title: Myers_BC_Uterus_BN0765_1_None_BioChain

description: Reduced Representation

value: Donor BN0765; Age 44; Asian; DNA Extract

value: Normal

value: Uterus

value: F

value: BioChain


title: Myers_MCF10A-Er-Src_2_None_Stanford

status: Public on Mar 01 2011

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description: Reduced Representation

library_source: genomic

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibMethylRrbs

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS(Struhl):MCF-10A_Struhl_protocol.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibMethylRrbs

tag: cell

tag: cell organism

value: Human

tag: cell description

value: mammary gland, non-tumorigenic epithelial, inducible cell line

tag: cell karyotype

value: stable and near-diploid

tag: cell lineage

value: derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

tag: cell sex

tag: replicate

tag: treatment

tag: obtainedby

value: Stanford


title: Myers_RPTEC_1_None_UW

description: Reduced Representation

source_name: RPTEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:RPTEC_Stam_protocol.pdf

value: RPTEC

value: Renal Proximal Tubule Epithelial Cells

value: U

value: UW


title: Myers_HeLa-S3_2_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HeLa-S3:HeLa-S3_protocol.pdf HeLa-S3_IFN_Crawford:HeLa-S3_IFN_Crawford_protocol.pdf

value: cervical carcinoma

value: cancer

value: ectoderm

value: HudsonAlpha


title: Myers_HSMMtube_3_None_Duke

description: Reduced Representation

source_name: HSMMtube

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:HSMMtube_Bernstein_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:HSMM_HSMMtube_Crawford_protocol.pdf

value: HSMMtube

value: Normal Human Skeletal Muscle Myotubes

value: normal

value: B

value: Duke


title: Myers_HSMMtube_2_None_Duke

description: Reduced Representation

value: Human


title: Myers_BC_Brain_H11058N_2_None_BioChain

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Myers_BioChain_protocol.pdf

value: Donor H11058N; Age 66; Asian; DNA Extract

value: Normal

value: Brain

value: M

value: BioChain


title: Myers_HPAEpiC_1_None_UW

description: Reduced Representation

source_name: HPAEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPAEpiC_Stam_protocol.pdf

value: HPAEpiC

value: Human Pulmonay Alevolar Epithelial Cells

value: U


title: Myers_MCF10A-Er-Src_3_None_Stanford

description: Reduced Representation

value: mammary gland, non-tumorigenic epithelial, inducible cell line

value: stable and near-diploid

value: derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

value: F

value: Stanford


title: Myers_NHDF-neo_1_None_UW

description: Reduced Representation

source_name: NHDF-neo

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:NHDF-neo_Stam_protocol.pdf

value: NHDF-neo

value: Neonatal Human Dermal Fibroblasts

value: UW


title: Myers_HepG2_1_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HepG2_protocol.pdf

value: Human

value: liver carcinoma

value: cancer

value: endoderm

value: Duke


title: Myers_Jurkat_1_None_UW

description: Reduced Representation

source_name: Jurkat

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Jurkat_protocol.pdf UW_Stam:Jurkat_Stam_protocol.pdf

value: Jurkat

value: T lymphoblastoid cell line derived from an acute T cell leukemia

value: "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC

value: M


title: Myers_BC_Placenta_UHN00189_1_None_BioChain

description: Reduced Representation

value: Donor UHN00189; Age 29; Native Indian; DNA Extract

value: Normal

value: Placenta

value: BioChain


title: Myers_MCF-7_2_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:MCF-7_Crawford_protocol.pdf Yale_TFBS(Farnham):MCF-7_Farnham_protocol.pdf UW_Stam:Stam_15_protocols.pdf

value: mammary gland, adenocarcinoma

value: F


title: Myers_MCF10A-Er-Src_2_TAM_1uM_36hr_Stanford

description: Reduced Representation

value: mammary gland, non-tumorigenic epithelial, inducible cell line

value: stable and near-diploid

value: derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

tag: treatment description

value: 36h, 1uM tamoxifen (Myers)

value: Stanford


title: Myers_AG10803_1_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG10803_Stam_protocol.pdf

value: Human

value: Adult human abdominal skin fibroblasts

value: UW


title: Myers_HNPCEpiC_2_None_UW

description: Reduced Representation

source_name: HNPCEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HNPCEpiC_Stam_protocol.pdf

value: HNPCEpiC

value: Human Non-Pigment Ciliary Epithelial Cells

value: U


title: Myers_PanIslets_3_None_Duke

description: Reduced Representation

source_name: PanIslets

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:PanIslets_Crawford_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin(Lieb):PanIslets_Lieb_protocol.pdf

value: PanIslets

value: human pancreatic islets

value: M

value: Duke


title: Myers_MCF-7_1_None_Duke

description: Reduced Representation

value: mammary gland, adenocarcinoma

value: cancer


title: Myers_NT2-D1_2_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:NT2-D1_protocol.pdf

value: malignant pluripotent embryonal carcinoma (Ntera2)

value: "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC


title: Myers_BC_Adrenal_Gland_H12803N_1_None_BioChain

description: Reduced Representation

value: Donor H12803N; Age 88; Caucasian; DNA Extract

value: Normal

value: Adrenal gland

value: F

value: BioChain


title: Myers_BC_Skeletal_Muscle_01-11002_1_None_BioChain

description: Reduced Representation

value: Human

value: Donor 01-11002; Age 83; Caucasian; DNA and RNA Extract

value: Skeletal muscle


title: Myers_HCT-116_1_None_Stanford

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:HCT-116_protocol.pdf UW_Stam:HCT116_Stam_protocol.pdf

value: colorectal carcinoma

value: endoderm

value: Stanford


title: Myers_NHBE_2_None_UW

description: Reduced Representation

source_name: NHBE

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:NHBE_Crawford_protocol.pdf

value: NHBE

value: normal human bronchial epithelial cells

value: UW


title: Myers_SKMC_2_None_UW

description: Reduced Representation

source_name: SKMC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:SkMC_Stam_protocol.pdf

value: SKMC

value: Human Skeletal Muscle Cells

value: U


title: Myers_ProgFib_2_None_Duke

description: Reduced Representation

source_name: ProgFib

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:progeria_Crawford_protocol.pdf

value: ProgFib

value: HGPS (HGADFN167, progeria research foundation)

value: progeria

value: Duke


title: Myers_K562_2_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/K562_protocol.pdf

value: leukemia

value: cancer

value: "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: F

value: HudsonAlpha


title: Myers_BJ_1_None_UW

description: Reduced Representation

source_name: BJ

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:BJ-tert_Stam_protocol.pdf

value: BJ

value: Human

value: skin fibroblast

value: normal

value: "The line was established from skin taken from normal foreskin." - ATCC

value: M


title: Myers_SK-N-SH_RA_1_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

value: neuroblastoma cell line differentiated w/ retinoic acid

value: "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC

value: UW


title: Myers_CMK_1_None_UW

description: Reduced Representation

source_name: CMK

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:CMK_Stam_protocol.pdf

value: CMK

value: Human Acute Megakaryocytic Leukemia Cells


title: Myers_BC_Testis_N30_1_None_BioChain

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Myers_BioChain_protocol.pdf

value: Donor N30; Age 41; Asian; DNA Extract

value: Normal

value: Testis

value: BioChain


title: Myers_GM19240_1_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:GM19240_Crawford_protocol.pdf

value: B-Lymphocyte

value: YORUBA, Epstein-Barr Virus, Female

value: F

value: Duke


title: Myers_LNCaP_2_androgen_Duke

description: Reduced Representation

source_name: LNCaP

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:LNCaP_Crawford_protocol.pdf Yale_TFBS(Farnham):LNCaP_protocol.pdf UW_Stam:LNCaP_Stam_protocol.pdf

value: LNCaP

value: Human

value: prostate adenocarcinoma

value: cancer

value: "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old Caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC

value: androgen

value: 12hrs, 1nM Methyltrienolone (R1881) (Crawford)


title: Myers_HRPEpiC_1_None_UW

description: Reduced Representation

source_name: HRPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRPEpiC_Stam_protocol.pdf

value: HRPEpiC

value: Human Retinal Pigment Epithelial Cells

value: U

value: UW


title: Myers_RPTEC_2_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:RPTEC_Stam_protocol.pdf

value: RPTEC

value: Renal Proximal Tubule Epithelial Cells


title: Myers_T-47D_2_DMSO_0.02pct_24hr_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:T47D_Myers_protocol.pdf

value: T-47D is a human epithelial cell line derived from an mammary ductal carcinoma.

value: hypotriploid

value: 24h,0.02% DMSO (Myers)

value: HudsonAlpha


title: Myers_H1-hESC_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/H1_ES_protocol.pdf

value: Human Embryonic Stem Cells

value: normal

value: embryonic stem cells

value: M


title: Myers_HEK293_2_None_Uw

description: Reduced Representation

value: Human

value: embryonic kidney

value: cancer

value: endoderm

value: Uw


title: Myers_AG09309_1_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09309_Stam_protocol.pdf

value: Adult human toe fibroblast

value: F


title: Myers_Fibrobl_1_None_Duke

description: Reduced Representation

source_name: Fibrobl

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:fibroblast_Crawford_protocol.pdf

value: Fibrobl

value: Normal child fibroblast; donor sex:female

value: Duke


title: Myers_LNCaP_2_None_UW

description: Reduced Representation

value: LNCaP

value: prostate adenocarcinoma

value: "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old Caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC

value: UW


title: Myers_Astrocy_1_None_Duke

description: Reduced Representation

source_name: Astrocy

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:Astrocytes_Crawford_protocol.pdf

value: Astrocy

value: Normal human astrocytes

value: normal

value: U


title: Myers_BC_Liver_01-11002_2_None_BioChain

description: Reduced Representation

value: Human

value: Donor 01-11002; Age 83; Caucasian; DNA and RNA Extract

value: Normal

value: Liver

value: BioChain


title: Myers_Myometr_2_None_Duke

description: Reduced Representation

source_name: Myometr

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:Myometr_Crawford_protocol.pdf

value: Myometr

value: Myometrial cells

value: F


title: Myers_Hepatocytes_1_None_Duke

description: Reduced Representation

source_name: Hepatocytes

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:Hepatocytes_Crawford_protocol.pdf

value: Hepatocytes

value: Primary Human Hepatocytes

value: Liver perfused by enzymes to generate single cell suspension

value: B

value: Duke


title: Myers_BJ_2_None_UW

description: Reduced Representation

value: BJ

value: skin fibroblast

value: "The line was established from skin taken from normal foreskin." - ATCC

value: M

value: UW


title: Myers_HTB-11_2_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:HTB-11_Myers_protocol.pdf

value: Human

value: Human neuroblastoma

value: HudsonAlpha


title: Myers_GM12878-XiMat_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:GM12878-XiMat_Myers_protocol.pdf

value: lymphoblastoid

value: relatively normal

value: International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus;Cloned for maternal X inactivation


title: Myers_BC_Breast_02-03015_2_None_BioChain

description: Reduced Representation

value: Donor 02-03015; Age 21; Caucasian; DNA Extract

value: Normal

value: Breast

value: F

value: BioChain


title: Myers_PrEC_2_None_UW

description: Reduced Representation

source_name: PrEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:PrEC_Stam_protocol.pdf

value: PrEC

value: Human Prostate Epithelial Cell line

value: Epithelial

value: U


title: Myers_BC_Leukocyte_UHN00204_2_None_BioChain

description: Reduced Representation

value: Donor UHN00204; Age 54; Caucasian; DNA Extract

value: Peripheral blood mononuclear cell

value: M


title: N33_CD24+_MSDKSeq

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing: 21 base pair (bp) of each read is used in this study. The first 4 bp is always CATG, as this is the recognition site of NlaIII. Our analysis was based around the alignment of the rest of the 17bp tags to human genome composed of segments between nearest NlaIII sites flanking BssHII recognition sites.

source_name: reduction mammoplasty

extract_protocol: 1-2ug of DNA was digested with methylation sensitive restriction enzyme BssHII (NEB) and ligated to biotinylated linker. DNA was then fragmented with another restriction enzyme NlaIII (NEB) and the resulting fragmented DNA with biotinylated linker was captured on streptavidin beads. Fragmented DNA was then ligated to Adapter 1 followed by release of DNA from beads by tagging enzyme MmeI (NEB) with subsequent ligation to Adapter 2. The resulting 85 bp DNA fragments were amplified by Primer 1 and Primer 2 and purified in 12% PAGE. Purified libraries were sequenced on the Illumina Solexa 1G platform. All the adapters and primers were from Illumina.

tag: tissue

value: breast

tag: cell type

value: epithelial cell

tag: disease state

value: normal

tag: cell marker

tag: cell purification antibody vendor

value: BD-Pharmingen

tag: cell purification antibody catalog number


title: N34_CD44+_SAGESeq

library_source: transcriptomic

data_processing: Sequencing was carried out at the Wistar Institute. The first 17bps of each read is used as a tag. The number of each unique tag is counted.   Processed data file includes tag sequences (17bps) in the first column and counts (frequencies) in the second column. Illumina software pipeline OLB version 1.6, 1.7, 1.8 with CASAVA 1.5 was used for generation  of sequence: frequency processed files.

molecule: polyA RNA

extract_protocol: cDNA made from polyA RNA isolated from purified cells using antibody attached to beads were fragmented with NlaIII/MmeI restriction enzyme with subsequent adapter ligation.

tag: antibody vender

tag: antibody catalog #


title: N40_CD44+_MSDKSeq


title: N37_CD44+_MSDKSeq


title: N34_CD44+_MSDKSeq


title: N35_CD44+_MSDKSeq


title: N33_CD44+_MSDKSeq


title: N40_CD24+_MSDKSeq


title: N39_CD44+_MSDKSeq


title: N37_CD24+_MSDKSeq


title: N34_CD24+_MSDKSeq


title: N58_CD24+_SAGESeq


title: H3K27me3_sample3_CD44+

description: Chromatin IP against H3K27me3

data_processing: Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.

extract_protocol: Following cell purification, cells were immediately cross-linked with formaldehyde (final concentration is 0.5%) at room temperature for 10 minutes. Cells were washed, lysed, and sonicated using a Bioruptor (Diagenode). The sonicated lysates were incubated with a specific antibody for 8 hours. The immunoprecipitates were sequentially washed, reverse-crosslinked, and purified by phenol-chloroform extraction and ethanol precipitation. ChIP-ed DNA was end-repaired by END-It DNA End Repair Kit (Epicentre), and 'A' base was added to 3'-ends by Klenow fragment. 1:10 diluted Adaptor oligo mix (ChIP-Seq Sample Preparation Kit, Illumina) were ligated using T4 DNA ligase HC (Invitrogen), and subjected to PCR amplification (18 cycles) using specific primers provided in the kit (Illumina). Fragments ranging from 150-300 bp were isolated from 8% polyacrylamide gel, and then sequenced by Illumina Genome Analyzer.

tag: chip antibody

tag: antibody vendor

value: Millipore

tag: antibody catalog number


title: Input_sample3_CD44+

description: input DNA


title: H3K27me3_sample2_CD24+

description: Chromatin IP against H3K27me3


title: H3K27me3_sample2_CD44+

description: Chromatin IP against H3K27me3


title: H3K27me3_sample3_CD24+

description: Chromatin IP against H3K27me3


title: Input_sample1_CD24+

description: input DNA


title: N39_CD24+_MSDKSeq


title: H3K4me3_sample1_CD24+

description: Chromatin IP against H3K4me3

value: Abcam


title: Input_sample2_CD44+

description: input DNA


title: Input_sample3_CD24+

description: input DNA


title: H3K27me3_sample1_CD24+

description: Chromatin IP against H3K27me3


title: N35_CD24+_MSDKSeq


title: Input_sample1_CD44+

description: input DNA


title: H3K4me3_sample1_CD44+

description: Chromatin IP against H3K4me3


title: H3K27me3_sample1_CD44+

description: Chromatin IP against H3K27me3


title: TAp73beta_RNASeq_replicate1

city: Nijmegen

first: Marion

last: Lohrum

department: Molecular Biology

country: Netherlands

institute: NCMLS

description: PolyA selected, fragmented and reverse transcribed RNA

data_processing: 35 bp reads were aligned to the human genome (hg18) using ELAND. Reads mapping in RefSeq genes were counted and average read numbers and expression changes were calculated using the R DEGseq package. Expression values are available from the Series record.

source_name: TAp73beta Saos-2 cell line

growth_protocol: The human osteosarcoma cell lines Saos-2 with inducible TAp73alpha, TAp73beta or p53 were maintained in Dulbecco modified Eagle medium supplemented with 10% fetal calf serum at 37C

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit according to protocol (Qiagen).To prepare samples for RNA-Seq 100 μg of total RNA were subjected to polyA-selection with Oligotex Kit according to protocol (Qiagen). Fragmentation of 100 ng polyA-selected mRNA was done for 105 seconds at 94°C in 1x fragmentation buffer (40 mM Tris acetate, pH 8.2; 100 mM potassium acetate; 30 mM magnesium acetate). After purification with RNeasy mini Kit, according to protocol (Qiagen) first strand cDNA synthesis was performed with 5 µg random hexamer primers, 0.5 mM dNTPS, 10 mM DTT, 5x buffer and Superscript Retrotranscriptase (Invitrogen). Second strand synthesis was done with 40 U E.coli DNA polymerase, 10 U E.coli DNA ligase, 0.2 mM dNTPs, 5X buffer and 2 U RNAseH. After purification with Minelute Reaction Cleanup Kit (Qiagen) the obtained material was used to prepare sequencing samples according to the manufacturers protocol (Illumina).

treatment_protocol: To induce stable transfected TAp73beta and p53, 2.0 µg/mL of doxycyclin were used for 24 hr, for TAp73alpha induction 0.5 µg/mL were used

tag: cell line

value: osteosarcoma

tag: genetic modification

value: Tet-on TAp73beta


title: TAp73alpha_RNASeq_replicate1

source_name: TAp73alpha Saos-2 cell line

value: Tet-on TAp73alpha


title: p53_ChIPSeq_replicate2

description: Chromatin IP against p53

data_processing: 35 bp reads were aligned to the human genome (hg18) using ELAND. Peaks were called using MACS with default settings and p-value threshold of 1e-5. Peaks files are available from the Series record.

source_name: p53 Saos-2 cell line

extract_protocol: Cells were crosslinked with 1% formaldehyde for 30 min at room temperature, quenched with 0.125 M glycine and washed at 4C with three buffers: (i) PBS, (ii) buffer of composition 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6 and (iii) 0.15 M NaCl in HEG buffer (1 mM EDTA, 0.5 mM EGTA, 50 mM HEPES pH 7.6). Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, HEG) and sonicated using a Bioruptor Sonicator.

tag: antibody

value: DO1 against p53

value: Tet-on FLp53


title: TAp73beta_ChIPSeq_replicate1

description: Chromatin IP against p73

value: BL906 against p73


title: TAp73beta_ChIPSeq_replicate2

description: Chromatin IP against p73


title: Input_sample2_CD24+

description: input DNA


title: TAp73beta_RNASeq_replicate2


title: p53_ChIPSeq_replicate1

description: Chromatin IP against p53


title: Control_RNASeq_replicate1

source_name: Saos-2 cell line


title: p53_RNASeq_replicate2


title: TAp73alpha_RNASeq_replicate2


title: TAp73alpha_ChIPSeq_replicate2

description: Chromatin IP against p73


title: TAp73alpha_ChIPSeq_replicate1

description: Chromatin IP against p73


title: ChIP_Input_control

description: Input


title: Neuron-PASSeq

status: Public on Feb 26 2011

city: Irvine

first: Peter

last: Shepard

address: Med Sci B233

department: M&G

institute: University of California, Irvine

description:
PAS-Seq
cDNA sequence upstream of poly(A) junctions

data_processing:
mRNA-SEQ reads were retrieved  GERALD (Generation of Recursive Analysis Linked by Dependency) the last step in the Illumina software. These reads were filtered by trimming Ts off the beginning reads and removing reads that have a string of 12 or more Ts.  The remaining mRNA-SEQ reads were mapped to the human (hg18)  and mouse genomes (mm9)  allowing up to two mismatches using the aligner Bowtie version 0.12.6  with the settings “bowtie -m 1 --best -p 4”. Alignments due to potential internal priming were removed if a read has 6 or more consecutive As or 7 or more As in the 10 nucleotides immediately downstream of the poly(A) junction.
the file "GSE25450_mouse_track.txt" has the deep sequencing reads for the poly(A) sites for the 3 mouse cell lines in the mm9 format

organism: Mus musculus

source_name: Mouse neurons

growth_protocol: HeLa cells were grown in DMEM plus 10% fetal bovine serum or FetalPlex (Gemini). Mouse C57BL/6NTac ES cells were a kind gift of Thomas Fielder from the Transgenic Mouse Facility at UCI. Mouse fetal-derived neural stem/progenitor cells (NSPCs) were isolated from cerebral cortical regions of wild-type CD1 mice at embryonic day 12.5 (E12.5) and neurons were derived from the same set of E12.5 mouse cortices.

extract_protocol: PAS-Seq: PolyA+ RNAs are fragmented to 60-200nt pieces. Reverse transcription is performed using the Clontech SMART system using Superscript III. After second strand synthesis, cDNAs are size-selected and amplified by PCR. A custom primer is used for sequencing on Solexa Genome Analyzer II.

value: neurons


title: HeLa-PASSeq

data_processing:
mRNA-SEQ reads were retrieved  GERALD (Generation of Recursive Analysis Linked by Dependency) the last step in the Illumina software. These reads were filtered by trimming Ts off the beginning reads and removing reads that have a string of 12 or more Ts.  The remaining mRNA-SEQ reads were mapped to the human (hg18)  and mouse genomes (mm9)  allowing up to two mismatches using the aligner Bowtie version 0.12.6  with the settings “bowtie -m 1 --best -p 4”. Alignments due to potential internal priming were removed if a read has 6 or more consecutive As or 7 or more As in the 10 nucleotides immediately downstream of the poly(A) junction.
the file "GSE25450_hela_custom_track.txt" has the deep sequencing reads for the poly(A) sites in the hg18 format

source_name: HeLa cell

value: HeLa


title: NSP-PASSeq

source_name: Mouse neural stem/progenitor cells

value: neural stem/progenitor cells


title: ES-PASSeq

source_name: Mouse embryonic stem cells

value: embryonic stem cells


title: LSF_A (091005_SOLEXA2_FC430VeAAXX) 2009-10-08-LANE 2

first: Anthony

last: James

address: 2315 McGaugh Hall

department: Molecular Biology and Biochemistry

data_processing:
Alignment: Sequence reads were obtained and mapped to the Aedes aegypti genome (assembly AaegL1) using Bowtie (Langmead et al., 2009) . All reads mapping with two or fewer mismatches were retained.
Image data were processed using the Illumina Standard Pipeline.

organism: Aedes aegypti

source_name: whole body

extract_protocol: Libraries prepared by UCDavis genome center following the Illumina standard protocol (Illumina RNA-seq Sample Preparation Guide: http://www.illumina.com/support/documentation.ilmn) and run for 40 cycles by the Expression Analysis Core at the UC Davis Genome Center (http://genomecenter.ucdavis.edu/expression_analysis/).

treatment_protocol: sugar feeding or blood-feeding

tag: strain

value: Liverpool

tag: status

value: sugar fed


title: H3K4me1_ChIPSeq

status: Public on Feb 25 2011

city: Worcester

first: Lihua

middle: Julie

last: Zhu

address: 364 Plantation St

department: Program in Gene Function and Expression

institute: Umass Medial School

description: Chromatin IP against H3K4me1

data_processing:
Alignments: Sequence reads were obtained and mapped to the zebrafish (Zv7) genome using the Illumina Genome Analyzer Pipeline. All reads uniquely mapped with two or fewer mismatches were retained for subsequent peak detection. The alignment files are in bed format.

Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS 1.3.6) algorithm (http://liulab.dfci.harvard.edu/MACS/)  with default setting except for these parameters --shiftsize=150 --oldfdr  --gsize=1700000000 --tsize=36 --bw=150 --mfold=10. The peak files are in wig format.

organism: Danio rerio

source_name: whole embryo at 24 hours post fertilization, H3K4me1 ChIP

growth_protocol: Wild type zebrafish embryos at 24 hours post fertilization.

extract_protocol: Histone-DNA complexes were isolated from sonicated chromatin using antibodies against H3K4me1 or H3K4me3. DNA was isolated and ends were polished using the END-IT DNA Repair Kit (Epicentre). Blunt ends were treated with exo-minus Klenow and dATP to add a protruding 3' adenosine.  Standard Illumina adaptors were ligated and the resulting library was PCR amplified with Illumina primers for 15 cycles followed by gel purification of approximately 250 bp library fragments. Cluster generation and subsequent sequencing was performed on a Genome Analyzer according to manufacturer's specifications.

value: whole embryo

tag: developmental stage

value: 24 hours post fertilization

tag: genotype

value: wild type


title: LSF_B (091005_SOLEXA2_FC430VEAAXX) 2009-10-08 LANE 5


title: Input

description: Input DNA

data_processing:
Alignments: Sequence reads were obtained and mapped to the zebrafish (Zv7) genome using the Illumina Genome Analyzer Pipeline. All reads uniquely mapped with two or fewer mismatches were retained for subsequent peak detection. The alignment files are in bed format.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS 1.3.6) algorithm (http://liulab.dfci.harvard.edu/MACS/)  with default setting except for these parameters --shiftsize=150 --oldfdr  --gsize=1700000000 --tsize=36 --bw=150 --mfold=10. The peak files are in wig format.

source_name: whole embryo at 24 hours post fertilization, input

tag: tissue


title: LBF_B (091023_SOLEXA2_FC431U5AAXX) 2009-10-23 LANE 5

value: blood fed


title: LBF_A (091023_SOLEXA2_FC431U5AAXX) 2009-10-23 LANE 4


title: H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

source_name: whole embryo at 24 hours post fertilization, H3K4me3 ChIP


title: Control_RNASeq_replicate2

tag: cell type


title: p53_RNASeq_replicate1


title: MEF TDG knockout 2

status: Public on Feb 24 2011

city: London

first: Gareth

last: Wilson

address: 23 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

description: DNA IP against 5-Methylcytosine

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse (July, 2007) genome using the software 'bwa' (http://bio-bwa.sourceforge.net/). Paired reads with a bwa alignment score of <10 were removed from downstream analysis.

source_name: Mouse embryonic fibroblast cells

growth_protocol: SV40 immortalized MEF cell lines were cultivated in growth medium (DMEM, 10% FCS, 2 mM L-glutamine) at 37°C in a humidified atmosphere containing 5% CO2. ES cells (ESC) were grown in the presence of feeder cells at 37°C in ES cell medium (ECM: DMEM, 15% heat inactivated FCS, LIF (1,000 U/ml), 1x nonessentialamino acids, 1 mM Na-pyruvate, 2 mM L-glutamine and 90 μM β-mercaptoethanol) in a humidified atmosphere containing 5% CO2.

extract_protocol: 5ug of DNA was sonicated giving fragment sizes <500bp.Fragments were end repaired, phosphorylated and A-tailed the fragmented DNA and ligated Illumina multiplex adapters to fragments in accordance with the Illumina Multiplex Sample Preparation protocol. These samples were then subjected to MeDIP as described previously (Weber et al. 2005; PMID: 16007088). The immunoprecipitated (IP) sample was purified using Zymo-5 kit according to the manufacturers instructions.The sample isolated by meDIP then underwent gel electrophoresis and library size selection, prior to PCR amplification using Illumina paired-end PCR primers for 18 cycles.  Bands were excised to produce libraries with insert sizes of 100-150 bp and 150-200bp, libraries were quantified using an Agilent Bioanalyzer 2100.

treatment_protocol: Before differentiation experiments for neuronal differentiation, ESC were grown in the absence of feeder cells for two passages. For embryoid body formation during neuronal differentiation 4 x 10e6 Tdg+/- or Tdg-/- ESC were plated into nonadherent bacterial dishes (Greiner Bio-one, Germany) in differentiation medium (ECM without LIF and with10% FCS) and grown at 37°C with a medium exchange after two days. After four days,5 μM all-trans retinoic acid (RA) was added and cells were further incubated for four days with a medium exchange after two days. Embryoid bodies were washed twice with 1x PBS and dissociated with freshly prepared trypsin solution (0.05% TPCK-treated trypsin in 0.05% EDTA/1x PBS) at 37°C for 3 min. Dissociated embryoid bodies were resuspended in 10 ml differentiation medium and collected by centrifugation at 700g for 5 min at room temperature (RT). The pellet was resuspended in N2 medium (DMEM:F12 nutrient mixture 1:1, 1x N2 supplement) and the cell suspension filtered through a 40 μm nylon cell strainer (BD, USA). Filtered cells were immediately plated onto poly-L-lysine (PLL) and laminin-coated dishes at a density of 5 × 10e6 cells/60 mm dish or 1.5× 10e7 cells/100 mm dish. The N2 medium was exchanged 2 hours after plating and cells were harvested after 4 hours for extraction of genomic DNA.

tag: genetic background

value: 129 C57BL/6 mixed

value: embryonic fibroblast cells

value: TDG knockout

tag: medip antibody

tag: antibody manufacturer

value: Eurogentec

tag: antibody lot #

tag: mean insert size

tag: insert size standard deviation


title: MEF TDG knockout 3

description: DNA IP against 5-Methylcytosine

tag: antibody catalog #


title: MEF TDG knockout 1

description: DNA IP against 5-Methylcytosine


title: MEF TDG homozygote wt 3

description: DNA IP against 5-Methylcytosine

value: TDG homozygote wt


title: MEF TDG homozygote wt 1

description: DNA IP against 5-Methylcytosine


title: NPC TDG knockout 3

description: DNA IP against 5-Methylcytosine

source_name: Mouse neural precursor cells

value: neural precursor cells


title: MEF TDG homozygote wt 2

description: DNA IP against 5-Methylcytosine


title: NPC TDG heterozygote 2

description: DNA IP against 5-Methylcytosine

value: TDG heterozygote


title: NPC TDG heterozygote 1

description: DNA IP against 5-Methylcytosine


title: NPC TDG knockout 1

description: DNA IP against 5-Methylcytosine


title: NPC TDG knockout 2

description: DNA IP against 5-Methylcytosine


title: ESC TDG knockout 3

description: DNA IP against 5-Methylcytosine


title: ESC TDG knockout 2

description: DNA IP against 5-Methylcytosine


title: ESC TDG knockout 1

description: DNA IP against 5-Methylcytosine


title: ESC TDG heterozygote 3

description: DNA IP against 5-Methylcytosine


title: ESC TDG heterozygote 1

description: DNA IP against 5-Methylcytosine


title: BMAL1_ZT22_ChIP-Seq_rep2

status: Public on Feb 23 2011

city: Geneva

first: Guillaume

last: Rey

address: Campus Biotech, Chemin des Mines 9

country: Switzerland

institute: University of Geneva

description:
Chromatin IP against BMAL1
sample 6b

data_processing:
Alignment: Sequence reads were aligned to the mouse genome (mm9) using Bowtie software
bedgraph: each read was shifted by +/- 75 bp for plus and minus strand respectively and then normalized by the total number of aligned reads in the library.

source_name: Liver cells

growth_protocol: Mice were housed under a 12-h light/12-h dark regimen with food and water available ad libitum. ZT0 is defined as the time when the lights are turned on. Animals were housed for 3 weeks under the indicated photoperiods.

extract_protocol: Crosslinked nuclei from liver cells were sonicated and protein-DNA complexes were isolated with a BMAL1 antibody (non-commercial). Libraries were prepared according to Illumina's instructions.

value: Liver

tag: time

tag: chip antibody


title: BMAL1_ZT22_ChIP-Seq_rep1

description:
Chromatin IP against BMAL1
sample 6a


title: Input_DNA

description:
input DNA
sample 7


title: BMAL1_ZT18_ChIP-Seq_rep2

description:
Chromatin IP against BMAL1
sample 5b


title: BMAL1_ZT18_ChIP-Seq_rep1

description:
Chromatin IP against BMAL1
sample 5a


title: Myb-activated B1T1

city: Brisbane

first: Evgeny

last: Glazov

address: Ipswich Road

department: Diamantina Institute

country: Australia

institute: University of Queensland

description: chromatin IP against ER-Myb fusion (Myb activated)

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse genome (USCS build mm9) using the Illumina Genome Analyzer Pipeline v.1.3. Reads with ambiguos aligmnets (2 or more hits) were excluded from further analyses.

source_name: Conditional Myb transformed myeloid cell line

growth_protocol: ERMYB cells were maintained in IMDM supplemented with 10% fetal bovine serum, 60 FDU/mL of GM-CSF and 1 μM of β-estradiol.

extract_protocol: Lysates were clarified from sonicated nuclei and Myb-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA prep Sample Kit (Part# 0801-0303). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: To inactivate Myb, estrogen was withdrawn by washing cells with PBS thrice and culturing them in IMDM supplemented with 10% FBS, 60 FDU/mL of GM-CSF and 100 nM of β-estradiol antagonist ICI-182780. ChIP samples were prepared from Myb-on cells (grown in the presence of estrogen) or Myb-off cells (estrogen withdrawn for 6 hr).

value: CBA

tag: cell line

value: ERMYB

value: ER Ab-10


title: Myb-inactivated isotype control

description: chromatin IP with isotype control Ab (Myb activated)


title: Myb-activated B1T2


title: Myb-activated B2


title: BMAL1_ZT14_ChIP-Seq_rep2

description:
Chromatin IP against BMAL1
sample 4b


title: Myb-inactivated B1

description: chromatin IP against ER-Myb fusion (Myb inactivated)


title: NPC TDG heterozygote 3

description: DNA IP against 5-Methylcytosine


title: Myb-inactivated B2


title: Myb-activated isotype control

description: chromatin IP with isotype control Ab (Myb inactivated)


title: BMAL1_ZT10_ChIP-Seq_rep1

description:
Chromatin IP against BMAL1
sample 3a


title: BMAL1_ZT14_ChIP-Seq_rep1

description:
Chromatin IP against BMAL1
sample 4a


title: BMAL1_ZT10_ChIP-Seq_rep2

description:
Chromatin IP against BMAL1
sample 3b


title: BMAL1_ZT06_ChIP-Seq_rep2

description:
Chromatin IP against BMAL1
sample 2b


title: BMAL1_ZT06_ChIP-Seq_rep1

description:
Chromatin IP against BMAL1
sample 2a


title: BMAL1_ZT02_ChIP-Seq_rep1

description:
Chromatin IP against BMAL1
sample 1a


title: ESC TDG heterozygote 2

description: DNA IP against 5-Methylcytosine

value: embryonic stem cells


title: INS-4C-pancreatic-islets-donor1

status: Public on Feb 22 2011

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

description:
4C-Seq with bait Bait1 at INS promoter
The sequence of PCR primers for the 4C-Seq analysis of donor1 sample.
Bait1-4C-1F: [5'-biotin]TCTCCCCTACCTCTCAACCCCTGC (5' to 3')
Bait1-4C-1R: ACAGGCTGCATCAGAAGAGGCCAT (5' to 3')
Bait1-4C-2F: [5'-biotin]CTGAGGCTGCAATTTCCGGACC (5' to 3')
Bait1-4C-2R: [5'-biotin]TCAAGCAGGTCTGTTCCAAGGGC (5' to 3')
library strategy: 4C-Seq
library selection: Restriction Digest

data_processing: Illumina Genome Analyzer Pipeline produced short sequence reads that were matched to the hg18 human genome    using ELAND alignment algorithm.

source_name: Pancreatic islets

growth_protocol: Isolated human pancreatic islets from independent  cadaver donors were obtained from the Islet Cell Resource Centers (ICRs).  Human islets were cultured in the shipping media for 2 h and placed on a 40 μm  cell strainer (BD Falcon) to get rid of the dead or single islet cells. Islets on the  cell strainer were washed twice with the fresh basal islet media, CMRL-1066 (99-  663-cv, Cellgro) and then cultured in fresh media for at least 3 h or overnight in a  37ºC cell incubator.

extract_protocol: 4C analysis was done as previously described (Zhao et al. Nat Genet 38, 1341-7 (2006)) except for the  last few steps. In brief, after reverse  cross-linking, 3C ligated DNAs were digested with NlaIII and then re-ligated to  make circular DNA. The first inverse PCR reaction was run for 23 cycles with  Phusion DNA polymerase (Finnzymes) and one 5′ biotinylated primer. The PCR  products were then digested with AvrII to cut the self-ligated products. The AvrII-digested  DNA was incubated with streptavidin dynabeads and DNA-bound  dynabeads were subject to nested PCR using two 5′ biotinylated primers. The  final PCR products were digested with BglII and NlaIII. After incubation with  streptavidin dynabeads, the known bait sequence located at both ends bound to  dynabeads and was discarded while the unknown bait-interacting DNA  sequences present in the supernatants were purified for preparation of the  sequencing library. Cluster generation and sequencing were performed as described earlier (Barski et al Cell, 2007) .

tag: cadaver donor

value: pancreatic islets


title: INS-4C-pancreatic-islets-donor2

description:
4C-Seq with bait Bait2 at INS promoter
The sequence of PCR primers for the 4C-Seq analysis of donor2 sample.
Bait2-4C-1F: [5'-biotin]CTGTCCCCAGTCCCGGAT (5' to 3')
Bait2-4C-1R: AGACCTGTCCCTGCTCACAG (5' to 3')
Bait2-4C-2F: [5'-biotin]GATGGCCCAAGATGCCGC (5' to 3')
Bait2-4C-2R: [5'-biotin]GGACCAGCGGGTCATTAGAG (5' to 3')
library strategy: 4C-Seq
library selection: Restriction Digest


title: Condition Thi2 - Thiamine starved - Insertions

status: Public on Feb 18 2011

city: Collegeville

first: David

last: Mayhew

state: PA

address: 1250 South Collegeville Road

department: Target Sciences, Computation Biology, R&D

institute: GlaxoSmithKline

description: Insertions of Ty5 in a strain expressing Thi2-Sir4 from its endogenous locus in cells grown in media without thiamine

data_processing: Paired-end DNA sequence reads were filtered by requiring the correct 17 bp LTR sequence in the first 17 bases of sequence from the first paired-end read, and an appropriate 5 bp barcode sequence and restriction enzyme digestion site sequence on the second paired-end read. Paired reads were mapped using a seeded hash approach. The first 12 genomic bases of each read were mapped to the yeast genome.  The remaining genomic fragments of each read were then aligned to the seeds using an ungapped alignment and allowing up to 2 mismatches on each read.  All alignments from the first read are compared to all alignments from the second read and screened for 3 requirements: (1) same chromosome, (2) within 1200 base-pairs, and (3) opposite strands. If a matched read pair passes all these tests it is accepted as a Calling Card insertion site.  If multiple matched read pairs meet these requirements, the pair with the fewest cumulative mismatches in the alignment is accepted as an insertion site.  If there is a tie and multiple pairs have the same minimum number of mismatches the read is discarded.  Single-end DNA reads were filtered by requiring the correct 17 bp LTR in the first half of the read and the remaining genomic bases were queried against 16-mer hash table of the yeast genome.  Only insertions with unique reads were accepted. Genome build: NCBI Saccharomyces cerevisiae S288c (2006)

organism: Saccharomyces cerevisiae

source_name: His+ FOAr colonies

growth_protocol: Yeasts were grown in complete synthetic media with the addition of 2% glucose or galactose.

extract_protocol: Calling Card Illumina libraries were prepared by harvesting all His+ FOAr colonies and extracting their genomic DNA. Each DNA sample was divided into three aliquots and digested with Hinp1I or HpaII or TaqI. Digested DNA was ligated overnight at 15°C in dilute solution (<10ng/ul) to encourage self-circularization. After ethanol precipitation, self-ligated DNA was resuspended in ddH2O and used as template in an inverse PCR. Primers that anneal to Ty5 sequences (OM8714: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTAATTCACTACGTCAACA; OM8827: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC) were used to amplify the genomic regions flanking Ty5 integrations and the bar codes within Ty5, as well as adding adapter sequences that allow the PCR products to be sequenced on the Illumina GA II analyzer. The PCR products were purified using the QIAquick PCR Purification Kit (Qiagen) and diluted to 10nM. For each sample, the same amount of PCR product from digestion with each restriction endonuclease was pooled and submitted for sequencing on the Illumina GAII.  The average insert size of the Paired-end libraries was 79.25 bp.

tag: strain

value: MATa his3∆1 leu2∆0 ura3∆0 met15∆0 sir4::KanMX trp1::Hyg THI2::sir4


title: Condition Thi2 - Complete media - Insertions

description: Insertions of Ty5 in a strain expressing Thi2-Sir4 from its endogenous locus in cells grown in complete media


title: Multiplex Rep 2 Sfg1 Insertions

description: Insertions of Ty5 containing the Sfg1 barcode in the 2nd Multiplex replicate

value: MATa /MATα his3∆1/ his3∆1 leu2∆0/ leu2∆0 ura3∆0/ ura3∆0 met15∆0/MET15 LYS2/lys2∆0 sir4::KanMX/ sir4::KanMX trp1::Hyg/ trp1::Hyg


title: Multiplex Rep 2 Sef1 Insertions

description: Insertions of Ty5 containing the Sef1 barcode in the 2nd Multiplex replicate


title: Multiplex Rep 2 Rpi1 Insertions

description: Insertions of Ty5 containing the Rpi1 barcode in the 2nd Multiplex replicate


title: Multiplex Rep 2 Rgm1 Insertions

description: Insertions of Ty5 containing the Rgm1 barcode in the 2nd Multiplex replicate


title: Multiplex Rep 2 Kar4 Insertions

description: Insertions of Ty5 containing the Kar4 barcode in the 2nd Multiplex replicate


title: Multiplex Rep 2 Gal4 Insertions

description: Insertions of Ty5 containing the Gal4 barcode in the 2nd Multiplex replicate


title: Multiplex Rep 1 Sef1 Insertions

description: Insertions of Ty5 containing the Sef1 barcode in the 1st Multiplex replicate


title: Multiplex Rep 1 Sfg1 Insertions

description: Insertions of Ty5 containing the Sfg1 barcode in the 1st Multiplex replicate


title: Multiplex Rep 1 Rgm1 Insertions

description: Insertions of Ty5 containing the Rgm1 barcode in the 1st Multiplex replicate


title: Multiplex Rep 1 Rpi1 Insertions

description: Insertions of Ty5 containing the Rpi1 barcode in the 1st Multiplex replicate


title: BMAL1_ZT02_ChIP-Seq_rep2

description:
Chromatin IP against BMAL1
sample 1b


title: Multiplex Rep 1 Lee1 Insertions

description: Insertions of Ty5 containing the Lee1 barcode in the 1st Multiplex replicate


title: Positive Control Gcn4 Insertions

description: Insertions of Ty5 in a strain overexpressing Gcn4-Sir4 from a plasmid


title: Multiplex Rep 1 Gal4 Insertions

description: Insertions of Ty5 containing the Gal4 barcode in the 1st Multiplex replicate


title: Multiplex Rep 1 Yrm1 Insertions

description: Insertions of Ty5 containing the Yrm1 barcode in the 1st Multiplex replicate


title: Positive Control Leu3 Insertions

description: Insertions of Ty5 in a strain overexpressing Leu3-Sir4 from a plasmid


title: Background Strain (Sir4 KO) Insertions

description: Insertions of Ty5 in a strain with no Sir4 present


title: Positive Control Gal4 Insertions

description: Insertions of Ty5 in a strain overexpressing Gal4-Sir4 from a plasmid


title: Multiplex Rep 1 Kar4 Insertions

description: Insertions of Ty5 containing the Kar4 barcode in the 1st Multiplex replicate


title: Multiplex Rep 2 Yrm1 Insertions

description: Insertions of Ty5 containing the Yrm1 barcode in the 2nd Multiplex replicate


title: Snyder_SKN-1_GFP_L1_rep2 extraction2_seq1 aliquote 2

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch2 is ChIP DNA; Antibody information listed below: official name: Anti-eGFP;target name: Enhanced Green Fluorescent Protein;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.;

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. This method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180

organism: Caenorhabditis elegans

extract_protocol:
Worms are grown on peptone-enriched plates seeded with E. coli (HB101) and maintained according to standard protocol. Briefly, starved and synchronized L1s are first obtained, and then plated on peptone-enriched plates with HB101, which serves as a food source. Worms are grown at 20ºC to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
In this ChIP Protocol whole C. elegans embryos are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents.  The cellular debris is removed by centrifugation and any formaldehyde cross-linked chromatin containing GFP epitopes is concentrated using an affinity-purified anti-GFP sera and Protein G-sepharose beads.  After extensive washing, any immune complexes are eluted and the protein-DNA cross-links are reversed.  The degree of sonication is assessed by running a small aliquot of DNA on an agarose gel.  The chromatin IP is verified using quantitative PCR to assay if the experimental sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

value: OP178(made_by :S Kim tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc119(ed3);wgIs178(skn-1::TY1 EGFP FLAG;unc119) official name :WBGene00004804 )

value: fed L1

tag: Sex

value: Hermaphrodite


title: Snyder_PQM-1_GFP_L3_rep1 extraction1_seq1 aliquote 2

value: OP201(made_by :S Kim description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PQM-1::EGFP fusion protein is expressed in the correct pqm-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PQM-1 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc119(ed3);wgIs201(pqm-1::TY1 EGFP FLAG C;unc119) official name :OP201 )

tag: developmental stage


title: Snyder_PQM-1_GFP_L3_rep2 extraction2_seq1 aliquote 2

tag: genotype

value: unc119(ed3);wgIs201(pqm-1::TY1 EGFP FLAG C;unc119)


title: Snyder_SKN-1_GFP_L1_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. This method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180


title: Snyder_PQM-1_GFP_L3_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_SKN-1_GFP_L1_rep1 extraction1_seq1 aliquote 2


title: Multiplex Rep 2 Lee1 Insertions

description: Insertions of Ty5 containing the Lee1 barcode in the 2nd Multiplex replicate


title: Snyder_EGL-27_GFP_L1_rep2 extraction2_seq1 aliquote 2

value: OP177(made_by :S Kim description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EGL-27::EGFP fusion protein is expressed in the correct egl-27 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-27 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc119(ed3);wgIs177(egl-27::TY1 EGFP FLAG;unc119) official name :OP177 )


title: Snyder_EGL-27_GFP_L1_rep1 extraction1_seq1 aliquote 2


title: Snyder_EGL-27_GFP_L1_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_EGL-27_GFP_L1_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_CEH-30_GFP_lemb_rep2 extraction2_seq1 aliquote 2

value: OP120(made_by :R Waterston description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-30::EGFP fusion protein is expressed in the correct ceh-30 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-30 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc119(ed3);wgIs120(ceh-30::TY1 EGFP FLAG;unc119) official name :OP120 )

value: late embryo


title: Snyder_SKN-1_GFP_L1_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_CEH-30_GFP_lemb_rep1 extraction1_seq1 aliquote 2


title: Snyder_PQM-1_GFP_L3_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_CEH-30_GFP_lemb_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ELT-3_GFP_L1_rep2 extraction2_seq1 aliquote 2

extract_protocol:
Large-scale worm samples are grown in S-basal medium and processed as described in Ercan et al., Nature Genetics 39: 403-408 (2007)and Stiernagle, T. Maintenance of C. elegans. in WormBook (ed. Community, T.C.e.R.)(WormBook doi/10.1895/wormbook.1.8.1, http://www.wormbook.org, February 11, 2006). Briefly, starved and synchronized L1s are first obtained, and then transferred to S-basal medium with concentrated E. coli (HB101), which serves as a food source. Worms are grown at 20ºC at 230 rpm rotation to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages, not growth time. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
In this ChIP Protocol whole C. elegans embryos are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents.  The cellular debris is removed by centrifugation and any formaldehyde cross-linked chromatin containing GFP epitopes is concentrated using an affinity-purified anti-GFP sera and Protein G-sepharose beads.  After extensive washing, any immune complexes are eluted and the protein-DNA cross-links are reversed.  The degree of sonication is assessed by running a small aliquot of DNA on an agarose gel.  The chromatin IP is verified using quantitative PCR to assay if the experimental sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

value: OP75(made_by :R Waterston description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ELT-3::EGFP fusion protein is expressed in the correct elt-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ELT-3 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119 (ed3) III; wgIs75 [elt-3::TY1::EGFP::FLAG; unc-119 (+)] official name :OP75 )


title: Snyder_LIN-13_GFP_emb_rep2 extraction2_seq1 aliquote 2

value: OP51(made_by :R Waterston description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-13::EGFP fusion protein is expressed in the correct LIN-13 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-13 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119 (ed3) III; wgIs73 [lin-13::TY1::EGFP::FLAG; unc-119 (+)] official name :OP51 )

value: embryo


title: Snyder_ELT-3_GFP_L1_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ELT-3_GFP_L1_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ELT-3_GFP_L1_rep1 extraction1_seq1 aliquote 2


title: Snyder_BLMP-1_GFP_L1_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;

value: OP109(made_by :R Waterston description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The BLMP-1::EGFP fusion protein is expressed in the correct blmp-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the BLMP-1 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119 (ed3) III; wgIs109 [blmp-1::TY1::EGFP::FLAG; unc-119 (+)] official name :OP109 )


title: Snyder_BLMP-1_GFP_L1_rep2 extraction2_seq1 aliquote 2


title: Snyder_LIN-13_GFP_emb_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_LIN-13_GFP_emb_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_LIN-15B_GFP_L3_rep2 extraction2_seq1 aliquote 2

value: OP184(made_by :S Kim description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-15B::EGFP fusion protein is expressed in the correct lin-15B spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-15B transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc119(ed3);wgIs184(lin-15B::TY1 EGFP FLAG;unc119) official name :OP184 )


title: Snyder_LIN-15B_GFP_L3_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_BLMP-1_GFP_L1_rep1 extraction1_seq1 aliquote 2


title: Snyder_LIN-15B_GFP_L3_rep1 extraction1_seq1 aliquote 2


title: Snyder_LIN-15B_GFP_L3_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_BLMP-1_GFP_L1_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_MDL-1_GFP_L1_rep2 extraction2_seq1 aliquote 2

value: OP106(made_by :R Waterston description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The MDL-1::EGFP fusion protein is expressed in the correct mdl-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MDL-1 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119 (ed3) III; wgIs106 [mdl-1::TY1::EGFP::FLAG; unc-119(+))] official name :OP106 )


title: Snyder_MDL-1_GFP_L1_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_MDL-1_GFP_L1_rep1 extraction1_seq1 aliquote 2


title: Snyder_MDL-1_GFP_L1_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_MEP-1_GFP_emb_rep2 extraction2_seq1 aliquote 2

value: OP70(made_by :R Waterston tags :GFP::3xFlag mutagen :Bombard genotype :unc119(ed3);wgIs70(mep-1::TY1 EGFP FLAG C;unc119) official name :WBGene00003218 )


title: Snyder_MEP-1_GFP_emb_rep1 extraction1_seq1 aliquote 2

value: unc119(ed3);wgIs70(mep-1::TY1 EGFP FLAG C;unc119)


title: Snyder_MEP-1_GFP_emb_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_PHA4_GFP_lemb_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;

value: OP37(made_by :R. Waterston and S. Kim description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] official name :OP37 )


title: Snyder_PHA4_GFP_lemb_rep2 extraction2_seq1 aliquote 2

value: unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG]


title: Snyder_LIN-13_GFP_emb_rep1 extraction1_seq1 aliquote 2


title: Snyder_PHA4_GFP_lemb_rep1 extraction1_seq1 aliquote 2


title: Snyder_CEH-30_GFP_lemb_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_PHA4_GFP_lemb_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_GEI11_GFP_L4_rep2 extraction2_seq1 aliquote 2

value: OP179(made_by :R. Waterston description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] official name :OP179 )


title: Snyder_GEI11_GFP_L4_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;

value: Hermaphrodite


title: Snyder_MEP-1_GFP_emb_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_YA_rep2 extraction2_seq1 aliquote 2

description: channel ch2 is ChIP DNA; Antibody information listed below: official name: RNA Polymerase II;target name: RNA Polymerase II;host: Mouse;antigen: 8WG16;clonal: Monoclonal;purified: Affinity;company: Covance;catalog: MMS-126R;short description: The recognizes the C terminal heptapeptide repeat present on the largest unit of POL II.;

value: N2(genotype :wild type genotype :DR subclone of DB original (Tc1 pattern I) official name :N2 )

value: Young Adult

value: wild type


title: Snyder_GEI11_GFP_L4_rep1 extraction1_seq1 aliquote 2


title: Snyder_N2_POLII_YA_rep1 extraction1_seq1 aliquote 2


title: Snyder_N2_POLII_L4_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_L4_rep1 extraction1_seq1 aliquote 2


title: Snyder_N2_POLII_L4_rep2 extraction2_seq1 aliquote 2


title: Snyder_N2_POLII_L3_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_L3_rep1 extraction1_seq1 aliquote 2


title: Snyder_N2_POLII_L3_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_YA_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_L2_rep2 extraction2_seq1 aliquote 2


title: Snyder_N2_POLII_L4_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_GEI11_GFP_L4_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_L3_rep2 extraction2_seq1 aliquote 2


title: Snyder_N2_POLII_L2_rep1 extraction1_seq1 aliquote 2


title: Snyder_N2_POLII_L1_rep2 extraction2_seq1 aliquote 2

value: fed L1


title: Snyder_N2_POLII_L2_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_L1_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_L1_rep1 extraction1_seq1 aliquote 2


title: Snyder_N2_POLII_L1_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_lemb_rep2 extraction2_seq1 aliquote 2

value: late embryo 20dC 4.5 hrs post-early embryo


title: Snyder_N2_POLII_lemb_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_lemb_rep1 extraction1_seq1 aliquote 2


title: Snyder_N2_POLII_eemb_rep2 extraction2_seq1 aliquote 2

value: early embryo


title: Snyder_N2_POLII_lemb_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_YA_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_eemb_rep1 extraction1_seq1 aliquote 2


title: Snyder_NHR-6_GFP_L2_rep2 extraction2_seq1 aliquote 2

value: OP90(made_by :R. Waterston description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-6::EGFP fusion protein is expressed in the correct nhr-6 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-6 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119(ed3) III; wgIs90 [unc-119(+) nhr-6::TY1::EGFP::3xFLAG] official name :OP90 )


title: Snyder_N2_POLII_eemb_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_eemb_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_NHR-6_GFP_L2_rep1 extraction1_seq1 aliquote 2

value: unc-119(ed3) III; wgIs90 [unc-119(+) nhr-6::TY1::EGFP::3xFLAG]


title: Snyder_LIN-39-GFP_L3_rep2 extraction2_seq1 aliquote 2

value: OP18(made_by :R. Waterston and S. Kim description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-39::EGFP fusion protein is expressed in the correct lin-39 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-39 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119(ed3) III; wgIs18 [unc-119(+) lin-39::TY1::EGFP::3xFLAG] official name :OP18 )


title: Snyder_NHR-6_GFP_L2_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_NHR-6_GFP_L2_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_N2_POLII_L2_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_LIN-39-GFP_L3_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_LIN-39-GFP_L3_rep1 extraction1_seq1 aliquote 2


title: Snyder_HLH-1_GFP_emb_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;

value: OP64(made_by :R. Waterston description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The HLH-1::EGFP fusion protein is expressed in the correct hlh-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HLH-1 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119(ed3) III; wgIs64 [unc-119(+) hlh-1::TY1::EGFP::3xFLAG] official name :OP64 )

value: embryo


title: Snyder_HLH-1_GFP_emb_rep2 extraction2_seq1 aliquote 2

value: unc-119(ed3) III; wgIs64 [unc-119(+) hlh-1::TY1::EGFP::3xFLAG]


title: Snyder_HLH-1_GFP_emb_rep1 extraction1_seq1 aliquote 2


title: Snyder_LIN-11_GFP_L2_rep2 extraction2_seq1 aliquote 2

value: OP62(made_by :R Waterston description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-11::EGFP fusion protein is expressed in the correct lin-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-11 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119(ed3) III; wgIs62 [unc-119(+) lin-11::TY1::EGFP::3xFLAG] official name :OP62 )


title: Snyder_HLH-1_GFP_emb_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_UNC-130_GFP_L1_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;

value: OP77(made_by :R. Waterston description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The UNC-130::EGFP fusion protein is expressed in the correct unc-130 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-130 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119(ed3) III; wgIs77 [unc-119(+) unc-130::TY1::EGFP::3xFLAG] official name :OP77 )


title: Snyder_UNC-130_GFP_L1_rep1 extraction1_seq1 aliquote 2


title: Snyder_UNC-130_GFP_L1_rep2 extraction2_seq1 aliquote 2


title: Snyder_LIN-11_GFP_L2_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_MAB5_POLII_L3_rep2 extraction2_seq1 aliquote 2

value: OP26(made_by :R. Waterston and S. Kim description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The MAB-5::EGFP fusion protein is expressed in the correct mab-5 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MAB-5 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119(ed3) III; wgIs26 [unc-119(+) mab-5::TY1::EGFP::3xFLAG] official name :OP26 )


title: Snyder_LIN-11_GFP_L2_rep1 extraction1_seq1 aliquote 2


title: Snyder_MAB5_POLII_L3_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;

value: unc-119(ed3) III; wgIs26 [unc-119(+) mab-5::TY1::EGFP::3xFLAG]


title: Snyder_MAB5_POLII_L3_rep1 extraction1_seq1 aliquote 2

value: Hermaphrodite


title: Snyder_MAB5_POLII_L3_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_LIN-39-GFP_L3_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Input DNA

status: Public on Feb 17 2011

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: Input DNA.

data_processing:
Alignment: Sequence reads were obtained and mapped to Drosophila melanogaster (dm3, April 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. PeakSeq was used to create the signal maps as wig files.

Peaks: Peak detection was performed with the PeakSeq program (http://www.gersteinlab.org/proj/PeakSeq/), using the Input DNA as a control. The final peak files are provided in BED format.

organism: Drosophila melanogaster

source_name: Wing imaginal discs, input

growth_protocol: Flies were grown in standard medium.

extract_protocol: Chromatin from Drosophila third instar larvae wing discs was immunoprecipitated with 2 ug of antibody using standard protocols. Libraries were prepared according to Illumina instructions.

tag: tissue

value: wing imaginal discs

value: third instar larvae


title: Pol2Ser5P_ChIPSeq

description: Chromatin IP against Pol2Ser5P.

source_name: Wing imaginal discs, Pol2Ser5P ChIP

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog number

tag: chip antibody lot number


title: Pol2Ser2P_ChIPSeq

description: Chromatin IP against Pol2Ser2P.

source_name: Wing imaginal discs, Pol2Ser2P ChIP


title: H3K36me3_ChIPSeq

description: Chromatin IP against H3K36me3.

source_name: Wing imaginal discs, H3K36me3 ChIP


title: H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3.

source_name: Wing imaginal discs, H3K4me3 ChIP

value: Upstate


title: H3K27me3_ChIPSeq

description: Chromatin IP against H3K27me3.

source_name: Wing imaginal discs, H3K27me3 ChIP


title: ASH2_ChIPSeq

description: Chromatin IP against ASH2.

source_name: Wing imaginal discs, ASH2 ChIP


title: Snyder_UNC-130_GFP_L1_rep2 extraction2_seq1 aliquote 1

description: channel ch1 is input DNA;

value: fed L1


title: Whole genome shotgun bisulfite sequencing: H1 cell line diff. into neural progenitor cells; methylC-seq_h1-npc_r1b

status: Public on Feb 16 2011

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
Design description: Whole genome shotgun bisulfite sequencing: H1 cell line diff. into neural progenitor cells
Library name: methylC-seq_h1-npc_r1b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6202
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6199
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM675543_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Bisulfite-Seq.methylC-seq_h1-npc_r1b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-npc_r1b.hg19.level.2.release.3
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells, Library methylC-seq_h1-npc_r1b were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6365
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HDNP BS 1b
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Library methylC-seq_h1-npc_r1b EA Release 3

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.86
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 40

**********************************************************************

ANALYSIS FILE NAME: GSM675543_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-npc_r1a-methylC-seq_h1-npc_r1b-methylC-seq_h1-npc_r1c-methylC-seq_h1-npc_r2a-methylC-seq_h1-npc_r2b.hg19.level.2.release.3
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6367
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HDNP BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Combined Libraries EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.91
SPECIAL NOTE: generated from combined data in GSM675542, GSM675543, GSM675544, GSM675545, GSM675546 (thus .wig files on these records are identical)

**********************************************************************

source_name: H1 cell line differentiated into neural progenitor cells, biological replicate 1 (r1); methylC-seq_h1-npc_r1b

extract_protocol: Library construction protocol: Five µg of genomic DNA was extracted from frozen cell pellets using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 100-150 bp, followed by end repair and addition of a 3' A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5 µl 10X PfuTurbo reaction buffer, 31 µM dNTPs, 1 µl Primer 1, 1 µl Primer 2 (50 µl final). The thermocycling parameters were: 95C 2 min, 98C 30 sec, then 4-8 cycles of 98C 15 sec, 60C 30 sec and 72C 4 min, ending with one 72C 10 min step. The reaction products were purified using AMPure XP beads (two rounds). Up to three separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to three independent libraries from the same biological sample.

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: embryonic stem cell differentiated into neural progenitor cells

value: H1 cells were differentiated by culturing in insulin, SB, Noggin

tag: passage

tag: medium

value: TeSR

value: Male

tag: batch

value: Replicate 1

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: >One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


title: Whole genome shotgun bisulfite sequencing: H1 cell line diff. into neural progenitor cells; methylC-seq_h1-npc_r1c

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing: H1 cell line diff. into neural progenitor cells
Library name: methylC-seq_h1-npc_r1c
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6203
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6199
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM675544_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Bisulfite-Seq.methylC-seq_h1-npc_r1c.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-npc_r1c.hg19.level.2.release.3
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells, Library methylC-seq_h1-npc_r1c were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6366
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HDNP BS 1c
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Library methylC-seq_h1-npc_r1c EA Release 3

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.86
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 40

**********************************************************************

ANALYSIS FILE NAME: GSM675544_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-npc_r1a-methylC-seq_h1-npc_r1b-methylC-seq_h1-npc_r1c-methylC-seq_h1-npc_r2a-methylC-seq_h1-npc_r2b.hg19.level.2.release.3
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6367
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HDNP BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Combined Libraries EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.91
SPECIAL NOTE: generated from combined data in GSM675542, GSM675543, GSM675544, GSM675545, GSM675546 (thus .wig files on these records are identical)

**********************************************************************

source_name: H1 cell line differentiated into neural progenitor cells, biological replicate 1 (r1); methylC-seq_h1-npc_r1c

value: genomic DNA

value: Thomson Laboratory

value: Cell Line

value: embryonic stem cell differentiated into neural progenitor cells

value: H1 cells were differentiated by culturing in insulin, SB, Noggin

value: TeSR

value: 16C for 16 hours with T4 DNA ligase (New England Biolabs)


title: Whole genome shotgun bisulfite sequencing: H1 cell line diff. into neural progenitor cells; methylC-seq_h1-npc_r2b

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: Whole genome shotgun bisulfite sequencing: H1 cell line diff. into neural progenitor cells
Library name: methylC-seq_h1-npc_r2b
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6205
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6200
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM675546_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Bisulfite-Seq.methylC-seq_h1-npc_r2b.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-npc_r2b.hg19.level.2.release.3
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells, Library methylC-seq_h1-npc_r2b were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6363
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HDNP BS 2b
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Library methylC-seq_h1-npc_r2b EA Release 3

QUALITY SCORES:
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.94
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 80

**********************************************************************

ANALYSIS FILE NAME: GSM675546_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-npc_r1a-methylC-seq_h1-npc_r1b-methylC-seq_h1-npc_r1c-methylC-seq_h1-npc_r2a-methylC-seq_h1-npc_r2b.hg19.level.2.release.3
ANALYSIS TITLE: Methylation Proportion Graphs of H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6367
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HDNP BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Bisulfite-Seq Combined Libraries EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.91
SPECIAL NOTE: generated from combined data in GSM675542, GSM675543, GSM675544, GSM675545, GSM675546 (thus .wig files on these records are identical)

**********************************************************************

source_name: H1 cell line differentiated into neural progenitor cells, biological replicate 2 (r2); methylC-seq_h1-npc_r2b

value: Male

value: Replicate 2

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg


title: Snyder_LIN-11_GFP_L2_rep1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;

tag: strain

value: OP62(made_by :R Waterston description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-11::EGFP fusion protein is expressed in the correct lin-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-11 transcription factor. tags :GFP::3xFlag mutagen :Bombard outcross :3 genotype :unc-119(ed3) III; wgIs62 [unc-119(+) lin-11::TY1::EGFP::3xFLAG] official name :OP62 )

value: Hermaphrodite