title: Input DNA

growth_protocol: ES cells were grown with in standard media composed of  DMEM supplemented with ES qualified FBS and Leukemia Inhibitory Factor (LIF).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and formaldehyde was inactivated by the addition of 125 mM glycine. Chromatin from each cell line was sonicated to a length of around 250-500bp and immunoprecipitated using the following antibodies: Klf antibody (custom made, a gift from Huck-Hui Ng, Chen et al., 2008, Cell, PMID:18555785) Klf5 antibody (custom made, a gift from Huck-Hui Ng, Jiang et al., 2008, Nat Biotechnology, PMID:18264089) and sequenced using the SOLEXA platform.
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 (3' to 5' exo minus) and dATP. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: CME211_Klf5_ChIP-seq

status: Public on Apr 25 2014

type: SRA

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

country: France

institute: Stem Cell and Brain Research Institute

library_source: genomic

data_processing:
ChIP-Seq reads were aligned using the Eland software to NCBI build 37 (mm9) of the mouse genome.
The MACS program (version 1.4) was used to detect peaks of ChIP enrichment. It was run with the default settings using a tag size of 35 and band width 280.
Genome_build: mm9
Supplementary_files_format_and_content: bed format. Chrom, ChromStart, ChromEnd, Name and Score.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse ESCs

tag: cell type

value: Undifferentiated mouse ESCs

tag: cell line

tag: chip antibody


title: CME186_Klf4_ChIP-seq


title: ADF04DF RNA-Seq

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

library_source: transcriptomic

data_processing:
reads aligned with tophat v2.0.8b with parameter –no-novel-juncs
transcript abundance estimated with cufflinks v2.1.1 with parameter –GTF
csv file created from column 5 and 10 from cufflinks output file genes.fpkm_tracking
Genome_build: hg19
Supplementary_files_format_and_content: csv with two columns; gene_short_name and fpkm value

molecule: total RNA

organism: Homo sapiens

source_name: normal primary dermal fibroblasts

growth_protocol: Human normal dermal fibroblasts (Lonza CC-2511; LDFs) and human normal primary dermal fibroblasts (Norwegian Stem Cell Center AD04DFs) were cultured in DMEM/F12 containing 13% FCS, 2 ng/ml basic fibroblast growth factor and antibiotics. Cells were exponentially growing and used at passage 5-7. AD04DFs were obtained with Norwegian Ethics Committee Approval REK2617A.

extract_protocol:
Total RNA was isolated using the Ambion TRIzol® Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation.
RNAseq library was prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center.

treatment_protocol: Cells were cultured as described under Growth protocol. 2x10e6 cells were cultured to confluency for RNA preparation before harvesting to ensure consistency of cell cycle stages between the two cell types.

value: normal primary dermal fibroblasts


title: ADF04DF_Input

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using bowtie2 version 2.1.0
Duplicate reads were removed using picard MarkDuplicates
ChIP and Input experiments were ensured to have equal read depth by downsampling the deeper sequenced experiment using picard DownsampleSam
Peak calling was done using EDD version 0.9
Genome_build: HG19
Supplementary_files_format_and_content: bed

extract_protocol:
Cells (107 per ChIP) were cross-linked in suspension for 10 min in PBS containing 1% formaldehyde before quenching with 1.25 mM glycine. Cells were lysed for 30 min at 4oC on a rotator in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 1 mM PMSF, 1x protease inhibitor cocktail) adjusted to 1% SDS, and sonicated for 3 times 15 min in a Bioruptor (Diagenode) with 30 sec ON/OFF at high power to generate chromatin fragments of ~200-400 base pairs (bp). After sedimentation, chromatin (supernatant from 107 cell-equivalents) was diluted 10 times in RIPA buffer without SDS, and incubated on a rotator overnight at 4oC with 50 µg anti-lamin A/C antibody (Santa Cruz sc-7292) pre-coupled to magnetic Dynabeads Protein G (Invitrogen). An irrelevant mouse IgG was used as control. ChIP material was collected and washed 3 times in 1 ml of ice-cold RIPA buffer without protease inhibitors. The crosslink was reversed and DNA eluted for 6 h on a shaker at 37oC in elution buffer (50 mM NaCl, 20 mM Tris-HCl, pH 7.5, 5 mM EDTA, 1% SDS) containing 0.5 µg/ml RNase A and 2 µg/ml Proteinase K). DNA was purified as described, processed for library preparation.
The sequencing library was prepared according to the Illumina protocol for the HSeq2500 at the Norwegian Sequencing Center.

treatment_protocol: Cells were cultured as described under Growth protocol. Cells were cultured to confluency before harvesting to ensure consistency of cell cycle stages between the two cell types.

tag: passages

tag: chip-antibody


title: LDF RNA-Seq

source_name: normal dermal fibroblasts

value: normal dermal fibroblasts


title: ADF04DF_LMNA_rep2

description: Processed file created with EDD using  as input HSF_AD04_Input.fastq.gz in addition to the raw file in this line

value: Santa Cruz sc-7292


title: ADF04DF_LMNA_rep1


title: LDF_Input

value: Lonza CC-2511


title: AR_DHT_exp2

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

country: USA

institute: University of Michigan

description: DHT

data_processing:
Basecalls performed using RTA 1.17.21.3 and CASAVA version 1.8.2
Reads were aligned to the HG19 genome using Bowtie2 with all default settings.
Resulting BAM files were sorted and duplicates were removed using samtools
Coverage profiles were calculated using bedtools genomecov as BedGraph files
BedGraph files wer converted to BigWig using BedGraphToBigWig from Kent Utils
Genome_build: hg19
Supplementary_files_format_and_content: Coverage profiles are normalized to sequencing depth

source_name: Prosate cancer cells

growth_protocol: Cells were grown in DMEM containing 10% FBS

extract_protocol:
ChIP was performed using HighCell ChIP kit following manufacturers protocol (Diagenode). ChIP DNA was isolated (IPure Kit, Diagenode) from samples by incubation with the antibody at 4°C overnight followed by wash and reversal of cross-linking.
The ChIP-seq sample preparation for sequencing was performed according to the manufacturer’s instructions (Illumina). ChIP-enriched DNA samples (1-10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3’ to 5’ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2000 Sequencer (100 nucleotide read length).

treatment_protocol: For BRD2/3/4 and ERG ChIP-seq experiments (sample21-33) with BET inhibitors, VCaP cells were treated with DMSO, 500 nM JQ1 or I-BET762 for 12hrs. For AR signaling ChIP-seq experiments (sample1-20), VCaP cells were grown in charcoal-stripped serum containing media for 48hrs. followed by 6hrs. pre-treatment with vehicle or 500nM JQ1 or 10µM MDV3100 or 25µM Bicalutamide and then stimulated with 10nM DHT for 12hrs

value: vertebral metastatic lesion derived prostate cancer cells

value: VCaP

value: AR (Millipore, 06-680)


title: LDF_LMNA

description: Processed file created with EDD using  as input HSF_lonzacc2511_Input.fastq.gz in addition to the raw file in this line


title: WT -GLU Ribosome Footprint 1

city: Cambridge

first: Pavanapuresan

last: Vaidyanathan

state: MA

address: 68-341, 31 Ames Street

department: Biology

institute: Massachusetts Institute of Technology

description: Small RNA sequencing by polyadenylation and circularization. RNA fragments were dephosphorylated, purified by filtration then gel to isolate ~28nt fragments. After subtractive hybridization to remove rRNA, fragments were poly(A) tailed and reverse transcribed with an anchored oligo-dT primer, followed by cDNA circularization and PCR

data_processing: Reads whose 5' ends map from 12nt 3' of CDS start to 14nt 5' of CDS end are assigned to that gene (first 8 codons are omitted to avoid artifacts due to the use of cylcoheximide in library preparation)

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were grown to mid-exponential phase (OD~0.7) at 30C in YPD

extract_protocol:
frozen cell pellets were thawed in lysis buffer and lysis was performed with glass beads as described in the text. Extracts were clarified by a 20' spin at 11,500 rpm in an SS-34 rotor
Footprints: 50 OD units of extract were treated with 50U of RNAse1 and subsequently purified from the monosome region of a sucrose gradient. RNA was extracted by hot acid phenol. Total RNA: RNA was extracted from 50 OD of extract by SDS and hot acid phenol, and poly(A) RNA was purified on DynaBeads. RNA was fragmented at 95C with zinc chloride

treatment_protocol: Cells were treated with 100ug/ml cycloheximide, then harvested by centrifugation. Cell pellet was frozen in liquid nitrogen.

tag: strain


title: WT +GLU RNA-seq 1

tag: poly-a selection

value: oligo-dT Cellulose


title: WT -GLU Ribosome Footprint 3


title: WT -GLU RNA-seq 1

description: Small RNA sequencing by polyadenylation and circularization. RNA fragments were dephosphorylated, purified by filtration then gel to isolate ~28nt fragments. Fragments were poly(A) tailed and reverse transcribed with an anchored oligo-dT primer, followed by cDNA circularization and PCR


title: WT +GLU RNA-seq 2

value: oligo-dT DynaBeads


title: WT -GLU RNA-seq 3


title: WT -GLU Ribosome Footprint 2


title: DcrKO_1_miR

first: Sidi

last: Chen

institute: MIT

description:
A3
The NSCLC cell lines used in this study (Chen et al. Genes Dev 2014) was derived from tumor samples of KrasG12D;p53-/-;Dicer1f/- mice, originally from this paper (Kumar et al. Genes Dev 2009):Dicer1 functions as a haploinsufficient tumor suppressor. Kumar MS, Pester RE, Chen CY, Lane K, Chin C, Lu J, Kirsch DG, Golub TR, Jacks T.Genes Dev. 2009 Dec 1;23(23):2700-4. doi: 10.1101/gad.1848209. Epub 2009 Nov 10.

data_processing:
adaptor clipping using fastxclipper of adaptors PE1.0 and PE2.0
discard reads shorter than 15bp
mapping to mm9 transcriptome (mRNA-seq) or miRbase release 19 (miRseq) using tophat 1.3
calculation of gene expression level in fpkm using cufflinks 2.0.3 (mRNA-seq)
calculation of gene expression level in rpm using custom scripts (miRseq)
Genome_build: mm9 transcriptome, miRbase release 19
Supplementary_files_format_and_content: text files containing fpkm or rpm values for Dicer het and Dicer KO

source_name: Dicer knockout NSCLC cells

growth_protocol: Tumor-derived non-small cell lung cancer cells were cultured in DMEM with 10% FBS, passage 1:5 or 1:10 every 2~3 days in cell-culture dish

extract_protocol:
Trizol-based total RNA extraction
NEBNext small RNA library prep

value: C57Bl6/129SV F1 hybrid

value: non-small cell lung cancer

tag: genotype

value: dicer knockout


title: WT -GLU RNA-seq 2


title: DcrKO_1_mRNA

extract_protocol:
Trizol-based total RNA extraction
Illumina Tru-Seq mRNA sequencing library prep


title: DcrHet_1_miR

description:
LCC111
The NSCLC cell lines used in this study (Chen et al. Genes Dev 2014) was derived from tumor samples of KrasG12D;p53-/-;Dicer1f/- mice, originally from this paper (Kumar et al. Genes Dev 2009):Dicer1 functions as a haploinsufficient tumor suppressor. Kumar MS, Pester RE, Chen CY, Lane K, Chin C, Lu J, Kirsch DG, Golub TR, Jacks T.Genes Dev. 2009 Dec 1;23(23):2700-4. doi: 10.1101/gad.1848209. Epub 2009 Nov 10.

source_name: Dicer Heterozygous NSCLC cells

value: dicer heterozygous


title: DcrHet_1_mRNA


title: WT +GLU Ribosome Footprint 3


title: WT +GLU RNA-seq 3


title: DcrHet_2_mRNA


title: WT +GLU Ribosome Footprint 1


title: CD49f-positive testicular cells

city: Yangling

first: wu

last: jiang

state: Shaanxi

address: Taicheng road #3

department: College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology

country: China

institute: Northwest A&F University

data_processing:
The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument.
Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70).
The extracted sequencing reads were stored in file and were then used in the sequencing data analysis.
The sequencing data analysis was analyzed using the ACGT101-miR v4.2 packages (LC Sciences, Houston, TX)
Genome_build: the latest release of miRBase (miRBase, http://www.mirbase.org/index.shtml), or genome based on the public releases of appropriate species. In this study, cattle and sheep were used as sequencing species for unique sequences to mirs, and goat was for unique sequences to genome
File contents and header definitions: See README_supplementary_file_contents.txt on Series record

organism: Capra hircus

source_name: testicular cells

extract_protocol:
The total RNAs of CD49f positive and negative testicular cells were extracted with RNAiso plus reagent (TaKaRa, Dalian, China) according to the manufacturer’s instructions,
A small RNA library was generated from the two RNA samples by the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide.

treatment_protocol: Three testes from three 5-month-old dairy goats were collected and delivered back to the laboratory on ice, respectively. Then, the testicular cells were separated  using CDD mixed digestive enzyme: 2 mg/mL collagenase (Invitrogen, Carlsbad, CA, USA) + 20 μg/ml DNase (Invitrogen) + 2 mg/ml decomposition enzyme (Invitrogen).Differential plating was performed to remove potential contamination of sertoli cells and myoid cells. The testicular cells were placed in a 10-cm diameter culture dish in DMEM/F12 medium supplemented with 10% FBS(Hyclone, Logan, UT, USA) at 37℃ overnight. Subsequently, the non-attached cells were collected for MACS by centrifuging at 1,000 rpm for 5 min.The CD49f-positive and negative testicular cells were obtained by MACS using a MiniMACS separation unit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).

value: primary testicular cell

value: Saanen dairy goat

tag: developmental stage

tag: cell surface markers


title: CD49f-negative testicular cells


title: ChIPseq_H3K27Ac_HPC7

status: Public on Apr 24 2014

first: Felicia

last: Ng

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

country: United Kingdom

institute: Cambridge Institute for Medical Research

data_processing:
ChIP-seq reads aligned to mm9 using Bowtie with default parameters.
bedGraphs were created with in-house script.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph – read density profiles

growth_protocol: Mast cells were derived from bone marrow cells collected from tibias and femurs of 3- to 5- month old adult mice. Cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% fetal bovine serum (Sigma), 1% penicillin/streptomycin (Sigma), 150 micromolar MTG (Sigma), 10% stem cell factor conditional media from BHK/MKL cells and 10ng/ml of recombinant mIL-3 (Peprotech). Cells were frequently transferred to new flasks to remove adherent cells and experiments were performed after 3 weeks, when cultures were homogenous. Homogeneity of culture was confirmed by presence of FcERI by FACS and toluidine blue staining of cytospins.

extract_protocol:
Total RNA was isolated using Tri-Reagent (Sigma) and subsequently digested with DNase I using TurboDNA (ambion), following manufacturer’s specifications. mRNA was enriched with oligoT, fragmented to an average size of 200 nt and retrotranscribed using random hexamers. cDNA was then amplified and sequenced. DNaseI-digested total RNA was processed and sequenced by BGI-Hong Kong.
ChIP assays were performed as previously described (Wilson NK et al., 2010 Cell Stem Cell) using polyclonal antibodies against CTCF (Upstate, 07-729), E2A (Santa Cruz, sc-763x), Erg (Santa Cruz, sc354x), FLI-1 (Abcam, ab15289-500), GATA2 (Santa Cruz, sc9008x), LMO2 (R&D, AF2726), Meis1 (Santa Cruz, sc-10599x), PU.1 (Santa Cruz, sc-352x), RUNX1 (Abcam, ab23980-100), TAL1 (Santa Cruz, sc12984x), Mitf (Cosmo Bio Co., BAM-73-107-EX), cFos (Santa Cruz, sc-253x). Each sample was amplified and sequenced using the Illumina Genome Analyzer II x, following manufacturer's instructions.

value: ES-derived mutipotent haematopoietic progenitor cell line


title: ChIPseq_H3K27Ac_mast

source_name: mast

value: primary mast cells


title: ChIPseq_Scl_mast

extract_protocol: ChIP assays were performed as previously described (Wilson NK et al., 2010 Cell Stem Cell) using polyclonal antibodies against CTCF (Upstate, 07-729), E2A (Santa Cruz, sc-763x), Erg (Santa Cruz, sc354x), FLI-1 (Abcam, ab15289-500), GATA2 (Santa Cruz, sc9008x), LMO2 (R&D, AF2726), Meis1 (Santa Cruz, sc-10599x), PU.1 (Santa Cruz, sc-352x), RUNX1 (Abcam, ab23980-100), TAL1 (Santa Cruz, sc12984x), Mitf (Cosmo Bio Co., BAM-73-107-EX), cFos (Santa Cruz, sc-253x). Each ChIPseq sample was amplified and sequenced using the Illumina Genome Analyzer IIx, following manufacturer's instructions.


title: ChIPseq_Mitf_mast


title: ChIPseq_cFos_mast


title: ChIPseq_Lmo2_mast


title: ChIPseq_Meis1_mast


title: ChIPseq_Runx1_mast


title: ChIPseq_PU1_mast

data_processing:
ChIP-seq reads aligned to mm9 using Bowtie with default parameters.
bedGraphs were created with in-house script.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph – read density profiles
Supplementary_files_format_and_content: fpkm values - tab-delimited text files include RPKM values for each sample


title: WT +GLU Ribosome Footprint 2


title: DcrKO_2_mRNA


title: ChIPseq_Erg_mast


title: ChIPseq_Fli1_mast


title: ChIPseq_E2A_HPC7


title: ChIPseq_Ctcf_mast


title: ChIPseq_Ctcf_HPC7


title: ChIPseq_E2A_mast


title: RNA_CD_replicate-2

city: London

first: Francesco

last: Gualdrini

address: 44 Lincoln's Inn Fields

institute: Francis Crick Institute

description: Sample 68

data_processing:
ChipSeq MRTFA MRTFB ELK1 NET1 SAP1: Fastq files for technical replicates prepared from the same library were pooled before alignment to improve the sensitivity of the analysis.
ChipSeq except total_h3: Basecalls performed using CASAVA version 1.4 & 1.5
ChipSeq except total_h3: Alignments performed using Eland for CASAVA version 1.4 & 1.5
ChipSeq total_h3: Basecalls performed using CASAVA version 1.8
ChipSeq total_h3: Alignments were performed using bwa version 0.5.9-r16
RNASeq: Alignments were performed using bwa version 0.5.9-r16
Genome_build: MM9
Supplementary_files_format_and_content: ChipSeq: Wig files are those generated by MACS at 1bp resolution and a set normalised to 15 million mapped reads is additionally provided.
Supplementary_files_format_and_content: ChipSeq total_h3: wig files generated by MACS at 1bp reolution
Supplementary_files_format_and_content: RNASeq: wig files generated by MACS at 1bp resolution

growth_protocol: NIH-3t3 were cultured in Dulbecco modified Eagles medium (DMEM) supplemented with 10% fetal calf serum (FCS), 100 IU/ml penicillin, and 100 μ/ml streptomycin.

extract_protocol:
Chip-Seq: DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation.  The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow use of the Invitrogen SizeSelect E-gel system.  Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip before clustering and subsequent 36bp single end sequencing on the GAIIx analyser or on a Hi-seq 2000/1000.
RNA-Seq: Total RNA was extracted using Genelute (Sigma). RNA samples were quality controlled (QC) using the 6000 Nano RNA Chip on the BioAnalyser 2100 (Agilent). Libraries were prepared using the Directional mRNA-Seq Library Prep. v1.0. Pre-Release Protocol from Illumina with minor adjustments. To minimise the ribosomal content of the samples a DSN treatment of the cDNA RNA-seq libraries was used (Evrogen JSC).The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix which reduced the overall volume of the PCR and the ratio for the Agencourt AMPure XP beads was adjusted accordingly.  The standard PCR cycling was also changed to match the concentration of the total RNA from the initial QC. After passing the final QC, the libraries were subjected to cluster formation and then 72bp single end sequencing on the GAIIx analyser.

treatment_protocol: Cells were starved overnight in 0.3%FCS. Where indicated, cells were stimulated for 30 minutes with 15% fetal calf serum (FCS) or with cytochalasin D (Calbiochem, CD, 2 μM). When indicated cells were pre-traeted with latrunculin B (Calbiochem, LatB, 0.3 μM) and/or U0126 (Promega, 10 μM). Pre-treatments were for 30 minutes prior stimulation.

value: NIH3T3 fibroblasts

value: normal


title: RNA_LAT_UO_replicate-1

description: Sample 69


title: RNA_CD_replicate-1

description: Sample 67


title: RNA_15_replicate-1

description: Sample 61


title: RNA_03_replicate-2

description: Sample 60


title: RNA_UO_replicate-2

description: Sample 66


title: RNA_LAT_replicate-2

description: Sample 64


title: Control_combined

description: Sample 58


title: RNA_LAT_UO_replicate-2

description: Sample 70


title: ChIPseq_Gata2_mast


title: xbp1 fl/+ cells transduced with p210-neo and ERT2-Cre, replicate 3

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description: mRNA isolated from mouse Xbp1 heterozygous deletion cells

data_processing:
Raw image data were converted into base calls and fastq files via the Illumina pipeline CASAVA version 1.8 with default parameters. All 50-bp-long reads were mapped to the reference mouse genome sequence, mm9, using Tophat aligner (Trapnell et al, Bioinformatics 2009, 25 (9): 1105-1111) with the default parameters. The mRNA expression level for each gene was represented as log2 RPKM (reads per kilobase per million reads), called by Seqgene (Deng et al, BMC Bioinformatics 2011, 12:267).
Genome_build: mm9
Supplementary_files_format_and_content: normalized abundance measurements log2 RPKM for the 6 samples

source_name: BCR-ABL1 transformed murine ALL-like cells, Xbp1 heterozygous deletion

growth_protocol: The murine p210 transduced murine Xbp1 fl/+ pre-B cells Xbp1 were maintained in Iscove’s modified Dulbecco’s medium (IMDM, Invitrogen) with GlutaMAX containing 20% fetal bovine serum, 100 IU ml−1 penicillin, 100 μg ml−1 streptomycin and 50 µM 2-mercaptoethanol.

extract_protocol:
Libraries were prepared according to a version of Illumina's mRNA-Seq protocol (Illumina, CA)
Libraries were prepared using the Illumina RNA-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA).

tag: genetic background

value: Xbp1 heterozygous deletion


title: xbp1 fl/+ cells transduced with p210-neo and ERT2-Cre, replicate 1

value: BCR-ABL1 transformed murine ALL-like cells


title: Control_LAT

description: Sample 56


title: xbp1 fl/+ cells transduced with p210-neo and ERT2, replicate 3

description: mRNA isolated from mouse Xbp1 wild type cells

source_name: BCR-ABL1 transformed murine ALL-like cells, Xbp1 wild type

value: Xbp1 wild type


title: xbp1 fl/+ cells transduced with p210-neo and ERT2, replicate 1


title: xbp1 fl/+ cells transduced with p210-neo and ERT2-Cre, replicate 2


title: Control_UO

description: Sample 57


title: Control_15

description: Sample 55


title: RNAseq_HPC7_rep2

data_processing:
RNA-seq reads aligned to mm9 transcriptome using Tophat and assembled using Cufflinks with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: fpkm values - tab-delimited text files include RPKM values for each sample

molecule: polyA RNA

extract_protocol: Total RNA was isolated using Tri-Reagent (Sigma) and subsequently digested with DNase I using TurboDNA (ambion), following manufacturer’s specifications. mRNA was enriched with oligoT, fragmented to an average size of 200 nt and retrotranscribed using random hexamers. cDNA was then amplified and sequenced. DNaseI-digested total RNA was processed and sequenced by BGI-Hong Kong. RNAseq samples were  sequenced using the Illumina HiSeq 2000 instrument.


title: RNA_UO_replicate-1

description: Sample 65


title: RNA_15_replicate-2

description: Sample 62


title: RNA_03_replicate-1

description: Sample 59


title: Control_03

description: Sample 54


title: RNAseq_HPC7_rep1


title: POLIIS5P_UO_replicate-2

description: Sample 49

tag: chip antibody vendor

value: covance

tag: chip antibody cat. #

tag: chip antibody lot #


title: RNAseq_mast_rep2


title: RNAseq_mast_rep1


title: TOTAL_H3_UO

description: Sample 53

value: Total H3

value: Abcam


title: OB_Input

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

data_processing:
ChIP-seq runs were all 50bp.  Barcoded samples were run over 4 lanes total and the fastq data were concatenated prior to BOWTIE mapping.  12 barcoded samples were run in each lane, over 4 lanes total.  Barcodes were decoded by Illumina HiSeq2000 software automatically.  All samples were mapped from fastq files using BOWTIE [-m 1 -- best] to mm9 [UCSCmouse genome build 9].  Replicate lanes were analyzed separately for reproducibility and normalization of the peak calls.
Peaks were called by using HOMER [http://biowhat.ucsd.edu/homer/] and QuEST [http://mendel.stanford.edu/sidowlab/downloads/quest/].
QuEST 2.4 was run using the recommend settings for transcription factor (TF) like binding with the following exceptions: kde_bandwith=30, region_size=600, ChIP threshold=30, enrichment fold=3, rescue fold=3
HOMER analysis was run using the default settings for peak finding.  Histone peaks were called with a 2-fold enrichment over input instead of 4-fold (for transcription factors) given the nature of histone chip-seq.
False Discovery Rate (FDR) cut off was 0.001 (0.1%) for all peaks.
Genome_build: mm9
Supplementary_files_format_and_content: fastq files are the raw sequence files [barcoded lanes (4 each) were concatenated for each sample for simplicity, no other modification was made], bedGraph files are for display in the UCSC genome browser, *replicate_overlap.bed are the resulting peaks found with QuEST and HOMER after normalization between both replicates

source_name: MC3T3-E1 cells differentiated for 15 days

growth_protocol: MC3T3-E1 cells were cultured in alpha MEM with 10% heat-inactivated fetal bovine serum from Hyclone (Logan, UT) and 1% penicillin-streptomycin.  Differentiated cells were cultured in complete media plus 10mM glycerol-2-phosphate and 50ug/mL ascorbic acid for 15 days, changing media every 2-3 days.

extract_protocol: Chromatin immunoprecipitation was performed as described previously (Meyer MB. Mol Endo. 2012).  Briefly, MC3T3-E1 cells were treated for 3 hrs with vehicle or 100nM 1,25(OH)2D3.  Samples were subjected to immunoprecipitation using either a control IgG antibody or the indicated experimental antibody (VDR, RXR, C/EBPβ, RUNX2, H3K5Ac, H3K9Ac, H3K4me1, H3K4me3, or H3K36me3).  For differentiated cells, there was substantial mineralized matrix.  To remove the matrix from the assay, the cell/matrix mix was subjected to 3x 15s pulses with a Polytron Homogenizer (Power Gen 125, Fisher Scientific) while in NCP 1 buffer (Hepes 10mM pH 6.5, EDTA 10mM, EGTA 0.5mM, Triton X-100 0.25%).  The resulting homogenate was centrifuged (200 x g) through a 10% sucrose buffer at a 1:1 ratio (10mM Tris-HCl, 15mM NaCl, 60mM KCl, 1mM EDTA, 10% Sucrose).  Resulting cell pellet was resuspended in NCP 2 buffer (Hepes 10mM pH 6.5, EDTA 1mM, EGTA 0.5mM, NaCl 200mM) and remainder of protocol was followed (Meyer MB. Mol Endo. 2012).  The isolated DNA (or Input DNA acquired prior to precipitation) was then validated by quantitative real time PCR (qPCR) and further prepared for ChIP-seq analysis.  ChIP-seq libraries were prepared using the NEBNext DNA sample prep kit (NEB, #E6000L) with the Bioo NEXTflex ChIP-seq Barcodes (Bioo Scientific, Austin, TX, #514122) according to manufacturer’s protocols, with few exceptions.  During the NEBNext prep, the Illumina adapters were replaced with the Bioo Scientific Barcoded adapters according to Bioo protocols. ChIP-DNA ligated libraries were cleaned up with Agencourt AMPureXP Magnetic Beads (Beckman-Coulter, #A63881).  A pre-size selection PCR was performed using Phusion polymerase, NEXTflex Primer Mix and purified ligation product for 4 cycles of PCR according to the Bioo Protocol.  Libraries were size selected using Invitrogen E-gels to a size of 400-500bp.  Samples were then PCR amplified for 14 cycles using Phusion polymerase, NEXTflex Primer mix and the size selected DNA as per Bioo protocol, followed by Agencourt bead clean up.  Libraries were validated for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Clusters were formed and sequenced on the Illumina GAIIx [for all samples sequenced before June, 2011] or the Illumina HiSeq2000 [after June, 2011] sequencers by the University of Wisconsin - Madison DNA Sequencing Facility in the University of Wisconsin- Madison Biotechnology Center.  DNA clusters were generated using a cBot Single Read Cluster Generation kit (ver. 3) on an Illumina cBot (Illumina) according to the manufacturer's instructions, to obtain an average of 1.5×108 clusters for each lane on a flowcell.  All sequencing runs for 50mers were performed on an Illumina HiSeq2000 using the Illumina Sequencing kit (ver. 3).  Fluorescent images were analyzed using the CASAVA 1.8.2 (Illumina) to obtain FASTQ formatted sequence data.  Twelve barcoded libraries were run per lane and this was repeated over 4 lanes.  After which, the raw FASTQ for each sample was concatenated from the 4 lanes prior to mapping to create a single sample.  Each ChIP sample was repeated in biological replicate in the same manner (minimum of 2 replicates).  Sequences were mapped to the mouse genome (mm9) using BOWTIE (--best –m 1) to yield unique alignments.

treatment_protocol: Cells were treated with 100nM 1,25(OH)2D3 [125] or with ethanol vehicle [Veh] for 3 hours prior to ChIP assay

tag: passage number

tag: treatment


title: POLIIS5P_UO_replicate-1

description: Sample 48


title: TOTAL_H3_15

description: Sample 51


title: POLIIS5P_LAT_replicate-2

description: Sample 47


title: TOTAL_H3_03

description: Sample 50


title: POB_Input

source_name: MC3T3-E1 cells

value: ethanol vehicle


title: xbp1 fl/+ cells transduced with p210-neo and ERT2, replicate 2


title: OB_H3K36me3Veh

tag: antibody

value: ethanol vehi differentiated for 15 dayscle


title: POLIIS5P_15_replicate-1

description: Sample 44


title: OB_H3K4me1Veh

value: MC3T3-E1 differentiated for 15 days


title: OB_H3K9AcVeh


title: OB_Runx2Veh

value: RUNX2 (Santa Cruz, M-70, sc10758, lot# D1411)


title: OB_H4K5AcVeh


title: OB_H3K4me3Veh


title: RNA_LAT_replicate-1

description: Sample 63


title: POLIIS5P_03_replicate-1

description: Sample 42


title: OB_CEBPbVeh

value: C/EBPβ (Santa Cruz, C-19, sc-150, lot# F3011)


title: POB_H3K36me3Veh


title: POB_H3K4me1Veh


title: TOTAL_H3_LAT

description: Sample 52


title: POLIIS5P_LAT_replicate-1

description: Sample 46


title: POLIIS2P_UO_replicate-2

description: Sample 41


title: POB_H4K5AcVeh


title: POB_H3K4me3Veh


title: POLIIS5P_15_replicate-2

description: Sample 45


title: POB_H3K9AcVeh


title: POB_CEBPbVeh


title: POB_Runx2Veh


title: ribosome profiling in minimal media 1

first: Gene-Wei

last: Li

address: 1700 4th Street, BH404

description:
ribosome protected mRNA
fp_min_pooled_f.wig
fp_min_pooled_r.wig

data_processing:
Basecalls performed using Casava versions 1.6 or 1.7.
Sequenced reads were trimmed for adaptor sequence.
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded.
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1.
Bowtie alignments against the E coli genome were converted to wiggle files. The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme.
Genome_build: NC000913.2
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

organism: Escherichia coli

source_name: bacteria

growth_protocol: All cultures were based on MOPS media with 0.2% glucose (Teknova), with either full supplement (Neidhardt et al., 1974). An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 2.8-liter flask at 37C with aeration (180 rpm) until OD600 reached 0.3.

extract_protocol:
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011). 200 ml of cell culture was rapidly filtered at 37C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C.
Ribosome protected mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, D. Burkhardt, C.A. Gross, J. S. Weissman (Cell).

tag: media

value: minimal MOPS glucose media


title: POLIIS2P_LAT_replicate-1

description: Sample 38

tag: cell line


title: POLIIS2P_LAT_replicate-2

description: Sample 39

tag: chip antibody


title: 8WG16_LAT_replicate-2

description: Sample 32

value: Santa Cruz Biotechnology


title: POLIIS2P_15_replicate-2

description: Sample 37


title: POLIIS5P_03_replicate-2

description: Sample 43


title: POLIIS2P_03_replicate-2

description: Sample 35


title: POLIIS2P_15_replicate-1

description: Sample 36


title: 8WG16_15_replicate-2

description: Sample 30


title: POLIIS2P_03_replicate-1

description: Sample 34


title: ribosome profiling in minimal media 2


title: NET_15

description: Sample 25

value: anti-Net 1996

tag: chip antibody information

value: Buchwalter, G et al 2005 MCB


title: 8WG16_UO_replicate-1

description: Sample 33

value: NIH3T3 fibroblasts


title: 8WG16_LAT_replicate-1

description: Sample 31

value: normal


title: NET_LAT

description: Sample 26


title: 8WG16_15_replicate-1

description: Sample 29


title: NET_03

description: Sample 24


title: NET_UO

description: Sample 27


title: 8WG16_03_replicate-1

description: Sample 28


title: SAP1_UO

description: Sample 23


title: POLIIS2P_UO_replicate-1

description: Sample 40


title: SAP1_03

description: Sample 20


title: SAP1_LAT

description: Sample 22


title: ELK1_15

description: Sample 16


title: ELK1_UO

description: Sample 18


title: SAP1_15

description: Sample 21


title: ELK1_LAT

description: Sample 17


title: MRTFB_UO

description: Sample 14

value: MRTF-B


title: MRTFB_LAT

description: Sample 13


title: ELK1_03

description: Sample 15


title: Growing WT

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

institute: Johns Hopkins University

data_processing:
Base calling was performed according to Illumina's protocols using RTA v1.13.48.0 and CASAVA v1.8.2.
Low-quality reads were removed if they met any of the following criteria: <18 nt, only homopolymer As, missing 3’ adapter, 5’-3’ adapter ligation products, 5’-5’ adapter ligation products, low quality (more than 4 bases with quality scores below 10 or more than 6 bases with a quality score below 13).
High-quality reads were aligned to S. cerevisiae transcriptome taken from the genome version sacCer3 using Bowtie2 v2.1.0 with the parameters -f --local -k 500 -p 2.
Read counts in each library were normalized to the total number of mapped reads in millions (RPM).
Reads mapping uniquely to the transcriptome with zero mismatches were were used to calculate RPM per kilobase of transcript (RPKM) for each gene.
Genome_build: SGD/sacCer3 (April 2011) from S288C strain
Supplementary_files_format_and_content: Normalized transcript abundance (RPKM) is presented for each transcript in each RNA-seq library.

source_name: Whole cell

growth_protocol: Yeast cells were grown in rich medium (YPD) to mid-log phase growth. Yeast cells subjected to starvation conditions were then shifted to SD-N for 2 hours.

extract_protocol:
Total RNAs were extracted using the Master-Pure yeast RNA purification Kit from Epicentre Biotechnologies.
cDNA library preparation was performed by the DNA sequencing core at the University of Michigan.

tag: condition

value: Growing

tag: barcode

value: CGATGT


title: MRTFB_03

description: Sample 11


title: Starvation WT

value: Nitrogen starved

value: GCCAAT


title: Starvation pho23Δ

value: SEY6210 pho23∆::HIS5 (JMY047)

value: CAGATC


title: MRTFB_15

description: Sample 12


title: MRTFA_UO

description: Sample 10

value: MRTF-A


title: MRTFA_LAT

description: Sample 9


title: MRTFA_03

description: Sample 7


title: SRF_UO

description: Sample 6

value: SRF


title: SRF_03_replicate-2

description: Sample 2


title: NFkB1_2

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the hg19 version of the human genome using tophat v1.4.1 and a GTF file of gene descriptions from ensembl 66.
FPKM values were calculated using cufflinks v1.3.0
Gene expression ratios between RelA or NFkB1 and Control were calculated using cuffdiff v1.0.3.
Genome_build: hg19
Supplementary_files_format_and_content: File fpkm.txt contains FPKM values from each sample for genes from ensembl 66 as determined by cufflinks.

source_name: HEK293T cells

extract_protocol:
Total RNA was isolated from approximately 1 x 108 HEK293T cells expressing either Halo-RelA, Halo-NFkB1(p105), or the Halo tag alone using RNeasy Midi kits (Qiagen). During purification, samples were treated with DNase to remove any contaminating DNA.
TruSeq RNA sample preparation kits (Illumina) were used to prepare individually barcoded libraries for Illumina sequencing according to the manufacturer's instructions.

tag: expression construct

tag: replicate


title: NFkB1_1


title: RelA_3

value: Halo-RelA


title: SRF_03_replicate-1

description: Sample 1

tag: genotype


title: SRF_15_replicate-2

description: Sample 4


title: SRF_LAT

description: Sample 5


title: NFkB1_3


title: RelA_2


title: DH9 teratoma AI91

city: Berkeley

first: Dirk

last: Hockemeyer

department: Molecular and Cellular Biology

institute: University of California Berkeley

data_processing:
Basecalls were performed by CASAVA_v1.8.0
Reads were aligned to Ensembl human transcriptome version GRCh37.72 (combined with LGR5+GFP fusions) using bowtie2 v.2.1.0 with the settings --rdg 6,5 --rfg 6,5 –score-min,L -.6,-.4
Abundance estimation was performed using eXpress v.1.4.0 with the settings -f0.75 -B20
Genome_build: hg19
Supplementary_files_format_and_content: eXpress results.xprs file containing FPKM and estimated read counts for each transcript

source_name: differentiated human embryonic stem cells

extract_protocol:
RNA was isolated from EBs or hESCs, which were mechanically separated from feeder cells, using the RNeasy Mini Kit (Qiagen) extraction with ethanol precipitation
cDNA libraries were prepared from 50~100ng of total RNA from each sample. Ribosomal RNAs were depleted using a oligo(dT)25 magnetic bead kit (Life Technologies), and the libraries were generated using the PrepXTM SPIA® RNA-Seq and PrepX Library kit(IntegenX) according to the manufacturer’s protocol, and samples were PCR amplified for 18 cycles to incorporate indexes and flow cell-binding regions.

treatment_protocol: hESCs were collected by collagenase treatment (1.5mg/ml) and separated from feeder cells by subsequent washes with medium and sedimentation by gravity. hESCs aggregates were collected by centrifugation, resuspended in 250µl of phosphate buffered saline (PBS) and injected subcutaneously in the back of NOD-SCID mice (Taconic). Tumors generally developed within 4-8 weeks and animals were sacrificed before tumor size exceeded 1.5 cm in diameter. Teratomas were isolated  from the subcutaneous compartment of NOD-SCID mice (Taconic) before tumor size exceeded 1.5 cm (4-8 weeks after injection), thoroughly separated from mouse tissues, and briefly washed in 70% EtOH followed by PBS supplemented with penicillin/streptomycin. Tissues were minced and disaggregated in 10ml trypsin for 10-15 minutes, treated with 750,000U DNaseI (Roche) and suspended in 30 ml of FBS-containing hES media to allow the isolation of single cells through a 70µM nylon mesh filter (Falcon) and either to FACS sorted or directly embedded into 3D organoid cultures.

tag: organoid stage

value: teratoma


title: Control_1

value: Halo


title: Control_2


title: Control_3


title: Growing pho23Δ

value: TGACCA


title: DH8 organoid 38-23

treatment_protocol: Single cells isolated from teratoma were embedded at 4°C in 50µl matrigel containing 1µM JAG-1 (AnaSpec; no. 61298) and allowed to solidify on the base of a 24 well plate at 37°C for 10 minutes.  Media (500µl/well) comprised 1:1 DMEM F-12 and Neurobasic containing N2 supplement (R&D Systems), B27 supplement (Invitrogen), L-glutamine, NEAA (Gibco), and penicillin/streptomycin with growth factors 200ngml-1WNT3A (R&D Systems), 1µgml-1RSPO1 (R&D Systems), 50ngml-1 EGF (R&D Systems), 100ngml-1 Noggin (R&D Systems) and 10µM ROCK inhibitor (Stemgent; Stemolecule™ Y27632) was replaced ever other day. Organoids were removed from matrix by 5 minutes dispase (Stemcell Technologies) digestion subcultured and enriched by gravity separation and aspiration of single cells using PBS 0.5%BSA wash. Organoids were incubated in PBS 0.5%BSA 2mM EDTA for 5 minutes and mechanically fragmented with a pipette, then further washed using hES media followed by PBS 0.5%BSA. Pelleted organoid fragments were resuspended in matrigel (BD Biosciences)

value: organoid


title: MRTFA_15

description: Sample 8

value: Santa Cruz Biotechnology


title: DH4 organoid 38-23

value: WIBR3 with fused GFP+LGR5


title: DH5 differentiated

treatment_protocol: For differentiated organoids, WNT was withdrawn and DAPT was added to the cultures at 10µM for four days to induce differentiation

value: differentiated organoid


title: DH6 hES C-termGFP

source_name: human embryonic stem cells

value: human embryonic stem cells


title: DH7 hES 38 nofusion


title: DH2 differentiated


title: DH32 differentiated C-termDENR


title: input

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi, Higashi

department: Faculty of Medical Sciences

country: Japan

institute: Kyushu University

data_processing:
illumina HCS2.0.5
ChIP-seq reads were aligned with the mouse reference geneme (mm9) using the bowtie program (v1.12.7) with the following parameters: -m 1 -v 3.
Duplicate reads were removed using samtools  (v0.1.18).
The normalized ChIP-seq signal was calculated by　subtracting the Reads Per Million mapped reads (RPM) of the Input signal from the IPed signal.
The signals were calculated at "window-size" bp genomic intervals with "step-size" bp window (e.g., The file name preffix of "w10000s1000" in our processed data means that the window-size is 10,000 bp and the step-size is 1,000 bp. )
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated for processed data containing chromosome, regions

source_name: MethylRO ES cells

extract_protocol:
the cross-linked chromatin was sheared by sonication, and MNase treatment.
To repair ChIP-DNA and input-DNA ends, T4 DNA polymerase, Klenow enzyme and T4 polynucleotide kinase were used (New England Biolabs), and an A base was subsequently added to the 3'-end by the treatment of Klenow exo-. The adaptor ligation and the PCR amplification for 18 cycles of DNA fragments were performed with Illumina (PCR primer InPE1.0 & InPE2.0).

tag: strain

tag: cell

value: ES cells


title: DH29 differentiated N-termDENR


title: DH30 hES C-termWENR


title: DH25 background

treatment_protocol: non-organoid cells from normally discarded from the organoid cultures were collected and prepared as total RNA

value: background contamination


title: SRF_15_replicate-1

description: Sample 3

value: NIH3T3 fibroblasts

value: normal

tag: chip antibody vendor

tag: chip antibody cat. #


title: 5MeC-Seq performed on MethylRO ES cells with mouse anti-5methylcytosine antibody

value: mouse anti-5methylcytosine antibody (positive control)


title: DH15 organoid 38-12C


title: DH1 organoid 38-23


title: mRNA-seq in rich defined media

description:
mRNA
mrna-rdm-pooled_f.wig
mrna-rdm-pooled_r.wig

value: fully supplemented MOPS glucose media


title: RelA_1


title: DH18 organoid AI92-25

value: WIBR3 with AAVS1-lox-stop-loxRFP


title: DH11 teratoma AI91-24


title: DH31 hES DAPT C-termDWENR

treatment_protocol: Cell culture was carried out as described previously (Soldner et all 2009). All hESC lines were maintained on a layer inactivated mouse embryonic fibroblasts (MEFs) in hESC medium (DMEM/F12 [Invitrogen] supplemented with 15% fetal bovine serum [Hyclone], 5% KnockOutTM Serum Replacement [Invitrogen], 1mM glutamine [Invitrogen], 1% nonessential amino acids [Invitrogen], 0.1 mM β-mercaptoethanol [Sigma], penicillin/streptomycin [Gibco],  and 4 ng/ml FGF2 [R&D systems]).  Cultures were passaged every 5-7 days either manually or enzymatically with collagenase typeIV (Invitrogen; 1.5 mg/ml) and gravitational sedimentation by washing 3x in wash media (DMEM/F12 [Invitrogen] supplemented with 5% fetal bovine serum [Hyclone], and pennecillin/streptomycin [Gibco]).


title: DH28 hES DAPT N-termDWENR


title: DH13 teratoma


title: DS hybrid Low_L1

status: Public on Apr 23 2014

city: Mississippi State

last: Arick II

state: MS

address: 650 Stone Blvd.

institute: Mississippi State University

data_processing:
OLB v1.9.4 used for base-calling
Bowtie2 v2.1.0 with default parameters used for aligning short reads to Liu et al. transcriptome of hybrid catfish
Gene counts were calculated by counting the number of times a read aligned to each transcript
DESeq package (v1.12.1) for R (v3.1.0) was used to find differential expressed transcripts.
Genome_build: NCBI Genbank  JT123347 – JT494144
Supplementary_files_format_and_content: Tab-delimited text files include transcript counts for each sample.

organism: Ictalurus punctatus x Ictalurus furcatus

source_name: Liver

growth_protocol: Chronic temperature trials were conducted for 6 weeks, during which fish were exposed to daily cycling temperatures of either optimal temperatures for best food conversion and greatest growth at 27-31°C or upper-range thermal temperatures of 32-36°C. Cycling temperature regimes mimicked natural pond daily temperature fluctuations. Each day starting at 0900, water temperature was increased from baseline temperatures of 27°C or 32°C to peak temperatures of 31°C or 36°C. Peak temperatures were reached by 1730, after which temperatures were slowly decreased to 27°C and 32°C for optimal and high thermal treatments respectively.

extract_protocol:
At the end of the 6 week chronic thermal trial, liver tissue was collected from fish euthanized with tricaine methanesulfonate (MS 222) (Argent Chemical Laboratories Inc., Redmond, WA) at 500 mg/L. Six fish from each tank were randomly chosen to extract samples. Two tissue samples (~50 mg each) were excised in a sterile setting using a sterile #24 stainless steel blade and each immediately placed in a polypropylene sterile 2 ml round bottom cryogenic vial (VWR, Atlanta, GA) containing 500 uL of TRI-reagent (Zymo Research, Irvine, CA), and flash frozen in liquid nitrogen. All samples were stored at -80°C until analysis.
For RNA extraction, one vial of liver tissue from each fish was allowed to thaw and was then homogenized in TRI-reagent using a TissueLyser (Qiagen, Germantown, MD). Liver was chosen for RNA extraction because of its metabolic and physiological importance with stress response and high rates of protein turnover. The Direct-zol RNA mini prep kit (Zymo Research) was used following homogenization according to manufacturer’s recommendations. To prevent degradation, only four to six samples were run at a time and kept on ice until transfer to a zymo-spin IIC column and collection tube (Zymo research). Samples were eluted twice for more complete RNA extraction. Spectrophotometry (NanoDrop, Thermo Scientific, Wilmington, DE) was run on extracted RNA samples to determine purity and concentration. Bioanalysis was performed with a 2200 TapeStation System (Agilent, Santa Clara, CA) at the Warmwater Aquaculture Research Unit in Stoneville, Mississippi to determine RNA quality. RNA samples that had the best RNA integrity numbers (RIN, ranging 8.2-9.9) were pooled from 3 fish per tank for a total of 18 samples to reduce the effects of individual genetic variation.
RNAseq libraries were prepared with the Tru-seq RNA Sample Preparation Kit V2 Illumina (catalog #RS-122-2001) at Global Biologics (Columbia, Missouri). DNA libraries were sequenced (50 bp, single-end reads) on an Illumina HiSeq 2000 using Illumina v3 chemistry and OLB1.9.4 software for base calling by the Institute for Genomics, Biocomputing & Biotechnology at Mississippi State University. Illumina was chosen due to being relatively cost-effective and technically efficient. Reads, a DNA sequence generated from a sequencer, were mapped to the Liu et al. (2013) transcriptome using Bowtie2 version 2.1.0 default parameters, which return the best mapping result for each read. The number of reads that map to each transcript were counted and used in the DE expression. DE was calculated using the DESeq package for the R programming language, by comparing the high and low temperature treatment of each fish strain. DE genes were characterized by a p-adjusted value equal to or less than 0.05 after adjustment for multiple testing with the Benjamini-Hochberg procedure using a false discovery rate of 10%.

value: Delta Select Strain

tag: tissue

value: liver

tag: temperature treatment

tag: catfish type

value: Hybrid


title: DS hybrid High_H8

department: Institute for Genomics, Biocomputing & Biotechnology


title: DH24 background


title: MeDIP-Seq performed on MethylRO ES cells with mouse anti-RFP antibody.

value: mouse anti-RFP antibody


title: DH14 teratoma

value: teratoma

value: WIBR3 with fused LGR5+GFP


title: DH16 organoid AI91-24

value: organoid


title: DH12 organoid AI92-25


title: ribosome profiling in rich defined media

description:
ribosome protected mRNA
fp_rdm_pooled_f.wig
fp_rdm_pooled_r.wig

tag: media


title: DS hybrid Low_L4


title: DH3 hES N-termGFP

tag: cell line

value: WIBR3 with fused GFP+LGR5


title: DS hybrid Low_L7


title: WT_2

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: Spo11-associated DNA oligonucleotides

data_processing:
Base calls perfomed using HiSeq Control Software v.1.5.15.1 for samples sequenced on Illumina HiSeq 2000, and HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 15 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 1001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Maps of 5' ends of sequence reads were compiled and analyzed in R (v. 2.15.3)
Genome_build: SacCer2
The SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: wig files include RPM (reads per million mapped) for each sample at each non-zero base position in the genome

source_name: meiotic culture

growth_protocol: Synchronized meiotic cultures were prepared in 2% potassium acetate at 30°C by the SPS pre-growth method as described in Murakami et al. (2009) Methods Mol Biol 557: 117-142.

extract_protocol:
Based on Pan et al. 2011 Cell 144:719-731. Whole cell extracts were prepared by grinding frozen cells in a bead mill and resuspending powder in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to affinity purification of Spo11-protein A fusion with IgG sepharose beads. Protein was digested with proteinase K and Spo11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell 144:719-731. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add Illumina HiSeq adaptors

tag: epitope tag

value: wild type

tag: time in meiosis

value: time = 5 hr in meiosis


title: zip3_2

description: Spo11-associated DNA oligonucleotides

value: zip3 deletion


title: DH10 organoid AI91-24


title: DS hybrid High_H2


title: RRxRR Low_L9

organism: Ictalurus punctatus

value: Red River Strain

value: Channel


title: WT_1

description: Spo11-associated DNA oligonucleotides

value: time = 4 hr in meiosis


title: DS hybrid High_H6


title: DSxDS Low_L8


title: Yki S2 ChIP rep2

city: Chicago

first: Jason

last: Grundstad

state: IL

address: 900 E 57th St

department: Division of Biological Sciences

institute: University of Chicago

description: GAF embryo ChIP, replicate 2

data_processing:
The Raw images were first processed with the Casava 1.7.0.
Base-called sequences with confidence metrics were obtained using OLB-1.9.0.  All multiplexed samples were demultiplexed using Casava 1.7.0
The BWA program was used to align the sequence reads to the Drosophila melanogaster (v5.32) genome, allowing up to 2 edit distance in the seed region and 3 in the full read length. Tags that aligned to more than one  location were excluded from our analysis for both ChIP sample and the corresponding control sample (input chromatin). Only properly aligned reads with mapping quality more than 30 were kept.
Peaks were called using MACS (v2), on merged replicates, using bandwidth of 100 and a p-value cutoff of 1E-5
Genome_build: dm3
Supplementary_files_format_and_content: peak file was generated using SPP from sorted bam file, which was generated by SAM/bowtie, under 100 bp step

organism: Drosophila melanogaster

source_name: S2 cell line ChIP; Yki antibody

growth_protocol: S2 cells were grown in schneiders medium and fixed with formaldehyde for ChIP (formaldehyde added direcly to culture media).

extract_protocol: Chromatin lysates were clarified from homogenized and sonicated tissues; protein-DNA complexes were isolated with antibody.  DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  Briefly, up to 12.5 ng DNA was included in the high molecular weight (HMW) tagmentation reaction (5 minutes at 55 degrees Celsius). Tagmented DNA was purified using a Qiagen MinElute column. Addition of barcoded PCR-compatible sites and library enrichment were performed using 12 cycles of PCR. Amplified DNA was purified using the Qiagen MinElute PCR Purification Kit. Library fragments of approximately 225 bp were gel purified and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a HiSeq2000 according to the manufacturer’s protocol.

tag: developmental stage

value: S2 (embryo cell line)

tag: chip antibody

value: anti-Yki


title: Yki S2 ChIP input

description: Yki embryo ChIP, replicate 1

source_name: S2 cell line ChIP; Input

value: no antibody (input control)


title: DSxDS Low_L3

value: Delta Select Strain


title: DSxDS High_H9

value: liver


title: RRxRR Low_L2


title: RRxRR High_H7


title: RRxRR Low_L6


title: RRxRR High_H4


title: DSxDS High_H3


title: zip3_1

description: Spo11-associated DNA oligonucleotides


title: FAPs TSA1

city: Roma

first: Pier Lorenzo

last: Puri

address: Via del Fosso di Fiorano, 64

country: Italy

institute: IRCCS Fondazione Santa Lucia

data_processing:
Fastq files were analyzed with miRDEEP* using the following parameters: genome mm10, adapter TGGAATTCTCGGGTGCCAAGG, miR length 18 to 23, min phred 20, max multimap 101, min reads 5, min score -10
the expression level were calculated as the number of reads covering the mature miRNA region
Genome_build: mm10
Supplementary_files_format_and_content: the expression level contain the number of reads covering the mature miRNA region

source_name: skeletal muscle

extract_protocol:
freshly isolated cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent
small-RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1.5 month old C57Bl6 mdx mice were treated for 15 days with daily i.p. injections of Trichostatin A, TSA (0.6 mg/Kg/day; Sigma)

value: C57Bl6 mdx

tag: cell type

tag: agent

value: Trichostatin A, TSA (0.6 mg/Kg/day)


title: FAPs NT1


title: Yki S2 ChIP rep1

description: GAF embryo ChIP, replicate 1


title: FAPs TSA2


title: FAPs NT2


title: LU.10580.tg2

status: Public on Apr 22 2014

city: Stanford

first: Zhipeng

last: Lu

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

data_processing:
Raw fastq files were mapped to dm3 Drosophila genome using tophat (Trapnel et al.). The mapped files were then converted to bedgraph format using samtools, BEDTools, and wigToBigWig and bigWigToBedGraph programs by Jim Kent. FPKM values are calculated using the Cufflinks package (Trapnell et al., 2012)
Genome_build: dm3

source_name: Drosophila pharate adults

growth_protocol: Flies were grown on standard cornmeal with yeast at room temperature 24±1°C.

extract_protocol: Total RNA was extracted from pharate adults and depleted of ribosomal RNA using the Ribo_zero kit from Invitrogen.RNA was digested with Dnase. A TruSeq RNA Sample Preparation Kit v2 (Illumina) was used for barcoding for multiplexing and cDNA library preparation. Paired end (2x48) sequencing was performed on an Illumina HiSeq 2000 platform.

tag: Stage

value: adult

value: pharate


title: LU.10580/CAG


title: DSxDS High_H5


title: DSxDS Low_L5


title: IL6ra T-KO

city: New Haven

first: Dominik

last: Schenten

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale University

description: Sample 3

data_processing:
The raw reads were mapped to the Mus musculus genome from UCSC genome browser using tophat.
Only read pairs thatmapped at both ends were kept.
CuffLinks was used to calculate the FPKM for all the annotated genes and calculate the fold change between two conditions.
The FPKMs from two groups are compared using t test and the multiple testing error correction was adjusted using John Story's q value method.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values are reported.

source_name: 2W:I-A(b)+ CD4+ T cells

growth_protocol: CD4 T cells were isolated 7 days after immunization

extract_protocol:
2W:I-A(b)+ CD4+ T cells were isolated from the draining lymph nodes (inguinal and popliteal) by flow cytometry
Total RNA was isolated and polyA-containing RNA were selected for library contstruction

treatment_protocol: Mice were immunized in the footpads with 2W1S peptide emulsified with LPS in IFA

tag: time

value: day 7 post immunization

tag: genotype/variation

value: Il-6 receptor a chain -/-

value: CD4+ T cells


title: WT

description: Sample 1

tag: strain

value: wild-type


title: MyD88 T-KO

description: Sample 2


title: infected T474D 20 days rep 1

status: Public on Apr 21 2014

city: Viçosa

first: Otavio Jose

middle: Bernardes

last: Brustolini

state: MG

address: Av. PHRolfs, S/N

department: Bioquimica e Biologia Molecular

country: Brazil

institute: Universidade Federal de Viçosa

data_processing:
Illumina Casava 1.8 software used for basecalling. The reads were filtered using the average of 20 phred quality.
Then the reads were mappped using arabidopsis transcriptome (cDNA) file with the Bowtie 2.1.0 aligner. The parameters for bowtie2 --very-sensitive --no-discordant --no-mixed  -p 8 -5 10 -3 10 -1
A posterior alignment  filter was performed by samtools samtools view -f 1 -F 12 -q 20
The normalization and differential expression analysis were performed by using the R/Bioconductor edgeR package. The normalization was the TMM factor implemented in this package.
Genome_build: TAIR10
Supplementary_files_format_and_content: normalized data in csv tables

organism: Arabidopsis thaliana

growth_protocol: The seeds were surface sterilized and cold treated at 4 °C for 2 days in the dark and then exposed to white light. The seedlings were grown at 22 °C on Murashige-Skoog medium for 3 weeks and then transferred to soil. The plants were grown in a growth chamber at 22 °C under long-day conditions (16 h light/8 h dark).

extract_protocol:
The transgenic and wild-type lines were infected at the seven-leaf stage with CaLCuV. After 10 days post-inoculation (dpi) or after 21 dpi, total RNA from systemically infected leaves, as diagnosed by PCR, and mock-inoculated leaves from wild-type, 35S::NIK1-5 and 35S::T474D-4 lines was isolated using TRIzol (Invitrogen)
RNA pair-ended libraries were prepared by the Illumina HiSeq 2000 standard protocols

treatment_protocol: The Columbia (Col-0) ecotype of Arabidopsis thaliana was used as the wild-type control, and the nik1 knockout line was used for plant transformation. A. thaliana plants at the seven-leaf stage were inoculated with plasmids containing partial tandem repeats of CaLCuV DNA-A and DNA-B by biolistic delivery

tag: infection

value: infected with CaLCuV

value: 20 dpi

value: leaves


title: mock T474D 20 days rep 2

value: mock


title: infected T474D 20 days rep 2


title: infected Col0 20 days rep 1

value: WT


title: infected Col0 20 days rep 2


title: LU.10580hom


title: mock Col0 20 days rep 1


title: infected T474D 10 days rep 2

value: 10 dpi


title: mock Col0 20 days rep 2


title: LU.10580.tg1


title: infected NIK 10 days rep 2

value: NIK


title: infected NIK 10 days rep 1


title: RRxRR High_H1

value: Red River Strain

value: Channel


title: mock T474D 10 days rep 1


title: infected T474D 10 days rep 1


title: mock T474D 10 days rep 2


title: mock NIK 10 days rep 2


title: infected Col0 10 days rep 2


title: infected Col0 10 days rep 1


title: mock T474D 20 days rep 1


title: mock NIK 10 days rep 1


title: mock Col0 10 days rep 1


title: rrp6Δdcr1Δ

city: Munich

first: Mario

last: Halic

address: Feodor-Lynenstr. 25

department: Department of Biochemistry

country: Germany

institute: Gene Center, University of Munich

description:
schizosaccharomyces_pombe_972h_20080716
rrp6Ddcr1D.igv; rrp6Ddcr1D-minus.igv; rrp6Ddcr1D-plus.igv;

data_processing:
base calling
sRNA-seq reads were aligned to the pombe genome assembly using Novoalign version 2 with the standard settings
Reads mapping with two or fewer mismatches were retained.
Enrichments were calculated with our house scripts
Genome_build: schizosaccharomyces_pombe_972h_20080716
Supplementary_files_format_and_content: can be viewed with IGV browser
Supplementary_files_format_and_content: http://www.broad.mit.edu/igv

organism: Schizosaccharomyces pombe

growth_protocol: S. pombe cells were grown on rich media (YES).

extract_protocol: Gel-purified Ago1-associated RNAs were incubated with 2μM pre-adenylated 3’-adaptor oligonucleotide (miRNA Cloning Linker-1 from IDT, AppCTGTAGGCACCATCAAT/ddC/), 1 U/μL RNAsin (Promega), 1 U/μL T4 ligase (Takara) in 10 μL ligation buffer without ATP at 20°C for 2h minutes. The 3´-ligation reaction was purified on a 17% gel. For the 5’-ligation, 3´-ligated products were incubated with 2 pmol 5’ adaptor oligonucleotide (GUU CAG AGU UCU ACA GUC CGA CGA UC), 1 U/μL RNAsin (Promega), 0.06 μg/μL BSA ,1 U/μL T4 ligase (Promega) in 10μL ligation buffer at 20°C for 2 hours. The ligated reaction was gel purified and used for first strand cDNA synthesis with RT oligo (ATT GAT GGT GCC TAC AG) for 1h at 44°C in 1x first strand buffer, 10mM DTT, 0.2 mM dNTP, 1 U/μL RNAsin (Promega) and Superscript III. cDNA was amplified using PCR with Illumina P5 (AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GAC GAT C) and Illumina P7 (CAA GCA GAA GAC GGC ATA CGA ATT GAT GGT GCC TAC AG ) oligos for 10-15 cycles and gel purified.

value: rrp6-delta dcr1-delta


title: rrp6Δtri1Δ, 1

description:
schizosaccharomyces_pombe_972h_20080716
rrp6Dtri1D.igv; rrp6Dtri1D-minus.igv; rrp6Dtri1D-plus.igv;

value: rrp6-delta tri1-delta


title: mock Col0 10 days rep 2


title: rrp6Δ, 2

description:
schizosaccharomyces_pombe_972h_20080716
rrp6D.igv; rrp6D-minus.igv; rrp6D-plus.igv;


title: dcr1Δtri1Δ, 2

description:
schizosaccharomyces_pombe_972h_20080716
dcr1tri1D.igv; dcr1tri1D-minus.igv; dcr1tri1D-plus.igv;

value: dcr1-delta tri1-delta


title: rrp6Δtri1Δ, 2


title: rrp6Δ, 1


title: dcr1Δ, 2

description:
schizosaccharomyces_pombe_972h_20080716
dcr1D.igv; dcr1D-minus.igv; dcr1D-plus.igv;


title: rrp6Δtri1Δ, 3


title: dcr1Δ, 1


title: dcr1Δtri1Δ, 1


title: wild type

description:
schizosaccharomyces_pombe_972h_20080716
wild_type.igv; wild_type-minus.igv; wild_type-plus.igv;

source_name: wild type

value: wild type


title: dcr1Δ, 3


title: Rery_PR4_Acet

city: Morahalom

first: Balazs

last: Horvath

address: Vallalkozok u. 7.

department: NGSP

country: Hungary

institute: SeqOmics Biotechnology Ltd.

description: Acet

data_processing:
Basecalls performed using ABI SOLiD 5500xl.
Data were filtered using the following specifications: minimum number of nucleotides in reads = 50.
RNA reads were aligned to the NC_007486, NC_007487, NC_007491, NC_012490 genome assembly using CLC Genomics Workbench version 7 with the following configurations:
-- Use annotations for gene and transcript identification = Yes
-- References = NC_007486, NC_007487, NC_007491, NC_012490
-- Additional upstream bases = 0
-- Additional downstream bases = 0
-- Maximum number of mismatches allowed (applies to short reads) = 2
-- Unspecific match limit = 10
-- Use colorspace encoding = Yes
-- Use strand specific assembly = No
-- Organism type = PROKARYOTE
-- Minimum number of reads = 10
-- Create report = No
-- Expression level = Genes
-- Calculate RPKM for genes without transcripts = No
-- Expression value = Read Per Kilobase of exon Model value
-- Normalization method = Total
-- Counts reported as = reads per 1000000
-- Normalized data = Original expression values
Calculate expression levels using CLC Genomics Workbench version 7.0.
Genome_build: NC_007486.1, NC_007487.1, NC_007491.1, NC_012490.1
Supplementary_files_format_and_content: Excel file 'GSE56474_Datasets_Rery_1.xls' contains normalized expression data and the fold change values of 3 samples: R. erythropolis PR4 grown on acetate, n-hexadecane or diesel oil.
Supplementary_files_format_and_content: In the Excel file 'GSE56474_Full_Datasets_Rery.xls', the data was supplemented with a preliminary experiment marked as Hex2, where the sampling point was at the end of the exponential phase.

organism: Rhodococcus erythropolis PR4

source_name: bacterial cell, acetate

growth_protocol: Rhodococcus erythropolis PR4 cells were inoculated into 5L minimal medium (1L medium consist of 50mL 'A' solution: 4.35 g/L KH2PO4, 29.2 g/L K2HPO4, 50mL 'B' solution: 11.7g/L NaCl, 2.5g/L MgSO4 x 7 H2O, 0.88g/L CaCl2 x 2 H2O, 2mL 'D' solution: 0.1g/L ZnSO4 x 7 H2O, 0.03g/L MnCl2 x 4 H2O, 0.3g/L H3BO3, 0.2g/L CoCl2 x 6 H2O, 0.01g/L CuCl2 x 2 H2O, 0.02g/L NiCl2 x 6 H2O, 0.023g/L NaMoO4 x 4 H2O, 1mL 'E' solution: 14g FeSO4, 9.3g EDTA x 2 H2O, 10mL 'F' solution: 120g/L NH4NO3) in a Biostat C Fermenter (B. Braun Biotech International GmbH, Melsungen, Germany) in 4% (V/V). The medium was supplemented with 30 g/L sodium acetate, or 1% (V/V) n-hexadecane, or diesel oil as carbon and energy source. All media was also supplemented with 0.5g/L amino acid mix (26.3 mg/L of each amino acids except glycine) to accelerate cell growth in the early phase of the fermentation. Temperature was kept at 25°C, pH was set to 7.5 and maintained with the addition of 1M NaOH and HCL. Pure oxygen 4.5 (Linde Gas Hungary Co. Cltd., Budapest) was used for the aeration at a gas flow of 100mL/min. Oxygen saturation was kept at 20% and stirring was set to 200-360 rpm. Initial stir velocity was set to 100 rpm in the case of cultures grown on sodium acetate. Samples for RNA extraction were taken in the late exponential phase (after 21 hours in the case of cultures grown on n-hexadecane and diesel oil and 31 hours in the case of cultures grown on acetate).

extract_protocol:
Total RNA was isolated with Qiagen RNeasy Mini Kit, followed by DNase I treatment using Invitrogen DNase I. RNA quality and quantity measurements were performed on Bioanalyzer (Agilent Technologies).
Libraries were processed according to the SOLiD transcriptome sequencing protocol (Publication Part Number 4452437). Briefly, total RNA was DNase I treated and rRNA-depleted using RiboMinus Plant Kit. After the fragmentation of RNA, the 50-200nt fraction was cleaned and was the subject of adaptor hybridization and reverse transcription. The cDNA library was cleaned with Qiagen MinElute PCR purification Kit and size-selected on a 6% TBE-Urea denaturing polyacrylamide gel. The 150-250nt cDNA fraction was amplified to generate sufficient template for SOLiD sequencing. To determine the accurate concentration of each library, a SOLiD Library TaqMan Quantitation Kit was used according to the manufacturer's instructions. After, each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR (ePCR). ePCR beads were enriched for template-positive beads by hybridization with capture beads. Template-enriched beads were extended at the 3' end in the presence of terminal transferase and 3' bead linker. Approximately 60 million beads per sample with clonally amplified DNA were deposited onto one lane of the 5500 SOLiD sequencing flowchip. The flowchip was then loaded onto a SOLiD 5500xl Instrument and the 50-base sequences were obtained according to manufacturer's protocol.

tag: strain/background

tag: growth condition

value: sodium acetate

tag: sample type

value: control


title: Rery_PR4_Hex1

source_name: bacterial cell, hexadecane

value: n-hexadecane

value: test


title: Rery_PR4_Diesel

description: Diesel

source_name: bacterial cell, diesel

value: diesel oil


title: HEK293_DMSO

city: Shanghai

first: Min

address: 50 Chifeng Rd., Yangpu District

department: Life Sciences and Technology

institute: Tongji University

description: Sample 3

data_processing:
Basecalls performed using Illumina Casava1.7 at BGI-Shenzhen (sequencing service provider).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by BGI-Shenzhen (sequencing service provider).
RNA-seq reads for each sample were aligned to hg19 whole genome and the human refseq genes using SOAPaligner version 2.21 with parameters –r 0 –p 4 or –r 2 –p 4, respectively.
Gene expression levels were quantified by RPKM, and then differentially expressed genes were defined by expression changes between two samples and their statistical significance q-value calculated with NOISeq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

growth_protocol: The human embryonic kidney 293 cells (HEK 293) were cultured at 37 ℃ in 5% CO2 as adherent monolayer in Dulbecco modified Eagle medim(DMEM) (Hiclone) supplemented with L-glutamine and 10% fetal bovine serum (FBS) (Hiclone).

extract_protocol:
Total RNA was extracted from each sample using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at BGI-Shenzhen (sequencing service provider).

treatment_protocol: BDE209 powder was dissolved in the dimethyl sulfoxide (DMSO) and added to culture medium. The final concentration of BDE209 and DMSO is 1E-06 M and 1E-03 M, respectively. For BDE209 treatment, cells were treated with 1E-06 M BDE209 for 48h. For DMSO treatment, cells were cultured in 1E-03 M DMSO medium for 48h. Meanwhile, cells cultured in both BDE209 and DMSO-free medium were used as the negative control.

tag: treatment

value: DMSO medium

value: HEK 293


title: PROB_H3K4ME3_TRI

status: Public on Apr 20 2014

city: Boston

first: David

last: Weinstock

address: 450 Brookline Ave

institute: DFCI

description: Chromatin IP against H3K4me3 in Ts1Rhr B cell progenitors

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m1 -n 2 --best. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences processed through MACS 1.4.2 and fragment pileup was outputted in .wig format

source_name: pro-B cell

growth_protocol: bone marrow harvested and placed in B cell methylcellulose medium to generate proB cell colonies

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: proB cell colonies were harvested at 1 week

tag: genotype

value: pro-B cell

tag: antibody catalog number

value: Abcam #ab8580


title: HEK293_Control

description: Sample 2

source_name: human embryonic kidney 293 cells (HEK 293)

value: control (normal; BDE209 in DMSO-free medium)

tag: cell line


title: PROB_H3K27AC_WT

description: Chromatin IP against H3K27ac in WT B cell progenitors

value: Abcam #ab4729


title: HEK293_BDE209

description: Sample 1

value: BDE209 in DMSO medium


title: PROB_H3K27AC_TRI

description: Chromatin IP against H3K27ac in Ts1Rhr B cell progenitors


title: Nanog-sg2-10ug-IP

first: Xuebing

last: Wu

address: 630 West 168th Street

department: Medicine/Systems Biology

institute: Columbia University

description: V6.5 cells expressing a stably integrated dCas9 gene

data_processing:
Reads were de-multiplexed and mapped to mouse genome mm9 or human genome hg19 using bowtie, requiring unique mapping with at most two mismatches (-n 2 -m 1 --best --strata). Mapped reads were collapsed and the same number of reads  were randomly sampled from each library to match sequencing depth. Peaks were called using MACS with default settings. For each sample, the other samples are each used as a control and only peaks called over all controls are defined as target sites.
Genome_build: mm9
Supplementary_files_format_and_content: MACS bed output. Columns are : chrom, start, end, peak_ID, peak_enrichment

source_name: embryonic stem cells

growth_protocol: standard ES cell culture conditions

extract_protocol:
Phenol choroform extraction
Aglient ChIP

treatment_protocol: Lipofectimine 2000 protocol for transfection

value: embryonic stem cells

value: V6.5 + dCas9

value: transfected with 10 ug sgRNA Nanog-sg2

value: anti-HA


title: SC 2.2 serum

city: Freiburg

first: Dominic

last: Grün

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10  and contained 31,109 isoforms derived from 23,480 gene loci. The right mate of each read pair was mapped to the ensemble of all RefSeq transcripts and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were distributed uniformly. For each cell barcode we counted the number of unique molecular identifiers (UMIs) for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics  we converted the number of observed UMIs into transcript counts. We finally discarded all genes that were not expressed with at least a single transcript in at least two cells and two control samples. Samples with less than 10 sequenced Oct4 transcripts were discarded, because sequencing efficiency was low or the cells are potentially undergoing differentiation.
Genome_build: mm10
Supplementary_files_format_and_content: data_transcript_counts.txt: Tab separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the nature of the sample (RNA: pool-and-split control, SC: single cell), condition (serum or 2i) and sample number, separated by an underscore. The first column lists the official gene symbol.

source_name: CEL-seq single cell RNA library 2_lane 2_in serum condition

growth_protocol: Serum medium consists of DMEM (Gibco) supplemented with 15% FCS (Gibco), 2mM GlutaMax (Gibco), 0.1 mM MEM nonessential amino acids, 0.1 mM β-mercaptoethanol (Sigma), 1% Pen/Strep (Gibco) and 1000u LIF/ml (ESGRO). J1 embryonic stem cells cultured in serum medium were maintained on a monolayer of MEFs. 2i medium consists of 50% DMEM/F12 and 50% N2B27 supplemented with 2mM GlutaMax (Gibco), 0.1 mM MEM nonessential amino acids, 0.1 mM β-mercaptoethanol (Sigma), 1% Pen/Strep (Gibco), 1000u LIF/ml (ESGRO) 1 μM PD0325901 (Stemgent) and 3 μM CHIR99021 (Stemgent). J1 embryonic stem cells cultured in 2i medium were maintained on culture dishes coated with gelatin. J1 cells cultured in serum medium were passaged every 2-3 days by dissociation with trypsin (Gibco). J1 cells cultured in 2i medium were passaged every 2-3 days by dissociation with Accutase (Gibco).

extract_protocol:
Cells were dissociated into a single cell suspension and picked under a stereomicroscope using a 30μm glass capillary and mouth pipette. Picked cells were deposited in the lid of an 0.5ml LoBind eppendorf tube and snap frozen in liquid nitrogen. For the pool and split controls, approximately 1 million cells were lysed, the amount of RNA was quantified on a bioanalyzer (Agilent) using the Eukaryote Total RNA pico kit. 20pg aliquots of total RNA were used for each pool and split control.
Single cells were processed using the previously described CEL-seq technique, with a few alterations. A 4bp random barcode as unique molecular identifier (UMI) was added to the primer in between the cell specific barcode and the poly T stretch. Instead of the 70° C lysis step, cells were lysed by adding 0.05% IGEPAL CA 630 (sigma) to the first strand synthesis mix. Libraries were sequenced on an Illumina HighSeq 2500 using 50bp paired end sequencing.

value: mouse embryonic stem cells

tag: culture condition

value: serum condition


title: Nanog-sg2-40ug-IP

value: transfected with 40 ug sgRNA Nanog-sg2


title: PROB_H3K4ME3_WT

description: Chromatin IP against H3K4me3 in WT B cell progenitors

value: wild type


title: SC 1.2 serum

source_name: CEL-seq single cell RNA library 1_lane 2_in serum condition


title: Nanog-sg3-0.02ug-IP

value: transfected with 0.02 ug sgRNA Nanog-sg3


title: SC 1.1 serum

source_name: CEL-seq single cell RNA library 1_lane 1_in serum condition


title: RNA 2.2 serum

source_name: CEL-seq control RNA library 2_lane 2_in serum condition


title: RNA 2.1 serum

source_name: CEL-seq control RNA library 2_lane 1_in serum condition


title: Nanog-sg3-2ug-IP

value: transfected with 2 ug sgRNA Nanog-sg3


title: Nanog-sg3-20ug-IP

value: transfected with 20 ug sgRNA Nanog-sg3


title: tri1Δ

description:
schizosaccharomyces_pombe_972h_20080716
tri1D.igv; tri1D-minus.igv; tri1D-plus.igv;


title: RNA 1.1 serum

source_name: CEL-seq control RNA library 1_lane 1_in serum condition


title: SC 2.2 2i

source_name: CEL-seq single cell RNA library 2_lane 2_in 2i condition

value: 2i condition


title: Phc1-sg1-Input

data_processing:
Reads were de-multiplexed and mapped to mouse genome mm9 using bowtie, requiring unique mapping with at most two mismatches (-n 2 -m 1 --best --strata). Mapped reads were collapsed and the same number of reads (about 9 million) were randomly sampled from each library to match sequencing depth. Peaks were called using MACS with default settings. For each sample, the other samples are each used as a control and only peaks called over all controls are defined as target sites.
Genome_build: mm9
Supplementary_files_format_and_content: MACS bed output. Columns are : chrom, start, end, peak_ID, peak_enrichment

source_name: Input

value: transfected with 20 ug sgRNA Phc1-sg1


title: Rery_PR4_Hex2

value: n-hexadecane

value: test


title: RNA 1.2 serum

source_name: CEL-seq control RNA library 1_lane 2_in serum condition


title: SC 1.2 2i

source_name: CEL-seq single cell RNA library 1_lane 2_in 2i condition


title: No-sgRNA-IP

source_name: No-sgRNA-IP


title: Nanog-sg3-transient-IP

description: wildtype v6.5 cells

value: transfected with 20 ug sgRNA Nanog-sg3 and 20 ug dCas9


title: Nanog-sg2-IP

value: transfected with 20 ug sgRNA Nanog-sg2


title: Phc1-sg2-IP

value: embryonic stem cells

value: transfected with 20 ug sgRNA Phc1-sg2


title: Nanog-sg3-IP

value: V6.5 + dCas9


title: RNA 2.2 2i

source_name: CEL-seq control RNA library 2_lane 2_in 2i condition


title: SC 2.1 serum

source_name: CEL-seq single cell RNA library 2_lane 1_in serum condition


title: SC 2.1 2i

source_name: CEL-seq single cell RNA library 2_lane 1_in 2i condition


title: Phc1-sg1-IP

value: anti-HA


title: SC 1.1 2i

source_name: CEL-seq single cell RNA library 1_lane 1_in 2i condition

value: mouse embryonic stem cells


title: RNA 1.1 2i

source_name: CEL-seq control RNA library 1_lane 1_in 2i condition


title: RNA 2.1 2i

source_name: CEL-seq control RNA library 2_lane 1_in 2i condition


title: Nanog-sg3-0.2ug-IP

source_name: embryonic stem cells

value: transfected with 0.2 ug sgRNA Nanog-sg3


title: Nanog-sg3-transient-Input

description: wildtype v6.5 cells


title: RNA 1.2 2i

source_name: CEL-seq control RNA library 1_lane 2_in 2i condition


title: EMX1-no-sgRNA-Input

description: cells purchased from Life Technology

data_processing:
Reads were de-multiplexed and mapped to mouse genome mm9 or human genome hg19 using bowtie, requiring unique mapping with at most two mismatches (-n 2 -m 1 --best --strata). Mapped reads were collapsed and the same number of reads  were randomly sampled from each library to match sequencing depth. Peaks were called using MACS with default settings. For each sample, the other samples are each used as a control and only peaks called over all controls are defined as target sites.
Genome_build: hg19
Supplementary_files_format_and_content: MACS bed output. Columns are : chrom, start, end, peak_ID, peak_enrichment

source_name: embryonal kidney cells

value: embryonal kidney cells


title: EMX1-no-sgRNA-IP

description: cells purchased from Life Technology


title: wild-type passage 1 R1

description: proB cells

data_processing:
The raw sequence data were subjected to data quality control checks based on per base sequence quality scores, per sequence quality scores, per sequence GC content, sequence length distribution, and overrepresented sequences, which are implemented in the FastQC tool: (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The RNA sequence reads that passed quality control filters were  aligned against the mouse reference genome (build mm9) by using the  ultra high-throughput long read aligner Bowtie2 (Langmead and Salzberg, 2012) available through TopHat 2.0.7 (http://tophat.cbcb.umd.edu) (Trapnell et al., 2012).
The mapping results were further analyzed with TopHat to identify splice junctions between exons. Genomic annotations in gene transfer format (GTF) were obtained from Ensembl mouse genome GRCm38: (http://useast.ensembl.org/Mus_musculus/Info/Index). Tophat command line-  tophat --output-dir <output_dir> --GTF <gtf_file> --no  -novel-juncs --transcriptome-only -p 2 -r 161 --mate-std-dev 35 <index_base> <read1(fastq)> <read2(fastq)>
Gene-level expression measurements for 23,021 Ensembl mouse genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples.
Cufflinks command line-cufflinks --GTF <gtf_file> -q -p 3 -u -b <genome.fa> -o <output directory> <bam_file_from_tophat>
Genome_build: mm9
Supplementary_files_format_and_content: ensembl transcripts fpkm

source_name: pro B cell colonies

extract_protocol:
For total RNA, 10e6 cells were harvested in Trizol according to the manufacturers instructions.
Quality control of total RNA was first performed using the RNA Qubit Assay (Invitrogen) and the Bioanalyzer RNA Nano 6000 Chip Kit (Agilent).  Samples containing at least 100ng of total RNA and a Bioanalyzer RNA Integrity Number of >7.0 passed quality control and proceeded into library construction. Library construction was performed using Illumina's TruSeq RNA Library Prep Kit according to the manufacturer's protocol, with 100ng of total RNA as input for each sample.  Final library quality control was performed using the DNA High Sensitivity Qubit Kit (Invitrogen), the Bioanalyzer High Sensitivity Chip Kit (Agilent) and the 7900HT Fast qPCR machine (Applied Biosystems). qPCR was performed  using the Illumina Universal Library Quantification Kit from KAPA Biosystems.  RNASeq libraries were then normalized to 2nM, pooled for multiplexing in equal volumes, and sequenced at 10pM on the Illumina HiSeq 2000.

tag: b cell stage

value: proB


title: Ts1Rhr passage 1 R1

description: proB cells


title: Ts1Rhr passage 1 R3

description: proB cells


title: EMX1.3-transient-IP

description: cells purchased from Life Technology

value: transfected with 20 ug sgRNA EMX1-sg3

tag: chip antibody


title: wild-type passage 1 R2

description: proB cells


title: Ts1Rhr passage 1 R2

description: proB cells


title: wild-type passage 1 R3

description: proB cells


title: EMX1.1-transient-IP

description: cells purchased from Life Technology

tag: cell type

value: transfected with 20 ug sgRNA EMX1-sg1


title: PROB_WCE_TRI

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences processed through MACS 1.4.2 and fragment pileup was outputted in .wig format

source_name: pro-B cell

value: pro-B cell

value: None WCE


title: PROB_WCE_WT

value: wild-type


title: PROB_H3K27ME3_TRI

value: Cell Signaling Technologies #9773


title: PROB_H3K27ME3_WT


title: HCT-116 shControl rep3

city: Madrid

first: Maria

middle: S

last: Soengas

address: Melchor Fernandez Almagro, 3

department: Molecular Pathology

country: Spain

institute: Spanish National Cancer Research Institute

description: Isolation of poly A+ RNA from total RNA

data_processing:
Read files were quality-checked with FastQC.
40-nt single-end reads were aligned against the human genome (GRCh37/hg19) with TopHat-2.0.4 (using Bowtie 0.12.7 and Samtools 0.1.16), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 1.3.0
Transcripts annotations used here were Homo_sapiens.GRCh37.65 from Ensembl
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tables were generated with Cufflinks 1.3.0 and contain transcripts abundance measured in FPKM values

source_name: Colon cancer cell line

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (Life Technologies, Rockville, MD, USA) supplemented with 10% fetal bovine serum (Nova-Tech Inc., Grand Island, NY, USA)

extract_protocol:
RNA was extracted from cell pellets using QIAshredder (Cat No. 79654) and Rneasy Mini Kit (Cat No. 74104) including DNase treatment step.
2 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 8.6 to 10 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ RNA fraction was extracted and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation v2 Protocol" (Part # 15026494 Rev. C). Adapter-ligated library was completed by 8 cycles of PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

treatment_protocol: Lentivirus-driven gene silencing of RAB7 was performed using the validated shRNA targeting the sequence GATTGACCTCGAAA, purchased from Sigma (St Louis, MO, USA). Parallel infections with the pLKO vector coding for scrambled shRNA (Sigma) served as controls. The lentiviral infections of the 3 different tumor cell lines were performed in parallel.

tag: time point

value: post infection day 3

value: shRNA scramble (pLKO backbone, sigma)


title: HCT-116 shRAB7 rep2

description: Isolation of poly A+ RNA from total RNA

value: shRNA RAB7 (pLKO backbone, sigma, GATTGACCTCGAAA)


title: UACC-62 shRAB7 rep1

description: Isolation of poly A+ RNA from total RNA

source_name: Melanoma cell line


title: UACC-62 shRAB7 rep2

description: Isolation of poly A+ RNA from total RNA


title: UACC-62 shControl rep3

description: Isolation of poly A+ RNA from total RNA


title: HCT-116 shRAB7 rep3

description: Isolation of poly A+ RNA from total RNA


title: HCT-116 shRAB7 rep1

description: Isolation of poly A+ RNA from total RNA


title: HCT-116 shControl rep2

description: Isolation of poly A+ RNA from total RNA


title: UACC-62 shControl rep2

description: Isolation of poly A+ RNA from total RNA


title: UACC-62 shControl rep1

description: Isolation of poly A+ RNA from total RNA


title: UACC-62 shRAB7 rep3

description: Isolation of poly A+ RNA from total RNA


title: SK-Mel-28 shRAB7 rep2

description: Isolation of poly A+ RNA from total RNA


title: SK-Mel-28 shRAB7 rep3

description: Isolation of poly A+ RNA from total RNA


title: SK-Mel-28 shRAB7 rep1

description: Isolation of poly A+ RNA from total RNA


title: SK-Mel-28 shControl rep3

description: Isolation of poly A+ RNA from total RNA


title: SK-Mel-28 shControl rep2

description: Isolation of poly A+ RNA from total RNA


title: SK-Mel-28 shControl rep1

description: Isolation of poly A+ RNA from total RNA


title: mouse_e11.5_forebrain_H3K4me1

status: Public on Apr 19 2014

first: Matthew

middle: James

last: Blow

address: 1 Cyclotron Road

department: Genomics Division

institute: Lawrence Berkeley National Laboratory

description: Tissue pooled from ~150 embryos Chromatin IP against H3K4me1

data_processing:
Bam: Sequence reads were mapped to the mouse (mm9) genome using bwa with default parameters. Reads mapping to multiple sites in the genome with an equivalent score, and duplicate reads with identical start sites were discarded.
Wig: Unique BWA-aligned read coordinates were extended to 300bp in the direction of the alignment. Coverage depth was calculated from extended reads at 25bp intervals throughout the genome.
peaks: Peak detection in FLAG ChIP samples was performed using MACS1.4 with the appropriate matched control sample where present. Parameters were: macs14 -t chip.bam –control=input.bam –name=chip_output  –format=BAM –gsize=mm –tsize=36 –bw=300 –mfold=10,30 –nolambda –nomodel –shiftsize=150 -p 0.00001. Peaks overlapping repeats, or duplicated regions of the genome were removed as likely mapping artifacts.
Genome_build: mm9
Supplementary_files_format_and_content: bed and wig

source_name: Mouse embryonic day 11.5 (e11.5) forebrain

extract_protocol: Embryonic heart and hindbrain was isolated from CD1 mouse embryos at e11.5  .Tissue samples were cross linked and cells were dissociated and subject to chromatin isolation, sonication and immunoprecipitation.  ChIP DNA was sheared by sonication, end-repaired, ligated to illumina sequencing adapters.   ChIP and input DNA between 300 and 500bp was sequenced on the  Illumina HiSeq 2000 to generate 50 or 36bp reads.

tag: developmental stage

tag: tissue

value: forebrain

tag: Sex

value: pooled male and female


title: mouse_e11.5_forebrain_inputforH3K4me1H3K4me3H3K27mme3

description: Tissue pooled from ~150 embryos sonicated input DNA

value: input

tag: strain


title: mouse_e11.5_forebrain_H3K27me3

description: Tissue pooled from ~150 embryos Chromatin IP against H3K27me3


title: mouse_e11.5_limb_H3K27ac

description: Tissue pooled from ~150 embryos Chromatin IP against H3K27ac

source_name: Mouse embryonic day 11.5 (e11.5) limb

value: limb


title: mouse_e11.5_forebrain_H3K4me3

description: Tissue pooled from ~150 embryos Chromatin IP against H3K4me3


title: mouse_e11.5_limb_H3K27me3


title: HCT-116 shControl rep1

description: Isolation of poly A+ RNA from total RNA


title: mouse_e11.5_limb_H3K4me3


title: mouse_e11.5_limb_inputforH3K27ac


title: mouse_e11.5_limb_inputforH3K4me1H3K4me3H3K27mme3


title: Sample 6

status: Public on Apr 18 2014

city: London

first: Michael

last: Lovett

state: London

address: Dovehouse St

department: NHLI

institute: Imperial College

data_processing:
Sequences were mapped to gga3 using Tophat v1.4.0 with default settings
Alignment files (.bam) were inputed to Partek Genomics Suite v6.6 to calculate RPKM
Genome_build: gga3
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values of individual samples

organism: Gallus gallus

source_name: Basal papilla

extract_protocol:
Chicken cochleae were dissected from E6.5 embryos.  Cochlea were divided into three approximately equal sized pieces to produce proximal, middle, and distal pieces.  Pieces from each region were pooled together and immediately transferred into three 1.5 mL eppendorf tubes containining 0.5 mL Tri Reagent RT (Molecular Research Center, Inc.).  Samples were then stored at -20C until further processing.  Samples from each section of the cochlea were then processed using Illumina mRNA-seq or TrueSeq preparation kits.  Separate biological replicates were also prepared and similarly analyzed.  mRNA was selected by oligo-dT magnetic beads and fragmented.  First-strand cDNA was then generated using random primers.  Second-strand synthesis, end repair and addition of a single A base and adaptor ligation were then performed.  Each RNA-seq library was DNA-sequenced the Illumina HiSeq 2000.
libraries were made using Illumina mRNA-seq or TrueSeq preparation kits.

value: cochlea

tag: cochlear region

tag: age

value: embryonic day 6.5


title: Sample 4

value: Proximal-BP