title: Jejunum_D10 [9031313012_H]

description:
D10
9031313012_H


title: CHN 0706009 d42

status: Public on May 01 2016

type: RNA

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: monkey no. 706009

hyb_protocol: After precipitation, purification and quantification the labeled samples were hybridized according to the supplier’s protocol (Agilent Technologies)

scan_protocol: Scanning of microarrays was performed with 5µm resolution 16 bit and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies)

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA ( Agilent Technologies). The extracted MAGE-ML files were further analyzed with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA). The values are the 'gProcessedSignal' from the Agilent Technologies Feature Extraction and represent signal intensities left after multiplicatively detrended background subtraction. Arrays were normalized to the mean of trimmed positive non-flagged/non-control Reporters.

molecule: total RNA

organism: Macaca mulatta

source_name: d42 post immunization

label_protocol: Total RNA labeling was performed with the one color Quick Amp Labeling Kit (Agilent Technologies)

extract_protocol: Total RNA from whole blood was isolated by the PAXgene protocol (PreAnalytiX)

treatment_protocol: PAXgene tubes were used for whole blood sampling.

tag: tissue

value: whole blood

tag: spectrotype

value: Chinese


title: Cecum_D10 [9031313012_L]

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

department: Pathology

country: USA

institute: Case Western Reserve University

description:
D10
9031313012_L

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

source_name: Subject: Monkey_5443

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: 44 outbred, Indian-origin, adult or juvenile female rhesus monkeys (Macaca mulatta) were genotyped and selected as negative for the protective MHC class I alleles Mamu-A*01, Mamu-B*08, and Mamu-B*17.  Animals were randomly allocated to groups.  All monkeys were housed at Bioqual, Rockville, MD.

extract_protocol: Plasma SIV RNA levels were measured using a gag targeted quantitative real-time RT-PCR assay, and tissue levels of SIV RNA and DNA were measured using gag targeted, nested quantitative hybrid real time/digital RT-PCR and PCR assays, essentially as described (Hansen et al., 2013). SIV-specific cellular immune responses in blood and tissues were assessed by multiparameter ICS assays essentially as previously described (Baden et al., 2015; Barouch et al., 2012; Li et al., 2011).  9-color ICS assays were performed with predetermined titers of mAbs against CD3 (SP34; Alexa700), CD4 (L200; AmCyan), CD8 (SK1; allophycocyanin-cyanine 7 [APC-Cy7]), CD28 (L293; peridinin chlorophyll-A-cyanine 5.5 [PerCP-Cy5.5]), CD95 (DX2; phycoerythrin [PE]), CD69 (TP1.55.3; phycoerythrin-Texas Red [energy coupled dye; ECD]; Beckman Coulter), IFN-γ (B27; phycoerythrin-cyanine 7 [PE-Cy7]), IL-2 (MQ1-17H12; allophycocyanin [APC]) and TNF-α (Mab11; fluorescein isothiocya [FITC]). IFN-γ backgrounds were consistently <0.01% in PBMC and <0.05% in tissues.

treatment_protocol: Animals were infected with 5x104 TCID50 of our SIVmac251 challenge stock (Barouch et al., 2012; Liu et al., 2010; Liu et al., 2009) by the intravaginal route and were necropsied on day 0, 1, 3, 7, or 10 following infection.

value: Cecum

tag: status

value: SIV


title: IND 8081 d42

description: monkey no. 8081

value: Indian


title: Tonsil_D10 [9031313012_J]

description:
D10
9031313012_J

value: Tonsil


title: IND 8010 d42

description: monkey no. 8010


title: IND 8093 d42

description: monkey no. 8093


title: Bone_Marrow_D7 [9031313012_B]

description:
D7
9031313012_B

source_name: Subject: Monkey_5355


title: IND 7063 d42

description: monkey no. 7063


title: Cecum_D7 [9031313012_D]

description:
D7
9031313012_D


title: pararectal_paracolonic_D7 [9031313012_F]

description:
D7
9031313012_F

source_name: Subject: Monkey_5442


title: IND 8199 d21

description: monkey no. 8199

source_name: d21 post immunization


title: ileocecal_LN_D10 [9031313012_E]

description:
D10
9031313012_E

source_name: Subject: Monkey_5441


title: CHN 0410009 d42

description: monkey no. 410009


title: CHN 0511009 d42

description: monkey no. 511009


title: CHN 0701003 d42

description: monkey no. 701003


title: CHN 0409005 d42

description: monkey no. 409005


title: CHN 0511007 d42

description: monkey no. 511007


title: Rectum_D7 [9031313012_C]

description:
D7
9031313012_C

value: Rectum


title: IND 8081 d21

description: monkey no. 8081


title: Liver_D7 [9031313009_J]

description:
D7
9031313009_J

source_name: Subject: Monkey_5438

value: Liver


title: Bone_Marrow_D10 [9031313009_K]

description:
D10
9031313009_K

source_name: Subject: Monkey_5440


title: Duodenum_D7 [9031313012_A]

description:
D7
9031313012_A

value: Duodenum


title: Inguinal_LN_D10 [9031313009_E]

description:
D10
9031313009_E


title: CHN 0706009 d21

description: monkey no. 706009


title: Brain_Lymphocyte_D7 [9031313009_H]

description:
D7
9031313009_H


title: IND 8010 d21

description: monkey no. 8010


title: Splenocytes_D10 [9031313009_F]

description:
D10
9031313009_F

value: Splenocytes


title: IND 8093 d21

description: monkey no. 8093


title: CHN 0701003 d21

description: monkey no. 701003


title: ileocecal_LN_D7 [9031313009_C]

description:
D7
9031313009_C

source_name: Subject: Monkey_5439


title: IND 7063 d21

description: monkey no. 7063


title: Blood_D7 [9031313009_L]

description:
D7
9031313009_L

tag: name used in manuscript

value: Blood

tag: subset


title: mesenteric_LN_D7 [9031313009_B]

description:
D7
9031313009_B

value: LN


title: CHN 0511009 d21

description: monkey no. 511009


title: mesenteric_LN_D7 [9031313003_L]

description:
D7
9031313003_L


title: Inguinal_LN_D7 [9031313009_D]

description:
D7
9031313009_D


title: IND 6053 d21

description: monkey no. 6053


title: CHN 0410009 d21

description: monkey no. 410009


title: IND 6053 d42

description: monkey no. 6053


title: CHN 0511007 d21

description: monkey no. 511007


title: Rectum_D10 [9031313009_G]

description:
D10
9031313009_G


title: Jejunum_D7 [9031313009_A]

description:
D7
9031313009_A

value: GI

value: Jejunum


title: CHN 0409005 d21

description: monkey no. 409005


title: Splenocytes_D7 [9031313003_K]

description:
D7
9031313003_K


title: IND 8199 d7

description: monkey no. 8199

source_name: d7 post immunization


title: IND 8081 d7

description: monkey no. 8081


title: Cervix_D10 [9031313003_J]

description:
D10
9031313003_J

value: FRT

value: Cervix


title: IND 8093 d7

description: monkey no. 8093


title: IND 6053 d7

description: monkey no. 6053


title: IND 8010 d7

description: monkey no. 8010


title: IND 7063 d7

description: monkey no. 7063


title: Thymus_D7 [9031313003_F]

description:
D7
9031313003_F

value: Thymus


title: Duodenum_D7 [9031313003_H]

description:
D7
9031313003_H


title: CHN 0511009 d7

description: monkey no. 511009

value: whole blood


title: CHN 0706009 d7

description: monkey no. 706009

value: Chinese


title: Duodenum_D7 [9031313003_D]

description:
D7
9031313003_D


title: genital_pelvic_LN_D7 [9031313003_G]

description:
D7
9031313003_G


title: Bone_Marrow_D7 [9023874014_E]

description:
D7
9023874014_E

source_name: Subject: Monkey_5358


title: CHN 0410009 d7

description: monkey no. 410009


title: CHN 0511007 d7

description: monkey no. 511007


title: CHN 0701003 d7

description: monkey no. 701003


title: Blood_D7 [9031313003_E]

description:
D7
9031313003_E


title: Colon_D10 [9021212001_L]

description:
D10
9021212001_L

value: Colon


title: CHN 0409005 d7

description: monkey no. 409005


title: IND 8093 d3

description: monkey no. 8093

source_name: d3 post immunization


title: genital_pelvic_LN_D10 [9031313003_B]

description:
D10
9031313003_B

value: SIV


title: Cervix_D7 [9021212001_J]

description:
D7
9021212001_J


title: Uterus_D10 [9031313003_C]

description:
D10
9031313003_C

value: Uterus


title: IND 8199 d3

description: monkey no. 8199

value: Indian


title: Brain_Lymphocyte_D7 [9021212001_K]

description:
D7
9021212001_K


title: Lung_D7 [9031313003_A]

description:
D7
9031313003_A

value: Lung


title: IND 8081 d3

description: monkey no. 8081


title: Mid_Vagina_D7 [9021212001_H]

description:
D7
9021212001_H


title: IND 7063 d3

description: monkey no. 7063


title: CHN 0706009 d3

description: monkey no. 706009


title: IND 8010 d3

description: monkey no. 8010


title: Cecum_D10 [9021212001_I]

description:
D10
9021212001_I

value: Cecum


title: Cervix_D7 [9021212001_G]

description:
D7
9021212001_G


title: CHN 0410009 d3

description: monkey no. 410009


title: Colon_D7 [9021212001_E]

description:
D7
9021212001_E


title: CHN 0511009 d3

description: monkey no. 511009


title: Uterus_D7 [8981245042_L]

description:
D7
8981245042_L

source_name: Subject: Monkey_5309


title: CHN 0701003 d3

description: monkey no. 701003


title: Ileum_D10 [9021212001_C]

description:
D10
9021212001_C

value: Ileum


title: IND 8093 d1

description: monkey no. 8093

source_name: d1 post immunization


title: CHN 0511007 d3

description: monkey no. 511007


title: Rectum_D7 [9021212001_F]

description:
D7
9021212001_F

value: Rectum


title: CHN 0409005 d3

description: monkey no. 409005


title: IND 6053 d3

description: monkey no. 6053


title: Lung_D7 [9021212001_D]

description:
D7
9021212001_D


title: genital_pelvic_LN_D7 [8981245042_J]

description:
D7
8981245042_J


title: IND 8199 d1

description: monkey no. 8199


title: Uterus_D7 [9021212001_A]

description:
D7
9021212001_A


title: IND 8010 d1

description: monkey no. 8010


title: pararectal_paracolonic_D7 [8981245042_H]

description:
D7
8981245042_H


title: Cecum_D7 [9021212001_B]

description:
D7
9021212001_B


title: IND 8081 d1

description: monkey no. 8081


title: Liver_D7 [8981245042_K]

description:
D7
8981245042_K

value: Liver


title: Thymus_D7 [8981245042_I]

description:
D7
8981245042_I


title: IND 7063 d1

description: monkey no. 7063


title: Colon_D7 [8981245042_G]

description:
D7
8981245042_G


title: IND 6053 d1

description: monkey no. 6053


title: CHN 0706009 d1

description: monkey no. 706009


title: CSF_D7 [8981245042_E]

description:
D7
8981245042_E

value: CSF


title: CHN 0410009 d1

description: monkey no. 410009


title: CHN 0409005 d1

description: monkey no. 409005


title: Inguinal_LN_D7 [8981245042_D]

description:
D7
8981245042_D


title: CHN 0511007 d1

description: monkey no. 511007


title: axillary_LN_D7 [8981245037_J]

description:
D7
8981245037_J

value: LN


title: CHN 0701003 d1

description: monkey no. 701003


title: mesenteric_LN_D7 [8981245042_F]

description:
D7
8981245042_F


title: Bone_Marrow_D7 [8981245037_L]

description:
D7
8981245037_L


title: Rectum_D7 [8981245037_I]

description:
D7
8981245037_I


title: Lung_D7 [8981245042_B]

description:
D7
8981245042_B


title: IND 8199 d0

description: monkey no. 8199

source_name: naive, pre-immunization d0


title: Duodenum_D7 [8981245037_K]

description:
D7
8981245037_K

value: Duodenum


title: IND 8093 d0

description: monkey no. 8093


title: IND 8010 d0

description: monkey no. 8010


title: Blood_D7 [8981245042_A]

description:
D7
8981245042_A

value: Blood


title: ileocecal_LN_D7 [8981245037_E]

description:
D7
8981245037_E


title: IND 7063 d0

description: monkey no. 7063


title: IND 6053 d0

description: monkey no. 6053


title: Splenocytes_D7 [8981245037_F]

description:
D7
8981245037_F

value: Splenocytes


title: Tonsil_D7 [8981245037_G]

description:
D7
8981245037_G

value: Tonsil


title: Brain_Lymphocyte_D7 [8981245042_C]

description:
D7
8981245042_C


title: Mid_Vagina_D7 [8981245037_D]

description:
D7
8981245037_D

value: FRT


title: Jejunum_D7 [8981245037_B]

description:
D7
8981245037_B

value: GI

value: Jejunum


title: CHN 0511009 d0

description: monkey no. 511009

value: whole blood

value: Chinese


title: CHN 0706009 d0

description: monkey no. 706009


title: Bone_Marrow_D7 [8981245022_K]

description:
D7
8981245022_K

source_name: Subject: Monkey_5307

value: SIV


title: Cervix_D7 [8981245037_H]

description:
D7
8981245037_H

value: Cervix


title: Ileum_D7 [8981245037_C]

description:
D7
8981245037_C


title: Cecum_D7 [8981245037_A]

description:
D7
8981245037_A

value: Cecum


title: CHN 0701003 d0

description: monkey no. 701003


title: IND 8099 d-14

description: monkey no. 8099

source_name: naive, pre-immunization d-14

value: Indian


title: Tonsil_D7 [8981245022_I]

description:
D7
8981245022_I


title: Liver_D7 [8981245022_L]

description:
D7
8981245022_L


title: IND 8081 d-14

description: monkey no. 8081


title: CHN 0409005 d0

description: monkey no. 409005


title: mesenteric_LN_D7 [8981245022_F]

description:
D7
8981245022_F


title: Jejunum_D7 [8981245022_J]

description:
D7
8981245022_J


title: IND 8093 d-14

description: monkey no. 8093


title: IND 6053 d-14

description: monkey no. 6053


title: CHN 0511007 d0

description: monkey no. 511007


title: pararectal_paracolonic_D7 [8981245022_H]

description:
D7
8981245022_H


title: IND 8010 d-14

description: monkey no. 8010


title: CHN 0706009 d-14

description: monkey no. 706009


title: CHN 0410009 d0

description: monkey no. 410009


title: IND 7063 d-14

description: monkey no. 7063


title: CHN 0701003 d-14

description: monkey no. 701003


title: Cecum_D7 [8981245022_E]

description:
D7
8981245022_E


title: ileocecal_LN_D7 [8981245022_C]

description:
D7
8981245022_C


title: CHN 0410009 d-14

description: monkey no. 410009


title: CHN 0511009 d-14

description: monkey no. 511009


title: CHN 0409005 d-14

description: monkey no. 409005


title: Brain_Lymphocyte_D7 [8981245022_A]

description:
D7
8981245022_A


title: Cecum_D7 [8981245021_L]

description:
D7
8981245021_L

source_name: Subject: Monkey_5319


title: Cervix_D7 [8981245022_G]

description:
D7
8981245022_G


title: Inguinal_LN_D7 [8981245021_H]

description:
D7
8981245021_H


title: genital_pelvic_LN_D7 [8981245021_K]

description:
D7
8981245021_K


title: CHN 0511007 d-14

description: monkey no. 511007


title: ileocecal_LN_D7 [8981245021_E]

description:
D7
8981245021_E


title: genital_pelvic_LN_D7 [8981245022_D]

description:
D7
8981245022_D


title: Rectum_D7 [8981245021_J]

description:
D7
8981245021_J

value: Rectum


title: Bone_Marrow_D7 [8981245021_I]

description:
D7
8981245021_I


title: Duodenum_D7 [8981245021_C]

description:
D7
8981245021_C


title: Colon_D7 [8981245021_D]

description:
D7
8981245021_D

value: Colon


title: Splenocytes_D7 [8981245021_B]

description:
D7
8981245021_B


title: JAR Romidepsin 16h

type: genomic

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Universitätsstr. 1

department: Urology

institute: University Hospital Düsseldorf

description: JAR treated with Romidepsin for 16h

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: A subset quantile normalization approach developed by N. Touleimat & J. Tost was applied (Touleimat, Tost, 2012, Pubmed ID: 22690668 ). This processing pipeline includes signal correction for the adjustment of the color balance and background level correction as well as the Infinium I/Infinium II shift correction between sample normalization. Technical quality parameters such as hybridization, extension, bisulfite conversion and specificity were evaluated using the ‚Genome Studio’ software. Beta-value signal distributions were inspected by density plots. Data was analysed using ‚Bioconductor R’ (http://www.bioconductor.org). To increase performance in terms of detection and true positive rate of highly methylated and unmethylated CpG-sites, beta-values were transformed to M-values (Du et al., 2010, Pubmed ID: 21118553)

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Choriocarcinoma-like cell line

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

extract_protocol:
Genomic DNA was isolated by phenol / chloroform / isoamylalcohol isolation as published (Nettersheim et al., 2015, Pubmed ID: 26226633). Quality was checked by Agilent Bioanalyser.
Bisulfite convesion: Genomic DNA was bisulfite converted using the EZ DNA methylation kit according to the manual (Zymo Research) and as published (Nettersheim et al., 2015, Pubmed ID: 26226633)
Cultivation protocol: TCam-2, 2102P, NCCIT and JAR cells were cultivated as published (Nettersheim et al., 2015, PubMed ID: 26226633)

tag: cell line

value: JAR


title: Thymus_D7 [8981245021_F]

description:
D7
8981245021_F

value: Thymus


title: Blood_D7 [8981245021_A]

description:
D7
8981245021_A


title: NCCIT Romidepsin 16h

description: NCCIT treated with Romidepsin for 16h

source_name: Embryonal carcinoma-like cell line

value: NCCIT


title: 2102EP Romidepsin 16h

description: 2102EP treated with Romidepsin for 16h


title: Inguinal_LN_D7 [8981245020_L]

description:
D7
8981245020_L


title: NCCIT Solvent 16h

description: NCCIT treated with DMSO for 16h


title: axillary_LN_D7 [8981245020_K]

description:
D7
8981245020_K

value: LN


title: Colon_D7 [8981245020_J]

description:
D7
8981245020_J


title: JAR Solvent 16h

description: JAR treated with DMSO for 16h


title: Duodenum_D7 [8981245020_I]

description:
D7
8981245020_I

value: Duodenum


title: TCam-2 Romidepsin 16h

description: TCam-2 treated with Romidepsin for 16h

source_name: Seminoma-like cell line


title: TCam-2 Solvent 16h

description: TCam-2 treated with DMSO for 16h


title: Thymus_D7 [8981245020_G]

description:
D7
8981245020_G


title: 2102EP Solvent 16h

description: 2102EP treated with DMSO for 16h


title: Uterus_D7 [8981245020_F]

description:
D7
8981245020_F

value: Uterus


title: Lung_D7 [8981245020_E]

description:
D7
8981245020_E

value: Lung


title: Ileum_D7 [8981245020_D]

description:
D7
8981245020_D

value: Ileum


title: Brain_Lymphocyte_D7 [8981245016_L]

description:
D7
8981245016_L


title: Blood_D7 [8981245020_C]

description:
D7
8981245020_C

value: Blood


title: mesenteric_LN_D7 [8981245016_H]

description:
D7
8981245016_H


title: Splenocytes_D7 [8981245020_A]

description:
D7
8981245020_A

value: Splenocytes


title: axillary_LN_D7 [8981245016_I]

description:
D7
8981245016_I


title: Haplogroup E1b1a1 sample 3

city: Los Angeles

first: Minjie

last: Zhang

state: CA

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences

institute: University of Southern California

description:
normal blood sample
F6

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudio Software
Unmethylated and methylated signal intensities in signal_intensities.txt

label: Cy5 and Cy3

source_name: whole blood 72

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from the whole blood using a QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany).

value: whole blood

tag: y haplotype

value: Haplogroup E1b1a1

tag: origin

value: Nigeria

tag: family relationship

tag: gender

value: Male

tag: disease state

value: Normal


title: Cervix_D7 [8981245016_J]

description:
D7
8981245016_J

value: FRT

value: Cervix

value: SIV


title: Tonsil_D7 [8981245016_K]

description:
D7
8981245016_K

value: Tonsil


title: Haplogroup O3a2c1* sample 3

description:
normal blood sample
513

source_name: whole blood 68

value: Haplogroup O3a2c1*

value: Nankang, China


title: Mid_Vagina_D7 [8981245016_G]

description:
D7
8981245016_G


title: Lung_D7 [8981245016_F]

description:
D7
8981245016_F


title: Haplogroup E1b1a1 sample 4

description:
normal blood sample
F7

source_name: whole blood 73


title: Haplogroup E1b1a1 sample 5

description:
normal blood sample
F24

source_name: whole blood 74


title: IND 8081 d0

description: monkey no. 8081

value: Indian


title: Haplogroup E1b1a1 sample 1

description:
normal blood sample
F1

source_name: whole blood 70


title: Haplogroup E1b1a1 sample 2

description:
normal blood sample
F4

source_name: whole blood 71


title: Ileum_D7 [8981245016_D]

description:
D7
8981245016_D


title: Haplogroup O3a2c1* sample 4

description:
normal blood sample
518

source_name: whole blood 69

value: Zhenhai, China


title: Haplogroup O3a2c1a sample 7

description:
normal blood sample
447

source_name: whole blood 63

value: Haplogroup O3a2c1a

value: Ningde, China


title: genital_pelvic_LN_D7 [8909358294_L]

description:
D7
8909358294_L

source_name: Subject: Monkey_5355

value: LN


title: Haplogroup O3a2c1a sample 8

description:
normal blood sample
450

source_name: whole blood 64

value: Pizhou, China


title: Haplogroup O3a2c1a sample 5

description:
normal blood sample
LACB0902

source_name: whole blood 61

value: whole blood

value: Shanxi, China


title: Fibroblast cell line F3, cell 21, sister cell 1

city: Leuven

first: Eftychia

last: Dimitriadou

address: Herestraat 49, ON1, bus 602

country: Belgium

institute: KU Leuven

description:
Sureplex whole genome amplified single-cell DNA
157

hyb_protocol: 200 ng of sample DNA and equal amount of commercially available reference DNA of the were labeled for 2 h by random primer labeling (BlueGnome/Illumina, USA) using Cy5- and Cy3-dCTPs, respectively.

scan_protocol: DNA-microarray scanner (Agilent Technologies, UK).

data_processing: Separation of the duplex raw images by ImageViewer and the analysis of the data by BlueFuse v3.0 software (BlueGnome/Illumina, USA).

source_name: Reference DNA

label_protocol: The fluorescent labeling system (BlueGnome/Illumina) was used for sample labeling. Samples and Reference DNAs were labeled using Cy5 or Cy3 for 2-4h at 37░C. Samples were combined with the respective references prior to hybridization.

growth_protocol: Primary fibroblasts were grown in 75-cm2 plastic flasks (BD Falcon, USA) under standard culture conditions in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium complemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA).

extract_protocol: The genome of collected single cells was amplified using the Sureplex amplification system (BlueGnome/Illumina, USA).

treatment_protocol: Single fibroblasts were plated separately and the two cells that derived following a cell division were isolated individually.

tag: sample type

value: reference

source_name: Primary single fibroblast, F3

tag: cell type

value: primary single fibroblast

value: Female


title: Uterus_D7 [8909358294_I]

description:
D7
8909358294_I

source_name: Subject: Monkey_5442

value: Uterus


title: Haplogroup O3a2c1a sample 3

description:
normal blood sample
JB3-Rep2

source_name: whole blood 59

value: Yiwu, China

value: Male

value: Normal


title: Haplogroup O3a2c1a sample 2

description:
normal blood sample
JB4-Rep1

source_name: whole blood 58


title: Haplogroup O3a2c1a sample 1

description:
normal blood sample
JB3-Rep1

source_name: whole blood 57


title: Haplogroup O3a2c1* sample 2

description:
normal blood sample
494

source_name: whole blood 67

value: Haplogroup O3a2c1*

value: Changchun, China


title: Haplogroup O3a2b sample 11

description:
normal blood sample
108

source_name: whole blood 54

value: Haplogroup O3a2b

value: Mashan, China


title: Haplogroup O3a2c1a sample 6

description:
normal blood sample
429

source_name: whole blood 62

value: Haplogroup O3a2c1a

value: Beijing, China


title: Fibroblast cell line F3, cell 19, sister cell 2

description:
Sureplex whole genome amplified single-cell DNA
130


title: Haplogroup O3a2c1* sample 1

description:
normal blood sample
BO003

source_name: whole blood 66

value: Anhui, China


title: Blood_D10 [8909358294_K]

description:
D10
8909358294_K

source_name: Subject: Monkey_5441

value: Blood

value: SIV


title: Haplogroup O3a2c1a sample 4

description:
normal blood sample
JB4-Rep2

source_name: whole blood 60

value: whole blood


title: Fibroblast cell line F3, cell 20, sister cell 1

value: reference


title: Liver_D7 [8981245016_E]

description:
D7
8981245016_E

source_name: Subject: Monkey_5319

value: Liver


title: Haplogroup O3a2c1a sample 9

description:
normal blood sample
471

source_name: whole blood 65


title: genital_pelvic_LN_D10 [8909358294_G]

description:
D10
8909358294_G

source_name: Subject: Monkey_5443

value: LN


title: Blood_D7 [8909358294_F]

description:
D7
8909358294_F


title: Fibroblast cell line F3, cell 18, sister cell 1

description:
Sureplex whole genome amplified single-cell DNA
131

value: primary single fibroblast

value: Female


title: Fibroblast cell line F3, cell 21, sister cell 2

value: Male


title: Fibroblast cell line F3, cell 18, sister cell 2


title: Fibroblast cell line F3, cell 19, sister cell 1


title: Fibroblast cell line F3, cell 17, sister cell 2


title: Haplogroup O3a2b sample 12

description:
normal blood sample
158

source_name: whole blood 55

value: Jishui, China

value: Normal


title: Fibroblast cell line F3, cell 17, sister cell 1


title: Fibroblast cell line F3, cell 12, sister cell 2


title: Haplogroup O3a2b sample 9

description:
normal blood sample
71

source_name: whole blood 52

value: Liaoyang, China


title: Haplogroup O3a2c* sample 1

description:
normal blood sample
QA6

source_name: whole blood 56

value: Haplogroup O3a2c*


title: Tonsil_D10 [8909358294_D]

description:
D10
8909358294_D

value: Tonsil


title: Haplogroup O3a2b sample 10

description:
normal blood sample
93

source_name: whole blood 53

value: Haplogroup O3a2b

value: Changchun, China


title: Fibroblast cell line F3, cell 12, sister cell 1

source_name: Reference DNA

source_name: Primary single fibroblast, F3


title: Fibroblast cell line F3, cell 11, sister cell 1


title: Haplogroup O3a2b sample 6

description:
normal blood sample
XB2

source_name: whole blood 49

value: She county, China


title: Haplogroup O3a2b sample 8

description:
normal blood sample
JF3

source_name: whole blood 51

value: Tonglu, China


title: Fibroblast cell line F3, cell 11, sister cell 2


title: Haplogroup O3a2b sample 7

description:
normal blood sample
JC5

source_name: whole blood 50

value: Jindong, China


title: Colon_D10 [8909358294_C]

description:
D10
8909358294_C

value: Colon

value: SIV


title: Fibroblast cell line F3, cell 8, sister cell 2

value: reference


title: Fibroblast cell line F3, cell 7, sister cell 2


title: Fibroblast cell line F3, cell 20, sister cell 2


title: Fibroblast cell line F3, cell 8, sister cell 1


title: Haplogroup O3a2b sample 5

description:
normal blood sample
XB0

source_name: whole blood 48

value: whole blood


title: Fibroblast cell line F3, cell 7, sister cell 1

value: primary single fibroblast


title: Fibroblast cell line F3, cell 6, sister cell 2

value: Female


title: Haplogroup O3a2b sample 4

description:
normal blood sample
XA7

source_name: whole blood 47

value: Male


title: pararectal_paracolonic_D7 [8981245016_A]

description:
D7
8981245016_A


title: Jejunum_D7 [8981245016_C]

description:
D7
8981245016_C

value: GI

value: Jejunum


title: Fibroblast cell line F3, cell 6, sister cell 1


title: mesenteric_LN_D10 [8909358279_L]

description:
D10
8909358279_L

value: LN


title: ileocecal_LN_D10 [8909358294_B]

description:
D10
8909358294_B


title: Fibroblast cell line F3, cell 4, sister cell 2


title: Liver_D10 [8909358294_A]

description:
D10
8909358294_A

value: Liver


title: Fibroblast cell line F3, cell 2, sister cell 2

description:
Sureplex whole genome amplified single-cell DNA
117


title: Fibroblast cell line F3, cell 4, sister cell 1


title: Fibroblast cell line F3, cell 2, sister cell 1


title: Haplogroup O3a2b sample 3

description:
normal blood sample
XA3

source_name: whole blood 46

value: Normal


title: Jejunum_D7 [8909358279_K]

description:
D7
8909358279_K

source_name: Subject: Monkey_5355


title: Fibroblast cell line F3, cell 1, sister cell 1


title: Splenocytes_D10 [8909358279_I]

description:
D10
8909358279_I

source_name: Subject: Monkey_5441

value: Splenocytes


title: Fibroblast cell line F2, cell 61, sister cell 1

source_name: Primary single fibroblast, F2


title: Fibroblast cell line F2, cell 61, sister cell 2


title: Haplogroup O3a2b sample 2

description:
normal blood sample
JF2

source_name: whole blood 45

value: Haplogroup O3a2b


title: Fibroblast cell line F3, cell 1, sister cell 2


title: ileocecal_LN_D7 [8909358294_E]

description:
D7
8909358294_E


title: Haplogroup O3a1c2a3 sample 2

description:
normal blood sample
460

source_name: whole blood 43

value: Haplogroup O3a1c2a3

value: Liaoning, China


title: genital_pelvic_LN_D10 [8909358279_J]

description:
D10
8909358279_J


title: Fibroblast cell line F2, cell 58, sister cell 1


title: Fibroblast cell line F2, cell 57, sister cell 2


title: Fibroblast cell line F2, cell 57, sister cell 1


title: Fibroblast cell line F2, cell 56, sister cell 2


title: Jejunum_D10 [8909358279_G]

description:
D10
8909358279_G


title: Duodenum_D10 [8909358279_F]

description:
D10
8909358279_F

source_name: Subject: Monkey_5443

value: Duodenum


title: Fibroblast cell line F2, cell 58, sister cell 2


title: Fibroblast cell line F2, cell 56, sister cell 1


title: Haplogroup O3a2b sample 1

description:
normal blood sample
JF1

source_name: whole blood 44

value: Tonglu, China


title: Haplogroup O3a1c2a3 sample 1

description:
normal blood sample
453

source_name: whole blood 42


title: Fibroblast cell line F2, cell 55, sister cell 2


title: Inguinal_LN_D10 [8909358279_H]

description:
D10
8909358279_H

value: SIV


title: Inguinal_LN_D10 [8909358279_C]

description:
D10
8909358279_C


title: Haplogroup O3a1c2a* sample 3

description:
normal blood sample
479

source_name: whole blood 40

value: Haplogroup O3a1c2a*

value: Tangshan, China


title: Fibroblast cell line F2, cell 54, sister cell 1

source_name: Reference DNA

value: reference

value: primary single fibroblast


title: Thymus_D7 [8909358279_D]

description:
D7
8909358279_D

value: Thymus


title: Haplogroup O3a1c2a* sample 4

description:
normal blood sample
425

source_name: whole blood 41

value: whole blood

value: Male


title: Fibroblast cell line F2, cell 54, sister cell 2

value: Female


title: Fibroblast cell line F2, cell 53, sister cell 2


title: Haplogroup O3a1c2a* sample 1

description:
normal blood sample
DA8

source_name: whole blood 38

value: Dayu, China


title: axillary_LN_D10 [8909358279_B]

description:
D10
8909358279_B

value: LN


title: Haplogroup O3a1c1* sample 2

description:
normal blood sample
HA5

source_name: whole blood 36

value: Haplogroup O3a1c1*

value: Caolou, China

value: Normal


title: Fibroblast cell line F2, cell 55, sister cell 1


title: Fibroblast cell line F2, cell 52, sister cell 1


title: Fibroblast cell line F2, cell 49, sister cell 2


title: Haplogroup O3a1c1* sample 3

description:
normal blood sample
254

source_name: whole blood 37

value: Guoyang, China


title: Haplogroup O3a1c2a* sample 2

description:
normal blood sample
DB5

source_name: whole blood 39


title: Fibroblast cell line F2, cell 51, sister cell 1


title: Fibroblast cell line F2, cell 51, sister cell 2


title: Fibroblast cell line F2, cell 49, sister cell 1


title: Uterus_D10 [8909358279_A]

description:
D10
8909358279_A

value: FRT

value: Uterus


title: Fibroblast cell line F2, cell 52, sister cell 2


title: Haplogroup O3a1c1* sample 1

description:
normal blood sample
HA4

source_name: whole blood 35


title: Mid_Vagina_D10 [8909358275_I]

description:
D10
8909358275_I

value: SIV


title: Fibroblast cell line F2, cell 48, sister cell 2


title: Rectum_D7 [8909358275_L]

description:
D7
8909358275_L

value: Rectum


title: Liver_D7 [8909358275_K]

description:
D7
8909358275_K

source_name: Subject: Monkey_5442

value: Liver


title: Fibroblast cell line F2, cell 53, sister cell 1

value: reference


title: Fibroblast cell line F2, cell 43, sister cell 2

value: primary single fibroblast


title: Haplogroup O3a1c sample 2

description:
normal blood sample
BO120

source_name: whole blood 32

value: Haplogroup O3a1c

value: Anhui, China


title: Haplogroup O3a1c1a sample 2

description:
normal blood sample
352

source_name: whole blood 34

value: whole blood

value: Haplogroup O3a1c1a

value: Baoding, China

value: Male


title: Fibroblast cell line F2, cell 48, sister cell 1

value: Female

source_name: Primary single fibroblast, F2


title: Fibroblast cell line F2, cell 43, sister cell 1


title: Fibroblast cell line F2, cell 3, sister cell 1


title: Fibroblast cell line F2, cell 3, sister cell 2


title: Fibroblast cell line F2, cell 40, sister cell 2


title: pararectal_paracolonic_D10 [8909358275_H]

description:
D10
8909358275_H


title: Brain_Lymphocyte_D10 [8909358275_F]

description:
D10
8909358275_F

source_name: Subject: Monkey_5441


title: Haplogroup O3a1c1a sample 1

description:
normal blood sample
351

source_name: whole blood 33

value: Zhuji, China


title: Fibroblast cell line F1, cell 20, sister cell 1

source_name: Primary single fibroblast, F1


title: Fibroblast cell line F1, cell 20, sister cell 2


title: Haplogroup O3a1c sample 1

description:
normal blood sample
LAD30601

source_name: whole blood 31

value: Yiwu, China

value: Normal


title: Fibroblast cell line F1, cell 19, sister cell 2


title: Liver_D7 [8909358275_D]

description:
D7
8909358275_D

source_name: Subject: Monkey_5355


title: mesenteric_LN_D10 [8909358275_G]

description:
D10
8909358275_G

source_name: Subject: Monkey_5443

value: LN


title: Jejunum_D7 [8909358275_C]

description:
D7
8909358275_C

value: GI

value: Jejunum


title: Haplogroup O1a1 sample 2

description:
normal blood sample
XA2

source_name: whole blood 30

value: Haplogroup O1a1

value: She county, China


title: Haplogroup O2* sample 27

description:
normal blood sample
SF01

source_name: whole blood 27

value: Haplogroup O2*

value: Shucheng, China


title: Fibroblast cell line F1, cell 18, sister cell 2

source_name: Reference DNA

value: reference

value: primary single fibroblast


title: mesenteric_LN_D7 [8909358275_J]

description:
D7
8909358275_J

value: SIV


title: Fibroblast cell line F1, cell 19, sister cell 1


title: Fibroblast cell line F1, cell 17, sister cell 1


title: Fibroblast cell line F1, cell 18, sister cell 1


title: Haplogroup O2* sample 28

description:
normal blood sample
SF91

source_name: whole blood 28

value: whole blood


title: Haplogroup O1a1 sample 1

description:
normal blood sample
XA1

source_name: whole blood 29


title: Fibroblast cell line F1, cell 17, sister cell 2


title: Fibroblast cell line F1, cell 16, sister cell 2


title: Fibroblast cell line F1, cell 16, sister cell 1


title: ileocecal_LN_D7 [8909358264_L]

description:
D7
8909358264_L


title: Colon_D7 [8909358275_A]

description:
D7
8909358275_A

value: Colon


title: Fibroblast cell line F1, cell 15, sister cell 2

value: Male


title: Cervix_D7 [8909358264_K]

description:
D7
8909358264_K

value: FRT

value: Cervix


title: Fibroblast cell line F1, cell 13, sister cell 2

value: Female


title: Fibroblast cell line F1, cell 15, sister cell 1


title: Inguinal_LN_D7 [8909358264_J]

description:
D7
8909358264_J


title: Fibroblast cell line F1, cell 13, sister cell 1


title: Fibroblast cell line F2, cell 40, sister cell 1


title: Haplogroup O2* sample 25

description:
normal blood sample
SE61

source_name: whole blood 25

value: Normal


title: Fibroblast cell line F1, cell 12, sister cell 1


title: Fibroblast cell line F1, cell 12, sister cell 2


title: Ileum_D7 [8909358264_H]

description:
D7
8909358264_H

value: Ileum


title: Haplogroup O2* sample 26

description:
normal blood sample
SE81

source_name: whole blood 26


title: Fibroblast cell line F1, cell 11, sister cell 2


title: Fibroblast cell line F1, cell 9, sister cell 2


title: Haplogroup O2* sample 24

description:
normal blood sample
SE51

source_name: whole blood 24


title: Haplogroup O2* sample 23

description:
normal blood sample
243

source_name: whole blood 23

value: Yancheng, China


title: Haplogroup O2* sample 22

description:
normal blood sample
235

source_name: whole blood 22

value: Xuwen, China


title: Fibroblast cell line F1, cell 9, sister cell 1


title: Fibroblast cell line F1, cell 11, sister cell 1


title: Ileum_D7 [8909358264_F]

description:
D7
8909358264_F

source_name: Subject: Monkey_5442


title: Haplogroup O2* sample 21

description:
normal blood sample
225

source_name: whole blood 21

value: Donggang, China


title: Uterus_D7 [8909358264_G]

description:
D7
8909358264_G

value: Uterus


title: Fibroblast cell line F1, cell 3, sister cell 2


title: Fibroblast cell line F1, cell 3, sister cell 1


title: Fibroblast cell line F1, cell 2, sister cell 1


title: mesenteric_LN_D7 [8909358264_E]

description:
D7
8909358264_E

value: LN


title: Brain_Lymphocyte_D7 [8909358264_B]

description:
D7
8909358264_B


title: Fibroblast cell line F1, cell 2, sister cell 2


title: Haplogroup O2* sample 19

description:
normal blood sample
XC4

source_name: whole blood 19

value: Haplogroup O2*

value: Jixi, China


title: pararectal_paracolonic_D7 [8909358264_D]

description:
D7
8909358264_D


title: Haplogroup O2* sample 20

description:
normal blood sample
XC5

source_name: whole blood 20


title: genital_pelvic_LN_D7 [8909358275_B]

description:
D7
8909358275_B


title: Haplogroup O2* sample 18

description:
normal blood sample
XC1

source_name: whole blood 18


title: Splenocytes_D7 [8909358261_L]

description:
D7
8909358261_L

source_name: Subject: Monkey_5355

value: Splenocytes


title: Wild type

city: Shanghai

first: Chengwen

last: Chen

address: No. 250 Bibo Road

country: China

institute: CHGC

description: Gene expression  at 72 hpf after 1hr heat-shock at 38°C wild type zebrafish embryos

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent zebrafish V3Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were processed using Feature Extraction software(Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Danio rerio

source_name: wild type, Total RNAs, 72hr, replicate 1

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.

growth_protocol: zebrafish strain was maintained at 28.5°C. Developmental stages refer to hours (hpf) or days (dpf) post-fertilization.

extract_protocol: Total RNAs were isolated with Trizol (Invitrogen).

treatment_protocol: Fertilized wild type (WT) AB fish eggs were microinjected through the chorion into the cytoplasm at the one-cell stage of development. The pSGH2-hRUNX1-Evi-1 plasmid was co-injected with I-SceI meganuclease enzyme (0.5units/μL) (New England Bio Labs). A pressure injector (IM-300, NARISHIGE) was used with borosilicate glass capillaries. After injection, the embryos were collected in Petri dishes and incubated at 28°C. Heat shock was executed at 38°C for 1 hour at between 14 to 18 hpf to induce EGFP and RUNX1-Evi-1 expression. EGFP+ fish were screened under the fluorescent microscope on the next day and bred up to sexual maturity, then crossed with the WT AB fish. The transgenetic (Tg) offspring also received heat shock for an hour to induce the target genes expression.

tag: genotype/variation

value: wild type AB

tag: Stage

value: embryo


title: Tg(RE:HSE:EGFP)

description: Gene expression at 72 hpf after 1hr heat-shock at 38°C Tg(RE:HSE:EGFP) zebrafish embryos

source_name: Tg(RE:HSE:EGFP), Total RNAs, 72hr, replicate 1

value: Tg(RE:HSE:EGFP) AB


title: Lung_D10 [8909358261_J]

description:
D10
8909358261_J

source_name: Subject: Monkey_5443

value: Lung

value: SIV


title: Haplogroup O2* sample 17

description:
normal blood sample
TA5

source_name: whole blood 17

value: whole blood

value: Tieling, China

value: Male


title: Thymus_D7 [8909358261_I]

description:
D7
8909358261_I

value: Thymus


title: axillary_LN_D10 [8909358264_A]

description:
D10
8909358264_A

source_name: Subject: Monkey_5441


title: Blood_D10 [8909358261_F]

description:
D10
8909358261_F

value: Blood


title: Haplogroup O2* sample 16

description:
normal blood sample
TA4

source_name: whole blood 16

value: Normal


title: Haplogroup O2* sample 15

description:
normal blood sample
TA3

source_name: whole blood 15


title: Brain_Lymphocyte_D7 [8909358261_H]

description:
D7
8909358261_H


title: Thymus_D10 [8909358261_E]

description:
D10
8909358261_E


title: Haplogroup O2* sample 11

description:
normal blood sample
RS3-3

source_name: whole blood 11

value: Rushan, China

value: Family 3 (son)


title: axillary_LN_D7 [8909358261_C]

description:
D7
8909358261_C

value: LN


title: Ileum_D10 [8909358261_D]

description:
D10
8909358261_D

value: Ileum


title: Ileum_D10 [8909358241_J]

description:
D10
8909358241_J


title: Haplogroup O2* sample 13

description:
normal blood sample
TA1

source_name: whole blood 13

value: Haplogroup O2*


title: Haplogroup O2* sample 12

description:
normal blood sample
RS4

source_name: whole blood 12


title: Haplogroup O2* sample 14

description:
normal blood sample
TA2

source_name: whole blood 14


title: Haplogroup O2* sample 10

description:
normal blood sample
RS3-2

source_name: whole blood 10

value: Family 3 (father)


title: Colon_D10 [8909358261_A]

description:
D10
8909358261_A

value: Colon


title: Blood_D7 [8909358241_F]

description:
D7
8909358241_F


title: Cervix_D7 [8909358241_D]

description:
D7
8909358241_D

source_name: Subject: Monkey_5442

value: FRT

value: Cervix


title: Haplogroup O2* sample 8

description:
normal blood sample
RS2-3

source_name: whole blood 8

value: Family 2 (son)


title: Thymus_D10 [8909358241_I]

description:
D10
8909358241_I

value: SIV


title: Inguinal_LN_D7 [8909358261_B]

description:
D7
8909358261_B


title: Lung_D7 [8909358241_C]

description:
D7
8909358241_C

value: Lung


title: Rectum_D10 [8909358241_G]

description:
D10
8909358241_G

value: Rectum


title: Haplogroup O2* sample 5

description:
normal blood sample
RS1-5

source_name: whole blood 5

value: whole blood

value: Family 1 (son)

value: Male


title: Splenocytes_D10 [8909358241_B]

description:
D10
8909358241_B

value: Splenocytes


title: Duodenum_D7 [8909358241_A]

description:
D7
8909358241_A

value: Duodenum


title: Haplogroup O2* sample 9

description:
normal blood sample
RS3-1

source_name: whole blood 9

value: Rushan, China

value: Family 3 (grandfather)

value: Normal


title: Haplogroup O2* sample 7

description:
normal blood sample
RS2-2

source_name: whole blood 7

value: Haplogroup O2*


title: Mid_Vagina_D7 [8909358129_L]

description:
D7
8909358129_L

source_name: Subject: Monkey_5354


title: endometrium in the proliferative phase_C2

city: Beijing

first: fa

middle: jian

last: jiang

address: Dongcheng District, Shuaifuyuan NO.1

department: Obstetrics and Gynecology

institute: Peking Union Medical College Hospital

hyb_protocol: Following fragmentation, 20 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Genechip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: normal endometrium in the proliferative phase

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: female

tag: age

value: 39 years old

value: control

value: endometrium

tag: tissue phase

value: proliferative


title: endometrium in the proliferative phase_C3

value: 47 years old

tag: tissue


title: endometrium in the secretory phase_C4

source_name: normal endometrium in the secretory phase

value: 51 years old

value: secretory


title: Haplogroup O2* sample 3

description:
normal blood sample
RS1-3

source_name: whole blood 3

value: whole blood

value: Family 1 (uncle)


title: Haplogroup O2* sample 4

description:
normal blood sample
RS1-4

source_name: whole blood 4

value: Male


title: endometrium in the secretory phase_C1

value: 42 years old


title: RBH049 9611518137_R03C02

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol, iScan

data_processing: Methylation data was background subtracted in GenomeStudio and normalized by beta-mixture quantile (BMIQ) normalization to adjust for the type II bias. Normalization was done using the waterRmelon Bioconductor R package (Pidsley R, CC YW, Volta M, Lunnon K, Mill J, Schalkwyk LC. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC genomics. 2013;14:293)

label: Cy3 and Cy5

source_name: Tumour

label_protocol: standard Illumina protocol

extract_protocol: Most DNA extractions were performed via the phenol-chloroform-isoamyl alcohol method [Maniatis T, Fritsch E, Sambrook J. Molecular cloning: A laboratory manual] a small set of 22 tumors/matched normal DNA was extracted AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA).

value: Tumour


title: PAH046 9611518137_R06C01


title: endometrium in the secretory phase_A3

source_name: eutopic endometrium in the secretory phase of adenomyosis

value: 41 years old

value: adenomyosis


title: PAH059 9611518137_R04C01

source_name: Normal

value: Normal


title: Cecum_D3 [8909358129_K]

description:
D3
8909358129_K

source_name: Subject: Monkey_5348

value: Cecum

value: SIV


title: JHH050 9611518137_R04C02


title: RBH058 9611518137_R03C01


title: Rectum_D7 [8909358129_J]

description:
D7
8909358129_J

value: Rectum


title: Duodenum_D7 [8909358129_H]

description:
D7
8909358129_H

source_name: Subject: Monkey_5353

value: GI

value: Duodenum


title: endometrium in the secretory phase_A2

value: female

value: 43 years old

value: endometrium


title: endometrium in the proliferative phase_A4

source_name: eutopic endometrium in the proliferative phase of adenomyosis

value: 50 years old

value: proliferative


title: 1417 9611518137_R05C02


title: Haplogroup O2* sample 1

description:
normal blood sample
RS1-1

source_name: whole blood 1

value: whole blood

value: Haplogroup O2*

value: Rushan, China

value: Family 1 (grandfather)


title: endometrium in the proliferative phase_A1

value: 44 years old


title: Thymus_D7 [8909358129_I]

description:
D7
8909358129_I

value: Thymus


title: Haplogroup O2* sample 2

description:
normal blood sample
RS1-2

source_name: whole blood 2

value: Family 1 (father)

value: Male

value: Normal


title: PAH053 9611518137_R01C01


title: Lung_D7 [8909358129_G]

description:
D7
8909358129_G

source_name: Subject: Monkey_5358

value: Lung

value: SIV


title: PAH052 9611518135_R06C02


title: Haplogroup O2* sample 6

description:
normal blood sample
RS2-1

source_name: whole blood 6

value: Family 2 (father)


title: genital_pelvic_LN_D7 [8909358129_E]

description:
D7
8909358129_E

value: LN


title: 1417 9611518137_R06C02

value: Tumour


title: RBH058 9611518137_R01C02


title: Inguinal_LN_D3 [8909358129_F]

description:
D3
8909358129_F


title: Blood_D7 [8909358129_B]

description:
D7
8909358129_B

value: Blood


title: JHH050 9611518135_R05C02


title: Brain_lymphocytes_D7 [8909358129_A]

description:
D7
8909358129_A


title: genital_pelvic_LN_D7 [8909358125_K]

description:
D7
8909358125_K


title: Ileum_D7 [8909358125_I]

description:
D7
8909358125_I

value: Ileum


title: PAH055 9611518137_R02C01


title: pararectal_paracolonic_D7 [8909358125_L]

description:
D7
8909358125_L


title: PAH044 9611518135_R06C01


title: axillary_LN_D3 [8909358125_J]

description:
D3
8909358125_J


title: PAH041 9611518135_R05C01


title: RBH049 9611518135_R04C02


title: PAH036 9611518135_R03C01


title: PAH040 9611518135_R04C01


title: Cervix_D3 [8909358129_D]

description:
D3
8909358129_D

value: FRT

value: Cervix


title: PAH018 9611518135_R01C01


title: 2291 7539308158_R06C02


title: Ileum_D7 [8909358125_B]

description:
D7
8909358125_B


title: JHH047 9611518135_R02C02


title: Thymus_D7 [8909358125_G]

description:
D7
8909358125_G


title: PAH046 9611518135_R01C02


title: Colon_D7 [8909358026_L]

description:
D7
8909358026_L

source_name: Subject: Monkey_5070

value: Colon


title: Bone_Marrow_D7 [8909358125_H]

description:
D7
8909358125_H


title: Splenocytes_D7 [8909358125_E]

description:
D7
8909358125_E

value: Splenocytes


title: Colon_D7 [8909358125_F]

description:
D7
8909358125_F


title: axillary_LN_D7 [8909358026_K]

description:
D7
8909358026_K


title: Bone_Marrow_D3 [8909358129_C]

description:
D3
8909358129_C


title: Thymus_D7 [8909358125_D]

description:
D7
8909358125_D


title: Splenocytes_D7 [8909358026_J]

description:
D7
8909358026_J


title: Inguinal_LN_D7 [8909358125_A]

description:
D7
8909358125_A


title: pararectal_paracolonic_D10 [8909358026_I]

description:
D10
8909358026_I

source_name: Subject: Monkey_5083


title: axillary_LN_D7 [8909358026_F]

description:
D7
8909358026_F

source_name: Subject: Monkey_5074


title: Inguinal_LN_D7 [8909358026_D]

description:
D7
8909358026_D


title: Rectum_D10 [8909358026_H]

description:
D10
8909358026_H

value: Rectum


title: mesenteric_LN_D7 [8909358026_E]

description:
D7
8909358026_E


title: 40335 7539308158_R06C01

source_name: BE

value: BE


title: 40361 7539308158_R04C02


title: Cervix_D7 [8909358026_B]

description:
D7
8909358026_B


title: 40357 7539308158_R04C01


title: ileocecal_LN_D7 [8909358026_C]

description:
D7
8909358026_C


title: 40341 7539308158_R05C01


title: 53015 7539308158_R01C01


title: 40336 7539308158_R01C02


title: Duodenum_D10 [8909358026_A]

description:
D10
8909358026_A

value: Duodenum


title: 2291 7539308158_R05C02


title: 40345 7539308158_R02C02


title: 40339 7539308158_R03C01


title: Ileum_D7 [8909358018_G]

description:
D7
8909358018_G


title: PAH006 7539308117_R06C01


title: PAH019 9611518135_R02C01


title: 53103 7539308158_R02C01


title: Cervix_D7 [8909358018_L]

description:
D7
8909358018_L


title: 40356 7539308158_R03C02


title: Defined-CD1-TS_rep3

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

country: Japan

institute: BRC, RIKEN

description:
Gene expression in CD1-TS-Tg(CAG-GFP)#3F cells
CD1-TS-Tg(CAG-GFP)#3F_3
amplified RNA

hyb_protocol: 600 ng Cy3-labelled RNAs were fragmented at 60°C for 30 minutes and hybridized at 65°C for 17 hours according to manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images of microarray slides were processed using Feature Extraction software 10.5.1 (Agilent Technologies). All raw data were loaded into Gene Spring GX 12.5 (Agilent Technologies) and transformed by default setting.
Raw signal intensities were normalized by default setting of GeneSpring12.5. Normalized data expressed in log2 scale.

organism: Mus musculus

source_name: CD1-TS-Tg(CAG-GFP)#3F, replicate 3

label_protocol: 5.0 ug of amplified RNA was labelled with Cianine-3 (Cy3) dye (GE Healthcare) for 90 minutes at RT. Labelled RNAs were purified with RNeasy MinElute kit (Qiagen) and checked with the NanoDrop ND-1000 Spectrophotometer

growth_protocol: Conventional TSC line were cultured on mitomycin-C (Sigma-Aldrich, St. Louis, MO, USA)-treated primary MEFs in RPMI1640 medium (Thermo Fisher Scientific, San Jose, CA,USA) with 20% fetal bovine serum (Thermo Fisher Scientific), 25 ng/ml human recombinant FGF4 (Wako, Osaka, Japan), 1 ug/ml heparin (Sigma-Aldrich), 100 μM 2-mercaptoethanol 100 (2-ME) (Sigma-Aldrich), 1% Glutamax (Thermo Fisher Scientific), and 1 mM sodium pyruvate (Thermo Fisher Scientific) at 37.5 ºC in a humidified incubator with 5% CO2. Defined TSC line was cultured in CDM/FAXY medium at 37.5 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted with TRIzol (Life Technologies) from 30–50 TSCs clonies and subjected to linear amplification using TargetAmp Two-Round Aminoallyl-aRNA Amplification Kits (Epicentre Biotechnologies).

tag: strain

value: trophoblast stem cell line

value: CD1-TS-Tg(CAG-GFP)#3F cells

tag: colony type

tag: culture medium

value: Chemically defined


title: Defined-CD1-TS_rep2

description:
Gene expression in CD1-TS-Tg(CAG-GFP)#3F cells
CD1-TS-Tg(CAG-GFP)#3F_2
amplified RNA

source_name: CD1-TS-Tg(CAG-GFP)#3F, replicate 2


title: Cecum_D7 [8909358018_E]

description:
D7
8909358018_E

value: Cecum

tag: status


title: mesenteric_LN_D10 [8909358018_H]

description:
D10
8909358018_H

tag: name used in manuscript

value: SIV

tag: subset


title: axillary_LN_D10 [8909358018_J]

description:
D10
8909358018_J


title: Thymus_D7 [8909358018_F]

description:
D7
8909358018_F

value: Thymus


title: PAH021 7539308117_R05C01


title: 53061 7539308117_R05C02

source_name: GERD

value: GERD


title: 52016 7539308117_R03C02

source_name: Control

value: Control


title: Defined-CD1-TS_rep1

description:
Gene expression in CD1-TS-Tg(CAG-GFP)#3F cells
CD1-TS-Tg(CAG-GFP)#3F_1
amplified RNA

source_name: CD1-TS-Tg(CAG-GFP)#3F, replicate 1

tag: cell line


title: GPH048 9611518135_R03C02

source_name: Normal

value: Normal


title: 55010 7539308117_R04C02


title: Conventional_XGFP-Type4_rep4

description:
Gene expression in type4 colonies of XGFP cells
XGFP_Type4_4
amplified RNA

source_name: XGFP, type4, replicate 4

value: XGFP cells

value: type 4

value: Conventional


title: 53042 7539308117_R02C02


title: 53118 7539308117_R06C02


title: Conventional_XGFP-Type4_rep3

description:
Gene expression in type4 colonies of XGFP cells
XGFP_Type4_3
amplified RNA

source_name: XGFP, type4, replicate 3


title: Thymus_D7 [8909358017_K]

description:
D7
8909358017_K


title: Blood_D10 [8909358018_A]

description:
D10
8909358018_A

value: Blood


title: Uterus_D10 [8909358017_J]

description:
D10
8909358017_J

value: FRT

value: Uterus


title: Conventional_XGFP-Type1_rep2

description:
Gene expression in type1 colonies of XGFP cells
XGFP_Type1_2
amplified RNA

source_name: XGFP, type1, replicate 2

value: type 1


title: Duodenum_D7 [8909358018_D]

description:
D7
8909358018_D

value: Duodenum


title: Conventional_XGFP-Type2_rep2

description:
Gene expression in type2 colonies of XGFP cells
XGFP_Type2_2
amplified RNA

source_name: XGFP, type2, replicate 2

value: trophoblast stem cell line

value: type 2


title: Conventional_XGFP-Type4_rep1

description:
Gene expression in type4 colonies of XGFP cells
XGFP_Type4_1
amplified RNA

source_name: XGFP, type4, replicate 1


title: Conventional_XGFP-Type2_rep3

description:
Gene expression in type2 colonies of XGFP cells
XGFP_Type2_3
amplified RNA

source_name: XGFP, type2, replicate 3


title: Conventional_XGFP-Type4_rep2

description:
Gene expression in type4 colonies of XGFP cells
XGFP_Type4_2
amplified RNA

source_name: XGFP, type4, replicate 2


title: Conventional_XGFP-Type1_rep3

description:
Gene expression in type1 colonies of XGFP cells
XGFP_Type1_3
amplified RNA

source_name: XGFP, type1, replicate 3


title: Conventional_XGFP-Type2_rep4

description:
Gene expression in type2 colonies of XGFP cells
XGFP_Type2_4
amplified RNA

source_name: XGFP, type2, replicate 4


title: Brain_Lymphocyte_D7 [8909358018_C]

description:
D7
8909358018_C

source_name: Subject: Monkey_5070


title: Conventional_XGFP-Type1_rep1

description:
Gene expression in type1 colonies of XGFP cells
XGFP_Type1_1
amplified RNA

source_name: XGFP, type1, replicate 1


title: Conventional_XGFP-Type2_rep1

description:
Gene expression in type2 colonies of XGFP cells
XGFP_Type2_1
amplified RNA

source_name: XGFP, type2, replicate 1


title: Conventional_EGFP-TS3.5-Type4_rep3

description:
Gene expression in type4 colonies of EGFP-TS3.5 cells
EGFP-TS3.5_Type4_3
amplified RNA

source_name: EGFP-TS3.5, type4, replicate 3

value: EGFP-TS3.5 cells


title: Conventional_EGFP-TS3.5-Type4_rep4

description:
Gene expression in type4 colonies of EGFP-TS3.5 cells
EGFP-TS3.5_Type4_4
amplified RNA

source_name: EGFP-TS3.5, type4, replicate 4


title: 54049 7539308117_R01C02

source_name: Control


title: Tonsil_D7 [8909358017_I]

description:
D7
8909358017_I

value: Tonsil


title: 833 7539308080_R05C01


title: Cecum_D10 [8909358017_G]

description:
D10
8909358017_G

source_name: Subject: Monkey_5083

value: Cecum

value: SIV


title: Conventional_EGFP-TS3.5-Type4_rep1

description:
Gene expression in type4 colonies of EGFP-TS3.5 cells
EGFP-TS3.5_Type4_1
amplified RNA

source_name: EGFP-TS3.5, type4, replicate 1


title: PAH035 7539308080_R04C02

source_name: Tumour

value: Tumour


title: Conventional_EGFP-TS3.5-Type1_rep3

description:
Gene expression in type1 colonies of EGFP-TS3.5 cells
EGFP-TS3.5_Type1_3
amplified RNA

source_name: EGFP-TS3.5, type1, replicate 3


title: Tonsil_D7 [8909358017_H]

description:
D7
8909358017_H

source_name: Subject: Monkey_5074


title: Conventional_EGFP-TS3.5-Type1_rep2

description:
Gene expression in type1 colonies of EGFP-TS3.5 cells
EGFP-TS3.5_Type1_2
amplified RNA

source_name: EGFP-TS3.5, type1, replicate 2


title: Conventional_EGFP-TS3.5-Type2_rep1

description:
Gene expression in type2 colonies of EGFP-TS3.5 cells
EGFP-TS3.5_Type2_1
amplified RNA

source_name: EGFP-TS3.5, type2, replicate 1


title: Bone_Marrow_D7 [8909358017_F]

description:
D7
8909358017_F


title: Conventional_EGFP-TS3.5-Type2_rep2

description:
Gene expression in type2 colonies of EGFP-TS3.5 cells
EGFP-TS3.5_Type2_2
amplified RNA

source_name: EGFP-TS3.5, type2, replicate 2


title: Conventional_EGFP-TS3.5-Type4_rep2

description:
Gene expression in type4 colonies of EGFP-TS3.5 cells
EGFP-TS3.5_Type4_2
amplified RNA

source_name: EGFP-TS3.5, type4, replicate 2


title: Conventional_EGFP-TS3.5-Type2_rep3

description:
Gene expression in type2 colonies of EGFP-TS3.5 cells
EGFP-TS3.5_Type2_3
amplified RNA

source_name: EGFP-TS3.5, type2, replicate 3


title: Conventional_EGFP-TS3.5-Type1_rep1

description:
Gene expression in type1 colonies of EGFP-TS3.5 cells
EGFP-TS3.5_Type1_1
amplified RNA

source_name: EGFP-TS3.5, type1, replicate 1


title: Brain_Lymphocyte_D7 [8909358017_D]

description:
D7
8909358017_D


title: 833 7539308080_R06C01


title: Conventional_B6TS4_Type4_rep3

description:
Gene expression in type4 colonies of B6TS4 cells
B6TS4_Type4_3
amplified RNA

source_name: B6TS4, type4, replicate 3

value: B6TS4 cells


title: 545 7539308080_R01C01


title: 890 7539308080_R01C02


title: 572 7539308080_R02C01


title: Duodenum_D7 [8909358017_C]

description:
D7
8909358017_C


title: Conventional_B6TS4_Type4_rep2

description:
Gene expression in type4 colonies of B6TS4 cells
B6TS4_Type4_2
amplified RNA

source_name: B6TS4, type4, replicate 2


title: Blood_D7 [8909358017_A]

description:
D7
8909358017_A


title: 3616 7539308075_R06C01


title: 505 7539308075_R06C02


title: 3616 7539308075_R05C01

source_name: Normal

value: Normal


title: Conventional_B6TS4_Type4_rep1

description:
Gene expression in type4 colonies of B6TS4 cells
B6TS4_Type4_1
amplified RNA

source_name: B6TS4, type4, replicate 1


title: Conventional_B6TS4_Type1_rep4

description:
Gene expression in type1 colonies of B6TS4 cells
B6TS4_Type1_4
amplified RNA

source_name: B6TS4, type1, replicate 4


title: 823 7539308080_R03C01


title: Conventional_B6TS4_Type1_rep3

description:
Gene expression in type1 colonies of B6TS4 cells
B6TS4_Type1_3
amplified RNA

source_name: B6TS4, type1, replicate 3


title: 3985 7539308075_R05C02


title: Blood_D7 [8909358015_K]

description:
D7
8909358015_K

source_name: Subject: Monkey_5070


title: Conventional_B6TS4_Type1_rep2

description:
Gene expression in type1 colonies of B6TS4 cells
B6TS4_Type1_2
amplified RNA

source_name: B6TS4, type1, replicate 2


title: PAH034 7539308080_R03C02


title: Rectum_D7 [8909358015_I]

description:
D7
8909358015_I

value: Rectum


title: Conventional_B6TS4_Type1_rep1

description:
Gene expression in type1 colonies of B6TS4 cells
B6TS4_Type1_1
amplified RNA

source_name: B6TS4, type1, replicate 1


title: E6.5_ICR_ectoplacental cone_rep3

description:
Gene expression in E6.5 ectoplacental cone
ICR_EPC3
amplified RNA

source_name: ICR, E6.5, embryo, ectoplacental cone, replicate 3

tag: developmental stage

value: embryo

value: ectoplacental cone


title: Conventional_B6TS4_Type2_rep2

description:
Gene expression in type2 colonies of B6TS4 cells
B6TS4_Type2_2
amplified RNA

source_name: B6TS4, type2, replicate 2

value: Conventional


title: Conventional_B6TS4_Type2_rep1

description:
Gene expression in type2 colonies of B6TS4 cells
B6TS4_Type2_1
amplified RNA

source_name: B6TS4, type2, replicate 1


title: Tonsil_D10 [8909358015_J]

description:
D10
8909358015_J

source_name: Subject: Monkey_5083


title: 54076 7539308075_R04C01

source_name: Tumour


title: E6.5_ICR_ectoplacental cone_rep2

description:
Gene expression in E6.5 ectoplacental cone
ICR_EPC2
amplified RNA

source_name: ICR, E6.5, embryo, ectoplacental cone, replicate 2


title: Colon_D7 [8909358015_H]

description:
D7
8909358015_H

source_name: Subject: Monkey_5074

value: Colon


title: E6.5_ICR_ectoplacental cone_rep1

description:
Gene expression in E6.5 ectoplacental cone
ICR_EPC1
amplified RNA

source_name: ICR, E6.5, embryo, ectoplacental cone, replicate 1


title: 3845 7539308075_R04C02


title: E6.5_ICR_extraembryonic ectoderm_rep2

description:
Gene expression in E6.5 extraembryonic ectoderm
ICR_ExE2
amplified RNA

source_name: ICR, E6.5, embryo, extraembryonic ectoderm, replicate 2

value: extraembryonic ectoderm


title: E6.5_ICR_extraembryonic ectoderm_rep3

description:
Gene expression in E6.5 extraembryonic ectoderm
ICR_ExE3
amplified RNA

source_name: ICR, E6.5, embryo, extraembryonic ectoderm, replicate 3


title: 40367 7539308075_R02C01


title: E6.5_C57B6_ectoplacental cone_rep2

description:
Gene expression in E6.5 ectoplacental cone
B6_EPC2
amplified RNA

source_name: B6, E6.5, embryo, ectoplacental cone, replicate 2


title: E6.5_ICR_extraembryonic ectoderm_rep1

description:
Gene expression in E6.5 extraembryonic ectoderm
ICR_ExE1
amplified RNA

source_name: ICR, E6.5, embryo, extraembryonic ectoderm, replicate 1


title: genital_pelvic_LN_D10 [8909358015_D]

description:
D10
8909358015_D

value: LN


title: Cervix_D10 [8909358015_F]

description:
D10
8909358015_F

value: FRT

value: Cervix


title: E6.5_C57B6_ectoplacental cone_rep1

description:
Gene expression in E6.5 ectoplacental cone
B6_EPC1
amplified RNA

source_name: B6, E6.5, embryo, ectoplacental cone, replicate 1


title: 54014 7539308075_R03C01


title: Colon_D10 [8909358015_L]

description:
D10
8909358015_L


title: mesenteric_LN_D7 [8909358015_G]

description:
D7
8909358015_G


title: 823 7539308080_R04C01


title: E6.5_C57B6_extraembryonic ectoderm_rep2

description:
Gene expression in E6.5 extraembryonic ectoderm
B6_ExE2
amplified RNA

source_name: B6, E6.5, embryo, extraembryonic ectoderm, replicate 2


title: 3845 7539308075_R03C02

source_name: Normal


title: 384 7539308075_R02C02


title: E6.5_C57B6_extraembryonic ectoderm_rep1

description:
Gene expression in E6.5 extraembryonic ectoderm
B6_ExE1
amplified RNA

source_name: B6, E6.5, embryo, extraembryonic ectoderm, replicate 1


title: 384 7539308075_R01C02


title: 54036 7539308074_R06C02

source_name: BE

value: BE


title: 40362 7539308075_R01C01


title: Inguinal_LN_D7 [8909358015_B]

description:
D7
8909358015_B


title: Uterus_D7 [8909358015_C]

description:
D7
8909358015_C

source_name: Subject: Monkey_5070

value: Uterus


title: WT_biological_rep2

city: Louisville

first: Brian

middle: F

last: Clem

state: KY

address: 505 S. Hancock St, CTRB, Rm. 422

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: Gene expression data from WT MEF

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Affymetrix Mouse 430.2 arrays according to the GeneChip 3' array Hybridization User Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 3.1 (Affymetrix)

data_processing: The CEL files were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization on a gene level, followed by a one-way ANOVA.

source_name: Wild-Type MEF

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix 3' IVT Express Reagent Kit from 100 ng total RNA

growth_protocol: All MEF cells were collected during exponential growth phase

treatment_protocol: No treatment

value: embryonic fibroblast

tag: genotype

value: Wild-Type


title: mesenteric_LN_D7 [8909358014_L]

description:
D7
8909358014_L

source_name: Subject: Monkey_5354

value: SIV


title: Liver_D7 [8909358014_K]

description:
D7
8909358014_K

source_name: Subject: Monkey_5358

value: Liver


title: WT_biological_rep3

description: Gene expression data from WT MEF


title: WT_biological_rep1

description: Gene expression data from WT MEF


title: TKO-Ras_biological_rep2

description: Gene expression data from TKO-Ras MEF

source_name: TKO MEF with mutated Ras

value: Rb1, p107, and p130 deletions; RasG12D


title: mesenteric_LN_D7 [8909358014_I]

description:
D7
8909358014_I

source_name: Subject: Monkey_5353


title: 54024 7539308074_R05C02

value: Normal


title: TKO-Ras_biological_rep3

description: Gene expression data from TKO-Ras MEF


title: SOG016 7539308074_R06C01


title: SOG018 7539308074_R05C01

source_name: Tumour

value: Tumour


title: Cecum_D7 [8909358015_E]

description:
D7
8909358015_E

source_name: Subject: Monkey_5074

value: Cecum


title: TKO_biological_rep3

description: Gene expression data from TKO MEF

source_name: MEF with Rb1, p107, and p130 deletions

value: Rb1, p107, and p130 deletions


title: TKO-Ras_biological_rep1

description: Gene expression data from TKO-Ras MEF


title: E6.5_C57B6_ectoplacental cone_rep3

description:
Gene expression in E6.5 ectoplacental cone
B6_EPC3
amplified RNA

source_name: B6, E6.5, embryo, ectoplacental cone, replicate 3

value: embryo

value: ectoplacental cone


title: E6.5_C57B6_extraembryonic ectoderm_rep3

description:
Gene expression in E6.5 extraembryonic ectoderm
B6_ExE3
amplified RNA

source_name: B6, E6.5, embryo, extraembryonic ectoderm, replicate 3

value: extraembryonic ectoderm


title: axillary_LN_D7 [8909358014_G]

description:
D7
8909358014_G

value: LN


title: TKO_biological_rep2

description: Gene expression data from TKO MEF


title: SOG017 7539308074_R04C01


title: Rb1KO_biological_rep2

description: Gene expression data from Rb1KO MEF

source_name: MEF with Rb1 deletion

value: Rb1 deletion


title: CSF_D7 [8909358014_E]

description:
D7
8909358014_E

value: CSF


title: Rb1KO_biological_rep1

description: Gene expression data from Rb1KO MEF


title: Tonsil_D7 [8909358014_H]

description:
D7
8909358014_H

value: Tonsil


title: TKO_biological_rep1

description: Gene expression data from TKO MEF


title: Rectum_D7 [8909358014_F]

description:
D7
8909358014_F

value: Rectum


title: 53160 7539308074_R03C02

source_name: GERD

value: GERD


title: FSH treated Granulosa cells Replicate 2

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.

organism: Bos taurus

source_name: Granulosa cells

label_protocol: The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: Two to six milimeters diameter follicles from bovine ovaries (kept on ice after collection) (n=4) for each biological replicate (n=8) from slaughterhouse were dissected individually. Then, the follicles were rinsed in culture medium 3 times and cut. The cells were then filtered on a mesh (opening size 104 µm) and rinsed in culture medium 3 times with centrifugation (800 rcf, 5 minutes). Cells were plated in 24 wells plates (BD Falcon) at the density of 106 cells/well and cultured for 48hrs with or without FSH treatment the last 4 hrs.

extract_protocol:
Total RNA extraction was performed using the PicoPure RNA Isolation Kit from Life Technologies. Total RNA was quantified using Bioanalyzer (Agilent)
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

treatment_protocol: FSH treatment for the last 4 hours of culture at a concentration of 1ng/ml

tag: treatment

value: FSH

tag: concentration

value: 1 ng/ml

tag: time

value: 4 hours

value: no FSH

value: 0 hour


title: SOG016 7539308074_R03C01

value: Tumour


title: Rb1KO_biological_rep3

description: Gene expression data from Rb1KO MEF

tag: cell type

value: embryonic fibroblast


title: axillary_LN_D7 [8909358014_D]

description:
D7
8909358014_D

value: SIV


title: FSH treated Granulosa cells Replicate 1


title: 53158 7539308074_R02C02


title: SOG015 7539308074_R02C01


title: Bovine Granulosa cells Replicate 4


title: FSH treated Granulosa cells Replicate 3


title: SOG017 7539308074_R01C02

source_name: Normal

value: Normal


title: Liver_D7 [8909358014_C]

description:
D7
8909358014_C

value: Liver


title: Inguinal_LN_D7 [8909358014_A]

description:
D7
8909358014_A


title: Cecum_D7 [8909358014_B]

description:
D7
8909358014_B

value: Cecum


title: FSH treated Granulosa cells Replicate 4


title: Bovine Granulosa cells Replicate 2


title: Bovine Granulosa cells Replicate 1


title: Ileum_D10 [8909358013_L]

description:
D10
8909358013_L

source_name: Subject: Monkey_5083

value: Ileum


title: 54016 7539308065_R06C01


title: Bovine Granulosa cells Replicate 3


title: ileocecal_LN_D7 [8909358013_K]

description:
D7
8909358013_K


title: 40364 7539308065_R06C02

source_name: BE

value: BE


title: 40365 7539308065_R05C02


title: Inguinal_LN_D10 [8909358013_J]

description:
D10
8909358013_J


title: 53161 7539308065_R05C01


title: Dermal Papilla Cell Cultures rep2

city: Bradford

first: Val

last: Randall

address: Richmond Road

country: United Kingdom

institute: University of Bradford

description: Primary dermal papilla cell cultures

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to Affymetrix Eukaryotic Target Hybridization protocol (GeneChip® Expression Analysis

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G and Affymetrix® Transcriptome Analysis Console (TAC) Software

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

source_name: Dermal Papilla cell Cultures

label_protocol: Samples were preperad according to Affymetrix GeneChip® WT Terminal Labelling Kit, according to manufactuer's protocol

growth_protocol: human hair follicle organ culture from occipital scalp

extract_protocol: Ambion® WT Expression Kit

treatment_protocol: not applicable

value: not applicable

value: Dermal Papilla

value: wild-type


title: genital_pelvic_LN_D7 [8909358013_I]

description:
D7
8909358013_I

source_name: Subject: Monkey_5070

value: LN


title: 53169 7539308065_R03C02


title: Dermal Papilla Cell Cultures rep3

description: Primary dermal papilla cell cultures


title: 54050 7539308065_R04C01

source_name: Control

value: Control


title: Human Hair Follicle Organ Cultures rep3

description: human hair follicle organ culture from occipital scalp

value: Hair follicles


title: Human Hair Follicle Organ Cultures rep1

source_name: human hair follicle organ culture from occipital scalp


title: 52039 7539308065_R02C02


title: 53114 7539308065_R04C02


title: Ileum_D7 [8909358013_E]

description:
D7
8909358013_E


title: ileocecal_LN_D10 [8909358013_H]

description:
D10
8909358013_H


title: Splenocytes_D10 [8909358013_G]

description:
D10
8909358013_G

value: Splenocytes


title: 53124 7539308065_R03C01


title: PAH010 7539308065_R02C01


title: Skin_Fibroblast_c217

description: Genomiphi V2 whole genome amplified material.

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA)

data_processing: Raw data were further processed using GenomeStudio.

source_name: Skin biopsy, fibroblast, cell 217

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 staining by extension, according to the manual of Infinium II Assay (Illumina, USA).

growth_protocol: Single fibroblasts were isolated from a fresh skin biopsy.

extract_protocol: The genome of collected single cells was amplified using GenomiphiV2 (GE Healthcare).

treatment_protocol: Following overnight treatment of the biopt with 400U/ml collagenase in culture medium, single cells were washed in 1xPBS (Thermo Scientific, USA).

tag: gender

value: Female

value: skin fibroblast


title: Human Hair Follicle Organ Cultures rep2

tag: age


title: pararectal_paracolonic_D7 [8909358013_D]

description:
D7
8909358013_D


title: Dermal Papilla Cell Cultures rep1

description: Primary dermal papilla cell cultures


title: 53103 7539308065_R01C02


title: PAH010 7539308065_R01C01

value: Tumour


title: Skin_Fibroblast_c214

scan_protocol: According to the manual of Infinium II Assay (Illumina, USA)

source_name: Skin biopsy, fibroblast, cell 214


title: Skin_Fibroblast_c210

source_name: Skin biopsy, fibroblast, cell 210


title: Liver_D7 [8909358013_C]

description:
D7
8909358013_C

source_name: Subject: Monkey_5074


title: Skin_Fibroblast_c212

source_name: Skin biopsy, fibroblast, cell 212


title: Liver_D7 [8909358013_B]

description:
D7
8909358013_B


title: Skin_Fibroblast_c211

source_name: Skin biopsy, fibroblast, cell 211


title: Skin_Fibroblast_c220

source_name: Skin biopsy, fibroblast, cell 220


title: Skin_Fibroblast_c209

source_name: Skin biopsy, fibroblast, cell 209


title: Rectum_D7 [8909358013_A]

description:
D7
8909358013_A

value: Rectum


title: Skin_Fibroblast_c200

source_name: Skin biopsy, fibroblast, cell 200


title: 1450 7539308063_R05C01

source_name: Tumour


title: Skin_Fibroblast_c215

source_name: Skin biopsy, fibroblast, cell 215


title: Colon_D3 [8909358010_L]

description:
D3
8909358010_L

source_name: Subject: Monkey_5348

value: Colon

value: SIV


title: Skin_Fibroblast_c204

source_name: Skin biopsy, fibroblast, cell 204


title: Skin_Fibroblast_c194

source_name: Skin biopsy, fibroblast, cell 194


title: Skin_Fibroblast_c197

source_name: Skin biopsy, fibroblast, cell 197


title: Brain_lymphocytes_D7 [8909358010_K]

description:
D7
8909358010_K

source_name: Subject: Monkey_5354


title: Skin_Fibroblast_c190

source_name: Skin biopsy, fibroblast, cell 190


title: genital_pelvic_LN_D7 [8909358010_J]

description:
D7
8909358010_J


title: PAH007 7539308063_R04C02


title: Splenocytes_D7 [8909358010_I]

description:
D7
8909358010_I

source_name: Subject: Monkey_5358


title: Skin_Fibroblast_c193

source_name: Skin biopsy, fibroblast, cell 193


title: Skin_Fibroblast_c186

source_name: Skin biopsy, fibroblast, cell 186


title: Skin_Fibroblast_c192

source_name: Skin biopsy, fibroblast, cell 192


title: Skin_Fibroblast_c191

source_name: Skin biopsy, fibroblast, cell 191


title: Lung_D7 [8909358010_G]

description:
D7
8909358010_G

source_name: Subject: Monkey_5353

value: Lung


title: Skin_Fibroblast_c202

source_name: Skin biopsy, fibroblast, cell 202


title: 1445 7539308063_R04C01


title: Cecum_D7 [8909358010_F]

description:
D7
8909358010_F

value: Cecum


title: Skin_Fibroblast_c188

source_name: Skin biopsy, fibroblast, cell 188


title: 1445 7539308063_R03C01

source_name: Normal

value: Normal


title: Skin_Fibroblast_c185

source_name: Skin biopsy, fibroblast, cell 185


title: PAH005 7539308063_R03C02

source_name: Tumour


title: PAH003 7539308063_R02C02


title: 1433 7539308063_R02C01


title: Colon_D7 [8909358010_D]

description:
D7
8909358010_D


title: Ileum_D3 [8909358010_E]

description:
D3
8909358010_E

source_name: Subject: Monkey_5348

value: Ileum


title: Skin_Fibroblast_c181

source_name: Skin biopsy, fibroblast, cell 181


title: Skin_Fibroblast_c176

source_name: Skin biopsy, fibroblast, cell 176


title: Skin_Fibroblast_c168

source_name: Skin biopsy, fibroblast, cell 168


title: Duodenum_D7 [8909358010_B]

description:
D7
8909358010_B

value: Duodenum


title: Skin_Fibroblast_c184

source_name: Skin biopsy, fibroblast, cell 184


title: PAH002 7539308063_R01C02


title: Skin_Fibroblast_c171

source_name: Skin biopsy, fibroblast, cell 171


title: Skin_Fibroblast_c182

source_name: Skin biopsy, fibroblast, cell 182


title: Skin_Fibroblast_c180

source_name: Skin biopsy, fibroblast, cell 180


title: Skin_Fibroblast_c170

source_name: Skin biopsy, fibroblast, cell 170


title: Skin_Fibroblast_c177

source_name: Skin biopsy, fibroblast, cell 177


title: Skin_Fibroblast_c183

source_name: Skin biopsy, fibroblast, cell 183


title: Skin_Fibroblast_c165

source_name: Skin biopsy, fibroblast, cell 165


title: Jejunum_D7 [8909358007_L]

description:
D7
8909358007_L

source_name: Subject: Monkey_5070

value: GI

value: Jejunum


title: Skin_Fibroblast_c162

source_name: Skin biopsy, fibroblast, cell 162


title: 1430 7539308054_R06C02


title: Skin_Fibroblast_c166

source_name: Skin biopsy, fibroblast, cell 166


title: ileocecal_LN_D7 [8909358010_A]

description:
D7
8909358010_A

source_name: Subject: Monkey_5354


title: Mid_Vagina_D7 [8909358007_K]

description:
D7
8909358007_K

value: FRT


title: Skin_Fibroblast_c164

source_name: Skin biopsy, fibroblast, cell 164


title: 1020 7539308054_R06C01

source_name: Normal


title: Lung_D7 [8909358007_J]

description:
D7
8909358007_J

source_name: Subject: Monkey_5074


title: 1430 7539308054_R05C02


title: Uterus_D7 [8909358007_I]

description:
D7
8909358007_I

value: Uterus


title: Skin_Fibroblast_c161

source_name: Skin biopsy, fibroblast, cell 161


title: 1433 7539308063_R01C01


title: Skin_Fibroblast_c167

source_name: Skin biopsy, fibroblast, cell 167


title: 40338 7539308054_R05C01

source_name: Tumour


title: Skin_Fibroblast_c159

source_name: Skin biopsy, fibroblast, cell 159


title: Skin_Fibroblast_c157

source_name: Skin biopsy, fibroblast, cell 157


title: Bone_Marrow_D7 [8909358007_H]

description:
D7
8909358007_H


title: Splenocytes_D7 [8909358007_G]

description:
D7
8909358007_G


title: pararectal_paracolonic_D7 [8909358007_F]

description:
D7
8909358007_F


title: Skin_Fibroblast_c160

source_name: Skin biopsy, fibroblast, cell 160


title: Skin_Fibroblast_c156

source_name: Skin biopsy, fibroblast, cell 156


title: Skin_Fibroblast_c158

source_name: Skin biopsy, fibroblast, cell 158


title: 1154 7539308054_R04C02


title: Thymus_D10 [8909358007_E]

description:
D10
8909358007_E

source_name: Subject: Monkey_5083

value: Thymus


title: Liver_D10 [8909358007_D]

description:
D10
8909358007_D

value: Liver


title: 1074 7539308054_R02C02


title: 1154 7539308054_R03C02


title: Skin_Fibroblast_c147

source_name: Skin biopsy, fibroblast, cell 147

value: Female


title: Skin_Fibroblast_c144

source_name: Skin biopsy, fibroblast, cell 144

value: skin fibroblast


title: 40325 7539308054_R03C01

value: Tumour


title: Skin_Fibroblast_c137

source_name: Skin biopsy, fibroblast, cell 137


title: Skin_Fibroblast_c140

source_name: Skin biopsy, fibroblast, cell 140


title: Skin_Fibroblast_c142

source_name: Skin biopsy, fibroblast, cell 142


title: Jejunum_D10 [8909358007_C]

description:
D10
8909358007_C


title: Skin_Fibroblast_c138

source_name: Skin biopsy, fibroblast, cell 138


title: Jejunum_D7 [8909358007_A]

description:
D7
8909358007_A


title: Skin_Fibroblast_c155

source_name: Skin biopsy, fibroblast, cell 155


title: 1020 7539308054_R01C02


title: Skin_Fibroblast_c148

source_name: Skin biopsy, fibroblast, cell 148


title: Skin_Fibroblast_c121

source_name: Skin biopsy, fibroblast, cell 121


title: Skin_Fibroblast_c136

source_name: Skin biopsy, fibroblast, cell 136


title: Skin_Fibroblast_c127

source_name: Skin biopsy, fibroblast, cell 127


title: 40320 7539308054_R02C01

source_name: Tumour


title: 40339 7539308054_R01C01

source_name: BE

value: BE


title: pararectal_paracolonic_D3 [8909358006_K]

description:
D3
8909358006_K

source_name: Subject: Monkey_5348


title: Skin_Fibroblast_c89

source_name: Skin biopsy, fibroblast, cell 89


title: Skin_Fibroblast_c115

source_name: Skin biopsy, fibroblast, cell 115


title: Skin_Fibroblast_c149

source_name: Skin biopsy, fibroblast, cell 149


title: mesenteric_LN_D3 [8909358006_H]

description:
D3
8909358006_H

value: LN


title: Skin_Fibroblast_c122

source_name: Skin biopsy, fibroblast, cell 122


title: Uterus_D7 [8909358006_I]

description:
D7
8909358006_I

source_name: Subject: Monkey_5358

value: SIV


title: Tonsil_D7 [8909358006_G]

description:
D7
8909358006_G

source_name: Subject: Monkey_5353

value: Tonsil


title: Skin_Fibroblast_c87

source_name: Skin biopsy, fibroblast, cell 87


title: 40320 7539308051_R06C02


title: 55024 7539308051_R06C01

source_name: Normal


title: Skin_Fibroblast_c114

source_name: Skin biopsy, fibroblast, cell 114


title: Skin_Fibroblast_c128

source_name: Skin biopsy, fibroblast, cell 128


title: Skin_Fibroblast_c86

source_name: Skin biopsy, fibroblast, cell 86


title: Jejunum_D7 [8909358006_F]

description:
D7
8909358006_F


title: 53022 7539308051_R04C01

source_name: GERD

value: GERD


title: genital_pelvic_LN_D3 [8909358006_E]

description:
D3
8909358006_E


title: 40334 7539308054_R04C01


title: 54082 7539308051_R05C01


title: Skin_Fibroblast_c82

source_name: Skin biopsy, fibroblast, cell 82


title: pararectal_paracolonic_D7 [8909358006_D]

description:
D7
8909358006_D


title: Skin_Fibroblast_c150

source_name: Skin biopsy, fibroblast, cell 150


title: 40320 7539308051_R04C02

value: Normal


title: Skin_Fibroblast_c77

source_name: Skin biopsy, fibroblast, cell 77


title: Skin_Fibroblast_c85

source_name: Skin biopsy, fibroblast, cell 85


title: 40341 7539308051_R05C02


title: Skin_Fibroblast_c50

source_name: Skin biopsy, fibroblast, cell 50


title: pararectal_paracolonic_D7 [8909358006_C]

description:
D7
8909358006_C


title: Skin_Fibroblast_c60

source_name: Skin biopsy, fibroblast, cell 60


title: Skin_Fibroblast_c53

source_name: Skin biopsy, fibroblast, cell 53


title: Cervix_D7 [8909358006_B]

description:
D7
8909358006_B

source_name: Subject: Monkey_5354

value: Cervix


title: 55024 7539308051_R02C02

source_name: BE


title: 54045 7539308051_R03C02


title: 54053 7539308051_R03C01

source_name: Control

value: Control


title: Skin_Fibroblast_c64

source_name: Skin biopsy, fibroblast, cell 64


title: Skin_Fibroblast_c65

source_name: Skin biopsy, fibroblast, cell 65


title: Skin_Fibroblast_c62

source_name: Skin biopsy, fibroblast, cell 62


title: Skin_Fibroblast_c83

source_name: Skin biopsy, fibroblast, cell 83


title: Skin_Fibroblast_c39

source_name: Skin biopsy, fibroblast, cell 39


title: Cervix_D7 [8909358006_A]

description:
D7
8909358006_A

source_name: Subject: Monkey_5353


title: Rectum_D7 [8909358005_L]

description:
D7
8909358005_L

source_name: Subject: Monkey_5358

value: Rectum


title: 54036 7539308051_R01C02

source_name: Normal


title: Skin_Fibroblast_c78

source_name: Skin biopsy, fibroblast, cell 78


title: Skin_Fibroblast_c5

source_name: Skin biopsy, fibroblast, cell 5


title: Skin_Fibroblast_c36

source_name: Skin biopsy, fibroblast, cell 36


title: Skin_Fibroblast_c47

source_name: Skin biopsy, fibroblast, cell 47


title: 54048 7539308051_R02C01


title: Skin_Fibroblast_c14

source_name: Skin biopsy, fibroblast, cell 14


title: Ileum_D7 [8909358005_I]

description:
D7
8909358005_I

value: Ileum


title: Blood_D7 [8909358005_K]

description:
D7
8909358005_K

value: Blood


title: WB_SB_Mother_MC

description: DNA extracted from whole blood.

source_name: Whole blood, Mother, multicell

value: Male

value: whole blood


title: WB_SB_Father_MC

description: DNA extracted from whole blood.

source_name: Whole blood, Father, multicell


title: Cervix_D7 [8909358005_H]

description:
D7
8909358005_H

value: FRT


title: Fibroblast_S2_c70_sc2

description: RepliG-sc whole genome amplified material.

source_name: Primary fibroblast cell line S2, cell 70, sister cell 2

extract_protocol: The genome of collected single cells was amplified using either Genomiphi V2 (GE Healthcare, UK) or RepliG-sc (Qiagen, NL) whole genome amplification kit.

value: Female


title: SOG018 7539308045_R06C02


title: 1924 7539308045_R06C01

source_name: Tumour


title: 1735 7539308045_R05C01


title: 53016 7539308051_R01C01

source_name: Control


title: Jejunum_D7 [8909358005_F]

description:
D7
8909358005_F

source_name: Subject: Monkey_5354

value: GI

value: Jejunum


title: PAH013 7539308045_R05C02


title: WB_SB_Sibling_MC

description: DNA extracted from whole blood.

source_name: Whole blood, Sibling, multicell


title: Fibroblast_S2_c68_sc1

source_name: Primary fibroblast cell line S2, cell 68, sister cell 1


title: Fibroblast_S2_c70_sc1

source_name: Primary fibroblast cell line S2, cell 70, sister cell 1


title: Fibroblast_S2_c68_sc2

source_name: Primary fibroblast cell line S2, cell 68, sister cell 2


title: Fibroblast_S2_c65_sc2

source_name: Primary fibroblast cell line S2, cell 65, sister cell 2


title: Fibroblast_S2_c64_sc2

source_name: Primary fibroblast cell line S2, cell 64, sister cell 2


title: Tonsil_D3 [8909358005_G]

description:
D3
8909358005_G

source_name: Subject: Monkey_5348


title: Fibroblast_S2_c61_sc2

source_name: Primary fibroblast cell line S2, cell 61, sister cell 2


title: mesenteric_LN_D7 [8909358005_D]

description:
D7
8909358005_D

source_name: Subject: Monkey_5358


title: Fibroblast_S2_c61_sc1

source_name: Primary fibroblast cell line S2, cell 61, sister cell 1


title: Fibroblast_S2_c65_sc1

source_name: Primary fibroblast cell line S2, cell 65, sister cell 1


title: Fibroblast_S2_c64_sc1

source_name: Primary fibroblast cell line S2, cell 64, sister cell 1


title: Inguinal_LN_D7 [8909358005_E]

description:
D7
8909358005_E


title: Fibroblast_S2_c54_sc2

source_name: Primary fibroblast cell line S2, cell 54, sister cell 2


title: Rectum_D3 [8909358005_C]

description:
D3
8909358005_C


title: Fibroblast_S2_c53_sc2

source_name: Primary fibroblast cell line S2, cell 53, sister cell 2


title: Bone_Marrow_D7 [8909358005_A]

description:
D7
8909358005_A


title: Fibroblast_S2_c53_sc1

source_name: Primary fibroblast cell line S2, cell 53, sister cell 1


title: Mid_Vagina_D7 [8909358002_L]

description:
D7
8909358002_L

source_name: Subject: Monkey_5353


title: Mid_Vagina_D7 [8909358005_B]

description:
D7
8909358005_B


title: Fibroblast_S2_c52_sc1

source_name: Primary fibroblast cell line S2, cell 52, sister cell 1


title: 1712 7539308045_R04C01

source_name: Tumour

value: Tumour


title: Blood_D3 [8909358002_K]

description:
D3
8909358002_K


title: Fibroblast_S2_c52_sc2

source_name: Primary fibroblast cell line S2, cell 52, sister cell 2


title: Fibroblast_S2_c54_sc1

source_name: Primary fibroblast cell line S2, cell 54, sister cell 1


title: 1712 7539308045_R03C01

source_name: Normal


title: Fibroblast_S2_c51_sc2

source_name: Primary fibroblast cell line S2, cell 51, sister cell 2


title: 1642 7539308045_R02C01


title: 1642 7539308045_R01C01


title: Fibroblast_S2_c51_sc1

source_name: Primary fibroblast cell line S2, cell 51, sister cell 1


title: Fibroblast_S2_c40_sc2

source_name: Primary fibroblast cell line S2, cell 40, sister cell 2


title: Cecum_D7 [8909358002_J]

description:
D7
8909358002_J

value: Cecum


title: 1636 7539308044_R05C02


title: Fibroblast_S2_c38_sc2

source_name: Primary fibroblast cell line S2, cell 38, sister cell 2


title: Fibroblast_S2_c37_sc1

source_name: Primary fibroblast cell line S2, cell 37, sister cell 1


title: Fibroblast_S2_c40_sc1

source_name: Primary fibroblast cell line S2, cell 40, sister cell 1


title: 1640 7539308044_R06C02


title: Fibroblast_S2_c38_sc1

source_name: Primary fibroblast cell line S2, cell 38, sister cell 1


title: Fibroblast_S2_c36_sc1

source_name: Primary fibroblast cell line S2, cell 36, sister cell 1


title: ileocecal_LN_D7 [8909358002_I]

description:
D7
8909358002_I

source_name: Subject: Monkey_5358

value: SIV


title: Fibroblast_S2_c35_sc1

source_name: Primary fibroblast cell line S2, cell 35, sister cell 1


title: Fibroblast_S2_c37_sc2

source_name: Primary fibroblast cell line S2, cell 37, sister cell 2


title: Uterus_D3 [8909358002_G]

description:
D3
8909358002_G

source_name: Subject: Monkey_5348

value: Uterus


title: PAH012 7539308045_R01C02


title: Fibroblast_S2_c35_sc2

source_name: Primary fibroblast cell line S2, cell 35, sister cell 2


title: Fibroblast_S2_c36_sc2

source_name: Primary fibroblast cell line S2, cell 36, sister cell 2


title: Fibroblast_S2_c34_sc2

source_name: Primary fibroblast cell line S2, cell 34, sister cell 2


title: Uterus_D7 [8909358002_E]

description:
D7
8909358002_E

source_name: Subject: Monkey_5353


title: Splenocytes_D7 [8909358002_F]

description:
D7
8909358002_F

source_name: Subject: Monkey_5354

value: Splenocytes


title: Duodenum_D3 [8909358002_H]

description:
D3
8909358002_H

value: Duodenum


title: 1636 7539308044_R04C02

source_name: Normal

value: Normal


title: Fibroblast_S2_c34_sc1

source_name: Primary fibroblast cell line S2, cell 34, sister cell 1


title: Jejunum_D3 [8909358002_D]

description:
D3
8909358002_D


title: 40323 7539308044_R04C01

source_name: Tumour


title: axillary_LN_D7 [8909358002_B]

description:
D7
8909358002_B

value: LN


title: Fibroblast_S2_c28_sc2

source_name: Primary fibroblast cell line S2, cell 28, sister cell 2


title: Fibroblast_S2_c33_sc2

source_name: Primary fibroblast cell line S2, cell 33, sister cell 2


title: 40331 7539308044_R05C01


title: Uterus_D7 [8909358002_A]

description:
D7
8909358002_A


title: Fibroblast_S2_c33_sc1

source_name: Primary fibroblast cell line S2, cell 33, sister cell 1


title: 1527 7539308044_R02C02


title: 1527 7539308044_R03C02


title: Fibroblast_S2_c30_sc1

source_name: Primary fibroblast cell line S2, cell 30, sister cell 1


title: 40358 7539308044_R03C01


title: Fibroblast_S2_c30_sc2

source_name: Primary fibroblast cell line S2, cell 30, sister cell 2


title: 1463 7539308044_R01C02


title: 40363 7539308044_R02C01


title: Fibroblast_S2_c26_sc1

source_name: Primary fibroblast cell line S2, cell 26, sister cell 1


title: ileocecal_LN_D7 [8909358001_L]

description:
D7
8909358001_L


title: Fibroblast_S2_c31_sc1

source_name: Primary fibroblast cell line S2, cell 31, sister cell 1


title: Fibroblast_S2_c26_sc2

source_name: Primary fibroblast cell line S2, cell 26, sister cell 2


title: cia-cGAS KO

first: Pengyan

last: Xia

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of biophysics, Chinese Academy of Sciences

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner. Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing:
Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.
Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through fold change. Hierarchical clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed using the standard enrichment computation method.

source_name: circular RNA cia-cGAS knockout LT-HSCs

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA).

growth_protocol: C57/BL6 mice were maintained in SPF conditions.

extract_protocol: Sorted cells were subjected to total RNA extraction with TRIZOL reagent.

treatment_protocol: 8 week-old mice were anesthetized and bone marrow cells were flushed out, followed by LT-HSCs sorting through a BD AriaIII sorter.

tag: genotype/variation

value: cia-cGAS knockout

value: bone marrow

value: LT-HSC


title: Fibroblast_S2_c24_sc2

source_name: Primary fibroblast cell line S2, cell 24, sister cell 2


title: Fibroblast_S2_c31_sc2

source_name: Primary fibroblast cell line S2, cell 31, sister cell 2


title: Lung_D3 [8909358001_K]

description:
D3
8909358001_K

source_name: Subject: Monkey_5348

tag: tissue

value: Lung


title: Duodenum_D7 [8909358001_J]

description:
D7
8909358001_J


title: Fibroblast_S2_c21_sc2

source_name: Primary fibroblast cell line S2, cell 21, sister cell 2


title: Fibroblast_S2_c19_sc2

source_name: Primary fibroblast cell line S2, cell 19, sister cell 2


title: Fibroblast_S2_c21_sc1

source_name: Primary fibroblast cell line S2, cell 21, sister cell 1


title: cia-cGAS WT

source_name: circular RNA cia-cGAS WT LT-HSCs

tag: strain

value: cia-cGAS WT


title: 40359 7539308044_R01C01

source_name: Tumour


title: Colon_D7 [8909358001_I]

description:
D7
8909358001_I

source_name: Subject: Monkey_5354

value: Colon


title: Fibroblast_S2_c28_sc1

source_name: Primary fibroblast cell line S2, cell 28, sister cell 1

value: Female


title: Fibroblast_S2_c18_sc1

source_name: Primary fibroblast cell line S2, cell 18, sister cell 1


title: Fibroblast_S2_c19_sc1

source_name: Primary fibroblast cell line S2, cell 19, sister cell 1


title: Fibroblast_S2_c24_sc1

source_name: Primary fibroblast cell line S2, cell 24, sister cell 1


title: Splenocytes_D3 [8909358001_F]

description:
D3
8909358001_F


title: ileocecal_LN_D3 [8909358001_G]

description:
D3
8909358001_G


title: 40341 7539308042_R06C02


title: Lung_D7 [8909358001_H]

description:
D7
8909358001_H


title: Fibroblast_S2_c18_sc2

source_name: Primary fibroblast cell line S2, cell 18, sister cell 2


title: 54080 7539308042_R06C01

source_name: BE

value: BE


title: 54043 7539308042_R05C02