title: WCE shNipbl mES MM8

description: Seq for WCE in shNipbl mouse ESCs

value: None WCE

value: Nipbl


title: CapD3 WT mES MM8

status: Public on Mar 14 2012

type: SRA

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

description: ChIP-Seq for CapD3 in asynchronous mESCs

library_source: genomic

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: chip antibody

tag: antibody catalog number

value: Tatsuya Hirano AFR319-3L

tag: antibody manufacturer

value: Tatsuya Hirano

tag: cell line

value: V6.5 embryonic stem cells


title: WCE shGFP mES MM8

description: Seq for WCE in shGFP mouse ESCs

tag: knockdown

value: control


title: CapH2 shNipbl mES MM8

description: ChIP-Seq for CapH2 in shNipbl mouse ESCs

value: Bethyl A302-275A

value: Bethyl


title: CapH2 shGFP mES MM8

description: ChIP-Seq for CapH2 in shGFP mouse ESCs


title: CapH2 Nocodazole mES MM8

description: ChIP-Seq for CapH2 in asynchronous mESCs

tag: treatment

value: 200 ng/ml nocodazole

tag: time

value: 12 hr


title: DP_miRNAseq

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

library_source: transcriptomic

data_processing: Reads were first clipped of any adaptor sequences (because miRNAs are shorter than the 36bp reads of the GAII platform). The processed reads were then aligned to mature microRNA sequences as annotated in miRBase. Sequences not mapping to mature microRNAs were then mapped to pre-miRNA sequences as annotated in miRBase.

molecule: total RNA

source_name: DP cells

extract_protocol: 19-24nt small RNAs fractionated by gel electrophoresis. Adaptors were ligated only to species with 5' phosphate and 3' hydroxyl

tag: strain

tag: source tissue

value: Thymus

tag: cell population

value: CD4+ CD8+ CD3lo CD90+


title: MEF_miRNAseq

source_name: Embryonic fibroblasts

value: E14.5 embryo

tag: cell type

value: embryonic fibroblast


title: CD8SP_miRNAseq

source_name: CD8SP cells

value: CD4- CD8+ CD3hi CD90+ CD24lo


title: DN3_miRNAseq

source_name: DN3 cells


title: DN4_miRNAseq

source_name: DN4 cells

value: CD4- CD8- CD3lo CD90+ CD44- CD25-


title: CD4SP_miRNAseq

source_name: CD4SP cells

value: CD4+ CD8- CD3hi CD90+ CD24lo


title: DN1_miRNAseq

source_name: DN1 cells


title: LMPP_miRNAseq

source_name: LMPP cells

value: Bone Marrow

value: Lineage - Sca+ cKit+ CD135+ CD106-


title: WCE Nocodazole mES MM8

description: WCE for nocodazole treated mES cells

value: None WCE


title: ProB_miRNAseq

source_name: Pro B cells

value: B220+ IgM- CD43hi


title: MPP_miRNAseq

source_name: MPP cells

value: Lineage - Sca+ cKit+ CD135+ CD106+


title: CD8 KO RNA-Seq

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9 assembly) using the Illumina Illumina ELAND software.

molecule: polyA RNA

source_name: KO CD4 cells

extract_protocol: PolyA RNAs were isolated and fragmented, then Ilumina compatible adaptors were ligated on.

value: CD8+ T cell

tag: genotype

value: Rnasen deficient


title: microRNA-Seq of timepoint2

status: Public on Mar 16 2012

city: Stanford

first: Hogune

last: Im

state: CA

address: 300 Pasteur Dr. Alway M308

department: Genetics

institute: Stanford

description:
Processed data file:
101103_COLUMBO_00039_FC62NP6_L1_clip3Ad5Ad_trim_tag_count.txt

data_processing:
TopHat  was used to align the reads to the hg19 reference genome, followed by Cufflinks for transcript assembly and RNA expression analysis.
Small RNA reads were analyzed after removal of 3' adapter and filtering of 5' adapter or 3' artifacts. Sequences larger than 27 nt were trimmed. Unique sequences were identified and the abundance of counts (number of reads).
processed data file build: hg19

organism: Homo sapiens

source_name: blood cell

growth_protocol: Blood was drawen

extract_protocol:
RNA from different blood component(PMBCs, plasma and sera) was used to prepare RNA-Seq ibraries according to Parkhomchuk D. et. al. 2009. Briefly, Total RNA was treated with DNaseI and rRNA removal by RiboZero. RNA was fragmented by RNA fragmentation kit from Ambion. Resulting RNA was converted to cDNA,  end-repaired using End-repair kit from Epicenter.  The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 300~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Average library fragment size is ~230 bp and SD of ~34 bp.
MicroRNA were isolated from 10 million PBMCs at five time points (Days 4, 21, 116, 185 and 186 from HRV infection) with the mirVanaTM miRNA Isolation Kit (Ambion). microRNA-Seq libraries were prepared from 1 microgram of isolated miRNA according to Illumina’s Small RNA v1.5 Sample Preparation Guide. Each library was sequenced with 36b single-end reads on 1 lane of Illumina’s GAIIx sequencer.

value: PBMC

tag: disease status

value: Recovery

tag: days


title: CD4 WT RNA-Seq

source_name: WT CD4 cells

value: CD4+ T cell

value: Wildtype


title: LSK_miRNAseq

source_name: LSK cells

value: Lineage - Sca+ cKit+


title: Starvation-15h-VI

status: Public on Mar 15 2012

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

country: China

institute: Institute of hydrobiology, CAS

data_processing: Sequence image analysis was performed using the Firecrest, Bustard and GERALD programs (Illumina). The low quality bases (Q<5) at the ends of the reads were trimmed. Tophat (Trapnell et al. 2009) were used to map the sequenced reads to the current T. thermophila reference genome (Coyne et al. 2008; October, 2008 release) (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/t_thermophila/annotation_dbs/final_release_oct2008/) and find the reads spanning one exon-exon junction. The NUCmer in MUMmer package (Delcher et al. 2002) and a custom script were used to find the reads possibly spanning two or more exon-exon junctions. The mapped reads allowed up to two mismatches and only the canonical GT-AG junction reads were accepted. Transcripts were assembled using the Cufflinks software (Trapnell et al. 2010), and was compared to the predicted gene models using cuffcompare (Trapnell et al. 2010) and custom scripts. Putative ORFs of assembled transcripts were found using GetOrf in EMBOSS package (Rice et al. 2000).

organism: Tetrahymena thermophila

source_name: Tetrahymena starvation, 15 hour cells, mating type VI

growth_protocol: Cells were cultured using 1X SPP (1%PP), 30 degrees, 150 rpm shaking.

extract_protocol:
Total RNA extracted using  Qiashredder (Cat # 79654) and the RNeasy kit (cat. # 74624), from Qiagen. Contains RNA Protect Cell Reagent (Cat. # 76526) and RNeasy Plus Mini Kit (50 samples).
Poly-A mRNA was selected using Dynal magnetic beads (Invitrogen) and fragmented by heating at 94 â. First strand cDNA were synthesized with random hexamer primers and second strand cDNA with DNA polymerase. Double strand cDNA was end-repaired and a single adenosine moiety was added. The Illumina adapters were ligated and gel-electrophoresis was used to select DNA fragments between 200â250 bps in size. Libraries were amplified by PCR with Phusion polymerase. Sequencing libraries were denatured with sodium hydroxide and diluted in hybridization buffer for loading onto a single lane of an Illumina GA flowcell. Cluster formation, primer hybridization and pair-end sequencing were performed using proprietary reagents according to hte manufacturer's recommended protocol (https://icom.illumina.com/).

treatment_protocol: For growth, mating type VI cells at a medium cell density (~200K cells/ml) were collected. For starvation, mating type V or VI cells were starved in 10 mM Tris (pH 7.5) for 3 and 15 hours. For conjugation, mating type V and VI cells that had been starved for 18 hours were resuspended in 10 mM Tris (pH 7.5) at 200K cells/ml and mixed, and samples were collected at 2 and 8 hours after the mixture.

tag: mating type

value: VI

tag: condition

value: starvation

value: 15 hrs


title: CD4 KO RNA-Seq


title: CD8 WT RNA-Seq

source_name: WT CD8 cells


title: CapD3 Nocodazole mES MM8

description: ChIP-Seq for CapD3 in nocodazole treated mESCs

source_name: Embryonic stem cells

value: Tatsuya Hirano AFR319-3L

value: Tatsuya Hirano

value: V6.5 embryonic stem cells

value: 200 ng/ml nocodazole

value: 12 hr


title: TEX_TCP_ATRA

city: New York

first: Hans-Ulrich

last: Klein

state: NY

department: Neurology

institute: Columbia University Medical Center

description: TEX cells are derived from primitive human cord blood cells immortalized by expression of the TLS-ERG oncogene. Warner, J.K., et al. Direct evidence for cooperating genetic events in the leukemic transformation of normal human hematopoietic cells. Leukemia 19, 1794-1805 (2005).

data_processing:
TEX_H3K4me2_TCP_ATRA.bed; genome build: hg19
Image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human hg19 reference genome using the using the BWA (Burrows-Wheeler Alignment) algorithm.

source_name: TEX cells

growth_protocol: HL-60 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS, Sigma), 100 U/ml penicillin and 100μg/ml streptomycin. TEX cells were maintained in IMDM supplemented with 15% FBS, 20ng/ml stem cell factor (SCF, Peprotech) and 2ng/ml IL-3 (Peprotech).

extract_protocol: ChIP was performed using the Histone ChIP kit (Diagenode) according to standard protocols and the supplier's directions. Libraries were prepared according to Illumina's instructions. Briefly, 20 ng enriched DNA as measured by Agilent 2100 BioAnalyzer (Agilent Technologies) was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters, which have a single 'T' base overhang at the 3’end. Adaptors ligated DNA fragments were subsequently size selected (300 base pairs). The adaptor-modified DNA fragments were subjected to limited PCR amplification (14 cycles) with Illumina primers and quality control was made by qPCR, as well as by running the PCR products on a Bioanalyzer. The purified DNA was captured on an Illumina flow cell for cluster generation and sequencing-by-synthesis (57 base pairs) was performed using the Illumina Genome Analyzer IIx (GAIIx) according to standard protocols of the manufacturer.

treatment_protocol: Cells were treated with the above described all-trans-retinoic acid (ATRA, 0.1 µM, HL-60; 1µM, TEX), tranycypromine (TCP, 10 µM) or ATRA + tranycypromine drug combinations for 4 days prior to analysis.

value: TEX

value: all-trans-retinoic acid and tranylcypromine

tag: antibody


title: DN2_miRNAseq

source_name: DN2 cells

value: Thymus


title: TEX_ATRA

data_processing:
TEX_H3K4me2_ATRA.bed; genome build: hg19
Image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human hg19 reference genome using the using the BWA (Burrows-Wheeler Alignment) algorithm.

value: all-trans-retinoic acid


title: TEX_TCP

data_processing:
TEX_H3K4me2_TCP.bed; genome build: hg19
Image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human hg19 reference genome using the using the BWA (Burrows-Wheeler Alignment) algorithm.

value: tranycypromine


title: TEX_untreated

data_processing:
TEX_H3K4me2_untreated.bed; genome build: hg19
Image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human hg19 reference genome using the using the BWA (Burrows-Wheeler Alignment) algorithm.

value: vehicle


title: HL60_TCP

description: HL-60 cells were established from the peripheral blood of a 35-year-old woman with acute myeloid leukemia (AML FAB M2) in 1976. Collins,S.J., Gallo,R.C. & Gallagher,R.E. (1977). Continuous growth and differentiation of human myeloid leukaemic cells in suspension culture. Nature 270(5635):347-349.

data_processing:
HL60_H3K4me2_TCP.bed; genome build: hg19
Image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human hg19 reference genome using the using the BWA (Burrows-Wheeler Alignment) algorithm.

source_name: HL-60 cells


title: HL60_TCP_ATRA

data_processing:
HL60_H3K4me2_TCP_ATRA.bed; genome build: hg19
Image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human hg19 reference genome using the using the BWA (Burrows-Wheeler Alignment) algorithm.


title: LMO1 ChIP-seq Jurkat 1

description: Chromatin IP against LMO1 ChIP Jurkat

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
hg18

source_name: T-ALL cell line

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

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

tag: chip antibody

value: Santa Cruz SC-10494

value: Santa Cruz

value: Jurkat E6-1


title: Input WCE ChIP-seq Prima5 T-ALL 2

description: Chromatin IP against WCE Input 5386 (6/15/11)

source_name: T-ALL primagraft

growth_protocol: Diagnostic T-ALL patient samples were obtained with informed consent and Institutional Review Board approval from children treated on Dana-Farber Cancer Institute study 05-01. Mononuclear cells were purified by Ficoll-Hypaque centrifugation prior to FACS analysis and viable cryopreservation in liquid nitrogen.  50,000 human CD34+ cells selected from above T-ALL samples with the aid of immunomagnetic beads (Miltenyi Biotec, Auburn, CA) or FACSAria were transplanted intrahepatically into RAG2-/-γc-/- neonatal mice within 48 hours of birth.  Mice were sacrificed at 8 weeks after transplantation.  Bone marrow (BM), spleen, thymus, liver and peripheral blood was collected for FACS analysis of human CD45, CD34, CD2, and CD7 expression.  Serial transplantation was done by intrahepatically injecting 50,000 human CD34+ cells selected from the T-ALL primary engrafted BM or thymus into the neonatal RAG2-/-γc-/- mice.  Human CD34+ cells used in TAL1 ChIP-seq analysis were isolated from the primary engraftments of T-ALL patients.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 4500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing using Beckman SPRIworks fragment library system with adapters from the Illumina TruSeq DNA kit. DNA fragments were end repaired, ligated and size selected using SPRIworks. DNA was then subjected to 18 cycles of PCR using oligos provided by Illumina.

tag: antibody catalog number

value: None WCE

tag: sample type

value: T-ALL primagraft 05-386


title: HL60_ATRA

data_processing:
HL60_H3K4me2_ATRA.bed; genome build: hg19
Image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human hg19 reference genome using the using the BWA (Burrows-Wheeler Alignment) algorithm.

tag: cell line


title: TAL1 ChIP-seq Prima5 T-ALL 2

description: Chromatin IP against TAL1 T-ALL(5386)

value: Santa Cruz SC-12984

tag: antibody manufacturer


title: TAL1 ChIP-seq Prima5 T-ALL 1

description: Chromatin IP against TAL1 T-ALL(5386)


title: TAL1 ChIP-seq Prima2 T-ALL 2

description: Chromatin IP against TAL1 T-ALL(5261)

value: T-ALL primagraft 05-261


title: Input WCE ChIP-seq Prima2 T-ALL 2

description: Chromatin IP against WCE Input 5261 (6/15/11)


title: microRNA-Seq of timepoint5

description:
Processed data file:
101103_COLUMBO_00039_FC62NP6_L3_clip3Ad5Ad_trim_tags_count.txt

value: PBMC

value: Healthy


title: TEX_IgG

data_processing:
TEX_IgG_untreated.bed; genome build: hg19
Image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human hg19 reference genome using the using the BWA (Burrows-Wheeler Alignment) algorithm.

tag: treatment

value: Immunoglobulin G


title: microRNA-Seq of timepoint3

description:
Processed data file:
101103_COLUMBO_00039_FC62NP6_L2_clip3Ad5Ad_trim_tags_count.txt

value: Recovery


title: TAL1 ChIP-seq Prima2 T-ALL 1

description: Chromatin IP against TAL1 T-ALL(5261)


title: TAL1 ChIP-seq CCRF-CEM 2

description: Chromatin IP against TAL1 ChIP CEM

growth_protocol: Human CCRF-CEM cells were purchased from the German Collection of Microorganisms and Cell Culture (DSMZ), Leibniz, Germany. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

value: CCRF-CEM


title: TAL1 ChIP-seq CCRF-CEM 1

description: Chromatin IP against TAL1 CCRF-CEM


title: RUNX1 ChIP-seq CCRF-CEM 1

description: Chromatin IP against RUNX1 CCRF-CEM

value: Santa Cruz SC-8563


title: LMO2 ChIP-seq CCRF-CEM 2

description: Chromatin IP against LMO2 CCRF-CEM

value: R&D Systems AF2726

value: R&D Systems


title: LMO2 ChIP-seq CCRF-CEM 1

description: Chromatin IP against LMO2 CCRF-CEM


title: Input WCE ChIP-seq CCRF-CEM 1

description: Chromatin IP against Input WCE CCRF-CEM


title: RUNX1 ChIP-seq CCRF-CEM 2

description: Chromatin IP against RUNX1 ChIP CEM


title: Input WCE ChIP-seq Prima5 T-ALL 1

description: Chromatin IP against Input WCE T-ALL(5386)


title: HEB ChIP-seq CCRF-CEM 2

description: Chromatin IP against HEB ChIP CEM

value: Santa Cruz SC-357


title: HEB ChIP-seq CCRF-CEM 1

description: Chromatin IP against HEB CCRF-CEM


title: LMO1 ChIP-seq Jurkat 2

description: Chromatin IP against LMO1 ChIP Jurkat


title: HL60_IgG

data_processing:
HL60_IgG_untreated.bed; genome build: hg19
Image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human hg19 reference genome using the using the BWA (Burrows-Wheeler Alignment) algorithm.

value: vehicle


title: Input WCE ChIP-seq CCRF-CEM 2

description: Chromatin IP against WCE Input CEM (6/22/11)


title: GATA3 ChIP-seq CCRF-CEM

description: Chromatin IP against GATA3 ChIP CEM

value: Santa Cruz SC-22206


title: HL60_untreated

data_processing:
HL60_H3K4me2_untreated.bed; genome build: hg19
Image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human hg19 reference genome using the using the BWA (Burrows-Wheeler Alignment) algorithm.


title: E2A ChIP-seq CCRF-CEM

description: Chromatin IP against E2A ChIP CEM

value: Santa Cruz SC-349

value: Santa Cruz


title: HAmCqG8 mRNA

status: Public on Mar 13 2012

city: Auburn

first: Nannan

last: Liu

state: AL

address: 301 Funchess Hall

department: Entomology

institute: Auburn University

description: mRNA

data_processing: Differential expression: Sequence reads were aligned to the Johannesburg strain Cx. quinquefasciatus genome v1.2 using Tophat, then expression values were estimated using Cufflinks-Cuffdiff. Values are given in Fragments Per Kilo of nucleotides per gene per Million reads mapped (FPKM) with the corresponding error estimates and Cuffdiff testing values

organism: Culex quinquefasciatus

growth_protocol: Larvae were reared at 27C (12:12 L:D) on a diet of Baker's yeast

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the mRNA Seq 8-sample kit by the Hudson Alpha Institute of Biotechnology, Huntsville, AL. Libraries were then sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: Untreated

value: High permethrin resistant strain HAmCqG8

tag: tissue

value: whole insect

tag: larval stage

value: fourth instar


title: HAmCqG0 mRNA

description: mRNA

tag: strain

value: Low permethrin resistant strain HAmCqG0


title: A375P

city: Farmington

first: Sam

last: Dadras

state: CT

address: Cell and Genome Science Building, 400 Farmington Ave.

department: Genetics and Cell Biology

institute: UCONN Health Center

description:
Sample 21
cDNA
Barcode: AF-PP-334: ACG CTC TTC CGA TCT rCrGrUrC

data_processing:
Bowtie was used to align sequences. miRDeep 2.0 was used for identifying expression levels of microRNA. The PAMR package from R was used for statistical analysis of microRNA as biomarkers between clinical groups.
Genome_build: hg19
Supplementary_files_format_and_content: *txt file: miRNA sequences and counts

source_name: A375P, cultured cells

growth_protocol:
A2058, A375P, C32, and A375SM cell lines were kindly provided by Dr. Stanley N. Cohen, Stanford School of Medicine, CA. These cells were cultured in Dulbecco's Modified Eagle's Medium supplemented with 10% FCS and 2 mM glutamine. WM35 and WM1552C cell lines were purchased (Wistar institute, Philadelphia, PA) and cultured in 80% MCDB153 (Sigma), 20% Leibovitz¹s L15 (Mediutech), 2% fetal bovine serum, 5ug/ml insulin (Sigma) and 1.68mM CaCl2.
Three types of epidermal primary melanocytes isolated from 3 individuals with light, medium and dark skin were purchased from ScienCell (Carlsbad, CA) and cultured in melanocyte medium as specified by ScienCell. All cell cultures were incubated at 37°C in a 5% CO2 completely humidified incubator.

extract_protocol: Total RNA was extracted from cultured cells and xylene extracted FFPE tissue sections with TRIzol (Invitrogen).  Small RNA libraries were constructed from total RNA (Ma, 2009) with the following modifications:  4 nt index tags were included in the 5' adapter oligonucleotide and the libraries were amplified with Illumina specific primers to enable multiplexed sequencing on an Illumina Genome Analyzer.


title: A2058

description:
Sample 20
cDNA
Barcode: AF-PP-333: ACG CTC TTC CGA TCT rArGrCrG

source_name: A2058, cultured cells


title: C32

description:
Sample 23
cDNA
Barcode: AF-PP-339: ACG CTC TTC CGA TCT rArCrUrU

source_name: C32, cultured cells


title: A375SM

description:
Sample 22
cDNA
Barcode: AF-PP-335: ACG CTC TTC CGA TCT rCrUrGrG

source_name: A375SM, cultured cells


title: Melanocyte-Medium4

description:
Sample 27_4
cDNA
Barcode: AF-PP-343: ACG CTC TTC CGA TCT rUrCrGrC

source_name: Melanocyte-medium, cultured cells

value: melanocyte-medium


title: Input WCE ChIP-seq Prima2 T-ALL 1

description: Chromatin IP against Input WCE T-ALL(5261)

value: None WCE

value: T-ALL primagraft 05-261


title: Metastatic Melanoma to skin3

description:
Sample 17
cDNA
Barcode: AF-PP-339: ACG CTC TTC CGA TCT rArCrUrU

source_name: Metastatic melanoma to skin, formalin-fixed paraffin embedded

value: metastatic melanoma to skin


title: Melanocyte-Medium3

description:
Sample 27_3
cDNA
Barcode: AF-PP-343: ACG CTC TTC CGA TCT rUrCrGrC


title: WM35

description:
Sample 24
cDNA
Barcode: AF-PP-340: ACG CTC TTC CGA TCT rGrGrGrU

source_name: WM35, cultured cells


title: Metastatic Melanoma to skin2

description:
Sample 16
cDNA
Barcode: AF-PP-335: ACG CTC TTC CGA TCT rCrUrGrG


title: Normal skin4

description:
Sample 19
cDNA
Barcode: AF-PP-341: ACG CTC TTC CGA TCT rGrUrUrA

source_name: Normal skin, formalin-fixed paraffin embedded

value: normal skin


title: WM1552C

description:
Sample 25
cDNA
Barcode: AF-PP-341: ACG CTC TTC CGA TCT rGrUrUrA

source_name: WM1552C, cultured cells


title: Melanocyte-Dark

description:
Sample 28
cDNA
Barcode: AF-PP-333: ACG CTC TTC CGA TCT rArGrCrG

source_name: Melanocyte-dark, cultured cells

value: melanocyte-dark


title: Primary Cutaneous Melanoma4 (2.5 mm, level IV)

description:
Sample 13
cDNA
Barcode: AF-PP-341: ACG CTC TTC CGA TCT rGrUrUrA

source_name: Primary cutaneous melanoma (2.5 mm, level IV), formalin-fixed paraffin embedded

value: primary cutaneous melanoma (2.5 mm, level IV)


title: Primary Cutaneous Melanoma3 (2.8 mm, level IV)

description:
Sample 12
cDNA
Barcode: AF-PP-340: ACG CTC TTC CGA TCT rGrGrGrU

source_name: Primary cutaneous melanoma (2.8 mm, level IV), formalin-fixed paraffin embedded

value: primary cutaneous melanoma (2.8 mm, level IV)


title: Melanocyte-Medium2

description:
Sample 27_2
cDNA
Barcode: AF-PP-343: ACG CTC TTC CGA TCT rUrCrGrC


title: Metastatic Melanoma to skin1

description:
Sample 15
cDNA
Barcode: AF-PP-334: ACG CTC TTC CGA TCT rCrGrUrC


title: Common Nevus2

description:
Sample 11
cDNA
Barcode: AF-PP-339: ACG CTC TTC CGA TCT rArCrUrU

source_name: Common nevus, formalin-fixed paraffin embedded

value: common nevus


title: Normal skin3

description:
Sample 18
cDNA
Barcode: AF-PP-340: ACG CTC TTC CGA TCT rGrGrGrU


title: Common Nevus1

description:
Sample 10
cDNA
Barcode: AF-PP-335: ACG CTC TTC CGA TCT rCrUrGrG


title: Normal lymph node

description:
Sample 8
cDNA
Barcode: AF-PP-333: ACG CTC TTC CGA TCT rArGrCrG

source_name: Normal lymph node, formalin-fixed paraffin embedded

value: normal lymph node


title: Normal skin2

description:
Sample 6
cDNA
Barcode: AF-PP-341: ACG CTC TTC CGA TCT rGrUrUrA


title: Primary Cutaneous Melanoma5 (2.0 mm, level IV)

description:
Sample 14
cDNA
Barcode: AF-PP-342: ACG CTC TTC CGA TCT rUrArUrG

source_name: Primary cutaneous melanoma (2.0 mm, level IV), formalin-fixed paraffin embedded

value: primary cutaneous melanoma (2.0 mm, level IV)


title: Melanocyte-Medium1

description:
Sample 27_1
cDNA
Barcode: AF-PP-343: ACG CTC TTC CGA TCT rUrCrGrC


title: Melanocyte-Light

description:
Sample 26
cDNA
Barcode: AF-PP-342: ACG CTC TTC CGA TCT rUrArUrG

source_name: Melanocyte-light, cultured cells

value: melanocyte-light


title: Metastatic Melanoma to Lymph Node3

description:
Sample 9
cDNA
Barcode: AF-PP-334: ACG CTC TTC CGA TCT rCrGrUrC

source_name: Metastatic melanoma to lymph node, formalin-fixed paraffin embedded

value: metastatic melanoma to lymph node


title: Primary Cutaneous Melanoma2 (4.0 mm, level IV)

description:
Sample 7
cDNA
Barcode: AF-PP-342: ACG CTC TTC CGA TCT rUrArUrG

source_name: Primary cutaneous melanoma (4.0 mm, level IV), formalin-fixed paraffin embedded

value: primary cutaneous melanoma (4.0 mm, level IV)


title: Primary Cutaneous Melanoma1 (11.5 mm, level V)

description:
Sample 5
cDNA
Barcode: AF-PP-340: ACG CTC TTC CGA TCT rGrGrGrU

source_name: Primary cutaneous melanoma (11.5 mm, level V), fresh frozen

value: primary cutaneous melanoma (11.5 mm, level V)


title: Normal skin1

description:
Sample 4
cDNA
Barcode: AF-PP-339: ACG CTC TTC CGA TCT rArCrUrU

source_name: Normal skin, fresh frozen


description:
Sample 2
cDNA
Barcode: AF-PP-334: ACG CTC TTC CGA TCT rCrGrUrC

source_name: Acrolentiginous melanoma (3.0 mm, level IV), fresh frozen

value: acrolentiginous melanoma (3.0 mm, level IV)


title: Metastatic Melanoma to Lymph Node1

description:
Sample 1
cDNA
Barcode: AF-PP-333: ACG CTC TTC CGA TCT rArGrCrG

source_name: Metastatic melanoma to lymph node, fresh frozen


title: Metastatic Melanoma to the Lymph Node2

description:
Sample 3
cDNA
Barcode: AF-PP-335: ACG CTC TTC CGA TCT rCrUrGrG

source_name: Metastatic melanoma to the lymph node, fresh frozen

value: metastatic melanoma to the lymph node


title: IP gH2AX Senescent Cells

city: Milan

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

country: Italy

institute: Università vita e Salute Ospedale San Raffaele

data_processing:
Samples coverage (bedGraph files) were created with bedTools. Cumulative distribution and coverage of gH2AX at telomeric (2Mbp) regions was calculated using DSPChIP: http://code.google.com/p/dspchip/
Genome Build:
s_4.bedGraph: hg18

source_name: IP gH2AX Senescent Cells

growth_protocol: standard

extract_protocol: Illumina Sequencing. Preparation of Illumina libraries. 10 ng of ChIP DNA was treated to remove 3' overhangs and fill in 5' overhangs resulted in blunt ended DNA fragments. An A residue was added by terminal transferase to the 3' end and the resulting fragments were ligated with Illumina adapters. The resulting Adapter- modified DNA fragments were separated by agarose gel electrophoresis and the band between 120-200 bp was excised from the gel. The DNA fragments were extracted from the agarose slice using a Qiaquick Gel Extraction Kit (Qiagen Inc). The specific band of DNA fragments were enriched by an 18 cycle PCR using a Illumina Primer 1.1 and Primer 2.1. The resulting PCR products were separated for the second time by agarose gel electrophoresis to purified DNA from an excess of PCR primers. The 25 DNA fragment library was quantitated with Bioanalyzer using High Sensitivity Chip, then diluted to a 10 nM working stock for cluster generation. Cluster generation. Adapter-ligated fragments (2 nM) were denatured in 0.1N NaOH for 5 minutes, then were further diluted to a final 8 pM concentration in 1 ml of pre- chilled hybridization buffer, and introduced onto the Illumina flow cell using the Cluster Station, an automated device supplied by Illumina. On this apparatus, the oligo-derivatized flow cell surfaces hybridize to library fragments by adapter-to-oligo pairing. 'Clusters', representing discrete populations of unique single-stranded library fragments amplified in situ, are generated by isothermal amplification using a proprietary process. Following isothermal amplification, clusters were made single- stranded by 0.1N NaOH denaturation, metered across the flow cell by the Illumina Cluster Station. A sequencing primer complementary to one Illumina adapter was added to prime the single strands of each cluster. Once hybridized and with excess primer removed by a wash, the flow cell was ready for sequencing. Sequencing process. The Illumina Genome Analyzer was programmed to provide up to 36 sequential flows of fluorescently labeled, 3'-OH blocked nucleotides and polymerase to the surface of the flow cell, thus producing a fixed 36bp read length. After each base incorporation step, the flow cell surface is washed to remove reactants and then imaged by microscope objective.

treatment_protocol: chip performed 30 days after no or 20Gy ionizing radiations

value: BJhTERT

value: Abcam, ab2893


title: IP gH2AX Quiescent Cells

data_processing:
Samples coverage (bedGraph files) were created with bedTools. Cumulative distribution and coverage of gH2AX at telomeric (2Mbp) regions was calculated using DSPChIP: http://code.google.com/p/dspchip/
Genome Build:
s_1.bedGraph: hg18

source_name: IP gH2AX Quiescent Cells


title: Arabidopsis_drought

status: Public on Mar 12 2012

city: Shanghai

first: Renyi

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

data_processing: Raw sequence reads were parsed to remove the 3'-adaptor, and those reads that do not have the 3'-adaptor, contain N, or have length less than 17nt were removed. The first column in a processed file contains clean reads, and the second column contains the number of copies of the reads in the library.

organism: Arabidopsis thaliana

source_name: adult plants

growth_protocol: 4-week-old plants grown at 23°C with 16h light

extract_protocol: Total RNA was isolated from shoots and fractionated on 15% denaturing polyacrylamide gel. RNA molecules ranging from 20 to 30 nt were excised and ligated to a preadenylated 3' adaptor and a 5’- adaptor using T4 RNA ligase. Ligation products were purified in polyacrylamide gels, followed by RT-PCR. The small RNA libraries were sequenced by the UCR core facility.

treatment_protocol: Four groups of plants are treated as follows: control (untreated), drought (40-50% relative water content), cold (5 ˚C for 24 hours), and salt (200mM NaCl for 5 hours)

value: Col gl1 RD29:LUC

value: Shoots

value: drought


title: Arabidopsis_cold

value: cold


title: Arabidopsis_control

value: control


title: rice_cold

organism: Oryza sativa

source_name: inflorescences

growth_protocol: Three-month-old plants grown at 28°C with 13h light

extract_protocol: Total RNA was isolated from inflorescences and fractionated on 15% denaturing polyacrylamide gel. RNA molecules ranging from 20 to 30 nt were excised and ligated to a preadenylated 3' adaptor and a 5’- adaptor using T4 RNA ligase. Ligation products were purified in polyacrylamide gels, followed by RT-PCR. The small RNA libraries were sequenced by the UCR core facility.

treatment_protocol: Four groups of plants are treated as follows: control (untreated), drought (drought for 3 days), cold (5 ˚C for 24 hours), and salt (400mM NaCl for 24 hours)

tag: subspecies

value: Japonica

value: inflorescences


title: Arabidopsis_salt

value: salt


title: Input Quiescent Cells

data_processing:
Samples coverage (bedGraph files) were created with bedTools. Cumulative distribution and coverage of gH2AX at telomeric (2Mbp) regions was calculated using DSPChIP: http://code.google.com/p/dspchip/
Genome Build:
s_3.bedGraph: hg18

source_name: Input Quiescent Cells

tag: cell type


title: rice_control


title: Arabidopsis_salt_pind

data_processing: Raw sequence reads were parsed to remove the 3'-adaptor, and those reads that do not have the 3'-adaptor, contain N, or have length less than 17nt were removed. The processed files are named as "prefix"_uniq.txt, where "prefix" is the prefix of the file that contains raw data.  The first column in a processed file contains clean reads, and the second column contains the number of copies of the reads in the library.

source_name: seedlings

growth_protocol: For AtCold library, 15-day-old plants grown at 22°C with 16h light; for AtPdep and AtPind libraries, 10-day-old plants grown at 22°C with 16h light

extract_protocol: Total RNA was isolated from shoots and fractionated on 15% denaturing polyacrylamide gel. RNA molecules ranging from 18 to 30 nt were excised. For AtCold and AtPdep libraries, excised RNAs were ligated to a preadenylated 3' adaptor and a 5’- adaptor using T4 RNA ligase. For AtPind library, excised RNAs were first de-phosphorylated at the 5’ end. After 3’ end adaptor was ligated, the 5’ end was phosphorylated before 5’ adaptor was ligated. Ligation products were purified in polyacrylamide gels, followed by RT-PCR. The small RNA libraries were sequenced using Illumina Genome Analyzer.

treatment_protocol: For AtCold library, plants were treated under 5 ˚C for 24 hours; For AtPdep and AtPind libraries, plants were treated with 300mM NaCl for 5 hours

tag: ecotype

value: Columbia

tag: stress

value: 300mM NaCl for 5 hours

tag: age


title: Arabidopsis_cold_stress

value: 5 ˚C for 24 hours


title: rice_drought


title: Arabidopsis_salt_pdep


title: SE_5hmC

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

description:
SE_5hmC_1
SE_5hmC_2

data_processing:
Sequenced reads were base-called using the standard Illumina software. 5 and 10 bases from the 5’ and 3’ ends of the reads were removed, respectively. The remaining 85 bases were aligned to the mouse genome (mm9) with Bowtie allowing up to three mismatches within the first 75 bases.
Genome Build:
5hmc_st.bw: mm9

source_name: Sertoli cells

extract_protocol:
Genomic DNAs were extracted using QiagenBlood & Cell Culture DNA Kits. Sperms were treated with DTT for a half hour at room temperature before DNA extraction. Briefly, cells were first lysed and the nuclei were collected using Buffer C1.The nuclei were treated with RNaseA (200ug/mL) in Buffer G2 for 5 min at room temperature and then incubated with proteinase K (500 ug/ml) overnight at 50 °C.On the second day, samples were loaded to mini-prep tips and the purified genomic DNAs were precipitated by adding 0.7 volumes room temperature isopropanol, washed with 1 ml of cold 70% ethanol, and dissolved in H2O. For each genomic DNA sample, 10~20 ug DNA was sonicatedinto short fragments in a range of 100 to 500 bp using a Covaris S2 instrument (Duty Cycle 10%, Intensity 5, Cycles per burst 200, 180 seconds). DNA was then concentrated to about 15 ul using an Eppendorf Concentrator plus instrument.
Enrichment of 5hmC containing DNA fragments was performed as previously described (ref 1,2). 10~20 ug fragmented DNA was glucosylated in a 20 μl solution containing 50 mM HEPES buffer (pH 7.9), 25 mM MgCl2, 100 μM UDP-6-N3-Glu and 2 μM β-glucosyltransferase for 1 hr at 37 °C, producing β-6-azide-glucosyl-5-hydroxymethyl-cytosine (N3-5-gmC). Click chemical reaction was then performed with a disulfide linkerat a concentration of 150 μM for 2 hr at 37 °C, yielding biotin-S-S-N3-5-gmC (ref 2). At the end of each reaction, DNA was purified on a Micro Bio-Spin 6 Column (Bio-Rad) whose buffer was exchanged with water for four times. The biotinylated DNA fragments were captured by DynabeadsMyOne Streptavidin C1 beads (Invitrogen) according to the manufacturer’s protocol. To release the DNA fragments, the beads were incubated in 70 µL of dithiothreitol (DTT) in H2O for 2 hr at room temperature using gentle rotation and separated with a magnet. The released DNA was applied to Micro Bio-Spin 6 Column and finally purified by QiagenMinElute PCR Purification Kit. Libraries were generated usingIlluminaTruSeqSample Preparation Kits following the manufacturer’s instruction. After PCR amplification, DNA fragments of 250 to 450 bp was gel-purified and then sequenced using IlluminaHiseq 2000.

treatment_protocol: Because different types of spermatogenic cells appear at different days postpartum (dpp), the cell type and the corresponding dpp pairs are as follows: primitive type A spermatogonia (priSG-A)/6 dpp, type A spermatogonia (SG-A)/8 dpp, type B spermatogonia (SG-B)/8 dpp mice, leptotene spermatocytes (lepSC)/17 dpp, pachytene spermatocytes (pacSC)/17 dpp, round spermatids (rST)/adult, elongative spermatids (eST)/adult. The only somatic cell type inside the seminiferous tubules, the Sertoli cells (SE), were isolated from 6 dpp mice. Spermatozoa (SZ) were isolated from epididymis.

value: Sertoli cells (somatic cell)

tag: generation

tag: gender

value: male

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/18NCrlVr female mice

tag: development stage


title: SZ_5hmC

description:
SZ_5hmC_1
SZ_5hmC_2

data_processing:
Sequenced reads were base-called using the standard Illumina software. 5 and 10 bases from the 5’ and 3’ ends of the reads were removed, respectively. The remaining 85 bases were aligned to the mouse genome (mm9) with Bowtie allowing up to three mismatches within the first 75 bases.
Genome Build:
5hmc_sz.bw: mm9

source_name: spermatozoa

value: spermatozoa (germ cell)

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/16NCrlVr female mice

value: adult


title: eST_5hmC

description:
eST_5hmC_1
eST_5hmC_2

data_processing:
Sequenced reads were base-called using the standard Illumina software. 5 and 10 bases from the 5’ and 3’ ends of the reads were removed, respectively. The remaining 85 bases were aligned to the mouse genome (mm9) with Bowtie allowing up to three mismatches within the first 75 bases.
Genome Build:
5hmc_ers.bw: mm9

source_name: elongative spermatids

value: elongative spermatids (germ cell)

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/14NCrlVr female mice


title: 5hmC_control

description:
5hmC_control_1
5hmC_control_2

data_processing:
Sequenced reads were base-called using the standard Illumina software. 5 and 10 bases from the 5’ and 3’ ends of the reads were removed, respectively. The remaining 85 bases were aligned to the mouse genome (mm9) with Bowtie allowing up to three mismatches within the first 75 bases.
Genome Build:
5hmc_control.bw: mm9

source_name: leptotene spermatocytes

value: leptotene spermatocytes (germ cell)

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/20NCrlVr female mice


title: rST_5hmC

description:
rST_5hmC_1
rST_5hmC_2

data_processing:
Sequenced reads were base-called using the standard Illumina software. 5 and 10 bases from the 5’ and 3’ ends of the reads were removed, respectively. The remaining 85 bases were aligned to the mouse genome (mm9) with Bowtie allowing up to three mismatches within the first 75 bases.
Genome Build:
5hmc_rs.bw: mm9

source_name: round spermatids

value: round spermatids (germ cell)

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/12NCrlVr female mice


title: lepSC_5hmC

description:
lepSC_5hmC_1
lepSC_5hmC_2

data_processing:
Sequenced reads were base-called using the standard Illumina software. 5 and 10 bases from the 5’ and 3’ ends of the reads were removed, respectively. The remaining 85 bases were aligned to the mouse genome (mm9) with Bowtie allowing up to three mismatches within the first 75 bases.
Genome Build:
5hmc_lps.bw: mm9

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/8NCrlVr female mice


title: SG-B_5hmC

description:
SG-B_5hmC_1
SG-B_5hmC_2

data_processing:
Sequenced reads were base-called using the standard Illumina software. 5 and 10 bases from the 5’ and 3’ ends of the reads were removed, respectively. The remaining 85 bases were aligned to the mouse genome (mm9) with Bowtie allowing up to three mismatches within the first 75 bases.
Genome Build:
5hmc_b.bw: mm9

source_name: type B spermatogonia

value: type B spermatogonia (germ cell)

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/6NCrlVr female mice


title: pacSC_5hmC

description:
pacSC_5hmC_1
pacSC_5hmC_2

data_processing:
Sequenced reads were base-called using the standard Illumina software. 5 and 10 bases from the 5’ and 3’ ends of the reads were removed, respectively. The remaining 85 bases were aligned to the mouse genome (mm9) with Bowtie allowing up to three mismatches within the first 75 bases.
Genome Build:
5hmc_ps.bw: mm9

source_name: pachytene spermatocytes

value: pachytene spermatocytes (germ cell)

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/10NCrlVr female mice


title: Input Senescent Cells

data_processing:
Samples coverage (bedGraph files) were created with bedTools. Cumulative distribution and coverage of gH2AX at telomeric (2Mbp) regions was calculated using DSPChIP: http://code.google.com/p/dspchip/
Genome Build:
s_6.bedGraph: hg18

source_name: Input Senescent Cells

value: BJhTERT

tag: antibody


title: priSG-A_5hmC

description:
priSG-A_5hmC_1
priSG-A_5hmC_2

data_processing:
Sequenced reads were base-called using the standard Illumina software. 5 and 10 bases from the 5’ and 3’ ends of the reads were removed, respectively. The remaining 85 bases were aligned to the mouse genome (mm9) with Bowtie allowing up to three mismatches within the first 75 bases.
Genome Build:
5hmc_pa.bw: mm9

source_name: primitive type A spermatogonia

value: primitive type A spermatogonia (germ cell)

value: male

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/2NCrlVr female mice


title: SG-A_5hmC

description:
SG-A_5hmC_1
SG-A_5hmC_2

data_processing:
Sequenced reads were base-called using the standard Illumina software. 5 and 10 bases from the 5’ and 3’ ends of the reads were removed, respectively. The remaining 85 bases were aligned to the mouse genome (mm9) with Bowtie allowing up to three mismatches within the first 75 bases.
Genome Build:
5hmc_a.bw: mm9

source_name: type A spermatogonia

value: type A spermatogonia (germ cell)

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/4NCrlVr female mice


title: SE_RNAseq

description:
SE_RNAseq_1
SE_RNAseq_2

data_processing:
The sequencing reads were mapped to mouse genome (mm9) using TopHat package
Genome Build:
RNA_ST.bw: mm9

extract_protocol: Total RNAs were extracted using QIAGEN RNeasy Mini Kits, and mRNA was isolated by Sera-Mag Oligo(dT) beads (Thermo Scientific) according to the manufacturer’s protocol. Libraries were prepared using NEBNext mRNA Sample PreP Master Mix Set 1 following the manufacturer’s instruction and sequenced using IlluminaHiseq 2000.

treatment_protocol: Because different types of spermatogenic cells appear at different days postpartum (dpp), the cell type and the corresponding dpp pairs are as follows: primitive type A spermatogonia (priSG-A)/6 dpp, type A spermatogonia (SG-A)/8 dpp, type B spermatogonia (SG-B)/8 dpp mice, leptotene spermatocytes (lepSC)/17 dpp, pachytene spermatocytes (pacSC)/17 dpp, round spermatids (rST)/adult, elongative spermatids (eST)/adult. The only somatic cell type inside the seminiferous tubules, the Sertoli cells (SE), were isolated from 6 dpp mice.

value: Sertoli cells (somatic cell)

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/18NCrlVr female mice


title: eST_RNAseq

description:
eST_RNAseq_1
eST_RNAseq_2

data_processing:
The sequencing reads were mapped to mouse genome (mm9) using TopHat package
Genome Build:
RNA_ERS.bw: mm9

value: elongative spermatids (germ cell)

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/14NCrlVr female mice

value: adult


title: pacSC_RNAseq

description:
pacSC_RNAseq_1
pacSC_RNAseq_2

data_processing:
The sequencing reads were mapped to mouse genome (mm9) using TopHat package
Genome Build:
RNA_PS.bw: mm9


title: rST_RNAseq

description:
rST_RNAseq_1
rST_RNAseq_2

data_processing:
The sequencing reads were mapped to mouse genome (mm9) using TopHat package
Genome Build:
RNA_RS.bw: mm9

value: round spermatids (germ cell)

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/12NCrlVr female mice


title: rice_salt

data_processing: Raw sequence reads were parsed to remove the 3'-adaptor, and those reads that do not have the 3'-adaptor, contain N, or have length less than 17nt were removed. The first column in a processed file contains clean reads, and the second column contains the number of copies of the reads in the library.

value: Japonica

value: inflorescences

value: salt


title: priSG-A_RNAseq

description:
priSG-A_RNAseq_1
priSG-A_RNAseq_2

data_processing:
The sequencing reads were mapped to mouse genome (mm9) using TopHat package
Genome Build:
RNA_PA.bw: mm9


title: SG-B_RNAseq

description:
SG-B_RNAseq_1
SG-B_RNAseq_2

data_processing:
The sequencing reads were mapped to mouse genome (mm9) using TopHat package
Genome Build:
RNA_B.bw: mm9

value: type B spermatogonia (germ cell)

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/6NCrlVr female mice


title: RNA_72hours_WNT_OFF_3

status: Public on Mar 09 2012

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the MAQ package
Genome Build:
TDOX3.bed: hg18

growth_protocol: We used Ls174T human colon cancer cells carrying an activating point mutation in β-catenin and Ls174T-pTER-β-catenin cell line carrying a doxycyclin-inducible short hairpin RNA (shRNA) against β-catenin.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. To deplete for non-informative ribosomal RNA, 5 µg of total RNA were purified using Ribominus kit (Invitrogen) according to manufacturer's instructions. Ribosome-depleted RNA was resuspended in 50 µl of diethylpyrocarbonate (DEPC)-treated water and fragmented for 60 s using the Covaris sonicator (6 ×16 mm AFA fiber Tube, duty cycle: 10%, intensity: 5, cycles/burst: 200, frequency sweeping). Sheared RNA fragments were phosphorylated using 30 U of Polynucleotide Kinase (Promega) with 0.5 mM adenosine triphosphate (ATP) for 30 min at 37°C. Phosphorylated RNA was purified using TRIzol according to the manufacturer's instruction and resuspended in 1.5 µl of DEPC-treated water with 1 µl of Adaptor mix A and 1.5 µl of Hybridization solution from SOLiD Small RNA Expression Kit (SREK) (Ambion). The mixture was incubated at 65°C in a thermocycler for 5 min and quickly cooled on ice. RNA with hybridized adaptors was mixed with 5 µl of SREK ligation buffer and 1 µl of SREK ligation enzyme and incubated at room temperature for 4 h. Ligated sample was mixed with 10 µl of denaturing buffer (90% formamide, bromphenol blue, crysol red) and size selected on 10% denaturing urea gel for the appropriate size fraction (150–300 bp). The piece of gel containing selected fragments was shredded and RNA was eluted in 300 µl 300 mM NaCl with gentle agitation for 4 h at room temperature. The eluate was separated from gel debris using SPIN-X centrifuge tube filters (Costar); the RNA was precipitated by isopropanol and resuspended in 5 µl of DEPC-treated water. Size-selected RNA was mixed with 2 µl of reverse transcription (RT) buffer, 1.5 µl of dNTPs (10 mMeach), 0.5 µl of barcode RT primer (10 µM), incubated in a thermocycler at 72°C for 4 min, 62°C for 2 min and then put on ice. The sample with hybridized barcode RT primer was mixed with MMLV-RT enzyme (Promega) and incubated at 37°C for 30 min. The library was amplified by ligation-mediated polymerase chain reaction (LM-PCR) by adding 2 µl of RT mix from the previous reaction into 100 µl of PCR mix from the SREK kit (Ambion) with P1 and P2 primer compatible with SOLiD/AB sequencing and cycled in a thermocycler with the following program: 95°C for 2 min; 15 cycles of 95°C for 30 s, 62°C for 30 s, 72°C for 30 s; 72°C for 7 min. The library was size selected on a 2% agarose gel for 150–400-bp long fragments and sequenced on SOLiD/AB sequencer in a multiplexed way to produce 50-bp long reads.

treatment_protocol: Cells were grown in the presence or absence of doxycyclin (1 µg/ml) for 72 h.

value: Ls174T human colon cancer cells

tag: wnt suppression

value: off


title: RNA_72hours_WNT_OFF_2

data_processing:
Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the MAQ package
Genome Build:
TDOX2.bed: hg18


title: SG-A_RNAseq

description:
SG-A_RNAseq_1
SG-A_RNAseq_2

data_processing:
The sequencing reads were mapped to mouse genome (mm9) using TopHat package
Genome Build:
RNA_A.bw: mm9

value: male


title: RNA_72hours_WNT_ON_3

data_processing:
Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the MAQ package
Genome Build:
TCON3.bed: hg18

value: on


title: RNA_72hours_WNT_OFF_1

data_processing:
Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the MAQ package
Genome Build:
TDOX1.bed: hg18


title: Reverb_alpha_null_5pm

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

data_processing:
Mapped read BED files: For all ChIP-Seq samples, sequence reads were mapped to the mouse genome (NCBI36/UCSC mm8) using ELAND software. Only the sequences uniquely mapped with no more than 2 mismatches in the first 32 bp were kept and used as valid reads. Redundant reads mapping to the same genomic loci were condensed to a single read to remove clonal amplification artifacts. Reads from replicate samples were pooled together prior to further analysis

Peak Call BED files: Peak calling was carried out by HOMER (version 3, 0.1% FDR, 1rpm cutoff).

Analysis BED files: To adjust for the higher read depth in the Rev-erb(alpha)-null ChIP-Seq sample, reads were randomly sampled from the Rev-erb(alpha)-null data 10 times, such that each random sample had a similar read count to the wild-type cistrome. The peak height was computed in each random sample, and the average height at each peak was used for subsequent analysis.  In order to obtain the most stringent high confidence cistrome, potential non-specific binding events in the Rev-erb(alpha) 5PM/ZT10 cistrome was identified, thereby removing 5,830 peaks where the Rev-erb(alpha) ChIP-Seq profile in the Rev-erb(alpha)-null animal was more than 50% of the peak height observed in the WT at 5PM/ZT10 from all subsequent analysis. The remaining peak calls for both Rev-erb(alpha) and Rev-erb(beta) were then merged together, such that any overlapping regions were combined into one region covering the peak calls for both isoforms. This resulted in 31,958 total Rev-erb binding regions, which contain a valid peak call for Rev-erb(alpha) and/or Rev-erb(beta). The ChIP-Seq signal for each subtype was then quantified at each region by computing the maximum stack height profile within the region, normalized to the total number of reads for that isoform (rpm).  Each region was categorized as being specific to either subtype, or common to both isoforms, as follows: First, Fisher’s Exact Test was applied to each region, comparing the peak height and total reads for each factor for significant changes that are unlikely to occur simply due to variability in the sequencing process. Regions with a Benjamini-Hochberg corrected p-value <= 0.05 from Fisher's Exact Test, and an absolute fold-change > 2 using the normalized (rpm) peak heights, were considered to be specific to the subtype with greater binding. All other sites were considered “common” sites because, regardless of peak calls, these sites did not show a significant quantitative difference in binding signal between the two subtypes. By this method, 29,462 sites are considered “common” sites (92%), 1,614 are considered "Alpha-specific" (5%), and 882 are considered "Beta-specific" (3%).

Genome Build:
ReverbA_KO_Liver_ZT10_masked.bed: mm8
reverb_alpha_KO_zt10_r1_223_2_rd.bed.gz: mm8

source_name: Homogenized mouse liver, Rev-erb(alpha) KO, 5pm/ZT10, Rev-erb(alpha) ChIP

growth_protocol: Male C57BL/6 WT and Rev-erbα KO mice, 8-12 weeks of age, were housed under 12h-light/12h-dark cycles (lights on at 7 AM, lights off at 7 PM), and euthanized at ZT10 (5PM) or ZT22 (5AM).

extract_protocol: ChIP experiments were performed independently on liver samples from 4 different mice and subsequently pooled. Libraries for each ChIP-Seq experiment were prepared as per Illumina's instructions (http://www.illumina.com). Briefly, DNA fragments were blunted, phosphorylated, and ligated to Illumina library adapters. Size selection was performed using gel electrophoresis by excising DNA fragments at 200 ± 50 base pairs. Following gel purification, PCR amplification was performed (30 s at 98°C; [10 s at 98°C, 30 s at 65°C, 30 s at 72°C] × 18 cycles; 5 min at 72°C). Amplified material was evaluated on an Agilent 2100 bioanalyzer to ensure proper size selection.

treatment_protocol: Liver was harvested immediately after euthanasia, quickly minced and cross-linked in 1% formaldehyde for 20min, followed by quenching with glycine solution. Nuclear extracts were prepared by Dounce homogenization. Chromatin fragmentation was performed by sonication using the Bioruptor (Diagenode). Proteins were immunoprecipited using Rev-erbβ antiserum or Rev-erbα antibody (Cell Signalling #2124). Cross-linking was reversed overnight at 65°C, and DNA was isolated using phenol/chloroform/isoamyl alcohol.

tag: genotype/variation

value: Rev-erb(alpha) KO

value: 8-12 weeks

value: liver

tag: time

tag: chip antibody

value: Rev-erb(alpha)

tag: antibody vendor

value: Cell Signalling

tag: antibody catalog #

tag: antibody lot#


title: RNA_72hours_WNT_ON_2

data_processing:
Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the MAQ package
Genome Build:
TCON2.bed: hg18


title: chd1 H3K27me3_ChIPSeq

status: Public on Mar 10 2012

city: paris

first: yongfeng

last: hu

address: univercite paris-sud Bat 630

country: France

institute: IBP

description: Chromatin IP against H3K27me3

data_processing:
Clean: After completing the sequencing,we removed the low-quality sequences, the adaptor sequences, and the pollutions.
Alignment: Sequence reads were obtained and mapped to the rice (Orazy JP_6.1) genomes using SOAP2.21 software. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 50 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm, the default parameters were bandwidth, 200bp; mfold, 32; P-value of 1.00e-05.

organism: Oryza sativa Japonica Group

growth_protocol: The rice  grew under long day conditions (14.5 h light and 8.5 h dark per day) and 28 C in the rooting medium.

extract_protocol: Full plant of 11 days old rice seedlings which were grew under the conditions (14.5h light and 8.5h dark at 28C) in the rooting medium were used for chromatin immunoprecipitation (CHIP) experiments. During the experiments, Chromatin was fragmented to 100-500bp by sonication and ChIP was performed using the following two antibodies: H3K4me3 (Millipore, DAM1731494) and H3K27me3 (Millipore, DAM166204). Briefly, The precipitated DNA was end-repaired using a combination of T4 DNA polymerase (Catalog NO.P708L), and T4 polynucleotide kinase (Catalog NO.Y904L). The blunt, phosphorylated ends were treated with Klenow Enzyme(Catalog NO.P706L) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end, all of above as discribled according to Illumina Paired-End DNA Sample Prep kit. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of 100~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced with the Equipment Illumina HISEQ2000.

tag: developmental stage

value: 11 days seedling

value: Full plants

tag: vendor

value: Millipore, DAM166204


title: HY H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

source_name: HY(Hwayong)

tag: cell type

value: Millipore, DAM1731494

value: Hwayong


title: RNAPII_72hours_WNT_ON_3

data_processing:
Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the MAQ package
Genome Build:
CON3.bed: hg18

extract_protocol: Chromatin was additionally sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by LMPCR. After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and sequenced on SOLiD/AB sequencer to produce 50-bp long reads.

value: anti-RNAPII

value: Euromedex

tag: catalog#


title: RNAPII_72hours_WNT_OFF_2

data_processing:
Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the MAQ package
Genome Build:
DOX2.bed: hg18


title: RNAPII_72hours_WNT_ON_2

data_processing:
Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the MAQ package
Genome Build:
CON2.bed: hg18


title: RNAPII_72hours_WNT_OFF_1

data_processing:
Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the MAQ package
Genome Build:
DOX1.bed: hg18


title: RNAPII_72hours_WNT_ON_1

data_processing:
Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the MAQ package
Genome Build:
CON1.bed: hg18


title: chd1 H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3


title: Input HELA Sample 1

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

description:
Sample 4
processed data file: Input_HELA_Pool_w1000s100.wig (available on Series records)

data_processing:
Sequence reads were mapped to the hg18 or mm9 genomes as appropriate using the Illumina Genome Analyser Pipeline.  Reads with less than two mismatches were not aligned.
Coverage was calculated in 1 Kb windows using a step of 100 nt across the genome.

source_name: HeLa_Input DNA

extract_protocol: Crosslinking for all the cell types used was carried out for 3 mins in 1% formaldehyde. Crosslinked chromatin from 10^7 cells and 60mg of antibody was used for each immunoprecipitation. Purified DNA was subjected to end-repair and adapter ligation using a sample preparation kit from Illumina according to the manufacturer’s protocol.

tag: cell line

value: HELA cell culture


title: Input HELA Sample 2

description:
Sample 5
processed data file: Input_HELA_Pool_w1000s100.wig (available on Series records)


title: RNAPII_72hours_WNT_OFF_3

data_processing:
Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the MAQ package
Genome Build:
DOX3.bed: hg18

value: Ls174T human colon cancer cells


title: HY H3K27me3_ChIPSeq

description: Chromatin IP against H3K27me3


title: HA-flag-Vezf1 ChIP-Seq Sample 2

description:
Sample 2
processed data file: Vezf1_HELA_Pool_w1000s100.wig (available on Series records)

source_name: HeLa_HA-flag-Vezf1 ChIP-Seq

value: Anti-FLAG M2


title: RNA Polymerase 2 ChIP-Seq HELA

description:
Sample 3
processed data file: Ser2Pol2_HELA_w1000s100.wig (available on Series records)

source_name: HeLa_RNA Polymerase 2 ChIP-Seq

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: lepSC_RNAseq

description:
lepSC_RNAseq_1
lepSC_RNAseq_2

data_processing:
The sequencing reads were mapped to mouse genome (mm9) using TopHat package
Genome Build:
RNA_LPS.bw: mm9

value: leptotene spermatocytes (germ cell)

tag: generation

tag: gender

value: male

tag: strain

value: F1 male mice of 129S2/SvPasCrlVr male and DBA/8NCrlVr female mice


title: Reverb_beta_5am

description: The Rev-erb(beta) antibody was custom developed for this project by Covance against amino acids 243-261 of the mouse Rev-erb(beta) protein (epitope: SDFAKEEVIGMVTRAHKDT). The validation of this antibody is described in the accompanying manuscript.

data_processing:
Mapped read BED files: For all ChIP-Seq samples, sequence reads were mapped to the mouse genome (NCBI36/UCSC mm8) using ELAND software. Only the sequences uniquely mapped with no more than 2 mismatches in the first 32 bp were kept and used as valid reads. Redundant reads mapping to the same genomic loci were condensed to a single read to remove clonal amplification artifacts. Reads from replicate samples were pooled together prior to further analysis

Peak Call BED files: Peak calling was carried out by HOMER (version 3, 0.1% FDR, 1rpm cutoff).

Analysis BED files: To adjust for the higher read depth in the Rev-erb(alpha)-null ChIP-Seq sample, reads were randomly sampled from the Rev-erb(alpha)-null data 10 times, such that each random sample had a similar read count to the wild-type cistrome. The peak height was computed in each random sample, and the average height at each peak was used for subsequent analysis.  In order to obtain the most stringent high confidence cistrome, potential non-specific binding events in the Rev-erb(alpha) 5PM/ZT10 cistrome was identified, thereby removing 5,830 peaks where the Rev-erb(alpha) ChIP-Seq profile in the Rev-erb(alpha)-null animal was more than 50% of the peak height observed in the WT at 5PM/ZT10 from all subsequent analysis. The remaining peak calls for both Rev-erb(alpha) and Rev-erb(beta) were then merged together, such that any overlapping regions were combined into one region covering the peak calls for both isoforms. This resulted in 31,958 total Rev-erb binding regions, which contain a valid peak call for Rev-erb(alpha) and/or Rev-erb(beta). The ChIP-Seq signal for each subtype was then quantified at each region by computing the maximum stack height profile within the region, normalized to the total number of reads for that isoform (rpm).  Each region was categorized as being specific to either subtype, or common to both isoforms, as follows: First, Fisher’s Exact Test was applied to each region, comparing the peak height and total reads for each factor for significant changes that are unlikely to occur simply due to variability in the sequencing process. Regions with a Benjamini-Hochberg corrected p-value <= 0.05 from Fisher's Exact Test, and an absolute fold-change > 2 using the normalized (rpm) peak heights, were considered to be specific to the subtype with greater binding. All other sites were considered “common” sites because, regardless of peak calls, these sites did not show a significant quantitative difference in binding signal between the two subtypes. By this method, 29,462 sites are considered “common” sites (92%), 1,614 are considered "Alpha-specific" (5%), and 882 are considered "Beta-specific" (3%).

Genome Build:
ReverbBeta_Liver_ZT22_homer_1rpm.bed: mm8
reverb_beta_zt22_r1_177_2_rd.bed.gz: mm8

source_name: Homogenized mouse liver, WT, 5am/ZT22, Rev-erb(beta) ChIP

value: WT

tag: age

value: 8-12 weeks

tag: tissue

value: liver

value: Rev-erb(beta)

value: Covance


title: Input Vezf1 ko

description:
Sample 9
processed data file: Input_mm9ES_Vezf1ko_w1000s100.wig (available on Series records)

source_name: mm9ES_Vezf1 ko_Input

tag: genotype/variation

value: embryonic stem (ES) cells


title: Reverb_beta_5pm

data_processing:
Mapped read BED files: For all ChIP-Seq samples, sequence reads were mapped to the mouse genome (NCBI36/UCSC mm8) using ELAND software. Only the sequences uniquely mapped with no more than 2 mismatches in the first 32 bp were kept and used as valid reads. Redundant reads mapping to the same genomic loci were condensed to a single read to remove clonal amplification artifacts. Reads from replicate samples were pooled together prior to further analysis

Peak Call BED files: Peak calling was carried out by HOMER (version 3, 0.1% FDR, 1rpm cutoff).

Analysis BED files: To adjust for the higher read depth in the Rev-erb(alpha)-null ChIP-Seq sample, reads were randomly sampled from the Rev-erb(alpha)-null data 10 times, such that each random sample had a similar read count to the wild-type cistrome. The peak height was computed in each random sample, and the average height at each peak was used for subsequent analysis.  In order to obtain the most stringent high confidence cistrome, potential non-specific binding events in the Rev-erb(alpha) 5PM/ZT10 cistrome was identified, thereby removing 5,830 peaks where the Rev-erb(alpha) ChIP-Seq profile in the Rev-erb(alpha)-null animal was more than 50% of the peak height observed in the WT at 5PM/ZT10 from all subsequent analysis. The remaining peak calls for both Rev-erb(alpha) and Rev-erb(beta) were then merged together, such that any overlapping regions were combined into one region covering the peak calls for both isoforms. This resulted in 31,958 total Rev-erb binding regions, which contain a valid peak call for Rev-erb(alpha) and/or Rev-erb(beta). The ChIP-Seq signal for each subtype was then quantified at each region by computing the maximum stack height profile within the region, normalized to the total number of reads for that isoform (rpm).  Each region was categorized as being specific to either subtype, or common to both isoforms, as follows: First, Fisher’s Exact Test was applied to each region, comparing the peak height and total reads for each factor for significant changes that are unlikely to occur simply due to variability in the sequencing process. Regions with a Benjamini-Hochberg corrected p-value <= 0.05 from Fisher's Exact Test, and an absolute fold-change > 2 using the normalized (rpm) peak heights, were considered to be specific to the subtype with greater binding. All other sites were considered “common” sites because, regardless of peak calls, these sites did not show a significant quantitative difference in binding signal between the two subtypes. By this method, 29,462 sites are considered “common” sites (92%), 1,614 are considered "Alpha-specific" (5%), and 882 are considered "Beta-specific" (3%).

Genome Build:
ReverbBeta_Liver_ZT10_homer_1rpm.bed: mm8
reverb_beta_zt10_r1_174_7_rd.bed.gz: mm8
reverb_beta_zt10_r2_177_1_rd.bed.gz: mm8
reverb_beta_zt10_r3_190_1_rd.bed.gz: mm8

source_name: Homogenized mouse liver, WT, 5pm/ZT10, Rev-erb(beta) ChIP

tag: time

tag: chip antibody


title: RNA Polymerase 2 ChIP-Seq mm9ES Vezf1 ko

description:
Sample 8
processed data file: Ser2Pol2_mm9ES_Vezf1ko_w1000s100.wig (available on Series records)

source_name: mm9ES_Vezf1_ko_RNA Polymerase 2 ChIP-Seq


title: Input mm9ES wt

description:
Sample 7
processed data file: Input_mm9ES_wt_w1000s100.wig (available on Series records)

source_name: mm9ES_wt_Input DNA

value: wild type


title: RNA_72hours_WNT_ON_1

data_processing:
Sequencing reads were mapped against the reference genome (hg18 assembly, NCBI build 36) using the MAQ package
Genome Build:
TCON1.bed: hg18

tag: wnt suppression

value: on


title: RNA Polymerase 2 ChIP-Seq mm9ES wt

description:
Sample 6
processed data file: Ser2Pol2_mm9ES_wt_w1000s100.wig (available on Series records)

source_name: mm9ES_wt_RNA Polymerase 2 ChIP-Seq


title: HA-flag-Vezf1 ChIP-Seq Sample 1

description:
Sample 1
processed data file: Vezf1_HELA_Pool_w1000s100.wig (available on Series records)


title: islet preparation 1 under cytokine treatment

city: Brussels

first: Guy

last: Bottu

address: U.L.B. CP618, Route de Lennik 808

department: Faculty of Medecine

country: Belgium

institute: Free University of Brussels

description: Sample 2

data_processing:
BED files: Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program gem-mapper from the GEM suite (http://gemlibrary.sourceforge.net). The GEM mapper reports exhaustively all mappings and split-mappings up to a user-defined amount of mismatches (default 2 mismatches), disregarding presumptive base-calling errors as identified by low associated quality values.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome Build:
ID1_cyt.bed: GRCh37/hg19
ID1_cyt.gtf: GRCh37/hg19

source_name: islet preparation_cytokine treatment

growth_protocol: Human islet preparations were obtained from heart-beating organ donors with no medical history of diabetes or metabolic disorders. The islets were isolated using collagenase digestion and density gradient purification. They were cultured in M199 culture medium containing 5.5 mM glucose and shipped within 1-5 days following isolation. Upon arrival, the human islet cells were cultured in Ham's F-10 medium containing 6.1 mM glucose, 10% fetal bovine serum (FBS), 2 mM GlutaMAX, 50 μM 3-isobutyl-1-methylxanthine, 1% BSA, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Venlo, The Netherlands), which favors purification of all RNA molecules longer than 200 nucleotides and sample preparation was done as described by the manufacturer (Illumina, Eindhoven, The Netherlands). Briefly, mRNA was purified from two μg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments. The generated cDNA had undergone paired-end repair to convert overhangs into blunt ends. After 3’-monoadenylation and adaptor ligation, cDNAs were purified on a 2% agarose gel and 200 basepair (bp) products were excised from the gel. Following gel digestion, purified cDNA was amplified by PCR using primers specific for the ligated adaptors. The generated libraries were submitted to quality control with the Agilent bioanalyzer 2100 (Agilent Technologies, Wokingham, UK) before sequencing. The RNA integrity number (RIN) values for all samples were 7.5 and above. 1 μL cDNA was loaded on an Agilent DNA chip (DNA-1000) to verify cDNA quality and quantity. Only libraries reaching satisfactory conditions were used for sequencing, on one sequencing lane of an Illumina Genome Analyzer II system (GAII, Illumina).

treatment_protocol: The islets were exposed or not to cytokines in the same medium as used for preparation but without FBS for 2 days. The following cytokine concentrations were used: recombinant human IL-1β (specific activity 1.8x107 U/mg; a kind gift from C.W. Reinolds, National Cancer Institute, Bethesda, MD, USA) at 50 U/ml; recombinant human IFN-γ (specific activity 2x107 U/mg; R&D Systems, Abingdon, UK) at 1000 U/ml. The evaluation of islet cell purity, i.e. the percentage of beta cells present in the preparations, was done by immunocytochemistry with an anti-insulin antibody (1/1000; Sigma, Bornem, Belgium) and donkey anti-mouse IgG rhodamine (1/200; Lucron Bioproducts, De Pinte, Belgium). Only preparations with more than 40% beta cells were used for the RNA-seq analyses; on average they contained 58% beta cells.

value: islets of Langerhans


title: islet preparation 3 under cytokine treatment

description: Sample 6

data_processing:
BED files: Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program gem-mapper from the GEM suite (http://gemlibrary.sourceforge.net). The GEM mapper reports exhaustively all mappings and split-mappings up to a user-defined amount of mismatches (default 2 mismatches), disregarding presumptive base-calling errors as identified by low associated quality values.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome Build:
ID3_cyt.bed: GRCh37/hg19
ID3_cyt.gtf: GRCh37/hg19


title: islet preparation 4 under cytokine treatment

description: Sample 8

data_processing:
BED files: Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program gem-mapper from the GEM suite (http://gemlibrary.sourceforge.net). The GEM mapper reports exhaustively all mappings and split-mappings up to a user-defined amount of mismatches (default 2 mismatches), disregarding presumptive base-calling errors as identified by low associated quality values.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome Build:
ID4_cyt.bed: GRCh37/hg19
ID4_cyt.gtf: GRCh37/hg19


title: islet preparation 2 under cytokine treatment

description: Sample 4

data_processing:
BED files: Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program gem-mapper from the GEM suite (http://gemlibrary.sourceforge.net). The GEM mapper reports exhaustively all mappings and split-mappings up to a user-defined amount of mismatches (default 2 mismatches), disregarding presumptive base-calling errors as identified by low associated quality values.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome Build:
ID2_cyt.bed: GRCh37/hg19
ID2_cyt.gtf: GRCh37/hg19


title: islet preparation 2 under control condition

description: Sample 3

data_processing:
BED files: Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program gem-mapper from the GEM suite (http://gemlibrary.sourceforge.net). The GEM mapper reports exhaustively all mappings and split-mappings up to a user-defined amount of mismatches (default 2 mismatches), disregarding presumptive base-calling errors as identified by low associated quality values.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome Build:
ID2_ctl.bed: GRCh37/hg19
ID2_ctl.gtf: GRCh37/hg19

source_name: islet preparation_control condition


title: islet preparation 1 under control condition

description: Sample 1

data_processing:
BED files: Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program gem-mapper from the GEM suite (http://gemlibrary.sourceforge.net). The GEM mapper reports exhaustively all mappings and split-mappings up to a user-defined amount of mismatches (default 2 mismatches), disregarding presumptive base-calling errors as identified by low associated quality values.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome Build:
ID1_ctl.bed: GRCh37/hg19
ID1_ctl.gtf: GRCh37/hg19


title: sh92.mH2A1-ChIP

status: Public on Mar 08 2012

first: Emily

last: Bernstein

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

data_processing:
100bp reads were aligned to the hg19 genome assembly (NCBI build 37) using Bowtie short read aligner (v 0.12.7) (Langmead et al. 2009), with the following parameters: seed of 50bp, maximum 2 mismatches, suppression (m) = 20, and reported alignments (k) = 20. Aligned reads were then converted to BED files (sh92.mH2A-ChIP.BED, shluc.mH2A-ChIP.BED and shluc.Input.BED) Wiggle files (HAFEZ, unpublished pipeline D.H.), were generated using a 500bp window sliding 250bp, counting the number of aligned reads (5' end of each aligned read), for both ChIP and Input samples. The number of alignments from each window was normalized to the total number of alignments and scaled by factor of 10^7, to allow comparison between different samples (sh92.mH2A-ChIP.wig, shluc.mH2A-ChIP.wig and shluc.Input.wig). The MACS software (v 1.4.1) (4) was used to identify peaks (pvalue cutoff = 1.00e-04, shift size = 75, max duplicate reads allowed =  2, (nomodel),  fragment size = 100 -t) (sh92.mH2A-ChIP.peaks.BED, shluc.mH2A-ChIP.peaks.BED) (Zhang et al. 2008).
Genome Build:
sh92.mH2A-ChIP.aligned.BED: hg19 (NCBI Build37)
sh92.mH2A1-ChIP.wig: hg19 (NCBI Build37)
sh92.mH2A1-ChIP.peaks.bed: hg19 (NCBI Build37)

source_name: ATRX knockdown

growth_protocol: Cells were grown in 75cm^2 suspension culture flasks (RPMI media) and maintained under puromycin selection (2ug/ml)

extract_protocol: mH2A1 ChIP (ab37264, ABCAM), was preformed with 100ug of MNase digested chromatin as previously described (Hori et al. 2008). Total of 25ng MNase-ChIPed DNA was processed for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the Hi-Seq 2000 illumina platform. Sh92 and shluc were multiplexed. We obtained a total of 67,219,237 reads for sh92, 56,540,184 for shluc and 148,165,330 for Input

treatment_protocol: Cells were depleted of ATRX using stably integrated lentiviral construct expressing shRNA constructs (Open Biosystems) targeting ATRX RNA for degradation (TRCN0000013592). Cells bearing lentiviral constucts targeting luciferase for degradation were used as the control. Cells were maintained under puromycin selection (2ug/ml) after being infected with virus (spin procotol).

tag: shRNA construct

value: ATRX (sh92)

value: mH2A1 (ab37264, ABCAM)


title: NCC-Rb-Rsi paired-end seq

status: Public on Mar 07 2012

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
H2BUb1-Rb-NCCIT-siRNF20.bed; genome build: hg18
The sequence tags were mapped to the human genome (UCSC hg18) by using Bowtie.

source_name: NCCIT

growth_protocol: NCCIT embryonic carcinoma cell lines on a 10cm dish were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS, Hyclone) and 1% antibiotic-antimycotic solution (Hyclone) at 37ºC in a humidified atmosphere composed of 5% CO2.

extract_protocol:
Genomic DNA extraction: Cross-linking was performed by incubating cells in 1% formaldehyde (Sigma) for 20 min at 25  C. Cells were quenched with 125 mM Glycine. PBS-washed cells were lysed in 400   l of SDS Lysis Buffer, and DNA was sonicated to create fragments of 400-500 nucleotides in length using a Sonic Dismembrator (Model 500, Fisher).

Chromatin immunoprecipitation: Chromatin cleared by centrifugation for 15 minutes at 13,000 rpm, 4  C were subjected to immunoprecipitation using antibodies of interest with a mixture of protein A and G agarose (GE Healthcare) for 2 hr at 4  C. Protein A and G agarose/antibody/chromatin complexes then were washed for 10 minutes with each of the following solutions: Low Salt Wash Buffer (150 mM NaCl lysis buffer without 0.2% SDS), High Salt Wash Buffer (500 mM NaCl lysis buffer without 0.2% SDS), LiCl buffer (10 mM Tris-Cl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Sodium deoxycholate), and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). The chromatin complexes were then eluted twice in 250   l elution buffer (1% SDS, 0.1M NaHCO3) by incubation at 25 C for 15min with rotation and were reverse-crosslinked by heating at 68  C for O/N with 400mM NaCl.
The purified ChIP DNA fragments were ligated to a pair of adaptors for sequencing on the HiSeq2000.

value: siRNF20-transfected NCCIT

value: embryonic carcinoma cells

tag: antibody vendor

value: Cell Signaling

tag: antibody catalog number

tag: antibody lot#


title: NCC-Rb-Esi paired-end seq

data_processing:
H2BUb1-Rb-NCCIT-siEGFP.bed; genome build: hg18
The sequence tags were mapped to the human genome (UCSC hg18) by using Bowtie.

value: siEGFP-transfected NCCIT

tag: cell type

tag: catalog/vendor

value: Cell Signaling (5546) with lot number #1


title: islet preparation 3 under control condition

description: Sample 5

data_processing:
BED files: Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program gem-mapper from the GEM suite (http://gemlibrary.sourceforge.net). The GEM mapper reports exhaustively all mappings and split-mappings up to a user-defined amount of mismatches (default 2 mismatches), disregarding presumptive base-calling errors as identified by low associated quality values.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome Build:
ID3_ctl.bed: GRCh37/hg19
ID3_ctl.gtf: GRCh37/hg19


title: islet preparation 5 under control condition

description: Sample 9

data_processing:
BED files: Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program gem-mapper from the GEM suite (http://gemlibrary.sourceforge.net). The GEM mapper reports exhaustively all mappings and split-mappings up to a user-defined amount of mismatches (default 2 mismatches), disregarding presumptive base-calling errors as identified by low associated quality values.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome Build:
ID5_ctl.bed: GRCh37/hg19
ID5_ctl.gtf: GRCh37/hg19


title: NCC-Rb-WT paired-end seq

data_processing:
H2BUb1-Rb-NCCIT-WT.bed; genome build: hg18
The sequence tags were mapped to the human genome (UCSC hg18) by using Bowtie.

tag: cell line

value: NCCIT


title: shluc.mH2A1-ChIP

data_processing:
100bp reads were aligned to the hg19 genome assembly (NCBI build 37) using Bowtie short read aligner (v 0.12.7) (Langmead et al. 2009), with the following parameters: seed of 50bp, maximum 2 mismatches, suppression (m) = 20, and reported alignments (k) = 20. Aligned reads were then converted to BED files (sh92.mH2A-ChIP.BED, shluc.mH2A-ChIP.BED and shluc.Input.BED) Wiggle files (HAFEZ, unpublished pipeline D.H.), were generated using a 500bp window sliding 250bp, counting the number of aligned reads (5' end of each aligned read), for both ChIP and Input samples. The number of alignments from each window was normalized to the total number of alignments and scaled by factor of 10^7, to allow comparison between different samples (sh92.mH2A-ChIP.wig, shluc.mH2A-ChIP.wig and shluc.Input.wig). The MACS software (v 1.4.1) (4) was used to identify peaks (pvalue cutoff = 1.00e-04, shift size = 75, max duplicate reads allowed =  2, (nomodel),  fragment size = 100 -t) (sh92.mH2A-ChIP.peaks.BED, shluc.mH2A-ChIP.peaks.BED) (Zhang et al. 2008).
Genome Build:
shluc.mH2A-ChIP.aligned.BED: hg19 (NCBI Build37)
shluc.mH2A1-ChIP.wig: hg19 (NCBI Build37)
shluc.mH2A1-ChIP.peaks.bed: hg19 (NCBI Build37)

source_name: control knockdown

value: luciferase (shluc)


title: shluc.Input

data_processing:
100bp reads were aligned to the hg19 genome assembly (NCBI build 37) using Bowtie short read aligner (v 0.12.7) (Langmead et al. 2009), with the following parameters: seed of 50bp, maximum 2 mismatches, suppression (m) = 20, and reported alignments (k) = 20. Aligned reads were then converted to BED files (sh92.mH2A-ChIP.BED, shluc.mH2A-ChIP.BED and shluc.Input.BED) Wiggle files (HAFEZ, unpublished pipeline D.H.), were generated using a 500bp window sliding 250bp, counting the number of aligned reads (5' end of each aligned read), for both ChIP and Input samples. The number of alignments from each window was normalized to the total number of alignments and scaled by factor of 10^7, to allow comparison between different samples (sh92.mH2A-ChIP.wig, shluc.mH2A-ChIP.wig and shluc.Input.wig). The MACS software (v 1.4.1) (4) was used to identify peaks (pvalue cutoff = 1.00e-04, shift size = 75, max duplicate reads allowed =  2, (nomodel),  fragment size = 100 -t) (sh92.mH2A-ChIP.peaks.BED, shluc.mH2A-ChIP.peaks.BED) (Zhang et al. 2008).
Genome Build:
shluc.Input.BED: hg19 (NCBI Build37)
shluc.Input.wig: hg19 (NCBI Build37)

source_name: Input control

value: none (input)


title: splenDC_H3K9me2_G9a_KO

first: Terry

last: Fang

address: 1230 York Ave

institute: Rockefeller University

description: chromatin IP against H3K9me2 in G9a f/f; Vav-cre splenic DCs

data_processing: Raw data processed using onboard SCS/RTA, alignments performed using Bowtie keeping only unique reads with 2 or fewer mismatches in 36bp. Alignments summed in 100bp windows for wig files

source_name: DC

growth_protocol: MEFs were grown in 10 cm plates with DMEM medium containing 15% FBS, Pen/Strep, Glutamine, NEAA and 2-mercaptoethanol. After immortalization with SV40-LTA, MEFs were grown in 15 cm plates with the same medium except FBS was 10%. DC were isolated from WT C57Bl/6, G9af/f, G9a;Vav-cre or IFNaR1 -/- mice that subcutaneously injected with B16-Flt3L cells. 2 weeks later splenic DCs were enriched for the CD11c+ population using CD11c MACS beads.  ChIP was carried out directly on ex vivo isolated cells.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Primary MEFs were immortalized at passage 2. At passage 5,  MEFs were treated witheither EtOH as a vehicle control or Tamoxifen to induce deletion of G9a.  MEFs were either left untreated, treated with Lipofectamine 200, the tranfection reagent or tranfected with PolyIC.

value: Splenic dendritic cells

tag: genotype

value: G9a f/f; Vav-cre

tag: passages

value: Ex-vivo isolated

tag: vendor

value: Abcam (ab1220)

tag: lot


title: splenDCs_H3K9me2_total_1h_unst

description: chromatin IP against H3K9me2 in G9af/f spenlic DCs

tag: strain

value: G9a f/f


title: MEFs_H3K9me2_DMSO

description: chromatin IP against H3K9me2 in WT MEFs treated with DMSO

source_name: MEF

value: Fibroblasts from day 13.5 embryos immortalized with SV40-LTA

value: Wild-type

value: Passaged 12-15 times


title: MEFs_H3K9me2_Unc

description: chromatin IP against H3K9me2 inWT MEFs treated with UNC0638


title: H3ac_ChIP-seq

data_processing: The sequence tags were mapped to the human genome (UCSC hg18) by using the Genome Analyzer data analysis pipeline. The mapped sequence reads were extended to the average size of fragment length (200bp).

source_name: NCCIT, H3Kac ChIP

extract_protocol:
Genomic DNA extraction: Cross-linking was performed by incubating cells in 1% formaldehyde (Sigma) for 20 min at 25°C. Cells were quenched with 125 mM Glycine. PBS-washed cells were lysed in 400 μl of SDS Lysis Buffer, and DNA was sonicated to create fragments of 400-500 nucleotides in length using a Sonic Dismembrator (Model 500, Fisher).

Chromatin immunoprecipitation: Chromatin cleared by centrifugation for 15 minutes at 13,000 rpm, 4°C were subjected to immunoprecipitation using antibodies of interest with a mixture of protein A and G agarose (GE Healthcare) for 2 hr at 4°C. Protein A and G agarose/antibody/chromatin complexes then were washed for 10 minutes with each of the following solutions: Low Salt Wash Buffer (150 mM NaCl lysis buffer without 0.2% SDS), High Salt Wash Buffer (500 mM NaCl lysis buffer without 0.2% SDS), LiCl buffer (10 mM Tris-Cl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Sodium deoxycholate), and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). The chromatin complexes were then eluted twice in 250 μl elution buffer (1% SDS, 0.1M NaHCO3) by incubation at 25°C for 15min with rotation and were reverse-crosslinked by heating at 68ºC for O/N with 400mM NaCl.
Antibodies: Antibodies recognizing H3ac, H3K4me3, H3K36me3, H3K79me1, H3K79me2, H3K79me3 were polyclonal rabbit antibodies purchased from Abcam or produced in-house. H2Bub antibody was obtained from Millipore (17-650).

The purified ChIP DNA fragments were ligated to a pair of adaptors for sequencing on the Illumina Genome Analyzer. The ligation products were size-fractioned to obtain 200- to 300-bp fragments on an agarose gel and subjected to 18 cycles of PCR amplification. Cluster generation and 72 cycles of single-read sequencing were done.

value: Millipore


title: H3K79me3_ChIP-seq

source_name: NCCIT, H3K79me3 ChIP

value: Abcam mixed with in-house antibody


title: islet preparation 5 under cytokine treatment

description: Sample 10

data_processing:
BED files: Sequencing reads were mapped to the human genome (version GRCh37/hg19) using the program gem-mapper from the GEM suite (http://gemlibrary.sourceforge.net). The GEM mapper reports exhaustively all mappings and split-mappings up to a user-defined amount of mismatches (default 2 mismatches), disregarding presumptive base-calling errors as identified by low associated quality values.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome Build:
ID5_cyt.bed: GRCh37/hg19
ID5_cyt.gtf: GRCh37/hg19

tag: tissue

value: islets of Langerhans


title: H3K79me2_ChIP-seq

source_name: NCCIT, H3K79me2 ChIP

value: embryonic carcinoma cells