title: CD34+cells_24hours_without NPs_rep1

source_name: Human umbilical cord blood CD34+ cells, 24 hours, without nanoparticles, replicate 1

value: Hematopoietic stem cells

tag: passage number

value: Passage 0 (Freshly isolated)

tag: days in culture

value: 24 hours


title: CNIT 97K1mo

status: Public on Jun 01 2014

type: RNA

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

country: USA

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Kidney biopsies from transplant recipients with histological diagnosis of calcineurin inhibitor toxicity (CNIT)

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

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

tag: tissue

value: kidney biopsy

tag: histological diagnosis

value: calcineurin inhibitor toxicity (CNIT)


title: Blood from Stage III (GP2477_WB_143174HP133A11)

city: Stevenage

first: steve

middle: matthew

last: fox

address: Gunnels Wood Road

department: Statistics

country: United Kingdom

institute: GlaxoSmithKline

hyb_protocol: Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on GeneChip HG-U133_plus_2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data was analysed with Rosetta Resolver version 5.0

label: Biotin

source_name: blood

label_protocol: NuGEN Ovation FLv2 methodology using NuGEN Ovation RNA amplification v2 including C1 spike with Agencourt RNAClean SPIA clean up. FLv2 biotin fragmentation and labelling.

value: blood

tag: age

tag: gender

value: M

tag: gold stage

value: Stage III

tag: plateid

tag: subject type

value: COPD Subjects


title: CNIT 62K6mo


title: CNIT 6-55-K


title: Blood from Stage I (GP2477_WB_143171HP133A11)

value: Stage I

value: Smoker Controls


title: testes_B6_ST_rep2

city: Prague

first: Petr

last: Simecek

state: Not Applicable

address: Vídeňská 1083

department: Department of Mouse Molecular Genetics

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR, v. v. i.

description: SAMPLE 8

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Bioconductor 1.9 and R statistics (version 2.3) using the gcRMA method with default settings and custom chip description file (probes were annotated to Ensembl).

organism: Mus musculus

label_protocol: Between 15 to 40 ng of total RNA were used to prepare biotinylated cRNA according to the standard Affymetrix Two-Cycle protocol (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: The mice had ad libitum access to a standard rodent diet (VELAS, ST-1, 3.4% fat) and acidified water.

extract_protocol: Total RNA was isolated Using Qiagen RNeasy Micro kit according to manufacturer's instructionsl

treatment_protocol: Testes of 8-10 weeks old mice were dissected, testicular tunica was removed, spermatogenic populations were isolated using FACS and the cells were placed into RLT buffer of the RNeasy Micro isolation kit (QIAGEN) and homogenized using syringe and needle.

tag: strain

value: 8-10 weeks

tag: cell type

value: spermatids (ST)


title: Blood from Stage II (GP2477_WB_143170HP133A11)

value: F

value: Stage II


title: testes_B6_RP_rep2

description: SAMPLE 5

value: pachytene spermatocytes (RP)


title: testes_B6_LP_rep2

description: SAMPLE 10

value: prepachytene spermatocytes (LP)


title: 1833-Treatment-1

city: Chicago

first: Miao

last: Sun

institute: University of Chicago

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA Array version 5th Generation (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 15.0 at the Sanger Institute.

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).

data_processing: Background correction was conducted to remove non-biological contributions.  The quantified signals were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: 1833 cells with depleted HMGA2 expression

label_protocol: The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 500 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: Cells were cultured in a complete medium consisting of DMEM supplemented with 10% FBS, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol: Total RNA was isolated from cells using miRNeasy Mini Kit following the manufacturer’s instructions.

treatment_protocol: HMGA2 depletion (shHMGA2) and control (SCR sh) were achieved by transducing the cells with HMGA2 shRNA or scrambled control in a pLKO.1 lentiviral vector.  After 48 h transduction, cells were selected and maintained in 0.5 μg/ml puromycin.

tag: cell line

value: breast cancer cells

tag: transduced with

value: HMGA2 shRNA in a pLKO.1 lentiviral vector

tag: treated with

value: breast cancer cells expressing shHMGA2

source_name: Common reference for ms1-ms6

tag: sample type

value: all 6 samples pooled (reference)


title: CNIT 17K3

value: kidney biopsy

value: calcineurin inhibitor toxicity (CNIT)


title: testes_B6_LP_rep1

description: SAMPLE 9


title: testes_PWD_ST_rep2

description: SAMPLE 6

value: PWD/Ph


title: testes_B6_ST_rep1

description: SAMPLE 7


title: testes_B6_RP_rep1

description: SAMPLE 4


title: Blood from Stage I (GP2477_WB_143173HP133A11)

value: blood


title: CNIT 30K9mo


title: 1833-Control-3

source_name: 1833 cells expressing control vector

value: scrambled control in a pLKO.1 lentiviral vector

value: breast cancer cells expressing control


title: 1833-Treatment-2


title: Blood from Stage II (GP2477_WB_143168HP133A11)

value: M

value: COPD Subjects


title: CNIT 45K6


title: testes_PWD_ST_rep1

description: SAMPLE 3

value: 8-10 weeks

value: spermatids (ST)


title: Blood from Stage III (GP2477_WB_143172HP133A11)

value: F

value: Stage III


title: Blood from Stage II (GP2477_WB_143169HP133A11)

value: Stage II


title: 1833-Control-2

value: breast cancer cells


title: 1833-Control-1


title: At061_YY_Col_H3_2

type: genomic

city: Athens

first: Xiaoyu

last: Zhang

state: GA

address: 4409 Miller Plant Sci. bldg

department: Department of Plant Biology

institute: University of Georgia

description:
15 min sonication + anti-H3
ChIP DNA

hyb_protocol: Hybridized as previously described (Zhang et al., 2006) according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing: Enrichment of H3K9ac and H3K14ac relative to H3 was calculated using TileMap (Hidden Markov model probabilities) as described (Ji and Wong 2005; Zhang et al 2006)

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: H3 ChIP-chip

label_protocol: Labelled as previously described (Zhang et al., 2006) according to Affymetrix specifications.

growth_protocol: Arabidopsis plants were grown on soil under 24-hour light.

extract_protocol: ChIP-chip was performed as described (Costas et al., 2011). Antibodies used for H3K9ac, H3K14ac and H3 are AB4441 (Abcam; Cambridge, MA; LOT# 511238), 07-353 (Millipore; Billerica, MA; LOT# DAM1462567), and AB1791 (Abcam; Cambridge, MA), respectively.

treatment_protocol: Above-ground tissues of 3-week-old seedlings were harvested for ChIP-chip experiments using the Affymetrix Arabidopsis Tiling 1.0R arrays as described

tag: antibody

tag: develpmental stage

value: 3-week-old seedlings

tag: antibody catalog/vendor

value: AB1791 (Abcam)


title: At062_YY_Col_H3_3

description:
15 min sonication + anti-H3
ChIP DNA


title: At060_YY_Col_H3_1

description:
15 min sonication + anti-H3
ChIP DNA


title: CNIT 40K9mo


title: ACR BxBC 30K_22mo

source_name: Kidney biopsies from transplant recipients with histological diagnosis of Acute Rejection (AR or ACR)

value: Acute Rejection (AR or ACR)


title: testes_PWD_RP_rep1

description: SAMPLE 1

value: pachytene spermatocytes (RP)


title: At068_YY_Col_H3K9ac_3

description:
15 min sonication + anti-H3K9ac
ChIP DNA

source_name: H3K9ac ChIP-chip

value: AB4441 (Abcam)


title: ACR BxBC 2K_40mo

value: kidney biopsy


title: Blood from Stage I (GP2477_WB_143164HP133A11)

value: blood

value: Stage I

value: Smoker Controls


title: At067_YY_Col_H3K9ac_2


title: Blood from Stage IV (GP2477_WB_143167HP133A11)

value: M

value: Stage IV


title: ACR BxBC 1K_4mo


title: Blood from Stage I (GP2477_WB_143163HP133A11)

value: Non-smoker Controls


title: Blood from Stage III (GP2477_WB_143160HP133A11)

value: COPD Subjects


title: ACR 164K69


title: ACR BxBC 31K_77mo


title: At066_YY_Col_H3K9ac_1


title: At059_YY_Col_H3K14ac_3

description:
15 min sonication + anti-H3K14ac
ChIP DNA

source_name: H3K14ac ChIP-chip

value: 07-353 (Millipore)


title: ACR 162K18


title: At058_YY_Col_H3K14ac_2


title: WT, vehicle treated, rep4

city: Lausanne

first: Tamara

last: Seredenin

address: AI2135 Station 15 EPFL

country: Switzerland

institute: EPFL

description: Gene expression data

hyb_protocol: cRNA (15 ug) was hybridized to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) at  45°C for 17 hours, washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: Microarray quality control was performed using the software package provided on RACE (http://race.unil.ch). Chips with a median normalized unscaled standard error  > 1.05 were excluded. Affymetrix annotations (version 30) were used for probeset-to-gene assignments. T-test was performed to assess the differences in gene expression between treated and untreated groups for each genotype.

source_name: WT mouse treated with vehicle

label_protocol: Biotinylated cRNAs were prepared from 200ng of total RNA using the GeneChip® 3’ IVT Express Kit (Affymetrix) following the instructions of the manufacturer.

growth_protocol: Mouse housing conditions, genotyping, behavioral assessment, and statistical analysis were performed as per (Hockly et al., 2006; Hockly et al., 2003; Woodman et al., 2007) except that RotaRod and open field analysis were performed over the course of 5 and 30 minutes respectively. Mice were sex matched for each treatment group for all experiments.

extract_protocol: QIAZOL (Qiagen) was added to frozen dissected brain regions (0.2 ml for striatum) prior to homogenisation. The homogenate was flash-frozen and stored at -80oC until all samples are prepared. The homogenate was thawed and placed at room temperature for five minutes to promote dissociation of nucleoprotein complexes. An equal volume of chloroform was added prior to thourough mixing. The homogenate was incubated at room temperature for 3 minutes then centrifuged at 13,000 x g for 15 min at 4°C.  The upper aqueous phase was transferred to a new eppendorf and one volume of 70% ethanol was added, then mixed thoroughly. 700μl of sample was transferred to a RNeasy Mini spin column (Qiagen) in a 2ml collection tube. The column/tube assembly was centrifuged for 15 sec at maximum speed at room temperature. The flow-through was discarded and the centrifugation step was repeated with remaining solution from the previous step. 350μl Buffer RW1 was added to the RNeasy spin column and centrifuged for 15 sec at max speed at room temperature prior to discarding the flow-through. DNase treatment was performed using Qiagen RNase-Free DNase Set. For each sample 10μl DNaseI stock solution (lypholised DNase was reconstituted in 550μl RNase free water, aliquoted & stored at -20°C) was diluted in 70μl RDD buffer (i.e. 1:8 dilution), and mixed gently by inverting the tube. 80μl of the DNaseI mix was added to each RNeasy spin column membrane, and incubated at room temperature for 15 min. The washes were performed by adding 350μl Buffer RW1 to the RNeasy spin column prior to centrifuging for 15 sec at max speed at room temperature and discarding the flow-through. 500μl Buffer RPE (with ethanol) was added to the RNeasy spin column, centrifuged for 15 sec at max speed at room temperature and the flow-through was discarded. The step was repeated with a further 500μl Buffer RPE.  The RNeasy spin column was placed in new 2ml collection tube & centrifuged for 15 sec at max speed at room temperature to remove any residual ethanol. The RNeasy spin column was placed in a new 1.5ml collection tube and 50μl RNase-free water was added directly to the membrane and incubated at room temperature for 1 min. The column assembly was centrifuged for 15 sec at max speed at room temperature. The elution step was repeated by reusing the eluate. The RNA was stored at -80°C. The RNA was quantified using an Agilent Bioanalyser according to the manufacturer’s instructions prior to cDNA synthesis.

treatment_protocol: HSP990 was obtained from Novartis pharmaceuticals via the CHDI foundation. In  order to administer HSP990 to mice, the compound was added to an opaque solution of Saline 10% NVP formulation solution. The mixture was briefly sonicated at high frequency in a water bath and mixed thoroughly to form a uniform suspension. Compound or vehicle alone were administered to mice by oral gavage with thorough mixing performed between dosing to ensure the suspension remained even. Mice were weighed and dosed in the afternoon, and typically dissected at the end of their light cycle.

value: WT

tag: treatment

value: vehicle

value: male

tag: genetic background

value: CBA X C57Bl/6

value: brain striatum

value: 12 weeks


title: WT, vehicle treated, rep7

description: Gene expression data

tag: tissue


title: ACR 113K_1mo

tag: histological diagnosis

value: Acute Rejection (AR or ACR)


title: Blood from Stage I (GP2477_WB_143158HP133A11)

tag: age

tag: gender

value: F


title: WT, vehicle treated, rep3

description: Gene expression data


title: WT, vehicle treated, rep6

description: Gene expression data


title: ACR 179K6

value: kidney biopsy


title: Blood from Stage III (GP2477_WB_143159HP133A11)

value: blood

tag: gold stage

value: Stage III

tag: plateid


title: Blood from Stage I (GP2477_WB_143161HP133A11)

value: Stage I

tag: subject type

value: Smoker Controls


title: At057_YY_Col_H3K14ac_1

value: 3-week-old seedlings


title: ACR 94-K


title: WT, vehicle treated, rep1

description: Gene expression data

tag: strain


title: WT, vehicle treated, rep2

description: Gene expression data


title: Blood from Stage I (GP2477_WB_143157HP133A11)

value: M


title: ACR 59K9


title: WT, HSP990 treated, rep9

description: Gene expression data

source_name: WT mouse treated with HSP90 inhibitor


title: ACR 17K20


title: Blood from Stage I (GP2477_WB_143154HP133A11)


title: ACR 4K18


title: WT, HSP990 treated, rep10

description: Gene expression data


title: Blood from Stage IV (GP2477_WB_143151HP133A11)

value: Stage IV

value: COPD Subjects


title: Blood from Stage II (GP2477_WB_143155HP133A11)

value: Stage II


title: testes_PWD_RP_rep2

description: SAMPLE 2

value: PWD/Ph

value: 8-10 weeks

tag: cell type

value: pachytene spermatocytes (RP)


title: WT, HSP990 treated, rep8

description: Gene expression data

value: WT

value: male

value: CBA X C57Bl/6

value: brain striatum


title: Blood from Stage II (GP2477_WB_143150HP133A11)


title: Blood from Stage II (GP2477_WB_143149HP133A11)

value: F


title: ACR 28K3

value: kidney biopsy

value: Acute Rejection (AR or ACR)


title: Blood from Stage I (GP2477_WB_143153HP133A11)

value: blood

value: Stage I


title: WT, HSP990 treated, rep4

description: Gene expression data

value: 12 weeks


title: IF/TA 175KCAN

source_name: Kidney biopsies from transplant recipients with histological diagnosis of IF/TA

value: IF/TA


title: WT, HSP990 treated, rep6

description: Gene expression data


title: WT, HSP990 treated, rep5

description: Gene expression data


title: IF/TA 117KCAN


title: IF/TA 136-K


title: Blood from Stage I (GP2477_WB_143156HP133A11)

value: M

value: Smoker Controls


title: Blood from Stage II (GP2477_WB_143152HP133A11)

value: Stage II

value: COPD Subjects


title: WT, HSP990 treated, rep3

description: Gene expression data


title: WT, HSP990 treated, rep7

description: Gene expression data


title: Blood from Stage I (GP2477_WB_143148HP133A11)


title: IF/TA 111-K


title: IF/TA 108-K


title: IF/TA 134-K


title: Blood from Stage II (GP2477_WB_143146HP133A11)


title: WT, HSP990 treated, rep2

description: Gene expression data


title: IF/TA 107-K


title: Blood from Stage IV (GP2477_WB_143145HP133A11)

value: Stage IV


title: Blood from Stage I (GP2477_WB_143147HP133A11)


title: HeLa PNPase Overexpressed_3

source_name: HeLa cells stably transfected with pTRIPZ-hPNPase induced with doxycycline _replicate 3

growth_protocol: The human melanoma cell line HO-1 and the HeLa cell line were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Invitrogen Life Technologies) supplemented with 10% fetal bovine serum (FBS; Sigma) and 5% penicillin/streptomycin (Gibco).

extract_protocol: Trizol lysates were used for the extraction of total RNA on the MagMAX™ Express Magnetic Particle Processor using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion/InvitrogenTM Life Technologies, Carlsbad, CA)

treatment_protocol: Lentiviral constructs (pGIPZ) expressing GFP were purchased from Open Biosystems that either contained non-silencing short hairpin RNA (shRNA) or shRNAs against hPNPaseold-35. For the overexpression experiments, The full-length cDNA of hPNPaseold-35 with a C-terminal HA tag was cloned into a Tet-On pTRIPZ vector (Open Biosystems).

value: pTRIPZ-hPNPase induced with doxycycline

tag: cell line

value: HeLa


title: IF/TA 2K-2KCAN


title: HeLa PNPase Overexpressed_2

source_name: HeLa cells stably transfected with pTRIPZ-hPNPase induced with doxycycline _replicate 2


title: Blood from Stage II (GP2477_WB_143165HP133A11)


title: Blood from Stage III (GP2477_WB_143142HP133A11)

value: Stage III


title: IF/TA 9KCAN


title: R6/2, vehicle treated, rep4

description: Gene expression data

source_name: R6/2 mouse treated with vehicle

value: vehicle

value: male

value: CBA X C57Bl/6


title: R6/2, vehicle treated, rep5

description: Gene expression data

value: brain striatum


title: WT, HSP990 treated, rep1

description: Gene expression data

value: WT


title: Blood from Stage III (GP2477_WB_143166HP133A11)

value: blood


title: Blood from Stage I (GP2477_WB_143141HP133A11)

value: F

value: Stage I


title: HeLa Control_3

source_name: HeLa cells transfected with scrambled shRNA_replicate 3

value: scrambled shRNA


title: HeLa PNPase Overexpressed_1

source_name: HeLa cells stably transfected with pTRIPZ-hPNPase induced with doxycycline _replicate 1


title: Blood from Stage III (GP2477_WB_143138HP133A11)

value: M


title: Blood from Stage II (GP2477_WB_143137HP133A11)


title: HeLa Control_1

source_name: HeLa cells transfected with scrambled shRNA_replicate 1


title: HeLa Control_2

source_name: HeLa cells transfected with scrambled shRNA_replicate 2


title: Blood from Stage II (GP2477_WB_143144HP133A11)

source_name: blood


title: R6/2, vehicle treated, rep7

description: Gene expression data

value: 12 weeks


title: R6/2, vehicle treated, rep1

description: Gene expression data


title: Blood from Stage I (GP2477_WB_143143HP133A11)

value: Smoker Controls


title: Blood from Stage III (GP2477_WB_143140HP133A11)

value: COPD Subjects


title: R6/2, vehicle treated, rep6

description: Gene expression data


title: R6/2, HSP990 treated, rep8

description: Gene expression data

source_name: R6/2 mouse treated with HSP90 inhibitor


title: R6/2, HSP990 treated, rep6

description: Gene expression data


title: R6/2, vehicle treated, rep3

description: Gene expression data


title: IF/TA 1K-1KCAN

value: kidney biopsy

value: IF/TA


title: R6/2, vehicle treated, rep2

description: Gene expression data


title: Blood from Stage I (GP2477_WB_143139HP133A11)


title: WT, vehicle treated, rep5

description: Gene expression data


title: R6/2, HSP990 treated, rep5

description: Gene expression data


title: Blood from Stage II (GP2477_WB_143136HP133A11)

value: Stage II


title: HO-1 PNPase shRNA stable knockdown_2 (2)

source_name: Human HO-1 melanoma cells transfected with PNPase shRNA_replicate 2

value: PNPase shRNA


title: HO-1 PNPase shRNA stable knockdown_3 (2)

source_name: Human HO-1 melanoma cells transfected with PNPase shRNA_replicate 3


title: R6/2, HSP990 treated, rep4

description: Gene expression data


title: Blood from Stage III (GP2477_WB_143135HP133A11)

value: Stage III


title: R6/2, HSP990 treated, rep7

description: Gene expression data

value: male


title: HO-1 Control_scrambled shRNA_2 (2)

source_name: Human HO-1 melanoma cells transfected with scrambled shRNA_replicate 2


title: HO-1 PNPase shRNA stable knockdown_1 (2)

source_name: Human HO-1 melanoma cells transfected with PNPase shRNA_replicate 1


title: R6/2, HSP990 treated, rep2

description: Gene expression data

value: CBA X C57Bl/6


title: Blood from Stage I (GP2477_WB_143133HP133A11)


title: R6/2, HSP990 treated, rep3

description: Gene expression data

value: brain striatum


title: Blood from Stage I (GP2477_WB_143129HP133A11)

value: Non-smoker Controls


title: Blood from Stage II (GP2477_WB_143132HP133A11)

value: blood


title: SkinWound_WT-3_3d_rep1

city: Nagasaki

first: Ryoichi

last: Mori

address: 1-12-4 Sakamoto

department: School of Biomedical Sciences

country: Japan

institute: Nagasaki University

description: Gene expression at wound site on 3 days after injury

hyb_protocol: Fragmentation Cy3-cRNA was hybridized to SurePrint G3 Mouse GE microarray, 8 x 60K (Agilent) at 65 ºC for 17 hrs in a rotating Agilent hybridization oven according to the manufacturers instructions. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Skin wound, 3 days, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, one color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Qiazol (QIAGEN) and further purified using RNeasy MinElute Cleanup kit (QIAGEN) according to manufacture’s instruction.

treatment_protocol: Made 4 full-thickness excisional (4-mm biopsy punch; Kai Industries) in dorsal skin after shaving under anesthesia, and then wounds were harvested using 6-mm biopsy punch.

value: Male

value: skin

value: wound

tag: genotype

value: wild type


title: Blood from Stage II (GP2477_WB_143131HP133A11)

value: M


title: HO-1 Control_scrambled shRNA_1 (2)

source_name: Human HO-1 melanoma cells transfected with scrambled shRNA_replicate 1

value: scrambled shRNA


title: Blood from Stage II (GP2477_WB_143130HP133A11)

value: COPD Subjects


title: Blood from Stage II (GP2477_WB_143127HP133A11)

value: F


title: E10.25_WT_3

city: Nice

first: Andreas

last: Schedl

address: Parc Valrose

department: iBV

country: France

institute: University of Nice

hyb_protocol: Each microarray was hybridized with 20ug of DIG- labeled cRNA  at 55C for 16h. Enhanced signals were generated by first incubating the micrarrays with an anti-digoxigenin-alkaline phosphatase (AP) and performing a rinse washing to remove any unbound antibody.  Finally,  enhancing solution was added to the microarray to increase the quantum yield of the chemiluminescent reaction.      ,

scan_protocol: Images were collected using the ABS1700 Chemiluminescent Microarray Analyzer. Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background and spatially normalized using the Expression Array System Analyzer Software Version 1.1.1)

data_processing: Data were processed in Gene Spring GSX version 7.3.1 software followed by per-chip median polishing and per gene normalization to specific samples. Statistical analysis was performed using Welch parametic t-test on genes given as present calls and using a p value equal or less than 0.05 as a measure of significance for differential epression.

label: DIG-UTP

source_name: metanephric kidney

label_protocol: UTP- Digoixigenin-labeled cRNA was generated and linearly amplified using the Nano Amp RT-IVT Labeling Kit (Applied Biosystems) according to maufacturers instructions. The equality and amount of labeled cRNA were assessed with the Agilent 2100 Bioanalyzer and the ND-1000 spectrophotometer, respectively. cRNA was fragmented to 100-400 bases by incubation with fragmentation buffer.

growth_protocol: Mice carrying the Wt1 mutant allele (Kreidberg et al., 1993, Cell) were kept on a mixed genetic background and allowed free access to a standard diet and water.

extract_protocol: Total RNA was extracted from microsurgically dissected metanephric kidneys using the RNeasy MicroKit (Qiagen) followed by column DNase digestion to remove any contaminating genomic DNA. To obtain 1ug of RNA, 16 kidneys of a given genotype were pooled for each sample.

treatment_protocol: Timed matings were performed and embryos dissected at  E10.25 (tail somite 8-13) .

value: kidney

value: mixed (C57Bl6/DBA)

tag: developmental stage

value: embryo

tag: genotype/variation


title: Blood from Stage I (GP2477_WB_143134HP133A11)

value: Stage I

value: Smoker Controls


title: SkinWound_ht-3_3d_rep1

value: FoxO1 +/-


title: SkinWound_ht-1_3d_rep1


title: HO-1 Control_scrambled shRNA_3 (2)

source_name: Human HO-1 melanoma cells transfected with scrambled shRNA_replicate 3


title: E10.25_WT_4


title: E10.25_WT_2


title: SkinWound_ht-2_3d_rep1


title: Blood from Stage I (GP2477_WB_143128HP133A11)


title: Blood from Stage I (GP2477_WB_143126HP133A11)


title: E10.25_WT_1


title: R6/2, HSP990 treated, rep1

description: Gene expression data

value: male

value: CBA X C57Bl/6

value: brain striatum

value: 12 weeks


title: Hyperglycemic 16 week old NOD PLN - sample 1

city: Stanford

first: Linda

last: Yip

state: CA

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

institute: Stanford University

description: Gene expression in the pancreatic lymph node of a hyperglycemic 16-week-old NOD mice compared to that of euglycemic age-matched NOD mice - sample 1

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels. Data was extracted using Feature Extraction software.

data_processing: Data were processed using Genespring 11.5.  Samples were filtered for detected entities.

source_name: pancreatic lymph nodes

label_protocol: 1 ug of total RNA was labeled using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: NOD mice were bred at the Stanford School of Medicine Animal facility.  All mice were maintained under pathogen-free conditions according to institutional guidelines under approved protocols in the Stanford Medical Center’s Department of Comparative Medicine.

extract_protocol: Total RNA was extracted using Trizol Reagent combined with the Qiagen Rneasy Mini Kit.

treatment_protocol: pancreatic lymph node tissues were extracted from mice and homogenized in Trizol Reagent.

value: NOD

value: 16 weeks old

tag: Sex

value: female

tag: glycemic state

value: hyperglycemic (blood glucose >500 mg/dl)

source_name: pancreatic lymph nodes (pool of 2 individuals)

value: euglycemic (blood glucose <200 mg/dl)


title: Hyperglycemic 16 week old NOD PLN - sample 2

description: Gene expression in the pancreatic lymph node of a hyperglycemic 16-week-old NOD mice compared to that of euglycemic age-matched NOD mice - sample 2


title: E10.25_KO_4


title: input replicate4

type: SRA

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

country: Italy

institute: EMBL

description:
input
inputreplicate1_2_3_4_Scaled.wig

library_source: genomic

data_processing:
In brief, all samples were sequenced on an Illumina Genome Analyzer (GAIIx for ChIP-seq and RNA-seq, or HIseq2000 for MNase-seq). Quality assessment and filtering of ChIP-seq and MNase-seq sequences were performed using either the Integrated Eland software or FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) to pre-process FastQ files. Quality score and nucleotide composition at each position of the sequenced tags were assessed by box and bar plotting using FastX-Toolkit standard functions. Quality controls (QC) and filtering of RNA samples were performed using fastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), FASTX-toolkit and Cutadapt (http://code.google.com/p/cutadapt/). Adapters were removed (Cutadapt) and a QC report was generated (fastQC). Sequences were further trimmed at nucleotide 55 and quality filtered as for DNA sample (FASTX-toolkit).
All samples were aligned to human genome (hg19, GRCh37) using Bowtie aligner (allowing 2 mismatches, keeping uniquely aligned reads only)
Piles of tags with same coordinates, due to artifacts of PCR or unannotated regions of the genome were removed according to a thresholding method, except for RNA-seq experiment
Uniquely aligned tags were further elongated after estimating optimal elongation size in silico and enabling to use the original fragment length for further processing.
For ChIP-seq experiments, all samples were input subtracted and signals were scaled so that the same number of units appeared in each experiment after merging of the replicates.
For nucleosome mapping, MNAse-seq experiment in Raji was sequenced in paired-end with higher depth than ChIP-seq in Hiseq2000. Two types of analyses were applied to this data: nucleosomes density and nucleosomes midpoint  that allow to score more specifically for depletion or positioning, respectively. For nucleosome density, paired tags were processed so to be directly connected and to retrieve original fragments (orphan tags were connected to the corresponding pairs using the estimated elongation size computed as described above). The input subtraction step was omitted. For nucleosomes midpoint analyses, the middle of elongated fragments was set as reference allowing locating the maximum signal approximately at the midpoint of the nucleosomes (dyads).
For all experiments, the number of tags covering each nucleotide of the genome was computed and averaged in bins of 50 nucleotides. The scores of bins were rescaled (after input subtraction when applicable) to reduce over-representation of particular genomic regions and signal/noise ratio.
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: wig, contains score of binding, nucleosomes occupancy and short RNAs expression.
Supplementary_files_format_and_content: raw.txt.gz, Eland processed file

source_name: Raji B-cell line

growth_protocol: Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum (FCS), 100U/ml penicillin, 100mg/ml streptomycin and 2mM L-glutamine (Gibco/Invitrogen) at 37°C and 5% CO2. For the removal of Pol II, cells were treated with 2.5 μg/ml of α-amanitin for the indicated time points for the WT Raji cells.

extract_protocol: Total RNA was extracted from 1x107 Raji cells using TRIzol (Life Technologies, USA) according to the manufacturer’s instructions with some modifications to ensure higher recovery rates of small RNAs. This was achieved by addition of 10μg of linear acrylamide (Life Technologies, USA) before RNA precipitation. DNA was digested using the rigorous Turbo DNase (Ambion, USA) treatment as per manufacturer’s instructions. RNA quantity was measured on a Qubit apparatus (Life Technologies, USA) using RNA assay kit the quality was verified using RNA pico chips on a 2100 Bioanalyzer (Agilent Technologies, USA).  Before preparation of sequencing libraries, small RNAs were enriched from 10µg total RNA by using mirVana RNA Isolation kit (Life Technologies, USA) using manufacturer’s protocol for small RNA enrichment. Strand specific RNA-seq library was constructed with ScriptMiner Small RNA-seq Library Preparation Kit (Epicenter, USA) according to manufacturer’s recommended protocol. Briefly, after both 5’ and 3’ adapter ligation, resulting cDNA library was PCR amplified with 14 amplification cycles. Purified library DNA was run on a 10% TBE-PAGE gel and library DNA corresponding to transcripts between 15nt-50nt was cut from the gel and transferred into 0.5mL tubes with punctured bottoms which were in turn placed in 2mL collection tubes. Gel slices were crushed into 2mL tubes by a 2 minutes centrifugation at 14000g. For library DNA elution by soaking, 0.4ml of 0.3M NaCl was added to each tube, before a 4 hour rotation at room temperature. After removal of gel particles using 0.22μm cellulose acetate filters, 10μg of linear acrylamide (Life Technologies, USA) and 2.5 volumes (approximately 1ml) of ice-cold absolute ethanol were added. After 30 minutes incubation at -80°C, the eluted cDNA was precipitated by centrifugation at 4°C and maximum speed for 45 minutes. The pellet was washed with 1ml of cold 80% ethanol, air dried and resuspended in 20μl of water. The size-selected small RNA library DNA was quantified using a Qubit apparatus with dsDNA High Sensitivity kit (Life Technologies, USA) and verified using DNA High Sensitivity 2100 Bioanalyzer chips (Agilent Technologies, USA).

value: Raji B


title: Blood from Stage I (GP2477_WB_143125HP133A11)

value: blood

value: F


title: SkinWound_WT-1_3d_rep1

value: Male

value: skin

tag: treatment

value: wound

value: wild type


title: SkinWound_WT-2_3d_rep1


title: E10.25_KO_1

value: kidney

value: mixed (C57Bl6/DBA)

value: embryo


title: E10.25_KO_3


title: Blood from Stage I (GP2477_WB_143122HP133A11)

value: M

value: Stage I

value: Smoker Controls

tag: hyb date


title: Blood from Stage II (GP2477_WB_143124HP133A11)

tag: tissue

value: Stage II

value: COPD Subjects


title: Blood from Stage III (GP2477_WB_143123HP133A11)

value: Stage III


title: Blood from Stage III (GP2477_WB_143121HP133A11)


title: 8W_2Gy_24h_03

city: Chiba

first: Kentaro

last: Ariyoshi

state: Chiba

address: Inage-ku, anagawa 4-9-1

institute: NIRS

description: Gene expression in 8 week old C3H Bone marrow tissue_24 hours after 2Gy exposure

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >11.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 8 week old C3H 2Gy_24h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Maxwell 16 Instrument and system (Promega) following the manufacturer's recommendations.

treatment_protocol: C3H female mice at 1 week and 8 weeks of age were irradiated 0.6 Gy/min gamm-ray.

tag: background strain

value: female

value: 8 weeks old

tag: tissue type

value: bone marrow


title: 8W_2Gy_24h_01

tag: gender

tag: age


title: Blood from Stage II (GP2477_WB_143118HP133A11)

value: blood

tag: gold stage

tag: plateid


title: 8W_2Gy_6h_03

description: Gene expression in 8 week old C3H Bone marrow tissue_6 hours after 2Gy exposure

source_name: 8 week old C3H 2Gy_6h


title: 8W_2Gy_6h_01


title: Blood from Stage II (GP2477_WB_143120HP133A11)

value: F

tag: subject type


title: 8W_2Gy_24h_02


title: Blood from Stage I (GP2477_WB_143119HP133A11)


title: E10.25_KO_2

tag: strain


title: 8W_0Gy_03

description: Gene expression in 8 week old C3H Bone marrow tissue_control

source_name: 8 week old C3H Control


title: Blood from Stage III (GP2477_WB_143116HP133A11)


title: Blood from Stage I (GP2477_WB_143117HP133A11)


title: Ser7P replicate1

description:
protein associated DNA
Ser7P_replicate1_replicate2_Scaled_BGSub.wig

tag: cell line

value: Raji B

tag: antibody


title: Ser5P replicate2

description:
protein associated DNA
Ser5P_replicate1_replicate2_Scaled_BGSub.wig


title: Ser5P replicate1


title: Blood from Stage I (GP2477_WB_143115HP133A11)


title: Ser7P replicate2


title: Blood from Stage III (GP2477_WB_143113HP133A11)


title: 8W_2Gy_6h_02


title: Blood from Stage II (GP2477_WB_143112HP133A11)


title: 1W_2Gy_24h_02

description: Gene expression in 1 week old C3H Bone marrow tissue_24 hours after 2Gy exposure

source_name: 1 week old C3H 2Gy_24h

value: 1 week old


title: 8W_0Gy_02


title: 8W_0Gy_01


title: Blood from Stage III (GP2477_WB_143114HP133A11)

source_name: blood


title: 1W_2Gy_24h_03


title: 1W_2Gy_24h_01


title: Blood from Stage II (GP2477_WB_143111HP133A11)


title: Blood from Stage II (GP2477_WB_143109HP133A11)


title: 1W_2Gy_6h_03

description: Gene expression in 1 week old C3H Bone marrow tissue_6 hours after 2Gy exposure

source_name: 1 week old C3H 2Gy_6h


title: 1W_0Gy_03

description: Gene expression in 1 week old C3H Bone marrow tissue_control

source_name: 1 week old C3H Control


title: 1W_2Gy_6h_01


title: 1W_2Gy_6h_02


title: Blood from Stage I (GP2477_WB_143108HP133A11)


title: H3K4me3 replicate1

description:
protein associated DNA
H3K4me3_replicate1_replicate2_Scaled_BGSub.wig

tag: antibody vendor/catalog

value: Abcam (ab8580)


title: H3K36me3 replicate1

description:
protein associated DNA
H3K36me3_replicate1_replicate2_ScaledBGSub.wig

value: Abcam (ab9050)


title: H3K36me3 replicate2


title: Blood from Stage III (GP2477_WB_143104HP133A11)


title: 1W_0Gy_01


title: Blood from Stage III (GP2477_WB_143106HP133A11)


title: Blood from Stage I (GP2477_WB_143102HP133A11)


title: IEC_IKK-AA_bCATca_rep. 2

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

country: Germany

institute: University Hospital Erlangen

hyb_protocol: Biotinylated cRNA was hybridized on MOE430A 2.0 GeneChips, that were stained, washed and scanned following Affymetrix standard procedures.

scan_protocol: standard Affymetrix protocol

data_processing: The probe level data (CEL files) were processed for global normalization and generation of expression values using the robust multi-array average algorithm (RMA) of the “affy package” in the R software environment (http://www.R-project.org).

source_name: IECs_inducible beta-Catenin-C.A. and IKKalphaAA/AA_15 days tamoxifen

label_protocol: Per sample, 200 ng total RNA was processed using Ambion’s MessageAmp II Biotin Enhanced labeling kit according to the manufacturer’s instructions.

growth_protocol: Mice were fed by gavage with tamoxifen on 5 consecutive days. 15 days after starting tamoxifen, intestinal epithelial cells were prepared.

extract_protocol: total RNA was extracted with Qiagen Rneasy Mini Kit.

tag: strain background

value: mixed C57BL/6 x 129Sv x FVB

tag: genotype/variation

tag: time point

value: 15 days after starting tamoxifen

tag: cell type

value: Intestinal epithelial cells (IECs)


title: IEC_bCATca_rep. 1

source_name: IECs_inducible beta-Catenin-C.A._15 days tamoxifen


title: 1W_0Gy_02

description: Gene expression in 1 week old  C3H Bone marrow tissue_control


title: Blood from Stage II (GP2477_WB_143105HP133A11)

value: M

tag: hyb date


title: IEC_IKK-AA_rep. 2

source_name: IECs_IKKalphaAA/AA_15 days tamoxifen

value: IkkαAA/AA


title: Blood from Stage III (GP2477_WB_143101HP133A11)

tag: tissue


title: Blood from Stage I (GP2477_WB_143103HP133A11)

value: Stage I

value: Smoker Controls


title: IEC_IKK-AA_bCATca_rep. 1


title: IEC_WT_rep. 1

source_name: IECs_WT control mice _15 days tamoxifen

value: wild type


title: IEC_bCATca_rep. 2


title: IEC_IKK-AA_rep. 1


title: IEC_WT_rep. 2


title: Blood from Stage I (GP2477_WB_143100HP133A11)


title: SD1c patient  in the SD1c family-aCGH

city: Chongqing

first: Hong

last: Guo

address: 30# Gaotanyan St. Shapingba District

department: Medical Genetics

country: China

institute: Third Military Medical University

hyb_protocol: The labeled genomic DNA (31μg) was dried at 45℃ and diluted in 5.6 μl Sample Tracking Control. Then hybridized in 14.4 μl Hybridization solution (containing 2X Hybridization Buffer, Hybridization Component A, Alignment Oligo). Arrays were hybridized in Maui hybridization stations for 40-72 hr at 42 °C, and then washed in 42 °C with buffer (containing VWR Water, 10X Wash Buffer (I, II or III), 1M DTT) by using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on a NimbleGen MS 200 Microarray Scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed by using Nimblegen's standard protocol for SignalMap.

source_name: lymphocyte

label_protocol: 1. Add 4μL β-mercaptoethanol to 2200μL Random Primer Buffer, Mix by pulse-vortexing. Use 1050 μL Random Primer Buffer (containing β-mercaptoethanol) to dilute cy3-Random Nonamers and cy5-Random Nonamers respectively. 2. Add 500ng genomic DNA to LHC(Labeling and Hybridization Control). Then add 2μLLCH-1 to test Sample, and 2μLLCH-2 to Reference Sample, amount to 40μL respectively. Add test Sample (containing LLCH-1) to cy3-Random Nonamers, and Reference Sample (containing LLCH-2) to cy5-Random Nonamers, amount to 80μL respectively. 98 °C for 10 min，4°C for 2min. 3. Prepare dNTP/Klenow Master Mix (20μL): 8μL Nuclease-free Water, 10μL 10mM dNTP Mix, 2μL Klenow Fragment (3’->5’ exo-)50U/μl. 4. Add dNTP/Klenow Master Mix (20μL) to Sample mixtures (80μL) respectively. 37 °C  for 2 hr. 5. Add 21.5μL Stop Solution to stop reaction. 6. Then purify the label reaction liquid.

extract_protocol: Use QIAamp DNA Blood Mini kit to extract genomic DNA. 1. Pipet 20 μl QIAGEN Protease (or proteinase K) into the bottom of a 1.5 ml microcentrifuge tube. 2. Add 200 μl whole blood in 200 μl PBS. Add 4 μl of an RNase A stock solution (100 mg/ml) to the sample. 3. Add 200 μl Buffer AL to the sample. Mix by pulse-vortexing for 15 s. 4. Incubate at 56°C for 10 min. DNA yield reaches a maximum after lysis for 10 min at 56°C. 5. Briefly centrifuge the 1.5 ml microcentrifuge tube to remove drops from the inside of the lid. 6. Add 200 μl ethanol (96–100%) to the sample, and mix again by pulse-vortexing for 15 s. After mixing, briefly centrifuge the 1.5 ml microcentrifuge tube to remove drops from the inside of the lid. 7. Carefully apply the mixture from step 6 to the QIAamp Mini spin column (in a 2 ml collection tube) without wetting the rim. Close the cap, and centrifuge at 6000 x g (8000 rpm) for 1 min. Place the QIAamp Mini spin column in a clean 2 ml collection tube (provided), and discard the tube containing the filtrate. 8. Carefully open the QIAamp Mini spin column and add 500 μl Buffer AW1 without wetting the rim. Close the cap and centrifuge at 6000 x g (8000 rpm) for 1 min. Place the QIAamp Mini spin column in a clean 2 ml collection tube (provided), and discard the collection tube containing the filtrate. 9. Carefully open the QIAamp Mini spin column and add 500 μl Buffer AW2 without wetting the rim. Close the cap and centrifuge at full speed (20,000 x g; 14,000 rpm) for 3 min. 10. Recommended: Place the QIAamp Mini spin column in a new 2 ml collection tube and discard the old collection tube with the filtrate. Centrifuge at full speed for 1 min. 11. Place the QIAamp Mini spin column in a clean 1.5 ml microcentrifuge tube, and discard the collection tube containing the filtrate. Carefully open the QIAamp Mini spin column and add 200 μl Buffer AE or distilled water. Incubate at room temperature (15–25°C) for 1 min, and then centrifuge at 6000 x g (8000 rpm) for 1 min.

tag: ethnic group

value: Chinese Han

value: male

value: lymphocyte

tag: sample type

value: SD1c patient

source_name: human genomic DNA

value: common control


title: Blood from Stage I (GP2477_WB_143110HP133A11)

value: blood

tag: gender


title: Healthy control in the SD1c family-aCGH

value: healthy control


title: iPSC from Gage Lab Donor: control line cent Region: cloneID: 3-6 DiffWk: 4

city: Chapel Hill

first: Jason

middle: L

last: Stein

state: NC

address: Neuroscience Research Building 8109C, 115 Mason Farm Rd

department: Genetics

institute: UNC Chapel Hill

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Log2 normalization, quantile normalization, and ComBat batch correction

source_name: iPSC from fibroblast

label_protocol: Biotin

growth_protocol: phNPC: Neurobasal A (Invitrogen) supplemented with 10% BIT (Stem Cell Technologies), Antibiotics and Antimycotics (Gibco), GlutaMAX (Gibco), and Heparin (1 μg/mL; Sigma)] with freshly added EGF, FGF2, PDGF (each at 20 ng/mL; Peprotech), and LIF (2 ng/mL; Millipore); iPSC Kosik Lab: N2 induction media with bFGF; iPSC Gage Lab: DMEM/F12; 1X N2; 1X B27 and FGF2

extract_protocol: phNPCs: RNA was isolated using TRIzol reagent (Invitrogen) according to standard protocols; iPSC Kosik Lab: RNA was extracted using miRVANA kit, following the manufacturer’s protocol for total RNA; iPSC Gage Lab: Total cellular RNA was extracted using the RNeasy Protect Mini kit (QIAGEN, Valencia, CA).

treatment_protocol: phNPC: Neurobasal A (Invitrogen) supplemented with B27 (Gibco), GlutaMAX (Gibco), and Antibiotics and Antimycotics (Gibco)] as well as Retinoic Acid (500 ng/mL; Sigma), Forskolin (100 μM; Sigma), BDNF (10 ng/mL; Peprotech), NT-3 (10 ng/mL; Peprotech), and KCl (10mM); iPSC Kosik Lab: neurobasal media supplemented with N2, B27 and neurotrophic factor cocktail that included NT3, BDNF, and GDNF; iPSC Gage Lab: DMEM/F12, N2, BDNF/GDNF, and laminin.

tag: donor id

value: control line cent

tag: region id

value: iPSC from Gage Lab

tag: differentiation wk

tag: passage

tag: rin

tag: gestation wk

tag: ancestry

tag: Sex

tag: array batch


title: Blood from Stage II (GP2477_WB_143095HP133A11)

tag: age

value: F

tag: gold stage

value: Stage II

tag: plateid

tag: subject type

value: COPD Subjects


title: Blood from Stage II (GP2477_WB_143097HP133A11)

tag: tissue

tag: hyb date


title: Blood from Stage III (GP2477_WB_143093HP133A11)

value: Stage III


title: iPSC from Gage Lab Donor: control line chap Region: cloneID: 1-5 DiffWk: 4

value: control line chap

tag: cell type


title: iPSC from Gage Lab Donor: control line cent Region: cloneID: 3-3 DiffWk: 0


title: iPSC from Gage Lab Donor: control line cove Region: cloneID: 3-1 DiffWk: 0

value: control line cove


title: iPSC from Gage Lab Donor: control line chap Region: cloneID: 1-2 DiffWk: 0


title: iPSC from Gage Lab Donor: control line cent Region: cloneID: 3-6 DiffWk: 0


title: Blood from Stage II (GP2477_WB_143098HP133A11)

tag: gender

value: M


title: iPSC from Gage Lab Donor: control line cove Region: cloneID: 3-1 DiffWk: 4

tag: donor id


title: Blood from Stage III (GP2477_WB_143092HP133A11)


title: Liver  from day 450 male rat offspring from mothers fed a control diet rep C

city: Los Angeles

first: William

middle: Alexander

last: Freije

address: 650 Charles Young Drive, South CHS B8-127

department: Obstetrics and Gynecology

institute: UCLA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Standard Affymetrix scanning

data_processing: Microarrays were normalized using RMA in the Affymetrix software Expression Console

organism: Rattus norvegicus

source_name: Liver

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

growth_protocol: Male offspring from timed mated and pregnant Sprague-Dawley rats were used for these experiments.

extract_protocol: RNA extraction through Trizol followed by Rneasy Cleanup

treatment_protocol: Control (Con) offspring born to mothers who were fed normally throughout gestation and lactation; intra-uterine calorie restricted offspring (IUCR) born to mothers who had 50% restriction of calories from e11 to e21; and combined intra-uterine and post-natal calorie restriction (IPCR) who were born to mothers who received calorie restriction during both fetal growth (e11 to e21) and post-natally (p1-p21). Livers were collected at p21(day 21 of life) for Con and IPCR groups (IUCR withheld owing to ‘catch up” growth, and at p450 (day 450 of life) for Con, IUCR, and IPCR.

value: liver

tag: strain

value: Sprague-Dawley

value: day 450

tag: treatment

value: mothers fed a control diet


title: Blood from Stage III (GP2477_WB_143096HP133A11)


title: Liver  from day 450 male rat offspring from mothers fed a 50% calorie restricted diet during gestation rep C

value: male


title: Liver  from day 450 male rat offspring from mothers fed a 50% calorie restricted diet during gestation rep A


title: Liver  from day 450 male rat offspring from mothers fed a 50% calorie restricted diet during gestation rep B


title: Liver  from day 450 male rat offspring from mothers fed a 50% calorie restricted diet during gestation + lactation rep B

value: mothers fed a 50% calorie restricted diet during gestation and lactation


title: Blood from Stage I (GP2477_WB_143094HP133A11)

value: blood

value: Stage I

value: Smoker Controls


title: Liver  from day 450 male rat offspring from mothers fed a control diet rep B


title: Liver  from day 450 male rat offspring from mothers fed a 50% calorie restricted diet during gestation + lactation rep C


title: iPSC from Gage Lab Donor: control line chap Region: cloneID: 1-5 DiffWk: 0

tag: region id

value: iPSC from Gage Lab

tag: differentiation wk

tag: passage


title: iPSC from Gage Lab Donor: control line cove Region: cloneID: 3-7 DiffWk: 4

tag: rin

tag: gestation wk

tag: ancestry


title: Blood from Stage IV (GP2477_WB_143091HP133A11)

tag: age

value: F

value: Stage IV


title: iPSC from Gage Lab Donor: control line cent Region: cloneID: 3-3 DiffWk: 4

value: control line cent

tag: Sex

tag: array batch


title: Liver  from day 450 male rat offspring from mothers fed a 50% calorie restricted diet during gestation + lactation rep A


title: Blood from Stage II (GP2477_WB_143088HP133A11)

tag: gold stage

value: Stage II

tag: plateid

tag: subject type

value: COPD Subjects


title: Blood from Stage III (GP2477_WB_143089HP133A11)

tag: tissue

value: Stage III

tag: hyb date


title: iPSC from Gage Lab Donor: control line cove Region: cloneID: 3-7 DiffWk: 0

tag: donor id

value: control line cove

tag: cell type


title: Liver  from day 21 male rat offspring from mothers fed a 50% calorie restricted diet during gestation + lactation rep C

value: liver

tag: gender

tag: strain

value: day 21

tag: treatment


title: Liver  from day 450 male rat offspring from mothers fed a control diet rep A

value: Sprague-Dawley

value: day 450


title: iPSC from Gage Lab Donor: control line chap Region: cloneID: 1-2 DiffWk: 4

value: control line chap

tag: region id

tag: differentiation wk

tag: passage


title: Liver  from day 21 male rat offspring from mothers fed a control diet rep C

value: male

value: mothers fed a control diet


title: iPSC from Kosik Lab morphogens 8 days Donor: Control Tau6(IN2R) DiffWk: 1

value: Control Tau6(IN2R)

value: iPSC from Kosik Lab morphogens 8 days

tag: rin

tag: gestation wk

tag: ancestry


title: Liver  from day 21 male rat offspring from mothers fed a 50% calorie restricted diet during gestation + lactation rep A

tag: age

value: mothers fed a 50% calorie restricted diet during gestation and lactation


title: Blood from Stage III (GP2477_WB_143087HP133A11)

value: blood

value: M

tag: gold stage


title: Blood from Stage I (GP2477_WB_143090HP133A11)

value: Stage I

tag: plateid

value: Smoker Controls


title: Liver  from day 21 male rat offspring from mothers fed a 50% calorie restricted diet during gestation + lactation rep B


title: Blood from Stage I (GP2477_WB_143086HP133A11)

value: F

tag: subject type


title: Blood from Stage IV (GP2477_WB_143081HP133A11)

tag: tissue

value: Stage IV

value: COPD Subjects


title: Liver  from day 21 male rat offspring from mothers fed a control diet rep B

value: liver


title: Liver  from day 21 male rat offspring from mothers fed a control diet rep A

value: day 21


title: Blood from Stage I (GP2477_WB_143082HP133A11)

tag: hyb date


title: iPSC from Kosik Lab morphogens 4 days Donor: Control Tau6(IN2R) DiffWk: 1

tag: donor id

value: iPSC from Kosik Lab morphogens 4 days

tag: Sex

tag: array batch


title: Blood from Stage I (GP2477_WB_143107HP133A11)

tag: gender


title: iPSC from Kosik Lab morphogens 4 days Donor: Tau mutant Tau104 DiffWk: 4

value: Tau mutant Tau104

tag: cell type


title: Blood from Stage I (GP2477_WB_143085HP133A11)


title: Blood from Stage III (GP2477_WB_143080HP133A11)

value: Stage III


title: Blood from Stage III (GP2477_WB_143079HP133A11)


title: control kidney #3

city: Ramat Gan

first: Achia

last: Urbach

address: Bar Ilan

department: Faculty of Life Sciences

country: Israel

institute: Bar Ilan University

description: normal kidney biological replicate #3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using the average background subtracted method

source_name: control kidney #3

label_protocol: biotin

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Quality control was performed with Agilent Bioanalyser.

value: kidney

tag: tumor status

value: non-tumorous


title: iPSC from Kosik Lab morphogens 4 days Donor: Control Tau6(IN2R) DiffWk: 8

value: Control Tau6(IN2R)

tag: region id

tag: differentiation wk


title: Blood from Stage I (GP2477_WB_143084HP133A11)


title: control kidney #4

description: normal kidney biological replicate #4

source_name: control kidney #4


title: iPSC from Kosik Lab morphogens 8 days Donor: Tau mutant Tau104 DiffWk: 4

value: iPSC from Kosik Lab morphogens 8 days

tag: passage

tag: rin


title: kidney tumor #4

description: Lin28 derived Wilms tumor biological replicate #4

source_name: kidney tumor #4

value: tumorous


title: kidney tumor #3

description: Lin28 derived Wilms tumor biological replicate #3

source_name: kidney tumor #3


title: iPSC from Kosik Lab morphogens 4 days Donor: Control Tau6(IN2R) DiffWk: 0

tag: gestation wk

tag: ancestry


title: Blood from Stage I (GP2477_WB_143077HP133A11)

value: blood

tag: age

tag: gold stage


title: control kidney #1

description: normal kidney biological replicate #1

source_name: control kidney #1


title: kidney tumor #2

description: Lin28 derived Wilms tumor biological replicate #2

source_name: kidney tumor #2


title: control kidney #2

description: normal kidney biological replicate #2

source_name: control kidney #2


title: Blood from Stage II (GP2477_WB_143078HP133A11)

source_name: blood

value: M

value: Stage II

tag: plateid

tag: subject type


title: iPSC from Kosik Lab morphogens 8 days Donor: Control Tau6(IN2R) DiffWk: 0


title: iPSC from Kosik Lab morphogens 8 days Donor: Tau mutant Tau104 DiffWk: 1


title: iPSC from Kosik Lab morphogens 8 days Donor: Tau mutant Tau104 DiffWk: 8


title: Blood from Stage III (GP2477_WB_143099HP133A11)

tag: tissue

tag: hyb date


title: Blood from Stage I (GP2477_WB_143075HP133A11)

value: Stage I

value: Smoker Controls


title: iPSC from Kosik Lab morphogens 4 days Donor: Control Tau6(IN2R) DiffWk: 4

tag: donor id

tag: Sex


title: iPSC from Kosik Lab morphogens 8 days Donor: Tau mutant Tau104 DiffWk: 0

tag: array batch


title: Blood from Stage I (GP2477_WB_143074HP133A11)

tag: gender

value: F


title: kidney tumor #1

description: Lin28 derived Wilms tumor biological replicate #1

source_name: kidney tumor #1

tag: tumor status


title: Blood from Stage I (GP2477_WB_143072HP133A11)


title: D8.3

first: and

last: PhD

state: Illinois

address: 5841 South Maryland Avenue, MC 5032 Room AB540

department: Department of Surgery

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-18

hyb_protocol: randomly hybridized to BeadChips

scan_protocol: Raw signal intensities of each probe were obtained using BeadStudio (Illumina).

data_processing: Statistical analyses were done in R (2008). Inadequate Illumina microarray probes due to misannotations or intronic coverage were removed from analysis using the Mouse WG V2.0 R0 file within ReMOAT (http://remoat.sysbiol.cam.ac.uk) (Barbosa-Morais et al. , 2010). Adequately annotated probes were considered to be above background if at least 2 of the 3 replicates measured were above background at P ≤ 0.01. The data were transformed using the variance stabilization transformation method (Lin et al. , 2008) and normalized by robust spline normalization (Du et al. , 2008).

source_name: Day 8 Repeat 3

label_protocol: mRNA samples were in vitro labeled using the TargetAmp 1-Round Aminoallyl-aRNA Kit (Epicentre, Madison, WI) a

growth_protocol: Multi-layered secondary follicles (150-180 µm in diameter) were mechanically isolated from ovaries of 16-day-old mice and individually encapsulated in alginate (FMC BioPolymers, Philadelphia, PA) as previously described (Kreeger et al. , 2006, West-Farrell et al., 2009, Xu et al. , 2006a). Alginate-encapsulated follicles were placed in individual wells of a 96-well plate containing 100 µl of growth medium (alpha minimum essential medium (alphaMEM) supplemented with 10 mIU/ml recombinant FSH (Organon, Roseland, NJ), 3 mg/ml bovine serum albumin (MP Biomedicals, Irvine, CA), 1 mg/ml bovine fetuin (Sigma, St. Louis, MO), 5 µg/ml insulin, 5 µg/ml transferrin, and 5 ng/ml selenium and cultured for 2, 4, 5, 6, or 8 days for microarray analysis. Half of the culture medium was exchanged every 2 days.

treatment_protocol: At each time point, follicles were pooled (for the microarray, 20-40 follicles per group, n = 3 independent experiments) and transferred into 1 ml of Liebovitz L-15 medium containing 10 U/ml alginate lyase (Sigma) for 20 min at 37°C to remove them from alginate. Follicles were aspirated, transferred into microcentrifuge tubes, flash frozen in liquid nitrogen, and stored at -80°C until RNA isolation was performed.

tag: strain

value: Multi-layered secondary follicles (150-180 µm in diameter) mechanically isolated from ovaries of 16-day-old mice

value: 16-day-old mice


title: REF0.5

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
REF 0-5

source_name: Day 0 Repeat 5


title: iPSC from Kosik Lab morphogens 8 days Donor: Control Tau6(IN2R) DiffWk: 4

tag: region id

tag: cell type

tag: differentiation wk


title: Blood from Stage II (GP2477_WB_143070HP133A11)

value: COPD Subjects


title: iPSC from Kosik Lab morphogens 4 days Donor: Tau mutant Tau104 DiffWk: 8

value: iPSC from Kosik Lab morphogens 4 days

tag: passage

tag: rin

tag: gestation wk


title: Blood from Stage I (GP2477_WB_143076HP133A11)

tag: age

tag: gold stage


title: iPSC from Kosik Lab morphogens 4 days Donor: Tau mutant Tau104 DiffWk: 1

value: Tau mutant Tau104

tag: ancestry


title: D2.2

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-5

source_name: Day 2 Repeat 2

tag: tissue


title: Blood from Stage I (GP2477_WB_143069HP133A11)

tag: plateid

tag: subject type

tag: hyb date


title: REFA.5

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
REFA 5

source_name: Reference Repeat 5

extract_protocol: RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA).

value: Murine brain sample


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 12 Replicate: 2 Passage: 5

source_name: Human fetal tissue

tag: donor id

value: phNPC from Geschwind Lab

value: ASW

tag: Sex

tag: array batch


title: Blood from Stage I (GP2477_WB_143067HP133A11)

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

tag: gender


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 1 Replicate: 1 Passage: 9

tag: region id

value: MEX


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 1 Replicate: 1 Passage: 6

tag: cell type


title: Blood from Stage IV (GP2477_WB_143066HP133A11)

value: Stage IV


title: Blood from Stage I (GP2477_WB_143065HP133A11)


title: D8.2

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-17

source_name: Day 8 Repeat 2

tag: strain


title: REFA.4

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
REFA-4

source_name: Reference Repeat 4


title: Blood from Stage III (GP2477_WB_143068HP133A11)

value: Stage III


title: D2.3

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-6

source_name: Day 2 Repeat 3


title: D4.3

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-9

source_name: Day 4 Repeat 3


title: REF0.4

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
REF0-4

source_name: Day 0 Repeat 4


title: Blood from Stage III (GP2477_WB_143071HP133A11)

value: blood


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 1 Replicate: 2 Passage: 9

tag: differentiation wk

tag: passage


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 4 Replicate: 1 Passage: 5

tag: rin

tag: gestation wk

value: M


title: Blood from Stage I (GP2477_WB_143064HP133A11)

tag: age

tag: gold stage


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 1 Replicate: 2 Passage: 5

tag: ancestry


title: D6.3

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-15

source_name: Day 6 Repeat 3

tag: tissue


title: Blood from Stage I (GP2477_WB_143063HP133A11)

tag: plateid

tag: subject type


title: Blood from Stage II (GP2477_WB_143062HP133A11)

value: Stage II

tag: hyb date


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 8 Replicate: 1 Passage: 5

tag: donor id

tag: Sex


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 1 Replicate: 2 Passage: 6

tag: array batch


title: REF0.3

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
REF0-3

source_name: Day 0 Repeat 3


title: D4.2

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-8

source_name: Day 4 Repeat 2


title: D5.3

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-12

source_name: Day 5 Repeat 3


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 4 Replicate: 2 Passage: 6

tag: region id


title: D5.2

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-11

source_name: Day 5 Repeat 2


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 8 Replicate: 2 Passage: 5

tag: cell type


title: Blood from Stage III (GP2477_WB_143061HP133A11)

source_name: blood

tag: gender


title: REFA.3

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
REFA-3

source_name: Reference Repeat 3


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 12 Replicate: 2 Passage: 6

tag: differentiation wk


title: Blood from Stage II (GP2477_WB_143058HP133A11)


title: iPSC from Kosik Lab morphogens 4 days Donor: Tau mutant Tau104 DiffWk: 0

source_name: iPSC from fibroblast

tag: passage


title: iPSC from Kosik Lab morphogens 8 days Donor: Control Tau6(IN2R) DiffWk: 8

value: Control Tau6(IN2R)

value: iPSC from Kosik Lab morphogens 8 days

tag: rin


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 8 Replicate: 1 Passage: 6

tag: gestation wk


title: D2.1

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-4

source_name: Day 2 Repeat 1

tag: strain

tag: age


title: D6.2

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-14

source_name: Day 6 Repeat 2


title: Blood from Stage II (GP2477_WB_143057HP133A11)

tag: gold stage


title: D6.1

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-13

source_name: Day 6 Repeat 1

tag: tissue


title: Blood from Stage I (GP2477_WB_143055HP133A11)

value: Stage I

tag: plateid

value: Smoker Controls


title: Blood from Stage I (GP2477_WB_143056HP133A11)

value: F

tag: subject type


title: Blood from Stage I (GP2477_WB_143054HP133A11)

tag: hyb date


title: Blood from Stage I (GP2477_WB_143052HP133A11)


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 12 Replicate: 2 Passage: 6

source_name: Human fetal tissue

tag: donor id

tag: ancestry


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 4 Replicate: 2 Passage: 6

tag: Sex

tag: array batch


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 4 Replicate: 1 Passage: 6

tag: region id

tag: cell type


title: REFA.2

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
REFA-2

source_name: Reference Repeat 2


title: Blood from Stage III (GP2477_WB_143051HP133A11)

tag: gender

value: COPD Subjects


title: D4.1

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-7

source_name: Day 4 Repeat 1

value: Multi-layered secondary follicles (150-180 µm in diameter) mechanically isolated from ovaries of 16-day-old mice

value: 16-day-old mice


title: REF0.2

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
REF0-2

source_name: Day 0 Repeat 2


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 1 Replicate: 2 Passage: 5

tag: differentiation wk

tag: passage


title: REFA.1

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
REFA-1

source_name: Reference Repeat 1

value: Murine brain sample


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 1 Replicate: 2 Passage: 6

value: phNPC from Geschwind Lab

tag: rin

tag: gestation wk


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 4 Replicate: 2 Passage: 7

value: ASW


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 1 Replicate: 2 Passage: 10

value: MEX


title: Blood from Stage I (GP2477_WB_143053HP133A11)

tag: age


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 4 Replicate: 2 Passage: 9


title: D5.1

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-10

source_name: Day 5 Repeat 1

tag: strain


title: Blood from Stage I (GP2477_WB_143050HP133a21)

tag: tissue

tag: gold stage


title: Blood from Stage II (GP2477_WB_143049HP133A11)

tag: plateid

tag: subject type


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 8 Replicate: 1 Passage: 5

tag: donor id


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 12 Replicate: 1 Passage: 5

tag: ancestry


title: D8.1

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
S2-16

source_name: Day 8 Repeat 1

value: Multi-layered secondary follicles (150-180 µm in diameter) mechanically isolated from ovaries


title: Blood from Stage III (GP2477_WB_143073HP133A11)

value: Stage III

tag: hyb date


title: Blood from Stage II (GP2477_WB_143048HP133A11)

value: blood


title: REF0.1

description:
TargetAmp 1-Round Aminoallyl-aRNA Kit
RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).
REF0-1

source_name: Day 0 Repeat 1


title: Blood from Stage I (GP2477_WB_143047HP133A11)

value: M


title: 1µg/ml 12 month rep 1

city: Callaghan

first: Belinda

last: Nixon

state: NSW

address: University Drive

country: Australia

institute: University of Newcastle

description: Sample name: 45

data_processing: The data were normalised using quantile normalisation using BioConductor's lumi package in R statistical software

source_name: mouse testis following 1 µg/ml acrylamide for 12 months

label_protocol: Biotinylated cRNA were prepared with Ambion's Illumina RNA Amplification kit for Illumina arrays

growth_protocol: Adult male Swiss mice were housed under controlled temperature and humidity conditions, 16 h light, 8 h dark, with food and water provided ad libitum. Animals were acclimated for at least 1 month prior to treatment. At each time point, animals were euthanized by CO2 asphyxiation and testes were extracted.

extract_protocol: RNA was extracted from individual testes of acrylamide exposed mice using RNeasy Mini Kit (Qiagen, Chadstone Centre, VIC) according to manufacturers' instructions.

treatment_protocol: Acrylamide drinking water solutions were prepared using research-grade acrylamide obtained from Sigma (≥ 99% purity, A9099) diluted in filtered, deionized water at concentrations 0.001, 0.01, 0.1, 1, and 10 ?g/ml. Drinking water containing acrylamide was prepared fresh on a weekly basis, and was substituted for normal drinking water at the commencement of treatment. Test animals were exposed to acrylamide via the drinking water for a period of 1, 6 or 12 months

value: Swiss

value: Male

value: 16-17 months

tag: agent

value: acrylamide

tag: dose

value: 1 µg/ml

tag: time

value: 12 months

value: testis


title: 10µg/ml 12 month rep 1

description: Sample name: 46

source_name: mouse testis following 10 µg/ml acrylamide for 12 months

tag: gender

value: 10 µg/ml


title: 0.01µg/ml 12 month rep 2

description: Sample name: 41

source_name: mouse testis following 0.01 µg/ml acrylamide for 12 months


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 4 Replicate: 1 Passage: 6

tag: region id

tag: cell type

tag: differentiation wk

tag: Sex

tag: array batch


title: Blood from Stage II (GP2477_WB_143045HP133A11)

first: steve

last: fox

data_processing: The data was analysed with Rosetta Resolver version 5.0

source_name: blood

tag: age

value: Stage II

value: COPD Subjects


title: 0.1µg/ml 12 month rep 2

description: Sample name: 43

source_name: mouse testis following 0.1 µg/ml acrylamide for 12 months

tag: strain

value: 0.1 µg/ml

tag: tissue


title: 0.1µg/ml 12 month rep 3

description: Sample name: 44


title: Blood from Stage I (GP2477_WB_143043HP133A11)

value: F

tag: gold stage

value: Stage I

tag: plateid

value: Smoker Controls


title: 0.1µg/ml 12 month rep 1

description: Sample name: 42


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 4 Replicate: 1 Passage: 9

tag: donor id

value: phNPC from Geschwind Lab

tag: passage

tag: rin

tag: gestation wk

value: MEX


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 12 Replicate: 1 Passage: 6

tag: ancestry

value: M


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 1 Replicate: 1 Passage: 7

value: ASW


title: Blood from Stage I (GP2477_WB_143046HP133A11)

value: blood

tag: subject type

tag: hyb date


title: Blood from Stage I (GP2477_WB_143042HP133A11)

tag: gender


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 12 Replicate: 1 Passage: 6

tag: region id

tag: cell type


title: 0.01µg/ml 12 month rep 1

description: Sample name: 40

value: Swiss

value: Male

value: 16-17 months

tag: agent

tag: dose

tag: time


title: 0.001µg/ml 12 month rep 2

description: Sample name: 39

source_name: mouse testis following 0.001 µg/ml acrylamide for 12 months

tag: strain

tag: age

value: acrylamide

value: 12 months


title: Blood from Stage III (GP2477_WB_143041HP133A11)

tag: tissue

tag: gold stage

value: Stage III


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 4 Replicate: 2 Passage: 6

tag: donor id

tag: differentiation wk

tag: Sex

tag: array batch


title: Blood from Stage III (GP2477_WB_143040HP133A11)

tag: plateid


title: Control 12 month rep 2

description: Sample name: 37

source_name: mouse testis following 0 µg/ml acrylamide for 12 months

value: control

value: 0 µg/ml

value: testis


title: Blood from Stage I (GP2477_WB_143036HP133A11)

tag: subject type


title: Blood from Stage II (GP2477_WB_143037HP133A11)

value: Stage II

value: COPD Subjects

tag: hyb date


title: 10µg/ml 6 month rep 3

description: Sample name: 35

source_name: mouse testis following 10 µg/ml acrylamide for 6 months

tag: gender

value: 11-12 months

value: 10 µg/ml

value: 6 months


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 4 Replicate: 1 Passage: 6

tag: region id

value: phNPC from Geschwind Lab

tag: passage

tag: rin

tag: gestation wk

tag: ancestry

value: M


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 12 Replicate: 2 Passage: 5

tag: cell type

value: ASW


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 4 Replicate: 1 Passage: 6


title: Blood from Stage I (GP2477_WB_143038HP133a12)

value: blood

tag: age

value: Stage I

value: Smoker Controls


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 12 Replicate: 1 Passage: 6


title: 0.001µg/ml 12 month rep 1

description: Sample name: 38

tag: strain

value: Swiss

value: Male

value: 16-17 months

tag: agent

value: acrylamide

tag: dose

tag: time

tag: tissue


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 1 Replicate: 2 Passage: 6

tag: donor id

tag: differentiation wk

tag: Sex

tag: array batch


title: Blood from Stage II (GP2477_WB_143035HP133A11)

tag: gender

tag: gold stage

tag: plateid

tag: subject type

tag: hyb date


title: 10µg/ml 6 month rep 2

description: Sample name: 34


title: Control 12 month rep 1

description: Sample name: 36

value: control

value: 0 µg/ml

value: 12 months


title: Blood from Stage III (GP2477_WB_143034HP133A11)

value: Stage III

value: COPD Subjects


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 8 Replicate: 1 Passage: 6

tag: region id

tag: passage

tag: rin

tag: gestation wk

tag: ancestry

value: MEX


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 1 Replicate: 2 Passage: 5

tag: cell type


title: Blood from Stage I (GP2477_WB_143032HP133A11)

tag: age


title: Blood from Stage I (GP2477_WB_143039HP133A11)

tag: tissue


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 8 Replicate: 2 Passage: 5

tag: donor id


title: 1µg/ml 6 month rep 3

description: Sample name: 32

source_name: mouse testis following 1 µg/ml acrylamide for 6 months

tag: strain

value: 11-12 months

tag: agent

tag: dose

value: 1 µg/ml

tag: time

value: 6 months

value: testis


title: Blood from Stage I (GP2477_WB_143031HP133A11)

value: blood

tag: gender

value: M

tag: gold stage


title: Blood from Stage IV (GP2477_WB_143060HP133A11)

value: Stage IV

tag: plateid

tag: subject type


title: 1µg/ml 6 month rep 1

description: Sample name: 30

value: Swiss


title: Blood from Stage I (GP2477_WB_143029HP133A11)

value: Stage I

value: Non-smoker Controls

tag: hyb date


title: Blood from Stage III (GP2477_WB_143028HP133A11)


title: Blood from Stage I (GP2477_WB_143030HP133A11)

value: Smoker Controls


title: 1µg/ml 6 month rep 2

description: Sample name: 31

value: Male

value: acrylamide


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 12 Replicate: 2 Passage: 7

source_name: Human fetal tissue

tag: region id

value: phNPC from Geschwind Lab

tag: differentiation wk

tag: passage

value: ASW

tag: Sex

tag: array batch


title: 10µg/ml 6 month rep 1

description: Sample name: 33

tag: age

value: 10 µg/ml


title: 0.01µg/ml 6 month rep 3

description: Sample name: 26

source_name: mouse testis following 0.01 µg/ml acrylamide for 6 months

tag: tissue


title: 0.1µg/ml 6 month rep 1

description: Sample name: 27

source_name: mouse testis following 0.1 µg/ml acrylamide for 6 months

value: 0.1 µg/ml


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 4 Replicate: 1 Passage: 5

tag: donor id

tag: cell type

tag: rin

tag: gestation wk

tag: ancestry

value: MEX


title: 0.1µg/ml 6 month rep 3

description: Sample name: 29

tag: strain

tag: gender

value: 11-12 months

tag: agent

tag: dose

tag: time


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 1 Replicate: 2 Passage: 6

tag: region id


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 12 Replicate: 1 Passage: 7

tag: differentiation wk


title: Blood from Stage I (GP2477_WB_143026HP133A11)

tag: gold stage

tag: plateid

tag: subject type

tag: hyb date


title: 0.01µg/ml 6 month rep 2

description: Sample name: 25

tag: age

value: 6 months

tag: tissue


title: 0.1µg/ml 6 month rep 2

description: Sample name: 28

value: testis


title: Blood from Stage II (GP2477_WB_143025HP133A11)

value: blood

value: Stage II

value: COPD Subjects


title: Blood from Stage IV (GP2477_WB_143024HP133A11)

value: M

value: Stage IV


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 1 Replicate: 1 Passage: 5

tag: donor id

tag: cell type

tag: passage

tag: Sex

tag: array batch


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 4 Replicate: 2 Passage: 5

tag: rin

tag: gestation wk

tag: ancestry


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 8 Replicate: 1 Passage: 9

value: F


title: 0.01µg/ml 6 month rep 1

description: Sample name: 24

tag: strain

value: Swiss

tag: gender

tag: agent

tag: dose

tag: time


title: 0.001µg/ml 6 month rep 3

description: Sample name: 23

source_name: mouse testis following 0.001 µg/ml acrylamide for 6 months

value: Male


title: 0.001µg/ml 6 month rep 2

description: Sample name: 22

value: acrylamide


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 8 Replicate: 1 Passage: 10

tag: region id

value: phNPC from Geschwind Lab

tag: differentiation wk


title: Blood from Stage IV (GP2477_WB_143021HP133A11)

tag: age

tag: gold stage

tag: plateid

tag: subject type

tag: hyb date


title: Blood from Stage I (GP2477_WB_143023HP133A11)

tag: tissue

value: Stage I

value: Smoker Controls


title: Blood from Stage III (GP2477_WB_143022HP133A11)

value: Stage III


title: Blood from Stage IV (GP2477_WB_143027HP133A11)


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 4 Replicate: 2 Passage: 10

tag: donor id

tag: cell type

tag: passage

value: MEX

tag: Sex

tag: array batch


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 12 Replicate: 2 Passage: 9

tag: rin

tag: gestation wk

tag: ancestry


title: Blood from Stage IV (GP2477_WB_143019HP133a12)

tag: gender


title: Control 6 month rep 3

description: Sample name: 20

source_name: mouse testis following 0 µg/ml acrylamide for 6 months

tag: strain

value: 11-12 months

tag: agent

value: control

tag: dose

value: 0 µg/ml

tag: time


title: Blood from Stage I (GP2477_WB_143016HP133A11)

value: blood

tag: age

tag: gold stage

tag: plateid


title: 10µg/ml 1 month rep 3

description: Sample name: 17

source_name: mouse testis following 10 µg/ml acrylamide for 1 month

value: 3-6 months

value: 10 µg/ml

value: 1 month

tag: tissue

value: testis


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 1 Replicate: 1 Passage: 6

tag: donor id

tag: region id

tag: differentiation wk

value: M


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 8 Replicate: 2 Passage: 10

tag: cell type

tag: passage

tag: Sex

value: F


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 4 Replicate: 2 Passage: 5

tag: rin

tag: gestation wk

value: ASW

tag: array batch


title: Blood from Stage II (GP2477_WB_143017HP133A11)

tag: gender

value: Stage II

tag: subject type

value: COPD Subjects

tag: hyb date


title: Blood from Stage II (GP2477_WB_143015HP133A11)


title: Blood from Stage I (GP2477_WB_143020HP133A11)

value: Stage I


title: Control 6 month rep 1

description: Sample name: 18

tag: strain

value: Swiss

value: Male

tag: agent

tag: dose

tag: time

value: 6 months


title: 0.001µg/ml 6 month rep 1

description: Sample name: 21

tag: age

value: 11-12 months

value: acrylamide

tag: tissue


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 8 Replicate: 2 Passage: 6

tag: donor id

tag: region id

value: phNPC from Geschwind Lab

tag: ancestry


title: 1µg/ml 1 month rep 3

description: Sample name: 14

source_name: mouse testis following 1 µg/ml acrylamide for 1 month

value: 1 µg/ml


title: 10µg/ml 1 month rep 2

description: Sample name: 16

value: 3-6 months


title: Blood from Stage III (GP2477_WB_143014HP133A11)

value: blood

tag: gold stage

value: Stage III

tag: plateid


title: Blood from Stage I (GP2477_WB_143018HP133A11)

value: Smoker Controls


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 8 Replicate: 1 Passage: 5

tag: cell type

tag: differentiation wk

tag: passage

tag: rin

tag: Sex

value: M


title: Control 6 month rep 2

description: Sample name: 19

tag: gender

value: control

value: 0 µg/ml

value: testis


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 12 Replicate: 2 Passage: 6

tag: gestation wk

value: ASW

tag: array batch


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 4 Replicate: 1 Passage: 10

value: MEX

value: F


title: 10µg/ml 1 month rep 1

description: Sample name: 15

tag: strain

value: Swiss

value: Male

tag: agent

tag: dose

value: 10 µg/ml

value: 1 month


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 8 Replicate: 2 Passage: 7

value: phNPC from Geschwind Lab


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 1 Replicate: 1 Passage: 10


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 12 Replicate: 2 Passage: 5


title: 1µg/ml 1 month rep 2

description: Sample name: 13

tag: age

value: acrylamide

value: 1 µg/ml

tag: time

tag: tissue


title: Blood from Stage II (GP2477_WB_143013HP133A11)

value: blood

value: Stage II

tag: subject type

value: COPD Subjects

tag: hyb date


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 8 Replicate: 1 Passage: 6

tag: donor id

tag: region id

tag: ancestry

value: M


title: Blood from Stage I (GP2477_WB_143010HP133A11)

tag: gold stage

value: Stage I

tag: plateid

value: Smoker Controls


title: Blood from Stage II (GP2477_WB_143012HP133A11)


title: Blood from Stage I (GP2477_WB_143009HP133A11)


title: 0.1µg/ml 1 month rep 1

description: Sample name: 10

source_name: mouse testis following 0.1 µg/ml acrylamide for 1 month

value: 3-6 months

value: 0.1 µg/ml

value: testis


title: 1µg/ml 1 month rep 1

description: Sample name: 12


title: Blood from Stage II (GP2477_WB_143008HP133A11)


title: Blood from Stage III (GP2477_WB_143011HP133a12)

value: Stage III


title: 0.01µg/ml 1 month rep 1

description: Sample name: 7

source_name: mouse testis following 0.01 µg/ml acrylamide for 1 month

value: Swiss


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 8 Replicate: 1 Passage: 6

tag: cell type

tag: differentiation wk

tag: passage

tag: rin

value: ASW

tag: Sex


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 8 Replicate: 2 Passage: 6

tag: gestation wk

tag: array batch


title: 0.01µg/ml 1 month rep 2

description: Sample name: 8

tag: strain

tag: gender

value: Male

tag: age

tag: agent

tag: dose


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 8 Replicate: 2 Passage: 6

tag: donor id


title: Blood from Stage II (GP2477_WB_143005HP133A11)

tag: tissue

tag: subject type

tag: hyb date


title: phNPC from Geschwind Lab Donor: 8 Region: 46 DiffWk: 12 Replicate: 1 Passage: 5

tag: region id

tag: ancestry


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 4 Replicate: 2 Passage: 6

tag: cell type

tag: differentiation wk

value: MEX


title: Blood from Stage III (GP2477_WB_143004HP133A11)

value: F

tag: gold stage

tag: plateid


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 8 Replicate: 2 Passage: 5

value: phNPC from Geschwind Lab

tag: passage

tag: rin

tag: gestation wk

tag: Sex


title: 0.1µg/ml 1 month rep 2

description: Sample name: 11

tag: strain

tag: gender

tag: age

value: acrylamide

tag: time

value: 1 month


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 8 Replicate: 1 Passage: 7

tag: donor id

tag: array batch


title: Control 1 month rep 2

description: Sample name: 2

source_name: mouse testis following 0 µg/ml acrylamide for 1 month

tag: agent

value: control

tag: dose

value: 0 µg/ml

tag: tissue


title: 0.001µg/ml 1 month rep 3

description: Sample name: 6

source_name: mouse testis following 0.001 µg/ml acrylamide for 1 month


title: 0.001µg/ml 1 month rep 1

description: Sample name: 4


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 8 Replicate: 2 Passage: 6

tag: region id

tag: cell type

tag: ancestry

value: M


title: Control 1 month rep 3

description: Sample name: 3


title: Blood from Stage II (GP2477_WB_143001HP133A11)

source_name: blood

value: blood

tag: gold stage

value: Stage II

tag: plateid

tag: subject type

value: COPD Subjects

tag: hyb date


title: Blood from Stage I (GP2477_WB_143007HP133A11)

value: Stage I

value: Smoker Controls


title: Blood from Stage III (GP2477_WB_143003HP133A11)

value: Stage III


title: 0.01µg/ml 1 month rep 3

description: Sample name: 9

value: Swiss

value: 3-6 months

value: testis


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 4 Replicate: 1 Passage: 5

tag: differentiation wk

tag: passage

tag: rin

tag: gestation wk

value: ASW

tag: Sex


title: Blood from Stage III (GP2477_WB_143006HP133A11)

tag: age

tag: gender

value: F


title: Blood from Stage II (GP2477_WB_143002HP133a12)


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 12 Replicate: 2 Passage: 6

tag: donor id

value: phNPC from Geschwind Lab

tag: array batch


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 1 Replicate: 2 Passage: 7


title: Control 1 month rep 1

description: Sample name: 1

tag: strain

value: Male

tag: agent

tag: dose

tag: time

tag: tissue


title: Blood from Stage I (GP2477_WB_143000HP133A11)

tag: gold stage

tag: plateid


title: Blood from Stage IV (GP2477_WB_142998HP133A11)

value: Stage IV

tag: subject type

tag: hyb date


title: Blood from Stage II (GP2477_WB_142999HP133A11)


title: Blood from Stage II (GP2477_WB_142995HP133A11)


title: phNPC from Geschwind Lab Donor: 5 Region: 17 DiffWk: 8 Replicate: 2 Passage: 9

tag: region id

tag: cell type

tag: differentiation wk

tag: passage

tag: ancestry

value: MEX


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 4 Replicate: 1 Passage: 7

tag: rin

tag: gestation wk

tag: Sex


title: Blood from Stage I (GP2477_WB_142997HP133A11)

tag: age

tag: gender


title: Blood from Stage III (GP2477_WB_142996HP133A11)


title: phNPC from Geschwind Lab Donor: 6 Region: 21 DiffWk: 4 Replicate: 2 Passage: 5

tag: donor id

tag: array batch


title: Blood from Stage II (GP2477_WB_142993HP133a12)

tag: tissue


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 1 Replicate: 1 Passage: 6


title: phNPC from Geschwind Lab Donor: 8 Region: 49 DiffWk: 1 Replicate: 1 Passage: 5


title: Blood from Stage I (GP2477_WB_142994HP133A11)

tag: gold stage

value: Non-smoker Controls


title: phNPC from Geschwind Lab Donor: 8 Region: 43 DiffWk: 12 Replicate: 1 Passage: 6

value: M


title: C.elegans MT KO  mtl-1,mtl-2(zs1) raised in the presence of Cd, rep3

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

description: Standard affymetrix recommended quality control parameters were used during entire experiment.

hyb_protocol: 10 μg of Biotin end labeled aRNA (amplified RNA) was fragmented and hybridized to the Affymetrix C. elegans GeneChips as recommended by Affymetrix. The quality & quantity of the aRNA probe preparation was assessed before hybridization using an Agilent 2100 bioanalyzer & Nanodrop-1000 spectrophotometer, receptively.

scan_protocol: Affymetrix GeneChip® Command Console (AGCC) software was used for the control of array washing (GeneChip Fluidics Station-450), data acquisition (Scanner 3000-7G) as well as for the preliminary data analysis.

data_processing:
Preprocessing of microarray raw data including probe-specific background correction, summarization of probe set values, and normalization was carried out using the GCRMA algorithm with CARMAweb 1.4, an R- and Bioconductor-based web service for microarray data analysis (Rainer et al., 2006).
Rainer J, Sanchez-Cabo F, Stocker G, Sturn A, Trajanoski Z (2006). CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. Nucleic Acids Res 34:W498–W503

organism: Caenorhabditis elegans

source_name: C.elegans MT KO Cd exposure

label_protocol: 200 ng of total RNA was subjected to aRNA amplification and Biotin labeling as described in the MessageAmpTM Premier RNA Amplification Kit (Ambion) for microarray analysis. aRNA cleanup was achieved using magnetic beads (Ambion).

extract_protocol: The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), however modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage. RNA was subsequently purified using an RNeasy kit (Qiagen) followed by a DNase digestion (Qiagen).

treatment_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach prepping and grown to L4 stage. Exposed to 30 µM Cd throughout from hatching to L4 stage.

value: larvae (L4)

value: whole animal

tag: strain

value: N2 (Bristol)

tag: genotype/variation

value: MT KO mtl-1,mtl-2(zs1)


title: C.elegans MT KO  mtl-1,mtl-2(zs1) raised in the presence of Cd, rep1

growth_protocol: Parent population (P0) maintained at 20 ºC on standard nematode growth media (NGM) plates using Escherichia coli OP50 as food source. A synchronous L1 culture was generated by standard bleach prepping and grown to L4 stage.