title: SPLN-Minus-3-2

city: Pasadena

first: Boyoung

last: Shin

address: 1200 E. California Blvd

institute: Californial Institute of Technology

description:
SPLN-Minus-3-2_GGCTAC_L001
Minus - SPLN-Minus-3-2_GE - RPKM

data_processing:
For the base-calling, Illumina Bal2fastq program, version 1.8.4 was used. During de-multiplexing, one mismatch was allowed for sample barcodes.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality (error rate<0.05) at the end.  After trimming, remaining sequence reads were aligned to the reference genome GRCm38.75 with CLC Genomics Server program.
After mapping, total gene hit counts were measured and Reads Per Kilobase of exon per Megabase of library size (RPKM) values were calculated using CLC Genomic workbench.
The total gene hit counts table was used for downstream differential expression analysis using DESeq2.
Genome_build: GRCm38.75
Supplementary_files_format_and_content: RPKM and DESeq2 output

source_name: IFNγ non-producing (Thy1.1-) CD4 T cells

growth_protocol: IFNγ K-in CD45RBhiCD25-CD4 T cells were transferred into Rag1 deficient mice for colitis induction. After 4 weeks post transfer, CD44+Thy1.1+ and CD44+Thy1.1-CD4 T cells from spleen and lymph nodes (8-10 colitic mice were pooled) were FACS sorted.

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing according to Illumina's instructions

value: 8-12 weeks

value: spleen and lymph nodes

value: CD44+ Thy1.1-  CD4+ T cells


title: LiSa2_HAase24h_2

status: Public on May 12 2018

type: RNA

city: Los Angeles

first: William

middle: Juster

last: Sullivan

state: California

address: 354-06 BSRB, 615 Charles E. Young Drive S

department: Biological Chemistry

country: USA

institute: University of California, Los Angeles

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Normalized data were not generated for this study. CEL files were used as input into the GSEA software: http://software.broadinstitute.org/gsea/index.jsp. The data tables associated with sample records were generated from the supplementary CHP files located at the foot the page. Although these files were not used in the analysis performed by the submitter, they have been provided for public use.

label: biotin (Affymetrix standard labeling)

molecule: total RNA

organism: Homo sapiens

label_protocol: Affymetrix standard protocol

growth_protocol: LiSa-2 liposarcoma cells were grown in standard 10cm plates with DMEM/F12 supplemented with 10% bovine serum and 1% penicillin/streptomycin

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit using manufacturer's guidelines

treatment_protocol: Cells were treated with bovine testicular hyaluronidase (HAase, 400ug/mL) or PBS control for times indicated

tag: cell line

tag: cell type

value: liposarcoma

tag: treatment

value: HAase, 400ug/mL, 24h


title: mammosphere cryopreserved donnor BT133

city: Rennes

first: Patrick

last: Legembre

address: CRLCC Eugène Marquis, Rue Bataille Flandres Dunkerque, Bat. D

department: Chemistry Oncogenesis Stress Signalling

country: France

institute: Inserm U1242

description: two weeks culture in mammocult medium (stemcell technologies) in low attachment plates

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® human Gene 2.0 ST (Affymetrix) at 45°C for 17 hours. After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix)

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The scanned images were analyzed with the Expression Console software (Affymetrix) to generate raw data (cel files) and metrics for quality controls. Probes were mapped using custom CDF files from Brainarray V22 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/22.0.0/entrezg.asp) and RMA normalization was performed using R. Supervised statistical analysis was performed using the LIMMA R package

label: biotin

source_name: TNBC tumor

label_protocol: 9 ng of total RNA were used to produce target CDNA using Ovation PicoSl WTA system V2 (Nugen) . After purification according to Nugen protocol, 3,6 ug of single strand DNA is used for fragmentation and biotin labelling using Encore Biotin Module (Nugen).

growth_protocol: cells were cultured in mammocult medium (stemcell technologies) in low attachment plates for 15 days

extract_protocol: Macherey Nagel total RNA isolation kit according to the manufacturer's instructions

treatment_protocol: cells weres cultured immediately after dissociation (fresh) or after a cryopreservation cycle of 15 days at -150ºC before thawing (cryopreserved)

tag: tissue

value: breast tumor

tag: histological subtype

value: triple negative

value: tumorosphere

value: cryopreserved


title: mammosphere cryopreserved donnor BT134


title: mammosphere fresh donnor BT134

value: fresh


title: BMDM c-Maf-/- LPS 5h

city: Hachioji

first: Kenta

last: Kikuchi

state: Tokyo

address: 1432-1, Horinouchi

country: Japan

institute: Immune regulation lab

description: Gene expression 5h after LPS stimulation

hyb_protocol: Labeled cRNA was hybridized to Agilent SurePrint G3 Mouse Gene Expression Arrays using Gene Expression Hybridization kit (Agilent Technologies).

scan_protocol: Slides were scanned with Agilent Technologies Microarray Scanner (Scan Resolution; 3 μm, TIFF file dynamic range; 20 bits).

data_processing: The scanned images were analyzed with Feature Extraction Software 10. 7. 3. 1 (Agilent). Array raw data was digitized and further analyzed using GeneSpring software.

organism: Mus musculus

source_name: BMDM LPS 5h

label_protocol: 50 ng of total RNA was labeled with Low Input Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: Mouse bone marrow cells were cultured in the presence of M-CSF (CMG14-12 culture medium) for 5 days to induce bone marrow-derived macrophages (BMDMs).

extract_protocol: Total RNA was prepared using the RNeasy mini kit (QIAGEN) according to the manufacturer's protocol. RNA concentration was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer series II (Agilent Technologies).

treatment_protocol: Those BMDMs were stimulated with 100 ng/ml LPS for 5 hours.

value: bone marrow derived macrophages

tag: genotype

value: c-Maf-/-

tag: stimulation

value: 100 ng/ml LPS 5h


title: LiSa2_HAase6h_3

value: HAase, 400ug/mL, 6h


title: AN14vsLAB-1

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

description:
AN14 vs LAB replicate 1
Sample 5

hyb_protocol: Labeled cRNA was pooled and hybridized  on a custome-made Agilent 8x60k slide using the Gene Expression Hybridization Kit (Agilent Technologies). Slides were kept in a rotating hybridization oven (17 hrs) and washed using reagentia from the Gene Expression Wash Buffer kit (Agilent Technologies).

scan_protocol: The 8x60k slide was scanned using an Agilent Microarray High Resolution Scanner with default settings for Agilent two-color GE micro-arrays.

data_processing: Raw intensity data was extracted using Agilent Feature Extraction Software 10.5 (GE2_107_Sep09 protocol). Subsequently, image data was transferred to limma (Smyth, 2004) for final statistical analysis. After background corrections, within- and between-array normalizations, significant differential expression was assessed (BH FDR-corrections).

organism: Bactrocera oleae

source_name: AN14_pooled 1-3 days old females

label_protocol: After Dnase treatment (Ambion), cyanine-labeled cRNA was synthesized following the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies). Quality was assessed using Nanodrop.

growth_protocol: Three field populations of B. oleae were collected and characterized in this study: AN12 and AN14 were collected from olive orchards that have been intensively treated with pyrethroid insecticides for several years in Agios Nikolaos (Crete, Greece) in 2012 and 2014, respectively. FOK14 was collected in 2014 from Fokida (central Greece), a region where the use of insecticides for B. oleae control is very limited. For all field caught insect populations, olives infested by B. oleae were collected from each sampling region, transferred to the laboratory and maintained in Petri dishes containing a layer of sawdust.

extract_protocol: Each RNA sample consisted of 10 pooled one-to-three days old females using the Rneasy minikit (Qiagen).

treatment_protocol: Upon pupation, pupae were transferred in plastic cages (8 × 8 × 8 cm) and the emerging females snap frozen in liquid nitrogen for further analysis.

tag: population

tag: age

value: 1-3 days

tag: Sex

value: female

value: whole-organism

source_name: LAB_pooled 1-3 days old females

value: LAB


title: LiSa2_PBS_2

value: PBS


title: AN14vsFOK14-4

description:
AN14 vs FOK14 replicate 4
Sample 12

source_name: FOK14_pooled 1-3 days old females


title: BMDM c-Maf+/- LPS 5h

value: c-Maf+/-


title: LiSa2_HAase6h_2

value: liposarcoma


title: mammosphere cryopreserved donnor BT138


title: AN14vsFOK14-1

description:
AN14 vs FOK14 replicate 1
Sample 9


title: AN14vsLAB-4

description:
AN14 vs LAB replicate 4
Sample 8


title: SPLN-Minus-2-2

type: SRA

description:
SPLN-Minus-2-2_ACTTGA_L001
Minus - SPLN-Minus-2-2_GE - RPKM

library_source: transcriptomic

tag: strain

value: 8-12 weeks

value: spleen and lymph nodes

value: CD44+ Thy1.1- CD4+ T cells


title: AN14vsFOK14-2

description:
AN14 vs FOK14 replicate 2
Sample 10


title: AN14vsFOK14-3

description:
AN14 vs FOK14 replicate 3
Sample 11


title: AN14vsLAB-3

description:
AN14 vs LAB replicate 3
Sample 7


title: mammosphere fresh donnor BT133

value: breast tumor

value: triple negative

value: tumorosphere


title: AN12vsHYB-4

description:
AN12 vs HYB replicate 4
Sample 4

source_name: AN12_pooled 1-3 days old females

source_name: HYB_pooled 1-3 days old females

value: HYB


title: mammosphere fresh donnor BT138

value: fresh


title: Non-stimulated

city: Minato-ku

first: Naoki

last: Takemura

address: 4-6-1 Shirokanedai

department: International Research and Development Center for Mucosal Vaccines

institute: Institute of Medical Science, The University of Tokyo

hyb_protocol: Samples were hybridized to GeneChip® Mouse Gene 2.0 ST Array (Affymetrix). The array was incubated for 18 hours at 45°C, then automatically washed and stained with GeneChip® Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned using with a GeneChip® Scanner 3000 7G.

data_processing: Raw signal values from the arrays were processed using the Affymetrix GeneChip® Command Console and Affymetrix Expression Console software for RMA summarization and background correction after scanning with a GeneChip® Scanner 3000 7G.  GeneSpring GX (Agilent Technologies) was then used to perform baseline transformation (to the median of control sample) and subsequent microarray analyses.

source_name: small intestinal eosinophils

label_protocol: Isolated total RNA were amplified and labeled using Affymetrix® GeneChip® WT Plus Reagent Kit (Affymetrix, Santa Clara, CA), according to the manufacturer’s protocol.

extract_protocol: RNA samples were isolated from small intestinal myofibroblsts using Trizol reagent  (Invitrogen).RNA was then further purified and concentrated using Rneasy MinElute Cleanup Kit (Qiagen).

treatment_protocol: Small intestinal myofibroblasts of BALB/c mice were cultured with or without homogenate of intestinal eosinphils (5 mg/ml) for 1 day.

tag: background mouse strain

value: BALB/c

tag: stimulation with homogenate

value: not treated


title: Stimulated

value: treated


title: dnaB-Ts_30°C

city: Newark

first: Yuzhi

last: Hong

state: NJ

address: 225 Warren St

department: PHRI, New Jersey Medical School

institute: Rutgers, the University of New Jersey

description:
Mixed samples of two independent cultures
dnaB-Ts_vs_dnaB-Ts-ahpC_30°C.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to E.coli K2 BW25113 whole genome using bowtie v0.12.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: E.coli K12 BW25113
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

organism: Escherichia coli

source_name: Bacterial cultures

growth_protocol: Overnight cultures of the dnaB-Ts single mutant (strain 2429) and the dnaB-Ts ΔahpC double mutant (strain 3780) were diluted 100-fold into fresh SB medium (3.2% peptone, 2% yeast extract and 1% NaCl), and they were then grown at 30 °C to early-log phase (OD600 = 0.15).  Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed, fresh SB medium, and they were grown at 30 °C for another 60 min.

extract_protocol:
After chilling on ice, each 100-ml culture was mixed with 25 ml ice-cold ethanol/phenol solution (5% (v/v), water-saturated phenol in 95% (v/v) ethanol).  Cells were harvested by centrifugation at 7,000 g for 2 min at 4 °C, flash-frozen with dry ice, and stored at –80 °C. Two independent cultures for each sample were mixed together for determination of transcriptional profiles. Total RNA was extracted from the collected bacterial cells using TRIzol reagent (Thermo Fisher Scientifc).
rRNA was removed from total RNA by using the Ribo-Zero rRNA removal kit. Reverse transcription and cDNA amplification were performed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Libraries were constructed using the Illumina Nextera XT kit and analyzed for concentration , size distribution and quantification of viable sequencing templates via qPCR.
To generate Illumina-compatible sequencing libraries for each sample, molecular indexes were added to each library, allowing samples to be pooled and sequenced on the Illumina HiSeq 2500 with a 1 x 50 bp single-end configuration. More than 250 million reads were generated per sample, and at least 80% bases had quality scores above Q30.

treatment_protocol: Samples (200-ml) of the above cultures for each strain were split into two aliquots (each 100 ml), and the aliquots were then incubated at 30 °C or 42 °C for another 60 min.

tag: culture temperature

value: 30 °C for 60 min

tag: medium

value: SB broth


title: dnaB-Ts Î”ahpC_30°C


title: dnaB-Ts_42°C

description:
Mixed samples of two independent cultures
dnaB-Ts_vs_dnaB-Ts-ahpC_42°C.txt

value: 42 °C for 60 min


title: dnaB-Ts Î”ahpC_42°C


title: AN14vsLAB-2

description:
AN14 vs LAB replicate 2
Sample 6

value: 1-3 days

value: female

value: whole-organism

value: LAB


title: AN12vsHYB-3

description:
AN12 vs HYB replicate 3
Sample 3


title: AN12vsHYB-2

description:
AN12 vs HYB replicate 2
Sample 2


title: skin NcstnΔKC mice rep2

status: Public on May 11 2018

city: Nanjing

first: Yanyan

last: He

address: Jiangwangmiao Street

department: Institute of Dermatology

country: China

institute: hinese Academy of Medical Sciences and Peking Union Medical College

description: miRNA expression of the skin tissue of NcstnΔKC mice and normal mice

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

source_name: NcstnΔKC mice

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat #5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: Eight-week-old male Ncstn flx/flx; Krt14 CreER+/- mice were first administrated 20 mg/kg body weight of tamoxifen per day for 5 consecutive days, followed by treatment every 10 days by oral gavage. The Ncstn flx/flx; Krt14 CreER+/- mice received the same volume of corn oil and were used as controls.

extract_protocol: Total RNA was extracted and purified using mirVana miRNA Isolation Kit, following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The NcstnΔKC and normal mice were sacrificed at the age of 16 weeks and skin lesions were excised for RNA isolation

value: Eight-week-old

value: male

value: skin tissue

tag: genotype/variation

value: NcstndeltaKC

value: 16 weeks


title: skin NcstnΔKC mice rep3


title: skin NcstnΔKC mice rep4


title: SPLN-Plus-2-2

description:
SPLN-Plus-2-2_ATCACG_L001
Plus - SPLN-Plus-2-2_GE - RPKM

source_name: IFNγ producing (Thy1.1+) CD4 T cells

value: 8-12 weeks

value: spleen and lymph nodes

value: CD44+ Thy1.1+ CD4+ T cells


title: skin normal mice rep3

source_name: normal mice

value: normal


title: SPLN-Plus-3-2

description:
SPLN-Plus-3-2_TAGCTT_L001
Plus - SPLN-Plus-3-2_GE - RPKM


title: skin NcstnΔKC mice rep1


title: skin normal mice rep2

description: miRNA expression  of the skin tissue of NcstnΔKC mice and normal mice


title: skin normal mice rep1


title: skin NCSTN 5

description: miRNA expression signatures of acne inversa (AI) patients with NCSTN mutations and healthy individuals

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA extracted using Ambion(AM1561) following manufacturer's instructions

treatment_protocol: This study was performed according to the principles of the Declaration of Helsinki. Written informed consent was provided by all the individuals participating in the experiments.Skin biopsies of AI patients with NCSTN mutations were obtained from surgical excision.Control skin tissues were obtained from healthy individuals undergoing cosmetic surgery procedures.

tag: disease

value: AI patients with NCSTN mutations


title: skin NCSTN 3

source_name: Skin biopsies of AI patients with NCSTN mutations


title: skin NCSTN 2


title: skin NCSTN 1


title: mRNA Phaseolus sanilac

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
MethylC-seq: MethylC-seq analysis was performed as described in (Schmtiz et al. 2013)
RNA-seq: RNA-seq was performed using TopHat v2.0.13 and Cufflinks v2.2.1
small RNAseq was performed using Illumina small RNA TruSeq library prep kit,and using bowtie for sequence mapping
Genome_build: Pvulgaris_218_v1.0
Supplementary_files_format_and_content: tab delimited text file, see "allc_header_descriptions.txt", "smallRNA.processedfile_description.txt" and "RNA_column_header_descriptions.txt" for column headers

organism: Phaseolus vulgaris

source_name: mRNA Phaseolus sanilac

extract_protocol: MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.

value: Young leaf tissue


title: skin control 5

source_name: skin tissues of healthy individuals

value: healthy


title: mRNA Phaseolus merlot

source_name: mRNA Phaseolus merlot


title: mRNA Phaseolus ui_111

source_name: mRNA Phaseolus ui_111


title: mRNA Phaseolus othello

source_name: mRNA Phaseolus othello


title: mRNA Phaseolus beryl

source_name: mRNA Phaseolus beryl


title: skin control 4


title: skin control 1


title: skin control 2


title: skin control 3


title: mRNA Phaseolus ip08_2

source_name: mRNA Phaseolus ip08_2


title: AN12vsHYB-1

description:
AN12 vs HYB replicate 1
Sample 1

value: HYB


title: skin normal mice rep4


title: mRNA Phaseolus croissant

source_name: mRNA Phaseolus croissant


title: mRNA Phaseolus raven

source_name: mRNA Phaseolus raven


title: skin NCSTN 4


title: mRNA Phaseolus santa_fe

source_name: mRNA Phaseolus santa_fe


title: mRNA Phaseolus ui_37

source_name: mRNA Phaseolus ui_37


title: mRNA Phaseolus avalanche

source_name: mRNA Phaseolus avalanche


title: mRNA Phaseolus ac_early_rose

source_name: mRNA Phaseolus ac_early_rose


title: mRNA Phaseolus zorro

source_name: mRNA Phaseolus zorro


title: mRNA Phaseolus ui_59

source_name: mRNA Phaseolus ui_59


title: mRNA Phaseolus beryl_r

source_name: mRNA Phaseolus beryl_r


title: mRNA Phaseolus remington

source_name: mRNA Phaseolus remington


title: mRNA Phaseolus common_pinto

source_name: mRNA Phaseolus common_pinto


title: mRNA Phaseolus roza

source_name: mRNA Phaseolus roza


title: mRNA Phaseolus gts_900

source_name: mRNA Phaseolus gts_900


title: mRNA Phaseolus quincy

source_name: mRNA Phaseolus quincy


title: mRNA Phaseolus ui_126

source_name: mRNA Phaseolus ui_126


title: mRNA Phaseolus gemini

source_name: mRNA Phaseolus gemini


title: mRNA Phaseolus norstar

source_name: mRNA Phaseolus norstar


title: mRNA Phaseolus bunsi

source_name: mRNA Phaseolus bunsi


title: mRNA Phaseolus poncho

source_name: mRNA Phaseolus poncho


title: mRNA Phaseolus seahawk

source_name: mRNA Phaseolus seahawk


title: mRNA Phaseolus orion

source_name: mRNA Phaseolus orion


title: mRNA Phaseolus ensign

source_name: mRNA Phaseolus ensign


title: mRNA Phaseolus sequoia

source_name: mRNA Phaseolus sequoia


title: mRNA Phaseolus dor_364

source_name: mRNA Phaseolus dor_364


title: mRNA Phaseolus ui_3

source_name: mRNA Phaseolus ui_3


title: mRNA Phaseolus yolano

source_name: mRNA Phaseolus yolano


title: mRNA Phaseolus cdc_nordic

source_name: mRNA Phaseolus cdc_nordic


title: mRNA Phaseolus sedona

source_name: mRNA Phaseolus sedona


title: mRNA Phaseolus black_magic

source_name: mRNA Phaseolus black_magic


title: mRNA Phaseolus ui_196

source_name: mRNA Phaseolus ui_196


title: mRNA Phaseolus cdc_rosalee

source_name: mRNA Phaseolus cdc_rosalee


title: mRNA Phaseolus oac_rex

source_name: mRNA Phaseolus oac_rex


title: mRNA Phaseolus windbreaker

source_name: mRNA Phaseolus windbreaker


title: mRNA Phaseolus midnight

source_name: mRNA Phaseolus midnight


title: mRNA Phaseolus fleetwood

source_name: mRNA Phaseolus fleetwood


title: mRNA Phaseolus vista

source_name: mRNA Phaseolus vista


title: mRNA Phaseolus fiesta

source_name: mRNA Phaseolus fiesta


title: mRNA Phaseolus gn_harris

source_name: mRNA Phaseolus gn_harris


title: mRNA Phaseolus lariat

source_name: mRNA Phaseolus lariat


title: mRNA Phaseolus viva

source_name: mRNA Phaseolus viva


title: mRNA Phaseolus amadeus_77

source_name: mRNA Phaseolus amadeus_77


title: mRNA Phaseolus bill_z

source_name: mRNA Phaseolus bill_z


title: mRNA Phaseolus mariah

source_name: mRNA Phaseolus mariah


title: mRNA Phaseolus midland

source_name: mRNA Phaseolus midland


title: mRNA Phaseolus marquis

source_name: mRNA Phaseolus marquis


title: mRNA Phaseolus seafarer

source_name: mRNA Phaseolus seafarer


title: mRNA Phaseolus pink_floyd

source_name: mRNA Phaseolus pink_floyd


title: mRNA Phaseolus buster

source_name: mRNA Phaseolus buster


title: mRNA Phaseolus la_paz

source_name: mRNA Phaseolus la_paz


title: mRNA Phaseolus medalist

source_name: mRNA Phaseolus medalist


title: mRNA Phaseolus nd041062_1

source_name: mRNA Phaseolus nd041062_1


title: mRNA Phaseolus domino

source_name: mRNA Phaseolus domino


title: mRNA Phaseolus albion

source_name: mRNA Phaseolus albion


title: mRNA Phaseolus ui_911

source_name: mRNA Phaseolus ui_911


title: mRNA Phaseolus t9905

source_name: mRNA Phaseolus t9905


title: mRNA Phaseolus ac_resolute

source_name: mRNA Phaseolus ac_resolute


title: mRNA Phaseolus ac_polaris

source_name: mRNA Phaseolus ac_polaris


title: mRNA Phaseolus stampede

source_name: mRNA Phaseolus stampede


title: mRNA Phaseolus nd060197

source_name: mRNA Phaseolus nd060197


title: mRNA Phaseolus condor

source_name: mRNA Phaseolus condor


title: mRNA Phaseolus ouray

source_name: mRNA Phaseolus ouray


title: mRNA Phaseolus t_39

source_name: mRNA Phaseolus t_39


title: mRNA Phaseolus matterhorn

source_name: mRNA Phaseolus matterhorn


title: mRNA Phaseolus sonora

source_name: mRNA Phaseolus sonora


title: mRNA Phaseolus usrm_20

source_name: mRNA Phaseolus usrm_20


title: mRNA Phaseolus nodak

source_name: mRNA Phaseolus nodak


title: mRNA Phaseolus starlight

source_name: mRNA Phaseolus starlight


title: mRNA Phaseolus medicine_hat

source_name: mRNA Phaseolus medicine_hat


title: mRNA Phaseolus navigator

source_name: mRNA Phaseolus navigator


title: mRNA Phaseolus ui_537

source_name: mRNA Phaseolus ui_537


title: mRNA Phaseolus nw_63

source_name: mRNA Phaseolus nw_63


title: mRNA Phaseolus olathe

source_name: mRNA Phaseolus olathe


title: mRNA Phaseolus le_baron

source_name: mRNA Phaseolus le_baron


title: mRNA Phaseolus abc_weihing

source_name: mRNA Phaseolus abc_weihing


title: mRNA Phaseolus harold

source_name: mRNA Phaseolus harold


title: mRNA Phaseolus crestwood

source_name: mRNA Phaseolus crestwood


title: mRNA Phaseolus nd_307

source_name: mRNA Phaseolus nd_307


title: mRNA Phaseolus mayflower

source_name: mRNA Phaseolus mayflower


title: mRNA Phaseolus eclipse

source_name: mRNA Phaseolus eclipse


title: mRNA Phaseolus sierra

source_name: mRNA Phaseolus sierra


title: mRNA Phaseolus frontier

source_name: mRNA Phaseolus frontier


title: mRNA Phaseolus a_55

source_name: mRNA Phaseolus a_55


title: mRNA Phaseolus garnet

source_name: mRNA Phaseolus garnet


title: mRNA Phaseolus ac_earlired

source_name: mRNA Phaseolus ac_earlired


title: mRNA Phaseolus ucd_9623

source_name: mRNA Phaseolus ucd_9623


title: mRNA Phaseolus jaguar

source_name: mRNA Phaseolus jaguar


title: mRNA Phaseolus puebla_152

source_name: mRNA Phaseolus puebla_152


title: mRNA Phaseolus maverick

source_name: mRNA Phaseolus maverick


title: mRNA Phaseolus cdc_nighthawk

source_name: mRNA Phaseolus cdc_nighthawk


title: mRNA Phaseolus envoy

source_name: mRNA Phaseolus envoy


title: Methylome Phaseolus nodak

library_source: genomic

molecule: genomic DNA

source_name: Methylome Phaseolus nodak


title: Methylome Phaseolus fiesta

source_name: Methylome Phaseolus fiesta


title: Methylome Phaseolus zorro

source_name: Methylome Phaseolus zorro


title: Methylome Phaseolus garnet

source_name: Methylome Phaseolus garnet


title: Methylome Phaseolus navigator

source_name: Methylome Phaseolus navigator


title: Methylome Phaseolus t_39

source_name: Methylome Phaseolus t_39


title: Methylome Phaseolus orion

source_name: Methylome Phaseolus orion


title: mRNA Phaseolus apache

source_name: mRNA Phaseolus apache


title: mRNA Phaseolus ui_114

source_name: mRNA Phaseolus ui_114


title: Methylome Phaseolus sonora

source_name: Methylome Phaseolus sonora


title: Methylome Phaseolus albion

source_name: Methylome Phaseolus albion


title: Methylome Phaseolus othello

source_name: Methylome Phaseolus othello


title: Methylome Phaseolus sedona

source_name: Methylome Phaseolus sedona


title: Methylome Phaseolus gts_900

source_name: Methylome Phaseolus gts_900


title: Methylome Phaseolus envoy

source_name: Methylome Phaseolus envoy


title: Methylome Phaseolus ac_polaris

source_name: Methylome Phaseolus ac_polaris


title: Methylome Phaseolus fleetwood

source_name: Methylome Phaseolus fleetwood


title: Methylome Phaseolus ensign

source_name: Methylome Phaseolus ensign


title: Methylome Phaseolus windbreaker

source_name: Methylome Phaseolus windbreaker


title: Methylome Phaseolus ip08_2

source_name: Methylome Phaseolus ip08_2


title: Methylome Phaseolus eclipse

source_name: Methylome Phaseolus eclipse


title: Methylome Phaseolus mariah

source_name: Methylome Phaseolus mariah


title: Methylome Phaseolus pink_floyd

source_name: Methylome Phaseolus pink_floyd


title: mRNA Phaseolus c_20

source_name: mRNA Phaseolus c_20


title: Methylome Phaseolus bill_z

source_name: Methylome Phaseolus bill_z


title: Methylome Phaseolus ouray

source_name: Methylome Phaseolus ouray


title: Methylome Phaseolus matterhorn

source_name: Methylome Phaseolus matterhorn


title: Methylome Phaseolus frontier

source_name: Methylome Phaseolus frontier


title: Methylome Phaseolus midland

source_name: Methylome Phaseolus midland


title: Methylome Phaseolus ui_3

source_name: Methylome Phaseolus ui_3


title: Methylome Phaseolus lariat

source_name: Methylome Phaseolus lariat


title: Methylome Phaseolus usrm_20

source_name: Methylome Phaseolus usrm_20


title: Methylome Phaseolus ucd_9623

source_name: Methylome Phaseolus ucd_9623


title: Methylome Phaseolus yolano

source_name: Methylome Phaseolus yolano


title: Methylome Phaseolus gemini

source_name: Methylome Phaseolus gemini


title: Methylome Phaseolus ui_126

source_name: Methylome Phaseolus ui_126


title: Methylome Phaseolus la_paz

source_name: Methylome Phaseolus la_paz


title: Methylome Phaseolus sierra

source_name: Methylome Phaseolus sierra


title: Methylome Phaseolus remington

source_name: Methylome Phaseolus remington


title: Methylome Phaseolus ac_earlired

source_name: Methylome Phaseolus ac_earlired


title: Methylome Phaseolus ac_early_rose

source_name: Methylome Phaseolus ac_early_rose


title: Methylome Phaseolus dor_364

source_name: Methylome Phaseolus dor_364


title: Methylome Phaseolus poncho

source_name: Methylome Phaseolus poncho


title: Methylome Phaseolus crestwood

source_name: Methylome Phaseolus crestwood


title: Methylome Phaseolus medalist

source_name: Methylome Phaseolus medalist


title: Methylome Phaseolus ui_911

source_name: Methylome Phaseolus ui_911


title: Methylome Phaseolus beryl_r

source_name: Methylome Phaseolus beryl_r


title: Methylome Phaseolus nd041062_1

source_name: Methylome Phaseolus nd041062_1


title: Methylome Phaseolus black_magic

source_name: Methylome Phaseolus black_magic


title: Methylome Phaseolus ui_111

source_name: Methylome Phaseolus ui_111


title: Methylome Phaseolus apache

source_name: Methylome Phaseolus apache


title: Methylome Phaseolus medicine_hat

source_name: Methylome Phaseolus medicine_hat


title: Methylome Phaseolus abc_weihing

source_name: Methylome Phaseolus abc_weihing


title: Methylome Phaseolus bunsi

source_name: Methylome Phaseolus bunsi


title: Methylome Phaseolus ui_59

source_name: Methylome Phaseolus ui_59


title: Methylome Phaseolus sequoia

source_name: Methylome Phaseolus sequoia


title: Methylome Phaseolus t9905

source_name: Methylome Phaseolus t9905


title: Methylome Phaseolus amadeus_77

source_name: Methylome Phaseolus amadeus_77


title: Methylome Phaseolus cdc_nordic

source_name: Methylome Phaseolus cdc_nordic


title: Methylome Phaseolus midnight

source_name: Methylome Phaseolus midnight


title: Methylome Phaseolus merlot

source_name: Methylome Phaseolus merlot


title: Methylome Phaseolus sanilac

source_name: Methylome Phaseolus sanilac


title: Methylome Phaseolus common_pinto

source_name: Methylome Phaseolus common_pinto


title: Methylome Phaseolus jaguar

source_name: Methylome Phaseolus jaguar


title: Methylome Phaseolus c_20

source_name: Methylome Phaseolus c_20


title: Methylome Phaseolus stampede

source_name: Methylome Phaseolus stampede


title: Methylome Phaseolus nd060197

source_name: Methylome Phaseolus nd060197


title: Methylome Phaseolus norstar

source_name: Methylome Phaseolus norstar


title: Methylome Phaseolus buster

source_name: Methylome Phaseolus buster


title: Methylome Phaseolus vista

source_name: Methylome Phaseolus vista


title: Methylome Phaseolus seafarer

source_name: Methylome Phaseolus seafarer


title: Methylome Phaseolus puebla_152

source_name: Methylome Phaseolus puebla_152


title: Methylome Phaseolus olathe

source_name: Methylome Phaseolus olathe


title: Methylome Phaseolus avalanche

source_name: Methylome Phaseolus avalanche


title: Methylome Phaseolus oac_rex

source_name: Methylome Phaseolus oac_rex


title: Methylome Phaseolus 115m

source_name: Methylome Phaseolus 115m


title: Methylome Phaseolus domino

source_name: Methylome Phaseolus domino


title: Methylome Phaseolus croissant

source_name: Methylome Phaseolus croissant


title: Methylome Phaseolus quincy

source_name: Methylome Phaseolus quincy


title: Methylome Phaseolus roza

source_name: Methylome Phaseolus roza


title: Methylome Phaseolus seahawk

source_name: Methylome Phaseolus seahawk


title: Methylome Phaseolus ui_37

source_name: Methylome Phaseolus ui_37


title: Methylome Phaseolus beryl

source_name: Methylome Phaseolus beryl


title: Methylome Phaseolus ac_resolute

source_name: Methylome Phaseolus ac_resolute


title: Methylome Phaseolus ui_537

source_name: Methylome Phaseolus ui_537


title: Methylome Phaseolus cdc_nighthawk

source_name: Methylome Phaseolus cdc_nighthawk


title: Methylome Phaseolus ui_114

source_name: Methylome Phaseolus ui_114


title: Methylome Phaseolus starlight

source_name: Methylome Phaseolus starlight


title: Methylome Phaseolus marquis

source_name: Methylome Phaseolus marquis


title: Methylome Phaseolus harold

source_name: Methylome Phaseolus harold


title: Methylome Phaseolus nw_63

source_name: Methylome Phaseolus nw_63


title: Methylome Phaseolus mayflower

source_name: Methylome Phaseolus mayflower


title: Methylome Phaseolus maverick

source_name: Methylome Phaseolus maverick


title: Methylome Phaseolus raven

source_name: Methylome Phaseolus raven


title: Methylome Phaseolus cdc_rosalee

source_name: Methylome Phaseolus cdc_rosalee


title: smallRNA Phaseolus usrm_20

source_name: smallRNA Phaseolus usrm_20


title: smallRNA Phaseolus beryl

source_name: smallRNA Phaseolus beryl


title: smallRNA Phaseolus marquis

source_name: smallRNA Phaseolus marquis


title: smallRNA Phaseolus beryl_r

source_name: smallRNA Phaseolus beryl_r


title: smallRNA Phaseolus matterhorn

source_name: smallRNA Phaseolus matterhorn


title: smallRNA Phaseolus orion

source_name: smallRNA Phaseolus orion


title: smallRNA Phaseolus starlight

source_name: smallRNA Phaseolus starlight


title: smallRNA Phaseolus bill_z

source_name: smallRNA Phaseolus bill_z


title: smallRNA Phaseolus poncho

source_name: smallRNA Phaseolus poncho


title: mRNA Phaseolus 115m

source_name: mRNA Phaseolus 115m


title: smallRNA Phaseolus crestwood

source_name: smallRNA Phaseolus crestwood


title: smallRNA Phaseolus zorro

source_name: smallRNA Phaseolus zorro


title: smallRNA Phaseolus nd_307

source_name: smallRNA Phaseolus nd_307


title: smallRNA Phaseolus c_20

source_name: smallRNA Phaseolus c_20


title: smallRNA Phaseolus sierra

source_name: smallRNA Phaseolus sierra


title: smallRNA Phaseolus gn_harris

source_name: smallRNA Phaseolus gn_harris


title: smallRNA Phaseolus ac_resolute

source_name: smallRNA Phaseolus ac_resolute


title: smallRNA Phaseolus medicine_hat

source_name: smallRNA Phaseolus medicine_hat


title: smallRNA Phaseolus mayflower

source_name: smallRNA Phaseolus mayflower


title: smallRNA Phaseolus apache

source_name: smallRNA Phaseolus apache


title: smallRNA Phaseolus la_paz

source_name: smallRNA Phaseolus la_paz


title: smallRNA Phaseolus roza

source_name: smallRNA Phaseolus roza


title: smallRNA Phaseolus ip08_2

source_name: smallRNA Phaseolus ip08_2


title: smallRNA Phaseolus common_pinto

source_name: smallRNA Phaseolus common_pinto


title: smallRNA Phaseolus amadeus_77

source_name: smallRNA Phaseolus amadeus_77


title: smallRNA Phaseolus ui_196

source_name: smallRNA Phaseolus ui_196


title: smallRNA Phaseolus quincy

source_name: smallRNA Phaseolus quincy


title: smallRNA Phaseolus avalanche

source_name: smallRNA Phaseolus avalanche


title: smallRNA Phaseolus maverick

source_name: smallRNA Phaseolus maverick


title: smallRNA Phaseolus fiesta

source_name: smallRNA Phaseolus fiesta


title: smallRNA Phaseolus lariat

source_name: smallRNA Phaseolus lariat


title: smallRNA Phaseolus oac_rex

source_name: smallRNA Phaseolus oac_rex


title: smallRNA Phaseolus sedona

source_name: smallRNA Phaseolus sedona


title: smallRNA Phaseolus ui_911

source_name: smallRNA Phaseolus ui_911


title: smallRNA Phaseolus medalist

source_name: smallRNA Phaseolus medalist


title: smallRNA Phaseolus sonora

source_name: smallRNA Phaseolus sonora


title: smallRNA Phaseolus vista

source_name: smallRNA Phaseolus vista


title: smallRNA Phaseolus santa_fe

source_name: smallRNA Phaseolus santa_fe


title: smallRNA Phaseolus yolano

source_name: smallRNA Phaseolus yolano


title: smallRNA Phaseolus seahawk

source_name: smallRNA Phaseolus seahawk


title: smallRNA Phaseolus ui_126

source_name: smallRNA Phaseolus ui_126


title: smallRNA Phaseolus stampede

source_name: smallRNA Phaseolus stampede


title: smallRNA Phaseolus albion

source_name: smallRNA Phaseolus albion


title: smallRNA Phaseolus t9905

source_name: smallRNA Phaseolus t9905


title: smallRNA Phaseolus midnight

source_name: smallRNA Phaseolus midnight


title: smallRNA Phaseolus garnet

source_name: smallRNA Phaseolus garnet


title: smallRNA Phaseolus merlot

source_name: smallRNA Phaseolus merlot


title: smallRNA Phaseolus ui_114

source_name: smallRNA Phaseolus ui_114


title: smallRNA Phaseolus norstar

source_name: smallRNA Phaseolus norstar


title: smallRNA Phaseolus cdc_nighthawk

source_name: smallRNA Phaseolus cdc_nighthawk


title: smallRNA Phaseolus cdc_nordic

source_name: smallRNA Phaseolus cdc_nordic


title: smallRNA Phaseolus sanilac

source_name: smallRNA Phaseolus sanilac


title: smallRNA Phaseolus nodak

source_name: smallRNA Phaseolus nodak


title: smallRNA Phaseolus black_magic

source_name: smallRNA Phaseolus black_magic


title: smallRNA Phaseolus olathe

source_name: smallRNA Phaseolus olathe


title: smallRNA Phaseolus ensign

source_name: smallRNA Phaseolus ensign


title: smallRNA Phaseolus ac_early_rose

source_name: smallRNA Phaseolus ac_early_rose


title: smallRNA Phaseolus pink_floyd

source_name: smallRNA Phaseolus pink_floyd


title: smallRNA Phaseolus t_39

source_name: smallRNA Phaseolus t_39


title: smallRNA Phaseolus croissant

source_name: smallRNA Phaseolus croissant


title: smallRNA Phaseolus ui_3

source_name: smallRNA Phaseolus ui_3


title: smallRNA Phaseolus mariah

source_name: smallRNA Phaseolus mariah


title: smallRNA Phaseolus ui_537

source_name: smallRNA Phaseolus ui_537


title: smallRNA Phaseolus frontier

source_name: smallRNA Phaseolus frontier


title: smallRNA Phaseolus cdc_rosalee

source_name: smallRNA Phaseolus cdc_rosalee


title: smallRNA Phaseolus envoy

source_name: smallRNA Phaseolus envoy


title: smallRNA Phaseolus ui_111

source_name: smallRNA Phaseolus ui_111


title: smallRNA Phaseolus nd060197

source_name: smallRNA Phaseolus nd060197


title: smallRNA Phaseolus buster

source_name: smallRNA Phaseolus buster


title: smallRNA Phaseolus a_55

source_name: smallRNA Phaseolus a_55


title: smallRNA Phaseolus bunsi

source_name: smallRNA Phaseolus bunsi


title: smallRNA Phaseolus le_baron

source_name: smallRNA Phaseolus le_baron


title: smallRNA Phaseolus 115m

source_name: smallRNA Phaseolus 115m


title: smallRNA Phaseolus dor_364

source_name: smallRNA Phaseolus dor_364


title: smallRNA Phaseolus gts_900

source_name: smallRNA Phaseolus gts_900


title: smallRNA Phaseolus puebla_152

source_name: smallRNA Phaseolus puebla_152


title: smallRNA Phaseolus midland

source_name: smallRNA Phaseolus midland


title: smallRNA Phaseolus remington

source_name: smallRNA Phaseolus remington


title: smallRNA Phaseolus othello

source_name: smallRNA Phaseolus othello


title: smallRNA Phaseolus domino

source_name: smallRNA Phaseolus domino


title: smallRNA Phaseolus ac_polaris

source_name: smallRNA Phaseolus ac_polaris


title: smallRNA Phaseolus nd041062_1

source_name: smallRNA Phaseolus nd041062_1


title: smallRNA Phaseolus jaguar

source_name: smallRNA Phaseolus jaguar


title: smallRNA Phaseolus raven

source_name: smallRNA Phaseolus raven


title: smallRNA Phaseolus windbreaker

source_name: smallRNA Phaseolus windbreaker


title: smallRNA Phaseolus harold

source_name: smallRNA Phaseolus harold


title: smallRNA Phaseolus viva

source_name: smallRNA Phaseolus viva


title: smallRNA Phaseolus ui_37

source_name: smallRNA Phaseolus ui_37


title: smallRNA Phaseolus ouray

source_name: smallRNA Phaseolus ouray


title: smallRNA Phaseolus navigator

source_name: smallRNA Phaseolus navigator


title: smallRNA Phaseolus condor

source_name: smallRNA Phaseolus condor


title: smallRNA Phaseolus abc_weihing

source_name: smallRNA Phaseolus abc_weihing


title: smallRNA Phaseolus gemini

source_name: smallRNA Phaseolus gemini


title: smallRNA Phaseolus fleetwood

source_name: smallRNA Phaseolus fleetwood


title: smallRNA Phaseolus ucd_9623

source_name: smallRNA Phaseolus ucd_9623


title: smallRNA Phaseolus ac_earlired

source_name: smallRNA Phaseolus ac_earlired


title: smallRNA Phaseolus nw_63

source_name: smallRNA Phaseolus nw_63


title: smallRNA Phaseolus eclipse

source_name: smallRNA Phaseolus eclipse


title: smallRNA Phaseolus sequoia

source_name: smallRNA Phaseolus sequoia


title: WT MPP rep2

city: Toronto

first: Rashim Pal

last: Singh

address: 101, College Street

country: Canada

institute: Princess Margaret Cancer Centre, UHN

description:
deseq.MPP.bfx312.xls
L4743_8.WT.MPP

data_processing:
After sequencing, FastQC (http://www.bioinformatics.babraham.ac.uk/) was used to perform a basic quality control on the sequencing data. As an additional control, library diversity was assessed by redundancy investigation in the reads. Next, the reads were aligned with BWA (v. 0.7.8) against the mouse reference (mm10) and an exon-exon junction library of 120 nucleotides, which was created according to the Ensembl annotation version 69. The uniquely aligned reads were counted with featureCounts (v1.4.4) and the same Ensembl annotation. Normalization of the raw read counts based on the library size and testing for differential expression between the two conditions was performed with the DESeq2 (v.1.4.0) R package. Genes with an adjusted p-value of less than 0.1 were considered as differentially expressed for comparison
DEseq gave 6629 significantly differentially expressed genes (DEGs) when comparing Tg and WT mice for HSC cells and 3801 DEGs for MPP cells (p-adjusted value <0.1). In order to compare DEGs between cell types we performed a simple overlap analysis (using Ensembl Gene IDs) to identify common and unique DEG, and performed a more fine-grained comparison by splitting DEGs into up-regulated and down regulated genes for each cell type
Genome_build: mm10
Supplementary_files_format_and_content: deseq .xls files (normalized read counts, log2FoldChange, etc.)

source_name: Multipotent Progenitors

growth_protocol: All transgenic mice  and their wild type littermates were bred and maintained in our animal facility with ad libitum water and food.

extract_protocol:
RNA was isolated using Rneasy micro kit from Qiagen.
Complete cDNA (pre-amplified for all HSC samples) was synthesized with the SMARTer® Ultra HV Kit (Clontech). After ultrasonic shearing of the amplified cDNA (Covaris S2) samples were subjected to standard Illumina fragment library preparation using the NEBNext® chemistries (New England Biolabs).

value: WT

value: Multipotent Progenitors


title: Tg MPP rep1

description:
deseq.MPP.bfx312.xls
L4745_10.Tg.MPP

value: EPO transgenic


title: Tg MPP rep2

description:
deseq.MPP.bfx312.xls
L4746_11.Tg.MPP


title: WT MPP rep1

description:
deseq.MPP.bfx312.xls
L4742_7.WT.MPP


title: WT HSC rep2

description:
deseq.HSC.bfx338.xls
L4737_2.WT.HSC

source_name: Hematopoietic stem cells

value: Hematopoietic stem cells


title: Tg MPP rep3

description:
deseq.MPP.bfx312.xls
L4747_12.Tg.MPP


title: WT MPP rep3

description:
deseq.MPP.bfx312.xls
L4744_9.WT.MPP


title: Tg HSC rep2

description:
deseq.HSC.bfx338.xls
L4740_5.Tg.HSC


title: Tg HSC rep1

description:
deseq.HSC.bfx338.xls
L4739_4.Tg.HSC


title: smallRNA Phaseolus ui_59

source_name: smallRNA Phaseolus ui_59


title: Tg HSC rep3

description:
deseq.HSC.bfx338.xls
L4741_6.Tg.HSC


title: smallRNA Phaseolus seafarer

source_name: smallRNA Phaseolus seafarer


title: WT HSC rep1

description:
deseq.HSC.bfx338.xls
L4736_1.WT.HSC


title: WT HSC rep3

description:
deseq.HSC.bfx338.xls
L4738_3.WT.HSC


title: Gril_H_8L

city: Bethesda

first: Patricia

middle: S

last: Steeg

state: MD

address: 37 Convent Dr

department: Women's Malignancies Branch

institute: National Cancer Institute

description: Human gene expression for highly permeable (L) metastases in mouse 8

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on  Affymetrix human U133 plus 2.0 ( or mouse 430 2.0) GeneChip,  washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Each chip were scanned on Affymetrix GeneChip scanner 3000.

data_processing: Data were collected using Affymetrix AGCC software.

source_name: Mouse brain

label_protocol: RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >8).  RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’ IVTexpress Labeling kit following manufacturer’s protocol.

growth_protocol: Female athymic NIH nu/nu mice were injected intracardiacally with the brain-tropic MDA-MB-231-BR cells. Brain metastases were established after 4 weeks. Diffusion of 3 kDa Texas red dextran was used to determine highly and poorly permeable metastases.

extract_protocol: Using laser capture microdissection highly and poorly permeable metastases were excised out and total RNA from the tissue was isolated using PicoPure® RNA isolation kit.

tag: subject

value: Female athymic NIH nu/nu mice


title: Gril_H_H4

description: Human gene expression of brains from healthy mouse H4

treatment_protocol: Diffusion of 3 kDa Texas red dextran was used to determine highly and poorly permeable metastases.


title: Gril_H_12NL

description: Human gene expression for poorly permeable (NL) metastases in mouse 12


title: Gril_H_H1

description: Human gene expression of brains from healthy mouse H1


title: Gril_H_H2

description: Human gene expression of brains from healthy mouse H2


title: Gril_H_12L

description: Human gene expression for highly permeable (L) metastases in mouse 12


title: Gril_H_13NL

description: Human gene expression for poorly permeable (NL) metastases in mouse 13


title: Gril_H_13L

description: Human gene expression for highly permeable (L) metastases in mouse 13


title: Gril_H_6NL

description: Human gene expression for poorly permeable (NL) metastases in mouse 6


title: Gril_H_11L

description: Human gene expression for highly permeable (L) metastases in mouse 11


title: Gril_H_H3

description: Human gene expression of brains from healthy mouse H3


title: OVCAR8 SiRNA1

city: Shanghai

first: Haiyan

last: Tai

address: Fangxie Road, Huangpu district,

institute: Obstetrics and Gynecology hospital of Fudan University

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45°C in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: OVCAR8 SiRNA1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA

growth_protocol: OVCAR8 and ES2 were cultured in plates

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

treatment_protocol: Ovarian cancer cell line OVCAR8 and ES2 were transiently transfected with control or FGFRL1 siRNA

tag: cell line

tag: sirna

value: tranfected with FGFRL1l SiRNA


title: Gril_H_8NL

description: Human gene expression for poorly permeable (NL) metastases in mouse 8


title: Gril_H_6L

description: Human gene expression for highly permeable (L) metastases in mouse 6


title: ES2 NC

source_name: ES2 NC

value: tranfected with control SiRNA


title: OVCAR8 NC

source_name: OVCAR8 NC


title: Gril_H_11NL

description: Human gene expression for poorly permeable (NL) metastases in mouse 11


title: treated [X_28]

city: Padova

first: Luca

last: Trentin

address: Via Giustiniani, 3

department: Department of Women's and Children's Health

country: Italy

institute: University of Padova

description: Gene expression data from leukemia cells treated  with I-BET151 10uM  ex vivo for 6h

hyb_protocol: 15 ug were fragmented; following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA

source_name: leukemia cell isolated from BM of NOD/SCID  mice with full-blown leukemia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting  from 100ng of Total RNA using the Affymetrix 3' IVT Plus Kit

growth_protocol: leukemia cells were cultured in serum-free StemSpan™ SFEM II Colture Medium in presence of SCF 10ng/mL and G-CSF 10ng/mL

extract_protocol: RNA was extracted using Trizol

treatment_protocol: I-BET151 10uM or control, for  6h

tag: treatment

tag: patient


title: treated [X_24]


title: treated [X_17]


title: treated [X_21bis]


title: treated [X_27]


title: treated [X_23]


title: treated [X_22bis]


title: ES2 SiRNA1

source_name: ES2 SiRNA1


title: treated [X_25]


title: treated [X_26]


title: treated [X_19]


title: treated [X_20]


title: treated [X_18]


title: treated [X_15]


title: treated [X_13]


title: DMSO [X_08]

description: Gene expression data from leukemia cells treated  with DMSO ex vivo for 6h

value: DMSO Control


title: DMSO [X_04]


title: treated [X_16]


title: DMSO [X_05]


title: DMSO [X_06]


title: DMSO [X_09]


title: DMSO [X_01]


title: DMSO [X_07]


title: DMSO [X_10]


title: DMSO [X_02]


title: DMSO [X_12]


title: 9VP

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: Ovation® FFPE WTA-Systems (NuGEN, San Carlos, USA) protocol in accordance with the standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using Illumina's BeadStudio Data Analysis Software.

source_name: pancreatitis formalin-fixed paraffin embedded

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

extract_protocol: RNA  from FF (Fresh Frozen) tissue samples was extracted with the  Universal RNA Purification Kit from Roboklon (Germany). RNA from FFPE (Formalin-Fixed Paraffin-Embedded) tissue samples was exttracted with the RNeasy FFPE Kit from Qiagen in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tissue storage

value: formalin-fixed paraffin embedded (FFPE)

tag: tissue type

value: pancreatitis

value: J


title: 8VP

value: I


title: 11VP

value: L


title: 1VP

value: B


title: DMSO [X_11]


title: treated [X_14]


title: 2VP

value: C


title: 7VP

value: H


title: 4VP

value: E


title: DMSO [X_03]


title: 6VP

value: G


title: 3VP

value: D


title: 2VFT

source_name: PDAC formalin-fixed paraffin embedded

value: PDAC


title: 10VP

value: K


title: 6VFT

source_name: normal formalin-fixed paraffin embedded

value: normal


title: 5VFT


title: 3VFT


title: 3VN

source_name: normal fresh-frozen

value: fresh frozen (FF)


title: 7VT

source_name: PDAC fresh-frozen


title: 6VT


title: 4VN


title: 8VT

value: F


title: T_53

hyb_protocol: Whole-Genome protocol from DASL HT Assay (Illumina, San Diego, USA) in accordance with the standard Illumina hybridization protocol

source_name: human PDAC tissue

value: tumor

tag: tumor grade

tag: tumor size

tag: tumor content

tag: metastasis

tag: number lymph nodes

tag: r classification


title: N_18

description:
matched pair T_28
Beads_9479614056_B

source_name: human non-tumor tissue


title: N_41

description:
matched pair T_44
Beads_9479614056_F


title: N_20

description:
matched pair T_20_2
Beads_9479614056_D


title: T_38

description:
matched pair N_19
Beads_9479187124_L

tag: lymphangiosis carcinomatosis

tag: hemangiosis carcinomatosis

tag: divorce invasion


title: T_20_2

description:
matched pair N_20
Beads_10010265016_G

value: pMx


title: T_PA36

description:
matched pair N_PA9
Beads_9479614056_L

value: formalin-fixed paraffin embedded (FFPE)


title: T_PA56_2

description:
matched pair N_PA56
Beads_10010265016_F


title: N_40

description:
matched pair T_43
Beads_9479614056_E


title: N_PA9

description:
matched pair T_PA36
Beads_9479614056_K


title: N_PA54

description:
matched pair T_PA54_2
Beads_10010265016_C


title: T_PA54_2

description:
matched pair N_PA54
Beads_10010265016_A


title: T_PA28

description:
matched pair N_PA18
Beads_9479614056_J


title: T_PA21

description:
matched pair N_PA11
Beads_9479614056_H


title: T_51


title: T_PA55_2

description:
matched pair N_PA55
Beads_10010265016_D


title: T_3_2

description:
matched pair N_3
Beads_10010265016_H


title: N_PA11

description:
matched pair T_PA21
Beads_9479614056_G


title: N_PA18

description:
matched pair T_PA28
Beads_9479614056_I


title: N_PA55

description:
matched pair T_PA55_2
Beads_10010265016_B


title: N_19

description:
matched pair T_38
Beads_9479614056_C


title: 2VN

value: A


title: T_32


title: T_34

description:
matched pair N_10
Beads_9479187124_H


title: T_28

description:
matched pair N_18
Beads_9479187124_D


title: N_15

description:
matched pair T_31
Beads_9479187111_L


title: N_PA56

description:
matched pair T_PA56_2
Beads_10010265016_E


title: N_13


title: T_21

description:
matched pair N_11
Beads_9479187124_A


title: T_23


title: RS-236_02, WT, technical replicate 2

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

description: Identification of differentially expressed genes

hyb_protocol: Following cRNA clean-up and quantification 600 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for One-Color based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). cRNA samples were hybridized at 65°C for 17 hours on separte SurePrint G3 Human GE Microarrays (8x60K format).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Fluorescent  signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies)  on the Agilent DNA Microarray Scanner and extracted from the images using Feature  Extraction 10.7.3.1 Software (Agilent Technologies)

source_name: iPSC-derived cardiomyocytes

label_protocol: 100 ng total RNA per sample were introduced into a reverse transcription reaction. Prior to this, the total RNA samples were spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy.The spiked total RNA was reverse transcribed into cDNA and then converted into labeled cRNA by in vitro transcription (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP.

growth_protocol: Wild-type and PKP2mut iPSCs were differentiated into cardiomyocytes. At day 20-30 of differentiation, contracting areas were manually micro-dissected, plated on fibronectin-coated plates, and maintained in culture for 3 months for maturation.

extract_protocol: Total mRNA was extracted using the Stratagene Absolutely RNA Nano kit according to the manufacturer's instructions.

treatment_protocol: 3-month-old cardiomyocytes were used for RNA isolation.

tag: cell type

value: iPSC-derived cardiomyocytes

tag: genotype

value: Wild-type

tag: age

value: 3 months of maturation


title: N_9

description:
matched pair T_36
Beads_9479187111_H


title: RS-236_02, WT, technical replicate 3


title: T_35


title: T_30

description:
matched pair N_6
Beads_9479187124_E

value: Rx


title: T_31

description:
matched pair N_15
Beads_9479187124_F


title: T_36

description:
matched pair N_9
Beads_9479187124_J


title: N_2

description:
matched pair T_22
Beads_9479187111_D


title: N_10

description:
matched pair T_34
Beads_9479187111_I


title: N_6

description:
matched pair T_30
Beads_9479187111_F


title: RS-236_01, PKP2mut, technical replicate 2


title: RS-236_01, PKP2mut technical replicate 3


title: RS-236_02, WT, technical replicate 1


title: T_43

description:
matched pair N_40
Beads_9479187111_B


title: T_44

description:
matched pair N_41
Beads_9479187111_C


title: N_3

description:
matched pair T_3_2
Beads_9479187111_E


title: N_11

description:
matched pair T_21
Beads_9479187111_J


title: T_42


title: T_22

description:
matched pair N_2
Beads_9479187124_B


title: Pax6cKO_M_3

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.
Reads were counted using FeaturesCount.
Genome_build: mm10
Supplementary_files_format_and_content: Count files.

source_name: embryonic cortex

extract_protocol:
RNA was isolated using Rneasy kit from Qiagen.
Libraries were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit.

tag: strain

tag: tissue

value: embryonic cortex


title: Pax6cKO_M_4


title: Pax6cKO_M_2


title: WT-72h-rep2 (part 1)

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Biological replicate 1 of 2, Cy3 is mouse RNA and Cy5 is mouse reference

hyb_protocol: Slides were hybridized to  Whole Mouse Genome Microarray 4x44K v2 (Agilent) according to manufacturer’s protocols

scan_protocol: The hybridized chips were scanned with SureScan Microarray Scanner D (Agilent) and the expression level was determined with Agilent Feature Extraction software 11.5.1.1.

data_processing:
Data are extracted with Agilent Feature Extraction Software. The data were further processed with NIA ANOVA tool utilities. See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal, rDyeNormSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 12 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr (adjust to UMR).

source_name: WT-KO CD8+ T-cells 72h after stimulation

label_protocol: RNA was labeled using Quick Amp Labeling two-color kit (Agilent)

extract_protocol: Cells were cultured in RPMI-1640 with 10% FBS, 10mM HEPES, 0.11nM beta-metcaptoethanol and 1x Pen/Strep/Glu from Thermo-Fisher. CD8+T cell stimulations performed using plate coated αCD3 (2C11) and soluble αCD28 (37.51) (Biolegend). Total RNA was extracted with RNaeasy Kit on QIAcube (Qiagen).

treatment_protocol: Ezh2 (Ezh2fl/fl) mice were generated as described20and obtained from MMRRC repository.CD4Cre was obtained from Taconic, and GzmbCre, OT-I, ROSA-26Sortm39(CAG-hop/EYFP, and B6.SJL-PtpraJ mice from Jackson Laboratory. Ezh2fl/flmice were crossed with CD4Cre to generate the Ezh2fl/fl-CD4Cre+(Ezh2-c-KO) strain. Ezh2fl/fl-CD4Cre mice were further crossed with OT-I to generate Ezh2fl/fl-CD4Cre -OT-I (Ezh2-c-KO OT-I) strain. Ezh2fl/flwas also crossed with GzmbCre and Gt(ROSA)26Sortm39(CAG-hop/EYFP)Hzeto create Ezh2fl/flGzmbCre-YFP (Ezh2-g-KO) mice. All mice were maintained under specific pathogen free conditions at the animal facility of National Institute on Aging and animal care was conducted in accordance with the guidelines of NIH.

tag: cell  type

tag: time point

source_name: Universal Mouse Reference

tag: biomaterial provider

value: Stratagene

tag: extract protocol

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


title: Pax6cKO_M_1


title: WT-72h-rep3 (part 1)

description: Biological replicate 2 of 2, Cy3 is mouse RNA and Cy5 is mouse reference

value: WT-KO CD8+ T-cells 72h after stimulation


title: Control_C_4


title: Control_C_2


title: Control_C_3


title: WT-16h-rep1 (part 1)

source_name: WT-KO CD8+ T-cells 16h after stimulation


title: Ezh2-16h-rep2 (part 1)

source_name: Ezh2-KO CD8+ T-cells 16h after stimulation


title: WT-72h-rep1 (part 1)


title: WT-0h-rep2 (part 1)

source_name: WT-KO CD8+ T-cells unstimulated

value: WT-KO CD8+ T-cells unstimulated


title: Ezh2-72h-rep1 (part 1)

value: Ezh2-KO CD8+ T-cells 72h after stimulation


title: WT-0h-rep3 (part 1)


title: Ezh2-72h-rep2 (part 1)

source_name: Ezh2-KO CD8+ T-cells 72h after stimulation


title: Control_C_1


title: BAF155cKO_M_4


title: WT-0h-rep1 (part 1)


title: Ezh2-16h-rep1 (part 1)

source_name: Ezh2-KO CD8+ T-cells unstimulated

value: Ezh2-KO CD8+ T-cells 16h after stimulation


title: Ezh2-0h-rep1 (part 1)

value: Ezh2-KO CD8+ T-cells unstimulated


title: Ezh2-0h-rep2 (part 1)


title: MDD_cerebellum_female_rat_21days_biological_replicate3

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

institute: INSERM

description: Gene expression in the cerebellum of 21-day-old female rat born to dams fed with methyl donor deficiency diet (MDD)

hyb_protocol: The fragmented cRNA was hybridized to a G4853A SurePrint G3 Rat GE 8X60K microarray (Agilent Technologies; Massy, France). The microarrays were performed in triplicate and washed, stabilized, and dried using acetonitrile and stabilization and drying solution (Agilent Technologies; Massy, France).

scan_protocol: The slides were scanned and the images were extracted using feature extraction software version 9.5.3 (Agilent Technologies; Massy, France).

data_processing: Normalized signal intensity using the Lowess procedure against a median profile of all samples.

organism: Rattus norvegicus

label_protocol: RNA samples were amplified, and labeled using the one-color microarray-based gene expression labeling kit (Agilent Technologies; Massy, France) following the manufacturer’s instructions. The RNA was denatured and reverse transcribed to cDNA. The cDNA was transcribed in vitro to RNA using T7 RNA polymerase and labeled with fluorescent cyanine 3-CTP.

growth_protocol: Experiments were performed on Wistar rats (Janvier Labs) in accordance with the National Institute of Health Guide for the Care and Use of Laboratory Animals in an accredited establishment (Institut National de la Santé et de la Recherche Médicale, Unité 954) according to the UE guidelines 2010-63-UE and to French governmental decree 2013-118). Adult rats were maintained under standard laboratory conditions on a 12h light / dark cycle with access to food and water ad libitum.

extract_protocol: Total RNA was extracted from 20 mg of grinded cerebellum from female P21 pups (control, N= 4; MDD, N=3) using TriZol (Invitrogen, Carlsbad, California, USA) according to the manufacturer’s recommendations. RNA was further digested with Turbo DNase (Thermo Fisher, Waltham, Massachusetts, USA) and phenol-chloroform extracted. Quality of total RNAs was attested by O.D.260 nm / O.D.280 nm and O.D.260 nm / O.D.230 nm determination by spectrophotometry (Multiskan GO, Thermo Fisher, Waltham, Massachusetts, USA).

treatment_protocol: One month before pregnancy,  female rats were either fed with a standard diet (A04 Standard Diet, Safe, Augy, France), or with a diet deficient in folate and vitamin B12 and lowered in choline (Special Diet Service, Saint-Gratien, France). These diets were maintained until the offspring was weaned at postnatal day 21 (P21). Rat pups were euthanized at postnatal day 21 with an overdose of isoflurane.

value: cerebellum

tag: gender

value: female

value: wistar

value: 21 days


title: BAF155cKO_M_3


title: MDD_cerebellum_female_rat_21days_biological_replicate2


title: BAF155cKO_M_1


title: genomic DNA from PM74 term control placenta

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

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

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

data_processing:
R version 3.2.5
The matrix_signal_Wilson_PEIUGR.csv contains Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted by standard salt method and purified using Qiagen DNeasy Kit according to standard instructions

tag: subject id

tag: pathology group

value: Term

tag: fetal sex

value: MALE

tag: gestational age

tag: sample tissue

value: Chorionic Villi

tag: 450k plate

tag: 450k sentrix_id

tag: 450k sentrix_position


title: control_cerebellum_female_rat_21days_biological_replicate4

description: Gene expression in the cerebellum of 21-day-old female rat born to dams fed with normal diet (CTRL)


title: control_cerebellum_female_rat_21days_biological_replicate3


title: MDD_cerebellum_female_rat_21days_biological_replicate1


title: Adv-Cre-4

city: Atlanta

first: Elizabeth

last: Millings

state: GA Georgia

address: 1510 Clifton Rd, Rm. G235

department: Biochemistry

institute: Emory University

description: Tissue collected 10 days post intravvenous adenoviral injection, following 12hr fast

data_processing:
Sample integrity for RNA utilized for RNA-Seq was assessed with an Agilent 2100 Bioanalyzer. All samples had RIN numbers greater than 9.0. mRNA was isolated using poly-A pulldown and reverse transcribed to generate cDNA.
cDNA was sequenced using single-ended sequencing on a HiSeq2000 according to manufacturer’s recommendations (Illumina)
The pass filter reads were mapped to mouse reference genome mm9 using TopHat (version 2.0.4).
For each read, up to 3 mismatches and 10 multiple hits were allowed during mapping.
FPKM values indicating relative abundance were determined using Cufflinks software (http://cole-trapnell-lab.github.io/cufflinks/).
Genome_build: mm9
Supplementary_files_format_and_content: Counts (.txt), FPKM (.csv)

source_name: Adv-Cre

extract_protocol:
Liver tissue was removed and flash frozen in liquid nitrogen. Total RNA was harvested using TRIzol® Reagent protocol or TRIzol® Reagent plus PureLink™ RNA Mini kit and columns were treated with DNase (all Life Technologies)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: male

value: 11 weeks

tag: genotype

value: Ildr2-/- (liver-specific)

value: liver


title: Adv-Cre-3

tag: strain

tag: age


title: Adv-Cre-2

tag: tissue


title: CTNNB1KO_PB_3

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: Agilent Mouse miRNA arrays (G4472B) were hybridised, washed and scanned on an Agilent Microarray Scanner following manufacturer instructions.

scan_protocol: Arrays ware scanned on an Agilent Microarray Scanner. Images from the scanner were processed using Agilent Feature Extraction Software v10.5.1.

data_processing: Raw signal data was RMA normalized using the limma package for R/Bioconductor.

source_name: C3H/CTNNB1ko mouse, liver, Phenobarbital, 0.05 %, 12 weeks

label_protocol: 100 ng Total RNA (diluted to 50ng/µl) were labelled using miRNA complete labelling and hybridization kit (Agilent# 5190-0456).

growth_protocol: Male C3H/He mice (wildtype and Ctnnb1 knockout) were used (see Baeuning et al., Histochem. Cell Biol 134, 469-481, 2010).  Alb-Cre mice (purchased from The Jackson Laboratory, Bar Harbor, ME) expressing Cre recombinase under the control of the hepatocyte-speciﬁc albumin promoter and transgenic mice with loxP sites inserted in the introns ﬂank-ing exons 3 and 6 of Ctnnb1 (gift from Dr. Huelsken, Swiss Institute for Experimental Cancer Research, Lausanne,Switzerland) were backcrossed for ﬁve generations into mice of the C3H/N strain leading to a genetic background which is highly susceptible for PB-mediated promotion. Mice with hepatocyte-speciﬁc KO of Ctnnb1 were obtained by interbreeding transgenic mice with Alb-Cre mice.

extract_protocol: Liver tissue was homogenized and RNA isolation was performed with Qiazol extraction (Qiagen, Hilden,Germany). RNA integrity was checked using the Agilent Bioanalyzer.

treatment_protocol: Mice were treated with 0.05% PB in the diet for 12 weeks; controls were kept on PB-free diet (see Baeuning et al., Histochem. Cell Biol 134, 469-481, 2010).

tag: genotype/variation

value: Phenobarbital

value: 12 weeks

tag: group


title: CTNNB1KO_PB_2


title: CTNNB1KO_PB_4


title: genomic DNA from PM167 term control placenta

value: FEMALE


title: genomic DNA from PM227 term control placenta


title: genomic DNA from PM263 term control placenta


title: control_cerebellum_female_rat_21days_biological_replicate1


title: genomic DNA from PM153 term control placenta


title: genomic DNA from PM205 term control placenta


title: genomic DNA from PM158 term control placenta


title: genomic DNA from PM142 term control placenta


title: Adv-Ildr2-shRNA-3

description: Tissue collected 3 days post intravenous adenoviral injection, following 24hr fast. Liver were not yet steatotic at this time point

value: 10 weeks

value: Ildr2 knockdown


title: Adv-Cre-1


title: Adv-Ildr2-shRNA-2


title: CTNNB1KO_H2O_4

source_name: C3H/CTNNB1ko mouse, liver, vehicle (Water), 0 %, 12 weeks

value: vehicle (Water)


title: CTNNB1KO_PB_1


title: CTNNB1KO_H2O_3


title: CTNNB1KO_H2O_2


title: genomic DNA from PM120 term control placenta


title: control_cerebellum_female_rat_21days_biological_replicate2

value: cerebellum


title: genomic DNA from PM136 term control placenta


title: RS-236_01, PKP2mut, technical replicate 1

tag: cell type

value: iPSC-derived cardiomyocytes

value: 3 months of maturation


title: genomic DNA from PM114 term control placenta


title: genomic DNA from PM112 term control placenta


title: genomic DNA from PM122 term control placenta


title: Adv-Ildr2-shRNA-1


title: CTNNB1KO_H2O_1


title: BAF155cKO_M_2

value: embryonic cortex


title: Adv-lacZ-shRNA-4

source_name: Adv-lacZ-shRNA

value: Wild-type


title: WT_PB_4

source_name: C3H mouse, liver, Phenobarbital, 0.05 %, 12 weeks

value: WT


title: Adv-lacZ-shRNA-2


title: Adv-lacZ-shRNA-1


title: genomic DNA from PM72r Technical Replicate placenta

value: REPLICATE

value: Chorionic Villi


title: genomic DNA from PM72 Technical Replicate placenta


title: WT_PB_3

value: male


title: WT_PB_1


title: WT_PB_2


title: WT_H2O_4

source_name: C3H mouse, liver, vehicle (Water), 0 %, 12 weeks


title: WT_H2O_1


title: WT_H2O_3


title: WT_H2O_2


title: Adv-Ildr2-shRNA-4


title: Adv-lacZ-shRNA-3


title: genomic DNA from PL64r1 Technical Replicate placenta


title: genomic DNA from PM139 Technical Replicate placenta

value: MALE


title: WT-16h-rep2 (part 2)

description: wide type naive CD8+ T-cells 16h after stimulation, replication 2

hyb_protocol: Slides were hybridized to  SurePrint G3 Mouse Gene Expression v2 8x60K Microarray (Agilent) according to manufacturer’s protocols

data_processing:
Data are extracted with Agilent Feature Extraction Software. The data were further processed with ExAtlas. See https://lgsun.irp.nia.nih.gov/exatlas for details.
The data is normalized with the following method:
(1) Take values from the columns gProcessedSignal, rProcessedSignal in the raw files and log-transform them using: log10(max(x,10)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 12 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr (adjust to UMR).

label_protocol: RNA was labeled using Quick Amp Labeling two-color kit (Agilent) and hybridized to SurePrint G3 Mouse Gene Expression v2 8x60K Microarray Kit (Agilent) according to manufacturer’s protocols.

extract_protocol: Cells were cultured in RPMI-1640 with 10% FBS, 10mM HEPES, 0.11nM beta-metcaptoethanol and 1x Pen/Strep/Glu from Thermo-Fisher. Naive CD8+ T cell stimulations performed using plate coated αCD3 (2C11) and soluble αCD28 (37.51) (Biolegend). Total RNA was extracted with RNaeasy Kit on QIAcube (Qiagen).

treatment_protocol: Ezh2 (Ezh2fl/fl) mice were obtained from MMRRC repository, CD4Cre mice was obtained from Taconic, and OT-I mice from Jackson Laboratory. Ezh2fl/fl mice were crossed with CD4Cre to generate the Ezh2fl/fl-CD4Cre+(Ezh2-c-KO) strain. Ezh2fl/fl-CD4Cre mice were further crossed with OT-I to generate Ezh2fl/fl-CD4Cre -OT-I (Ezh2-c-KO OT-I) strain.  All mice were maintained under specific pathogen free conditions at the animal facility of National Institute on Aging and animal care was conducted in accordance with the guidelines of NIH.

tag: cell  type

value: wide type CD8+ T-cell

tag: time point

source_name: Mix of resting and activated mouse T cells

tag: biomaterial provider

value: Home-made

tag: extract protocol


title: genomic DNA from PL64 Technical Replicate placenta

tag: subject id

tag: pathology group

tag: fetal sex

tag: gestational age


title: WT-0h-rep3 (part 2)

description: wide type naive CD8+ T-cells unstimulated, replication 3

value: Total RNA was extracted with RNaeasy Kit on QIAcube (Qiagen)


title: genomic DNA from PM139r1 Technical Replicate placenta

tag: sample tissue

tag: 450k plate

tag: 450k sentrix_id

tag: 450k sentrix_position


title: Ezh2-0h-rep3 (part 2)

description: Ezh2-CD4cre-KO naïve CD8+ T-cells unstimulated, replication 3

value: Ezh2-c-KO CD8+ T-cell


title: WT-16h-rep1 (part 2)

description: wide type naive CD8+ T-cells 16h after stimulation, replication 1


title: WT-0h-rep1 (part 2)

description: wide type naive CD8+ T-cells unstimulated, replication 1


title: Ezh2-16h-rep2 (part 2)

description: Ezh2-CD4cre-KO naïve CD8+ T-cells 16h after stimulation, replication 2


title: genomic DNA from PL21r Technical Replicate placenta


title: Ezh2-16h-rep1 (part 2)

description: Ezh2-CD4cre-KO naïve CD8+ T-cells 16h after stimulation, replication 1


title: Ezh2-72h-rep1 (part 2)

description: Ezh2-CD4cre-KO naïve CD8+ T-cells 72h after stimulation, replication 1


title: genomic DNA from PM249 pre-term control placenta

value: PreT

value: FEMALE


title: genomic DNA from PM77 pre-term control placenta


title: genomic DNA from PL21 Technical Replicate placenta


title: genomic DNA from PM17 pre-term control placenta


title: genomic DNA from PM161 pre-term control placenta


title: Ezh2-0h-rep2 (part 2)

description: Ezh2-CD4cre-KO naïve CD8+ T-cells unstimulated, replication 2


title: Ezh2-0h-rep1 (part 2)

description: Ezh2-CD4cre-KO naïve CD8+ T-cells unstimulated, replication 1


title: genomic DNA from PM20 pre-term control placenta


title: genomic DNA from PL65 pre-term control placenta


title: genomic DNA from PL96 pre-term control placenta


title: 35S::WOX1:GR_DEX-IAA_line2

city: Tsukuba

first: Miyuki

middle: T

last: Nakata

state: Ibaraki

address: 1-1-1, Higashi

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). 1.65 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 ºC) to Agilent Whole Genome Oligo Microarrays 4x44K V4. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at root temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 ºC) for 1 min. The last washing was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.

organism: Arabidopsis thaliana

source_name: DEX, 6 hours, IAA, 3 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's recommendations.

growth_protocol: Plants were grown on solid medium contains 0.5x Murashige and Skoog (MS) salts, 1% sucrose, 0.05% MES-KOH (w/v) pH 5.7, 1.2 % purified agar for 6 days (continuous light condition, 22 ºC).

extract_protocol: RNA was extracted from shoot apices of 6-dps seedlings using the Plant RNeasy Mini Kit (QIAGEN) following the manufacturer's recommendations.

treatment_protocol: Plants were treated with liquid medium containing 0.5x MS salts, 1% sucrose and 0.05% MES-KOH (w/v) pH 5.7 with or without 10 µM DEX, 10 µM cycloheximide (CHX) and 20 µM IAA  for 6 hours, 6 hours and 3 hours, respectively (continuous light condition, 22 ºC).

value: shoot apices including leaf primordia

tag: strain

value: 35S::WOX1:GR line 2


title: 35S::WOX1:GR_DEX-IAA_line1

tag: tissue

value: 35S::WOX1:GR line 1


title: Gril_M_H3

description: Murine gene expression of brains from healthy mouse H3

source_name: Mouse brain

tag: subject

value: Female athymic NIH nu/nu mice


title: Gril_M_H2

description: Murine gene expression of brains from healthy mouse H2


title: genomic DNA from PL58 pre-term control placenta


title: genomic DNA from PL59 pre-term control placenta


title: Gril_M_H4

description: Murine gene expression of brains from healthy mouse H4


title: 35S::WOX1:GR_Mock-IAA_line2

source_name: Mock, 6 hours, IAA, 3 hours


title: genomic DNA from PL56 pre-term control placenta


title: genomic DNA from PL33 pre-term control placenta


title: genomic DNA from PL43 pre-term control placenta


title: 35S::WOX1:GR_DEX-Mock_line2

source_name: DEX, 6 hours, Mock, 3 hours


title: Gril_M_H1

description: Murine gene expression of brains from healthy mouse H1


title: genomic DNA from PL64r2 pre-term control placenta


title: genomic DNA from PL76 pre-term control placenta


title: Gril_M_8L

description: Murine gene expression for highly permeable (L) metastases in mouse 8


title: 35S::WOX1:GR_Mock-IAA_line1


title: 35S::WOX1:GR_Mock-Mock_line2

source_name: Mock, 6 hours, Mock, 3 hours


title: Gril_M_8NL

description: Murine gene expression for poorly permeable (NL) metastases in mouse 8


title: genomic DNA from PL38 pre-term control placenta


title: genomic DNA from PL32 pre-term control placenta


title: 35S::WOX1:GR_DEX-Mock_line1


title: genomic DNA from PL25 pre-term control placenta


title: Gril_M_6L

description: Murine gene expression for highly permeable (L) metastases in mouse 6


title: 35S::WOX1:GR_Mock-Mock_line1


title: Gril_M_6NL

description: Murine gene expression for poorly permeable (NL) metastases in mouse 6


title: genomic DNA from PL113 pre-term control placenta


title: 35S::WOX1:GR_DEXCHX_line2_rep2

source_name: DEX & CHX, 6 hours

value: 35S::WOX1:GR line 2 experiment 2


title: genomic DNA from PL26 pre-term control placenta


title: Gril_M_12NL

description: Murine gene expression for poorly permeable (NL) metastases in mouse 12


title: genomic DNA from PL11 pre-term control placenta


title: Gril_M_13L

description: Murine gene expression for highly permeable (L) metastases in mouse 13


title: 35S::WOX1:GR_DEXCHX_line1_rep2

value: 35S::WOX1:GR line 1 experiment 2


title: 35S::WOX1:GR_DEXCHX_line2_rep1

value: 35S::WOX1:GR line 2 experiment 1


title: Gril_M_12L

description: Murine gene expression for highly permeable (L) metastases in mouse 12


title: genomic DNA from PL112 pre-term control placenta


title: Gril_M_11NL

description: Murine gene expression for poorly permeable (NL) metastases in mouse 11


title: Gril_M_11L

description: Murine gene expression for highly permeable (L) metastases in mouse 11


title: 35S::WOX1:GR_DEXCHX_line1_rep1

value: 35S::WOX1:GR line 1 experiment 1


title: 35S::WOX1:GR_CHX_line2_rep2

source_name: CHX, 6 hours


title: genomic DNA from PL21r2 pre-term control placenta

value: Chorionic Villi


title: genomic DNA from PL102 pre-term control placenta


title: 35S::WOX1:GR_CHX_line2_rep1


title: 35S::WOX1:GR_CHX_line1_rep2


title: WT_PB_4

hyb_protocol: cRNA synthesis, target hybridization, washing, staining and subsequent probe array scanning was done according to the manufacturer's instructions (3'IVT Express Kit User Manual Affymetrix)

scan_protocol: Scanner 3000 7G; Software GCOS (Genechip Operating Software) version 1.4.0

data_processing: Raw signal data was RMA normalized using the affy package for R/Bioconductor.

label_protocol: Labeling according to 3'IVT Express Kit User Manual Affymetrix

extract_protocol: Liver tissue was homogenized and RNA isolation was performed with Qiazol extraction (Qiagen, Hilden,Germany). RNA integrity was checked using the Agilent Bioanalyser.

tag: genotype/variation

value: WT

value: liver

value: Phenobarbital

value: 12 weeks

tag: Sex

value: male

tag: group


title: WT_PB_3


title: 35S::WOX1:GR_CHX_line1_rep1


title: 35S::WOX1:GR_DEX_line2_rep2

source_name: DEX, 6 hours


title: WT_PB_1


title: WT_PB_2


title: 35S::WOX1:GR_DEX_line1_rep2


title: WT_H2O_5

value: vehicle (Water)


title: 35S::WOX1:GR_DEX_line2_rep1


title: WT_H2O_3


title: 35S::WOX1:GR_DEX_line1_rep1


title: WT_H2O_2


title: 35S::WOX1:GR_Mock_line1_rep2

source_name: Mock, 6 hours


title: genomic DNA from PM54 LOPE placenta

value: LOPE


title: 35S::WOX1:GR_Mock_line2_rep1


title: WT_H2O_4


title: 35S::WOX1:GR_Mock_line2_rep2


title: 35S::WOX1:GR_Mock_line1_rep1


title: CTNNB1KO_PB_7


title: CTNNB1KO_PB_6


title: genomic DNA from PM58 LOPE placenta

value: FEMALE


title: genomic DNA from PM52 LOPE placenta

value: MALE


title: 35S::GFP:GR_DEX_line1

value: shoot apices including leaf primordia

value: 35S::GFP:GR line 1


title: 35S::GFP:GR_DEX_line2

value: 35S::GFP:GR line 2


title: CTNNB1KO_PB_5


title: WT_H2O_1


title: genomic DNA from PM46 LOPE placenta


title: genomic DNA from PM55 LOPE placenta


title: 35S::GFP:GR_Mock_line2


title: CTNNB1KO_PB_4


title: 35S::GFP:GR_Mock_line1


title: CTNNB1KO_PB_3


title: Gril_M_13NL

description: Murine gene expression for poorly permeable (NL) metastases in mouse 13

value: Female athymic NIH nu/nu mice


title: CTNNB1KO_PB_2


title: cartilage-OA-rep5 (exon-level)

city: changsha

first: haibin

last: zhang

state: China

address: Xiangya Hospital, Central South University, Changsha

department: Department of Orthopedics

description: Exon-level expression data from OA cartilage

hyb_protocol: the 2nd cycle cDNAs were hybridized onto the microarray

scan_protocol: After washing and staining, the arrays were scanned by the Affymetrix Scanner 3000(Affymetrix).

data_processing:
Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data
Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Then the gene expression analysis and alternative splice analysis proceeded separately

source_name: OA cartilage

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNAs were transcribed to double strand cDNAs and then synthesized cRNAs. Next, 2nd cycle cDNAs were synthesized from cRNAs. Followed fragmentation and biotin labeling

extract_protocol: Total RNAs was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNAs integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies)

value: cartilage

tag: disease state

value: OA

tag: age

tag: gender


title: cartilage-OA-rep4 (exon-level)

institute: Xiangya Hospital, Central South University

value: female


title: cartilage-OA-rep3 (exon-level)


title: genomic DNA from PM32 LOPE placenta

tag: subject id

value: Chorionic Villi


title: CTNNB1KO_H2O_6


title: CTNNB1KO_PB_1


title: CTNNB1KO_H2O_7


title: Celf1-WT_P0_A

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using rank invariant normalisation method  in R

source_name: Lens tissue, post-natal day 0

label_protocol: Standard protocol for Illumina arrays

extract_protocol: Standard total RNA isolation protocol by RNeasy mini kit (Qiagen)

value: mixed background (C57BL/6J, FVB) wild-type


title: cartilage-OA-rep2 (exon-level)


title: Celf1_KO_P0_C

value: mutant (Celf1cKO/lacZKI; Pax6GFPCre)


title: cartilage-normal-rep5 (exon-level)

description: Exon-level expression data from non-OA cartilage

source_name: normal cartilage

value: control


title: cartilage-normal-rep4 (exon-level)


title: cartilage-normal-rep3 (exon-level)


title: CTNNB1KO_H2O_5

source_name: C3H/CTNNB1ko mouse, liver, vehicle (Water), 0 %, 12 weeks

value: liver

value: 12 weeks


title: Celf1_KO_P0_A


title: Celf1_KO_P0_B


title: Celf1-WT_P0_B


title: cartilage-normal-rep2 (exon-level)


title: cartilage-OA-rep1 (exon-level)


title: cartilage-normal-rep1 (exon-level)

value: male


title: genomic DNA from PM31 LOPE placenta

tag: pathology group

value: LOPE


title: CTNNB1KO_H2O_2

value: vehicle (Water)


title: CTNNB1KO_H2O_3


title: Sp9_E13_ChIP

first: Qifei

last: Liang

address: 138 Yi Xue Yuan Road

institute: Fudan University

data_processing:
Base-calls were performed with CASAVA (v1.8.2) and bcl2fastq (v1.8.4).
ChIP-seq reads were filtered and aligned to whole mouse genome mm9 using BWA (v0.6.2).
Peak-calling was performed with MACS2 (v2.1.0).
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing coverage and txt files containing MACS2 peak-calls.

source_name: basal ganglia

extract_protocol:
Tissue was micro-dissected, cross-linked and sheared to 200-1000bp fragment. Protein/DNA complexes were isolated with antibodies and collected using Dynabeads.
ChIP-seq libraries were generated using the Ovation Ultralow DR Multiplex System (NuGEN #0330)

value: basal ganglia

tag: developmental stage

value: Embryonic day 13.5

tag: chip-antibody


title: Sp9_E16_ChIP

value: Embryonic day 16.5


title: Sp9_E16_Input


title: Sp9_E13_Input


title: CTNNB1KO_H2O_4


title: CTNNB1KO_H2O_1


title: cartilage-OA-rep2 (gene-level)

description: Gene-level expression data from OA cartilage


title: cartilage-OA-rep1 (gene-level)


title: cartilage-OA-rep3 (gene-level)


title: cartilage-OA-rep5 (gene-level)


title: cartilage-OA-rep4 (gene-level)


title: cartilage-normal-rep5 (gene-level)

description: Gene-level expression data from non-OA cartilage


title: cartilage-normal-rep4 (gene-level)


title: genomic DNA from PL135 LOPE placenta

tag: fetal sex

value: MALE

tag: gestational age

tag: sample tissue


title: cartilage-normal-rep1 (gene-level)


title: cartilage-normal-rep3 (gene-level)


title: cartilage-normal-rep2 (gene-level)


title: genomic DNA from PL142 LOPE placenta

tag: 450k plate

tag: 450k sentrix_id

tag: 450k sentrix_position


title: aged_olfactory_epithelium_2

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

description: Gene expression after silica aspiration in lung CD45 negative cells

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Mouse GE 8X60K, V2 Microarrays (Agilent Technologies). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven and then washed at room temperature.

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies)

data_processing:
Raw data were extracted using Agilent Feature Extraction Software (Agilent Technologies, v11.0.1.1). Background correction, averaging the expression values of duplicated probes and between-sample normalization of raw data were performed using limma35 and R 3.2.1（https://cran.r-project.org/）. Normalization was performed using quantile method.
All expression values for the probes was log2 transformed and normalized between groups using quantile method.

source_name: olfactory epithelium, B6, 16 months old (aged)

label_protocol: RNA labeling and hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kits (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

extract_protocol: RNA was prepared using TRIzol Reagent (Life Technologies) and RNeasy Mini Kits (QIAGEN) following the manufacturer's recommendations. RNA purity and integrity were confirmed based on its OD 260/280 ratio before analysis using an Agilent 2100 Bioanalyzer (Agilent Technologies). Each total RNA sample pooled from 5 biological replicates (two experimental replicate).

treatment_protocol: Septal nasal mucosa were collected from young-adult or aged mice immediately after euthanization, and then snap-freezed with liquid nitrogen.

tag: tissue

value: olfactory epithelium

tag: strain

tag: days post silica aspiration

value: 16 months


title: young_olfactory_epithelium_2

source_name: olfactory epithelium, B6, 8 weeks old (young-adult)

value: 8 weeks


title: Corneal tissue KC_18

status: Public on May 10 2018

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

description:
counts_table.txt
KC_18

data_processing:
RNA samples were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina,USA) according to the manufacturer’s instructions. One μg of total RNA was used as input to the Ribozero rRNA-depletion step of the assay. The adapter-ligated cDNA was enriched using 12 cycles of PCR. The libraries were sequenced on a NextSeq500 (Illumina) using a 75bp paired end read high output v2 run. This produced between 27 M and 60 M paired end reads per sample
The samples were processed in 2 batches each with the same number of KC (n=5 per batch) and control subjects (n=5 per batch). We mapped the 75 nucleotide reads to the human genome (GRCh38) using TopHat2 (v 2.0.4) 56, calling the Bowtie aligner (v 2-2.0.0-beta7) 57, allowing up to 2 bp mismatches per read (default position)
HTSeq-count (Python package HTSeq, python v 2.7.3) was used to generate counts of reads uniquely mapped to known and annotated genes using the Ensembl annotation file GRCh38.79.gtf (mode=union, –t = exon, –i = gene_name). The number of uniquely mapped reads varied between 41-50 million per sample in the first batch and 18-32 million per sample in the second batch
The count table of uniquely mapped reads was then used and differential expression was tested using the Bioconductor packages, edgeR (v3.16.0) and DESeq2 (v1.14.0).
Genome_build: Ensembl Home sapiens genome (GRCh38)
Supplementary_files_format_and_content: Tab-delimited text file with read count for each sample.

source_name: Corneal tissue 18

extract_protocol:
RNeasy mini kit (Qiagen) was used to extract the RNA from tissues, following the manufacturer’s instruction with minor modifications. Briefly, RNALater was carefully removed from Eppendorf tubes containing tissues, and 300 μL of RLT containing 2-mercaptoethanol in a 100:1 ratio was added to each tube and the tubes were vortexed until the tissues were dissolved. Equal portions of 70% ethanol (300 μL) were added to each tube, vortexed, and centrifuged at 12,000xg for 20s at room temperature (RT). The cartridge was washed wash buffer I (700 μL) at 12,000g for 20s followed by two more wash with wash buffer II (500 μL) at 12,000g for 15s. The cartridge was dried at 12,000xg for 1min at RT and 30μL of RNase-Free water was added to center of the cartridge and incubated at RT for 2min. Purified RNA was eluted by centrifuging at 20,000xg for 2min at RT and then stored at -80 °C for further use.
mRNA libraries  were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia). The Illumina TruSeq Stranded mRNA Prep Kit was used. AllRNA-Seq libraries  were sequenced  using the Illumina NextSeq 500. R1.fastq and R2.fastq files were produced for each sample.

tag: individual

value: Kerataconus patient

value: Corneal tissue

tag: batch

tag: Sex

value: Male


title: Corneal tissue KC_S4

description:
counts_table.txt
KC_S4

source_name: Corneal tissue S4


title: Corneal tissue KC_19

description:
counts_table.txt
KC_19

source_name: Corneal tissue 19


title: Corneal tissue KC_S6

description:
counts_table.txt
KC_S6

source_name: Corneal tissue S6


title: Corneal tissue KC_21

description:
counts_table.txt
KC_21

source_name: Corneal tissue 21


title: Corneal tissue KC_S5

description:
counts_table.txt
KC_S5

source_name: Corneal tissue S5


title: Corneal tissue KC_20

description:
counts_table.txt
KC_20

source_name: Corneal tissue 20


title: young_olfactory_epithelium_1


title: Corneal tissue Con_S9

description:
counts_table.txt
Con_S9

source_name: Corneal tissue S9

value: Control, myopia patient


title: Corneal tissue Con_S10

description:
counts_table.txt
Con_S10

source_name: Corneal tissue S10

value: Female


title: Corneal tissue KC_17

description:
counts_table.txt
KC_17

source_name: Corneal tissue 17


title: aged_olfactory_epithelium_1


title: Corneal tissue KC_S3

description:
counts_table.txt
KC_S3

source_name: Corneal tissue S3


title: Corneal tissue KC_S1

description:
counts_table.txt
KC_S1

source_name: Corneal tissue S1


title: Corneal tissue Con_S7

description:
counts_table.txt
Con_S7

source_name: Corneal tissue S7


title: Corneal tissue Con_S8

description:
counts_table.txt
Con_S8

source_name: Corneal tissue S8


title: genomic DNA from PM43 EOPE placenta

value: EOPE

value: FEMALE

value: Chorionic Villi