title: ovarian cancer surgical sample P251

value: surgical tumor sample

value: mutation

value: accumulation

value: IIIB

value: CR

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)

value: DOD


title: Endometrium_afterProg_2B

status: Public on Dec 06 2014

type: RNA

city: Chicago

first: Gulum

last: Kosova

address: 920 E 58th Street

department: Human Genetics

country: USA

institute: University of Chicago

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: 19,591probes were filtered out because they did not meet the following quality control  (QC) criteria: 1) map uniquely to the HG19 genome using BWA (and there were no secondary  hits with 1 mismatch), 2) overlap an Ensembl gene (release 65) on the same strand, 3) do not  encompass any SNPs included in HapMap CEU with QC+ designation. For the remaining probes, data was log2 transformed and normalized with quantile normalization using the Bioconductor package lumi in the R statistical environment.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human endometrium

label_protocol: standard Illumina protocol

growth_protocol: Endometrial biopsies were collected during midsecretory phase

extract_protocol: RNA was extracted using Trizol reagent, followed by Qiagen Rneasy mini kit for clean up in accordance with the recommended protocol provided by Qiagen. RNA quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Biopsy samples were frozen immediately and stored in -80C until RNA extraction

tag: tissue

value: endometrium

tag: gender

value: Female

tag: classification

value: corrected cyclin E after progesterone treatment

tag: age

tag: bmi

tag: microarraychip

value: E

tag: season of biopsy collection

value: sp

tag: extraction order

value: B


title: ovarian cancer surgical sample P115

city: Gliwice

first: Katarzyna

middle: Marta

last: Lisowska

address: ul. Wybrzeże Armii Krajowej 15

department: Center for Translational Research  and Molecular Biology of Cancer

country: Poland

institute: MSC Memorial Cancer Center and Institute of Oncology, Gliwice Branch

description: gene expression data from serous ovarian cancer

hyb_protocol: 16 ug of fragmented cRNA were hybridized for 16 hr at 45ͦC on HG U133 Plus 2.0 Gene Chip oligonucleotide arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing:
acquired by GCOS 1.2 software (Affymetrix); preprocessed by Robust Multiarray Analysis (RMA, Bioconductor)
The data were analyzed with Bioconductor and rma package with default normalization parameters settings

source_name: frozen surgical sample of serous ovarian cancer; p53-mutated

label_protocol: Total RNA (8 ug) was used for synthesis of double stranded cDNA according to manufacturer's instructions. Biotinylated cRNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics).

extract_protocol: Total RNA was isolated using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: clinical sample

tag: histophatological type of tumor

value: serous ovarian ca.

tag: adjuwant chemotherapy

value: platinum/cyclophosphamide

tag: brca1 mutation

value: no mutation

tag: somatic tp53 mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):moderately sensitive


title: Endometrium_afterProg_2A

tag: tissue

tag: gender

value: C

value: A


title: ovarian cancer surgical sample X342

source_name: frozen surgical sample of serous ovarian cancer; BRCA1-mutated; p53-mutated

value: surgical tumor sample

value: mutation

value: no accumulation

value: IIIC

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)

value: AWD


title: Endometrium_beforeProg_2A

value: endometrium

tag: classification

value: abnormal high cyclin E before progesterone

tag: age

tag: bmi

tag: microarraychip

value: F

tag: season of biopsy collection

value: f


title: Endometrium_beforeProg_2B

value: Female

tag: extraction order


title: Endometrium_afterProg_1A

value: corrected cyclin E after progesterone treatment

value: sp


title: ovarian cancer surgical sample T610

tag: clinical sample

tag: histophatological type of tumor

value: serous ovarian ca.

tag: adjuwant chemotherapy

value: taxane/platinum

tag: brca1 mutation

tag: somatic tp53 mutation

value: accumulation

value: IIIA

value: CR

value: DOD


title: ovarian cancer surgical sample E609

description: gene expression data from endometrioid ovarian cancer

source_name: frozen surgical sample of endometrioid ovarian cancer; p53-mutated

value: surgical tumor sample

value: endometrioid ovarian ca.

value: no mutation

value: mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):moderately sensitive

value: NED


title: Endometrium_beforeProg_1B

tag: tissue

value: endometrium

tag: gender

value: abnormal high cyclin E before progesterone

value: D

value: B


title: Endometrium_afterProg_1B

value: Female

tag: classification

value: corrected cyclin E after progesterone treatment

tag: age

value: E

value: sp


title: Endometrium_beforeProg_3A

tag: bmi

tag: microarraychip

value: G

value: su

value: A


title: Endometrium_beforeProg_1A

value: C

tag: season of biopsy collection

value: f

tag: extraction order


title: Endometrium_normal_13B

value: normal histology and cyclin E

value: F


title: ovarian cancer surgical sample P11

tag: clinical sample

value: surgical tumor sample

tag: histophatological type of tumor

value: serous ovarian ca.

value: platinum/cyclophosphamide

value: no mutation

value: mutation

value: accumulation

value: IIIA

value: CR

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):moderately sensitive

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)

value: DOD


title: ovarian cancer surgical sample T340

source_name: frozen surgical sample of serous ovarian cancer

tag: adjuwant chemotherapy

value: taxane/platinum

tag: brca1 mutation

tag: somatic tp53 mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: no accumulation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

value: IIIC


title: ovarian cancer surgical sample T197

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

tag: platinium sensitivity (resistant

value: NED


title: ovarian cancer surgical sample T316

description: gene expression data from serous ovarian

value: IIIB


title: ovarian cancer surgical sample P272


title: ovarian cancer surgical sample P162


title: ovarian cancer surgical sample T306


title: Endometrium_normal_12B

tag: tissue

value: endometrium

tag: gender

value: Female

tag: classification

value: normal histology and cyclin E

tag: age

tag: bmi

value: B

value: su


title: ovarian cancer surgical sample T420

tag: clinical sample

value: surgical tumor sample

tag: histophatological type of tumor

value: serous ovarian ca.


title: Endometrium_normal_13A

tag: microarraychip

value: C

tag: season of biopsy collection

value: f

tag: extraction order

value: A


title: Endometrium_normal_12A

value: H


title: Endometrium_normal_11B

value: D


title: Endometrium_normal_10A

value: sp


title: Endometrium_normal_9B


title: ovarian cancer surgical sample P284

tag: adjuwant chemotherapy

value: platinum/cyclophosphamide

tag: brca1 mutation

value: no mutation

value: mutation

value: no accumulation

value: CR

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):moderately sensitive

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)

value: DOD


title: Endometrium_normal_9A

value: endometrium

value: Female

value: normal histology and cyclin E

value: F


title: ovarian cancer surgical sample T415

value: surgical tumor sample

value: serous ovarian ca.

value: taxane/platinum

tag: somatic tp53 mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

value: IV

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)


title: Endometrium_normal_10B

tag: tissue

tag: gender

tag: classification

tag: age

value: E

value: B


title: ovarian cancer surgical sample P160

tag: clinical sample

tag: histophatological type of tumor

value: platinum/cyclophosphamide

value: IIIC

tag: platinium sensitivity (resistant


title: Endometrium_normal_8B

tag: bmi

tag: microarraychip

value: A

tag: season of biopsy collection

value: su

tag: extraction order


title: ovarian cancer surgical sample T389

tag: adjuwant chemotherapy

tag: brca1 mutation

value: mutation

value: accumulation

value: CR

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: Endometrium_normal_8A

value: endometrium


title: ovarian cancer surgical sample P127

value: no mutation

tag: somatic tp53 mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):moderately sensitive

value: DOD


title: Endometrium_normal_11A

tag: tissue

tag: gender

value: Female

tag: classification

value: normal histology and cyclin E

tag: age

value: G


title: ovarian cancer surgical sample T320

tag: clinical sample

value: surgical tumor sample

tag: histophatological type of tumor

value: serous ovarian ca.

value: taxane/platinum

tag: platinium sensitivity (resistant


title: ovarian cancer surgical sample T351

tag: adjuwant chemotherapy


title: Endometrium_normal_7A

tag: bmi

tag: microarraychip

value: B

tag: season of biopsy collection

tag: extraction order


title: ovarian cancer surgical sample P30

value: platinum/cyclophosphamide

tag: brca1 mutation

tag: somatic tp53 mutation

value: no accumulation

value: IV

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: ovarian cancer surgical sample T200

description: gene expression data from undifferentiated ovarian cancer

source_name: frozen surgical sample of undifferentiated ovarian cancer; p53-mutated

value: undifferentiated ovarian ca.

value: mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

value: IIIC

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)


title: ovarian cancer surgical sample P281

tag: clinical sample

value: accumulation

value: CR

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):resistant


title: Endometrium_normal_7B

tag: tissue

value: endometrium

tag: gender

tag: classification

tag: age

value: D

value: su


title: Endometrium_normal_6B

value: Female

value: normal histology and cyclin E

tag: bmi

tag: microarraychip

value: C

value: sp


title: ovarian cancer surgical sample T324

value: surgical tumor sample

tag: histophatological type of tumor

value: serous ovarian ca.

tag: adjuwant chemotherapy

value: taxane/platinum

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):moderately sensitive

value: DOD


title: Endometrium_normal_5A

value: H

tag: season of biopsy collection

value: w

tag: extraction order

value: A


title: ovarian cancer surgical sample P145

value: platinum/cyclophosphamide

tag: brca1 mutation

tag: somatic tp53 mutation

value: mutation

value: accumulation

value: IIIC

value: CR

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: ovarian cancer surgical sample T257

tag: clinical sample

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: no accumulation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):resistant


title: Endometrium_normal_4A

tag: tissue

value: endometrium

tag: gender

value: Female

tag: classification

value: normal histology and cyclin E

tag: age

tag: bmi

value: G


title: ovarian cancer surgical sample P253

value: surgical tumor sample

tag: histophatological type of tumor

value: serous ovarian ca.

tag: adjuwant chemotherapy

tag: platinium sensitivity (resistant


title: Endometrium_normal_4B

tag: microarraychip

value: F

tag: season of biopsy collection

tag: extraction order

value: B


title: Endometrium_normal_6A

value: H

value: sp


title: Endometrium_normal_3B

value: E

value: su


title: ovarian cancer surgical sample T313

value: taxane/platinum

tag: brca1 mutation

value: no mutation

tag: somatic tp53 mutation

value: mutation

value: accumulation

value: IIIB

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)

value: DOD


title: Endometrium_normal_5B

value: endometrium

value: Female

value: D

value: w


title: ovarian cancer surgical sample T353

tag: clinical sample

value: surgical tumor sample

value: serous ovarian ca.

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: no accumulation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

value: IIIC

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

value: SD

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):resistant


title: ovarian cancer surgical sample P271

value: platinum/cyclophosphamide

value: CR


title: ovarian cancer surgical sample T383

value: taxane/platinum

value: no mutation


title: Endometrium_normal_3A

tag: tissue

tag: gender

tag: classification

value: normal histology and cyclin E

tag: age

tag: bmi

value: G

value: su

value: A


title: Endometrium_normal_1A

value: endometrium

value: Female

tag: microarraychip

value: F

tag: season of biopsy collection


title: Endometrium_normal_2A

value: C

value: sp

tag: extraction order


title: ovarian cancer surgical sample P146

value: surgical tumor sample

tag: histophatological type of tumor

value: serous ovarian ca.

tag: adjuwant chemotherapy

tag: brca1 mutation

tag: somatic tp53 mutation

value: mutation

value: accumulation

value: IIIB

value: PR

tag: platinium sensitivity (resistant

value: DOD


title: ovarian cancer surgical sample T375

tag: clinical sample

value: taxane/platinum

value: no mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: IIIC

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):resistant

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: Endometrium_normal_2B

tag: tissue

tag: gender

value: normal histology and cyclin E

value: E

value: B


title: Endometrium_normal_1B

value: endometrium

value: Female

tag: classification

tag: age

value: w


title: ovarian cancer surgical sample P279

value: surgical tumor sample

value: platinum/cyclophosphamide

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

value: CR


title: Endometrium_cyclinE_9B

value: abnormal high cyclin E

tag: bmi

tag: microarraychip

value: A

tag: season of biopsy collection

value: f

tag: extraction order


title: Endometrium_cyclinE_8B

value: su


title: ovarian cancer surgical sample P100

tag: histophatological type of tumor

value: serous ovarian ca.

tag: adjuwant chemotherapy

tag: brca1 mutation

tag: somatic tp53 mutation

value: mutation

value: no accumulation

value: IV

value: SD

tag: platinium sensitivity (resistant

value: DOD


title: Endometrium_cyclinE_9A


title: ovarian cancer surgical sample T422

source_name: frozen surgical sample of undifferentiated ovarian cancer; BRCA1-mutated; p53-mutated

tag: clinical sample

value: undifferentiated ovarian ca.

value: taxane/platinum

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: accumulation

value: PR

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):resistant

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: ovarian cancer surgical sample T386

value: surgical tumor sample

value: no mutation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

value: IIIC


title: ovarian cancer surgical sample T337

value: IIC

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

value: CR

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):moderately sensitive


title: Endometrium_cyclinE_8A

tag: tissue

value: endometrium

tag: gender

value: Female

tag: classification

value: abnormal high cyclin E

tag: age

value: H

value: su

value: A


title: Endometrium_cyclinE_7A

tag: bmi

tag: microarraychip

value: B

tag: season of biopsy collection

value: f

tag: extraction order


title: ovarian cancer surgical sample X381

tag: histophatological type of tumor

value: serous ovarian ca.

tag: adjuwant chemotherapy

value: platinum/cyclophosphamide

tag: brca1 mutation

tag: somatic tp53 mutation

value: mutation

value: accumulation

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

value: AWD


title: ovarian cancer surgical sample P273

tag: clinical sample

value: surgical tumor sample

value: no mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: IIIC

value: PR

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):resistant

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]

value: DOD


title: ovarian cancer surgical sample T352

value: taxane/platinum

value: no accumulation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: ovarian cancer surgical sample P130

value: IIIB

value: CR

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):moderately sensitive


title: Endometrium_cyclinE_6B

tag: tissue

value: endometrium

tag: gender

value: Female

tag: classification

value: abnormal high cyclin E

tag: age

tag: bmi

value: B

value: f


title: ovarian cancer surgical sample P136

tag: histophatological type of tumor

value: serous ovarian ca.

tag: adjuwant chemotherapy

value: platinum/cyclophosphamide

value: mutation

value: accumulation


title: ovarian cancer surgical sample T319

description: gene expression data from somatic serous ovarian cancer

source_name: frozen surgical sample of serous ovarian cancer; BRCA1-mutated somaticaly; p53-mutated

value: surgical tumor sample

tag: brca1 mutation

value: A5335T (somatic mutation)

tag: somatic tp53 mutation

value: IV

value: PR


title: Endometrium_cyclinE_5A

tag: microarraychip

value: C

tag: season of biopsy collection

tag: extraction order

value: A


title: ovarian cancer surgical sample P70

tag: clinical sample

value: no mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: IIIC

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

value: P

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):resistant

tag: dfs - disease-free survival [days]

value: DOD


title: Endometrium_cyclinE_5B

tag: tissue

value: endometrium

value: Female

value: abnormal high cyclin E

value: E

value: B


title: ovarian cancer surgical sample T398

value: serous ovarian ca.

value: taxane/platinum

value: mutation

value: no accumulation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: ovarian cancer surgical sample T325

value: surgical tumor sample

tag: histophatological type of tumor

value: undifferentiated ovarian ca.

value: accumulation

value: PR


title: Endometrium_cyclinE_6A

tag: gender

tag: classification

tag: age

tag: bmi

value: F

value: f

value: A


title: Endometrium_cyclinE_7B

tag: microarraychip

value: D

tag: season of biopsy collection


title: ovarian cancer surgical sample P255

tag: clinical sample

tag: adjuwant chemotherapy

value: platinum/cyclophosphamide

tag: brca1 mutation

value: no mutation

tag: somatic tp53 mutation

value: IIIC

value: P

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):resistant

value: DOD


title: Endometrium_cyclinE_3B

value: endometrium

value: Female

value: abnormal high cyclin E

value: G

value: su

tag: extraction order

value: B


title: ovarian cancer surgical sample T369

value: surgical tumor sample

value: serous ovarian ca.

value: taxane/platinum

value: mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: no accumulation

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

value: PR

tag: platinium sensitivity (resistant

tag: dfs - disease-free survival [days]


title: ovarian cancer surgical sample T360

value: no mutation

value: accumulation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: os - overall survival [days]

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)


title: Endometrium_cyclinE_3A

tag: tissue

tag: gender

tag: classification

tag: age

value: H

value: A


title: ovarian cancer surgical sample T331

tag: clinical sample

tag: histophatological type of tumor

value: IIIC

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):resistant

value: DOD


title: Endometrium_cyclinE_4B

value: endometrium

value: Female

value: abnormal high cyclin E

tag: bmi

tag: microarraychip

value: E

tag: season of biopsy collection


title: Endometrium_cyclinE_4A

value: F

value: su

tag: extraction order


title: Endometrium_cyclinE_2A

value: w


title: ovarian cancer surgical sample T382

value: surgical tumor sample

value: serous ovarian ca.

tag: adjuwant chemotherapy

value: taxane/platinum

tag: brca1 mutation

tag: somatic tp53 mutation

value: mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)


title: ovarian cancer surgical sample T174

value: no mutation

value: no accumulation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

value: IIIA

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

value: PR

tag: platinium sensitivity (resistant

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]


title: Endometrium_cyclinE_2B

tag: tissue

tag: gender

tag: classification

tag: age

value: C

value: B


status: Public on Dec 05 2014

type: genomic

city: Durham

first: Jason

middle: Alan

last: Belsky

state: NC

address: LSRC Room C333

department: Pharmacology and Cancer Biology

institute: Duke University

description: Biological Replicate 1 Array: Mcm2-7 ChIP relative to input

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: Array scanning protocol; Scanning per Agilent recommendations.

data_processing: Data was normalized with the R package limma and log2 ratio of probe intensities (.tsv format) were determined via MA2C. Other MAC2C formats are the wiggle file for viewing along the genome and a peaks file in the BED format.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Mcm2-7 ChIP: Kc Mcm2-7 Late S Phase Replicate 1

label_protocol: Sequenase labeling protocol; 1.Thaw DNA samples on ice 2.Transfer to 0.2ml pcr tubes. Open tubes and place inside a 1.5ml tube 3.Speed vac samples on medium heat for approx. 15-18 minutes 4.Resusp DNA in sequenase primer mix: 5X sequenase buffer 2ul (US Biochemicals) random nonamer 5ul (NNNNNNNNN; hand mixed 25,25,25,25) Ambion dH2O 1ul 5.Thaw Cy dyes (Cy 3 dUTP and Cy 5 dUTP; Perkin Elmer) on ice and in the dark 6.Add 2ul of cy dye to DNA sample 7.Start pcr program: 95C 3' 4C 2' 37C 30' ramp 95C 2' 4C 2' 37C 30' ramp 4C hold 8.At the first 4C step in program, add the following: 5X sequenase buffer 1ul Low T 1.5ul (5ul dATP, 5ul dCTP, 5ul dGTP, 2ul dTTP, 83ul ambion dH2O) 100 mM BSA 1ul 100mM DTT 0.75ul sequenase 1ul 9.At the second 4C step, add additional sequenase and finish program sequenase buffer DLT 0.7ul sequenase 0.3ul 10.Clean samples on YM-30 microcon column (Millipore) according to directions 11.Spec samples

growth_protocol: Cells were cultured in 150-mm plates at an approximate density of 1 x 10E6 cells/mL in Schneider's Insect Cell Medium (Invitrogen) supplemented with 10% heat-inactivated FBS (Hyclone) and 1% penicillin/streptomycin/glutamine (Invitrogen).

extract_protocol: ChIP crosslinking and isolation protocol; 1. Crosslink cells at room temperature with 1% formaldehyde (Ted Pella #18505) for 10 min. 2. Quench reaction with 125 mM glycine for 5 min at room temp. 3. Centrifuge cross-linked cells, 1,000 rpm, 10 min. 4. Wash cells with 2X cold 1X PBS. 5. Freeze pellet with liquid nitrogen and store at -80C for at least two hours 6. Thaw pellet on ice and prepare lysis buffers: Lysis Buffer 1: 50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1/2 mini protease tablet (Roche) per 5ml of buffer; Lysis Buffer 2: 10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5 EGTA, 1/2 protease tablet per 5ml of buffer; Lysis Buffer 3: 10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1/2 mini protease tablet per 5ml buffer 7. Keep lysis buffers on ice 8. Resuspend pellet in 5ml lysis buffer 1 and incubate with rotation at 4C for 10min. 9. Centrifuge, 4C, 1350xg, 5 min 10.Resuspend pellet in 5ml lysis buffer 2 and incubate with rotation at room temperature for 10 min. 11. Centrifuge, 4C, 1350xg, 5 min 12. Resuspend in 3 mL lysis buffer 3 13. sonicate extract to an average size of 1Kb. 14. Add Triton X-100 to 1%. vortex gently 15. Centrifuge at 4C, 20,000xg, 10min. 16. Aliquot extracts into ~500ul samples.  The chromatin was immunoprecipitated with the Mcm2-7 monoclonal mouse antibody (AS1.1) and used at a 1/25 dilution.

treatment_protocol: Cells were incubated with 1 mM HU for 24 h to arrest cells in G1/S, and then released for 6 hours to collect cells in Late S Phase.

tag: cell line

source_name: Input: Kc Mcm2-7 Late S Phase Replicate 1 Array


title: ovarian cancer surgical sample T175

tag: clinical sample

tag: histophatological type of tumor

value: accumulation

value: IIIC

value: P

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):resistant

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)

value: DOD


description: Biological Replicate 2 Array: Mcm2-7 ChIP relative to input

source_name: Mcm2-7 ChIP: Kc Mcm2-7 Late S Phase Replicate 2

source_name: Input: Kc Mcm2-7 Late S Phase Replicate 2 Array


title: ovarian cancer surgical sample P67

tag: adjuwant chemotherapy

value: platinum/cyclophosphamide

tag: brca1 mutation


title: ovarian cancer surgical sample P343

tag: somatic tp53 mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: IV

value: SD


title: C57BL6_saline_8h_rep1

city: Philadelphia

first: Konstantinos

last: Drosatos

state: PA

address: 3500 N. Broad st

department: Pharmacology

institute: Temple University

description:
368296_5_CTRL
Gene expression profile 8h post-saline intraperitoneal injection_replicate 1

hyb_protocol: Biotinylated cRNA samples were fragmented, diluted in a formamide-containing hybridization buffer, and loaded on to the surface of MEEBO microarray slides enclosed in custom hybridization chambers. The slides were hybridized for 16-18 hours under constant rotation in a Model 400 hybridization oven (Scigene, Sunnyvale, CA). After hybridization, the microarray slides were washed under stringent conditions and stained with Streptavidin-Alexa-647 (Invitrogen).

scan_protocol: The microarray slides were scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Spot intensities for each probe were calculated by subtracting median local background from median local foreground for each spot. Spot intensities were transformed by taking the base 2 logarithm of each value. The spot intensities were then normalized by subtracting the 70th percentile of the spot intensities of probes against mouse constitutive exons and adding back a scaling factor (grand mean of 70th percentile). After removing data for low-quality spots, control sequences, and non-mouse probes, 34,945 mouse probe intensities remained. The mouse probes intensities were filtered to identify all probes with intensity above a normalized threshold [log2 (3* standard deviation of raw local background) + mean of log2-transformed negative controls], to arrive at 12,495 probes above threshold in all samples from at least one treatment group.

label: Biotin

organism: Mus musculus

source_name: heart, control

label_protocol: Biotin-labeled complementary RNA (cRNA) was prepared from total RNA. Briefly, an oligonucleotide containing a 5'-T7-promoter sequence and a 3' T24VN sequence was used to prime reverse transcription of RNA catalyzed by Superscript II (Invitrogen, Carlsbad, CA). Double-stranded cDNA was prepared from the 1st strand product, and purified on a PCR purification column (Qiagen, Valencia, CA). The double-stranded cDNA was then used as a template for in vitro transcription with T7 RNA polymerase using a high yield transcription kit (Ambion) and including biotin-16-UTP (Ambion) in the reaction mixture.

growth_protocol: C57BL/6 mice were grown in a barrier facility on chow diet.

extract_protocol: Hearts were perfused with PBS and excised. RNA was purified with TRIZOL (Invitrogen) according to manufacturer's instructions.

treatment_protocol: Mice received 5mg/kg LPS or saline (control treatment) by intraperitoneal injection and were sacrificed 8h post-injection.

tag: strain/background

value: heart

value: female

value: 12 weeks

tag: treatment

value: saline injection

tag: time point

value: 8h post-injection


title: PorcineConcept_D20_biorep3

city: Olsztyn

first: Monika

middle: M

last: Kaczmarek

address: Tuwima 10

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

description: microRNA expression in D20 porcine trophoblast

hyb_protocol: Dried (MiVac DNA Concentrator, Genevac, USA) samples were resuspended in nuclease free water with addition of 10x GE Blocking Agent and 2x Hi-RPM Hybridization Buffer, and incubated at 100°C for 5 minutes. Afterwards cooled mixtures were hybridized to Agilent miRNA microarrays for 20 h at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x15 K array slides (Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent Technologies) using default parameters (protocol miRNA_107_Sep09 and Grid: 031147_D_F_20101114) to obtain background subtracted and spatially detrended Processed Signal intensities. Data was normalized using the vsn package for BioConductor R, followed by quality control with a distance matrix and a heatmap based on pair-wise distances (geneplotter package). In order to find differentially expressed miRNAs, empirical Bayes analysis was applied using the Linear Models for Microarray Data (LIMMA) package.

organism: Sus scrofa

source_name: Porcine trophoblast Day 20 of pregnancy, biological replicate 3

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 100 ng RNA fallowing the manufacturer’s instructions supplied with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Waldbronn, Germany). First 100 ng of RNA was dephosphorylated in 37°C for 30 minutes in a reaction volume of 7 µl containing 1x Calf Intestinal Phosphatase Buffer and 0.7 µl of Calf Intestinal Phosphatase. On completion of the dephosphorylation 5 µl of 100% DMSO was added and incubated at 100°C for 10 minutes. Labelling was accomplished by addition of 10x T4 RNA Ligase Buffer, Cyanine3-pCp, and T4 RNA ligase to the abovementioned mixture and incubation at 16°C for 2 hours, followed by Micro BioSpin 6 column (Bio-Rad, USA) purification.

growth_protocol: Hampshire x Duroc crossbred gilts of similar age (7-8 months) and genetic background from one commercial herd were inseminated 12 and 24 hours after detection of the third estrus.

extract_protocol: Total RNA was isolated with the miRVana miRNA isolation kit (Ambion, Life Technologies, USA) according to the manufacturer’s instructions. The protocol includes sample disruption in lysis buffer, acid phenol:chloroform extraction and an on-column RNA isolation. Quality and quantity of RNA was determined using UV spectrophotometry (NanoDrop 1000). RNA with RNA Integrity number higher than 7 (Agilent 2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA) was used for microarray analysis of each individual sample.

treatment_protocol: Samples were collected post mortem on day (D) 10 (n=9), 11 (n=5), 12 (n=5), 16 (n=5) and 20 (n=5) of pregnancy. Until D16 of gestation, concepti were flushed from uterine horns with 20 ml of 0.01 M PBS. On D20, uterine horns were opened longitudinally and trophoblasts were dissected away from embryos. Samples were snap-frozen in liquid nitrogen and stored at -80°C for further use.

value: trophoblast

tag: breed

value: Hampshire x Duroc

tag: day of pregnancy

value: Day 20


title: PorcineConcept_D20_biorep5

source_name: Porcine trophoblast Day 20 of pregnancy, biological replicate 5

tag: tissue


title: PorcineConcept_D20_biorep2

source_name: Porcine trophoblast Day 20 of pregnancy, biological replicate 2


title: PorcineConcept_D20_biorep4

source_name: Porcine trophoblast Day 20 of pregnancy, biological replicate 4


title: PorcineConcept_D20_biorep1

source_name: Porcine trophoblast Day 20 of pregnancy, biological replicate 1


title: CEP_uninduced

city: Wien

first: Julia

last: Testori

address: Lazarettgasse 19

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Medical University Vienna

description: Gene expression data

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed using RMA (Robust multiarray average) Signal extraction and normalization.

source_name: CEP, starved, uninduced

label_protocol: Affymetrix protocol

growth_protocol: Endothelial cells were kept in complete EGM-2 Medium in dense culture without change of medium and before the stimulation in EGM-2 medium without growth factors over night.

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

tag: cell type

value: Circulating endothelial progenitor cells, isolated from cord blood

value: uninduced


title: PorcineConcept_D16_biorep5

description: microRNA expression in D16 porcine conceptus

source_name: Porcine conceptus, Day 16 of pregnancy, biological replicate 5

value: Day 16


title: C57BL6_saline_8h_rep3

description:
368283_7_CTRL
Gene expression profile 8h post-saline intraperitoneal injection_replicate 3

tag: gender


title: C57BL6_saline_8h_rep4

description:
368284_8_CTRL
Gene expression profile 8h post-saline intraperitoneal injection_replicate 4

tag: age


title: PorcineConcept_D16_biorep4

source_name: Porcine conceptus, Day 16 of pregnancy, biological replicate 4

value: conceptus


title: ovarian cancer surgical sample P8

source_name: frozen surgical sample of serous ovarian cancer; p53-mutated

value: surgical tumor sample

value: serous ovarian ca.

value: no mutation

value: mutation

value: accumulation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

value: IIIC

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

value: P

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):resistant

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]


title: C57BL6_LPS_8h_rep1

description:
368289_1_Treated
Gene expression profile 8h post-LPS intraperitoneal injection (5 mg/kg)_replicate 1

source_name: heart, LPS

value: heart

value: female

value: 12 weeks

value: lipopolysaccharide (LPS) injection


title: C57BL6_saline_8h_rep2

description:
368297_6_CTRL
Gene expression profile 8h post-saline intraperitoneal injection_replicate 2

value: saline injection

value: 8h post-injection


title: C57BL6_LPS_8h_rep3

description:
366330_3_Treated
Gene expression profile 8h post-LPS intraperitoneal injection (5 mg/kg)_replicate 3


title: C57BL6_LPS_8h_rep4

description:
366350_4_Treated
Gene expression profile 8h post-LPS intraperitoneal injection (5 mg/kg)_replicate 4


title: PorcineConcept_D16_biorep3

source_name: Porcine conceptus, Day 16 of pregnancy, biological replicate 3

value: Hampshire x Duroc


title: CEP_VEGF_30min

description: Gene expression data

source_name: CEP, starved, 30min VEGF induced

treatment_protocol: Endothelial cells were induced for 30min with 100ng/ml VEGF-A.

value: Circulating endothelial progenitor cells, isolated from cord blood

value: VEGF

tag: time

value: 30 min


title: CEP_VEGF_60min

description: Gene expression data

source_name: CEP, starved, 60min VEGF induced

treatment_protocol: Endothelial cells were induced for 60min with 100ng/ml VEGF-A.

value: 60 min


title: PorcineConcept_D16_biorep2

source_name: Porcine conceptus, Day 16 of pregnancy, biological replicate 2

value: conceptus

value: Day 16


title: ovarian cancer surgical sample P264

source_name: frozen surgical sample of serous ovarian cancer

tag: clinical sample

value: surgical tumor sample

tag: histophatological type of tumor

value: serous ovarian ca.

tag: adjuwant chemotherapy

value: platinum/cyclophosphamide

tag: brca1 mutation

value: no mutation

tag: somatic tp53 mutation

tag: tp53 accumulation in cancer cells (assesed by immunohistochemistry)

value: accumulation

tag: clinical status at last follow-up (awd - alive with disease; dod - dead from disease; ned - no evidence of disease)

value: DOD


title: CEP_VEGF_150min

description: Gene expression data

source_name: CEP, starved, 150 min VEGF-A induced

treatment_protocol: Endothelial cells were induced for 150min with 100ng/ml VEGF-A.

tag: cell type

tag: treatment

value: 150 min


title: CD34 pos

description: Gene expression data

source_name: CD34 pos cells

treatment_protocol: CD34 pos cells, isolated from cord blood


title: C57BL6_LPS_8h_rep2

description:
366327_2_Treated
Gene expression profile 8h post-LPS intraperitoneal injection (5 mg/kg)_replicate 2

tag: strain/background

tag: tissue

value: heart

tag: gender

value: female

tag: age

value: 12 weeks

value: lipopolysaccharide (LPS) injection

tag: time point


title: PorcineConcept_D12_biorep5

description: microRNA expression in D12 porcine conceptus

source_name: Porcine conceptus, Day 12 of pregnancy, biological replicate 5

tag: breed

value: Hampshire x Duroc

tag: day of pregnancy

value: Day 12


title: PorcineConcept_D12_biorep3

source_name: Porcine conceptus, Day 12 of pregnancy, biological replicate 3


title: PorcineConcept_D12_biorep4

source_name: Porcine conceptus, Day 12 of pregnancy, biological replicate 4


title: PorcineConcept_D12_biorep2

source_name: Porcine conceptus, Day 12 of pregnancy, biological replicate 2


title: PorcineConcept_D12_biorep1

source_name: Porcine conceptus, Day 12 of pregnancy, biological replicate 1


title: ovarian cancer surgical sample T348

description: gene expression data from serous ovarian cancer

value: taxane/platinum

value: mutation

tag: tumor grade (g1 - well differentiated; g2 - moderately differentiated; g3 - poorly differentiated; g4 - undifferentiated)

value: IV

tag: residual tumor size (r0 < 1 cm;  1 < r1 < 5 cm; r2 > 5cm)

tag: clinical status post 1st line chemotherapy (cr - complete response; pr - partial response; sd - stable disease; p - progression)

value: P

tag: platinium sensitivity (resistant

value: DFS<180 days; moderately sensitive:180>DFS>732; highly sensitive:DFS>732 days):resistant

tag: dfs - disease-free survival [days]

tag: os - overall survival [days]


title: PorcineConcept_D16_biorep1

source_name: Porcine conceptus, Day 16 of pregnancy, biological replicate 1

value: conceptus

value: Day 16


title: PorcineConcept_D10_biorep9

description: microRNA expression in D10 porcine conceptus

source_name: Porcine conceptus, Day 10 of pregnancy, biological replicate 9

value: Day 10


title: PorcineConcept_D11_biorep3

description: microRNA expression in D11 porcine conceptus

source_name: Porcine conceptus, Day 11 of pregnancy, biological replicate 3

value: Day 11


title: PorcineConcept_D11_biorep4

source_name: Porcine conceptus, Day 11 of pregnancy, biological replicate 4


title: PorcineConcept_D11_biorep5

source_name: Porcine conceptus, Day 11 of pregnancy, biological replicate 5


title: PorcineConcept_D11_biorep2

source_name: Porcine conceptus, Day 11 of pregnancy, biological replicate 2


title: PorcineConcept_D10_biorep8

source_name: Porcine conceptus, Day 10 of pregnancy, biological replicate 8


title: PorcineConcept_D10_biorep7

source_name: Porcine conceptus, Day 10 of pregnancy, biological replicate 7


title: PorcineConcept_D11_biorep1

source_name: Porcine conceptus, Day 11 of pregnancy, biological replicate 1


title: PorcineConcept_D10_biorep5

source_name: Porcine conceptus, Day 10 of pregnancy, biological replicate 5


title: PorcineConcept_D10_biorep4

source_name: Porcine conceptus, Day 10 of pregnancy, biological replicate 4


title: PorcineConcept_D10_biorep3

source_name: Porcine conceptus, Day 10 of pregnancy, biological replicate 3


title: PorcineConcept_D10_biorep2

source_name: Porcine conceptus, Day 10 of pregnancy, biological replicate 2


title: At_stem of 35S::AtC3H14

city: Yongin

first: Jae-Heung

last: Ko

state: Gyeonggi

address: 1 Seocheon-dong, Giheung-gu

department: Plant & Environmental Resources

country: South Korea

institute: Kyung Hee University

description: Gene expression data from Arabidopsis stem overexpressing AtC3H14 gene.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to the array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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 100.

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The wild-type and transgenic Arabidopsis plants were grown on soil in a growth chamber (16 h light/ 8 h dark) at 23 °C, after stratification.

value: Stem tissue (basal to 3rd internode)

tag: genetic background

value: Columbia (Col-0)

value: 30-days old soil grown plants

tag: genotype


title: Kc ORC HU

description: ORC ChIP relative to input

source_name: ORC ChIP: Kc ORC HU

extract_protocol: ChIP crosslinking and isolation protocol; 1. Crosslink cells at room temperature with 1% formaldehyde (Ted Pella #18505) for 10 min. 2. Quench reaction with 125 mM glycine for 5 min at room temp. 3. Centrifuge cross-linked cells, 1,000 rpm, 10 min. 4. Wash cells with 2X cold 1X PBS. 5. Freeze pellet with liquid nitrogen and store at -80C for at least two hours 6. Thaw pellet on ice and prepare lysis buffers: Lysis Buffer 1: 50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1/2 mini protease tablet (Roche) per 5ml of buffer; Lysis Buffer 2: 10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5 EGTA, 1/2 protease tablet per 5ml of buffer; Lysis Buffer 3: 10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1/2 mini protease tablet per 5ml buffer 7. Keep lysis buffers on ice 8. Resuspend pellet in 5ml lysis buffer 1 and incubate with rotation at 4C for 10min. 9. Centrifuge, 4C, 1350xg, 5 min 10.Resuspend pellet in 5ml lysis buffer 2 and incubate with rotation at room temperature for 10 min. 11. Centrifuge, 4C, 1350xg, 5 min 12. Resuspend in 3 mL lysis buffer 3 13. sonicate extract to an average size of 1Kb. 14. Add Triton X-100 to 1%. vortex gently 15. Centrifuge at 4C, 20,000xg, 10min. 16. Aliquot extracts into ~500ul samples.  The chromatin was immunoprecipitated with the anti-dORC2 antibody.

treatment_protocol: Cells were incubated with 1 mM HU for 24 h to arrest cells in G1/S.

tag: cell line

source_name: Input: Kc ORC HU


title: PorcineConcept_D10_biorep6

source_name: Porcine conceptus, Day 10 of pregnancy, biological replicate 6


title: At_stem of wild-type

description: Gene expression data from wild-type Arabidopsis stem.

source_name: Wild-type Arabidopsis stem tissue

value: wild type


title: PorcineConcept_D10_biorep1

source_name: Porcine conceptus, Day 10 of pregnancy, biological replicate 1


title: Liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 7

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 7

data_processing: Data including background subtraction (GenomeStudioV2011.1 software, gene expression module version 1.9.0), removal of negative values by introducing an offset, quantile normalisation

source_name: Liver tissue

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: Animals housed under spf conditions

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: Isocaloric diets containing either sucrose or palatinose as described in the paper

tag: treatment

value: palatinose

value: liver

value: 18 weeks

tag: strain

value: male


title: Liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 6

description: Gene expression data from liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 6

tag: tissue


title: Liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 7

description: Gene expression data from liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 7

value: sucrose

tag: gender


title: Liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 2

description: Gene expression data from liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 2

tag: age


title: Liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 5

description: Gene expression data from liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 5


title: Liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 4

description: Gene expression data from liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 4


title: Liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 3

description: Gene expression data from liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 3


title: Liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 4

description: Gene expression data from liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 4


title: Liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 3

description: Gene expression data from liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 3


title: Liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 1

description: Gene expression data from liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 1


title: Liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 5

description: Gene expression data from liver tissue from mice fed with a palatinose-containing diet for 22 weeks, biological replicate 5


title: Liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 1

description: Gene expression data from liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 1


title: Liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 6

description: Gene expression data from liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 6


title: Chronic Treg, 16 d, rep1

city: Seoul

first: Sang-Jun

last: Ha

address: 50 Yonsei-ro, Science Research Center, Room S423

department: Biochemistry

institute: Yonsei University

description: Biological replicate 1 of 3, CD4+CD25+ Treg cells, 16 d after chronic infection, isolated from spleen using CD4+CD25+ regulatory T Cell Isolation Kit (MiltenyiBiotec)

hyb_protocol: Following fragmentation, fragmented cRNA were hybridized for 16 hr at 45C on AffymetrixGeneChip® HT MG-430 PM Array plate. The GeneChips were washed and stained in the Affymetrix GeneTitan® MC Instrument.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® HT Scanner.

data_processing: The Micorarray Suite version 5 (MAS5) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: Splenic CD4+CD25+ Treg cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® 3’IVT Express kit P/N 901229, Affymetrix).

extract_protocol: Splenic CD4+CD25+ regulatory T (Treg) cells were isolated from naïve and infected mice at 0 and 16 day after acute and chronic virus infection using a CD4+CD25+ regulatory T Cell Isolation Kit (MiltenyiBiotec). Total RNA was extracted from isolated Treg cells using the RNeasyPlus Micro Kit (Qiagen). RNA purity was confirmed through the Agilent Bioanalyzer 2100 and nano drop 8000 analysis.

treatment_protocol: Mice were infected with LCMV Arm and LCMV CL13 by intraperitoneal and intravenous injection, respectively.

value: Spleen

tag: cell type

value: CD4+CD25+ regulatory T cells

tag: infection

value: 16 days after chronic infection with LCMV CL13


title: Acute Treg, 16 d, rep2

description: Biological replicate 2 of 3, CD4+CD25+ Treg cells, 16 d after acute infection, isolated from spleen using CD4+CD25+ regulatory T Cell Isolation Kit (MiltenyiBiotec)

value: 16 days after acute infection with LCMV Arm


title: Peripheral whole blood-AIM-B1-P019

city: Prague

first: Michal

last: Kolář

address: Pod Vodárenskou věží 2

country: Czech Republic

institute: Institute of Computer Science, Academy of Sciences of the Czech Republic

hyb_protocol: The cRNA samples (1.5 μg) were hybridized on HumanWG-6 v2 Expression BeadChips (Illumina Inc.) according to manufacturer’s protocol.

data_processing: The data were background corrected using the Illumina background model and quantile normalised with GenomeStudio Version 2010.3.0.30128

source_name: Peripheral whole blood, AIM, B1, P019

label_protocol: The cRNA was amplified using Illumina® TotalPrep™ RNA Amplification Kit, precipitated and controlled on Nanodrop (Thermo Scientific) and Bioanalyzer 2100 (Agilent Technologies).

extract_protocol: Samples of peripheral whole blood were collected from all subjects using commercial 3 ml Vacutainer sets with EDTA. The tubes were inverted several times and 2.4 ml of the content was immediately mixed with 7.6 ml RNAlater (Applied Biosystems) in 15 ml tubes, stabilized blood samples were inverted several times until they were homogenous and the samples were stored in -70°C. The RNA was isolated from 1.8 ml aliquot of stabilized blood with RiboPure-Blood Kit (Applied Biosystems), precipitated and purified with GLOBINclear–Human kit (Applied Biosystems).

tag: group

value: AIM

tag: pair

tag: Sex

value: Female

tag: age [year]

tag: diabetes status

value: yes

tag: smoking status

value: no

tag: height [cm]

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers

tag: statins

tag: fibrates

tag: other medication

value: whole blood

tag: technical replicate

value: replicate 1

tag: sentrix id and position


title: Chronic Treg, 16 d, rep2

description: Biological replicate 2 of 3, CD4+CD25+ Treg cells, 16 d after chronic infection, isolated from spleen using CD4+CD25+ regulatory T Cell Isolation Kit (MiltenyiBiotec)

tag: strain

tag: tissue

tag: cell type

tag: infection


title: Liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 2

description: Gene expression data from liver tissue from mice fed with a sucrose-containing diet for 22 weeks, biological replicate 2

tag: treatment

tag: age

tag: gender


title: Peripheral whole blood-AIM-A-P011

source_name: Peripheral whole blood, AIM, A, P011

tag: group

tag: pair

value: A

tag: Sex

value: Male

tag: age [year]

tag: diabetes status

tag: smoking status

tag: height [cm]

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]


title: Peripheral whole blood-AIMD6-E-P010

source_name: Peripheral whole blood, AIMD6, E, P010

value: E

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers

tag: statins

tag: fibrates

tag: other medication

tag: technical replicate

tag: sentrix id and position


title: Acute Treg, 16 d, rep1

description: Biological replicate 1 of 3, CD4+CD25+ Treg cells, 16 d after acute infection, isolated from spleen using CD4+CD25+ regulatory T Cell Isolation Kit (MiltenyiBiotec)

tag: strain

tag: tissue

tag: cell type

tag: infection


title: Naïve Treg, 0 d, rep3

description: Biological replicate 3 of 3, Control CD4+CD25+ Treg cells, Naive, isolated from spleen using CD4+CD25+ regulatory T Cell Isolation Kit (MiltenyiBiotec)


title: Chronic Treg, 16 d, rep3

description: Biological replicate 3 of 3, CD4+CD25+ Treg cells, 16 d after chronic infection, isolated from spleen using CD4+CD25+ regulatory T Cell Isolation Kit (MiltenyiBiotec)


title: Peripheral whole blood-AIM-S-P009

source_name: Peripheral whole blood, AIM, S, P009

tag: group

tag: pair

value: S

tag: Sex

tag: age [year]

tag: diabetes status

tag: smoking status

tag: height [cm]


title: Peripheral whole blood-AIM-M-P008

source_name: Peripheral whole blood, AIM, M, P008

value: M

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers


title: Acute Treg, 16 d, rep3

description: Biological replicate 3 of 3, CD4+CD25+ Treg cells, 16 d after acute infection, isolated from spleen using CD4+CD25+ regulatory T Cell Isolation Kit (MiltenyiBiotec)

tag: strain

tag: tissue


title: Peripheral whole blood-AIM-M-P008dup

tag: statins

tag: fibrates

tag: other medication

tag: technical replicate

value: replicate 2

tag: sentrix id and position


title: Naïve Treg, 0 d, rep2

description: Biological replicate 2 of 3, Control CD4+CD25+ Treg cells, Naive, isolated from spleen using CD4+CD25+ regulatory T Cell Isolation Kit (MiltenyiBiotec)

tag: cell type

tag: infection


title: Peripheral whole blood-AIM-P1-P003

source_name: Peripheral whole blood, AIM, P1, P003

tag: group

tag: pair

tag: Sex

tag: age [year]

tag: diabetes status

tag: smoking status

tag: height [cm]


title: Peripheral whole blood-control-C1-C348dup

source_name: Peripheral whole blood, control, C1, C348

value: control

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers


title: Peripheral whole blood-control-E1-C302

source_name: Peripheral whole blood, control, E1, C302

tag: statins

tag: fibrates

tag: other medication

tag: tissue

tag: technical replicate

tag: sentrix id and position


title: Peripheral whole blood-control-A-C282

source_name: Peripheral whole blood, control, A, C282

tag: group

tag: pair

tag: Sex

tag: age [year]


title: Peripheral whole blood-control-C1-C348

tag: diabetes status

tag: smoking status

tag: height [cm]

tag: weigth [kg]


title: Naïve Treg, 0 d, rep1

description: Biological replicate 1 of 3, Control CD4+CD25+ Treg cells, Naive, isolated from spleen using CD4+CD25+ regulatory T Cell Isolation Kit (MiltenyiBiotec)

tag: strain

value: Spleen

tag: cell type

tag: infection


title: Peripheral whole blood-control-U-C274

source_name: Peripheral whole blood, control, U, C274

value: U

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers

tag: statins


title: Peripheral whole blood-control-O-C294

source_name: Peripheral whole blood, control, O, C294

tag: group

tag: pair

value: O

tag: fibrates

tag: other medication

tag: tissue

tag: technical replicate

tag: sentrix id and position


title: Peripheral whole blood-control-N-C310

source_name: Peripheral whole blood, control, N, C310

value: N

tag: Sex

tag: age [year]

tag: diabetes status

tag: smoking status

tag: height [cm]

tag: weigth [kg]


title: Peripheral whole blood-AIM-E1-C284

source_name: Peripheral whole blood, AIM, E1, C284

value: AIM

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers


title: Peripheral whole blood-control-D1-C304

source_name: Peripheral whole blood, control, D1, C304

tag: group

tag: diuretics

tag: ca blockers

tag: statins


title: Peripheral whole blood-control-G-C213

source_name: Peripheral whole blood, control, G, C213

tag: pair

value: G

tag: fibrates

tag: other medication

tag: tissue


title: Peripheral whole blood-AIM-W-C289

source_name: Peripheral whole blood, AIM, W, C289

value: W

tag: Sex

tag: age [year]

value: yes

tag: technical replicate

tag: sentrix id and position


title: Peripheral whole blood-control-G1-C272__1

source_name: Peripheral whole blood, control, G1, C272

tag: diabetes status

tag: smoking status

value: no

tag: height [cm]

tag: weigth [kg]

value: whole blood


title: Peripheral whole blood-control-H1-C287

source_name: Peripheral whole blood, control, H1, C287

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

value: replicate 1


title: Peripheral whole blood-control-ID-C250

source_name: Peripheral whole blood, control, ID, C250

tag: group

value: ID

value: Male

tag: diuretics

tag: ca blockers

tag: statins


title: Peripheral whole blood-control-B1-C221

source_name: Peripheral whole blood, control, B1, C221

tag: pair

value: Female

tag: fibrates

tag: other medication

tag: tissue


title: Peripheral whole blood-control-X1-C210

source_name: Peripheral whole blood, control, X1, C210

tag: Sex

tag: age [year]

tag: technical replicate

tag: sentrix id and position


title: Peripheral whole blood-AIM-A1-C269

source_name: Peripheral whole blood, AIM, A1, C269

tag: diabetes status

tag: smoking status

tag: height [cm]

tag: weigth [kg]


title: Peripheral whole blood-control-P1-C209

source_name: Peripheral whole blood, control, P1, C209

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers


title: Peripheral whole blood-AIM-G1-C238

source_name: Peripheral whole blood, AIM, G1, C238

tag: group

tag: diuretics

tag: ca blockers

tag: statins


title: Peripheral whole blood-control-A1-C206

source_name: Peripheral whole blood, control, A1, C206

tag: pair

tag: fibrates

tag: other medication

tag: tissue


title: Peripheral whole blood-control-B-C260

source_name: Peripheral whole blood, control, B, C260

value: B

tag: Sex

tag: age [year]

tag: technical replicate

tag: sentrix id and position


title: Peripheral whole blood-control-Z-C207

source_name: Peripheral whole blood, control, Z, C207

value: Z

tag: diabetes status

tag: smoking status

tag: height [cm]

tag: weigth [kg]


title: Peripheral whole blood-AIM-R-C205

source_name: Peripheral whole blood, AIM, R, C205

value: R

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers


title: Peripheral whole blood-control-P-C187

source_name: Peripheral whole blood, control, P, C187

tag: group

value: control

value: P

tag: diuretics

tag: ca blockers

tag: statins


title: Peripheral whole blood-AIM-C1-C185dup

source_name: Peripheral whole blood, AIM, C1, C185

tag: pair

tag: fibrates

tag: other medication

tag: tissue

value: replicate 2


title: Peripheral whole blood-AIM-C1-C185

tag: Sex

tag: age [year]

tag: technical replicate

tag: sentrix id and position


title: Peripheral whole blood-AIM-D1-C195

source_name: Peripheral whole blood, AIM, D1, C195

tag: diabetes status

tag: smoking status

tag: height [cm]

tag: weigth [kg]


title: Peripheral whole blood-AIM-F1-C194

source_name: Peripheral whole blood, AIM, F1, C194

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers


title: Peripheral whole blood-control-M1-C198

source_name: Peripheral whole blood, control, M1, C198

tag: group

tag: diuretics

tag: ca blockers

tag: statins


title: Peripheral whole blood-AIM-ID-C184

source_name: Peripheral whole blood, AIM, ID, C184

tag: pair

tag: fibrates

tag: other medication

tag: tissue


title: Peripheral whole blood-control-E-C208

source_name: Peripheral whole blood, control, E, C208

value: E

tag: Sex

tag: age [year]

tag: technical replicate

tag: sentrix id and position


title: Peripheral whole blood-control-N1-C204

source_name: Peripheral whole blood, control, N1, C204

tag: diabetes status

tag: smoking status

tag: height [cm]

tag: weigth [kg]


title: Peripheral whole blood-AIM-F-C181

source_name: Peripheral whole blood, AIM, F, C181

value: AIM

value: F

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers


title: Peripheral whole blood-AIM-V-C182

source_name: Peripheral whole blood, AIM, V, C182

tag: group

value: V

tag: diuretics

tag: ca blockers

tag: statins


title: Peripheral whole blood-AIM-U-C174

source_name: Peripheral whole blood, AIM, U, C174

tag: pair

value: U

tag: fibrates

tag: other medication

tag: tissue


title: Peripheral whole blood-AIM-K-C172

source_name: Peripheral whole blood, AIM, K, C172

value: K

tag: Sex

tag: age [year]

value: yes

value: no

tag: technical replicate

tag: sentrix id and position


title: Blood_schizophrenia 18 [Sch62]

city: Wuxi

first: Fuquan

last: Zhang

address: 156 Qianrong Rd

country: China

institute: Wuxi mental health center

description: early onset schizophrenia < 18 years

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 20 out of 30 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

note from submitter: The raw file is the most original data received from the company, containing ~17000 probes.

source_name: schizophrenia patient

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Integrity and concentration of RNA were assessed after RNA extraction and prior to sample labeling.

value: peripheral blood mononuclear cells


title: Peripheral whole blood-AIM-J-C170

source_name: Peripheral whole blood, AIM, J, C170

value: J

tag: diabetes status

tag: smoking status

tag: height [cm]

tag: weigth [kg]

value: whole blood

value: replicate 1


title: Blood_schizophrenia 16 [Sch60]

description: early onset schizophrenia < 18 years


title: Peripheral whole blood-control-D-C163

source_name: Peripheral whole blood, control, D, C163

value: D

value: Female

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers


title: Blood_schizophrenia 12 [Sch54]

description: early onset schizophrenia < 18 years


title: Peripheral whole blood-control-T1-C150

source_name: Peripheral whole blood, control, T1, C150

tag: group

value: control

value: Male

tag: diuretics

tag: ca blockers

tag: statins


title: Peripheral whole blood-control-V-C168

source_name: Peripheral whole blood, control, V, C168

tag: pair

tag: fibrates

tag: other medication

tag: tissue


title: Blood_schizophrenia 14 [Sch57]

description: early onset schizophrenia < 18 years


title: Blood_schizophrenia 11 [Sch53]

description: early onset schizophrenia < 18 years


title: Blood_schizophrenia 15 [Sch58]

description: early onset schizophrenia < 18 years


title: Blood_schizophrenia 13 [Sch56]

description: early onset schizophrenia < 18 years


title: Peripheral whole blood-control-S-C149

source_name: Peripheral whole blood, control, S, C149

value: S

tag: Sex

tag: age [year]

tag: technical replicate

tag: sentrix id and position


title: Blood_schizophrenia 17 [Sch61]

description: early onset schizophrenia < 18 years


title: Blood_schizophrenia 7 [Sch47]

description: early onset schizophrenia < 18 years


title: Peripheral whole blood-AIM-O-C139

source_name: Peripheral whole blood, AIM, O, C139

value: O

tag: diabetes status

tag: smoking status

tag: height [cm]

tag: weigth [kg]


title: Peripheral whole blood-AIM-B-C147

source_name: Peripheral whole blood, AIM, B, C147

value: AIM

value: B

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers


title: Blood_schizophrenia 10 [Sch52]

description: early onset schizophrenia < 18 years


title: Peripheral whole blood-control-H-C133

source_name: Peripheral whole blood, control, H, C133

tag: group

value: H

tag: diuretics

tag: ca blockers

tag: statins


title: Peripheral whole blood-control-L-C138dup

source_name: Peripheral whole blood, control, L, C138

tag: pair

value: L

tag: fibrates

tag: other medication

tag: tissue

value: replicate 2


title: Peripheral whole blood-AIM-HD-C129

source_name: Peripheral whole blood, AIM, HD, C129

value: HD

tag: Sex

tag: age [year]

value: yes

tag: technical replicate

tag: sentrix id and position


title: Blood_schizophrenia 8 [Sch49]

description: early onset schizophrenia < 18 years

value: peripheral blood mononuclear cells


title: Blood_schizophrenia 3 [Sch42]

description: Healthy controls < 18 years


title: Peripheral whole blood-control-L-C138

tag: diabetes status

value: no

tag: smoking status

tag: height [cm]

tag: weigth [kg]


title: Blood_schizophrenia 5 [Sch44]

description: early onset schizophrenia < 18 years


title: Blood_schizophrenia 6 [Sch45]

description: early onset schizophrenia < 18 years


title: Blood_schizophrenia 4 [Sch43]

description: early onset schizophrenia < 18 years


title: Peripheral whole blood-AIM-P-C120

source_name: Peripheral whole blood, AIM, P, C120

value: P

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

value: whole blood


title: Peripheral whole blood-AIM-N-C125

source_name: Peripheral whole blood, AIM, N, C125

tag: group

value: N

tag: diuretics

tag: ca blockers

tag: statins

value: replicate 1


title: Peripheral whole blood-control-L1-C124dup

source_name: Peripheral whole blood, control, L1, C124

value: control

tag: pair

value: Female

tag: fibrates

tag: other medication

tag: tissue


title: Blood_schizophrenia 1 [Sch35]

description: Healthy controls < 18 years


title: Peripheral whole blood-AIM-V1-C119

source_name: Peripheral whole blood, AIM, V1, C119

tag: Sex

value: Male

tag: age [year]

tag: technical replicate

tag: sentrix id and position


title: Blood_schizophrenia 2 [Sch38]

description: Healthy controls < 18 years


title: Blood_control 11 [NC90]

description: Healthy controls < 18 years

source_name: healthy control


title: Blood_schizophrenia 9 [Sch50]

description: early onset schizophrenia < 18 years


title: Blood_control 12 [NC91]

description: Healthy controls < 18 years


title: Peripheral whole blood-control-W1-C118

source_name: Peripheral whole blood, control, W1, C118

tag: diabetes status

tag: smoking status

tag: height [cm]

tag: weigth [kg]


title: Peripheral whole blood-control-R-C116

source_name: Peripheral whole blood, control, R, C116

value: R

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers


title: Peripheral whole blood-control-S1-C110

source_name: Peripheral whole blood, control, S1, C110

tag: group

tag: diuretics

tag: ca blockers

tag: statins


title: Peripheral whole blood-AIM-U1-C108

source_name: Peripheral whole blood, AIM, U1, C108

value: AIM

tag: pair

tag: fibrates

tag: other medication

tag: tissue


title: Blood_control 8 [NC85]

description: Healthy controls < 18 years


title: Peripheral whole blood-control-J-C109

source_name: Peripheral whole blood, control, J, C109

value: J

tag: Sex

tag: age [year]

tag: technical replicate

tag: sentrix id and position


title: Peripheral whole blood-control-Y-C106

source_name: Peripheral whole blood, control, Y, C106

value: Y

tag: diabetes status

tag: smoking status

tag: height [cm]

tag: weigth [kg]


title: Blood_control 10 [NC89]

description: Healthy controls < 18 years


title: Blood_control 7 [NC79]

description: Healthy controls < 18 years


title: Heart_from_aMHC_KLF5_ko_mouse_rep4

description: Gene expression profile at basal levels

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, mRNAs that at least 1 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed mRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Heart from aMHC-KLF5-/- mice

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA was purified from total hearts with TRIZOL (Invitrogen) following the manufacturer's instructions. Briefly, the protocol includes cell lysis in TRIZOL reagent, phenol/chloroform extraction of RNA, isopropanol precipitation and two washes with 70% ethanol in DEPC-treated water.

treatment_protocol: Basal levels of cardiac RNA were measured for KLF5 floxed mice vs. aMHC-KLF5-/- mice

value: whole heart

tag: gender

tag: age

value: 8-12 weeks


title: Peripheral whole blood-control-I-C101

source_name: Peripheral whole blood, control, I, C101

tag: group

value: I

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

tag: diuretics


title: Heart_from_aMHC_KLF5_ko_mouse_rep1

description: Gene expression profile at basal levels

tag: tissue


title: Peripheral whole blood-control-F1-C098

source_name: Peripheral whole blood, control, F1, C098

tag: pair

tag: Sex

value: yes

tag: ca blockers

tag: statins

tag: fibrates

tag: other medication


title: Heart_from_KLF5_flox_flox_mouse_rep1

description: Gene expression profile at basal levels

source_name: Heart from KLF5 floxed mice


title: Heart_from_aMHC_KLF5_ko_mouse_rep2

description: Gene expression profile at basal levels


title: Heart_from_aMHC_KLF5_ko_mouse_rep3

description: Gene expression profile at basal levels


title: Peripheral whole blood-AIM-I-C099

source_name: Peripheral whole blood, AIM, I, C099

tag: age [year]

tag: diabetes status

tag: smoking status

tag: height [cm]

tag: technical replicate

tag: sentrix id and position


title: Heart_from_KLF5_flox_flox_mouse_rep4

description: Gene expression profile at basal levels

tag: gender

tag: age


title: Heart_from_KLF5_flox_flox_mouse_rep3

description: Gene expression profile at basal levels


title: Old without severe cognitive disability_47

city: Krakow

first: Miroslaw

last: Bik-Multanowski

address: ul. Wielicka 265

department: Dept. of Medical Genetics

institute: Jagiellonian University

data_processing: GeneSpring software was used with default workflow-type; single-color analysis

source_name: Blood white cells

extract_protocol: RNA extraction from blood samples with use of PAXgene system (PreAnalytiX)

value: Old

tag: condition

value: without severe cognitive disability

tag: cell type

value: white blood cell


title: Blood_control 6 [NC78]

description: Healthy controls < 18 years

tag: tissue

value: peripheral blood mononuclear cells


title: Heart_from_KLF5_flox_flox_mouse_rep2

description: Gene expression profile at basal levels


title: Old without severe cognitive disability_48


title: Blood_control 4 [NC76]

description: Healthy controls < 18 years


title: Blood_control 9 [NC86]

description: Healthy controls < 18 years


title: Blood_control 3 [NC75]

description: Healthy controls < 18 years


title: Peripheral whole blood-control-M-C081

source_name: Peripheral whole blood, control, M, C081

tag: group

tag: pair

value: M

value: no

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

tag: diuretics

value: whole blood


title: Blood_control 1 [NC72]

description: Healthy controls < 18 years


title: Old without severe cognitive disability_45


title: Old without severe cognitive disability_46


title: Blood_control 2 [NC74]

description: Healthy controls < 18 years


title: Peripheral whole blood-control-M-C081dup

value: control

tag: Sex

value: Female

tag: age [year]

tag: diabetes status

tag: smoking status

tag: ca blockers

tag: statins

tag: fibrates

tag: other medication

value: replicate 2


title: Old without severe cognitive disability_44

tag: age

tag: condition

tag: cell type


title: Peripheral whole blood-AIMD6-H1-C078

source_name: Peripheral whole blood, AIMD6, H1, C078

tag: group

tag: pair

value: Male

tag: height [cm]

tag: weigth [kg]

tag: tissue

tag: technical replicate

value: replicate 1

tag: sentrix id and position


title: Blood_control 5 [NC77]

description: Healthy controls < 18 years


title: Old with severe cognitive disability_40

value: severe cognitive disability


title: Peripheral whole blood-control-HD-C083

source_name: Peripheral whole blood, control, HD, C083

value: HD

tag: Sex

tag: age [year]

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: acei

tag: betablockers

tag: diuretics


title: Old with severe cognitive disability_42

tag: age


title: Old with severe cognitive disability_41

tag: condition


title: Old with severe cognitive disability_39

tag: cell type


title: Old with severe cognitive disability_37


title: Peripheral whole blood-AIM-N1-C074

source_name: Peripheral whole blood, AIM, N1, C074

tag: group

value: AIM

tag: diabetes status

tag: smoking status

tag: ca blockers

tag: statins

tag: fibrates

tag: other medication


title: Old with severe cognitive disability_43


title: Old with severe cognitive disability_38


title: Old with severe cognitive disability_36


title: Young without severe cognitive disability_33

value: Young


title: Young without severe cognitive disability_31


title: Young without severe cognitive disability_34


title: Sox9_3/IgG_3

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: SOX9 experimental sample 3 is compared to IgG control sample 3

hyb_protocol: The ChIP-Chip hybridization used a Roche Nimblegen's Rat ChIP-chip 3×720K RefSeq Promoter Array. The enrichment for each probe on the array was calculated as the log ratio of the intensities of hybridization for SRY or SOX9 ChIP DNA (Cy5) to control DNA from IgG control (Cy3). Array contained on average 4,000 bp of promoter for each of 15,287 promoters in the rat genome corresponding to 15,600 RefSeq transcripts (approximately 3880 bp upstream and 970 bp downstream from transcription start site). Two different comparative (ChIP vs ChIP) hybridizations experiments were performed, each encompassing 4 samples (2 treatment and 2 control) and 4 array sets. The first was a dye balance design as follows: C1 in the green channel against V1 in the red channel; V1 in the green channel against C2 in the red channel; C2 in the green channel against V2 in the red channel; V2 in the green channel against C1 in the red channel. The second one was a dye swap design as follows: C1 in the green channel against V1 in the red channel; V1 in the green channel against C1 in the red channel; C2 in the green channel against V2 in the red channel; V2 in the green channel against C2 in the red channel.

scan_protocol: Scanning and image acquisition was performed in-house by Nimblegen Inc.

data_processing:
For each hybridization experiment raw data from both the Cy3 can Cy5 channels were imported into R (R Development Core Team (2010), R: A language for statistical computing, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org), and data checked for quality and converted to MA values (M = Cy5-Cy3; A = (Cy5+Cy3)/2). The R codes that were used for analysis and annotation are available in the following website: http//www.skinner.wsu.edu. All the tiling array Chip data was deposited in the NCBI GEO site. Within each array, probes were separated into groups by GC content and each group was separately normalized using the LOESS normalization procedure. This allowed for groups with optimal GC content, which exhibited a reduced quality issue, to receive a normalization curve specific to that group. After each array was normalized within array, the arrays were then normalized across arrays using the A-quantile normalization procedure. Following normalization the probe's normalized M values (and then A) were replaced with the median value of all probe M values (and then A) within a sliding window of 600 bp, due to the size of DNA fragments used. Following normalization each probe's M value represents the median intensity difference between Cy5 and Cy3 of a 600 bp window. Significance was assigned to probe differences between experimental (SRY or SOX9) and IgG control by calculating the median value of the intensity differences as compared to a normal distribution scaled to the experimental mean and standard deviation of M. Regions of interest were then determined by combining consecutive probes with significance p-values less than 10−3. Significance was assigned to probe differences between experimental and control by calculating the median value of the increasing differences as compared to a normal distribution scaled to the experimental mean and standard deviation of the mean. A Z-score and P-value were computed from that distribution with the use of R code analysis. The statistically significant peaks of hybridization were identified and P-value associated with each peak presented. Each peak of interest was then annotated for the gene. Every promoter exceeding the intensity threshold was considered positive for SRY or SOX9 binding. The final list of SRY or SOX9 targets includes the promoter-proximal regions that made the threshold in an average of the three replicates. Hybridization signals for all the candidate promoters that were within the cutoff line (p≤1×10−7) were plotted (average of the three replicates), Supplemental Figure S1. The genes that were not in the list but seemed to be masked by IgG negative signals were designated as questionable positives. These questionable positive promoters were manually chosen and confirmed by PCR, Supplemental Figure S2.
Nimblescan software-generated Cy3/Cy5 expression ratios are presented in the processed data files, but R-code data processing of raw data as described was used as the basis for conlusions in this study. Value definitions for processed data files: #ClusterID= ID and chrolosomal location for cluster of probes showing a significant difference (p<1.0E-5) between red and green channel hybridization (treated vs. control),  #Chromosome= Chromosome number, #cSTART= Cluster start site,  #cSTOP= Cluster stop site,  #meanM= mean log2 intensity ratio (treated vs. control) across all microarray chips for this treatment/control group,  #meanA= mean log2 hybridization intensity (both red and green channel) across all microarray chips for this treatment/control group,  #minP= p-value for difference between treated and control intensity as calculated by indicated R-code from raw data files. P-value must be p<1.0E-5 or less for inclusion,  #nProbes= number of consecutive probes with p<1.0E-5 included in cluster,  #CG= CG content of cluster,  #CpG= CpG content of cluster, and #CpGdensity= number of CpGs per hundred base pairs.

organism: Rattus norvegicus

source_name: SOX9 ChIP DNA from embryonic day 13 gonads

label_protocol: SRY or SOX9 ChIP DNA where labeled with Cy5 and control DNA from IgG control were labeled with Cy3

extract_protocol: Harlan Sprague-Dawley rats were used for the study. All the rats were kept in a temperature controlled environment and given food and water ad libitum. Estrous cycles of female rats were monitored by cellular morphology from vaginal smears. Rats in early estrus were paired with males overnight and mating confirmed by sperm positive smears, denoted day 0 of pregnancy. Pregnant rats were euthanized at embryonic day 13 (E13) of pregnancy, and embryonic gonads were collected for chromatin immunoprecipitation. Sex was determined by PCR using primers specific for Sry on genomic DNA isolated from embryo tails was preformed by using 1 μl of genomic DNA with the consensus SRY primers 5′ CGGGATCCATGTCAAGCGCC CCATGAATGCATTTATG 3′ and 5′ GCGGAATTCACTTTAGCCCTCCGATGAGGCTGA TAT 3′, producing a PCR product of 240 base pairs (bp). PCR was performed using an annealing temperature of 55°C for 30 cycles. All procedures were approved by the Washington State University Animal Care and Use Committee (IACUC approval # 02568-026). A modified ChIP (cChIP) assay was adopted from O'Neill et al., (2006) and performed according to Bhandari et al (2011).  To run ChIP assay, male and female gonads (gonad+mesonephros) were dissected from approximately twenty to twenty five 13 dpc (12–18 tail somite stage) rat embryos per array and snap-frozen in liquid nitrogen. Drosophila SL2 cells were used as a carrier. Densely-grown cells (approximately 5×107 cells) were pelleted and washed three times in ice-cold PBS, 5 mM sodium butyrate and resuspended in 0.5 ml NB buffer (15 mM Tris-HCL, pH 7.4, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.5 mM 2-mercaptoethanol, 0.1 mM PMSF). Frozen testis samples were thawed, mixed with SL2 cells and homogenized to make single cell suspension. Nuclei were pelleted, resuspended in 20 ml NB buffer, 5% (vol/vol) sucrose, pelleted and resuspended again in 5 ml digestion buffer (50 mM Tris-HCl pH 7.4, 0.32 M sucrose, 4 mM MgCl2, 1 mM CaCl2, 0.1 mM PMSF). Following micrococcal nuclease digestion (NEB, USA) for 10 minutes at 37 degree, the digested samples were gently spun (800×g) for 10 minutes and supernatant set aside on ice. The pellet was resuspended in 250 ul incubation buffer (50 mM Nacl, 20 mM Tris HCl pH 7.5, 20 mM Na-butyrate, 5 mM Na2EDTA, and 0.1 mM PMSF) and again centrifuged gently for 10 minutes. Both the supernatants were pooled and a fraction (50 ul) out of it was kept aside to use as input. The remaining supernatant was incubated with either non-immune IgG or anti-SRY or anti-Gata4 antibodies at 4°C overnight. After incubation with 100 µl of preswollen protein A-Sepharose beads (Sigma) for 2 h at 4°C, the bead-bound immunoprecipitates were centrifuged gently and washed five times with wash buffer (50 mM TrisHCl pH 7.5, 10 mM EDTA, 5 mM Na butyrate and 50–150 mM NaCl). The protein-DNA complexes were incubated at room temperature with elution buffer (1% SDS in TE) and centrifuged at 11500×g at 4°C for 10 minutes. Elution was repeated two times and eluted DNA was pooled. Co-immunoprecipitated DNA was purified by proteinase K digestion, phenol/chloroform extraction, and ethanol precipitation. Final concentration of immunoprecipitated DNA varied from 100 to 300 ng per assay. Two rounds of PCR reactions were run for 25 cycles before evaluating samples by gel electrophoresis. Identity of the PCR-amplified fragments was verified by sequencing. The conditions for the native-ChIP (not including cross linking) were optimized for immunoprecipitating with SRY and SOX9 antibodies. The native-ChIP was used to identify high affinity binding sites and reduce low affinity sites, and was validated with PCR for Sox9, Tcf21 and Ntf3. To run a replicate of the ChIP assay, at least twenty male gonads from thirty 13 dpc (12–18 tail somite stage) rat embryos were used per array. All three ChIP experiments were with different biological samples. Drosophila SL2 cells (American Type Culture Collection (ATCC) Catalog no. CRL-1963) were used as a carrier. Densely-grown cells (approximately 5×107 cells) were pelleted and washed three times in ice-cold phosphate buffered salve (PBS), 5 mM sodium butyrate and resuspended in 0.5 ml NB buffer (15 mM Tris-HCL, pH 7.4, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.5 mM 2-mercaptoethanol, 0.1 mM PMSF). Testis samples were mixed with SL2 cells and homogenized to make single cell suspension. Nuclei were pelleted, resuspended in 10 ml NB buffer, 5% (vol/vol) sucrose, pelleted and resuspended again in 1.5 ml digestion buffer (50 mM Tris-HCl pH 7.4, 0.32 M sucrose, 4 mM MgCl2, 1 mM CaCl2, 0.1 mM PMSF). Following micrococcal nuclease digestion (NEB, USA) for 5 minutes at 28°C, the digested samples were gently spun (800× g) for 15 minutes and supernatant set aside on ice. The pellet was resuspended in 250 ul digestion buffer and again centrifuged gently at 800× g for 15 minutes at 4 degrees. Both the supernatants were pooled and a fraction (50 ul) out of it was kept aside to use as input. The remaining supernatant was incubated with either non-immune IgG or anti-SRY (Santa Cruz, CA, USA) or anti-SOX9 (ABcam, CA, USA) antibodies at 4°C overnight. The specificity of these antibodies on western blots have been previously described and validated. After incubation with 100 µl of pre-swollen protein A-Sepharose beads (SL2 DNA blocked) for 2 h at 4°C, the bead-bound immunoprecipitates were centrifuged gently and washed five times with wash buffer (50 mM TrisHCl pH 7.5, 10 mM EDTA, 5 mM Na butyrate and 50–150 mM NaCl). The protein-DNA complexes were incubated at room temperature with elution buffer (1% SDS in TE) and centrifuged at 11500× g for 10 minutes. Elution was repeated two times and eluted DNA was pooled. Co-immunoprecipitated DNA was purified by phenol/chloroform extraction, and ethanol precipitation. Final concentration of immunoprecipitated DNA varied from 200 to 500 ng per assay. Three different experiments and ChIP assays were performed. Exactly 30 ng of immunoprecipitated DNA from each assay was amplified by whole genome amplification kit developed by Sigma (Sigma #WGA2 50 RXN). At least five separate whole genome amplifications were performed and DNA was pooled. Pooled whole genome amplified DNA was purified by using Promega's Wizard SV40 PCR cleanup kit (Promega). Purified DNA was checked on the gel and sent to Nimblegen for ChIP-chip hybridization (Nimblegen, Iceland).

tag: developmental stage

value: Embryonic day 13 (E13)

tag: strain

value: Harlan Sprague-Dawley

tag: tissue

value: gonads

source_name: IgG ChIP DNA from embryonic day 13 gonads

treatment_protocol: IgG-Control


title: Peripheral whole blood-AIM-Q-C063

source_name: Peripheral whole blood, AIM, Q, C063

tag: pair

value: Q

tag: Sex

tag: age [year]

tag: height [cm]

tag: weigth [kg]

tag: sbp [mmhg]

tag: dbp [mmhg]

value: yes

tag: technical replicate

tag: sentrix id and position


title: Young without severe cognitive disability_35

tag: age

tag: condition

value: without severe cognitive disability

tag: cell type

value: white blood cell


title: Peripheral whole blood-control-V1-C066

source_name: Peripheral whole blood, control, V1, C066

tag: group

tag: diabetes status

value: no

tag: smoking status

tag: acei

tag: betablockers

tag: diuretics

tag: ca blockers

tag: statins

tag: fibrates

value: whole blood


title: Peripheral whole blood-AIM-G-C069

source_name: Peripheral whole blood, AIM, G, C069

tag: pair

value: G

tag: Sex

tag: age [year]

tag: height [cm]

tag: weigth [kg]

tag: other medication

tag: tissue


title: Peripheral whole blood-AIM-W1-C065

source_name: Peripheral whole blood, AIM, W1, C065

value: Female

tag: sbp [mmhg]

tag: dbp [mmhg]

tag: technical replicate

tag: sentrix id and position


title: Peripheral whole blood-control-W-C061

source_name: Peripheral whole blood, control, W, C061

tag: group

value: control

value: W

value: Male

tag: diabetes status

tag: smoking status

tag: acei


title: Young without severe cognitive disability_28

tag: age

tag: condition

tag: cell type


title: Young without severe cognitive disability_25


title: Young without severe cognitive disability_32


title: Young without severe cognitive disability_30


title: Young without severe cognitive disability_26


title: Young without severe cognitive disability_24


title: Young without severe cognitive disability_27


title: Sox9_2/IgG_2

description: SOX9 experimental sample 2 is compared to IgG control sample 2

growth_protocol: Harlan Sprague-Dawley rats were used for the study. All the rats were kept in a temperature controlled environment and given food and water ad libitum. Estrous cycles of female rats were monitored by cellular morphology from vaginal smears. Rats in early estrus were paired with males overnight and mating confirmed by sperm positive smears, denoted day 0 of pregnancy. Pregnant rats were euthanized at embryonic day 13 (E13) of pregnancy, and embryonic gonads were collected for chromatin immunoprecipitation.

tag: developmental stage

tag: strain


title: Young without severe cognitive disability_29


title: Sox9_1/IgG_1

description: SOX9 experimental sample 1 is compared to IgG control sample 1


title: Peripheral whole blood-AIM-L-C056dup

source_name: Peripheral whole blood, AIM, L, C056

tag: pair

value: L

tag: Sex

tag: age [year]

tag: height [cm]

tag: betablockers

tag: diuretics

tag: ca blockers

tag: statins

tag: fibrates

value: replicate 2