title: WT Bcell -IL21 IRF4

description: Chromatin IP against IRF4

value: IRF4 (Santa Cruz, sc-6059)


title: BrdU_IP Total DNA

status: Public on Sep 18 2012

type: SRA

city: Milano

first: Lucilla

last: Luzi

address: Via Adamello 16

country: Italy

institute: IFOM FIRC Institute for Molecular Oncology Foundation

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.3
ChIP-seq reads were aligned to the hg18 genome assembly using bwa version 0.5.7 with the default parameters
H3K4me3 reads were trimmed to 36bps before alignment using fastx toolkit
Peaks were called using FindPeaks version 4.0.10 with the following setting: -dist type 1 (200), -qualityfilter (1), -duplicatefilter
To enhance signal-to-noise ratio from BrdU-positive regions (RepliSeq), data from all anti-BrdU IPs (S1-S6 windows and control) were processed with dspchip (v0.8.5, http://code.google.com/p/dspchip/). Control signal was subtracted from each S-phase window (S1-S6).
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph files were generated using BEDtools (v 2.7.1)

molecule: genomic DNA

organism: Homo sapiens

source_name: cervical cancer cell line

growth_protocol: HeLaS3 cells were grown by plating typically 300,000 cells/ml into a T75 flask in Dulbecco's Modified Eagle's Medium (Lonza) supplemented with South American Fetal Bovin Serum, Glutamine, penicillin and streptomicyn. For ChIP or IP assays cells were used at a concentration of 600,000-700,000 cells/ml

extract_protocol: ChIP enriched or control DNA (1-10 ng) were blunt ended, 3'-dA overhangs were created by adding Klenow exo¯ with dATP and adapters were ligated. Unligated ADP was removed prior to PCR amplification (18 cycles)

treatment_protocol: Formaldehyde was added to the culture medium to a final concentration of 1% (4 min at RT). Cross-linking was stopped by addition of glycine to a final concentration of 125 mM. Cells were washed twice with PBS and lysed in SDS buffer: 100 mM NaCl, 50 mM Tris HCl (pH 8.1), 5 mM EDTA (pH 8), 0.5% SDS and protease inhibitors. Chromatin lysate was then pelleted and washed once in IP buffer (100 mM NaCl, 100 mM Tris HCl (pH 8.1), 5 mM EDTA (pH 8), 0.3% SDS, 1.7% Triton X-100) and twice in sonication buffer (10 mM Hepes pH 7.6, 1 mM EDTA, 0.5 mM EGTA, protease inhibitors). The cells were resuspended in sonication buffer to a concentration of 3x107 cells/ml. Sonication, sample preparation for equilibrium density centrifugation, dialysis of collected fractions and analysis of DNA or protein content of each fraction were performed as previously described (Schwartz et al. 2005), with minor modifications. The sample volume was adjusted to 12 ml before centrifugation, transferred into a 14x89 mm Beckman Ultra-Clear centrifuge tubes and spun for 120 to 144 h at +20°C (34,000 rpm in a Sorvall S52-ST rotor). 750 μl fractions were collected with a peristaltic pump from the top of the tube.

tag: cell line

value: HeLa S3

tag: chip antibody

value: BrdU

tag: chip vendor

value: Becton Dickinson

tag: chip catalog#

tag: chip lot


title: BrdU_RepliSeq S1


title: BrdU_RepliSeq S3


title: BrdU_RepliSeq S4


title: BrdU_RepliSeq S2


title: High-density fractions(fr14-15-16)


title: input DNA (low-density fractions)


title: Orc1_ChIPseq

source_name: cervical cancer cell line (low-density fractions)

value: polyclonal, gift of Mauro Giacca


title: BrdU_RepliSeq S6


title: H3K4me3_ChIPSeq

value: Active Motif


title: input DNA


title: UAE_FLI1(Abcam_ab15289)_no

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

country: USA

institute: Radboud University

description: chromatin IP against FLI1

data_processing: Reads (32 bp) were aligned to the Human (Homo Sapiens) reference genome HG18. Peaks were called using MACS. MethylCap tracks for the different fractions were equalized for the total number of mapped tags by random removal of sequenced tags and combined.For RNAPII number of tags within ENSEMBLE genes (from +500 from TSS to end of gene) were counted and gene regulation was expressed as ratio of tags on a given hour divided by tags in same gene region on T= 0.

source_name: UAE(leukemic)

growth_protocol: Leukemic cells were cultured in normal cell culture containing 10% serum.

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.

treatment_protocol: U937AML1ETO cells were treated with zinc for 5 hours, K562-ERG cells for 72 hrs with doxycyclin.

tag: treatment

value: no

tag: antibody

value: antibody FLI1 (Abcam, Ab15289)


title: UAE_FLI1(Abcam_ab15289)_5hrs zinc

description: chromatin IP against FLI1

value: 5 hrs zinc


title: NB4_FLI1(Abcam_ab15289)_no

description: chromatin IP against FLI1


title: SKNO_RNA

description: RNA extraction

library_source: transcriptomic

data_processing: RNA-seq reads were mapped to HG18 and used for bioinformatical analysis. RPKM (reads per kilobase of gene length per million reads) (Mortazavi  et al. 2008) values for RefSeq genes were computed using tag counting scripts and used to analyze gene expression levels.

molecule: total RNA

extract_protocol: Total RNA was extracted from SKNO-1 cells with the RNeasy kit and on-column DNase treatment (Qiagen) and the concentration was measured with a Qubit fluorometer (Invitrogen). 250 ng of total RNA was treated by Ribo-Zero rRNA Removal Kit (epicentre) to remove  ribosomal RNAs  according to manufacturer instructions. 16 µl of purified RNA was fragmented by addition of 4 µl 5x fragmentation buffer (200 mM Tris acetate pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and incubated at 94°C for exactly 90 seconds. After ethanol precipitation first strand cDNA was synthesized from the fragmented RNA with SuperscriptIII (Invitrogen) using random hexamers. First strand cDNA was purified by Qiagen mini elute columns and second strand cDNA was prepared in the presence of dUTP instead of dTTP.  Double stranded cDNA was purified by Qiagen mini elute columns and used for Illumina sample prepping and sequencing according to the manufacturars instructions.

value: SKNO-1 cell line


title: H3K79me2_ChIPSeq

value: Abcam


title: K562-ERG_ERG(SantaCruz_sc353_C20)_72hrsdox

description: chromatin IP against ERG

source_name: K562 (leukemic)

tag: cell type

value: hematopoietic cell

tag: disease state

value: leukemic

value: 72 hrs dox

value: ERG

tag: antibody vendor

value: SantaCruz

tag: antibody catalog number

tag: antibody lot/batch number


title: MCF7_AE(A706_Diagenode)_no

description: chromatin IP against AE (A706)

source_name: MCF7 (cancer)

value: cancer

value: n/a (commercialization pending manuscript publication)


title: K562-ERG_AE(SA706_Diagenode)_72hrsdox

description: chromatin IP against AE (A706)


title: K562-ERG_AE(A706_Diagenode)_no

description: chromatin IP against AE (A706)


title: K562-ERG_ERG(SantaCruz_sc353_C20)_no

description: chromatin IP against ERG


title: MCF7_ERG(SantaCruz_sc353_C20)_no

description: chromatin IP against ERG


title: BrdU_RepliSeq S5

value: HeLa S3


title: SKNO-1_CBFb (A1329_Diagenode)_no

description: chromatin IP against CBFb (A1329_Diagenode)

source_name: SKNO-1 (leukemic)

value: CBFb

value: Diagenode


title: SKNO-1_RUNX1 (Abcam ab23980, Gr21798-1)_no

description: chromatin IP against RUNX1 (Abcam ab23980, Gr21798-1)


title: UAE_H4K5K8K12K16ac  (Upstate_06-866)_5 hrs zinc

description: chromatin IP against H4K5K8K12K16ac (Upstate)

data_processing: Reads (32 bp) were aligned to the Human (Homo Sapiens) reference genome HG18. Peaks were called using MACS. MethylCap tracks for the different fractions were equalized for the total number of mapped tags by random removal of sequenced tags and combined.

source_name: UAE (leukemic)

treatment_protocol: U937AML1ETO cells were treated with zinc for 5 hours.

value: Upstate


title: UAE_AE (A706_Diagenode)_no

description: chromatin IP against AE (A706)


title: UAE_H3K9K14ac (Diagenode_pAb-ACHBHS-044_DA-0010)_5 hrs zinc

description: chromatin IP against H3K9K14ac (Diagenode)


title: AML pz229_ MethylCap_no [42D36AAXX_3]

description: chromatin IP against MethylCap

source_name: AML pz229 (leukemic)

value: MethylCap


title: CD34+ nr30_H3K9K14ac (Diagenode_pAb-ACHBHS-044_DA-0010)_no

source_name: CD34+ nr30 (normal)

value: normal

value: no


title: UAE_RNAPII(8WG16, Diagenode)_no

description: chromatin IP against RNAPII(8WG16) (Diagenode)

value: RNAPII


title: AML pz186_ MethylCap_no[42E0CAAXX_3]

description: chromatin IP against MethylCap

source_name: AML pz186 (leukemic)


title: UAE_H4K5K8K12K16ac  (Upstate_06-866)_no


title: WT Bcell +IL21 IRF4

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: Chromatin IP against IRF4

data_processing:
For ChIP-Seq, Basecalls performed using CASAVA version 1.4 (Genome analyzer), 1.7 (GAII) and 1.8 (GAII and HiSeq2000); For RNA-Seq, Basecalls performed using CASAVA version 1.7 (Genome Analyzer) and 1.8 (HiSeq2000)
ChIP-Seq reads were aligned to the mm8 genome assembly using CASAVA pipeline 1.4, 1.7 and Bowtie 0.12.4
Aligned reads are converted to BED format and removed redundancies using unpublished python and perl scripts
For ChIP-Seq, peaks are called using MACS 1.3.7.1; For RNA-Seq, Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using mm8 refseq database
Genome_build: mm8
Supplementary_files_format_and_content: BED files are generated using CASAVA pipeline 1.4, 1.7 and unpublished python scripts, rpkm (abundance measurement) files are generated using definition in [Mortazavi et al., 2008] and unpublished python scripts

organism: Mus musculus

source_name: B cells

growth_protocol: For ChIP-Seq, T and B cells were isolated using kits (Miltenyi). Cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum. For pre-activation, cells were stimulated with plate-bound anti-CD3 (2 ug/ml) + anti-CD28 (1 ug/ml) for 3 days, washed, rested overnight.

extract_protocol: For ChIP-Seq, chromatin was prepared from cells cross-linked with 1% formaldehyde at 37oC for 15 min. Chromatin was fragmented by sonication and the ChIP DNA was blunt-ended, ligated to the Solexa adaptor and amplified using adaptor primers for 17 cycles. Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols.

treatment_protocol: not treated or treated with IL-21 (100 ng/ml) for 1 hr

tag: strain

value: B cells

tag: tissue

value: Spleen

value: IRF4 (Santa Cruz, sc-6059)


title: AML pz186_ MethylCap_no[42E0CAAXX_4]

description: chromatin IP against MethylCap

value: hematopoietic cell

value: leukemic


title: AML pz229_ MethylCap_no [42D36AAXX_5]

description: chromatin IP against MethylCap


title: AML pz186_ MethylCap_no [42E1UAAXX_5]

description: chromatin IP against MethylCap


title: AML pz186_H3K9K14ac (Diagenode_pAb-ACHBHS-044_DA-0010)_no


title: CD34+ nr29_ERG(SantaCruz_sc353_C20)_no

description: chromatin IP against ERG

source_name: CD34+ nr29 (normal)

value: ERG


title: APL pz74_ERG(SantaCruz_sc353_C20)_no

description: chromatin IP against ERG

source_name: APL pz74 (leukemic)

value: SantaCruz


title: AML pz229_AE (A706_Diagenode)_no

description: chromatin IP against AE (A706)


title: UAE_AE (A706_Diagenode)_5 hrs zinc

description: chromatin IP against AE (A706)

value: 5 hrs zinc


title: UAE_H3K9K14ac (Diagenode_pAb-ACHBHS-044_DA-0010)_no


title: UAE_RNAPII(8WG16, Diagenode)_5 hrs zinc


title: SKNO-1_FLI1(SantaCruz_sc356_C19)_no

description: chromatin IP against FLI1


title: AML pz12_AE (A706_Diagenode)_no

description: chromatin IP against AE (A706)

source_name: AML pz12 (leukemic)

value: n/a (commercialization pending manuscript publication)


title: AML pz229_H3K9K14ac (Diagenode_pAb-ACHBHS-044_DA-0010)_no


title: AML pz186_AE (A706_Diagenode)_no

description: chromatin IP against AE (A706)


title: SKNO-1_AE (A706_Diagenode)_no

description: chromatin IP against AE (A706)


title: Kasumi-1_ETOsc(SantaCruz_sc9737_E0106)_no

description: chromatin IP against ETOsc

source_name: Kasumi-1 (leukemic)

value: ETOsc


title: Kasumi-1_HEB(SantaCruz_sc357_A20)_no

description: chromatin IP against HEB

value: HEB


title: AML pz12_ERG(SantaCruz_sc353_C20)_no

description: chromatin IP against ERG


title: AML pz229_ MethylCap_no [42D36AAXX_4]

description: chromatin IP against MethylCap


title: Breast milk exosomes 28d

status: Public on Sep 17 2012

city: Ya'an

first: Mingzhou

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

description: female pig when the infant were aged at 28 days

data_processing:
The reads that passed through a series of additional filters are called “mappable reads”, which are sequences satisfy the following criteria from the statistics of mammalian miRNAs in miRBbase 18.0: (1) not sequencing adapters; (2) containing no more than 80% A, C, G, or T; (3) containing no more than two N (undermined bases); (4) containing not only A and C or G and T, (5) containing no stretches of A7, C8, G6, or T7; (6) being longer than 14 nt and shorter than 27 nt; (7) not containing more than nine repeats of any dimer, more than five repeats of any trimer, or more than four repeats of any tetramer; (8) been observed more than two times; and (9) not originating from porcine known classes of RNAs (i.e., mRNA in NCBI database; rRNA, tRNA, snRNA and snoRNA in Rfam database; and repetitive sequence elements in Repbase database). All identical reads were counted and combined into one kind. The “mappable reads” then were mapped to the 228 porcine pre-miRNAs registered in miRBase 18.0.
Genome_build: miRBbase 18.0

organism: Sus scrofa

source_name: Breast milk exosomes 28d

extract_protocol: Porcine breast milk samples (20-30 ml) were separately collected from three healthy sows when the infant were aged at 0, 3, 7, 14, 21 and 28 days. The exosomes in the breast milk are enriched using ExoQuick Exosome Precipitation Solution (SBI, CA, USA) following manufacturer’s instruction. Total RNA of exosomes was extracted using TRIzol-LS (Invitrogen, CA, USA) following manufacturer’s instruction. Small RNAs were analyzed with the Agilent Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA). The small RNA fraction between 10-40 nt was isolated by polyacrylamide gel electrophoresis (PAGE) and ligated with proprietary adaptors (Illumina). The short RNAs were then converted to cDNA by RT-PCR and each small RNA library was sequenced individually using Illumina Genome Analyzer II according to manufacturer instructions.

tag: gender

value: female

tag: infant age

value: 28 days


title: Breast milk exosomes 14d

description: female pig when the infant were aged at 14 days

source_name: Breast milk exosomes 14d

value: 14 days


title: Breast milk exosomes 21d

description: female pig when the infant were aged at 21 days

source_name: Breast milk exosomes 21d

value: 21 days


title: Kasumi-1_AE (A706_Diagenode)_no

description: chromatin IP against AE (A706)

value: no


title: Breast milk exosomes 7d

description: female pig when the infant were aged at 7 days

source_name: Breast milk exosomes 7d

value: 7 days


title: Breast milk exosomes 3d

description: female pig when the infant were aged at 3 days

source_name: Breast milk exosomes 3d

value: 3 days


title: Breast milk exosomes 0d-rep3

description: female pig when the infant were aged at 0 day

source_name: Breast milk exosomes 0d-rep3

value: 0 day


title: Breast milk exosomes 0d-rep2

source_name: Breast milk exosomes 0d-rep2


title: M1-3 H3K9me3 #1926

status: Public on Sep 16 2012

city: Freiburg im Breisgau

first: Thomas

last: Manke

address: Stuebeweg 51

department: Bioinformatics and Deep-Sequencing Unit

country: Germany

institute: Max-Planck-Institute for Immunobiology and Epigenetics

description: Sample 2

data_processing:
Illumina Casava 1.7 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.3 with the following parameters: -v 2 -X 1000 --tryhard -m 1 --best --strata
For each wt (M1-1) versus ko (M1-3, M1-3/9) combination the two corresponding BAM files were compared based on the number of reads as follows: The reads were elongated to a fragment size of 300 nucleotides. The number of reads in each BAM file was normalized based on the SES method proposed by Diaz et al. (2012), "Normalization, bias correction, and peak calling for ChIP-seq", Statistical applications in genetics and molecular biology, 11(3). The genome was partitioned into bins of size 25bp and then the number of reads found in each BAM file was counted for those bins. The log2 of the ratio (wt vs. ko) of those counts was written to a bigWiggle file.
Genome_build: mm9
Supplementary_files_format_and_content: bigWiggle files containing log2 ratios

source_name: Embryonic Fibroblasts

growth_protocol: Cell were growth in normal MEFs medium.

extract_protocol: ChIP was performed on formaldehyde fixed cells, lysates were incubated with the corresponding antibodies, histones-DNA complexes were immunoprecipitated with dynabeads and DNA was purified using columns. Libraries were prepared following the standard illumina Pair-end protocol. Libraries were sequenced on the GAIIx, 2x36 bases following the standard protocols.

treatment_protocol: For Pax9 kd, 5 shRNAs were obtained from the Sigma Mission RNAi library, packaged into lentiviral particles and transduced into wt and Pax3-deficient iMEFs. Transduced cells were selected with puromycin and kd efficiency was corroborated by qRT-PCR.

value: In house anti-H3K9me3 #1926

tag: genotype

value: Pax3 null

value: Embryonic Fibroblasts


title: M1-3/9 H3K9me3 #1926

description: Sample 3

value: Pax3 null/ Pax9 knock down


title: M1-3 H3K9me3 #4861

description: Sample 5

value: In house anti-H3K9me3 #4861


title: M1-3/9 H3K9me3 #4861

description: Sample 6


title: M1-1 H3K9me3 #4861

description: Sample 4

value: wt


title: M1-1 H3K9me3 #1926

description: Sample 1


title: Breast milk exosomes 0d-rep1

source_name: Breast milk exosomes 0d-rep1


title: SKNO-1_ERG(SantaCruz_sc353_C20)_no

description: chromatin IP against ERG

source_name: SKNO-1 (leukemic)

value: hematopoietic cell

value: leukemic

value: ERG

value: SantaCruz


title: Kasumi-1_ETO1(A710_Diagenode)_no

description: chromatin IP against ETO1

value: n/a (commercialization pending manuscript publication)


title: Stanford_ChipSeq_MEL_Input_DMSO_2.0pct_std

status: Public on Sep 14 2012

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

source_name: MEL

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeSydhTfbs

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

tag: cell sex

value: M

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: treatment description

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

tag: replicate

value: Unknown

tag: strain description

value: Unknown strain origin


title: Pericarp_P-ww_14DAP_ChIP_2

city: East Lansing

first: Erich

last: Grotewold

state: MI

address: 603 Wilson Road

institute: Michigan State University

description: processed data file: P1_Prr-14_Pww-14_2_peaks.bed

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-Seq reads were aligned to the maize genome assembly version 2 using Bowtie.
MACS ver. 1.4.0beta was used for calling peaks by using uniquely aligned reads.
Genome_build: Maize Golden Path B73 RefGen_v2
Supplementary_files_format_and_content: bed files generated by MACS contains information of peak positions (genome coordinates) and hights.

organism: Zea mays

source_name: Pericarp at 14DAP of P1-ww

growth_protocol: The P1-rr stock designated as 65-CFS-305 (Brink and Styles, 1966) was obtained from the National Seed Storage Laboratory, Ft. Collins CO. Near isogenic lines containing P1-rr and P1-ww were generated by six backcross generations of 65-CFS-305 with A619 (P1-ww) followed by 3 selfing generations to confirm homozygousity.  The original 65-CFS-305 line has both P1-rr and the P2 gene in the 4 County 63 background while the inbred line A619 has a non-functional P1 locus (P1-ww) and lacks P2 (Szalma et al., 2005).  The introgressed region from 65-CFS-305 in A619 was determined to extend on chromosome 1 from 35-66 Mb (AGPv2) by mapping with Illumina Maize SNP50 array (Ganal et al., 2011).  The final NIL also contained a second, non-target introgressed region of chromosome 6 89-102 Mb. Pericarps were peeled from 14 and 25 days after pollination (DAP) maize ears avoiding any aleurone tissue.

extract_protocol:
ChIP-Seq library preparation was performed according to Quail’s method (Quail et al., 2008). ChIP DNA were subjected to end-repair and A-base addition, followed by ligation with custom adapters. ChIP experiments were performed by using bilogical duplicates. Barcode sequences of each adaptor correspond to: AGGCC, ChIP of P1-ww at 14 DAP; AGAAG, ChIP of P1-rr at 14 DAP.
Chromatin immunoprecipitation (ChIP) was performed by methods previously described (Morohashi and Grotewold, 2009; Morohashi et al., 2009; Falcone Ferreyra et al., 2010), with modifications to accommodate for the high concentration of flavonoids present in P1-rr pericarps. Briefly, 0.3 g of dissected pericarps were fixed in Buffer A (0.4 M sucrose, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1 mM phenylmethylsμlfonyl fluoride, and 0.1% formaldehyde) for 10 minutes under vacuum conditions. Glycine was added to a final concentration of 0.1 M and incubation was continued for an additional 5 minutes. Fixed pericarps were washed in distilled water and frozen in liquid N2. The tissue was ground in liquid N2, followed by nuclear isolation using the Plant Nuclei Isolation/Extraction Kit according to the manufacturer’s instruction (Sigma). Nuclear-enriched extracts were resuspended in 100 μl Lysis Buffer (50 mM HEPES, pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS, 1 mM phenylmethylsulfonyl fluoride, 10 mM sodium butyrate) and plant proteinase inhibitor cocktail (Sigma), followed by sonication with a Bioruptor (Diangenode) to approximately 300 bp of average fragment size, estimated by agarose electrophoresis. For quantitative (real time) PCR analyses of ChIPed materials, to correct for PCR bias, 1 pg of pUC19 plasmid was spiked into input and immunoprecipitated (ChIP) DNA. Quantitative PCR (qPCR) was performed by using 0.1-1 uL of input or ChIPed DNA with Buffer J of the FailSafeTM PCR System (Epicentre Biotechnologies). ChIP-Seq library preparation was performed according to Quail’s method (Quail et al., 2008). Input and ChIP DNA were subjected to end-repair and A-base addition, followed by ligation with custom adapters. Barcode sequences of each adaptor correspond to: AGGTT, input of P1-ww at 14 DAP; AGGCC, ChIP of P1-ww at 14 DAP; AACCA, input of P1-rr at 14 DAP, AGAAG, ChIP of P1-rr at 14 DAP.

tag: genotype/variation

value: P-ww (P1 not expressed)

tag: tissue

value: Pericarp

value: 14 after pollination (DAP)

tag: chip antibody

value: P1 polyclonal antibodies (alphaP1344)

tag: chip antibody provider

value: Dr. Erich Grotewold and Dr. Kengo Morohash

tag: chip antibody reference

tag: chip antibody information


title: Broad_ChipSeq_NH-A_H3K9ac

source_name: NH-A

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K9ac

tag: antibody targetdescription

value: Histone H3 (acetyl K9). As with H3K27ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases.

tag: antibody vendorname

value: abcam

tag: antibody vendorid

tag: softwareversion

value: U

tag: antibody

value: Abcam

tag: treatment

value: No special treatment or protocol applies

value: NH-A/Input/std


title: Pericarp_P-ww_14DAP_ChIP_1

description: processed data file: P1_Prr-14_Pww-14_1_peaks.bed

tag: age


title: Broad_ChipSeq_NH-A_H3K4me2

value: rabbit polyclonal. Antibody Target:H3K4me2

value: Histone H3 (di methyl K4). Marks promoters and enhancers. Most CpG islands are marked by H3K4me2 in primary cells. May be associated also with poised promoters.

tag: controlid

tag: replicate

tag: cell sex

tag: treatment description

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.


title: Pericarp_P-rr_14DAP_ChIP_1

source_name: Pericarp at 14DAP of P1-rr

growth_protocol: The P1-rr stock designated as 65-CFS-305 (Brink and Styles, 1966) was obtained from the National Seed Storage Laboratory, Ft. Collins CO. Near isogenic lines containing P1-rr and P1-ww were generated by six backcross generations of 65-CFS-305 with A619 (P1-ww) followed by 3 selfing generations to confirm homozygousity.  The original 65-CFS-305 line has both P1-rr and the P2 gene in the 4 County 63 background while the inbred line A619 has a non-functional P1 locus (P1-ww) and lacks P2 (Szalma et al., 2005).  The introgressed region from 65-CFS-305 in A619 was determined to extend on chromosome 1 from 35-66 Mb (AGPv2) by mapping with Illumina Maize SNP50 array (Ganal et al., 2011).  The final NIL also contained a second, non-target introgressed region of chromosome 6 89-102 Mb. Pericarps were peeled from 14 days after pollination (DAP) maize ears avoiding any aleurone tissue.

tag: genotype/variation

value: P-rr (P1 expressed)

tag: tissue

value: Pericarp

tag: chip antibody

tag: chip antibody provider

tag: chip antibody reference

tag: chip antibody information


title: Stanford_ChipSeq_ES-E14_ZC3H11A_(NB100-74650)_std

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: mouse embryonic stem cell line E14

value: M

tag: antibody antibodydescription

value: Rabbit polyclonal antibody. The immunogen recognized by this antibody maps to a region between residue 250 and 300 of human zinc finger CCCH-type containing 11A.

tag: antibody targetdescription

value: ZC3H11A is a C3H1-type zinc finger protein. ZC3H11A has been identified as a protein that is phosphorylated upon DNA damage by ATM or ATR. The function of ZC3H11A remains uncharacterized.

tag: antibody vendorname

value: NovusBio

tag: antibody vendorid

tag: age description

value: Embryonic day 0 (stem cell)

tag: strain

tag: strain description

value: The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice.


title: Stanford_ChipSeq_ES-E14_Input_std

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell sex

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

tag: control description

tag: age

tag: controlid

tag: replicate


title: Stanford_ChipSeq_ES-E14_MafK_(ab50322)_std

tag: lab

tag: lab description

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

tag: antibody antibodydescription

value: Rabbit polyclonal. Raised against synthetic peptide:TTNPKPNKALKVKKEA conjugated to KLH by a C-terminal Cysteine residue linker, corresponding to amino acids 2-17 of Human MAFK. Antibody Target:MafK

value: NFE2 DNA-binding activity consists of a heterodimer containing an 18-kD Maf protein (MafF, MafG, or MafK) and p45. Both subunits are members of the activator protein-1 superfamily of basic leucine zipper (bZIP)proteins. Since they lack a putative transactivation domain, small Mafs behave as transcriptional repressors when they dimerize among themselves. They serve as transcriptional activators by dimerizing with other (usually larger) bZip proteins and recruiting them to specific DNA-binding sites.

value: Abcam

value: std

value: Standard input signal for most experiments.

tag: labversion


title: Stanford_ChipSeq_ES-E14_ZNF384_(HPA004051)_std

value: Stanford-m

value: Snyder - Stanford University

value: mouse

value: mouse embryonic stem cell line E14

tag: cell sex

tag: antibody

value: Rabbit polyclonal generated using the immunogen:Zinc finger protein 384 recombinant protein epitope signature tag (PrEST)

tag: antibody targetdescription

value: This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7.

tag: antibody vendorname

value: SIGMA

tag: antibody vendorid

tag: age description

tag: strain

tag: strain description


title: Stanford_ChipSeq_MEL_MafK_(ab50322)_DMSO_2.0pct_std

tag: lab

value: ChipSeq

value: MEL

value: Leukemia (K562 analog)

value: M

tag: treatment

tag: treatment description

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

tag: control

tag: control description

tag: age

value: immortalized

value: Immortal cells

tag: controlid

value: Unknown

value: Unknown strain origin


title: Stanford_ChipSeq_MEL_CHD1_(NB100-60411)_IgG-rab

tag: lab description

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

tag: antibody antibodydescription

value: Rabbit polyclonal, The epitope recognized by this antibody maps to a region between residue 1660 and 1710 of human chromodomain helicase DNA binding protein 1 using the numbering given in entry NP_001261.2 (GeneID 1105). Antibody Target:CHD1

value: ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells

value: Novus Biologicals

value: No special treatment or protocol applies

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Stanford_ChipSeq_MEL_GCN5_IgG-rab

value: Stanford-m

value: Snyder - Stanford University

value: mouse

tag: cell sex

tag: antibody

value: Rabbit polyclonal anti-GCN5 antibody (2676), Immunogen :synthetic peptide coupled to Ovalbumin (sequence-MAEPSQAPTPAPAAQPRPLC). Antibody Target:GCN5

tag: antibody targetdescription

value: KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4

tag: antibody vendorname

value: Laszlo Tora

tag: antibody vendorid

value: Missing

tag: age description


title: Stanford_ChipSeq_CH12_MAZ_(ab85725)_IgG-rab

tag: lab

value: ChipSeq

value: B-cell lymphoma (GM12878 analog)

value: F

value: Rabbit polyclonal, immunogen is synthetic peptide, corresponding to a region within amino acids 427-477 of Human MAZ, GenBank BAA33064.1. Antibody Target:MAZ

value: May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors.

value: Abcam

tag: treatment

tag: treatment description

tag: control

value: immortalized

value: Immortal cells

tag: labversion

tag: strain

tag: strain description

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: Stanford_ChipSeq_CH12_Nrf2_IgG-rab

tag: lab description

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: Rabbit polyclonal IgG. Antibody Target:Nrf2

value: epitope corresponding to amino acids 1-180 mapping at the N-terminus of GABP-alpha of human origin

value: Santa Cruz Biotech

value: No special treatment or protocol applies

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: age

tag: controlid


title: Stanford_ChipSeq_ES-E14_HCFC1_(NB100-68209)_std

value: Stanford-m

value: Snyder - Stanford University

tag: cell organism

value: mouse

tag: cell description

value: mouse embryonic stem cell line E14

tag: cell sex

value: M

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonalantibody against residue 1700 and 1750 of human host cell factor C1

tag: antibody targetdescription

value: The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein).

tag: antibody vendorname

value: NovusBio

value: std

value: Standard input signal for most experiments.

value: Embryonic day 0 (stem cell)

value: The mice have yellow coats and late onset severe vacuolation in brain (700+ days). Inbred strain used as a control group to compare with null PrP mice.


title: Stanford_ChipSeq_MEL_ZNF-MIZD-CP1_(ab65767)_IgG-rab

tag: lab

value: ChipSeq

value: Chromatin IP Sequencing

value: MEL

value: Leukemia (K562 analog)

value: Rabbit Polyclonal against synthetic peptide conjugated to KLH derived from within residues 200 - 300 of Human Zinc finger MIZ domain-containing protein 1.

value: Zinc finger MIZ domain-containing protein 1 that increases ligand-dependent transcriptional activity of AR and promotes AR sumoylation. The stimulation of AR activity is dependent upon sumoylation.

value: Abcam

tag: antibody vendorid

tag: treatment

tag: treatment description

tag: control

value: immortalized

tag: age description

value: Immortal cells

value: Unknown

value: Unknown strain origin


title: Stanford_ChipSeq_CH12_ZNF384_(HPA004051)_IgG-rab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: datatype

tag: datatype description

tag: cell

value: mouse

value: B-cell lymphoma (GM12878 analog)

value: F

value: Rabbit polyclonal generated using the immunogen:Zinc finger protein 384 recombinant protein epitope signature tag (PrEST)

value: This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7.

value: SIGMA

value: No special treatment or protocol applies

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: strain

tag: strain description

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: Stanford_ChipSeq_CH12_HCFC1_(NB100-68209)_IgG-rab

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

tag: cell description

tag: cell sex

value: Rabbit polyclonalantibody against residue 1700 and 1750 of human host cell factor C1

value: The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein).

value: NovusBio

tag: control description

tag: age

tag: controlid


title: Stanford_ChipSeq_MEL_BHLHE40_(NB100-1800)_IgG-rab

tag: lab

value: Stanford-m

value: MEL

value: Leukemia (K562 analog)

value: M

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonal, maps to a region between residues 350 and the C-terminus (residue 412). Antibody Target:BHLHE40

tag: antibody targetdescription

value: This gene encodes a basic helix-loop-helix protein expressed in various tissues. Expression in the chondrocytes is responsive to the addition of Bt2cAMP. The encoded protein is believed to be involved in the control of cell differentiation.

tag: antibody vendorname

value: Novus

tag: antibody vendorid

value: immortalized

value: Immortal cells

tag: labversion

value: Unknown

value: Unknown strain origin


title: Pericarp_P-rr_14DAP_ChIP_2

tag: genotype/variation

value: P-rr (P1 expressed)

tag: tissue

value: Pericarp

value: 14 after pollination (DAP)

tag: chip antibody

value: P1 polyclonal antibodies (alphaP1344)

tag: chip antibody provider

value: Dr. Erich Grotewold and Dr. Kengo Morohash

tag: chip antibody reference

tag: chip antibody information


title: Stanford_ChipSeq_CH12_ZC3H11A_(NB100-74650)_IgG-rab

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: B-cell lymphoma (GM12878 analog)

tag: cell sex

value: F

value: Rabbit polyclonal antibody. The immunogen recognized by this antibody maps to a region between residue 250 and 300 of human zinc finger CCCH-type containing 11A.

value: ZC3H11A is a C3H1-type zinc finger protein. ZC3H11A has been identified as a protein that is phosphorylated upon DNA damage by ATM or ATR. The function of ZC3H11A remains uncharacterized.

value: NovusBio

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: age description

tag: strain

tag: strain description

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: Stanford_ChipSeq_CH12_ZNF-MIZD-CP1_(ab65767)_IgG-rab

tag: lab

value: Stanford-m

tag: antibody

tag: antibody antibodydescription

value: Rabbit Polyclonal against synthetic peptide conjugated to KLH derived from within residues 200 - 300 of Human Zinc finger MIZ domain-containing protein 1.

tag: antibody targetdescription

value: Zinc finger MIZ domain-containing protein 1 that increases ligand-dependent transcriptional activity of AR and promotes AR sumoylation. The stimulation of AR activity is dependent upon sumoylation.

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: control description

tag: age

value: immortalized

value: Immortal cells

tag: controlid


title: Stanford_ChipSeq_MEL_Nrf2_IgG-rab

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: MEL

tag: cell organism

tag: cell description

value: Leukemia (K562 analog)

value: M

value: Rabbit polyclonal IgG. Antibody Target:Nrf2

value: epitope corresponding to amino acids 1-180 mapping at the N-terminus of GABP-alpha of human origin

value: Santa Cruz Biotech

value: Unknown

value: Unknown strain origin


title: Silks_P-ww

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the maize genome assembly version 2 using TopHat version 1.2.0 -G option using the gff file for Filtered Gene Set provided by maizegenome.org
Alignment files were compared for differential gene expression using Cuffdiff option of the Cufflink program (version 1.0.3)
Genome_build: Maize Golden Path B73 RefGen_v2
Supplementary_files_format_and_content: Maize_Silks_mRNA-Seq_genes.fpkm_tracking and Maize_Silks_mRNA-Seq_gene_exp.diff are tabulator delimiter files generated with Cuffdiff. genes.fpkm_tracking tracks the summed FPKM of transcripts sharing each gene_id and gene_exp.dif tracks the results of tests difference sin the summed FPKM of transcripts sharing each gene_id.

growth_protocol: The P1-rr stock designated as 65-CFS-305 (Brink and Styles, 1966) was obtained from the National Seed Storage Laboratory, Ft. Collins CO. Near isogenic lines containing P1-rr and P1-ww were generated by six backcross generations of 65-CFS-305 with A619 (P1-ww) followed by 3 selfing generations to confirm homozygousity.  The original 65-CFS-305 line has both P1-rr and the P2 gene in the 4 County 63 background while the inbred line A619 has a non-functional P1 locus (P1-ww) and lacks P2 (Szalma et al., 2005).  The introgressed region from 65-CFS-305 in A619 was determined to extend on chromosome 1 from 35-66 Mb (AGPv2) by mapping with Illumina Maize SNP50 array (Ganal et al., 2011).  The final NIL also contained a second, non-target introgressed region of chromosome 6 89-102 Mb. Pericarps were peeled from 14 and 25 days after pollination (DAP) maize ears avoiding any aleurone tissue

extract_protocol: The preparation of mRNA-Seq libraries was performed according to instructions from the Illumina mRNA-Seq Sample Preparation Kit (RS-100-0801 Illumina). Total RNA extracted from P1-rr and P1-ww pericarps harvested at 14 and 25 DAP and from P1-rr and P1-ww unfertilized silks obtained promptly (< 72 hrs) after emergence. were treated with DNaseI (Promega) twice to ensure no genomic DNA contamination. Two μg of total RNA was subjected to two rounds of hybridization to oligo(dT) beads (Illumina). The polyA-enriched mRNA was fragmented by heating at 94 °C for 5 minutes in Fragmentation Buffer supplied by Illumina, followed by ethanol precipitation. The fragmented mRNA was added into 1x First Strand Buffer (2.5mM dNTP, 10mM DTT, RNaseOUT, and random primers mix). After adding Superscript II, first strand cDNA synthesis was performed at 25°C for 10 minutes, 42°C for 50 minutes and 70°C for 15 minutes. The second strand cDNA synthesis was carried out in GEX Second Strand Buffer (25mM dNTP, 1μl RNase H and μl DNA Pol I for 2.5 hours at 16°C), and purified by PCR Purification Kit (Qiagen). After end repair and A-base addition, adapter ligation was performed using custom made adapters or Illumina multiplexing system. For custom-made adapters, reverse oligo-adapters consisting of SLX-R_P1 and SLX-R_P2 and forward oligo adapters consisting of SLX-N_P1 and SLX-N_P2, where underlined nucleotides (see Table S6) corresponds to a barcode sequence, which was either AATCG, AACAC, AACGT, or AACTG in P1-ww at 14 or 25 DAP and P1-rr 14 or 25 DAP, respectively. For using Illumina multiplexing system, the overall procedure was according to the manufacturer’s instructions (MultiplexPE_SamplePrep_1005361_RevB). We used Index 1 (ATCACG) or 2 (CGATGT) for P1-rr or P1-ww silk, respectively. For both procedures, ligated fragments were subjected to electrophoresis for selection of fragments of ~300 bp in length, followed by PCR amplification (20 cycles). PCR products were purified with Agencourt AMPure (Beckman Coulter). Library DNA was checked for concentration and size distribution in an Agilent Bioanalyzer before being subjected to Illuimina GA sequencing using the OSUCCC Nucleic Acid Shared Resource-Illumina GAII Core and the OARDC Molecular and Cellular Imaging Center (The Ohio State University, Ohio).

tag: tissue

value: silk

tag: isogenic line

value: P-ww


title: Stanford_ChipSeq_MEL_COREST_(sc-30189)_IgG-rab

tag: lab

value: Stanford-m

value: mouse

tag: cell sex

value: Rabbit polyclonal, epitope corresponding to amino acids 246-310 mapping within an internal region of CoREST of human origin recommended for detection of CoREST of mouse, rat and human origin. Antibody Target:COREST (sc30189)

value: Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells.  In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates.

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: age description

tag: labversion

tag: strain

tag: strain description


title: Silks_P-rr

value: P-rr


title: Stanford_ChipSeq_MEL_GATA-1_DMSO_2.0pct_std

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

value: MEL

value: Leukemia (K562 analog)

tag: antibody

tag: antibody antibodydescription

value: Anti-GATA-1 rabbit polyclonal antibody was generated by using a purified GST fusion to amino acids 1-89 of mouse GATA-1. Antibody Target:GATA1

tag: antibody targetdescription

value: GATA-1 is a transcriptional activator which probably serves as a general switch factor for erythroid development. It binds to DNA sites with the consensus sequence [AT]GATA[AG} within regulatory regions of globin genes and of other genes expressed in erythroid cells.

tag: antibody vendorname

value: Donated by Dr. E.H. Bresnick, UW Madison

tag: antibody vendorid

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

value: std

tag: control description

value: Standard input signal for most experiments.

tag: age

value: immortalized

value: Immortal cells

tag: controlid


title: Stanford_ChipSeq_MEL_MAZ_(ab85725)_IgG-rab

tag: lab

value: Stanford-m

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

value: M

value: Rabbit polyclonal, immunogen is synthetic peptide, corresponding to a region within amino acids 427-477 of Human MAZ, GenBank BAA33064.1. Antibody Target:MAZ

value: May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors.

value: Abcam

value: No special treatment or protocol applies

value: Unknown

value: Unknown strain origin


title: Stanford_ChipSeq_MEL_UBF_(sc-13125)_IgG-mus

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

value: MEL

value: Leukemia (K562 analog)

value: UBF (F-9) is a mouse monoclonal antibody raised against amino acids 1-220 of UBF of human origin. Antibody Target:UBF

value: Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes

value: Santa Cruz Biotech

tag: treatment

tag: treatment description

tag: control

value: IgG-mus

value: Input signal from Normal Mouse IgG ChIP-seq.

tag: age description

tag: strain

tag: strain description


title: Pericarp at 25DAP of P1-ww

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the maize genome assembly version 2 using TopHat version 1.2.0 -G option using the gff file for Filtered Gene Set provided by maizegenome.org
Alignment files were compared for differential gene expression using the Cuffdiff option of the Cufflink program (version 1.0.3)
Genome_build: Maize Golden Path B73 RefGen_v2
Supplementary_files_format_and_content: genes.fpkm_tracking and gene_exp.diff are tabulator delimiter files generated with Cuffdiff. genes.fpkm_tracking tracks the summed FPKM of transcripts sharing each gene_id and gene_exp.dif tracks the results of tests difference sin the summed FPKM of transcripts sharing each gene_id.

source_name: Pericarp at 25DAP of P1-ww

extract_protocol: The preparation of mRNA-Seq libraries was performed according to instructions from the Illumina mRNA-Seq Sample Preparation Kit (RS-100-0801 Illumina). Total RNA extracted from P1-rr and P1-ww pericarps harvested at 14 and 25 DAP and silks harvested 1-2 days post emergence were treated with DNaseI (Promega) twice to ensure no genomic DNA contamination. Two μg of total RNA was subjected to two rounds of hybridization to oligo(dT) beads (Illumina). The polyA-enriched mRNA was fragmented by heating at 94 °C for 5 minutes in Fragmentation Buffer supplied by Illumina, followed by ethanol precipitation. The fragmented mRNA was added into 1x First Strand Buffer (2.5mM dNTP, 10mM DTT, RNaseOUT, and random primers mix). After adding Superscript II, first strand cDNA synthesis was performed at 25°C for 10 minutes, 42°C for 50 minutes and 70°C for 15 minutes. The second strand cDNA synthesis was carried out in GEX Second Strand Buffer (25mM dNTP, 1μl RNase H and μl DNA Pol I for 2.5 hours at 16°C), and purified by PCR Purification Kit (Qiagen). After end repair and A-base addition, adapter ligation was performed using custom made adapters or Illumina multiplexing system. For custom-made adapters, reverse oligo-adapters consisting of SLX-R_P1 and SLX-R_P2 and forward oligo adapters consisting of SLX-N_P1 and SLX-N_P2, where underlined nucleotides (see Table S6) corresponds to a barcode sequence, which was either AATCG, AACAC, AACGT, or AACTG in P1-ww at 14 or 25 DAP and P1-rr 14 or 25 DAP, respectively. For using Illumina multiplexing system, the overall procedure was according to the manufacturer’s instructions (MultiplexPE_SamplePrep_1005361_RevB). We used Index 1 (ATCACG) or 2 (CGATGT) for P1-rr or P1-ww silk, respectively. For both procedures, ligated fragments were subjected to electrophoresis for selection of fragments of ~300 bp in length, followed by PCR amplification (20 cycles). PCR products were purified with Agencourt AMPure (Beckman Coulter). Library DNA was checked for concentration and size distribution in an Agilent Bioanalyzer before being subjected to Illuimina GA sequencing using the OSUCCC Nucleic Acid Shared Resource-Illumina GAII Core and the OARDC Molecular and Cellular Imaging Center (The Ohio State University, Ohio).

tag: tissue

value: pericarp

tag: Stage

tag: isogenic line


title: Pericarp at 14DAP of P1-ww


title: Broad_ChipSeq_Monocytes-CD14+_RO01746_H3K4me1

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K4me1

tag: antibody targetdescription

value: Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.

tag: antibody vendorname

value: abcam

tag: antibody vendorid

tag: controlid

tag: replicate

tag: softwareversion

value: F

tag: antibody

value: std

tag: control description

value: Standard input signal for most experiments.


title: Stanford_ChipSeq_MEL_Input_DMSO_2.0pct_IgG-rat

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

value: M

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: treatment

tag: treatment description

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

value: IgG-rat

value: Input signal from Normal Rat IgG ChIP-seq

tag: age

value: immortalized

value: Immortal cells

value: Unknown

value: Unknown strain origin


title: Pericarp at 14DAP of P1-rr

tag: tissue

value: pericarp

tag: Stage

tag: isogenic line


title: Pericarp at 25DAP of P1-rr

source_name: Pericarp at 25DAP of P1-rr


title: Stanford_ChipSeq_CH12_CHD1_(NB100-60411)_IgG-rab

value: ChipSeq

value: Chromatin IP Sequencing

value: B-cell lymphoma (GM12878 analog)

value: F

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonal, The epitope recognized by this antibody maps to a region between residue 1660 and 1710 of human chromodomain helicase DNA binding protein 1 using the numbering given in entry NP_001261.2 (GeneID 1105). Antibody Target:CHD1

tag: antibody targetdescription

value: ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells

tag: antibody vendorname

value: Novus Biologicals

tag: antibody vendorid

value: No special treatment or protocol applies

tag: control

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: age description

tag: controlid

tag: strain

tag: strain description

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: Broad_ChipSeq_NH-A_EZH2_(39875)

tag: datatype

tag: datatype description

value: This EZH2 antibody was raised against a recombinant protein corresponding to amino acids 353-451 of human EZH2. Antibody Target:EZH2

value: EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers.

value: Active Motif

tag: replicate

tag: softwareversion

tag: cell sex

value: U

value: std

tag: control description

value: Standard input signal for most experiments.

value: NH-A/Input/std


title: Broad_ChipSeq_NHLF_H3K9me3

source_name: NHLF

value: ChipSeq

value: Chromatin IP Sequencing

value: rabbit polyclonal, ChIP grade. Antibody Target:H3K9me3

value: Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.

value: abcam

value: Abcam

tag: treatment

tag: treatment description

value: NHLF/Input/std


title: Broad_ChipSeq_NHLF_H2A.Z

tag: antibody antibodydescription

value: Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminus of H2AZ. Antibody Target:H2AZ

value: H2A.Z is a sequence variant of Histone H2A.

value: Millipore

tag: antibody

value: Upstate (Millipore)

value: No special treatment or protocol applies


title: Stanford_ChipSeq_CH12_COREST_(sc-30189)_IgG-rab

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: B-cell lymphoma (GM12878 analog)

value: F

value: Rabbit polyclonal, epitope corresponding to amino acids 246-310 mapping within an internal region of CoREST of human origin recommended for detection of CoREST of mouse, rat and human origin. Antibody Target:COREST (sc30189)

tag: antibody targetdescription

value: Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells.  In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates.

tag: antibody vendorname

value: Santa Cruz Biotech

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: age

value: immortalized

value: Immortal cells

tag: labversion

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: Stanford_ChipSeq_MEL_ZNF384_(HPA004051)_IgG-rab

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: MEL

value: Leukemia (K562 analog)

value: M

value: Rabbit polyclonal generated using the immunogen:Zinc finger protein 384 recombinant protein epitope signature tag (PrEST)

value: This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7.

value: SIGMA

tag: antibody vendorid

tag: control

tag: age description

tag: controlid

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: Stanford_ChipSeq_MEL_USF2_IgG-rab

tag: lab

value: Stanford-m

value: Snyder - Stanford University

value: mouse

tag: cell sex

tag: antibody

tag: antibody antibodydescription

value: Mouse monoclonal. Immunogen corresponds to amino acids 1-101 of Human USF2. Antibody Target:USF2

value: Encodes a member of the basic helix-loop-helix leucine zipper family. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs (5'-CACGTG-3').

value: abcam

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control description


title: Broad_ChipSeq_NHLF_EZH2_(39875)

value: ChipSeq

value: This EZH2 antibody was raised against a recombinant protein corresponding to amino acids 353-451 of human EZH2. Antibody Target:EZH2

tag: antibody targetdescription

value: EZH2 (Enhancer of Zeste homolog 2, also designated Enx1 and SETDB1) is a human homolog of the Drosophila Polycomb-group protein Enhancer of Zeste protein. It contains a SET domain that catalyzes the methylation of histone H3 at lysine 27 (Histone H3 Lys27 monomethylated, dimethylated and trimethylated). Polycomb-group proteins repress gene expression by binding to chromatin and locally altering chromatin structure. EZH2, BMI-1 and Suz12 are present in the PRC2 and PRC3 protein complexes that function as mediators of epigenetic transcriptional silencing. EZH2 associates with the embryonic ectoderm development protein, the VAV1 oncoprotein, and the X-linked nuclear protein. EZH2 may play a role in the hematopoietic and central nervous systems. Deregulation of EZH2 is linked to a variety of cancers.

tag: antibody vendorname

value: Active Motif

tag: replicate

tag: softwareversion

value: U

value: std

value: Standard input signal for most experiments.

value: NHLF/Input/std


title: Stanford_ChipSeq_CH12_GCN5_IgG-rab

tag: lab description

tag: datatype

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

value: B-cell lymphoma (GM12878 analog)

value: F

value: Rabbit polyclonal anti-GCN5 antibody (2676), Immunogen :synthetic peptide coupled to Ovalbumin (sequence-MAEPSQAPTPAPAAQPRPLC). Antibody Target:GCN5

value: KAT2A, or GCN5, is a histone acetyltransferase (HAT) that functions primarily as a transcriptional activator. Acetylation of histones gives a specific tag for epigenetic transcription activation. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Component of the SAGA and ATAC complexes, complexes with histone acetyltransferase activities on histones H3 and H4

value: Laszlo Tora

tag: antibody vendorid

value: Missing

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: age

value: immortalized

value: Immortal cells

tag: labversion

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: Stanford_ChipSeq_CH12_ZKSCAN1_(HPA006672)_IgG-rab

tag: lab

value: Stanford-m

value: Snyder - Stanford University

value: ChipSeq

value: mouse

tag: cell sex

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonal, Immunogen:Zinc finger with KRAB and SCAN domain-containing protein 1 recombinant protein epitope signature tag (PrEST). Antibody Target:ZKSCAN1

value: The ZKSCAN1 gene encodes a transcriptional regulator of the KRAB (Kruppel-associated box) subfamily of zinc finger proteins, which contain repeated Cys2-His2 (C2H2) zinc finger domains that are connected by conserved sequences, called H/C links. Transcriptional regulatory proteins containing tandemly repeated zinc finger domains are thought to be involved in both normal and abnormal cellular proliferation and differentiation.

value: Sigma-Aldrich

value: No special treatment or protocol applies

tag: control

tag: age description

tag: controlid

tag: strain

tag: strain description


title: Stanford_ChipSeq_CH12_UBF_(sc-13125)_IgG-rab

tag: lab description

tag: datatype

value: Chromatin IP Sequencing

value: B-cell lymphoma (GM12878 analog)

value: F

value: UBF (F-9) is a mouse monoclonal antibody raised against amino acids 1-220 of UBF of human origin. Antibody Target:UBF

tag: antibody targetdescription

value: Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP (MIM 600075) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human (Bell et al., 1988 (PubMed 3413483)). UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains. Sequence-specific DNA binding to the core and upstream control elements of the human rRNA promoter is mediated through several HMG boxes

tag: antibody vendorname

value: Santa Cruz Biotech

tag: treatment

tag: treatment description

tag: control description


title: Stanford_ChipSeq_MEL_SIN3A_(NB600-1263)_IgG-rab

tag: datatype description

tag: cell

value: MEL

tag: cell organism

tag: cell description

value: Leukemia (K562 analog)

value: M

value: Rabbit polyclonal, Immunogen:Synthetic peptide:MKRRLDDQESDVYAAQQRR, corresponding to amino acids 1-19 of Mouse mSin3A. Antibody Target:SIN3A (NB600-1263)

value: Mammalian Sin 3 (mSin 3) is closely related to the yeast SIN3 repressor protein involved in the transcriptional repression of many genes. Containing 4 paired amphipathic helix domains (PAH domains), mSin 3A and mSin 3B have been shown to directly interact with several other transcriptional repressor proteins including HDAC 1, HDAC 2, RbAp 46, the methyl CpG binding protein MeCP 2, the Mad/Max heterodimer, and the corepressors silencing mediator of retinoic acid & thyroid hormone receptor (SMRT) and nuclear receptor corepressor (N-CoR).

value: Novus Biologicals

tag: antibody vendorid

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: age

value: immortalized

tag: labversion

value: Unknown

value: Unknown strain origin


title: Stanford_ChipSeq_CH12_SIN3A_(NB600-1263)_IgG-rab

tag: lab

value: Stanford-m

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

value: mouse

tag: cell sex

tag: antibody

tag: antibody antibodydescription

value: No special treatment or protocol applies

tag: control

tag: age description

value: Immortal cells

tag: controlid

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: Stanford_ChipSeq_MEL_HCFC1_(NB100-68209)_IgG-rab

tag: lab description

tag: datatype

value: MEL

value: Leukemia (K562 analog)

value: M

value: Rabbit polyclonalantibody against residue 1700 and 1750 of human host cell factor C1

tag: antibody targetdescription

value: The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein).

tag: antibody vendorname

value: NovusBio

tag: treatment

tag: strain

tag: strain description


title: Stanford_ChipSeq_MEL_ZKSCAN1_(HPA006672)_IgG-rab

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: Rabbit polyclonal, Immunogen:Zinc finger with KRAB and SCAN domain-containing protein 1 recombinant protein epitope signature tag (PrEST). Antibody Target:ZKSCAN1

value: The ZKSCAN1 gene encodes a transcriptional regulator of the KRAB (Kruppel-associated box) subfamily of zinc finger proteins, which contain repeated Cys2-His2 (C2H2) zinc finger domains that are connected by conserved sequences, called H/C links. Transcriptional regulatory proteins containing tandemly repeated zinc finger domains are thought to be involved in both normal and abnormal cellular proliferation and differentiation.

value: Sigma-Aldrich

tag: antibody vendorid

tag: treatment description

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

value: immortalized


title: Stanford_ChipSeq_MEL_ETS1_IgG-rab

tag: lab

value: Stanford-m

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell sex

tag: antibody

tag: antibody antibodydescription

value: Rabbit polyclonal IgG. Antibody Target:ETS1

value: ETS transcriptions factors, such as ETS1, regulate numerous genes and are involved in stem cell development, cell senescence and death, and tumorigenesis

value: Santa Cruz Biotech

tag: control

tag: age

tag: labversion

value: Unknown

value: Unknown strain origin


title: Stanford_ChipSeq_MEL_ZC3H11A_(NB100-74650)_IgG-rab

tag: lab description

tag: datatype

value: MEL

value: mouse

value: Leukemia (K562 analog)

value: M

value: Rabbit polyclonal antibody. The immunogen recognized by this antibody maps to a region between residue 250 and 300 of human zinc finger CCCH-type containing 11A.

tag: antibody targetdescription

value: ZC3H11A is a C3H1-type zinc finger protein. ZC3H11A has been identified as a protein that is phosphorylated upon DNA damage by ATM or ATR. The function of ZC3H11A remains uncharacterized.

tag: antibody vendorname

tag: treatment

value: No special treatment or protocol applies

tag: age description

value: Immortal cells

tag: controlid


title: Stanford_ChipSeq_CH12_ETS1_IgG-rab

value: Stanford-m

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: B-cell lymphoma (GM12878 analog)

value: F

tag: antibody vendorid

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

value: immortalized

tag: strain

tag: strain description

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: Stanford_ChipSeq_SK-N-SH_CTCF_(SC-15914)_IgG-rab

status: Public on Sep 13 2012

source_name: SK-N-SH

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeSydhTfbs

tag: lab

value: Stanford

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

value: SK-N-SH

value: human

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

tag: treatment description

tag: antibody

tag: antibody antibodydescription

value: Goat polyclonal, epitope mapping near the C-terminus of CTCF of human origin. Antibody Target:CTCF

value: Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites.

value: Santa Cruz Biotech

tag: control

tag: control description


title: Stanford_ChipSeq_SK-N-SH_JunD_IgG-rab

tag: lab description

tag: datatype

value: F

tag: treatment

value: No special treatment or protocol applies

value: JunD

value: rabbit polyclonal IgG. Antibody Target:JunD

tag: antibody targetdescription

value: The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq)

tag: antibody vendorname

tag: controlid


title: Stanford_ChipSeq_SK-N-SH_Mxi1_(AF4185)_IgG-rab

value: Stanford

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: Goat IgG. Raised against E. coli-derived rhMxi1. Antibody Target:Mxi1

value: Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX

value: R&D Systems

tag: antibody vendorid

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Stanford_ChipSeq_SK-N-SH_p300_(SC-584)_IgG-rab

tag: lab

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

value: SK-N-SH

value: human

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

tag: cell karyotype

tag: cell lineage

tag: cell sex

value: Rabbit polyclonal IgG, epitope mapping at the N-terminus of p300 of human origin. Antibody Target:P300

value: Encodes the adenovirus E1A-associated cellular p300 transcriptional co-activator protein. Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein


title: Stanford_ChipSeq_GM12878_JunD_IgG-rab

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: normal

value: mesoderm

value: F

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: JunD

tag: antibody antibodydescription

value: Santa Cruz Biotech

tag: control


title: Stanford_ChipSeq_SK-N-SH_Rad21_IgG-rab

value: Stanford

tag: lab description

tag: datatype

value: cancer

value: ectoderm

tag: treatment

value: Rabbit polyclonal. Antibody Target:RAD21

value: Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14

value: Abcam

value: IgG-rab

tag: control description


title: Stanford_ChipSeq_SK-N-SH_Nrf1_IgG-rab

value: Snyder - Stanford University

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: SK-N-SH

value: human

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: Mouse monoclonal, Immunogen corresponding to amino acids 201-286 of Human NRF1. Antibody Target:NRF1

tag: antibody targetdescription

value: NRF1 is the mammalian homolog to the erect wing (ewg) Drosophila protein that is required for proper development of the central nervous system and indirect flight muscles. In mammals NRF1 functions as a transcription factor that activates the expression of the EIF2S1 (EIF-alpha) gene. This protein links the transcriptional modulation of key metabolic genes to cellular growth and development, and has been implicated in the control of nuclear genes required for respiration, heme biosynthesis and mitochondrialDNA transcription and replication. NRF1 forms a homodimer and binds DNA as a dimer. NRF1 shows a nuclear localization and is expressed widely in embryonic, fetal and adult tissues. Phosphorylation of NRF1 enhances DNA binding.

tag: antibody vendorname

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid


title: Stanford_ChipSeq_MEL_Pol2_DMSO_2.0pct_IgG-rab

value: Stanford-m

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

value: M

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

tag: antibody vendorid

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: labversion

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: Stanford_ChipSeq_SK-N-SH_Input_IgG-rab

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

value: ChipSeq

value: Chromatin IP Sequencing

value: SK-N-SH

value: human

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: control

value: IgG-rab

tag: replicate


title: Stanford_ChipSeq_SK-N-SH_RFX5_(200-401-194)_IgG-rab

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

tag: treatment

tag: antibody antibodydescription

value: Rabbit polyclonal against RFX5 peptide corresponding to a region at amino acids 320 to 494 of the human protein conjugated to Keyhole Limpet Hemocyanin. Antibody Target:RFX5

tag: antibody targetdescription

value: Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding betweenRFX and NF-Y. RFX binds the X1 box of MHC-II promoters

tag: antibody vendorname

value: Rockland Immunochemicals

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid


title: Stanford_ChipSeq_IMR90_CHD1_(NB100-60411)_IgG-rab

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: normal

tag: cell lineage

value: endoderm

tag: cell sex

value: Rabbit polyclonal, The epitope recognized by this antibody maps to a region between residue 1660 and 1710 of human chromodomain helicase DNA binding protein 1 using the numbering given in entry NP_001261.2 (GeneID 1105). Antibody Target:CHD1

value: ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells

value: Novus Biologicals

tag: antibody vendorid


title: Stanford_ChipSeq_MEL_CTCF_(SC-15914)_DMSO_2.0pct_std

value: Stanford-m

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: MEL

value: mouse

value: Leukemia (K562 analog)

value: M

tag: antibody

value: Goat polyclonal, epitope mapping near the C-terminus of CTCF of human origin. Antibody Target:CTCF

value: Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites.

value: Santa Cruz Biotech

tag: treatment description

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

tag: control

value: std

value: Standard input signal for most experiments.

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: labversion

tag: strain

value: Unknown

tag: strain description

value: Unknown strain origin


title: Stanford_ChipSeq_K562_HCFC1_(NB100-68209)_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: datatype description

tag: cell

tag: cell organism

value: human

tag: cell description

value: leukemia, "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: cancer

value: mesoderm

value: F

tag: treatment

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit polyclonalantibody against residue 1700 and 1750 of human host cell factor C1

tag: antibody targetdescription

value: The epitope recognized by this antibody maps to a region between residue 1700 and 1750 of human host cell factor C1 (VP16-accessory protein).

tag: antibody vendorname

value: NovusBio

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Stanford_ChipSeq_K562_CDP_(sc-6327)_IgG-rab

tag: lab

tag: lab description

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell karyotype

tag: cell lineage

tag: cell sex

tag: antibody

value: CDP (C-20) is an affinity purified goat polyclonal antibody raised against a peptide mapping at the C-terminus of CDP of mouse origin.

value: CDP (for CCAAT displacement protein) was identified as a repressor for tran- scription of developmentally regulated genes. It is a homeodomain protein that appears to compete with transcriptional activating proteins for binding to the promoter regions of various genes. CDP contains three cut repeats which function as DNA binding domains. It has been demonstrated that cut repeat domains have the capacity to bind to DNA in conjunction with or independently of homeodomain DNA binding. CDP has been shown to be the DNA-binding subunit of the HiNF-D complex, which contains cyclin A, Cdc2 and an Rb-related protein in addition to CDP. Histone expression is required for the transition to S phase in the cell cycle. The HiNF-D complex regulates the transcription of Histone H4, H3 and H1 genes, allowing cells to progress from G1 to S phase.

value: Santa Cruz Biotechnology

tag: antibody vendorid

tag: controlid


title: Stanford_ChipSeq_HeLa-S3_HCFC1_(NB100-68209)_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: datatype description

tag: cell

value: cervical carcinoma

value: ectoderm

tag: treatment description

tag: control


title: Stanford_ChipSeq_K562_ZNF384_(HPA004051)_IgG-rab

tag: cell organism

value: human

tag: cell description

value: leukemia, "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: cancer

value: mesoderm

tag: treatment

tag: antibody antibodydescription

value: Rabbit polyclonal generated using the immunogen:Zinc finger protein 384 recombinant protein epitope signature tag (PrEST)

value: This gene encodes a C2H2-type zinc finger protein, which may function as a transcription factor. This gene also contains long CAG trinucleotide repeats that encode consecutive glutamine residues. The protein appears to bind and regulate the promoters of the extracellular matrix genes MMP1, MMP3, MMP7 and COL1A1. Studies in mouse suggest that nuclear matrix transcription factors (NP/NMP4) may be part of a general mechanical pathway that couples cell construction and function during extracellular matrix remodeling. Alternative splicing results in multiple transcript variants. Recurrent rearrangements of this gene with the Ewing's sarcoma gene, EWSR1 on chromosome 22, or with the TAF15 gene on chromosome 17, or with the TCF3 (E2A) gene on chromosome 19, have been observed in acute leukemia. A related pseudogene has been identified on chromosome 7.

value: SIGMA

tag: labversion


title: USC_ChipSeq_H1-hESC_ZNF274_(M01)_UCDavis

growth_protocol: missing

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

value: embryonic stem cells

value: normal

value: inner cell mass

value: M

value: No special treatment or protocol applies

value: Mouse monoclonal antibody raised against a partial recombinant ZNF274 (corresponding to amino acids 420-531 of the human ZNF274 protein). Antibody Target:ZNF274

tag: antibody targetdescription

value: ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor and interacts with the KAP1 corepressor complex.

tag: antibody vendorname

value: Abnova ZNF74

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.


title: Rem

city: Qingdao

first: Fei

last: Xu

address: 7 Nanhai Road

institute: Institute of Oceanology, Chinese Academy of Sciences

description: Sequenced reads were generated from mixture of the adult tissues after sampling the main part of hemolymph, mantle, gonad, digestive gland, gill, labial palp, and adductor muscle.

data_processing:
use Pacific oyster Crassostrea gigas genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except  -r 20 --mate-std-dev 5 -g 20 -I 10000 --solexa1.3-quals
Genome_build: oyster_v9 genome
Supplementary_files_format_and_content: bedgraph: TopHat - read coverage

organism: Magallana gigas

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 ug total RNA of each sample. First strand cDNA synthesis was  performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp  fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200 +/-20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using a 1G Illumina Genome Analyzer and the paired-end sequencing module.

treatment_protocol: total RNA is extracted by TRIzol Reagent

tag: developmental stage

value: adult

tag: tissue


title: Stanford_ChipSeq_GM12878_SREBP1_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: cell karyotype

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: antibody

value: Rabbit polyclonal. Antibody Target:SREBP1

value: Sterol regulatory element binding transcription factor 1

value: Santa Cruz Biotech

tag: antibody vendorid

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: controlid


title: late

description: Sequenced reads were generated from late planktonic stages and spat in Crassostrea gigas, including the stage of D-shaped larvae at 21.5 h, D-shaped larvae at 1.75 day, D-shaped larvae at 3.77 day, early umbo larvae at 5.73 day, umbo larvae at 7.75 day, umbo larvae at 9.75 day, umbo larvae at 11.75 day, umbo larvae at 13.75 day, umbo larvae at 15.75 day, eyed larvae at 16.75 day, and spat at 22.15 day.

data_processing: use oyster_v9 genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except  -r 20 --mate-std-dev 5 -g 20 -I 10000 --solexa1.3-quals

source_name: late planktonic stages and spat

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 Î¼g total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3â dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200Â±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using a 1G Illumina Genome Analyzer and the paired-end sequencing module.

value: late planktonic stages and spat

tag: exptl group

value: tissue


title: early

description: Sequenced reads were generated from early developmental stages in Crassostrea gigas. The early developmetnal stages including the stage of second polar body ejected at 35 min after insemination, four cells stage at 1.5 h, morula stage at 3.5 h, the stage when embryo can rotate at 5.5 h, early gastrula stage at 7.5 h, early trochophore stage at 9.5 h, trochophore at 11.5 h, trochophore at 13.5 h, early D-shaped larvae at 15.5 h, D-shaped larvae at 17.5 h, and D-shaped larvae at 19.5 h.

source_name: early developmental stages

value: early developmental stages


title: Zn9d_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (1 mg/L) for 9 days.

source_name: Pool of three oyster digestive gills, sampled at time 9d, Zn

value: adult

value: digestive gland


title: Stanford_ChipSeq_IMR90_MAZ_(ab85725)_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: normal

value: endoderm

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: antibody antibodydescription

value: Rabbit polyclonal, immunogen is synthetic peptide, corresponding to a region within amino acids 427-477 of Human MAZ, GenBank BAA33064.1. Antibody Target:MAZ

value: May function as a transcription factor with dual roles in transcription initiation and termination. Binds to two sites, ME1a1 and ME1a2, within the MYC promoter having greater affinity for the former. Also binds to multiple G/C-rich sites within the promoter of the Sp1 family of transcription factors.

value: Abcam

tag: control


title: Stanford_ChipSeq_SK-N-SH_SMC3_(ab9263)_IgG-rab

tag: lab

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

value: SK-N-SH

value: human

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: cancer

value: ectoderm

value: F

value: Rabbit polyclonal raised against synthetic peptide representing a portion within the last 100 amino acids of the human Structural Maintenance of Chromosomes-3 conjugated to KLH. Antibody Target:SMC3

tag: antibody targetdescription

value: Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex.  The cohesin complex is required for the cohesion of sister chromatids after DNA replication.

tag: antibody vendorname

tag: control description


title: Stanford_ChipSeq_IMR90_Mxi1_(AF4185)_IgG-rab

value: Stanford

value: Snyder - Stanford University

tag: datatype

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

tag: cell lineage

tag: cell sex

tag: antibody

value: Goat IgG. Raised against E. coli-derived rhMxi1. Antibody Target:Mxi1

value: Transcriptional repressor. Binds with MAX to form recognize the core sequence 5'-CAC[GA]TG-3', antagonizes MYC transcriptional activity by competing for MAX

value: R&D Systems

value: IgG-rab

value: Input signal from Normal Rabbit IgG ChIP-seq.


title: Zn13d_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (1 mg/L) for 13 days.

source_name: Pool of three oyster digestive gills, sampled at time 13d, Zn

tag: developmental stage

value: adult

tag: tissue

value: digestive gland

tag: exptl group

value: tissue


title: Zn7d_gills

description: Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (1 mg/L) for 7 days.

source_name: Pool of three oyster digestive gills, sampled at time 7d, Zn


title: Zn9d_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (1 mg/L) for 9 days.

source_name: Pool of three oyster digestive glands, sampled at time 9d, Zn


title: Zn13d_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (1 mg/L) for 13 days.

source_name: Pool of three oyster digestive glands, sampled at time 13d, Zn


title: Stanford_ChipSeq_K562_GATA1_(SC-266)_IgG-mus

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

value: leukemia, "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: mesoderm

tag: treatment

value: No special treatment or protocol applies

value: Rat monoclonal raised against bacterially expressed murine GATA-1. Antibody Target: GATA1

value: GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes.

value: Santa Cruz Biotech

tag: antibody vendorid

value: IgG-mus

value: Input signal from Normal Mouse IgG ChIP-seq.

tag: controlid


title: Stanford_ChipSeq_K562_c-Jun_IgG-rab

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

value: cancer

value: F

tag: treatment description

value: c-Jun

tag: antibody antibodydescription

value: Rabbit polyclonal to amino acids 1-79 mapping at the N-terminus of c-Jun p39 of human origin. Antibody Target:c-Jun

tag: antibody targetdescription

value: Heterodimer of Fos and Jun constitute transcription factor AP1.  Proto-oncogene c-Jun is a leucine-zipper.

tag: antibody vendorname

tag: control


title: Stanford_ChipSeq_K562_ELK1_(1277-1)_IgG-rab

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell karyotype

tag: cell lineage

tag: cell sex

tag: antibody

value: Rabbit polyclonal, a synthetic peptide corresponding to residues in C-terminus of human ELK-1 was used as immunogen. The antibody does not cross-react with other ETS family members. Antibody Target:ELK1

value: Elk-1 is a transcription factor that is part of the ets oncogene superfamily. Elk-1 forms a ternary complex with the serum response factors, SRE and SRF, mediating gene activity in response to serum and growth factors. Activation by several mitogen- activated protein kinases (Erk1 and Erk2) mediates the immediate early responses of the c-fos promoter to growth factors and other stimuli.

value: Epitomics

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: labversion


title: Zn7d_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (1 mg/L) for 7 days.

source_name: Pool of three oyster digestive glands, sampled at time 7d, Zn

tag: developmental stage

value: adult

tag: tissue

value: digestive gland

tag: exptl group

value: tissue


title: Stanford_ChipSeq_K562_ZNF-MIZD-CP1_(ab65767)_IgG-rab

tag: lab

value: Stanford

tag: datatype description

tag: cell

tag: cell organism

value: human

tag: cell description

value: leukemia, "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: mesoderm

tag: treatment

value: No special treatment or protocol applies

value: Rabbit Polyclonal against synthetic peptide conjugated to KLH derived from within residues 200 - 300 of Human Zinc finger MIZ domain-containing protein 1.

value: Zinc finger MIZ domain-containing protein 1 that increases ligand-dependent transcriptional activity of AR and promotes AR sumoylation. The stimulation of AR activity is dependent upon sumoylation.

value: Abcam

tag: antibody vendorid

tag: controlid


title: Zn5d_DG

description: Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (1 mg/L) for 5 days.

source_name: Pool of three oyster digestive glands, sampled at time 5d, Zn


title: Stanford_ChipSeq_A549_CTCF_(SC-15914)_IgG-rab

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

value: Chromatin IP Sequencing

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

value: endoderm

value: M

tag: treatment description

tag: antibody antibodydescription

value: Goat polyclonal, epitope mapping near the C-terminus of CTCF of human origin. Antibody Target:CTCF

tag: antibody targetdescription

value: Transcriptional regulator with 11 highly conserved zinc finger domains. Depending on context, can bind a histone acetyltransferase (HAT)-containing complex and function as transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as transcriptional repressor. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation. Can dimerize, mediating long-range chromatin looping. When bound to chromatin, provides an anchor point for nucleosomes positioning. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: control