title: 5h-OKF6.uninfected.sc.rep1

description:
SRX132006
10_5h_o


title: 8hr-hRSV-infected

status: Public on Mar 30 2014

type: SRA

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

country: USA

institute: University of Maryland Baltimore

description:
intrument models: Illumina Hiseq 2000 and Illumina Genome Analyzer II
infected sample

library_source: transcriptomic

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Human GRCh37 whole genome reference using TopHat v1.4.0 and/or human respiratory syncytial virus (hRSV, AF035006) reference using Bowtie v0.12.9
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: H. sapiens(GRCh37), hRSV(AF035006)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

molecule: total RNA

organism:
Homo sapiens
human respiratory syncytial virus

source_name: human lung epithelial cell

growth_protocol: A549 cells infected with hRSV

extract_protocol:
Ambion miRVANA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells collected by trypsinization; immediately put in Ambion reagent; stored at -80

tag: cell line

tag: time point


title: 90m-HUVEC.infected-Candida.WO1.rep1

description:
SRX123452
16_90m_hc_w

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Human GRCh38 whole genome reference and/or C. albicans SC5314 or WO1 reference using TopHat v1.4.0
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: H. sapiens (GRCh38), C. albicans (sc5314; GCF_000182965.2), C. albicans (wo1; GCA_000149445.2)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism:
Candida albicans
Homo sapiens

source_name: huvec infected

growth_protocol: C. albicans cells were used to infect HUVEC cells or OKF6-TERT2 cells in tissue culture media for the indicated amount of time at 37 degrees celcius. The negative control samples were the host or C. albicans cells alone in tissue culture media for the indicated amount of time.

extract_protocol:
RNA extractions were performed using RiboPure RNA Purification Kit, yeast (Life Technologies, AM1926) following manufacturer's protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: candida strain

tag: infected human culture

value: HUVEC

value: 90 minutes


title: 5h-HUVEC.uninfected.wo.rep1

description:
SRX123584
19_5h_h_w

organism: Homo sapiens

source_name: huvec uninfected

value: none (uninfected)

value: 5 hours


title: 20hr-hRSV-infected


title: 4hr-hRSV-infected


title: PF intermediate-size RNA

city: Beijing

first: Chunyan

last: Wei

address: 5# Dong Dan San Tiao

department: Department of Microbiology and Parasitology

country: China

institute: Institute of Basic Medical Sciences, CAMS & School of Basic Medicine, PUMC

description: RNA (50-500nt)

data_processing:
The 5' and 3' adaptors in the raw paired-end sequencing data were removed, and reads with abnormal adaptors or inserted sequences shorter than 30 nt were filtered.
The remaining clean reads were mapped to the P. falciparum 3D7 genome (UCSC malaria genome, 2007) using Bowtie (Langmead 2010). Only reads containing no more than one mismatch were used for further analysis.
Overlapping reads were clustered into contigs, and "wig" profiles were generated for visualisation in the Integrated Genome Brower (Nicol, Helt, Blanchard, Raja and Loraine 2009).
Genome annotation, sequence, and conservation data were downloaded from the UCSC genome browser, which was accessed via http://areslab.ucsc.edu/data_downloads/. And the ncRNAs reported in in five previous studies  were aslo considered in the annotation
Genome_build: PlasmoDB P. falciparum Dec 2007 (pf5) assembly
Supplementary_files_format_and_content: An data table including genome location, contig number, gene annotation, sequence for each unique contigs assembled from the sequencing data.

organism: Plasmodium falciparum

source_name: mixed intraerythrocytic stage

growth_protocol: P. falciparum strain 3D7 was cultured in complete medium using the standard growth conditions originally described by Trager and Jensen (Trager and Jensen 1976), with minor modifications. Briefly, the parasites were cultured at 37°C in petri dishes containing 5% haematocrit human red blood cells in RPMI Medium 1640 supplemented with 25 mM HEPES, 10 mg/L glucose, 0.5% Albumax II, 0.3 g/L L-glutamine, 0.015% hypoxanthine, 0.125 g/L gentamicin, and 25 mM sodium bicarbonate. For synchronisation,  the cultures were treated with a 5% sorbitol solution treatment (Lambros and Vanderberg 1979).

extract_protocol: The is-ncRNA-specific library was constructed as previously described (Deng, Zhu, Skogerbo, Zhao, Fu, Wang, He, Cai, Sun, Liu et al. 2006), with modifications. Briefly, 200 μg of DNAse I-treated RNA was size fractionated via anion exchange chromatography on an RNA/DNA Midi Tip (QIAGEN) according to the manufacturer’s instructions. RNAs that ranged in size from 50 to 500 nt were pooled. RNA sizes were estimated using the RiboRuler™ Low-Range RNA Ladder (Fermentas). Highly abundant 5S and 5.8S rRNAs, U3 snoRNA, and U1-U6 snRNAs were removed using the Ambion MICROBExpress kit (Ambion) with specifically designed Capture Oligonucleotides (Table S6 in Additional file 1). The is-ncRNA sample was separated into a 50-200 nt fraction and 200-500 nt fraction on a 6% denaturing urea PAGE gel. After the gel fragments were excised and the RNA was purified, the 50-200 nt fractions were dephosphorylated, ligated to a 3′ adaptor (3′AD, 5-p-GAUCGGAAGAGCGGUUCAGCAGGAAUGCCGAG-3) and reverse transcribed with a universal primer (3′RT, CTCGGCTTTCCTGCTGTTCCG). The 200-500 nt fractions were directly reverse transcribed with a random primer (5-CTCGGCTTTCCTGCTGTTCCGNNNNNN-3). A 5′ adaptor (5-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3) was ligated to the two cDNA fractions. PCR was performed, and the amplified products were sequenced on a standard paired-end Illumina/Solexa platform.

tag: strain

tag: developmental stage

value: mixed intraerythrocytic stage


title: 0hr-mock-infected

description:
intrument models: Illumina Hiseq 2000 and Illumina Genome Analyzer II
control sample


title: 2hr-hRSV-infected


title: MB_input_rep3

status: Public on Mar 29 2014

city: New York

first: Roy

last: Blum

state: NY

address: 552 First Ave

department: Cancer Institute

institute: New York University

library_source: genomic

data_processing:
Sequence reads within each individual replicate were filtered to remove identical sequence tags since those were likely generated by the LM-PCR amplification process while identical sequences present after the merging of replicates were retained. The sequence reads were aligned against the mouse mm9 genome build using the Illumina Pipeline and only tags locating to a single unique position were retained.
Peaks were identified using Qeseq, an algorithm developed in collaboration with Dr Klugers bioinformatics group. Setting for all MNAse libraries: sigma=50 and cut-off=15. For sonicated libraries the settings used were: sigma=100 and cut-off=15.
For RNA-seq, all raw sequencing reads were mapped to the mouse genome (NCBI37/mm9) using Bowtie aligner (0.12.9) with v2 and m1 parameters. The mapped reads were subsequently sorted and filtered by removing the PCR duplicates with samtools (0.1.19) before further analysis. To generate the visualization files for IGV, each individual filtered bam file was converted to bigwig files with bedtools (2.17.0) and the UCSC bigwig conversion script.  After removal of PCR duplicates, the reads were then assigned to the Ensemble gene model (Mus_musculus.NCBIM37.67.gff) (Morgan et al., 2009). The raw read counts were normalized using the trimmed mean of M-values normalization method (Robinson and Oshlack, 2010). The common dispersion and statistical significance for genes across sample groups were estimated and calculated using a generalized linear model (Robinson and Oshlack, 2010, Robinson et al., 2010). To obtain an adjusted p-value for each gene, we applied the FDR method for multiple hypothesis testing to genes that have summed read counts (from all samples) greater than 10.
Genome_build: mm9
Supplementary_files_format_and_content: bed file format for enriched peaks for ChIP-seq, Tdf format for RNA-seq

molecule: genomic DNA

organism: Mus musculus

growth_protocol: C2C12 myoblasts were grown in DMEM containing 10% FBS and harvested at ~40% confluency for MB chromatin. For myotube differentiation, cells were allowed to grow to complete confluence at which point differentiation was induced by changing the media to DMEM containing 2% horse serum. Induced cells were incubated for 4 days with one change of media (DMEM/2% horse serum) after two days and myotubes were harvested after 4 days of differentiation.

extract_protocol: Libraries were generated from input chromatin or ChIP enriched chromatin according to Illumina's standard protocol but using reagents from other companies: DNA end-repair was performed using the End-It DNA repair kit, Epicentre (cat:ER81050). A-overhang generation was performed uising Klenow from NED (cat: M0212). Adapter ligation was performede using the LigaFast kit from Promega (cat:M8225). LM-PCR was performed using Phusion DNA pol master mix from NEB (cat:F-531S). Very stringent quality controls were applied to the libraries: 1. Enrichment of a given site had to be preserved in the libraries in a manner comparable to the original ChIP. 10-12 positive and negative sites were tested for library preparation. 2. The total yield of the LM-PCR had to be ~500 ng. 3. The size distribution had to be centred around 350 bp for sonicated with a variation no larger than +/- 75 bp. Libraries that did not pass these criteria were considered substandard and were not used for sequencing.  RNA concentrations were measured using a NanoDrop 8000 Spectrophotometer. 1 ug of total RNA was used for the library preparation, using the Illumina TruSeq RNA Sample Prep Kit (polyA selection-based), following the TruSeq RNA Sample Preparation V2 Guide. TruSeq adapters 1, 3, 8, 9, 10, and 11 were used during the ligation step. 15 cycles of PCR were run during the amplification step. The samples were mixed into one pool and run in one 50-nucleotide single-end read Rapid run flow cell with the Illumina HiSeq 2500 sequencer, to generate a total of 288 million reads passing filter.

treatment_protocol: Isolated chromatin was either sonicated to an average size of 250 bp

tag: cell type

value: Growing C1C12 myoblasts

tag: chromatin preparation method

value: Sonication

tag: chip antibody


title: MB_input_rep2


title: MT_input_rep2

value: C1C12 myotubes differentiated for 96h


title: Input_ING1_flag_MT_rep3

description: Stable cell lines ectopically expressing Flag-tagged ING1 were generated by cloning cDNA from Open Biosystems into pBabe-puro. Virus was produced by transfecting constructs into 293T cells.  Viral supernatant was harvested and added with polybrene to C2C12 myoblasts.  Myoblasts were then selected using puromycin.

tag: genotype/variation

value: ectopically expressing Flag-tagged ING1


title: MB_input_rep1


title: siMLL3_1

source_name: C1C12 myoblasts_siRNA targeting MLL3

value: growing myoblasts (MB)

tag: transfected with

value: siRNA targeting MLL3


title: MLL3_MB

source_name: Growing C1C12 myoblasts

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#


title: siNS_2

source_name: C1C12 myoblasts_non-specific siRNA (siNS)

value: non-specific siRNA (siNS)


title: siNS_1


title: siMLL3_2


title: LSD1_MB

value: Active Motif


title: MT_input_rep1


title: Input_ING1_flag_MT_rep2


title: LSD1_MT

source_name: C1C12 myotubes differentiated for 96h

value: fully differentiated myotubes (MT)


title: Input_ING1_flag_MT_rep1


title: siMLL3_4_2

source_name: C1C12 myoblasts_siRNA targeting MLL3 and MLL4

value: siRNA targeting MLL3 and MLL4


title: Input_ING1_flag_MB_rep1


title: Wdr5_MB_rep3

description: processed data file: Wdr5_MB_merged_100_15.bed

tag: chip antibody provider

value: kind gift from D. Reinberg


title: siMLL3_4_1


title: 5h-HUVEC.uninfected.sc.rep1

description:
SRX124666
7_5h_h

value: HUVEC


title: Wdr5_MB_rep2


title: Sin3A_MT_rep2

description: processed data file: Sin3A_MT_merged_100_15.bed

value: kind gift from D. Ayer


title: Sin3A_MT_rep1


title: MLL_MB_rep2

description: processed data file: MLL1_MB_merged_100_15.bed

value: Bethyl Laboratories

tag: chip antibody cat. #


title: PLHCX

city: Tianjin

first: jintang

last: dong

address: Weijin road

institute: Nankai university

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit version 0.0.13 and Perl version 5.8.8.
mRNA-seq reads were aligned to the UCSC hg19 genome assembly using Tophat version 2.0.9 with parameters: -r 100 -I 50000 --max-segment-intron 50000 -a 10 -g 1
Gene abundance measurements were generated and normalized using Cufflink version 2.1.1.Linux_x86_64; the normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression were analysed using DEGseq function package in R program version 2.10.0.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file includes normalized FPKM values and raw fragment counts for each Sample.

source_name: Xenografts of nude mice BALB/c, vector control

growth_protocol: Male BALB/c nude mice 3- to 4-weeks-old were used in this assay. Cancer cells were resuspended in a mixture of PBS and Matrigel (equal volumes) at 2 x 10^7 cells/ml. 100 µl of cells were injected subcutaneously into both flanks. At day 38 after injection, mice were sacrificed, and tumors were surgically isolated.

extract_protocol:
RNA was harvested using TRIZOL reagent (Invitrogen, Beijing, China). 4ug total RNA of each sample was pooled and purified by RNeasy Micro kit (catalogue #74004, Qiagen), respectively. The quality and concentration of RNA samples were determined by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, US). 10 μg total RNA of each pool was used for library construction and RNA-Seq.
Non-directional RNA-Seq libraries (300nt average insert size) of three pools were established following the manufacturer's instruction of TruSeq RNA-Seq Library Prep Kit v2 (Illumina, SanDiego, CA, US) and quantified by Qubit 2.0 Fluorometer (Invitrogen) and validated by Agilent 2100 Bioanalyzer. Clusters were generated by cBot with the libraries diluted to 20 pM and subsequently sequenced on HiSeqTM 2500 (Illumina) platform.

treatment_protocol: After isolating, tumors were flash frozen in liquid nitrogen.

tag: tissue

value: tumor

value: prostate cancer cell line DU-145 xenograft

tag: expression

value: empty vector


title: MLL_MB_rep1

tag: cell line

value: Growing C1C12 myoblasts

value: Sonication


title: Input_ING1_flag_MB_rep2

value: ectopically expressing Flag-tagged ING1


title: Menin_MB_rep2

description: processed data file: Menin_MB_merged_100_15.bed

value: Menin


title: Menin_MB_rep1


title: ING1_flag_MT_rep3

description:
processed data file: ING1_MT_merged_100_15.bed
Stable cell lines ectopically expressing Flag-tagged ING1 were generated by cloning cDNA from Open Biosystems into pBabe-puro. Virus was produced by transfecting constructs into 293T cells.  Viral supernatant was harvested and added with polybrene to C2C12 myoblasts.  Myoblasts were then selected using puromycin.

value: C1C12 myotubes differentiated for 96h

value: anti-FLAG

value: Sigma


title: ING1_flag_MB_rep2

description:
processed data file: ING1_MB_merged_100_15.bed
Stable cell lines ectopically expressing Flag-tagged ING1 were generated by cloning cDNA from Open Biosystems into pBabe-puro. Virus was produced by transfecting constructs into 293T cells.  Viral supernatant was harvested and added with polybrene to C2C12 myoblasts.  Myoblasts were then selected using puromycin.


title: ING1_flag_MB_rep1


title: K369R

source_name: Xenografts of nude mice BALB/c, KLF5 mutant

value: KLF5 mutant K369R


title: ING1_flag_MT_rep1


title: ING1_flag_MT_rep2


title: papain 3'UTRKO lung natural helper cells #1

status: Public on Mar 28 2014

city: Yokohama

first: Yasutaka

last: Motomura

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Read mapping,Bowtie0.12.7,Tophat v1.4.0
Estimate the transcript abundances,Cufflinks v1.3.0
Genome_build: NCBI Build 37(UCSC mm9)

molecule: polyA RNA

source_name: Lung natural helper cells

growth_protocol: We sorted FceR1+,CD49b+,c-kit- cells as basophils,Lineage-,Thy1.2+,IL7Ra+,CD25+ cells as natural helper cells and SiglecF+,CD11c(+/-),Gr1lo,autofluorescence- cells as eosinophils from the lung by BD FACS AriaⅡ

extract_protocol:
mRNA was isolated with TRIzol and NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB Biolabs, Inc. Ipswich, MA,USA) .
10ng of isolated RNA  were used for production of the RNA-Seq cDNA library with NEBNext Ultra RNA Library Prep  Kit for Illumina (NEB Biolabs, Inc.) according to the  manufacturer's protocol that included cDNA synthesis and fragmentation, the  addition of adaptors, size selection, amplification and quality control.

treatment_protocol: Mice were intranasally administrated with papain (50ug/mouse) for consective three days.

value: Lung

tag: treatment

value: papain


title: papain lung CD11c+ eosinophil#1

source_name: Lung eosinophil


title: papain lung natural helper cells #1


title: papain lung CD11c+ eosinophil#2


title: naïve lung natural helper cells #2


title: papain lung CD11c- eosinophil#2


title: papain lung natural helper cells #2


title: Wdr5_MB_rep1

value: kind gift from D. Reinberg


title: papain lung CD11c- eosinophil#1


title: naïve lung eosinophil#2


title: naïve lung eosinophil#1


title: papain lung basophils #1

source_name: Lung basophils


title: KLF5

source_name: Xenografts of nude mice BALB/c, KLF5

value: wild type KLF5


title: papain lung basophils #2


title: naïve lung basophils #1


title: heart #7 endocardium

city: Belfast

first: Anthony

last: Collins

state: NI

address: Clinical Sciences, Block A, Grosvenor Rd.

department: Centre for Experimental Medicine

country: United Kingdom

institute: Queen's University Belfast

description: small RNA

data_processing:
CLC Genomics Workbench v4.0 used to trim adapter sequences
sequences aligned and annotated to known rat miRNA, miRBase V18
remaining unannotated sequences annotated to all other species in miRBase V18 - Novel Orthologs
Known rat and novel ortholog sequences normalised on total annotated sequences per sample, sequences grouped on mature/mature*  allowing 3 additions/deletions upstream/downstream and up to 2 mismatches within the sequence
minimun expression level set at 10 raw reads in any one sample of the 9 samples for grouped on mature data
Genome_build: miRBase v18
Supplementary_files_format_and_content: tab-delimited text files for all annotated sequences and groups normalised in RPMM for each sample;  Grouped_data.txt = sequences grouped on mature sequences in miRBase v18; All_annotated_reads.txt = reads annotated to miRBase v18; unannotated_minimum_10_reads.txt = reads unannotated to miRBase v18

organism: Rattus norvegicus

source_name: heart; left ventricular free wall

extract_protocol:
30mg of chopped tissue flash frozen in Liquid Nitrogen, miRNA extracted with MiRNeasy Extraction Kit, Qiagen, as per manufacturers protocol
miRNA with a RIN value ≥8.0 were adapted, RT'ed and amplified using the TruSeq Small RNA Sample Preparation Kit, Illumina, as per maunfacturers protocol. Barcodes indicated in raw data file names.
TruSeq SR Cluster Kit v5, Illumina

value: Sprague-Dawley

tag: gender

value: male

tag: age (months)

value: heart


title: heart #8 endocardium

description: small RNA

tag: strain


title: heart #8 midmyocardium

description: small RNA


title: heart #8 epicardium

description: small RNA


title: heart #6 midmyocardium

description: small RNA


title: WT seedling at 38°c

city: Perpignan

first: Jean-Marc

last: Deragon

address: 58 avenue Paul Alduy

department: Biology

country: France

institute: Université de Perpignan, CNRS

data_processing:
Sequencing quality was assessed with a PhiX reference spiked in the flow-cell that gave a sequencing error rate of 0.19% with 95.5% of the reference nucleotides having a Q-score >=30 (Phred calculation).
For each library, 42-46.10E6 reads were obtained with 94-95% of the bases displaying a Q-score >=30, with a mean Q-score of 36.
Reads mapping was performed with BWA 0.5.9 alignment tool (Li and Durbin, 2010) using A.thaliana full genome TAIR10 version as reference.
A maximum of 2 mismatches was allowed in the first 32 bases of the sequences and a maximum of n mismatches in total, with n ranging from 2 to 7 according to the sequence length. Expression estimation, sample counts comparison and normalization of the mapped data was performed with SeqMonk (version 0.16.0, http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk).
Counts were normalized as reads per million, by dividing with the total number of reads and multiplying by 10E6, giving counts comparable between samples. Reads per million from mRNAs encoded from the same locus were summed up and genes that did not give at least one read per 106 bases in any of the four conditions were filtered out, leaving for further analyses 19,084 different loci (among which 18,950 are nuclear encoded) representing 76% of the total estimated number of genes in the Arabidopsis genome.
Genome_build: TAIR10
Supplementary_files_format_and_content: Data_before_filtering.txt: the full set of normalized counts data prior to statistical filtering for each Sample save in a tab-delimited .txt format

organism: Arabidopsis thaliana

source_name: WT seedling at 38°c

growth_protocol: Analyses were carried out with 21 days old whole plantlets grown on synthetic MS medium (Duchefa) containing 1% sucrose and 0.8% plant agar, at 20°C under continuous light.

extract_protocol:
Total RNA was isolated from liquid nitrogen pulverized tissues. cDNA libraries preparation on ribosomal RNA depleted transcripts, high-throughput sequencing, quality control and bio-informatic analyses of the RNA-seq were performed by FASTERIS Life Sciences (http://www.fasteris.com)
cDNA libraries preparation on ribosomal RNA depleted transcripts, high-throughput sequencing, quality control and bio-informatic analyses of the RNA-seq were performed by FASTERIS Life Sciences (http://www.fasteris.com)
The RNA-seq and differential accumulation analyses were conducted by Fasteris SA as follow: ribosomal RNAs were removed using using duplex-specific nuclease (DSN) from 0.5-1mg of total RNA, after zinc breaking cDNA libraries were prepared and sequenced as single-end 100 bp tags with an Illumina Hi-seq 2000 instrument.

treatment_protocol: Heat stress was carried as follow: 6-8 plantlets were transferred to 5ml liquid MS medium-1% sucrose pre-warmed at 38°C (heat stressed plants) or at 20°C (control plants). Heat stressed plants were incubated 15 min at 38°C while control plants were kept at 20°C for 15 min. Plants were harvested and immediately frozen in liquid nitrogen.

value: 21 days-old seedlings

tag: genotype

value: WT

tag: ecotype


title: larp1 seedling at 38°C

source_name: larp1 seedling at 38°C

value: larp1 mutant


title: heart #7 midmyocardium

description: small RNA


title: heart #7 epicardium

description: small RNA


title: h17kds

city: Jacksonville

first: Michael

middle: Patrick

last: Walsh

state: Florida

address: 4500 San Pablo Road

department: Cancer Basic Science

institute: Mayo Clinic Jacksonville

data_processing:
Basecalls performed using CASAVA version 1.4
reads aligned using Tophat version 1.4
gene counts calculated using Htseq version 0.5.3p3
Genome_build: hg19
Supplementary_files_format_and_content: tab delimietd text files containing the number of reads that alingned to each gene in the genome. ModeNormalizedCntsForLSCCcellLines.txt contains counts that have been normalized using mode normalization (described in Kalari et. Al. 2012, PMID: 22655260). CntsForLSCCcellLines.txt contains raw counts.

source_name: TICs from the H1703 cell line (PRKCI knock down)

extract_protocol:
Qiagen RNEasy
NuGen

tag: phenotype

value: tumo initiating cells

tag: cell type


title: h12ntp

source_name: Adherent/parental cells from the H1299 cell line

value: adehrent cells


title: h12nts

source_name: TICs from the H1299 cell line

value: TICs from the H1299 cell line


title: chants

source_name: TICs from the CHAGO cell line

value: TICs from the CHAGO cell line


title: chantp

source_name: Adherent/parental cells from the CHAGO cell line


title: h17nts

source_name: TICs from the H1703 cell line

value: TICs from the H1703 cell line


title: naïve lung natural helper cells #1


title: larp1 seedling at 20°C

source_name: larp1 seedling at 20°C


title: heart #6 epicardium

description: small RNA


title: naïve lung basophils #2


title: calnts

source_name: TICs from the CALU cell line

value: TICs from the CALU cell line


title: heart #6 endocardium

description: small RNA


title: chakds

source_name: TICs from the CHAGO cell line (PRKCI knock down)


title: CpG methylatio/coveragen in HSPCs from wild-type mice

city: Houston

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

description: [[deletion]]

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Analyzed using Zymo Research proprietary pipeline, outlined in the supplementary methods file
Sequence reads from bisulphite-treated EpiQuest libraries were identified using standard Illumina base-calling software and then analyzed using a Zymo Research proprietary computational pipeline. Residual cytosines (Cs) in each read were first converted to thymines (Ts), with each such conversion noted for subsequent analysis. A reference sequence database was constructed from the 36-bp ends of each computationally predicted MspI-TaqI fragment in the 40-220-bp size range. All Cs in each fragment end were then converted to Ts (only the C-poor strands are sequenced in the RRBS process; The converted reads were aligned to the converted reference by finding all 12-bp perfect matches and then extending to both ends of the treated read, not allowing gaps (reverse complement alignments were not considered). The number of mismatches in the induced alignment was then counted between the unconverted read and reference, ignoring cases in which a T in the unconverted read is matched to a C in the unconverted reference. For a given read, the best alignment was kept if the second-best alignment had 2 more mismatches; otherwise the read was discarded as non-unique. The mean CpG coverages ranged between 5-11X and total number of unique mapped reads ranged between 3,378,764-10,295,957 for each condition. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. A bioinformatics pipeline was used to score epigenetic alterations according to strength and significance, and links them to potentially affected genes. To that end, we collected a comprehensive set of regions of interest, which includes promoters, CpG islands and repetitive elements. For each of these regions, the number of methylated and unmethylated CpG observations is determined, and a p-value is assigned using Fisher's exact test. Once all p-values are calculated, multiple-testing correction is performed separately for each region type using the q-value method, which controls the false discovery rate to be below a user-specified threshold (typically 10%). The software pipeline is implemented in Python (alignment processing module) and R (statistical analysis module).  Unsupervised clustering was performed on methylation ratio data from each condition using Kendall tau rank correlation.
Genome_build: mm9
Supplementary_files_format_and_content: Files containing the string 'cpgMethylation' are reads from methylated CpGs
Supplementary_files_format_and_content: Files containing the string 'cpgReads' are reads showing total CpG coverage
Supplementary_files_format_and_content: the 'results.xls' contains Zymo research promoter analysis results

source_name: HSPCs

growth_protocol: All animal work has been conducted according to relevant national and international guidelines and it has been approved by the Bioethics Committee of University of Salamanca and by the Bioethics Subcommittee of Consejo Superior de Investigaciones Cientificas (CSIC).

extract_protocol:
DNeasy Blood and Tissue Kit (Qiagen)
EpiQuest Library Preparation Kit (Zymo Research); EpiQuest libraries were prepared from 200-500 ng mouse genomic DNA obtained from primary cells (Sca1+Lin- cells from bone marrow, and B220+ cells and Gr1+Mac1+ from peripheral blood) purified from Sca1-Bcl6Δ mice and/or wild-type mice. DNA were pooled from 6-9 mice to provide one pooled replicate per condition, as performed previously.The DNA was digested with 60 units of TaqI and 30 units of MspI (New England Biolabs) sequentially. Size-selected TaqI-MspI fragments (40-120 bp and 120-350 bp) were filled in and 3'-terminal-A extended, extracted with a DNA Clean & Concentrator kit (Zymo Research). Ligation to pre-annealed adapters containing 5'-methyl-cytosine instead of cytosine was performed using the Illumina DNA preparation kit and protocol. Purified, adaptor ligated fragments were bisulphite-treated using the EZ DNA Methylation-Direct Kit (Zymo Research). Preparative-scale PCR (18 cycles) was performed and purified PCR products were subjected to a final size selection on a 4% NuSieve 3:1 agarose gel. SYBR-green-stained gel slices containing adaptor-ligated fragments of 130-210 bp or 210-460 bp in size were excised. Library material was recovered from the gel using a Zymoclean Gel DNA Recovery Kit (Zymo Research) and sequenced on an GAIIx genome analyzer (Illumina), yielding between 43,930,708 and 60,139,994 total reads for each condition.

tag: strain background

tag: genotype/variation

value: Wild-type

value: bone marrow

value: Hematopoeitic stem/progentior cells (HSPC, Sca1+Lin-)


title: h17ntp

source_name: Adherent/parental cells from the H1703 cell line


title: calntp

source_name: Adherent/parental cells from the CALU cell line


title: CpG methylation/coverage in mature B-cells from wild-type mice

description: [[deletion]]

source_name: Mature B-cells

value: peripheral blood

value: mature B-cells (B220+)


title: CpG methylation/coverage in mature B-cells from Sca1-BCL6Δ mice

description: [[deletion]]


title: CpG methylation/coverage in HSPCs from Sca1-BCL6Δ mice

description: [[deletion]]


title: calukds

source_name: TICs from the CALU cell line (PRKCI knock down)


title: WT seedlling at 20°C

source_name: WT seedlling at 20°C


title: 103_index3

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH-Science for Life Laboratory

description: Sample 13

data_processing:
Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite
Potential fusions were analyzed using FusionMap
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include output from FusionMap for each Sample 1-13

source_name: cortical ischemic stroke tissue

extract_protocol:
RNAeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols and clustered on cBot

treatment_protocol: frozen material

value: cortical ischemic stroke tissue


title: 101_index1

description: Sample 11

source_name: healthy cortex

value: healthy cortex


title: 102_index2

description: Sample 12


title: 108_STROKE-DD147-12

description: Sample 8


title: 107_STROKE-2012L5

description: Sample 7


title: 109_STROKE-D2421

description: Sample 9


title: 110_STROKE-D202-11

description: Sample 10


title: h12kds

source_name: TICs from the H1299 cell line (PRKCI knock down)


title: 106_STROKE-OL274

description: Sample 6


title: 103_OC-D11472

description: Sample 3


title: 104_OC-DD332

description: Sample 4


title: 101_OC-OL127

description: Sample 1


title: 105_OC-2002UD

description: Sample 5


title: Xu_WT_rep1_Input

city: madison

first: Lu

last: Wang

state: wisconsin

address: 1400 university ave

department: Oncology

institute: UW madison

description: Sample 6

data_processing:
ChIP-seq runs were all 100bp.  Barcoded samples were run over 4 lanes total and the fastq data were concatenated prior to BOWTIE mapping. Fastq files are the raw sequence files [barcoded lanes (4 each) were concatenated for each sample for simplicity, no other modification was made], Barcodes were decoded by Illumina HiSeq2000 software automatically.  All samples were mapped from fastq files using BOWTIE [-m 1 -- best] to mm9 [UCSCmouse genome build 9].  Replicate lanes were analyzed separately for reproducibility and normalization of the peak calls.
Peaks were called by using HOMER [http://biowhat.ucsd.edu/homer/] and QuEST [http://mendel.stanford.edu/sidowlab/downloads/quest/].
QuEST 2.4 was run using the recommend settings for transcription factor (TF) like binding with the following exceptions: kde_bandwith=30, region_size=600, ChIP threshold=30, enrichment fold=3, rescue fold=3
HOMER analysis was run using the default settings for peak finding.
False Discovery Rate (FDR) cut off was 0.001 (0.1%) for all peaks.
Genome_build: hg19
Supplementary_files_format_and_content: *peak.bed are the resulting peaks found with QuEST and HOMER

growth_protocol: MCF-7 cells were obtained from ATCC, and maintained with DMEM (Gibco, Gaithersburg, MD) containing 10% FBS (Gibco)

extract_protocol:
Chromatin immunoprecipitation was performed as described previously (Meyer MB. Mol Endo. 2012)
The isolated DNA (or Input DNA acquired prior to precipitation) was then validated by quantitative real time PCR (qPCR) and further prepared for ChIP-seq analysis.  ChIP-seq libraries were prepared using the NEBNext DNA sample prep kit (NEB, #E6000L) with the Bioo NEXTflex ChIP-seq Barcodes (Bioo Scientific, Austin, TX, #514122) according to manufacturer’s protocols, with few exceptions.  During the NEBNext prep, the Illumina adapters were replaced with the Bioo Scientific Barcoded adapters according to Bioo protocols. ChIP-DNA ligated libraries were cleaned up with Agencourt AMPureXP Magnetic Beads (Beckman-Coulter, #A63881).  A pre-size selection PCR was performed using Phusion polymerase, NEXTflex Primer Mix and purified ligation product for 4 cycles of PCR according to the Bioo Protocol.  Libraries were size selected using Invitrogen E-gels to a size of 400-500bp.  Samples were then PCR amplified for 14 cycles using Phusion polymerase, NEXTflex Primer mix and the size selected DNA as per Bioo protocol, followed by Agencourt bead clean up.  Libraries were validated for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Clusters were formed and sequenced on the Illumina HiSeq2000 sequencer by the University of Wisconsin - Madison DNA Sequencing Facility in the University of Wisconsin- Madison Biotechnology Center.  DNA clusters were generated using a cBot Single Read Cluster Generation kit (ver. 3) on an Illumina cBot (Illumina) according to the manufacturer's instructions, to obtain an average of 1.5×108 clusters for each lane on a flowcell.  All sequencing runs for 50mers were performed on an Illumina HiSeq2000 using the Illumina Sequencing kit (ver. 3).  Fluorescent images were analyzed using the CASAVA 1.8.2 (Illumina) to obtain FASTQ formatted sequence data.  Twelve barcoded libraries were run per lane and this was repeated over 4 lanes.  After which, the raw FASTQ for each sample was concatenated from the 4 lanes prior to mapping to create a single sample.  Each ChIP sample was repeated in biological replicate in the same manner (minimum of 2 replicates).  Sequences were mapped to the human genome (hg19) using BOWTIE (--best –m 1) to yield unique alignments.

value: breast cancer cells

tag: passages

value: wild type


title: Xu_WT_rep2_BAF155

description: Sample 7

tag: chip antibody

tag: chip antibody vendor

value: Santa cruz


title: Xu_MUT_rep2_Input

description: Sample 4

value: CARM1 KO


title: Xu_MUT_rep1_Input

description: Sample 2


title: Xu_WT_rep1_BAF155

description: Sample 5

tag: chip antibody cat. #


title: Xu_MUT_rep1_BAF155_MUT

description: Sample 1


title: Xu_MUT_rep2_BAF155_MUT

description: Sample 3


title: Xu_WT_rep2_Input

description: Sample 8


title: d0 input

city: Chicago

first: Jozef

last: Madzo

state: Illinois

address: 900 E 57th Street, KCBD

department: Medicine Hem/Onc.

institute: The University of Chicago

description: genomic DNA

data_processing:
5-hmC reads were mapped to the reference genome hg19 using BWA
Peak calling for each sample was performed using MACS
Genome_build: hg19
Supplementary_files_format_and_content: wig file generated with MACS1.4

source_name: CD34-pos cell in erythroid differentiation

growth_protocol: Primary human CD34+, stem/progenitor cells were purified from growth factor mobilized blood using the CliniMACSTM. The purity of CD34+ cells were greater than 95% based on flow cytometry analysis. Cells were maintained in Isocove's modified Dulbecco's medium (IMDM, Life Technologies) supplemented with 15% fetal bovine serum (Life Technologies), 15% human serum, 1% penicillin-streptomycin (Life Technologies), Erythropoietin (EPO) at 2 units/mL, human interleukin-3 (R&D systems) at 10 ng/mL and human stem cell factor (SCF) at 50 ng/mL until day 3 of culture. During subsequent feedings IL-3 was omitted but EPO concentration was maintained at 2U/ml. Concentration of SCF was tapered at each feeding (day 3, SCF at 25 ng/mL; day 6, SCF at 10 ng/mL day 8, SCF at 2 ng/mL and day 10, 0 ng/ml). The overall cell concentration was maintained at 2 million cells/ml or less during the first week of culture. The cultured were continued until day 16 without further manipulation until the cells reached the reticulocytes stage. Samples for NGS analysis were collected at day0, day3, day7 and day10 time point.

extract_protocol: Genomic DNA  (gDNA)  was isolated and sonicated into 200-400bp, in total 20 mg gDNA were labeled with chemically modified uridine diphosphoglucose glucose (UDP-6-N3-Glu) by viral β-glucosyltransferase (β-GT). The click chemistry reaction was performed by addition of 150 μM dibenzocyclooctyne modified biotin into the eluted DNA. Labeled DNA was pull-down with streptavidine coated magnetic beads. After washing captured DNA was released from bead with access of DTT.

tag: time point

value: primary CD34+ stem/progenitor cells


title: d7 5hmC Affinity pull-down

description: affinity pull-down DNA


title: d10 input

description: genomic DNA


title: d7 input

description: genomic DNA


title: d10 5hmC Affinity pull-down

description: affinity pull-down DNA


title: 102_OC-OL114

description: Sample 2

tag: tissue


title: d0 5hmC Affinity pull-down

description: affinity pull-down DNA


title: d3 5hmC Affinity pull-down

description: affinity pull-down DNA


title: d7_RNAseq

description: polyA RNA

extract_protocol: Total RNAs were isolated using Trizol Reagent (Invitrogen) and the integrity of total RNAs was validated using the Agilent 2100 Bioanalyzer. Libraries were generated following the Illumina protocol.


title: d3_RNAseq

description: polyA RNA


title: d10_RNAseq

description: polyA RNA


title: MS275_5_24h

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

data_processing:
All sequencing results were mapped  on the Mus musculus NCBI m37 genome assembly (MM9; assembly July 2007)
Normalized expression values were obtained by Genomatix (www.genomatix.de).
Cut-Off apply of 0.001 on NE value
Imputed value and ratio with control
Genome_build: Mus musculus NCBI m37 genome assembly (MM9)
Supplementary_files_format_and_content: The *list files represent all NE values.  Column 1:  the Genomatix geneid, column 2: the NE ( Normalized Expression) value, column 3:  the Genomatix gene symbol.
Supplementary_files_format_and_content: The *0.001.txt files represent NE values with Cut-Off of 0.001 applied.  Column 1:  the gene symbol, column 2: the NE ( Normalized Expression) value with Cut-Off of 0.001.
Supplementary_files_format_and_content: The *imputed .txt files represent MS275/Solvent ratios.  Col1: Genomatix Genesymbol, col2: NE value from solvent, col3: NE from MS275 5 micromolar  treatment, col4: Ratio calculated by dividing col3 by col2.

source_name: TBV2 embryonic stem cells

growth_protocol: TBV2 ES cells were maintained on a feeder layer containing LIF, to avoid differentiation, and were cultured onto gelatin-coated plates, to favour adhesion. The medium was replaced every day and cells were maintained in plate until at a confluence of 70-80% (generally for 2 days) and then removed with trypsin and reseed cells at about density three times lowest.

extract_protocol:
RNA was harvested using Trizol reagent and 100 μg total RNA was subjected to two rounds of poly(A) selection (Oligotex mRNA Mini Kit; QIAGEN), followed by DNaseI treatment (QIAGEN). 100–200 ng mRNA was fragmented by hydrolysis (5x fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 seconds and purified (RNAeasy Minelute Kit; QIAGEN). cDNA was synthesized with 5 μg random hexamers by Superscript III Reverse Transcriptase (Invitrogen). Double strand cDNA synthesis was performed according to the manufacturer's recommendations and purified (Minelute Reaction Cleanup Kit; QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols, starting from 20 ng cDNA

treatment_protocol: 24h stimulation with HDACi Class I specific MS-275

tag: agent

value: HDACi Class I specific MS-275


title: d3 input

description: genomic DNA


title: MS275_5_24h_Duplicate


title: ATCC_0pct

first: Kent

last: Shefchek

address: 801 West Baltimore Street

institute: University of Maryland School of Medicine

description: no serum control

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 Bordetella holmesii ATCC51541T whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: CP007494
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Bordetella holmesii

source_name: Bordetella holmesii ATCC51541T

growth_protocol: B. holmesii ATCC51541T was grown in tryptic soy (TS) medium without serum to an OD600 of 0.35 at 37C with shaking.

extract_protocol:
Total Bordetella RNAs were purified at Columbia University (Ratner laboratory) with the Ambion RiboPure Bacteria kit, treated with DNase which was then inactivated with the Ambion DNase inhibitor beadsand the beads removed, and resuspended in the Ambion elution buffer.
RNA samples were depleted of rRNA with the RiboZero Gram Negative Bacterial kit. Libraries were then prepared for sequencing using standard Illumina protocols.

treatment_protocol: 5ml cultures were treated with either vehicle control (TS), 0.5% human serum in TS, or 5% human serum in TS for 1 hr at 37C with shaking. The serum had been heat-inactivated at 56C x 1 hr to inactivate complement. At the end of the 1 hr incubation, bacteria were pelleted by centrifugation and RNA was isolated.

tag: treatment

value: no serum control


title: ATCC_5pct

description: exposed to 5% heat-inactived human serum

value: 5% heat-inactivated human serum


title: ATCC_0_5pct

description: exposed to .5% heat-inactivated human serum

value: 0.5% heat-inactivated human serum


title: Solvent_24h_Duplicate

value: Solvent


title: Solvent_24h


title: s_3_23_4.0_rz

status: Public on Mar 27 2014

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

institute: University of Exeter Medical School

description:
RiboZero RNA
Series_3_Sample_23_4.0_hpf_rz
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 8352.463313

data_processing:
Series 1&2 basecalling performed with Illumina RTA 1.9.35
Series 3 basecalling performed with Illumina RTA 1.17.21.3
Read pairs were aligned to a transcriptome containing Xenopus Tropicalis v7 gene models and additional off-genome EST sequences with Bowtie 0.12.7 with parameters -a -y --best -v 3 -X 0 -I 10000.  The assembly of these off-genome ESTs is described here: "Gilchrist, M. J., Zorn, A. M., Voigt, J., Smith, J. C., Papalopulu, N. and Amaya, E. (2004). Defining a large set of full-length clones from a Xenopus tropicalis EST project. Dev Biol 271, 498-516."  The assembled contigs themselves do not have accession numbers, but the contig sequences will be included in a supplemental file with our paper.
Pairs aligning to transcripts from more than one gene were discarded, pairs aligning to one or more transcripts from the same gene were counted once.
Reads were normalized by total mapped reads to a standard library size of 25 million reads.
Genome_build: Xtropicalis_v7
Supplementary_files_format_and_content: Tab delimited .txt files containing raw and normalized read counts for each sample

organism: Xenopus tropicalis

source_name: Whole embryo

extract_protocol:
Series 1&2: total RNA was isolated using TriPure (Invitrogen) followed by LiCl precipitation. RNA was dissolved in 100 µl H2O, and 10 µg total RNA from each sample was used for PolyA+ RNA library preparation using Illumina kit RS-930-1001
Series 3: total RNA was extracted, samples were suspended in 40 µl DEPC H2O, and 1 µg was taken for library preparation. PolyA+ RNA was isolated using beads from TruSeq RNA Sample Prep Kit v2 (Illumina kit RS-122-2001), and PolyA+ RNA-seq libraries were prepared using Epicentre ScriptSeq v2. Ribosomal RNA depleted RNA-seq libraries were prepared using Epicentre ScriptSeq Complete Kit (BHMR1224) combining Ribo-Zero and ScriptSeq v2.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: series

tag: time/hpf


title: s_3_21_2.0_rz

description:
RiboZero RNA
Series_3_Sample_21_2.0_hpf_rz
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 10496.147218


title: s_3_27_8.0_rz

description:
RiboZero RNA
Series_3_Sample_27_8.0_hpf_rz
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 8468.956317


title: s_3_22_3.0_rz

description:
RiboZero RNA
Series_3_Sample_22_3.0_hpf_rz
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 8147.011174


title: s_3_24_5.0_rz

description:
RiboZero RNA
Series_3_Sample_24_5.0_hpf_rz
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 8038.49438


title: s_3_20_1.0_rz

description:
RiboZero RNA
Series_3_Sample_20_1.0_hpf_rz
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 7999.535319


title: s_3_18_9.0_polyA

description:
Series_3_Sample_18_9.0_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 11453.255431


title: s_3_13_6.5_polyA

description:
Series_3_Sample_13_6.5_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 7382.667231


title: s_3_14_7.0_polyA

description:
Series_3_Sample_14_7.0_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 6963.750586


title: d0_RNAseq

description: polyA RNA


title: s_3_16_8.0_polyA

description:
Series_3_Sample_16_8.0_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 8997.192772


title: s_3_19_0.0_rz

description:
RiboZero RNA
Series_3_Sample_19_0.0_hpf_rz
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 8361.580141


title: s_3_08_4.0_polyA

description:
Series_3_Sample_08_4.0_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 7530.804818


title: s_3_17_8.5_polyA

description:
Series_3_Sample_17_8.5_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 10380.068036


title: s_3_12_6.0_polyA

description:
Series_3_Sample_12_6.0_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 5774.971933


title: s_3_10_5.0_polyA

description:
Series_3_Sample_10_5.0_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 6168.579258


title: s_3_09_4.5_polyA

description:
Series_3_Sample_09_4.5_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 6269.286559


title: s_3_07_3.5_polyA

description:
Series_3_Sample_07_3.5_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 5589.066014


title: s_3_11_5.5_polyA

description:
Series_3_Sample_11_5.5_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 5627.432803


title: s_3_15_7.5_polyA

description:
Series_3_Sample_15_7.5_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 7394.464404


title: s_3_25_6.0_rz

description:
RiboZero RNA
Series_3_Sample_25_6.0_hpf_rz
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 8335.336797


title: s_3_04_2.0_polyA

description:
Series_3_Sample_04_2.0_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 6774.029507


title: s_3_03_1.5_polyA

description:
Series_3_Sample_03_1.5_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 5914.907634


title: s_3_02_1.0_polyA

description:
Series_3_Sample_02_1.0_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 5717.282297


title: s_3_01_0.5_polyA

description:
Series_3_Sample_01_0.5_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 5996.164824


title: s_3_00_0.0_polyA

description:
Series_3_Sample_00_0.0_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 8399.464152


title: sel-1_hj41_2

city: Kansas City

first: Huan

last: Yang

state: MO

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

data_processing:
Sequencing reads were clipped with Fastx_clipper (v0.0.13) to remove adaptor sequence
Alignment was performed using TopHat (1.4.1) using the ce6 reference genome. Alignment was performed on each replicate separately and then the resulting alignments were merged using samtools. These merged alignments were used for the rest of the downstream analysis
Bedtools was used to determine the number of reads aligned to the different types of small RNA.
Genome_build: ce6
Supplementary_files_format_and_content: tab-delimited text files include counts of small RNA for each sample in listed genes or regions. File (small RNA expression.txt) shows the abundance of small RNA that we quantified, OP50_N2_sample_1_counts represents small RNA counts in sample 1 of N2 animals fed with OP50; OP50_N2_sample_2_counts represents small RNA counts in sample 2 of N2 animals fed with OP50; OP50_hj41_sample_1_counts represents small RNA counts in sample 1 of hj41 animals fed with OP50; OP50_hj41_sample_2_counts represents small RNA counts in sample 2 of hj41 animals fed with OP50. File(sel-1 siRNA expression.txt) shows the small RNA abundance in gene sel-1 locus; region represents the region where small RNAs were mapped to; counts represents the number of small RNA that were mapped to that region.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Synchronized L1 worms were grown on RNAi plates seeded with HT115 E. coli expressing a sel-1 RNAi trigger as previously described (Pak and Fire 2007) or OP50. After 50 hrs at 20oC, ~50000 worms were washed 5 times with 10ml M9, and then homogenized in Tri-reagent. Samples were kept at -80oC.

extract_protocol:
Purified total RNA were processed with MirVana kit (Invitrogen) for small RNA enrichment. Equal amount of small RNAs (30~40ug) were resolved on 15% TBE-Urea Acrylamide gels. Gels containing small RNAs of 20-26nt were cut out and purified with a small-RNA PAGE Recovery Kit (Zymo Research, R1070).
Each small RNA sample was treated with TAP and processed with the ScriptMiner Small RNA-Seq Library Preparation Kit (Epicentre, SMMP1012). Libraries from different samples were indexed with RNA-Seq Barcode Primers (Epicentre, RSBC10948). Two biological samples of each condition (wild type +sel-1 RNAi, rde-12+sel-1 RNAi, wild type+OP50 and rde-12+OP50) were used for library preparation

tag: strain/genotype

tag: developmental stage

value: young adult

tag: bacteria

value: HT115(sel-1 RNAi)


title: sel-1_hj41_1


title: OP50_hj41_2


title: OP50_hj41_1


title: OP50_N2_2


title: OP50_N2_1


title: s_2_13_9.0_polyA

description:
Series_2_Sample_13_9.0_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 4183.187697


title: s_3_05_2.5_polyA

description:
Series_3_Sample_05_2.5_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 5892.016311


title: s_3_26_7.0_rz

description:
RiboZero RNA
Series_3_Sample_26_7.0_hpf_rz
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 7826.888673


title: s_2_10_7.5_polyA

description:
Series_2_Sample_10_7.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 8103.689289


title: Menin_KO_Th_H3K27me3

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

institute: Ehime University

description: Menin-KO CD4 T cells

data_processing:
Illumina Casava1.8.2 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie 0.12.7
peaks were called using MACS 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: BED

source_name: naive CD4 T cells

growth_protocol: KJ1+ naïve CD4 T cells from DO11.10 OVA-specific TCR TG mice were stimulated with plate bound anti-TCR-b mAb (3 μg/ml, H57-597, BioLegend) plus anti-CD28 mAb (1 μg/ml, 37.5, BioLegend) in the presence of IL-2 (2.5 ng/ml) for 2 days, and then cells were further expanded with IL-2 another 3 days in vitro.  We termed these cells “primary effector CD4 T cells”.  The primary effector CD4 T cells were transferred intravenously into syngeneic BALB/c nu/nu recipient mice to induce homeostatic expansion in vivo.  Four weeks after transfer, KJ1+ transferred CD4 T cells were recovered from the spleen of recipient mice, and expanded same way as primary stimulation.  The secondary expanded effecter CD4 T cells, we termed “secondary effector CD4 T  cells”.  Naïve CD4 T cells from Menin-WT and -KO mice were stimulated with immobilized anti-TCR-β mAb and an anti-CD28 mAb for 2 days with IL-2 (2.5 ng/ml). Next, cells were transferred to a new plate and cultured for 5 day in the presence of IL-2.

extract_protocol:
Lysates were clarified from sonicated nuclei and transcription factor- or histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the ChIP Sample Prep Kit

value: Menin knockout

value: spleen

value: splenic naive CD4 T cells

value: Active Motif

tag: chip antibody lot#


title: s_2_14_9.5_polyA

description:
Series_2_Sample_14_9.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 5375.215525


title: s_2_15_4.5_polyA

description:
Series_2_Sample_15_4.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 5411.955723


title: s_2_09_7.0_polyA

description:
Series_2_Sample_09_7.0_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 9198.652338


title: Menin_WT_Th_H3K27me3

description: Menin-WT CD4 T cells

value: Menin wild type

tag: cell type


title: Menin_KO_Th_H3K27ac

description: Menin-KO CD4 T cells

tag: strain background

value: lot 105


title: s_2_11_8.0_polyA

description:
Series_2_Sample_11_8.0_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 5600.172126


title: s_3_06_3.0_polyA

description:
Series_3_Sample_06_3.0_hpf_polyA
processed data file: series_3_raw_counts.txt.gz
processed data file: series_3_norm_counts.txt.gz
Paired-end files_variance: 5820.743988


title: s_2_16_6.5_polyA

description:
Series_2_Sample_16_6.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 5029.541825


title: Menin_WT_Th_H3K27ac

description: Menin-WT CD4 T cells

tag: genotype/variation


title: s_2_08_6.5_polyA

description:
Series_2_Sample_08_6.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 6668.473375


title: Menin_KO_Th_H3K4me3

description: Menin-KO CD4 T cells


title: s_2_05_5.0_polyA

description:
Series_2_Sample_05_5.0_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 5094.686209


title: sel-1_N2_1


title: s_2_07_6.0_polyA

description:
Series_2_Sample_07_6.0_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 7431.988984


title: Secondary_Th_Menin_ChIP

description: secondary effector CD4 T  cells

source_name: KJ1+ transferred CD4 T cells

value: BALB/c

value: DO11.10 OVA-specific TCR transgenic

value: KJ1+ transferred CD4 T cells

value: Menin

value: Bethyl Laboratories


title: Menin_WT_Th_H3K4me3

description: Menin-WT CD4 T cells


title: sel-1_N2_2


title: Primary_Th_Menin_ChIP

description: primary effector CD4 T cells

source_name: KJ1+ naive CD4 T cells

value: KJ1+ naive CD4 T cells


title: s_2_03_4.0_polyA

description:
Series_2_Sample_03_4.0_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 4690.284463


title: IPF8

city: Stanford

first: Tracy

middle: L

last: Nance

state: CA

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University

description: library strategy: RNA-Seq, strand specificity was performed

data_processing:
Base calls were made using an Illumina HiSeq 2000 and standard Illumina software.
Paired-end reads were aligned to hg19 using STAR 2.2.0.c with splice junction annotation from gencode 14.
Reads with mapping quality < 10 or mapping to mitochondrial DNA were discarded.
Counts of reads in genes were determined by the in-house script samtoexoncoverage_gencode.pl, with gencode 14 annotation.
Counts of reads in exonic bins were determined by the DEXSeq script dexseq_count.py with options -p yes -s reverse.
Genome_build: hg19
Supplementary_files_format_and_content: *.genes.txt files are tab-separated text files containing ensembl gene ID and count; *.exon.count files are tab-separated text files containing gene/exonbin ID and count

source_name: lung tissue

extract_protocol:
RNA was isolated from frozen lung samples with Trizol and rRNA was depleted using the Ribo-Zero Magnetic Kit.
RNA libraries were prepared for sequencing using Illumina TruSeq RNA preparation kit.

tag: Sex

value: Male

tag: demographic group

value: European ancestry

value: lung

tag: phenotype

value: Idiopathic pulmonary fibrosis


title: s_2_12_8.5_polyA

description:
Series_2_Sample_12_8.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 4526.198367


title: s_2_02_3.5_polyA

description:
Series_2_Sample_02_3.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 3998.333215


title: OSC_STARRseq_with_ecd_rep1

city: Vienna

first: Daria

last: Shlyueva

address: Dr. Bohr-gasse,7

country: Austria

institute: IMP

description: PCR amplified cDNA (STARR-seq transcript)

data_processing:
Library strategy: STARR-Seq
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
STARR-Seq:
Reads were mapped to the dm3 genome using bowtie (bowtie -p 12 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa) excluding chrU, chrUextra, and chrM. For all subsequently analysis we used only reads collapsed on chromosome, start, end, strand (fragments). Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of cDNA and input and an hypergeometric test to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
RNA-seq:
Reads were mapped to the dm3 genome and transcriptome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -) and bfast reconciling the outputs. We estimated RPKM values for each gene based on the number of reads falling over each exon merging exons from a all genes' isoforms into one meta-transcript. Reads counts were normalized by the total reads per library and the merged meta-gene exons lengths.
Genome_build: dm3
Supplementary_files_format_and_content: All processed data files are in plain text. For STARR-seq we report for each peak the chromosome, the summit position, the enrichment over input (log2-scale) at the summit, and the p-value. For the RNA-seq data we report 3 different gene identifiers and the RPKM value for each gene.

organism: Drosophila melanogaster

source_name: OSC cells

extract_protocol: Genomic DNA (source: embryos of the sequenced strain: y; cn bw sp) was isolated, sheared and size selected (~500bp). Following the instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L), Illumina Multiplexing Adapters (Illumina Inc; cat. no. PE-400-1001) were ligated and homology arms for In-Fusion® recombination were added by PCR, followed by recombination into the STARR-seq vector (pGL3-Promotor backbone (Promega; cat. no. E1751) with the sequence between BglII and FseI replaced with the following sequence, containing a Drosophila Synthetic Core Promoter (DSCP) (1), an ORF (sgGFP, Qbiogene, Inc), a ccdB suicide gene flanked by homology arms (used for cloning the genomic enhancer candidates during library generation), and the pGL3’s SV40 late polyA-signal.). The In-Fusion® reactions were transformed (MegaX DH10B; Invitrogen), grown in liquid culture and plasmids were isolated.

treatment_protocol: For all experiments cells were treated with ecdysone. The final concentration of ecdysone was 41 μM (10 mg of 20-hydroxyecdysone (Sigma; cat. no. H5142) per 500 ml of growth medium). After 24 hrs incubation with the hormone, cells were harvested.

value: OSC cells

value: ecdysone


title: IPF6


title: OSC_STARRseq_no_ecd_rep2

value: no ecdysone


title: s_1_06_3.0_polyA

description:
Series_1_Sample_06_3.0_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 3435.686891


title: OSC_STARRseq_no_ecd_rep1


title: IPF4


title: OSC_STARRseq_with_ecd_rep2


title: IPF3

value: Female


title: s_2_00_2.5_polyA

description:
Series_2_Sample_00_2.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 2497.754984


title: IPF7

value: Asian ancestry


title: S2_RNAseq_with_ecd_rep1

description: PCR amplified cDNA (cellular polyA+ RNA)

data_processing:
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
STARR-Seq:
Reads were mapped to the dm3 genome using bowtie (bowtie -p 12 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa) excluding chrU, chrUextra, and chrM. For all subsequently analysis we used only reads collapsed on chromosome, start, end, strand (fragments). Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of cDNA and input and an hypergeometric test to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
RNA-seq:
Reads were mapped to the dm3 genome and transcriptome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -) and bfast reconciling the outputs. We estimated RPKM values for each gene based on the number of reads falling over each exon merging exons from a all genes' isoforms into one meta-transcript. Reads counts were normalized by the total reads per library and the merged meta-gene exons lengths.
Genome_build: dm3
Supplementary_files_format_and_content: All processed data files are in plain text. For STARR-seq we report for each peak the chromosome, the summit position, the enrichment over input (log2-scale) at the summit, and the p-value. For the RNA-seq data we report 3 different gene identifiers and the RPKM value for each gene.

source_name: S2 cells

extract_protocol: RNA was isolated using QIAShredder (QIAGEN; cat.no. 79654) and RNeasy Mini Kit (QIAGEN; cat.no. 74106; including DNase I on column digestion) from 5-10 x 10^6 cells. 5ug total RNA was then processed as described before (S. Zhong et al., High-throughput illumina strand-specific RNA sequencing library preparation., Cold Spring Harbor protocols 2011, 940-9 (2011)) with minor adjustments. End-repair, dA-tailing and adapter ligation were performed with the NEBNext DNA Library Prep Reagent Set for Illumina (NEB, cat.no. E6000L) with proportionally reduced enzyme amounts to account for low RNA concentrations. Indexed library amplification was carried out using KAPA Library Amp Real Time (KAPA biosystems: cat.no. KK2701).

value: S2 cells


title: s_1_04_2.0_polyA

description:
Series_1_Sample_04_2.0_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 4117.358998


title: IPF5


title: IPF2

value: Admixed or American ancestry


title: s_1_03_1.5_polyA

description:
Series_1_Sample_03_1.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 3991.76628


title: S2_RNAseq_no_ecd_rep1


title: s_2_06_5.5_polyA

description:
Series_2_Sample_06_5.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 5573.196769


title: s_2_04_4.5_polyA

description:
Series_2_Sample_04_4.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 7789.413588


title: S2_RNAseq_no_ecd_rep2


title: Norm8

value: normal


title: IPF1


title: S2_STARRseq_input

description:
PCR amplified Plasmid library, used for S2 STARR-seq
plasmid DNA (containing genomic DNA fragments)

source_name: whole genome library (in STARR-seq vector)

tag: genotype

value: y; cn bw sp - sequenced strain (Adams et al. 2000)


title: s_1_01_0.5_polyA

description:
Series_1_Sample_01_0.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 5705.410726


title: Norm6


title: S2_STARRseq_with_ecd_rep2


title: s_1_00_0.0_polyA

description:
Series_1_Sample_00_0.0_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 5079.8863


title: s_1_05_2.5_polyA

description:
Series_1_Sample_05_2.5_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 5944.538106


title: S2_RNAseq_with_ecd_rep2


title: s_2_01_3.0_polyA

description:
Series_2_Sample_01_3.0_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 3208.769392


title: Norm5


title: S2_STARRseq_with_ecd_rep1


title: S2_STARRseq_no_ecd_rep2


title: Norm4


title: s_1_02_1.0_polyA

description:
Series_1_Sample_02_1.0_hpf_polyA
processed data file: series_1_2_raw_counts.txt.gz
processed data file: series_1_2_norm_counts.txt.gz
Paired-end files_variance: 6656.412824


title: Norm2

description: library strategy: RNA-Seq, strand specificity was performed


title: SPF 3

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Hi-Seq 2000 for sequencing
Sequenced reads were trimmed of adaptors and barcodes, filtered of reads with quality threshold <= 30, multiply mapped reads, and number of N's > 0.  Remaining reads were aligned to the mm9 genome in GeneSpring NGS
Reads per kilobase per megabase (RPKM) was calculated, and normalized using the DeSeq normalization procedure, thresholding the number of reads per entity to 1.
Normalized expression values were baselined to the median of all samples
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files containing RPKM values (*RPKM.txt), and normalized and baselined RPKM values, for each sample.

source_name: Ileal sample from obese mouse, pair fed after sham surgery

extract_protocol:
Illumina TruSeq RNA preparation kit
RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq RNA preparation kit and sequenced on the Illumina Hi-Seq 2000 with single-end 50-bp reads (Illumina, San Diego, CA)

tag: gender

tag: strain

tag: surgery

value: Sham surgery

tag: feeding after surgery

value: Pair-fed

tag: diet

value: 60 kcal % high fat diet for 6 weeks prior to surgery

tag: age at surgery

value: 8 weeks


title: SPF 4

value: Male


title: SPF 2


title: ChIPseq_input

description: PCR amplified DNA

data_processing:
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
Reads were mapped to the dm3 genome using bowtie (bowtie -p 12 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa) excluding chrU, chrUextra, and chrM.
ChIP-seq peaks were called using STARR-seq pipeline using following parameters: -M 50 -W 1000 -D 600 -Z 1.67 -g dm3 -P 0.001
Genome_build: dm3
Supplementary_files_format_and_content: ChIP-Seq processed files supplement_ChIP_peaks_no_ecd.txt and supplement_ChIP_peaks_with_ecd.txt contain chr, summit, enrichment and p-values for called peaks.

extract_protocol: 10^8 cells with and without treatment were harvested. Chromatin was sonicated with Tip sonicator (Omni Sonic Ruptor 250 Watt Ultrasonic Homogenizer) for 7 cycles (1 min on (duty cycle 30%, output 20%)) 1 min off) in 2 ml of Lysis buffer 3. The anti-EcR monoclonal antibody (DDA2.7) developed by C. Thummel in D. Hogness laboratory was obtained from the Developmental Studies Hybridoma Bank developed under the auspices of the NICHD and maintained by The University of Iowa, Department of Biology, Iowa City, IA 52242. 1 ml of chromatin was incubated with 3 μl of antibody (135 μg/ml) overnight. Chromatin and 25 μl of blocked Dynabeads Protein G (Invitrogen, cat. no. 10004D) were combined and incubated at 4° C for additional 2 hrs. 3 ng of material was used for library generation.  Library was constructed following instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L). Library amplifcation was done using KAPA Library Amp Real Time (KAPA biosystems: cat.no. KK2701).

tag: chip antibody


title: S2_STARRseq_no_ecd_rep1

tag: agent


title: SPF 5


title: S2_ChIPseq_with_ecd

description:
S2_ChIPseq_with_ecd_rep1
S2_ChIPseq_with_ecd_rep2
PCR amplified DNA

value: anti-EcR monoclonal antibody (DDA2.7) developed by C. Thummel in D. Hogness laboratory


title: SPF 1


title: S2_DHSseq_with_ecd_24hrs_rep2

description: PCR amplified DNaseI digested chromatin

data_processing:
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
STARR-Seq:
Reads were mapped to the dm3 genome using bowtie (bowtie -p 12 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa) excluding chrU, chrUextra, and chrM. For all subsequently analysis we used only reads collapsed on chromosome, start, end, strand (fragments). Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of cDNA and input and an hypergeometric test to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
DNase-Hypersensitivity
Reads were mapped to the dm3 genome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -) excluding chrU, chrUextra, and chrM. We estimated the enrichment and p-values for specific genomic regions using the cDNA and the input together with a hypergeometric test. To call peaks we also used MACS14 with default parameters and an FDR cutoff of 5%.
RNA-seq
Reads were mapped to the dm3 genome and transcriptome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -) and bfast reconciling the outputs. We estimated RPKM values for each gene based on the number of reads falling over each exon merging exons from a all genes' isoforms into one meta-transcript. Reads counts were normalized by the total reads per library and the merged meta-gene exons lengths.
Genome_build: dm3
Supplementary_files_format_and_content: All processed data files are in plain text. The DHS-seq peaks are directly taken from the MACS output. For STARR-seq we report for each peak the chromosome, the summit position, the enrichment over input (log2-scale) at the summit, and the p-value.For the RNA-seq data we report 3 different gene identifiers and the RPKM value for each gene.

extract_protocol: 5-7 10^7 cells were harvested. DNase treatment was done as in (L. Cappabianca, H. Thomassin, R. Pictet, T. Grange, Genomic footprinting using nucleases., Methods in molecular biology (Clifton, N.J.) 119, 427-42 (1999)). For size selection (~120bp) a sucrose gradient was emplyed (SW TI40, 30000rpm, 16h). Library was constructed following instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L). Library amplifcation was done using KAPA Library Amp Real Time (KAPA biosystems: cat.no. KK2701).


title: S2_ChIPseq_no_ecd

description:
S2_ChIPseq_no_ecd_rep1
S2_ChIPseq_no_ecd_rep2
PCR amplified DNA


title: VSG 5

source_name: Ileal sample from obese mouse following vertical sleeve gastrectomy

value: Vertical sleeve gastrectomy

value: Ad libitum


title: VSG 4


title: Input sequencing in endoderm cells

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description: Sequenced input

data_processing:
Basecalling: Performed with CASAVA v1.7
Alignment: Sequence reads were aligned to the mouse genome (version mm9) using Bowtie (Langmead, et al. Genome Biology 2009) version 0.12.7 with options "-q --best --strata -m 1 -p 4 --chunkmbs 1024". Only uniquely mapping reads were analyzed further. All alignment data is provided here in BAM format.
BIGWIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 20bp was used for calculating overlapping read counts. Read counts per starting base pair were limited to 1 in full-length Cdx2 replicates 3 & 4, and the truncated Cdx2 experiment, due to lower library complexity than sequencing depth. WIG files were converted to bigWig using wigToBigWig (UCSC).
Genome_build: mm9
Supplementary_files_format_and_content: Alignment files are BAM format output from Bowtie; bigwig files are generated from aligned reads as described in the data processing steps.

source_name: endoderm

growth_protocol: Prior to differentiation, ES cells were passaged onto gelatin-coated plates for 25 minutes to deplete MEFs. MEF-depleted ES cells were then seeded at 1 *10^4 cells/cm2 onto gelatin-coated dishes in Advanced DMEM (Life Technologies) supplemented with N-2 (Life Technologies), B27 Supplement without vitamin A (Life Technologies), and Glutamax. After 36 hours, media was changed to Advanced DMEM with 2% FBS, Glutamax, 5 nM GSK-3 inhibitor XV and 50 ng/mL E. coli-derived Activin A (Peprotech) for 24 hours to produce mesendoderm. For endoderm differentiation, cells were then fed with Advanced DMEM with 2% FBS, Glutamax, 50 ng/mL Activin A and 1 µM Dorsomorphin (Sigma) for 48 hours. For intestinal endoderm differentiation, cells at the endoderm stage were fed for 24 hours with Advanced DMEM with B-27 supplement without vitamin A, Glutamax, and 100 nM GSK-3 inhibitor XV.

extract_protocol: Cells were fixed with 1% formaldehyde for 15 minutes at room temperature. Pellets containing ~40 x10^6 cells were flash frozen and stored at -80 oC. Cells were thawed on ice, resuspended in 5ml of Lysis Buffer A and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 5ml Lysis Buffer B and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 3ml of Sonication Buffer (SB). Nuclear extracts were sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp. Sonicated chromatin was incubated for 16 hours at 4C with Protein-G beads (Invitrogen) conjugated with either rabbit anti-V5 (Abcam) or anti-FLAG (Sigma). After incubation and with the aid of a magnetic device, beads were washed once with SB+500nM NaCl, once with LiCl Wash Buffer and 1ml of TE. Then, beads were centrifugated at 950g for 3 min and remove residual TE with a pipette. 210ul of Elution Buffer was added to the beads followed by incubation at 65 oC for 45 minutes with a brief pulse of vortex every 10 minutes. 200ul of supernatant was removed after a 1 minute centrifugation at 16,000g. The crosslink was reversed by 16 hours incubation at 65 oC. RNA was digested by the addition of 200ul of TE and RNAseA (Sigma) at a final concentration of 0.2mg/ml and incubated for 2 hours at 37C. Protein was digested by the addition of Proteinase K (0.2 mg/ml final, Invitrogen) supplemented with CaCl2 followed by a 30 minutes incubation at 55 oC. DNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and then recovered with an ethanol precipitation with glycogens as carrier. The pellets were suspended in 70ul of water. Purified DNA fragments were processed according to the Illumina/Solexa library protocol and sequenced using a Genome Analyzer II (Illumina, http://www.illumina.com/pages.ilmn?ID=252).

treatment_protocol: During this last 24 hour step, Doxycycline was added to the culture medium at 2ug/ml to induce the iCdx2 construct.

tag: cell line

value: Ainv15 (ATCC SCRC-1029) with Dox-inducible Cdx2-V5 construct

tag: Stage

value: endoderm


title: ChIP-seq analysis of induced V5-tagged Cdx2 (iCdx2-V5) in endoderm cells

description: Chromatin IP against V5

value: anti-V5 (Abcam, ab15828)


title: S2_DHSseq_with_ecd_24hrs_rep1

description: PCR amplified DNaseI digested chromatin

tag: cell type


title: VSG 3


title: S2_DHSseq_no_ecd_24hrs_rep2

description: PCR amplified DNaseI digested chromatin


title: Norm3

value: Female

value: European ancestry

tag: tissue

value: lung


title: VSG 2


title: induced FLAG-tagged truncated Cdx2 (iFLAG-Cdx2-truncated) in embryonic stem cells [ChIP-seq]

description: Chromatin IP against FLAG

data_processing:
Basecalling: Performed with CASAVA v1.7
BIGWIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 20bp was used for calculating overlapping read counts. Read counts per starting base pair were limited to 1 in full-length Cdx2 replicates 3 & 4, and the truncated Cdx2 experiment, due to lower library complexity than sequencing depth. WIG files were converted to bigWig using wigToBigWig (UCSC).
Peaks: TF binding events were detected using GPS (Guo, et al. Bioinformatics 2010) version 2.0. In GPS, the scaling ratio between IP and control channels was estimated using the median ratio of all 10Kbp windows along the genome. The GPS binding model was initialized to the default and iteratively updated over up to 3 training rounds. In this study, we require that reported peaks contain a ChIP-seq enrichment level that is significantly greater than 1.5 times the control level with p-value <0.01 as tested using the Binomial distribution. Signal-to-noise ratios are estimated by comparing the ChIP-seq read count occurring at any peak found for a given transcription factor in any condition to the count of remaining reads in that experiment.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files are generated from aligned reads as described in the data processing steps.

source_name: embryonic stem cells

growth_protocol: ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol, 100 U/ml LIF, and 100 ng/ml bFGF (PeproTech).  For ChIP experiments, we scaled to seed 1x10^7 cells on Day 0. Doxycycline (Sigma) was added to the culture medium for 36 hours at 2ug/ml to induce Cdx2 construct expression.

extract_protocol: Cells were fixed with 1% formaldehyde for 15 minutes at room temperature. Pellets containing ~40 x10^6 cells were flash frozen and stored at -80 oC. Cells were thawed on ice, resuspended in 5ml of Lysis Buffer A and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 5ml Lysis Buffer B and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 3ml of Sonication Buffer (SB). Nuclear extracts were sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp. Sonicated chromatin was incubated for 16 hours at 4C with Protein-G beads (Invitrogen) conjugated with either rabbit anti-V5 (Abcam) or anti-FLAG (Sigma). After incubation and with the aid of a magnetic device, beads were washed once with SB+500nM NaCl, once with LiCl Wash Buffer and 1ml of TE. Then, beads were centrifugated at 950g for 3 min and remove residual TE with a pipette. 210ul of Elution Buffer was added to the beads followed by incubation at 65 oC for 45 minutes with a brief pulse of vortex every 10 minutes. 200ul of supernatant was removed after a 1 minute centrifugation at 16,000g. The crosslink was reversed by 16 hours incubation at 65 oC.  RNA was digested by the addition of 200ul of TE and RNAseA (Sigma) at a final concentration of 0.2mg/ml and incubated for 2 hours at 37C.  Protein was digested by the addition of Proteinase K (0.2 mg/ml final, Invitrogen) supplemented with CaCl2 followed by a 30 minutes incubation at 55 oC. DNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and then recovered with an ethanol precipitation with glycogens as carrier. The pellets were suspended in 70ul of water. Purified DNA fragments were processed according to the Illumina/Solexa library  protocol and sequenced using a Genome Analyzer II (Illumina, http://www.illumina.com/pages.ilmn?ID=252).

treatment_protocol: Doxycycline (Sigma) was added to the culture medium at 2ug/ml for 36 hours to induce the iCdx2 construct.

tag: cell-line

value: Ainv15 (ATCC SCRC-1029) with Dox-inducible FLAG-Cdx2 construct where amino acids 1-59 have been removed from the Cdx2 gene

tag: cell-treatment

value: +Dox +FGF

tag: cell-stage

value: embryonic stem cells

tag: chip-antibody

value: anti-Flag (Sigma, F1804-200UG)


title: VSG 1


title: Norm1

tag: Sex

tag: demographic group

tag: phenotype

value: normal


title: Pseudo-ChIP control using anti-V5 in progenitor motor neurons (Day_4 )

description: progenitor motor neurons (Day4 directed differentiation)

data_processing:
Alignment: Sequence reads were aligned to the mouse genome (version mm9) using Bowtie (Langmead, et al. Genome Biology 2009) version 0.12.5 with options "-q --best --strata -m 1 -p 4 --chunkmbs 1024". Only uniquely mapping reads were analyzed further. All alignment data is provided here in BAM format.
Peaks: Binding events were detected using GPS (Guo, et al. Bioinformatics 2010) version 1.0. In GPS, the scaling ratio between IP and control channels was estimated using the median ratio of all 10Kbp windows along the genome. The GPS binding model was initialized to the default and iteratively updated over up to 3 training rounds. In this study, we require that reported peaks contain a ChIP-seq enrichment level that is significantly greater than 1.5 times the control level with p-value <0.01 as tested using the Binomial distribution. Signal-to-noise ratios are estimated by comparing the ChIP-seq read count occurring at any peak found for a given transcription factor in any condition to the count of remaining reads in that experiment. Peaks are provided here in two formats, BED and GPS raw output. The BED format shows the GPS-predicted binding position, and the Q-value calculated by GPS is provided in the score field. The GPS raw output has the following fields (tab-separated): 1) Binding event coordinate, 2) IP read count assigned to event, 3) Control read count assigned to event, 4)Fold enrichment (IP/Control), 5) Q-value (multiple hypothesis corrected), 6) P-value, 7) Shape deviation from the empirical read distribution (log10(KL)), 8) Shape deviation between IP vs Control (log10(KL)).
WIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 20bp was used for calculating overlapping read counts.

source_name: Pseudo IP against V5

growth_protocol: ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described (Wichterle, et al. Cell 2002).  Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x105 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 1, Day 2 and Day 5 of differentiation.  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 ÂµM all-trans-Retinoic acid (RA, Sigma) and 0.5 ÂµM agonist of hedgehog signaling (SAG, Calbiochem). For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0. Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

extract_protocol: Differentiating embryoid bodies were washed with PBS and then dissociated by mild Trypsinization (Invitrogen) followed by mechanical dissociation until single-cell suspension was obtained. Cells were fixed with 1% formaldehyde for 15 minutes at room temperature. Pellets containing ~40 x106 cells were flash frozen and stored at -80 oC. Cells were thawed on ice, resuspended in 5ml of Lysis Buffer A and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 5ml Lysis Buffer B and incubated for 10 minutes at 4 oC in a rotating platform. Samples were spun down for 5 minutes at 1,350g, resuspended in 3ml of Sonication Buffer (SB). Nuclear extracts were sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp. Sonicated chromatin was incubated for 16 hours at 4C with Protein-G beads (Invitrogen) conjugated with either rabbit anti-V5 (Abcam), mouse anti-Flag M2 (Sigma) or rabbit anti-Olig2 (Millipore). After incubation and with the aid of a magnetic device, beads were washed once with SB+500nM NaCl, once with LiCl Wash Buffer (LiClB) and 1ml of TE. Then, beads were centrifugated at 950g for 3 min and remove residual TE with a pipette. 210ul of Elution Buffer was added to the beads followed by incubation at 65 oC for 45 minutes with a brief pulse of vortex every 10 minutes. 200ul of supernatant was removed after a 1 minute centrifugation at 16,000g. The crosslink was reversed by 16 hours incubation at 65 oC.  RNA was digested by the addition of 200ul of TE and RNAseA (Sigma) at a final concentration of 0.2mg/ml and incubated for 2 hours at 37C.  Protein was digested by the addition of Proteinase K (0.2 mg/ml final, Invitrogen) supplemented with CaCl2 followed by a 30 minutes incubation at 55 oC. DNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and then recovered with an ethanol precipitation with glycogens as carrier. The pellets were suspended in 70ul of water. Purified DNA fragments were processed according to the Illumina/Solexa sequencing protocol using a Genome Analyzer II (Illumina, http://www.illumina.com/pages.ilmn?ID=252).

treatment_protocol: Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 ÂµM all-trans-Retinoic acid (RA, Sigma) and 0.5 ÂµM agonist of hedgehog signaling (SAG, Calbiochem). Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

value: Ainv15 (ATCC SCRC-1029) with inducible V5-tagged Olig2

tag: treatment

tag: cell stage


title: S2_DHSseq_no_ecd_24hrs_rep1

description: PCR amplified DNaseI digested chromatin

data_processing:
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
STARR-Seq:
Reads were mapped to the dm3 genome using bowtie (bowtie -p 12 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa) excluding chrU, chrUextra, and chrM. For all subsequently analysis we used only reads collapsed on chromosome, start, end, strand (fragments). Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of cDNA and input and an hypergeometric test to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
DNase-Hypersensitivity
Reads were mapped to the dm3 genome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -) excluding chrU, chrUextra, and chrM. We estimated the enrichment and p-values for specific genomic regions using the cDNA and the input together with a hypergeometric test. To call peaks we also used MACS14 with default parameters and an FDR cutoff of 5%.
RNA-seq
Reads were mapped to the dm3 genome and transcriptome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -) and bfast reconciling the outputs. We estimated RPKM values for each gene based on the number of reads falling over each exon merging exons from a all genes' isoforms into one meta-transcript. Reads counts were normalized by the total reads per library and the merged meta-gene exons lengths.
Genome_build: dm3
Supplementary_files_format_and_content: All processed data files are in plain text. The DHS-seq peaks are directly taken from the MACS output. For STARR-seq we report for each peak the chromosome, the summit position, the enrichment over input (log2-scale) at the summit, and the p-value.For the RNA-seq data we report 3 different gene identifiers and the RPKM value for each gene.
Supplementary_files_format_and_content: shlyueva_supplement_DHS.txt contains enhancer_class, log2 enrichments before and after treatment and quantile normalized enrichments.

value: S2 cells


title: cntl_neo_5hr_1

status: Public on Mar 26 2014

first: Chris

middle: W

last: Seidel

department: Genomics

institute: Stowers Institute

data_processing:
Data was processed with CASAVA version 1.8.2
Sequence reads in fastq format were mapped to danRer7using tophat-1.4.1 with options –g 1 and a GTF description of transcripts based on Ensembl 63. FPKM values for these transcripts were generated using cufflinks v1.3.
Genome_build: danRer7
Supplementary_files_format_and_content: FPKM values per gene.

organism: Danio rerio

source_name: GFP negative cells from 5 dpf larvae

growth_protocol: Larvae were generated by paired matings and raised in 0.5X E2 medium at 28.5°C. GFP positive larvae were sorted from wild-type larvae at 48 hpf under fluorescent stereoscope.

extract_protocol:
Two hundred 5dpf untreated Tg(sqET20) control or neomycin treated Tg(sqET20) larvae were anesthetized, collected in a 2mL tube, dissociated with trypsin and filtered to remove un-dissociated tissue. A two-gate FACS strategy was used to select only living target cells from excesses of dead cells and cellular debris of the larval cell suspensions (see Materials and Methods of associated manuscript for detailed FACS protocol). Approximately 30,000 GFP- or GFP+ cells were used for total RNA extraction using Trizol (Invitrogen) following the manufacturer’s manual.
Libraries for RNA sequencing were made with poly-A selected mRNA using the Illumina TruSeq RNA library construction kit v2 (Illumina). The resulting libraries were purified using Agencourt AMPure XP system (Backman Coulter), then quantified using a Bioanalyzer or Qubit Fluorometer (Life Technologies).

treatment_protocol: For neomycin treatment, 5dpf larvae were treated for 30min with 300μM neomycin (Fisher BioReagents) diluted in 0.5X E2 medium, rinsed three times and recovered in 0.5X E2 medium at 28.5°C for the indicated time.

tag: drug

value: neomycin

tag: time

tag: gfp status

value: negative

tag: genotype


title: induced V5-tagged Cdx2 (iCdx2-V5) in embryonic stem cells [ChIP-seq]

description: Chromatin IP against V5


title: cntl_neo_5hr_3


title: cntl_neo_5hr_2


title: gfp_neo_5hr_3

source_name: GFP positive cells from 5 dpf larvae

value: positive


title: cntl_neo_3hr_1


title: gfp_neo_3hr_2


title: gfp_neo_5hr_1


title: gfp_neo_3hr_3


title: cntl_neo_3hr_2


title: gfp_neo_5hr_2


title: gfp_neo_3hr_1


title: cntl_neo_3hr_3


title: gfp_nt_1hr_2

value: no drug


title: gfp_nt_1hr_1


title: gfp_nt_1hr_3


title: gfp_neo_1hr_1


title: gfp_neo_1hr_2


title: gfp_neo_1hr_3


title: cntl_nt_1hr_3


title: cntl_nt_1hr_1


title: cntl_nt_1hr_2


title: HIF1a_Hypoxia_ChIPSeq

city: Beijing

first: Jing

last: Zhang

address: 1130 St Nicholas Ave ICRC, room403

institute: Columbia University Medical Center

data_processing:
ChIP-seq reads were aligned to the hg18 genome assembly using BWA with default configurations.
The aligned reads were filtered to get uniquely mapped reads.
Peaks were called using MACS1.4 with p value cutoff <= 0.00001.
Genome_build: hg18
Supplementary_files_format_and_content: Chr represents chromosome; start represents the start position of the peak; end represents the end position of the peak; length represents the length of the peak; summit represents the relative position of summit of the peak; tags represent the number of reads in the peak; -10*log10(pvalue) represent the p value of the peak; fold_enrichment represents the fold change of the peak compared with local genome background.

source_name: Caki-2 cell line

growth_protocol: Caki-2 was maintained in McCoy's 5a modified medium supplemented with 10% (vol/vol) fetal bovine serum

extract_protocol:
Chromatin immunoprecipitation was performed in Caki-2 cells with a HIF-1a antibody (Novus, NB100-134) and control IgG antibody
Libraries were prepared according to Solid's insruction for single-end library.

treatment_protocol: Cells were treated with 100 μM desferoxamine (DFO) induced hypoxic conditions

value: ccRCC

value: kidney

value: HIF-1a antibody (Novus, NB100-134)


title: cntl_neo_1hr_2


title: cntl_neo_1hr_3