA is then amplified with 12-14 cycles of PCR.

tag: cell line

value: hFF

value: cultured human foreskin fibroblasts


title: Lung fibroblasts batch 3

description:
hLF_b2
Reanalysis of GSM759892.
polyA RNA

source_name: Cultured human lung fibroblast

value: hLF

value: cultured human lung fibroblasts


title: Lung fibroblasts batch 1, sample 2

description:
hLF_b1_2
Reanalysis of GSM759891.
polyA RNA


title: Lung fibroblasts batch 1, sample 1

description:
hLF_b1_1
Reanalysis of GSM759890.
polyA RNA


title: Control 6 tp2

description:
Control: day 131 with ad libitum diet.
00584_tp2_cont
mRNA

source_name: Muscle, high energy diet followed by realimentation period, day 131

value: crossbred Aberdeen Angus x Holstein Friesian

value: male

value: muscle

value: control


title: Control 5 tp2

description:
Control: day 131 with ad libitum diet.
00521_tp2_cont
mRNA

value: mixed ration of grass silage:concentrates with ratio of 80:20

value: day 131 of study period

value: realimentation period


title: Control 5 tp1

description:
Control: day 99 with ad libitum diet.
00521_tp1_cont
mRNA

source_name: Muscle, high energy diet, day 99

value: high energy diet of concentrates ad libitum plus 7kg grass silage

value: day 99 of study period


title: Restricted 1 tp1

description:
Experimental: day 99 with restricted diet.
00465_tp1_rest
mRNA

value: energy restricted diet of grass silage ad libitum plus 0.5 kg of concentrates

value: undergoing restricted feed intake

value: differential feeding


title: Control 4 tp2

description:
Control: day 131 with ad libitum diet.
00468_tp2_cont
mRNA


title: Control 4 tp1

description:
Control: day 99 with ad libitum diet.
00468_tp1_cont
mRNA


title: Control 2 tp2, rep2

description:
Control: day 131 with ad libitum diet.
00030_tp2_cont_r2
mRNA


title: Control 3 tp2

description:
Control: day 131 with ad libitum diet.
00414_tp2_cont
mRNA


title: Control 2 tp1

description:
Control: day 99 with ad libitum diet.
00030_tp1_cont
mRNA


title: Control 1 tp2

description:
Control: day 131 with ad libitum diet.
00023_tp2_cont
mRNA


title: Control 2 tp2, rep1

description:
Control: day 131 with ad libitum diet.
00030_tp2_cont_r1
mRNA


title: Restricted 1 tp2

description:
Experimental: day 131 (32 days post restricted diet) with ad libitum following 99 days of restricted diet.
00465_tp2_rest
mRNA

value: undergoing compensatory growth


title: Control 3 tp1

description:
Control: day 99 with ad libitum diet.
00414_tp1_cont
mRNA


title: Control 1 tp1, rep2

description:
Control: day 99 with ad libitum diet.
00023_tp1_cont_r2
mRNA


title: TruSeq - 20%

city: Stanford

first: Peter

middle: Acuña

last: Combs

state: CA

address: Gilbert Rm 309, 371 Serra Mall

department: Biology

institute: Stanford University

data_processing:
CASAVA v1.8
STAR --runMode genomeGenerate --sjdbGTFfile dmel_dvir.gtf
STAR --outSAMstrandField intronMotif --outReadsUnmapped Fastx
htseq-count --idattr='gene_name' --stranded=no --order=pos
Genome_build: D. virilis r1.2
Genome_build: D. melanogaster r5.54

organism:
Drosophila melanogaster
Drosophila virilis

source_name: Pooled embryos 0-4hrs

growth_protocol: Standard conditions

extract_protocol:
TRIzol extraction of pools of whole embryos
Illumina TruSeq mRNA Unstranded
Epicentre TotalScript: oligo(dT) Primed
Clontech Low Volume Library Construction Kit
SMARTseq v2
SMARTseq v2 - Tagmentation volume 1/2.5
SMARTseq v2 - Tagmentation volume 1/5

tag: fraction d. virilis

tag: library prep protocol

value: Illumina TruSeq mRNA Unstranded

tag: input rna volume


title: SMARTseq2 - 5x dilution - 5%

value: SMARTseq v2 - Tagmentation volume 1/5


title: SMARTseq2 - 5x dilution - 1%


title: TruSeq - 10%


title: SMARTseq2 - 5x dilution - 20%


title: SMARTseq2 - 5x dilution - 10%


title: TruSeq - 5%


title: TruSeq - 0%


title: SMARTseq2 - 5x dilution - 0%


title: Control 6 tp1

description:
Control: day 99 with ad libitum diet.
00584_tp1_cont
mRNA


title: SMARTseq2 - 2.5x dilution - 1%

value: SMARTseq v2 - Tagmentation volume 1/2.5


title: SMARTseq2 - 2.5x dilution - 5%


title: SMARTseq2 - 2.5x dilution - 10%


title: SMARTseq2 - 20%

value: SMARTseq v2


title: Control 1 tp1, rep1

description:
Control: day 99 with ad libitum diet.
00023_tp1_cont_r1
mRNA

value: crossbred Aberdeen Angus x Holstein Friesian


title: SMARTseq2 - 5%


title: PANC1 siTCF7L2 1

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

description: siRNA RNAseq

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 hg19 whole genome using bowtie2 with ultrasensitive parameters.
RNA-seq reads were counted over gene exons using HTSeq using the hg19_refFlat.gtf file from UCSC Genome Browser.
EdgeR was used for statistical analyses of siControl and siTCF7L2 samples, and a fold change (FC) of 2 was used to call the differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include HTSeq count values for each Sample in a matrix

growth_protocol: PANC1 cells were grown in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
Total RNA was collected 48 hours post-transfection using Trizol according to manufacturer’s instructions (Life Technologies).
Total RNA was used for polyA+ RNA selection using oligo-dT beads and subjected to library construction by True-Seq library preparation kits (Illumina), followed by Illumina HiSeq2000 sequencing.

treatment_protocol: Transfections were performed using Lipofectamine RNAiMax (Life Technologies) according to manufacturer’s instructions. A final concentration of 40nM siRNAs targeting either TCF7L2 (catalog # 4392420, Life Technologies) or a non-specific negative control siRNA (catalog # AM4611, Life Technologies) were used using reduced serum OptiMEM media (Life Technologies).

value: pancreatic ductal carcinoma cell line

tag: sirna

value: TCF7L2 siRNA


title: PANC1 siTCF7L2 2

description: siRNA RNAseq


title: PANC1 siTCF7L2 3

description: siRNA RNAseq


title: Epicentre Oligo dT - 10%

value: Epicentre TotalScript:oligo(dT) Primed


title: SMARTseq2 - 2.5x dilution - 20%


title: PANC1 control siRNA 3

description: siRNA RNAseq

value: control siRNA


title: Epicentre Oligo dT - 5%


title: PANC1 control siRNA 1

description: siRNA RNAseq


title: Clontech - 20%

value: Clontech Low Volume Library Construction Kit


title: Clontech - 5%


title: Clontech - 10%


title: REP Dnase-seq rep 1

first: Ann

last: Harris

state: Illinois

address: 2430 N Halsted

institute: Northwestern University

data_processing:
Bowtie v 1.0.0 used for alignment
Sequences are mapped to hg19 reference genome with parameters:  -q -m 1 -l 20 -n 3 --best --strata  --chunkmbs 256 -p 10
The peak calls for the DNase-seq data were made with the F-seq application to give a discrete number of DHS within the REP cells. These sites were determined by F-seq by fitting the data to a gamma distribution to calculate p-values. P-values below a 0.05/0.01 threshold in contiguous regions were considered significant.
Genome_build: hg19
Supplementary_files_format_and_content: BED file containing the locations of DNase hypersensitive sites

source_name: immortalized primary fetal human epididymis cells

growth_protocol: Cells are cultured in Primaria flasks (Falcon) in CMRL 1066 medium, containing 20% foetal calf serum (FCS) (Gibco, UK); L-glutamine (4mM); insulin (0.2 unit/ml); cholera toxin (10-10M) and hydrocortisone (1μg/ml), all from Sigma. Cultures were routinely maintained at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
genomic DNA is digested with different concentrations of DNaseI (NEB) and purified for library construction
DNase-seq libraries were prepared using the Crawford lab method

value: SV-40 transformed primary human fetal epididymis cells


title: REP Dnase-seq rep 2


title: Epicentre Oligo dT - 0%


title: REP PAX2 siRNA rep 4

data_processing:
Paired-end reads are mapped back to hg19 reference genome with Tophat v 2.0.9 with default parameters.
The aligned reads were then processed by Cufflinks (v2.1.1) to assemble expressed genes and transcripts against the UCSC hg19 gene structure annotation, and estimate expression levels for each transcript.
The assembly files for each of the 8 samples were then merged to create a single transcriptome annotation and differentially expressed genes identified by Cuffdiff.
Samples were then normalized and expressed as fragments per kilobase of transcript per million fragments mapped (FPKM) and both a test statistic (p-value) and an adjusted p-value (q-value) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene and fold difference between control and PAX2 siRNA samples.

extract_protocol:
TRIzol® (Life Technologies) used for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells at 40-50% confluence were transfected with non-targeting control- or PAX2-targeting siRNA (sc-37007 and sc-38745, Santa Cruz, Dallas, TX) using RNAiMax Lipofectamine 2000 reagent (Life Technologies, Grand Island, NY) at a final concentration of 20 nM. After 24h, media was replaced with fresh media. At 72h post transfection, the cells were washed in PBS and immediately harvested for RNA extraction using TRIzol® (Life Technologies).


title: REP PAX2 siRNA rep 3


title: REP PAX2 siRNA rep 2


title: Clontech - 0%


title: SMARTseq2 - 2.5x dilution - 0%


title: SMARTseq2 - 0%


title: REP control siRNA rep 3


title: Epicentre Oligo dT - 20%


title: REP control siRNA rep 1


title: SMARTseq2 - 10%


title: REP control siRNA rep 2


title: PANC1 control siRNA 2

description: siRNA RNAseq


title: hFF_2

description:
hFF_scramble2
polyA RNA

source_name: human foreskin fibroblast, scramble siRNA

extract_protocol:
Total RNA from human cell lines was extracted with Trizol (Invitrogen) and purified via the RNeasy mini kit (Qiagen) according to the manufacturers' instructions. RNA quality was assessed using an Agilent Bioanalyzer.
RNA-Seq libraries were prepared with the TruSeq mRNA-Seq kit (v1) according to manufacturer's instructions (polyA selection). Sequenced insert length for all libraries was approximately 180bp with a standard deviation of 50bp.

value: BJ (ATCC CRL-2522)

value: foreskin fibroblast cell line

tag: transfection

value: scramble siRNA

tag: barcode

value: ATCACG

tag: lane number


title: hFF_1

description:
hFF_scramble1
polyA RNA


title: REP control siRNA rep 4


title: RNA-seq_Sample 10

city: Suzhou

first: Yifeng

last: Zhou

state: Jiangsu

address: Ren Ai road #199

institute: Soochow University

description:
RNA-seq replicate 1 read1
RNA-seq replicate 1 read2
RNA-seq replicate 2 read1
RNA-seq replicate 2 read2

data_processing:
RNA-seq Alignment: Sequence reads were obtained and mapped to the human (hg19) genomes using the Tophat2. All reads mapping with five or fewer mismatches were retained.
FPKM: FPKMs were generated by Cufflinks2 using the alignment output from tophat.
Genome_build: hg19
Supplementary_files_format_and_content: The fpkm.txt processed files are the output files from Cufflinks with gene FPKM information

source_name: endometrial tumor

extract_protocol:
Purified mRNA was fragmented and reverse-transcribed with random hexamers into cDNA for Illumina 100-nucleotide paired-end sequencing, by using the RNA-Seq Sample Prep kit (Illumina Inc).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: sample donor

value: donor No.5

value: female

tag: organ

value: endometrium

value: endometrial tumor


title: RNA-seq_Sample 9

source_name: adjacent normal tissue

tag: gender

value: adjacent normal tissue


title: RNA-seq_Sample 17

value: donor No.9


title: RNA-seq_Sample 8

value: donor No.4


title: RNA-seq_Sample 16

value: donor No.8


title: RNA-seq_Sample 13

value: donor No.7


title: RNA-seq_Sample 7


title: RNA-seq_Sample 5

value: donor No.3


title: RNA-seq_Sample 6


title: RNA-seq_Sample 11

value: donor No.6


title: RNA-seq_Sample 14


title: RNA-seq_Sample 12


title: REP PAX2 siRNA rep 1


title: RNA-seq_Sample 4

value: donor No.2


title: RNA-seq_Sample 2

value: donor No.1


title: RNA-seq_Sample 3


title: hFF_3

description:
hFF_scramble3
polyA RNA

value: BJ (ATCC CRL-2522)


title: RNA-seq_Sample 1


title: RNA-seq_Sample 15


title: RNA-seq_Sample 18


title: m15_2b_130

status: Public on Jan 06 2015

city: New York

first: Joseph

middle: M

last: Luna

address: 1230 York Ave #64

institute: The Rockefeller University

description: CLIP-seq

data_processing:
Sequenced reads were trimmed for adaptor sequence, if any, and then mapped to hg18 whole genome using novoalign. Mapped reads were collapsed on the basis of the 5'prime degenerate linker, as in Moore et al., Nature Protocols, 2014.
Collapsed mapped reads were clustered, where the peak cluster coordinate +/- 32 nt was searched for the presence of miRNA 6-8mers, for those miRNAs with CLIP evidence.
Fold changes were calculated by adding a psuedocount of 1 to every cluster, normalizing each cluster for read depth (reads per million mapped), and dividing by condition.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text file includes HiTS-CLIP cluster definition and locations, miRNA seed search results, and genomic annotations.

growth_protocol: Cells were maintained in DMEM supplemented with 5%FBS and 1% Non-essential amino acids, under 5% Co@ at 37C.

extract_protocol:
UV crosslinked cells were lysed in 1x PXL buffer, lystates were Dnase treated, partially RnaseA digested, clarified by centrifugation, and Argonaute-mRNA complexes isolated with pan-Ago 2A8 antibody.
Libraries were prepared as in Moore M et al. 2014 but with the following modifications. The 2nd PCR step was used to introduce library specific indices that were additionally compatible with MiSeq sequencers using version2 chemistry.

treatment_protocol: Cells were infected with m15 J6/JFH1 Clone 2 virus at an MOI of 1-2. Virus inoculum was washed off 6 hours post infection. Cells underwent harvest, with appropriate Mock infected controls at 96 hours post-infection.

tag: infection status

value: m15 J6/JFH Clone2

tag: biologic replicate

tag: antibody

value: anti-AGO1-4 (2A8 monoclonal)

tag: rna species

value: miRNA


title: m15_2a_130

description: CLIP-seq


title: m15_1b_130

description: CLIP-seq


title: m15_1a_130

description: CLIP-seq

value: mRNA


title: Mock2a_130

description: CLIP-seq

value: Mock


title: Mock1b_130

description: CLIP-seq


title: Mock 96 hours replicate 1

description: polyA RNA

data_processing:
Fastq files were groomed for quality (min score 20) and aligned with bowtie allowing up to 2 mismatched and discarding reads with multiple hits.
Mapped read coordinates were then intersected with a meta-transcript file of the longest isoform of every coding gene in RefSeq and then counted. The resulting reads per gene count, for each RNA-Seq replicate then underwent statistical analysis and quantification using EdgeR (Robinson et al., 2009).
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text file counts per gene matrix, fold change, counts per million and FDR values for virus versus mock infection comparisons.

extract_protocol:
Total RNA was isolated via Trizol extraction, RQ1 DNAse treated, and re-extracted using phenol:chlorofom.
RNA libraries were prepared for sequencing using standard Illumina protocols with polyA selection.

treatment_protocol: Cells were infected with WT or m15 HCV viruses at an MOI of 1-2. Virus inoculum was washed off 6hours post infection. Cells underwent harvest, with appropriate Mock infected controls at 72 and 96 hours, for WT and m15 HCV infections respectively.


title: Mock1a_130

description: CLIP-seq


title: 4C-Seq for hoxa13a promoter in 24hpf zebrafish

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
Library strategy: 4C-Seq
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the Danio rerio (danRer7 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
Raw reads were converted into reads/DpnII fragment, and a running 30 bins-window smoothing algorithm was used to smooth the data.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: danRer7
Supplementary_files_format_and_content: bedGraph, they contain smoothed data of 2Mb around each viewpoint that can be directly uploaded to UCSC for visualization.

organism: Danio rerio

source_name: 24hpf zebrafish embryos

growth_protocol: Embryos were raised at 28ºC untill they reached the desired developmental stage. They were dechorionated manually before fixation.

extract_protocol:
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

tag: tissue

value: whole embryos

tag: developmental stage


title: 4C-Seq for hoxa13b promoter in 60hpf zebrafish

source_name: 60hpf zebrafish embryos


title: 4C-Seq for hoxa13b promoter in 48hpf zebrafish

source_name: 48hpf zebrafish embryos


title: 4C-Seq for hoxa13b promoter in 24hpf zebrafish


title: ATACseq in whole 24hpf zebrafish embryos

data_processing:
Library strategy: ATAC-seq
Alignment: reads were aligned using zebrafish July 2010 assembly (danRer7) and mouse July 2007 (mm9) as reference genomes and Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using UCSC Genome Browser.
Genome_build: mm9 / danRer7
Supplementary_files_format_and_content: bigWig format for visualization

source_name: Zebrafish whole embryos

growth_protocol: Wild type embryos were raised at 28ºC until 24hpf stage.

extract_protocol:
10 zebrafish embryos were manually dechorionated and disrupted in Ginzburg Fish Ringers.
Cells were processed for ATAC-seq as previously described (Buenrostro et al., 2013) with the following modifications: 12 total cycles of PCR were used, and DNA cleanups were performed using a Nucleospin Gel and PCR Clean up kit (Macherey-Nagel).


title: m15 virus 96 hours replicate 2

description: polyA RNA

tag: cell line

value: m15 J6/JFH1 Clone2


title: 4C-Seq for hoxa13a promoter in 60hpf zebrafish


title: m6A-seq in Mettl3-KO ESCs, Input

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
ES_m6A_KO_Input
negative control

data_processing:
library strategy: m6A-seq
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm10 reference genome (downloaded from ensemble) using TopHat version 2.0.10. Flags used: -M
We identified enriched intervals using MACS version 1.4.1, while using the input as control in order to define a background model.
Final peak list includes peaks that appaer in at least 2 out of 3 replicates (or 2 out of 2 in MEF), their MACS fold-change is >2, and FDR < 5%, and they fall in annotated gene whose expression level was equal or over the first quartile of the expression level of all genes.
Genome_build: mm10
Supplementary_files_format_and_content: final_peaks.xlsx: final list of peaks in ESC, EBs and MEFs, and their mapping to genes

source_name: Embryonic Stem Cells

growth_protocol: Maintenance of grounds state naïve murine pluripotent cells was conducted in FBS free N2B27-based media, and included 10μg recombinant human LIF and small-molecule inhibitors CHIR99021 (CH, 1-3 μM- Axon Medchem) and PD0325901 (PD, 1 μM - TOCRIS) termed 2i. For embryoied bodies formation 5x10^6 ESCs were disaggregated with trypsin and transfer to low non-adherent palte and culture in MEF medium (DMEM supplemented with 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin/streptomycin and 15% FBS) for 8-21 days. MEF generation: E13.5 mouse embryo was decapitated and disaggregated with trypsin and culture in MEFs medium until MEFs population were expended.

extract_protocol:
Cells were harvested and RNA was extracted using the 5 PRIME PerfectPure RNA Cell culture Kit (cat#2302340 ), according to manufacturer's manual
Libraries were prepared according to NEB's instructions accompanying the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Cat# 7530).

tag: strain

tag: genotype/variation

value: Input

tag: cell type

value: Embryonic Stem Cells


title: Mock 96 hours replicate 2

description: polyA RNA


title: 4C-Seq for hoxa13a promoter in 48hpf zebrafish


title: Restricted 2 tp1, rep3

description:
Experimental: day 99 with restricted diet.
00553_tp1_rest_r3
mRNA

tag: breed

value: crossbred Aberdeen Angus x Holstein Friesian

value: male

value: muscle

tag: diet

value: energy restricted diet of grass silage ad libitum plus 0.5 kg of concentrates

tag: restriction model

value: undergoing restricted feed intake

tag: biopsy day

value: day 99 of study period

tag: feeding period

value: differential feeding


title: m6A-seq in Mettl3-KO ESCs, IP

description:
ES_m6A_KO_IP
negative control


title: WT 72 hours replicate 2

description: polyA RNA

value: J6/JFH1 Clone2


title: 4C-Seq for hoxd13a promoter in 60hpf zebrafish


title: m15 virus 96 hours replicate 1

description: polyA RNA


title: ATACseq in 60hpf zebrafish fin cells

source_name: Cells from zebrafish fins

growth_protocol: Transgenic zebrafish embryos that express GFP only in the distal cells of the fin were raised until 60hpf stage.

extract_protocol:
Fin tissue was dissected and disrupted and GFP expressing cells were selected using Fluorescence-activated cell sorting (FACS).
Cells were processed for ATAC-seq as previously described (Buenrostro et al., 2013) with the following modifications: 12 total cycles of PCR were used, and DNA cleanups were performed using a Nucleospin Gel and PCR Clean up kit (Macherey-Nagel).

value: fin distal cells


title: 4C-Seq for hoxd13a promoter in 48hpf zebrafish


title: Mock 72 hours replicate 2

description: polyA RNA


title: WT 72 hours replicate 1

description: polyA RNA


title: 4C-Seq for hoxd13a promoter in 24hpf zebrafish


title: 122KO replicate 2

description: CLIP-seq

data_processing:
Sequenced reads were trimmed for adaptor sequence, if any, and then mapped to hg18 whole genome using novoalign. Mapped reads were collapsed on the basis of the 5'prime degenerate linker, as in Moore et al., Nature Protocols, 2014.
Collapsed mapped reads were clustered, where the peak cluster coordinate +/- 32 nt was searched for the presence of miRNA 6-8mers, for those miRNAs with CLIP evidence.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text file includes HiTS-CLIP cluster definition and locations, miRNA seed search results, and genomic annotations.

tag: genotype

value: anti-AGO1-4 (2A8 monoclonal)


title: Mock 72 hours replicate 1

description: polyA RNA


title: Mock2b_130

description: CLIP-seq


title: 122KO replicate 3

description: CLIP-seq

value: miRNA


title: Mock replicate 4

description: CLIP-seq

treatment_protocol: Cells were electroporated with J6/JFH1 Clone 2 U3 virus RNA or treated with LNA or miravirsen.  Cells underwent harvest with appropriate mock treated controls at 48 hours post-treatment for small RNA inhibitors, or 17days post electroporation for U3 virus infections.

tag: treatment


title: 122KO replicate 1

description: CLIP-seq

value: mRNA


title: Mock replicate 3

description: CLIP-seq

value: Mock


title: GFP replicate 2

description: CLIP-seq

value: WT


title: GFP replicate 1

description: CLIP-seq


title: Mock replicate 1

description: CLIP-seq

tag: timepoint harvested


title: WT replicate 1

description: CLIP-seq


title: miravirsen 30nM replicate 4

description: CLIP-seq

value: miravirsen 30nM


title: Mock replicate 2

description: CLIP-seq


title: miravirsen 30nM replicate 3

description: CLIP-seq


title: WT replicate 2

description: CLIP-seq


title: miravirsen 30nM replicate 2

description: CLIP-seq


title: miravirsen 30nM replicate 1

description: CLIP-seq


title: LNA122 30nM replicate 4

description: CLIP-seq

value: LNA122 30nM


title: LNA122 30nM replicate 3

description: CLIP-seq


title: HCV-U3 LNA 30nM replicate 2

description: CLIP-seq

value: U3 J6/JFH Clone2 virus + LNA122 30nM


title: LNA122 30nM replicate 2

description: CLIP-seq


title: HCV-U3 LNA 3nM replicate 2

description: CLIP-seq

value: U3 J6/JFH Clone2 virus + LNA122 3nM


title: HCV-U3 replicate 1

description: CLIP-seq

value: U3 J6/JFH Clone2 virus


title: HCV-U3 LNA 30nM replicate 1

description: CLIP-seq


title: HCV110 miRNA replicate2

description: CLIP-seq

treatment_protocol: Cells were infected with J6/JFH1 Clone 2 virus at an MOI of 1-2. Virus inoculum was washed off 6 hours post infection. Cells underwent harvest, with appropriate Mock infected controls at 72 hours post-infection.

tag: infection status

tag: biologic replicate


title: LNA122 30nM replicate 1

description: CLIP-seq

tag: antibody

tag: rna species


title: HCV-U3 replicate 2

description: CLIP-seq


title: HCV110 miRNA replicate3

description: CLIP-seq


title: HCV150 miRNA replicate1

description: CLIP-seq


title: HCV-U3 LNA 3nM replicate 1

description: CLIP-seq


title: HCV-U3 replicate 3

description: CLIP-seq


title: HCV150 mRNA replicate1

description: CLIP-seq


title: HCV110 mRNA replicate3

description: CLIP-seq


title: HCV130 mRNA replicate3

description: CLIP-seq


title: HCV130 mRNA replicate2

description: CLIP-seq


title: E47.9

city: Tartu

first: Merli

last: Saare

address: Puusepa 8

department: Obstetrics and Gynecology

country: Estonia

institute: University of Tartu

description: Adjacent healthy peritoneal tissue

data_processing:
Fastq_quality_filter -q 20 -p 100
mapper.pl (mirdeep2) against hg19 with options -e -h -i -j -k TGGAATTCTCGGGTGCCAAGG -l 17 -m
miRDeep2.pl (mirdeep2) against Human mirbase v18
Genome_build: hg19
Supplementary_files_format_and_content: csv files of miRNAs expressed were generated by miRDeep2.pl, expressing the miRNA counts

source_name: Adjacent healthy peritoneal tissue

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Small RNA fraction (< 200nt) was eluted separately from large RNA fraction.
Small RNA libraries were prepared using Bioo Scientific NEXTflex Small RNA Sequencing Kit and NEXTflex small RNA Barcode Primer Set A (Bioo Scientific Corporation) following the manufacturer’s protocol. Size selection of 140-160 bp fragments corresponding to mature miRNAs and adapters was carried out by gel electrophoresis with 10% Mini-PROTEAN TBE Precast gels (Bio-Rad Laboratories). 0.66 pM of individual indexed samples were pooled for template hybridization and clustering/amplification was performed using TruSeq SR Cluster Kit v2-cBot-GA (Illumina).

tag: subject

tag: tissue

value: Adjacent healthy peritoneal tissue


title: HCV110 mRNA replicate2

description: CLIP-seq

tag: cell line


title: E47.6

description: Adjacent healthy peritoneal tissue


title: E47.4

description: Adjacent healthy peritoneal tissue


title: Mock150 miRNA replicate1

description: CLIP-seq


title: Mock110 miRNA replicate3

description: CLIP-seq


title: E47.5

description: Peritoneal endometriotic lesion

source_name: Peritoneal endometriotic lesion

value: Peritoneal endometriotic lesion


title: Mock110 mRNA replicate3

description: CLIP-seq


title: Mock110 miRNA replicate2

description: CLIP-seq


title: E47.3

description: Peritoneal endometriotic lesion


title: Mock130 mRNA replicate3

description: CLIP-seq


title: Mock110 mRNA replicate2

description: CLIP-seq


title: E47.1

description: Eutopic endometrium of endometriosis patient


title: Mock130 mRNA replicate2

description: CLIP-seq


title: E101.4

description: Peritoneal endometriotic lesion


title: E101.3

description: Adjacent healthy peritoneal tissue


title: HCV130 mRNA replicate1

description: CLIP-seq


title: Mock130 mRNA replicate1

description: CLIP-seq


title: HD31_T_7_SL17311

city: Nashville

first: Andrew

middle: J

last: Link

state: Tennessee

address: 1161 21st Ave South

department: Pathology, Microbiology and Immunology

institute: Vanderbilt University School of Medicine

description: poly-A enriched mRNA

data_processing:
Image analysis and base calling was performed using the standard Illumina Pipeline consisting of Real time Analysis (RTA) version v1.13.
Raw reads were de-multiplexed using a bcl2fastq conversion software v1.8.3 (Illumina, Inc.) with default settings.
Quality control checks on raw sequence data from each sample were performed using FastQC (Babraham Bioinformatics).
 Raw reads were mapped to the reference human genome hg19/GRCh37 using TopHat v1.4
The alignment metrics of the mapped reads were estimated using SAMtools.
Aligned reads were imported onto the commercial data analysis platform AvadisNGS v1.5 (Strand Life Sciences) and were filtered on the basis of read quality metrics where reads with a base quality score less than 30, alignment score less than 95, and mapping quality less than 40 were removed. Remaining reads were then filtered on the basis of their read statistics, where missing mates, translocated, unaligned and flipped reads were removed. The reads list was then filtered to remove duplicates.
Quantification of transcript abundance in AvadisNGS v 1.5 was performed on this final read list using Trimmed Means of M-values (TMM) as the normalization method
Genome_build: hg19
Supplementary_files_format_and_content: Output data was a normalized signal value generated by AvadisNGS v1.5. This data is presented in a tab-delimited text file.

source_name: T cells

extract_protocol:
PBMC and PMN were fractionated from fresh human blood via ficoll separation. CD3+ T cells, CD11c+ mDC, CD14+ monocytes, CD15+ Neutrophils, CD19+ B cells and CD56+ NK cells were isolated from PBMC/PMN by MACS enrichment followed by FACS sorting. Total RNA was extracted from PBMC and sorted immune cells (≤0.5x106 cells) from the two TIV-vaccinated subjects using the automated Maxwell 16® magnetic particle processor and a Maxwell 16 LEV simply RNA kit (Promega Corp.).
Polyadenylated RNAs were isolated using NEBNext magnetic oligo d(T)25 beads. NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs Inc.) was used to prepare individually bar-coded next generation sequencing expression libraries.
50bp, paired end RNA-seq (25 million read)

tag: time

value: 7 d

value: primary human T cells

tag: assay

value: RNA-seq

tag: donor


title: E101.2

description: Peritoneal endometriotic lesion


title: HD31_T_3_SL17303

description: poly-A enriched mRNA

value: 3 d

tag: cell type


title: E101.1

source_name: Eutopic endometrium of endometriosis patient


title: HD31_T_1_SL17295

description: poly-A enriched mRNA

value: 1 d


title: HD31_PBMC_7_SL17305

description: poly-A enriched mRNA

source_name: PBMC

value: primary human PBMC


title: E47.8

description: Peritoneal endometriotic lesion


title: HD31_T_0_SL17287

description: poly-A enriched mRNA

value: 0 d


title: HD31_PBMC_3_SL17297

description: poly-A enriched mRNA


title: HD31_PBMC_1_SL17289

description: poly-A enriched mRNA


title: ATACseq in E12.5 mouse limb cells

source_name: Cells from mouse autopods

extract_protocol:
5 mouse autopods (cut at the zeugopod/autopod boundary) were harvested at e12.5 and placed in 500 uL of PBS supplemented with 0.125% collagenase.  This solution was incubated at 37 degrees C with shaking at 300 rpms for 1.5 hours, with gentle pipetting every 20 minutes to assist in homogenization of the tissue.
Cells were processed for ATAC-seq as previously described (Buenrostro et al., 2013) with the following modifications: 12 total cycles of PCR were used, and DNA cleanups were performed using a Nucleospin Gel and PCR Clean up kit (Macherey-Nagel).

value: autopod cells

tag: developmental stage


title: Red7

city: Portland

first: Qingshuo

last: Zhang

state: OR

address: 3181 SW Sam Jackson Park Road

department: Department of Pediatrics

institute: Oregon Health & Science University

description: mRNA-enriched total RNA

data_processing:
Standard Illumina Cassava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to the mouse reference genome (version mm9) using Bowtie short read aligner software.
Data analysis was performed using EdgeR GLM algorithms.
Data-mining and pathway analysis were carried out with the MetaCore integrated software suite (Thomson Reuters, New York, USA).
Genome_build: mm9

source_name: Ter119+/CD71high/FSChigh cells

extract_protocol:
Trizol followed by RNAeasy kit and mRNA purification with Dynabeads Oligo (dT)25
Libraries were prepared according to Illumina's instructions accompanying TruSeq RNA Sample Prep Kit. (Part#RS-122-2001)

treatment_protocol: Mutant mice and controls were given either OXM diet or placebo for 3 months. OXM was obtained from Sigma (Saint Louis, MO, USA), milled into standard rodent chow at 300mg/kg diet (Bio-Serv, NJ, USA), and given to the mice upon weaning (3 - 4 weeks of age).

tag: strain background

tag: age

value: 4 month

tag: gender

value: male

tag: genotype/variation

value: Wildtype

tag: treated with

value: palcebo

tag: cell population

value: Ter119+/CD71high/FSChigh cells


title: HD31_NEU_0_SL17282

description: poly-A enriched mRNA

source_name: Neutrophils

value: primary human neutrophils


title: HD31_MO_1_SL17292

description: poly-A enriched mRNA

source_name: Monocytes

value: primary human monocytes


title: HD31_NEU_7_SL17306

description: poly-A enriched mRNA


title: HD31_NK_0_SL17286

description: poly-A enriched mRNA

source_name: NK cells

value: primary human NK cells


title: HD31_PBMC_0_SL17281

description: poly-A enriched mRNA


title: HD31_NK_3_SL17302

description: poly-A enriched mRNA


title: HD31_NEU_3_SL17298

description: poly-A enriched mRNA


title: Red10

description: mRNA-enriched total RNA


title: HD31_NK_7_SL17310

description: poly-A enriched mRNA


title: HD31_NK_1_SL17294

description: poly-A enriched mRNA


title: HD31_MO_7_SL17308

description: poly-A enriched mRNA


title: HD31_NEU_1_SL17290

description: poly-A enriched mRNA


title: HD31_MO_0_SL17284

description: poly-A enriched mRNA


title: Red11

description: mRNA-enriched total RNA

value: oxymetholone


title: Red9

description: mRNA-enriched total RNA


title: Red8

description: mRNA-enriched total RNA


title: HD31_DC_7_SL17309

description: poly-A enriched mRNA

source_name: myeloid DC

value: 7 d

value: primary human myeloid DC


title: HD31_DC_1_SL17293

description: poly-A enriched mRNA

value: RNA-seq


title: HSC_27

description: mRNA-enriched total RNA

source_name: pooled library from whole bone marrow cells


title: HSC_26

description: mRNA-enriched total RNA

value: pooled library from whole bone marrow cells


title: HD31_DC_0_SL17285

description: poly-A enriched mRNA


title: HD31_DC_3_SL17301

description: poly-A enriched mRNA

value: 3 d


title: COM16

description: mRNA-enriched total RNA

source_name: cKit+ Sca1+ Lin- cells

value: cKit+ Sca1+ Lin- cells


title: HD31_B_7_SL17312

description: poly-A enriched mRNA

source_name: B cells

value: primary human B cells


title: HSC_24

description: mRNA-enriched total RNA


title: Red6

description: mRNA-enriched total RNA


title: HD31_MO_3_SL17300

description: poly-A enriched mRNA


title: HD31_B_3_SL17304

description: poly-A enriched mRNA


title: QZ_36

description: mRNA-enriched total RNA


title: HD30_T_7_SL27224

description: poly-A enriched mRNA

value: primary human T cells


title: HD31_B_0_SL17288

description: poly-A enriched mRNA

value: 0 d


title: COM15

description: mRNA-enriched total RNA

value: 4 month

value: male


title: HD30_T_1_SL27210

description: poly-A enriched mRNA

value: 1 d


title: HD31_B_1_SL17296

description: poly-A enriched mRNA


title: HSC_22

description: mRNA-enriched total RNA

value: Wildtype


title: HSC_10b

description: mRNA-enriched total RNA

value: palcebo


title: QZ_35

description: mRNA-enriched total RNA


title: HSC_18

description: mRNA-enriched total RNA


title: HD30_PBMC_7_SL27220

description: poly-A enriched mRNA

value: primary human PBMC


title: HSC_23

description: mRNA-enriched total RNA


title: HSC_3

description: mRNA-enriched total RNA


title: HSC_13

description: mRNA-enriched total RNA


title: HD30_PBMC_1_SL27206

description: poly-A enriched mRNA


title: HD30_PMBC_0_SL27199

description: poly-A enriched mRNA


title: HD30_NK_7_SL27225

description: poly-A enriched mRNA

value: primary human NK cells


title: HD30_PBMC_3_SL27213

description: poly-A enriched mRNA


title: COM17

description: mRNA-enriched total RNA

value: oxymetholone


title: HD30_NK_3_SL27218

description: poly-A enriched mRNA


title: double_MethylC-Seq

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: treated with bisulfite

data_processing:
Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position ( unconverted_C / ( converted_C+ unconverted_C ) ).

organism: Arabidopsis thaliana

extract_protocol:
Genomic DNA was extracted from 14-d-old seedlings and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing.
Bisulfite sequencing libraries were prepared using standard Illumina protocols.

tag: genotype

value: 14-day old seedlings


title: mock treated stage 6

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

description: ribosomal RNA (rRNA) depleted

data_processing:
A to I hyper-edit site detection: Identification of A to I hyper-edit sites was carried out as described in Porath et al. 2014 study.
Human A to I hyper-edit site detection: For the detection of human A to I hyper edit site we used the following datasets SRR364681.sra, SRR384965.sra, SRR384964.sra, SRR364680.sra, SRR384963.sra, SRR364679.sra, as well as datasets available under SRP050149 accession number.
C.elegans A to I hyper-edit site detection: For the detection of C.elegans A to I hyper edit site we used the sequencing datasets listed below as well as the following datasets SRR1050768.sra ,SRR1050771.sra, SRR1050774.sra, SRR1050775.sra, SRR1050776.sra, SRR1050777.sra, SRR1272311.sra, SRR1272312.sra, SRR1272313.sra
Supplementary_files_format_and_content: The processed files are in bed-like txt format and contain 3 columns: chromosome, start and end position of hyper-edited nucleotide. C.elegans processed files contain additional 3 columns with 4:triplet nucleotide sequence (centered around hyper edited site), 5:number of reads supporting the site and 6:strand information.

source_name: worm

growth_protocol: C. elegans Bristol N2 wild type worms used in this study were cultured as described previously in Brenner 1974.

extract_protocol:
Total RNA was extracted using TRIZOL (Invitrogen), ribosomal RNA (rRNA) was depleted using a Ribominus kit (Ambion) according to manufacturer's protocol. rRNA depleted RNA was either treated with the exonuclease Rnase-R (to enrich for exonuclease-resistant circular RNA) or simply left at room temperature for the same time (“mock” treated).
Sequencing library was constructed according to default Illumina RNA-Seq for HiSeq2000 (TruSeq) protocol.

value: Young Adult

tag: strain

value: Bristol N2

tag: treatment


title: HD30_NK_1_SL27211

description: poly-A enriched mRNA

value: RNA-seq


title: ago6-2_MethylC-Seq

description: treated with bisulfite


title: mock treated stage 5

description: ribosomal RNA (rRNA) depleted


title: RNase R treated stage 5

description: ribosomal RNA (rRNA) depleted

value: exonuclease Rnase-R


title: ago4-6_MethylC-Seq

description: treated with bisulfite


title: HD30_NK_0_SL27204

description: poly-A enriched mRNA


title: HD30_T_3_SL27217

description: poly-A enriched mRNA

value: 3 d


title: HD30_T_0_SL27203

description: poly-A enriched mRNA


title: HD30_NEU_7_SL27222

description: poly-A enriched mRNA

value: 7 d

value: primary human neutrophils


title: RNase R treated stage 3

description: ribosomal RNA (rRNA) depleted


title: HD30_NEU_3_SL27215

description: poly-A enriched mRNA


title: RNase R treated stage 6

description: ribosomal RNA (rRNA) depleted


title: mock treated stage 2

description: ribosomal RNA (rRNA) depleted


title: mock treated stage 3

description: ribosomal RNA (rRNA) depleted


title: RNase R treated stage 2

description: ribosomal RNA (rRNA) depleted


title: RNase R treated stage 1

description: ribosomal RNA (rRNA) depleted

value: embryo


title: HD30_MO_3_SL27216

description: poly-A enriched mRNA

value: primary human monocytes


title: HD30_NEU_0_SL27201

description: poly-A enriched mRNA

value: 0 d


title: HD30_MO_0_SL27202

description: poly-A enriched mRNA


title: HD30_MO_1_SL27209

description: poly-A enriched mRNA

value: 1 d


title: HD30_DC_7_SL27226

description: poly-A enriched mRNA

value: primary human myeloid DC


title: HD30_MO_7_SL27223

description: poly-A enriched mRNA


title: HD30_DC_3_SL27219

description: poly-A enriched mRNA


title: mock treated stage 1

description: ribosomal RNA (rRNA) depleted


title: HD30_DC_1_SL27212

description: poly-A enriched mRNA


title: HD30_B_7_SL27221

description: poly-A enriched mRNA

value: primary human B cells


title: HD30_DC_0_SL27205

description: poly-A enriched mRNA


title: HD30_B_1_SL27207

description: poly-A enriched mRNA


title: HD30_B_3_SL27214

description: poly-A enriched mRNA


title: HD30_B_0_SL27200

description: poly-A enriched mRNA


title: RNase R treated stage 4

description: ribosomal RNA (rRNA) depleted


title: mock treated stage 4

description: ribosomal RNA (rRNA) depleted


title: HD30_NEU_1_SL27208

description: poly-A enriched mRNA


title: NFAT1 curdlan Input

status: Public on Jan 05 2015

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

data_processing:
The raw data was mapped to mm9 genome assembly using bowtie with default parameters, duplicate reads were removed, the peaks were called using MACS by comparing treatment sample to a control
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadsheet peak call file from MACS

source_name: dendritic cells, NFAT1 curdlan Input

growth_protocol: Murine dendritic cells (D1) were cultured as previously described  (Granucci et al., 2001; Winzler et al., 1997)

extract_protocol:
Lysates were clarified from sonicated nuclei andNFAT1-v5-DNA complexes were isolated with antibody.
Illumina TruSeq DNA version 2 kit according to the manufacturer's protocol, with the following modifications; 30X adaptor dilution, 18 PCR cycles of amplification. Batches of 5-8 samples were sequenced as a multiplex in individual lanes of an Illumina HiSeq 2000 apparatus using a single-end run (1X51) together with the SBS kit v3. Reads were mapped to the mouse genome (version mm9) with bowtie 1 (Langmead et al., 2009) using default parameters.

treatment_protocol: NFAT1 ChIP-seq, we used 10ug/ml for 30 minutes. For H3K4me3 ChIP-seq, we used 10ug/ml for 2 hours.

value: splenic long term dendritic cells

tag: treatment/control

value: control


title: D1 NT Input

source_name: dendritic cells, D1 NT Input


title: D1 curdlan 2h H3K4me3

source_name: dendritic cells, D1 curdlan 2h H3K4me3

value: treatment


title: NFAT1 curdlan V5

source_name: dendritic cells, NFAT1 curdlan V5


title: D1 curdlan Input

source_name: dendritic cells, D1 curdlan Input


title: D1 NT H3K4me3

source_name: dendritic cells, D1 NT H3K4me3


title: D1 curdlan + Fk506 Input

source_name: dendritic cells, D1 curdlan + Fk506 Input


title: D1 curdlan+Fk506 2h H3K4me3

source_name: dendritic cells, D1 curdlan+Fk506 2h H3K4me3


title: AGG-QC footprint

first: Cristina

last: Pop

address: 353 Serra Mall

department: Computer Science

description: tRNA sequence from tR(UCU)B was mutated in the anticodon to CCU using QuikChange site-directed mutagenesis kit (Stratagene) in order for the tRNA product from tR(UCU)B to recognize the AGG codon. The mutated tRNA was cloned in the URA marked 2micron plasmid pRS426 and transformed into 288C

data_processing:
Library strategy: Ribosome profiling
Raw fastq files were stripped of the linker sequence (CTGTAGGCACCATCAAT) using the FASTX-Toolkit v0.0.13 clipper.
Reads were aligned to the yeast genome (R63 from SGD, www.yeastgenome.org) using bowtie v1.0.0 and the following parameters (-l 18 -n 2 -v 2 -m 1 -k 1). Namely, only uniquely mapped reads with less than two mismatches were kept.
The final processed mRNA and fooprint counts are filtered for the mRNA reads with length greater than 26 and footprint reads with length between 28 and 31 inclusive.
Genome_build: R63
Supplementary_files_format_and_content: Processed txt files per sample show a matrix (with columns: gene name, gene length, total mRNA counts, total ribosome footprint counts, and the ribosome footprint counts per position) for the reliable genes in each sample.

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast were grown to OD=0.6

extract_protocol:
To collect the ribosomal footprints, samples were digested with RNAseI and run through a sucrose gradient. Monosomes were collected and 27-32bp fragments were size selected by gel. Library Construction Protocol: Footprints were ligated to linker-1(IDT) using Truncated RNA ligase II(NEB). After reverse transcription, 5' end sequencing adapters were added by circularization with circ ligase II.
Footprints were ligated to linker-1(IDT) using Truncated RNA ligase II(NEB). After reverse transcription, 5' end sequencing adapters were added by circularization with circ ligase II.

treatment_protocol: Cells were filtered and frozen on liquid nitrogen


title: WT footprint

description: wild type yeast


title: AGG-QC mrna

data_processing:
Raw fastq files were stripped of the linker sequence (CTGTAGGCACCATCAAT) using the FASTX-Toolkit v0.0.13 clipper.
Reads were aligned to the yeast genome (R63 from SGD, www.yeastgenome.org) using bowtie v1.0.0 and the following parameters (-l 18 -n 2 -v 2 -m 1 -k 1). Namely, only uniquely mapped reads with less than two mismatches were kept.
The final processed mRNA and fooprint counts are filtered for the mRNA reads with length greater than 26 and footprint reads with length between 28 and 31 inclusive.
Genome_build: R63
Supplementary_files_format_and_content: Processed txt files per sample show a matrix (with columns: gene name, gene length, total mRNA counts, total ribosome footprint counts, and the ribosome footprint counts per position) for the reliable genes in each sample.

extract_protocol: Total RNA was isolated with hot acid phenol. mRNA was selected using oligo dT Dynabeads


title: WT-URA mrna

description: Wild-type yeast with a URA marked 2micron plasmid (pRS426).


title: AGG-OE footprint

description: tRNA arginine (tR(CCU)J) recognizing the AGG codon was overexpressed by cloning into the URA marked 2micron plasmid pRS426 and transforming wild-type yeast using â€"URA selection.


title: ACA-K footprint

description: 3/4 copies of Threonine tRNA (tT(UGU)G2, tT(UGU)H, tT(UGU)P), recognizing the ACA codon, were knocked out using the standard technique of homologous recombination from a plasmid PCR product. The resulting strain was marked with nourseothricin, kanamycin, and hygromycin B resistance respectively. Successfully transformed yeast were identified by check PCR.


title: AGG-OE mrna


title: WT mrna

description: wild type yeast


title: RNASeq_htz1-rrp6-del_rep2

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: University of Cambridge

description: Strand-specific mRNA-seq of htz1Δrrp6Δ, replicate 2

data_processing:
Sequence reads were mapped to the S. cerevisiae genome assembly sacCer1 using Bowtie version 0.12.9, allowing up to 2 mismatches and no ambiguously mapped reads.Mapped reads were then converted to WIG files.
Genome_build: sacCer1
Supplementary_files_format_and_content: BedGraph (WIG)

source_name: Saccharomyces cerevisiae grown in SD medium

growth_protocol: Yeast cells were grown in SD medium to mid-log phase before harvesting for ChIP or RNA extraction.

extract_protocol: Total RNA was purified using the Ribopure Purification Kit (Life Technologies) and contaminating genomic DNA was removed by DNaseI digestion. Illumina TruSeq stranded mRNA sample preparation kits were used for library preparation.

value: MATalpha can1-delta::STE2pr-SP_his5 lyp1-delta his3-delta-1 ura3-delta-0 met15-delta-0 htz1-delta::HpH rrp6-delta::KanMX


title: ACA-K mrna


title: H2A.Z_ChIPSeq_rrp6-del_rep2

description: Htz1 ChIP-seq of rrp6Δ, replicate 2

extract_protocol: Cultures were crosslinked with 1% (v/v) formaldehyde, quenched with glycine, and cells were lysed with beads in a FastPrep-24 (MP Biomedicals) cell homogeniser.  Sonicated, clarified extracts were immunoprecipitated with anti-Htz1 antibodies before washing and DNA extraction, or were used directly to prepare input DNA. Illumina TruSeq ChIP Sample Prep Kit were used for library preparation.

value: MATalpha can1-delta::STE2pr-SP_his5 lyp1-delta his3-delta-1 ura3-delta-0 met15-delta-0 HTZ1-HpH rrp6-delta::KanMX

tag: chip antibody


title: Input_DNA_ChIP-seq

description: ChIP-seq of input DNA wild type S.cerevisiae

value: MATalpha can1-delta::STE2pr-SP_his5 lyp1-delta his3-delta-1 ura3-delta-0 met15-delta-0 HTZ1-HpH


title: in vivo

city: Braunschweig

first: Diego

last: Chaves-Moreno

address: inhoffenstrasse 7

department: Department of Medical Microbiology (MMIK)

institute: Helmholtz Centrum for Infection Research

data_processing:
Base calls for the  GAIIx were done using the GA II x  CASAVA-1.8.1 pipeline and for the MISeq was performed using MiSeq RTA 1.14.23 pipeline
Filtering and trimming with the following parameters: Q ≥ 15, Seq. length ≥ 80nt, Homopolymers ≤ 8nt and N's = 0.
Two sequencing events were done for all in vitro S. aureus samples. After quality filtering, libraries were merged into one file and collapsed into representative reads
From the In vivo sample (Metatranscriptome) human reads were removed using BLAT against a human genome repository downloaded from NCBI ftp site. Sequences with >70% identity were removed
Ribosomal sequences were removed using HMMER (V3.0) using as a database models build with alignments of the Ribosomal fractions (5S,16S, and 23S) and BLASTN against a database of Ribosomal proteins of S. aureus genomes
Reads were assigned as belonging to S. aureus via blastn using a database of 25 concatenated genomes
Remaining reads were blasted (RPS-BLASTN) against a reference database of Position Scoring Matrices (PSM) build from a comparison of 25 Genomes of S. aureus
Read counts were down-sampled by a random resampling using an in-house script written in perl
A rank-ordering (from highest to lowest expression) of all genes in each sample was performed
Supplementary_files_format_and_content: text file with abundance (by counting the number of transcripts) for each gene (groups of genes, OG) within each condition

organism: Staphylococcus aureus

source_name: ANS

growth_protocol: Two S. aureus strains (USA300 and T032) were grown in rich (BHI) and minimun media (SNM) and harvested at different phases (mid-log and stationary). The in vivo sample was taken from the anterior nares of a human nose known to be an S. aureus carrier.

extract_protocol:
RNA was extracted using Qiagen's Rneasy Mini Kit following manufacturer's instructions, the where the samples were treated by beat beating in a solution of RLT Buffer (Qiagen) and 1% of β-mercaptoethanol.
Enriched mRNA fractions were amplified using the MessageAMP II-Bacteria RNA amplification according to manufacturer's instructions. Amplified samples were converted to ds-cDNA using SuperScript Double-Stranded cDNA Synthesis Kit and purified using GeneClean Turbo for PCR Kit (MP Biomed).
Paired-End DNA Sample Prep Kit (Illumina, San Diego, USA) according to manufacturer's instructions

treatment_protocol: Stabilization of the RNA in the samples was performed by incubating with RNAprotect for 30 mins before proceeding with the RNA isolation.

value: Unknown

tag: media

value: In vivo

tag: harvest phase

tag: sequence events

tag: specific host

value: human


title: RNASeq_htz1-del_rep2

description: Strand-specific mRNA-seq of htz1Δ, replicate 2

value: MATalpha can1-delta::STE2pr-SP_his5 lyp1-delta his3-delta-1 ura3-delta-0 met15-delta-0 htz1-delta::HpH


title: RNASeq_rrp6-del_rep2

description: Strand-specific mRNA-seq of rrp6Δ, replicate 2


title: RNASeq_WT_rep2

description: Strand-specific mRNA-seq of wild type S.cerevisiae, replicate 2


title: H2A.Z_ChIPSeq_htz1-del

description: Htz1 ChIP-seq of htz1Δ


title: H2A.Z_ChIPSeq_rrp6-del_rep1

description: Htz1 ChIP-seq of rrp6Δ, replicate 1


title: H2A.Z_ChIPSeq_WT_rep1

description: Htz1 ChIP-seq of wild type S.cerevisiae, replicate 1


title: H2A.Z_ChIPSeq_WT_rep2

description: Htz1 ChIP-seq of wild type S.cerevisiae, replicate 2


title: WT-URA footprint


title: Nascent_RNA_shXPB_DMSO

city: Kansas City

first: Joan

last: Conaway

institute: Stowers Institute

description:
Ribosomal RNA-depleted total RNA
library strategy: nascent-seq
nascent RNA in starved HCT116 cells targeted by shXPB and treated with TPL for 1 hour

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to three mismatches of a 50bp seed length.
Nascent-seq alignments were done using TopHat v2.0.9 with bowtie1 v0.12.9, using -g 1 option and allowing up to two mismatches.
ChIP-seq: Alignments were extended to a total fragment length of 150 bases in the orientation of the read alignment.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Nascent-seq: Reads were aligned using Ensembl 67 GTF human annotations using TopHat v2.0.9 and Bowtie v0.12.9.  Alignments were not extended.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

source_name: Colon cancer cell line

growth_protocol: HCT116 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol:
For ChIP-seq, HCT116 cells were crosslinked with 1% paraformaldehyde for 10 minutes at room temperature with gentle rotation, and then quenched by 0.125 M glycine solution. After washing, nuclei were sonicated on a Misonix Sonicator 3000 Ultrasonic Cell Disruptor, and the supernatant was used for immunoprecipitation with the indicated antibody. ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit. For nascent RNA-seq, HCT116 cells was harvested and washed 3 times with cold PBS, then suspended in 10 ml Buffer A (10 mM HEPES at pH=7.9, 10 mM KCl, 2 mM MgCl2, 1 mM DTT, 1× Complete protease inhibitors [Roche]). After incubating on ice for 15 minutes, the cells were homogenized in pre-cooled 15 ml Dounce tissue homogenizer for 15 times. Nuclei were then washed twice with Buffer B (10 mM HEPES at pH=7.9, 250 mM Sucrose, 1 mM DTT, 1× Complete protease inhibitors). The pellet was vigorously suspended with 1 ml NUN buffer (20 mM HEPES at pH=7.9, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% v/v Nonidet P40, 1 mM DTT, 20 U/ml SUPERase.In RNase Inhibitor [Ambion]) that was freshly prepared. The chromatin was then washed twice more with 5 ml NUN buffer each time. The supernatant was removed and TRIzol reagent (Invitrogen) was added to the pellet for purification of RNA. The RNA was subjected to polyA depletion with Oligo(dT) magnetic beads (Invitrogen) and DNase I treatment (NEB) for 20 minutes, and then was re-purified. For sequencing, 2 μg of resulting RNA was used for ribosomal RNA depletion with the RiboZero kit (Epicenter) and libraries were made with the TruSeq RNA sample Prep Kit (Illumina).
ChIP-seq and Nascent-RNA-seq libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: human colon cancer cell

value: DMSO for 1 hour

tag: serum

value: starved

tag: targeted by

value: shXPB


title: Nascent_RNA_starved_rep3

description:
Ribosomal RNA-depleted total RNA
library strategy: nascent-seq
nascent RNA in starved HCT116 cells


title: Nascent_RNA_shScr_TPL

description:
Ribosomal RNA-depleted total RNA
library strategy: nascent-seq
nascent RNA in starved HCT116 cells targeted by scramble shRNA and treated with TPL for 1 hour

value: TPL for 1 hour

value: scramble shRNA


title: Nascent_RNA_starved_rep1


title: T032(EX)SNM

source_name: Nasal isolate from Northern Germany

value: SNM

value: Exponential


title: Ser5P_starved_rep1_ChIPSeq

description: Chromatin IP of Ser5P Pol II in starved HCT116 cells

tag: antibody

value: CTD Ser5P rat monoclonal 3E8 (Millipore, 04-1572-I)


title: Nascent_RNA_shScr_DMSO

description:
Ribosomal RNA-depleted total RNA
library strategy: nascent-seq
nascent RNA in starved HCT116 cells targeted by scramble shRNA and treated with DMSO for 1 hour


title: Ser5P_starved_rep2_ChIPSeq


title: USA300(EX)SNM

source_name: Reference Strain


title: Pol_II_shNELF-A_starved_rep1_ChIPSeq

description: Chromatin IP of Pol II in starved HCT116 cells targeted by shNELF-A

value: RNAPII rabbit polyclonal N20 (Santa Cruz, sc-899)

value: shNELF-A


title: Pol_II_shNELF-A_starved_rep2_ChIPSeq