title: ENS-TRIM8_1

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

institute: IRCCS Casa Sollievo della Sofferenza

description: RIN: 8.90

data_processing:
Reads trimming performed using Trimmomatic
Residual adapter removed using cutadapt
Reads aligned with TopHat 2
Reads were RPKM-normalized
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample ...

source_name: Embryonic telencephalon

growth_protocol: Cells were grown in proliferation medium containing Dulbecco’s modified Eagle’s medium (DMEM)-F12/Neurobasal and B27 supplement, 2 mM L-glutamine (Gibco-Invitrogen), recombinant human fibroblast growth factor-2  (bFGF, 10 ng/ml, Gibco-Invitrogen) and recombinant human epidermal growth factor (EGF, 20 ng/ml, Gibco-Invitrogen).

extract_protocol:
Total RNA was reverse transcribed using the Quantitect Transcription kit (Qiagen), according to the manufacturer's instructions
Indexed libraries were prepared from purified RNA with the TruSeq Total Stranded RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Libraries were quantified using the Agilent 2100 Bioanalyzer (Agilent Technologies). Index-tagged samples were equimolar and the overall concentration was 2 nM. The pooled samples were subject to cluster generation and sequenced using an Illumina HiSeq 2500 System (Illumina) in a 2x100 paired-end format at a final concentration of 8 pmol.

treatment_protocol: After plating, cells were infected with replication incompetent retrovirus expressing the murine FLAG-tagged Trim8 upstream of an IRES-GFP cassette or a control vector expressing only the IRES-GFP cassette. The infected cells were then FACS-sorted to obtain a pure population of GFP-positive cells that were used for RNA-Seq analysis

value: Embryonic Neural Stem Cells

value: Brain

tag: age

value: gestation day 14th


title: 286-3: ovarian cancer

status: Public on Apr 07 2018

type: RNA

city: Atlanta

first: Cai

last: Huang

state: Georgia

address: North Ave NW

country: USA

institute: Georgia Institute of Technology

description: ovarian cancer patients were snap frozen in liquid nitrogen within one minute of surgical removal and transferred to the lab for laser capture microdissection of cancer cells

hyb_protocol: Chips were hybridized to platform GPL570 platform (Gene Chip Human Transcriptome Array 2.0 (Affymetrix) and GeneChip® miRNA 3.0 Array (Affymetrix)) using Affymetrix HWS KIT and FS450_0004 Protocol.

scan_protocol: Scan on 7G Affymetrix GeneChip scanner.

data_processing: The data were analyzed with Robust Multi-Array Average (RMA) using Affymetrix default analysis.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: primary tumors collected from ovarian cancer patients

label_protocol: Total RNA was amplified with Applause 3'-Amplification KIT (NuGen) and labeled with Encor Biotin Module (NuGen). Labeling of miRNAs was performed with the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, ThermoFisher).

extract_protocol: Cells were collected from frozen sections using LCM. RNA was isolated with PicoPure RNA KIT (LifeTechnologies). miRNAs were isolated from the cells using the miRNeasy Micro KIT (Qiagen, Germantown, MD). The quality and quantity of mRNA and miRNAs were assessed on the Bioanalyzer RNA PicoChip (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: primary ovarian cancer tumor

tag: gender

value: female

tag: diagnosis

value: ovarian cancer


title: 286-2: ovarian cancer


title: PDXEx-A

city: Houston

first: Geoffrey

middle: Arthur

last: Bartholomeusz

state: Texas

address: 1901 East Road

department: Experimental Therapeutics

institute: UT MD Anderson Cancer Center

description: 06_Tumor A star_(Clariom_D_Human).CEL(normalized)

hyb_protocol: Following fragmentation, 5 micrograms of biotin-labeled sense-strand cDNA fragments in 200 µL of hybridization mix was loaded onto a human Clariom D array and hybridized to probes on the array in a GeneChip Hybridization Oven 645 (Affymetrix) for 16 h at 45°C with 60 rpm rotation.

scan_protocol: GeneChips were scanned using GeneArray G7 scanner (Affymetrix) and quantified into .CEL files with image and signal intensities.

data_processing: Transcriptome Analysis Console software v4.0 (Affymetrix) was used for probe set summarization and robust multiarray average (RMA) normalization procedures.

source_name: ex-vivo tissue

label_protocol: The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase using the Affymetrix proprietary DNA labeling reagent, which is covalently linked to biotin.

growth_protocol: Cells harvested from IBC PDX tumors were incubated overnight with poly-L-lysine–covered iron nanoparticles for about 18-24 h at a ratio of 1 µL of nanoshells to 150,000 cells to permit the binding of the iron nanoparticles to the surface of the cells. The nanoparticle-coated cells were then placed in the Bio-Assembler system. Cells were maintained within the Bio-Assembler system for 10 to 14 days at 370C in a humidified environment with medium changed every 3 to 4 days. The best results were obtained from cells released from PDX tumors that were vascular with a fat content between 20% and 30% of the total tumor weight. Tumors weighing 0.8 gram to 1 gram generally yielded the best results.

extract_protocol: Total RNA isolated from the PDX tumors as well as from the ex vivo tumor tissue after 5 days of growth in culture was purified with the Trizol method (Invitrogen) according to the manufacturer’s instructions

treatment_protocol: To compare the molecular signatures, we utilized magnetic 3D bio-printing (n3D BiosciencesTM, Inc.).  Briefly, viable cells released from the PDX tumor and tagged with poly-L-lysine–tagged magnetic nanoparticle assembly for 24hr were harvested and dispensed into a 96-well ultra-low attachment tissue culture plate at a concentration of 50,000 cells per well, and the plate was placed on a 96 well magnetic bioprinter. Well-formed and equally sized PDXEx “bio-prints” were observed at 5 days of incubation, a time corresponding to the duration of the planned high-throughput drug screens.

value: IBC patient-derived xenograft (PDX)-derived ex vivo tumor tissue

tag: original tumor type

value: triple negative inflammatory breast cancer


title: ENS-EGFP_1

type: SRA

country: Italy

description: RIN: 8.60

library_source: transcriptomic

organism: Mus musculus

tag: cell type


title: 286-1: ovarian cancer


title: PDXEx-D

description: 08_Tumor D star_(Clariom_D_Human).CEL(normalized)


title: PDXEx-C

description: 07_Tumor C star_(Clariom_D_Human).CEL(normalized)


title: 272-3: ovarian cancer


title: PDX tumor E

description: 05_Tumor E_(Clariom_D_Human).CEL(normalized)

source_name: PDX tumor

tag: host organism

value: Mus musculus

value: patient-derived xenograft (PDX)-derived tumor


title: ENS-TRIM8

description: RIN: 8.70


title: PDX tumor D

description: 04_Tumor D_(Clariom_D_Human).CEL(normalized)


title: gDNA-100E_409_2-vs-PreMA

type: genomic

city: College Station

first: Vaishali

last: Katju

address: Veterinary Integrative Bioscience, MS 4458

department: Veterinary Integrative Bioscience

institute: Texas A&M University

description: Genome variation profiling by genome tiling array

hyb_protocol: The sample was rehydrated in 40 μl of NimbleGen Hybridization Buffer (NimbleGen Systems, Inc.), denatured at 95 °C for 5 min, and then cooled to 42 °C. Hybridizations were carried out for 18 hr at 42 °C in the NimbleGen Service Laboratory. The arrays were washed using a NimbleGen Wash Buffer System (NimbleGen Systems, Inc.) and immediately dried down by centrifugation. See Selzer,R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44:305-319 (PMID 16075461).

scan_protocol: The scanner used was an Axon Scanner (Model # 40008). See Selzer,R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44:305-319 (PMID 16075461).

data_processing: The raw log2 intensity ratios were normalized with the LOESS regression.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: PreMA gDNA from ancestral population

label_protocol: Cy3/Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 μl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 μl/ml β-Mercaptoethanol. 1 μg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 °C and then chilled on ice in 0.2 ml PCR tubes. 10 μl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP, and dTTP), 8 μl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixede well with a pipet. Samples were centrifuged and incubated at 37 °C for 2 hours. 10 μl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precpitated by adding 11.5 μl 0.5 M NaCl and 110 μl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrfuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 μl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 μl DI water. DNA concentration was measured using a spectrophotometer. See Maydan JS, Lorch A, Edgley ML, Flibotte S, and Moerman DG. 2010. Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. BMC Genomics Jan 25;11:62 (PMID: 20100350)

growth_protocol: The population was grown on NGM plates (Nematode Growth Medium) at 20˚C and maintained on 90x15 mm petri dishes seeded with 750μl of Escherichia coli (OP50) in YT medium.

extract_protocol: DNA was prepared either by standard phenol-chloroform extraction followed by ethanol precipitation, or with the Puregene DNA Purification Kit (D-7000A, Gentra Systems) using solid tissue protocol.

treatment_protocol: This is the ancestral control line. It was cryogenically frozen at −86°C throughout the MA period of the other lines.

tag: population

value: Ancestral

tag: generations

tag: individual

tag: sample

value: final

source_name: 100E_409_2 gDNA from populations

treatment_protocol: Spontaneous mutation accumulation via population bottlenecks of N = 100 every generation.


title: PDX tumor C

description: 03_Tumor C_(Clariom_D_Human).CEL(normalized)


title: gDNA-100E_409_1-vs-PreMA

source_name: 100E_409_1 gDNA from populations


title: ENS-EGFP

description: RIN: 9.10


title: gDNA-100D_409_3-vs-PreMA

source_name: 100D_409_3 gDNA from populations


title: gDNA-100D_409_1-vs-PreMA

source_name: 100D_409_1 gDNA from populations


title: 272-2: ovarian cancer


title: gDNA-100C_409_4-vs-PreMA

source_name: 100C_409_4 gDNA from populations


title: INS-KD rep3

status: Public on Apr 06 2018

city: Bethesda

first: Gary

last: Felsenfeld

state: MD

address: 5 Memorial Drive, Room 212

department: NIDDK

institute: National Institutes of Health

description: replicate 2 in *read_group_tracking file

data_processing:
The reads for each library were mapped to the hg19 human genome assembly using TopHat2
Quantification and differential analysis of the reads were performed using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: zip archive  of cufflinks output. Merged transcriptome annotation merged.gtf

source_name: EndoC βH1

growth_protocol: EndoC βH1 cells were grown in were cultured in low-glucose Dulbecco's modified Eagle's medium (Life Technology, cat. # 11885) with 2% BSA (fatty acid free and heat shocked, Equitech, cat. #BAH66), 50 μM 2-mercaptoethanol, 10 mM nicotinamide, 5.5 mg/ml human transferrin (Sigma–Aldrich, cat. #T8158), 6.7 ng/ml sodium selenite, 100 U/ml penicillin, and 0.1 mg/ml streptomycin. Cells were seeded at a density of 6 × 10^5/cm2 on ECM-gel (1%) (Sigma-Aldrich, cat. # E1270) /fibronectin (2 µg/ml; Sigma–Aldrich, cat #. F1141) coated plates and cultured at 37 °C and 5% CO2.

extract_protocol:
The total RNA from 5 × 10^5 EndoC-βH1 cells that were induced with shRNA was isolated with a NucleoSpin RNA XS kit (Clontech).
The c-DNA library was prepared with a SMART-Seq® v4 Ultra® Low Input RNA Kit (Clontech, Cat. #634888) with 10 ng input RNA. The full-length cDNA output of the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing was processed with the Nextera XT DNA Library Preparation Kit (Illumina, Cat. # FC-131-1024).

treatment_protocol: A lenti-viral system were used to deliver shRNA construct into EndoC-βH1 cells. To performing knockdown experiments, the viral transduced cells were treated with 1 mg/mL doxycycline for 7 days. ). The media was changed every 48 h. No doxycycline was added in the negative control samples.

value: Pancreatic Beta cells

tag: treatment

value: shRNA induced

tag: cell line

value: EndoC BetaH1


title: Negative Control rep 2

description: replicate 1 in *read_group_tracking file

value: Negative Control


title: Negative Control rep 1

description: replicate 0 in *read_group_tracking file


title: INS-KD rep1


title: Input genomic DNA rep 3

library_source: genomic

data_processing:
The sequencing was performed on an Illumina HiSeq 2500 system.
The alignment was performed by illumina sequencing analysis pipeline at NIDDK Genomic Core.
The regions enriched with the relevant histone mark were analyzed using CCAT3.0
Genome_build: hg19
Supplementary_files_format_and_content: Peak bed files containing called peaks.

growth_protocol: EndoC βH1 cells were grown in were cultured in low-glucose Dulbecco's modified Eagle's medium (Life Technology, cat. # 11885) with 2% BSA (fatty acid free and heat shocked, Equitech, cat. #BAH66), 50 μM 2-mercaptoethanol, 10 mM nicotinamide, 5.5 mg/ml human transferrin (Sigma–Aldrich, cat. #T8158), 6.7 ng/ml sodium selenite, 100 U/ml penicillin, and 0.1 mg/ml streptomycin. Cells were seeded at a density of 6 × 105/cm2 on ECM-gel (1%) (Sigma-Aldrich, cat. # E1270) /fibronectin (2 g/ml; Sigma–Aldrich, cat #. F1141) coated plates and cultured at 37 °C and 5% CO2. Hela cells were grown in low-glucose Dulbecco's modified Eagle's medium with 10% Fetal Bovine Serum and cultured at 37 °C and 5% CO2.

extract_protocol:
The chromatin immune-precipitation was performed with 50,000 EndoC-βH1 cells using True MicroChIP Kit Kit (Diagenode Cat. # C01010130).
The sequencing library was generated using MicroPlex Library Preparation Kit v2 (Diagenode Cat. # C05010012) on an IP-Star® Compact Automated System (Diagenode Cat. # B03000002)

treatment_protocol: The chromatin was sheared by a Bioruptor Plus sonication device.

tag: chip antibody


title: 272-1: ovarian cancer


title: H3K27Ac rep3

value: anti-H3K27Ac(Abcam Cat. # ab4729, Lot # GR132150-4)


title: INS-KD rep2


title: H3K27Ac rep2


title: gDNA-100D_409_2-vs-PreMA

source_name: 100D_409_2 gDNA from populations


title: PDX tumor A

description: 01_Tumor A_(Clariom_D_Human).CEL(normalized)


title: PDX tumor B

description: 02_Tumor B_(Clariom_D_Human).CEL(normalized)


title: Input genomic DNA rep 2


title: 545R-1: ovarian cancer


title: gDNA-100C_409_3-vs-PreMA

source_name: 100C_409_3 gDNA from populations


title: gDNA-100C_409_2_2-vs-PreMA

source_name: 100C_409_2_2 gDNA from populations


title: gDNA-100B_409_4-vs-PreMA

source_name: 100B_409_4 gDNA from populations


title: Negative Control rep 3


title: H3K27Ac rep1


title: gDNA-100B_409_1-vs-PreMA

source_name: 100B_409_1 gDNA from populations


title: gDNA-100C_409_1-vs-PreMA

source_name: 100C_409_1 gDNA from populations


title: wt_rep3

city: Wuhan

first: Zhongmin

last: Xu

state: Hubei Province

address: No.1,Shizishan Street

country: China

institute: Huazhong Agricultural University

description:
Gene expression of 05ZY strain
WT_3

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Streptococcus suis

source_name: Streptococcus suis 05ZY strain

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: The strains was grown in tryptic soy broth (TSB) to OD600=0.7 in the absence of antibiotics.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen), and purified using RNeasy Mini Kit (Qiagen).

treatment_protocol: The strains were harvested at the logarithmic phase of growth and preserved in liquid nitrogen and subsequently stored in a -80℃ freezer immediately.

tag: genotype

value: wildtype


title: wt_rep4

description:
Gene expression of 05ZY strain
WT_4


title: gDNA-100C_409_2-vs-PreMA

value: pre

source_name: 100C_409_2 gDNA from populations


title: PRSS3 KD #337 replicate a

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description:
SAMPLE 5
Gene expression data from cell culture.

hyb_protocol: cRNA was hybridized onto chips for 18 h at 45 degrees C. GeneChips were washed in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4_450 wash protocol.

scan_protocol: Chips were scanned in an Affymetrix 3000 (7G) Confocal Scanner.

data_processing: The data were analyzed with GeneSpring GX13 using Affymetrix default analysis settings (RMA processing), chips were normalized to 50th percentile, and genes were normalized to average NT values (samples #1-#4).

source_name: PC9 cells infected with PRSS3 knockdown virus #337 replicate a

label_protocol: This project used the Affymetrix.GeneChip.HG-U133_Plus_2. 200 ng of total RNA was used as input.

growth_protocol: PC9 cells were maintained in RPMI 1640 (ATCC 30-2001) supplemented with 10% fetal bovine serum (FBS) (Gemini Bio-Products, Sacramento, CA, USA).

extract_protocol: Phenol/Chloroform

treatment_protocol: Cells were plated in 35 mm dishes, infected with NT lentivirus, PRSS3 KD #C24 lentivirus (NM_002771.2-454s1c1, Sigma), or PRSS3 KD #337 lentivirus (NM_002771.3-337s21c1, Sigma), then harvested after 2 days.

value: lung cancer cell line

value: infection with PRSS3 knockdown virus #337 lentivirus


title: NT (control) Experiment B replicate A

description:
SAMPLE 3
Gene expression data from cell culture.

source_name: PC9 cells infected with NT control lentivirus experiment B replicate a

treatment_protocol: Cells were plated in 35 mm dishes, and infected with NT lentivirus.

value: infection with NT control lentivirus


title: gDNA-100B_409_2-vs-PreMA

source_name: PreMA gDNA from ancestral population

source_name: 100B_409_2 gDNA from populations


title: NT (control) Experiment A replicate a

description:
SAMPLE 1
Gene expression data from cell culture.

source_name: PC9 cells infected with NT control lentivirus experiment A replicate a


title: NT (control) Experiment A replicate b

description:
SAMPLE 2
Gene expression data from cell culture.

source_name: PC9 cells infected with NT control lentivirus experiment A replicate b


title: KLK5 KD #42 replicate b

description:
SAMPLE 8
Gene expression data from cell culture.

source_name: PC9 cells infected with KLK5 knockdown virus #42 replicate b

treatment_protocol: Cells were plated in 35 mm dishes, infected with NT lentivirus, KLK5 KD #40 lentivirus (NM_012427.31248s1c1, Sigma), or KLK5 KD #42 lentivirus (NM_012427.3650s1c1, Sigma).

value: infection with KLK5 knockdown virus #42 lentivirus


title: gDNA-100A_409_3-vs-PreMA

source_name: 100A_409_3 gDNA from populations


title: gDNA-100B_409_3-vs-PreMA

source_name: 100B_409_3 gDNA from populations


title: wt_rep1

description:
Gene expression of 05ZY strain
WT_1


title: KLK5 KD #40 replicate b

description:
SAMPLE 6
Gene expression data from cell culture.

source_name: PC9 cells infected with KLK5 knockdown virus #40 replicate b

value: infection with KLK5 knockdown virus #40 lentivirus


title: KLK5 KD #42 replicate a

description:
SAMPLE 7
Gene expression data from cell culture.

source_name: PC9 cells infected with KLK5 knockdown virus #42 replicate a


title: mutant_rep4

description:
Gene expression of SSU05_0930 isogenic mutant
S0930_4

source_name: SSU05_0930 isogenic mutant strain

value: SSU05_0930 isogenic mutant


title: mutant_rep3

description:
Gene expression of SSU05_0930 isogenic mutant
S0930_3


title: gDNA-100A_409_2-vs-PreMA

source_name: 100A_409_2 gDNA from populations


title: mutant_rep2

description:
Gene expression of SSU05_0930 isogenic mutant
S0930_2


title: Guo_138_m35

city: Morgatown

first: Nancy

middle: Lan

last: Guo

state: WV

address: 2816 Health Sciences Center

department: Occupational and Environmental Health Sciences

institute: West Virginia University

description: Gene expression from mouse lung tissue

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 arrays, and were washed and stained using the Affymetrix GeneTitan system (software version 3.2.4.1515)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical language version 3.0.0. RMA was used to fit log2 transformed expression values

source_name: 40ug MWCNT 12 month

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

growth_protocol: Male C57BL/J6 mice (7 weeks old, average weight 21.19 g ± 0.06 g) were obtained from Jackson Laboratories (Bar Harbor, ME). Individual mice were housed 1 per cage in polycarbonate isolator ventilated cages and provided HEPA-filtered air with fluorescent lighting from 0700 to 1900 hr. Autoclaved Alpha-Dri virgin cellulose chips and hardwood Beta-chips were used as bedding. Mice were monitored to be free of adventitous viral pathogens, parasites, mycoplasms, Helicobacter, and CAR Bacillus. Mice were maintained on Harlan Teklad Rodent Diet 7913 (Indianapolis, IN), and tap water was provided ad libitum. Animals were allowed to acclimate for at least 5 days before use.

extract_protocol: Total RNA was isolated from mouse lung tissue using a mirVana miRNA Isolation Kit from Ambion per the manufacturer's protocol. Mouse lungs were initially disrupted by transferring them to a 2 mL microcentrifuge tube containing 400 μL silica beads and 600 μL Lysis/Binding Solution.

treatment_protocol: A stock suspension of MWCNT (1.6 mg/mL) was prepared in DM (Ca2+ and Mg2+-free phosphate-buffered saline, pH 7.4, supplemented with 5.5 mM d-glucose, 0.6 mg/mL mouse serum albumin, and 0.01 mg/mL 1,2-dipalmitoyl-sn-glycero-3-phosphocholine) with sonication as previously described by Porter et al. (2008; 2010). Serial dilutions of MWCNT suspension were made using DM as the diluent. Crocidolite asbestos (2.4 mg/mL) was suspended in DM by brief vortexing. Mice were anesthetized with isoflurane (Abbott Laboratories, North Chicago, IL). When fully anesthetized, the mouse was positioned with its back against a slant board and suspended by the incisor teeth using a rubber band. The mouth was opened, and the tongue gently pulled aside from the oral cavity. A 50 μL aliquot of sample was pipetted at the base of the tongue, and the tongue was restrained until at least 2 deep breaths were completed (but for not longer than 15 sec). Following release of the tongue, the mouse was gently lifted off the board, placed on its left side, and monitored for recovery from anesthesia. Mice received either DM; 1, 10, 40 or 80 μg MWCNT; or 120 μg asbestos.

tag: treatment dose and postexposure time

value: 40 ug MWCNT 12 mo

tag: animal

value: Male C57BL/J6

value: lung tissue


title: Guo_139_m41

description: Gene expression from mouse lung tissue

source_name: 120ug crocidolite 12 month

value: 120 ug crocidolite 12 mo


title: PRSS3 KD #C24 replicate b

source_name: PC9 cells infected with PRSS3 knockdown virus #C24 replicate b

value: infection with PRSS3 knockdown virus #C24 lentivirus


title: PRSS3 KD #337 replicate b

source_name: PC9 cells infected with PRSS3 knockdown virus #337 replicate b


title: PRSS3 KD #C24 replicate a

source_name: PC9 cells infected with PRSS3 knockdown virus #C24 replicate a


title: gDNA-100E_409_3-vs-PreMA

description: Genome variation profiling by genome tiling array

value: Ancestral

value: final

source_name: 100E_409_3 gDNA from populations


title: mutant_rep1

description:
Gene expression of SSU05_0930 isogenic mutant
S0930_1


title: LFD BAT 1

city: Oxford

first: Haifei

last: Shi

state: Ohio

address: 700 E High St

department: Biology

institute: Miami University

data_processing:
Remove Truseq3-SE adapter sequence using Trimmomatic (version 0.36)
Single-end sequencing reads were aligned to the mouse genome (ENSEMBL 84 release, GRCm38.p4) using RSEM (version 1.3.0)
Differential gene expression analysis was performed by DESeq2 (version 1.10.1) using the estimated gene-level counts from RSEM
RNA-Seq clean reads  were mapped to mouse genome (ENSEMBL 84 release, GRCm38.p4)
Genome_build: GRCm38.p4

source_name: brown adipose tissue

extract_protocol:
RNA extraction using E.Z.N.A® Total RNA kit II (Omega Bio-tek)
Libraries were sequenced as single-end 75 bp on Illumina NextSeq500 sequencing system at Cofactor Genomics Inc (St. Louis, MO). Approximately 30 millions of reads were retrieved from each sample
Ribosomal RNA was removed by using TruSeq Standard Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina)

treatment_protocol: Diet

value: brown adipose tissue

tag: strain

value: wild type

tag: diet

value: standard rodent diet


title: LFD BAT 3

tag: tissue


title: HFD BAT 3

value: 45% high-fat diet


title: LFD BAT 2


title: Input genomic DNA rep 1

source_name: EndoC βH1

value: EndoC BetaH1

value: Pancreatic Beta cells


title: HFD BAT 2


title: Guo_132_m330

description: Gene expression from mouse lung tissue

source_name: 1ug MWCNT 12 month

value: 1 ug MWCNT 12 mo


title: Guo_133_m168

description: Gene expression from mouse lung tissue


title: Guo_137_m71

description: Gene expression from mouse lung tissue


title: Guo_130_m10

description: Gene expression from mouse lung tissue

source_name: 1ug MWCNT 1 month

value: 1 ug MWCNT 1 mo


title: Guo_135_m152

description: Gene expression from mouse lung tissue


title: NT (control) Experiment B replicate b

description:
SAMPLE 4
Gene expression data from cell culture.

source_name: PC9 cells infected with NT control lentivirus experiment B replicate b

value: lung cancer cell line

value: infection with NT control lentivirus


title: gDNA-100A_409_1-vs-PreMA

source_name: PreMA gDNA from ancestral population

value: pre

source_name: 100A_409_1 gDNA from populations


title: gDNA-100A_409_1_2-vs-PreMA

source_name: 100A_409_1_2 gDNA from populations


title: Guo_134_m265

description: Gene expression from mouse lung tissue

source_name: DM 12 month

value: DM 12 mo

value: Male C57BL/J6


title: HFD BAT 1


title: Guo_128_m347

description: Gene expression from mouse lung tissue

source_name: 1ug MWCNT 6 month

value: 1 ug MWCNT 6 mo

value: lung tissue


title: Guo_125_m2

description: Gene expression from mouse lung tissue


title: Guo_127_m98

description: Gene expression from mouse lung tissue

source_name: 10ug MWCNT 12 month

value: 10 ug MWCNT 12 mo


title: Guo_120_m225

description: Gene expression from mouse lung tissue

source_name: 80ug MWCNT 6 month

value: 80 ug MWCNT 6 mo


title: Guo_129_m189, replacement

description: Gene expression from mouse lung tissue

source_name: 40ug MWCNT 6 month

value: 40 ug MWCNT 6 mo


title: Guo_123_m429

description: Gene expression from mouse lung tissue


title: Guo_122_m402

description: Gene expression from mouse lung tissue


title: Guo_126_m67

description: Gene expression from mouse lung tissue

source_name: DM 1 month

value: DM 1 mo


title: Guo_121_m281

description: Gene expression from mouse lung tissue

source_name: 40ug MWCNT 6month

value: 40 ug MWCNT 6month


title: NoAF-RA3

city: Chicago

first: Dawood

last: Darbar

state: IL

address: 840 S. Wood St. 920S CSB

department: Cardiology

institute: University of Illinois at Chicago

data_processing:
Read quality was checked for each sample using FastQC v0.10.1.
Raw reads were then aligned to the human reference genome (biospyder platform) using BWA MEM v0.7.5a, which efficiently maps reads with read-through into polyA tails and adapter sequences.
We quantified the expression level of genes as raw read counts by parsing the BAM files using samtools v1.4, which are suitable for differential expression analyses, and also normalized to reads-per-million for direct comparison between samples.
We used principle component analysis (PCA) to check for potential biological outliers.
The differentially expressed genes were identified by using edgeR v3.4.2.
Genome_build: biospyderBiospyder TempO-Seq human gene expression assay platform.
Supplementary_files_format_and_content: Excel, Differentially expressed genes and counts per million data; raw_read_count.txt: raw read counts

source_name: human iPSC derived CM

growth_protocol: HiPSCs were maintained on human recombinant vitronectin (hrVTN) coated plates in Essential 8 Flex medium (Gibco). iPSCs were then differentiated using medium A of conditioned cardiomyocyte differentiation kit (Gibco) for two days. At day 3, medium is replaced for CM differentiation medium B for two days.

extract_protocol:
Cells were harvested and RNA extracted using phenol chloroform extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To guide iPSC-derived CMs into atrial maturation, at day 5, we used an adaptation of the method previously described by Devala et al (Devalla et al., 2015) whereby hiPSC-CMs are treated with 1 μmol/l all-trans retinoic acid (RA). We treated cells with RA during five days with media changes every other day. Control cells were treated with equivalent concentrations of DMSO. At day 10, a low-glucose metabolic selection step is used to enrich CM culture (Sharma et al., 2015).

tag: agent

value: Retinoic Acid


title: NoAF-RA2


title: NoAF-RA1


title: NoAF-CT1

value: DMSO


title: NoAF-CT3


title: NoAF-CT2


title: Guo_119_m263

description: Gene expression from mouse lung tissue

source_name: 120ug crocidolite 6 month

value: 120 ug crocidolite 6 mo


title: Guo_124_m201

description: Gene expression from mouse lung tissue

source_name: 10ug MWCNT 6 month

value: 10 ug MWCNT 6 mo


title: Guo_131_m118

description: Gene expression from mouse lung tissue

value: 1 ug MWCNT 12 mo


title: Guo_117_m410

description: Gene expression from mouse lung tissue

source_name: 80ug MWCNT 12 month

value: 80 ug MWCNT 12 mo


title: Guo_118_m13

description: Gene expression from mouse lung tissue


title: KLK5 KD #40 replicate a

source_name: PC9 cells infected with KLK5 knockdown virus #40 replicate a

value: lung cancer cell line

value: infection with KLK5 knockdown virus #40 lentivirus


title: Guo_140_m362

description: Gene expression from mouse lung tissue

source_name: 40ug MWCNT 12 month

value: 40 ug MWCNT 12 mo


title: Guo_116_m218

description: Gene expression from mouse lung tissue

source_name: 120ug crocidolite 1 month

value: 120 ug crocidolite 1 mo

value: Male C57BL/J6


title: Guo_115_m296

description: Gene expression from mouse lung tissue

value: lung tissue


title: wt_rep2

description:
Gene expression of 05ZY strain
WT_2

source_name: Streptococcus suis 05ZY strain

value: wildtype


title: Guo_111_m223

description: Gene expression from mouse lung tissue


title: Guo_112_m23

description: Gene expression from mouse lung tissue

value: 10 ug MWCNT 12 mo


title: Guo_114_m113

description: Gene expression from mouse lung tissue

source_name: 1ug MWCNT 1 month

value: 1 ug MWCNT 1 mo


title: Guo_108_m97

description: Gene expression from mouse lung tissue

value: DM 12 mo


title: Guo_109_m250

description: Gene expression from mouse lung tissue

source_name: DM 6 month

value: DM 6 mo


title: Guo_113_m351

description: Gene expression from mouse lung tissue

source_name: 40ug MWCNT 1 month

value: 40 ug MWCNT 1 mo


title: Guo_106_m409, replacement

description: Gene expression from mouse lung tissue


title: Guo_105_m54

description: Gene expression from mouse lung tissue

value: 40 ug MWCNT 6 mo


title: Guo_110_m323

description: Gene expression from mouse lung tissue

value: 120 ug crocidolite 6 mo


title: Guo_094_m36, replacement

description: Gene expression from mouse lung tissue


title: Guo_107_m254

description: Gene expression from mouse lung tissue


title: Guo_092_m407, replacement

description: Gene expression from mouse lung tissue

value: 10 ug MWCNT 6 mo


title: Guo_100_m138

description: Gene expression from mouse lung tissue


title: Guo_090_m320, replacement

description: Gene expression from mouse lung tissue

value: DM 1 mo


title: Guo_089_m174

description: Gene expression from mouse lung tissue

value: 80 ug MWCNT 6 mo


title: Guo_103_m340

description: Gene expression from mouse lung tissue


title: Guo_088_m404

description: Gene expression from mouse lung tissue


title: Guo_104_m185

description: Gene expression from mouse lung tissue

source_name: 10ug MWCNT 1 month

value: 10 ug MWCNT 1 mo


title: Guo_097_m164

description: Gene expression from mouse lung tissue

source_name: DM 12 month


title: Guo_086_m247

description: Gene expression from mouse lung tissue

source_name: 1ug MWCNT 6 month

value: 1 ug MWCNT 6 mo


title: Guo_091_m133

description: Gene expression from mouse lung tissue


title: Guo_085_m119

description: Gene expression from mouse lung tissue


title: Guo_095_m257, replacement

description: Gene expression from mouse lung tissue

source_name: 1ug MWCNT 12 month

value: 1 ug MWCNT 12 mo


title: Guo_102_m366

description: Gene expression from mouse lung tissue

source_name: 10ug MWCNT 12 month


title: Guo_087_m65

description: Gene expression from mouse lung tissue

source_name: 80ug MWCNT 6 month


title: Guo_093_m85

description: Gene expression from mouse lung tissue

source_name: 40ug MWCNT 6 month


title: Guo_099_m306, replacement

description: Gene expression from mouse lung tissue


title: Guo_098_m160

description: Gene expression from mouse lung tissue

value: 80 ug MWCNT 12 mo


title: Guo_101_m300, replacement

description: Gene expression from mouse lung tissue

value: 40 ug MWCNT 12 mo

value: Male C57BL/J6


title: Guo_084_m135

description: Gene expression from mouse lung tissue

value: lung tissue


title: Guo_082_m390

description: Gene expression from mouse lung tissue


title: Guo_077_m78, replacement

description: Gene expression from mouse lung tissue

source_name: 120ug crocidolite 12 month

value: 120 ug crocidolite 12 mo


title: Guo_083_m123, replacement

description: Gene expression from mouse lung tissue

source_name: DM 1 month


title: Guo_096_m274

description: Gene expression from mouse lung tissue


title: Guo_079_m101

description: Gene expression from mouse lung tissue

value: 1 ug MWCNT 1 mo


title: Guo_081_m355, replacement

description: Gene expression from mouse lung tissue

source_name: 80ug MWCNT 12 month


title: Guo_075_m240, replacement

description: Gene expression from mouse lung tissue


title: Guo_078_m132

description: Gene expression from mouse lung tissue

source_name: 120ug crocidolite 6 month


title: Guo_072_m200, replacement

description: Gene expression from mouse lung tissue


title: Guo_074_m105

description: Gene expression from mouse lung tissue


title: Guo_069_m417, replacement

description: Gene expression from mouse lung tissue


title: Guo_067_m288, replacement

description: Gene expression from mouse lung tissue

value: 10 ug MWCNT 12 mo


title: Guo_068_m337, replacement

description: Gene expression from mouse lung tissue


title: Guo_064_m214, replacement

description: Gene expression from mouse lung tissue

source_name: 40ug MWCNT 12 month


title: Guo_062_m492

description: Gene expression from mouse lung tissue


title: Guo_066_m205, replacement

description: Gene expression from mouse lung tissue


title: Guo_055_m425

description: Gene expression from mouse lung tissue


title: Guo_065_m243

description: Gene expression from mouse lung tissue


title: Guo_073_m327, replacement

description: Gene expression from mouse lung tissue

value: DM 12 mo


title: Guo_080_m399

description: Gene expression from mouse lung tissue


title: THAP_insoluble_TEDseq_rep5

city: Ithaca

first: Yumi

last: Woo

state: NY

address: 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Whole genome alignment: We aligned all TED-seq reads to the hg38 reference genome as follows. We tagged the sequence reads with the first 8 bases of the reads as the unique molecular identifiers (UMIs). Then we aligned the reads to the hg38 reference genome using the STAR aligner with default parameters. We generated the read count positions (bedgraphs) of the 5′ ends of the mapped reads and collapsed reads that have the same UMI at the same 5′ end positions. These 5′ ends are the positions where the mRNA tail ends are displaced upstream by the selected insert size. We generated pilot TED-seq libraries with the insert sizes of 100 and 300 bp.  3′ transcriptome alignment: When a TED-seq read is split between two exons, we observed the clipping of 5′ end of sequence reads. This lead to inaccurate quantification of the tail length distributions, and we used a complementary mapping approach using the annotated transcriptome.  We used the refFlat mRNA annotation (n=58,135), and extracted the last 400 bp of the transcripts longer than 400 bp (n=55,362; Table 1a). Then we generated a reduced 3′ transcriptome as the reference and aligned TED-seq reads to the new reference using the STAR aligner. We collapsed the UMI and generated 5′ end read distributions for the 300 bp TED-seq libraries for the downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files are BedGraph which represents the read count positions of the 5' ends of the mapped reads and collapsed reads that have the same UMI at the same 5' end positions.

growth_protocol: HEK293 cells were cultured in MEM (Gibco) media with 10% fetal bovine serum in a humidified 5% CO2 atmosphere at 37 degrees Celsius.

extract_protocol:
Cell fractionation was performed by differential centrifugation following by THAP treatment (2 μM for 2 hr). Briefly, the cells were washed with cold PBS twice and lysed by cold Buffer L (50 mM Tris-HCL (pH7.6), 50 mM NaCl, 5 mM MgCl2, 0.1% NP-40, 1 mM β-mercaptoethanol, 1x Roche complete protease inhibitor EDTA-free, 10 μl SUPERaseIN/ml) by scraping and pipetting. Cell lysates were homogenized and centrifuged at 2,000g at 4°C for 2 min. Pellet is nucleus fraction and aqua phase includes cytoplasmic fraction. Cytoplasmic fraction was centrifuged at 10,000g at 4°C for 10 min and insoluble fraction was obtained from the pellet. The insoluble fraction includes stress granules in TAHP-treated cells.  For TED-seq, total RNA was isolated using TRIzol or TRIzol-LS according to the manufacturer’s protocol (Invitrogen Life Technologies). Poly(A) RNA was isolated from 5~10 μg of total RNA using Dynabeads® mRNA purification kit (Ambion) according to the manufacturer’s protocol.   The ribosome footprint strategy was followed as the previous paper (Ingolia et al., 2012) and partially modified for the generation of RNA-seq library. In brief, cultured cells were washed twice with ice-cold 1x PBS and lyzed by adding lysis buffer (20 mM Tris-Cl (pH7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml cycloheximide, 1% (v/v) Triton X-100, 25 U/ml Turbo DNase I) and triturating the cells ten times through a 26-gauge needle. After centrifuging the cell lysate at 20,000g at 4°C for 10 min, the supernatant was divided into two groups for ribosome profiling library and mRNA expression profiling library.  For ribosome profiling library, RNase I (100 U/μl) was treated in lysate and incubated at room temperature for 45 min. After nuclease digestion, ribosome footprinted RNAs were purified by sedimenting through a 1 M sucrose cushion and excising the urea gel between 26-34 nucleotides.  For mRNA expression profiling library, TRIzol was added into the supernatant and total RNA was extracted according to the manufacturer's protocol.  For nuclei isolation of PRO-seq, cells were washed twice with 1X cold PBS. Cells were scrapped with 1ml of Buffer D (50mM Tris-Cl, pH 8.0, 25% glycerol, 5mM M MgCl2, 0.1mM EDTA, 5mM DTT). Cells were pelleted at 1000 x g for 5min and then resuspended in 50 µl of Buffer D. And then flash frozen in liquid nitrogen.
In TED-seq libralies, for 3′ RNA adaptor ligation, 40 pmol of RA3 adaptor (5′phosphate-UGGAAUUCUGGGGUGCCAAGG-/3InvdT/-3′) was treated into each poly(A) RNA and incubated in 20°C for 6 hr. After RNA extraction with TRIzol, RNA fragmentation with 1N NaOH was performed by incubating on ice for 10 min. To remove un-ligated adaptors, poly(A) RNA was isolated from the fragmented RNA using Dynabeads® mRNA purification kit (Ambion). 5′ end phosphorylation was performed using T4 polynucleotide kinase (PNK, NEB) according to the manufacturer’s protocol, following by RNA extraction with TRIzol, For 5′ RNA adaptor ligation, 30 pmol of RA5 (5′-GUUCAGAGUUCUACAGUCCGACGAUCNNNNNNNN-3′) and 50 pmol of RT primer (RTP, 5′-GCCTTGGCACCCGAGAATTCCA-3′) were treated into each RNA and incubated in 20°C for 6 hr. 5′-ligated RNA was reverse-transcribed using Superscript II Reverse Transcriptase kit (Invitrogen) including 0.1 M DTT, 12.5 mM dNTP mixture, SUPERaseIN (Ambion). For first size selection of the library, first round amplification was performed with 8 cycles. Following by loading the PCR products to big native 6% polyacrylamide gel, gel bands between 350-360 bp (insert 300 bp) from each sample were excised and then DNA was recovered using Ampure XP beads (Beckman Coulter, Inc.) as provided by the manufacturer’s protocol. To obtain precisely size-selected library, recovered DNA was used for second amplification with optimal cycles and different RPI-X barcode index primer according to TruSeq Library Prep Pooling guide (Illumina). Finally, gel extraction was repeated with bands with 426 bp for each selected insert size. The libraries were pooled and sequenced on Illumina NextSeq500 (75 bp) with PhiX control library and the spike-in mixture.

treatment_protocol: For ER stress induction, thapsigargin (THAP, Sigma-Aldrich) was treated with 2 µM for 2 h in HEK293 cells.

value: Fetus derived cell line from female human embryonic kidney

tag: passages

tag: drug treatment

value: THAP (2µM) for 2h

tag: molecule subtype

value: total RNA from cytosol fraction


title: Guo_070_m14, replacement

description: Gene expression from mouse lung tissue

source_name: 120ug crocidolite 1 month

value: 120 ug crocidolite 1 mo


title: Guo_056_m184, replacement

description: Gene expression from mouse lung tissue


title: Guo_071_m345

description: Gene expression from mouse lung tissue

value: 40 ug MWCNT 6 mo


title: Guo_060_m403

description: Gene expression from mouse lung tissue


title: Guo_054_m391, replacement

description: Gene expression from mouse lung tissue

value: DM 1 mo


title: Guo_061_m314, replacement

description: Gene expression from mouse lung tissue


title: DMSO_insoluble_TEDseq_rep5

tag: cell type


title: Guo_058_m286

description: Gene expression from mouse lung tissue


title: Guo_063_m216, replacement

description: Gene expression from mouse lung tissue


title: Guo_053_m84

description: Gene expression from mouse lung tissue

value: DM 6 mo


title: Guo_059_m196, replacement

description: Gene expression from mouse lung tissue

source_name: 80ug MWCNT 1 month

value: 80 ug MWCNT 1 mo


title: THAP_cytosol_TEDseq_rep5

value: DMSO for 2h


title: Guo_076_m275, replacement

description: Gene expression from mouse lung tissue

value: 80 ug MWCNT 12 mo


title: DMSO_cytosol_TEDseq_rep5


title: Guo_052_m74

description: Gene expression from mouse lung tissue

source_name: 10ug MWCNT 6 month

value: 10 ug MWCNT 6 mo


title: Guo_051_m11

description: Gene expression from mouse lung tissue

value: 80 ug MWCNT 6 mo

value: Male C57BL/J6


title: Guo_057_m220

description: Gene expression from mouse lung tissue

value: lung tissue


title: Guo_049_m384, replacement

description: Gene expression from mouse lung tissue


title: DMSO_cytosol_TEDseq_rep4


title: Guo_050_m412

description: Gene expression from mouse lung tissue

value: 120 ug crocidolite 6 mo


title: THAP_cytosol_TEDseq_rep3


title: DMSO_cytosol_TEDseq_rep3


title: Guo_046_m298, replacement

description: Gene expression from mouse lung tissue

value: 1 ug MWCNT 12 mo


title: Guo_047_m82

description: Gene expression from mouse lung tissue


title: sALS_PBL_2701

city: Seattle

first: James

middle: Douglas

last: Thomas

state: WA

address: 1100 Fairview Ave. N., B3-111

department: Computational Biology

institute: Fred Hutchinson Cancer Research Center

data_processing:
Illumina Casava software was used for base calling.
Reads were mapped to the human genome (hg19) using STAR, and only uniquely mapped reads were kept for downstream analysis.
IRFinder was used to detect intron retention events.
Genome_build: hg19
Supplementary_files_format_and_content: All intron retention events described in this study are provided in an excel document associated with this entry.

source_name: PBLs

extract_protocol:
All samples were collected into TRIzol or flash-frozen in liquid nitrogen and stored at -80°C until RNA was isolated.
rRNA-depletion

value: PBLs

tag: disease

value: sALS


title: Guo_045_m372, replacement

description: Gene expression from mouse lung tissue


title: sALS_PBL_2601


title: THAP_cytosol_TEDseq_rep4

value: Fetus derived cell line from female human embryonic kidney

value: THAP (2µM) for 2h


title: C9-ALS/FTD_PBL_2801


title: C9-ALS/FTD_PBL_1701


title: DM2_PBL_1155


title: DM2_PBL_1048


title: Guo_043_m55

description: Gene expression from mouse lung tissue


title: DM2_PBL_1047


title: Guo_044_m154

description: Gene expression from mouse lung tissue

value: 1 ug MWCNT 6 mo


title: C9-ALS/FTD_PBL_4901


title: Guo_042_m4

description: Gene expression from mouse lung tissue


title: TA1628

source_name: Fibroblast

value: Fibroblast


title: Guo_040_m333, replacement

description: Gene expression from mouse lung tissue

source_name: 10ug MWCNT 1 month

value: 10 ug MWCNT 1 mo


title: Guo_039_m170

description: Gene expression from mouse lung tissue


title: Guo_041_m406

description: Gene expression from mouse lung tissue

value: 40 ug MWCNT 6 mo


title: HA29


title: Guo_036_m7

description: Gene expression from mouse lung tissue


title: HA26


title: Guo_038_m262, replacement

description: Gene expression from mouse lung tissue

value: 120 ug crocidolite 12 mo


title: HA28

value: Control


title: Guo_037_m397

description: Gene expression from mouse lung tissue


title: 863


title: 337


title: 653


title: Guo_034_m114

description: Gene expression from mouse lung tissue

value: 120 ug crocidolite 1 mo


title: Guo_033_m315, replacement

description: Gene expression from mouse lung tissue

value: 80 ug MWCNT 1 mo


title: A15-015

source_name: Cerebellum

value: Cerebellum


title: C1


title: Guo_032_m342

description: Gene expression from mouse lung tissue

value: Male C57BL/J6


title: Guo_035_m309

description: Gene expression from mouse lung tissue

source_name: 1ug MWCNT 6 month

value: lung tissue


title: Guo_048_m235

description: Gene expression from mouse lung tissue

source_name: 1ug MWCNT 1 month

value: 1 ug MWCNT 1 mo


title: Guo_031_m155, replacement

description: Gene expression from mouse lung tissue

source_name: DM 12 month

value: DM 12 mo


title: Guo_028_m90

description: Gene expression from mouse lung tissue


title: Guo_026_m100

description: Gene expression from mouse lung tissue


title: HA25


title: Guo_030_m231

description: Gene expression from mouse lung tissue

value: 10 ug MWCNT 6 mo


title: Guo_029_m8

description: Gene expression from mouse lung tissue

value: 120 ug crocidolite 6 mo


title: Guo_025_m129

description: Gene expression from mouse lung tissue

source_name: 40ug MWCNT 1 month

value: 40 ug MWCNT 1 mo


title: naïve sample 3

city: Aurora

first: Ross

middle: M.

last: Kedl

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description: gene expression in naïve CD8+ T cells

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array (MoGene-1_0-st) . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner M10.

data_processing: The data were analyzed with TAC software using Affymetrix default analysis settings.

source_name: CD44lo T cells. From B6 spleen

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiagen Rneasy

treatment_protocol: mice immunized IP or listeria challenge IV.  7 days later, spleen cells stained with SIINFEKL-Kb tetramer to identify anitgen specific T cells, flow sorted, and gene expression analyzed by affymetric gene array MoGene-1_0-st-v1

value: spleen

value: CD8+ T cell

tag: stimulation


title: Guo_021_m175

description: Gene expression from mouse lung tissue

value: 1 ug MWCNT 6 mo


title: vaccine sample 2

description: gene expression in activated T cells day 7 post combined adjuvant vaccination

source_name: SIINFEKL tetramer+ cells from spleen d7 PI

value: combined adjuvant vaccination


title: Guo_020_m197

description: Gene expression from mouse lung tissue


title: naïve sample 1

description: gene expression in naïve CD8+ T cells


title: LM sample 3

description: gene expression in activated T cells day 7 post listeria infection

value: listeria infection


title: vaccine sample 1


title: naïve sample 2

description: gene expression in naïve CD8+ T cells


title: Guo_023_m289, replacement

description: Gene expression from mouse lung tissue

source_name: 120ug crocidolite 12month

value: 120 ug crocidolite 12month


title: Guo_02_ m72, replacement

description: Gene expression from mouse lung tissue

source_name: 80ug MWCNT 12 month

value: 80 ug MWCNT 12 mo


title: Guo_027_m169

description: Gene expression from mouse lung tissue

source_name: DM 6 month

value: DM 6 mo


title: vaccine sample 3


title: LM sample 2


title: LM sample 1


title: Guo_022_m50

description: Gene expression from mouse lung tissue

value: 80 ug MWCNT 1 mo


title: Guo_018_m319

description: Gene expression from mouse lung tissue


title: Guo_017_m350

description: Gene expression from mouse lung tissue

source_name: DM 1 month

value: DM 1 mo


title: siMyolinc.3-transfected at Day 2 of differentiation, biological rep1 [Undiff-Day_2 dataset]

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

description: siMyolinc.3.1 [Undiff-Day_2 dataset]

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained in the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol.

data_processing:
The data were analyzed using noncoder web interface (http://noncoder.mpi-bn.mpg.de).
The CEL files were analyzed through the updated version of noncoder web interface (Gellert et al., 2013) using the pipeline set up for Gene Array Analyzer (GAA) web interface (Gellert et al., 2012). After the normalization by Robust Multi-array Average (RMA) (Irizarry et al., 2003) and the application of moderate t-statitsics via the limma package (Ritchie et al., 2015), Transcript Cluster IDs that match that do not match to a gene or to multiple genes were discarded. Then, a standard deviation is calculated across samples. For a gene that matches to multiple Transcript Cluster IDs, the Transcript Cluster ID with the highest standard deviation was kept for further analysis.  siMyolinc-C2C12-Militello2015.xlsx is linked as a supplementary file on the Series record:
“Day_2” sheet: siMyolinc-knockdown C2C12 cells on day 2 of the differentation were compared to C2C12 cells transfected with siRNA against scramble control (siScr) and differentiated for 2 days.
“Undiff-Day_2” sheet: siMyolinc-knockdown C2C12 cells on day 2 of the differentation were compared to normally cultured C2C12 cells in the growth medium (“Undiff”), one and two days after the differentiation (“Day_1” and “Day_2”, respectively).

source_name: C2C12 cells, siMyolinc.3-transfected at Day 2 of differentiation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Murine myoblast cell line C2C12 cells were cultured in the growth medium containing 20% FBS (Life Technologies, #10270106) in DMEM with high glucose, pyruvate (Life Technologies, # 41966-029) supplemented with antibiotics (penicillin and streptomycin, Sigma-Aldrich, #P4333) at 37°C in a humidified atmosphere containing 5% CO2.

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

treatment_protocol: Transient siRNA transfection (10nM final concentration) was carried out using RNAiMax (Life Technologies) according to the manufacturer’s protocol. To induce the differentiation process (initiated 24 hours after the transfection), C2C12 cells were cultured in the differentiation medium containing 2% horse serum (Sigma-Aldrich, #H1270) in DMEM with low glucose, pyruvate (Life Technologies, #31885-023) supplemented with antibiotics (penicillin and streptomycin, Sigma-Aldrich, #P4333).

value: myoblast cell line C2C12

tag: transfection

tag: time

value: Day 2 of differentiation


title: siMyolinc.1-transfected at Day 2 of differentiation, biological rep1 [Undiff-Day_2 dataset]

description: siMyolinc.1.1 [Undiff-Day_2 dataset]

source_name: C2C12 cells, siMyolinc.1-transfected at Day 2 of differentiation

tag: cell line


title: siMyolinc.3-transfected at Day 2 of differentiation, biological rep2 [Undiff-Day_2 dataset]

description: siMyolinc.3.2 [Undiff-Day_2 dataset]


title: siMyolinc.2-transfected at Day 2 of differentiation, biological rep1 [Undiff-Day_2 dataset]

description: siMyolinc.2.1 [Undiff-Day_2 dataset]

source_name: C2C12 cells, siMyolinc.2-transfected at Day 2 of differentiation


title: Day 1 of differentiation, biological rep1 [Undiff-Day_2 dataset]

description: Day_1.1 [Undiff-Day_2 dataset]

source_name: C2C12 cells, Day 1 of differentiation

value: Day 1 of differentiation


title: siMyolinc.2-transfected at Day 2 of differentiation, biological rep2 [Undiff-Day_2 dataset]

description: siMyolinc.2.2 [Undiff-Day_2 dataset]


title: Guo_019_m343

description: Gene expression from mouse lung tissue

value: Male C57BL/J6

value: lung tissue


title: siMyolinc.1-transfected at Day 2 of differentiation, biological rep2 [Undiff-Day_2 dataset]

description: siMyolinc.1.2 [Undiff-Day_2 dataset]


title: Day 2 of differentiation, biological rep2 [Undiff-Day_2 dataset]

description: Day_2.2 [Undiff-Day_2 dataset]

source_name: C2C12 cells, Day 2 of differentiation


title: Day 1 of differentiation, biological rep2 [Undiff-Day_2 dataset]

description: Day_1.2 [Undiff-Day_2 dataset]


title: Guo_015_m48

description: Gene expression from mouse lung tissue


title: siMyolinc.3-transfected at Day 2 of differentiation, biological rep1 [Day2 dataset]

description: siMyolinc.3.1 [Day2 dataset]


title: Guo_014_m336

description: Gene expression from mouse lung tissue

source_name: 120ug crocidolite 6 month

value: 120 ug crocidolite 6 mo


title: Undifferentiated, biological rep2 [Undiff-Day_2 dataset]

description: Undiff.2 [Undiff-Day_2 dataset]

source_name: C2C12 cells, Undifferentiated

value: Day 0 of differentiation


title: Guo_012_m221

description: Gene expression from mouse lung tissue

source_name: 80ug MWCNT 1 month


title: siMyolinc.2-transfected at Day 2 of differentiation, biological rep2 [Day2 dataset]

description: siMyolinc.2.2 [Day2 dataset]


title: Day 2 of differentiation, biological rep1 [Undiff-Day_2 dataset]

description: Day_2.1 [Undiff-Day_2 dataset]


title: Undifferentiated, biological rep1 [Undiff-Day_2 dataset]

description: Undiff.1 [Undiff-Day_2 dataset]


title: TRA2B4 siRNA

city: Toskushima

first: Yuki

last: Kuwano

address: Kuramoto-cho

department: Pathophysiology

country: Japan

institute: The University of Tokushima Graduate School

description: TRA2B4 siRNA

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol. The fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4858A) for 17 hours at 65C in a rotating Agilent hybridization oven.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner (P/N G2600D).

data_processing: Data extracted using Agilent's Feature Extraction software. Raw data output was imported into Genespring GX14.9 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization).

source_name: colon cancer cell line

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis’ Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. For microarray analysis, total RNA (400 ng) was used for amplification and labeling of complementary RNA (cRNA) using a Low RNA Input Liner Amplification Kit PLUS and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol (Agilent).

extract_protocol: The total RNA was extracted using RNAiso Plus reagent (Thermo Fisher Scientific).

treatment_protocol: HCT116 cells were treated with 10 nM of control, NCL, or TRA2B4 siRNA using Lipofectamine RNAiMax (Thermo Fisher Scientific) for 48 hours.

value: TRA2B4 siRNA


title: Guo_013_m101, replacement

description: Gene expression from mouse lung tissue

source_name: 1ug MWCNT 1 month

value: 1 ug MWCNT 1 mo


title: Nucleolin siRNA

description: Nucleolin siRNA

value: Nucleolin siRNA


title: control siRNA

description: control siRNA

value: control siRNA


title: siMyolinc.3-transfected at Day 2 of differentiation, biological rep2 [Day2 dataset]

description: siMyolinc.3.2 [Day2 dataset]


title: Guo_011_m383, replacement

description: Gene expression from mouse lung tissue

source_name: 120ug crocidolite 1 month

value: 120 ug crocidolite 1 mo


title: Guo_009_m102

description: Gene expression from mouse lung tissue

source_name: 40ug MWCNT 1 month

value: 40 ug MWCNT 1 mo


title: siMyolinc.1-transfected at Day 2 of differentiation, biological rep2 [Day2 dataset]

description: siMyolinc.1.2 [Day2 dataset]


title: Guo_008_m411

description: Gene expression from mouse lung tissue


title: siMyolinc.1-transfected at Day 2 of differentiation, biological rep1 [Day2 dataset]

description: siMyolinc.1.1 [Day2 dataset]


title: siScramble-transfected at Day 2 of differentiation, biological rep1 [Day2 dataset]

description: siScr.1 [Day2 dataset]

source_name: C2C12 cells, siScramble-transfected at Day 2 of differentiation

value: siScramble


title: VP_Mock_root, biological rep3

city: Yokohama

first: Takatoshi

last: Kiba

state: Kanagawa

address: Suehiro 1-7-22

department: CSRS

institute: RIKEN

description:
VP_Mock_R_3
Gene expression data of 10 day-old AtNIGT1.2-VP inducuble-overexpressor seedling root without b-estradiole

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Arabidopsis thaliana

source_name: AtNIGT1.2-VP overepxressor without b-estradiole

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA with 3′ IVT Express Kit (Affymetrix)

growth_protocol: Seedlings werer pre-grown half-strength Murashige-Skoog (1/2MS) vertical agar plates containing 1% sucrose and 2.3 mM MES buffer (pH 5.8) at 22°C under fluorescent light (100 µmol m-2 s-1, 16 h light/8 h dark)

extract_protocol: Total RNA was extracted using an RNeasy Plant Mini kit with the RNase-Free DNase set (QIAGEN)

treatment_protocol: Seven-day-old Col-0 and AtNIGT1.2 overexpressor seedlings were transferred to and incubated in MGRL plates with 5 mM NH4NO3 (WT_Nsuf) or without nitrogen source (WT_Nstv) for 3 days. Nine-day-old AtNIGT1.2-VP inducible overepxressor seedlings were transfered to  MGRL plates (5 mM NH4NO3) with 10 mM b-estradiole (VP_+Est) or without b-estradiole for 24h.

value: Root


title: siScramble-transfected at Day 2 of differentiation, biological rep2 [Day2 dataset]

description: siScr.2 [Day2 dataset]


title: Guo_010_m121

description: Gene expression from mouse lung tissue

value: 80 ug MWCNT 1 mo


title: Guo_007_m312

description: Gene expression from mouse lung tissue

source_name: 10ug MWCNT 1 month

value: 10 ug MWCNT 1 mo


title: siMyolinc.2-transfected at Day 2 of differentiation, biological rep1 [Day2 dataset]

description: siMyolinc.2.1 [Day2 dataset]

value: myoblast cell line C2C12


title: VP_+Est_root , biological rep3

description:
VP_bER_R_3
Gene expression data of 10 day-old AtNIGT1.2-VP inducuble-overexpressor seedling root with 10 mM b-estradiole for 24h

source_name: AtNIGT1.2-VP overepxressor with b-estradiole


title: VP_Mock_root, biological rep2

description:
VP_Mock_R_2
Gene expression data of 10 day-old AtNIGT1.2-VP inducuble-overexpressor seedling root without b-estradiole


title: Empty vector, biological rep2

description:
Transfected with pcDNA3.1/Zeo(+) vector.
Empty_Vec.2

data_processing: The CEL files were analyzed through the updated version of noncoder web interface (Gellert et al., 2013) using the pipeline set up for Gene Array Analyzer (GAA) web interface (Gellert et al., 2012). After the normalization by Robust Multi-array Average (RMA) (Irizarry et al., 2003) and the application of moderate t-statitsics via the limma package (Ritchie et al., 2015), Transcript Cluster IDs that match that do not match to a gene or to multiple genes were discarded. Then, a standard deviation is calculated across samples. For a gene that matches to multiple Transcript Cluster IDs, the Transcript Cluster ID with the highest standard deviation was kept for further analysis. Over_Expression-Myolinc-C2C12-Militello2015.xlsx is linked as a supplementary file on the Series record.  Polyclonal Myolinc-over-expressing C2C12 cells were compared to C2C12 cells transfected with an empty vector.  The .xls file reports the ratio (in log2 scale) and p-value calculated via moderate t-statistics along with RMA-normalized values.

source_name: C2C12 cells, Empty vector

treatment_protocol: Transfection was performed using Lipofectamine 2000 (Life Technologies) according to the manufacturer’s protocol.Clones were selected with Zeocin.

value: pcDNA3.1/Zeo(+) vector


title: VP_+Est_root , biological rep1

description:
VP_bER_R_1
Gene expression data of 10 day-old AtNIGT1.2-VP inducuble-overexpressor seedling root with 10 mM b-estradiole for 24h


title: OX_Nstv_root,  biological rep3

description:
OX_Nstv_R_3
Gene expression data of N-starved 10 day-old AtNIGT1.2 overexpressor seedling root

source_name: AtNIGT1.2 overexpressor grown under N-starvation


title: Polyclonal line, biological rep2

description:
Transfected with Myolinc in the pcDNA3.1/Zeo(+) vector.
Polyclonal.2

source_name: C2C12 cells, Polyclonal line

value: Myolinc in the pcDNA3.1/Zeo(+) vector


title: PIWI2: Piwi RNAi 7 days 2

city: Novato

first: Pedro

last: Sousa-Victor

state: CALIFORNIA

address: 8001 Redwood Blvd.

institute: Buck Institute for Research on Aging

data_processing:
TopHat was used to align RNA-seq reads to the reference genome
Cufflinks was used for final transcriptome reconstruction and expression quantification
Genome_build: Drosophila genome release 5.2

organism: Drosophila melanogaster

source_name: sorted ISCs - PiwiRNAi (7d 29ºC)

growth_protocol: Flies were kept at 29C to express RNAi against Piwi or mCherry for 7 days.

extract_protocol:
RNA was extracted from sorted ISCs using Trizol (Invitrogen)
RNA libraries were prepared for sequencing using standard protocol of TruSeq RNA Library Prep Kit

value: Intestinal Stem Cells


title: WT2: mCherry RNAi 7 days 2

source_name: sorted ISCs - yw (7d 29º)


title: Polyclonal line, biological rep1

description:
Transfected with Myolinc in the pcDNA3.1/Zeo(+) vector.
Polyclonal.1


title: VP_+Est_root , biological rep2

description:
VP_bER_R_2
Gene expression data of 10 day-old AtNIGT1.2-VP inducuble-overexpressor seedling root with 10 mM b-estradiole for 24h


title: Guo_003_m51

description: Gene expression from mouse lung tissue

value: Male C57BL/J6

value: lung tissue


title: Guo_005_m376

description: Gene expression from mouse lung tissue

source_name: 10ug MWCNT 6 month

value: 10 ug MWCNT 6 mo


title: OX_Nstv_root,  biological rep2

description:
OX_Nstv_R_2
Gene expression data of N-starved 10 day-old AtNIGT1.2 overexpressor seedling root


title: Guo_006_m142, replacement

description: Gene expression from mouse lung tissue

source_name: 80ug MWCNT 6 month

value: 80 ug MWCNT 6 mo


title: Guo_004_m187

description: Gene expression from mouse lung tissue


title: Guo_002_m217

description: Gene expression from mouse lung tissue

source_name: DM 1 month

value: DM 1 mo


title: Empty vector, biological rep1

description:
Transfected with pcDNA3.1/Zeo(+) vector.
Empty_Vec.1


title: VP_Mock_root, biological rep1

description:
VP_Mock_R_1
Gene expression data of 10 day-old AtNIGT1.2-VP inducuble-overexpressor seedling root without b-estradiole


title: OX_Nstv_root,  biological rep1

description:
OX_Nstv_R_1
Gene expression data of N-starved 10 day-old AtNIGT1.2 overexpressor seedling root


title: WT_Nstv_root, biological rep3

description:
WT_Nstv_R_3
Gene expression data of N-starved 10 day-old Col-0 seedling root

source_name: Wild type (Col-0) seedlings grown under N-starvation


title: Uterine_SqCC_SC37 (SqC-withoutMeta)

city: Seongnam-si

first: Ah-Young

last: Kwon

state: Gyeonggi-do

address: 351 Yatap-dong, Bundang-gu

department: Department of Pathology

country: South Korea

institute: College of Medicine, CHA University

hyb_protocol: Desalted labeled RNA were hybridized to the Agilent miRNA expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: Squamous cell carcinoma of uterine cervix (SC37)

label_protocol: Desalted Labeled RNA were prepared from 100ng total RNA Agilent’s miRNA Complete Labeling and Hyb Kit

extract_protocol: RNeasy FFPE kit for FFPE tissues (QIAGEN, Germany) according to the protocol provided by the manufacturer

treatment_protocol: Microdissected formalin-fixed paraffin-embedded (FFPE) tissue

tag: phenotype

value: uterine cervical squamous cell carcinoma, without metastasis

tag: description

value: formalin-fixed paraffin-embedded tissue

value: uterine cervix

value: Squamous cell carcinoma


title: Guo_016_m161

description: Gene expression from mouse lung tissue

source_name: 10ug MWCNT 12 month

tag: treatment dose and postexposure time

value: 10 ug MWCNT 12 mo


title: WT_Nstv_root, biological rep2

description:
WT_Nstv_R_2
Gene expression data of N-starved 10 day-old Col-0 seedling root

value: Root


title: Uterine_SqCC_SC34 (SqC-withoutMeta)

source_name: Squamous cell carcinoma of uterine cervix (SC34)


title: WT_Nsuf_root, biological rep3

description:
WT_Nsup_R_3
Gene expression data of N-sufficient 10 day-old Col-0 seedling root

source_name: Wild type (Col-0) seedlings grown under high N-availability


title: WT_Nsuf_root, biological rep1

description:
WT_Nsup_R_1
Gene expression data of N-sufficient 10 day-old Col-0 seedling root


title: Uterine_SqCC_SC38 (SqC-withMeta)

source_name: Squamous cell carcinoma of uterine cervix (SC38)

value: uterine cervical squamous cell carcinoma, with metastasis


title: WT_Nstv_root, biological rep1

description:
WT_Nstv_R_1
Gene expression data of N-starved 10 day-old Col-0 seedling root


title: Uterine_SqCC_SC41 (SqC-withMeta)

source_name: Squamous cell carcinoma of uterine cervix (SC41)


title: Guo_001_m267

description: Gene expression from mouse lung tissue

source_name: 10ug MWCNT 1 month

value: 10 ug MWCNT 1 mo

tag: animal


title: WT_Nsuf_root, biological rep2

description:
WT_Nsup_R_2
Gene expression data of N-sufficient 10 day-old Col-0 seedling root


title: Deep-layer astrocytes rep3

city: Tokyo

first: Yukiko

last: Gotoh

state: Tokyo

address: 7-3-1 Hongo, Bunkyo-ku

institute: University of Tokyo

description: ExpressionProfile.txt

data_processing:
Basecalling : RTA : 1.18.64 , bcl2fastq-1.8.4
Alignment : CASAVA-1.8.2 (eland_rna)
Sequences aligning to rRNA were discarded and the remaining reads were aligned to mm9 genomes. The tags uniquely aligned to the genome region with permissive two base mismatches were counted with normalization to region length (reads per kilobase per million mapped reads [RPKM])
Genome_build: mm9
Supplementary_files_format_and_content: RPKMs

source_name: Neocortex

extract_protocol:
Total RNA was isolated from sorted cells with TRIzol (Invitrogen) or RNAiso Plus (Takara) and was then subjected to reverse transcription with the use of a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech).
RNA libraries were prepared using the SMARTer Ultra Low Input RNA for Sequencing kit (Clontech Laboratories) followed with Nextera XT DNA Library Prep kit (Illumina) and RNA sequencing performed using the Illumina HiSeq 2500 platform.

value: neocortex

value: Deep-layer astrocytes

tag: age

tag: genotype


title: Deep-layer astrocytes rep1

description: ExpressionProfile.txt

tag: tissue


title: Uterine_NormalSqEpi_NC13 (normal epi)

source_name: Normal squamous epithelium from uterine cervix (NC13)

value: normal

value: Normal squamous epithelium


title: Uterine_NormalSqEpi_NC2 (normal epi)

source_name: Normal squamous epithelium from uterine cervix (NC2)


title: VP_+Est_shoot , biological rep3

description:
VP_bER_L_3
Gene expression data of 10 day-old AtNIGT1.2-VP inducuble-overexpressor seedling shoot with 10 mM b-estradiole for 24h

source_name: AtNIGT1.2-VP inducible-overepxressor with b-estradiole

value: Shoot


title: Uterine_SqCC_SC35 (SqC-withoutMeta)

source_name: Squamous cell carcinoma of uterine cervix (SC35)


title: Upper-layer astrocytes rep2

description: ExpressionProfile.txt

value: Upper-layer astrocytes


title: Upper-layer astrocytes rep1

description: ExpressionProfile.txt


title: Deep-layer astrocytes rep2

description: ExpressionProfile.txt


title: VP_+Est_shoot , biological rep1

description:
VP_bER_L_1
Gene expression data of 10 day-old AtNIGT1.2-VP inducuble-overexpressor seedling shoot with 10 mM b-estradiole for 24h


title: VP_Mock_shoot, biological rep3

description:
VP_Mock_L_3
Gene expression data of 10 day-old AtNIGT1.2-VP inducuble-overexpressor seedling shoot without b-estradiole

source_name: AtNIGT1.2-VP inducible-overepxressor without b-estradiole


title: Upper-layer astrocytes rep3

description: ExpressionProfile.txt


title: OX_Nstv_shoot,  biological rep2

description:
OX_Nstv_L_2
Gene expression data of N-starved 10 day-old AtNIGT1.2 overexpressor seedling shoot

source_name: AtNIGT1.2 overexpressor grown under N-starvation


title: OX_Nstv_shoot,  biological rep3

description:
OX_Nstv_L_3
Gene expression data of N-starved 10 day-old AtNIGT1.2 overexpressor seedling shoot


title: VP_+Est_shoot , biological rep2

description:
VP_bER_L_2
Gene expression data of 10 day-old AtNIGT1.2-VP inducuble-overexpressor seedling shoot with 10 mM b-estradiole for 24h


title: VP_Mock_shoot, biological rep1

description:
VP_Mock_L_1
Gene expression data of 10 day-old AtNIGT1.2-VP inducuble-overexpressor seedling shoot without b-estradiole


title: OX_Nstv_shoot,  biological rep1

description:
OX_Nstv_L_1
Gene expression data of N-starved 10 day-old AtNIGT1.2 overexpressor seedling shoot


title: VP_Mock_shoot, biological rep2

description:
VP_Mock_L_2
Gene expression data of 10 day-old AtNIGT1.2-VP inducuble-overexpressor seedling shoot without b-estradiole


title: WT_Nstv_shoot, biological rep3

description:
WT_Nstv_L_3
Gene expression data of N-starved 10 day-old Col-0 seedling shoot


title: WT_Nstv_shoot, biological rep2

description:
WT_Nstv_L_2
Gene expression data of N-starved 10 day-old Col-0 seedling shoot


title: WT_Nstv_shoot, biological rep1

description:
WT_Nstv_L_1
Gene expression data of N-starved 10 day-old Col-0 seedling shoot


title: Uninfected

status: Public on Apr 05 2018

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v2.0.1)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v2.0.1)
barcode processing, Cell Ranger Single Cell Software Suite (v2.0.1)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v2.0.1)
alignment, Cell Ranger Single Cell Software Suite (v2.0.1)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

molecule: polyA RNA

source_name: Neural stem cells from subventricular zone

growth_protocol: WT mouse adult neuronal stem cells were isolated from 4-6 week old C57BL/6 mice and cultured in media containing Neurobasal media (Thermo Fisher) without phenol red, supplemented with B27 without vitamin A (Thermo Fisher) and N-2 supplement (Thermo Fisher) at 37°C in 5% CO2

extract_protocol:
NSCs were resuspended at 103 cells/µL in PBS containing 0.04% (w/v) BSA to minimize cell loss and aggregation. ~17,500 cells were partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum of 10,000 individual cells per sample. Utilizing the v2 Chromium™ Single Cell 3’ Library Kit and Chromium instrument (10x Genomics), poly-adenylated mRNA from an individual cell was tagged with a unique 16 basepair 10x barcode and 10 basepair Unique Molecular Identifier. Full length cDNA was amplified to generate sufficient mass for library construction.
Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size (~400 basepair) for the library. The final library was sequence-ready and contained four unique sample indexes. The concentration of the 10x single cell library was determined through qPCR (Kapa Biosystems). The libraries were normalized, pooled, and sequenced with a custom recipe (26-8-98) on the HiSeq4000 platform (Illumina). Five single cell libraries were sequenced across an entire HiSeq4000 flow cell targeting ~45,000 reads per cell.

treatment_protocol: WT mouse adult neuronal stem cells were infected with ZIKV-Dakar or ZIKV-Dakar NS4B G18R at an MOI 1 for 24 to 48 hours or mock infected.

tag: strain

value: NSCs

tag: mouse genotype

value: WT

tag: infection

tag: time post infection


title: NS4B G18R 24h

value: NS4B G18R (ZIKV-Dak strain 41525)


title: WT 48h

value: WT (ZIKV-Dak strain 41525)


title: NS4B G18R 48h

value: NS4B G18R  (ZIKV-Dak strain 41525)


title: WT_Nsuf_shoot, biological rep3

description:
WT_Nsup_L_3
Gene expression data of N-sufficient 10 day-old Col-0 seedling shoot


title: WT 24h


title: Differentiated C2C12 cells (Day 2.5)

description: 2.5 days after the differentiation

data_processing: The data were analyzed using noncoder web interface (http://noncoder.mpi-bn.mpg.de).

source_name: Differentiated C2C12 cells (Day 2.5)

treatment_protocol: To induce the differentiation process, C2C12 cells were cultured in the differentiation medium containing 2% horse serum (Sigma-Aldrich, #H1270) in DMEM with low glucose, pyruvate (Life Technologies, #31885-023) supplemented with antibiotics (penicillin and streptomycin, Sigma-Aldrich, #P4333).

value: myoblast cell line C2C12

value: 2.5 days differentiation


title: Differentiated C2C12 cells (Day 7)

description: 7 days after the differentiation

source_name: Differentiated C2C12 cells (Day 7)

value: 7 days differentiation


title: WT_Nsuf_shoot, biological rep2

description:
WT_Nsup_L_2
Gene expression data of N-sufficient 10 day-old Col-0 seedling shoot


title: WT_Nsuf_shoot, biological rep1

description:
WT_Nsup_L_1
Gene expression data of N-sufficient 10 day-old Col-0 seedling shoot


title: Differentiated C2C12 cells (Day 5)

description: 5 days after the differentiation

source_name: Differentiated C2C12 cells (Day 5)

value: 5 days differentiation


title: Undifferentiated C2C12 cells

description: Undifferentiated cells

source_name: Undifferentiated C2C12 cells

value: control


title: CB_WT_4

city: SYDNEY

first: Irina

last: VOINEAGU

address: High ST

country: Australia

institute: UNSW

description: RNA sample from CB of 22 weeks-old WT mouse 4

data_processing:
Standard Illumina  software was used for basecalling.
RNA sequencing reads were trimmed using Trimmomatic (trimmomatic v0.32)  to remove adapter sequences
Sequencing reads were aligned to the reference mouse genome mm10 (GRCm38 release 90) using the STAR spliced aligner, in paired-end mode.
Gene-level quantification was carried out using featureCounts as implemented in STAR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes RPKM (reads per kilobase per million) values for all Samples

growth_protocol: To generate adult MeCP2 conditionally deleted mice, we crossed MeCP2 flox/flox mice (B6;129P2-Mecp2tm1Bird/J, Jackson Laboratories) with B6.Cg-Tg(UBC::cre/ERT2)1Ejb/1J, Jackson Laboratories).

extract_protocol:
The mice were housed individually and sacrificed at 22 weeks of age following the behavioral tests. Their brain was immediately removed and cut using Adult Mouse Brain Slicer (Zivik Instruments), and then the cerebellum (CB) and the all cortex (CTX) were isolated and frozen at -80.
RNA-seq libraries were generated using the TruSeq RNA Library Prep Kit v2 (RS-122-2001, RS-122-2002), with poly-A selection.

treatment_protocol: At the age of 12 weeks mice were injected with tamoxifen for 5 days and after 3 weeks were placed in a reversed light and dark cycle room. Behavioral tests were conducted on males one month after the tamoxifen treatment (16 weeks of age).

value: MeCP2 flox/flox mice (B6;129P2-Mecp2tm1Bird/J, Jackson Laboratories) crossed with B6.Cg-Tg(UBC::cre/ERT2)1Ejb/1J, Jackson Laboratories).

value: 22 weeks

tag: genotype/variation

value: wild type

value: Brain - Cerebellum (CB)


title: CB_MECP2_KO_4

description: RNA sample from CB of 22 weeks-old MECP2 conditional KO mouse 4

value: MECP2 conditional KO


title: CTX_WT_4

description: RNA sample from CTX of 22 weeks-old WT mouse 4

value: Brain - Cerebral cortex (CTX)


title: CTX_MECP2_KO_3

description: RNA sample from CTX of 22 weeks-old MECP2 conditional KO mouse 3


title: CB_MECP2_KO_1

description: RNA sample from CB of 22 weeks-old MECP2 conditional KO mouse 1


title: CB_WT_1

description: RNA sample from CB of 22 weeks-old WT mouse 1


title: CTX_MECP2_KO_4

description: RNA sample from CTX of 22 weeks-old MECP2 conditional KO mouse 4


title: CB_MECP2_KO_3

description: RNA sample from CB of 22 weeks-old MECP2 conditional KO mouse 3


title: CB_WT_3

description: RNA sample from CB of 22 weeks-old WT mouse 3


title: CTX_MECP2_KO_1

description: RNA sample from CTX of 22 weeks-old MECP2 conditional KO mouse 1


title: CB_MECP2_KO_2

description: RNA sample from CB of 22 weeks-old MECP2 conditional KO mouse 2


title: CTX_MECP2_KO_2

description: RNA sample from CTX of 22 weeks-old MECP2 conditional KO mouse 2


title: CTX_WT_3

description: RNA sample from CTX of 22 weeks-old WT mouse 3


title: CTX_WT_2

description: RNA sample from CTX of 22 weeks-old WT mouse 2


title: CTX_WT_1

description: RNA sample from CTX of 22 weeks-old WT mouse 1


title: CB_WT_2

description: RNA sample from CB of 22 weeks-old WT mouse 2


title: WM1366_ctrl_4

city: Philadelphia

first: Andrew

middle: E

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

data_processing:
Reads were quality and adaptor trimmed with skewer
Trimmed reads were aligned with STAR with default options to GRCh38 gencode v22
Counts were extracted using --quantMode TranscriptomeSAM GeneCounts
Normalized counts were generated by edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file for log normalized counts per million for each sample

source_name: metastatic melanoma cells

growth_protocol: Melanoma cells were grown in Tu2% medium (MCDB153 80%, Leibovitz's L-15 20%, FBS 2%, Insulin (bovine) 5 5 ug/mL, CaCl2 1.68 mM)

extract_protocol:
Qiagen RNeasy mini kit
TruSeq RNA Library Prep Kit v2

treatment_protocol: Melanoma cells were treated with Palbociclib (PD0332991, 0.1uM) and PD0325901 (1nM)

tag: diet

value: control diet


title: WM1366_combo_R2_3

value: combination of MEK plus CDK4/6 inhibitor diet


title: WM1366_combo_R2_2


title: WM1366_combo_R2_1


title: WM1366_combo_R2_4


title: WM1366_ctrl_2


title: WM1366_ctrl_3


title: qNSC_rep2_Dam vs qNSC_rep2_DamPol

city: Cambridge

first: Andrea

middle: H

last: Brand

address: Tennis Court Road

department: University of Cambridge

country: United Kingdom

institute: Gurdon Institute

description: Methylated genomic DNA

hyb_protocol: Amplified DNA from Dam-Pol II and Dam-only samples labelled with Cy3 or Cy5 were co-hybridized to whole genome tiling arrays as recommended by Nimblegen.

scan_protocol: Microarrays were scanned using a Genepix 4000B dual laser scanner (Axon) at FlyChip (Cambridge, UK).

data_processing:
Data were extracted using Nimblescan software (Nimblegen).
Data were processed as described in Southall et al. 2013.

source_name: Neural stem cells, 10 hours expression during quiescence, Dam-only control

label_protocol: Amplified DNA from Dam-Pol II and Dam-only samples were labelled with Cy3 or Cy5 as recommended by Nimblegen.

growth_protocol: Embryos were collected onto an apple juice plate for a 1 hour period and developed at 18oC for 28 hours until ~Stage 16. Embryos were shifted to 29oC for 10 hours to inactivate GAL80ts and induce expression of TaDa constructs. ~250 L1 larval brains were dissected for each condition.

extract_protocol: Targeted DamID was performed as described in Southall et al. 2013.

tag: cell type

value: quiescent neural stem cells

source_name: Neural stem cells, 10 hours expression during quiescence, Dam-Pol II test


title: WM1366_combo_R1_3


title: WM1366_combo_R1_4


title: WM1366_ctrl_1


title: WM1366_combo_R1_1


title: WM1366_combo_R1_2


title: qNSC_rep1_Dam vs qNSC_rep1_DamPol

description: Methylated genomic DNA


title: whole blood gene expression profile_ALS02864

city: Utrecht

first: Jan

middle: Herman

last: Veldink

state: Utrecht

address: Heidelberglaan 100, F.02.230

department: Neurology, Brain Center Rudolf Magnus

country: Netherlands

institute: University Medical Center Utrecht

description: unique sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
Before RNA hybridization, samples were randomized to avoid batch effects correlated to the diagnosis. Samples were hybridized to Illumina’s HumanHT-12 version 3 BeadChips according to manufacturer’s protocol (Illumina, Inc., San Diego, CA, U.S.A.).
Final Reports from Illumina’s GenomeStudio were imported in R (http://.cran.r-project.org). After quantile normalization, gender was checked by expression of gender-specific Y chromosomal probes (JARID1D and RPS4Y1). Samples with gender mismatches were excluded. Subsequently expression values were log2 transformed and quantile normalized. Arrays were projected along the first and second principal component and outliers were dismissed. This resulted in the exclusion of 34 patients and 33 control subjects from the training set and exclusion of 13 patients and 7 control subjects from the test-validation set.
High quality probes were selected, including true autosomal probes only. Using the BLAT function in UCSC’s Genome Browser, all probes were aligned to the NCBI reference genome build 36. Probes with multiple BLAT hits with a sequence homology of > 95% were defined as aspecific and excluded from further analysis. We looked for retired probes using the RefSeq and UniGene (build #228) databases. Retired probes were excluded from further analysis. Finally, probes with identical probe IDs that overlapped between the Illumina HumanHT12 v3 and v4 platform were selected.
Surrogate variable analysis: To eliminate expression heterogeneity caused by known and unknown technical and biological background, data from both training and test sets were combined and normalized, applying surrogate variable analysis (SVA). This produces surrogate variables for which expression levels can be corrected by calculating residuals in a linear regression model. In previous studies, this correction has been proven to reduce batch-specific background noise, thereby increasing the ability to detect biologically meaningful signals.

source_name: whole blood_CON

label_protocol: The Illumina TotalPrep‐96 RNA Amplification Kit was used to generate Biotin labeled (biotin‐16‐UTP), amplified cRNA starting from 200ng total RNA.

extract_protocol: Venous blood was collected in PAXgene tubes stabilizing messengerRNA (mRNA). PAXgene extraction kits (Qiagen) for RNA extraction were used according to the manufacturer’s protocol. Globin reduction treatments were not performed. Quality of isolated RNA was assessed using the Agilent 2100 Bioanalyzer system.

tag: Sex

value: m

tag: diagnosis

value: CON

tag: censored


title: whole blood gene expression profile_ALS01321

description: unique sample

source_name: whole blood_ALS

value: ALS

value: s


title: whole blood gene expression profile_ALS01274

description: unique sample

value: f

value: b


title: whole blood gene expression profile_ALS02754

description: unique sample


title: whole blood gene expression profile_ALS01303

description: unique sample


title: whole blood gene expression profile_ALS04040

description: unique sample


title: whole blood gene expression profile_ALS04367

description: unique sample


title: whole blood gene expression profile_ALS01249

description: unique sample


title: whole blood gene expression profile_ALS04273

description: unique sample


title: whole blood gene expression profile_ALS00507

description: unique sample


title: whole blood gene expression profile_ALS04873

description: unique sample


title: whole blood gene expression profile_ALS02906

description: unique sample


title: whole blood gene expression profile_ALS04233

description: unique sample


title: whole blood gene expression profile_ALS03010

description: unique sample


title: whole blood gene expression profile_ALS04055

description: unique sample


title: whole blood gene expression profile_ALS02683

description: unique sample


title: whole blood gene expression profile_ALS00710

description: unique sample


title: whole blood gene expression profile_ALS04313

description: unique sample


title: whole blood gene expression profile_ALS02900

description: unique sample


title: whole blood gene expression profile_ALS02853

description: unique sample


title: whole blood gene expression profile_ALS04319

description: unique sample


title: whole blood gene expression profile_ALS01284

description: unique sample


title: whole blood gene expression profile_ALS02910

description: unique sample


title: whole blood gene expression profile_ALS03787

description: unique sample


title: whole blood gene expression profile_ALS00493

description: unique sample


title: whole blood gene expression profile_ALS04226

description: unique sample


title: whole blood gene expression profile_ALS03897

description: unique sample


title: whole blood gene expression profile_ALS04246

description: unique sample


title: whole blood gene expression profile_ALS02664

description: unique sample


title: whole blood gene expression profile_ALS00480

description: unique sample


title: whole blood gene expression profile_ALS04340

description: unique sample


title: whole blood gene expression profile_ALS02915

description: unique sample


title: whole blood gene expression profile_ALS04308

description: unique sample


title: whole blood gene expression profile_ALS02792

description: unique sample


title: whole blood gene expression profile_ALS04117

description: unique sample


title: whole blood gene expression profile_ALS02822

description: unique sample


title: whole blood gene expression profile_ALS04283

description: unique sample


title: whole blood gene expression profile_ALS04336

description: unique sample


title: whole blood gene expression profile_ALS04053

description: unique sample


title: whole blood gene expression profile_ALS04261

description: unique sample


title: whole blood gene expression profile_ALS04238

description: unique sample


title: whole blood gene expression profile_ALS04201

description: unique sample


title: whole blood gene expression profile_ALS04361

description: unique sample


title: whole blood gene expression profile_ALS04081

description: unique sample


title: whole blood gene expression profile_ALS04021

description: unique sample


title: whole blood gene expression profile_ALS03068

description: unique sample


title: Uterine_SqCC_SC39 (SqC-withMeta)

source_name: Squamous cell carcinoma of uterine cervix (SC39)

tag: phenotype

value: uterine cervical squamous cell carcinoma, with metastasis

value: formalin-fixed paraffin-embedded tissue

value: uterine cervix

value: Squamous cell carcinoma


title: whole blood gene expression profile_ALS02948

description: unique sample


title: whole blood gene expression profile_ALS04328

description: unique sample


title: whole blood gene expression profile_ALS04295

description: unique sample


title: whole blood gene expression profile_ALS02581

description: unique sample


title: whole blood gene expression profile_ALS03841

description: unique sample


title: whole blood gene expression profile_ALS02997

description: unique sample


title: whole blood gene expression profile_ALS03008

description: unique sample


title: whole blood gene expression profile_ALS02605

description: unique sample


title: whole blood gene expression profile_ALS04286

description: unique sample


title: whole blood gene expression profile_ALS02617

description: unique sample


title: whole blood gene expression profile_ALS02628

description: unique sample


title: whole blood gene expression profile_ALS03070

description: unique sample


title: whole blood gene expression profile_ALS02870

description: unique sample


title: whole blood gene expression profile_ALS02818

description: unique sample


title: whole blood gene expression profile_ALS04294

description: unique sample


title: whole blood gene expression profile_ALS02998

description: unique sample


title: whole blood gene expression profile_ALS02882

description: unique sample


title: whole blood gene expression profile_ALS03829

description: unique sample


title: whole blood gene expression profile_ALS00543

description: unique sample


title: whole blood gene expression profile_ALS04052

description: unique sample


title: whole blood gene expression profile_ALS02986

description: unique sample


title: whole blood gene expression profile_ALS04318

description: unique sample


title: whole blood gene expression profile_ALS02648

description: unique sample


title: whole blood gene expression profile_ALS02782

description: unique sample


title: whole blood gene expression profile_ALS04383

description: unique sample


title: whole blood gene expression profile_ALS02862

description: unique sample


title: whole blood gene expression profile_ALS02817

description: unique sample


title: whole blood gene expression profile_ALS02835

description: unique sample


title: whole blood gene expression profile_ALS04406

description: unique sample


title: whole blood gene expression profile_ALS00503

description: unique sample


title: whole blood gene expression profile_ALS04173

description: unique sample


title: whole blood gene expression profile_ALS04469

description: unique sample


title: whole blood gene expression profile_ALS02509

description: unique sample


title: whole blood gene expression profile_ALS02962

description: unique sample


title: whole blood gene expression profile_ALS04391

description: unique sample


title: whole blood gene expression profile_ALS04245

description: unique sample


title: whole blood gene expression profile_ALS04439

description: unique sample


title: whole blood gene expression profile_ALS04311

description: unique sample


title: whole blood gene expression profile_ALS04203

description: unique sample


title: whole blood gene expression profile_ALS04225

description: unique sample


title: whole blood gene expression profile_ALS04360

description: unique sample


title: whole blood gene expression profile_ALS04326

description: unique sample


title: whole blood gene expression profile_ALS02909

description: unique sample


title: whole blood gene expression profile_ALS02564

description: unique sample


title: whole blood gene expression profile_ALS04325

description: unique sample


title: whole blood gene expression profile_ALS02520

description: unique sample


title: whole blood gene expression profile_ALS04351

description: unique sample


title: whole blood gene expression profile_ALS04329

description: unique sample


title: whole blood gene expression profile_ALS03084

description: unique sample


title: whole blood gene expression profile_ALS04043

description: unique sample


title: whole blood gene expression profile_ALS02832

description: unique sample


title: whole blood gene expression profile_ALS04285

description: unique sample


title: whole blood gene expression profile_ALS04042

description: unique sample


title: whole blood gene expression profile_ALS04189

description: unique sample


title: whole blood gene expression profile_ALS04174

description: unique sample


title: whole blood gene expression profile_ALS04188

description: unique sample


title: whole blood gene expression profile_ALS04191

description: unique sample


title: whole blood gene expression profile_ALS04087

description: unique sample


title: whole blood gene expression profile_ALS02638

description: unique sample


title: whole blood gene expression profile_ALS04020

description: unique sample


title: whole blood gene expression profile_ALS03786

description: unique sample


title: whole blood gene expression profile_ALS04236

description: unique sample


title: whole blood gene expression profile_ALS04322

description: unique sample


title: whole blood gene expression profile_ALS04205

description: unique sample


title: whole blood gene expression profile_ALS03021

description: unique sample


title: whole blood gene expression profile_ALS04267

description: unique sample


title: whole blood gene expression profile_ALS02567

description: unique sample


title: whole blood gene expression profile_ALS04080

description: unique sample


title: whole blood gene expression profile_ALS02640

description: unique sample


title: whole blood gene expression profile_ALS04258

description: unique sample


title: whole blood gene expression profile_ALS04366

description: unique sample


title: whole blood gene expression profile_ALS03902

description: unique sample


title: whole blood gene expression profile_ALS04348

description: unique sample


title: whole blood gene expression profile_ALS02845

description: unique sample


title: whole blood gene expression profile_ALS04293

description: unique sample


title: whole blood gene expression profile_ALS02781

description: unique sample


title: whole blood gene expression profile_ALS04190

description: unique sample


title: whole blood gene expression profile_ALS04111

description: unique sample


title: whole blood gene expression profile_ALS04076

description: unique sample


title: whole blood gene expression profile_ALS04106

description: unique sample


title: whole blood gene expression profile_ALS04288

description: unique sample


title: whole blood gene expression profile_ALS04049

description: unique sample


title: whole blood gene expression profile_ALS04320

description: unique sample