title: sample34_IR

city: Heidelberg

first: Thorsten

last: Zenz

address: Im Neuenheimer Feld 460

department: Department of Translational Oncology

institute: German Cancer Research Center (DKFZ)

description:
MatureMiRNA_readcounts_DESeq2_normalized.xlsx
ncRNA.excludingMatureMiRNA_readcounts_DESeq2_normalized.xlsx
mRNA_readcounts_DESeq2_normalized.xlsx

data_processing:
Basecalling was performed with Illumina RTA 1.13.48, CASAVA 1.8.2.
Sequencing reads were trimmed for adaptor sequences with cutadapt v1.2.1.
Sequencing reads were quality artifact filtered with FastX.
Reads of 17-25 nt length were selected for mature miRNA analyses.
Reads ≥15 nt were selected for non-coding RNA and mRNA analyses (excluding mature miRNA).
Reads were aligned using Bowtie with the following configurations: -v -a --best --strata --norc.
Reads were normalized by standardizing read counts by a sample-specific size factor using DESeq2 1.0.19 in R 3.0.1.
Genome_build: For mature miRNA analyses, reads were aligned to miRBase v19 hsa sequences.
Genome_build: For non-coding RNA (excluding mature miRNA sequences) and mRNA analyses, hsa sequences of Ensembl 71, GtRNAdb, Rfam 11.0, piRNA cluster database were used as reference.
Supplementary_files_format_and_content: Excel files containing normalized read counts.

source_name: Primary CLL MNCs

growth_protocol: CLL cells were cultured for 24h in RPMI supplemented with 10% human serum.

extract_protocol:
Total RNA was isolated using Trizol reagent.
Small RNA libraries were constructed using the NEBNext Small RNA Library Prep Set for Illumina following the manufacturer's instructions. Nucleic acids of approximately 15-35 nt length were gel purified during library preparation.

treatment_protocol: CLL cells were irradiated with 5 Gy (IR) or left untreated (NT) and harvested after 24h.

value: irradiation

value: Primary CLL MNCs

tag: tp53 status

tag: del11q and/or atmmut

value: no

tag: patient treatment status

value: previously treated


title: sample34_NT

status: Public on May 01 2015

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment

tag: cell type


title: sample33_IR


title: sample32_IR

value: untreated


title: sample33_NT


title: sample31_IR


title: sample31_NT


title: sample30_NT


title: sample29_NT


title: sample32_NT


title: sample28_IR


title: sample27_IR


title: sample30_IR


title: BLS279 replicate 3

city: Ithaca

first: Adam

last: Bogdanove

state: NY

address: 334 Plant Science Building

department: Plant Pathology and Plant-Microbe Biology

country: USA

institute: Cornell University

data_processing:
Adapters were trimmed using the Trimmomatic v0.22 ILLUMINACLIP function (Bolger et al., 2014) for single end reads with seedMismatches=2, palindromeClipThreshold=30, and simpleClipThreshold=7
Low quality bases at the ends of reads were trimmed using BRAT trim v2.0.1 (Harris et al., 2010) with the parameters "-q 20 -L 33"
Reads were aligned using Tophat v2.06  with command line options '--num-threads 8 --max-intron-length 10000' and with the -G option specifying that the the MSU Release 7.0 annotation downloaded from the Rice Genome Annotation Project be used to guide transcript assembly
The number of reads aligned to each gene was determined using HTSeq-count (Anders et al., 2014) from the HTSeq framework version 0.5.4p3 with the command line options ‘-i ID -t gene -s no’
Genome_build: The Oryza sativa L. ssp. japonica (cv. Nipponbare) reference genome v.7.0 was downloaded from Phytozyme 10
Supplementary_files_format_and_content: the processed files are text tab-delimited files output by HTSeq-count with locus IDs in the first column and the number of reads aligned to each locus in the second column. The last five lines in each file don't include reads aligned to specific loci, but the number of reads in the following categories: those aligned to no annotated feature (no_feature), those that cannot be unambiguously assigend to a single feature (ambiguous), reads with an alignment quality lower than ten (too_low_aQual), reads that are not aligned (not_aligned), and reads that are aligned to multiple locations (alignment_not_unique)

organism: Oryza sativa Japonica Group

source_name: 48 hrs after inoculation with BLS279

growth_protocol: Oryza sativa L. ssp. japonica cv. Nipponbare plants to be inoculated were grown in LC-1 soil mixture (Sungro, Bellevue, WA) in PGC15 growth chambers (Percival Scientific, Perry, IA) in trays approximately 60 cm below a combination of fluorescent and incandescent bulbs providing approximately 1,000 μmoles/m2/s measured at 15 cm, under a cycle of 12 h of light at 28 °C and 12 h of dark at 25 °C.

extract_protocol:
RNA was extracted using a modified hot Trizol protocol (Huang et al., 2005) followed by treatment with RNase-free DNase I (Life Technologies, Carlsbad, CA), then purified using the RNeasy MinElute Cleanup kit (Qiagen, Valencia, CA).
These libraries were prepped with the Illumina TruSeq RNA Sample Prep v2 kit

treatment_protocol: Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaf. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.

tag: cultivar

value: cv. Nipponbare

tag: x. oryzae pv.oryzicola strain

tag: tissue

value: leaf


title: sample29_IR


title: sample28_NT


title: sample26_IR


title: sample25_IR


title: I_Hi_siCtrl_-

city: Toronto

first: Rod

last: Bremner

state: ON

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

country: Canada

institute: Mount Sinai Hospital

data_processing:
The fast files were obtained using Illumina CASAVA v1.8
The quality of fast reads was examined by FASTQC and low quality 5' nucleotides were removed before mapping
The trimmed fast reads were mapped on human genome (hg19) using Tophat 1.4.1
The read counts were calculated using custom R scripts to obtain exon union reads
The counts were normalized by using R package DESeq before differential expression analysis by using R package NOISeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include counts as gene expression of all the samples in this study, with rows named by Ensemble gene identifier and columns named as sample names.

source_name: Cell lines

extract_protocol:
RNA extraction was done using Trizol according to the manufacturer
For RNAseq library construction, Oligo-dT beads were first used to isolate poly(A)+ mRNA, after randomly fragmented, RNA fragments around 300bp were selected to prepare multiplexed cDNA libraries using Illumina TruSeq RNA Sample Preparation Kit.

value: Cervical cancer cells

tag: cell line

value: HeLa

value: control siRNA without IFNg treatment


title: sample27_NT


title: sample25_NT


title: sample24_IR

value: yes


title: sample23_NT


title: sample24_NT


title: sample22_IR


title: sample22_NT


title: CFBP2286 replicate 1

source_name: 48 hrs after inoculation with CFBP2286


title: sample21_NT


title: sample21_IR


title: sample20_IR


title: sample19_IR


title: sample20_NT


title: sample19_NT


title: sample18_NT


title: sample18_IR


title: sample17_NT


title: sample26_NT


title: sample15_IR


title: sample16_NT


title: sample17_IR


title: sample14_NT


title: sample13_II_NT

description:
technical replicate of sample 25; the average was used for further analyses
MatureMiRNA_readcounts_DESeq2_normalized.xlsx
ncRNA.excludingMatureMiRNA_readcounts_DESeq2_normalized.xlsx
mRNA_readcounts_DESeq2_normalized.xlsx


title: sample13_NT


title: sample13_II_IR

description:
technical replicate of sample 26, the average was used for further analyses
MatureMiRNA_readcounts_DESeq2_normalized.xlsx
ncRNA.excludingMatureMiRNA_readcounts_DESeq2_normalized.xlsx
mRNA_readcounts_DESeq2_normalized.xlsx


title: sample15_NT


title: sample14_IR


title: sample12_IR


title: sample16_IR


title: sample13_IR


title: sample12_NT


title: sample23_IR


title: sample11_IR


title: sample10_NT


title: sample10_IR


title: sample9_IR


title: sample9_NT


title: sample8_IR


title: sample7_IR


title: sample8_NT


title: sample7_NT


title: sample6_IR


title: sample6_NT


title: sample5_IR


title: sample4_IR


title: sample5_NT


title: sample3_IR


title: sample3_NT


title: sample1_IR


title: sample4_NT


title: sample2_NT


title: sample_IR


title: sample11_NT


title: sample1_NT


title: TS121

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

country: Italy

institute: National Research Council

data_processing:
Reads mapping was performed using TopHat v.2.0.7
PCR duplicates were removed using Picard tools v1.117
SNP calling was carried out using GATK v3.3 workflow optimized from RNA-Seq data; Nucleotide variants were annotated using ANNOVAR and COSMIC database was used to label variants as "somatic in cancer".
For gene expression analysis we used reads count per gene obtained with HTSeq. RPKM (Reads per kilobase transcript per million reads) normalization was used.
Fusion transcripts analysis was erformed using TopHat Fusion and Chimerascan v0.4.5
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression data are provided in tab-delimited file as normalized RPKM.

source_name: Thyroid

extract_protocol:
Total RNA was extracted from tumor biopsies using Trizol standard procedure according to manufacturer's protocol. RNA integrity was assessed using digital gel electrophoresis (Experion) and spectrophotometry.
Paired-end libraries (75 and 100x2 bp) were prepared using TruSeq RNA Sample Preparation Kit (Illumina) and sequenced on Illumina HiSeq2000 NGS platform at high coverage according to manufacturer's instructions

tag: sample type

value: Tumor sample

value: thyroid

tag: diagnosis

value: papillary thyroid carcinoma


title: TS126


title: NS129

value: Control sample

value: healthy


title: TS127


title: TS128


title: TS117


title: TS125


title: NS130


title: TS122


title: TS123


title: NS119


title: TS116


title: NS118


title: TS115


title: TS120


title: TS114


title: TS131


title: TS124


title: TS113


title: TS110


title: TS111


title: Sample12113

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Samples were run on 2 lanes of a HiSeq 2000 (Illumina) generating 8,612,682 to 16,469,501 single-ended 50 bp reads per sample.
These reads were aligned to the human genome (Ensembl GRCh37.74, GenBank Assembly ID GCA_000001405.14) using TopHat version 2.0.10, Bowtie 2 version 2.1.0 and Samtools version 0.1.18.
Reads were mapped to known genes using HTseq. Gene expression was analyzed using DESeq2 version 1.2.10.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for each Sample.

source_name: Adipose, acromegaly

extract_protocol:
During the course of pituitary surgery, a routine subcutaneous fat graft is utilized to seal the surgical field upon completion of the procedure. 500 mg of this fat graft was used for the study. ~100 mg were utilized for ex-vivo lipolysis assay, and ~200 mg was snap frozen in liquid nitrogen and stored at -80 degrees for RNA preparation. 25 mg pieces of adipose tissue were pre-incubated for 15 minutes in KRBH buffer (Sigma) at 37°C and then incubated for 1 hour at 37°C in 300 μl KRBH in the presence or absence of isoproterenol 30nM in duplicate. Glycerol was assayed in supernatants using a glycerol assay kit (Sigma) as instructed by the manufacturer.
At the University of Michigan DNA Sequencing Core, cDNA libraries from polyA mRNA were prepared using the TruSeq cDNA synthesis kit and sequenced using a HiSeq 2000 (Illumina).

tag: phenotype

value: acromegaly

value: adipose

tag: patient #


title: Sample12108


title: Sample12100


title: Sample12103


title: Sample12107


title: Sample12102


title: Sample12111


title: Sample12127

source_name: Adipose, control

value: non-functioning pituitary adenoma


title: Sample12119


title: Sample12120


title: Sample12109


title: Sample12104


title: Sample12101


title: Sample12105


title: IgG_ChIPseq_HCT116

city: MONTPELLIER CEDEX 5

first: Jérôme

last: Déjardin

address: 141, rue de la Cardonille

country: France

institute: Institute of Human Genetics

library_source: genomic

data_processing:
Base-calling performed by Fasteris SA (CASAVA pipeline v.1.8.2)
50 nt-long sequenced reads were mapped onto the sequence genome of Homo sapiens (hg19 assembly) according to sequencing quality using Bowtie.
For genome-wide enrichment analysis, only reads perfectly matching the human genome were retrieved (one mismatch was nevertheless allowed on low-quality nucleotides using –e 20 option). Redundant reads as well as reads mapping to multiple genomic locations were also discarded.
Enrichment peaks were called using SISSRs v 1.4 (Jothi et al., 2008) with default parameters using input DNA as background. Peaks corresponding to repetitive regions were discarded using BEDTools (Quinlan & Hall, 2010) (satellites 2/3, alpha/beta satellites and ribosomal DNAs genomic positions were retrieved from the UCSC repeatmasker track (http://genome.ucsc.edu/)) as well as peaks identified in IgG control library.
Annotation of the identified peaks as well as peak overlap and motif discovery were performed using HOMER tool suite (Heinz et al., 2010)
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated using HOMER tool suite (Heinz et al., 2010) and represent normalized fragment density profile (based on genome-unique unredundant perfectly mapping reads). BED files contain coordinates (chromosome, start and end) of called peaks.

molecule: genomic DNA

growth_protocol: Cells were cultured in McCoy medium with 10% FBS.

extract_protocol:
ChIP experiment was performed using formaldehyde-crosslinked chromatin from HCT116 cells (human carcinoma cell line) and antibody against SMCHD1 protein. Non-specific rabbit polyclonal IgG was used in control experiment.
Libraries were prepared by Fasteris SA (Switzerland) and were sequenced on HiSeq2000.

value: Colon carcinoma cells

tag: chip antibody

value: Normal rabbit IgG

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: Sample12115


title: SMCHD1_ChIPseq_HCT116

value: Anti-SMCHD1 Rabbit polyclonal IgG

value: Sigma-Aldrich

tag: chip antibody lot #


title: D546R_H3K79me3

status: Public on Apr 30 2015

city: Charlottesville

first: John

middle: H

last: Bushweller

state: VA

address: 1340 Jefferson Park Avenue

department: Molecular Physiology and Biological Physics

institute: University of Virginia

description: BAM files were final files used for analyses and include reads from multiple runs that were merged

data_processing:
The sequencing reads from Illumina MiSeq were aligned to mouse mm9 genome using the BOWTIE alignment tool. These aligned reads were then processed and converted into BigWig format, which were loaded in the UCSC Genome browser for visualization. Reads from multiple runs were merged. BEDTOOLS suite commands were used for format conversions and the reads were converted to BED format. To identify genes enriched for H3K79me2 and H3K79me3, we calculated the total number of reads in the gene body regions for each gene. To calculate the enrichments, Transcription Start Site (TSS) and Transcription End Site (TES) coordinates were downloaded from UCSC Genome browser for the mouse (mm9) gene list. BED file of regions of interest were created and defined as coordinates from TSS(-2000bp) to TES, for each gene. Once peaks were obtained for all the tracks, we selected regions of interest for the genes that overlapped with these peaks, with the BEDTOOLS intersect command.
Differentially enriched genes were identified using the DEseq package from Bioconductor using (FDR < 0.1) and the ngs.plot program was used to visualize H3K79me2 and H3K79me3 marks across the genebody.
Genome_build: mm9
Supplementary_files_format_and_content: Table containing ChIP-seq data (raw counts, not normalized) with read counts per each gene from the Transcription start site (-2000bp) to the Transcription End Site for each mutant and wildtype for both H3K79me2 and H3K79me3.

organism: Mus musculus

source_name: Hematopoietic progenitor cells

extract_protocol:
Cross-linked cells were sonicated go get 300bp average fragments and incubated with either H3K79me2 or H3K79me3 antibodies.
For DNA sequencing, approximately 0.5-3 ng ChIP-DNA was processed for whole genome library preparation using Illumina TruSeq Chip Library Kit according to the manufacturer’s protocol.

tag: cell-type

value: Primary Hematopoietic progenitor cells

tag: genotype/variation

value: MLL-AF9 (D546R)

value: H3K79me3, Diagenode cat#pAb-068-050


title: Sample12110


title: HCT116_inputDNA


title: Sample12112


title: TS112


title: WT_H3K79me3

value: MLL-AF9 (WT)


title: D546R_H3K79me2

value: H3K79me2, Abcam ab3594


title: D544R_H3K79me2

value: MLL-AF9 (D544R)


title: HPCa177N_B

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

country: China

institute: Hunan University

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
Reads were mapped onto the hg19 reference genome using TopHat v2.0.9 and Bowtie v2.1.0 with default options.
BAM files were further processed with Samtools v0.1.18, and read counts were quantified using HTSeq v0.5.3p9 based on the hg19 gtf file in the Tophat package.
The read count matrix was normalized by geometric mean normalization built in DESeq R package v1.10.1
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file reports normalized read counts

source_name: Freshly purified human benign prostatic basal cells

extract_protocol:
The FACS purified human prostate basal (Trop2+CD49fhi) and luminal (Trop2+CD49flo) epithelial populations are subject to total RNA extraction by RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq Stranded Total RNA Preparation Kit (Illumina, cat#: RS-122-2301) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Prostate

value: basal epithelial cells

tag: patient number

tag: patient age


title: HPCa173N_L

source_name: Freshly purified human benign prostatic luminal cells

tag: cell type

value: luminal epithelial cells


title: HPCa177N_L


title: HPCa175N_L


title: WOC

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description: genomic DNA

data_processing:
Basecalling was performed using CASAVA version 1.8
Quality control of FastQ sequences was assessed using the FastQC software version 0.9.3.
ChIP-seq reads were aligned to the dm3 genome assembly using Bowtie 0.12.5, rejecting reads aligning to more than one genomic location, allowing up to 2 mismatches in the first 28 bases of the reads and no gapped alignments.
Aligned reads were filtered with the htSeqTools R package. PCR artifacts were detected and removed with the filterDuplicateReads function using a FDR of 1%. Strand shift bias was removed using the alignPeaks function with the default options.
A first step for peak calling was done using the enrichedRegions function from the htSeqTools package to find genomic regions with coverage above 10 reads, comparing the proportion of reads inside/outside of each region between each IP sample and the Input with a logistic regression likelihood-ratio test. Enriched regions were defined as those with a Benjamini–Yekutieli adjusted P-value below 0.05.
In a second step, we used the function enrichedPeaks from htSeqTools to define peaks (i.e. putative binding sites) as locations within the enriched regions with a coverage difference between IP and Input above 30 reads for WOC/ROW/Z4 and 20 reads for HP1c/Dsk2.
After peak calling, we used the mergeRegions function from htSeqTools to merge adjacent peaks closer than 300bp.
Genome_build: dm3
Supplementary_files_format_and_content: BED files include chromosome, start and end of the identified peaks in the dm3 Drosophila melanogaster  genome.

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were grown on Schneider’s insect Medium (Sigma) supplemented with 100 μg/ml streptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with polyclonal αWOC, αROW, αZ4, αDsk2 and αHP1c antibodies. Finally DNA was purified by standard phenol extraction.
10 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 18 cycles was performed using TruSeqRNA Sample Prep Kit (Illumina) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).

tag: type

value: IP

value: S2 cells

value: rabbit αWOC


title: Z4

description: genomic DNA

value: guinea pig αZ4


title: WT_H3K79me2


title: ROW

description: genomic DNA

value: rabbit αROW


title: HPCa175N_B


title: Sample12121

value: non-functioning pituitary adenoma

value: adipose


title: Input1

description: genomic DNA

value: Input for WOC/ROW/Z4


title: Input2

description: genomic DNA

value: Input for HP1c/Dsk2


title: HPCa173N_B


title: D544R_H3K79me3

value: Primary Hematopoietic progenitor cells


title: Rep2_flox_IgG

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

country: United Kingdom

institute: School of Life Sciences, University of Dundee

description: Sonicated chromatin

data_processing:
Image capture, analysis and base calling were performed using Illumina’s CASAVA 1.8. Raw sequencing reads obtained from ChIP-seq experiments were split according to the sample index, and 3'-adaptor sequences as well as low quality nucleotides were trimmed prior to mapping to the GRCm38 (mm10) mouse genome using bowtie (Langmead et al., 2009), with parameters “-m1 --strata --best”. Potential PCR duplicates were removed by only keeping a single read if multiple reads mapped to the exact same genomic sequence. Peak calling of ChIP-seq datasets was performed using MACS 1.4 (Zhang et al., 2008) with the corresponding IgG sample as control and a p-value cut-off of 1E-12. All analyses of ChIP-seq sequencing data were performed on the public server of the Galaxy Project using a prepublished workflow (Helin Group).
Genome_build: mm10
Supplementary_files_format_and_content: BED files: Tab-delimited text files containing genomic intervals representing ChIP-seq peaks. BIGWIG files: Binary bigWig files were generated from output of MACS using the Wig/Bedgraph-to-bigWig tool on the public Galaxy Server.

source_name: Tet2fl/fl; AML1-ETO_IgG control

growth_protocol: Primary Kit-enriched bone marrow cells from Tet2fl/fl;CreER mice were freshly transduced with MigR1-AE-IRES-GFP, sorted for GFP and plated in methylcellulose medium (M3534, StemCell Technologies). After three rounds of replating, the cells were shifted to grow in suspension in non-tissue culture treated plasticware in media containing 1× StemPro®-34 SFM (Invitrogen), 1x L-Glutamine, with SCF (CHO producer cell line), 10ng/ml IL-3 (Peprotech), 10ng/ml IL-6 (Peprotech) and 0.1mM 2-mercapto-ethanol.

extract_protocol:
Immature myeloid cells (iGMP cells; GFP+, CD11b-, Gr1-, CD16/32+) were sorted from cultures. Genomic DNA was isolated using the AllPrep DNA/RNA micro kit (Qiagen).
Duplicate cultures of Tet2fl/fl;AE or Tet2-/-:AE cells grown in vitro for 10 passages after Tet2 disruption were fixed for 10 minutes in 1% formaldehyde dissolved in PBS and the reaction was quenched by addition of glycine to a final concentration of 0.125M. The crosslinked cells were harvested in SDS lysis buffer (100 mM NaCl, 50mM Tris-HCl (pH8.1), 5mM EDTA (pH 8.0), 0.2% NaN3, 0.5% SDS) and nuclei were pelleted and resuspended in IP buffer (100mM Tris-HCl (pH 8.6), 100mM NaCl, 5mM EDTA (pH 8.0), 0.2% NaN3, 5% Triton X-100, 0.3% SDS). The obtained DNA was then sheared to an average size of 150-300bp (Bioruptor, Diagenode) and 40ug of solubilized chromatin was immunoprecipitated with Protein A Sepharose beads (GE healthcare) after overnight incubation with the respective antibodies. Finally, adaptor-ligated libraries were generated from 10ng of precipitated DNA using the NEBNext® DNA library Sample Prep Master kit (New England Biolabs), PCR-amplified (15x PCR cycles) using indexed multiplex primers for illumina sequencing (New England Biolabs), and sequenced on a HiSeq2000 using 50bp single-end sequencing at the National High-Throughput Sequencing Centre (University of Copenhagen).

treatment_protocol: To induce the CreER-mediated excision of Tet2, the cells were treated with 200 nM 4-OHT (Experimental) or EtOH (Control) for 2 passages (4 days). The cells were subsequently washed to remove residual 4-OHT and passaged every 2 days for a total of 10 passages.

tag: strain background

value: Tet2fl/fl; AML1-ETO

value: Kit-enriched hematopoietic bone marrow cells

tag: passage number

value: Passage 10

tag: transduced with

value: IgG control (Gamma-globulin (10760815, Pierce))


title: Rep2_KO_K4me3

description: Sonicated chromatin

source_name: Tet2-/-: AML1-ETO_anti-H3K4me3

value: anti-H3K4me3 (9751S, Cell signalling)


title: Rep2_KO_K27ac

description: Sonicated chromatin

source_name: Tet2-/-: AML1-ETO_anti-H3K27ac

value: anti-H3K27ac (ab4729, Abcam)


title: Rep2_flox_K4me1

description: Sonicated chromatin

source_name: Tet2fl/fl; AML1-ETO_anti-H3K4me1

value: anti-H3K4me1 (39635, Active Motif)


title: Rep2_KO_IgG

description: Sonicated chromatin

source_name: Tet2-/-: AML1-ETO_IgG control


title: Rep2_flox_K4me3

description: Sonicated chromatin

source_name: Tet2fl/fl; AML1-ETO_anti-H3K4me3


title: Rep1_KO_K4me3

description: Sonicated chromatin


title: Rep1_KO_K4me1

description: Sonicated chromatin

source_name: Tet2-/-: AML1-ETO_anti-H3K4me1


title: Rep1_KO_K27ac

description: Sonicated chromatin


title: Rep2_KO_K4me1

description: Sonicated chromatin


title: Rep2_flox_K27ac

description: Sonicated chromatin

source_name: Tet2fl/fl; AML1-ETO_anti-H3K27ac


title: Rep1_flox_K27ac

description: Sonicated chromatin


title: Rep1_KO_IgG

description: Sonicated chromatin


title: Rep1_flox_K4me3

description: Sonicated chromatin


title: Rep1_flox_IgG

description: Sonicated chromatin


title: Rep1_flox_K4me1

description: Sonicated chromatin


title: non-hair cell control

city: Los Angeles

first: Litao

last: Tao

state: California

address: 1425 San Pablo St.

department: Stem Cell and Regenerative Medicine

institute: University of Southern California

description: GFP negative

data_processing:
Illumina Hi-seq 2000 for sequencing
Sequenced reads were trimmed based on qualitiy scores and then aligned to genome build mm10 using TopHat2 in PartekFlow with default settings.
Aligned raw reads were quantified using Refseq coordinates, and normalized using "classic" RPKM method (PartekFlow).
Differential gene expression was analyzed using the Gene-Specific Analysis algorithm in PartekFlow
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited txt files include normalized reads for each replicate.

molecule: polyA RNA

source_name: cochlea

growth_protocol: Cochleae were dissected from postnatal day 1 animals and cultured under 5% CO2 - 5% O2 conditions overnight prior to treatment. Cultures were maintained on polycarbonate membranes floating on DMEM F12 supplemented with 1% N2 and 100U/ml penicillin.

extract_protocol:
Cells were FACS purified into RNA lysis buffer, and RNA was extracted with Zymo RNA microprep kit.
Libraries were construced according to Illumina True-seq mRNA-seq kit protocol.

treatment_protocol: Organs were treated with 0.5mM gentamicin for 3 hours.

tag: strain

tag: developmental stage

value: post natal day 1

tag: tissue

value: cochlea


title: hair cell control

description: GFP positive


title: hair cell gentamicin

description: GFP positive


title: miRNA_LPS_120_min

city: Boston

first: Trent

last: Fowler

state: MA

address: 150 Harrison Ave

department: Dept. of Devleopmental, Chemical, and Molecular Biology

institute: Tufts University

data_processing:
Sequence data was aligned with Illumina ELAND software and mapped against the mm9/ENSEMBL build 67 genome reference using Tophat v2.0.0 (Trapnell et al., 2009), for RNA, bowtie 1.0.0 for ChIP (Langmead et al., 2009).  Mapping was performed for unique reads with a 1bp possible mismatch.
RNA was harvested by trizol treatment, phenol extraction, and DNAse treatment. Sequencing was performed at Tufts as stated above. 50 bp single end reads were analyzed with Mirdeep2 (Friedlander et al., 2012) using the mirBase reference v14 with standard settings. Mapped miRNAs were confirmed by visual inspection of miRNA structure and UCSC Genome Browser tracks (Raney et al., 2014), and inclusion in the Ensembl data base (Flicek et al., 2013). Differential expression from the resting state was identified by a minimal two fold difference in Mirdeep2 normalized reads.
Genome_build: mm9/ENSEMBL build 67
Supplementary_files_format_and_content: bigwig-custom R scripts were used to produce bedgraphs from mapped bam files which were then converted to BigWig files with bedgraphToBigwig

source_name: CD43- splenic B cells

extract_protocol:
Naïve resting B cells from splenocytes of 8 week old male C57BL6 mice were incubated with anti-CD43 beads (Miltenyi) and the negatively selected population isolated and confirmed as 95% CD19+ by flow cytometry (FACS Calibur).
RNA libraries were prepared with the NuGEN Ovation RNA-Seq v2 library preparation kit, which amplifies both mRNA and non-polyadenylated transcripts. The resulting cDNA was fractionated by sonication and prepared using the Illumina TruSeq library preparation kit which was then multiplexed across single-end, 100bp (RNA), 50bp (ChIP and miRNA), lanes of an Illumina HiSeq2000 sequencer using the Illumina pipeline RTA version 1.12.4.2 and de-multiplexing with CASAVA v1.8.2.  ChIP-seq was performed at NIH using an Illumina TruSeq ChIP library kit according to the manufacturer’s protocol followed by cluster generation with a TruSeq Cluster generation kit v5. ChIP libraries were sequenced on an Illumina Genome Analyzer (GA-II) with sequencing performed for 42 cycles using the Illumina RTA version1.8.

treatment_protocol: For induction, either 10 ug/ml anti-mouse IgM goat IgG Fab fragments (Jackson Immunology) or 25 ug/ml Salmonella typhimurium typhus LPS (Sigma) were added. After addition of media and ligands, cells were rested on ice for 30 minutes following a previously published method (Damdinsuren et al., 2010) and incubated at 37C/5%CO2 for the experimental times.

tag: cell population

value: CD43- splenic B cells


title: miRNA_BCR_120_min


title: miRNA_0_min


title: Input_LPS_120_min

tag: chip antibody

value: None (input)


title: PolII_0_min

value: RNA Pol II (N-20)(Santa Cruz sc-816x)


title: PolII_BCR_120_min


title: RNA_LPS_120_min_2


title: Input_BCR_120_min


title: RNA_0_min_2


title: Input_0_min


title: RNA_LPS_120_min


title: RNA_BCR_120_min


title: RNA_BCR_120_min_2


title: RNA-dark-2

city: Chicago

first: Guan-Zheng

last: Luo

state: IL

address: 929 E 57th St

department: Chemistry

institute: UChicago

data_processing:
After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1
Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01.
For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide.
Methylation ratios are determined by the the reads ends information.
Genome_build: Cre4
Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample.

organism: Chlamydomonas reinhardtii

source_name: Algae cultured in constant dark

growth_protocol: Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+)  was grown in standard Tris-Acetate-Phosphate (TAP) medium in  at 25 ºC with 220 rpm shaking and constant light.

extract_protocol:
For RNA samples, poly-A tailed RNA is extracted by Oligo(dT)/Magnetic Capture Method. Then Stranded RNA library is constructed by the instruction of Illumina.
Standard DNA sequencing and Stranded RNA-seq protocol from Illumina

tag: culture media

value: Tris-Acetate-Phosphate (TAP)


title: MNase-seq

source_name: Algae cultured in constant light

extract_protocol:
For nucleosome profiling, nuclei is extracted and digested by Mnase for 12 minutes. After agarose gel electrophoresis, 150 bp band is cutted and purifiled for standard illumina DNA library construction.
Standard DNA sequencing and Stranded RNA-seq protocol from Illumina


title: RNA-light-1


title: RNA-light-2


title: m6A-CviAII-light

description: enzyme-treated

extract_protocol:
For enzyme digested samples, CviAII or DpnII are added to 10 U/ug and incubated overnight. Digested DNA is sonicated to ~500 bp segments which is subject to DNA library construction.
Standard DNA sequencing and Stranded RNA-seq protocol from Illumina


title: RNA_0_min


title: m6A-CviAII-dark

description: enzyme-treated


title: PolII_LPS_120_min


title: non-hair cell gentamicin

description: GFP negative


title: m6A-DpnII-dark

description: enzyme-treated


title: m6A-DpnII-light

description: enzyme-treated


title: m6A-Input-light

extract_protocol:
Genomic DNA was isolated using phenol-chloroform-isoamyl alcohol with overnight RNase A treatment. For MeDIP, genomic DNA is sonicated to 200-400 bp segments, then m6A antibody is used to pull down DNA pieces containing m6A modification which is subject for standard Illumina DNA library construction.
Standard DNA sequencing and Stranded RNA-seq protocol from Illumina


title: m6A-IP-light-2

tag: antibody

value: m6A antibody, rabbit polyclonal (SYSY, 202003, lot 202003/32)


title: m6A-IP-dark

value: m6A antibody, rabbit polyclonal (SYSY, 202003, lot 202003/33)


title: m6A-IP-light-1


title: H3K27me3_LPS_120_min

value: H3K27me3 Abcam ab6002)


title: HeLa transfected with siRNAs for TUT2, 4, 7

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: RNA-seq for subset of pre-miRNAs in TUT2/4/7 knockdown HeLa cells

data_processing:
The sequencing data were analyzed using Illumina RTA 1.18.42. The sequences were processed using Cutadapt to trim the 5′-most fifteen nucleotides and clip 3′ adapter sequences out. The sequence at the 5′-end was removed because they originate from PCR primers for specific enrichment of pre-miRNAs and often include significant number of mismatches to known pre-miRNA sequences. Short sequences (<15nt) after trimming and clipping, and sequences without a 3′ adapter part were removed from the final sequence pool.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated files with nucleotide sequences clipped out of 3' adapters with their number of occurrence in the libraries

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM (Welgene) supplemented with 9% fetal bovine serum (Welgene).

extract_protocol:
Total RNAs were extracted by TRIzol (Invitrogen) following the manufacturer's instructions.
To prepare pre-miRNA cDNA libraries, total RNAs were separated on 15% urea-PAGE and RNAs of 40-120nt were gel-purified. Size fractionated RNAs were ligated to 3ʹ adapter by using T4 RNA ligase 2, truncated (NEB). The 3ʹ adapter-ligated RNA was separated on 12.5% urea-PAGE and RNAs of 60-140nt were gel-purified. Size fractionated RNAs were hybridized with an RT primer that is complementary to the 3ʹ adapter and reverse-transcribed by using SuperScript III (Life Technologies) and the cDNA was PCR-amplified with miRNA specific primers using Phusion DNA polymerase (NEB). The cDNA libraries were separated on 6% native polyacrylamide gel and RNAs of 150-225nt.

treatment_protocol: HeLa cells were transfected twice with 42 nM of siRNAs using Lipofectamine 2000 (Invitrogen).

tag: cell line

value: HeLa

tag: transfection

value: siRNAs for TUT2, 4, 7


title: RNA-dark-1


title: H3K27me3_BCR_120_min


title: ATAC-Seq from v6.5 embryonic stem cells

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were aligned to mm10 mouse genome using Bowtie2 with the parameter -X2000 (allowing fragments up to 2 kb to align). Duplicated aligned reads were removed using Picard MarkDuplicates tool.
To identify chromatin accessibility signal we considered only short reads (≤ 100bp) that correspond to nucleosome free regions. To detect and separate accessible loci in each sample, we used MACS version 1.4.2-1 with --call-subpeaks flag (PeakSplitter version 1.0).
Genome_build: mm10
Supplementary_files_format_and_content: bed format, significant accessibility signal peaks (MACS output)

source_name: mouse embryonic stem cells

growth_protocol: Intermediate ES like cells (IES 9 cells): Nanog-CreER Reporter MEFs were plated at day 0 in MEF medium: DMEM supplemented with 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin/streptomycin and 10% FBS. On day 1 medium was changed to KO-DMEM with supplemented 15% FBS and 5% KSR with added JAK1 inhibitor (Calbiochem 420099, 0.5ϻM) for 6 days, followed by switching to 1% FBS and 14% KSR and JAK1 inhibitor for 3 days. The medium was supplemented with 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin/streptomycin and 0.1 mM β-mercaptoethanol. Doxycycline hyclate (Dox) and 4-Hydroxytamoxifen (4OHT) were added to the medium at day 1 and continuously kept in the medium until day 9.

extract_protocol:
Nanog-CreER reporter MEFs were reprogrammed using OSKM-TD protocol until the end of OSKM induction step, at which point tdTomato+ intermediate cells were sorted and applied for ATAC sequencing. Briefly, 50,000 sorted cells were centrifuged at 500g for 3 minutes, followed by a wash using 50 μL of cold PBS and centrifugation at 500g for 3 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. Next, the pellet was re-suspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 minutes at 37 °C and immediately put on ice. Directly afterwards, the sample was purified using a Qiagen MinElute kit.
Following purification, the library fragments were amplified using custom Nextera PCR primers 1 and 2 for a total of 12 cycles. Following PCR amplification the libraries were purified using a Qiagen MinElute Kit.

treatment_protocol: IES9 sample was generated by addting dox and 4OHT to the medium from day 1- 9


title: H3K4me3_BCR_120_min

value: H3K4me3 (Abcam ab8580)


title: H3K4me3_0_min


title: ATAC-Seq from induced pluripotent stem cells

source_name: mouse induced pluripotent stem cells

value: A12 (Mbd3 flox/-)

tag: transgene


title: ATAC-Seq from day 9 of OSKM trans-differentiation to Neural Stem Cells

description: Sorted tdTomato positive cells. No  MEF feeders

source_name: day 6 of OSKM-trans differentiation to Neural Stem Cells

value: Rosa26-TdTomato B6 female + Col1a-OSKM 129 male


title: ATAC-Seq from Mouse Embryonic Fibroblasts

source_name: mouse embryonic fibroblasts


title: H3K27me3_0_min


title: m6A-Input-dark


title: RNA-Seq from Nerual Stem Cells negative for Nanog-Tomato

description: Mechanicly subcloned NSCs. No MEF feeders

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
We aligned reads to mm10 reference genome (index downloaded from bowtie) using TopHat version 2.0.10.
Read counts per exon were calculated over all 628,052 exons in mm10 ensemble GTF, using bedtools coverage command
Exon counts were normalized by the exon length in Kbp and by million number of aligned reads per sample, to give RPKM values.
Gene expression was defined by the average expression level (RPKM) of all exons associated with a certain gene.
Genome_build: mm10
Supplementary_files_format_and_content: exons.txt contains RPKM values calculated per-exon in all samples.

source_name: neural stem cells received with OSKM trans-differentiation

growth_protocol: Intermediate ES like cells (IES 6 cells): Nanog-CreER Reporter MEFs were plated at day 0 in MEF medium: DMEM supplemented with 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin/streptomycin and 10% FBS. On day 1 medium was changed to knock-out DMEM medium (Gibco 10829-018) with 10% KSR, 5% FBS, 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin/streptomycin, 0.05 mM β-mercaptoethanol and Dox+4OHT were added for a period of 6 days. By the end of day 6 tdTomato positive cells were sorted out using FACS sorter and used for RNA production.    Primary Brain NSC: BDF2 mouse embryos were sacrificed at E13.5 of gestation according to standard protocols, and brain vesicles were mechanically dissociated and plated on Poly-D-Lysine and Laminin coated plates  and were cultured in NSC medium: DMEM/F12 supplemented with 1XB27 and 1XN2 cell-supplements, 0.01% Fraction V BSA 7.5 % solution (Life Technologies), 1% Penicillin-streptomycin and 20ng/mL bFGF and 20ng/mL EGF.

extract_protocol:
Cells were harvested and RNA was extracted using the 5 PRIME PerfectPure RNA Cell culture Kit (cat#2302340 ), according to manufacturer's manual
RNA was extracted from Trizol pellets, and utilized for RNA-Seq by TruSeq RNA Sample Preparation Kit v2 (Illumina) according to manufacturer’s instruction

treatment_protocol: IES6 sample was generated by adding dox and 4OHT to the medium from day 1- 6


title: RNA-Seq from day 6 of OSKM trans-differentiation to Neural Stem Cells

source_name: day 6 of OSKM-trans differentiation to neural stem cells


title: RNA-Seq from v6.5 embryonic stem cells

description: ESCs with MEF feeders

source_name: embryonic stem cells


title: RNA-Seq from Mouse Embryonic Fibroblasts

source_name: Mouse Fibroblasts


title: mutant (saePQRS deleted) 4

city: Little Rock

first: Chia

middle: Y

last: Lee

state: AR

address: 4301 W. Markham St.

department: Microbiology and Immunology

institute: University of Arkansas for Medical Sciences

data_processing:
Illumina MiSeq standard protocols for raw sequence data files,
Genesifter analysis software for RNAseq alignment to designated reference genome.  GATKv3.0 assembly algorithm
Genome_build: NC_009641.1
Supplementary_files_format_and_content: counts

organism: Staphylococcus aureus

source_name: mutant (saePQRS deleted)

growth_protocol: grown to early stationary phase in tryptone broth

extract_protocol:
cold acetone-ethanol was added to bacterial cultures, RNA was extracted using standard protocols, rRNA was removed using the Microbexpress© kit from Ambion
RNA libraries were prepared using standard Illumina protocols.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA-Seq - Illumina TruSeq RNA library modified so that poly A enrichment is not performed due to these being prokaryotic RNA samples

value: Newman

tag: genotype

value: mutant (saePQRS deleted)


title: repaired [saeS(P18) repaired to saeS(L18)] 3


title: wild type 3

source_name: wild type

value: wild type


title: wild type 2


title: repaired [saeS(P18) repaired to saeS(L18)] 2


title: mutant (saePQRS deleted) 2


title: mutant (saePQRS deleted) 1


title: mutant (saePQRS deleted) 3


title: wild type 1


title: HeLa transfected with a control siRNA

description: RNA-seq for subset of pre-miRNAs in control knockdown HeLa cells

value: control siRNA


title: H3K4me3_LPS_120_min


title: RNA-Seq from induced pluripotent stem cells

description: ESCs with MEF feeders ??

source_name: induced pluripotent stem cells


title: RNA-Seq from Neural Stem Cells

description: Brain derived NSC from E12.5 embryo

source_name: primary neural stem cells


title: WT rep2

city: Stanford

first: Juthamas

last: Chaiwanon

state: CA

address: 260 Panama St.

department: Plant Biology

institute: Carnegie Institution

description: replicate 2

data_processing:
Total reads were mapped to the Arabidopsis thaliana genome (TAIR10, www.arabidopsis.org) using TopHat v1.4.0, with parameters --min-segment-intron 40 --max-segment-intron 2000 --bowtie --no-novel-juncs --read-mismatches 2 -G
Read counts for each gene were quantified using HTSeq-count with union mode.
Genome_build: TAIR10, www.arabidopsis.org
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Arabidopsis thaliana

source_name: Col-0 wild-type

growth_protocol: Seedlings were grown vertically on half-strength MS regular media under continuous light for 7 days.

extract_protocol:
Roots were sectioned in half and the root tip section was harvested for total RNA extraction using the Spectrum Plant Total RNA kit (Sigma, USA).
Libraries were constructed using TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Seedlings were treated with 100 nM BL and/or 5 uM IAA or mock solution for 4 hr.

value: wild-type Col-0

tag: genetic background

value: primary root

value: 7-day-old seedling

tag: treatment

value: untreated

tag: sequencing read length

value: 36 bp


title: dwf4 rep1

description: replicate 1

value: dwf4 mutant


title: RNA-Seq from Nerual Stem Cells positive for Nanog-Tomato


title: dwf4 rep2

description: replicate 2


title: dwf4 BL 4hr rep1

description: replicate 1

source_name: dwf4, BL 4 hr

value: 100 nM BL, 4 hr


title: WT rep1

description: replicate 1


title: bri1-116;bzr1-1D rep2

description: replicate 2

value: bri1-116;bzr1-1D mutant


title: dwf4 BL 4hr rep2

description: replicate 2


title: bri1-116;bzr1-1D rep1

description: replicate 1


title: bri1-116 rep1

description: replicate 1

value: bri1-116 mutant


title: Col IAA+BL 4hr rep2

description: replicate 2

source_name: Col-0, IAA+BL 4 hr

value: 100 nM BL + 5 µM IAA, 4 hr, cotreatment


title: Col IAA 4hr rep2

description: replicate 2

source_name: Col-0, IAA 4 hr

value: 5 µM IAA, 4 hr


title: Col BL 4hr rep2

description: replicate 2

source_name: Col-0, BL 4 hr


title: Col BL 4hr rep1

description: replicate 1


title: repaired [saeS(P18) repaired to saeS(L18)] 1


title: Col mock rep2

description: replicate 2

source_name: Col-0 mock

value: mock, 4 hr


title: Col mock rep1

description: replicate 1


title: trf4delta

city: Paris

first: Marc

last: Descrimes

address: 26 rue d'Ulm

institute: Institut Curie

description: BY4741 strain deleted for trf4 gene

data_processing:
Mapping with bowtie 0.12.7, uniquely mapped read, 3 mismatches.
Sorting with samtools sort
Tag densities were obtained using uniquely mapped reads, after normalization on the total number of reads that uniquely mapped on ORFs.

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: YPD

extract_protocol:
total RNA hot phenol
ribominus SOLiD kit (SOLiD whole transcriptome analysis kit)

treatment_protocol: standard

tag: genotype/variation

tag: growth

value: exponential asynchronous culture


title: 4C-seq CorticalNeurons-FOS

status: Public on Apr 29 2015

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

data_processing:
Processing of sequenced 4C-seq reads is performed using a special purpose computational analysis pipeline, 4Cseqpipe, which can be downloaded along with a detailed manual at: http://compgenomics.weizmann.ac.il/tanay/?page_id=367
Briefly, unique reads are mapped on the predesigned restriction fragment region.  Dense genomic profiles are genarated by linear interpolation of mapped reads.  One interpolated profile is selected and the three other profiles are quantile-normalized to match its distribution. Resulting profiles are combined by direct summation, resulting in a coverage profile. Geometric mean of normalized coverage, as well as 20th and 80th percentiles, are calculated for sliding windows ranging from 3kb to 49kb in size.
Supplementary_files_format_and_content: ID.nearcis.norm.trunc_log_mean.scales – geometric mean of truncated (default value: top and bottom 2%) normalized contact intensity in 1kb genomic bins. Each row represents a genomic bin of size 1kb. Includes the following tab-delimited columns: column 1 – the starting coordinate of the 1kb bin, column 2 – the log of geometric mean of values within a 3kb window, centered on the 1kb genomic bin  column 3 – the 80th percentile of values in the window  column 4 – the 20th percentile of values in the window  column 5-145 – as columns 2-4, but with linearly increasing window size, going up to 49kb
Genome_build: mm9

source_name: cortical neurons

growth_protocol: Cortical neurons were dissected from E15.5 embryos and cultured for 10-11 DIV. Hippocampal tissue was dissected from 3 months old mice.

extract_protocol: Samples were fixed usinng 1% formaldehyde. Fixation was stopped by adding Glycine (0.125M). After lysis, soluble chromatin was subjected to restriction endonuclease digestion overnight. First digestion with HindII, second digestion with DpnII. Intra-molecular ligations were performed using T4 DNA ligase (NEB) for four hours at 16C. Decross-linked, purified chromatin was subkjected to RNase digestion and further purified. PCR reactions were performed  using a first primer designed on the viewpoint and a second outer primer designed beside the DpnII site. Both primers contained illumina sequencing adapters and Barcodes for multiplexing. Approximately 16 reactions were performed for each viewpoint to generate complex libraries.

tag: sample type

value: primary cortical neurons

tag: cell type

value: cortical neurons


title: xrn1delta trf4delta

description: BY4741 strain deleted for trf4 and xrn1 genes

value: xrn1delta trf4delta

tag: strain


title: 4C-seq hippocampus-FOS

source_name: hippocampus

value: hippocampal tissue

tag: tissue

value: hippocampus


title: bri1-116 rep2

description: replicate 2

value: primary root

tag: developmental stage


title: maize_DGE_IV

city: Wenjiang,Chengdu

first: hongjun

last: liu

state: Sichuan

address: 211 Huimin Road

institute: Sichuan Agricultural University

data_processing:
DGE reads were aligned to the B73 RefGen_v2 (release 5b. 60 in February 2011) reference sequences by SOAP2.
Data were filtered as follows: (1) 3' adaptor sequence removal: since Tags are only 21nt long while the sequencing reads are 35nt long, raw sequences are with 3' adaptor sequences; (2) Empty reads removal (reads with only 3' adaptor sequences but no tags); (3) 3.Low quality tags removal (Tags with unknown sequences 'N'); (4) Removal of tags which are too long or too short, leaving Tags of 21nt long; (5) Generate clean tags.
Raw sequencing image data were transformed by base calling into sequences. Those raw data reads were stored in FASTA format, and their analysis was conducted as described by Shen et al,. Briefly, prior to mapping to the reference database, all sequences were ﬁltered to trim the 3’ adaptor sequence, filter empty tags (reads with only 3’ adaptor sequences but no tags) and low-quality tags containing Ns, and remove tags which are too long or too short. We used the B73 RefGen_v2 (release 5b. 60 in February 2011)) reference sequences as reference, which is a virtual library containing all possible CATG+17 base-length sequences. All clean tags were mapped to the reference sequences and a mismatch of only 1bp was considered. Clean tags that were mapped to the maize genome reference sequences from multiple genes were filtered. The remaining clean tags were designed as unambiguous clean tags. The expression level of each gene was estimated by the frequency of clean tags and then normalized to TPM (number of transcripts per million clean tags), which is a standard method and extensively used in DGE analysis.
Genome_build: the B73 RefGen_v2 (release 5b. 60 in February 2011)

organism: Zea mays

source_name: ears (female inflorescences)

extract_protocol:
All the samples were harvested and immediately frozen in liquid nitrogen and stored at -80°C. The total RNA from each sample was then isolated using Trizol (Invitrogen) according to the manufacturer’s instructions.
For RNA library construction and deep sequencing, an extract of 6 μg of total RNA was obtained and treated with Oligo(dT) magnetic bead adsorption to purify mRNA. Oligo(dT) was then used as a primer to synthesize the ﬁrst- and second-strand cDNA. The 5' ends of tags were generated by two endonucleases Nla III or Dpn II. The bead-bound cDNA was subsequently digested with restriction enzyme Nla III, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to Oligo(dT) beads were washed away and the Illumina adaptor 1 was ligated to the sticky 5' end of the digested bead-bound cDNA fragments. The junction of Illumina adaptor 1 and CATG site is the recognition site of Mme I, which is a type of Endonuclease with separates recognition and digestion sites. It cuts 17 bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads by precipitation, Illumina adaptor 2 was ligated to the 3' ends of tags, acquiring tags with different adaptors at both ends to form a tag library. After 15 cycles of linear PCR amplification, 95bp fragments were purified by 6% TBE PAGE Gel electrophoresis. After denaturation, the single-chain molecules were fixed onto the Illumina Sequencing flowcell. Each molecule grows into a single-molecule cluster sequencing template through in situ amplification. The four types of nucleotides were labeled by four colors, and added to perform sequencing by synthesis (SBS). Each tunnel will generate millions of raw reads with sequencing length of 35bp. Raw data (tag sequences) were deposited in the GEO database (No.GSE43058).

value: ears

tag: phase

value: floret organ differentiation phase


title: maize_DGE_I

value: growth point elongation phase


title: maize_DGE_II

value: spikelet differentiation phase


title: maize_DGE_III

value: floret primordium differentiation phase


title: RNA-Seq plus BIC

description: RNA-seq in primary cortical neurons treated with 50uM Bicuculline

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

growth_protocol: Cortical neurons were dissected from E15.5 embryos and cultured for 10-11 DIV.

extract_protocol: Total RNA was exctracted with the Qiagen RNAeasy kit

treatment_protocol: Cortical neurons were treated with 10nM purified recombinant Reelin for 1 hour.


title: RNA-Seq minus BIC

description: RNA-Seq in primary cortical neurons in restin condition


title: Gro-Seq plus Reelin

description: Gro-seq in primary cortical neurons treated with 10nM purified recombinant Reelin protein

data_processing:
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: mm9
Supplementary_files_format_and_content: biwWig

growth_protocol: Primary cortical neurons were isolated from E15.5 embryos

extract_protocol:
Primary cortical neurons were incubated in swellinig ice-cold buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5min. Cells were lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol). The resultant nuclei were washed once again with 10 ml lysis buffer and then re-suspended in 100ml of freezing buffer (50mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA).
For run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase In, 1% sarkosyl, 500mM ATP, GTP, and Br-UTP, 2mM CTP) and incubated for 5 min at 30°C. The nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Invitogen) following manufacturer’s instructions. NRO-RNA was then subjected to base hydrolysis on ice for 40 min and followed by treatment with DNase I and antarctic phosphatase. To purify the Br-UTP labeled nascent RNA, the NRO-RNA was immunoprecipitated with an anti-BrdU agarose beads (Santa Cruz Biotech) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween-20) for 1h at 4°C while rotating.  To repair the end, the immunoprecipitated BrU-RNA was re-suspended in 50mL reaction (43mL DEPC water, 5.2mL T4 PNK buffer, 1mL SUPERase In and 1mL T4 PNK (New England BioLabs)) and incubated at 37°C for 1h. RNA was then extracted, precipitated using acidic phenol-chloroform (Ambion) and subjected to poly-A tailing reaction by using poly-A polymerase (New England BioLabs) for 30 min at 37°C. Subsequently, reverse transcription was performed using oNTI223- primers (5’- pGATCGTCGGACTGTAGAACTCT; CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3’) where the p indicates 5’ phosphorylation, ‘;’ indicates the abasic dSpacer furan and VN indicates degenerate nucleotides. Specifically, tailed RNA (8.0mL) was subjected to reverse transcription using superscript III (Invitrogen), after which the cDNA products were separated on a 10% polyacrylamide TBE-urea gel. The extended first-strand product (100-500bp) was excised and recovered by gel extraction. After that, the first-strand cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1 (New England BioLabs). Re-linearized single strand cDNA (sscDNA) was separated in a 10% polyacrylamide TBE gel as described above and the product of needed size was excised (~170-400bp) for gel extraction. Finally, sscDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB) according to the manufacturer’s instructions. Primers oNTI200 (5’-CAAGCAGAAGACGGCATA-3’) and oNTI201 (5’- AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACG-3’) were used to generate DNAs for deep sequencing.

treatment_protocol: Cortical neurons were treated with 10nM purified recombinant Reelin for 1 hour

value: Nascent RNA sequencing


title: Col IAA+BL 4hr rep1

description: replicate 1

value: wild-type Col-0

value: 7-day-old seedling


title: ChIP-Seq Hippocampus Input

data_processing:
Basecalls performed using CASAVA version 1.4
reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

extract_protocol:
For ChIP-seq, samples were fixed for 45 minutes with 2mM DSG followed by 10 minutes with 1% formaldehyde. Fixation was stopped by adding Glycine (0.125M). Chromatin DNA was sheared to 200–500 bp average in size by sonication. Soluble sheared chromatin was immunoprecipitated with specific antibodies coupled with protein G dynabeads (Invitrogen) overnight at 4°C. After washing and elution, the protein–DNA complex was decross-linked by heating at 65°C for 4 hours. Immunoprecipitated DNA was purified by using iPure Diagenode kit.
the libraries were constructed following Illumina’s Chip-Seq Sample prep kit.


title: ChIP-Seq H3K27ac plus Reelin

source_name: CorticalNeurons

value: CorticalNeurons

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: Abcam ab4729

value: cortical neuron


title: ChIP-Seq H3K27ac minus Reelin


title: Col IAA 4hr rep1

description: replicate 1

value: 5 µM IAA, 4 hr


title: Gro-Seq minus Reeln

description: Gro-seq in primary cortical neurons treated with vehicle

value: primary cortical neurons


title: RNA-Seq minus Reelin


title: RNA-Seq plus Reelin-GSI

description: RNA-seq in primary cortical neurons treated with 10nM purified recombinant Reelin protein in presence of GSI


title: ChIP-Seq H3K27Ac HET


title: ChIP-Seq H4K16Ac WT

value: Millipore 07-329


title: ChIP-Seq NCor minus Reelin

value: Rosenfeld Lab


title: ChIP-Seq NCor plus Reelin

value: Rosenfeld lab


title: ChIP-Seq H4K16Ac HET

value: hippocampal tissue

value: hippocampus


title: ChIP-Seq MEF2 plus Reelin

value: Santa Cruz Biotechnologies sc-313


title: ChIP-Seq MEF2C minus Reelin

value: Abcam ab79436


title: ChIP-Seq H3K27Ac WT


title: ChIP-Seq MED23 plus Reelin

value: Novus NB200-337


title: ChIP-Seq MEF2 minus Reelin


title: ChIP-Seq MED1 plus Reelin

value: Bethyl Laboratories A300-793A


title: RNA-Seq plus Reelin

description: RNA-seq in primary cortical neurons treated with 10nM purified recombinant Reelin protein


title: ChIP-Seq MED1 minus Reelin


title: ChIP-Seq H3K4me2 plus Reelin

value: Millipore 07-030


title: ChIP-Seq Cortical Neurons Input


title: ChIP-Seq H4K16ac plus Reelin


title: ChIP-Seq H4K16ac minus Reelin


title: ChIP-Seq CREB plus Reelin

value: Millipore 17-600


title: ChIP-Seq H3K4me2 minus Reelin


title: ChIP-Seq CREB minus Reelin


title: ChIP-Seq CBP plus Reelin

value: abcam ab2832


title: ChIP-Seq CBP minus Reelin

value: CorticalNeurons


title: WT Input

first: Kenneth

middle: N

last: Ross

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Other: CMS-IP

data_processing:
Sequencing reads derived from S6KO and WT ESCs CMS-IP and Input assays were mapped against mm9 as previously described for bisulfite treated samples (Pastor et al., 2011, PMID: 21552279).
After discarding all reads that map to multiple positions in the genome, there are 11,679,660 reads for S6KO CMS-IP, 13,916,523 reads for WT CMS-IP, 24,157,471 reads for S6KO input, and 16,743,260 reads for WT input.
To identify genome wide differentially hydroxymethylated regions (DHMRs) in S6KO compared to WT, we calculated differential coverage at genome wide 500 bp windows by employing the Bioconductor package MEDIPS (Lienhard et al., 2014, PMID: 24227674) v1.12.0 (extend = 200, uniq = T, window_size = 500, BSgenome = BSgenome.Mmusculus.UCSC.mm9, adj = F, diff.method = edgeR, p.value = 1e-3), resulting in 1,562 genomic windows with significant loss of 5hmC in S6KO, and 2,218 genomic windows with significant gain of 5hmC.
Genome_build: mm9
Supplementary_files_format_and_content: Result table contains counts, rpkm, log2FC, and p-values at genome wide 500 bp windows as returned by the MEDIPS software for significant DHMRs (p.value < 1e-3).

source_name: mouse embryonic stem cells

growth_protocol: WT and S6KO ES cells were grown in ES media conditions

extract_protocol:
WT and S6KO ES cells were harvested at approximately 80% - 90% confluence, washed with PBS and kept at -20°C
Genomic DNA was sheared using Covaris Adaptive Focused Acoustic to the center at 200 bp. DNA fragments were size selected and ligated with methylated adaptors and treated with sodium bisulfite (invitrogen). The extra adapters were removed by AmpurXP (Beckman). The DNA was then denatured for 10 minutes at 95 °C (0.4 M NaOH, 10 mM EDTA), neutralized by the addition of cold 2M ammonium acetate (pH 7.0) for 10 min on ice. Then denatured DNA fragments were incubated with 1 μl anti-CMS antiserum in 1x IP buffer (10 mM sodium phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100) for 2 h at 4 °C, and then precipitated with protein G beads. Precipitated DNA was eluted with proteinase K, purified with phenol chloroform, amplified and enriched by 8 cycles PCR using Pfu TurboCx hotstart DNA polymerase (Stratagene).  DNA sequencing was carried out using Illumina HiSeq sequencing systems.

value: wild type

value: input


title: 2 Control heart

city: Claremont

first: Alexander

middle: C

last: Zambon

address: 517 Watson Drive

department: Biopharmaceutical Sciences

institute: Keck Graduate Institute

data_processing:
Low quality reads were trimmed off of ends with Trim_galore
Reads were mapped to exons and junctions with Tophat2 using the following -G -r -28 --mate-std-dev 100
AltAnalyze was used to generate RPKM normalization for samples with the following parameters database: EnsMart72   species: Mm   method: RNASeq   constitutive_source: Ensembl   dabg_p: 1.0   junction expression threshold: 2.0   exon_exp_threshold: 5.0   gene_exp_threshold: 10.0   exon_rpkm_threshold: 0.5   gene_rpkm_threshold: 0.5   expression_data_format: non-log   include_raw_data: yes   run_from_scratch: Process RNA-seq reads   perform_alt_analysis: yes   calculate_gene_expression_using: core
Genome_build: Mm10
Supplementary_files_format_and_content: text file continaing a matrix of RPKM values for each Sample and included with the latest annotation Identifiers

source_name: embryonic heart

extract_protocol:
Hearts from E12.5 embryos were rapidly dissected in ice cold 1x PBS and placed directly into TRIzol (Invitrogen), dounce homogenized (20 strokes) and total RNA isolated according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Black-Swiss

value: NKX2-5 Cre/WT; Hif1a WT/flox


title: 5 Control heart


title: 5 Hif1a Mutant Heart

value: NKX2-5 Cre/WT; Hif1a Null/flox


title: 9 Control heart


title: S6KO Input

description: Other: CMS-IP

value: Sirt6 knockout


title: 10 Hif1a Mutant Heart


title: ChIP-Seq MEF2C plus Reelin

value: cortical neuron


title: S6KO CMS-IP

description: Other: CMS-IP

value: IP


title: 8 Hif1a Mutant Heart


title: Input_Starved_ChIPseq

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Mapped using LifeScope
peaks were called using MACS version 1.4.2 with the following setting: Default parameters were used for peak calling using Stimulated input. While peak calling by using Starved input the pvalue used is 1e-15 rest all parameters are default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files generated using MACS version 1.4.2

source_name: Cultured Human Cells

growth_protocol: 37C, 5% CO2, humidity, 10%BCS, 0.5% Glutamine, MEM (All SIGMA)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibody.
Libraries were prepared according to 5500 series SOLiD system instructions accompanying the Library Builder™ Fragment Core Kit for 5500 SOLiD™ (#Part no. 4463763).

treatment_protocol: Normal human fibroblasts were serum-starved for 72 h. One set of cells were continued to be starved for additional 12h while another set was stimulated with 10% FBS for 12h.

value: control

value: Normal human foreskin 1064Sk

tag: chip antibody


title: WT CMS-IP

description: Other: CMS-IP


title: ChIP-Seq MED23 minus Reelin


title: HH34803_GCCAAT

city: Houston

first: Jason

last: Heaney

state: Texas

address: One Baylor Plaza, R810

department: Molecular & Human Genetics

institute: Baylor College of Medicine

data_processing:
fastq files were uploaded to usegalaxy.org and converted to fastqsanger
files were trimmed to 5-95 bp, adapter sequences were removed, and files were filtered by quality with a value of 20 and percentage of 90
datasets were concatenated and aligned to the genome using TopHat
transcripts were assembled with Cufflinks with no quartile normalization, bias correction, or multi-read correct and using a reference annotation
files were merged in Cuffmerge using a reference annotation and reference file for sequence data
Cuffdiff was used to analyze replicates with geometric library normalization, pooled dispersion estimation, a false discover rate of .05, minimum alignment count of 10, no quartile normalization but with multi-read correct and bias correction
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of assembled transcripts from all reads for each sample and FPKM values

source_name: colonic myofibroblasts_rhIL-33

growth_protocol: CCD-18Co cells were obtained from ATCC, grown in EMEM medium containing 10% FBS and supplemented with non-essential amino acids until 80% confluency

extract_protocol:
RNA prepped according to Qiagen RNeasy Mini Kit (#74106) with QiaShredder columns (#79656)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: media was removed and replaced with medium containing 10 ng/ml rhIL-33 or vehicle (1X PBS) for 6 hours until removal by trypsinization

tag: cell line

value: normal intestinal subepithelial myofibroblasts

value: 10 ng/ml rhIL-33

tag: duration

value: 6 hours


title: HH34804_CAGATC


title: HH34801_TGACCA

source_name: colonic myofibroblasts_vehicle

value: vehicle (1X PBS)


title: Stimulated_ChIPseq

description:
Stimulated_peaks
Stimulated+AndStarved-

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Lifescope version 2.5 with default parameters.
Mapped using BioScope
peaks were called using MACS version 1.4.2 with the following setting: Default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files generated using MACS version 1.4.2

value: stimulated with FBS

value: Proteintech 10716-1-AP, Abcam ab126095 and ab56412, Santacruz sc-102434 and sc-102433


title: HH34800_CGATGT


title: Starved_ChIPseq

description:
Starved_peaks
Stimulated+AndStarved-

value: starved


title: Dyrk1a_shRNA rep2

first: Bernard

last: Khor

address: 185 Cambridge St MCPZN 7106

institute: Massachusetts General Hospital

description: Sample 6

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads from run 1 and 2 were combined for each of the 6 samples respectively
Sequenced reads were mapped to mm10 whole genom using Tophat 2.0.13
RSEM-based quantification using known transcripts was performed using protocol described by Li et al (BMC Bioinformatics 2011, 12:323)
The (raw) count matrix was then further processed with DESeq (Anders et al., Genome Biology 2010, 11:R106): The data was normalized by library size followed by variance estimation and evaluation of pairwise differential expression based on a negative binomial distribution model.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include matrix of fragment counts …

source_name: Splenic CD4+CD62L+

growth_protocol: Mouse (Balb/c) splenic CD4+CD62L+ MACS purified, stimulated on plate anti-CD3/28

extract_protocol:
Cells PBS washed, polyA RNA isolated using Dynabeads mRNA DIRECT kit (610-12)
RNA libraries were prepared for sequencing using standard Illumina protocols; PolydT primed reverse transcription followed by Nextera library prep according to manufacturers instructions

treatment_protocol: After 24h anti-CD3/28, +20x conc shRNA (scrmblr vs DYRK1a) @ 10ul per well, 24h later fed media + IL-2; scrmblr also +/- harmine 3.7uM. Harvest 48h later.

value: Dyrk1a shRNA

value: Balb/c

value: Splenic CD4+CD62L+

tag: age

value: 12 wks

value: TAGGCATG

tag: barcode

tag: i5 index 2

value: TATCCTCT


title: Input_Stimulated_ChIPseq

tag: treatment


title: Scrmblr rep2

description: Sample 4

value: scramble

value: TCCTGAGC

value: TAGATCGC


title: Scrmblr_Harmine rep2

description: Sample 5

value: scramble, harmine

value: GGACTCCT

value: CTCTCTAT


title: Dyrk1a_shRNA rep1

description: Sample 3

value: AGGCAGAA


title: HH34805_CTTGTA

value: normal intestinal subepithelial myofibroblasts

value: 10 ng/ml rhIL-33

value: 6 hours


title: NHEK-TM3C-1

city: La Jolla

first: Ferhat

last: Ay

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description: TM3C library constructed using only DpnII restriction enzyme.

data_processing:
We mapped the paired-end reads to the human reference genome (hg19) using the short read alignment mode  of BWA (v0.5.9) with default parameter settings. Each end of the paired reads was mapped individually.  We post-processed the alignment results to extract the reads that satisfy the following three criteria: (i)  mapped uniquely to one location in the reference genome, (ii) mapped with an alignment quality score of  at least 30, (iii) mapped with an edit distance of at most 3. Reads that satisfy these criteria are named  fully-mapped (F), and the rest of the mapped reads that did not satisfy these criteria are discarded from  further analysis. We identified pairs of fully-mapped reads that share a common identifier to generate the  set of contacts that we denote as F-F (fully-mapped - fully-mapped). The reads that did not map to any  location in this phase of mapping are named non-mapped and are analyzed further.
Within each non-mapped read, we first counted the number of cleavage sites, taking into account all the  restriction enzymes that are used in the digestion step for that specific library. We discarded reads that  contain more than two cleavage sites. We also discarded reads that contain no cleavage sites because such  reads surely are not chimeric.
We split the remaining reads, which contain one or two cleavage sites, into  two or three smaller fragments, respectively, preserving the entire cleavage site on both adjacent fragments.  We only kept the largest two fragments from each read. We mapped the resulting fragments to the genome  using BWA with default parameter settings. The 3-point filtering criteria mentioned in the previous section  are applied to the aligned reads, but allowing an edit distance of at most 1 to make sure we only extract  the unique and high quality mappings.
The reads that are extracted from this phase of mapping are named  partially-mapped (P) because they did not map as a whole, but their constituent fragments were successfully  mapped to different loci. The two classes of mapped reads (fully-mapped (F) and partially-mapped (P))  yield three possible types of contacts, namely F-F, F-P/P-F and P-P. The first set (F-F) is extracted after the  initial mapping in which each paired-end read can contribute at most one interaction between two loci. The  second set (F-P/P-F) consists of paired-end reads with one end fully mapped and the other end having either one  or two smaller fragments that mapped to the genome. If the latter contains only one mapped fragment, then  the only interaction is between this fragment and the fully-mapped end. However, if the end has two mapped  fragments, then this paired-end read produces three contacts: one between the two mapped fragments on  the partially-mapped end and two others that have one side from a fragment from the partially-mapped end  and the other side from the fully-mapped end. In addition, the same paired-end read produces one triple  (i.e., interaction among three loci) of type F-P/P-F. For the contacts of the third type (P-P), each paired-end  can produce either one, three or six binary contacts, depending on whether one or two fragments from each  end are successfully mapped. If only one fragment from one end and two from the other is mapped, then,  similar to the case of P-F, three binary contacts and one triple is produced. If both ends have two mapped  fragments, then six binary contacts, four triples (of type P-P) and one quadruple (i.e., contact among four  loci) are produced.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contain the pairwise (doubles) and multi-locus contacts for each library that is not an experimental control. For pairwise contacts we used BEDPE file format (see http://bedtools.readthedocs.org/en/latest/content/general-usage.html) with name field (column 7) representing the contact type (F-F or F-P or P-F or P-P) and score field (column 8) listing the read ID for cross referencing with fastq files. For contacts that link more than two loci simultaneously, we extended the BEDPE format to include triples (extension BEDTE) and quadruples (extension BEDQE) of genomic regions. Each line of a BEDTE or a BEDQE file first lists the coordinates of each locus then the contact type and read ID columns and finally the mapping strands of each locus in order.

source_name: normal human epidermal keratinocyte cells

extract_protocol:
Approximately six million NHEK and ten million KBM7 cells were fixed in 1.5% formaldehyde at room temperature for 10 minutes. The fixed cells were washed with TN buffer (10 mM Tris, 40 mM NaCl, pH 7.5) and collected by centrifugation at 600 g for 3 minutes. To increase digestion efficiency, fixed cells (6 or 10 million / 122 ul) were treated with SDS (add 3.8 ul of 10% SDS to a final of 0.30% SDS) at 64°C for 10 minutes and then at 37°C overnight (15 hours). The SDS concentration was reduced gradually to 0.10% by adding five times of 50 ul (1 x DpnII digestion buffer or NEB buffer 4 for multiple enzymes) with mixing. Triton X-100 (38 ul of 20% Triton X) was added to 1.8% concentration and the sample was incubated at  37°C for 1 hour. Sample volume was adjusted to 600 ul by adding 1 X restriction buffer, ATP (0.2 mM final) and BSA (100 ug/ml final). Digestion with appropriate restriction enzymes (300 units each) was carried out on a rotate shaker at 37°C for 15 hours. We used high concentration NEB enzymes to keep the final volume of the enzyme mixture less than 60 ul (1/10 reaction volume). The digested samples were deactivated at 65°C for 15 minutes and then centrifuged at 15,000 g for 5 min. We recovered ~95% of cellular DNA in the pellet fraction. The pellet fraction was re-suspended with T4 ligation buffer (15 ul 10 x buffer, 65 ul total) heated at 65°C and mixed with 100 ul of melted 2.5% low-melting agarose. We used 200 ul pipette to deliver the hot agarose sample to ice-cold ligation buffer (800 ul of 1 x ligation buffer containing T4 ligase (4000 units, NEB) in a steady fashion within ~5 seconds, on melted ice. Strings of gel bead appeared instantly at 0°C. We sealed the tube with parafilm and perform ligation at RT (23°C.) overnight on top of a shaker (~300 rpm), then transfer the tube to a iced water bath. The sample pellet was recovered by centrifugation at 20,000 g for 2 minutes, then 10 ul of 1% SDS (0.05% final) was added and heated at 80°C for 1 hour. Cross-links were reversed by treatment with Proteinase K (200 ug/ml) at 65°C and 300 rpm overnight (12 hours). Melted TM3C-agarose sample was incubated with RNase A (10 ug / 210 ul) at 55°C for 15 minutes and then purified by QIAquick gel extraction protocol (QUIAGEN Inc., CA). Purified TM3C DNA was quantified using both a NanoDrop spectrophotometer (Thermo Scientific) and a Qubit 2.0 Fluorometer. The Qubit quantification represents the more accurate DNA concentration.
Size-selected fragments were paired-end sequenced (100 bp per end) after adding sequencing adaptors using Illumina Hi-Seq 2000.

value: NHEK


title: KBM7-MCcont-4

description: Multiple 3C control library constructed using four different restriction enzymes (AluI, MspI, DpnIIm NlaIII). Tethering step (in-gel ligation) is omitted.

source_name: near-haploid human chronic leukemia cells


title: KBM7-TM3C-1


title: Scrmblr_Harmine rep1

description: Sample 2

value: CGTACTAG


title: Scrmblr rep1

description: Sample 1

value: Balb/c

value: TAAGGCGA


title: Hif1a pulldown replicate 2

data_processing:
Reads were mapped to mm10 genome build with Bowtie2
Homer software was used to make tag directory with default settings
Homer was used for peak calls using findPeaks function using cIP1/Input and cIP2/Input files separately using the -F 2 and -P .05 modifications to default
Peaks were merged with Homer's software MergePeaks function
Genome_build: Mm10
Supplementary_files_format_and_content: Data fields with Peak IDs and coordinates are saved as tab delimited .txt files

extract_protocol:
E12.5 mouse hearts were dissected and cross-linked in 1.5% of formaldehyde methanol-free for 10 minutes at room temperature. Samples were quenched by incubation with 2.5M glycine for 5 minutes. Hearts were ressuspended in lysis buffer (50 mM HEPES-KOH pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% Glycerol; 0.5% NP40; 0.25% Triton X-100) and dounce homogenized for nuclei isolation. The cross-linked chromatin was sonicated in Shearing buffer (1mM EDTA; 10mM Tris-HCl pH 7.6; 0.1% SDS) using a Covaris S2 (2% Duty cycle, 3 Intensity; 200 cycles per burst; for 8 minutes) to an average size of 200 bp. Precleared chromatin extract was incubated overnight at 4°C with 4μg of rabbit anti-HIF-1α antibody (Novus) and immunoprecipitated with protein A–Sepharose beads. 10 ng of ChIP DNA was used to generate a standard Illumina sequencing library.
libraries were prepared for sequencing using standard Illumina protocols

value: Black-Swiss

tag: genotype

value: Wild-type

tag: antibody


title: Pause sites in E. coli wild-type strain identified by RNET-seq

city: Frederick

first: Masahiko

last: Imashimizu

state: MD

department: NCI/CCR

institute: NCI

data_processing:
The fastq files of 36-bp sequenced reads were generated with the CASAVA v1.8 (Illumina). For the bulk RNET-seq analysis, the specific adapter sequences were trimmed with the Trimmomatic v0.25 to obtain reads ≥ 21-nt from the 5’ end. The reads ≥ 21-nt were mapped to the reference genome of E. coli K-12 strain W3110 (NC_007779.1) using the Bowtie2 v2.1.0 with the default parameter. A gene annotation file of E. coli W3110 was downloaded from the ftp server of Ensembl.
To analyze RNAP pausing on the E. coli chromosome, we counted the number of reads at every genomic nucleotide position using the mpileup command of SAM tools v0.1.18 with –A –B parameters. Pausing sites were defined P(φ, δ), where φ is the minimal fraction of having 3’ RNA ends in the mapped reads and δ is the minimal read depth for any genomic position. We chose δ to be 100 for WT and 160 for ΔgreAB, which normalized these respective numbers for each strain since there were 1.6-fold more total reads in the ΔgreAB strain. The high φ parameter allowed us to define a reliable pause-inducing element for WT or ΔgreAB cells.
The processed data file (csv) includes information about genomic position, reference/non-reference bases, read count, the fraction of 3’ RNA end, DNA strand (+/-), gene name, and mapping/base qualities in transcriptional pause sites that are defined by the parameters P(0.9,100).

organism: Escherichia coli

source_name: W3110 rpoC-6xHis::kan gal490

growth_protocol: The cells were grown in ~300 ml LB broth +25 mg/ml kanamycin with shaking at 37˚C until OD600 of ~0.5. The cells of 150 mg (wet weight) were harvested by centrifugation at 6,500 × g for 4 min at 4˚C, aliquoted in three 1.5 ml tubes, flash frozen in liquid nitrogen, and stored at -80˚C.

extract_protocol:
The 200 ml eluate from the Ni-NTA agarose was mixed with equal volume of pre-warmed PCI and incubated for 2 min at 70˚C. The mixture was centrifuged, and RNA and DNA were precipitated with isopropanol from the supernatant. The pellet was dissolved in 30 ml DNase I buffer with 5 U DNaseI (Takara Bio) and 20 U SUPERase, incubated for 10 min at RT. RNA was separated from the digested DNA by the PCI extraction and RNA was precipitated with isopropanol. The pellet was dissolved in diethylpyrocarbonate-treated water and used for cDNA synthesis.
cDNA library of the nascent RNA was constructed according to Churchman and Weissman, Nature 2011 (PMID: 21248844).

treatment_protocol: Each tube of the cell pellet stored at -80˚C was resuspended in 650 ml TES buffer (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 100 mM NaCl, 0.1% TritonX 100, 0.3 mM PMSF) at room temperature (RT). The cell suspension was mixed with 100 kU Ready-Lyse Lysozyme (Epicentre) and 50 µg RNaseA (Sigma) and incubated for 5 min, allowing rapid cell lysis. To digest the nucleoide, 62.5 U DNaseI (Roche) and 250 µg/ml heparin at the final concentrations as well as 74 ml DNaseI buffer (10 mM MnCl2 10 mM Tris-HCl, pH 7.5) were added to the mixture and incubated for 10 min at RT. To remove cell debris, the mixture was centrifuged at 20,000 x g for 3 min at 4˚C and the supernatant was collected into a new 1.5 ml tube. The supernatant including RNAPs that form ternary complexes with RNA/DNA were immobilized on ~155 µl Ni-NTA agarose (Qiagen) pre-equilibrated with the binding buffer (0.5 M NaCl, 5 mM imidazole, 5% glycerol, 20 mM Tris-HCl, pH7.9, 1 mM 2-mercaptoethanol) with shaking for 10 min at 4˚C. The immobilized ternary complexes were washed five times with the wash buffer (1M NaCl, 15 mM imidazole, 5% glycerol, pH7.9, 1 mM 2-mercaptoethanol) at 4˚C, washed twice with the nuclease buffer (40 mM KCl, 15 mM imidazole, 20 mM Tris-HCl, pH 7.9, 0.3 mM MgCl2 5% glycerol, 1 mM 2-mercaptoethanol) at 4˚C. The RNA transcript and DNA unprotected by RNAP were cleaved by the additions of 0.4 U RNase V1 (Invitrogen), 0.7 U RNase T1 (Sigma), and 5 U DNase I (Takara Bio) to the immobilized complexes and incubation for 7 min at RT. The nuclease-treated complexes were washed twice with the wash buffer, twice with the MnCl2-free nuclease buffer at 4˚C, and eluted by increasing the concentration of imidazole to 100 mM followed by shaking for 10 min at 4˚C in the presence of 30 U SUPERase RNase inhibitor (Ambion).

tag: genotype/variation

value: W3110 rpoC-6xHis::kan gal490

tag: molecule subtype

value: nascent 3' RNA


title: H111 wt #2

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Bc H111 genome using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: H111 genome sequence (accession no. HG938370, HG938371, and HG938372)
Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample

organism: Burkholderia cenocepacia H111

source_name: Bc H111 planktonic cells

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007) . Ds cDNA was produced and nugen librairies obtained.
RNA libraries were prepared using Ovation® Complete Prokaryotic RNA-Seq Library System

value: wt

tag: growth

value: planktonic cells, OD600 equal 0.5

tag: medium

value: minimal medium shift experiment (15 mM to 0.3 mM)


title: H111 s54 complemented mutant

tag: strain

value: s54 complemented mutant


title: Hif1a pulldown replicate 1

tag: developmental stage


title: Pause sites in E. coli ΔgreAB strain identified by RNET-seq

data_processing:
The fastq files of 36-bp sequenced reads were generated with the CASAVA v1.8 (Illumina). For the bulk RNET-seq analysis, the specific adapter sequences were trimmed with the Trimmomatic v0.25 to obtain reads ≥ 21-nt from the 5’ end. The reads ≥ 21-nt were mapped to the reference genome of E. coli K-12 strain W3110 (NC_007779.1) using the Bowtie2 v2.1.0 with the default parameter. A gene annotation file of E. coli W3110 was downloaded from the ftp server of Ensembl.
To analyze RNAP pausing on the E. coli chromosome, we counted the number of reads at every genomic nucleotide position using the mpileup command of SAM tools v0.1.18 with –A –B parameters. Pausing sites were defined P(φ, δ), where φ is the minimal fraction of having 3’ RNA ends in the mapped reads and δ is the minimal read depth for any genomic position. We chose δ to be 100 for WT and 160 for ΔgreAB, which normalized these respective numbers for each strain since there were 1.6-fold more total reads in the ΔgreAB strain. The high φ parameter allowed us to define a reliable pause-inducing element for WT or ΔgreAB cells.
The processed data file (csv) includes information about genomic position, reference/non-reference bases, read count, the fraction of 3’ RNA end, DNA strand (+/-), gene name, and mapping/base qualities in transcriptional pause sites that are defined by the parameters P(0.9, 160).

source_name: W3110 rpoC-6xHis::kan greA::tet, greB::amp

growth_protocol: The cells were grown in ~300 ml LB broth +25 mg/ml kanamycin with shaking at 37˚C until OD600 of ~0.5.The cells of 150 mg (wet weight) were harvested by centrifugation at 6,500 × g for 4 min at 4˚C, aliquoted in three 1.5 ml tubes, flash frozen in liquid nitrogen, and stored at -80˚C.


title: H111 wt nitrogen starved

value: minimal medium 0.3 mM NH4


title: Input


title: HH34802_ACAGTG

tag: cell type

value: vehicle (1X PBS)


title: H111 wt nitrogen replete

value: planktonic cells, OD600 equal 0.9

value: minimal medium 30 mM NH4


title: H3K4me3-scrambledshRNA

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to mouse genome mm9 using bowtie 1.0 with n = 1 and m = 3
The wiggle files has been created in the Cistrome platform using MACS
The difference Wiggle for H3K4me3 has been made via a custom workflow in cistrome
Genome_build: mm9
Supplementary_files_format_and_content: wiggle

growth_protocol: E14 mouse ES cells (ES-E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine (Invitrogen), 1 x Non-essential amino acids (Invitrogen), 1 x Penicillin/Streptavidin (Invitrogen) and LIF (Millipore) on gelatin-coated plates

extract_protocol:
Genomic DNA were extracted using antibodies for Flag, C17orf96, H3K4me3 or H3K27me3
Libraries were constructed of 10 ng of ChIP DNA following Illumina’s® protocol

treatment_protocol: For ChIP cells were crosslinked with 1% formaldehyd for 10 min and sonicated to 200 bps.

value: Millipore, #04-745


title: H3K27me3-C17orf96shRNA

value: Millipore, #07-449


title: H3K27me3-scrambledshRNA


title: KBM7-TM3C-4

description: TM3C library constructed using four different restriction enzymes (AluI, MspI, DpnIIm NlaIII).


title: C17orf96-C17orf96shRNA


title: C17orf96-scrambledshRNA


title: Flag-C17orf96

value: Flag-M2 (Sigma Aldrich)


title: Input


title: WT_CO_2

status: Public on Apr 28 2015

city: Ansan-si

first: Min-Sik

last: Kim

state: Gyeonggi-do

address: Haean-ro

department: Department of Marine Biotechnology

institute: Korea Institute of Ocean Science and Technology

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic 0.32 as default parameter, then mapped to mm8 whole genome using bowtie v 2.2.4 with parameters -t --very-sensitive
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v 2.2.1.
Genome_build: ASM1836v1 (PRJNA59043) (2013-06-10)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and locus tags for genes of T. onnurineus NA1

organism: Thermococcus onnurineus NA1

source_name: RNA from Archaeal cells

extract_protocol:
After cell harvest, RNA samples were prepared using TRIzol reagent. Genomic DNA was eliminated by DNaseI treatment.
To remove rRNA in total RNA, Ribo-Zero rRNA Removal Kits (Human/Mouse/Rat) (MRZH-11124, Epicentre, USA) was used. Illumina Stranded TruSeq Total RNA Sample Prep Kit (Cat#FC-122-2201) was used with 1 ug of rRNA depleted RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: media

value: MM1-CO (CO-supplied media)

tag: growth phase

value: exponential phase


title: ORCA Knockdown H3K9me3

city: Urbana

first: Supriya

middle: G

last: Prasanth

address: 601 S. Goodwin Avenue

department: Cell and Developmental Biology

institute: University of Illinois, Urbana-Champaign

data_processing:
The libraries were pooled, quantitated by qPCR and sequenced on one lane for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and analyzed with Casava1.8.2 (pipeline 1.8)
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: U2OS osteosarcoma cell line

growth_protocol: U2OS cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing high glucose and supplemented with 10% fetal bovine serum (FBS – Hyclone)

extract_protocol:
Formaldehyde (Sigma) was added to culture medium to a final concentration of 1%. Crosslinking was allowed to proceed for 10 min at room temperature and stopped by addition of glycine at a final concentration of 0.125 M. Fixed cells were washed and harvested with PBS. Chromatin was prepared by two subsequent extraction steps (10 min at 4°C) with Buffer 1 (50 mM Hepes/KOH pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% Glycerol; 0.5% NP-40; 0.25% Triton) and Buffer 2 (200 mM NaCl; 1mM EDTA; 0.5mM EGTA; 10 mM Tris pH 8). Nuclei were then pelleted by centrifugation, resuspended in Buffer 3 (50 mM Tris pH 8; 0.1% SDS; 1% NP-40; 0.1% Na-Deoxycholate; 10 mM EDTA; 150 mM NaCl) and subjected to sonication with Bioruptor Power-up (Diagenode) yealding genomic DNA fragments with a bulk size of 150-300 bp.
The ChIPseq libraries were prepared with Illumina's 'TruSeq DNA Sample Prep kit'.

treatment_protocol: Cells were grown to 30% confluency and siRNA against ORCA or control luciferease gene were delivered into the cells at a final concentration of 100nM using Lipofectamine RNAimax (Invitrogen). The siRNAs were delivered twice at the gap of 24 hours and the cells were collected 24 hours after the second round of transfection for subsequent analysis.

value: Cell line derived from a bone cancer patient

tag: cell line

tag: chip antibody

value: ORCA knockdown


title: ORCA knockdown Input

value: input


title: Control Input

value: control


title: Control H3K9me3


title: H3K4me3-C17orf96shRNA


title: human C6 (IL3Ra-low)

city: Amsterdam

first: yanling

last: xiao

address: Plesmanlaan 121

country: Netherlands

institute: NKI

data_processing:
Sequence reads were mapped to NCBI build 37 using tophat version 2.0.6 with parameters --bowtie1, --library-type fr-unstranded, --no-coverage-search, --mate-inner-dist, --mate-std-dev, -M, -G, --transcriptome-index, Ensembl GTF version 66
Readcounts were calcultated using HTSeq-count with default parameters
Genome_build: GRCh37
Supplementary_files_format_and_content: The file genecounts.txt contains the absolute gene expression values for each of the samples.

source_name: Bone marrow

growth_protocol: human BM IL3Ra-high- or IL3Ra-low hematopoietic progenitor cells were sorted from three different healthy individuals

extract_protocol:
sorted cells were immediately put in 1ml trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were sorted from direct ex-vivo cryo-preserved human BM samples, sorted cells were without additional treatment

tag: date of birth

tag: bm sample date

tag: cell sorting date

value: 15-May-2013 (BD FACS Aria)

value: BM progenitor

tag: cell population

value: IL3Ra-low progenitor cells


title: WT_CO_1


title: human C5 (IL3Ra-low)


title: human C7 (IL3Ra-low)


title: Input

city: Philadelphia

first: Feng

last: Zhang

state: PA

address: 415 Curie Boulevard

department: Department of Neuroscience and Mahoney Institute for Neurosciences

institute: Perelman School for Medicine, University of Pennsylvania

data_processing:
ChIP-seq reads mapping: Alignment of the ChIP-seq data to the reference genome (rn3) was carried out using SOAP2.21 software allowing at most 2 mismatches. Reads that are mapped to a unique genomic location were chosen for further analysis.
ChIP-seq peak calling: peaks were called using MACS 1.4.0 software, with p-value < 10e-5.
Genome_build: rn3
Supplementary_files_format_and_content: wig file with the relative binding level to each position.

organism: Rattus norvegicus

source_name: embryonic cerebral cortex

extract_protocol:
Histone-DNA complexes of lysates from sonicated nuclei were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Sample Prep kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase and Klenow polymerase. A single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through being treated with Klenow fragment, and then the 3-'A' ended DNA was ligated to Illumina's adapters which have a single 3-'T' base using DNA ligase. After adapter ligation DNA was PCR amplified with primers and library fragments of 100-300 bp (insert plus adaptor and PCR primer sequences) were selected. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: tissue

value: brain

value: embryonic 15.5 days

value: Sprague Dawley


title: human C7 (IL3Ra-high)

value: IL3Ra-high progenitor cells


title: human C5 (IL3Ra-high)


title: LSD1_ChIPSeq