title: CD8+ T cells from tumor infiltrating lymphocytes, ccRCC patient no.4

status: Public on Oct 17 2020

type: RNA

city: Montreal

first: Anne

last: Monette

state: Quebec

address: Centre de recherche du CHUM (CRCHUM), 900 rue St-Denis

country: Canada

institute: University of Montreal

description: RMA expression value derived from Expression Console Affymetrix software; gene level and exon level analyses

hyb_protocol: Hybridization was performed using the Affymetrix GeneChip system according to the manufacturer’s recommendations, and was evaluated using the Affymetrix GeneChip Command Console Software (AGCC). Chip quality was assessed using the Affymetrix Expression Console.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data was normalized using Partek Genomics Suite™ 6.6 (Partek, St. Louis, Missouri). GC content adjustment, background adjustment, quantile normalization and mean probe set summarization were performed using the Robust Multichip Average (RMA) algorithm. Quality control analysis was then performed and included: QC metrics (pos vs neg area under curve (AUC), all probe set mean absolute deviation (MAD) residual mean, all probe set relative log expression (RLE) mean, hybridization controls (BAC spike), synthesis controls (poly(A) spike), and log expression signal box plots), signal histograms, and principle component analysis (PCA). CHP data files were generated using Affymetrix Expression console, with HTA 2.0 libraries for gene- and exon-level analysis.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: ccRCC patient

label_protocol: Microarray experiments were performed using the GeneChip® Human Transcriptome array 2.0 (Affymetrix, Santa Clara, CA). 1 ng of total RNA for each sample was processed using the Affymetrix GeneChip WT Pico Reagent Kit. This kit uses a reverse transcription priming method that specifically primes non-ribosomal RNA, including both poly(A) and non-poly(A) mRNA, and is used to generate sense-stranded cDNA. 5.5 µg of the single-stranded cDNA was then fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit and it this product was hybridized onto the chip.

growth_protocol: Tissue and blood specimens were kept on ice for all short-term transport from operating rooms, to pathology units, and to TIL extraction laboratories. Expert renal pathologists classified and selected experimental tissues according to WHO guidelines. CD8+ and CD19+ immune cell subsets were simultaneously and rapidly isolated from tumors, tissues and blood, and total RNA was extracted for microarray analyses.

extract_protocol: Total RNA was purified using QIAshredder cell-lysate homogenizers followed by the RNeasy Plus Micro Kit (QIAGEN). The quality of the total RNA was evaluated with the RNA 6000 nano LabChip kit on an Agilent 2100 Bioanalyzer system (Agilent Technologies).

treatment_protocol: For the isolation of TILs and TIICs from freshly resected kidney tumors and normal adjacent tissues, cold tissues were homogenized using three consecutive cycles of the h_tumor_01 program of the gentleMACS™ Dissociator (Miltenyi Biotec, USA), and resulting cellular suspensions were passed through a 0.45 μm filter fit onto a 50 mL falcon tubes (Fisher), were pelleted by centrifugation (4 °C, 10 min, 300 g), and were subjected to Ficoll gradient separating lymphocytes from tumoral material (Lymphocyte separation medium; WISENT Bioproducts) followed by an additional two 50 mL PBS washes prior to cell pelleting by centrifugation (4 °C, 10 min, 300 g). 40 mL of blood from patients and matched control donors were treated alongside tumors, via dilution in PBS for Ficoll gradient separation of immune cells (Lymphocyte separation medium; WISENT Bioproducts), pelleting of cells (4 °C, 10 min, 300 g), and followed by two additional 50 mL PBS washes prior to cell pelleting by centrifugation. Cell pellets were resuspended in EasySep™ Buffer (STEMCELL Technologies), and cells were counted and resuspended at appropriate dilutions for extraction using Human CD8 and CD19 Positive Selection Kits (STEMCELL Technologies), used as recommended by the manufacturer.

tag: disease state

value: ccRCC patient

tag: tissue

value: CD8+ T cell from tumor


title: CD19+ T cells from peripheral blood lymphocytes, ccRCC patient no.4

value: CD19+ T cell from blood


title: CD19+ T cells from normal tissue infiltrating immune cells, ccRCC patient no.2

value: CD19+ T cell from tissue


title: CD19+ T cells from peripheral blood lymphocytes, ccRCC patient no.2


title: CD19+ T cells from peripheral blood lymphocytes, ccRCC patient no.1


title: CD19+ T cells from normal tissue infiltrating immune cells, ccRCC patient no.1


title: CD8+ T cells from tumor infiltrating lymphocytes, ccRCC patient no.3


title: CD19+ T cells from normal tissue infiltrating immune cells, ccRCC patient no.5


title: CD19+ T cells from tumor infiltrating lymphocytes, ccRCC patient no.1

value: CD19+ T cell from tumor


title: CD8+ T cells from tumor infiltrating lymphocytes, ccRCC patient no.5


title: CD19+ T cells from tumor infiltrating lymphocytes, ccRCC patient no.3


title: CD19+ T cells from normal tissue infiltrating immune cells, ccRCC patient no.4


title: CD19+ T cells from peripheral blood lymphocytes, control donor no.3

source_name: Healthy control donor

value: Healthy control donor


title: CD19+ T cells from peripheral blood lymphocytes, ccRCC patient no.5


title: CD19+ T cells from normal tissue infiltrating immune cells, ccRCC patient no.3


title: CD19+ T cells from peripheral blood lymphocytes, control donor no.1


title: CD19+ T cells from tumor infiltrating lymphocytes, ccRCC patient no.2


title: CD19+ T cells from tumor infiltrating lymphocytes, ccRCC patient no.5


title: CD19+ T cells from peripheral blood lymphocytes, control donor no.5


title: CD8+ T cells from tumor infiltrating lymphocytes, ccRCC patient no.2


title: CD19+ T cells from peripheral blood lymphocytes, control donor no.2


title: CD19+ T cells from tumor infiltrating lymphocytes, ccRCC patient no.4


title: CD19+ T cells from peripheral blood lymphocytes, control donor no.4


title: Sgo1-brain-3

status: Public on Jul 31 2018

type: SRA

city: Oklahoma City

first: Hiroshi

middle: Y

last: Yamada

state: Oklahoma

department: Medicine

country: USA

institute: OUHSC

library_source: transcriptomic

data_processing:
Strand software  was used for base-calling and alignment.
BWA  Paired-End (GATKv3) pipeline was used to align with Mus musculus (build 37.2) genome. Pairwise and Cluster analyses were done using Genesifter software and differential gene lists were exported as tab delimited files.
Pairwise settings were as follows: normalize to mapped reads, statistical analysis using EdgeR differential genes originally shown if 2.0 fold minimum change in expression and significant FDR value of <0.05
Genome_build: Mus musculus build 37.2
Supplementary_files_format_and_content: Differential gene lists provided as excel file format

organism: Mus musculus

source_name: brain

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the RNA TruSeq V2 Library construction kit.   Libraries were sequenced on the Illumina MiSeq following the manufacturer's protocols.

tag: genotype/variation

tag: gender

value: female

tag: run

value: Run 259

tag: strain


title: CD19+ T cells from peripheral blood lymphocytes, ccRCC patient no.3


title: Sgo1-brain-2

value: male


title: Sgo1-brain-1


title: CD8+ T cells from normal tissue infiltrating immune cells, ccRCC patient no.4

value: CD8+ T cell from tissue


title: CD8+ T cells from normal tissue infiltrating immune cells, ccRCC patient no.3


title: CD8+ T cells from normal tissue infiltrating immune cells, ccRCC patient no.2


title: CD8+ T cells from tumor infiltrating lymphocytes, ccRCC patient no.1


title: CD8+ T cells from peripheral blood lymphocytes, control donor no.4

value: CD8+ T cell from blood


title: WT-brain-3

value: Run 258


title: CD8+ T cells from normal tissue infiltrating immune cells, ccRCC patient no.5


title: WT-brain-2


title: WT-brain-1


title: CD8+ T cells from peripheral blood lymphocytes, control donor no.3


title: CD8+ T cells from peripheral blood lymphocytes, ccRCC patient no.2


title: CD8+ T cells from peripheral blood lymphocytes, control donor no.2


title: CD8+ T cells from peripheral blood lymphocytes, ccRCC patient no.5


title: CD8+ T cells from peripheral blood lymphocytes, control donor no.5


title: CD8+ T cells from peripheral blood lymphocytes, ccRCC patient no.1


title: CD8+ T cells from peripheral blood lymphocytes, ccRCC patient no.3


title: CD8+ T cells from normal tissue infiltrating immune cells, ccRCC patient no.1


title: CD8+ T cells from peripheral blood lymphocytes, ccRCC patient no.4


title: CD8+ T cells from peripheral blood lymphocytes, control donor no.1


title: Hnf6/Oc2_04_spinal cord_e11.5

city: Brussels

first: Frederic

last: Clotman

address: avenue Hippocrate, 55 boxB1.55.11

department: Institute of Neuroscience

country: Belgium

institute: UCLouvain

description: Gene expression data from mouse embryonic spinal cord at e11.5

hyb_protocol: Following fragmentation, 5.2 ug of ss-cDNA were hybridized for 16h at 45C on GeneChip® MoGene 2.0 ST array. GeneChip were washed and stained in the Genechip ® Fluidics Station 450

scan_protocol: GeneChip were scanned using the Affymetrix Genechip® scanner

data_processing: The data were analyzed with R software.

label: Biotin

source_name: Hnf6/Oc2 mouse embryonic spinal cord

label_protocol: Biotinylated ss-cDNA were prepared according to the Affymetrix protocol from 100ng total RNA (GeneChip® WT PLUS reagent Kit)

growth_protocol: Mouse embryos were harvested at e11.5

extract_protocol: Tripur dissociation of the embryonic spinal cords. The RNA were next isolated and precipitated by chloroform and isopropanol. The pellets were washed with ethanol and resuspend in RNAse free water.

treatment_protocol: The spinal cords were dissected and directly processed for RNA extraction

tag: genotype

value: spinal cord

tag: developmental stage

value: e11.5 embryo


title: Hnf6/Oc2_03_spinal cord_e11.5


title: Hnf6/Oc2_01_spinal cord_e11.5


title: Hnf6/Oc2_02_spinal cord_e11.5


title: ML24_R8_2

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix mouse GeneChip 2.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

source_name: isolated microglia

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse Gene-2_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652). After hybridization, the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: an experimental intruder C57BL/6 or mutant mouse was placed into a resident CD-1 mouse's home cage (polycarbonate cage 24.0 × 46.0 × 15.5 cm; Lab Products) into which a 5.5-mm-thick perforated transparent polycarbonate partition had been placed down the middle to separate the pair. Defeats commenced after a 2-day accommodation period.  The partition was removed for 5 min/day at approximately 11:00 AM to allow agonistic encounters between the mice.  Defeat sessions were monitored to ensure that defeats reliably occurred65.  The 24 h/day dyadic social housing exposed the defeated mouse to continuous psychological stress via sensory interaction with the aggressor.  After 14 days of CSD, mice were killed 2 h after the last defeat and tissues harvested.  Home-caged (HC) control mice were pair-housed in a divided 14.0 × 35.5 × 13.0 cm polycarbonate cage (Tecniplast) with one mouse on each side of the perforated divider.

value: isolated microglia

value: WT

tag: stress

value: Resilient


title: ML28_R10_2


title: ML19_R6_2


title: ML17_R4_2


title: ML18_R5_2


title: ML14_R1_2


title: ML23_R7_2


title: ML20_S7

value: Susceptible


title: Control_01_spinal cord_e11.5

source_name: Control mouse embryonic spinal cord

value: Control


title: Control_05_spinal cord_e11.5


title: ML29_R11_2


title: ML16_R3_2


title: ML07_HC8

value: Control home caged


title: Control_04_spinal cord_e11.5


title: ML06_HC6


title: ML10_S3


title: ML12_S5


title: Control_03_spinal cord_e11.5


title: ML13_S6


title: ML11_S4


title: ML09_S2


title: ML03_HC3


title: ML04_HC4


title: ML01_HC1


title: ML05_HC5


title: Vi vaccine 1

city: Seoul

first: Se-Na

last: Lee

address: SNU Research Park, 1 Gwanak-gu

country: South Korea

institute: International Vaccine Institute

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse 2.0 ST Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix). Signal values were computed using the Affymetrix® GeneChip™ Command Console software. Command Console software.

data_processing: The raw data (CEL file) were normalized using a robust multi-array analysis (RMA) with the affy R package.

source_name: Vi vaccine_terminal ileum tissues

label_protocol: Expression array process was executed according to the manufacturer's protocol (GeneChip Whole Transcript PLUS reagent Kit). The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

extract_protocol: Total RNA was extracted from terminal ileum using the TRIzol(Invitrogen, Carlsbad, CA)protocol and single strandzA cDNA was synthesized of total RNA using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster city, CA). For the quality control, RNA purity and integrity were evaluated by OD 260/280 ratio, and analyzed by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

tag: oral fed with

value: Vi vaccine

tag: feeding days

value: terminal ileum tissues


title: Probiotics mixture 3

source_name: Probiotics mixture_terminal ileum tissues

value: Probiotics mixture


title: only AB cocktails in the drinking water 1

source_name: only AB cocktails in the drinking water_terminal ileum tissues

value: only AB cocktails in the drinking water


title: only 4% DSS in the drinking water 3

source_name: only 4% DSS in the drinking water_terminal ileum tissues

value: only 4% DSS in the drinking water


title: Probiotics mixture 1


title: Vi vaccine 3


title: only 4% DSS in the drinking water 2


title: only AB cocktails in the drinking water 3


title: Probiotics mixture 2


title: distilled water 1

source_name: distilled water_terminal ileum tissues

value: distilled water


title: distilled water 2


title: ink_poly_rep3

city: New York

first: Robert

middle: J

last: Schneider

state: NY

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

hyb_protocol: label, hybridization, and scanning protocols were performed by the NYUMC genomics core facitlity, located at NYU Health NY, NY

data_processing: Gene-level probeset summary of microarray data were obtained using the GCCN and SST transformation algorithms, RMA background correction, and quantile normalization provided in Expression Console Software, version 1.4.1 (Affymetrix).  Control probesets and probesets lacking mRNA accession tags were removed from further analysis.  To quantify translational efficiency, the difference in log2 intensity between matched polysomal RNA and total RNA was determined.  To examine differences in transcription and translation, total RNA and polysome RNA were quantile normalized separately.  Statistical analysis was performed using the limma R package

growth_protocol: OVCAR-3 cells were derived from a patient with a platinum resistant recurrence of high-grade serous ovarian cancer with acquired resistance to platinum drugs, Cells were cultured at 37oC, 5% CO2 in RPMI 1640 medium with L-glutamine and supplemented with bovine insulin at 0.01 mg/mL, penicillin/streptomycin at 10 mL/L, plasmocin at 50 μL/500 mL, and 20% fetal bovine serum (FBS).  Cells were routinely tested and found to be mycoplasma free.

extract_protocol: RNA was isolated from each fraction by extraction using the QIAGEN RNeasy MinElute Cleanup Kit. Fractions 7–14, representing high density polysomes, were combined and extracted.  For normalization, an aliquot of total RNA was extracted from the same cell lysates used for polysome sedimentation and purified using the QIAGEN protocol.  RNA quantity and quality for all samples were determined by bioanalysis (Agilent Technologies), and samples stored in nuclease-free water at −80°C. 10 μg of pooled RNA was used for microarray analysis using GeneChip Human Gene 2.0 ST Array (Affymetrix), according to the manufacturer instructions

treatment_protocol: Cells (3x150 mm plates per condition) were treated with DMSO as control, 1 μM carboplatin, 0.25 μM INK128, 1 μM carboplatin + 0.25 μM INK128.  Cells were treated with INK128 for 19 h prior to addition of carboplatin for 5 h.  Plates with only carboplatin were treated at the same time point as the combination plates.  Total combination drug treatment was 24 h

tag: cell line

tag: cell type

value: Ovarian cancer cell line

tag: rna fraction

value: polysome RNA


title: distilled water 3


title: ink_total_rep2

scan_protocol: label, hybridization, and scanning protocols were performed by the NYUMC genomics core facitlity, located at NYU Health NY, NY

value: total RNA


title: Vi vaccine 2


title: ink_total_rep1

label_protocol: label, hybridization, and scanning protocols were performed by the NYUMC genomics core facitlity, located at NYU Health NY, NY


title: only 4% DSS in the drinking water 1


title: ink_poly_rep2


title: carbo+ink_poly_rep3

source_name: Carboplatin + Ink128


title: dmso_poly_rep2

source_name: DMSO


title: carbo_poly_102_rep3

source_name: Carboplatin


title: dmso_poly_rep3


title: ink_poly_rep1


title: carbo_poly_022_rep2


title: dmso_total_rep2


title: dmso_total_rep1


title: carbo+ink_poly_rep1


title: carbo+ink_poly_rep2


title: carbo+ink_total_rep2


title: carbo+ink_total_rep1


title: dmso_poly_rep1


title: carbo_total_101_rep1


title: carbo_total_rep3


title: carbo_poly_rep2


title: carbo_poly_rep3


title: carbo_total_rep1


title: GIF9

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression profile of normal gastric epithelial cell line #GIF9

hyb_protocol: Hybridization of SurePrint G3 Mouse Gene Expression 8x60K Microarray Kit (G4852A, Agilent) were performed following the manufacturer's instruction by using the Agilent DNA Microarray Hybridization Oven.

scan_protocol: Microarray chips were scanned with Agilent DNA Microarray Scanner.

data_processing: The data were normalized by using Feature Extraction Software (Agilent, , Ver.9.5.3), and then transformed into log 2 base.

source_name: Normal gastric epithelial cell line #GIF9 derived from the p53-null mouse model

label_protocol: Cyanine-3 labeled complementary RNA was prepared from total RNA for each mouse sample by using the Low Input Quick Amp Labeling kit (Agilent).

extract_protocol: Total RNA was isolated from cells with TRIzol Reagent (Invitrogen). Contaminated DNA was removed by digestion with RNase-free DNase using DNA-free Kit (Applied Biosystems). Integrity of obtained RNA was assessed by using the Agilent 2100 BioAnalyzer (Agilent Technologies).

treatment_protocol: The cell lines were grown in appropriate culture conditions described in the overall design section.


title: MDGC7

description: Gene expression profile of gastric cancer cell line #MDGC7

source_name: Gastric cancer cell line #MDGC7 derived from the DCKO mouse model

value: gastric cancer cell line #MDGC7


title: Control_02_spinal cord_e11.5

value: spinal cord

value: e11.5 embryo


title: MDGC9

description: Gene expression profile of gastric cancer cell line #MDGC9

source_name: Gastric cancer cell line #MDGC9 derived from the DCKO mouse model

value: gastric cancer cell line #MDGC9


title: MDGC4C1

description: Gene expression profile of gastric cancer cell line #MDGC4SC1

source_name: Gastric cancer cell line #MDGC4SC1 derived from the DCKO mouse model

value: gastric cancer cell line #MDGC4SC1


title: carbo_poly_rep1


title: GIF13

description: Gene expression profile of normal gastric epithelial cell line #GIF13

source_name: Normal gastric epithelial cell line #GIF13 derived from the p53-null mouse model


title: MDGC8

description: Gene expression profile of gastric cancer cell line #MDGC8

source_name: Gastric cancer cell line #MDGC8 derived from the DCKO mouse model

value: gastric cancer cell line #MDGC8


title: GIF7

description: Gene expression profile of normal gastric epithelial cell line #GIF7

source_name: Normal gastric epithelial cell line #GIF7 derived from the p53-null mouse model


title: I2: S2 input DNA rep1

first: Jongbum

last: Kim

address: 254, Beotkkot-ro, Geumcheon-gu

institute: Macrogen, Inc.

library_source: genomic

data_processing:
Basecalls performed using CASAVA
Sequencing reads which include low base quality or adapter sequence were removed using Trimmomatic version 0.32
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.1.2
PCR duplicate reads were removed using Picard MarkDuplicates version 1.118
peaks were called using MACS version 2.1.1.20160309 with the following parameters: --qvalue 0.01, --mfold 5,50, --keep-dup 1
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using bedtools version 2-2.20.1 ; peak files were generated using MACS version 2.1.1.20160309

molecule: genomic DNA

growth_protocol: HEK293 cells were grown in DMEM media including 10% FBS and 1% antibiotics. For serum starvation, cells were grown in DMEM including 0.1% serum for 18.5–20 h.  For serum induction, the media were exchanged to 18% FBS-including DMEM for 15 min.

extract_protocol:
HEK293 cells were cross-linked using formaldehyde, washed with cold PBS twice, and scraped in a small amount of PBS. The cells were collected and lysed using ChIP cell and nuclei lysis buffers (refer to the manuscript associated with the submission).  The chromatins were sheared in nuclei lysis buffer by sonication. S2 Pol II antibody was used for immunoprecipitation of the chromatin associated with the target protein.
Illumina libraries were prepared using a Beckan-Coulter SPRIworks system and sequenced on an Illumina  HiSeq2000 using a 40nt single end read.

treatment_protocol: For flavopiridol treatment, a final concentration of 1 microM was applied for 1 h before serum induction and during serum induction for 15 min.

value: Human embryonic kidney cells

tag: chip antibody

tag: inhibitor

value: None (DMSO)


title: I6: S6 input DNA rep1

value: Flavopiridol


title: dI2: S2 input DNA rep2


title: dI1: S1 input DNA rep2


title: I5: S5 input DNA rep1


title: carbo_total_rep2


title: I1: S1 input DNA rep1


title: dI6: S6 input DNA rep2


title: dI5: S5 input DNA rep2


title: dS6: S6 ChIP-seq rep2

value: S2 Pol II


title: MDGC4C7

description: Gene expression profile of gastric cancer cell line #MDGC4SC7

source_name: Gastric cancer cell line #MDGC4SC7 derived from the DCKO mouse model

value: gastric cancer cell line #MDGC4SC7


title: S6: S6 ChIP-seq rep1


title: dS5: S5 ChIP-seq rep2


title: S5: S5 ChIP-seq rep1


title: S2: S2 ChIP-seq rep1


title: S1: S1 ChIP-seq rep1


title: dS2: S2 ChIP-seq rep2


title: dS1: S1 ChIP-seq rep2


title: Untreated, JAK2V617F-, rep2

city: Salt Lake City

first: Michael

middle: W.

last: Deininger

state: UT

address: 2000 Circle of Hope HCI 4280

department: Hematology & Hematologic Malignancies

institute: Huntsman Cancer Institute

hyb_protocol: The cDNA target samples were each hybridized to an Affymetrix Mouse Expression 430 2.0 array.

scan_protocol: Image processing was performed using Affymetrix Command Console (AGCC) v.3.1.1 software.

data_processing: Expression analysis was performed using Affymetrix Expression Console build 1.4.1.46.

source_name: Untreated,  JAK2V617F-

label_protocol: cDNA was prepared with the Ovation Pico WTA System V2 (NuGEN) and labeled with the Encore Biotin Module (NuGEN).

growth_protocol: After isolation bone marrow cells were cultured in RPMI with 10% FBS, 50 ng/mL IL-3 and 100 ng/mL SCF.

extract_protocol: RNA was isolated with a Qiagen Rneasy micro kit with on-column DNA digestion according to the manufactures specifications. RNA was further purified using Clean & Concentrator columns (Zymo Research)

treatment_protocol: TNFR blocking antibodies were used at 10 μg/mL

value: bone marrow

tag: treatment

value: untreated and sorted for Lin-Kit+GFP- cells


title: Untreated, JAK2V617F+, rep2

source_name: Untreated,  JAK2V617F+

value: untreated and sorted for Lin-Kit+GFP+ cells


title: TNFR1 BA, JAK2V617F+, rep2

source_name: TNFR1 BA treated,  JAK2V617F+

value: treated with a TNFR1 blocking antibody and sorted for Lin-Kit+GFP+ cells


title: Untreated, JAK2V617F-, rep3


title: TNFR1 BA, JAK2V617F-, rep3

source_name: TNFR1 BA treated,  JAK2V617F-

value: treated with a TNFR1 blocking antibody and sorted for Lin-Kit+GFP- cells


title: TNFR1 BA, JAK2V617F+, rep3


title: Untreated, JAK2V617F+, rep1


title: TNFR2 BA, JAK2V617F-, rep2

source_name: TNFR2 BA treated,  JAK2V617F-

value: treated with a TNFR2 blocking antibody and sorted for Lin-Kit+GFP- cells


title: TNFR1 BA, JAK2V617F+, rep1


title: TNFR2 BA, JAK2V617F+, rep3

source_name: TNFR2 BA treated,  JAK2V617F+

value: treated with a TNFR2 blocking antibody and sorted for Lin-Kit+GFP+ cells


title: TNFR2 BA, JAK2V617F-, rep3


title: TNFR2 BA, JAK2V617F-, rep1


title: Untreated, JAK2V617F+, rep3


title: TNFR2 BA, JAK2V617F+, rep1


title: TNFR2 BA, JAK2V617F+, rep2


title: Untreated, JAK2V617F-, rep1


title: mouse macrophage cells after LPS and menthol treatment, biological rep2

city: Boston

first: Hoon

last: Ryu

address: 150 S. Huntington Ave.

institute: Boston University School of Medicine

hyb_protocol: cRNA were hybridized with Affymetrix hybrization kit on Affymetrix Mouse Genome 430 Plus 2.0 Arrays for 16 hr at 45°C

scan_protocol: Scanned with the Affymetrix GeneChip Scanner 3000 G7 by following  manufacture's protocol.

data_processing: The data was processed with R Package gcrma version 2.10.0 in R 2.6.1.

source_name: RAW 264.7 macrophage

label_protocol: RNA was amplified and labeled with Life technologies MessageAmp Premier RNA Amplification Kit.  All MessageAmp™ kits employ the proven methodology for RNA sample preparation and labeling based on the original T7 in vitro transcription (IVT) amplification technology, known as the Eberwine or reverse transcription-IVT (RT-IVT) method.

growth_protocol: The mouse macrophage cell line RAW 264.7 was obtained from Sigma Cells which were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS in a humidified incubator with 5% CO2 at 37 °C. The medium was replaced every day and the cells were passed every two to three days to maintain logarithmic growth.

extract_protocol: Cells were extacted with Qiagen RNeasy mini kit by following manufacture's protocol.

treatment_protocol: Cells were treated with menthol or control for 1 hr and followed by induction with LPS (100ng/ml) for 6 hrs.

value: mouse macrophage cells

value: LPS and menthol


title: mouse macrophage cells after LPS and menthol treatment, biological rep1


title: TNFR1 BA, JAK2V617F-, rep2


title: TNFR1 BA, JAK2V617F-, rep1


title: Human glomeruli Control 18

city: Nanjing

first: Jingsong

last: Shi

state: China

address: No.305, Zhongshan East Road

department: National Clinical Research Center of Kidney Disease

country: China

institute: Jinling Hospital, Nanjing University School of Medicine

description: SST RMA expression value derived from Expression Console software

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

data_processing: Raw data were processed with Expression Console software (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 3.3.1, http://www.r-project.org/).

source_name: unaffected portion of tumor nephrectomies

label_protocol: Total RNA was amplified, labeled and purified by Ovation® Pico WTA System V2(Cat#3302, NuGEN, San Carlos, CA, US)and FL-Ovation™ cDNA Biotin Module V2(Cat#4200, NuGEN, San Carlos, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Kidney tissues were put into RNAlater (Ambion, Austin, TX) and stored at -80°C.

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) 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: Microdissection of glomeruli was performed manually under a stereomicroscope using two dissection needle holders in RNAlater at 4°C.

value: glomeruli

tag: Sex

value: male


title: mouse macrophage cells after control treatment, biological rep2

value: control


title: mouse macrophage cells after LPS treatment, biological rep2

value: LPS


title: mouse macrophage cells after LPS treatment, biological rep1


title: Human glomeruli Control 20

tag: tissue


title: mouse macrophage cells after menthol treatment, biological rep2

value: menthol


title: mouse macrophage cells after control treatment, biological rep1


title: Human glomeruli Control 19

value: female


title: mouse macrophage cells after menthol treatment, biological rep1


title: Human glomeruli Control 17


title: Human glomeruli Control 16


title: Human glomeruli Control 15


title: Human glomeruli Control 11


title: Human glomeruli Control 09


title: Human glomeruli Control 06


title: Human glomeruli Control 10


title: Human glomeruli Control 07


title: Human glomeruli Control 12


title: Human glomeruli Control 13


title: Human glomeruli Control 05


title: Human glomeruli Control 01


title: Human glomeruli Control 03


title: Human glomeruli Control 04


title: Human glomeruli DN 41

source_name: diabetic nephropathy


title: Human glomeruli Control 08


title: Human glomeruli DN 40


title: Human glomeruli Control 14


title: Human glomeruli DN 39


title: Human glomeruli DN 38


title: Human glomeruli DN 34


title: Human glomeruli DN 32


title: Human glomeruli DN 36


title: Human glomeruli Control 02


title: Human glomeruli DN 30


title: Human glomeruli DN 35


title: Human glomeruli DN 37


title: Human glomeruli DN 33


title: Human glomeruli DN 29


title: Human glomeruli DN 31


title: only AB cocktails in the drinking water 2

source_name: only AB cocktails in the drinking water_terminal ileum tissues

value: only AB cocktails in the drinking water

value: terminal ileum tissues


title: Human glomeruli DN 27


title: Human glomeruli DN 25


title: Human glomeruli DN 26


title: Human glomeruli DN 28


title: Human glomeruli DN 22


title: Human glomeruli DN 23


title: Human glomeruli DN 21


title: Human glomeruli DN 15


title: Human glomeruli DN 18


title: Human glomeruli DN 20


title: Human glomeruli DN 13


title: Human glomeruli DN 16


title: Human glomeruli DN 17


title: Human glomeruli DN 11


title: Human glomeruli DN 04


title: GFP_NEG_c10_r39

first: George

last: Murphy

state: MA

address: 670 Albany Street

institute: Center for Regenerative Medicine of Boston University and Boston Medical Center

description:
c10_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt

data_processing:
Due to the limited length of R1 reads, they were discarded from the analysis. R2 Reads were aligned to the human genome (hg19) and quantified using the STAR aligner.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: raw_count_matrix.txt: Tab-delimited text file; raw counts matrix.
Supplementary_files_format_and_content: cell_metadata.txt: Tab-delimited text file; metadata containing information for each cell.

source_name: Erythroid Cells

extract_protocol:
GFP-positive and -negative cells were sorted and entered into the Fluidigm C1 HT workflow, which was used to capture individual cells, lyse, reverse transcribe, and prepare libraries for sequencing (See: Using the C1 High-Throughput IFC to Generate Single-Cell cDNA Libraries for mRNA Sequencing, PN 100-9886).
Sequencing was performed on a Nextseq 500 using a high-output kit, resulting in a total of 475 million, paired-end, 75 bp reads.

treatment_protocol: hiPSC were differentiated towards a hematopoietic stem and progenitor cell (HSPC) fate, followed by commitment to and maturation along the erythroid lineage. To induce erythroid specification, d15 hiPSC-derived HSPCs were embedded in a semi-solid extra-cellular matrix mimetic (MethocultTM), yielding burst-forming unit-erythroid (BFU-E) colonies, which were picked on d28 and cultured in StemSpan™ Serum-Free Expansion Medium II (SFEM II) supplemented with 4U/ml hEPO over night. The following day (d29), floating cells were collected over a strainer, spun and resuspended in sort buffer. Cells were sorted for viability (PI-) and β-globin expression (GFP+ versus GFP-) and resuspended in sort buffer at a concentration of 400 cells/μL for loading onto the C1 platform.

value: d29 iPSC-derived erythroid cells

tag: sort

value: GFP Negative reporting for beta globin


title: GFP_NEG_c10_r37

description:
c10_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r38

description:
c10_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r35

description:
c10_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r36

description:
c10_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Human glomeruli DN 12


title: GFP_NEG_c10_r40

description:
c10_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Human glomeruli DN 03


title: GFP_NEG_c10_r32

description:
c10_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Human glomeruli DN 09


title: GFP_NEG_c10_r33

description:
c10_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Human glomeruli DN 07


title: Human glomeruli DN 10


title: GFP_NEG_c10_r31

description:
c10_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Human glomeruli DN 19


title: Human glomeruli DN 02


title: Human glomeruli DN 08


title: Human glomeruli DN 06


title: Human glomeruli DN 14


title: GFP_NEG_c10_r30

description:
c10_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Human glomeruli DN 01


title: GFP_NEG_c10_r29

description:
c10_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r25

description:
c10_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r22

description:
c10_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r27

description:
c10_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r28

description:
c10_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r24

description:
c10_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r23

description:
c10_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r26

description:
c10_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r34

description:
c10_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r18

description:
c10_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r17

description:
c10_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r14

description:
c10_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r10

description:
c10_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r09

description:
c10_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r16

description:
c10_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r12

description:
c10_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r19

description:
c10_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r21

description:
c10_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r11

description:
c10_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r13

description:
c10_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r07

description:
c10_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Human glomeruli DN 05

description: SST RMA expression value derived from Expression Console software


title: GFP_NEG_c10_r05

description:
c10_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r20

description:
c10_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r08

description:
c10_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r06

description:
c10_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r03

description:
c10_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r01

description:
c10_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r40

description:
c09_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r39

description:
c09_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r38

description:
c09_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r37

description:
c09_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r02

description:
c10_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r15

description:
c10_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r36

description:
c09_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r35

description:
c09_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r34

description:
c09_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r33

description:
c09_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r30

description:
c09_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r31

description:
c09_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r29

description:
c09_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r27

description:
c09_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r28

description:
c09_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r25

description:
c09_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r24

description:
c09_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r23

description:
c09_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c10_r04

description:
c10_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r20

description:
c09_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r18

description:
c09_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r21

description:
c09_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r19

description:
c09_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r17

description:
c09_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r15

description:
c09_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r11

description:
c09_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r12

description:
c09_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r13

description:
c09_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r16

description:
c09_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r14

description:
c09_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r10

description:
c09_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r09

description:
c09_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r26

description:
c09_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r07

description:
c09_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r04

description:
c09_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r32

description:
c09_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r06

description:
c09_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r05

description:
c09_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r03

description:
c09_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r02

description:
c09_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r40

description:
c08_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r22

description:
c09_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r38

description:
c08_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r01

description:
c09_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r39

description:
c08_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r37

description:
c08_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r34

description:
c08_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r35

description:
c08_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r32

description:
c08_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r33

description:
c08_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r36

description:
c08_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r29

description:
c08_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r27

description:
c08_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r30

description:
c08_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r31

description:
c08_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r28

description:
c08_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r26

description:
c08_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c09_r08

description:
c09_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r25

description:
c08_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: Eccrine sweat gland RNA-Seq

city: Baltimore

first: Garry

middle: R

last: Cutting

state: MD

address: 700 N. Broadway, Suite 551

department: Institute of Genetic Medicine

institute: Johns Hopkins University

description: Transcriptome profiling of human eccrine sweat glands

data_processing:
CASAVA for base calling
Adaptor trimming and quality trimming using 'Fqtrim v0.9.5'
Alignment using HISAT2 v2.0.1
Assembly and quantification using StringTie v1.3.3, HTSeq 0.6.1p1 and RNA-SeQC v1.1.8
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: counts

source_name: Human eccrine sweat glands

extract_protocol:
The dissected eccrine sweat glands were placed in RNAlater (Qiagen # 76104) immediately after they were dissected out from the skin. The collection tube was centrifuged to remove RNA later solution and Trizol was added to the sample and mixed. The samples were processed in a bead-beater (FastPrep-24, MP) at a setting of 4 m/s for 20 seconds and subsequently placed on ice for five minutes. This was repeated three times. Chloroform was then added to the samples and incubated for five minutes at room temperature. The samples were then centrifuged at 8,000 x g for 5 minutes at 4°C. The aqueous phase was separated from the organic phase containing the DNA and protein. Ethanol was added to the sample for precipitation and immediately applied to RNeasy columns (RNeasy Kit, Qiagen # 74104). The manufacturer’s cleanup procedure was followed except that the RNA sample was treated with the Turbo DNA-Free kit to remove residual DNA contamination (ThermoFisher # AM1907). The RNA was stored at -80°C. The quality of RNA was measured by RNA integrity number (RIN) using Agilent 2100 Bioanalyzer.
Using 1 µg of total RNA isolated from eccrine sweat glands, library preparation and RNA-seq were performed at the Deep Sequencing and Microarray Core Facility at Johns Hopkins University. RNA-seq library was constructed using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA), and 200 million paired-end reads were obtained on Illumina’s Next Seq 500 platform.

value: Skin

tag: organ

value: Eccrine sweat glands


title: GFP_NEG_c08_r22

description:
c08_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r21

description:
c08_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r23

description:
c08_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r24

description:
c08_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r20

description:
c08_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r18

description:
c08_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r17

description:
c08_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r19

description:
c08_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r16

description:
c08_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r15

description:
c08_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r13

description:
c08_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r14

description:
c08_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r10

description:
c08_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r11

description:
c08_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r09

description:
c08_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r12

description:
c08_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r05

description:
c08_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r08

description:
c08_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r06

description:
c08_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r07

description:
c08_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r04

description:
c08_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r03

description:
c08_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r01

description:
c08_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c08_r02

description:
c08_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r37

description:
c07_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r38

description:
c07_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r39

description:
c07_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r33

description:
c07_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r32

description:
c07_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r29

description:
c07_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r30

description:
c07_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r28

description:
c07_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r31

description:
c07_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r25

description:
c07_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r36

description:
c07_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r35

description:
c07_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r23

description:
c07_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r19

description:
c07_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r40

description:
c07_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r17

description:
c07_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r18

description:
c07_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r27

description:
c07_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r26

description:
c07_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r13

description:
c07_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r24

description:
c07_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r34

description:
c07_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r09

description:
c07_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r10

description:
c07_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r11

description:
c07_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r08

description:
c07_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r07

description:
c07_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r05

description:
c07_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r03

description:
c07_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r22

description:
c07_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r21

description:
c07_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r04

description:
c07_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r01

description:
c07_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r20

description:
c07_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r40

description:
c06_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r02

description:
c07_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r15

description:
c07_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r12

description:
c07_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r38

description:
c06_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r35

description:
c06_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r34

description:
c06_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r39

description:
c06_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r14

description:
c07_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r37

description:
c06_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r31

description:
c06_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r36

description:
c06_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r29

description:
c06_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r30

description:
c06_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r27

description:
c06_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r06

description:
c07_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r28

description:
c06_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r26

description:
c06_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r23

description:
c06_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r25

description:
c06_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r24

description:
c06_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r21

description:
c06_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r22

description:
c06_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r19

description:
c06_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r16

description:
c06_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r18

description:
c06_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r15

description:
c06_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r14

description:
c06_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r32

description:
c06_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r13

description:
c06_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r12

description:
c06_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r10

description:
c06_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r11

description:
c06_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r33

description:
c06_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r17

description:
c06_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r07

description:
c06_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r09

description:
c06_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r05

description:
c06_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r04

description:
c06_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c07_r16

description:
c07_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r03

description:
c06_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r06

description:
c06_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r01

description:
c06_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r02

description:
c06_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r20

description:
c06_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r40

description:
c05_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r39

description:
c05_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r38

description:
c05_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r37

description:
c05_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r36

description:
c05_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r29

description:
c05_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r31

description:
c05_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r33

description:
c05_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c06_r08

description:
c06_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r17

description:
c05_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r21

description:
c05_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r27

description:
c05_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r12

description:
c05_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r26

description:
c05_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r14

description:
c05_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r34

description:
c05_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r10

description:
c05_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r18

description:
c05_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r16

description:
c05_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r09

description:
c05_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r02

description:
c05_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r40

description:
c04_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r04

description:
c05_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r19

description:
c05_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r39

description:
c04_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r38

description:
c04_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r36

description:
c04_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r35

description:
c04_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r05

description:
c05_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r32

description:
c04_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r37

description:
c04_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r30

description:
c04_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r31

description:
c04_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r28

description:
c04_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r26

description:
c04_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r27

description:
c04_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r25

description:
c04_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r22

description:
c04_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r24

description:
c04_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r23

description:
c04_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r18

description:
c04_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r21

description:
c04_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r16

description:
c04_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r15

description:
c04_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r14

description:
c04_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r20

description:
c04_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r19

description:
c04_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r13

description:
c04_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r17

description:
c04_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r34

description:
c04_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r11

description:
c04_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r12

description:
c04_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r10

description:
c04_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r08

description:
c04_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r33

description:
c04_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r29

description:
c04_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r07

description:
c04_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r06

description:
c04_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r04

description:
c04_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r03

description:
c04_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r02

description:
c04_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r01

description:
c04_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r40

description:
c03_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r39

description:
c03_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r35

description:
c03_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r32

description:
c03_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r31

description:
c03_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r33

description:
c03_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r09

description:
c04_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r37

description:
c03_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r28

description:
c03_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r26

description:
c03_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r22

description:
c03_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r24

description:
c03_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c05_r01

description:
c05_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r25

description:
c03_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r21

description:
c03_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r27

description:
c03_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c04_r05

description:
c04_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r20

description:
c03_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r18

description:
c03_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r19

description:
c03_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r16

description:
c03_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r17

description:
c03_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r38

description:
c03_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r13

description:
c03_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r29

description:
c03_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r30

description:
c03_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r15

description:
c03_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r14

description:
c03_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r36

description:
c03_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r34

description:
c03_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r10

description:
c03_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r06

description:
c03_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r07

description:
c03_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r12

description:
c03_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r04

description:
c03_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r03

description:
c03_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r01

description:
c03_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r11

description:
c03_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r02

description:
c03_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r39

description:
c02_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r05

description:
c03_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r40

description:
c02_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r08

description:
c03_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r23

description:
c03_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r37

description:
c02_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r38

description:
c02_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r36

description:
c02_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r35

description:
c02_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r33

description:
c02_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r32

description:
c02_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r34

description:
c02_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c03_r09

description:
c03_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r31

description:
c02_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r29

description:
c02_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r26

description:
c02_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r30

description:
c02_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r28

description:
c02_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r27

description:
c02_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r23

description:
c02_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r25

description:
c02_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r24

description:
c02_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r22

description:
c02_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r21

description:
c02_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r05

description:
c02_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r14

description:
c02_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r01

description:
c02_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r11

description:
c02_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r12

description:
c02_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r02

description:
c02_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r04

description:
c02_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r06

description:
c02_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r03

description:
c02_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r18

description:
c02_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r17

description:
c02_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r10

description:
c02_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r16

description:
c02_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r09

description:
c02_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r08

description:
c02_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r19

description:
c02_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r15

description:
c02_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r07

description:
c02_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r13

description:
c02_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c02_r20

description:
c02_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r32

description:
c01_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r39

description:
c01_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r37

description:
c01_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r36

description:
c01_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r40

description:
c01_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r38

description:
c01_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r33

description:
c01_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r35

description:
c01_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r34

description:
c01_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r31

description:
c01_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r29

description:
c01_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r30

description:
c01_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r17

description:
c01_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r23

description:
c01_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r22

description:
c01_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r24

description:
c01_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r15

description:
c01_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r28

description:
c01_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r13

description:
c01_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r18

description:
c01_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r26

description:
c01_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r25

description:
c01_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r21

description:
c01_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r19

description:
c01_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r14

description:
c01_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r20

description:
c01_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r27

description:
c01_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r07

description:
c01_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r05

description:
c01_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r12

description:
c01_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r08

description:
c01_r08
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r09

description:
c01_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r10

description:
c01_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r04

description:
c01_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r03

description:
c01_r03
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r11

description:
c01_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r16

description:
c01_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r01

description:
c01_r01
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_NEG_c01_r02

description:
c01_r02
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r40

description:
c19_r40
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt

value: GFP Positive reporting for beta globin


title: GFP_POS_c19_r35

description:
c19_r35
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r39

description:
c19_r39
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r37

description:
c19_r37
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r38

description:
c19_r38
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r33

description:
c19_r33
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r31

description:
c19_r31
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r26

description:
c19_r26
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r30

description:
c19_r30
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r29

description:
c19_r29
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r25

description:
c19_r25
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r27

description:
c19_r27
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r23

description:
c19_r23
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r24

description:
c19_r24
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r34

description:
c19_r34
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r36

description:
c19_r36
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r22

description:
c19_r22
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r28

description:
c19_r28
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r21

description:
c19_r21
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r20

description:
c19_r20
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r17

description:
c19_r17
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r19

description:
c19_r19
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r15

description:
c19_r15
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r18

description:
c19_r18
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r14

description:
c19_r14
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r16

description:
c19_r16
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r13

description:
c19_r13
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: ES Cells_10Gy_4hr_replicate3

city: St. Louis

first: Girdhar

last: Sharma

state: MO

address: 4511 Forest Park

department: Radiation Oncology - Cancer Biology

institute: Washington University School of Medicine

description: gene-expression in 10Gy irradiated ES at 4hr post-IR

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

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

source_name: 10Gy irradiated ES at 4hr post-IR

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

growth_protocol: ES cells were grown on gelatin coated plates in stem cell media containing LIF following standard mouse embryonic stem cell culture procedures of growth without MEF feeder layers. In parallel ES cells were cultured in absence of LIF in normal growth media for 1 week or until expression of stem cell markers (Oct4, Sox2, Nanog, SSEA1 etc.) were lost in these isogenic non-stem differentiated ED cells.

extract_protocol: Total RNA was isolated from cells using RNeasy Kit (QIAGEN Inc. Valencia, CA, USA) following manufacturer's protocol.

treatment_protocol: Isogenic early passage, primary ES cells and non-stem differentiated ED cells were irradiated with 10 Gy in triplicates and RNA isolated at early (15 minutes) and late (4 hours) timepoints post irradiation.

value: late radiation response

value: undifferentiated stem cells


title: ES Cells_10Gy_15min_replicate3

description: gene-expression in 10Gy irradiated ES at 15min post-IR

source_name: 10Gy irradiated ES at 15min post-IR

value: early radiation response


title: GFP_POS_c19_r12

description:
c19_r12
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: ES Cells_10Gy_15min_replicate1


title: Mouse Embryonic Stem Cell unirradiated_replicate2

description: gene-expression in unirradiated early passage embryonic stem cell

source_name: early passage embryonic stem cell


title: ES Cells_10Gy_4hr_replicate2


title: Mouse Embryonic Stem Cell unirradiated_replicate3


title: ES Cells_10Gy_4hr_replicate1


title: GFP_POS_c19_r11

description:
c19_r11
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: ED Cells_10Gy_4hr_replicate2

description: gene-expression in 10Gy irradiated ED at 4hr post-IR

source_name: 10Gy irradiated ED at 4hr post-IR

value: differentiated primary cells


title: ES Cells_10Gy_15min_replicate2


title: Mouse Embryonic Stem Cell unirradiated_replicate1


title: cucumber degradome

city: Beijing

first: Xiaohui

last: Zhang

address: Zhong-Guan-Cun South Street 12

institute: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science

data_processing:
BaseCall V1.6
SOAP
BLAST
Bowtie
RSEM
Genome_build: Cucumis sativus L. var. sativus cv. 9930 _v20; ftp://cucurbitgenomics.org/pub/cucurbit/genome/cucumber/Chinese_long/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Cucumis sativus

source_name: shoot apical tissue

growth_protocol: Seedlings were grown in artificial climate chambers

extract_protocol:
When four true-leaves were unfolded, shoot apical tissues (1 mm) were dissected under a microscope and snap-frozen in liquid nitrogen and kept at −80 °C for further use. In each experiment, more than 500 shoot apices and three biological replicates were used. Total RNA was extracted using the TRIzol reagent (Invitrogen, USA). DNase (Promega, USA) was used to remove potential DNA contamination.
1.  For RNA seq, Total RNAs (10 μg) were subjected to poly-A selection, fragmentation, random priming and cDNA synthesis with the Illumina Gene Expression Sample Prep kit (CA, USA). The cDNA fragments were end repaired, ligated to adapters and then enriched by PCR. The fragments were purified with 6% TBE PAGE gel electrophoresis. After denaturation, the single-chain fragments were fixed onto the Solexa Sequencing Chip (Flowcell) and consequently grown into single-molecule cluster sequencing templates through in situ amplification.
2.  For miRNA seq, A total of 30 μg of RNA was resolved on denatured polyacrylamide gels. Gel fragments with the size range of 18-30 nt were excised and recovered. These small RNAs were ligated with 5’ and 3’RNA adapters using T4 RNA ligase. The adapter-ligated small RNAs were subsequently transcribed into cDNA by Super-Script II Reverse Transcriptase (Invitrogen) and amplified using primers specific for the ends of the adapters.
3.  For degradome seq, Approximately 200 μg of total RNA was polyadenylated using the Oligotex mRNA mini kit (Qiagen). A 5′ RNA adapter was added to the cleavage products (which possessed a free 5′-monophosphate at their 3’ termini) using the T4 RNA ligase (Takara). Then, the ligated products were purified using the Oligotex mRNA mini kit (Qiagen) for reverse transcription to generate the first strand of cDNA using an oligo dT primer via SuperScript II RT (Invitrogen). After the cDNA library was amplified for 6 cycles (94 °C for 30 s, 60 °C for 20 s, and 72 °C for 3 min) using Phusion Taq (NEB), the PCR products were digested with restriction enzymes and further ligated to double-stranded DNA adapters. The ligated products were subjected to PCR amplification and gel purification and finally used for high-throughput sequencing with the Illumina HiSeq 2000.

treatment_protocol: conditions set as follows: 16 h light in 28 °C /8 h dark in 25 °C (high temperature, long day, HL), 8 h light in 28 °C /16 h dark in 25 °C (high temperature, short day, HS), 16 h light in 20 °C /8 h dark in 15 °C (low temperature, long day, LL), and 8 h light in 20 °C /16 h dark in 15 °C (low temperature, short day, LS). A 70% humidity was used for all of these plants.

tag: common name

value: Chinese long 9930

tag: cultivar

value: shoot apical tissue

value: four-week-seedling

value: mix of 4 temperature-photoperiod treatments


title: ED Cells_10Gy_4hr_replicate1


title: ED Cells_10Gy_4hr_replicate3


title: GFP_POS_c19_r32

description:
c19_r32
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: ED Cells_10Gy_15min_replicate1

description: gene-expression in 10Gy irradiated ED at 15min post-IR

source_name: 10Gy irradiated ED at 15min post-IR


title: ED Cells_10Gy_15min_replicate3


title: GFP_POS_c19_r09

description:
c19_r09
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: cucumber miRNA HL-3

description: miRNA.txt

value: grown in 16 h light at 28°C /8 h dark at 25°C


title: GFP_POS_c19_r10

description:
c19_r10
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r07

description:
c19_r07
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: cucumber miRNA HL-1

description: miRNA.txt


title: ED Cells_10Gy_15min_replicate2


title: differentiated primary non-stem cells_replicate1

description: gene-expression in unirradiated isogenic non-stem cells differentiated from ES cells


title: differentiated primary non-stem cells_replicate2

source_name: isogenic non-stem cells differentiated from ES cells


title: GFP_POS_c19_r06

description:
c19_r06
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r05

description:
c19_r05
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt


title: GFP_POS_c19_r04

description:
c19_r04
processed data file: raw_count_matrix.txt
processed data file: cell_metadata.txt