title: C20_leaf_control-20d-rep3

description: mature leaf from a day 20 control plant

value: control

value: mature leaf


title: C20_leaf_control-20d-rep2

status: Public on Jul 26 2012

type: RNA

city: Pullman

first: Glenn

middle: W

last: Turner

state: WA

address: PO Box 646340, Washington State University

department: Institute of Biological Chemistry

country: USA

institute: Washington State University

description: mature leaf from a day 20 control plant

hyb_protocol: 15ug biotinylated cRNA hybridized for 16 hr at 45C in Affymetrix 640 hybridization oven at 50rpm

scan_protocol: Standard Affymetrix Scan on Affymetrix 7G scanner

data_processing: The data were analyzed using GeneChip Operating Software with affymetrix default  settings utilizing global scaling for normalization and a target intensity value of 125.

label: biotin

molecule: total RNA

organism: Glycine max

source_name: mature leaf

label_protocol: Standard Affymetrix one cycle labeling and fragmentation protocol

growth_protocol: Plants were grown in growth chambers, in 4-L pots, with a minimum ligh intensity of 360-400 umol m2/s, with 16h daylengths, and day/night temperatures of 25/18oC.

extract_protocol: RNA was extracted from leaf samples using a method developed for tissues containing abundant polysaccharides and polyphenols (Gehrig et al., 2000).  In addition, the extracted RNA was further purified using the RNeasy kit (Qiagen, Valencia, CA).

treatment_protocol: Soybean plants were cultivated in growth chambers for 30 days.  Experimental plants were then subjected to a daily removal of all axillary and terminal buds for a period of 15 days (designated D1-15; “Detip” period), while controls were left untreated (C0-15) through the same time period.  Following the Detip period, shoot tips on experimental plants were allowed to regrow for another 15 days (R16-30; “Retip” period) while control plants continued to be grown without treatment (C16-30).  Samples were collected at 5 day intervals, frozen in liquid nitrogen immediately after harvest, and stored at -80oC until further analysis.

tag: sample type

tag: tissue


title: Retina from control mouse at ZT20, biological rep 1

city: Bethesda

first: Margaret

last: Ochocinska

address: 49 Convent Dr. Rm.6A71

department: NICHD/PDEGEN

institute: National Institutes of Health

description:
CR_N1
Gene expression from the retina of a control mouse at ZT20.

hyb_protocol: GeneChip® One-Cycle Target Labeling from Affymetrix. Fluidics script EukGE_Ws2v5 was used with GeneChip® Fluidics Station 450.

scan_protocol: Affymetrix GCOS default settings and GeneChip Scanner 3000.

data_processing: GCOS software statistical algorithm (Affymetrix).

organism: Mus musculus

source_name: Control at ZT20, retina

label_protocol: Nugen Ovation RNA amplification system V2 and FL-Ovation cDNA Biotin Module V2.

growth_protocol: NeuroD1 conditional knockout (cKO) mice were generated by crossing NeuroD1flox/flox mice with NeuroD1+/flox::Crx-cre+/- mice to produce NeuroD1flox/flox/Crx-cre+/- (cKO) mice and  NeuroD1flox/flox::Crx-cre-/- (CON) mice. CON and cKO mice (both genders, 2 months of age) were bred and housed in LD 12:12 light cycles with food and water ad libitum.

extract_protocol: Total mouse pineal and retina RNA was isolated using the RNeasy Micro RNA isolation kit (Qiagen).

treatment_protocol: Pineal glands and retinas were collected during the day (ZT6) and night (ZT20). 6 pineal glands or retinas were pooled per sample. ZT20 samples were collected under dim red lighting conditions.

tag: strain

value: C57BL/6J; NeuroD1flox::Crx-Cre-/-

tag: genotype

tag: age

value: 2 months

value: retina

tag: time


title: HC-45

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were quantile normalized using Matlab software

label: biotin / SA-Cy3

organism: Homo sapiens

source_name: PBMC

label_protocol: 300 ng of total RNA from each sample was labeled using the Illumina Total Prep RNA Amplification Kit following manufacturer's directions (Ambion)

extract_protocol: Total RNA was isolated from frozen PBMCs using QIAshredder columns for cell homogenization followed by use of the RNeasy Micro Kit.  DNA was eliminated through on-column DNase I treatment according to the manufacturer’s directions (Qiagen).

treatment_protocol: Whole blood was drawn into BD Vacutainer K2EDTA tubes. PBMCs were isolated over a Ficoll-paque Plus density gradient.  PBMCs were frozen in FBS and 10% DMSO and stored in liquid nitrogen.

tag: disease

value: healthy control

value: PBMC


title: MDD-395

value: major depressive disorder


title: C20_leaf_control-20d-rep1

description: mature leaf from a day 20 control plant


title: D15_leaf_detip-15d-rep1

description: mature leaf from a detip plant after 15 days of vegetative bud removal

value: bud removal


title: Retina from control mouse at ZT6, biological rep 1

description:
CR_D1
Gene expression from the retina of a control mouse at ZT6.

source_name: Control at ZT6, retina


title: sALS mRNA subject-10

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

description: Nanostring  GX Human Immunology and Nanostring Human Inflammation assays detected RNAs in sorted CD14+/CD16- blood-derived monocytes (RNA transcriptom per 100 ng total RNA)

hyb_protocol: Hybrdization reactions were performed according to the manufacturer's instructions (NanoString.com) with 5 µl of the sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions.  For each assay, a high-density scan (600 fields of view) was performed

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using vsn normalization

source_name: CD14+CD16- monocytes

label_protocol: 100 ng of total RNA was used in 5 µl with specific mRNA tag probes from Nanostring using the Nanostring  GX Human Immunology and Nanostring Human Inflammation assays

extract_protocol: Blood monocytes were sorted and total RNA was extracted using mirVana RNA isolation kit (Ambion) according to the manufacturer’s protocol

tag: cell type

value: CD14+CD16- monocytes

value: 78 years

tag: Sex

value: Male

tag: disease state

value: Sporadic amyotrophic lateral sclerosis (SALS)

tag: ethnicity

value: Non-hispanic

tag: onset site

value: both limbs

tag: fvc

tag: alsfrs


title: D15_leaf_detip-15d-rep2


title: sALS mRNA subject-9

value: 59 years

value: limb


title: sALS mRNA subject-8

value: 62 years

value: U


title: sALS mRNA subject-7

value: 58 years

value: Female


title: Pineal gland from NeuroD1 cKO mouse at ZT20, biological rep 2

description:
TP_N2
Gene expression from the pineal gland of a NeuroD1 cKO mouse at ZT20.

source_name: NeuroD1 cKO at ZT20, pineal gland

value: C57BL/6J; NeuroD1flox::Crx-Cre+/-

value: NeuroD1 cKO

value: 2 months

value: pineal gland


title: BD2-282

value: bipolar disorder

value: PBMC


title: sALS mRNA subject-6

value: CD14+CD16- monocytes

value: 50 years


title: C15_leaf_control_15d-rep2

description: mature leaf from a day 15 control plant

value: control

value: mature leaf


title: D15_leaf_detip-15d-rep3

value: bud removal


title: Retina from control mouse at ZT6, biological rep 2

description:
CR_D2
Gene expression from the retina of a control mouse at ZT6.

value: C57BL/6J; NeuroD1flox::Crx-Cre-/-

value: retina


title: MDD-329

value: major depressive disorder


title: C15_leaf_control_15d-rep1

description: mature leaf from a day 15 control plant


title: MDD-397


title: BD1-351


title: HC-284

value: healthy control


title: C15_leaf_control_15d-rep3

description: mature leaf from a day 15 control plant


title: MDD-456


title: MDD-425


title: sALS mRNA subject-4

value: 68 years

value: Sporadic amyotrophic lateral sclerosis (SALS)

value: Non-hispanic

value: limb


title: sALS mRNA subject-5

value: 56 years

value: Male


title: C0_leaf_control_0d-rep4

description: mature leaf from a day 0 control plant


title: Pineal gland from NeuroD1 cKO mouse at ZT20, biological rep 1

description:
TP_N1
Gene expression from the pineal gland of a NeuroD1 cKO mouse at ZT20.

value: C57BL/6J; NeuroD1flox::Crx-Cre+/-

value: NeuroD1 cKO

value: 2 months

value: pineal gland


title: Pineal gland from NeuroD1 cKO mouse at ZT6, biological rep 3

description:
TP_D3
Gene expression from the pineal gland of a NeuroD1 cKO mouse at ZT6.

source_name: NeuroD1 cKO at ZT6, pineal gland


title: HC-3

value: PBMC


title: C0_leaf_control_0d-rep3

description: mature leaf from a day 0 control plant

value: control

value: mature leaf


title: sALS mRNA subject-3

value: CD14+CD16- monocytes

value: 61 years


title: Pineal gland from NeuroD1 cKO mouse at ZT6, biological rep 2

description:
TP_D2
Gene expression from the pineal gland of a NeuroD1 cKO mouse at ZT6.


title: HC-365


title: C0_leaf_control_d0-rep1

description: mature leaf from a day 0 control plant


title: sALS mRNA subject-1

value: 48 years

value: Female


title: Pineal gland from NeuroD1 cKO mouse at ZT6, biological rep 1

description:
TP_D1
Gene expression from the pineal gland of a NeuroD1 cKO mouse at ZT6.


title: BD2-231

value: bipolar disorder


title: C0_leaf_control_0d-rep2

description: mature leaf from a day 0 control plant


title: HC-513

value: healthy control


title: Pineal gland from control mouse at ZT20, biological rep 3

description:
CP_N3
Gene expression from the pineal gland of a control mouse at ZT20.

source_name: Control at ZT20, pineal gland

value: C57BL/6J; NeuroD1flox::Crx-Cre-/-


title: MDD-465

value: major depressive disorder


title: S2 SMC1 ChIP-chip

type: genomic

city: Rotterdam

first: Yuri

last: Moshkin

address: Dr. Molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center

description:
SMC1 ChIP S2 cells Biological Rep 1-2.

Input/Mock-ChIP DNA (control) CEL files:
S2_input_1.CEL
S2_input_2.CEL
S2_input_3.CEL
S2_input_4.CEL
S2_input_5.CEL
S2_mock_ChIP_1.CEL
S2_mock_ChIP_2.CEL
S2_mock_ChIP_3.CEL
S2_mock_ChIP_4.CEL
S2_mock_ChIP_5.CEL
S2_mock_ChIP_6.CEL
S2_mock_ChIP_7.CEL
S2_mock_ChIP_8.CEL
S2_mock_ChIP_9.CEL
S2_mock_ChIP_10.CEL

hyb_protocol: according to the manufacturer protocols

scan_protocol: according to the manufacturer protocols

data_processing:
ChIP-chip hybridization intensities scanned from Drosophila tiling 2.0R arrays were analyzed using R and R/Bioconductor packages. In brief, log2-scaled ratios of ChIP hybridization profiles to input DNA hybridization profile were quantile normalized and averaged for each antibody ChIP-chip profile. The same was done for the Mock ChIP hybridization intensities, and both ChIP and Mock ratios to input were scaled by the median. To obtain ChIP-chip enrichment score Mock/input ratio was subtracted from ChIP/input ratio. We noted that input DNA hybridization profile provides only a minor correction to the resulting ChIP score. For each antibody we perform 2 independent biological replicates. Peaks were selected based on random permutations at false discovery rate (FDR) < 0.01 using algorithm described by Simonis et al., 2006 and some of the selected sites were verified by ChIP-qPCR analysis. Cohesin binding sites were obtained by intersecting SA and SMC1 filtered sites.
Results file descriptions:
1) bar files contain ChIP.score calculated for each antibody.
2) sgr files contain chromosome, position and ChIP.score.
3) bed files contain binding sites selected at false discovery rate (FDR) of < 0.01.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2 SMC1 ChIP DNA

label_protocol: according to the manufacturer protocols

growth_protocol: Drosophila S2 cells were cultured in Schneider's media (Invitrogen 21720-024) supplied with 10% FBS and Penicillin/Streptomycin mixture at 25°C

extract_protocol: The following antibodies were used: anti-NAP1 (Moshkin et al., 2009), anti-SA (12-312 aa) and anti-SMC1 (a gift from D. Dorsette). Log-phase S2 cells were fixed for 10 min with 1% formaldehyde. Fixation was stopped by 125 mM glycine, cells were washed with PBS and resuspended in ice-cold L buffer (1% sodium dodecyl sulfate, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, 0.5 mM phenylmethylsulfonyl fluoride - PMSF, and 100 ng/ml of leupeptin and aprotinin). Cross-linked chromatin was sonicated to an apparent length of ~500 bp. 100 mkg of cross-linked chromatin was diluted with 9 volumes of buffer D (150 mM NaCl, 20 mM Tris-HCl pH8.1, 2 mM EDTA pH8.0, 1% Triton-X100, 0.5 mM PMSF, and 100 ng/ml of leupeptin and aprotinin), pre-cleared with 10 mkl (bed volume) protein A agarose blocked with salmon sperm DNA (16-157, Upstate), incubated ON at 4°C with ~10 mkl of appropriate antibodies, followed by 1 hr incubation with 20 mkl of pre-blocked protein A agarose. For Mock ChIP, chromatin was incubated with 10 mkl of preimmune serum. Beads were washed 5x with buffer W (20 mM Tris-HCl pH 8.1, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5 mM PMSF, and 100 ng/ml of leupeptin and aprotinin) containing 150 mM NaCl, and 1 x with buffer W/500 mM NaCl. DNA was eluted with 250 mkl buffer E (1% SDS, 0.1 M NaHCO3, 500 mkg/ml Proteinase K) for 2 hrs at 37°C and overnight at 65°C. DNA was then extracted with QIAquick PCR purification kit (Qiagen Cat. 28106). Isolated DNA was amplified with REPLI-g (Qiagen Cat. 150025), digested with DNase, labeled and hybridized on Affymetrix Drosophila tiling 2.0R arrays.

tag: cell line

value: S2 cells

tag: chip antibody

value: SMC1 rabbit polyclonal (from D. Dorsette)

source_name: Input/Mock-ChIP DNA

value: Mock ChIPs were performed with preimmune serum (preimmune) or protein A beads (protA)


title: S2 SA ChIP-chip

description:
SA Ab1 ChIP S2 cells Biological Rep 1-3.

Input/Mock-ChIP DNA (control) CEL files:
S2_input_1.CEL
S2_input_2.CEL
S2_input_3.CEL
S2_input_4.CEL
S2_input_5.CEL
S2_mock_ChIP_1.CEL
S2_mock_ChIP_2.CEL
S2_mock_ChIP_3.CEL
S2_mock_ChIP_4.CEL
S2_mock_ChIP_5.CEL
S2_mock_ChIP_6.CEL
S2_mock_ChIP_7.CEL
S2_mock_ChIP_8.CEL
S2_mock_ChIP_9.CEL
S2_mock_ChIP_10.CEL

source_name: S2 SA ChIP DNA

value: SA rabbit polyclonal (against 12-312 aa; in-house)


title: S2 NAP1 ChIP-chip

description:
NAP1 ChIP S2 cells Biological Rep 1-2.

Input/Mock-ChIP DNA (control) CEL files:
S2_input_1.CEL
S2_input_2.CEL
S2_input_3.CEL
S2_input_4.CEL
S2_input_5.CEL
S2_mock_ChIP_1.CEL
S2_mock_ChIP_2.CEL
S2_mock_ChIP_3.CEL
S2_mock_ChIP_4.CEL
S2_mock_ChIP_5.CEL
S2_mock_ChIP_6.CEL
S2_mock_ChIP_7.CEL
S2_mock_ChIP_8.CEL
S2_mock_ChIP_9.CEL
S2_mock_ChIP_10.CEL

source_name: S2 NAP1 ChIP DNA

value: NAP1 rabbit polyclonal (Moshkin et al., 2009)


title: sALS mRNA subject-2

value: Male

value: Sporadic amyotrophic lateral sclerosis (SALS)

value: Non-hispanic

value: limb


title: Pineal gland from control mouse at ZT20, biological rep 1

description:
CP_N1
Gene expression from the pineal gland of a control mouse at ZT20.

value: control

value: 2 months

value: pineal gland


title: HC-104

value: PBMC


title: Pineal gland from control mouse at ZT6, biological rep 2

description:
CP_D2
Gene expression from the pineal gland of a control mouse at ZT6.

source_name: Control at ZT6, pineal gland


title: Soybean_PP1_rep1

description: Gene expression within paraveinal mesophyll cells of mature soybean leaves.

label: Biotin

source_name: palisade mesophyll parenchyma cells

growth_protocol: Plants were grown in growth chambers in 4-L pots in growth chambers, with 16 hour day-lengths and 8 hour night  periods.   The daytime temperature was set to 25 oC. The night time temperature was 18oC. The minimum light intensity was 360-400 umol m2/s.

extract_protocol: Soybean leaves were fixed with 5:1 ethanol: acetic acid, embedded in low-temp paraffin, and sectioned before used for laser microdissection. RNA was extracted from the laser-microdissected cells using Qiagen Micro Rneasy kit.

treatment_protocol: None, untreated plants were used.

value: palisade mesophyll chlorenchyma


title: Soybean_PP1_rep3


title: Soybean_PP1_rep2


title: HC mRNA subject-3

value: CD14+CD16- monocytes

value: 40 years

value: Healthy control


title: HC-261

value: healthy control


title: Soybean_PVM_rep3

source_name: paraveinal mesophyll cells

value: paraveinal mesophyll cells


title: Pineal gland from control mouse at ZT6, biological rep 3

description:
CP_D3
Gene expression from the pineal gland of a control mouse at ZT6.

value: C57BL/6J; NeuroD1flox::Crx-Cre-/-


title: Pineal gland from control mouse at ZT20, biological rep 2

description:
CP_N2
Gene expression from the pineal gland of a control mouse at ZT20.


title: Soybean_PVM_rep2


title: Retina from control mouse at ZT6, biological rep 3

description:
CR_D3
Gene expression from the retina of a control mouse at ZT6.

value: retina


title: MDD-376

value: major depressive disorder


title: Soybean_PVM_rep1


title: H3K36A H3 IP Replicate 1

status: Public on Jul 25 2012

city: Kansas City

first: Swaminathan

last: Venkatesh

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

description: Biological Replicate 1 of 3 ChIP enrichment of AcH4 IP over Input in the WT BY4741 strain

hyb_protocol: The hybridization mixture (Oligo CGH/Chip-on-chip hybridization kit, Agilent) was prepared according to manufacturer’s instructions with the addition of 20 ug of T7 blocking oligo (ttt ttt ttt ttt tt cac gcg tct ccc) , and hybridized overnight at 65C. Microarrays were washed using the Oligo aCCH/Chip-on-chip Wash buffers (Agilent) according to  manufacturer’s instructions.

scan_protocol: Scanned on Agilent Technologies Scanner G2505C US45102919 Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Data processed on R. Median normalization carried out.

organism: Saccharomyces cerevisiae

source_name: IP DNA H3 antibody

label_protocol: Briefly, up to 50 ng of IP or input DNA was treated with 2.5 U CIP enzyme (NEB) for 1 hour at 37C, followed by phenol:chloroform extraction and ethanol precipitation. The CIP-treated template was incubated with 20 U TdT (NEB) for 20 minutes at 37C for T-tailing the ends, and the product isolated with the MinElute Reaction Cleanup Kit (Qiagen). An anchored T7 promoter-(dA)18 oligo was added by annealing and filling with 5 U Exo- Klenow (NEB) for 4 hours at 37C, followed by phenol:chloroform extraction and ethanol precipitation. In vitro transcription was performed at 37C overnight using the Ampliscribe T7 transcription kit (Epicentre Biotechnologies). RNAs purified using the RNeasy Mini Kit (Qiagen) and quantified on a Nanodrop 2000 Spectrophotometer (Thermo Scientific). For the second round amplification, 100–150 ng of RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen) and purified with the MinElute Reaction Cleanup Kit (Qiagen). The T7 promoter primer was added to the product through a Klenow filling reaction as described above, followed by in vitro transcription with amino allyl-UTP (Ambion) instead of UTP. Final reaction cleanup was performed with the RNeasy Mini Kit (Qiagen). For the labeling reactions, 8 ug of amino allyl-incorporated RNA in a 5 uL volume of 0.1 M Carbonate Buffer, pH 8.7, was mixed with 5 uL (0.01 nmol) Cy3 or Cy5 dye (GE Healthcare) in DMSO (Sigma) and incubated at room temperature for 2 hours. Reactions were quenched with 5 uL 4 M hydroxylamine at room temperature for 15 minutes, purified by RNeasy MinElute Cleanup Kit (Qiagen), and the dye incorporation measured using the Nanodrop 2000 (Thermo Scientific). 2.5-4 ug of input and IP were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate histone H3K56 acetylated nucleosomes. The immune complexes were pulled down with 50 ml of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with250mM NaCl). The eluates were RNase treated and Proteinase K was added to remove the bound proteins. Crosslinks were reversed by incubating at 65 C overnight. Samples werte phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase step.

value: anti H3

source_name: Input DNA


title: H3K36A H3K56ac IP Replicate 1

source_name: IP DNA H3K56ac antibody

value: anti-acetyl-Histone H3

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #


title: set2 Ioc3 Flag-IP Replicate 1

first: Michaela

last: Smolle

state: Missouri

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG-IP over Input in the YMS114 IOC3-3xFLAG set2 strain.

hyb_protocol: The hybridization mixture (Oligo CGH/Chip-on-chip hybridization kit, Agilent) was prepared according to manufacturer’s instructions with the addition of 20 ug of T7 blocking oligo (ttt ttt ttt ttt tt cac gcg tct ccc), and hybridized overnight at 65°C. Microarrays were washed using the Oligo aCCH/Chip-on-chip Wash buffers (Agilent) according to  manufacturer’s instructions.

data_processing: Data processed in R (version 2.12.1) using Bioconductor MEDIAN normalization (within arrays) and SCALE normalization (between arrays).

source_name: IP DNA FLAG antibody

label_protocol: Briefly, 50 ng of IP or input DNA were treated with 2.5 U CIP enzyme (NEB) for 1 hour at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. The CIP-treated template was incubated with 20 U TdT (NEB) for 20 minutes at 37°C for T-tailing the ends, and the product isolated with the MinElute Reaction Cleanup Kit (Qiagen). An anchored T7 promoter-(dA)18 oligo was added by annealing and filling with 5 U Exo- Klenow (NEB) for 4 hours at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. In vitro transcription was performed at 37°C overnight using the Ampliscribe T7 transcription kit (Epicentre Biotechnologies). RNAs purified using the RNeasy Mini Kit (Qiagen) and quantified on a Nanodrop 2000 Spectrophotometer (Thermo Scientific). For the second round amplification, 100 ng of RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen) and purified with the MinElute Reaction Cleanup Kit (Qiagen). The T7 promoter primer was added to the product through a Klenow filling reaction as described above, followed by in vitro transcription with amino allyl-UTP (Ambion) instead of UTP. Final reaction cleanup was performed with the RNeasy Mini Kit (Qiagen). For the labeling reactions, 8 ug of amino allyl-incorporated RNA in a 5 uL volume of 0.1 M Carbonate Buffer, pH 8.7, was mixed with 5 uL (0.01 nmol) Cy3 or Cy5 dye (GE Healthcare) in DMSO (Sigma) and incubated at room temperature for 2 hours. Reactions were quenched with 5 uL 4 M hydroxylamine at room temperature for 15 minutes, purified by RNeasy MinElute Cleanup Kit (Qiagen), and the dye incorporation measured using the Nanodrop 2000 (Thermo Scientific). 4ug of input and IP were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.

growth_protocol: These strains were grown in YPD to an OD of 1.0. Cells were cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate 3xFLAG tagged Ioc4 or Ioc3 (2 ul αFLAG per IP).

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate FLAG-tagged Ioc4 or Ioc3. The immune complexes were pulled down with 50 ul of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with 250mM NaCl). The eluates were RNase A treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65 C overnight. Samples were phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase A step.

tag: antibody

value: Flag M2

tag: vendor

value: Sigma #F1804


title: Pineal gland from control mouse at ZT6, biological rep 1

description:
CP_D1
Gene expression from the pineal gland of a control mouse at ZT6.

tag: strain

tag: genotype

value: control

value: 2 months

tag: tissue


title: WT H3 IP Replicate 1

value: wild type


title: set2 Ioc4 Flag-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG-IP over Input in the YMS087 IOC4-3xFLAG set2 strain.


title: Pineal gland from NeuroD1 cKO mouse at ZT20, biological rep 3

description:
TP_N3
Gene expression from the pineal gland of a NeuroD1 cKO mouse at ZT20.

value: C57BL/6J; NeuroD1flox::Crx-Cre+/-

value: NeuroD1 cKO

tag: age

value: pineal gland

tag: time


title: WT H3 IP Replicate 2

description: Biological Replicate 2 of 3 ChIP enrichment of AcH4 IP over Input in the WT BY4741 strain


title: WT H3K36me3 IP Replicate 2

source_name: IP DNA H3K36me3 antibody

label_protocol: Briefly, up to 50 ng of IP or input DNA was treated with 2.5 U CIP enzyme (NEB) for 1 hour at 37C, followed by phenol:chloroform extraction and ethanol precipitation. The CIP-treated template was incubated with 20 U TdT (NEB) for 20 minutes at 37C for T-tailing the ends, and the product isolated with the MinElute Reaction Cleanup Kit (Qiagen). An anchored T7 promoter-(dA)18 oligo was added by annealing and filling with 5 U Exo- Klenow (NEB) for 4 hours at 37C, followed by phenol:chloroform extraction and ethanol precipitation. In vitro transcription was performed at 37C overnight using the Ampliscribe T7 transcription kit (Epicentre Biotechnologies). RNAs purified using the RNeasy Mini Kit (Qiagen) and quantified on a Nanodrop 2000 Spectrophotometer (Thermo Scientific). For the second round amplification, 100–150 ng of RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen) and purified with the MinElute Reaction Cleanup Kit (Qiagen). The T7 promoter primer was added to the product through a Klenow filling reaction as described above, followed by in vitro transcription with amino allyl-UTP (Ambion) instead of UTP. Final reaction cleanup was performed with the RNeasy Mini Kit (Qiagen). For the labeling reactions, 8 ug of amino allyl-incorporated RNA in a 5 uL volume of 0.1 M Carbonate Buffer, pH 8.7, was mixed with 5 uL (0.01 nmol) Cy3 or Cy5 dye (GE Healthcare) in DMSO (Sigma) and incubated at room temperature for 2 hours. Reactions were quenched with 5 uL 4 M hydroxylamine at room temperature for 15 minutes, purified by RNeasy MinElute Cleanup Kit (Qiagen), and the dye incorporation measured using the Nanodrop 2000 (Thermo Scientific). 2.5-4ug of input and IP were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.

growth_protocol: These strains were grown in YPD to an OD of 0.6. a-factor was added to a final concentration of 1 mM and the cells were grown for an additional 4 hrs. Cells were cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate H3 K36 me3 (2 ul per IP, Abcam ab9050).

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate histone H3K36 trimethylated nucleosomes. The immune complexes were pulled down with 50 ml of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with250mM NaCl). The eluates were RNase treated and Proteinase K was added to remove the bound proteins. Crosslinks were reversed by incubating at 65 C overnight. Samples werte phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase step.

value: anti H3 K36 me3

value: Abcam


title: WT Ioc3 Flag-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG-IP over Input in the YMS099 IOC3-3xFLAG strain.


title: WT H3K36me3 IP Replicate 3

description: Biological Replicate 3 of 3 ChIP enrichment of AcH4 IP over Input in the WT BY4741 strain


title: WT H3K56ac IP Replicate 2


title: set2 Ioc3 Flag-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of FLAG-IP over Input in the YMS114 IOC3-3xFLAG set2 strain.


title: H3K36A H3 IP Replicate 3


title: H3K36A H3 IP Replicate 2


title: set2 Ioc3 Flag-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG-IP over Input in the YMS114 IOC3-3xFLAG set2 strain.


title: WT H3K56ac IP Replicate 3


title: H3K36A H3K56ac IP Replicate 2


title: H3K36A H3K56ac IP Replicate 3


title: WT H3K36me3 IP Replicate 1


title: WT Ioc3 Flag-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of FLAG-IP over Input in the YMS099 IOC3-3xFLAG strain.


title: WT Ioc3 Flag-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG-IP over Input in the YMS099 IOC3-3xFLAG strain.


title: WT H3 IP Replicate 3


title: WT H3K56ac IP Replicate 1


title: set2 Ioc4 Flag-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG-IP over Input in the YMS087 IOC4-3xFLAG set2 strain.


title: set2 Ioc4 Flag-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of FLAG-IP over Input in the YMS087 IOC4-3xFLAG set2 strain.


title: WT Ioc4 Flag-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG-IP over Input in the YMS079 IOC4-3xFLAG strain.


title: WT Ioc4 Flag-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG-IP over Input in the YMS079 IOC4-3xFLAG strain.


title: WT Ioc4 Flag-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of FLAG-IP over Input in the YMS079 IOC4-3xFLAG strain.


title: ASF1SET2 deletion AcH4 IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4 IP over Input in the ASF1SET2 deletion BY4741 strain.

hyb_protocol: The hybridization mixture (Oligo CGH/Chip-on-chip hybridization kit, Agilent) was prepared according to manufacturer’s instructions with the addition of 20 ug of T7 blocking oligo (ttt ttt ttt ttt tt cac gcg tct ccc) , and hybridized overnight at 65°C. Microarrays were washed using the Oligo aCCH/Chip-on-chip Wash buffers (Agilent) according to  manufacturer’s instructions.

data_processing: Data processed in GeneSpring

source_name: ASF1SET2 deletion AcH4 IP

label_protocol: Briefly, up to 50 ng of IP or input DNA was treated with 2.5 U CIP enzyme (NEB) for 1 hour at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. The CIP-treated template was incubated with 20 U TdT (NEB) for 20 minutes at 37°C for T-tailing the ends, and the product isolated with the MinElute Reaction Cleanup Kit (Qiagen). An anchored T7 promoter-(dA)18 oligo was added by annealing and filling with 5 U Exo- Klenow (NEB) for 4 hours at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. In vitro transcription was performed at 37°C overnight using the Ampliscribe T7 transcription kit (Epicentre Biotechnologies). RNAs purified using the RNeasy Mini Kit (Qiagen) and quantified on a Nanodrop 2000 Spectrophotometer (Thermo Scientific). For the second round amplification, 100–150 ng of RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen) and purified with the MinElute Reaction Cleanup Kit (Qiagen). The T7 promoter primer was added to the product through a Klenow filling reaction as described above, followed by in vitro transcription with amino allyl-UTP (Ambion) instead of UTP. Final reaction cleanup was performed with the RNeasy Mini Kit (Qiagen). For the labeling reactions, 8 ug of amino allyl-incorporated RNA in a 5 uL volume of 0.1 M Carbonate Buffer, pH 8.7, was mixed with 5 uL (0.01 nmol) Cy3 or Cy5 dye (GE Healthcare) in DMSO (Sigma) and incubated at room temperature for 2 hours. Reactions were quenched with 5 uL 4 M hydroxylamine at room temperature for 15 minutes, purified by RNeasy MinElute Cleanup Kit (Qiagen), and the dye incorporation measured using the Nanodrop 2000 (Thermo Scientific). 2.5-4µgg of input and IP were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate acetylated H4 and histone H3. The immune complexes were pulled down with 50 ml of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with250mM NaCl). The eluates were RNase treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65 C overnight. Samples werte phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase step.


title: ASF1 AcH4 IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4 IP over Input in the ASF1 BY4741 strain.

source_name: ASF1 AcH4 IP


title: ASF1SET2 deletion AcH4 IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4 IP over Input in the ASF1SET2 deletion BY4741 strain.


title: ASF1 H3 IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of H3 IP over Input in the ASF1 BY4741 strain.

source_name: ASF1 H3 IP


title: ASF1SET2 deletion H3 IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of H3 IP over Input in the ASF1SET2 deletion BY4741 strain.

source_name: ASF1SET2 deletion H3 IP


title: ASF1 H3 IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of H3 IP over Input in the ASF1 BY4741 strain.


title: ASF1SET2 deletion AcH4 IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of AcH4 IP over Input in the ASF1SET2 deletion BY4741 strain.


title: ASF1SET2 deletion H3 IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of H3 IP over Input in the ASF1SET2 deletion BY4741 strain.


title: SET2 deletion AcH4 IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of AcH4 IP over Input in the SET2 deletion BY4741 strain.

source_name: SET2 deletion AcH4 IP


title: SET2 deletion AcH4 IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4 IP over Input in the SET2 deletion BY4741 strain.


title: ASF1 AcH4 IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of AcH4 IP over Input in the ASF1 BY4741 strain.


title: WT AcH4 IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4 IP over Input in the WT BY4741 strain.

source_name: WT AcH4 IP


title: WT AcH4 IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of AcH4 IP over Input in the WT BY4741 strain.


title: ASF1 H3 IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of H3 IP over Input in the ASF1 BY4741 strain.


title: SET2 deletion H3 IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of H3 IP over Input in the SET2 deletion BY4741 strain.

source_name: SET2 deletion H3 IP

growth_protocol: These strains were grown in YPD to an OD of 0.6. a-factor was added to a final concentration of 1 mM and the cells were grown for an additional 4 hrs. Cells were cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate H3 K56ac (2 ul per IP), H3 K9ac (2 ul per IP), H4 K12ac (2 ul per IP), H3 (2 ul per IP).

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate H3K9ac, H3K56ac, H4K12ac and histone H3. The immune complexes were pulled down with 50 ml of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with250mM NaCl). The eluates were RNase treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65 C overnight. Samples werte phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase step.


title: SET2 deletion AcH4 IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4 IP over Input in the SET2 deletion BY4741 strain.


title: ASF1SET2 deletion H3 IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of H3 IP over Input in the ASF1SET2 deletion BY4741 strain.


title: WT H3 IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of H3 IP over Input in the WT BY4741 strain.

source_name: WT H3 IP


title: SET2 deletion H3 IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of H3 IP over Input in the SET2 deletion BY4741 strain.


title: WT H3 IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of H3 IP over Input in the WT BY4741 strain.


title: SET2 deletion H3 IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of H3 IP over Input in the SET2 deletion BY4741 strain.


title: SET2 deletion H4K12ac IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of H4K12ac IP over Input in the SET2 deletion BY4741 strain.

source_name: SET2 deletion H4K12ac IP


title: WT H3 IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of H3 IP over Input in the WT BY4741 strain.


title: WT H4K12ac IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of H4K12ac IP over Input in the WT BY4741 strain.

source_name: WT H4K12ac IP


title: SET2 deletion H4K12ac IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of H4K12ac IP over Input in the SET2 deletion BY4741 strain.


title: WT H4K12ac IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of H4K12ac IP over Input in the WT BY4741 strain.


title: WT H3K56ac IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of H3K56ac IP over Input in the WT BY4741 strain.

source_name: WT H3K56ac IP


title: SET2 deletion H3K9ac IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of H3K9ac IP over Input in the SET2 deletion BY4741 strain.

source_name: SET2 deletion H3K9ac IP


title: WT H3K56ac IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of H3K56ac IP over Input in the WT BY4741 strain.


title: SET2 deletion H3K56ac IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of H3K56ac IP over Input in the SET2 deletion BY4741 strain.

source_name: SET2 deletion H3K56ac IP


title: WT H4K12ac IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of H4K12ac IP over Input in the WT BY4741 strain.

source_name: Input DNA


title: WT H3K9ac IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of H3K9ac IP over Input in the WT BY4741 strain.

source_name: WT H3K9ac IP


title: SET2 deletion H3K9ac IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of H3K9ac IP over Input in the SET2 deletion BY4741 strain.


title: SET2 deletion H3K56ac IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of H3K56ac IP over Input in the SET2 deletion BY4741 strain.


title: WT AcH4 IP Replicate 3 (MDY510)

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4 IP over Input in the WT exchange strain.

growth_protocol: The exchange strains were grown in YP + 2% raffinose at 25°C to an OD of 0.5. a-factor was added to a final concentration of 1 mM and the cells were grown in raffinose containing medium for an additional 4 hrs. After the a-factor arrest, cells were collected washed in 1x PBS with protease inhibitors, resuspended and grown in YP + 2% galactose with 1 mM a-factor at 25°C for 45 min. Cells were cross-linked with 1% formaldehyde at room temperature for 15 min. with continuous shaking. The reaction was quenched by adding glycine to a final concentration of 125mM. Cells were collected by centrifugation and processed for the ChIP assay

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate Flag, Myc and acetylated H4. The immune complexes were pulled down with 50 ml of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with250mM NaCl). The eluates were RNase treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65 C overnight. Samples werte phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase step.

value: Exchange strain MDY510


title: WT H3K9ac IP Replicate 2 (BY4741)

description: Biological Replicate 2 of 3. ChIP enrichment of H3K9ac IP over Input in the WT BY4741 strain.


title: SET2 deletion H3K56ac IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of H3K56ac IP over Input in the SET2 deletion BY4741 strain.


title: WT H3K56ac IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of H3K56ac IP over Input in the WT BY4741 strain.


title: WT H3K9ac IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of H3K9ac IP over Input in the WT BY4741 strain.


title: SET2 deletion H3K9ac IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of H3K9ac IP over Input in the SET2 deletion BY4741 strain.


title: SET2 deletion AcH4 IP Replicate 3 (MDY510)

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4 IP over Input in the SET2 deletion exchange strain.


title: SET2 deletion AcH4 IP Replicate 2 (MDY510)

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4 IP over Input in the SET2 deletion exchange strain.


title: SET2 deletion myc IP Replicate 1 (MDY510)

description: Biological Replicate 1 of 3. ChIP enrichment of Myc IP over Input in the SET2 deletion exchange strain.

source_name: SET2 deletion myc IP

value: Myc


title: SET2 deletion AcH4 IP Replicate 1 (MDY510)

description: Biological Replicate 1 of 3. ChIP enrichment of AcH4 IP over Input in the SET2 deletion exchange strain.


title: WT myc IP Replicate 3 (MDY510)

description: Biological Replicate 3 of 3. ChIP enrichment of Myc IP over Input in the WT exchange strain.

source_name: WT myc IP


title: WT AcH4 IP Replicate 2 (MDY510)

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4 IP over Input in the WT exchange strain.


title: WT AcH4 IP Replicate 1 (MDY510)

description: Biological Replicate 1 of 3. ChIP enrichment of AcH4 IP over Input in the WT exchange strain.


title: SET2 deletion myc IP Replicate 3 (MDY510)

description: Biological Replicate 3 of 3. ChIP enrichment of Myc IP over Input in the SET2 deletion exchange strain.


title: SET2 deletion myc IP Replicate 2 (MDY510)

description: Biological Replicate 2 of 3. ChIP enrichment of Myc IP over Input in the SET2 deletion exchange strain.


title: WT myc IP Replicate 2 (MDY510)

description: Biological Replicate 2 of 3. ChIP enrichment of Myc IP over Input in the WT exchange strain.


title: WT myc IP Replicate 1 (MDY510)

description: Biological Replicate 1 of 3. ChIP enrichment of Myc IP over Input in the WT exchange strain.


title: SET2 deletion Flag IP Replicate 2 (MDY510)

description: Biological Replicate 2 of 3. ChIP enrichment of Flag IP over Input in the SET2 deletion exchange strain.

source_name: SET2 deletion Flag IP

value: Flag


title: SET2 deletion Flag IP Replicate 1 (MDY510)

description: Biological Replicate 1 of 3. ChIP enrichment of Flag IP over Input in the SET2 deletion exchange strain.


title: WT Flag IP Replicate 2 (MDY510)

description: Biological Replicate 2 of 3. ChIP enrichment of Flag IP over Input in the WT exchange strain.

source_name: WT Flag IP


title: SET2 deletion Flag IP Replicate 3 (MDY510)

description: Biological Replicate 3 of 3. ChIP enrichment of Flag IP over Input in the SET2 deletion exchange strain.


title: WT Flag IP Replicate 1 (MDY510)

description: Biological Replicate 1 of 3. ChIP enrichment of Flag IP over Input in the WT exchange strain.


title: WT Flag IP Replicate 3 (MDY510)

description: Biological Replicate 3 of 3. ChIP enrichment of Flag IP over Input in the WT exchange strain.


title: WT AcH4 IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4 IP over Input in the WT BY4741 strain.


title: ASF1 AcH4 IP Replicate 3 (BY4741)

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4 IP over Input in the ASF1 BY4741 strain.

source_name: ASF1 AcH4 IP


title: set2 Isw1 Flag-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG-IP over Input in the YMS085 ISW1-3xFLAG set2 strain.

source_name: IP DNA FLAG antibody

growth_protocol: These strains were grown in YPD to an OD of 1.0. Cells were cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate 3xFLAG tagged Ioc4, Ioc3 or Isw1 (2 ul αFLAG per IP).


title: WT-197 H3-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of H3-IP over Input in the YMS197 bar1 strain.

data_processing: Data processed in R (version 2.13.0) using Bioconductor MEDIAN normalization.

source_name: IP DNA H3 antibody

label_protocol: Briefly, up to 50 ng of IP or input DNA were treated with 2.5 U CIP enzyme (NEB) for 1 hour at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. The CIP-treated template was incubated with 20 U TdT (NEB) for 20 minutes at 37°C for T-tailing the ends, and the product isolated with the MinElute Reaction Cleanup Kit (Qiagen). An anchored T7 promoter-(dA)18 oligo was added by annealing and filling with 5 U Exo- Klenow (NEB) for 4 hours at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. In vitro transcription was performed at 37°C overnight using the Ampliscribe T7 transcription kit (Epicentre Biotechnologies). RNAs purified using the RNeasy Mini Kit (Qiagen) and quantified on a Nanodrop 2000 Spectrophotometer (Thermo Scientific). For the second round amplification, 100 ng of RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen) and purified with the MinElute Reaction Cleanup Kit (Qiagen). The T7 promoter primer was added to the product through a Klenow filling reaction as described above, followed by in vitro transcription with amino allyl-UTP (Ambion) instead of UTP. Final reaction cleanup was performed with the RNeasy Mini Kit (Qiagen). For the labeling reactions, 8 ug of amino allyl-incorporated RNA in a 5 uL volume of 0.1 M Carbonate Buffer, pH 8.7, was mixed with 5 uL (0.01 nmol) Cy3 or Cy5 dye (GE Healthcare) in DMSO (Sigma) and incubated at room temperature for 2 hours. Reactions were quenched with 5 uL 4 M hydroxylamine at room temperature for 15 minutes, purified by RNeasy MinElute Cleanup Kit (Qiagen), and the dye incorporation measured using the Nanodrop 2000 (Thermo Scientific). 4ug of input and IP were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.

growth_protocol: These strains were grown in YPD to an OD of 0.4. Cells were arrested with 2uM of α-factor for 4 hours, cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate acetylated histone H3 K56 (2 ul αK56ac per IP; Millipore 07-677) or histone H3 (2 ul αH3 per IP; ab1791).

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate AcH4  or H3. The immune complexes were pulled down with 50 ul of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with 250mM NaCl). The eluates were RNase A treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65 C overnight. Samples were phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase A step.

value: histone H3

value: Abcam #ab1791


title: ISW1[K227R]  H3-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  H3-IP over Input in the YMS204 ISW1[K227R] bar1 strain.


title: ISW1[K227R]  H3-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of  H3-IP over Input in the YMS204 ISW1[K227R] bar1 strain.


title: WT-197 H3-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of H3-IP over Input in the YMS197 bar1 strain.


title: WT-197 H3-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of H3-IP over Input in the YMS197 bar1 strain.


title: set2 Isw1 Flag-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of FLAG-IP over Input in the YMS085 ISW1-3xFLAG set2 strain.


title: ISW1[K227R]  H3-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of  H3-IP over Input in the YMS204 ISW1[K227R] bar1 strain.


title: ISW1[K227R]  K56ac-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of K56ac-IP over Input in the YMS204 ISW1[K227R] bar1 strain.

source_name: IP DNA K56ac antibody

value: acetylated histone H3 K56

value: Millipore 07-677


title: isw1 chd1  K56ac-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  K56ac-IP over Input in the YMS127 isw1 chd1 bar1 strain.


title: WT-197 K56ac-IP Replicate 1

description: Biological Replicate 1 of 2. ChIP enrichment of K56ac-IP over Input in the YMS197 bar1 strain.


title: isw1 chd1  K56ac-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of K56ac-IP over Input in the YMS127 isw1 chd1 bar1 strain.


title: ISW1[K227R]  K56ac-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  K56ac-IP over Input in the YMS204 ISW1[K227R] bar1 strain.


title: set2 Isw1 Flag-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG-IP over Input in the YMS085 ISW1-3xFLAG set2 strain.

value: Flag M2


title: ISW1[K227R]  K56ac-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of K56ac-IP over Input in the YMS204 ISW1[K227R] bar1 strain.


title: isw1 chd1  K56ac-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of K56ac-IP over Input in the YMS127 isw1 chd1 bar1 strain.


title: WT-197 K56ac-IP Replicate 2

description: Biological Replicate 2 of 2. ChIP enrichment of K56ac-IP over Input in the YMS197 bar1 strain.


title: chd1  K56ac-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of K56ac-IP over Input in the YMS125 chd1 bar1 strain.


title: isw1  K56ac-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  K56ac-IP over Input in the YMS124 isw1 bar1 strain.


title: chd1  K56ac-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of K56ac-IP over Input in the YMS125 chd1 bar1 strain.


title: isw1  K56ac-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of K56ac-IP over Input in the YMS124 isw1 bar1 strain.


title: WT K56ac-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of  K56ac-IP over Input in the YMS123 bar1 strain.


title: isw1 set2  H3-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of H3-IP over Input in the YMS139 isw1 set2 bar1 strain.

growth_protocol: These strains were grown in YPD to an OD of 0.4. Cells were arrested with 2uM of α-factor for 4 hours, cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate acetylated histone H4 (2 ul αAcH4 per IP; Millipore 06-866) or histone H3 (2 ul αH3 per IP; ab1791).


title: WT K56ac-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of K56ac-IP over Input in the YMS123 bar1 strain.


title: isw1  K56ac-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of  K56ac-IP over Input in the YMS124 isw1 bar1 strain.


title: isw1 set2  H3-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of H3-IP over Input in the YMS139 isw1 set2 bar1 strain.


title: set2  H3-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of H3-IP over Input in the YMS126 set2 bar1 strain.


title: chd1 set2  H3-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of H3-IP over Input in the YMS141 chd1 set2 bar1 strain.


title: SET2 deletion H4K12ac IP Replicate 1 (BY4741)

description: Biological Replicate 1 of 3. ChIP enrichment of H4K12ac IP over Input in the SET2 deletion BY4741 strain.


title: chd1 set2  H3-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  H3-IP over Input in the YMS141 chd1 set2 bar1 strain.


title: WT K56ac-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of K56ac-IP over Input in the YMS123 bar1 strain.


title: chd1 set2  AcH4-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  AcH4-IP over Input in the YMS141 chd1 set2 bar1 strain.

source_name: IP DNA AcH4 antibody

value: acetylated histone H4

value: Millipore #06-866


title: chd1 set2  H3-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of H3-IP over Input in the YMS141 chd1 set2 bar1 strain.


title: isw1 chd1  H3-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  H3-IP over Input in the YMS127 isw1 chd1 bar1 strain.


title: isw1 set2  H3-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  H3-IP over Input in the YMS139 isw1 set2 bar1 strain.


title: set2  H3-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  H3-IP over Input in the YMS126 set2 bar1 strain.


title: chd1 set2  AcH4-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4-IP over Input in the YMS141 chd1 set2 bar1 strain.


title: chd1 set2  AcH4-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4-IP over Input in the YMS141 chd1 set2 bar1 strain.


title: set2  H3-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of H3-IP over Input in the YMS126 set2 bar1 strain.


title: isw1 chd1  H3-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of H3-IP over Input in the YMS127 isw1 chd1 bar1 strain.


title: isw1 chd1  H3-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of H3-IP over Input in the YMS127 isw1 chd1 bar1 strain.


title: set2  AcH4-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4-IP over Input in the YMS126 set2 bar1 strain.


title: isw1 set2  AcH4-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4-IP over Input in the YMS139 isw1 set2 bar1 strain.


title: isw1 set2  AcH4-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4-IP over Input in the YMS139 isw1 set2 bar1 strain.


title: isw1 chd1  AcH4-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4-IP over Input in the YMS127 isw1 chd1 bar1 strain.


title: isw1 set2  AcH4-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  AcH4-IP over Input in the YMS139 isw1 set2 bar1 strain.


title: set2  AcH4-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4-IP over Input in the YMS126 set2 bar1 strain.


title: isw1 chd1  AcH4-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  AcH4-IP over Input in the YMS127 isw1 chd1 bar1 strain.


title: set2  AcH4-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  AcH4-IP over Input in the YMS126 set2 bar1 strain.


title: isw1 chd1  AcH4-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4-IP over Input in the YMS127 isw1 chd1 bar1 strain.


title: isw1  H3-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of H3-IP over Input in the YMS124 isw1 bar1 strain.

growth_protocol: These strains were grown in YPD to an OD of 0.4. Cells were arrested with 2uM of α-factor for 4 hours, cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate acetylated histone H4 (2 ul αAcH4 per IP) or histone H3 (2 ul αH3 per IP).

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate AcH4 or H3. The immune complexes were pulled down with 50 ul of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with 250mM NaCl). The eluates were RNase A treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65 C overnight. Samples were phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase A step.


title: chd1  H3-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of H3-IP over Input in the YMS125 chd1 bar1 strain.


title: isw1  H3-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of H3-IP over Input in the YMS124 isw1 bar1 strain.


title: chd1  H3-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of H3-IP over Input in the YMS125 chd1 bar1 strain.


title: Caucasian sample no.90

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

description: Caucasian lung cancer sample 19

hyb_protocol: Labeled tumor and reference DNA were combined together with 100 μg human Cot-1 DNA (Invitrogen). Hybridization was performed using MAUI hybridization system (BioMcro Systems, Salt Lake City, UT), agitating the hybridization solution for 50 hours at 50℃.

scan_protocol: The arrays were scanned using scanner GenePix4000B (Axon Instruments, Foster City, CA) and the images were segmented and transformed to Cy3-Cy5 log ratio using GenePix software by Axon Instruments, Inc. (http://www.axon.com).

data_processing: Further data processing, a normalization method called “block-wise normalization”, which normalized the array-CGH data by the log ratio of the self-self hybridization of reference DNA according to the mean and the standard deviations of each array block, was established.

source_name: Tumor sample

label_protocol: 500 ng of tumor genomic DNA and reference DNA (for Asian samples: 28 matched-normal genomic DNA pool; for Caucasian samples: commercial human genomic DNA, Invitrogen) were labeled by random priming using BioPrime DNA Labeling System (Invitrogen) with Cy3-dCTP (tumor) or Cy5-dCTP (reference).

extract_protocol: The genomic DNA was prepared using proteinase K digestion and phenol-chloroform extraction.

value: lung

tag: disease status

value: non-small cell lung cancer (NSLCL)

tag: race

value: Caucasian

source_name: Reference sample

tag: reference source


title: chd1  H3-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of H3-IP over Input in the YMS125 chd1 bar1 strain.


title: WT H3-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of H3-IP over Input in the YMS123 bar1 strain.


title: Caucasian sample no.91

description: Caucasian lung cancer sample 20

value: commercial human genomic DNA, Invitrogen


title: WT H3-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of H3-IP over Input in the YMS123 bar1 strain.


title: chd1  AcH4-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4-IP over Input in the YMS125 chd1 bar1 strain.


title: WT H3-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of H3-IP over Input in the YMS123 bar1 strain.


title: isw1  H3-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of H3-IP over Input in the YMS124 isw1 bar1 strain.


title: Caucasian sample no.84

description: Caucasian lung cancer sample 14


title: Caucasian sample no.86

description: Caucasian lung cancer sample 15


title: Caucasian sample no.87

description: Caucasian lung cancer sample 16


title: Caucasian sample no.88

description: Caucasian lung cancer sample 17


title: Caucasian sample no.83

description: Caucasian lung cancer sample 13


title: chd1  AcH4-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of AcH4-IP over Input in the YMS125 chd1 bar1 strain.


title: isw1  AcH4-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4-IP over Input in the YMS124 isw1 bar1 strain.


title: mt-2 vs IHF-, rep3

city: Campus de Cantoblanco

first: Victor

last: de Lorenzo

state: Madrid

address: Darwin 3

department: Systems Biology

country: Spain

institute: CNB-CSIC

description: Biological replicate 3 of 3.  P. putida mt-2 vs mutant IHF-.

hyb_protocol: Slides were prehybridized in 6x SSC, 0.5% SDS (w/v), and 1% BSA (w/v) at 44ºC for 10 min, followed by five rinses with milliQ water. Excess water was drained with a 2000-rpm spin for 2 min. 300 pmol of dye of each cDNA labeled with either Cy3 or Hyper5 were resuspended in 50% formamide, 3x SSC, 5x Denhardt's, 1% SDS and 5% Dextransulphate. This mix was boiled for 5 min at 95ºC and then added to the prehybridized slide. Hybridization took place overnight at 42ºC in a hybridization chamber. Arrays were then washed for 5 min at 37ºC in 0.5x SSPE, tween20 0.1%, twice for 5 min at room temperature (21ºC) with 0.5x SSPE, tween20 0.1%, three times with 0.5x SSPE at room temperature, and 5 min with 0.1x SSPE. The slides were drained with a 2000-rpm spin for 2 min and stored in darknesss until they were scanned.

scan_protocol: The slides were scanned with a GenePix 4000B scanner and the images were quantified with GenePix Pro 5.1 software (Molecular Devices).

data_processing: Data processing was carried-out using the LIMMA package (Smyth, 2003) of the Bioconductor project. Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization), followed by adjustment of their quantiles (inter-arrays normalization).

organism: Pseudomonas putida

source_name: Pseudomonas putida mt-2

label_protocol: RNA was labeled with Cy3 or Hyper5 by using the SuperScript indirect cDNA labeling system (invitrogen) as described in the instruction manual.

growth_protocol: Mineral medium M9 with Glucose 0.3% as carbon source. The samples were taken in exponential phase (OD600 = 0.5-0-6).

extract_protocol: 10 ml aliquots of the corresponding cultures were added with 1.25 ml of ice-cold stop mix (5% water-saturated phenol in ethanol) and the tubes subsequently centrifuged 3000 g, 15 min at 4ºC. The pellets were then snap-frozen in liquid nitrogen and kept at -80ºC until further processing. RNA was subsequently extracted with the NucleoSpin RNA II kit (Macherey-Nagel, Germany) according to the manufacturer’s instructions. The quality of RNA was verified as the ratio the 28s/18s rRNAs using an Agilent Bionalyzer 2100.

value: wild type

tag: growth phase

value: exponential

source_name: Pseudomonas putida mutant IHF-

value: IHF-


title: Caucasian sample no.89

description: Caucasian lung cancer sample 18


title: mt-2 vs IHF-, rep2

description: Biological replicate 2 of 3.  P. putida mt-2 vs mutant IHF-.


title: Caucasian sample no.82

description: Caucasian lung cancer sample 12


title: chd1  AcH4-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4-IP over Input in the YMS125 chd1 bar1 strain.


title: isw1  AcH4-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4-IP over Input in the YMS124 isw1 bar1 strain.


title: mt-2 vs IHF-, rep1

description: Biological replicate 1 of 3.  P. putida mt-2 vs mutant IHF-.


title: isw1  AcH4-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of AcH4-IP over Input in the YMS124 isw1 bar1 strain.


title: WT AcH4-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of AcH4-IP over Input in the YMS123 bar1 strain.


title: Caucasian sample no.81

description: Caucasian lung cancer sample 11


title: Caucasian sample no.59

description: Caucasian lung cancer sample 10


title: Caucasian sample no.58

description: Caucasian lung cancer sample 9


title: WT AcH4-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of AcH4-IP over Input in the YMS123 bar1 strain.


title: chd1  K56ac-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of  K56ac-IP over Input in the YMS125 chd1 bar1 strain.


title: Caucasian sample no.57

description: Caucasian lung cancer sample 8


title: chd1 K36me3-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of K36me3 IP over Input in the chd1 YMS136 strain.

source_name: IP DNA K36me3 antibody

label_protocol: Briefly, up to 50 ng of IP or input DNA was treated with 2.5 U CIP enzyme (NEB) for 1 hour at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. The CIP-treated template was incubated with 20 U TdT (NEB) for 20 minutes at 37°C for T-tailing the ends, and the product isolated with the MinElute Reaction Cleanup Kit (Qiagen). An anchored T7 promoter-(dA)18 oligo was added by annealing and filling with 5 U Exo- Klenow (NEB) for 4 hours at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. In vitro transcription was performed at 37°C overnight using the Ampliscribe T7 transcription kit (Epicentre Biotechnologies). RNAs purified using the RNeasy Mini Kit (Qiagen) and quantified on a Nanodrop 2000 Spectrophotometer (Thermo Scientific). For the second round amplification, 100 ng of RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen) and purified with the MinElute Reaction Cleanup Kit (Qiagen). The T7 promoter primer was added to the product through a Klenow filling reaction as described above, followed by in vitro transcription with amino allyl-UTP (Ambion) instead of UTP. Final reaction cleanup was performed with the RNeasy Mini Kit (Qiagen). For the labeling reactions, 8 ug of amino allyl-incorporated RNA in a 5 uL volume of 0.1 M Carbonate Buffer, pH 8.7, was mixed with 5 uL (0.01 nmol) Cy3 or Cy5 dye (GE Healthcare) in DMSO (Sigma) and incubated at room temperature for 2 hours. Reactions were quenched with 5 uL 4 M hydroxylamine at room temperature for 15 minutes, purified by RNeasy MinElute Cleanup Kit (Qiagen), and the dye incorporation measured using the Nanodrop 2000 (Thermo Scientific). 4 ug of input and IP were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.

growth_protocol: These strains were grown in YPD to an OD of 0.4. a-factor was added to a final concentration of 2 uM and the cells were grown for an additional 5 hrs. Cells were cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate K36me3 (2 ul per IP) antibodies.

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate histone H3 K36me3. The immune complexes were pulled down with 50 ul of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with250mM NaCl). The eluates were RNase A treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65°C overnight. Samples werte phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase A step.

value: Abcam #ab9050


title: V108_UNINTERRUPTED

city: Melbourne

first: Celine

last: Latouche

state: VICTORIA

address: 75 Commercial Road

country: Australia

institute: Baker IDI Heart and Diabetes Institute

description:
uninterrupted sitting_ repl8
SAMPLE 22

hyb_protocol: Hybridization to the Illumina Human HT-12 v4 BeadChip was for 16 hours at 58ºC on a BeadChip Hyb Wheel using 1,500ng biotin-labeled cRNA as input. The chip was then washed, blocked and stained with Cy3-streptavidin (Amersham Bioscience, Piscataway, NJ, USA) according to manufacturer’s protocols (Illumina, SanDiego, CA, USA).

scan_protocol: The iScan Control Software V1.6.20.7 (Illumina) together with the Illumina iSCAN platform (Illumina) was used for RNA quantification.

data_processing: Processing and analysis of the microarray data were performed with the Illumina Beadstudio 3.1.3.0 software. Raw data were background subtracted and normalized using the “Quantile” algorithm.

source_name: vastus lateralis muscle

label_protocol: Biotin-labeled cRNA was produced by means of a linear amplification kit (AMIL1791; Ambion, Austin, TX, USA) using 250ng of quality checked total RNA as input.

extract_protocol: Total RNA was extracted from frozen muscle with TRIzol reagent (InVitrogen, Carlsbad, CA, USA) using the manufacturer’s recommended protocol. RNA quality was determined by the MultiNA system (Shimadzu Biotech, Sydney, NSW, Australia).

tag: individual

tag: gender

value: MALE

tag: weight (kg)

tag: bmi

tag: treatment protocol

value: uninterrupted sitting

value: vastus lateralis


title: chd1 K36me3-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of K36me3 IP over Input in the chd1 YMS136 strain.

source_name: Input DNA


title: C4EH_LIGHT BREAKS

description:
light-intinsity breaks_repl6
SAMPLE 16

value: light-intensity breaks


title: C4EH_UNINTERRUPTED

description:
uninterrupted sitting_ repl6
SAMPLE 18


title: Caucasian sample no.56

description: Caucasian lung cancer sample 7


title: 9WEZ_UNINTERRUPTED

description:
uninterrupted sitting_ repl5
SAMPLE 14


title: TPCW_LIGHT BREAKS

description:
light-intinsity breaks_repl7
SAMPLE 20

value: TPCW


title: V108_LIGHT BREAKS

description:
light-intinsity breaks_repl8
SAMPLE 24


title: V108_MODERATE BREAKS

description:
moderate-intensity breaks_repl8
SAMPLE 23

value: moderate-intensity breaks


title: isw1  K36me3-IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of K36me3 IP over Input in the isw1 YMS131 strain.


title: WT AcH4-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of AcH4-IP over Input in the YMS123 bar1 strain.


title: 8S33_LIGHT BREAKS

description:
light-intinsity breaks_repl4
SAMPLE 12


title: TPCW_UNINTERRUPTED

description:
uninterrupted sitting_ repl7
SAMPLE 21


title: isw1 K36me3-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of K36me3 IP over Input in the isw1 YMS131 strain.


title: isw1 K36me3-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of K36me3 IP over Input in the isw1 YMS131 strain.


title: Caucasian sample no.55

description: Caucasian lung cancer sample 6


title: TPCW_MODERATE BREAKS

description:
moderate-intensity breaks_repl7
SAMPLE 19


title: chd1 K36me3-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of K36me3 IP over Input in the chd1 YMS136 strain.


title: C4EH_MODERATE BREAKS

description:
moderate-intensity breaks_repl6
SAMPLE 17


title: 9WEZ_LIGHT BREAKS

description:
light-intinsity breaks_repl5
SAMPLE 13


title: 9WEZ_MODERATE BREAKS

description:
moderate-intensity breaks_repl5
SAMPLE 15


title: 8S33_MODERATE BREAKS

description:
moderate-intensity breaks_repl4
SAMPLE 11


title: Caucasian sample no.53

description: Caucasian lung cancer sample 5


title: Caucasian sample no.51

description: Caucasian lung cancer sample 3


title: Caucasian sample no.52

description: Caucasian lung cancer sample 4


title: Caucasian sample no.50

description: Caucasian lung cancer sample 2


title: WT K36me3-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of K36me3 IP over Input in the WT MDY510 strain.


title: isw1chd1/WT sense transcripts Replicate 3

description: Biological Replicate 3 of 3. Sense gene expression for isw1chd1/WT

hyb_protocol: The hybridization mixture was prepared according to the Agilent protocol with the addition of Kreatech Blocking Reagent, and hybridized overnight at 65°C. Wash conditions used were as outlined in the Agilent processing manual (protocol version 4.0).

molecule: polyA RNA

source_name: mRNA isw1chd1

label_protocol: Briefly, 2.3ug of mRNA were labeled directly with Cy dyes using the Kreatech ULS system according to manufacturer's instructions. Dye incorporation was measured using the Nanodrop 2000 (Thermo Scientific). 2ug of labeled mutant and wildtype mRNA were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.

growth_protocol: These strains were grown in YPD at 30ºC  to an OD of 0.8. RNA was isolated using hot acid phenol. mRNA was subsequently purified by oligo (dT) cellulose affinity chromatography.

extract_protocol: TOTAL RNA ISOLATION: 1. Spin down the cells (approximately 250 ml at OD600=0.8). Dump the supernatant. 2. Resuspend the pellet in 12 ml AE Buffer (AE=50mM NaAcetate pH 5.2, 10mM EDTA). Transfer to an RNase-free Nalgene Oak Ridge phenol-resistant centrifuge tube (50ml size). 3. Add 800 μl 25% SDS (w/v), 12 ml acid phenol (pH 4.3, purchased as unbuffered saturated liquefied phenol (Fischer BP1751I-400)). Vortex to mix. 4. Incubate 10' in 65 °deg;C water bath, vortexing every minute. 5. Incubate 5' on ice. 6. Spin down 15' at 10,000 rpm in an SS34 rotor. (Get Phase Lock tubes ready - Step7) 7. Pour the supernatant into a pre-spun (5' at 1500 rpm) 50 ml Phase Lock Gel tube (Eppendorf 0032 005.330). Add 13 ml chloroform (Fischer BP1145-1) and shake to mix. 8. Spin down 10' at 3,000 rpm in a tabletop centrifuge (Beckman). 9. Pour the supernatant into a new RNase-free Nalgene Oak Ridge centrifuge tube. 10. Add 1/10 volume 3 M NaAcetate (pH 5.2-5.6) and equal volume of room temperature Isopropanol. 11. Spin down 35'-45' at 12,000 rpm in an SS34 rotor. 12. Wash the pellet with 5 ml 70% Ethanol and spin again 20' at 12,000 rpm. 13. Pour off the Ethanol. Dry the pellet in a speed vac (rotor off) on low heat for 15'. 14. Resuspend in 500 μl water and transfer to an RNase-free Eppendorf tube.  POLY-A RNA PREP: 1. Resuspend at least 2 mg (up to 4mg) of total RNA in 750 μl RNase-free water.  2. Wash the oligo dT cellulose 3X with 750 μl 1X NETS. (Spin down gently between washes and aspirate off the wash.) 3. Aspirate off final 1X NETS wash and resuspend the cellulose in 750 μl 2X NETS. 4. Incubate the RNA at 65 °C for 10 minutes. 5. Add the RNA to the cellulose and mix on rotator for 1 hour at room temperature. 6. Prepare a BIO-RAD Disposable Chromatography Column (BIO-RAD cat. #732-6008) by washing it out once with 750 μl 1X NETS. 7. Gently pour the RNA/cellulose mixture into the column and allow it to settle by gravity. (do not mix) 8. Gently wash the column 3X with 750 μl 1X NETS. (Pipette down the side of the column without disrupting the cellulose.) 9. Elute the mRNA into a fresh Eppendorf tube by pipetting 650 μl of 65 °C 1X ETS directly and forcibly into the oligo dT cellulose. Repeat 1X into a second tube. 10. Add 65 μl 3M NaAcetate to all samples. Fill the remainder of the tube with room temperature isopropanol (~700 μl). Mix well by inverting several times. 11. The sample can now sit at -20 °C to precipitate as long as desired (up to overnight). To proceed, spin sample in a 4 °C microfuge at max speed for 30 minutes to 1 hour. 12. Aspirate off supernatant and wash pellet with 250 μl 70% EtOH and spin down 5'. 13. Aspirate off the EtOH and let pellet air dry (or speed vac dry on low heat). 14. Resuspend in 20-40 μl RNase-free water.

source_name: mRNA WT


title: Caucasian sample no.49

description: Caucasian lung cancer sample 1


title: Asian sample no.171

description: Asian lung cancer sample 37

value: Asian

value: 28 matched-normal genomic DNA pool from Aaian lung cancer


title: isw1chd1/WT sense transcripts Replicate 2

description: Biological Replicate 2 of 3. Sense gene expression for isw1chd1/WT


title: 71XM_UNINTERRUPTED

description:
uninterrupted sitting_ repl3
SAMPLE 8


title: isw1chd1/WT sense transcripts Replicate 1

description: Biological Replicate 1 of 3. Sense gene expression for isw1chd1/WT


title: Asian sample no.221

description: Asian lung cancer sample 40


title: H3K36AK56R/WT sense transcripts Replicate 3

description: Biological Replicate 2 of 3

source_name: mRNA H3K36AK56R

label_protocol: Briefly, 1.5ug of mRNA were labeled directly with Cy dyes using the Kreatech ULS system according to manufacturer's instructions. Dye incorporation was measured using the Nanodrop 2000 (Thermo Scientific). 2ug of labeled mutant and wildtype mRNA were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.


title: Asian sample no.190

description: Asian lung cancer sample 39


title: WT K36me3-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of K36me3 IP over Input in the WT MDY510 strain.


title: 71XM_LIGHT BREAKS

description:
light-intinsity breaks_repl3
SAMPLE 7


title: 71XM_MODERATE BREAKS

description:
moderate-intensity breaks_repl3
SAMPLE 9


title: 8S33_UNINTERRUPTED

description:
uninterrupted sitting_ repl4
SAMPLE 10


title: H3K36AK56R/WT sense transcripts Replicate 2

description: Biological Replicate 2 of 3


title: WT K36me3-IP Replicate

description: Biological Replicate 2 of 3. ChIP enrichment of K36me3 IP over Input in the WT MDY510 strain.


title: 389C_MODERATE BREAKS

description:
moderate-intensity breaks_repl2
SAMPLE 6

value: FEMALE


title: ioc4  FLAG-H3 IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG IP over Input in the ioc4 YMS134 strain.

label_protocol: Briefly, up to 50 ng of IP or input DNA was treated with 2.5 U CIP enzyme (NEB) for 1 hour at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. The CIP-treated template was incubated with 20 U TdT (NEB) for 20 minutes at 37C for T-tailing the ends, and the product isolated with the MinElute Reaction Cleanup Kit (Qiagen). An anchored T7 promoter-(dA)18 oligo was added by annealing and filling with 5 U Exo- Klenow (NEB) for 4 hours at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. In vitro transcription was performed at 37°C overnight using the Ampliscribe T7 transcription kit (Epicentre Biotechnologies). RNAs purified using the RNeasy Mini Kit (Qiagen) and quantified on a Nanodrop 2000 Spectrophotometer (Thermo Scientific). For the second round amplification, 100 ng of RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen) and purified with the MinElute Reaction Cleanup Kit (Qiagen). The T7 promoter primer was added to the product through a Klenow filling reaction as described above, followed by in vitro transcription with amino allyl-UTP (Ambion) instead of UTP. Final reaction cleanup was performed with the RNeasy Mini Kit (Qiagen). For the labeling reactions, 8 ug of amino allyl-incorporated RNA in a 5 uL volume of 0.1 M Carbonate Buffer, pH 8.7, was mixed with 5 uL (0.01 nmol) Cy3 or Cy5 dye (GE Healthcare) in DMSO (Sigma) and incubated at room temperature for 2 hours. Reactions were quenched with 5 uL 4 M hydroxylamine at room temperature for 15 minutes, purified by RNeasy MinElute Cleanup Kit (Qiagen), and the dye incorporation measured using the Nanodrop 2000 (Thermo Scientific). 4ug of input and IP were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.

growth_protocol: These strains were grown in YPD to an OD of 0.4. a-factor was added to a final concentration of 2 uM and the cells were grown for an additional 5 hrs. Cells were cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate FLAG (15 ul per IP) or Myc (2 ul per IP) antibodies.

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate FLAG- and Myc-tagged histone H3. The immune complexes were pulled down with 50 ul of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with250mM NaCl). The eluates were RNase A treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65°C overnight. Samples werte phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase A step.

value: Flag M2

value: Sigma #F1804


title: ioc4  Myc-H3 IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of Myc IP over Input in the ioc4 YMS134 strain.

source_name: IP DNA Myc antibody

value: -c-myc

value: Sigma #4439


title: 389C_LIGHT BREAKS

description:
light-intinsity breaks_repl2
SAMPLE 5


title: 389C_UNINTERRUPTED

description:
uninterrupted sitting_ repl2
SAMPLE 4


title: H3K56R/WT sense transcripts Replicate 2

description: Biological Replicate 2 of 3

source_name: mRNA H3K56R

value: wild type


title: ioc4  Myc-H3 IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of Myc IP over Input in the ioc4 YMS134 strain.


title: H3K36AK56R/WT sense transcripts Replicate 1

description: Biological Replicate 2 of 3


title: H3K56R/WT sense transcripts Replicate 1

description: Biological Replicate 2 of 3


title: ioc4  Myc-H3 IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of Myc IP over Input in the ioc4 YMS134 strain.


title: Asian sample no.172

description: Asian lung cancer sample 38

value: lung

value: non-small cell lung cancer (NSLCL)


title: Asian sample no.112

description: Asian lung cancer sample 35


title: Asian sample no.136

description: Asian lung cancer sample 36


title: Asian sample no.104

description: Asian lung cancer sample 34


title: Asian sample no.103

description: Asian lung cancer sample 33


title: isw1chd1/WT antisense transcripts Replicate 3

description: Biological Replicate 3 of 3. Antisense gene expression for isw1chd1/WT


title: 35T7_MODERATE BREAKS

description:
moderate-intensity breaks_repl1
SAMPLE 3


title: 12 h after chitin oligosaccharide treatment replicate 2

city: Tokyo

first: Kazunori

last: Okada

address: 1-1-1, Yayoi, Bunkyo-ku

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

description: Biological replicate 2 of 2.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent scanner model G2505B, software G2565BA

data_processing: Data was analyzed by Fearure Extraction software (Agilent)

organism: Oryza sativa

source_name: untreated rice cells

label_protocol: Low RNA input Linear Amplification/Labeling Kit (Agilent)

growth_protocol: Rice suspension cultured cells (Oryza sativa L. cv. Nipponnbare) used for total RNA extraction were maintained using N-6 medium and incubated on a rotary shaker at 25 C and 120 rpm in a dark. Cells were transferred to a fresh medium every week.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: Rice cells 6 days after transfer to the new medium were used experiment and chitin oligosaccharide (1 ppm) was added to the culture medium.

tag: cultivar

value: Nipponnbare

tag: agent

value: control (un-treated)

source_name: rice cells treated with chitin oligosaccharide for 12 h

value: chitin oligosaccharide


title: ioc4  FLAG-H3 IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of FLAG IP over Input in the ioc4 YMS134 strain.

source_name: IP DNA FLAG antibody

tag: antibody

tag: vendor


title: 6 h after chitin oligosaccharide treatment replicate 2

description: Biological replicate 2 of 2.

source_name: rice cells treated with chitin oligosaccharide for 6 h

value: 6 h


title: H3K36AK56R/WT antisense transcripts Replicate 3

description: Biological Replicate 2 of 3

tag: genotype

tag: strain


title: Asian sample no.85

description: Asian lung cancer sample 31

tag: tissue


title: 4 h after chitin oligosaccharide treatment replicate 2

description: Biological replicate 2 of 2.

source_name: rice cells treated with chitin oligosaccharide for 4 h

tag: time

value: 4 h


title: ioc4  FLAG-H3 IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG IP over Input in the ioc4 YMS134 strain.


title: 35T7_UNINTERRUPTED

description:
uninterrupted sitting_ repl1
SAMPLE 1

value: MALE

tag: age

value: uninterrupted sitting

value: vastus lateralis


title: Asian sample no.80

description: Asian lung cancer sample 30

source_name: Tumor sample

tag: disease status

tag: race

value: Asian

value: 28 matched-normal genomic DNA pool from Aaian lung cancer


title: isw1 chd1  Myc-H3 IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of Myc IP over Input in the isw1 chd1 YMS172 strain.


title: 35T7_LIGHT BREAKS

description:
light-intinsity breaks_repl1
SAMPLE 2

value: light-intensity breaks


title: Asian sample no.92

description: Asian lung cancer sample 32

source_name: Reference sample

tag: reference source


title: isw1chd1/WT antisense transcripts Replicate 1

description: Biological Replicate 1 of 3. Antisense gene expression for isw1chd1/WT


title: H3K36A/WT sense transcripts Replicate 3

description: Biological Replicate 2 of 3

source_name: mRNA H3K36A


title: 2 h after chitin oligosaccharide treatment replicate 2

description: Biological replicate 2 of 2.

source_name: rice cells treated with chitin oligosaccharide for 2 h

value: 2 h


title: isw1 chd1  Myc-H3 IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of Myc IP over Input in the isw1 chd1 YMS172 strain.

value: -c-myc


title: H3K36A/WT sense transcripts Replicate 2

description: Biological Replicate 2 of 3


title: 8 h after chitin oligosaccharide treatment replicate 2

description: Biological replicate 2 of 2.

source_name: rice cells treated with chitin oligosaccharide for 8 h

value: 8 h


title: isw1 chd1  Myc-H3 IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of Myc IP over Input in the isw1 chd1 YMS172 strain.

value: Sigma #4439


title: H3K36A/WT sense transcripts Replicate 1

description: Biological Replicate 1 of 3

value: wild type


title: isw1 chd1  FLAG-H3 IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG IP over Input in the isw1 chd1 YMS172 strain.

value: Flag M2

value: Sigma #F1804


title: isw1 chd1 FLAG-H3 IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG IP over Input in the isw1 chd1 YMS172 strain.


title: Asian sample no.79

description: Asian lung cancer sample 29

value: lung

value: non-small cell lung cancer (NSLCL)


title: isw1chd1/WT antisense transcripts Replicate 2

description: Biological Replicate 2 of 3. Antisense gene expression for isw1chd1/WT


title: H3K36AK56R/WT antisense transcripts Replicate 2

description: Biological Replicate 2 of 3


title: Asian sample no.76

description: Asian lung cancer sample 28


title: 1 h after chitin oligosaccharide treatment replicate 2

description: Biological replicate 2 of 2.

value: Nipponnbare

value: control (un-treated)

source_name: rice cells treated with chitin oligosaccharide for 1 h

value: chitin oligosaccharide

value: 1 h


title: isw1 chd1  FLAG-H3 IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of FLAG IP over Input in the isw1 chd1 YMS172 strain.

source_name: Input DNA


title: chd1  Myc-H3 IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of Myc IP over Input in the chd1 YMS136 strain.


title: Asian sample no.75

description: Asian lung cancer sample 27


title: H3K36AK56R/WT antisense transcripts Replicate 1

description: Biological Replicate 2 of 3


title: Asian sample no.71

description: Asian lung cancer sample 25


title: 8 h after chitin oligosaccharide treatment replicate 1

description: Biological replicate 1 of 2.


title: 12 h after chitin oligosaccharide treatment replicate 1

description: Biological replicate 1 of 2.


title: chd1  FLAG-H3 IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG IP over Input in the chd1 YMS136 strain.


title: chd1  Myc-H3 IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of Myc IP over Input in the chd1 YMS136 strain.


title: H3K56R/WT antisense transcripts Replicate 2

description: Biological Replicate 2 of 3


title: chd1  FLAG-H3 IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of FLAG IP over Input in the chd1 YMS136 strain.


title: 1 h after chitin oligosaccharide treatment replicate 1

description: Biological replicate 1 of 2.


title: chd1  Myc-H3 IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of Myc IP over Input in the chd1 YMS136 strain.


title: H3K56R/WT antisense transcripts Replicate 1

description: Biological Replicate 2 of 3


title: H3K36A/WT antisense transcripts Replicate 3

description: Biological Replicate 2 of 3


title: H3K36A/WT antisense transcripts Replicate 1

description: Biological Replicate 1 of 3


title: 4 h after chitin oligosaccharide treatment replicate 1

description: Biological replicate 1 of 2.

value: 4 h


title: 6 h after chitin oligosaccharide treatment replicate 1

description: Biological replicate 1 of 2.

value: 6 h


title: H3K36A/WT antisense transcripts Replicate 2

description: Biological Replicate 2 of 3


title: Asian sample no.66

description: Asian lung cancer sample 23

value: Asian

value: 28 matched-normal genomic DNA pool from Aaian lung cancer


title: 2 h after chitin oligosaccharide treatment replicate 1

description: Biological replicate 1 of 2.

value: 2 h


title: Asian sample no.72

description: Asian lung cancer sample 26


title: Asian sample no.69

description: Asian lung cancer sample 24


title: chd1  FLAG-H3 IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG IP over Input in the chd1 YMS136 strain.


title: isw1  Myc-H3 IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of Myc IP over Input in the isw1 YMS131 strain.

value: -c-myc


title: Asian sample no.62

description: Asian lung cancer sample 21


title: Asian sample no.54

description: Asian lung cancer sample 19


title: Asian sample no.63

description: Asian lung cancer sample 22


title: isw1  Myc-H3 IP Replicate 2

description: Biological Replicate 2 of 3. ChIP enrichment of Myc IP over Input in the isw1 YMS131 strain.


title: Asian sample no.49

description: Asian lung cancer sample 18


title: Asian sample no.55

description: Asian lung cancer sample 20


title: isw1  Myc-H3 IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of Myc IP over Input in the isw1 YMS131 strain.


title: brainstem_Atxn2 Knock-In_replicate2

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse [HT_MG-430_PM] Affymetrix HT MG-430 PM Array Plate. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner with GCOS 1.4.

data_processing: The data were analysed using Bioconductor package 'affy' under R-2.7.0. Background correction, normalization and probe summarization was performed with RMA (function just.rma()).

source_name: brainstem_Atxn2 Knock-In

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were housed in Type II L cages (365x207x140 mm, floor area 530 cm2; IVC-based)at an environmental temperature 20-24°C, humidity: 55±10%and under 12/12 h light/dark cycle with food and water ad libitum.

extract_protocol: RNA  was extracted by using RNeasy Midi Kit (Qiagen) following manufacturers instructions for animal tissues.

value: brainstem

tag: genotype/variation

value: Atxn2 Knock-In


title: ES_CTCFL_DOX

first: frank

last: sleutels

address: Dr Molewaterplein 50

department: cell biology and genetics

institute: ErasmusMC

description: Gene expression data from CTCFL induced ES cells

hyb_protocol: cRNA was hybridized to the Affymetrix Mouse Gene 1.0ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station Fluidics 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner 3000

data_processing: The data was normalized by Robust Multi-Array average (RMA) algorithm

source_name: CTCFL_V5_GFP induced ES cells

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 300 ng total RNA

growth_protocol: CTCFL_V5_GFP transgenic ES cell were grown in ES+LIF medium on gelatin coated plastic

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were induced with doxycyclin during 3 days for CTCFL_V5_GFP expression and sorted for GFP expression or not-induced with doxycyclin and not sorted.

tag: cell type

value: embryonic stem


title: ES_CTCFL_NODOX

description: Gene expression data from CTCFL uninduced ES cells

source_name: CTCFL_V5_GFP uninduced ES cells


title: brainstem_Atxn2 Knock-In_replicate4


title: Asian sample no.45

description: Asian lung cancer sample 16


title: Asian sample no.48

description: Asian lung cancer sample 17


title: isw1  FLAG-H3 IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG IP over Input in the isw1 YMS131 strain.

value: Flag M2


title: cerebellum_Atxn2 Knock-In_replicate3

source_name: cerebellum_Atxn2 Knock-In

value: cerebellum