title: QSC_o_H3K4me3_ChIPSeq

city: Palo Alto

first: Ling

last: Liu

address: 300 Pasteur Drive

data_processing:
Basecalling was performed using Illumina RTA 1.8.70.0
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie.
Unique reads mapped to a single genomic location (allowing a maximal of 2 mismatches) were used for peak detection by Model-based Analysis of ChIP-Seq (MACS) with alignment of the ChIP input DNA as control.
Genome_build: mm9
Supplementary_files_format_and_content: .bed files for ChIP-seq analysis containing peak location and −10*log10(p value) are provided.

source_name: hindlimb muscles

growth_protocol: QSCs were FACS-purified from hindlimb muscle of healthy mice at the indicated ages.

extract_protocol:
FACS-sorted cells were crosslinked with 1% formaldehyde at room temperature with gentle agitation for 10 minutes. The crosslink was terminated by Glycine at a final concentration of 0.125 M. Cells were then washed three times with ice-cold PBS and stored at -80°C until a sufficient number of cells had been obtained. ChIP was performed following standard ChIP protocols with the following major modifications: 10E6 cells were resuspended in 200 ml lysis buffer and sonicated to obtain DNA fragments from 150 to 500 bp in size. Each ChIP reaction was performed with 10E6 cells and 5 ug of antibody.
The ChIP DNA was size-selected for fragments between 150-400 bp by 2% low-melt agarose gel electrophoresis (NuSieve). A library for deep sequencing was generated with Illumina ChIP-seq Sample Prep Kit (Part# IP-102-1001) with the following modification to the standard protocol: The adaptor solution was diluted 50 times for ligation. 15 cycles of PCR amplification were performed immediately following adaptor ligation. Size-selection of fragments between 200-400 bp was performed after PCR amplification. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

treatment_protocol: FACS-purified QSCs from young mice were plated on ECM coated surface in F10 media supplemented with 10% horse serum for 3 days to obtain ASCs.

value: male

value: 22-24 months

tag: sorting markers

value: H3K4me3 (Abcam 8580)


title: ASC_y_input DNA

status: Public on Aug 13 2013

type: SRA

country: USA

institute: Stanford University

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: gender

tag: age

value: 2-3 months

tag: chip antibody


title: QSC_y_input DNA


title: QSC_y_H3K36me3_ChIPSeq


title: ASC_y_H3K36me3_ChIPSeq


title: ASC_y_H3K4me3_ChIPSeq


title: Background_Plus_LY

city: Stanford

first: Anne

last: Brunet

state: California

address: 300 Pasteur Drive,

department: Genetics

data_processing:
Reads with low quality scores (sequences that have phred <15 on 85% seq) were filtered using the fastx toolbox (fastq_quality_filter -v -Q 33 -q 15 -p 85)
Reads were aligned to mm9 using bowtie-0.12.7 (bowtie -p 4 -S -q -v 2 -m 3 --best --strata)
For chromatin marks, peaks were generated using Macs (version 2) software with "broad option" and with default settings (macs2 --broad)
For transcription factor, peaks were generated using QuEST 2.1 using the highest stringency peak calling parameters (Fold enrichment > 50, bandwidth=30)
Genome_build: mm9
Supplementary_files_format_and_content: H3K27me3, H3K4me1 and H3K4me1 peak files were generated using MACS 2, Ascl1 and FoxO3 peak bed files were generated using QuEST 2.1

source_name: Neural progenitor cells

growth_protocol: Adult (12-week-old) mouse NPCs were isolated as previously described (Renault et al., Cell Stem Cell 2009). Briefly, whole mouse forebrains were homogenized and incubated for 30 min in HBSS (Invitrogen) with 1 U/ml DispaseII (Roche), 250 U/ml DNaseI (Sigma) and 2.5 U/ml Papain (Worthington) at 37oC. After mechanical dissociation, cells were purified by sequential 25% and 65% Percoll (Amersham) gradients. Cells were cultured in high growth factor signaling conditions: Neurobasal A (Invitrogen) medium supplemented with penicillin/streptomycin/glutamine (Invitrogen), 2% B27 (Invitrogen) and 20 ng/ml each of FGF2 (Peprotec) and EGF (Peprotec).

extract_protocol:
Chromatin was cross-linked with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. Cells were washed and incubated in swelling buffer (10 mM HEPES pH 7.8, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT, 0.5 mM PMSF) for 15 min on ice, followed by nuclei isolation by dounce homogenization. Nuclei were pelleted and resuspended in RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 1% SDS in PBS pH 7.4), and chromatin was sheared with a Vibra-Cell Sonicator VC130 (Sonics) six times for 30 sec at 60% amplitude.
Single end libraries were generated according to the manufacturer’s instructions (Illumina).

treatment_protocol: To induce FOXO3 nuclear accumulation, cells were incubated in low growth factor signaling conditions: Neurobasal A medium supplemented with penicillin/streptomycin/glutamine and 2% B27 for 4 hours, followed by a 1.5 hour incubation with 20 mM LY294002 (LY, Calbiochem-Novabiochem Corp.), a specific PI3K inhibitor, to inhibit residual growth factor signaling.

value: FVB/N

tag: cell type

value: Primary adult neural progenitor cell

tag: passages

value: No Antibody


title: QSC_y_H3K4me3_ChIPSeq


title: HCT116_MeCP2_GA3247_ChIPseq

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

description: fastq

data_processing:
BED files were generated by aligning ChIP-seq reads to hg18 genome using Bowtie algorithm (version 0.12.5). UCSC genome browser displayable bedGraph files for ChIP-Seq data were generated by counting shifted tags in 200-bp windows across the genome and normalizing window tag counts by 5 million total sequenced reads to make different libraries directly comparable.
Genome_build: hg18
Supplementary_files_format_and_content: The bed files report alignments.  Most of the results reported in our manuscript were obtained by processing BED files (however, too many and too heterogeneous, making it difficult to deposit them all).
Supplementary_files_format_and_content: The bedGraph files report the number of ChIP-Seq sequencing reads in a  genomic interval, normalized to 5 million uniquely aligned sequenced reads.

organism: Homo sapiens

growth_protocol: Human IMR90 cells (American Type Culture Collection; ATCC) were cultured under optimal growth conditions as specified by ATCC, and only cells at early passage were used for experiments. HCT116 cells were generous gifts from Dr. B. Vogelstein (Johns Hopkins University). These cells were cultured in McCoy's 5A medium with 10% FBS.

extract_protocol:
Chromatin from 5 million cells per ChIP was prepared by formaldehyde cross-linking and sonication as described previously. Antibodies against MeCP2 (Abcam; ab2828) and ser2p-PolII (Abcam; ab5095) were added in manufacturer-recommended amounts per ChIP. For input control samples, DNA was isolated from 10% (vol.) of chromatin material used for ChIP by phenol/chloroform extraction and ethanol purification procedures.
ChIP-Seq was carried out according to established protocols and prepared libraries were sequenced with the Illumina Genome Analyzer II or HiSeq 2000 sequencer according to the manufacturer’s instructions.

tag: cell line

value: MeCP2 (Abcam; ab2828)


title: HCT116_6hr_TSA_GA3816_RNAseq

library_source: transcriptomic

data_processing:
RNA-Seq reads were aligned to hg18 genome using TopHat algorithm (version 1.3.1)  with '-g 1' option.
Genome_build: hg18
Supplementary_files_format_and_content: exon junction BED files generated using Tophat

molecule: polyA RNA

source_name: HCT116 cells treated with trichostatin-A (TSA) for 6 hours

growth_protocol: Human IMR90 cells (American Type Culture Collection; ATCC) were cultured under optimal growth conditions as specified by ATCC, and only cells at early passage were used for experiments15. HCT116-WT and HCT116-DKO (DKO1 line) cells were generous gifts from Dr. B. Vogelstein (Johns Hopkins University)17. These cells were cultured in McCoy's 5A medium with 10% FBS.

extract_protocol:
Total mRNA was isolated from all cells using the RNeasy kit (Qiagen) and converted to cDNA using the Superscript ds-cDNA synthesis kit (Invitrogen) according to the manufacturer’s instructions.
For RNA-Seq, double-stranded DNAs were fragmented to 100–200 bp using sonication, followed by end-repair, Illumina adaptor ligation, and sequencing using the Illumina HiSeq 2000 platform according to the manufacturer’s protocol for paired-end reads.

treatment_protocol: (1) Primary IMR90 cells were seeded at 1 × 10^5 cells per well of a 6-well plate, incubated for 24 hours in Eagle's Minimum Essential Medium (EMEM, ATCC) high glucose with 10% serum, and then supplemented with fresh media containing 20 μM 5azadC (Sigma-Aldrich) for 72 hours. Media containing drug was changed every 24 hours. (2) For HDAC inhibition, IMR90 or HCT116-WT cells were seeded at a density of 2 × 10^6 cells in 100-mm plates with EMEM or McCoy’s 5A medium (ATCC) supplemented with 10% serum, respectively, incubated overnight, and mock treated (media only; ‘CTR’) or treated with 300 nM TSA (Sigma-Aldrich) for 6 hours in an CO2 incubator at 37°C. MeCP2 shRNA, 5’- CATTAGGGTCCAGGGATGTGT - 3’; shRNA constructs were designed and cloned into the pGreenPuro lentiviral vector according to specifications provided by System Biosciences and their shLuc construct was used as a negative, non-specific control. Sequences were confirmed by automated DNA sequencing (not shown). (3) The shMeCP2 and shLuc constructs were transfected into HEK-293T cells for packaging according to System Biosciences’ instructions. Viral supernatants were collected for infection of IMR90 cells. 2 × 10^6 early passage IMR90 cells or HCT116-WT cells were seeded in the presence of viral supernatant and 8 μg/ml polybrene per well of a 12-well plate. After 24 hours, cells were trypsinized and transferred into 6-well plates with fresh media and 5 μg/ml puromycin. Selection was visually monitored by GFP positivity and cells were collected for experiments at day 3 post-infection when >95% of cells by count were GFP positive.

tag: genotype/variation

value: wild type

tag: treated with

value: 300nM TSA for 6 hrs


title: HCT116_ser2p_PolII_GA3249_ChIPseq

description: fastq

value: ser2p-PolII (Abcam; ab5095)


title: IMR90_6hr_TSA_GA3263_RNAseq

source_name: IMR90 cells treated with trichostatin-A (TSA) for 6 hours


title: HCT116_GA3814_RNAseq

source_name: HCT116 cells


title: IMR90_GA3259_RNAseq

source_name: IMR90 cells


title: HCT116_Input_GA3250_ChIPseq

description: fastq

value: none (input)


title: HCT116_MeCP2_GA1576_ChIPseq

description: phred+64 fastq


title: HCT116_shLuc_GA3255_RNAseq

source_name: HCT116 cells infected with the negative control shRNA-luciferase (shLuc) construct

tag: infected with


title: HCT116_shMeCP2_GA3256_RNAseq

source_name: HCT116 cells infected with the shRNA-MeCP2 construct

value: shRNA-MeCP2 construct


title: IMR90_Input_GA2460_replicate_ChIPseq

description: phred+64 fastq


title: IMR90_Input_GA2460_ChIPseq

description: phred+64 fastq


title: IMR90_MeCP2_GA1580_replicate_ChIPseq

description: phred+64 fastq


title: IMR90_MeCP2_GA1580_ChIPseq

description: phred+64 fastq


title: QSC_o_input DNA


title: QSC_o_H3K27me3_ChIPSeq

value: H3K27me3 (Millipore 07-449)


title: IMR90_MeCP2_GA1110_ChIPseq

description: phred+64 fastq


title: IMR90_shMeCP2_GA2349_RNAseq

source_name: IMR90 cells infected with the shRNA-MeCP2 construct


title: ASC_y_H3K27me3_ChIPSeq


title: IMR90_shLuc_GA2348_RNAseq

source_name: IMR90 cells infected with the negative control shRNA-luciferase (shLuc) construct


title: QSC_y_H3K27me3_ChIPSeq


title: HCT116_DKO_GA2067_RNAseq

source_name: HCT116 cells expressing hypomorphic DNMT1 and lack DNMT3b (HCT116-DKO)


title: HCT116_GA2066_RNAseq


title: IMR90_GA2064_RNAseq


title: A37

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
Basecalling with Illumina pipeline software (SCS v2.8 / RTA v1.8)
36 bp reads were checked for quality using FastQC.
Reads were aligned to the Rat genome (build RN4) using BWA (aln algorithm v0.6) with default settings in Galaxy UI.
Reads aligning to exons with a mapping quality score above 20 were counted and summed over genes for each sample using HTSeq.
The resulting count matrix was tested for differential gene expression (DGE) between control and HFD offspring using the edgeR package
Genome_build: RN4
Supplementary_files_format_and_content: Count matrix

organism: Rattus norvegicus

source_name: Hind limb skeletal muscle (soleus)

growth_protocol: Female Sprague-Dawley rats weighing 200 to 300g were obtained from ARC (Animal Resources Centre, WA) and housed under standard animal facility conditions (22-23°C, 30-33% humidity, 12-hour light/dark cycle). Water and food were given ad libitum.

extract_protocol:
Skeletal muscle (soleus) was collected from the hind limb of offspring and immediately snap frozen and stored at -80˚C for RNA and protein analysis. Frozen muscle (~50 mg) was homogenised with a motorized rotor-stator homogenizer (3 pulses of 15 seconds).  Total RNA was extracted using RNeasy isolation kit (QIAGEN, Valencia, CA) using the manufacturer’s recommended protocol. RNA quality was determined by the MultiNA capillary electrophoresis system (Shimadzu Biotech, Sydney, NSW, Australia). Messenger RNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) from 2 μg total RNA.
Sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina® (New England Biolabs). Libraries were quantified on MultiNA system and sequenced at a concentration of 12 pM on the Genome Analyzer IIx (Illumina Inc, CA, USA) using TruSeq version 5 cluster kit (cBot) and SBS kit (36 cycles).

treatment_protocol: Female breeder rats were fed either a normal fat diet (NFD, 6% soy oil, 10% sucrose w/w, 16.1 MJ/Kg digestible energy; Specialty Feeds, Glen Forest, WA) or a diet rich in saturated fat (sourced mainly from animal lard) and sucrose (HFD, 23.3% fat, 20% sucrose wt/wt, 19.6MJ/Kg digestible energy; Specialty Feeds) for the 3 weeks prior to mating and throughout pregnancy and lactation. This time period was chosen to ensure that offspring were exposed to a high fat/sucrose diet throughout the developmental period. Offspring of NFD and HFD dams were weaned at postnatal day 21 and maintained on a standard chow diet (ad libitum) for the remainder of their life. For tissue collection at 12 months, 11 male offspring (6 of control dams, 5 of high fat/sucrose-fed dams) were fasted 1 to 2 hours before being anaesthetized using inhaled isofluorane.

value: Sprague Dawley rats

tag: litter

tag: diet

value: High Fat

tag: weight(g)

tag: mesentericfat(g)

tag: %bw

tag: perirenalfat(g)

tag: abdominalfat(g)

tag: totalfat

tag: heart(g)

tag: liver(g)

tag: pancreas(g)

tag: lkid(g)

tag: brain(g)

tag: plasmainsulin(ng/ml)

tag: plasmainsulin(mu/l)

tag: glucose(mmol)

tag: homa-ir


title: A75

tag: strain

tag: litter

value: Control


title: C25

tag: diet

tag: weight(g)


title: H20

tag: mesentericfat(g)

tag: %bw


title: H1

tag: perirenalfat(g)

tag: abdominalfat(g)


title: A89

tag: totalfat

tag: heart(g)


title: C91

tag: liver(g)

tag: pancreas(g)


title: C60

tag: lkid(g)

tag: brain(g)


title: C73

tag: plasmainsulin(ng/ml)

tag: plasmainsulin(mu/l)


title: H10

tag: glucose(mmol)

tag: homa-ir


title: Hi-C Tcell Rad21WT R3

city: Barcelona

first: Andre

middle: J

last: Faure

address: Dr. Aiguader 88

department: EMBL-CRG Systems Biology Unit

country: Spain

institute: Centre for Genomic Regulation (CRG)

data_processing:
DEKKER ICE METHOD - all relevant HiC data (binned at 4 resolutions) raw + iced data
UCSC GENOME BROWSER BED FILE - coordinates of all chip-seq peaks
Tab delmited file of all gene  expression values (count equivalents) across all 4 samples.
Genome_build: mm9
Supplementary_files_format_and_content: peak bed (ChIP-seq), counts (RNA-Seq), and HiC data

source_name: CD4+ CD8+ Double Positive Thymocytes

extract_protocol: Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: A comprehensive technique to capture the conformation of genomes. Methods. 2012 Nov; 58(3):268-76.

tag: cell type

value: CD4+ CD8+ Double Positive Thymocytes

tag: genotype

value: Rad21 KO

tag: genetic background

value: C57BL\6 and 129 mixed


title: Hi-C Tcell Rad21KO R3


title: WT DP R1

molecule: total RNA

extract_protocol: Total RNA was extracted from sorted CD4+ CD8+ DP thymocytes using RNABee. 10 μg RNA were used with the Ribominus kit (Life Technologies) to deplete rRNA. rRNA-depleted transcripts were used with the Illumina TrueSeq kit to obtain high throughput sequencing libraries.


title: WT DP R2


title: Hi-C Tcell Rad21WT R1


title: Nipbl ChIP DP

extract_protocol: 50 million sorted CD4+ CD8+ DP thymocytes were fixed in 10% FCS DMEM media containing 1% formaldehyde. The cells were lysed and sonicated in [20 mM Tris-HCl, pH8, 150 mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X, protease inhibitors]. Lysates were cleared by centrifugation and NIPBL-DNA complexes were captured with 5 μg anti-NIPBL antibody (Bethyl, #A301-779A) and 25 μl Dynabeads. The captured DNA was eluted from the beads with a mixture of RnaseA, proteinaseK in [TE, 1% SDS] for 2 hours at 37° and then 16 hours at 65°. DNA was purified by phenol-chloroform extraction and 10ng was used with a Illumina ChIP-seq sample preparation according to the manufacturer instructions.

tag: chip antibody

value: NIPBL (Bethyl Laboratories, A301-779A, lot A301-779A-2)


title: Rad21KO DP R1


title: Hi-C Tcell Rad21KO R1


title: Pre-immune sequencing reads

city: University Park

first: David

middle: Scott

last: Gilmour

state: Pennsylvania

address: 465 North Frear

department: Biochemistry and Molecular Biology

institute: Penn State University

description: sequencing reads for DNA recovered with preimmune serum

data_processing:
Sequence reads were obtained and mapped to the Drosophila melanogaster dm3 (April, 2006) genome using Bowtie 1.1.2 with a seed length of 28 nucleotides.
All unique reads mapping with two or fewer mismatches were retained.
The reads on both strands were shifted 50 base pairs towards the center of the ChIP'ed DNA fragments and binned into 25 nucleotide widows to make bedgraph files for both M1BP ChIP-seq and Pre-immune ChIP-seq results.
Genome_build: dm3 (April, 2006)

organism: Drosophila melanogaster

source_name: S2R+ cells

growth_protocol: Cells were grown in Schneider's media with 10% FBS at 24 degrees C

extract_protocol:
Crosslinked chromatin from 20 million cells was immunoprecipitated by either M1BP antisera or preimmune sera.  DNA precipitated from two biologically independent experiments was combined and subjected to library preparation for SOLiD sequencing
DNA libraries were prepared as described by Motallebipour et al. (2009) Genome Biology 10, R129

treatment_protocol: Crosslinked chromatin was prepared from cells as described by Petesch, S.J. and J.T. Lis (2008) Cell 134, p 74-84

tag: antibody

value: Preimmune sera

tag: cell line


title: Rad21 ChIP DP

extract_protocol: Sorted CD4+ CD8+ DP thymocytes were fixed in 10% FCS DMEM media containing 1% formaldehyde. The cells were lysed and sonicated in [10 mM Tris-HCl, pH7.4, 800 mM NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X, 0.1% Sodium Deoxycholate, protease inhibitors]. Lysates were cleared by centrifugation and 150 μg were incubated with 5 μg anti-Rad21 antibody (Abcam, ab992) and 25 μl Dynabeads to capture Rad21-DNA complexes. DNA was eluted with a mixture of RNaseA and proteinaseK for 2 hours at 37° followed by 16 hours at 65° to reverse the cross-links. DNA was purified by phenol-chloroform extraction and 10ng was used with a Illumina ChIP-seq sample preparation according to the manufacturer instructions.

value: Rad21 (Abcam, ab992, Multiple Lots)


title: Med1 ChIP DP

extract_protocol: 50 million sorted CD4+ CD8+ DP thymocytes were fixed in 10% FCS DMEM media containing 1% formaldehyde. The cells were lysed and sonicated in [20 mM Tris-HCl, pH8, 150 mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X, protease inhibitors]. Lysates were cleared by centrifugation and Med1-DNA complexes were captured with 5 μg anti-Med1 antibody (Bethyl, #A300-793A) and 25 μl Dynabeads. The captured DNA was eluted from the beads with a mixture of RnaseA, proteinaseK in [TE, 1% SDS] for 2 hours at 37° and then 16 hours at 65°. DNA was purified by phenol-chloroform extraction and 10ng was used with a Illumina ChIP-seq sample preparation according to the manufacturer instructions.

value: Med1 (Bethyl Laboratories, A300-793A, lot A300-793A-1)


title: Input DP (for Rad21 ChIP)

extract_protocol: Sorted CD4+ CD8+ DP thymocytes were fixed in 10% FCS DMEM media containing 1% formaldehyde. The cells were lysed and sonicated in [10 mM Tris-HCl, pH7.4, 800 mM NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X, 0.1% Sodium Deoxycholate, protease inhibitors]. Lysates were cleared by centrifugation and incubated with a mixture of RNaseA and proteinaseK for 2 hours at 37° and then 16 hours at 65° to reverse the cross-links. DNA was purified by phenol-chloroform extraction and 10ng was used with a Illumina ChIP-seq sample preparation according to the manufacturer instructions.

value: input DNA


title: IMR90_Aza_GA2065_RNAseq

source_name: IMR90 cells treated with 5azadC

tag: genotype/variation

value: wild type

tag: treated with

value: 20 μM 5azadC for 72 hrs


title: M1BP sequencing reads

description: sequencing reads for DNA crosslinked to M1BP

value: M1BP antisera generated in a rabbit using recombinant M1BP isolated from E. coli.


title: Input DP (for Input DP for Nipbl and Med1 ChIP)

extract_protocol: Sorted CD4+ CD8+ DP thymocytes were fixed in 10% FCS DMEM media containing 1% formaldehyde. The cells were lysed and sonicated in [20 mM Tris-HCl, pH8, 150 mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X, protease inhibitors]. Lysates were cleared by centrifugation and incubated with a mixture of RNaseA and proteinaseK for 2 hours at 37° and then 16 hours at 65° to reverse the cross-links. DNA was purified by phenol-chloroform extraction and 10ng was used with a Illumina ChIP-seq sample preparation according to the manufacturer instructions.


title: A110

tag: strain

tag: litter

tag: diet

tag: weight(g)

tag: mesentericfat(g)

tag: %bw

tag: perirenalfat(g)

tag: abdominalfat(g)

tag: totalfat

tag: heart(g)


title: HCT116_Input_GA2462_ChIPseq

description: phred+64 fastq

value: none (input)


title: TCF_WPP_ChIP-seq_ChIP_Rep3

status: Public on Aug 11 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: tgo mouse Crews;target name: tango;host: Mouse;antigen: unknown;clonal: Monoclonal;purified: Crude;company: Lab;catalog: Stephen Crews (http://www.unc.edu/~crews/SteveC.html);short description: Gift from Stephen Crews.

data_processing: Solexa_Alignment protocol. Raw image files were processed following the following Illumina-compatible pipeline:1.  The Raw images were first processed with the Casava 1.7.0.2.  Base-called sequences with confidence metrics were obtained using OLB-1.9.0.  All multiplexed samples were demultiplexed using Casava 1.7.0.3. Finally the BWA program was used to align the sequence reads to the Drosophila melanogaster (v5.32) genome, allowing up to 2 edit distance in the seed region and 3 in the full read length. Tags that aligned to more than one  location were excluded from our analysis for both ChIP sample and the corresponding control sample (input chromatin). Only properly aligned reads with mapping quality more than 30 were kept. MACS_Peak-calling protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software, version 2 (MACS2). MACS2 was supplied with the following parameters:tagSize = 50mfold = 2genomeSize = 120000000bandwidth = 100pvalue = 1e-5  Processed data are obtained using following parameters: genome version is flybase BDGPv5

extract_protocol:
Collection of White pre-pupae for chromatin extraction
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

value: Y cn bw sp

tag: developmental stage

value: White Prepupae (WPP)

tag: genotype


title: sensor_head_18C

city: Blacksburg

first: Kevin

last: Myles

state: VA

address: Fralin Biotechnology Center

department: Fralin Life Science Institute

institute: Virginia Tech

data_processing:
Basecalls performed using CASAVA version 1.4.
Randomly 25 million sequences were selected for analysis from each library using an in-house perl script.
VectorBase Aedes aegypti genome AaegL1.2 was used for both Ae. aegypti and Ae. albopictus alignments.
Mosquito ncRNAs were taken out using bowtie v12.7 (-q -t -p 8 -v 3 -k 1 -m 1).
CHIK viral small RNAs were removed using bowtie v12.7 (-q -t -p 8 -v 1 -k 1 -B 1 --best).
Mosquito miRNAs, transposable elements, and endosiRNAs were removed using bowtie v12.7 (-q -t -p 8 -v 1 -k 1 -B 1 --best).
Individual counts for each small RNA class was totaled using in-house perl scripts.
Libraries were normalized using edgeR, using counts from viRNAs, miRNAs, TE, and endosiRNAs.
Genome_build: AaegL1
Supplementary_files_format_and_content: Processed counts were pasted into excel spreadsheet

organism: Aedes aegypti

source_name: head, 18C, non-infected

growth_protocol: All mosquito strains [Ae. aegypti Liverpool, khw (white eye) and all transgenic strains, Ae. albopictus Wise County strain] were reared in environmental chambers with a light cycle of 14:10 (day:night) and humidity of 80%. For all experiments, mosquitoes were hatched under vacuum for ~30 minutes, counted, and dispensed (n=~400) into 4 L of water pre-chilled at 18oC or pre-warmed at 28oC.

extract_protocol:
Small RNA libraries derived from head tissue of transgenic sensor strain mosquitoes were constructed using Illumina's small RNA sample prep kit and sequenced on an Illumina GAIIx (single replicate per temperature).
RNA from pools of 5 females was extracted using TRIreagent following manufacturer's instructions.

treatment_protocol: Mosquitoes reared at 18oC or 28oC were injected with equivalent amounts of virus, transferred to 28oC, and processed 8 hours later.

value: Liverpool sensor

tag: gender

value: female

tag: tissue

value: head

tag: growth temperature

tag: treatment

value: no infection


title: TCF_WPP_ChIP-seq_Input_Rep3

description: input DNA


title: TCF_WPP_ChIP-seq_Input_Rep1

description: input DNA


title: Rad21KO DP R2

tag: cell type

value: CD4+ CD8+ Double Positive Thymocytes

value: Rad21 KO


title: TCF_W3L_ChIP-seq_ChIP_Rep2

extract_protocol:
1. y; bw cn sp flies are cultivated in standard fly food covered with yeast powder.2. Flies are removed from the bottles after 24 hours and eggs are allowed to grow at 25 C for several days until they reach the desired growth stage.3. Wandering third instal larvae are collected from the side of the bottles using a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

tag: strain

tag: Sex

value: Unknown


title: TCF_WPP_ChIP-seq_Input_Rep2

description: input DNA


title: TCF_W3L_ChIP-seq_ChIP_Rep1


title: TCF_WPP_ChIP-seq_ChIP_Rep1


title: TCF_W3L_ChIP-seq_Input_Rep1

description: input DNA


title: TCF_nonISO1_0-8_embryonic_ChIP-seq_ChIP_Rep2

extract_protocol:
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.   2. For a 8-16 hours egg laying, new plates are added after a 2 hours pre-egglaying at 12 pm and flies are allowed to lay eggs for 8 hours.   3. Embryos are collected at 7.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 8am in 1.8% formaldehyde at room temperature for 15 min.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

value: Embryo 0-8

tag: transgene

value: Hr46 genomic coding region


title: TCF_nonISO1_0-8_embryonic_ChIP-seq_Input_Rep1

description: input DNA


title: TCF_W3L_ChIP-seq_Input_Rep3

description: input DNA


title: dTBP_0-8h_embryonic_ChIP-seq_Input_Rep2

description: input DNA

value: exd genomic coding region with stop codon replaced with GFP


title: dTBP_0-8h_embryonic_ChIP-seq_Input_Rep1

description: input DNA


title: dTBP_0-8h_embryonic_ChIP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: Tbp;target name: Tbp;host: Rabbit;antigen: Drosophila TATA binding protein;clonal: Polyclonal;purified: Crude;company: Lab;catalog: James Kadonaga Lab;short description: Gift to modENCODE from James Kadonaga


title: TCF_nonISO1_0-8_embryonic_ChIP-seq_Input_Rep2

description: input DNA


title: sensor_head_28C

source_name: head, 28C, non-infected


title: Su(H)_0-8_embryonic_ChIP-seq_ChIP_Rep3

description: ChIP DNA; Antibody information listed below: official name: Su(H);target name: fly genes:Su(H);host: Rabbit;antigen: Epitope corresponding to amino acids 259-594;clonal: Polyclonal;purified: Protein A/G;company: Santa Cruz Biotechnology Inc.;catalog: sc-25761;reference: http://www.scbt.com/datasheet-25761-suppressor-of-hairless-d-300-antibody.html;short description: Santa Cruz antibody agains Suppressor of Hairless


title: Su(H)_0-8_embryonic_ChIP-seq_ChIP_Rep1


title: Su(H)_0-8_embryonic_ChIP-seq_ChIP_Rep2


title: Su(H)_0-8_embryonic_ChIP-seq_Input_Rep3

description: input DNA


title: Su(H)_0-8_embryonic_ChIP-seq_Input_Rep2

description: input DNA


title: TCF_WPP_ChIP-seq_ChIP_Rep2


title: TCF_W3L_ChIP-seq_ChIP_Rep3


title: Su(H)_0-8_embryonic_ChIP-seq_Input_Rep1

description: input DNA


title: TCF_W3L_ChIP-seq_Input_Rep2

description: input DNA


title: Stat92E-GFP_12-24h_embryonic_ChIP-seq_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: GFP ab290;target name: Green Fluorescent Protein;host: Rabbit;antigen: entire GFP sequence;clonal: Polyclonal;purified: Crude;company: Abcam;catalog: ab290;reference: abcam website Jungreis et al. Genome Res. 2011 Dec;21(12):2096-113.;short description: This antibody is reactive against all variants of Aequorea victoria GFP such as S65T-GFP RS-GFP YFP and EGFP.

extract_protocol:
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 12-24 hours egg laying, new plates are added after a 2 hours pre-egglaying at 9 pm and flies are allowed to lay eggs for 12 hours.3. Embryos are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9am in 1.8% formaldehyde at room temperature for 15 min.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

value: Embryo 12-24h

value: Stat92E genomic coding region


title: Stat92E-GFP_12-24h_embryonic_ChIP-seq_ChIP_Rep2


title: Stat92E-GFP_12-24h_embryonic_ChIP-seq_Input_Rep2

description: input DNA


title: dMyc_W3L_ChIP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: MycN;target name: fly genes:dm;host: Rabbit;antigen: raised against amino acids 46-507 of Drosophila Myc;clonal: Polyclonal;purified: Protein A/G;company: Santa Cruz Biotechnology Inc.;catalog: sc-28208;reference: http://www.scbt.com/datasheet-28208-mycn-d46-507-antibody.html


title: dMyc_W3L_ChIP-seq_ChIP_Rep1


title: shGFP_RA_12h_RNAseq

city: Kansas City

first: Joan

last: Conaway

state: MO

institute: Stowers Institute

description:
RNAseq after non-targeting-RNAi and RA treatment 12 hours
Ribosomal RNA-depleted total RNA

data_processing:
Reads were aligned using Ensembl 67 GTF mouse annotations using TopHat v2.0.8 and Bowtie v0.12.9.  Alignments were not extended.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to three mismatches of a 50bp seed length.
Peak detection was done using MACS, version 1.4.2 (Zhang, Y. et al, 2008) using the indicated criteria.
RNA-seq alignments were done using TopHat v2.0.8 with bowtie1 v0.12.9, allowing uniquely mapping reads only and allowing up to two mismatches. Differential expression analysis was done using Cuffdiff v1.3.0.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

source_name: ES cell culture

growth_protocol: Mouse V6.5 embryonic stem cells were cultured in 0.1% gelatin-coated (Stem Cell Technology #07903) tissue culture flasks with irradiated mouse embryonic fibroblast (MEF) feeder cells. Cells were grown in DMEM (Sigma #06546) supplemented with 15% fetal bovine serum (Hyclone #SH30070.03), 2 mM L-glutamine, 0.1mM nonessential amino acids (Stem Cell Technology #07600) and 1000 U/ml recombinant LIF (Millipore #ESG1107).

extract_protocol:
ChIP assays were performed as previously described (Lee et al., 2006) . Briefly, 5x10^7 cells were crosslinked with 1% paraformaldehyde (Electron microscropy science #15710) at room temperature for 10 min and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody. Total RNA was extracted with Trizol (Invitrogen #15596), treated with DNAase I (NEB #M0303) for 20 min at room temperature and purified with RNeasy Mini kit (Qiagen #74106).
ChIP libraries were prepared with the TruSeq DNA Sample Kit (Illumina #FC-121-2001) according to Illumina's instructions. 2 µg of total RNA was depleted of ribosomal RNA with the Ribo Zero kit (Epicentre #MRZG12324) and libraries were made with the TruSeq RNA sample Pre Kit (Illumina #RS-122-2001).

treatment_protocol: For Mll2 and Mll3 knockdown, mouse V6.5 ES cells were infected with lentiviruses expressing short-hairpin RNA (shRNA) for Mll2 (GGAGAACTCTGATTGAGAAAG) or Mll3 (GGAGAGGACTACAAATGAAGT) for 24 hours and then were subjected to selection with 2ug/ml puromycin (Invitrogen #A11138) for 5 days. For ChIP-seq and RNA-seq experiments, cells were grown for one passage without feeder cells for 30 min before harvesting. For RA induction experiments, Mll2 knockdown and control shGFP mouse embryonic stem cells were cultured on MEF feeders in ES medium (DMEM, 15% fetal bovine serum, 1mM sodium pyruvate, 1x MEM-NEAA, 100uM 2-mercaptoethanol, 1,000U/ml leukemia inhibitory factor [Millipore, #ESG1107]) containing 1.5ug/ml Puromycin (Sigma, #P8833). To induce differentiation, cells were switched to medium without leukemia inhibitory factor containing 2uM all-trans retinoic acid (Sigma, #R2626) for 0, 6 and 12 hours. Prior to RNA extraction, cells were trypsinized and MEFs were allowed to adhere to gelatinized tissue culture dishes for 30 minutes and Non-adherent cells were collected.

value: mouse embryonic stem cell

tag: transfection

value: shGFP


title: Stat92E-GFP_12-24h_embryonic_ChIP-seq_Input_Rep1

description: input DNA


title: TCF_nonISO1_0-8_embryonic_ChIP-seq_ChIP_Rep1


title: shmMLL2_RA_6h_RNAseq

description:
RNAseq after MLL2 RNAi and RA treatment 6 hours
Ribosomal RNA-depleted total RNA


title: shmMLL2_RA_12h_RNAseq

description:
RNAseq after MLL2 RNAi and RA treatment 12 hours
Ribosomal RNA-depleted total RNA


title: shGFP_RA_6h_RNAseq

description:
RNAseq after non-targeting-RNAi and RA treatment 6 hours
Ribosomal RNA-depleted total RNA


title: lola-PJ-GFP_12-24h_embryo_ChIP-seq_ChIP_Rep2

value: lola-RJ-GFP

value: lola-RJ genomic coding region


title: dTBP_0-8h_embryonic_ChIP-seq_ChIP_Rep1


title: dMyc_W3L_ChIP-seq_Input_Rep1

description: input DNA

value: Y cn bw sp


title: dMyc_W3L_ChIP-seq_Input_Rep2

description: input DNA


title: lola-PJ-GFP_12-24h_embryo_ChIP-seq_ChIP_Rep1


title: lola-PJ-GFP_12-24h_embryo_ChIP-seq_Input_Rep1

description: input DNA


title: lola-PJ-GFP_12-24h_embryo_ChIP-seq_Input_Rep2

description: input DNA


title: shmMLL2_RA_0h_RNAseq

description:
RNAseq after MLL2 RNAi and RA treatment 0 hour
Ribosomal RNA-depleted total RNA


title: Input_V6.5

description: Input DNA from whole cell extract

data_processing:
Alignments were extended to a total fragment length of 150 bases in the orientation of the read alignment.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to three mismatches of a 50bp seed length.
Peak detection was done using MACS, version 1.4.2 (Zhang, Y. et al, 2008) using the indicated criteria.
RNA-seq alignments were done using TopHat v2.0.8 with bowtie1 v0.12.9, allowing uniquely mapping reads only and allowing up to two mismatches. Differential expression analysis was done using Cuffdiff v1.3.0.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

tag: antibody


title: shGFP_RA_0h_RNAseq

description:
RNAseq after non-targeting-RNAi and RA treatment 0 hour
Ribosomal RNA-depleted total RNA


title: MLL2_V6.5

description: Chromatin IP of MLL2

value: (rb) α-H3K4me3 (#528; Ali  Shilatifard)


title: shMLL3_Input_rep2

description: Input DNA from whole cell extract following RNAi of MLL3; Replicate 2


title: lola-PJ-GFP_0-12h_embryo_ChIP-seq_ChIP_Rep2

extract_protocol:
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 0-12 hours egg laying, new plates are added after a 2hours pre-egglaying at 9pm and flies are allowed to lay eggs for 12 hours.3. Embryos are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9am in 1.8% formaldehyde at room temperature for 15 min.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

value: Embryo 0-12h


title: lola-PJ-GFP_0-12h_embryo_ChIP-seq_Input_Rep2

description: input DNA


title: shMLL2_Input_rep2

description: Input DNA from whole cell extract following RNAi of MLL2; Replicate 2


title: shMLL3_H3K4me3_rep2

description: Chromatin IP of H3K4me3 following RNAi of MLL3; Replicate 2


title: shMLL2_H3K27me3_rep2

description: Chromatin IP of H3K27me3 following RNAi of MLL2; Replicate 2

value: Bethyl Laboratories (#A302-175A)


title: lola-PJ-GFP_0-12h_embryo_ChIP-seq_Input_Rep1

description: input DNA


title: H_0-8h_embryonic_ChIP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: KW3-h-D1;target name: Hairy;host: Rabbit;antigen: PMLVSMPQRTASTGSASSHSSAGYESAPGSSSSCSYAPPSPANSSYEPMDIKPSVIQRVPMEQQPLSLVIKKQIKEEEQPWRP;clonal: Polyclonal;purified: Protein A/G;company: Other;catalog: Aviva-KW3-h-D1;short description: Antisera raised against a peptide from the Hairy protein. Produced commercially for the modENCODE Project by K. White's group.


title: shMLL2_H3K4me3_rep2

description: Chromatin IP of H3K4me3 following RNAi of MLL2; Replicate 2


title: lola-PJ-GFP_0-12h_embryo_ChIP-seq_ChIP_Rep1


title: H_0-8h_embryonic_ChIP-seq_ChIP_Rep1


title: H_0-8h_embryonic_ChIP-seq_Input_Rep2

description: input DNA


title: shGFP_H3K27me3_rep2

description: Chromatin IP of H3K27me3 following RNAi of GFP (non-targeting); Replicate 2

value: Active Motif (#39155)


title: H_0-8h_embryonic_ChIP-seq_Input_Rep1

description: input DNA


title: gro_WPP_ChIP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: KW0:GRO;target name: GROUCHO;host: Rabbit;antigen: IKFTIADTLERIKEEFNFLQAQYHSIKLECEKLSNEKTEMQRHYVMYYEMSYGLNVEMHKQTEIAKRLNTLINQLLPFLQADHQQQVLQAVERAKQVTMQELNLIIGQQIHA;clonal: Polyclonal;purified: Protein A/G;company: Other;catalog: KW0:GRO;short description: Antisera raised against a peptide from the GRO protein.  Produced commercially for the modENCODE Project by K. White's group.

value: White Prepupae (WPP)


title: shMLL2_H3K4me1

description: Chromatin IP of H3K4me1 following RNAi of MLL2 ; Replicate 1

data_processing:
1st basepair was trimmed before alignment due to the low quality
Alignments were extended to a total fragment length of 150 bases in the orientation of the read alignment.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to three mismatches of a 50bp seed length.
Peak detection was done using MACS, version 1.4.2 (Zhang, Y. et al, 2008) using the indicated criteria.
RNA-seq alignments were done using TopHat v2.0.8 with bowtie1 v0.12.9, allowing uniquely mapping reads only and allowing up to two mismatches. Differential expression analysis was done using Cuffdiff v1.3.0.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

value: (rb) α-H3K4me1 (#524; Ali  Shilatifard)


title: shGFP_H3K4me3_rep2

description: Chromatin IP of H3K4me3 following RNAi of GFP (non-targeting); Replicate 2


title: shGFP_H3K4me1

description: Chromatin IP of H3K4me1 following RNAi of GFP (non-targeting); Replicate 1


title: gro_WPP_ChIP-seq_Input_Rep2

description: input DNA


title: shMLL2_RNAseq_rep2

description:
Ribosomal RNA-depleted total RNA
RNAseq after MLL2 RNAi; Replicate 2

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to three mismatches of a 50bp seed length.
Peak detection was done using MACS, version 1.4.2 (Zhang, Y. et al, 2008) using the indicated criteria.
RNA-seq alignments were done using TopHat v2.0.8 with bowtie1 v0.12.9, allowing uniquely mapping reads only and allowing up to two mismatches. Differential expression analysis was done using Cuffdiff v1.3.0.
ChIP-seq alignments were extended to a total fragment length of 150 bases in the orientation of the read alignment.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
RNA-seq reads were aligned using Ensembl 67 GTF mouse annotations using TopHat v2.0.8 and Bowtie v0.12.9.  Alignments were not extended.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Genome_build: UCSC mm9
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

treatment_protocol: For Mll2 and Mll3 knockdown, mouse V6.5 ES cells were infected with lentiviruses expressing short-hairpin RNA (shRNA) for Mll2 (GGAGAACTCTGATTGAGAAAG) or Mll3 (GGAGAGGACTACAAATGAAGT) for 24 hours and then were subjected to selection with 2ug/ml puromycin (Invitrogen #A11138) for 5 days. For ChIP-seq and RNA-seq experiments, cells were grown for one passage without feeder cells for 30 min before harvesting.


title: shMLL2_RNAseq_rep1

description:
Ribosomal RNA-depleted total RNA
RNAseq after MLL2 RNAi; Replicate 1


title: shGFP_RNAseq_rep2

description:
Ribosomal RNA-depleted total RNA
RNAseq after non-targeting-RNAi; Replicate 2


title: gro_WPP_ChIP-seq_Input_Rep1

description: input DNA


title: shGFP_RNAseq_rep1

description:
Ribosomal RNA-depleted total RNA
RNAseq after non-targeting-RNAi; Replicate 1


title: Eip74EF-GFP_8-16h_embryonic_ChIP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: GFP ab290;target name: Green Fluorescent Protein;host: Rabbit;antigen: entire GFP sequence;clonal: Polyclonal;purified: Crude;company: Abcam;catalog: ab290;reference: abcam website Jungreis et al. Genome Res. 2011 Dec;21(12):2096-113.;short description: This antibody is reactive against all variants of Aequorea victoria GFP such as S65T-GFP RS-GFP YFP and EGFP.

extract_protocol:
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder.2. For a 8-16 hours egg laying, new plates are added after a 2 hours pre-egglaying at 12 pm and flies are allowed to lay eggs for 8 hours.3. Embryos are collected at 7.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 8am in 1.8% formaldehyde at room temperature for 15 min.
Solutions and MaterialsLysis buffer: (see above)5mg/ml RNaseA (DNase free)PAS suspension: 100 mg of CL-4B (Amersham, 17-0780-01) PAS shoµld be resuspended in 1 ml of lysis buffer + protease inhibitors + 0.1 mg/ml BSA for 50 %v suspension. Wash in lysis buffer 2-3 times, overall equilibration time 1h. Store up to one week at 4 C.TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTAElution buffer1: 10 mM EDTA, 1% SDS, 50 mM Tris-Cl pH 8.Elution buffer2: TE+0.67% SDS.LiCL 4M? Protocol 1. To an amount of chromatin corresponding to 150 mg of biological material, suspended in a final volume of chromatin extract of 1 ml (in lysis buffer + protease inhibitors), add 100 µl of PAS suspension for preincubation. Incubate several hours or overnight at 4°C, then remove PAS. Crosslinked chromatin at this stage can be stored several days at 4°C or frozen at ?70°C.2. [Optional : Check for amount of DNA. From the 1 ml solution above, take a 100 µl aliquot, Add proteinase K up to 100 ug/ml and SDS to 1%, incubate 6h at 60°C, then 20 min at 70°C, add RNAse to 50 ug/ml and incubate additional 2h at 37°C. Phenol-chlorophorm extract, ethanol precipitate. Run on an agarose gel to check amount and size of DNA.]3. Separate chromatin sample into 4x250 µl aliquots (one aliquot is enough for one IP but the amount may be decreased further). Immunoprecipitate chromatin by adding the antibody (Ab) of interest (amount of Ab shoµld be determined empirically, usually the same concentration than for a successfµl IF experiement). Keep a control sample without Ab IP, named "Mock".4. Incubate 4 h at 4°C on a head to head rotating wheel, then add 50 µl of PAS suspension and incubate 4 h or overnight. Spin down PAS and proceed to washes.5. Wash PAS 4x with lysis buffer, followed by 2x with TE (without protease inhibitors). Each wash is for 5 min at 4°C, using 1 ml of solution.6. Elution of precipitated material. Spin down PAS. Add 100 µl of elution buffer, mix and incubate 10 min at 65°C. Spin down PAS and transfer supernatant to new tube. Add 150 µl of elution buffer 2 to PAS, mix, centrifuge at fµll speed and transfer eluate to a tube together with the eluate from the first centrifugation. The combined material is the "chromatin precipitate" (approx. 250 µl).7. Incubate precipitate 6 h (or overnight) at 65 C to reverse cross-links. Add 250 µl of Proteinase K solution, incubate at 50°C 2-3 h.8. Add 55 µl of 4M LiCl and 500 µl of phenol-chlorophorm. Mix and microfuge at fµll speed at RT. Transfer aqueous phase to a new tube and precipitate with 1 ml of 100% ethanol. Wash with 750 µl of 70% ethanol. Spin down and dry precipitate.9. Dissolve in 25 µl of water. This is the chromatin immunoprecipitate or ?Native ChIP? sample.
DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911).  After a final gel purification step the DNA is loaded into a flow cell for multiplexed sequencing.

value: Embryo 8-16h

value: Eip74EF genomic coding region


title: Eip74EF-GFP_8-16h_embryonic_ChIP-seq_ChIP_Rep1


title: shMLL3_input

description: Input DNA from whole cell extract following RNAi of MLL3

data_processing:
1st basepair was trimmed before alignment due to the low quality
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to three mismatches of a 50bp seed length.
Peak detection was done using MACS, version 1.4.2 (Zhang, Y. et al, 2008) using the indicated criteria.
RNA-seq alignments were done using TopHat v2.0.8 with bowtie1 v0.12.9, allowing uniquely mapping reads only and allowing up to two mismatches. Differential expression analysis was done using Cuffdiff v1.3.0.
ChIP-seq alignments were extended to a total fragment length of 150 bases in the orientation of the read alignment.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
RNA-seq reads were aligned using Ensembl 67 GTF mouse annotations using TopHat v2.0.8 and Bowtie v0.12.9.  Alignments were not extended.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Genome_build: UCSC mm9
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html


title: Eip74EF-GFP_8-16h_embryonic_ChIP-seq_Input_Rep1

description: input DNA


title: Eip74EF-GFP_8-16h_embryonic_ChIP-seq_Input_Rep2

description: input DNA


title: gro_WPP_ChIP-seq_ChIP_Rep1


title: shMLL2_input

description: Input DNA from whole cell extract following RNAi of MLL2


title: shMLL3_H3K4me3

description: Chromatin IP of H3K4me3 following RNAi of MLL3


title: Dll_WPP_ChIP-seq_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: dll;target name: DLL;host: Rabbit;antigen: MDAPDAPHTPKYMDGGNTAASVTPGINIPGKSAFVELQQHAAAGYGGIRS TYQHFGPQGGQDSGFPSPRSALGYPFPPMHQNSYSGYHLGSYAPPCASPP KDDFSISDKCEDSGLRVNGKGKKMRKPRTIYSSLQLQQLNRRFQRTQYLA LPERAELAASLGLTQTQVKIWFQNRRSKYKKMMKAAQGPGTNSGMPLGGG GPNPGQHSPNQMHSGGNNGGGSNSGSPSHYLPPGHSPTPSSTPVSELSPE FPPTGLSPPTQAPWDQKPHWIDHKPPPQMTPQPPHPAATLHPQTHHHNPP PQMGGYVPQYWYQPETNPSLVT;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Sean Carroll Lab;short description: This is a gift from Tom Williams in Sean Carroll's Lab to Nicolas Negre for the modENCODE project.


title: Dll_WPP_ChIP-seq_ChIP_Rep1


title: shGFP_Input

description: Input DNA from whole cell extract following RNAi of GFP (non-targeting)


title: shMLL2_H3K4me3

description: Chromatin IP of H3K4me3 following RNAi of MLL2


title: shGFP_H3K4me3

description: Chromatin IP of H3K4me3 following RNAi of GFP (non-targeting)


title: shGFP_Input_rep2


title: hESC passage#10 -Cell#26

status: Public on Aug 10 2013

city: Beijing

first: Mingyu

last: Yang

address: 5 Yiheyuan Road

country: China

institute: Peking University

description:
Sample 145
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S15.expression.txt: hg19

source_name: hESC passage#10

growth_protocol: Donated human preplantation embryos were dissociated into individual blastmeres and were separately amplied to set up single cell cDNA libraries.

extract_protocol: Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol

value: human embryonic stem cell

value: peri-implantation stem cells

value: human embryonic stem cell line


title: hESC passage#10 -Cell#25

description:
Sample 144
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S14.expression.txt: hg19


title: hESC passage#10 -Cell#23

description:
Sample 142
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S12.expression.txt: hg19


title: hESC passage#10 -Cell#19

description:
Sample 138
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S8.expression.txt: hg19


title: hESC passage#10 -Cell#24

description:
Sample 143
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S13.expression.txt: hg19


title: hESC passage#10 -Cell#16

description:
Sample 135
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S5.expression.txt: hg19


title: hESC passage#10 -Cell#17

description:
Sample 136
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S6.expression.txt: hg19


title: hESC passage#10 -Cell#18

description:
Sample 137
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S7.expression.txt: hg19


title: hESC passage#10 -Cell#21

description:
Sample 140
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S10.expression.txt: hg19


title: Pou5f1-Flag ChIP

city: Freiburg

first: Manuel

last: Leichsenring

address: Hauptstr. 1

country: Germany

institute: Albert-Ludwigs-University Freiburg

data_processing:
Basecalls were performed using CASAVA.
Reads were trimmed to 20bps and aligned to the zv9 genome using "CLC Genomics Workbench" using the following parameters: Match Mode = Random; Sequence Masking = No; Limit = 8; Mismatch Cost = 2; Aligment = Ungapped; Global Aligment = No; Result Handling = Save
Peaks were called using "CLC Genomics Workbench" using the following parameters: Analyze each reference separately = No; Filter peaks on read orientation = No; Filter peaks using Wilcoxon test = No; Shift reads based on fragment length = Yes; Fragment length = 150; Peak refinement = No; Maximum FDR = 5%; Window Size = 50
Peaks were filtered according to the following criteria: Normalized read orientation difference <0.5; Wilcoxons test p-value < 0.05. Further, peaks were discarded that showed a larger than 20bp overlap with annotated repeats.
Peaks were normalized to 320 basepairs surrounding the peak center (Average peak size) for applications requiring fixed sequence length.
Genome_build: zv9
Supplementary_files_format_and_content: Filtered peak information was exported from CLC workbench. NOTE: Background peaks (Input Control) are not subtracted yet in these lists. Closest gene TSS in 5' and 3' direction were obtained using Galaxy. Processed data files include the following information: Peak ID, Position (Chromosome, Start, End), Length, False Discovery Rate, Number of total reads, Number of forward reads, Number of reverse reads, Normalized difference between forward and reverse, Wilcoxon p-value, Closest 5' and 3' gene (RefSeq ID).

organism: Danio rerio

source_name: MZspg zebrafish embryos, Pou5f1-Flag ChIP

growth_protocol: Zebrafish were routinely kept and mated. Eggs were collected and either left untreated (Sox2) or microinjected (Pou5f1). Unfertilized and dead eggs were removed. Eggs were cultivated in 0.3x Danio's at 28.5°C until the appropriate stage was reached.

extract_protocol: Embryos were homogenized and fixed with 1% PFA. Cells were lysed and nuclei purified and snap-frozen. 2*10^7 nuclei were pooled and fully lysed. Chromatin was sheared and DNA-Protein complexes were isolated with the respective antibodies and purified. ChIP-libraries were generated using the Illumina "ChIP-Seq DNA Sample Prep Kit" (Cat. No. IP-102-1001) according to the manufacturer's instructions. Nuclei were lysed in 50mM Tris-HCl pH7.5, 10mM EDTA, 1% (w/v) SDS including protease inhibitors (Roche Complete, EDTA free).

treatment_protocol: Maternal-zygotic spg (MZspg) zygotes were injected at the 1-cell stage with a defined amount of Pou5f1-Flag mRNA that was just sufficient to rescue the MZspg mutant phenotype.

value: MZspg injected with Pou5f1-Flag mRNA

value: embryos

value: late blastula

tag: chip antibody

value: anti-FLAG® M2

tag: antibody vendor

value: Sigma Aldrich

tag: antibody catalog #


title: hESC passage#10 -Cell#14

description:
Sample 133
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S3.expression.txt: hg19


title: hESC passage#10 -Cell#13

description:
Sample 132
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S2.expression.txt: hg19


title: Input DNA

source_name: wildtype zebrafish embryos, input

value: wildtype


title: seq-SDQ2946_HCP4_N2_Mxemb_Input_Rep1

description: input DNA

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10   ChIP-Seq_MACS_Peak-calling:JL:1 protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters:tagSize = 25mfold = 10,30genomeSize = 90000000bandwidth = 300pvalue = 1e-5  Processed data are obtained using following parameters: genome version is ce10

organism: Caenorhabditis elegans

growth_protocol: Worm_embryo_growth_and_harvest_vRG2. Synchronized worm cultures were grown at 20 °C in batches of 500 ml using 2.8-L Fernbach flasks shaking at 230 rpm. Gravid adults were separated from debris by sucrose floating. Embryos were isolated by bleaching and fixed after EPS treatment with 1 % formaldehyde for 5 min on ice. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vRG2. Fixed embryos were suspended in 8mL of ChIP buffer (50 mM Hepes-KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) and sonicated on ice with a Branson sonifier microtip (25 % power setting for 2 min; 30 % power setting for 2 min; 35 % power setting for 10 min; 40 % power setting for 2 min; 45 % power setting for 2 min).  Debris were pelleted at 10 000 g for 20 min and the supernatant was made 10 % in glycerol.  The extract was snap frozen in liquid nitrogen aliquots containing 3 mg of protein and stored at ? 80 °C.  For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_vRG2. For each ChIP reaction, 3 mg of protein extract was diluted with ChIP buffer (50 mM Hepes KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) to 900 ?l. Then 35 ?l 30 % sarcosyl (1 % final) and 20 ?l 5 % Na-deoxycholate (0.1 % final) were added. 50 ?l of the diluted extract were removed (input sample), mixed with Elution buffer (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 250 mM NaCl, 1 % SDS) and processed as described for ChIP samples. 100 ?l antibody/bead suspension (5?g antibody pre-bound to 50 ?l Dynabeads, suspended in ChIP buffer) was added and the mixture and rotated at least 1.5 hr to over night at 4 °C. Beads were washed with 2 × 1 ml FA Buffer (50 mM Hepes-KOH pH 7.6, 150 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 5 min each; with 1 ml FA-1000 buffer (50 mM Hepes-KOH pH 7.6, 1 M NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml FA-500 buffer (50 mM Hepes-KOH pH 7.6, 500 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml TEL buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% NP-40, 1% Na-deoxycholate) for 10 min; and briefly with 1 ml TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA). Immunocomplexes were eluted with 50 ?l Elution buffer for 15 min at 67 °C. Eluates were incubated over night at 65 °C to reverse cross-links, then treated with Proteinase K (0.44 mg/ml) at 37 °C for 2 h. Nucleic acids were recovered by phenol/chloroform extraction and ethanol precipitation. After digestion with RNAse A (0.33 mg/ml) for 2h at 37 °C, DNA was purified using the Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/.
DNA for Library Prep is incubated with an End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends. It is then purified and incubated with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends (a single A-overhang for more efficient and directed ligation of the adaptors). After a second purification, the DNA fragments is ligated with single-end ?Homebrew? adaptors which contain an index sequence within (Corbin Jones? lab). After ligation, the samples are purified TWICE using SPRI beads, allowing for a size selection step getting rid of excess adaptors. Samples are then amplified by PCR with single end primers. Depending on the original fragmentation of the DNA, samples can either be purified by SPRI or by separation and purification from an agarose gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

value: Mixed Embryo

value: wild type

tag: sex type

value: mixed Male and Hermaphrodite population


title: seq-SDQ2946_HCP4_N2_Mxemb_ChIP_Rep2

description: ChIP DNA; Antibody information listed below: official name: HCP-4 SDQ2946;target name: HCP-4;host: Rabbit;antigen: PDGVRRSTRVRVKPVRSWLGEQPVYVNSPISGCKRLTGVTAVVIKDPRLCYYRTADVRTATERELKDKANKRALAQEKKQQRQNARSGRRHDSDDDEEDD;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ2946;short description: An Affinity purified Rabbit Polyclonal antibody to HCP-4 obtained from SDI (HCP-4 SDQ2946)


title: seq-SDQ2946_HCP4_N2_Mxemb_ChIP_Rep1


title: hESC passage#10 -Cell#12

description:
Sample 131
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S1.expression.txt: hg19


title: seq-SDQ2946_HCP4_N2_Mxemb_Input_Rep2

description: input DNA


title: Dll_WPP_ChIP-seq_Input_Rep1

description: input DNA

data_processing: Solexa_Alignment protocol. Raw image files were processed following the following Illumina-compatible pipeline:1.  The Raw images were first processed with the Casava 1.7.0.2.  Base-called sequences with confidence metrics were obtained using OLB-1.9.0.  All multiplexed samples were demultiplexed using Casava 1.7.0.3. Finally the BWA program was used to align the sequence reads to the Drosophila melanogaster (v5.32) genome, allowing up to 2 edit distance in the seed region and 3 in the full read length. Tags that aligned to more than one  location were excluded from our analysis for both ChIP sample and the corresponding control sample (input chromatin). Only properly aligned reads with mapping quality more than 30 were kept. MACS_Peak-calling protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software, version 2 (MACS2). MACS2 was supplied with the following parameters:tagSize = 50mfold = 2genomeSize = 120000000bandwidth = 100pvalue = 1e-5  Processed data are obtained using following parameters: genome version is flybase BDGPv5

value: Y cn bw sp


title: Sox2 ChIP

source_name: wildtype zebrafish embryos, Sox2 ChIP

value: R&D Systems


title: hESC passage#10 -Cell#22

description:
Sample 141
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S11.expression.txt: hg19


title: hESC passage#10 -Cell#11

description:
Sample 130
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_P17.expression.txt: hg19


title: hESC passage#10 -Cell#10

description:
Sample 129
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_P15.expression.txt: hg19


title: Dll_WPP_ChIP-seq_Input_Rep2

description: input DNA

value: White Prepupae (WPP)


title: hESC passage#10 -Cell#9

description:
Sample 128
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_P14.expression.txt: hg19


title: hESC passage#10 -Cell#15

description:
Sample 134
cDNAs of individual cell of human embryonic stem cells

data_processing:
Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_S4.expression.txt: hg19