title: Tubulointerstitium from IgAN patient_IgA26 [HG-U133A_ENTREZG_10]

status: Public on Feb 02 2012

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description:
Tub_IgA26
Gene expression data from the tubulointerstitial compartment of human IgAN kidney

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using GenePattern pipeline: RMA method and Human Entrez Gene custom CDF annotation version 10 were used for the normalization.

source_name: Kidney biopsy from human IgAN

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

extract_protocol: Total RNA was isolated using the RNeasy mini kit from Qiagen, following the manufacturer’s instructions.

value: Tubulointerstitium from kidney biopsy


title: UNP-April 2008_201:73_human_liver_EAM7467

status: Public on Feb 10 2012

type: RNA

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

country: USA

institute: University of Washington

description: Agilent Oligo Hyb

hyb_protocol: The Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred ng of each RNA sample was hybridized to one Agilent 22K Human oligo array.

scan_protocol: Scanned on an Agilent Scanner G2505B US23502338. Images were quantified using Agilent Feature Extraction Software (version A.8.1.1.1).

data_processing: The limma package was used. Background correction was performed (method=normexp, offset=1). Data was normalized within arrays with the loess method, then normalized between arrays with the quantile normalization method, and then log2 transformed.

molecule: total RNA

organism: Homo sapiens

source_name: UNP-April 2008, human liver, Cy3

label_protocol: The Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA and Cy5-cDNA probe preparation.

extract_protocol: Biopsy specimens were disrupted in TRIzol reagent (Life Technologies, Carlsbad, CA) using a Polytron homogenizer (PowerGene 700; Fisher Scientific, Pittsburgh, PA).  Total RNA was isolated according to the manufacturer’s protocol.  All total RNA samples were amplified using the RiboAmp RNA Amplification Kit (Arcturus/MDS, Mountain View, CA).  The quality of amplified RNA was determined by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: PCT study Utah Normal Pool (UNP): Liver biopsies used to compare transcriptional profiles of responders (with sustained virologic response:SVR) vs. non-responders to IFN treatment during HCV infection.

value: normal

tag: tissue

value: liver

tag: patient/unp identifier

value: UNP-April 2008

source_name: 201:73, human liver, Cy5

value: HCV-infected


title: Tubulointerstitium from IgAN patient_IgA27 [HG-U133A_ENTREZG_10]

description:
Tub_IgA27
Gene expression data from the tubulointerstitial compartment of human IgAN kidney

label: biotin


title: 120:12:00_UNP-May 2008_human_EAM7551

description: Agilent Oligo Hyb

source_name: 120:12, human liver, Cy3

source_name: UNP-May 2008, human, Cy5

value: UNP-May 2008


title: 397:84_UNP-April 2008_human_liver_EAM7465

description: Agilent Oligo Hyb

source_name: 397:84, human liver, Cy3

source_name: UNP-April 2008, human liver, Cy5


title: Tubulointerstitium from IgAN patient_IgA25 [HG-U133A_ENTREZG_10]

description:
Tub_IgA25
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: UNP-May 2008_109:33_human_liver_EAM7517

description: Agilent Oligo Hyb

source_name: UNP-May 2008, human, Cy3

source_name: 109:33, human liver, Cy5


title: Tubulointerstitium from IgAN patient_IgA23 [HG-U133A_ENTREZG_10]

description:
Tub_IgA23
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA24 [HG-U133A_ENTREZG_10]

description:
Tub_IgA24
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: UNP-April 2008_201:96_human_liver_EAM7483

description: Agilent Oligo Hyb

source_name: 201:96, human liver, Cy5


title: Tubulointerstitium from IgAN patient_IgA22 [HG-U133A_ENTREZG_10]

description:
Tub_IgA22
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: 179:63_UNP-April 2008_human_liver_EAM7473

description: Agilent Oligo Hyb

source_name: 179:63, human liver, Cy3


title: 120:12:00_UNP-May 2008_human_EAM7552

description: Agilent Oligo Hyb


title: Tubulointerstitium from IgAN patient_IgA20 [HG-U133A_ENTREZG_10]

description:
Tub_IgA20
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: UNP-April 2008_179:74_human_liver_EAM7475

description: Agilent Oligo Hyb

source_name: 179:74, human liver, Cy5


title: UNP-April 2008_201:96_human_liver_EAM7484

description: Agilent Oligo Hyb


title: Tubulointerstitium from IgAN patient_IgA21 [HG-U133A_ENTREZG_10]

description:
Tub_IgA21
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: 179:63_UNP-April 2008_human_liver_EAM7474

description: Agilent Oligo Hyb


title: UNP-April 2008_179:63_human_liver_EAM7472

description: Agilent Oligo Hyb

source_name: 179:63, human liver, Cy5


title: 201:96_UNP-April 2008_human_liver_EAM7486

description: Agilent Oligo Hyb

source_name: 201:96, human liver, Cy3


title: 201:96_UNP-April 2008_human_liver_EAM7485

description: Agilent Oligo Hyb


title: Tubulointerstitium from IgAN patient_IgA19 [HG-U133A_ENTREZG_10]

description:
Tub_IgA19
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA16 [HG-U133A_ENTREZG_10]

description:
Tub_IgA16
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA18 [HG-U133A_ENTREZG_10]

description:
Tub_IgA18
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA14 [HG-U133A_ENTREZG_10]

description:
Tub_IgA14
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA13 [HG-U133A_ENTREZG_10]

description:
Tub_IgA13
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: UNP-April 2008_179:63_human_liver_EAM7471

description: Agilent Oligo Hyb


title: Tubulointerstitium from IgAN patient_IgA7 [HG-U133A_ENTREZG_10]

description:
Tub_IgA7
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA8 [HG-U133A_ENTREZG_10]

description:
Tub_IgA8
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA6 [HG-U133A_ENTREZG_10]

description:
Tub_IgA6
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA9 [HG-U133A_ENTREZG_10]

description:
Tub_IgA9
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA5 [HG-U133A_ENTREZG_10]

description:
Tub_IgA5
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA3 [HG-U133A_ENTREZG_10]

description:
Tub_IgA3
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA4 [HG-U133A_ENTREZG_10]

description:
Tub_IgA4
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA10 [HG-U133A_ENTREZG_10]

description:
Tub_IgA10
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA11 [HG-U133A_ENTREZG_10]

description:
Tub_IgA11
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA1 [HG-U133A_ENTREZG_10]

description:
Tub_IgA1
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Tubulointerstitium from IgAN patient_IgA12 [HG-U133A_ENTREZG_10]

description:
Tub_IgA12
Gene expression data from the tubulointerstitial compartment of human IgAN kidney


title: Patient P3  @LS

status: Public on Jan 30 2012

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: Patient P3  @LS

extract_protocol: Whole skin punch biopsies were homogenized in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

tag: patient

tag: group

value: LS

value: skin

tag: treatment

value: efalizumab

tag: disease state

value: psoriasis

tag: time

value: baseline

tag: disease status

value: lesional


title: Patient P1  @NL

source_name: Patient P1  @NL

label_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

value: NL

value: non-lesional


title: Patient P1  @LS

source_name: Patient P1  @LS


title: Patient P4  @FLARE

source_name: Patient P4  @FLARE

value: FLARE

value: week 12

value: relapse


title: Patient P4  @LS

source_name: Patient P4  @LS


title: Patient P2  @LS

source_name: Patient P2  @LS


title: Patient P1  @Week 12

source_name: Patient P1  @Week 12

value: Week 12

value: non-relapse


title: Patient P4  @Week 12

source_name: Patient P4  @Week 12


title: Patient P1  @FLARE

source_name: Patient P1  @FLARE


title: Patient P2  @FLARE

source_name: Patient P2  @FLARE


title: Patient P2  @Week 12

source_name: Patient P2  @Week 12


title: Tubulointerstitium from IgAN patient_IgA2 [HG-U133A_ENTREZG_10]

description:
Tub_IgA2
Gene expression data from the tubulointerstitial compartment of human IgAN kidney

source_name: Kidney biopsy from human IgAN

value: Tubulointerstitium from kidney biopsy


title: Patient P3  @Week 12

source_name: Patient P3  @Week 12


title: Patient P3  @FLARE

source_name: Patient P3  @FLARE


title: 89_pT1

status: Public on Jan 23 2012

city: Boston

first: Markus

last: Riester

state: MA

address: 3 Blackfan Circle

department: Biostatistics & Computational Biology

institute: Dana-Farber Cancer Institute

hyb_protocol: Following quality assessment using an Agilent Bioanalyzer, the aRNA was fragmented and hybridized onto Affymetrix U133 Plus 2.0 arrays

scan_protocol: Standard Affymetrix protocol.

data_processing: Expression estimates were obtained with GCRMA from Bioconductor with default parameters.

source_name: Bladder Cancer

label_protocol: Expression profiling was performed in the MSKCC Genomics Core Facility. In brief, 5-10 ug of RNA was transcribed utilizing a T7-oligo dT primer and converted to cDNA (Invitrogen cDNA synthesis kit). Biotinylated aRNA was produced from the cDNA using an in vitro transcription kit (Enzo Diagnostics).

extract_protocol: RNA was isolated with Trizol (Invitrogen) and RNA was cleaned with Rneasy mini kits (Qiagen) according to manufacturer protocols

treatment_protocol: Frozen bladder tissues were examined by a genitourinary pathologist  to identify tumor content, which was microdissected. Ten 50-um sections were cut, with confirmation of tumor content by pathologic review.

tag: gender

value: male

tag: preopclinstage

tag: age at rc

value: TCC

tag: plnd result

value: Positive

tag: rc grade

value: High

tag: nomogram score

tag: distant mets

tag: local recurrence

tag: urothelial recurrence

tag: metastasis

tag: last known status

value: DOD

value: No

tag: post rc_chemo

value: Yes

tag: postchemo type

value: adjuvant

tag: smoking

value: Former

tag: smokingpack-years

tag: recurrence free survival months (distant and local)

tag: recurrence/dod

tag: cluster


title: 90_pT2

tag: gender

tag: preopclinstage

value: NED


title: 86_pT3

tag: age at rc

tag: plnd result

value: Negative

value: salvage

value: Current


title: 91_pT2

value: female

tag: rc grade

tag: nomogram score

value: Never


title: Patient P4  @NL

source_name: Patient P4  @NL

tag: patient

tag: group

value: NL

tag: tissue

value: skin

tag: treatment

value: efalizumab

tag: disease state

value: psoriasis

tag: time

value: baseline

tag: disease status

value: non-lesional


title: 82_pT1

value: male

value: Ta

value: TCC

value: High

tag: distant mets

tag: local recurrence

tag: urothelial recurrence

tag: metastasis

tag: last known status

tag: post rc_chemo

tag: smoking

tag: smokingpack-years


title: 84_pT2

tag: gender

tag: preopclinstage

tag: age at rc

tag: plnd result

tag: rc grade

value: No

tag: recurrence free survival months (distant and local)

tag: recurrence/dod

tag: cluster


title: 85_pT4

value: Positive

tag: nomogram score

value: NED

value: Yes

tag: postchemo type

value: adjuvant

value: Former


title: 92_pT3

tag: distant mets

tag: local recurrence

value: DOD


title: 88_pT3

tag: urothelial recurrence

tag: metastasis

value: salvage

value: Current


title: 83_pT2

value: Negative

tag: last known status

tag: post rc_chemo


title: 13:06_UNP-Aug 2007_human_EAM7169

description: Agilent Oligo Hyb

source_name: 13:6, human liver, Cy3

value: HCV-infected

tag: tissue

value: liver

tag: patient/unp identifier

source_name: UNP-Aug 2007, human, Cy5

value: normal

value: UNP-Aug 2007


title: 87_pT3

tag: gender

value: female

tag: preopclinstage

tag: smoking

value: Never


title: 93_pT2

value: male

tag: age at rc

value: TCC

tag: plnd result

value: Nx

tag: rc grade

value: High

tag: smokingpack-years


title: 81_pT3

tag: nomogram score

value: NED

value: No

value: Yes

tag: recurrence free survival months (distant and local)

tag: recurrence/dod

tag: cluster


title: 76_pT2

tag: distant mets

tag: local recurrence

tag: urothelial recurrence

value: DOC

value: Former


title: 77_pT2

tag: metastasis

tag: last known status

value: DOD

value: no

tag: post rc_chemo

tag: postchemo type

value: salvage


title: 72_pT2

tag: gender

tag: preopclinstage

value: Negative


title: 71_pT4

tag: age at rc

value: high

tag: smoking


title: 79_pT3

tag: plnd result

value: Positive

tag: rc grade

value: adjuvant

value: Current


title: 74_pT3

value: male

tag: nomogram score

tag: smokingpack-years


title: 70_pT3

value: TCC

tag: recurrence free survival months (distant and local)

tag: recurrence/dod


title: 80_pT3

value: Nx

tag: distant mets

tag: cluster


title: 68_pT1

value: female

value: Ta

value: NX

value: Low

tag: local recurrence

tag: urothelial recurrence


title: 69_pT1

value: High

tag: metastasis

tag: last known status

value: NED

value: No


title: 73_pT3

value: DOD

tag: post rc_chemo

value: Yes

tag: postchemo type

value: Never


title: 78_pT3

tag: gender

tag: preopclinstage


title: 75_pT1

tag: age at rc

value: Negative

tag: smoking


title: 67_pT3

tag: plnd result

tag: rc grade

value: DOC


title: 66_pTa

value: pTa

tag: nomogram score

value: Former

tag: smokingpack-years

value: unk


title: 65_pT1

value: male

value: TCC

tag: recurrence free survival months (distant and local)

tag: recurrence/dod


title: 59_pT3

tag: distant mets

value: salvage

tag: cluster


title: 60_pT3

tag: local recurrence

tag: urothelial recurrence


title: 61_pT3

value: female

tag: metastasis

tag: last known status

value: adjuvant


title: 64_pT3

tag: post rc_chemo

value: Current


title: 56_pT4

tag: gender

value: Nx

value: High


title: 63_pT4

tag: preopclinstage

value: Positive

value: NED

value: No

tag: postchemo type


title: 62_pT3

tag: age at rc

tag: smoking


title: 52_pT4

tag: plnd result

tag: rc grade

value: DOD

value: Yes

value: Never


title: 58_pT2

value: Negative

tag: nomogram score

value: DOC

tag: smokingpack-years


title: 57_pT3

value: Former

tag: recurrence free survival months (distant and local)

tag: recurrence/dod


title: 49_pTa

value: pTa

tag: distant mets

tag: cluster


title: 50_pT4

value: male

value: TCC

tag: local recurrence

tag: urothelial recurrence


title: 53_pT3

value: TCC/Squamous

tag: metastasis

tag: last known status


title: 44_pT1

tag: gender

tag: post rc_chemo


title: 54_pT3

value: female

tag: preopclinstage

tag: postchemo type

value: salvage


title: 40_pT3

tag: age at rc

value: NX

tag: smoking


title: 45_pT3

tag: plnd result

tag: rc grade

value: High


title: 55_pT3

value: Nx

tag: nomogram score

tag: smokingpack-years


title: 48_pT2

tag: recurrence free survival months (distant and local)

tag: recurrence/dod


title: 41_pT3

tag: distant mets

tag: cluster


title: 47_pT2

tag: local recurrence

tag: urothelial recurrence

value: unk


title: 42_pT3

value: Positive

tag: metastasis

tag: last known status

value: No


title: 46_pT4

tag: gender

value: DOD

tag: post rc_chemo

value: Yes


title: 36_pT3

tag: preopclinstage

value: NED


title: 51_pTa

value: Ta

tag: age at rc

value: Negative

value: DOC


title: 43_pT3

value: male

tag: postchemo type

tag: smoking

value: Former


title: 35_pT4

value: TCC

tag: plnd result

tag: rc grade

value: Current


title: 34_pT3

tag: nomogram score

value: adjuvant

tag: smokingpack-years


title: 38_pT3

value: female

tag: recurrence free survival months (distant and local)

tag: recurrence/dod


title: 31_pT4

value: High

tag: distant mets

tag: cluster


title: 39_pT3

tag: local recurrence

tag: urothelial recurrence

value: Never


title: 33_pTa

value: pTa

value: Low

tag: metastasis

tag: last known status


title: 29_pT3

tag: gender

value: Positive

value: No

tag: post rc_chemo


title: 37_pTa

tag: preopclinstage

tag: age at rc


title: 28_pT3

value: DOD

value: Yes

tag: postchemo type

value: salvage

tag: smoking


title: 30_pT4

value: TCC/Squamous

tag: plnd result

value: Negative

tag: rc grade

value: unk


title: 26_pT4

value: Nx

tag: nomogram score

value: Former

tag: smokingpack-years


title: 32_pT3

value: male

value: NED

value: Current

tag: recurrence free survival months (distant and local)

tag: recurrence/dod


title: 27_pT1

value: TCC

value: High

tag: distant mets

tag: cluster


title: 21_pT4

tag: local recurrence

tag: urothelial recurrence

value: DOC


title: 17_pT3

value: female

tag: metastasis

tag: last known status


title: 24_pT4

tag: gender

value: Positive

tag: post rc_chemo

value: adjuvant


title: 16_pT3

tag: preopclinstage

tag: age at rc

value: DOD

value: No


title: 20_pT4

value: Yes

tag: postchemo type

value: salvage

tag: smoking


title: 25_pT3

tag: plnd result

value: Negative

tag: rc grade

value: Never


title: 22_pT3

tag: nomogram score

tag: smokingpack-years


title: 19_pT2

value: Nx

tag: recurrence free survival months (distant and local)

tag: recurrence/dod


title: 14_pT4

tag: distant mets

value: Former

tag: cluster


title: 12_pT2

value: male

tag: local recurrence

tag: urothelial recurrence


title: 11_pT1

value: Low

tag: metastasis

tag: last known status

value: NED


title: 13_pT3

tag: gender

value: TCC/Squamous

tag: post rc_chemo


title: 15_pT4

tag: preopclinstage

tag: age at rc

value: High

value: Current


title: 18_pT3

value: TCC

tag: postchemo type

tag: smoking


title: 23_pT4

tag: plnd result

tag: rc grade

value: DOC

value: unk


title: 7_pT1

value: Positive

tag: nomogram score

tag: smokingpack-years


title: 9_pT2

value: DOD

value: No

tag: recurrence free survival months (distant and local)

tag: recurrence/dod


title: 5_pT4

value: female

value: TCC/CIS

tag: distant mets

tag: cluster


title: 8_pT3

value: Negative

tag: local recurrence

tag: urothelial recurrence

value: Never


title: 6_pT3

value: Nx

tag: metastasis

tag: last known status

value: Former

value: Yes


title: 3_pT2

tag: gender

tag: post rc_chemo


title: 2_pT2

value: male

tag: preopclinstage

tag: age at rc

value: salvage


title: 1_pT2

value: High

tag: smoking


title: Basal cochlea at postnatal day 0 [P0-Base_2011]

status: Public on Dec 13 2011

city: Seoul

first: Heejei

last: Yoon

address: 134 Shinchondong, Seodaemoongu

department: Anatomy

country: South Korea

institute: Yonsei University

description: pooled basal cochlea

hyb_protocol: End-labeled cDNA was hybridized for 16 hours at 45℃ and 60 rpm according to Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: GeneChips were stained and washed in a Genechip Fluidics Station 450 (Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix)

data_processing: Affymetrix Command Console Software version 1.1 was used to process the raw images into CEL files. Gene expression estimates were normalized using the robust multiarray averaging (RMA) method.

organism: Mus musculus

source_name: wild-type, basal cochlea

label_protocol: Three hundred nano-gram of high quality total RNA was converted into double-stranded cDNA using a random hexamer conjugated with a T7 promoter sequence. cRNA was generated from the double-stranded cDNA using an in vitro transcription (IVT) reaction and then re-converted into cDNA with dNTPs mix containing dUTP. This cDNA was then fragmented by uracil-DNA glycosylase (UDG) and APE1 restriction endonucleases and labeled with a biotinylated dideoxynucleotide by terminal transferase reaction

growth_protocol: Mouse cochlea dissected from day 0 and 8 pups

extract_protocol: Eighty temporal bones were dissected from mice at P0 and P8. After removing the otic capsule, The cochlear tissues were divided into three equal pieces representing the basal, middle and apical turns, and pooled separately. The pooled cochlear tissues were homogenized with a micro-homogenizer, and total RNA was extracted using an RNeasy Mini Kit.

treatment_protocol: Not applicable

tag: age

tag: tissue

tag: genetic background


title: Apical cochlea at postnatal day 8 [P8-Apex_2011]

description: pooled apical cochlea

source_name: wild-type, apical cochlea


title: Middle cochlea at postnatal day 8 [P8-Mid_2011]

description: pooled middle cochlea

source_name: wild-type, middle cochlea


title: 4_pT4

tag: plnd result

tag: rc grade

tag: nomogram score

tag: smokingpack-years


title: Middle cochlea at postnatal day 0 [P0-Mid_2011]

description: pooled middle cochlea


title: Basal cochlea at postnatal day 8 [P8-Base_2011]

description: pooled basal cochlea


title: Adrenocortical Carcinoma 051 [ACC]

status: Public on Nov 02 2011

first: Rork

last: Kuick

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Ann Arbor quantile-normalized trimmed-mean method

source_name: Adrenocortical Carcinoma

label_protocol: 3-5 Âµg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from the tissue lysate using Trizol (Invitrogen) and cleanup performed with an RNeasy kit (Qiagen)

tag: Sex

value: F

tag: side of body

value: Right

tag: clinical characteristics

value: Right adrenal mass; elevated androgens and cortisol

tag: tumor diameter (cm)

tag: tumor weight (gm)

tag: weiss score of tumor

tag: mitotic rate of tumor

tag: tumor stage

tag: years to last followup

tag: dead or alive at last followup

value: dead

tag: beta-catenin staining

value: Nuclear

tag: beta-catenin sequence result

value: unknown

tag: hormone expression

value: Testosterone


title: Adrenocortical Carcinoma 055 [ACC]

tag: age

value: not applicable

value: History of Adrenocortical carcinoma

value: Low


title: Adrenocortical Carcinoma 017 [ACC]

value: History of adrenal mass; 2 month history of abdominal pain

value: Cortisol+Testosterone


title: Adrenocortical Carcinoma 038 [ACC]

value: Cushing Syndrome; Right adrenalectomy 4 years prior

value: alive

value: Cortisol


title: Adrenocortical Carcinoma 057 [ACC]

value: Left

value: Cortisol secreting tumor


title: Adrenocortical Carcinoma 014 [ACC]

value: M

value: Right adrenal tumor; Leg edema

value: High

value: Non-functional


title: Adrenocortical Carcinoma 056 [ACC]

value: F

value: Right

value: Hyperaldosteronism

value: Nuclear

value: Aldosterone


title: Adrenocortical Carcinoma 102 [ACC]

value: Left adrenal mass

value: unknown

value: dead


title: Adrenocortical Carcinoma 094 [ACC]


title: Adrenocortical Carcinoma 042 [ACC]

value: Cushing Syndrome


title: Adrenocortical Carcinoma 039 [ACC]


title: Adrenocortical Carcinoma 047 [ACC]

value: Elevated serum aldosterone and DHEA-S; History of left nephrectomy


title: Adrenocortical Carcinoma 046 [ACC]

value: Low


title: Adrenocortical Carcinoma 033 [ACC]

value: Left

value: Increased testosterone

value: Testosterone


title: Adrenocortical Carcinoma 048 [ACC]

value: Liver tumor; Severe abdominal pain

value: alive

value: Membrane

value: Cortisol


title: Adrenocortical Carcinoma 054 [ACC]

value: F


title: Apical cochlea at postnatal day 0 [P0-Apex_2011]

description: pooled apical cochlea

tag: tissue

tag: genetic background


title: Adrenocortical Carcinoma 001 [ACC]

value: DHEAS


title: Adrenocortical Carcinoma 019 [ACC]

value: Right

value: Right flank pain; Masses in right kidney, liver and both lungs

value: High

value: Non-functional


title: Adrenocortical Carcinoma 058 [ACC]

value: Left adrenal mass

value: unknown


title: 10_pT3

tag: gender

value: female

tag: preopclinstage

tag: age at rc

value: TCC

tag: plnd result

value: Nx

tag: rc grade

tag: nomogram score

tag: distant mets

tag: local recurrence

tag: urothelial recurrence

tag: metastasis

tag: last known status

value: DOC

value: No

tag: post rc_chemo

tag: smoking

value: Former

tag: smokingpack-years

tag: recurrence free survival months (distant and local)

tag: recurrence/dod

tag: cluster


title: Adrenocortical Carcinoma 035 [ACC]

tag: age

tag: Sex

value: M

tag: side of body

value: Left

tag: clinical characteristics

tag: tumor diameter (cm)

tag: tumor weight (gm)

tag: weiss score of tumor

value: Low

tag: mitotic rate of tumor

tag: tumor stage

tag: years to last followup

tag: dead or alive at last followup

value: alive

tag: beta-catenin staining

tag: beta-catenin sequence result

tag: hormone expression


title: Adrenocortical Carcinoma 101 [ACC]

value: Membrane


title: Adrenocortical Carcinoma 013 [ACC]

value: F

value: History of Adrenocortical carcinoma with lung, liver and bone metastises 1 year prior

value: dead

value: Cortisol


title: Adrenocortical Carcinoma 089 [ACC]

value: High

value: Non-functional


title: Adrenocortical Carcinoma 018 [ACC]

value: Cushing Syndrome

value: unknown


title: Adrenocortical Carcinoma 084 [ACC]

value: not applicable

value: Tumor of left hepatic lobe


title: Adrenocortical Carcinoma 098 [ACC]

value: Status post adrenalectomy


title: Adrenocortical Carcinoma 103 [ACC]

value: Left adrenal mass


title: Adrenocortical Carcinoma 016 [ACC]

value: Right

value: Virilization and microcephaly

value: Testosterone


title: Adrenocortical Carcinoma 032 [ACC]

value: M

value: Left

value: Cushing Syndrome; Left adrenalectomy 3 years prior for adrenocortical tumor

value: Low


title: Adrenocortical Adenoma 095 [ACA]

source_name: Adrenocortical Adenoma

value: Right adrenal mass

value: Nuclear

value: wild type


title: Adrenocortical Adenoma 070 [ACA]

value: F

value: Right pheochromocytoma

value: mutant

value: Non-functional


title: Adrenocortical Adenoma 065 [ACA]

value: not applicable

value: unknown

value: Membrane

value: Cortisol


title: Adrenocortical Adenoma 075 [ACA]

value: Abdominal pain


title: Adrenocortical Adenoma 077 [ACA]

value: Cushing Syndrome


title: Adrenocortical Carcinoma 011 [ACC]

value: History of Adrenocortical carcinoma

value: High

value: dead


title: Adrenocortical Adenoma 081 [ACA]

value: Right


title: Adrenocortical Adenoma 078 [ACA]

value: Aldosteronoma

value: Aldosterone


title: Adrenocortical Adenoma 071 [ACA]

value: Left

value: Conn's syndrome

value: wild type


title: Adrenocortical Adenoma 079 [ACA]

value: F

value: Hyperaldosteronism


title: Adrenocortical Adenoma 082 [ACA]

value: Bilateral adrenal masses

value: not applicable

value: Non-functional


title: Adrenocortical Adenoma 080 [ACA]

value: M

value: unknown

value: Membrane


title: Adrenocortical Adenoma 099 [ACA]

value: Left adrenal mass

value: Nuclear

value: mutant


title: Adrenocortical Adenoma 064 [ACA]


title: Adrenocortical Adenoma 021 [ACA]

value: Right

value: Hypertension

value: Cortisol


title: Adrenocortical Adenoma 068 [ACA]

value: Left

value: Aldosteronoma

value: Aldosterone


title: Adrenocortical Carcinoma 053 [ACC]

value: Low


title: Total RNA 1 (20111110_gDNA_vs_total_3_507526-2)

status: Public on Dec 05 2011

type: mixed

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Expression profiling of nuclear RNA from total nuclei.

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Standard NimbleGen protocol.

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Total_RNA_1.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.

organism: Caenorhabditis elegans

source_name: total RNA

label_protocol: Standard NimbleGen protocol using 6 hour labeling reaction rather than 2 hour reaction.

extract_protocol: RNA isolation was done with Qiagen RNeasy mini kit. cDNA preparation and amplification were done with the Sigma WTA2 kit. Detailed protocol in supplementary file INTACT_ChIP_protocol.rtf .

tag: strain

value: adult

tag: cell type

value: whole organism

tag: sample type

value: total cell

molecule: genomic DNA

source_name: Fragmented genomic DNA

extract_protocol:
Genomic DNA was fragmented by sonication to
about 400bp.

tag: tissue

value: fragmented genomic DNA


title: Adrenocortical Adenoma 072 [ACA]

tag: age

tag: Sex

value: F

value: not applicable

value: wild type


title: Total nuclei RNA 4 (20110624_gDNA_vs_nucA_1_453625-3)

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Total_nuclei_RNA_4.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.

molecule: nuclear RNA

source_name: total nuclei

extract_protocol: RNA isolation was done with Qiagen RNeasy micro kit. cDNA preparation and amplification were done with the Sigma WTA2 kit. Detailed protocol in supplementary file INTACT_ChIP_protocol.rtf .

value: total nuclei

extract_protocol: Genomic DNA was fragmented by sonication to about 400bp.


title: Adrenocortical Adenoma 040 [ACA]

tag: side of body

tag: clinical characteristics

value: Cushing Syndrome

value: unknown

value: Membrane

value: Cortisol+Testosterone


title: Total RNA 2 (20111110_gDNA_vs_total_4_507308-2)

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Total_RNA_2.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.


title: Adrenocortical Adenoma 059 [ACA]

value: Right

value: Hyperaldosteronism

tag: tumor diameter (cm)

tag: tumor weight (gm)


title: Muscle nuclei RNA 1 (20110323_gDNA_vs_PmyoL1_453631)

description: Expression profiling of nuclear RNA from affinity-purified muscle nuclei.

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Muscle_nuclei_RNA_1.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.

source_name: INTACT-purified muscle nuclei

value: muscle cell

value: INTACT affinity-purified muscle nuclei


title: Total nuclei RNA 6 (20111110_gDNA_vs_nuc120_2_507524-2)

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Total_nuclei_RNA_6.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.

tag: background


title: Adrenocortical Carcinoma 034 [ACC]

value: Right adrenal mass

tag: weiss score of tumor

value: Low

tag: mitotic rate of tumor

tag: tumor stage

value: dead

value: Non-functional


title: Adrenocortical Adenoma 028 [ACA]

value: Left

tag: years to last followup

tag: dead or alive at last followup

tag: beta-catenin staining

value: Cortisol


title: Adrenocortical Adenoma 029 [ACA]

value: F

value: not applicable

tag: beta-catenin sequence result

tag: hormone expression


title: Adrenocortical Adenoma 022 [ACA]

value: wild type


title: Adrenocortical Adenoma 030 [ACA]

value: Cushing Syndrome


title: Normal Adrenal Cortex 076 [NC]

source_name: Normal Adrenal Cortex

value: M

value: Adrenalectomy for ACA; Conn's syndrome

value: unknown


title: Total nuclei RNA 3 (20110624_gDNA_vs_nuc_4_453614-3)

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Total_nuclei_RNA_3.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.

value: adult

tag: strain

value: whole organism

tag: sample type

value: total nuclei

value: fragmented genomic DNA


title: Normal Adrenal Cortex 085 [NC]

tag: age

value: Adrenalectomy for pheochromocytoma (Multiple Endocrine Neoplasia, Type IIA)

value: Membrane


title: Normal Adrenal Cortex 097 [NC]

tag: Sex

value: Adrenalectomy for pheochromocytoma


title: Normal Adrenal Cortex 069 [NC]

tag: side of body

value: Right

value: Adrenalectomy for renal cell carcinoma


title: Normal Adrenal Cortex 063 [NC]

tag: clinical characteristics


title: Normal Adrenal Cortex 088 [NC]

value: Left

tag: tumor diameter (cm)


title: Normal Adrenal Cortex 087 [NC]

value: Adrenalectomy for multinodular cortical hyperplasia; Conn's syndrome

tag: tumor weight (gm)


title: Normal Adrenal Cortex 092 [NC]

value: not applicable


title: Normal Adrenal Cortex 083 [NC]

value: F

value: Adrenalectomy for ACA


title: Muscle nuclei RNA 5 (20111012_gDNA_vs_unc120_1_507460)

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Muscle_nuclei_RNA_5.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.

tag: background

tag: cell type

value: muscle cell

value: INTACT affinity-purified muscle nuclei

tag: tissue


title: Fibroblast_HELP

status: Public on Aug 06 2011

type: genomic

city: Bronx

first: John

last: Greally

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

hyb_protocol: The HpaII and MspI representations were co-hybridized to the microarray and scanned to quantify the 532 and 635 nm fluorescence at each oligonucleotide on the microarray.

scan_protocol: see manufacturer's web site www.nimblegen.com

data_processing: HELP assay data analysis was performed using our published pipeline (Thompson, Reimers, Khulan, Gissot, Richmond, Chen, Zheng, Kim and Greally 2008), an open source resource available through BioConductor (HELP package)

source_name: LM-PCR products from HpaII digested DNA

label_protocol: The HELP samples were labeled for microarray analysis as described previously[Selzer, Genes Chromosomes Cancer 44:305–319] using Cy3 or Cy5-conjugated oligonucleotides and random primers.

growth_protocol: The cells were grown in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% Fetal Bovine Serum, 2 mM Glutamine and Penicillin-Streptomycin (Invitrogen) in a 37°C incubator with 5% CO2.

extract_protocol: DNA was isolated using proteinase K digestion, phenol-chloroform extraction, dialysis against 0.2X SSC and concentration by surrounding the dialysis bag with PEG 20,000 to reduce water content by osmosis.  The quality of the DNA was checked by gel electrophoresis and spectrophotometry.

value: Foreskin fibroblast

tag: digestive enzyme

value: HpaII

source_name: LM-PCR products

value: Msp 1


title: GM06990_HELP

growth_protocol: The cells were cultured as recommended by the Coriell repository.

value: Lymphoblastoid

source_name: LM-PCR products from MspI digested DNA


title: Muscle nuclei RNA 3 (20110624_gDNA_vs_myoL_4_454304-2)

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Muscle_nuclei_RNA_3.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.

value: adult

value: whole organism

value: fragmented genomic DNA


title: Muscle nuclei RNA 6 (20111012_gDNA_vs_unc120_2_507461)

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Muscle_nuclei_RNA_6.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.


title: Muscle nuclei RNA 4 (20110624_gDNA_vs_LmyoA_1_454479)

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Muscle_nuclei_RNA_4.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.


title: Total nuclei RNA 5 (20111110_gDNA_vs_nuc120_1_507461-2)

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Total_nuclei_RNA_5.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.

value: total nuclei


title: Normal Adrenal Cortex 006 [NC]

value: Adrenalectomy for metastatic lung carcinoma

tag: weiss score of tumor

tag: mitotic rate of tumor

tag: tumor stage

tag: years to last followup

value: unknown

value: Membrane


title: Muscle_AQM_Control_4

status: Public on Oct 19 2011

city: uppsala

first: sudhakar

middle: reddy

last: aare

address: Ing 85, 3 tr, Akademiska sjukhuset

department: neuroscience

country: Sweden

institute: uppsala university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip  Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 800.

organism: Sus scrofa

source_name: control treated with sedation and mechanical ventilation_Day5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

extract_protocol: Total RNA was extracted according to the standard Affymetrix protocol including Trizol extraction and Rneasy column cleanup

treatment_protocol: Four female domestic piglets (Sus scrofa, average body weight 25.5 kg) were used in this study. Piglets were immobilized by anesthesia and mechanically ventilated via a tracheotomy for a period of five days. During this study period, the animals were sedated using isoflurane inhalation (Abbott Laboratories, Chicago, Il, USA, 0.8 – 1.3% end-tidal concentration) supplemented by intravenous bolus doses of morphine and ketamine as needed.  Core body temperature (blood) was maintained in the range of 38.5 – 40°C by a servo controlled heating pad.  The animals received intravenous crystalloid fluid (Ringeracetat) to maintain stable blood pressure and urinary output and a glucose infusion (Rehydrex, Fresenius Kabi, Stockholm, Sweden, 25 mg glucose /mL) in the range of 0.5 – 1.5 mg/kg/minute to decrease the effects of catabolism.  Each animal received prophylactic streptomycin 750 mg/d and bensylpenicillin 600 mg/d (Streptocillin Vet, Boeringer-Ingelheim, Hellerup, Denmark). Arterial blood gas analysis as well as electrolytes and blood glucose levels were monitored regularly and kept in the normal range throughout the study period.Endotoxemia was induced by a continuous infusion of Escherichia coli endotoxin, serotype O26:B6 (Sigma Labkemi, Stockholm, Sweden) at 36 µg/kg/h for 1h.

tag: gender

value: female

value: biceps femoris muscle

tag: disease

value: acute quadriplegic myopathy (AQM)

tag: time period

value: 5 days


title: Adrenocortical Carcinoma 008 [ACC]

tag: age

value: F

value: Left

value: Left adrenal mass

value: High

tag: dead or alive at last followup

value: dead

tag: beta-catenin staining

tag: beta-catenin sequence result

tag: hormone expression

value: Testosterone


title: Muscle_AQM_Control_2


title: Muscle_AQM_Control_3


title: Muscle_AQM_Control_1


title: Total nuclei RNA 1 (20110323_gDNA_vs_nuc_453625)

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Total_nuclei_RNA_1.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.

value: adult

tag: strain

tag: sample type


title: pRJ-FR. 5 fed 3

status: Public on Jul 22 2011

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

country: Japan

institute: Toyohashi University of Technology

description: Gene expression of a pRJ-FR. 5-fed worm.

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C. After hybridization, the microarrays were washed according to the manufacturer’s protocol.

scan_protocol: Microarrays were scanned on an Agilent DNA Microarray Scanner with the Scan Control software (Agilent Technologies).

data_processing: The resulting images were processed, and raw data were collected using Agilent’s Feature Extraction software. The gene expression data were analyzed using GeneSpring GX 10 (Agilent). The signal intensity for each probe was normalized by a percentile shift, in which each measurement was divided by the 75th percentile of all measurements in its array.

source_name: pRJ-FR. 5 treated

label_protocol: Five hundred ng of the RNA sample was transcribed using oligo(dT)-based T7 promoter primer and MMLV-RT in the first- and second-strand cDNA synthesis reactions. The double-stranded cDNAs were used as templates in the preparation of fluorescent complementary RNAs (cRNAs) in the presence of T7 RNA polymerase and cyanine 3-CTP dye in an in vitro transcription reaction.

extract_protocol: Total RNA was prepared from non-treated control nematodes and those exposed to 25 mg/ml pRJ Fr. 5 for 24 h. Worms were homogenized with TRIzol® Reagent by using a Precellys 24 and total RNA was extracted with a PureLinkTM RNA Mini kit.

treatment_protocol: The Bristol N2 strain of C. elegans was maintained at 20°C on nematode growth agar medium (NGM) with UV-irradiated Escherichia coli OP50 as a food source. Worms were treated with or not with pRJ-Fr. 5 (25mg/ml) for 24 h starting at the L4 stage.

value: Bristol N2

tag: genotype

value: wild type

tag: Sex

value: hermaphrodite

value: whole body

value: larval 4 (L4)

tag: treatment

value: protease-treated royal jelly, fraction 5 (pRJ-FR. 5)


title: pRJ-FR. 5 fed 2

tag: tissue


title: Control 2

description: Gene expression of a control worm.

source_name: Untreated


title: Total nuclei RNA 2 (20110527_gDNA_vs_nuc_2_453529-2)

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Total_nuclei_RNA_2.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.

value: whole organism

value: total nuclei

value: fragmented genomic DNA


title: Control 3

description: Gene expression of a control worm.


title: Chip-24 Day21 Rep4 Blue & Day7 Rep4 Red

status: Public on Apr 05 2011

city: Fargo

first: Munevver

last: Dogramaci

state: ND

address: 1605 Albrecht Blvd N

institute: USDA-ARS

description: See Dogramaci et al. Plant Molecular Biology 2010 (PMID 20340040) for more details.

hyb_protocol: Labeled cDNAs were hybridized to a custom-made 23K element microarray that contained 19,808 UniGenes from a leafy spurge EST database (Anderson et al. 2007) and an additional 4,129 UniGenes from a cassava EST database (Lokko et al. 2007). Comparison of gene expression between samples was accomplished using a rolling circle dye-swap hybridization scheme (Churchill 2002) to provide every biological replicate with technical replicates. In this experiment, each of the four biological replicates included two technical replicates.

scan_protocol: Microarray hybridization was visualized using a GenePix 4000B scanner and probe intensities and background were quantified using GenePix 6.0 software (Molecular Devices, Sunnyvale, California, USA).

data_processing: A quality control value of “1” was assigned to all probes that had intensity values greater than 2 times the standard deviation over average of the negative control and empty probe intensities (after deleting 1% of the most intense negative/empty probe values). Intensity values of control spots (a total of 1455 spots including 3X SSC, blanks, and mouse) from MA chips were removed before bioinformatics. In this submission, the original “GPR” files include information for the control spots, while the Sample data tables include information only for the spots that were used for data analyses (a total of: 23937). Raw signal intensities of all DNA-containing spots were up-loaded into the GeneMaths XT 5.1 microarray data analysis program (Applied Maths Inc., Austin, TX, USA) for normalization following the "Layer/Normalization/Arrays" path with default settings (Offset: Average; Scaling: Standard deviation), and for statistical analysis and clustering of the dataset. Hybridization intensities were log2 transformed, and arrays were centered and normalized against each other; technical replicates within each biological replicate were averaged.

organism: Euphorbia esula

source_name: 21-day dehydration-stressed endodormant crown buds

label_protocol: For microarray hybridizations, labeled cDNAs were prepared from 30 µg of total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen, Carlsbad, CA, USA) according to manufacturer's protocols.

growth_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype 1984-ND001 and maintained in a greenhouse as described by Anderson and Davis (2004). Shoot cuttings were grown in No. 1 Ray Leach Cone-tainers (Stuewe and Sons Inc. Corvallis, OR, USA) in the greenhouse for three months prior to application of experimental treatments. The greenhouse was set at 25°C with a 16 h:8 h day:night photoperiod. Average daily light fluencies were approximately 350 μmol m-2 s-1 and 400 W high-pressure sodium lamps were used as to extend the day-length. Each treatment was replicated four times, and thirty plants were used per biological replication. Prior to the start of each experiment, plants were randomly chosen from the greenhouse and acclimated in a growth chamber (PGR15 Model of Conviron, Winnipeg, Canada) for one week at 27°C, 16 h:8 h day:night photoperiod. At the end of each treatment, crown bud samples were collected between 1100 and 1300 Central Standard times to avoid diurnal variation.

extract_protocol: At the end of each treatment, crown bud samples were collected, flash frozen in liquid N2, and stored at -80°C until RNA extraction. Crown bud samples were ground to a fine powder in liquid N2, and RNA was extracted from approximately one gram of tissue according to the pine tree RNA extraction protocol (Chang et al. 1993). RNA quality and quantity was confirmed by spectrophotometry and agarose gel electrophoresis.

treatment_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype and maintained in a greenhouse. Induction of endodormancy in crown buds was accomplished by subjecting paradormant plants to a ramp down treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light) for 12 weeks as described by Dogramaci et al. (2010); plants were watered daily. After endodormancy induction, water was withheld from these plants for 21 days to study effect of dehydration stress on transcriptome profiles and dormancy status.

tag: biotype

value: crown bud

value: dehydration stress

tag: treatment time

value: 21 days

source_name: 7-day dehydration-stressed endodormant crown buds

treatment_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype and maintained in a greenhouse. Induction of endodormancy in crown buds was accomplished by subjecting paradormant plants to a ramp down treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light) for 12 weeks as described by Dogramaci et al. (2010); plants were watered daily. After endodormancy induction, water was withheld from these plants for 7 days to study effect of dehydration stress on transcriptome profiles and dormancy status.

value: 7 days


title: Muscle nuclei RNA 2 (20110527_gDNA_vs_myoL1_3_453614-2)

data_processing: Standard NimbleGen bi-weight mean adjusted log base 2 ratios (Cy5/Cy3) were converted to standard deviates by subtracting their mean and dividing by their standard deviation. Per-gene expression values in supplementary file Muscle_nuclei_RNA_2.txt were computed as described in http://nettie.fhcrc.org/labuser/protocols/expression.html: The standardized log ratios for all exonic probes starting with the 20th probe from the 3' ends of WS220 genes were averaged to give a single expression value for each gene.

tag: cell type

value: muscle cell

value: INTACT affinity-purified muscle nuclei


title: Chip-19 Day0 Rep4 Blue & Day3 Rep4 Red

source_name: 0-day dehydration-stressed endodormant crown buds

treatment_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype and maintained in a greenhouse. Induction of endodormancy in crown buds was accomplished by subjecting paradormant plants to a ramp down treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light) for 12 weeks as described by Dogramaci et al. (2010); plants were watered daily. In this study, endodormant crown buds were used as controls, and referred as Day-0 dehydration.

value: 0 days

source_name: 3-day dehydration-stressed endodormant crown buds

treatment_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype and maintained in a greenhouse. Induction of endodormancy in crown buds was accomplished by subjecting paradormant plants to a ramp down treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light) for 12 weeks as described by Dogramaci et al. (2010); plants were watered daily. After endodormancy induction, water was withheld from these plants for 3 days to study effect of dehydration stress on transcriptome profiles and dormancy status.

value: 3 days


title: Chip-20 Day1 Rep4 Blue & Day14 Rep4 Red

source_name: 1-day dehydration-stressed endodormant crown buds

treatment_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype and maintained in a greenhouse. Induction of endodormancy in crown buds was accomplished by subjecting paradormant plants to a ramp down treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light) for 12 weeks as described by Dogramaci et al. (2010); plants were watered daily. After endodormancy induction, water was withheld from these plants for 1 day to study effect of dehydration stress on transcriptome profiles and dormancy status.

value: 1 day

source_name: 14-day dehydration-stressed endodormant crown buds

treatment_protocol: A population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype and maintained in a greenhouse. Induction of endodormancy in crown buds was accomplished by subjecting paradormant plants to a ramp down treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C → 10°C) and a decreasing photoperiod of 40 min week-1 (16h → 8h light) for 12 weeks as described by Dogramaci et al. (2010); plants were watered daily. After endodormancy induction, water was withheld from these plants for 14 days to study effect of dehydration stress on transcriptome profiles and dormancy status.

value: 14 days


title: pRJ-FR. 5 fed 1

value: Bristol N2

value: wild type

value: hermaphrodite


title: Chip-22 Day7 Rep4 Blue & Day1 Rep4 Red


title: Chip-21 Day3 Rep4 Blue & Day21 Rep4 Red


title: Chip-17 Day14 Rep3 Blue & Day0 Rep3 Red


title: Chip-16 Day7 Rep3 Blue & Day1 Rep3 Red


title: Chip-7 Day0 Rep2 Blue & Day3 Rep2 Red


title: Chip-14 Day1 Rep3 Blue & Day14 Rep3 Red


title: Chip-18 Day21 Rep3 Blue & Day7 Rep3 Red


title: Chip-9 Day3 Rep2 Blue & Day21 Rep2 Red


title: Control 1

description: Gene expression of a control worm.

value: whole body

value: larval 4 (L4)


title: Chip-13 Day0 Rep3 Blue & Day3 Rep3 Red


title: Chip-11 Day14 Rep2 Blue & Day0 Rep2 Red


title: Chip-15 Day3 Rep3 Blue & Day21 Rep3 Red


title: Chip-10 Day7 Rep2 Blue & Day1 Rep2 Red


title: Chip-5 Day14 Rep1 Blue & Day0 Rep1 Red


title: Chip-12 Day21 Rep2 Blue & Day7 Rep2 Red


title: Chip-8 Day1 Rep2 Blue & Day14 Rep2 Red


title: Chip-4 Day7 Rep1 Blue & Day1 Rep1 Red


title: MG_CGH extraction2_array2

status: Public on Mar 25 2011

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Agilent hybridization protocol;  Setting up hybridization 1.Thaw samples on ice, in the dark 2.Set up hyb reaction: (Oligo aCGH/ChOP-on-Chip Hyb kit; Agilent) sample 25ul Ambion dH2O 175ul 10X Blocking Solution 50ul 2X Hybridization buffer 250ul 3.Inc 95C, 5 minutes 4.Spin down briefly and keep at 37C while getting slide ready 5.Place gasket with agilent side facing up on metal chamber 6.Pipet 490ul of hyb reaction on gasket 7.Lay down microarray on hyb reaction with Agilent side down. 8.Assemble metal chamber 9.inc. 16-20 hours in rotating hyb oven at 65C Washing microarrays 10.Dissamble arrays in tip box lid containing Buffer 1 (Agilent) 11.Wash slide in buffer 1 with stirring, 5 minutes 12.Wash slide in buffer 2 with stirring, 5 minutes 13.Wash slide in acetonitrile, 30 seconds 14.Wash slide in buffer 3, 30 seconds 15.Store in light proof holder and scan

scan_protocol: This scanning protocol outputs raw images of intensity values resulting from the hybridization of the DNA sample to the microarray slide.  The raw tiffs are quantified and output in an Agilent text format. We then mangle the Agilent data into a pseudo nimblegen format.

data_processing: Normalization_and_peak_calling:DM:1 protocol. Normalization and peak calling protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Parameters are passed as a tag file which we generate in Array Scanning protocol.   Processed data are obtained using following parameters: tag file is http://macalpine-lab.duhs.duke.edu/files/modencode/Midgut_CGH/400K_Array/midgut_400K.tag

organism: Drosophila melanogaster

source_name: MG_CGH extraction2_array2 channel_1

label_protocol: Labeling WI protocol;  For All Tissue Types Protocol Adapted from Agilent Technologies’ “Oligonucleotide Array-Based CGH for Genomic DNA Analysis” Protocol Handbook (Version 2.0, August 2005). The BioPrime Array CGH Genomic Labeling System (18095-011, Invitrogen) was used to prepare samples for CGH arrays. Cye-dyes were purchased from Amersham (25nmol, PA53022/PA55022). Label 3ug of genomic DNA (recovered from 150 larval salivary glands or 16C follicle cell nuclei from 300 pairs of ovaries). 50uL of embryos yields about 7-9ug of DNA. 1. Add 20uL of the 2.5x Random Primers solution to your previously prepared salivary gland gDNA. Transfer tube to a heat block at 95C and incubate for 5 minutes. Afterwards, immediately incubate sample on ice for an additional 5 minutes. 2. Prepare the labeling reaction mix on ice in the order indicated. 10x dUTP mix 5uL Cy3 or Cy5 –dUTP 3uL Exo-Klenow 1uL Mix this labeling reaction mix with your salivary gland gDNA (incubating on ice). 3. Transfer sample to a water bath at 37C for 2 hours. 4. Remove sample from water bath and add 5uL of Stop Buffer. 5. Concentrate labeled DNA with a microcon YM-30 filter according to manufacturer’s instructions for a final volume of 150uL, for each tube. 6. Quantitate total amount of incorporated dye in each sample using a Nanodrop. Combine up to 200 picomoles of labeled sample into a single tube, for a maximum volume of 150uL. Save the rest for technical replicates.

growth_protocol:
From a Drosophila culture, manually remove larvea of selected type.
Collection and dissection of biologicial tissues, to include:embryo 0-2hfollicle cellsnurse cellsadult fat bodysalivary gland

extract_protocol: DNA isolation WI protocol;  For all tissues Protocol adapted from Qiagen DNeasy Blood and Tissue Handbook (July 2006). Using the DNeasy Blood and Tissue Kit: 1. Spin down samples and resuspend in 180uL ATL buffer. 2. Add 20uL proteinase K. Incubate at 56C until tissues are lysed (typically overnight for salivary gland tissues, four hours for other cell types). Vortex occasionally. 3. Vortex for 15s. Add 200uL buffer AL. Vortex again, and then add 200uL 100% EtOH. Vortex again to mix. 4. Pipet mixture into supplied DNeasy Mini Spin column placed in provided 2mL collective tube. Centrifuge for 1min at >6000g (14000rpm in a tabletop centrifuge is fine). 5. Place column in a fresh collection tube. Add 500uL buffer AW1, centrifuge for 1min at >6000g. Discard collection tube. 6. Transfer spin column to a fresh microcentrifuge tube. Pipet 50uL buffer AE onto column membrane. Incubate at room temperature for 1min, and elute by centrifuging for 1min at >6,000g.

value: Oregon-R(official name :Oregon-R-modENCODE genotype :wild type )

value: midgut

tag: developmental stage

value: L3 stage wandering larvae

source_name: MG_CGH extraction2_array2 channel_2


title: expt.1092 extraction1_array1

status: Public on Mar 09 2011

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ISWI Q4095;target name: ISWI;host: Rabbit;antigen: Amino acid 589-688;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4095;short description: ISWI;

Input: pirrota_1362_Kc-5_Input.1114.CEL

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.

source_name: expt.1092 extraction1_array1 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: embryo-derived cell-line

value: late embryonic stage

value: se/e

value: Female


title: FB_CGH extraction1_array1

data_processing: Normalization_and_peak_calling:DM:1 protocol. Normalization and peak calling protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Parameters are passed as a tag file which we generate in Array Scanning protocol.   Processed data are obtained using following parameters: tag file is http://macalpine-lab.duhs.duke.edu/files/modencode/Fatbody_CGH/1M_Array/fatbody_1M.tag

source_name: FB_CGH extraction1_array1 channel_1

value: fat body

source_name: FB_CGH extraction1_array1 channel_2


title: Chip-3 Day3 Rep1 Blue & Day21 Rep1 Red

value: crown bud

value: dehydration stress

value: 21 days


title: expt.1098 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ISWI Q4095;target name: ISWI;host: Rabbit;antigen: Amino acid 589-688;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4095;short description: ISWI;

Input: pirrota_1205_B5_Input.936.CEL

source_name: expt.1098 extraction3_array1 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.

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

value: Unknown


title: Chip-6 Day21 Rep1 Blue & Day7 Rep1 Red

value: 7 days


title: expt.1097 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: ISWI Q4095;target name: ISWI;host: Rabbit;antigen: Amino acid 589-688;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4095;short description: ISWI;

Input: pirrota_1204_B3_Input.935.CEL

source_name: expt.1097 extraction1_array1 channel_1


title: FB_CGH extraction2_array2

data_processing: Normalization_and_peak_calling:DM:1 protocol. Normalization and peak calling protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Parameters are passed as a tag file which we generate in Array Scanning protocol.   Processed data are obtained using following parameters: tag file is http://macalpine-lab.duhs.duke.edu/files/modencode/Fatbody_CGH/400K_Array/fatbody_400K.tag

source_name: FB_CGH extraction2_array2 channel_1

value: wild type

source_name: FB_CGH extraction2_array2 channel_2


title: MG_CGH extraction1_array1

data_processing: Normalization_and_peak_calling:DM:1 protocol. Normalization and peak calling protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Parameters are passed as a tag file which we generate in Array Scanning protocol.   Processed data are obtained using following parameters: tag file is http://macalpine-lab.duhs.duke.edu/files/modencode/Midgut_CGH/1M_Array/midgut_1M.tag

source_name: MG_CGH extraction1_array1 channel_1

value: Oregon-R(official name :Oregon-R-modENCODE genotype :wild type )

source_name: MG_CGH extraction1_array1 channel_2


title: Chip-2 Day1 Rep1 Blue & Day14 Rep1 Red

value: 1 day

value: 14 days


title: Chip-1 Day0 Rep1 Blue & Day3 Rep1 Red

value: 0 days

value: 3 days


title: expt.681 extraction4_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HP2 (Ab2-90);target name: HP2;host: Rabbit;antigen: cDNA identified in Y2H that corresponds to C-terminal end;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Elgin Ab2-90;short description: rabbit polyclonal;

Input: pirrota_602_B5_Input_20cycles_391.CEL

source_name: expt.681 extraction4_array1 channel_1


title: expt.680 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HP2 (Ab2-90);target name: HP2;host: Rabbit;antigen: cDNA identified in Y2H that corresponds to C-terminal end;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Elgin Ab2-90;short description: rabbit polyclonal;

Input: pirrota_646_B3_Input2_20cycles_423.CEL

source_name: expt.680 extraction1_array1 channel_1


title: expt.992 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1b Q4114;target name: HP1b;host: Rabbit;antigen: AA's 151-240;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4114;short description: affinity purified antibody from 80mL rabbit antisera;

Input: pirrota_1012_A21_Input_20cyc_774.CEL

source_name: expt.992 extraction1_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage

value: Male


title: expt.720 extraction3_array1

source_name: expt.720 extraction3_array1 channel_1


title: expt.872 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1b (Henikoff);target name: HP1b;host: Rabbit;antigen: CASPIGSINQDENIKPDESSELDN;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Henikoff;short description: HP1b antibody from Henikoff lab;

Input: pirrota_1040_Kc4_Input_20cyc_814.CEL

source_name: expt.872 extraction3_array1 channel_1

value: se/e

value: Female


title: expt.873 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1b (Henikoff);target name: HP1b;host: Rabbit;antigen: CASPIGSINQDENIKPDESSELDN;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Henikoff;short description: HP1b antibody from Henikoff lab;

Input: pirrota_1041_Kc5_Input_20cyc_815.CEL

source_name: expt.873 extraction1_array1 channel_1


title: expt.157 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H4K20me;target name: H4K20me;clonal: Polyclonal;company: abcam;catalog: ab9051-25;short description: H4K20me polyclonal 0.5mg/ml (mono methyl K20);

Input: pirrota_272_S11_Input.111.CEL

source_name: expt.157 extraction3_array1 channel_1


title: expt.871 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1b (Henikoff);target name: HP1b;host: Rabbit;antigen: CASPIGSINQDENIKPDESSELDN;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Henikoff;short description: HP1b antibody from Henikoff lab;

Input: pirrota_826_CL8-2_Input_DNA_20cyc_597.CEL

source_name: expt.871 extraction1_array1 channel_1

value: dorsal mesothoracic disc


title: expt.870 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1b (Henikoff);target name: HP1b;host: Rabbit;antigen: CASPIGSINQDENIKPDESSELDN;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Henikoff;short description: HP1b antibody from Henikoff lab;

Input: pirrota_825_CL8-1_InputDNA_20cyc_596.CEL

source_name: expt.870 extraction3_array1 channel_1


title: expt.726 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me2-Ab2 (new lot);target name: H3K9me2;host: Mouse;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 di methylated at K9.;clonal: Monoclonal;purified: Affinity;company: Abcam;catalog: ab1220;reference: http://www.abcam.com/Histone-H3-di-methyl-K9-antibody-mAbcam-1220-ChIP-Grade-ab1220.html;short description: mouse monoclonal to histone H3 di-methyl K9 chIP grade;

Input: pirrota_963_A17_Input_20cyc_724.CEL

source_name: expt.726 extraction3_array1 channel_1


title: expt.631 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me2-Ab2 (new lot);target name: H3K9me2;host: Mouse;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 di methylated at K9.;clonal: Monoclonal;purified: Affinity;company: Abcam;catalog: ab1220;reference: http://www.abcam.com/Histone-H3-di-methyl-K9-antibody-mAbcam-1220-ChIP-Grade-ab1220.html;short description: mouse monoclonal to histone H3 di-methyl K9 chIP grade;

Input: pirrota_684_A15_Input.453.CEL

source_name: expt.631 extraction1_array1 channel_1


title: expt.931 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K36me3;target name: H3K36me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 tri methylated at K36.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9050;reference: http://www.abcam.com/Histone-H3-tri-methyl-K36-antibody-ChIP-Grade-ab9050.html;short description: Rabbit polyclonal to Histone H3 (tri methyl K36) - ChIP Grade;

Input: pirrota_477_C18-1_Input_14cyc_288.CEL

source_name: expt.931 extraction3_array1 channel_1


title: expt.991 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HP1b Q4114;target name: HP1b;host: Rabbit;antigen: AA's 151-240;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4114;short description: affinity purified antibody from 80mL rabbit antisera;

Input: pirrota_1011_A20_Input_20cyc_773.CEL

source_name: expt.991 extraction3_array1 channel_1


title: expt.932 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K36me3;target name: H3K36me3;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 tri methylated at K36.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9050;reference: http://www.abcam.com/Histone-H3-tri-methyl-K36-antibody-ChIP-Grade-ab9050.html;short description: Rabbit polyclonal to Histone H3 (tri methyl K36) - ChIP Grade;

Input: pirrota_478_C18-2_Input_14cyc_289.CEL

source_name: expt.932 extraction1_array1 channel_1


title: expt.75 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H4K20me;target name: H4K20me;clonal: Polyclonal;company: abcam;catalog: ab9051-25;short description: H4K20me polyclonal 0.5mg/ml (mono methyl K20);

Input: pirrota_273_S12_Input.112.CEL

source_name: expt.75 extraction1_array1 channel_1


title: expt.926 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K36me1;target name: H3K36me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 mono methylated at K36.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9048;reference: http://www.abcam.com/Histone-H3-mono-methyl-K36-antibody-ChIP-Grade-ab9048.html;short description: Rabbit polyclonal to Histone H3 (mono methyl K36) - ChIP Grade;

Input: pirrota_480_Kc-2_Input_14cyc_291.CEL

source_name: expt.926 extraction3_array1 channel_1


title: expt.921 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H2B-ubiq (NRO3);target name: H2Bubi;host: Mouse;antigen: This antibody was raised against a branched peptide corresponding to the conjugation site of ubiquitin on human histone H2B.;clonal: Monoclonal;purified: Affinity;company: Medimabs;catalog: #MM-0029;short description: Ubiquitinated Histone H2B Mouse Monoclonal Antibody: Isotype: IgG2a;

Input: pirrota_478_C18-2_Input_14cyc_289.CEL

source_name: expt.921 extraction3_array1 channel_1


title: expt.862 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K18Ac (new lot);target name: H3K18Ac;host: Rabbit;antigen: Synthetic peptide derived from within residues 1 - 100 Histone H3 acetylated at K18.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab1191;reference: http://www.abcam.com/Histone-H3-acetyl-K18-antibody-ChIP-Grade-ab1191.html;short description: rabbit polyclonal to Histone H3K18ac ChIP grade;

Input: pirrota_1038_Kc4_Input_14cyc_812.CEL

source_name: expt.862 extraction3_array1 channel_1


title: expt.863 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K18Ac (new lot);target name: H3K18Ac;host: Rabbit;antigen: Synthetic peptide derived from within residues 1 - 100 Histone H3 acetylated at K18.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab1191;reference: http://www.abcam.com/Histone-H3-acetyl-K18-antibody-ChIP-Grade-ab1191.html;short description: rabbit polyclonal to Histone H3K18ac ChIP grade;

Input: pirrota_1039_Kc5_Input_14cyc_813.CEL

source_name: expt.863 extraction1_array1 channel_1


title: expt.920 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H2B-ubiq (NRO3);target name: H2Bubi;host: Mouse;antigen: This antibody was raised against a branched peptide corresponding to the conjugation site of ubiquitin on human histone H2B.;clonal: Monoclonal;purified: Affinity;company: Medimabs;catalog: #MM-0029;short description: Ubiquitinated Histone H2B Mouse Monoclonal Antibody: Isotype: IgG2a;

Input: pirrota_477_C18-1_Input_14cyc_288.CEL

source_name: expt.920 extraction1_array1 channel_1


title: expt.887 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H2AV 9751;target name: H2AV;host: Rabbit;antigen: QDPQRKGNVILSQAY;clonal: Polyclonal;purified: Affinity;company: Lake Placid;catalog: Rabbit 9751;short description: Raised against peptide;

Input: pirrota_803_A14.input.566.CEL

source_name: expt.887 extraction3_array1 channel_1


title: expt.693 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H2AV 9751;target name: H2AV;host: Rabbit;antigen: QDPQRKGNVILSQAY;clonal: Polyclonal;purified: Affinity;company: Lake Placid;catalog: Rabbit 9751;short description: Raised against peptide;

Input: pirrota_802_A12.input.565.CEL

source_name: expt.693 extraction1_array1 channel_1


title: expt.672 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: EZ-Q3421;target name: E(Z);host: Rabbit;antigen: Peptide based on the aa 190-289 of the E(Z) protein;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3421;short description: Rabbit polyclonal antibody raised against E(Z) protein;

Input: pirrota_873_S15_Input-18cycles.644.CEL

source_name: expt.672 extraction1_array1 channel_1


title: expt.893 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: Su(var)3-9-Q2598;target name: Su(var)3-9;host: Rabbit;antigen: AA's 320-419;clonal: Unknown;purified: Affinity;company: SDI;catalog: Q2598;short description: Affinity purified antibodies from 80mL rabbit antisera;

Input: pirrota_1012_A21_Input_20cyc_774.CEL

source_name: expt.893 extraction3_array1 channel_1


title: expt.665 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: dSFMBT Q2642;target name: dSFMBT;host: Rabbit;antigen: aa 14-113 of dSFMBT protein;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2642;short description: Rabbit polyclonal Ab raised against the dSFMBT protein;

Input: pirrota_916_B4_Input-18cycles.671.CEL

source_name: expt.665 extraction3_array1 channel_1

value: CNS-derived cell-line


title: expt.892 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: Su(var)3-9-Q2598;target name: Su(var)3-9;host: Rabbit;antigen: AA's 320-419;clonal: Unknown;purified: Affinity;company: SDI;catalog: Q2598;short description: Affinity purified antibodies from 80mL rabbit antisera;

Input: pirrota_1011_A20_Input_20cyc_773.CEL

source_name: expt.892 extraction1_array1 channel_1


title: expt.784 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: EZ-Q3421;target name: E(Z);host: Rabbit;antigen: Peptide based on the aa 190-289 of the E(Z) protein;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3421;short description: Rabbit polyclonal antibody raised against E(Z) protein;

Input: pirrota_916_B4_Input-18cycles.671.CEL

source_name: expt.784 extraction1_array1 channel_1

value: third instar larval stage


title: expt.820 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: EZ-Q3421;target name: E(Z);host: Rabbit;antigen: Peptide based on the aa 190-289 of the E(Z) protein;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3421;short description: Rabbit polyclonal antibody raised against E(Z) protein;

Input: pirrota_1065_B10_Input-18cycles.823.CEL

source_name: expt.820 extraction3_array1 channel_1

value: y v f mal


title: expt.783 extraction3_array1

source_name: expt.783 extraction3_array1 channel_1


title: expt.821 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: dSFMBT Q2642;target name: dSFMBT;host: Rabbit;antigen: aa 14-113 of dSFMBT protein;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q2642;short description: Rabbit polyclonal Ab raised against the dSFMBT protein;

Input: pirrota_1064_B9_Input-18cycles.822.CEL

source_name: expt.821 extraction1_array1 channel_1

value: Unknown


title: expt.925 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K36me1;target name: H3K36me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 mono methylated at K36.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9048;reference: http://www.abcam.com/Histone-H3-mono-methyl-K36-antibody-ChIP-Grade-ab9048.html;short description: Rabbit polyclonal to Histone H3 (mono methyl K36) - ChIP Grade;

Input: pirrota_479_Kc-1_Input_14cyc_290.CEL

source_name: expt.925 extraction1_array1 channel_1


title: expt.945 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: POF (MO 459);target name: POF;host: Rabbit;antigen: aa1-150;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: MO 459;short description: Custom produced by Covance;

Input: pirrota_602_B5_Input_20cycles_391.CEL

source_name: expt.945 extraction3_array1 channel_1


title: expt.908 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: PR-Set7 Q3484;target name: PR-Set7;host: Rabbit;antigen: DQYFASPKRK DCRLMKVTQN GQLPEATMMA HNKDNKAGRT IGVPLATRSQ TRTIENFFKA NAAAKDSQKT IHTEEQLNLG NQELKLDDEE LNGQIKLDDE ; clonal: Unknown;purified: Affinity;company: SDI;catalog: Q3484;short description: (PR/SET domain-containing protein 07) (dSET8) (Lysine N-methyltransferase 5A)(KMT5A) (CG3307). Against 45-144;

Input: pirrota_803_A14.input.566.CEL

source_name: expt.908 extraction3_array1 channel_1


title: expt.944 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: POF (MO 459);target name: POF;host: Rabbit;antigen: aa1-150;clonal: Polyclonal;purified: Affinity;company: Covance;catalog: MO 459;short description: Custom produced by Covance;

Input: pirrota_646_B3_Input2_20cycles_423.CEL

source_name: expt.944 extraction1_array1 channel_1


title: expt.850 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: PR-Set7 Q3484;target name: PR-Set7;host: Rabbit;antigen: DQYFASPKRK DCRLMKVTQN GQLPEATMMA HNKDNKAGRT IGVPLATRSQ TRTIENFFKA NAAAKDSQKT IHTEEQLNLG NQELKLDDEE LNGQIKLDDE ; clonal: Unknown;purified: Affinity;company: SDI;catalog: Q3484;short description: (PR/SET domain-containing protein 07) (dSET8) (Lysine N-methyltransferase 5A)(KMT5A) (CG3307). Against 45-144;

Input: pirrota_802_A12.input.565.CEL

source_name: expt.850 extraction1_array1 channel_1


title: expt.826 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: Nurf301 Q4159;target name: Nurf301;host: Rabbit;antigen: Amino acid 448-547;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4159;short description: Nurf301;

Input: pirrota_760_A17_Input.530.CEL

source_name: expt.826 extraction1_array1 channel_1


title: expt.827 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: Nurf301 Q4159;target name: Nurf301;host: Rabbit;antigen: Amino acid 448-547;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4159;short description: Nurf301;

Input: pirrota_761_A18_Input.531.CEL

source_name: expt.827 extraction3_array1 channel_1


title: expt.838 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MOF Q4145;target name: MOF;host: Rabbit;antigen: Amino acid 362-461;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4145;short description: MOF;

Input: pirrota_1088_A21_Input.846.CEL

source_name: expt.838 extraction3_array1 channel_1


title: expt.839 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MOF Q4145;target name: MOF;host: Rabbit;antigen: Amino acid 362-461;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4145;short description: MOF;

Input: pirrota_1089_A20_Input.847.CEL

source_name: expt.839 extraction1_array1 channel_1


title: expt.1103 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MOF Q4145;target name: MOF;host: Rabbit;antigen: Amino acid 362-461;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4145;short description: MOF;

Input: pirrota_1361_Kc-4_Input.1113.CEL

source_name: expt.1103 extraction3_array1 channel_1


title: expt.1107 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MOF Q4145;target name: MOF;host: Rabbit;antigen: Amino acid 362-461;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4145;short description: MOF;

Input: pirrota_477_C18-1_Input_14cyc_288.CEL

source_name: expt.1107 extraction3_array1 channel_1


title: expt.1104 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MOF Q4145;target name: MOF;host: Rabbit;antigen: Amino acid 362-461;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4145;short description: MOF;

Input: pirrota_1362_Kc-5_Input.1114.CEL

source_name: expt.1104 extraction1_array1 channel_1


title: expt.1105 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MOF Q4145;target name: MOF;host: Rabbit;antigen: Amino acid 362-461;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4145;short description: MOF;

Input: pirrota_1204_B3_Input.935.CEL

source_name: expt.1105 extraction3_array1 channel_1


title: expt.1108 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MOF Q4145;target name: MOF;host: Rabbit;antigen: Amino acid 362-461;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4145;short description: MOF;

Input: pirrota_478_C18-2_Input_14cyc_289.CEL

source_name: expt.1108 extraction1_array1 channel_1


title: expt.1106 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MOF Q4145;target name: MOF;host: Rabbit;antigen: Amino acid 362-461;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4145;short description: MOF;

Input: pirrota_1205_B5_Input.936.CEL

source_name: expt.1106 extraction1_array1 channel_1


title: mixed transgenic HTG male somatic vs male somatic C57B/6 gDNA

status: Public on Jul 23 2011

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

country: Austria

institute: University of Vienna

description: CNV analysis of HTGmale vs C57B/6 male

hyb_protocol: hybridization were performed by a commercial provider; Imagenes, Berlin

scan_protocol: scanning were performed by a commercial provider; Imagenes, Berlin

source_name: gDNA from HTG somatic control

label_protocol: sample processing, labelling and data processing were performed by a commercial provider; Imagenes, Berlin

growth_protocol: male kidney

extract_protocol: gDNA was extracted using the Quiagen Gentra Puregene Kit

treatment_protocol: kidney was collected from a mouse from a mixed transgenic background

value: mixed transgenic

tag: dna source

value: male somatic kidney

source_name: C57B/6 male kidney control

label_protocol: labelling were performed by a commercial provider; Imagenes, Berlin

growth_protocol: gDNA extracted from male kidney

treatment_protocol: kidney was collected from an inbred C57B/6 mouse


title: expt.913 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JIL1 Q3433;target name: JIL1;host: Rabbit;antigen: Amino Acids: 919-1018;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3433;short description: JIL1 Accession number AAV11898   JIL-1 isoform A;

Input: pirrota_479_Kc-1_Input_14cyc_290.CEL

source_name: expt.913 extraction1_array1 channel_1


title: expt.830 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MBD-R2(Q4167);target name: MBD-R2;host: Rabbit;antigen: Amino acid 511-610;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4167;short description: MBD-R2;

Input: pirrota_760_A17_Input.530.CEL

source_name: expt.830 extraction1_array1 channel_1


title: expt.914 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JIL1 Q3433;target name: JIL1;host: Rabbit;antigen: Amino Acids: 919-1018;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3433;short description: JIL1 Accession number AAV11898   JIL-1 isoform A;

Input: pirrota_480_Kc-2_Input_14cyc_291.CEL

source_name: expt.914 extraction3_array1 channel_1


title: expt.916 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JIL1 Q3433;target name: JIL1;host: Rabbit;antigen: Amino Acids: 919-1018;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3433;short description: JIL1 Accession number AAV11898   JIL-1 isoform A;

Input: pirrota_478_C18-2_Input_14cyc_289.CEL

source_name: expt.916 extraction3_array1 channel_1


title: expt.880 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HP2 (Ab2-90);target name: HP2;host: Rabbit;antigen: cDNA identified in Y2H that corresponds to C-terminal end;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Elgin Ab2-90;short description: rabbit polyclonal;

Input: pirrota_825_CL8-1_InputDNA_20cyc_596.CEL

source_name: expt.880 extraction3_array1 channel_1


title: expt.915 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: JIL1 Q3433;target name: JIL1;host: Rabbit;antigen: Amino Acids: 919-1018;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q3433;short description: JIL1 Accession number AAV11898   JIL-1 isoform A;

Input: pirrota_477_C18-1_Input_14cyc_288.CEL

source_name: expt.915 extraction1_array1 channel_1


title: expt.856 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me3 abcam;target name: H3K9me3;host: Rabbit;antigen: synthetic peptide conjugated to KLH derived from within residues 1-100 of Human Histone H3 tri methylated at K9;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8898;reference: http://www.abcam.com/Histone-H3-tri-methyl-K9-antibody-ChIP-Grade-ab8898.html;short description: rabbit polyclonal to Histone H3 (tri methyl K9) ChIP grade;

Input: pirrota_1038_Kc4_Input_14cyc_812.CEL

source_name: expt.856 extraction3_array1 channel_1


title: expt.881 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: HP2 (Ab2-90);target name: HP2;host: Rabbit;antigen: cDNA identified in Y2H that corresponds to C-terminal end;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Elgin Ab2-90;short description: rabbit polyclonal;

Input: pirrota_826_CL8-2_Input_DNA_20cyc_597.CEL

source_name: expt.881 extraction1_array1 channel_1


title: expt.857 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9me3 abcam;target name: H3K9me3;host: Rabbit;antigen: synthetic peptide conjugated to KLH derived from within residues 1-100 of Human Histone H3 tri methylated at K9;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab8898;reference: http://www.abcam.com/Histone-H3-tri-methyl-K9-antibody-ChIP-Grade-ab8898.html;short description: rabbit polyclonal to Histone H3 (tri methyl K9) ChIP grade;

Input: pirrota_1039_Kc5_Input_14cyc_813.CEL

source_name: expt.857 extraction1_array1 channel_1


title: expt.808 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K9ac;target name: H3K9ac;host: Rabbit;antigen: Peptide including acetyl-lysine 9 of histone 3;clonal: Polyclonal;purified: Crude;company: Lake Placid;catalog: AR-0102;short description: rabbit polyclonal against a peptide including acetyl-lysine 9 of histone H3.;

Input: pirrota_1039_Kc5_Input_14cyc_813.CEL

source_name: expt.808 extraction1_array1 channel_1


title: expt.831 extraction3_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: MBD-R2(Q4167);target name: MBD-R2;host: Rabbit;antigen: Amino acid 511-610;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: Q4167;short description: MBD-R2;

Input: pirrota_761_A18_Input.531.CEL

source_name: expt.831 extraction3_array1 channel_1


title: expt.927 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: H3K36me1;target name: H3K36me1;host: Rabbit;antigen: Synthetic peptide conjugated to KLH derived from within residues 1 - 100 of Human Histone H3 mono methylated at K36.;clonal: Polyclonal;purified: Affinity;company: Abcam;catalog: ab9048;reference: http://www.abcam.com/Histone-H3-mono-methyl-K36-antibody-ChIP-Grade-ab9048.html;short description: Rabbit polyclonal to Histone H3 (mono methyl K36) - ChIP Grade;

Input: pirrota_477_C18-1_Input_14cyc_288.CEL

source_name: expt.927 extraction1_array1 channel_1