title: ThioMac-p65-Input

city: La Jolla

first: Nathanael

middle: Judge

last: Spann

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description: ThioMac genomic DNA, notx (input)

data_processing:
Libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer, Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions.
Reads were aligned to the mm9 genome (NCBI build using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location.
For ChIP-Seq, Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, and perform other analyses in the study. Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped. UCSC Genome Browser BigWig or BigWig hub text files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.
Genome_build: mm9

source_name: Primary thioglycollate-elicited peritoneal macrophages

growth_protocol: Primary cells were isolated from 6-8 week-old C57Bl/6 (Harlan Laboratories) male mice. Thioglycollate-elicited macrophages were isolated by peritoneal lavage 3-4 days following peritoneal injection of 2.5 ml thioglycollate. Cells were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after adherence and again fed with fresh medium. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 100 ng/ml of Kdo2-Lipid A for 1 – 24 hours. For LXR experiments cells were treated with 1uM GW3965 for 2 hours.

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Alternatively, lysates clarified from isolated nuclei were treated with MNase and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina Genomic adaptors or with NEXTflex DNA barcodes adaptors for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size-selected (150-250bp) from a 2% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina Genome Analyzer II or Illumina HiSeq 2000 according to the manuactuere’s instructions.

value: Macrophage

tag: strain

tag: treatment


title: ThioMac-WT-p65-KLA1h

status: Public on Oct 09 2013

type: SRA

state: CA

country: USA

description: p65 ChIP-Seq, KLA 1h

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

value: C57BL/6 NCoR fl/fl Lys M-Cre -/-

value: Kdo2 Lipid A (KLA) 1h

tag: chip ab

value: p65 (Santa Cruz sc-372)


title: ThioMac-NCoRKO-p65-KLA1h

description: p65 ChIP-Seq, KLA 1h

value: C57BL/6 NCoR fl/fl Lys M-Cre +/-


title: ThioMac-NCoRKO-p65-notx

description: p65 ChIP-Seq, notx


title: ThioMac-WT-p65-notx

description: p65 ChIP-Seq, notx


title: ChIP-seq_spt6-1_Input_II

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

data_processing:
ChIP-seq reads were aligned to S. Pombe assembly ASM294v2 using bowtie with ‘-m 10 --best’ options.
The samples were normalized with BEADS. The fragments were extended in the 3’ end direction to be 100 bp long ("beads extend -threePrim <100-read length>”).  Spp defined broad enrichment clusters (z=3) were excluded in the BEADS calculation.  Downstream ChIP-seq analysis was performed in 10 bp bins as out by BEADS (“beads tagCount -base 10”).
The input samples were normalized to per 1M fragments over nuclear chromosomes.
The IP samples were normalized such that the median fold enrichment over input is set to 1.
Genome_build: ASM294v2
Supplementary_files_format_and_content: wig files at 10bp resolution show fold enrichment for IP samples and normalized tag counts for input samples

organism: Schizosaccharomyces pombe

growth_protocol: Strains were cultured at 30°C, using Yeast Extract Supplemented (YES) medium

extract_protocol:
100 ml cultures grown to 1-2 x 107 cells/ml were crosslinked (1% formaldehyde, 30 min) and lysed by bead beating.  The chromatin fraction was isolated and sheared to 200-500 bp fragments using a Bioruptor sonicator (Diagenode) or Sonicator 3000 (Misonix).  Immunoprecipitations (IPs) were performed overnight at 4°C with 1 μg of anti-H3 (ab1791; Abcam), 2 μg of anti-H2B (ab1970; Abcam), 3 μg of anti-H3K36me3 (ab9050; Abcam), 5 μg of anti-H3K4me3 (ab8580; Abcam), 5 μL of anti-Rpb1 (8WG16; Covance), 5 μg of anti-HA (ab9110; Abcam), or 5 μL of anti-Myc (9E10; Santa Cruz Biotechnology).  IPs were coupled to 50 μL of protein-G-sepharose beads (GE Healthcare Life Sciences) at 4°C for 4 hours.  Beads were washed and eluted; eluate was reverse-crosslinked overnight at 65°C and incubated with proteinase K and glycogen for 2 hours at 37°C.  DNA was purified by phenol chloroform extraction and precipitated in ethanol overnight at -20°C.
Between 1-10 ng of ChIP DNA were processed for each ChIP-seq library.  DNA was end repaired with T4 DNA Polymerase (Invitrogen), T4 PNK (NEB) and DNA Pol I, Large Klenow fragment (Invitrogen), and an 'A' base was added using Klenow 3' to 5' exo minus (NEB).  1 pmol of barcoded adaptors were ligated on with T4 DNA ligase (Roche) and the products were PCR amplified with Phusion DNA Polymerase (NEB) and size selected by purification on 2% agarose-EX E-gels (Invitrogen) for fragments between 200-600 bp.  Library size and concentration was determined by Bioanalyzer or Tapestation analysis (Agilent) and libraries were pooled equimolar amounts with up to 26 in each sequencing lane.  Pooled libraries were gel purified twice, followed by column purification on MinElute columns (Qiagen).  At least 10 nM were submitted for analysis on the Illumina Hi-Seq at Tufts University Core Facility.

tag: genotype/variation

value: spt6-1; spt6 mutant

tag: chip-antibody


title: ChIP-seq_spt6-1_Set2-myc_II

value: Set2-myc (anti-Myc)

tag: chip-antibody vendor

value: Santa Cruz Biotechnology

tag: chip-antibody cat. #


title: ThioMac-NCoRKO-H3K4me2-KLA-24h

description: H3K4me2 nucleosomal DNA, KLA 24h

value: Kdo2 Lipid A (KLA) 24h

value: H3K4me2 (Millipore 07-030)


title: ChIP-seq_spt6-1_Rpb1_II

value: Covance


title: ChIP-seq_spt6-1_Input_I


title: ChIP-seq_spt6-1_Input_III


title: ChIP-seq_spt6-1_Input_Ctr9-myc_II


title: ChIP-seq_spt6-1_Input_Ctr9-myc_I


title: ThioMac-NCoRKO-H3K4me2-KLA-6h

description: H3K4me2 nucleosomal DNA, KLA 6h

value: Kdo2 Lipid A (KLA) 6h


title: Brpf2

city: Quebec city

first: Marie-Eve

last: Lalonde

state: Qc

address: 9 McMahon street

country: Canada

institute: CHUQ

data_processing:
Raw reads were mapped on the human genome build hg18 using Burrows-Wheeler Aligner (bwa http://bio-bwa.sourceforge.net/). Uniquely mapped reads were kept for further analysis. Samtools and the script genomeCoverageBed were used to produce bedgraph files.
Genome_build: hg18
Supplementary_files_format_and_content: bw or bed

organism: Homo sapiens

source_name: human colon carcinoma

growth_protocol: DMEM, 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and DNA was PCR amplified with Illumina primers for 18 cycles. Amplicons were purified with Qiagen QIA Quick MinElute PCR purification kit and libraries were sequenced on the Illumina Genome analyzer or HiSeq2000 following the manufacturer's protocols.

treatment_protocol: no treatment

tag: ChIP

tag: cell line

value: RKO

tag: growth conditions

value: untreated cells, normal growth conditions

tag: antibody vendor/catalog

value: abcam, ab71877


title: ChIP-seq_spt6-1_Set2-myc_I


title: ChIP-seq_spt6-1_H3_II

value: Abcam


title: ChIP-seq_spt6-1_Input_Ctr9-myc_III


title: ChIP-seq_spt6-1_H3_III


title: ChIP-seq_spt6-1_Rpb1_I


title: ChIP-seq_spt6-1_H3K4me3_III


title: ThioMac-NCoRKO-H3K4me2-notx

description: H3K4me2 nucleosomal DNA, notx


title: ChIP-seq_spt6-1_H3K4me3_II


title: ChIP-seq_spt6-1_H2B_III


title: ChIP-seq_spt6-1_H2B_II


title: ChIP-seq_spt6-1_Ctr9-myc_II

value: Ctr9-myc (anti-Myc)


title: ChIP-seq_spt6-1_H2B_I


title: ChIP-seq_WT_Swd1-myc_III

value: wild type

value: Swd1-myc (anti-Myc)


title: ChIP-seq_spt6-1_Ctr9-myc_III


title: ChIP-seq_WT_Swd1-myc_I


title: ChIP-seq_spt6-1_Ctr9-myc_I


title: ChIP-seq_WT_Spt6-HA_I

value: Spt6-HA (anti-HA)


title: ChIP-seq_WT_Set2-myc_II


title: ChIP-seq_WT_Rpb1_I


title: ChIP-seq_WT_Rpb1_II


title: ChIP-seq_WT_Set2-myc_I


title: ChIP-seq_WT_Input_Swd1-Myc_III


title: ChIP-seq_WT_Input_Swd1-Myc_I


title: ChIP-seq_WT_Input_III


title: ChIP-seq_WT_Input_Set2-myc_I


title: ChIP-seq_WT_Input_Set2-myc_II


title: ChIP-seq_WT_H3_III


title: ChIP-seq_WT_H3_II


title: ChIP-seq_WT_H3K4me3_II


title: ChIP-seq_WT_Input_Ctr9-myc_I


title: ChIP-seq_WT_Input_Ctr9-myc_II


title: ChIP-seq_WT_H3K36me3_II


title: ThioMac-NCoRKO-H4K5ac-KLA1h

description: H4K5ac nucleosomal DNA,  KLA 1h

value: Macrophage

value: Kdo2 Lipid A (KLA) 1h

value: H4K5ac (Millipore 07-327)


title: ChIP-seq_WT_Input_I


title: ChIP-seq_WT_Input_Ctr9-myc_III


title: ChIP-seq_WT_H3K4me3_III


title: ChIP-seq_WT_H3K36me3_III


title: ChIP-seq_WT_Spt6-HA_Ib


title: ThioMac-WT-H4K5ac-KLA1h

description: H4K5ac nucleosomal DNA, KLA 1h

value: C57BL/6 NCoR fl/fl Lys M-Cre -/-


title: ChIP-seq_WT_H2B_II


title: ThioMac-NCoRKO-H4K5ac-notx

description: H4K5ac nucleosomal DNA, notx

value: C57BL/6 NCoR fl/fl Lys M-Cre +/-


title: ThioMac-WT-H4K5ac-notx

description: H4K5ac nucleosomal DNA, notx


title: ChIP-seq_WT_H2B_III


title: ChIP-seq_WT_Input_Spt6HA_I


title: ThioMac-WT-H3K4me2-KLA-6h

description: H3K4me2 nucleosomal DNA, KLA 6h


title: ThioMac-WT--H3K4me2-notx

description: H3K4me2 nucleosomal DNA, notx


title: ThioMac-NCoRKO-GroSeq-KLA-12h

description: Gro-Seq for nascent RNA, KLA 12h

library_source: transcriptomic

data_processing:
Library strategy: Gro-Seq
Libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer, Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions.
Reads were aligned to the mm9 genome (NCBI build using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location.
Gro-Seq results were trimmed to remove A-stretches originating from the library preparation. Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://biowhat.ucsd.edu/homer/
Genome_build: mm9

molecule: nuclear RNA

extract_protocol: Nuclei were extracted from 8-12 million cells grown on 10 cm plates and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified for 10-16 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina Genome Analyzer II or HiSeq 2000.

value: Kdo2 Lipid A (KLA) 12h


title: ChIP-seq_WT_Input_II


title: ChIP-seq_WT_H2B_I


title: ThioMac-WT-GroSeq-KLA-12h

description: Gro-Seq for nascent RNA, KLA 12h


title: ThioMac-NCoRKO-GroSeq-notx

description: Gro-Seq for nascent RNA, notx


title: ThioMac-NCoRKO-GroSeq-KLA-1h

description: Gro-Seq for nascent RNA, KLA 1h


title: ChIP-seq_WT_Ctr9-myc_II

value: Santa Cruz Biotechnology


title: ThioMac-WT-GroSeq-notx

description: Gro-Seq for nascent RNA, notx


title: ChIP-seq_WT_Ctr9-myc_I


title: ThioMac-WT-GroSeq-KLA-1h

description: Gro-Seq for nascent RNA, KLA 1h


title: MNase_spt6_150Uml_N2

data_processing:
The sequenced reads were aligned using Bowtie allowing up to 10 matches ('-m 10 --best' options).
Paired end sequenced (PE) fragments with an inferred length between 90 bp and 200 bp were kept for downstream analysis.
A home-brew GC-content normalization, similar to BEADS, was applied to reduce variability in GC content of different samples.  Instead of normalizing all samples to a flat GC distribution, the normalization brought the GC content of all samples similar to one of the samples, deemed to be midway.  The final conclusions were independent of this normalization procedure.
The MNase-seq profile was calculated using a Gaussian Kernel smoothing (bandwidth=20 bp) on the positions of paired-end fragment centers.
Genome_build: ASM294v2
Supplementary_files_format_and_content: wig files show normalized smoothed fragment center density

growth_protocol: cells from strains FWP172 (wild-type) and FWP371 (spt6-1) were grown in 200 ml of YES media to OD600=0.5.

extract_protocol:
Cells were spheroplasted in 2 ml of CES buffer (50mM Citric acid/50mM Na2HPO pH 5.6; 40mM EDTA pH=8.0; 1.2M Sorbitol) containing 1 mg/ml Zymolyase 100T (United States Biological) and 20 mM  _-mercaptoethanol for 1 hour at 30¡ C.  Spheroplasts were pelleted, washed with 50 ml of Tris/Sorbitol buffer (40 mM TrisHCl pH=8.0; 1.2 M Sorbitol; 50 mM NaCl; 1 mM EDTA) and subjected to MNase digestion in 2 ml of NP-buffer (40 mM TrisHCl pH=8.0; 1.2 M Sorbitol; 50 mM NaCl; 1 mM EDTA, 0.1% NP-40, 0.75% Sigma Fungal Protease Inhibitor Cocktail; 10 mM _-mercaptoethanol; 5mM spermidine; 10 mM CaCl2) containing 150 u/ml of Nuclease S7 (Roche) for 5 min at 37¡ C.  Reactions were stopped by addition of EDTA and EGTA mix to final concentration 25 mM each.  Crosslinking was reversed overnight at 65¡ C in the presence of 0.5% SDS and 1 mg/ml proteinase K.  DNA was purified by phenol/chloroform extraction and ethanol precipitation. RNA was removed by treatment with RNAseA/T1 mix (Fermentas). Purified DNA was resolved on 1% agarose gel and a band corresponding to mono-nucleosomal fragments was excised and subjected to gel-extraction.
DNA was end repaired with T4 DNA Polymerase (Invitrogen), T4 PNK (NEB) and DNA Pol I, Large Klenow fragment (Invitrogen), and an 'A' base was added using Klenow 3' to 5' exo minus (NEB).  1 pmol of barcoded adaptors were ligated on with T4 DNA ligase (Roche) and the products were PCR amplified with Phusion DNA Polymerase (NEB) and size selected by purification on 2% agarose-EX E-gels (Invitrogen) for fragments between 200-600 bp.  Library size and concentration was determined by Bioanalyzer or Tapestation analysis (Agilent) and libraries were pooled equimolar amounts with up to 26 in each sequencing lane.  Pooled libraries were gel purified twice, followed by column purification on MinElute columns (Qiagen).  At least 10 nM were submitted for analysis on the Illumina Hi-Seq at Tufts University Core Facility.

treatment_protocol: cells were shifted to the non-permissive temperature of 37˚C for two hour.

value: spt6-1; spt6 mutant

tag: mnase concentration


title: MNase_spt6_150Uml_N1


title: RNA-seq_spt6II

data_processing:
The sequenced reads from each sample were aligned twice using TopHat 77 with default parameters, except setting the intron length range to between 30 and 200 bp, to S. pombe genome assembly ASM294v2, ('-i 30 -I 2000' options).  In the first round, no annotation guide was provided.
The splice junctions that were discovered for the four samples were merged with annotated splice junctions (ASM294v2.18) to obtain a complete list of splice candidates.  In the second round of alignment, these junctions were provided as a guide to the aligner. ('-j <junction file>, --no-novel-juncs' options).
The reads per kb of exon per million mapped read (RPKM) score was calculated for each transcription unit on the sense and antisense strands; sense scores reflected only exonic reads, whereas the complete transcription unit was used in the antisense direction.
Different samples were normalized relative to each other to account for differences in ratios of antisense and intergenic reads, intron retention rates and t/rRNA filtering efficiency.  The RPKM values for each of the samples was scaled by a linear factor, such that the mode of the log fold-change distribution for sense RPKM values between each sample and the average of the four samples fell at 0.  The linear factor was between 0.75 and 1.1 for the four samples.
A continuous RNA-seq signal was calculated at single bp resolution for the whole genome as: RNA signal = (number of reads covering the position) / (total number of aligned reads) / (read length in sample) * (normalization factor determined using RPKM values above) * 10^10
Genome_build: ASM294v2
Supplementary_files_format_and_content: wig files show log(RNA-seq coverage signal+1) for either strand at every 10bp

molecule: polyA RNA

extract_protocol:
Total RNA was isolated from S. pombe cells using a hot phenol method followed by phenol-chloroform extractions, precipitation, and purification using Qiagen RNeasy columns.
10 μg of total RNA were used as starting material for strand-specific library preparation using the Illumina Universal RNA-seq samples prep kit.  This kit is an unreleased early version provided by Illumina of the Illumina TruSeq Small RNA Sample Prep Kit.  Briefly, poly(A)+ RNA was enriched by two rounds of poly(dT) Sera-Mag magnetic beads purification, then fragmented to an average size of ~200 nucleotides.  Fragmented RNA was 3’ de-phosphorylated with Antarctic phosphatase and 5’ phosphorylated with polynucleotide kinase to prepare RNA fragments for subsequent ligation.  Illumina RNA adaptors were ligated to the 5’ and 3’ ends using a 3’ RNA ligase and a T4 RNA ligase, respectively.  First strand cDNA was produced using a primer specific for the Illumina 3’ adaptor.  The library was amplified with 15 cycles of PCR using primers specific for the Illumina adaptors and purified using SPRI-beads (Agencourt, Beckman Coulter).  Library size distributions and concentrations were determined on an Agilent Bioanalyzer.  RNA-seq libraries were sequenced on an Illumina Genome Analyzer IIx instrument.

treatment_protocol: prototrophic wild-type and spt6-1 strains shifted to 37°C for 2 hours.


title: MNase_spt6_100Uml_N2


title: H3

value: abcam, ab1791


title: RNA-seq_WTI

source_name: WT


title: IgG

value: rabbit IgG

value: RKO

value: homemade


title: ThioMac-WT-H3K4me2-KLA-24h

description: H3K4me2 nucleosomal DNA, KLA 24h

value: Kdo2 Lipid A (KLA) 24h

value: H3K4me2 (Millipore 07-030)


title: MNase_WT_150Uml_N1

value: wild type


title: MNase_WT_150Uml_N2


title: RNA-seq_spt6I


title: RAW-Blrp-Ctrl-Input

description: Blrp-Ctrl RAW264.7 cell line genomic DNA, GW3965 (input)

source_name: Blrp-Ctrl RAW264.7 cells

growth_protocol: The Indicated RAW264.7 stable cell lines were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after adherence and again fed with fresh medium. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 1uM GW3965 for 2 hours.

value: Macrophage Cell line RAW264.7


title: MNase_WT_100Uml_N2


title: ChIP-seq_WT_Ctr9-myc_III


title: H3K4me3

value: untreated cells, normal growth conditions

value: abcam, ab8580


title: ING2

value: epitomics, 3683-1


title: ING5

value: abcam, ab96851


title: MNase_WT_100Uml_N1


title: Prostate-Post-R5

status: Public on Oct 07 2013

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

description: Post treatment tumour sample from patient 5

data_processing:
Basecalling was preformed using standard Illumina pipeline
Reads were mapped to the genome using TopHat v1.4.1, allow upto 2 mismatches and using a custom junctions library derived from Ensembl version 68
Reads falling in each gene model from Ensembl 68 were counted using HTSeq verion 0.5.3
Read counts were normalized using the TMM method via the edgeR bioconductor package and differentially expressed genes identified using a paired negative bionomial generalized linear model with the same package
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited table containing the read counts for each sample for each gene, and tab-delimited table of fitted expression changes with statistcal significance for each gene

molecule: total RNA

source_name: TRUSS-guided prostatic biopsy of clinically advanced/metastatic prostate cancer tissue

extract_protocol:
Total RNA was extracted from pre- and post-AAT samples using the RNeasy Mini Kit (QIAgen, 74104) according to manufacturer’s instructions.  RNA quantity and quality was evaluated by spectrophotometry using the NanoDrop 2000 spectrophotometer (Thermo Scientific) and 2100 Bioanalyzer (Agilent) RNA electropherograms, with calculation of RNA integrity number (RIN) (35).  Samples were included for RNA sequencing if RIN > 6 and total RNA > 500 ng
Samples were processed using the Illumina RNA-Seq protocol (Illumina) according to manufacturer’s instructions without poly(A) mRNA selection.  The cDNA sample library was subsequently normalized using the Illumina DSN (Duplex-specific Nuclease) protocol according to manufacturer’s instructions.

treatment_protocol: standard AAT consisting Luteinising hormone-releasing hormone (LHRH) agonists with anti-androgen “flare” protection. Repeat TRUSS biopsy was performed at ~22 weeks following initiation of AAT, specifically targeting tumour-rich areas

tag: tissue

value: Prostate Tumour

tag: time point

value: Post-Treatment


title: Prostate-Post-R6

description: Post treatment tumour sample from patient 6


title: Prostate-Post-R4

description: Post treatment tumour sample from patient 4


title: Prostate-Post-R3

description: Post treatment tumour sample from patient 3


title: MNase_spt6_100Uml_N1


title: RNA-seq_WTII


title: Prostate-Pre-R5

description: Pre treatment tumour sample from patient 5

value: Pre-treament


title: Prostate-Post-R2

description: Post treatment tumour sample from patient 2


title: Prostate-Pre-R7

description: Pre treatment tumour sample from patient 7


title: Prostate-Pre-R4

description: Pre treatment tumour sample from patient 4


title: Prostate-Pre-R3

description: Pre treatment tumour sample from patient 3


title: Prostate-Pre-R6

description: Pre treatment tumour sample from patient 6


title: Smoker with Lung Cancer

first: Avrum

last: Spira

address: 72 East Concord Street, E631

department: Computational Biomedicine

institute: Boston University

description: ABI SOLID small RNA-seq, 36 bp sequencing

data_processing: The adapter was trimmed off of the 3’ end of each read.  Reads were aligned to the human genome build 19 (hg19) using Bowtie version 0.12.3  allowing up to two mismatches and limiting the number of locations a read can map to the genome to 4 or fewer.  The number of reads that overlap with the genomic locations of known mature microRNA from miRBase v16 and from the miRDeep predictions for miR- 4423 was counted using BEDTools v2.9.0.

source_name: Large airway epithelial cells

extract_protocol: 300ng of small molecular weight fraction (<200bp) RNA was pooled from individuals within each phenotype, never smoker (NS), current smoker (S), no cancer (NC) and cancer (C), for a total of 4 samples (900ng each).  Each pooled sample was size fractioned using the Ambion flashPAGE fractionator to obtain small RNAs of 10-40nts. Small RNA sequencing libraries were created using SOLiD Small RNA Expression Kit (Ambion) starting with 200ng of the size fractionated small RNA following the manufacturer’s instructions.  Libraries were sequenced on an Applied Biosystems SOLiD System to obtain 36 bp reads.

tag: Sex

value: 2 Male, 1 Female

tag: average age

tag: smoking status

value: 2 Former, 1 Current

tag: packyears

tag: lung cancer

value: 3 Yes


title: Prostate-Pre-R2

description: Pre treatment tumour sample from patient 2


title: Smoker without Lung Cancer

value: 1 Male, 2 Female

value: 3 No


title: GA rep1

status: Public on Oct 05 2013

city: Nanjing

first: Changnian

last: Song

address: Weigang No.1

department: College of Horticulture

country: China

institute: Nanjing Agricultural University

description:
four-year old ‘Summer Black’ grapevine (hybrids of V. vinifera and V. labrusca)
Instrument model: Illumina 1G Genome Analyzer

data_processing:
To identify conserved and potential Vv-miRNAs in grapevine, the raw sequences were processed as described by Axtell et al. 2005 (PMID:15849273) and Sunkar et al. 2005 (PMID:16077027, PMID:15805478).  All sRNAs sequences from 18nt to 30nt obtained were removed from the vector sequences, then the modified sequences were further subjected to removal of rRNA, tRNA, snRNA, snoRNA and those containing the polyA tails, and finaly the remaining sequences were compared against known plant Vv-miRNAs existing in the miRBase 17.0 (http://www.mirbase.org/, Morin et al. 2008).  Only matching (0-3mismatches) sequences were considered as conserved Vv-miRNAs. To study potential Vv-miRNAs precursor sequences, all sRNAs from grapevine were aligned against the grapevine genome and then the miRNA candidates were processed by miRCat (http://srna-tools.cmp.uea.ac.uk/; Moxon et al. 2008), using default parameters, to generate the secondary structures.
Supplementary_files_format_and_content: File processed_data_conservedVv-miRNAs.fa represents abundance counts of the conserved Vv-miRNAs.

organism: Vitis labrusca x Vitis vinifera

source_name: berries

extract_protocol: Mixed ‘Summer Black’ grapevine young berries (one week after flowering) large berries (five week after flowering after flowering), and old berries (nine week after flowering) treated with gibberellin, respectively, which were used for RNA extraction. The total RNA samples were first extracted in which modified CTAB (Chang et al. 1993) was employed.  Isolation of small RNAs and preparing small RNA libraries were performed based on the procedure of Song et al. (2010). SRNAs were first separated from the total RNA by size fractionation with 15 % TBE urea polyacrylamide gel (TBU) and small RNA regions corresponding to the 18–30 nucleotide bands in the marker lane were excised and recovered. The 18-30 nt small RNAs were 5’ and 3’ RNA adapter-ligated by T4 RNA ligase and at each step, length validated and purified by TBU electrophoretic separation.  The adapter-ligated small RNA was subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen) and PCR amplified, using primers that annealed to the ends of the adapters.  The amplified cDNA constructs were purified and recovered. 18 ng cDNA was loaded into the Illumina 1 G Genome Analyzer for sequencing.

value: berries

tag: developmental stage

tag: agent

value: gibberellin


title: Prostate-Post-R7

description: Post treatment tumour sample from patient 7


title: RNA-Seq_TMC_mutant_KOb_1

status: Public on Oct 04 2013

city: Ann Arbor

first: Tomonori

last: Hosoya

state: MI

address: 109 Zina Pitcher Place

department: CDB

institute: University of Michigan

data_processing:
tophat-2.0.8b
bowtie2-2.1.0
cuffdiff-2.1.1
--max-bundle-frags 1000000000
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff output gene_exp.diff file.This tab delimited file lists the results of differential expression testing between samples for genes.Gene differential FPKM.

extract_protocol:
QIAGEN RNeasy Mini Kit with in-column DNase treatment
NuGEN Encore Complete RNA-Seq Library Systems

tag: strain background

tag: genotype/variation

tag: cell type

value: bone marrow immature erythroid cells (severely-deleted)

tag: cell surface molecule expression


title: Prostate-Pre-R1

description: Pre treatment tumour sample from patient 1


title: Healthy non-smoker

value: 3 Female

value: 3 Never


title: Healthy smoker

value: 3 Current


title: RNA-Seq_TMC_mutant_KOa_0

value: bone marrow immature erythroid cells (modestly-deleted)


title: RNA-Seq_TMC_mutant_KOa_1


title: RNA-Seq_control_FFa_2

value: bone marrow immature erythroid cells


title: RNA-Seq_control_FFa_1


title: Vitis vinifera flowers and berries

first: Chen

last: Wang

state: Jiangshu

address: Weigang 1#

department: Horticulture College

institute: Nanjing Agriculture University

data_processing: The sequenced small RNA were compared to known plant miRNAs from miRBase using a BLASTn search. No mismatches were allowed between identified grapevine miRNAs and currently known miRNAs in other plant species.

organism: Vitis vinifera

source_name: Flowers and berries

extract_protocol: Small RNA samples were sequenced by Beijing Genomics Institute (BGI) (Shenzhen, Guangdong, China) using the high throughput pyrosequencing technology developed by Illumina. Small RNAs with 16-30 nt in length were first separated from the total RNA by size fractionation with 15% TBE urea polyacrylamide gel (TBU). The small RNA (16-30 nt in length) were excised from the gel and submerged in 600 μL of 0.3 M sodium chloride overnight at 4 °C. The gel slurry was then passed through a Spinfilter column (Corning, Beijing, China), and RNA precipitated by addition of 3 μL of 5 mg/mL mussel glycogen (Invitrogen, Carlsbad, CA, USA) and 800 μL of ethanol. The RNA pellets were then washed with 75% ethanol and air dried at 25 °C. The small RNA was resuspended in 5.0 μL of diethylpyrocarbonate (DEPC) treated water (Ambion, Austin, TX, USA). The isolated small RNAs were then ligated to 5’ adaptor (5’UCAGAGUUCUACAGUCCGACGAUC) using T4 RNA ligase (Promega, Madison, WI) in the presence of RNase Out (Invitrogen) overnight at 4 °C according to the manufacturer’s instructions. After selecting the ligated products by size fractionation, a 3’adaptor (5’UCGUAUGCCGUCUUCUGCUUGUidT) was ligated to the small RNAs following the same procedure as the ligation of the 5’adaptor. Finally, the ligated RNAs were size fractionated on a 10% TBE urea polyacrylamide gel and the 70 nt RNAs were excised. The 3’adaptorgated small RNAs were then purified from the gel and precipitated as described above followed by resuspension in 5.0 μL DEPCeated water (Ambion). The small RNA with 5’ and 3’adaptors were selected and reversely transcribed to cDNA with the RT primer (CAAGCAGAAGACGGCATACGA) using Superscript II reverse transcriptase (Invitrogen). The cDNA was further purified by 15% TBU followed by dissolving in 100 μL1× NEB. The cDNA was quantified by Agilent 2100 and dilutioned to 10 nM at final concentration, 18 ng cDNA was loaded into the Illumina 1 G Genome Analyzer for sequencing.

tag: sample type

value: Inflorescence, flower, young fruit(15 days after flowering), big fruit (60 days after flowering)

value: mixed stage flowers and berries

tag: cultivar

value: Summer Black


title: RNA-Seq_TMC_mutant_KOa_2


title: Prostate-Post-R1

description: Post treatment tumour sample from patient 1

value: Prostate Tumour

value: Post-Treatment


title: RNA-Seq_control_FFa_0


title: MNase_ES

city: Montpellier

first: Michael

last: Girardot

state: France

address: 1919 route de Mende

country: France

institute: IGMM CNRS UMR5535

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned on the M. musculus genome (mm9) with Bowtie 0.12.7
The smoothed tag density compared to the input tag density was computed with the Sequence Processing Pipeline (spp v1.11) and exported as bedgraph file.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated by the spp v1.11 suite

organism: Mus musculus domesticus x M. m. molossinus

source_name: Embryonic Stem Cells

growth_protocol: ES cell lines were routinely cultured on 0.1% gelatin-coated plates in feeder-free and serum-free conditions with ESgro complete plus medium (Millipore, SF001-500P) and were serially passaged using Accutase (Millipore, SF006). Primary mouse embryonic fibroblasts (MEFs) were derived from 13.5 d.p.c. foetuses and were cultured up to passage 6 in DMEM medium supplemented with 15% foetal bovine serum (FBS).

extract_protocol:
ChIP on native chromatin was performed as described (Wagschal et al, 2007). Briefly, nuclei from 5 million cells were extracted and purified through a sucrose gradient and incubated for 15 min with 50 units of micrococal nuclease (MNase) at 37 °C. The chromatin fragmented as mono to tri-nucleosomes was then immunoprecipitated with an anti-H4R3me2s antibody (abcam: ab5823; batch n° 885940) and Dynabeads protein A (Invitrogen). After extensive washes the precipitated DNA was eluted and purified with the ‘ChIP DNA purification kit’ (Zymo Research).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq-2000 following the manufacturer's protocols.

value: embryonic stem cells

tag: strain

value: C57BL6/J (Mus m. domesticus) x JF1 (Mus m. molossinus)

tag: passages

value: passages 5-10


title: MNase_MEF

source_name: E13.5 embryos derived Mouse Embryonic Fibroblasts

value: E13.5 embryos derived MEF

value: passages 2-6


title: H4R3me2s_ES


title: H4R3me2s_MEF


title: RNA-Seq_TMC_mutant_KOb_2


title: MID5_GBM_100U

status: Public on Oct 03 2013

city: Gainesville

first: Nancy

middle: H

last: Nabilsi

state: FL

address: 2033 Mowry Rd

department: Biochemistry and Mol Bio

institute: University of Florida

description: deaminated

data_processing:
library strategy: Bisulfite-seq (amplicon)
Base and quality scores from instrument software
Barcodes called by fastools called through Python
Sequences aligned to references by blastn following in silico deamination by Python
Images generated by MethylMapper
(Python pipeline software, fastools, MethylMapper available on request)
Genome_build: AluBIpatch (amplicon reference library). There is no a publication reference or URL for the AluBI patch. Rather, sequences have been provided as AluBIpatch.fa (linked as supplementary file on Series record). AluBIpatch.fa is a database of reference sequences (no reads are aligned to them in this ".fa" file).
Supplementary_files_format_and_content: report.tsv table reporting reads assigned to each sample/locus/strand (linked as supplementary file on Series record), *.tsv tables reporting methylation/accessiblity of sites/patches on indivdiual molecules.

source_name: glioblastoma cells

growth_protocol: Cells were grown in serum-free spheroid suspension culture (i.e. neurosphere culture conditions)

extract_protocol:
Genomic DNA was extracted with phenol:chloroform:isoamylalcohol and perceipitated with ethanol and salt.
Libraries were prepared for each sample using bisulfite-patch-PCR protocol. Briefly, purified genomic DNA is digested by a restriction enzyme into fragments with defined ends. After denaturation, in a multiplexed reaction, both ends of selected target loci are hybridized and ligated to specific patch oligonucleotides and universal priming sequences. After enzymatic enrichment of ligated loci, PCR is performed using primers with platform-specific adapter and universal sequences. Barcoded products are then pooled, purified and sequenced.

treatment_protocol: Nuclei were prepared and probed with 0U or 100U M.CviPI activity according to standard MAPit protocol.

value: glioblastoma tumor cells

tag: m.cvipi activity


title: RNA-Seq_TMC_mutant_KOb_0

value: bone marrow immature erythroid cells (severely-deleted)


title: CAP-H input

city: Parkville

first: Ji Hun

last: Kim

state: VIC

address: Royal Childrens Hospital, 50 Flemington Rd

department: Paediatrics

country: Australia

institute: Murdoch Childrens Research Institute / The Univesity of Melbourne

data_processing:
Duplicate and triplicate SMC2 and CAP-H ChIP-seq and input raw sequencing data were provided by Beijing Genome Institute in FASTQ format.
Sequencing reads were aligned into the chicken genome Galgal4 using Burrows-Wheeler Aligner (BWA) v0.5.8
Peaks were called using Model-based Analysis for ChIP-seq (MACS) v1.4.1. The parameters used for peak calling includes the chicken reference genome size as 1,016M bp (excluding the repetitive sequences from the original chicken genome size 1.2G bp), tag size as 49bp, band width as 200 bp, other parameters remained default. The sequence data were pooled before peak calling.
For the sequence tag density at TSS analysis, the numbers of sequence tags of ChIP-seq and input aligned at or near the 5' transcription start sites of all RefSeq genes in the Galgal4 chicken genome were counted using EpiChIPv0.9.7
Genome_build: Gallus_gallus-4.0
Supplementary_files_format_and_content: SMC2 and CAP-H peaks generated as above in Bed format.
Supplementary_files_format_and_content: The wiggle files were generated by MACS using the aligned sequence data (in bam) to the canonical chromosomes of the chicken genome (galGal4). Each file includes the concatenated wiggle data for all of the chromosomes.

organism: Gallus gallus

source_name: DT40 cells

growth_protocol: SBP-tagged SMC2 and CAP-H transgene rescued the knockout DT40 cells. The cells were grown in 2ng/ml doxycycline in order to suppress the un-tagged SMC2 or CAP-H proteins and for the transgene to be the only form of the proteins in the cells.

extract_protocol:
Lysates from the crosslinked cells in 1% formaldehyde was sonicated and condensin-associated DNA was isolated using streptavidin beads.
Library was prepared by Beijing Genome Institute for Illumina Hiseq2000 sequencing for single-ended 50bp reading length.

treatment_protocol: Cells were blocked in mitosis in 500ng/ml nocodazole.

tag: cell line

value: DT40 lymphoma B cells

tag: transgene

value: SBP-tagged CAP-H

tag: chip antibody


title: CAP-H ChAP-seq

value: streptavidin


title: MID4_NSC_100U

description: deaminated

source_name: neural stem cells

value: neural stem cells derived from fetal subventricular zone


title: T7107_stat

status: Public on Oct 02 2013

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

description: In the processed data file the values for each chromosome were generated by dividing by 0.58.

data_processing:
Sequence reads were mapped to the S. cerevisiae reference genome.
Sequence reads mapping to a single genomic location were summed in 1 kb bins. Windows where fewer than 250 reads were mapped in either sample were excluded.
Normalised copy numbers were generated by dividing the sequence read counts from the replicating sample by counts from the non-replicating (alpha factor arrested,  G2 phase or stationary phase) sample for each strain.
The resulting absolute ratios reflect the read numbers; therefore data was normalized by dividing by an empirically determined factor. This resulted in >95% of the data points lying between 1 and 2 (a biologically imposed restraint).
Genome_build: sacCer1
Supplementary_files_format_and_content: Wig file containing normalised replication profile.

organism: Saccharomyces cerevisiae

source_name: Genomic DNA from stationary phase cells

growth_protocol: Cells were harvested from stationary phase cultures grown in rich medium.

extract_protocol:
DNA was purified by phenol chloroform extraction.
Library preparation and sequencing was carried out according to SOLiD/Illumina instructions.

tag: relevant genotype

value: MATa; RAD5; BUD4; leu2; ura3; trp1; ade2; his3

tag: treatment protocol


title: T7107_exp

source_name: Genomic DNA from exponential phase cells

growth_protocol: Cells were harvested from early-log phase cultures grown in rich medium.


title: SMC2 ChAP-seq

value: SBP-tagged SMC2


title: SMC2 input


title: T9475_S

description: In the processed data file the values for each chromosome were generated by dividing by 0.379.

source_name: Genomic DNA from S phase cells

growth_protocol: Cells were harvested from mid-log phase cultures grown in rich medium.

value: MATa/MATalpha; RAD5/RAD5; BUD4/BUD4; leu2/leu2; ura3/ura3; trp1/trp1; ade2/ade2;, his3/his3

value: Cells were sorted by DNA content, selecting (S phase and) G2 phase cells


title: 6 hour infected (replicate 3)

city: Meath

first: Nathan

last: Lawless

address: Grange

country: Ireland

institute: Teagasc

data_processing:
Basecalls performed using CASAVA version 1.8.2
FastQC version 0.10.0 for QC checks
Adapter removal with Cutadapt version 1.0
Fastq quality filter version 0.0.13
Alignment to bovine genome with Novoalign version 2.07.11
Count of aligned reads with HTSeq-count (part of the HTSeq framework, version 0.5.3p3), using miRNA gene annotations from Ensembl version 66.
Discovery of novel miRNAs with miRDeep2 version 2.0.0.3, using Fastq quality filtered data (from step 4)
Genome_build: UMD3.1 Ensembl 66
Supplementary_files_format_and_content: Tab-delimited text containing the tag per million counts for miRNA genes in all 24 samples

organism: Bos taurus

source_name: IE3_6 hr infected

growth_protocol: Primary bovine mammary epithelial cells were purchased from AvantiCell. Cells were isolated from mammary parenchyma. The source animal was in her third trimester of first pregnancy, aged between 26-30 months and negative for bovine viral diarrhoea & BSE free. Cells were plated (seed density of 1x106) directly onto collagen coated plastic flasks (Greiner bio-one) and immersed in AvantiCell medium – (medium 199/Ham’s F12 (50:50) pH 7.4 containing 5% (v/v) horse serum, 5% (v/v) fetal bovine serum, 5 μg/mL bovine insulin, 1 μg/mL hydrocortisone, 3 μg/mL cortisol, 10 ng/mL epidermal growth factor (EGF), 2 mM sodium acetate, 10 mM Hepes, U/mL penicillin/streptomycin and single strength Fungizone™). Media was initially replaced after 48 hrs and every 48 hrs thereafter. Cells were split twice (75 cm2 & 175 cm2). Cells were then seeded at a concentration of 1.8 x 10^5 cells/well into collagen coated 6-well plates. Media was changed after 24 hrs, and cells were inspected under microscopy for confluence. Cells were harvested by washing with Hanks Balanced Salt Solution (HBSS) pH 7.4 and treated with 4 ml of 0.25 % trypsin for approximately 5 min at 37 °C. An equal volume of medium to trypsin (1:1) neutralised trypsin.

extract_protocol:
The mirVana™ miRNA isolation kit was used to size select & enrich for small RNA. Procedures were performed according to the manufacturer’s protocol.
Libraries were prepared according to the manufacturer's protocol of the ScriptMiner Small RNA-Seq Library Preparation Kit (MultiPlex; Illumina-Compatible, Cat. No. SMMP101212), using 8uL small RNA as input material.

treatment_protocol: Streptococcus uberis 0140J was purchased from ATCC. S. uberis 0140J was first isolated in milk obtained from a clinical case of bovine mastitis in the United Kingdom in 1972. In this study, S. uberis was cultured as per ATCC instructions. The cells were challenged with S. uberis 0140J at a multiplicity of infection (MOI) of 50, over a time course of 1, 2, 4, & 6 hrs. Three technical replicates were infected at each time point. Three technical replicate uninfected controls were maintained for each time point.

tag: tissue source

value: mammary parenchyma

value: Mammary epithelial cell

tag: challenged with

value: S. uberis 0140J at MOI of 50

tag: timepoint

value: 6 hour

tag: molecule subtype

value: miRNA


title: 6 hour control (replicate 3)

source_name: CE3_6 hr control

value: none (uninfected control)


title: 6 hour control (replicate 2)

source_name: CE2_6 hr control


title: 6 hour infected (replicate 1)

source_name: IE1_6 hr infected


title: 6 hour control (replicate 1)

source_name: CE1_6 hr control


title: 4 hour infected (replicate 1)

source_name: ID1_4 hr infected

value: 4 hour


title: 4 hour control (replicate 3)

source_name: CD3_4 hr control


title: 4 hour infected (replicate 3)

source_name: ID3_4 hr infected


title: 4 hour infected (replicate 2)

source_name: ID2_4 hr infected


title: 4 hour control (replicate 2)

source_name: CD2_4 hr control


title: 4 hour control (replicate 1)

source_name: CD1_4 hr control


title: MID2_GBM_0U

description: deaminated

source_name: glioblastoma cells

value: glioblastoma tumor cells


title: 2 hour infected (replicate 1)

source_name: IC1_2 hr infected

value: 2 hour


title: 2 hour control (replicate 3)

source_name: CC3_2 hr control


title: MID1_NSC_0U

description: deaminated

source_name: neural stem cells


title: 2 hour infected (replicate 2)

source_name: IC2_2 hr infected


title: 2 hour infected (replicate 3)

source_name: IC3_2 hr infected


title: 2 hour control (replicate 2)

source_name: CC2_2 hr control


title: T9475_G2

source_name: Genomic DNA from G2 phase cells

value: Cells were sorted by DNA content, selecting S phase (and G2 phase) cells.


title: 1 hour infected (replicate 3)

source_name: IB3_1 hr infected

value: 1 hour


title: 1 hour infected (replicate 2)

source_name: IB2_1 hr infected


title: 2 hour control (replicate 1)

source_name: CC1_2 hr control


title: 1 hour infected (replicate 1)

source_name: IB1_1 hr infected


title: 1 hour control (replicate 3)

source_name: CB3_1 hr control


title: 6 hour infected (replicate 2)

source_name: IE2_6 hr infected


title: 1 hour control (replicate 1)

source_name: CB1_1 hr control


title: CAY106_hu

description: In the processed data file the values for each chromosome were generated by dividing by 0.6.

data_processing:
Sequence reads were mapped to the S. cerevisiae reference genome using BioScope (version 1.3.1).
Sequence reads mapping to a single genomic location were summed in 1 kb bins. Windows where fewer than 250 reads were mapped in either sample were excluded.
Normalised copy numbers were generated by dividing the sequence read counts from the replicating sample by counts from the non-replicating (alpha factor arrested or G2 phase) sample for each strain.
The resulting absolute ratios reflect the read numbers; therefore data was normalized by dividing by an empirically determined factor. This resulted in >95% of the data points lying between 1 and 2 (a biologically imposed restraint).
Genome_build: sacCer1
Supplementary_files_format_and_content: Wig file containing normalised replication profile.

source_name: CAY106 genomic DNA from cells 60 min post release from alpha factor into HU

extract_protocol:
DNA was purified by phenol chloroform extraction.
Library preparation and sequencing was carried out according to SOLiD instructions.

value: MATa; ade2-1; trp1-1; can1-100; leu2,3-112; his3-11,15; ura3; ssd1; bar1::TRP1; sml1::URA3; rad53::LEU2; disomic for chrX

tag: growth protocol

value: Cells were released from alpha factor in rich media plus 200 mM HU and a sample taken after 60 min.

value: None.


title: CAY106_alpha

source_name: CAY106 genomic DNA from alpha factor arrested cells

value: Cells were grown to early-log phase in rich medium and then arrested with alpha factor.


title: 1 hour control (replicate 2)

source_name: CB2_1 hr control

tag: cell type


title: AUY077_45min

description: In the processed data file the values for each chromosome were generated by dividing by 0.88.

source_name: AUY077 genomic DNA 45 min released from alpha factor

value: Cells were released from alpha factor in rich media and a sample taken after 45 min.


title: AUY077_50min

description: In the processed data file the values for each chromosome were generated by dividing by 0.76.

source_name: AUY077 genomic DNA 50 min released from alpha factor

value: Cells were released from alpha factor in rich media and a sample taken after 50 min.


title: AUY077_40min

description: In the processed data file the values for each chromosome were generated by dividing by 1.15.

source_name: AUY077 genomic DNA 40 min released from alpha factor

value: Cells were released from alpha factor in rich media and a sample taken after 40 min.


title: AUY077_30min

description: In the processed data file the values for each chromosome were generated by dividing by 1.34.

source_name: AUY077 genomic DNA 30 min released from alpha factor

value: Cells were released from alpha factor in rich media and a sample taken after 30 min.


title: AUY077_90min

description: In the processed data file the values for each chromosome were generated by dividing by 0.93.

source_name: AUY077 genomic DNA 90 min released from alpha factor

value: Cells were released from alpha factor in rich media and a sample taken after 90 min.


title: AUY077_alpha

source_name: AUY077 genomic DNA from alpha factor arrested cells


title: AUY077_35min

description: In the processed data file the values for each chromosome were generated by dividing by 1.27.

source_name: AUY077 genomic DNA 35 min released from alpha factor

value: Cells were released from alpha factor in rich media and a sample taken after 35 min.


title: cL5

status: Public on Oct 01 2013

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

country: Germany

institute: University of Luebeck

data_processing:
Brain and liver samples were sequenced on seven different flow cells of an Illumina Genome Analyzer I. Sequencing data was analyzed starting from Illumina 'chastity' filtered FastQ files. For these files, quality scores were converted to PHRED-scale (Ewing and Green 1998). Heart, kidney and testis samples were sequenced on ten different flow cells on the Genome Analyzer II platform, and sequences called with Ibis (Kircher, Stenzel, and Kelso 2009).
PHRED-scaled FastQ files from both platforms were filtered for adapter and chimera sequences (Kircher, Heyn, and Kelso 2011) and reads with at least 9nt of the adapter sequence (TCGTATGCCGTCTTCTGCTTG) at the read end removed. The last read base (the first adapter base) of the remaining 18nt reads was clipped off, and reads with more than 1 base below a quality score of 10 were discarded. Further, reads with sequence entropy below 0.85 were removed, as these are likely to originate from flow cell artifacts (Kircher, Heyn, and Kelso 2011).
We extended the reads by a 'CATG' restriction motif and aligned these using bowtie 0.12.4 (Langmead et al. 2009) to the following versions of the human, chimpanzee and rhesus macaque genomes: hg19/GRCh37 (excluding additional haplotypes), pantro2/CGSC 2.1 and rhemac2/MGSC Merged 1.0 (with the addition of a mitochondrial genome sequence from the Ensembl MMUL_1.54 build). Bowtie was configured to report up to 100 equally good alignments (with up to two mismatches) and to discard reads that produce more than 100 alignments (parameters -a -m 100 --best --strata).
We used the non-symmetrical UCSC liftOver chains and the command line tool liftOver in a reciprocal manner, to transfer gene start and end coordinates of the human Ensembl v59 annotation separately, and required the projected coordinates to be on the same chromosome and strand. Further, the new gene length was not permitted to change length by more than a factor of 10, or at most 100kb. The rhesus genome does not include a mitochondrial genome in the assembly version provided by UCSC. Hence, all 37 mitochondrially encoded genes were projected using a ClustalW (Thompson, Higgins, and Gibson 1994) mitochondrial genome alignment of the three species. From a total of 51,715 genes, 43,020 (83%) could be projected to chimpanzee and 33,259 (64%) to chimpanzee and rhesus macaque.
For quantifying gene expression, bowtie outputs of mapped tags were sorted by coordinates. Per-site counts were determined and sites observed fewer than three times were removed, to reduce the effect of including erroneous alignments in long transcripts.
Genome_build: hg19/GRCh37, pantro2/CGSC 2.1 and rhemac2/MGSC Merged 1.0

organism: Pan troglodytes

source_name: Big Male Zurich

extract_protocol:
Samples were obtained from brain (pre-frontal cortex), heart, kidney, liver, and testis tissues of male humans, chimpanzees and rhesus macaques. Samples were processed in tissue batches, randomizing species in library preparation and sequencing.
Illumina NlaIII DGE libraries for all samples were generated following the vendor protocol. Expressed 3' tags from polyA RNAs

tag: Sex

value: male

tag: age

tag: rin

tag: tissue

value: liver


title: cL1

description: Half sibling Herman, Japie, Koos

source_name: Antoine


title: cB5

value: brain


title: cL3

description: Full sibling to Koos, half sibling Herman, Antoine

source_name: Japie


title: cB4

description: Full sibling to Japie half sibling Herman, Antoine

source_name: Koos


title: cB3


title: cB2

description: Half sibling Antoine, Japie, Koos

source_name: Herman


title: Neuronal nuclei from P21 hypothalamus_rep5

city: Houston

first: Ge

last: Li

state: TX

address: 1100 Bates St.

department: Pediatrics

institute: Baylor College of Medicine

description: P21 neuron biological replicate 5 of 5.

data_processing:
Quality control was checked by FastQC (version 0.10.1).
Sequencing adptors and remaining MSA adaptors were trimmed by cutadapt program.
The trimmed reads were alignned to mouse genomes using bowtie aligner (version 0.12.9)
Sum of number of reads overlapping for each SmaI/XmaI interval wer counted. The SmaI/XmaI intervals refer to genomic regions with SmaI/XmaI cut sites (cccggg) at both ends and within the distance of 60bp to 3kb, which are the regions that examined by MSA-seq.
A read depth threshold is set as no less than 20 in-group total reads per age per cell-type.
Genome_build: NCBI37/mm9 mouse genome (Jul 2006 release)
Supplementary_files_format_and_content: The processed data are presented in .xlsx format, and present the read depth of each sample in each SmaI/XmaI interval.

source_name: Hypothalamus

extract_protocol:
Genomic DNA was isolated with phenol/chloroform extraction followed by ethanol precipitation
Libraries were constructed by MSA-seq. As a brief description of the MSA: 500ng of genomic DNA was serially digested with SmaI and XmaI followed by an adaptor ligation and adaptor mediated PCR amplification (Waterland et al, 2010 Plos Genetics). MSA products were sheared to 200-500bp, ligated to sequencing adaptors for paired-end read, and submitted for sequencing by Illumina HiSeq.

tag: strain

value: neuron


title: MNase-seq-open replicate1

city: Shenzhen

first: Xia

address: No.1 Fuhua Road, Futian District, Shenzhen, P.R. China

department: Department of Pathology

institute: Shenzhen Traditional Chinese Medicine Hospital

description: Mild digestion by MNase

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using BWA with the default parameters and all uniquely aligned reads (mapping quality >= 10) were kept.
File format was transferred and duplicates removal was done using samtools.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited bed files include the uniquely aligned reads.

source_name: MilliTrace Nanog GFP Reporter Mouse Embryonic Stem Cells

growth_protocol: mouse Embyronic stem cells were maintained under feeder-free condition with the presence ot Lif(Leucaemia Ihibitor Factor ) and passaged routinly

extract_protocol:
The DNA fragment corresponding to mono-nucleasome was extracted from agrarose gel by QIAquick Gel Extraction kit.
ChIP libraries were prepared for sequencing using standard Hi-seq 2000 protocols.

treatment_protocol: mES nuclei were released,then treated with Microccoccal Nuclease under mild digestion or extensive digestion conditions.

tag: treatment

value: mild digestion


title: Neuronal nuclei from P21 hypothalamus_rep2

description: P21 neuron biological replicate 2 of 5.


title: MNase-seq-position replicate1

description: Extensive digestion by MNase

value: extensive digestion

tag: cell line


title: Neuronal nuclei from P21 hypothalamus_rep3

description: P21 neuron biological replicate 3 of 5.


title: MNase-seq-open replicate2

description: Mild digestion by MNase


title: cL4


title: MNase-seq-position replicate2

description: Extensive digestion by MNase


title: Neuronal nuclei from P21 hypothalamus_rep4

description: P21 neuron biological replicate 4 of 5.


title: AUY077_25min

description: In the processed data file the values for each chromosome were generated by dividing by 1.29.

source_name: AUY077 genomic DNA 25 min released from alpha factor

value: Cells were released from alpha factor in rich media and a sample taken after 25 min.


title: Non-neuronal nuclei from P21 hypothalamus_rep4

description: P21 non-neuron biological replicate 4 of 5.

value: non-neuronal cell


title: Non-neuronal nuclei from P21 hypothalamus_rep5

description: P21 non-neuron biological replicate 5 of 5.


title: Non-neuronal nuclei from P21 hypothalamus_rep2

description: P21 non-neuron biological replicate 2 of 5.


title: Neuronal nuclei from P0 hypothalamus_rep1

description: P0 neuron biological replicate 1 of 5.


title: Neuronal nuclei from P0 hypothalamus_rep2

description: P0 neuron biological replicate 2 of 5.


title: Non-neuronal nuclei from P21 hypothalamus_rep3

description: P21 non-neuron biological replicate 3 of 5.


title: Non-neuronal nuclei from P21 hypothalamus_rep1

description: P21 non-neuron biological replicate 1 of 5.


title: Neuronal nuclei from P21 hypothalamus_rep1

description: P21 neuron biological replicate 1 of 5.


title: Neuronal nuclei from P0 hypothalamus_rep4

description: P0 neuron biological replicate 4 of 5.


title: Neuronal nuclei from P0 hypothalamus_rep5

description: P0 neuron biological replicate 5 of 5.


title: Non-neuronal nuclei from P0 hypothalamus_rep5

description: P0 non-neuron biological replicate 5 of 5.


title: cB1

description: Half sibling Herman, Japie, Koos


title: Non-neuronal nuclei from P0 hypothalamus_rep4

description: P0 non-neuron biological replicate 4 of 5.


title: Non-neuronal nuclei from P0 hypothalamus_rep3

description: P0 non-neuron biological replicate 3 of 5.


title: Non-neuronal nuclei from P0 hypothalamus_rep1

description: P0 non-neuron biological replicate 1 of 5.


title: Non-neuronal nuclei from P0 hypothalamus_rep2

description: P0 non-neuron biological replicate 2 of 5.


title: POLR3GL_Hepa_2

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

data_processing:
Basecalls was performed using Illumina CASAVA pipeline v1.8.2.
Human,respectively Mouse ChIP-seq reads were aligned to the hg18 (resp. mm9) genome assembly via the eland_extended mode of Eland v2e in the Illumina CASSAVA pipeline v1.8.2. The tags with multiple but perfect matches on the genome were then mapped with the “fetchGWI” software.
Tags with up to 500 matches in the genome were attributed a weight corresponding to the number of times they were sequenced divided by the number of matches in the genome.
Scores were calculated as log2((Immunoprecipitation tag counts +30)/(Input tag counts+30)) over regions encompassing the RNA coding sequence as well as 150 base pairs (bp) upstream and 150 bp downstream of the RNA coding region.
Genome_build: hg19 for Human IMR90 cells
Genome_build: mm9 for Mouse liver and hepatocarcinoma cells
Supplementary_files_format_and_content: bedGraph files for genome releases hg18 (human data) and mm9 (Mouse data) showing the regions around Pol3 transcribed features for each IP and for the Inputs.

source_name: Hepa 1-6 cells

growth_protocol: Cell lines : cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% foetal bovine serum, 4 mM glutamine, 100 units/ml of penicillin, and 100 μg/ml of streptomycin.

extract_protocol:
Cell lines : approximately 10 million subconfluent IMR90 or Hepa 1-6 cells were used per ChIP. The protocol used was similar to the one described by (O'Geen et al. 2006). Cells were directly crosslinked in the culture medium for seven minutes with 1% formaldehyde. The chromatin was sonicated to an average size of 200-600 base pairs.
Mouse livers : livers were perfused with 5 ml of PBS through the spleen, immediately homogenized in PBS containing 1% formaldehyde, and then processed as described in (Ripperger and Schibler 2006).
Aliquots of sonicated chromatin were mixed with different antibodies and incubated overnight at 4˚C on a rotating wheel. Immunoprecipitated material was recovered by addition of 15 µl of protein A agarose beads (pre-blocked with 10 µg/ml of BSA and 10 µg/ml of salmon sperm DNA) and incubation for 1 h at room temperature on a rotating wheel. The beads were washed with dialysis and wash buffer (O’Green et al., 2006). De-crosslinking, RNase A treatment, proteinase K treatment, and DNA purification were performed as described in (O’Green et al., 2006).Ten ng of immunopurified chromatin as well as input DNA was used to prepare sequencing libraries with the ChIP-Seq Sample Preparation Kit (Illumina; San Diego, California, USA; Cat. No IP-102-1001) according to the protocol supplied by the manufacturer

value: Hepa 1-6 cells

value: anti-mouse POLR3GL ZCH10079-1434 Ab, raised against peptide RPPKSTDDKEETIQK


title: POLR3GL_Hepa_1


title: POLR3G_Hepa_2

value: anti-mouse POLR3G ZCH10075-1430 Ab, raised against peptide VGFSRGEKLPDVVLK


title: POLR3G_Hepa_1


title: Neuronal nuclei from P0 hypothalamus_rep3

description: P0 neuron biological replicate 3 of 5.


title: Input_Hepa


title: POLR3G_Liver_1

source_name: Liver

value: Liver

value: post natal week 12


title: POLR3GL_Liver_2


title: POLR3G_Liver_2


title: POLR3GL_Liver_1


title: POLR3D_Hepa_2

value: anti-POLR3D (mouse and human) CS681 Ab,  raised against peptide CSPDFESLLDHKHR {Chong, 2001 #96}


title: Input_Liver_1


title: Input_Liver_2


title: POLR3D_Hepa_1


title: POLR3D_Liver_2


title: POLR3D_Liver_1


title: NMD_MOCK_R2

city: New York

first: Andre

last: Kahles

state: New York

address: 1275 York Avenue

department: Computational Biology Center

institute: Memorial Sloan-Kettering Cancer Center

description: Col-0 t=4h contrl. #2

data_processing:
Illumina Raw Data processing with SHORE 4.1 pipeline with application 'mRNA' and disabled illumina filter
Fastq file were aligned to the TAIR10 genome with the spliced aligner PALMapper (version 4)
Alignment postprocessing (filtering and multimapper resolution) using RNAgeeq
Reads were counted as overlapping to a gene, if they shared at least one exonic position
Expression values were transformed to RPKM (Reads per kilobase per million mapped reads)
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text-file, with following columns: (1) gene id; (2) WT; (3) UPF1; (4) UPF3; (5) UPF1UPF3; (6) MOCK; (7) CHX

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: seedlings were grown on 1/2 MS medium containing 2% sucrose for 11 days under continuous light conditions

extract_protocol:
seedlings were ground in liquid N2 and total RNA was isolated using the Universal RNA purification kit (Roboklon)
Libraries were prepared using the Illumina TruSeq™ sample prep kit starting from 2-4 µg of total RNA and following the instruction manual (TruSeq RNA Sample Preparation v2 Guide; November 2010)

tag: ecotype

value: Columbia

tag: genotype

value: wild type

tag: developmental stage

value: 11 days old seedlings

value: incubated for 4 h in liquid MS medium (mock treatment)


title: NMD_CHX_R2

description: Col-0 t=4h CHX #2

value: incubated for 4 h in liquid MS medium containing 10 µg/ml cycloheximide


title: cL2

description: Half sibling Antoine, Japie, Koos

value: male

value: liver


title: NMD_UPF3_R2

description: upf3-1 #2

value: untreated


title: NMD_UPF1_R2

description: lba1 #2


title: NMD_WT_R2

description: Col-0 WT #3


title: NMD_MOCK_R1

description: Col-0 t=4h contrl. #1


title: NMD_UPF1UPF3_R1

description: lba1 upf3-1 #2


title: NMD_CHX_R1

description: Col-0 t=4h CHX #1


title: NMD_WT_R1

description: Col-0 WT #2


title: NMD_UPF1_R1

description: lba1 #1


title: NMD_UPF3_R1

description: upf3-1 #1


title: H3K27me3 ChIP-seq for GM19239

first: Graham

last: McVicker

address: 10010 N Torrey Pines Rd

institute: Salk Institute

data_processing:
Basecalls by Illumina CASAVA 1.7.0
Mapped reads to hg18 using BWA 0.6.1, allowing up to 2 mismatches per read (-n 2), and excluding gapped alignments (-o 0)
Discarded reads that did not uniquely map, taking into account SNPs in YRI 1000 genomes samples as described in Degner 2012.
Discarded reads overlapping multiple SNPs and reads overlapping indels
Discarded duplicate reads mapping to same location and strand randomly (rather than retaining highest scoring)
Extracted reads in 2kb surrounding each segregating SNP and counted reads that could be assigned to each haplotype
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited files containing all information used for tests of genetic association. Each row represents 2kb region flanking a test-SNP and gives total number of reads for one individual as well as number of allele-specific reads that can be assigned to each haplotype.

source_name: lymphoblastoid cell line

growth_protocol: Ten lymphoblastoid cell lines from unrelated Yoruba individuals were obtained from the Coriell Institute. Cells were grown in RPMI media with 15% FBS, supplemented with 2mM L-glutamate, 100 I.U./mL penicillin, and 100 ug/mL streptomycin.

extract_protocol:
Chromatin was extracted using protocol described in Cain et al. 2011, except that for some samples chromatin was sheared with a Covaris S2 (settings: 40 min duty cycle 20%, intensity 8, 200 cycles/burst, 500 uL at a time in 12 x 24 mm tubes).
Prepared Illumina sequencing libraries as described by the ENCODE Project Consortium (2011), starting with 20 uL of ChIP output or 4 ng of pooled input sample.

value: lymphoblastoid cell line

tag: population

value: YRI

tag: ethnicity

value: Yoruba

tag: country of origin

value: Nigeria

tag: chip antibody

value: H3K27me3 (Millipore 07-449)

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #


title: H3K27me3 ChIP-seq for GM19204

tag: cell type


title: H3K27me3 ChIP-seq for GM19238


title: NMD_UPF1UPF3_R2

description: lba1 upf3-1 #3


title: H3K27me3 ChIP-seq for GM18522


title: H3K27me3 ChIP-seq for GM19193


title: H3K27ac ChIP-seq for GM19239

value: H3K27ac (Abcam ab4729)

value: Abcam


title: H3K27me3 ChIP-seq for GM18507


title: H3K27me3 ChIP-seq for GM18516


title: H3K27ac ChIP-seq for GM19204


title: H3K27me3 ChIP-seq for GM18505


title: H3K27ac ChIP-seq for GM19141


title: H3K27ac ChIP-seq for GM19238


title: H3K27ac ChIP-seq for GM19193


title: H3K27ac ChIP-seq for GM18522


title: H3K27ac ChIP-seq for GM18508


title: H3K27ac ChIP-seq for GM18505


title: H3K4me3 ChIP-seq for GM19204

value: H3K4me3 (Abcam ab8580)


title: H3K27ac ChIP-seq for GM18516


title: H3K27ac ChIP-seq for GM18507


title: H3K4me3 ChIP-seq for GM19239


title: H3K4me3 ChIP-seq for GM19193


title: H3K4me3 ChIP-seq for GM19238


title: H3K4me3 ChIP-seq for GM18522


title: H3K4me3 ChIP-seq for GM18508


title: H3K4me3 ChIP-seq for GM18516


title: H3K4me3 ChIP-seq for GM19141


title: H3K27me3 ChIP-seq for GM19141


title: H3K4me3 ChIP-seq for GM18507


title: H3K4me3 ChIP-seq for GM18505


title: H3K27me3 ChIP-seq for GM18508


title: H3K4me1 ChIP-seq for GM19238

value: H3K4me1 (Millipore 07-436)


title: H3K4me1 ChIP-seq for GM19239


title: H3K4me1 ChIP-seq for GM18516


title: H3K4me1 ChIP-seq for GM18507


title: 54-1_untreated

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing:
Base calls and quality scores were generated using Illumina's Real-Time Analysis software v1.8.7.  Binary base call files were converted to text formatted qseq files via OLB 1.9.0, which were then filtered and converted to fastq format by CASAVA 1.7, using the default Chastity threshold of 0.6.
Read counts for the genes are collected by Bioconductor Biostrings and IRanges packages.  Reads that are mapped ambiguously to M locations are counted as 1/M at each occurrence.
Genome_build: hg19

source_name: untreated myoblasts

growth_protocol: Primary human myoblasts were collected and cultured as previously described (Snider et al., 2010, PubMed ID 21060811).

extract_protocol:
Myoblasts were collected and total RNA was harvested from the cells using the RNeasy kit (Qiagen) according to the manufacturer's protocol.
mRNA purification, mRNA fragmentation and cDNA synthesis were performed with the TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer's protocol.

treatment_protocol: Human primary myoblasts were transduced with lentivirus carrying DUX4 (samples 1 and 3), GFP (sample 2), or were left untransduced (sample 4). Treatment times were 24h (samples 1 and 2) or 48h (samples 3 and 4).

tag: transduction


title: 54-1_DUX4

source_name: myoblasts transduced with lentivirus carrying DUX4-fl

value: lentivirus carrying DUX4-fl


title: MB135_DUX4


title: H3K4me1 ChIP-seq for GM18522

city: La Jolla


title: H3K4me1 ChIP-seq for GM19141


title: H3K4me1 ChIP-seq for GM19193


title: H3K4me1 ChIP-seq for GM18505


title: H3K4me1 ChIP-seq for GM19204


title: H3K4me1 ChIP-seq for GM18508


title: SW1398 Methylation

city: Gent

first: Joachim

last: De Schrijver

address: Coupure Links 653

country: Belgium

institute: Universiteit Gent

description: Methylated DNA

data_processing:
Basecalling performed using CASAVA
Bed files generated using MHM (http://h2g2.ugent.be/?page_id=32)
Genome_build: NCBI 37
Supplementary_files_format_and_content: MBD data: Methylation peaks in bed format

source_name: SW1398 Colorectal cancer cell line

extract_protocol:
Methylated DNA from cell lines was extracted using a column based method (MethylCollector kit ) and sheared by sonication.
Paired end standard illumina kit.

value: Colorectal cancer

tag: dsn time


title: Colo205 Methylation

description: Methylated DNA

source_name: Colo205 Colorectal cancer cell line


title: LS513 Methylation

description: Methylated DNA

source_name: LS513 Colorectal cancer cell line


title: SW480 Methylation

description: Methylated DNA

source_name: SW480 Colorectal cancer cell line


title: MB135_GFP

source_name: myoblasts transduced with lentivirus carrying GFP

value: lentivirus carrying GFP


title: HT29 Methylation

description: Methylated DNA

source_name: HT29 Colorectal cancer cell line


title: HCT116 Methylation

description: Methylated DNA

source_name: HCT116 Colorectal cancer cell line


title: SW480 total RNA

description: Bidirectional total RNA

data_processing:
Basecalling performed using CASAVA
Transcription data is calculated as the average number of bases mapping in the exons of a transcript (i.e. Normalized over transcript length). Intra sample normalization can be done using the matrix in the GEO_RNA_normalization.txt file.
Genome_build: NCBI 37
Supplementary_files_format_and_content: RNA data: Average exon coverage per base.

extract_protocol:
Total RNA was isolated using TRIzol reagent and subjected to purification using RNeasy Mini Kit. PolyA RNA was extracted using the standard Illumina protocol.
Single-end standard illumina kit.


title: SW1398 total RNA

description: Bidirectional total RNA


title: Colo205 total RNA

description: Bidirectional total RNA


title: LS513 total RNA

description: Bidirectional total RNA


title: RKO total RNA

description: Bidirectional total RNA

source_name: RKO Colorectal cancer cell line

value: RKO


title: HT29 total RNA

description: Bidirectional total RNA


title: DKO polyA mRNA

description: Bidirectional PolyA mRNA

source_name: HCT116 DNMT1/3b double knockout


title: DKO total RNA

description: Bidirectional total RNA


title: HCT116 total RNA 11h DSN

description: Bidirectional total RNA


title: Colo320 Methylation

description: Methylated DNA

source_name: Colo320 Colorectal cancer cell line


title: HCT116 total RNA 9h DSN

description: Bidirectional total RNA


title: HCT116 polyA mRNA

description: Bidirectional polyA mRNA


title: HCT116 total RNA 10h DSN

description: Bidirectional total RNA


title: HCT116 total RNA 6h DSN

description: Bidirectional total RNA


title: RKO Methylation

description: Methylated DNA


title: hT5

tag: Sex

value: male

tag: age

tag: rin

value: testis


title: HCT116 total RNA 8h DSN

description: Bidirectional total RNA


title: hT2

tag: tissue


title: HCT116 total RNA 7h DSN

description: Bidirectional total RNA

tag: cell line


title: hT3


title: hH4

value: heart


title: hH3


title: HCT116 total RNA 5h DSN

description: Bidirectional total RNA


title: hK5

source_name: Finn 1

value: kidney


title: hT1


title: hK1


title: hL1_GAII

description: Resequencing of hL1 library on Genome Analyzer II

value: liver


title: hB1_GAII

description: Resequencing of hB1 library on Genome Analyzer II

source_name: Holland 3

value: brain


title: hT4


title: Colo320 total RNA

description: Bidirectional total RNA


title: hH2


title: POLR3GL_IMR90

source_name: IMR90 cells

value: IMR90 cells

value: anti-human POLR3GL SZ3072 Ab, raised against peptide RPPKTTEDKEETIK


title: POLR3G_IMR90

value: anti-human POLR3G SZ3070 antibody (Ab), raised against peptide DYKPVPLKTGEGEEYML


title: POLR3D_IMR90

value: anti-POLR3D (mouse and human) CS681 Ab,  raised against peptide CSPDFESLLDHKHR {Chong, 2001 #96}


title: VKR_9.4OB_14dpc

first: Vanessa

middle: K.

last: Ridaura

state: MO

address: 4444 Forest Park Parkway, Box 8510

department: Pahtology and Immunology

institute: Washington University in St. Louis, School of Medicine

description: Microbial metatranscriptome

data_processing:
Illumina Hiseq 2000
Reads were split according to 4-bp barcodes used to label each of four samples pooled together per HiSeq lane. After dividing sequences by barcode, reads were mapped to genes in a custom database of 148 sequenced human gut bacterial genomes using the Bowtie 2 algorithm (63). A minimum score threshold of 42 was selected based on the distribution of scores for the reads. If a read mapped to more than one location in a genome or to multiple genomes, the counts for each gene were added according to the gene’s fraction of unique-match counts. Pseudocounts were added (i.e. 1 count) to each gene prior to normalization to account for different sampling depths (data expressed as reads/kb/million mapped reads).
Genome_build: genomes of various organisms
Supplementary_files_format_and_content: genes and counts

organism: mouse gut metagenome

source_name: Fecal sample from humanized mice

extract_protocol: RNA was treated with RNAse-free TURBO-DNAse (Ambion) and 5S rRNA and tRNAs were removed (MEGAClear columns, Ambion). A second DNAse treatment was performed (Baseline-ZERO DNAse; Epicenter). rRNA was initially depleted using MICROBexpress kit (Ambion) followed by a second MEGAClear purification. In addition, custom biotinylated oligonucleotides, directed against conserved regions of sequenced human gut bacterial rRNA genes were employed for streptavidin bead-based pulldowns. cDNA was synthesized using SuperScript II (Invitrogen), followed by second strand synthesis with RNAseH, E. coli DNA polymerase (NEB) and E. coli DNA ligase (NEB). Samples were sheared using a BioRuptor XL sonicator (Diagenode); 150-200 bp fragments were gel selected and prepared for sequencing. Multiplex microbial cDNA sequencing was performed using an Illumina Hi-Seq2000 instrument to generate 23.7 ± 16.4 million unidirectional 101 nt reads per sample.

tag: sample type

value: Fecal sample from humanized mice

tag: donor bmi

value: Obese culture collection (co-housed with mice with the complete Lean culture collection)


title: BDP1_IMR90

value: anti-human BDP1:CS914, raised against peptide CSDRYRIYKAQK, like CS913 {Schramm, 2000 #97}


title: hK4


title: VKR_8.3V73_14dpc

description: Microbial metatranscriptome

value: Lean culture consortia


title: VKR_7.4OB_14dpc

description: Microbial metatranscriptome


title: VKR_9.3V73_14dpc

description: Microbial metatranscriptome


title: VKR_6.3V73_14dpc

description: Microbial metatranscriptome

value: Lean culture consortia (co-housed with mice harboring the Obese culture)


title: VKR_8.4OB_14dpc

description: Microbial metatranscriptome


title: hH1


title: VKR_5.4LN_14dpc

description: Microbial metatranscriptome

value: Lean culture collection (co-housed with mice colonized with the Ob culture collection)


title: VKR_6.4OB_14dpc

description: Microbial metatranscriptome


title: VKR_1ob.15_14dpc

description: Microbial metatranscriptome

value: Obese culture collection


title: VKR_1ob.14_14dpc

description: Microbial metatranscriptome


title: VKR_1ob.12_14dpc

description: Microbial metatranscriptome


title: VKR_2.4LN_14dpc

description: Microbial metatranscriptome


title: VKR_4.4LN_14dpc

description: Microbial metatranscriptome


title: VKR_1ob.16_14dpc

description: Microbial metatranscriptome


title: VKR_1ln.1_14dpc

description: Microbial metatranscriptome

value: Lean culture collection


title: VKR_1ob.11_14dpc

description: Microbial metatranscriptome


title: VKR_1ln.5_14dpc

description: Microbial metatranscriptome


title: VKR_1ln.2_14dpc

description: Microbial metatranscriptome


title: VKR_15.3OB_14dpc

description: Microbial metatranscriptome

value: Obese culture collection (co-housed with mice with the Lean culture consortia)


title: VKR_1ln.6_14dpc

description: Microbial metatranscriptome


title: VKR_1.4LN_14dpc

description: Microbial metatranscriptome


title: VKR_14.3OB_14dpc

description: Microbial metatranscriptome


title: VKR_13.3OB_14dpc

description: Microbial metatranscriptome


title: VKR_12.3OB_14dpc

description: Microbial metatranscriptome


title: VKR_11.3OB_14dpc

description: Microbial metatranscriptome


title: VKR_10.4OB_14dpc

description: Microbial metatranscriptome


title: VKR_7.3V73_14dpc

description: Microbial metatranscriptome


title: VKR_3.4LN_14dpc

description: Microbial metatranscriptome


title: VKR_10.3V73_14dpc

description: Microbial metatranscriptome


title: VKR_1ln.4_14dpc

description: Microbial metatranscriptome


title: D9_FECAL_14dpc

description: Microbial metatranscriptome

value: Obese


title: F1_FECAL_14dpc

description: Microbial metatranscriptome


title: E13_FECAL_14dpc

description: Microbial metatranscriptome

value: Lean


title: E15_FECAL_14dpc

description: Microbial metatranscriptome


title: C6_FECAL_14dpc

description: Microbial metatranscriptome


title: D12_FECAL_14dpc

description: Microbial metatranscriptome


title: C5_FECAL_14dpc

description: Microbial metatranscriptome


title: F4_FECAL_14dpc

description: Microbial metatranscriptome


title: PM98_FECAL_14dpc

description: Microbial metatranscriptome


title: E16_FECAL_14dpc

description: Microbial metatranscriptome


title: C8_FECAL_14dpc

description: Microbial metatranscriptome


title: F3_FECAL_14dpc

description: Microbial metatranscriptome


title: C7_FECAL_14dpc

description: Microbial metatranscriptome


title: PM96_FECAL_14dpc

description: Microbial metatranscriptome


title: PM93_FECAL_14dpc

description: Microbial metatranscriptome


title: PM94_FECAL_14dpc

description: Microbial metatranscriptome


title: PM97_FECAL_14dpc

description: Microbial metatranscriptome


title: PM78_FECAL_14dpc

description: Microbial metatranscriptome


title: PM91_FECAL_14dpc

description: Microbial metatranscriptome


title: PM75_FECAL_14dpc

description: Microbial metatranscriptome


title: PM74_FECAL_14dpc

description: Microbial metatranscriptome


title: PM76_FECAL_14dpc

description: Microbial metatranscriptome


title: PM77_FECAL_14dpc

description: Microbial metatranscriptome


title: PM72_FECAL_14dpc

description: Microbial metatranscriptome


title: PM61_FECAL_14dpc

description: Microbial metatranscriptome


title: PM71_FECAL_14dpc

description: Microbial metatranscriptome


title: D10_FECAL_14dpc

description: Microbial metatranscriptome


title: PM73_FECAL_14dpc

description: Microbial metatranscriptome


title: DCA_9hpi_rep2

city: Newark

first: Sridhara

middle: G

last: Kunjeti

state: DE

address: 531, S. college Ave

department: Plant and Soil Sciences

institute: University of Delaware

description: 9 hours post-inoculation into 1x PBS buffer with mutant bacterial cells

data_processing:
Primary analysis and quality filtering of the Illumina HiSeq data was performed using the default parameters. Bowtie alignment was performed considering the best alignment with zero mismatches. The abundance of reads per gene was calculated by using a custom Perl script which used the Bowtie output file as its input file.
The abundance files was later used as an input data to analyze in LOX program.
Genome_build: MG8
Supplementary_files_format_and_content: see readme.txt

organism: Pyricularia oryzae

source_name: fungal mycelium and spores and bacterial L. enzymogenes mutant strain DCA cells in buffer

growth_protocol: The cultures of the L. enzymogenes wild-type strain C3 and mutant DCA were grown overnight in LB medium at 200 rpm at 30ºC. The fungus was grown on oatmeal-agar medium (50 g/L oatmeal, 15 g/L agar) for 10 days, under continuous light at 25ºC for conidia production.

extract_protocol:
RNA was extracted from each sample using the Trizol reagent following manufacturer's protocols. Initially, the frozen tissue was ground to a fine powder in liquid nitrogen, RNA was extracted with Trizol, and the ensuing pellet was re-suspended in 50 microliters of nuclease-free water.
RNA was extracted from all  the samples (plate-grown and plant-grown P. phaseoli race F) using Tri reagent (Ambion Inc., Austin, TX) according to manufacturer’s instructions. After nanodrop, total RNA from all tewelve libraries were processed for RNA-Seq according to Illumina manufacturer’s instructions (Illumina, San Diego, CA). These libraries were multiplexed.

tag: time point

value: 9 hours post-inoculation


title: DCA_9hpi_rep1


title: DCA_3hpi_rep2

description: 3 hours post-inoculation into 1x PBS buffer with mutant bacterial cells

value: 3 hours post-inoculation


title: PM95_FECAL_14dpc

description: Microbial metatranscriptome


title: DCA_3hpi_rep1


title: C3_3hpi_rep1

description: 3 hours post-inoculation into 1x PBS buffer with wild-type bacterial cells

source_name: fungal mycelium and spores and bacterial wild-type L. enzymogenes strain C3 cells in buffer


title: C3_9hpi_rep1

description: 9 hours post-inoculation into 1x PBS buffer with wild-type bacterial cells


title: CON_9hpi_rep1

description: 9 hours post-inoculation into 1x PBS buffer

source_name: fungal mycelium and spores in buffer


title: C3_9hpi_rep2


title: CON_9hpi_rep2


title: CON_3hpi_rep2

description: 3 hours post-inoculation into 1x PBS buffer


title: C3_3hpi_rep2


title: CON_3hpi_rep1


title: hL4

source_name: Witthe 1

value: male

value: liver


title: hL2


title: hL1


title: hB5

value: brain


title: hL1_rep

description: Technical replicate (new library) for hL1


title: hB4


title: hB3


title: rT3

description: One zoo colony

organism: Macaca mulatta

value: testis


title: hB2

source_name: Finn II


title: hB1


title: rT4

description: One zoo colony


title: rK6

description: One zoo colony

value: kidney


title: rK4

description: One zoo colony


title: hL5


title: rH5

description: One zoo colony

value: heart


title: rK1

description: One zoo colony


title: rK2

description: One zoo colony


title: rH4

description: One zoo colony


title: hL3


title: rH1

description: One zoo colony


title: cT1

source_name: Geoff


title: cT2

description: Half sibling Antoine, Japie, Koos

source_name: Herman


title: cT3

description: Full sibling to Koos, half sibling Herman, Antoine

source_name: Japie


title: rT5

description: One zoo colony


title: cT4

description: Full sibling to Japie half sibling Herman, Antoine

source_name: Koos


title: cT5

source_name: Big Male Zurich


title: rH3

description: One zoo colony


title: cK2

description: Half sibling Antoine, Japie, Koos


title: cK1

description: Half sibling Herman, Japie, Koos

source_name: Antoine


title: rH2

description: One zoo colony


title: cH4


title: cH3


title: cH2

description: Half sibling Antoine, Japie, Koos


title: rT1

description: One zoo colony


title: LoVoSTTnocodazole0_RAD21_Rabbit

city: Stockholm

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: Files generated using MACS 1.4

source_name: LoVo

growth_protocol: LoVo (ATCC CCL-229)  colon adenocarcinoma cells were cultured in DMEM supplemented with penicillin/streptomycin and 10% FBS under standard culture conditions.

extract_protocol: Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit.

treatment_protocol: For S-phase synchronization, LoVo cells were arrested in early S phase by double thymidine block essentially as described in (Whitfield et al., 2002). Briefly, cells were cultured to 30 to 40% confluence and washed with PBS. Block medium (DMEM containing 10% FBS and 2 mM thymidine) was applied to cells for 12 h, followed by washing with PBS, and continued culture in culture medium for 8 h. The second thymidine block was applied by changing the medium to the block medium followed by another 12 h of culture before harvesting the cells. Genomic DNA was extracted from the synchronized cells and sequenced as described below. For M-phase synchronization, cells were cultured and incubated in block medium for 12 h as above. Then the block medium was replaced by culture medium (DMEM with 10% FBS) containing 200 ng/ml nocodazole (Sigma), in which cells were cultured for 8 h before harvest.

value: LoVo

value: colon adenocarcinoma

tag: hgn

tag: antibody

value: Santa Cruz Biotechnology, Inc. :sc-98784

tag: control sample

tag: blocking protocol

value: Thymidine block + nocodazole

tag: number of peaks, fdr < 5%


title: LoVoSTTnocodazole0_MYC_Rabbit

value: MYC

value: MILLIPORE :06-340


title: LoVoSTTnocodazole0_KLF5_Rabbit

value: Santa Cruz Biotechnology, Inc. :sc-22797


title: LoVoSTTnocodazole0_IgG_Rabbit

value: IgG

value: Santa Cruz Biotechnology, Inc. :sc-2027


title: LoVoSTTnocodazole0_HNF4A_Rabbit

value: Santa Cruz Biotechnology, Inc. :sc-8987


title: cK4


title: LoVoSTTnocodazole0_H3_Rabbit

value: Abcam :ab1791


title: cK3

value: male


title: LoVoDTT0_RAD21_Rabbit

value: Double Thymidine block


title: PolII ChIP-seq for GM19239

source_name: lymphoblastoid cell line

value: lymphoblastoid cell line

tag: population

value: YRI

tag: ethnicity

value: Yoruba

tag: country of origin

value: Nigeria

tag: chip antibody

value: PolII (Santa Cruz sc-9001)

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #


title: PolII ChIP-seq for GM18522

tag: cell type


title: PolII ChIP-seq for GM19141


title: LoVoDTT0_IgG_Rabbit

value: LoVo

value: colon adenocarcinoma


title: Input_IMR90

value: IMR90 cells


title: LoVoDTT0_MYC_Rabbit

value: MYC

value: MILLIPORE :06-340


title: PolII ChIP-seq for GM19238


title: PolII ChIP-seq for GM18516


title: LoVoDTT0_KLF5_Rabbit

value: Santa Cruz Biotechnology, Inc. :sc-22797


title: LoVoDTT0_HNF4A_Rabbit


title: PolII ChIP-seq for GM19204


title: PolII ChIP-seq for GM18508


title: LoVoDTT0_H3_Rabbit


title: PolII ChIP-seq for GM18507


title: CD4+_ATACseq_Day3_Rep1

city: Stanford

first: William

last: Greenleaf

address: 279 Campus Dr West, Beckman Center

department: Genetics

institute: Stanford University

description:
insert size: 50-500
Processed data file: CD4+_ATACseq_AllDays_AllReps_ZINBA_pp08.bed.gz

data_processing:
Library strategy: ATAC-Seq
Basecalls were performed using CASAVA.
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard.
Genome-wide read density was calculated as the number of insertions found within 150bp sliding window with 20 bp step size.
Peaks were called using the ZINBA algorithm, which was first applied to each dataset independently, using the following parameters: a 300bp window, 50bp offset, background and enriched components were modeled using the intercept, while the zero-inflated component was modeled using alignability, a posterior probability of 0.8 was used to select the set of significant regions. The peak sets from the same cell-type and number of cells were merged.
Genome_build: GRCh37
Supplementary_files_format_and_content: Peak files are in UCSC broadPeak format, which includes the following columns: chromosome, start, stop, name, arbitrary score (1000), strand, read count within peaks, -log10(1-posterior probability), -log10(qvalue).

source_name: CD4+ T cells, day 3

growth_protocol: GM12878 cells were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks, cells were maintained between 200,000-800,000 cells/ml.

extract_protocol:
GM12878 cells were harvested at a concentration of 500,000 cells/ml, CD4+ T cells were isolated from 5 ml of blood using negative selection. For both cell types, 50,000 cells were used for each transposition reaction. For the GM12878 cells, an additional experiment was performed using 500 cells. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

value: CD4+ T-cells purified using negative selection

tag: day


title: CD4+_ATACseq_Day3_Rep2


title: cH1

description: Half sibling Herman, Japie, Koos

tag: Sex

tag: age

tag: rin

tag: tissue

value: heart


title: CD4+_ATACseq_Day2_Rep1

source_name: CD4+ T cells, day 2


title: GM12878_ATACseq_500_Rep3

description:
insert size: 50-500
Processed data file: none

tag: cell line

value: EBV-transformed lymphoblastoid cell line

tag: number of cells


title: CD4+_ATACseq_Day1_Rep1

source_name: CD4+ T cells, day 1


title: GM12878_ATACseq_500_Rep2


title: GM12878_ATACseq_500_Rep1


title: PolII ChIP-seq for GM19193


title: GM12878_ATACseq_50k_Rep4

description:
insert size: 50-500
Processed data file: GM12878_ATACseq_50k_AllReps_ZINBA_pp08.bed.gz

source_name: GM12878, 50k cells


title: PolII ChIP-seq for GM18505


title: GM12878_ATACseq_50k_Rep2


title: GM12878_ATACseq_50k_Rep3


title: CD4+_ATACseq_Day2_Rep2


title: GM12878_ATACseq_50k_Rep1


title: HelaHA1_smRNA

first: Mien-Chie

last: Hung

address: 1515 Holcombe Boulevard

institute: MD Anderson Cancer Center

data_processing:
50 nt colorspace reads were trimmed to 35nt. Resulting 35nt reads were trimmed of adaptor sequence and mapped against human pre-miR sequences (miRBase version 16.0).
Reads per million mapped reads (RPM) values were based on mapped reads with no more than 2 mismatches total. A read was considered to come from a mature miRNA if it mapped to pre-miRNA sequences with no more than three upstream or downstream bases, and missing no more than two upstream or downstream bases from predicted mature or mature* sequences as defined in miRBase version 16.0. All the other pre-miRNA mapped reads were assigned as pre-miRNA signal.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each miR

source_name: Cervical Cancer Cells

growth_protocol: Cells were cultured in DMEM/F12 medium with 10%FBS

extract_protocol:
Total RNA was extracted from HeLa stable clones expressing scrambled control or EGFR shRNA-E1 that were seeded at same density and cultured under normoxia or hypoxia (1% O2) for 24h using miRNeasy Mini Kit (Qiagen). All RNA samples passed quality test with RIN-values greater than 8 as measured by Agilent Technologies Bioanalyzer, were subjected to RNA deep sequencing.
RNA libraries were prepared according to the standard procedures instructed by Applied Biosystems for Deep Sequencing

treatment_protocol: Same density of HeLa cells expressing scrambled control (S) or EGFR shRNA-E1 (A1) were seed and allowed for 6-8h attachment. After that, half of the experimental groups (HS and HA1) were moved into hypoxia chamber (1% O2) while the other groups (S and A1) were continuingly cultured under normoxia for another 24h.

value: ATCC-HeLa

tag: shRNA expression

value: EGFR shRNA-E1

tag: culture condition

value: Hypoxia


title: HelaHS_smRNA

value: Scrambled Control


title: rL2

description: One zoo colony

value: male

value: liver


title: control

city: Shanghai

first: Guang

address: 320 Yueyang Lu

institute: PICB

data_processing:
Raw sequence reads were mapped to the Danio rerio genome (Danio rerio Zv9), using TopHat (ver.  2.0.9) and gene transfer format (gtf) data (ref_Zv9_scaffolds.gff3.gz from ncbi).
Normalized transcription profiles were estimated based on the mapping results using cufflinks. For each transcript, the number of fragments per kilobase of transcript per million fragments mapped (FPKM) was converted from the raw read counts.
Genome_build: Danio rerio Zv9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample from cufflinks output.

organism: Danio rerio

source_name: larvae

growth_protocol: WT larvae, control and impdh knock-down larvae were raised raised at 28°C under 14h: 10h light/dark cycle from birth and sampled simultaneously at 32 hpf.

extract_protocol:
Total RNA of each sample was extracted using Trizol (Invitrogen).The quantity and quality of the RNA samples were assessed with a Qbit and an Agilent 2100 bioanalyzer.
mRNA-seq libraries were constructed using the TruSeq RNA Sample Preparation v2 Kit following the manufacturer's protocol (Illumina).

treatment_protocol: The larvae in each group were sucked into freezing tubes, removed of water, frozen immediately in liquid nitrogen, and stored at -80°C.

tag: treatment

value: control knockdown

tag: strain

value: AB strain

tag: developmental stage

tag: tissues

value: whole embryo


title: MO_impdh1b

value: MO impdh1b


title: rL4

description: One zoo colony


title: MO_impdh1a

value: MO impdh1a


title: CD4+_ATACseq_Day1_Rep2


title: rL1

description: One zoo colony


title: MO_impdh2

value: MO impdh2


title: HelaS_smRNA

value: Normoxia


title: rB5

description: One zoo colony

value: brain


title: HelaA1_smRNA


title: HelaHA1_WT

data_processing:
SOLiD fragment colorspace transcriptome reads (50nt) were mapped to the human genome (hg19) and assigned to Ensembl transcripts using default settings in Bioscope 1.3.1 (Life Technologies).
RPKM values were determined using the Bioscope 1.3.1 CountTags tool using default parameters.  Primary alignments with a minimum mapping quality of 10 and minimum alignment score of 10 were counted.
Genome_build: Hg19
Supplementary_files_format_and_content: Tab delimited file text file with RPKM measurements for each transcript feature


title: rB4

description: One zoo colony


title: rL3

description: One zoo colony


title: HelaHS_WT


title: HelaA1_WT


title: rB3

description: One zoo colony


title: rB1

description: One zoo colony


title: HelaS_WT


title: rB2

description: One zoo colony


title: WT

value: untreated