title: Liver_Cancer-HCC_QD131_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient QD131 vs. Normal liver tissue mixed (Cy3)


title: Whsc2_72h_shRNAtrasient #2

status: Public on Mar 14 2013

type: RNA

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

country: USA

institute: NIH

description: shRNA transient transfection

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 246 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

molecule: total RNA

organism: Mus musculus

source_name: shRNA transient transfection

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: The samples were dissolved in the well with TRIzol reagent 1 mL.  They were then transferred to Phase Lock Gel Heavy tubes (eppendorf) and 0.2 volumes of chloroform (Sigma-Aldrich) was added to each sample.  They were mixed by hand and allowed to stand for 2-5 min at room temperature. The samples were then separated by centrifugation for 5 minutes at 15,300 rpm on an eppendorf centrifuge at 4C. The aqeous phase was transferred to another eppendorf tube, and 0.8 volumes of ice-cold isopropanol was added. They were allowed to incubate  for a minimum of 10 minutes at room temperature. If longer, they were placed at 4C. The sample was centrifuged again at the same conditions for 15 minutes. After centrifugation, the liquid was dumped out of the tubes and the pellet was washed with 1 mL of ice-cold 70% ethanol. The tube was spun  for 5 minutes, then the ethanol was dumped out.  Excess was removed with a pipette and the pellet was allowed to air dry until no liquid remained, but no longer.  ddH2O was then added in the appropriate volume, the sample was allowed to dissolve for 5 minutes at 55C and then transferred to -80C for storage.

treatment_protocol: Cells (2,000,000 cells) were co-transfected with 1.6ug of shRNA expression vector and 0.4ug of expression vector for puromycine resistant gene and plated onto 1 well of 6 well plate. After 24h and 48h, medium was changed to medium containing puromycine (1.5ug/ml). At 72 hours after the transfection, the cells were harvested in Trizol.For time couse experiments, cell were harvetsed  at 48h, 72h, and 96h. For rescue experiments, NIA mouse ES cell bank clone were co-trasnfeteced with shRNA expression vector and expression vector for Blasticidin S and cultured in presence of puromycine (0.5 or 1.5 ug/ml) and presence/absence of doxycyclin (0.2 ug/ml). Blasticidin S (40 or 100 ug/ml) was used for selection. ZHtc6 cells were cultured with doxycyclin and Zeocin (20 ug/ml) and co-transfected wuith shRNA expression vector and expression vector for puromycine resistant gene in presence/absence of doxycyclin. puromycine (1.5 ug/ml) was used for selection.

tag: cell type

value: Embryonic Stem Cells

tag: strain

tag: individual identifier

value: Whsc2 shRNA transient transfection , 72h, Replictaion 2; Whsc2_72h_shRNAtrasient #2; 251508710727A2

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

value: Universale Mouse Reference


title: NS 2

city: Kingston

first: Harriet

last: Feilotter

state: Ontario

address: 88 Stuart St

department: Pathology and molecular department

country: Canada

institute: Queen's University

hyb_protocol: Labeled RNA was hybridized to Agilent miRNA array (8 arrays per slide) at 55°C for 22h in rotisserie in a hybridization oven. Disassembled arrays were washed in GE wash buffer 1&2 for 5 minutes each.

scan_protocol: Images were scanned with Agilent scanner at 5µm resolution.

data_processing: Raw data (probe view file) from feature extracted file was imported into GeneSpring, GeneSpring software (v.11.5.1) was used to quantile normalize and log transform raw data and perform unsupervised hierarchical clustering. Differential expression between MCC and non-MCC groups was assessed by an unpaired t-test. p-values were adjusted for multiplicity using the Benjamini-Hochberg approach to control the false discovery rate (FDR). miRNAs were considered differentially expressed if theFDR was <0.05 and the fold change 2.

organism: Homo sapiens

source_name: Normal skin

label_protocol: 100ng total RNA was dephosphorylated in the presence of calf intestine alkaline phsphatase, then a Cy3-pCp molecule was ligated to the 3' end of the RNA molecule according to Agilent miRNA protocol version 2.0.

extract_protocol: The RecoverAll total RNA Isolation kit (Ambion, Streetsville, Canada) was used to extract total RNA (including miRNA) from FFPE samples.

treatment_protocol: Formalin-fixed paraffin-embedded (FFPE) tissues

tag: tissue type

value: FFPE normal skin tissue


title: MCC 5

source_name: Mercel cell carcinoma (MCC)

value: FFPE MCC tissue


title: MCC 6


title: NS 1


title: Tcea3_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Tcea3 shRNA transient transfection , 72h, Replictaion 2; Tcea3_72h_shRNAtrasient #2; 251508710726A2


title: Trp63 cHet uterus, rep1

city: Columbus

first: Takeshi

last: Kurita

state: OH

address: 460 W. 12th Avenue,

department: Molecular Virology, Immunology & Medical Genetics

institute: Ohio State University

description: Total RNA was extracted from the uteri of 3 Trp63 cHet mice.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The average signal intensity for each array was normalized to the average total signal intensity of all 12 arrays by average normalization utilizing Excel.

label: biotin

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain/background

value: mixed (C57BL/6, S129/5 and CD-1)

tag: genotype

value: Trp63 flox/wt ; Pax2-cre

tag: tissue

value: uterus

tag: gender

value: female

tag: age

value: postnatal day 3


title: Sample 11_Cyclin ET74A T393A

city: Chicago

first: Yanfei

last: Xu

state: IL

address: 303 E. Superior Street., Lurie 5-250

department: Medicine

institute: Northwestern University

description: Sample 11

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio Gene Expression Module

source_name: cyclin E (T74A T393A) knock-in_erythroblasts

label_protocol: Biotinylated cRNA were prepared with the Direct Hybridization Whole-Gene Exrpession assay for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol

tag: strain background

value: bone marrow erythroid progenitors

value: sorted erythroid cells

tag: genotype/variation

value: cyclin E (T74A T393A) knock-in


title: Liver_Pericancer_HK043_P_P3vsN5

city: Shanghai

first: Lin

last: Wei

address: No.25/Ln.2200, Xie Tu Road

country: China

institute: Shanghai Cancer Institute

description: Periancerous liver tissue (Cy3) from HCC patient HK043 vs. Normal liver tissue mixed (Cy5)

hyb_protocol: Labeled controls and test samples labeled with Cy5-dCTP and Cy3-dCTP were dissolved in 80 µL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a CapitalBio BioMixer II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned with a confocal LuxScan scanner and the images obtained were then analyzed using LuxScan 3.0 software (Both from CapitalBio).

data_processing: Faint spots (intensity < 400) removed, background subtracted data were normalized by LOWESS program.

source_name: Liver tissue, Pericancer

label_protocol: Eberwine’s linear RNA amplification method and subsequent enzymatic reaction

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, CA, USA).

value: P, Pericancerous

value: Male

tag: survival

value: No

tag: recurrence

value: Yes

tag: cirrhosis

tag: edmonson

tag: metastasis

source_name: Liver tissue, Normal

value: N, Normal


title: Trp63 cHet vagina, rep1

description: Total RNA was extracted from the vaginae of 3 Trp63 cHet mice.

value: vagina


title: Liver_Pericancer_HK041_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient HK041 vs. Normal liver tissue mixed (Cy3)


title: T_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: T shRNA transient transfection , 72h, Replictaion 1; T_72h_shRNAtrasient #1; 251508710725A3

value: Universale Mouse Reference


title: MCC 4

value: FFPE MCC tissue


title: Liver_Pericancer_QD127_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient QD127 vs. Normal liver tissue mixed (Cy3)


title: T_72h_shRNAtrasient #2

description: shRNA transient transfection

value: T shRNA transient transfection , 72h, Replictaion 2; T_72h_shRNAtrasient #2; 251508710725A4


title: Liver_Cancer-HCC_HK042_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient HK042 vs. Normal liver tissue mixed (Cy3)

source_name: Liver tissue, Hepatocellular carcinoma

value: C, Cancer


title: Liver_Pericancer_QD128_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient QD128 vs. Normal liver tissue mixed (Cy3)


title: Liver_Cancer-HCC_HK041_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient HK041 vs. Normal liver tissue mixed (Cy3)


title: Sample 12_Cyclin ET74A T393A

description: Sample 12


title: Tcea3_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Tcea3 shRNA transient transfection , 72h, Replictaion 1; Tcea3_72h_shRNAtrasient #1; 251508710726A1


title: Sample 9_wild type

description: Sample 9

source_name: wild type_erythroblasts

value: wild type


title: Liver_Cancer-HCC_HK039_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient HK039 vs. Normal liver tissue mixed (Cy3)


title: Suz12_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Suz12 shRNA transient transfection , 72h, Replictaion 1; Suz12_72h_shRNAtrasient #1; 251508710725A1


title: Sample 8_wild type

description: Sample 8

value: bone marrow erythroid progenitors

value: sorted erythroid cells


title: Liver_Cancer-HCC_QD128_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient QD128 vs. Normal liver tissue mixed (Cy3)


title: Sample 10_wild type

description: Sample 10


title: Sample 7_wild type

description: Sample 7


title: Liver_Pericancer_HK039_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient HK039 vs. Normal liver tissue mixed (Cy3)

value: P, Pericancerous


title: Stat3_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Stat3 shRNA transient transfection , 72h, Replictaion 1; Stat3_72h_shRNAtrasient #1; 251508710724A3


title: Suz12_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Suz12 shRNA transient transfection , 72h, Replictaion 2; Suz12_72h_shRNAtrasient #2; 251508710725A2


title: MCC 1


title: MCC 3


title: Sample 6_Cyclin ET74A T393A

description: Sample 6

value: cyclin E (T74A T393A) knock-in


title: Liver_Cancer-HCC_HK035_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient HK035 vs. Normal liver tissue mixed (Cy3)

value: Male

value: No

value: Yes

value: N, Normal


title: Smad7_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Smad7 shRNA transient transfection , 72h, Replictaion 1; Smad7_72h_shRNAtrasient #1; 251508710724A1

value: Universale Mouse Reference


title: Liver_Pericancer_HK032_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient HK032 vs. Normal liver tissue mixed (Cy3)

value: Female


title: Liver_Pericancer_HK042_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient HK042 vs. Normal liver tissue mixed (Cy3)


title: Smad4_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Smad4 shRNA transient transfection , 72h, Replictaion 2; Smad4_72h_shRNAtrasient #2; 251508710723A4


title: Sample 2_wild type

description: Sample 2

value: wild type


title: Sample 4_Cyclin ET74A T393A

description: Sample 4


title: Sample 3_Cyclin ET74A T393A

description: Sample 3


title: MCC 2

value: FFPE MCC tissue


title: Smad7_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Smad7 shRNA transient transfection , 72h, Replictaion 2; Smad7_72h_shRNAtrasient #2; 251508710724A2


title: Liver_Pericancer_HK035_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient HK035 vs. Normal liver tissue mixed (Cy3)


title: Smad4_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Smad4 shRNA transient transfection , 72h, Replictaion 1; Smad4_72h_shRNAtrasient #1; 251508710723A3


title: Liver_Pericancer_HK017_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient HK017 vs. Normal liver tissue mixed (Cy3)

value: P, Pericancerous


title: miR-203 induced, biological rep2

city: Boulder

first: Zhaojie

last: Zhang

state: CO

address: 2300 Arapahoe Ave

institute: University of Colorado at Boulder

description: Gene expression data

hyb_protocol: standard Affymetrix protocol for Mouse 430 2.0 array

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Bioconductor with RMA as the background adjustment and normalization method.

source_name: Cells sorted from P4 old miR-203 inducible animals

label_protocol: standard Affymetrix protocol from 0.5 ug total RNA

growth_protocol: Mice were housed in the Mouse Facility under standard conditions.

extract_protocol: Cells sortd with FACS were put into Trizol and RNA extraction was performed according to the Trizol manufacturer's instructions.

treatment_protocol: We use two pairs of biological duplicates to perform the microarray analysis from the epidermal samples harvested from K14-rtTA/TRE-miR-203/K14-H2BGFP (DP) and TRE-miR-203/K14-H2BGFP (SP) littermates at P4, 24h after the Dox injection.

value: skin

value: miR-203 inducible

tag: background stain

value: FVB


title: Sample 5_Cyclin ET74A T393A

description: Sample 5

value: bone marrow erythroid progenitors

tag: cell type

value: sorted erythroid cells

value: cyclin E (T74A T393A) knock-in


title: Liver_Cancer-HCC_HK017_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient HK017 vs. Normal liver tissue mixed (Cy3)

value: C, Cancer

value: Male

value: No

value: Yes

value: N, Normal


title: Sall4_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Embryonic Stem Cells

tag: strain

value: Sall4 shRNA transient transfection , 72h, Replictaion 2; Sall4_72h_shRNAtrasient #2; 251508710723A2

value: Universale Mouse Reference


title: Sall4_72h_shRNAtrasient #1

description: shRNA transient transfection

tag: individual identifier

value: Sall4 shRNA transient transfection , 72h, Replictaion 1; Sall4_72h_shRNAtrasient #1; 251508710723A1


title: Liver_Pericancer_HK014_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient HK014 vs. Normal liver tissue mixed (Cy3)

tag: tissue type


title: Liver_Cancer-HCC_HK014_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient HK014 vs. Normal liver tissue mixed (Cy3)


title: uninduced WT control, biological rep1

description: Gene expression data

source_name: Cells sorted from P4 old WT animals

value: WT


title: miR-203 induced, biological rep1

description: Gene expression data


title: TetR2-C

city: Innsbruck

first: Daniel

last: Bindreither

state: Tirol

address: Innrain 82

department: Division of Molecular Pathophysiology

country: Austria

institute: Medical University Innsbruck

hyb_protocol: Target samples were hybridized to Human Gene 1.0 ST v2 microarrays according to the manufacturer's protocols.The microarrays were washed and stained in an Affymetrix fluidic station 450.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw data were preprocessed using the RMA method. For transcript probe set definition the custom CDF package from the brainarray group (hugene10stv1enstcdf version 13, defining probe sets for transcripts from Ensemble core database version 58) was used.

source_name: knock-down

label_protocol: Target RNA was labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station.

growth_protocol: CaCo2 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing high Glucose supplemented with 10 % heat-inactivated fetal bovine serum, 100 U/ml Penicillin, 100 µg/ml Streptomycin and Sodium Pyruvate. Cells were incubated in a humidified atmosphere with 5 % CO2 at 37 °C. To allow differentiation, CaCo2 cells were grown for 10 days on 24 mm Costar © Transwell filters (pore size 0.4 µm, Corning, Boston, Massachusettes). MYO5B RNAi in CaCo2 cells was performed using lentiviral shRNA against human myosin Vb. Small hairpin RNAs against human MYO5B were generated using the Gateway Multicloning System (Invitrogen). Three different shRNA were designed to facilitate MYO5B knock down. The targeted sequences were as follows: shRNA#1: 5’ggacttacctcttggagaa3’, shRNA#2: 5’aggcagatgatgagaggaa 3’ and shRNA#3: 5’gagaacagcaggacagcaa 3’. All 3 shRNA sequences were first cloned into a pENTR- THT III vector expressing the 5’TO promoter   and finally cloned into a pHR – DEST Puro vector. For stably expression of shRNA against human myosin Vb, CaCo2 cells were transfected with the pHR-DEST Puro vector containing the shRNA sequences against human MYO5B and afterwards selected with 12 µg Puromycin (Sigma Aldrich).To generate an inducible MYO5B RNAi cell system, wild type CaCo2 cells were transfected with pLenti-CMV-TetR BLAST plasmid from Addgene for stable expression of the TetR system. Afterwards transfected CaCo2 cells were selected with 12 µg Blasticidin (Invitrogen).CaCo2 cells stably expressing TeTR were cotransfected with pHR-DEST Puro vector containing the shRNA sequences against human myosin Vb and afterwards selected with 12 µg Puromycin (Sigma Aldrich). For infections of CaCo2 cells, lentivirus was packaged into 293T cells. 293T cells were transfected using Lipofectamine LTX plus Reagent (Invitrogen) with the plasmids containing the shRNA sequences together with the vesicular stomatitis virus-G (VSV-G) plasmid and the lentiviral gag-pol packaging vector PAX2. After 48 and 72 hours, respectively, the supernatant containing the virus was harvested and directly used for CaCo2 cell infection. After 48 hours post infection, CaCo2 cells were selected with 12 µg Puromycin (Sigma Aldrich) and 12 µg Blasticidin (Invitrogen).

treatment_protocol: Inducible MYO5B RNAi CaCo2 cells were treated for 5 days with 1 µg of Doxycycline obtaining efficient knock down of the myosin Vb protein. Knock down efficiency of induced MYO5B RNAi CaCo2 cells were tested with western blot analysis (supporting information 1).RNA was extracted using the RNeasy kit from Quiagen out of 3 different non-induced and induced MYO5B RNAi CaCo2 cells clone showing equally MYO5B knock down efficiency (supporting information 1). Thereby non-induced MYO5B RNAi CaCo2 cell clones served as controls and induced as knock down samples.

tag: cell line

value: colon carcinoma

tag: transfection

value: shRNA against Myosin V B induced by doxycyclin


title: TetR2-B

extract_protocol: RNA was extracted using the RNeasy kit from Quiagen out of 3 different non-induced and induced MYO5B RNAi CaCo2 cells clone showing equally MYO5B knock down efficiency (supporting information 1). Thereby non-induced MYO5B RNAi CaCo2 cell clones served as controls and induced as knock down samples.


title: Nr0b1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Nr0b1 shRNA transient transfection , 72h, Replictaion 2; Nr0b1_72h_shRNAtrasient #2; 251508710722A2


title: Liver_Pericancer_HK009_P_N3vsP5

description: Periancerous liver tissue (Cy5) from HCC patient HK009 vs. Normal liver tissue mixed (Cy3)

value: P, Pericancerous


title: Liver_Cancer-HCC_HK009_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient HK009 vs. Normal liver tissue mixed (Cy3)


title: Ring1+Rnf2+_E13.5_female_rep1

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: samples were hybridized to Mouse Gene 1.0 arrays from Affymetrix for 16h

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing: Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.15) / Bioconductor package affy (version 1.36).

source_name: Primordial germ cells

label_protocol: total RNA of 500 cells was converterd into OnmiPlex WTA cDNA libraries and amplified by WTA PCR usin greagetns supplied with the TansPlex Whole Transcriptome Amplification kit (WTA1, Sigma, USA) following the manufacturer's instructions but with the addition of 2mM UTP added to the dNTP mix. The obtained cDNA was purified using the GeneChip cDNA Sample Cleanyp Module (Affymetrix). The labeling and fragmentation of cDNA was performed according to Affymetrix instructions (GeneChip Whole Transcription Sense Target labeling technical manual, Rev. 2)

extract_protocol: Arcturus PicoPure™ RNA Isolation Kit (Invitrogen KIT0202)

treatment_protocol: Gonads from embryos carrying Oct4(deltaPE)-GFP transgene were treated with Trypsin to obtain single cell suspensions, which were subsequently processed by FACS to isolate GFP-positive PGCs.

value: Primordial germ cells

tag: genotype

tag: developmental stage

value: female

tag: genetic background

value: mixed129/Sv and C57BL6J


title: TetR2-A


title: Sample 1_wild type

description: Sample 1

tag: strain background

tag: tissue

value: bone marrow erythroid progenitors

value: sorted erythroid cells

value: wild type


title: Nr5a2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Nr5a2 shRNA transient transfection , 72h, Replictaion 2; Nr5a2_72h_shRNAtrasient #2; 251508710722A4


title: Ring1+Rnf2+_E13.5_female_rep2

tag: gender


title: Nr0b1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Nr0b1 shRNA transient transfection , 72h, Replictaion 1; Nr0b1_72h_shRNAtrasient #1; 251508710722A1


title: Tet3-ctr

source_name: control

value: shRNA against Myosin V B


title: Myc_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Myc shRNA transient transfection , 72h, Replictaion 2; Myc_72h_shRNAtrasient #2; 251508710721A4


title: Ring1+Rnf2+_E13.5_male_rep2

value: male


title: Tet2-ctr


title: Ring1+Rnf2+_E13.5_male_rep3


title: Nr5a2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Nr5a2 shRNA transient transfection , 72h, Replictaion 1; Nr5a2_72h_shRNAtrasient #1; 251508710722A3

value: Universale Mouse Reference


title: CN vs CN+MAC_biological replicate 3_technical replicate 2 (dye-flip)

city: St. Louis

first: Michael

last: Heinz

state: MO

address: 4320 Forest Park Blvd.

department: Genetics

institute: Washington University School of Medicine

description: Biological replicate 3 of 3

hyb_protocol: Each sample pair (~20ul) is suspended in Formamide-based  hybridization buffer (vial 7-Genisphere) (26ul), Array 50dT blocker (Genisphere) (2ul), and Rnase/Dnase-free water (4ul).  Two hybridizations are carried out in a sequential manner. The primary hybridization is performed by adding 48ul of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity.  Prior to the secondary hybridization, slides are gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. Secondary hybridization is carried out using the complimentary capture reagents provided in the 3DNA Array 350 kit (Genisphere).  For each reaction, the following are added: 3DNA capture reagent with Cy3 (2.5ul), 3DNA capture reagent with Cy5 (2.5ul), SDS-based hybridization buffer (vial 6-Genisphere) (26ul), and Rnase/Dnase-free water (21ul).  The secondary hybridization solution is incubated in the dark at 80C for 10 min. then 50C for 15 min.  Hybridization is performed by adding 48ul secondary hybridization solution to the slide under a supported glass coverslip at 65C for 3 hr at high humidity in the dark. At hybridization termination, arrays are gently submerged into 2X SSC, 0.2% SDS (at 65C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.  To prevent fluorophore degredation, the arrays are treated with Dyesaver (Genisphere).

scan_protocol: Slides are scanned on a Molecular Devices Genepix 4000B microarray scanner to detect Cy3 fluorescence.  Laser power is kept constant and PMT voltage is established for all 12 arrays on the glass such that the each array has less than 1% signal saturation in either dye. Images were quantitated with Genepix Pro, v6.1 (Molecular Devices).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of test/reference.

organism: Cryptococcus neoformans

source_name: H99 yeast cells, phagocytosed by J774.A1 macrophages at 37C/5%CO2, six hours

label_protocol: First strand cDNA is generated by polyT primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array350  kit (Genisphere).  For cDNA synthesis, 1ul of fluorophore specific oligo-dT primer is added to 8ug of total RNA and the solution is incubated at 80C for 10 minutes then cooled on ice for 2 minutes.  To each sample are added RNase inhibitor (Superase-In; Ambion) (1ul), 5X first strand buffer (4ul), dNTP mix (10mM each dATP, dCTP, dGTP, and dTTP) (1ul), 0.1M DTT (2ul), and Superscript II RNase H- Reverse Transcriptase (1ul).  Reverse transcription is carried out at 42C for 2 hours.  The reaction is terminated by adding 0.5M NaOH/ 50mM EDTA (3.5ul) and incubation at 65C for 15 minutes then neutralized with 1M Tris-HCL, pH 7.5 (5ul).  For RNA expression level comparison, samples are paired and concentrated using Microcon YM30 microconcentrators (Millipore) according to the manufacturer’s protocol.

growth_protocol: Yeast cells were grown on YPD medium for 24 hours at 30C prior to co-incubation with phagocytes.

extract_protocol: TRIzol RNA extraction followed by purification through a QIAGEN RNEasy column

treatment_protocol: For amoeba co-cultures, yeast cells were added to amoeba monolayers at MOI of five and incubated for six hours at 28C in PYG medium. For macrophage co-cultures, MOI and incubation times were kept; medium was DMEM and incubation was at 37C/5% CO2.

tag: treatment

value: phagocytosed by J774.A1 macrophages at 37C/5%CO2, for 6 hours

source_name: H99 yeast cells, vegetative growth at 37C

value: vegetative growth at 37C


title: CN vs CN+MAC_biological replicate 3_technical replicate 1

description: Biological replicate 3 of 3


title: Myc_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Myc shRNA transient transfection , 72h, Replictaion 1; Myc_72h_shRNAtrasient #1; 251508710721A3


title: Ring1+Rnf2delta_E12.5_female_rep3

value: Primordial germ cells


title: Tet1-ctr

value: colon carcinoma


title: Mybl2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Mybl2 shRNA transient transfection , 72h, Replictaion 2; Mybl2_72h_shRNAtrasient #2; 251508710721A2


title: Ring1+Rnf2delta_E12.5_female_rep2

value: female

value: mixed129/Sv and C57BL6J


title: CN vs CN+MAC_biological replicate 2_technical replicate 1

description: Biological replicate 2 of 3


title: CN vs CN+MAC_biological replicate 1_technical replicate 2 (dye-flip)

description: Biological replicate 1 of 3


title: CN vs CN+MAC_biological replicate 2_technical replicate 2 (dye-flip)

description: Biological replicate 2 of 3


title: CN vs CN+MAC_biological replicate 1_technical replicate 1

description: Biological replicate 1 of 3


title: Ring1+Rnf2+_E13.5_male_rep1


title: Mybl2_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Mybl2 shRNA transient transfection , 72h, Replictaion 1; Mybl2_72h_shRNAtrasient #1; 251508710721A1


title: Ring1+Rnf2+_E12.5_female_rep2


title: Ring1+Rnf2+_E12.5_female_rep3


title: Klf4_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Klf4 shRNA transient transfection , 72h, Replictaion 2; Klf4_72h_shRNAtrasient #2; 251508710720A4


title: CN vs CN+AC_biological replicate 3_technical replicate 2 (dye-flip)

description: Biological replicate 3 of 3

source_name: H99 yeast cells, phagocytosed by Acanthamoeba castellanii at 28C, six hours

value: phagocytosed by Acanthamoeba castellanni at 28C for 6 hours

source_name: H99 yeast cells, vegetative growth at 28C

value: vegetative growth at 28C


title: Ring1+Rnf2delta_E12.5_female_rep1


title: Ring1+Rnf2+_E12.5_female_rep1


title: Klf4_72h_shRNAtrasient #1

description: shRNA transient transfection

source_name: shRNA transient transfection

value: Embryonic Stem Cells

value: Klf4 shRNA transient transfection , 72h, Replictaion 1; Klf4_72h_shRNAtrasient #1; 251508710720A3

source_name: Universal Mouse Reference 129ES Cell


title: CN vs CN+AC_biological replicate 2_technical replicate 1

description: Biological replicate 2 of 3


title: Id1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Id1 shRNA transient transfection , 72h, Replictaion 1; Id1_72h_shRNAtrasient #1; 251508710720A1


title: Ring1+Rnf2delta_E12.5_male_rep3

value: male


title: CN vs CN+AC_biological replicate 3_technical replicate 1

description: Biological replicate 3 of 3


title: CN vs CN+AC_biological replicate 2_technical replicate 2 (dye-flip)

description: Biological replicate 2 of 3


title: Ring1+Rnf2delta_E12.5_male_rep1


title: Ring1+Rnf2delta_E12.5_male_rep2


title: Fem1b_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Fem1b shRNA transient transfection , 72h, Replictaion 2; Fem1b_72h_shRNAtrasient #2; 251508710719A4

value: Universale Mouse Reference


title: Id1_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Id1 shRNA transient transfection , 72h, Replictaion 2; Id1_72h_shRNAtrasient #2; 251508710720A2


title: CN vs CN+AC_biological replicate 1_technical replicate 2 (dye-flip)

description: Biological replicate 1 of 3


title: Eed_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Eed shRNA transient transfection , 72h, Replictaion 2; Eed_72h_shRNAtrasient #2; 251508710719A2


title: Fem1b_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Fem1b shRNA transient transfection , 72h, Replictaion 1; Fem1b_72h_shRNAtrasient #1; 251508710719A3


title: Dppa5a_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Dppa5a shRNA transient transfection , 72h, Replictaion 1; Dppa5a_72h_shRNAtrasient #1; 251508710718A3


title: Ring1+Rnf2+_E12.5_male_rep2

value: Primordial germ cells


title: NCI-HPN-M2G Kid_p36

type: genomic

city: Bethesda

first: Hesed

middle: Maria

last: Padilla-Nash

address: 50 South Drive

department: Genetics Branch

institute: NCI

hyb_protocol: The differentially labeled targets sample and reference DNA  were combined with Agilent 10X Blocking Agent, Agilent 2X Hybridization Buffer,  and Cot-1 DNA , denatured at 95C for 3 min and preannealed for 30 min at 37C according to the Agilent Oligonucleotide Array-Based CGH for Genomic Analysis Protocol. The denatured probe was applied to the Agilent Mouse Genome CGH 44K Microarray Kit according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using an Agilent Scanner System. Images were quantified using Agilent Feature Extraction Software (version 8.1.1).

data_processing: DNA copy package from Bioconductor was used to analyze aCGH data. The data were smoothed using smooth.CNA (with smooth.region = 2, and smooth.SD.scale = 3), then CBS was performed using segment (with alpha = 0.02, undo.split = sdundo and undo.SD = 0.9).

molecule: genomic DNA

source_name: mouse epithelial kidney cells_passage 36

label_protocol: 7ug of digested DNA was prepared for labeling with the BioPrime Array Genomic Labeling Kit using Cy3 -dUTP for the test DNA and Cy5-dUTP for the reference DNAas described in Agilent Oligonucleotide Array-Based CGH for Genomic Analysis Protocol.

growth_protocol: The epithelial cells were grown in DMEM/F12 media supplemented with low fetal bovine serum (2-5%).The cells were fed every 10 days to promote in vitro cellular transformation (Padilla Nash et al., 2012).

extract_protocol: DNA was extracted from the murine epithelial cells and the mouse C57BL/6 liver cells (normal reference DNA) using protocols described in http://www.riedlab.nci.nih.gov/protocols.

value: kidney

tag: Stage

value: transformed

tag: passage

source_name: Male Mouse DNA

value: mouse liver cells

tag: sample type

value: normal reference DNA


title: NCI-HPN-M2C Kid_p55

source_name: mouse epithelial kidney cells_passage 55


title: Eed _72h_shRNAtrasient #1

description: shRNA transient transfection

value: Eed shRNA transient transfection , 72h, Replictaion 1; Eed _72h_shRNAtrasient #1; 251508710719A1


title: NCI-HPN-M1C Kid_p41

source_name: mouse epithelial kidney cells_passage 41


title: Liver_Cancer-HCC_HK032_C_N3vsC5

description: Cancer liver tissue (Cy5) from HCC patient HK032 vs. Normal liver tissue mixed (Cy3)

source_name: Liver tissue, Hepatocellular carcinoma

value: C, Cancer

value: Female

tag: age

tag: survival

value: No

tag: recurrence

tag: cirrhosis

value: Yes

tag: edmonson

tag: metastasis

source_name: Liver tissue, Normal

value: N, Normal


title: CN vs CN+AC_biological replicate 1_technical replicate 1

description: Biological replicate 1 of 3

tag: strain

value: vegetative growth at 28C

value: phagocytosed by Acanthamoeba castellanni at 28C for 6 hours


title: Ring1+Rnf2+_E12.5_male_rep1

tag: cell type

tag: genotype

value: male

value: mixed129/Sv and C57BL6J


title: Ring1+Rnf2+_E13.5_female_rep3

tag: developmental stage

value: female

tag: genetic background


title: Ring1+Rnf2delta_E11.5_female_rep3


title: NCI-HPN-F2G Kid_p35

source_name: mouse epithelial kidney cells_passage 35

tag: tissue

source_name: Female Mouse DNA


title: Ring1+Rnf2delta_E11.5_female_rep2

tag: gender


title: Dppa5a_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Embryonic Stem Cells

tag: individual identifier

value: Dppa5a shRNA transient transfection , 72h, Replictaion 2; Dppa5a_72h_shRNAtrasient #2; 251508710718A4

value: Universale Mouse Reference


title: Dnmt3b_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Dnmt3b shRNA transient transfection , 72h, Replictaion 2; Dnmt3b_72h_shRNAtrasient #2; 251508710718A2


title: Ring1+Rnf2delta_E11.5_female_rep1

value: Primordial germ cells


title: Ring1+Rnf2+_E12.5_male_rep3


title: AY350 5360-2 500193-4

city: Seattle

first: Toshio

last: Tsukiyama

state: WA

address: 1100 Fairview Ave N

department: Basic Science

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Equal concentrations of WT Isw2 and Isw2-K215R or input and Ume6 were competitively hybridized onto custom Nimblegen microarrays according to manufactures protocol.

scan_protocol: Scan was performed per manufactures protocol

data_processing:
Log2 ratios and normalization was performed individually for forward and reverse strands using Ringo (Toedling et al. 2007) and chipchipnorm (nlag=30) (Peng et al. 2007) R packages followed by median adjustment and pseudomedian smoothing (150 bp window) (Royce et al. 2007).
The scaled and normalized Log2 ratio  for each of the forward and reverse strands was then averaged across all biological replicates for a given strain (as indicated by the sample name - the same sample name denotes biological replicates) to generate a single average log2 ratio for each strain as reported.

organism: Saccharomyces cerevisiae

label_protocol: DNA was fragmented and Cy-dye labeled (WT Isw2=Cy3, Isw2-K215R=Cy5, or input=Cy3, Ume6=Cy5) as described (Yadon et al. 2010a).

extract_protocol: Chromatin from strains with either 3X-Flag-tagged Isw2 or 3X-Flag-tagged Ume6 were crosslinked for 20 min, fragmented by sonication, and immunoprecipitated using approximately 6 mL (of OD660=0.70 +/- 0.05) of cell equivalent as described (Gelbart et al. 2005). Purified DNA was amplified using linker-mediated PCR amplification.  dUTP incorporation was achieved by boiling of 3 µg DNA, 55 µM Tris-HCl pH6.8, 5.55 mM MgCl2, 15 µg Random Hexamers, and H2O to final volume of 45 µL for 5 min followed by 5 min incubation on ice.  5 µL dNTP mix (1.2 mM dATP, 1.2 mM dCTP, 1.2 mM dGTP, 0.95 mM dTTP, and 0.25 mM dUTP) and 1 µL 50 U/µL Klenow (exo-) was incubated 10 min at 22°C, 30 min at 37°C, 5 min at 95°C, and 5 min at 4°C.  Incubation was repeated following the addition of 1 µL Klenow (exo-).  DNA was finally phenol-chloroform extracted and ethanol precipitated.

tag: strain number

value: MAT@ cyc1-5000 cyc7-67 ura3-52 leu2-3, 112 cyh2 sua7-1 Ume6-3XFLAG-KanMX

value: Genomic DNA

tag: chip antibody

value: input DNA

tag: label

value: Ume6 ChIP DNA

value: Anti-Flag for Ume6-3XFlag


title: NCI-HPN-F1G Kid_p40

source_name: mouse epithelial kidney cells_passage 40

value: kidney

tag: Stage

value: transformed

tag: passage

value: mouse liver cells

tag: sample type

value: normal reference DNA


title: Dnmt3b_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Dnmt3b shRNA transient transfection , 72h, Replictaion 1; Dnmt3b_72h_shRNAtrasient #1; 251508710718A1


title: AY350 331-5354 500193-4

value: MATa s288c his3-1 leu2-0 ura3-0 met+ lys+ Ume6-3XFlag-KanMX


title: Ring1+Rnf2+_E11.5_female_rep3

source_name: Primordial germ cells

value: female

value: mixed129/Sv and C57BL6J


title: Ring1+Rnf2+_E11.5_female_rep2


title: NCI-HPN-F1B Kid_p38

source_name: mouse epithelial kidney cells_passage 38


title: AY350 5361-1 500193-4


title: Ring1+Rnf2+_E11.5_female_rep1


title: Mycn_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Mycn shRNA transient transfection , 72h, Replictaion 2; Mycn_72h_shRNAtrasient #2; 251508710717A2


title: NCI-HPN-M2C Blad_p63

source_name: mouse epithelial bladder cells_passage 63

value: male

value: bladder


title: NCI-HPN-M1C Blad_p67

source_name: mouse epithelial bladder cells_passage 67


title: Ring1+Rnf2delta_E11.5_male_rep3

value: Primordial germ cells


title: NCI-HPN-F2G Blad_p53

source_name: mouse epithelial bladder cells_passage 53


title: NCI-HPN-M1I Blad_p55

source_name: mouse epithelial bladder cells_passage 55


title: Sox2_72h_shRNAtrasient #1

description: shRNA transient transfection

source_name: shRNA transient transfection

value: Sox2 shRNA transient transfection , 72h, Replictaion 1; Sox2_72h_shRNAtrasient #1; 251508710716A3

value: Universale Mouse Reference


title: Sox2_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Sox2 shRNA transient transfection , 72h, Replictaion 2; Sox2_72h_shRNAtrasient #2; 251508710716A4

source_name: Universal Mouse Reference 129ES Cell


title: uninduced WT control, biological rep2

description: Gene expression data

source_name: Cells sorted from P4 old WT animals

value: skin

value: WT

tag: age

tag: background stain

value: FVB


title: AY345 5354 452821-3

value: Genomic DNA

value: input DNA

value: Ume6 ChIP DNA

value: Anti-Flag for Ume6-3XFlag


title: Mycn_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Mycn shRNA transient transfection , 72h, Replictaion 1; Mycn_72h_shRNAtrasient #1; 251508710717A1


title: AY345 5360-1 452821-3

value: MAT@ cyc1-5000 cyc7-67 ura3-52 leu2-3, 112 cyh2 sua7-1 Ume6-3XFLAG-KanMX


title: AY327 sua7-1 a 452821-2

value: MAT@ cyc1-5000 cyc7-67 ura3-52 leu2-3 112 cyh2 sua7-1 isw2-3XFLAG (KAN)

value: Isw2 ChIP DNA

value: Anti-Flag for Isw2-3XFlag

value: MAT@ cyc1-5000 cyc7-67 ura3-52 leu2-3 112 cyh2 sua7-1 isw2-K215R-3XFLAG (KAN)

value: Isw2-K215R ChIP DNA


title: NCI-HPN-F1G Blad_p56

source_name: mouse epithelial bladder cells_passage 56

value: female

value: bladder

value: transformed

value: mouse liver cells

value: normal reference DNA


title: Pou5f1(2)_72h_shRNAtrasient #2

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Pou5f1 shRNA transient transfection , 72h, Replictaion 2; Pou5f1(2)_72h_shRNAtrasient #2; 251508710716A2

value: Universale Mouse Reference


title: AY345 5355 452821-3

value: MATa s288chis3-1 leu2-0 ura3-0 met+ lys+ Ume6-3XFlag-KanMX

value: Genomic DNA

value: input DNA

value: Ume6 ChIP DNA


title: Ring1+Rnf2delta_E11.5_male_rep1

value: Primordial germ cells

value: male

value: mixed129/Sv and C57BL6J


title: Pou5f1(2)_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Pou5f1 shRNA transient transfection , 72h, Replictaion 1; Pou5f1(2)_72h_shRNAtrasient #1; 251508710716A1


title: Ctnnb1_72h_shRNAtrasient #1

description: shRNA transient transfection

value: Ctnnb1 shRNA transient transfection , 72h, Replictaion 1; Ctnnb1_72h_shRNAtrasient #1; 251508710717A3


title: AY304 sua7-1 471425-3

value: MAT@ cyc1-5000 cyc7-67 ura3-52 leu2-3 112 cyh2 sua7-1 isw2-3XFLAG (KAN)

value: Isw2 ChIP DNA

value: Anti-Flag for Isw2-3XFlag

value: MAT@ cyc1-5000 cyc7-67 ura3-52 leu2-3 112 cyh2 sua7-1 isw2-K215R-3XFLAG (KAN)

value: Isw2-K215R ChIP DNA


title: NCI-HPN-M2G Kid_p35

hyb_protocol: The differentially labeled targets sample and reference DNA  were combined with Agilent 10X Blocking Agent, Agilent 2X Hybridization Buffer,  and Cot-1 DNA , denatured at 95C for 3 min and preannealed for 30 min at 37C according to the Agilent Oligonucleotide Array-Based CGH for Genomic Analysis Protocol. The denatured probe was applied to the Agilent Mouse Genome CGH 244K Microarray Kit according to the manufacturer's instructions.

data_processing: Rank Segmentation algorithm of Nexus Copy Number 6 was used to analyze aCGH data. Significance Threshold: 5E-6; Max Contiguous Probe Spacing: 3000; Min number of probes per segment: 6; Systematic correction: linear correction with correction file provided by Nexus.

value: kidney

value: transformed

source_name: Male Mouse DNA

value: mouse liver cells

value: normal reference DNA


title: Ring1+Rnf2+_E11.5_male_rep3


title: H2AV 9751 ML-DmBG3-c2 D.melanogaster ChIP Rep2

status: Public on Mar 13 2013

city: Toronto

first: DCC

last: modENCODE

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

institute: Ontario Institute for Cancer Research

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

organism: Drosophila melanogaster

source_name: H2AV 9751 DmBG3 ChIP expt.1151 channel_1

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: cell line

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

tag: Sex

value: Unknown


title: Ring1+Rnf2+_E11.5_male_rep2

tag: cell type

value: Primordial germ cells

value: male


title: H2AV 9751 ML-DmBG3-c2 D.melanogaster Input Rep1

description: Served as Input for: 1147.Mvalues.bedgraph

source_name: H2AV 9751 DmBG3 Input expt.1153 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

tag: genotype


title: H2AV 9751 ML-DmBG3-c2 D.melanogaster Input Rep2

description: Served as Input for: 1151.Mvalues.bedgraph

source_name: H2AV 9751 DmBG3 Input expt.1154 channel_1

tag: developmental stage


title: AY327 sua7-1 b 452821-2


title: H3K9ac 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K9ac 2-4 hr OR Em. ChIP expt.811 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: strain

value: Oregon-R

value: Embryo 2-4hr OR

value: wild type


title: AY308 sok2 500193

value: MATa s288c MET+ LYS+ Isw2-3XFLAG (HYG) sok2::KanMX his3-1 leu2-0 ura3-0

value: Isw2 ChIP DNA

value: MATa s288c MET+ LYS+ Isw2-K215R-3XFLAG (HYG) sok2::KanMX his3-1 leu2-0 ura3-0


title: Ring1+Rnf2+_E11.5_male_rep1

tag: genetic background

value: mixed129/Sv and C57BL6J


title: H3K9ac 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K9ac 2-4 hr OR Em. ChIP expt.806 channel_1


title: AY295 cin5 471425

value: MATa s288c MET+ LYS+ Isw2-3XFLAG (HYG) cin5::KanMX his3-1 leu2-0 ura3-0

value: Anti-Flag for Isw2-3XFlag

value: MATa s288c MET+ LYS+ Isw2-K215R-3XFLAG (HYG) cin5::KanMX his3-1 leu2-0 ura3-0

value: Isw2-K215R ChIP DNA


title: Nanog _72h_shRNAtrasient #1

description: shRNA transient transfection

value: Embryonic Stem Cells

value: Nanog shRNA transient transfection , 72h, Replictaion 1; Nanog _72h_shRNAtrasient #1; 251508710715A3

value: Universale Mouse Reference


title: H3K9ac 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 811.Mvalues.bedgraph

source_name: H3K9ac 2-4 hr OR Em. Input expt.690 channel_1


title: H4K16ac(M) L3 Nuclear Sexed Male Jil Mutant Heterozygous D.melanogaster ChIP Rep2

source_name: H4K16ac(M) L3 Nuc. SexedMJilMutant-HZ ChIP expt.1900 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Sexed male Jil mutant-heterozygous

value: 3rd Instar Larvae Sexed Male

value: Jil-1 z2/TM3 Ser-GFP

value: Male

tag: transgene

value: deletion


title: NCI-HPN-M2C Blad_p59

source_name: mouse epithelial bladder cells_passage 59

tag: tissue

value: bladder

value: transformed

tag: gender

value: male

value: mouse liver cells

value: normal reference DNA


title: Ring1+Rnf2delta_E11.5_male_rep2

source_name: Primordial germ cells

value: Primordial germ cells

value: mixed129/Sv and C57BL6J


title: H2AV 9751 ML-DmBG3-c2 D.melanogaster ChIP Rep1

source_name: H2AV 9751 DmBG3 ChIP expt.1147 channel_1

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

value: Unknown


title: AY296 cin5 293393-2

tag: strain number

value: MATa s288c MET+ LYS+ Isw2-3XFLAG (HYG) cin5::KanMX his3-1 leu2-0 ura3-0

value: Isw2 ChIP DNA

tag: chip antibody

value: Anti-Flag for Isw2-3XFlag

value: MATa s288c MET+ LYS+ Isw2-K215R-3XFLAG (HYG) cin5::KanMX his3-1 leu2-0 ura3-0

value: Isw2-K215R ChIP DNA


title: H4K16ac(M) L3 Nuclear Sexed Male Jil Mutant Heterozygous D.melanogaster Input Rep2

description: Served as Input for: 1900.Mvalues.bedgraph

source_name: H4K16ac(M) L3 Nuc. SexedMJilMutant-HZ Input expt.1907 channel_1

value: Sexed male Jil mutant-heterozygous

value: 3rd Instar Larvae Sexed Male

value: Jil-1 z2/TM3 Ser-GFP

value: Male

value: deletion


title: H4K16ac(M) L3 Nuclear Sexed Male Jil Mutant D.melanogaster ChIP Rep2

source_name: H4K16ac(M) L3 Nuc. SexedMJil ChIP expt.1492 channel_1

value: Sexed male Jil mutant

value: Jil-1 z2/Jil-1z2


title: H4K16ac(M) L3 Nuclear Sexed Male Jil Mutant Heterozygous D.melanogaster Input Rep1

description: Served as Input for: 1898.Mvalues.bedgraph

source_name: H4K16ac(M) L3 Nuc. SexedMJilMutant-HZ Input expt.1906 channel_1


title: H4K16ac(M) L3 Nuclear Sexed Male Jil Mutant Heterozygous D.melanogaster ChIP Rep1

source_name: H4K16ac(M) L3 Nuc. SexedMJilMutant-HZ ChIP expt.1898 channel_1


title: H4K16ac(M) L3 Nuclear Sexed Male Jil Mutant D.melanogaster ChIP Rep1

source_name: H4K16ac(M) L3 Nuc. SexedMJil ChIP expt.1416 channel_1


title: H4K16ac(M) L3 Nuclear Sexed Male Jil Mutant D.melanogaster Input Rep2

description: Served as Input for: 1492.Mvalues.bedgraph

source_name: H4K16ac(M) L3 Nuc. SexedMJil Input expt.1182 channel_1


title: H4K16ac(M) L3 Nuclear Sexed Male Jil Mutant D.melanogaster Input Rep1

description: Served as Input for: 1416.Mvalues.bedgraph

source_name: H4K16ac(M) L3 Nuc. SexedMJil Input expt.1180 channel_1


title: H4K16ac(M) L3 Nuclear Sexed Female Jil Mutant D.melanogaster ChIP Rep1

source_name: H4K16ac(M) L3 Nuc. SexedFJil ChIP expt.1417 channel_1

value: Sexed Female Jil mutant

value: 3rd Instar Larvae Sexed Female

value: Jil-1 z2/ Jil-1 z2

value: Female


title: AY296 sok2 293393-2

value: MATa s288c MET+ LYS+ Isw2-3XFLAG (HYG) sok2::KanMX his3-1 leu2-0 ura3-0

tag: label

value: MATa s288c MET+ LYS+ Isw2-K215R-3XFLAG (HYG) sok2::KanMX his3-1 leu2-0 ura3-0


title: Nanog _72h_shRNAtrasient #2

description: shRNA transient transfection

source_name: shRNA transient transfection

value: Embryonic Stem Cells

tag: individual identifier

value: Nanog shRNA transient transfection , 72h, Replictaion 2; Nanog _72h_shRNAtrasient #2; 251508710715A4

source_name: Universal Mouse Reference 129ES Cell

value: Universale Mouse Reference


title: H4K16ac(M) L3 Nuclear Sexed Female Jil Mutant D.melanogaster Input Rep2

description: Served as Input for: 1493.Mvalues.bedgraph

source_name: H4K16ac(M) L3 Nuc. SexedFJil Input expt.1183 channel_1


title: H4K16ac(M) L3 Nuclear Sexed Female Jil Mutant D.melanogaster ChIP Rep2

source_name: H4K16ac(M) L3 Nuc. SexedFJil ChIP expt.1493 channel_1


title: H4K16ac(M) L3 Nuclear Sexed Female Jil Mutant D.melanogaster Input Rep1

description: Served as Input for: 1417.Mvalues.bedgraph

source_name: H4K16ac(M) L3 Nuc. SexedFJil Input expt.1181 channel_1


title: H3K9me2 Ab2 (new lot 3) Nuclear L3 G9a Mutant D.melanogaster ChIP Rep1

source_name: H3K9me2 Ab2 (new lot 3) Nuc. L3 G9a ChIP expt.2163 channel_1

value: G9a mutant

value: 3rd Instar Larvae


title: H3K9me2 Ab2 (new lot 3) Nuclear L3 G9a Mutant D.melanogaster ChIP Rep2

source_name: H3K9me2 Ab2 (new lot 3) Nuc. L3 G9a ChIP expt.2164 channel_1


title: H3K9me2 Ab2 (new lot 3) Nuclear L3 G9a Mutant D.melanogaster Input Rep2

description: Served as Input for: 2164.Mvalues.bedgraph

source_name: H3K9me2 Ab2 (new lot 3) Nuc. L3 G9a Input expt.2160 channel_1


title: H3K9me2 Ab2 (new lot 3) Nuclear L3 G9a Mutant D.melanogaster Input Rep1

description: Served as Input for: 2163.Mvalues.bedgraph

source_name: H3K9me2 Ab2 (new lot 3) Nuc. L3 G9a Input expt.2159 channel_1


title: AY327 ume6 452821-2

value: MATa s288c MET+ LYS+ Isw2-3XFLAG (HYG) ume6::KanMX his3-1 leu2-0 ura3-0

tag: sample type

value: Isw2 ChIP DNA

value: Anti-Flag for Isw2-3XFlag

value: MATa s288c MET+ LYS+ Isw2-K215R-3XFLAG (HYG) ume6::KanMX his3-1 leu2-0 ura3-0

value: Isw2-K215R ChIP DNA


title: H3K9ac 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 806.Mvalues.bedgraph

source_name: H3K9ac 2-4 hr OR Em. Input expt.800 channel_1

value: Oregon-R

value: Embryo 2-4hr OR

value: wild type


title: RNA Pol II (abcam) L3 Nuclear HP1b Mutant D.melanogaster Input Rep1

description: Served as Input for: 1850.Mvalues.bedgraph

source_name: RNA Pol II (abcam) L3 Nuc. HP1b Input expt.1844 channel_1

value: HP1b mutant


title: RNA Pol II (abcam) L3 Nuclear HP1b Mutant D.melanogaster ChIP Rep2

source_name: RNA Pol II (abcam) L3 Nuc. HP1b ChIP expt.1851 channel_1


title: RNA Pol II (abcam) L3 Nuclear HP1b Mutant D.melanogaster ChIP Rep1

source_name: RNA Pol II (abcam) L3 Nuc. HP1b ChIP expt.1850 channel_1


title: AY295 nrg1 293393

value: MATa s288c MET+ LYS+ Isw2-3XFLAG (HYG) nrg1::KanMX his3-1 leu2-0 ura3-0


title: RNA Pol II (abcam) L3 Nuclear G9a Mutant D.melanogaster Input Rep2

description: Served as Input for: 2170.Mvalues.bedgraph

source_name: RNA Pol II (abcam) L3 Nuc. G9a Input expt.2160 channel_1


title: RNA Pol II (abcam) L3 Nuclear G9a Mutant D.melanogaster ChIP Rep1

source_name: RNA Pol II (abcam) L3 Nuc. G9a ChIP expt.2169 channel_1


title: H3K9me3 abcam L3 Nuclear G9a Mutant D.melanogaster ChIP Rep2

source_name: H3K9me3 abcam L3 Nuc. G9a ChIP expt.2166 channel_1


title: RNA Pol II (abcam) L3 Nuclear G9a Mutant D.melanogaster ChIP Rep2

source_name: RNA Pol II (abcam) L3 Nuc. G9a ChIP expt.2170 channel_1


title: H3K9me3 abcam L3 Nuclear G9a Mutant D.melanogaster ChIP Rep1

source_name: H3K9me3 abcam L3 Nuc. G9a ChIP expt.2165 channel_1


title: AY296 nrg1 471425-2

value: MATa s288c MET+ LYS+ Isw2-K215R-3XFLAG (HYG) nrg1::KanMX his3-1 leu2-0 ura3-0


title: H3K9me3 abcam L3 Nuclear G9a Mutant D.melanogaster Input Rep1

description: Served as Input for: 2165.Mvalues.bedgraph

source_name: H3K9me3 abcam L3 Nuc. G9a Input expt.2159 channel_1


title: HP1b Q4114 L3 Nuclear HP1b Mutant D.melanogaster ChIP Rep2

source_name: HP1b Q4114 L3 Nuc. HP1b ChIP expt.1847 channel_1


title: RNA Pol II (abcam) L3 Nuclear G9a Mutant D.melanogaster Input Rep1

description: Served as Input for: 2169.Mvalues.bedgraph

source_name: RNA Pol II (abcam) L3 Nuc. G9a Input expt.2159 channel_1


title: HP1b Q4114 L3 Nuclear HP1b Mutant D.melanogaster Input Rep2

description: Served as Input for: 1847.Mvalues.bedgraph

source_name: HP1b Q4114 L3 Nuc. HP1b Input expt.1845 channel_1


title: HP1b Q4114 L3 Nuclear HP1b Mutant D.melanogaster ChIP Rep1

source_name: HP1b Q4114 L3 Nuc. HP1b ChIP expt.1846 channel_1


title: H3K9me2 antibody2 L3 Nuclear Sexed Male Jil Mutant Heterozygous D.melanogaster ChIP Rep2

source_name: H3K9me2 antibody2 L3 Nuc. SexedMJilMutant-HZ ChIP expt.1944 channel_1

value: Sexed male Jil mutant-heterozygous

value: 3rd Instar Larvae Sexed Male

value: Jil-1 z2/TM3 Ser-GFP

value: Male

value: deletion


title: H3K9me2 antibody2 L3 Nuclear Sexed Male Jil Mutant Heterozygous D.melanogaster ChIP Rep1

source_name: H3K9me2 antibody2 L3 Nuc. SexedMJilMutant-HZ ChIP expt.1942 channel_1


title: H3K9me2 antibody2 L3 Nuclear Sexed Male Jil Mutant Heterozygous D.melanogaster Input Rep2

description: Served as Input for: 1944.Mvalues.bedgraph

source_name: H3K9me2 antibody2 L3 Nuc. SexedMJilMutant-HZ Input expt.1907 channel_1


title: AY362 sua7-1 452821-4

value: MAT@ cyc1-5000 cyc7-67 ura3-52 leu2-3 112 cyh2 sua7-1 isw2-3XFLAG (KAN)

value: MAT@ cyc1-5000 cyc7-67 ura3-52 leu2-3 112 cyh2 sua7-1 isw2-K215R-3XFLAG (KAN)


title: HP1b Q4113 L3 Nuclear HP1b Mutant D.melanogaster ChIP Rep2

source_name: HP1b Q4113 L3 Nuc. HP1b ChIP expt.2537 channel_1

value: 3rd Instar Larvae


title: HP1b Q4113 L3 Nuclear HP1b Mutant D.melanogaster Input Rep1

description: Served as Input for: 2535.Mvalues.bedgraph

source_name: HP1b Q4113 L3 Nuc. HP1b Input expt.2536 channel_1


title: H3K9me3 abcam L3 Nuclear G9a Mutant D.melanogaster Input Rep2

description: Served as Input for: 2166.Mvalues.bedgraph

source_name: H3K9me3 abcam L3 Nuc. G9a Input expt.2160 channel_1

value: G9a mutant


title: HP1b Q4113 L3 Nuclear HP1b Mutant D.melanogaster Input Rep2

description: Served as Input for: 2537.Mvalues.bedgraph

source_name: HP1b Q4113 L3 Nuc. HP1b Input expt.2538 channel_1


title: H3K9me2 antibody2 L3 Nuclear Sexed Male Jil Mutant Heterozygous D.melanogaster Input Rep1

description: Served as Input for: 1942.Mvalues.bedgraph

source_name: H3K9me2 antibody2 L3 Nuc. SexedMJilMutant-HZ Input expt.1906 channel_1


title: HP1b Q4113 L3 Nuclear HP1b Mutant D.melanogaster ChIP Rep1

source_name: HP1b Q4113 L3 Nuc. HP1b ChIP expt.2535 channel_1


title: AY308 ume6 500193

value: MATa s288c MET+ LYS+ Isw2-3XFLAG (HYG) ume6::KanMX his3-1 leu2-0 ura3-0

value: Isw2 ChIP DNA

value: Anti-Flag for Isw2-3XFlag

value: MATa s288c MET+ LYS+ Isw2-K215R-3XFLAG (HYG) ume6::KanMX his3-1 leu2-0 ura3-0


title: ZW5 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: ZW5 2-4 hr OR Em. ChIP expt.2285 channel_1

value: Oregon-R

value: Embryo 2-4hr OR

value: wild type


title: ZW5 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2285.Mvalues.bedgraph

source_name: ZW5 2-4 hr OR Em. Input expt.2099 channel_1


title: ZW5 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2075.Mvalues.bedgraph

source_name: ZW5 2-4 hr OR Em. Input expt.2070 channel_1


title: ZW5 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: ZW5 2-4 hr OR Em. ChIP expt.2075 channel_1


title: HP1 wa191 Nuclear L2 AGO2 414 Mutant D.melanogaster ChIP Rep2

source_name: HP1 wa191 Nuc. L2 AGO2 414 ChIP expt.2085 channel_1


title: HP1 wa191 Nuclear L2 AGO2 414 Mutant D.melanogaster Input Rep2

description: Served as Input for: 2085.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L2 AGO2 414 Input expt.1922 channel_1


title: AY362 ume6 1 452821-4

value: Isw2-K215R ChIP DNA


title: dSFMBT Q2642 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: dSFMBT Q2642 2-4 hr OR Em. ChIP expt.2102 channel_1


title: HP1 wa191 Nuclear L2 AGO2 414 Mutant D.melanogaster Input Rep1

description: Served as Input for: 2084.Mvalues.bedgraph

source_name: HP1 wa191 Nuc. L2 AGO2 414 Input expt.1921 channel_1


title: dSFMBT Q2642 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2138.Mvalues.bedgraph

source_name: dSFMBT Q2642 2-4 hr OR Em. Input expt.2129 channel_1


title: dRING Q3200 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2151.Mvalues.bedgraph

source_name: dRING Q3200 2-4 hr OR Em. Input expt.2130 channel_1


title: dRING Q3200 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: dRING Q3200 2-4 hr OR Em. ChIP expt.2151 channel_1


title: dRING Q3200 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2286.Mvalues.bedgraph

source_name: dRING Q3200 2-4 hr OR Em. Input expt.2129 channel_1


title: RNA Pol II (abcam) L3 Nuclear HP1b Mutant D.melanogaster Input Rep2

description: Served as Input for: 1851.Mvalues.bedgraph

source_name: RNA Pol II (abcam) L3 Nuc. HP1b Input expt.1845 channel_1

value: HP1b mutant


title: HP1 wa191 Nuclear L2 AGO2 414 Mutant D.melanogaster ChIP Rep1

source_name: HP1 wa191 Nuc. L2 AGO2 414 ChIP expt.2084 channel_1


title: dSFMBT Q2642 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: dSFMBT Q2642 2-4 hr OR Em. ChIP expt.2138 channel_1


title: WDS Q2691 ML-DmBG3-c2 D.melanogaster ChIP Rep2

source_name: WDS Q2691 BG3 ChIP expt.889 channel_1

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

value: Unknown


title: HP1b Q4114 L3 Nuclear HP1b Mutant D.melanogaster Input Rep1

description: Served as Input for: 1846.Mvalues.bedgraph

source_name: HP1b Q4114 L3 Nuc. HP1b Input expt.1844 channel_1


title: WDS Q2691 ML-DmBG3-c2 D.melanogaster Input Rep2

description: Served as Input for: 888.Mvalues.bedgraph

source_name: WDS Q2691 BG3 Input expt.332 channel_1


title: dRING Q3200 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: dRING Q3200 2-4 hr OR Em. ChIP expt.2286 channel_1


title: AY296 WT 471425-2

value: MATa s288c MET+ LYS+ Isw2-3XFLAG (HYG) his3-1 leu2-0 ura3-0

value: MATa s288c MET+ LYS+ Isw2-K215R-3XFLAG (HYG) his3-1 leu2-0 ura3-0


title: AY304 WT KO 471425-3


title: SPT16(Cosmo) S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 1244.Mvalues.bedgraph

source_name: SPT16(Cosmo) S2 Input expt.846 channel_1

value: embryo-derived cell-line

value: late embryonic stage

value: Male


title: SPT16(Cosmo) S2-DRSC D.melanogaster ChIP Rep2

source_name: SPT16(Cosmo) S2 ChIP expt.1244 channel_1


title: SPT16(Cosmo) S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 1243.Mvalues.bedgraph

source_name: SPT16(Cosmo) S2 Input expt.847 channel_1


title: SPT16(Cosmo) S2-DRSC D.melanogaster ChIP Rep1

source_name: SPT16(Cosmo) S2 ChIP expt.1243 channel_1


title: JHDM1 Q2634 ML-DmBG3-c2 D.melanogaster Input Rep2

description: Served as Input for: 2178.Mvalues.bedgraph

source_name: JHDM1 Q2634 BG3 Input expt.1643 channel_1


title: JHDM1 Q2634 ML-DmBG3-c2 D.melanogaster Input Rep1

description: Served as Input for: 2177.Mvalues.bedgraph

source_name: JHDM1 Q2634 BG3 Input expt.1153 channel_1


title: JHDM1 Q2634 ML-DmBG3-c2 D.melanogaster ChIP Rep1

source_name: JHDM1 Q2634 BG3 ChIP expt.2177 channel_1


title: H4K12ac S2-DRSC D.melanogaster ChIP Rep2

source_name: H4K12ac S2 ChIP expt.174 channel_1


title: H4K12ac S2-DRSC D.melanogaster ChIP Rep1

source_name: H4K12ac S2 ChIP expt.24 channel_1


title: JHDM1 Q2634 ML-DmBG3-c2 D.melanogaster ChIP Rep2

source_name: JHDM1 Q2634 BG3 ChIP expt.2178 channel_1


title: WDS Q2691 ML-DmBG3-c2 D.melanogaster ChIP Rep1

source_name: WDS Q2691 BG3 ChIP expt.888 channel_1


title: dSFMBT Q2642 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2102.Mvalues.bedgraph

source_name: dSFMBT Q2642 2-4 hr OR Em. Input expt.2100 channel_1


title: H3K79me3 Abcam ab2621 lot1 S2-DRSC D.melanogaster ChIP Rep1

source_name: H3K79me3 Abcam ab2621 lot1 S2 ChIP expt.2048 channel_1


title: H4K12ac S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 174.Mvalues.bedgraph

source_name: H4K12ac S2 Input expt.136 channel_1


title: AY308 WT sua7 500193

value: MAT@ cyc1-5000 cyc7-67 ura3-52 leu2-3 112 cyh2 isw2-3XFLAG (KAN)

value: Isw2 ChIP DNA

value: MAT@ cyc1-5000 cyc7-67 ura3-52 leu2-3 112 cyh2 isw2-K215R-3XFLAG (KAN)


title: WDS Q2691 ML-DmBG3-c2 D.melanogaster Input Rep1

description: Served as Input for: 889.Mvalues.bedgraph

source_name: WDS Q2691 BG3 Input expt.315 channel_1


title: AY304 WT sua7 471425-3

value: Anti-Flag for Isw2-3XFlag


title: H3K79me1 (Abcam lot1) 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K79me1 (Abcam lot1) 2-4 hr OR Em. ChIP expt.2284 channel_1

value: Oregon-R

value: Embryo 2-4hr OR


title: H3K79me1 (Abcam lot1) 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K79me1 (Abcam lot1) 2-4 hr OR Em. ChIP expt.2140 channel_1

value: wild type


title: H3K79me3 Abcam ab2621 lot1 S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 2049.Mvalues.bedgraph

source_name: H3K79me3 Abcam ab2621 lot1 S2 Input expt.2040 channel_1


title: H3K79me3 Abcam ab2621 lot1 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 2048.Mvalues.bedgraph

source_name: H3K79me3 Abcam ab2621 lot1 S2 Input expt.1883 channel_1


title: H3K79me3 Abcam ab2621 lot1 S2-DRSC D.melanogaster ChIP Rep2

source_name: H3K79me3 Abcam ab2621 lot1 S2 ChIP expt.2049 channel_1


title: H3K79me1 (Abcam lot1) 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2140.Mvalues.bedgraph

source_name: H3K79me1 (Abcam lot1) 2-4 hr OR Em. Input expt.2130 channel_1


title: H3K79me1 (Abcam lot1) 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2284.Mvalues.bedgraph

source_name: H3K79me1 (Abcam lot1) 2-4 hr OR Em. Input expt.2099 channel_1


title: H4K12ac S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 24.Mvalues.bedgraph

source_name: H4K12ac S2 Input expt.10 channel_1


title: H3K4me3 ab8580 lot2 Kc167 D.melanogaster ChIP Rep2

source_name: H3K4me3 ab8580 lot2 Kc ChIP expt.1772 channel_1

value: se/e

value: Female


title: H3K4me3 ab8580 lot2 Kc167 D.melanogaster ChIP Rep1

source_name: H3K4me3 ab8580 lot2 Kc ChIP expt.1759 channel_1


title: H3K4me1 ab8895 new lot2 Kc167 D.melanogaster ChIP Rep1

source_name: H3K4me1 ab8895 new lot2 Kc ChIP expt.1757 channel_1


title: H3K4me1 ab8895 new lot2 Kc167 D.melanogaster ChIP Rep2

source_name: H3K4me1 ab8895 new lot2 Kc ChIP expt.1770 channel_1


title: H3K4me2 (Abcam lot2) 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2279.Mvalues.bedgraph

source_name: H3K4me2 (Abcam lot2) 2-4 hr OR Em. Input expt.2130 channel_1


title: H3K4me3 ab8580 lot2 Kc167 D.melanogaster Input Rep2

description: Served as Input for: 1759.Mvalues.bedgraph

source_name: H3K4me3 ab8580 lot2 Kc Input expt.1756 channel_1


title: H3K4me2 (Abcam lot2) 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K4me2 (Abcam lot2) 2-4 hr OR Em. ChIP expt.2139 channel_1


title: H3K4me1 ab8895 new lot2 Kc167 D.melanogaster Input Rep2

description: Served as Input for: 1756.Mvalues.bedgraph

source_name: H3K4me1 ab8895 new lot2 Kc Input expt.1756 channel_1


title: H3K4me2 (Abcam lot2) 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K4me2 (Abcam lot2) 2-4 hr OR Em. ChIP expt.2279 channel_1


title: H3K4me1 ab8895 new lot2 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K4me1 ab8895 new lot2 2-4 hr OR Em. ChIP expt.2148 channel_1


title: H3K4me3 ab8580 lot2 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2135.Mvalues.bedgraph

source_name: H3K4me3 ab8580 lot2 2-4 hr OR Em. Input expt.2099 channel_1


title: H3K4me1 ab8895 new lot2 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K4me1 ab8895 new lot2 2-4 hr OR Em. ChIP expt.2281 channel_1


title: H3K4me1 ab8895 new lot2 Kc167 D.melanogaster Input Rep1

description: Served as Input for: 1770.Mvalues.bedgraph

source_name: H3K4me1 ab8895 new lot2 Kc Input expt.1750 channel_1


title: H3K4me3 ab8580 lot2 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K4me3 ab8580 lot2 2-4 hr OR Em. ChIP expt.2135 channel_1


title: H3K4me1 ab8895 new lot2 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2148.Mvalues.bedgraph

source_name: H3K4me1 ab8895 new lot2 2-4 hr OR Em. Input expt.2130 channel_1


title: H3K4me3 ab8580 lot2 Kc167 D.melanogaster Input Rep1

description: Served as Input for: 1772.Mvalues.bedgraph

source_name: H3K4me3 ab8580 lot2 Kc Input expt.1750 channel_1


title: H3K4me3 ab8580 lot2 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2106.Mvalues.bedgraph

source_name: H3K4me3 ab8580 lot2 2-4 hr OR Em. Input expt.2100 channel_1


title: H3K4me3 ab8580 lot2 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K4me3 ab8580 lot2 2-4 hr OR Em. ChIP expt.2106 channel_1


title: H3K4me1 ab8895 new lot2 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2281.Mvalues.bedgraph

source_name: H3K4me1 ab8895 new lot2 2-4 hr OR Em. Input expt.2100 channel_1


title: H3K27me3 (Abcam lot3) Kc167 D.melanogaster ChIP Rep2

source_name: H3K27me3 (Abcam lot3) Kc ChIP expt.1769 channel_1


title: H3K27me3 (Abcam lot3) Kc167 D.melanogaster ChIP Rep1

source_name: H3K27me3 (Abcam lot3) Kc ChIP expt.1763 channel_1


title: H3K27me3 (Abcam lot3) 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2145.Mvalues.bedgraph

source_name: H3K27me3 (Abcam lot3) 2-4 hr OR Em. Input expt.2130 channel_1


title: H3K27me3 (Abcam lot3) 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K27me3 (Abcam lot3) 2-4 hr OR Em. ChIP expt.2110 channel_1


title: H3K27me3 (Abcam lot3) Kc167 D.melanogaster Input Rep1

description: Served as Input for: 1763.Mvalues.bedgraph

source_name: H3K27me3 (Abcam lot3) Kc Input expt.1671 channel_1


title: H3K27me3 (Abcam lot3) 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2110.Mvalues.bedgraph

source_name: H3K27me3 (Abcam lot3) 2-4 hr OR Em. Input expt.2070 channel_1


title: H1 Kc167 D.melanogaster ChIP Rep1

source_name: H1 Kc ChIP expt.354 channel_1


title: H1 Kc167 D.melanogaster Input Rep1

description: Served as Input for: 354.Mvalues.bedgraph

source_name: H1 Kc Input expt.290 channel_1


title: H3K4me2 (Abcam lot2) 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2139.Mvalues.bedgraph

source_name: H3K4me2 (Abcam lot2) 2-4 hr OR Em. Input expt.2129 channel_1


title: H3K27me3 (Abcam lot3) Kc167 D.melanogaster Input Rep2

description: Served as Input for: 1769.Mvalues.bedgraph

source_name: H3K27me3 (Abcam lot3) Kc Input expt.1750 channel_1


title: H1 Clone 8 D.melanogaster ChIP Rep1

source_name: H1 Clone 8 ChIP expt.358 channel_1

value: dorsal mesothoracic disc

value: third instar larval stage


title: H3K27me3 (Abcam lot3) 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K27me3 (Abcam lot3) 2-4 hr OR Em. ChIP expt.2145 channel_1


title: H1 Clone 8 D.melanogaster ChIP Rep2

source_name: H1 Clone 8 ChIP expt.359 channel_1


title: dSFMBT Q2642 Kc167 D.melanogaster Input Rep2

description: Served as Input for: 1754.Mvalues.bedgraph

source_name: dSFMBT Q2642 Kc Input expt.1750 channel_1


title: dSFMBT Q2642 Kc167 D.melanogaster ChIP Rep2

source_name: dSFMBT Q2642 Kc ChIP expt.1754 channel_1


title: H1 Clone 8 D.melanogaster Input Rep2

description: Served as Input for: 359.Mvalues.bedgraph

source_name: H1 Clone 8 Input expt.289 channel_1


title: dSFMBT Q2642 Kc167 D.melanogaster ChIP Rep1

source_name: dSFMBT Q2642 Kc ChIP expt.1675 channel_1


title: dSFMBT Q2642 Kc167 D.melanogaster Input Rep1

description: Served as Input for: 1675.Mvalues.bedgraph

source_name: dSFMBT Q2642 Kc Input expt.1671 channel_1


title: CP190-HB 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: CP190-HB 2-4 hr OR Em. ChIP expt.2072 channel_1


title: CP190-HB 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: CP190-HB 2-4 hr OR Em. ChIP expt.2137 channel_1


title: H1 Kc167 D.melanogaster ChIP Rep2

source_name: H1 Kc ChIP expt.355 channel_1


title: H1 Kc167 D.melanogaster Input Rep2

description: Served as Input for: 355.Mvalues.bedgraph

source_name: H1 Kc Input expt.291 channel_1


title: SU(HW)-HB 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2136.Mvalues.bedgraph

source_name: SU(HW)-HB 2-4 hr OR Em. Input expt.2099 channel_1


title: WDS Q2691 L3 Nuclear D.melanogaster Input Rep1

description: Served as Input for: 1579.Mvalues.bedgraph

source_name: WDS Q2691 L3 Nuc. Input expt.1571 channel_1

value: 3rd Instar Larvae


title: WDS Q2691 L3 Nuclear D.melanogaster Input Rep2

description: Served as Input for: 1580.Mvalues.bedgraph

source_name: WDS Q2691 L3 Nuc. Input expt.1572 channel_1


title: BEAF-HB 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2276.Mvalues.bedgraph

source_name: BEAF-HB 2-4 hr OR Em. Input expt.2130 channel_1


title: BEAF-HB 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2071.Mvalues.bedgraph

source_name: BEAF-HB 2-4 hr OR Em. Input expt.2070 channel_1


title: SU(HW)-HB 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: SU(HW)-HB 2-4 hr OR Em. ChIP expt.2136 channel_1


title: CP190-HB 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2072.Mvalues.bedgraph

source_name: CP190-HB 2-4 hr OR Em. Input expt.2070 channel_1


title: BEAF-HB 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: BEAF-HB 2-4 hr OR Em. ChIP expt.2276 channel_1


title: SU(HW)-HB 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: SU(HW)-HB 2-4 hr OR Em. ChIP expt.2074 channel_1


title: WDS Q2691 L3 Nuclear D.melanogaster ChIP Rep2

source_name: WDS Q2691 L3 Nuc. ChIP expt.1580 channel_1


title: BEAF-HB 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: BEAF-HB 2-4 hr OR Em. ChIP expt.2071 channel_1


title: SU(HW)-HB 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2074.Mvalues.bedgraph

source_name: SU(HW)-HB 2-4 hr OR Em. Input expt.2070 channel_1


title: WDS Q2691 L3 Nuclear D.melanogaster ChIP Rep1

source_name: WDS Q2691 L3 Nuc. ChIP expt.1579 channel_1


title: PR-Set7 Q3484 ML-DmBG3-c2 D.melanogaster ChIP Rep2

source_name: PR-Set7 Q3484 BG3 ChIP expt.1256 channel_1

value: CNS-derived cell-line

value: y v f mal

value: Unknown


title: PR-Set7 Q3484 ML-DmBG3-c2 D.melanogaster ChIP Rep1

source_name: PR-Set7 Q3484 BG3 ChIP expt.1255 channel_1


title: CP190-HB 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2137.Mvalues.bedgraph

source_name: CP190-HB 2-4 hr OR Em. Input expt.2129 channel_1


title: PR-Set7 Q3484 ML-DmBG3-c2 D.melanogaster Input Rep2

description: Served as Input for: 1256.Mvalues.bedgraph

source_name: PR-Set7 Q3484 BG3 Input expt.1154 channel_1


title: PR-Set7 Q3484 ML-DmBG3-c2 D.melanogaster Input Rep1

description: Served as Input for: 1255.Mvalues.bedgraph

source_name: PR-Set7 Q3484 BG3 Input expt.1153 channel_1


title: NURF301 Q2602 ML-DmBG3-c2 D.melanogaster ChIP Rep1

source_name: NURF301 Q2602 BG3 ChIP expt.1888 channel_1


title: NURF301 Q2602 ML-DmBG3-c2 D.melanogaster ChIP Rep2

source_name: NURF301 Q2602 BG3 ChIP expt.1889 channel_1


title: Pc 2-4 hr OR Embryo D.melanogaster Input Rep3

description: Served as Input for: 2103.Mvalues.bedgraph

source_name: Pc 2-4 hr OR Em. Input expt.2100 channel_1


title: Pc 2-4 hr OR Embryo D.melanogaster ChIP Rep3

source_name: Pc 2-4 hr OR Em. ChIP expt.2107 channel_1


title: Pc 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: Pc 2-4 hr OR Em. ChIP expt.1017 channel_1


title: Pc 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: Pc 2-4 hr OR Em. ChIP expt.2103 channel_1


title: H1 Clone 8 D.melanogaster Input Rep1

description: Served as Input for: 358.Mvalues.bedgraph

source_name: H1 Clone 8 Input expt.288 channel_1


title: Pc 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 1017.Mvalues.bedgraph

source_name: Pc 2-4 hr OR Em. Input expt.1023 channel_1


title: NURF301 Q2602 ML-DmBG3-c2 D.melanogaster Input Rep1

description: Served as Input for: 1888.Mvalues.bedgraph

source_name: NURF301 Q2602 BG3 Input expt.1902 channel_1


title: ISWI Q3445 S2-DRSC D.melanogaster ChIP Rep2

source_name: ISWI Q3445 S2 ChIP expt.527 channel_1

value: embryo-derived cell-line

value: late embryonic stage


title: ISWI Q3445 S2-DRSC D.melanogaster ChIP Rep1

source_name: ISWI Q3445 S2 ChIP expt.516 channel_1

value: Male


title: ISWI Q3445 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 516.Mvalues.bedgraph

source_name: ISWI Q3445 S2 Input expt.530 channel_1


title: H4K8ac ML-BG3-c2 D.melanogaster Input Rep2

description: Served as Input for: 1247.Mvalues.bedgraph

source_name: H4K8ac BG3 Input expt.935 channel_1


title: H4K8ac ML-BG3-c2 D.melanogaster ChIP Rep1

source_name: H4K8ac BG3 ChIP expt.349 channel_1


title: H4K8ac ML-BG3-c2 D.melanogaster ChIP Rep3

source_name: H4K8ac BG3 ChIP expt.1248 channel_1


title: H4K8ac ML-BG3-c2 D.melanogaster Input Rep3

description: Served as Input for: 1248.Mvalues.bedgraph

source_name: H4K8ac BG3 Input expt.936 channel_1


title: ISWI Q3445 S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 527.Mvalues.bedgraph

source_name: ISWI Q3445 S2 Input expt.531 channel_1


title: H4K8ac ML-BG3-c2 D.melanogaster ChIP Rep2

source_name: H4K8ac BG3 ChIP expt.1247 channel_1


title: dmTopo II ML-DmBG3-c2 D.melanogaster Input Rep1

description: Served as Input for: 1501.Mvalues.bedgraph

source_name: dmTopo II BG3 Input expt.292 channel_1


title: H4K8ac ML-BG3-c2 D.melanogaster Input Rep1

description: Served as Input for: 349.Mvalues.bedgraph

source_name: H4K8ac BG3 Input expt.292 channel_1


title: dmTopo II ML-DmBG3-c2 D.melanogaster ChIP Rep1

source_name: dmTopo II BG3 ChIP expt.1501 channel_1


title: dmTopo II ML-DmBG3-c2 D.melanogaster ChIP Rep2

source_name: dmTopo II BG3 ChIP expt.1502 channel_1


title: NURF301 Q2602 ML-DmBG3-c2 D.melanogaster Input Rep2

description: Served as Input for: 1889.Mvalues.bedgraph

source_name: NURF301 Q2602 BG3 Input expt.1903 channel_1


title: CTCF 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2143.Mvalues.bedgraph

source_name: CTCF 2-4 hr OR Em. Input expt.2130 channel_1


title: CTCF 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2101.Mvalues.bedgraph

source_name: CTCF 2-4 hr OR Em. Input expt.2100 channel_1


title: CTCF 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: CTCF 2-4 hr OR Em. ChIP expt.2101 channel_1


title: CTCF 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: CTCF 2-4 hr OR Em. ChIP expt.2143 channel_1


title: dmTopo II ML-DmBG3-c2 D.melanogaster Input Rep2

description: Served as Input for: 1502.Mvalues.bedgraph

source_name: dmTopo II BG3 Input expt.936 channel_1


title: Pc 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2107.Mvalues.bedgraph

source_name: Pc 2-4 hr OR Em. Input expt.2070 channel_1


title: ACF1 Q3443 S2-DRSC D.melanogaster ChIP Rep1

source_name: ACF1 Q3443 S2 ChIP expt.518 channel_1


title: H3K27ac (Active Motif) 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K27ac (Active Motif) 2-4 hr OR Em. ChIP expt.2105 channel_1


title: H3K27ac (Active Motif) 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K27ac (Active Motif) 2-4 hr OR Em. ChIP expt.2146 channel_1


title: H3K79me3 (Abcam ab2621 lot1) 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K79me3 (Abcam ab2621 lot1) 2-4 hr OR Em. ChIP expt.2144 channel_1


title: H3K27ac (Active Motif) 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2105.Mvalues.bedgraph

source_name: H3K27ac (Active Motif) 2-4 hr OR Em. Input expt.2100 channel_1


title: ACF1 Q3443 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 518.Mvalues.bedgraph

source_name: ACF1 Q3443 S2 Input expt.530 channel_1


title: ACF1 Q3443 S2-DRSC D.melanogaster ChIP Rep2

source_name: ACF1 Q3443 S2 ChIP expt.529 channel_1


title: ACF1 Q3443 S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 529.Mvalues.bedgraph

source_name: ACF1 Q3443 S2 Input expt.531 channel_1


title: H3K27ac (Active Motif) 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2146.Mvalues.bedgraph

source_name: H3K27ac (Active Motif) 2-4 hr OR Em. Input expt.2130 channel_1


title: H3K79me2 Abcam ab3594 lot1 2-4 hr OR Embryo D.melanogaster ChIP Rep2

source_name: H3K79me2 Abcam ab3594 lot1 2-4 hr OR Em. ChIP expt.2277 channel_1


title: H3K79me3 (Abcam ab2621 lot1) 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2133.Mvalues.bedgraph

source_name: H3K79me3 (Abcam ab2621 lot1) 2-4 hr OR Em. Input expt.2100 channel_1


title: H3K79me2 Abcam ab3594 lot1 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2277.Mvalues.bedgraph

source_name: H3K79me2 Abcam ab3594 lot1 2-4 hr OR Em. Input expt.2130 channel_1


title: H3K79me2 Abcam ab3594 lot1 2-4 hr OR Embryo D.melanogaster Input Rep1

description: Served as Input for: 2132.Mvalues.bedgraph

source_name: H3K79me2 Abcam ab3594 lot1 2-4 hr OR Em. Input expt.2100 channel_1


title: H3K79me3 (Abcam ab2621 lot1) 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K79me3 (Abcam ab2621 lot1) 2-4 hr OR Em. ChIP expt.2133 channel_1


title: H3K79me2 Abcam ab3594 lot1 2-4 hr OR Embryo D.melanogaster ChIP Rep1

source_name: H3K79me2 Abcam ab3594 lot1 2-4 hr OR Em. ChIP expt.2132 channel_1


title: H3K79me3 (Abcam ab2621 lot1) 2-4 hr OR Embryo D.melanogaster Input Rep2

description: Served as Input for: 2144.Mvalues.bedgraph

source_name: H3K79me3 (Abcam ab2621 lot1) 2-4 hr OR Em. Input expt.2130 channel_1


title: H3K4me2 Abcam Kc167 D.melanogaster ChIP Rep2

source_name: H3K4me2 Abcam Kc ChIP expt.1758 channel_1


title: H3K79me3 (Abcam ab2621 lot1) ML-DmBG3-c2 D.melanogaster Input Rep1

description: Served as Input for: 1882.Mvalues.bedgraph

source_name: H3K79me3 (Abcam ab2621 lot1) BG3 Input expt.1880 channel_1


title: H3K79me3 (Abcam ab2621 lot1) ML-DmBG3-c2 D.melanogaster Input Rep2

description: Served as Input for: 2050.Mvalues.bedgraph

source_name: H3K79me3 (Abcam ab2621 lot1) BG3 Input expt.2041 channel_1


title: H3K79me3 (Abcam ab2621 lot1) ML-DmBG3-c2 D.melanogaster ChIP Rep1

source_name: H3K79me3 (Abcam ab2621 lot1) BG3 ChIP expt.1882 channel_1


title: JHDM1 Q2634 S2-DRSC D.melanogaster Input Rep1

description: Served as Input for: 459.Mvalues.bedgraph

source_name: JHDM1 Q2634 S2 Input expt.417 channel_1


title: JHDM1 Q2634 S2-DRSC D.melanogaster ChIP Rep1

source_name: JHDM1 Q2634 S2 ChIP expt.459 channel_1


title: Su(var) 3-7 Q3448 OR Head Nuclear D.melanogaster ChIP Rep2

source_name: Su(var) 3-7 Q3448 OR Head Nuc. ChIP expt.1865 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Collection of fly heads from whole adults using sieves of varying sizes.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Mixed Adult


title: JHDM1 Q2634 S2-DRSC D.melanogaster Input Rep2

description: Served as Input for: 1024.Mvalues.bedgraph

source_name: JHDM1 Q2634 S2 Input expt.767 channel_1


title: JHDM1 Q2634 S2-DRSC D.melanogaster ChIP Rep2

source_name: JHDM1 Q2634 S2 ChIP expt.1024 channel_1


title: H3K4me2 Abcam Kc167 D.melanogaster Input Rep1

description: Served as Input for: 1771.Mvalues.bedgraph

source_name: H3K4me2 Abcam Kc Input expt.1750 channel_1


title: H3K4me2 Abcam Kc167 D.melanogaster ChIP Rep1

source_name: H3K4me2 Abcam Kc ChIP expt.1771 channel_1


title: H3K79me3 (Abcam ab2621 lot1) ML-DmBG3-c2 D.melanogaster ChIP Rep2

source_name: H3K79me3 (Abcam ab2621 lot1) BG3 ChIP expt.2050 channel_1


title: Su(var) 3-7 Q3448 OR Head Nuclear D.melanogaster ChIP Rep1

source_name: Su(var) 3-7 Q3448 OR Head Nuc. ChIP expt.1864 channel_1


title: Su(var) 3-7 Q3448 OR Head Nuclear D.melanogaster Input Rep2

description: Served as Input for: 1865.Mvalues.bedgraph

source_name: Su(var) 3-7 Q3448 OR Head Nuc. Input expt.1790 channel_1


title: H3K4me2 Abcam Kc167 D.melanogaster Input Rep2

description: Served as Input for: 1758.Mvalues.bedgraph

source_name: H3K4me2 Abcam Kc Input expt.1756 channel_1


title: PIWI-Q2569 L3 Nuclear Sexed Female D.melanogaster Input Rep2

description: Served as Input for: 1070.Mvalues.bedgraph

source_name: PIWI-Q2569 L3 Nuc. SexedF Input expt.978 channel_1

value: 3rd Instar Larvae Sexed Female


title: PIWI-Q2569 L3 Nuclear Sexed Female D.melanogaster ChIP Rep2

source_name: PIWI-Q2569 L3 Nuc. SexedF ChIP expt.1071 channel_1


title: PIWI-Q2569 L3 Nuclear Sexed Female D.melanogaster ChIP Rep1

source_name: PIWI-Q2569 L3 Nuc. SexedF ChIP expt.1070 channel_1


title: Su(var) 3-7 Q3448 OR Head Nuclear D.melanogaster Input Rep1

description: Served as Input for: 1864.Mvalues.bedgraph

source_name: Su(var) 3-7 Q3448 OR Head Nuc. Input expt.1789 channel_1


title: PIWI-Q2569 L3 Nuclear Sexed Female D.melanogaster Input Rep1

description: Served as Input for: 1071.Mvalues.bedgraph

source_name: PIWI-Q2569 L3 Nuc. SexedF Input expt.960 channel_1


title: HP1b Q4114 L3 Nuclear HP1c Mutant D.melanogaster ChIP Rep1

source_name: HP1b Q4114 L3 Nuc. HP1c ChIP expt.1206 channel_1

value: HP1c mutant

value: PBac insertion


title: HP1b Q4114 L3 Nuclear HP1c Mutant D.melanogaster ChIP Rep2

source_name: HP1b Q4114 L3 Nuc. HP1c ChIP expt.1533 channel_1


title: H3 antibody3 OR Head Nuclear D.melanogaster ChIP Rep2

source_name: H3 antibody3 OR Head Nuc. ChIP expt.1812 channel_1

value: Oregon-R


title: HP1b Q4114 L3 Nuclear HP1c Mutant D.melanogaster Input Rep1

description: Served as Input for: 1206.Mvalues.bedgraph

source_name: HP1b Q4114 L3 Nuc. HP1c Input expt.1213 channel_1


title: HP1b Q4114 L3 Nuclear HP1c Mutant D.melanogaster Input Rep2

description: Served as Input for: 1533.Mvalues.bedgraph

source_name: HP1b Q4114 L3 Nuc. HP1c Input expt.1214 channel_1