title: TALL_JS_48 (polyA+ RNA)

source_name: bone marrow


title: TALL_JS_49 (polyA+ RNA)

status: Public on Sep 11 2018

type: SRA

city: Ghent

first: Karen

last: Verboom

address: De Pintelaan 185

department: Pediatrics and Genetics

country: Belgium

institute: Ghent University

library_source: transcriptomic

data_processing:
fastq files were aligned to GRCh38 primary annotation with STARv2.4.2a using a 2-pass strategy. In the first pass gencode.v25 was used as guide, in the second pass all sjdb files from the first pass were used as guide
Genes were quantified by STARv2.4.2a on Gencode.v25
Genome_build: GRCh38
Supplementary_files_format_and_content: reads per gene as generated by STAR2.4.2a

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
RNA was extracted using the miRNAeasy mini kit (Qiagen). Truseq stranded mRNA  sample preparation kit (Illumina) was used for the preparation of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subgroup

value: TAL


title: Temsirolimus (iv) followed by Sunitinib (po) in Liver for 1 hr(s) (5M56)

type: RNA

city: Bethesda

first: Myrtle

last: Davis Millin

state: MD

address: 31 Center Drive

country: USA

institute: The National Cancer Institute

description: The rat was administered a single bolus intravenous (iv) dose of temsirolimus or appropriate vehicle formulation.  Thirty (30) minutes after iv administration of temsirolimus or vehicle formulation, sorafenib, sunitinib, or respective vehicle formulation was administered po.  IV doses were administered in a dose volume of 5 mL/kg.  PO doses were administered in a dose volume of 10 mL/kg.  Dose volumes were based on the most recent body weight taken.

hyb_protocol: 11 μg of purified cRNA was applied to Affymetrix GeneChip Rat Genome 230 2.0 Arrays, and incubated at 45°C for 16 hours. Following hybridization, arrays were washed and stained using standard Affymetrix procedures.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 using factory PMT settings. Data extraction was completed with Expression Console software using a target scaling of 500.

data_processing: Data analysis was performed using the Bioconductor R package using the affyQCReport, simpleaffy and arrayQualityMetrics packages. The raw data was normalized using the robust multichip average (RMA) algorithm (Irizarry et. al. Biostatistics, 2003) with log2 transformation.

label: Biotin

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Total RNA samples were converted into labeled target antisense RNA (cRNA) using the Single-Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: Rats used in this study were procured with an indwelling femoral vein cannula.  Prior to dosing on day 1, the catheter of each rat was checked for patency. Rats with patent catheters were randomly assigned to one of 8 treatment groups. On day 1, the rats weighed between 197.6–274.4 grams. Teklad Certified Rodent Diet 2016C (Harlan; Madison, WI) and tap water (Birmingham public water supply) were provided ad libitum to the rats prior to and throughout the study. The animals were individually housed in solid-bottom polycarbonate cages on stainless steel racks in a room maintained at a temperature of 70-79°F and a relative humidity of 44-66%. Room lights were controlled by an automatic timer set to provide a 12/12 light:dark cycle

extract_protocol: RNA isolation from individual tissues was accomplished using an RNeasy microarray kit (QIAGEN Inc.). After extraction, the RNA concentration of each sample was determined using a RiboGreen assay. The RNA Integrity Number (RIN) of each sample was determined using an Agilent 2100 Bioanalyzer with 2100 Expert Software. Only samples with a RIN of 7.5 or higher were deemed acceptable for gene expression analysis.

treatment_protocol: At 1, 6, or 24 hours after the completion of dosing, rats were euthanized by CO2 asphyxiation. Immediately after euthanasia, tissues of interest were collected for RNA isolation.  Bone marrow (left femur), heart (apex, with left and right ventricles), liver (left lateral and median lobes).   Samples of the heart and liver collected for RNA isolation were cut into sections ≤ 2 mm in thickness and immediately placed into pre-filled tubes containing RNAlater® (Applied Biosystems; Foster City, CA).  Bone marrow was flushed from bone using RNAlater®.  After collection into RNAlater®, tissues were maintained refrigerated (approximately 4-5 °C) for at least 24 hours and then stored at or below -20 °C.

tag: strain

value: Sprague-Dawley

tag: Sex

value: Male

tag: age

value: 7-8 weeks

tag: tissue

value: Liver

tag: compound given 1st

value: Temsirolimus

tag: dose (mg/kg) compound given 1st

tag: compound given 2nd

value: Sunitinib

tag: dose (mg/kg) compound 2nd

tag: time

value: 1 hr


title: TALL_JS_47 (polyA+ RNA)


title: subject S_1 [expression]

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

description:
S_1
Gene expression data from liver biopsy from subject S_1.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: The Affymetrix GeneChip Command Console Software (AGCC) was used to generate probe level data that were then converted to expression values using the Robust Multiarray Average (RMA) procedure.

label: biotin

source_name: subject S_1

label_protocol: Standard Affymetrix procedures.

extract_protocol: Total RNA (including miRNAs) was extracted using the mirVana miRNA Isolation Kit (Ambion), following manufacturer’s instructions.

tag: disease

value: normal

value: 59 years


title: TALL_JS_46 (polyA+ RNA)

value: IMM


title: subject S_21 [methylation]

type: genomic

description: DNA methylation data from liver biopsy from subject S_21.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Infinium HumanMethylation450 BeadChip using standard Illumina protocol.

scan_protocol: HiScan SQ scanner (Illumina).

data_processing: Signal intensities files were extracted using the methylumi Bioconductor package. Data preprocessing and normalization were performed using the wateRmelon Bioconductor package. Beta-values were normalized using the dasen function.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: subject S_21

label_protocol: DNA was bisulfite-converted using the EZDNA Methylation-Gold Kit (Zymo Research).

extract_protocol: Genomic DNA was extracted from liver biopsies using the Qiagen kit QiAmp mini Kit®, following manufacturer’s instructions.

value: 60 years

value: Female


title: Temsirolimus (iv) followed by Sunitinib (po) in Heart for 24 hr(s) (5M54)

value: Heart

value: 24 hr


title: TALL_JS_45 (polyA+ RNA)

value: TLX


title: subject S_28 [methylation]

description: DNA methylation data from liver biopsy from subject S_28.

source_name: subject S_28

value: 58 years


title: subject S_21 [expression]

description:
S_21
Gene expression data from liver biopsy from subject S_21.


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 24 hr(s) (4M48)

value: Bone Marrow


title: TALL_JS_44 (polyA+ RNA)

value: TAL


title: subject S_26 [methylation]

description: DNA methylation data from liver biopsy from subject S_26.

source_name: subject S_26

value: 66 years

value: Male


title: subject S_28 [expression]

description:
S_28
Gene expression data from liver biopsy from subject S_28.

value: Liver


title: TALL_JS_43 (polyA+ RNA)


title: subject S_8 [methylation]

description: DNA methylation data from liver biopsy from subject S_8.

source_name: subject S_8

value: 73 years


title: subject S_17 [methylation]

description: DNA methylation data from liver biopsy from subject S_17.

source_name: subject S_17

value: 23 years


title: TEM_vehicle (iv) followed by sterile water (po) in Heart for 6 hr(s) (1M3)

value: Sprague-Dawley

value: 7-8 weeks

value: sterile water

value: 6 hr


title: TALL_JS_42 (polyA+ RNA)


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Liver for 6 hr(s) (4M45)

value: Temsirolimus


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Heart for 1 hr(s) (4M37)

value: 1 hr


title: subject S_24 [expression]

description:
S_24
Gene expression data from liver biopsy from subject S_24.

source_name: subject S_24

value: normal

value: 50 years


title: subject S_7 [methylation]

description: DNA methylation data from liver biopsy from subject S_7.

source_name: subject S_7

value: 44 years


title: subject S_16 [methylation]

description: DNA methylation data from liver biopsy from subject S_16.

source_name: subject S_16

value: 13 years

value: Female


title: subject S_23 [expression]

description:
S_23
Gene expression data from liver biopsy from subject S_23.

source_name: subject S_23

value: 53 years


title: subject S_6 [methylation]

description: DNA methylation data from liver biopsy from subject S_6.

source_name: subject S_6

value: 43 years


title: TALL_JS_40 (polyA+ RNA)

value: HOXA


title: Temsirolimus (iv) followed by Sorafenib (po) in Heart for 1 hr(s) (6M62)

value: Male

value: Heart

value: Sorafenib


title: subject S_14 [expression]

description:
S_14
Gene expression data from liver biopsy from subject S_14.

source_name: subject S_14

value: Liver

value: 54 years


title: Temsirolimus (iv) followed by Sunitinib (po) in Bone Marrow for 1 hr(s) (5M50)

value: Sprague-Dawley

value: 7-8 weeks

value: Bone Marrow

value: Sunitinib


title: subject S_14 [methylation]

description: DNA methylation data from liver biopsy from subject S_14.

value: normal


title: TALL_JS_37 (polyA+ RNA)

value: TLX


title: Temsirolimus (iv) followed by sterile water (po) in Heart for 24 hr(s) (3M29)

value: Temsirolimus

value: sterile water

value: 24 hr


title: TEM_vehicle (iv) followed by Sorafenib (po) in Bone Marrow for 24 hr(s) (8M96)


title: subject S_7 [expression]

description:
S_7
Gene expression data from liver biopsy from subject S_7.

value: 44 years


title: subject S_10 [methylation]

description: DNA methylation data from liver biopsy from subject S_10.

source_name: subject S_10

value: 37 years


title: subject S_15 [expression]

description:
S_15
Gene expression data from liver biopsy from subject S_15.

source_name: subject S_15

value: 50 years


title: TALL_JS_39 (polyA+ RNA)


title: TALL_JS_35 (polyA+ RNA)

value: HOXA


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (4M44)

description: The rat was administered a single bolus intravenous (iv) dose of temsirolimus or appropriate vehicle formulation.  Thirty (30) minutes after iv administration of temsirolimus or vehicle formulation, sorafenib, sunitinib, or respective vehicle formulation was administered po.  IV doses were administered in a dose volume of 5 mL/kg.  PO doses were administered in a dose volume of 10 mL/kg.  Dose volumes were based on the most recent body weight taken.

value: Male

value: 1 hr


title: TALL_JS_34 (polyA+ RNA)

value: TAL


title: subject S_45 [expression]

description:
S_45
Gene expression data from liver biopsy from subject S_45.

source_name: subject S_45

value: Liver

value: 45 years


title: Temsirolimus (iv) followed by sterile water (po) in Bone Marrow for 1 hr(s) (3M25)

value: Sprague-Dawley

value: 7-8 weeks


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 24 hr(s) (4M47)

value: Bone Marrow


title: subject S_44 [expression]

description:
S_44
Gene expression data from liver biopsy from subject S_44.

source_name: subject S_44

value: normal

value: 43 years


title: Temsirolimus (iv) followed by sterile water (po) in Heart for 6 hr(s) (3M34)

value: Heart

value: Temsirolimus

value: 6 hr


title: TALL_JS_32 (polyA+ RNA)

source_name: bone marrow


title: subject S_3 [methylation]

description: DNA methylation data from liver biopsy from subject S_3.

source_name: subject S_3

value: 69 years

value: Female


title: TALL_JS_31 (polyA+ RNA)

value: TLX


title: subject S_79 [methylation]

description: DNA methylation data from liver biopsy from subject S_79.

source_name: subject S_79

value: 54 years


title: subject S_5 [methylation]

description: DNA methylation data from liver biopsy from subject S_5.

source_name: subject S_5

value: 30 years

value: Male


title: subject S_27 [expression]

description:
S_27
Gene expression data from liver biopsy from subject S_27.

source_name: subject S_27


title: TALL_JS_30 (polyA+ RNA)

value: IMM


title: TEM_vehicle (iv) followed by Sorafenib (po) in Liver for 1 hr(s) (8M92)

value: Liver

value: Sorafenib

value: 1 hr


title: subject S_67 [methylation]

description: DNA methylation data from liver biopsy from subject S_67.

source_name: subject S_67

value: 82 years


title: subject S_6 [expression]

description:
S_6
Gene expression data from liver biopsy from subject S_6.


title: subject S_76 [methylation]

description: DNA methylation data from liver biopsy from subject S_76.

source_name: subject S_76

value: 49 years


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (4M38)

value: Sprague-Dawley

value: 7-8 weeks


title: subject S_5 [expression]

description:
S_5
Gene expression data from liver biopsy from subject S_5.

value: normal


title: subject S_107 [methylation]

description: DNA methylation data from liver biopsy from subject S_107.

source_name: subject S_107

value: 64 years


title: subject S_1 [methylation]

description: DNA methylation data from liver biopsy from subject S_1.

source_name: subject S_1

value: 59 years


title: subject S_22 [expression]

description:
S_22
Gene expression data from liver biopsy from subject S_22.

source_name: subject S_22

value: 29 years


title: subject S_20 [expression]

description:
S_20
Gene expression data from liver biopsy from subject S_20.

source_name: subject S_20

value: 26 years


title: TALL_JS_28 (polyA+ RNA)

value: TLX


title: subject S_10 [expression]

description:
S_10
Gene expression data from liver biopsy from subject S_10.

value: 37 years


title: TALL_JS_29 (polyA+ RNA)


title: subject S_17 [expression]

description:
S_17
Gene expression data from liver biopsy from subject S_17.

source_name: subject S_17

value: 23 years


title: TALL_JS_27 (polyA+ RNA)


title: Asp72h3

city: saint paul

first: Jonathan

last: Schilling

state: minnesota

address: 2004 folwell ave

institute: University of Minnesota

data_processing:
The 50-base short read sequences produced by the SOLiD sequencer were mapped in color space using the Whole Transcriptome analysis pipeline in Life Technologies LifeScope software version 2.5 against the P. placenta genome below and normalized as counts per Million mapped reads (CPM) as gene expression level. The test of differential expression was made using edgeR's (v3.14) “glmQLFit” routine on the design matrix.
Genome_build: Postia placenta MAD-698-R-v1.0 from JGI (https://genome.jgi.doe.gov/programs/fungi/index.jsf)
Supplementary_files_format_and_content: Excel file (.xlsx) includes pairwise comparison and cpm levels.

organism: Rhodonia placenta

source_name: liquid culture

growth_protocol: The 100 ml MEY liquid medium (1.5% malt extract and 0.2% yeast extract) was used to grow the P. placenta biomass in 500 ml flasks at 100 rpm and 25°C for about 7 days. About 10 g pre-grown P. placenta wet mycelium were transferred to the basal salts liquid with various treatment of carbon substrates, e.g., no-carbon control, 1% glucose, 1% cellobiose and 1% aspen powder (Populus sp.). Then the incubation was performed at 25°C and 90-100 rpm for 15 and 72 hours. The basal salt (per liter) contains: 2 g NH4NO3, 2 g KH2PO4, 0.5 g MgSO4·7H2O, 0.1 g CaC12·2H2O, 0.57 mg H3BO4, 0.036 mg MnC12·4H2O, 0.31 mg ZnSO4·7H2O, 0.039 mg CuSO4·5H2O, 0.018 mg (NH4)6Mo7O24·4H2O, 0.015 mg FeSO4·7H2O, and 0.001 g thiamine hydrochloride (Highley, 1973). Three bioreplicates were included for each treatment.

extract_protocol:
Total fungal RNA was extracted from mycelium with TRIzol (Life Technologies) and cleaned up with a Qiagen RNeasy Mini Kit (Qiagen, Inc.) prior to RNA sequencing or quantitative RT-PCR (qRT-PCR), a method validated in Zhang et al. (2016).
For RNA-Seq, RNA was extracted using Qiagen RNeasy mini kit (cat74104), followed by genomic DNA removal and cleaning using Qiagen RNase-Free DNase Set kit (cat#79254) and Qiagen Mini RNeasy™ kit (cat#74104). Integrity of the RNA samples was assessed using the Alegient 2100 Bioanalyzer. RNA samples having RNA Integrity Number between 9 – 10 were used in this work.  Ribo-Zero rRNA removal Kit (cat#MRZPL1224) was used for enrichment of transcripts.  The SOLiD® Total RNA-Seq Kit (cat#4445374) was used to construct template cDNA for RNA-Seq following the protocol recommended by Applied Biosystems. Briefly, mRNA was fragmented using chemical hydrolysis followed by ligation with strand specific adapters and reverse transcript to generate cDNA.  The cDNA fragments, 150 to 250 bp in size, were isolated and  amplified through 15 amplification cycles to produce the required number of templates for the SOLiD™ EZ Bead™ system, which was used to generate the template bead library for ligation base sequencing by 5500xl SOLiD™ instrument (LifeTechnologies).

tag: carbon sources

value: aspen

tag: cultring time


title: subject S_85 [methylation]

description: DNA methylation data from liver biopsy from subject S_85.

source_name: subject S_85

value: Female


title: Asp72h2


title: subject S_115 [methylation]

description: DNA methylation data from liver biopsy from subject S_115.

source_name: subject S_115

value: Liver

value: 46 years


title: TALL_JS_26 (polyA+ RNA)


title: subject S_39 [expression]

description:
S_39
Gene expression data from liver biopsy from subject S_39.

source_name: subject S_39

value: 20 years

value: Male


title: TEM_vehicle (iv) followed by sterile water (po) in Heart for 24 hr(s) (1M6)

description: The rat was administered a single bolus intravenous (iv) dose of temsirolimus or appropriate vehicle formulation.  Thirty (30) minutes after iv administration of temsirolimus or vehicle formulation, sorafenib, sunitinib, or respective vehicle formulation was administered po.  IV doses were administered in a dose volume of 5 mL/kg.  PO doses were administered in a dose volume of 10 mL/kg.  Dose volumes were based on the most recent body weight taken.

value: Heart

value: sterile water

value: 24 hr


title: Asp15h3


title: TALL_JS_24 (polyA+ RNA)

value: TAL


title: TALL_JS_25 (polyA+ RNA)


title: Asp72h1


title: subject S_16 [expression]

description:
S_16
Gene expression data from liver biopsy from subject S_16.

source_name: subject S_16

value: normal

value: 13 years


title: subject S_66 [methylation]

description: DNA methylation data from liver biopsy from subject S_66.

source_name: subject S_66

value: 82 years


title: Hyl1_rep1

city: Rosario

first: Uciel

middle: Pablo

last: Chorostecki

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

data_processing:
For data processing, adapters were trimmed using cutadapt only reads no shorter than 18 nt were kept
Then, sequences were trimmed and reads shorter than 18  were discarded.
Sequence data processing was conducted using in-house Perl scripts developed by Palatnik lab in Institute of Molecular and Cell Biology of Rosario.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include precursor name, strand, match position, tag, length, numer of hits and abundance for each Sample

organism: Arabidopsis thaliana

source_name: Arabidopsis mutant

growth_protocol: continous ligth for ten days

extract_protocol:
Trizol Total RNA extraction
After DNase, treatment and RNA-RNA processing intermediaries ligation was done using T4 RNA ligase.cDNA was synthesized using specific primers. Then two rounds of PCR were performed for enrichemen and incorporation of Ilumina sequence to every DNA fragment.

tag: genotype/variation

value: seedling whole bud


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Heart for 24 hr(s) (2M17)

value: Sprague-Dawley

value: 7-8 weeks


title: subject S_58 [methylation]

description: DNA methylation data from liver biopsy from subject S_58.

source_name: subject S_58

value: 55 years


title: Temsirolimus (iv) followed by sterile water (po) in Bone Marrow for 24 hr(s) (3M30)

value: Bone Marrow

value: Temsirolimus


title: Se_rep2


title: TEM_vehicle (iv) followed by Sorafenib (po) in Bone Marrow for 1 hr(s) (8M85.N2)

value: Sorafenib

value: 1 hr


title: subject S_65 [methylation]

description: DNA methylation data from liver biopsy from subject S_65.

source_name: subject S_65

value: Liver

value: 79 years

value: Female


title: TALL_JS_23 (polyA+ RNA)

source_name: bone marrow

value: HOXA


title: Col_rep2 [col_22c_2s]

data_processing:
For data processing, adapters were trimmed using cutadapt only reads no shorter than 18 nt were kept
Sequence data processing was conducted using in-house Perl scripts developed by Palatnik lab in Institute of Molecular and Cell Biology of Rosario.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include sequence mapped and count

source_name: Arabidopsis Col_WT seedling

extract_protocol:
Trizol Total RNA extraction
A sRNA library was constructed using the Illumina TruSeq sRNA kit

tag: ecotype background

value: Col

value: wild-type


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Liver for 1 hr(s) (4M43)

value: Male


title: TEM_vehicle (iv) followed by Sorafenib (po) in Heart for 24 hr(s) (8M89)

value: Heart

value: 24 hr


title: TEM_vehicle (iv) followed by Sunitinib (po) in Bone Marrow for 1 hr(s) (7M73.N2)

value: Sunitinib


title: Col_rep1 [col_22c_1s]

value: seedling whole bud


title: Asp15h1

value: aspen


title: subject S_81 [methylation]

description: DNA methylation data from liver biopsy from subject S_81.

source_name: subject S_81

value: normal

value: 89 years


title: TALL_JS_21 (polyA+ RNA)

value: TAL


title: Cell72h3

value: cellobiose


title: Cell72h2


title: subject S_57 [methylation]

description: DNA methylation data from liver biopsy from subject S_57.

source_name: subject S_57

value: 53 years


title: TALL_JS_20 (polyA+ RNA)

value: IMM


title: Hyl1_rep2

tag: genotype/varation


title: Se_rep1


title: Fiery1_rep2

value: Fiery1 -/-


title: TEM_vehicle (iv) followed by Sorafenib (po) in Heart for 6 hr(s) (8M88)

value: Sprague-Dawley

value: 7-8 weeks

value: Sorafenib

value: 6 hr


title: subject S_51 [methylation]

description: DNA methylation data from liver biopsy from subject S_51.

source_name: subject S_51

value: Liver

value: 70 years

value: Male


title: Cell72h1


title: Cell15h3


title: TALL_JS_19 (polyA+ RNA)

value: TLX


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Bone Marrow for 6 hr(s) (2M22)

value: Bone Marrow


title: TEM_vehicle (iv) followed by sterile water (po) in Liver for 1 hr(s) (1M8)

value: sterile water

value: 1 hr


title: TEM_vehicle (iv) followed by Sunitinib (po) in Bone Marrow for 24 hr(s) (7M83)

value: Sunitinib

value: 24 hr


title: Col_rep2

value: wild-type

value: seedling whole bud


title: Cell15h2

value: cellobiose


title: subject S_55 [methylation]

description: DNA methylation data from liver biopsy from subject S_55.

source_name: subject S_55

value: normal

value: 68 years


title: Fiery1_rep1

value: Fiery1 -/-


title: Asp15h2

value: aspen


title: Col_rep1


title: TALL_JS_16 (polyA+ RNA)

value: TAL


title: HCASMC siSMAD3 knockdown_S24

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

data_processing:
Reads were processed using rnaSeqFPro, a workflow for full processing of RNASeq data starting from fastq files. In brief, the quality control was performed using FastQC, mapping to the human genome hg19 was performed using STAR second pass mapping to increase the percentage of mapped reads, and counting was done with featureCounts using GENCODE gtf annotation. Next, rnaSeqFPro performed differential analysis using DESeq2, conducted principal component analysis and hierarchical clustering using standard R functions, plotPCA and heatmap.2 and generated graphs using gglot2. DESeq2 gave 493 differentially expressed (DE) genes (FDR £ 0.05).
Genome_build: hg19
Supplementary_files_format_and_content: text file with raw counts.

source_name: Cultured coronary artery smooth muscle cells

growth_protocol: Primary human coronary artery smooth muscle cells (HCASMCs) were purchased from three different manufacturers, PromoCell, Lonza and Cell Applications at passage 2 and were cultured in smooth muscle cell basal media along with hEGF, insulin, hFGF-B and fetal bovine serum (FBS) (Lonza # CC-3182) according to the manufacturer’s instructions. HCASMCs between passages 5-8 were used for all the experiments.

extract_protocol:
RNA for all samples was extracted using the RNAeasy mini kit (Qiagen). HCASMC RNA (500 ng) were reverse transcribed using the High capacity RNA-to-cDNA Synthesis kit (Applied Biosystems).
Three experimental and three control samples were generated, RNA was converted to cDNA library as per workflow at Novogene, and sequenced on a HiSeq 4000 machine, 125 bp paired end reads.

treatment_protocol: SMAD3 (s8401 and s8402) silencer select siRNAs were purchased from Life Technologies. siRNA transfection was performed using Lipofectamine RNAiMAX (Life Technologies). For each well treated with the SMAD3 siRNA or scrambled control (Life technologies, #4390843), the final concentration was 20 nM. HCASMCs were seeded in 6 well plates and grown to 75% confluence before siRNA transfection. HCASMCs were transfected with the SMAD3 siRNA or scrambled control for 12 hours and subsequently collected and processed for RNA isolation after 48 hrs of transfection using the RNeasy kit (Qiagen).

tag: cell type

value: coronary artery smooth muscle cells

tag: culture method

value: Grown in serum

tag: knockdown


title: subject S_50 [methylation]

description: DNA methylation data from liver biopsy from subject S_50.

source_name: subject S_50

value: Liver

value: 18 years

tag: Sex

value: Female


title: TALL_JS_18 (polyA+ RNA)

tag: subgroup

value: IMM


title: TALL_JS_15 (polyA+ RNA)


title: TALL_JS_14 (polyA+ RNA)

value: HOXA


title: HCASMC siSMAD3 knockdown_S25


title: Glu72h3

source_name: liquid culture

tag: strain

value: glucose


title: Glu72h2


title: Temsirolimus (iv) followed by sterile water (po) in Bone Marrow for 24 hr(s) (3M35)

value: Sprague-Dawley

value: Male

tag: age

value: 7-8 weeks

tag: tissue

value: Bone Marrow

tag: compound given 1st

value: Temsirolimus

value: sterile water

value: 24 hr


title: TALL_JS_17 (polyA+ RNA)


title: HCASMC siSMAD3 knockdown_S23


title: Cell15h1

value: cellobiose


title: Glu72h1


title: subject S_19 [methylation]

description: DNA methylation data from liver biopsy from subject S_19.

source_name: subject S_19

value: normal

value: 87 years


title: TALL_JS_13 (polyA+ RNA)

value: TAL


title: Glu15h3


title: TALL_JS_12 (polyA+ RNA)


title: Temsirolimus (iv) followed by sterile water (po) in Liver for 1 hr(s) (3M26)

value: Liver

tag: dose (mg/kg) compound given 1st

tag: compound given 2nd

tag: dose (mg/kg) compound 2nd

value: 1 hr


title: TEM_vehicle (iv) followed by Sunitinib (po) in Bone Marrow for 1 hr(s) (7M74.N2)

value: Sunitinib

tag: time


title: TALL_JS_11 (polyA+ RNA)


title: TEM_vehicle (iv) followed by sterile water (po) in Bone Marrow for 6 hr(s) (1M3)

value: 6 hr


title: Temsirolimus (iv) followed by F68/PG/PEG400 (po) in Heart for 6 hr(s) (4M40)

value: Heart


title: Glu15h2

tag: carbon sources

value: glucose

tag: cultring time


title: TEM_vehicle (iv) followed by F68/PG/PEG400 (po) in Liver for 24 hr(s) (2M18)

value: Sprague-Dawley


title: Glu15h1


title: TEM_vehicle (iv) followed by Sorafenib (po) in Heart for 6 hr(s) (8M94)

value: Male

value: Sorafenib


title: TALL_JS_10 (polyA+ RNA)

value: TLX


title: NC72h3

value: no carbon source


title: TEM_vehicle (iv) followed by Sunitinib (po) in Liver for 1 hr(s) (7M79)

value: 7-8 weeks


title: TALL_JS_9 (polyA+ RNA)


title: TALL_JS_8 (polyA+ RNA)


title: NC72h1


title: TALL_JS_7 (polyA+ RNA)

value: IMM


title: NC72h2


title: TALL_JS_6 (polyA+ RNA)

value: HOXA


title: NC15h2


title: TALL_JS_5 (polyA+ RNA)


title: TALL_JS_4 (polyA+ RNA)


title: NC15h1


title: Pbalm_6_2

city: Quebec

first: Julien

last: Prunier

state: QC

address: 1030 av. de la medecine

department: Forestry

country: Canada

institute: Université Laval

description: DNA extraction from leaf punch

hyb_protocol: Array CGH hybridizations were performed with the SureTag DNA Labeling Kit (Agilent, protocol version 7.2), following manufacturer’s instructions

scan_protocol: arrays were scanned using Tecan scanner station

data_processing:
The fluorescence intensities were analyzed using an in-house pipeline of R (v3.1.3) and Python (v2.7.9) scripts (available in https://bitbucket.org/jprunier/git-CNVgene-discovery) in order to correct for dye bias, take into account the GC content in the intensity variations and finally compare the 'test' genome (a descendant or a reference genome) to the 'pseudo-ref' genome of the opposite dye. The 'pseudo-ref' genome is an in silico array representing the average of all reference genome hybridizations within each dye corrected for batch-effect. Hence, one "pseudo-reference genome" was calculated for Cy3 and one was calculated for Cy5. Afterwards, reference DNA (KUU-4, repetition from 1 to 12) were recompared to the pseudo-reference DNA of the opposite dye in order to access the False Discovery Rate.  Please see the files array_design.xlsx and sup_fig1.tiff for more information on the array hybridization strategy.
Please note that the left-most ID column in the raw data files does not contain the Feature Numbers found on the platform supplementary file PtrichocarpaV2_085113_D_GEO_20171001.txt (in 'ID' column).
The file "normalized_data.txt" contains the normalized log2 ratios sample/pseudo reference DNA.  The 'source name' field includes the sample name used in the processed data file.

organism: Populus balsamifera

label_protocol: 250 ng of DNA were labelled using the Agilent consumable and protocol

growth_protocol: Samples were obtained cutting branches in outdoor sites

extract_protocol: Total DNA extracted using DNeasy Plant Mini Kit (QIAgen, http://www.qiagen.com/)

tag: sample type

value: reference DNA (an unlinked individual coming from the 58th parallel in Canada) rep3

value: leaf

value: reference DNA (an unlinked individual coming from the 58th parallel in Canada) rep12


title: TALL_JS_3 (polyA+ RNA)


title: Pbalm_6_3

description: DNA extraction from leaf punch

value: inter-provenance descendant#3

value: inter-provenance descendant#4


title: Liver hepatocytes (LKB6)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description:
LKB1 overexpressed liver hepatocytes (LKB6)
LKB6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor (v2.5) Lumi package.

organism: Mus musculus

source_name: Liver hepatocytes

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

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

treatment_protocol: Overexpression with the LKB1 WT plasmid was performed by tail vein injections once a week during 8 weeks in FVB mice

value: FVB

value: liver

tag: treatment

value: LKB1 overexpressed


title: Liver hepatocytes (LKB4)

description:
LKB1 overexpressed liver hepatocytes (LKB4)
LKB4


title: Liver hepatocytes (LKB7)

description:
LKB1 overexpressed liver hepatocytes (LKB7)
LKB7


title: Pbalm_6_1

description: DNA extraction from leaf punch

value: intra-provenance descendant#20

value: intra-provenance descendant#9


title: TALL_JS_1 (polyA+ RNA)

value: TAL


title: NTC_siRNA_rep3

source_name: ALL-SIL cell line

growth_protocol: Cells were grown in RPMI supplemented with 20% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol:
RNA was extracted using the miRNAeasy mini kit (Qiagen). Truseq unstranded mRNA  sample preparation kit was used for the preparation of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were electroporated with a TLX1 or NTC siRNA

tag: cell line

value: ALL-SIL


title: Pbalm_5_4

description: DNA extraction from leaf punch

value: intra-provenance descendant#1

value: intra-provenance descendant#4


title: NC15h3

value: no carbon source


title: TLX1_siRNA2_rep3


title: Pbalm_5_2

description: DNA extraction from leaf punch

value: inter-provenance descendant#1

value: inter-provenance descendant#6


title: Pbalm_5_3

description: DNA extraction from leaf punch

value: reference DNA (an unlinked individual coming from the 58th parallel in Canada) rep7

value: reference DNA (an unlinked individual coming from the 58th parallel in Canada) rep6


title: Liver hepatocytes (LKB5)

description:
LKB1 overexpressed liver hepatocytes (LKB5)
LKB5


title: 401p

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced clean reads were mapped to Homo sapiens (hg19) whole genome using tophat v1.4.1 with parameters -i 10 -I 80000 --solexa1.3-quals --min-coverage-intron 20 --max-coverage-intron 11000 --min-segment-intron 10 --max-segment-intron 81000 --segment-length 20
Gene annotation and calculation of FPKM values was carried out using Cufflinks (v2.0.2) with the provision of a GTF annotation file (hg19).
Gene expression differences were assessed by Cuffdiff use upper-quartile normalization, with false discovery rate correction for multiple testing.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: lung

extract_protocol:
Tumor and adjacent tissues were ground into powder in liquid nitrogen; total RNA was harvested using RNeasy Plant Mini Kit (QIAGEN); then total RNA samples were treated with DNase I and the mRNA is enriched by using the oligo(dT) magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: normal lung

tag: age (yrs)

tag: gender

value: male

tag: survival time

value: living


title: 448p


title: 401c

value: adenocarcinoma


title: 448c


title: TLX1_siRNA1_rep3


title: Liver hepatocytes (LKB1)

description:
LKB1 overexpressed liver hepatocytes (LKB1)
LKB1

value: FVB

value: liver


title: Liver hepatocytes (LKB2)

description:
LKB1 overexpressed liver hepatocytes (LKB2)
LKB2

value: LKB1 overexpressed


title: Liver hepatocytes (Control4)

description:
Untreated liver hepatocytes (Control4)
Control4

value: untreated


title: Liver hepatocytes (Control2)

description:
Untreated liver hepatocytes (Control2)
Control2


title: Liver hepatocytes (Control1)

description:
Untreated liver hepatocytes (Control1)
Control1


title: Pbalm_5_1

description: DNA extraction from leaf punch

value: inter-provenance descendant#7

value: leaf

value: inter-provenance descendant#2


title: TALL_JS_2 (polyA+ RNA)

tag: subgroup

value: IMM


title: NTC_siRNA_rep2

value: ALL-SIL


title: TLX1_siRNA2_rep2


title: 126c

value: female


title: Liver hepatocytes (Control3)

description:
Untreated liver hepatocytes (Control3)
Control3

tag: strain


title: 126p


title: Pbalm_4_3

description: DNA extraction from leaf punch

value: intra-provenance descendant#8

value: intra-provenance descendant#7


title: TLX1_siRNA1_rep2


title: Pbalm_4_2

description: DNA extraction from leaf punch

value: intra-provenance descendant#18

value: intra-provenance descendant#19


title: NTC_siRNA_rep1


title: Pbalm_4_1

description: DNA extraction from leaf punch

value: inter-provenance descendant#19

value: inter-provenance descendant#18


title: TLX1_siRNA2_rep1


title: NK +adenosine 2

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

data_processing:
FastQC v.0.11.3 was used to observe read quality
FastX v. 0.0.14 was used to trim data
STAR v. 2.5.4bq was used to align reads to the genome with max-intron-length set to 560, min-intron-length set to 60,  and strandedness set to "fr-firststrand".
HTSeq Count v. 0.6.1  was used to count reads aligning to genes, feature was set to "exon" and attribute was set to "gene id", stranded was set to "reverse" and intersection-nonempty was used
EdgeR v. 3.12.1 (using Bioconductor v 3.2) were used to normalize and perform DE analysis. The number of reads for the control and experimental groups were then compared to identify differentially expressed genes (false discovery raye of 1%)
GSEA v. 3 was used in performing the GSEA analysis
Genome_build: GRCh38.p12 Ensembl reference genome
Supplementary_files_format_and_content: raw abundance measurements

source_name: whole cell

growth_protocol: NK cells

extract_protocol: NuGen Universal Plus mRNA-Seq kit  (NuGen Technologies Inc., San Carlos, USA)

treatment_protocol: treated with adenosine or no adenosine

tag: cell type

value: NK cells

tag: agent

value: adenosine


title: NK +adenosine 1


title: NK +adenosine 3


title: Pbalm_3_4

description: DNA extraction from leaf punch

value: inter-provenance descendant#5

tag: tissue

value: inter-provenance descendant#13


title: Pbalm_3_2

description: DNA extraction from leaf punch

value: intra-provenance descendant#12

value: intra-provenance descendant#23


title: Pbalm_3_3

description: DNA extraction from leaf punch

value: reference DNA (an unlinked individual coming from the 58th parallel in Canada) rep9

value: leaf

value: reference DNA (an unlinked individual coming from the 58th parallel in Canada) rep4


title: input DNA

library_source: genomic

data_processing:
fastq files were aligned with STARv2.4.2a to GRCh38 with --alignIntronMax 1 --alignMatesGapMax 1000 to avoid splice awareness.
Peak calling was performed with MACS2 using broad setting
Genome_build: GRCh38
Supplementary_files_format_and_content: xls file with MACS2 output

extract_protocol: DNA was purified by phenol/chloroform extraction, assisted by phase lock gel tubes (5Prime).

treatment_protocol: The ChIP-protocol has been adapted from previous studies (Lee et al. 2006). In brief, 1*107 cells were cross-linked with 1,1 % formaldehyde (Sigma-Aldrich, F1635) at room temperature for 10 min and the cross-linking reaction was quenched with glycine (125 mM final concentration, Sigma-Aldrich, G-8790). Nuclei were isolated and chromatin was purified by chemical lysis. Next, the purified chromatin was fragmented to 200-300 bp fragments by sonication (Covaris, M220, Focused-ultrasonicator). Chromatin immunoprecipitation was performed by incubation of the chromatin fraction overnight with 20 μl of protein-A coated beads (Thermo-Scientific, catalog number 53139) and 2 μg of H3K4me1 specific (Abcam, ab8895) or H3K4me3 specific (Abcam, ab8580) antibody. The next day, beads were washed to remove non-specific binding events and enriched chromatin fragments were eluted from the beads, followed by reverse cross-linking by incubation at 65°C overnight.

value: ALL-SIL


title: NK untreated 1


title: NK untreated 3


title: MCT_RV_4_S10

city: Kingston

first: Stephen

last: Archer

state: Ontario

address: 94 Stuart Street

department: Medicine

institute: Queen's University

description:
mct_rv
MCT_RV_4_S10

data_processing:
Bcl2Fastq
Fastqc - to perfom quality control
Cutadapt - to remove adapter sequences and trim low quality reads
HISAT2 to align reads
StringTie to assemble reads
Genome_build: Rn6
Supplementary_files_format_and_content: condition_res_ct_rv-mct_rv.csv: Differentially regulated genes file
Supplementary_files_format_and_content: all_counts.csv: All counts file

source_name: Right Ventricle_mct

extract_protocol: Right ventricles were dissected free from the LV and vasculature and ground with a mortar and pestle in liquid nitrogen. total RNA was extracted in TrIzol using Zymo DirectZol columns (Zymotech Inc., Austin, TX, USA). Libraries were generated using an Illumina RiboGold ribodepletion and Truseq stranded LT library generation kit (Illumina Inc., San Diego, CA, USA), and sequenced using the Illumina NextSeq550 Sequencer (Illumina).

value: Sprague Dawley

value: Right Ventricle

value: Monocrotaline


title: MCT_RV_6_S12

description:
mct_rv
MCT_RV_6_S12


title: Pbalm_3_1

description: DNA extraction from leaf punch

value: intra-provenance descendant#10

value: intra-provenance descendant#17


title: Pbalm_4_4

description: DNA extraction from leaf punch

value: reference DNA (an unlinked individual coming from the 58th parallel in Canada) rep5

value: reference DNA (an unlinked individual coming from the 58th parallel in Canada) rep2


title: MCT_RV_3_S9

description:
mct_rv
MCT_RV_3_S9


title: Pbalm_2_4

description: DNA extraction from leaf punch

value: inter-provenance descendant#12

value: inter-provenance descendant#15


title: MCT_RV_2_S8

description:
mct_rv
MCT_RV_2_S8


title: TALL_JS_22 (polyA+ RNA)

value: IMM


title: SAMPLE 7

city: México City

first: Eric

middle: Gustavo

last: Ramírez-Salazar

address: Periferico Sur 4809, Arenal Tepepan, 14610 Ciudad de México

country: Mexico

institute: INMEGEN

data_processing: The relative amount of microRNAs was calculated using the software Expression Suite 1.3 (Applied Biosystems, Foster City, CA); normalization method was performed using levels of RNU6 as normalizer. The levels of miRNAs that showed a 2-fold change and a p < 0.05 were considered to be differentially present in the osteoporotic group of samples.

label: FAM

source_name: pool of osteoporotic women

label_protocol: We prepared four pools of five postmenopausal osteoporotic women and four pools of five postmenopausal healthy women. Quantitative global profiling of serum miRNAs was performed on the Applied Biosystems ViiA7 system using TaqMan Array Human MicroRNA A+B Cards Set v3.0 (Applied Biosystems, Foster City, CA) designed to identify 754 human miRNAs following manufacturer's protocol. Briefly, 30 ng of RNA was reverse transcribed to cDNA using TaqMan miRNA Reverse Transcription kit and Megaplex RT Primers Human Pool A v2.1 and Pool B v3.0, (Applied Biosystems, Foster city, CA). The mixture was incubated for 40 cycles at 16ºC for 2 min, 42ºC for 60s, and 50ºC 1 s, followed for incubation at 85ºC for 5 min to generate a library of miRNA cDNAs. Pre-amplification stage was performing using TaqMan PreAmp Master Mix and Megaplex™ PreAmp Primers (Applied Biosystems, Foster City, CA), following the manufacturer’s instructions. qPCR was then performed using TaqMan Universal PCR Master Mix and TaqMan Human MicroRNA Array Card A and Card B v3.0 at 95ºC for 10 min, followed by 40 cycles at 95ºC for 15s and at 60ºC for 60s.

extract_protocol: Total RNA from serum was extracted using miRNaeasy Serum/Plasma kit (QIAGEN) following the manufacturer instructions.

tag: disease state

value: Osteoporosis

value: Serum

value: Women

tag: Stage

value: Postmenopausal


title: Pbalm_2_2

description: DNA extraction from leaf punch

value: reference DNA (an unlinked individual coming from the 58th parallel in Canada) rep11

value: leaf

value: reference DNA (an unlinked individual coming from the 58th parallel in Canada) rep10


title: SAMPLE 6


title: SAMPLE 8


title: CT_RV_6_S6

description:
ct_rv
CT_RV_6_S6

source_name: Right Ventricle_vehicle

value: Sprague Dawley

value: Vehicle


title: SAMPLE 5


title: Pbalm_2_1

description: DNA extraction from leaf punch

value: intra-provenance descendant#14

value: intra-provenance descendant#11


title: CT_RV_5_S5

description:
ct_rv
CT_RV_5_S5

value: Right Ventricle


title: NK untreated 2

value: NK cells


title: SAMPLE 4

source_name: pool of normal women

value: Normal


title: TLX1_siRNA1_rep1

value: ALL-SIL


title: Pbalm_1_4

description: DNA extraction from leaf punch

value: intra-provenance descendant#5

value: intra-provenance descendant#13


title: PAX8_Tfx

city: Seattle

first: Marshall

middle: S

last: Horwitz

state: Washington

address: 850 Republican Street N431

department: Pathology

institute: University of Washington

data_processing:
Illumina NextSeq System Suite v2.1.3 was used for basecalling.
Cutadapt v1.12 was used to remove adapter sequences and filter low quality bases (Q20 cuttoff).
Reads were aliged to GRCh38 with HISAT2 v2.0.5. Reads mapping to GRCh38.88 defined exons were counted and per gene expression was reported as transcripts per million (TPM) using Stringtie v1.3.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file containing individual sample expression (TPM) matrix.

source_name: Reh cells

growth_protocol: Reh cells were grown in 10% FBS/RPMI 1640 (Gibco, 11875-093). Cells were grown at 37°C, under 5% CO2 and were passaged every 3-4 days at confluencies suggested by their supplier. Cell aliquots were cultured for no more than ~20 passages.

extract_protocol: PolyA selected mRNA libraries were prepared from total RNA (~ 1 µg per sample) using the Illumina TruSeq Stranded mRNA Library Prep kit.

treatment_protocol: Two separate transfections of PAX2, PAX5, PAX8, or empty vector (pRRL-CMV-IRES-hrGFPII) control were performed via electroporation in 400µL OPTI-MEM on 1.5X106 REH cells / treatment (BioRad GenePulser Xcell, Square wave, 210V, 15ms, 2x pulse, .1sec gap). The transfected cells were incubated for 24 hours post transfection in normal growth media (RPMI, 10% FBS). Cells were washed twice in PBS plus 1% FBS, and 4-6x105 GFP (+) cells / treatment were harvested via FACS for RNA. Total RNA was isolated from sorted cells using the Qiagen RNeasy Plus kit. The 2 replicates were then combined equally to create one sample per condition for deep sequencing.

tag: facs sorting

value: GFP (+)

value: Transfection

tag: treatment condition

value: PAX8, 24 hrs.


title: Empty_Vector_Tfx

value: Empty Vector, 24 hrs.


title: CT_RV_4_S4

description:
ct_rv
CT_RV_4_S4


title: SAMPLE 3

value: Serum

value: Women

value: Postmenopausal


title: No_Salt_Control

treatment_protocol: 1X106 REH cells, cultured in RPMI supplemented with 10% FBS, were exposed to either Potassium Gluconate or Calcium Chloride (80 mM concentration added to media) for 24 hours. The cells were then washed twice with PBS and total RNA was isolated using the Qiagen RNeasy Plus kit. Each condition along with a no treatment control was repeated for a total of 3 replicates. The 3 replicates were then combined equally to create one sample per condition for deep sequencing.

value: Salt Exposure

value: No Salt, 24 hrs.


title: PAX2_Tfx

value: PAX2, 24 hrs.


title: CT_RV_3_S3

description:
ct_rv
CT_RV_3_S3

value: Sprague Dawley

value: Vehicle


title: SAMPLE 2


title: MCT_RV_1_S7

description:
mct_rv
MCT_RV_1_S7

value: Right Ventricle

value: Monocrotaline


title: PAX5_Tfx

value: PAX5, 24 hrs.


title: CT_RV_2_S2

description:
ct_rv
CT_RV_2_S2


title: Pbalm_1_3

description: DNA extraction from leaf punch

value: inter-provenance descendant#17

value: leaf

value: inter-provenance descendant#8


title: SAMPLE 1

value: Normal


title: Pbalm_1_2

description: DNA extraction from leaf punch

value: inter-provenance descendant#14

value: inter-provenance descendant#11


title: Calcium_Chloride_80mM

value: Calcium Chloride, 80 mM, 24 hrs.


title: Pbalm_2_3

description: DNA extraction from leaf punch

value: inter-provenance descendant#9

value: inter-provenance descendant#20


title: Potasium_Gluconate_80mM

value: Salt Exposure

value: Potasium Gluconate, 80 mM, 24 hrs.


title: Pbalm_1_1

description: DNA extraction from leaf punch

value: reference DNA (an unlinked individual coming from the 58th parallel in Canada) rep1

value: reference DNA (an unlinked individual coming from the 58th parallel in Canada) rep8


title: CT_RV_1_S1

description:
ct_rv
CT_RV_1_S1

value: Sprague Dawley

value: Vehicle


title: PV5T_D79H_WT-1: Poliovirus-5T D79H mutant passage 4 replicate 1

status: Public on Sep 10 2018

city: New York

first: Benjamin

last: tenOever

state: NY

address: 1468 Madison Avenue

department: Microbiology

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Libraries were run on an Illumina NextSeq
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Reads were aligned to viral genomes using Bowtie2
BAM files from each lane were consolidated into a single file
Reads were visualized using IGV

extract_protocol: mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was extracted from cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used to prepare 1 ug of total RNA for the sequencing libraries.

tag: infection

value: Poliovirus D79H


title: PV5T_WT-1: Poliovirus-5T passage 4 replicate 1

value: Poliovirus


title: PV5T_WT-2: Poliovirus-5T passage 4 replicate 2


title: PV5T_D79H_WT-2: Poliovirus-5T D79H mutant passage 4 replicate 2


title: PV5T_RIII-2: Poliovirus-5T passage 4 replicate 2

source_name: RNaseIII-/-


title: PV5T_D79H_RIII-1: Poliovirus-5T D79H mutant passage 4 replicate 1


title: PV5T_RIII-1: Poliovirus-5T passage 4 replicate 1


title: Human10_ChIP_Pol2_ZIKVpositive_input

city: La Jolla

first: Aaron

middle: F

last: Carlin

state: California

address: 9500 Gilman Drive GPL Rm 118

department: Pathology and Medicine

institute: University of California, San Diego

data_processing:
Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14)
RNA-seq reads were mapped to the human genome (hg38) using STAR (v2.2.0c). Only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis. Gene FPKM values were defined for primary Gencode transcripts using HOMER (v4.10) using only strand-specific exonic reads for each transcript.
ChIP-seq reads were aligned to the human genome (hg38) using bowtie2 (Langmead and Salzberg, 2012), keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). ChIP-seq peaks were called on pooled replicates using HOMER’s findPeaks program in either “histone” (histone marks, Pol II) or “factor” (CTCF) mode using default parameters to identify spreading or focal peaks, respectively.
Gene expression was measured using HOMER with the following parameters analyzeRepeats rna hg38 -count exons -noadj -pc 3 -condenseGenes followed by DESeq normalized abundance measurements
ChIP-Seq: Tab-delimited BED files containing peak positions for each ChIP-seq experiment (one peak file per set of replicates, hg38) Columns: 1:chromosome,2:start,3:end,4:peakName,5:set to 1,6:strand.  RNA-seq: Tab-delimited table of FPKM values for all RNA-seq experiments Columns: 1:transcript ID, 2:chr, 3:start, 4:end, 5:strand, 6:mRNA length, 7:gene name, 8:Annotation/Divergence, 9:gene ID, 10: gene type, 10-43: FPKM for each experiment.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq tab-delimited text files include FPKM values for each Sample and pooled samples at each time point, Tab-delimited BED files containing peak positions for each ChIP-seq experiment

source_name: Human blood monocytes derived

growth_protocol: Human blood was obtained from healthy volunteers and separated using Histopaque 1077 spun at 300xg for 30-60’ at 4C. The buffy coat was washed once, red blood cells lysed and monocytes isolated by negative selection using the pan monocyte isolation kit [Miltenyi Biotech cat. #130-096-537]. Cells were seeded onto tissue coated plates and differentiated for 7 days in complete macrophage media (macrophage serum-free media [Gibco cat #12065] supplemented with 1% penicillin/ streptomycin, 1% nutridoma-SP [Roche cat #11011375001], 1% fungizone [Gibco cat#15290-018], and 100ng/ml human macrophage-colony stimulating factor (M-CSF) [Peprotech cat# 300-25]) at 37o C, 5% CO2. Media was changed every 2-3days.

extract_protocol:
For RNA-seq acrophages were washed once with 1XPBS, gently scraped off in 1XPBS, pelleted at 4C and stained with zombie violet viability dye [BioLegend] in the dark. Cells were washed once with FACS buffer (1X PBS, 3% fetal bovine serum, and 1 mM EDTA) and fixed and permeabilized with 4% PFA [Electron Microscopy Sciences, 15710-S], 0.1% saponin [Sigma-Aldrich, 47036] in molecular grade PBS supplemented with 1:100 RNasin Plus RNase Inhibitor [Promega, N2615] for 30’ at 4C. Cells were washed in Wash Buffer: 1XPBS containing 0.2% BSA, 0.1% saponin, and 1:100 RNasin Plus RNase Inhibitor and blocked for 10’ with Human Fc Block (1:500) [BioLegend] in Staining Buffer: 1XPBS containing 1%BSA, 0.1% saponin, and RNasin Plus RNase Inhibitor. HMDMs were then stained with 4G2 antibody [BioXcell] conjugated to AF647 [Thermo Scientific Cat#A20186] for 30’ at 4C, washed twice, resuspended at 5-10E6 cells/ml in Sort Buffer (PBS containing 0.5% BSA, and 1:25 RNasin Plus RNase Inhibitor) and sorted into ZIKV+ and ZIKV- cells on the FACSAria [BD Biosciences] at La Jolla Institute for Allergy for Immunology. Gates were set with reference to negative controls. After sorting, cells were pelleted at at 4C, supernatant discarded and total RNA isolated using Ambion’s RecoverAll Total Nucleic Acid Isolation Kit [AM1975], starting at the protease digestion step. All steps were performed per manufacturer recommendations with the following modification. Cells were incubated in digestion buffer for 3 hours at 50C supplemented with RNasin Plus RNase Inhibitor. RNA was treated with in column DNase per manufacturer instructions, eluted and RNA quality determined by BioAnalyzer using the Eukaryote Total RNA Pico Chip. Samples with RIN values greater than 8.0 were used for library preparation. For ChIP-seq macrophages were cross-linked with 1% formaldehyde for 15 minutes in the presence of 1 mM sodium butyrate and quenched with 0.125M glycine. Preparation of HMDMs for FACS was performed as described above for RNA-seq except that 1x cOmplete protease inhibitors (Roche) and 1 mM sodium butyrate [Sigma] were included in all buffers instead of RNasin Plus RNase Inhibitor. Following FACS cells were washed, pelleted and snap-frozen.
Strand-specific total RNA-seq libraries from ribosomal RNA-depleted were prepared using the TruSeq kit (Illumina) according to the supplied protocol. ChIP-seq was essentially performed as described (Heinz et al., 2013), except that libraries were prepared using NEB Ultra II DNA library prep kit reagents.

treatment_protocol: On day 7 of culture, macrophages were infected with Zika virus clinical isolates SD001 or FSS13025 at indicated multiplicity of infection (MOI) with or without antibody-dependent enhancement (ADE) (MOI= 1 + 0.6% (v/v) DENV human immune serum). The virus was incubated with HMDMs for 2 hours with rocking every 10-15’ at 37oC, 5% CO2. The supernatant was removed, and cells were washed 3x with 1XPBS, before addition of fresh warm complete macrophage media. Both RNA-seq and flow cytometry confirmed that no infectious DENV is present in the human immune serum.

tag: human donor

value: monocyte derived macrophage

tag: chip antibody

value: input

tag: viral infection

value: ZIKV-infected

tag: viral strain

tag: time post infection viral infection


title: Human10_ChIP_CTCF_ZIKVnegative_input

value: ZIKV-bystander


title: Human10_ChIP_CTCF_Mock_input

value: mock infected


title: Human10_ChIP_Pol2_Mock_input


title: Human10_ChIP_Pol2_ZIKVnegative_24h

value: RPB2 protein of RNApol2, GeneTex #GTX102535


title: Human10_ChIP_Pol2_ZIKVpositive_24h


title: Human10_ChIP_CTCF_ZIKVnegative_24h

value: CTCF, Active Motif #61311


title: Human10_ChIP_Pol2_ZIKVnegative_input


title: Human10_ChIP_CTCF_Mock_24h


title: Human10_ChIP_CTCF_ZIKVpositive_input


title: Human10_ChIP_Pol2_Mock_24h


title: Human10_ChIP_CTCF_ZIKVpositive_24h


title: Human9_ChIP_H3K27Ac_Mock_24h

value: Histone H3 lysine 27 acetyl, Active Motif #39133, (H3K27ac)


title: PV5T_D79H_RIII-2: Poliovirus-5T D79H mutant passage 4 replicate 2


title: Human9_ChIP_H3K27Ac_ZIKVnegative_24h


title: Human8_ChIP_H3K27Ac_Mock_24h


title: Human9_ChIP_H3K27Ac_ZIKVpositive_24h


title: Human8_ChIP_H3K27Ac_ZIKVnegative_24h


title: Human8_ChIP_H3K27Ac_ZIKVpositive_24h


title: Human7_ChIP_H3K27Ac_ZIKVnegative_24h


title: Human8_ChIP_H3K27Ac_input


title: Human7_ChIP_H3K27Ac_Mock_24h


title: Human7_ChIP_H3K27Ac_input


title: siLINC00152_B

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1300 Jefferson Park Ave

department: Biochemistry & Molecular Genetics

institute: University Of Virginia

data_processing:
Illumina software was used for basecalling to generate the .bcl files which were converted to fastq file using a software named bcl2fastq
RNA-seq reads were aligned to the hg38 reference genome using HISAT. Reads mapping to each gene were counted using htseq-count and differentially expressed genes were identified using DESeq R package.
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq output file with raw counts of sequencing reads for each gene

source_name: U87 cell line

extract_protocol:
TRIzol and subsequently purified using RNeasy Isolation kit (Qiagen)
NEB NEXT Ultra directional RNA Library prep kit (NEB)
Sequencing was run using a NextSeq 150 cycle V2 kit with HighOutput. A paired-end (R1_75 & R2_75) run with indexing (6 cycles) were included in the workflow.

tag: cell line

value: brain


title: siGL2_A


title: siGL2_C


title: siGL2_B


title: siLINC00152_A


title: siLINC00152_C


title: Human7_ChIP_H3K27Ac_ZIKVpositive_24h


title: SeV-5R in RNaseIII-/-  replicate 2

description:
SeV_alignments.xlsx
CO74-SeV5R-R3-Rep2_S17

data_processing:
Libraries were run on an Illumina NextSeq
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Raw sequencing reads were aligned to the corresponding reference viral genome using Bowtie2 with default paramaters
BAM files from each lane were consolidated into a single file
The resulting aligned reads were visualized, and the read counts for each residue per site obtained, using the Integrative Genomics Viewer (IGV)
Relative read counts and variation analyses were performed using in-house Perl scripts. Major variant for each site was defined as the residue (nucleotide) with higher read counts compared to all other possible residues for the same site.
For the analysis of junction sites, raw sequencing reads were aligned to the corresponding reference viral genome using HISAT2
Resulting alignments were filtered for low mapping quality reads using samtools(-q 10), and junction counts were obtained using regtools
Further consolidation of junction sites and their corresponding counts was performed using in-house Perl scripts.
Genome_build: As these are recombinant viruses, they do not have references on UCSC or  NCBI that are perfect matches.  See viral_genome sequences linked to the Series record.
Supplementary_files_format_and_content: Processed excel spread sheets contain, for each sample, Variability Ratio, Total Read Number, Number of Minor Variable reads, Number of mapped reads, Percentage, Coverage, and Minor Variable Reads for each position in the indicated viral genome

extract_protocol:
Total RNA was extracted from cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used to prepare 1 ug of total RNA for the sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: Sendai virus, control


title: SeV-5R in RNaseIII-/-  replicate 1

description:
SeV_alignments.xlsx
CO-SeV5R-RnaseIIIKO_S3


title: D8N

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

data_processing:
Cufflinks
Cuffdiff
Genome_build: hg19/rheMac8
Supplementary_files_format_and_content: Gene-level differential expression. Tests differences in the summed FPKM of transcripts sharing each gene_id

source_name: Homo sapiens_Normoxia

growth_protocol: CHIR 8uM x 2d + IWR 5uM x 2d + Glucose starvation on day 12 for 4 days. Cells were collected on day 30 of differentiation.

extract_protocol:
Trisol/ Qiagen RNA extract kit
Ion Total RNA Seq Kit v2 with ERCC RNA Spike-in Mix 1 added

treatment_protocol: Normoxia (control) vs. 24hr Hypoxia

tag: treatment

value: Normoxia

value: iPSC-Cardiomyocytes (iPSC-CM)


title: SeV-5R in RNaseIII-/-  replicate 3

description:
SeV_alignments.xlsx
CO80-SeV5R-R3-Rep3_S12


title: D737N


title: D740N


title: D740H

source_name: Homo sapiens_Hypoxia

value: Hypoxia


title: D8H


title: SeV-5T in RNaseIII-/-  replicate 1

description:
SeV_alignments.xlsx
CO-SeV5T-RnaseIIIKO_S15

value: Sendai virus, targeted


title: SeV-5T in RNaseIII-/-  replicate 2

description:
SeV_alignments.xlsx
CO73-SeV5T-R3-Rep2_S22


title: RAT-seq random control in iPSC

city: Palo Alto

first: Jifan

last: Hu

address: 3801 Miranda Ave, Bldg 100, Room E4-200

department: Palo Alto Veterans Institute for Research

institute: Stanford University Medical School

description: PSC RAT Ct34

data_processing:
Library strategy: RAT-Seq
The low quality reads were filtered using Fastx (version:0.0.13). Clean reads were mapped to the mouse genome (genome version: mm10) using the Bowtie (version:0.12.8) software with default parameters.
Enriched regions of the genome were identified by comparing the RAT-Seq peaks to input samples using MACS2 (version:2.1.1) and q-value of 0.05 was used as the initial cutoff threshold.
Differential binding analysis was performed with the DiffBind package using parameters of fold change difference ≥2 and p-value < 0.05, with false discovery rate (FDR) <0.1.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: iPS cells

growth_protocol: Fibroblasts were reprorammed by Oct4-Sox2-Klf4-c-Myc defined factors. Fibroblasts and iPS cells were collacted for the study.

extract_protocol:
iPS cells were treated with formaldehyde to fix the lncRNA-chromatin structure. RNAs were reverse transcribed in situ using lncRNA-specific complementary primers or random oligo primers containing biotin-dCTP. The lncRNA-interacting chromatin complex was pulled down with streptavidin beads and the target gene DNAs were eluted for library sequencing.
RAT-DNA libraries were prepared using Illumina's Kit (Part# 0801-0303).

value: Induced pluripotent stem cells

tag: project

value: Reprogramming


title: Peln4 RAT-seq in FIB

description: Peln4 RAT

source_name: Fibroblasts

value: Fibroblasts


title: Palr35 RAT-seq in iPSC

description: Palr35 RAT


title: RAT-seq random control in FIB

description: FIB RAT Ct33


title: RIP1i-3

first: Varshini

last: Vasudevaraja

address: 550 1st Avenue

institute: NYU Langone Health

data_processing:
Basecalls performed using CASAVA version 1.8.4
Sequenced reads were checked for contaminations using fastqscreen v0.5.2 and were mapped to mm10 referece genome using STAR aligner v2.5.3a d with default parameters.
Raw read counts were obtained using featureCounts from subread package v1.4.6-p3
Normalization and differential gene exrpression analysis was performed using DESeq2 v1.14.0
Heatmaps and other statistics was performed using R3.2
Genome_build: mm10
Supplementary_files_format_and_content: csv files include raw read counts table for genomic features and Transcript FPKM counts.

source_name: Bone marrow

growth_protocol: Bone marrow derived macrophages (BMDMs) were isolated and plated with cRPMI and GM-CSF in a standard cell incubator

extract_protocol:
Bone marrow derived macrophages were collected and flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO or RIP1i were added to day 7 BMDM cultures overnight

value: Bone marrow

tag: strain

value: Bone marrow derived macrophage


title: RIP1i-2

tag: cell type


title: Osclr8 RAT-seq in iPSC

description:
Osclr8 lncRNA-binding chromatin DNA target sequence identified by RAT-Seq
PSC RAT Osclr8


title: PSC RNA-Seq

data_processing:
Raw data were filtered with Seqtk
Clean reads were mapped by mouse genome mm10 with STAR software
Cuffdiff was used to calculate the differentially expressed RNAs when the fold-change was > 2 and p < 0.05 with an unpaired two-sided t-test
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: iPS cells (BC170039)

growth_protocol: Fibroblasts were reprogrammed by Oct4-Sox2-Klf4-c-Myc defined factors.  Induced pluripotent stem cells (iPSCs) were isolated and expanded for characterization of pluripotency. Fibroblasts (FIB or FBC) and induced pluripotent stem cells (iPSC) were collected at different stages of reprogramming and used for RNA-seq.

extract_protocol:
RNA was extracted by TRIZOL Reagent (15596-018, Invitrogen, CA)
Ribosome RNA was removed by TruSeq Stranded Total RNA LT -(Ribo-Zero TM Gold)-Set A/B (#RS-122-2301/2302, Illumina, CA). The first-strand cDNA was synthesized using random hexamer-primed reverse transcription (#18064014, SupperScript II reverse Transcriptase, Invitrogen, CA) and was followed by a second-strand cDNA synthesis (#Q32850, Qubit dsDNA HS Assay Kit, Invitrogen, CA).  The synthesized cDNA fragments were 3′ adenylated and ligated with adaptors for PCR amplification for library construction. The library quality was checked using Agilent2100, producing average 370-380 bp fragments including adapters. The libraries were clustered on Illumina cBot Instrument and pair-sequenced.

value: iPSCs at 20 passages


title: RIP1i-1


title: DMSO-3

value: DMSO


title: DMSO-2


title: DMSO-1


title: GC_Bcells_KO-D83V_303

first: Riccardo

last: Dalla-Favera

address: 1130 St Nicholas Avenue

institute: Columbia University

description: Mouse genotype is Mef2bD83Vstop/Fl; Cg1cre/+. Mice are littermates obtained by crossing Mef2bFl/+; Cg1cre/+ with Mef2bD83Vstop/+; Cg1+/+ mice.

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the mouse genome (UCSC mm10) using hisat2 with the following options: --threads 4 --add-chrname --ignore-quals -q -x mm10 -k 5. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v0.1.19 using the rmdup option.
Reads were mapped to exons to produce count tables which were converted to transcript per million (TPM) values.
Genome_build: mm10
Supplementary_files_format_and_content: TPM tables containing the normalized transcripts per million mapped reads (TPM) counts for genes.

source_name: Germinal center B cells

growth_protocol: Mice were immunized by intraperitoneal injection with sheep red blood cells. Analysis was performed 12 days after immunization.

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA XS kit (Machery Nagel), according to the manufacturer's instructions.
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina).

treatment_protocol: Germinal center B cells (B220+/PNA+/CD95+)  were isolated by cytofluorimetric sorting.

value: Spleen

tag: genotype/variation

value: Mef2bD83Vstop/Fl; Cg1cre/+


title: GC_Bcells_KO-D83V_335

tag: tissue


title: SeV-5T in RNaseIII-/-  replicate 3

description:
SeV_alignments.xlsx
CO79-SeV5T-R3-Rep3_S10


title: GC_Bcells_KO-D83V_313


title: GC_Bcells_KO-D83V_332


title: FIB RNA-seq

source_name: Fibroblasts (BC160340)

value: Fetal skin fibroblasts (E18 embryo)


title: GC_Bcells_HET_341

description: Mouse genotype is Mef2bFl/+; Cg1cre/+. Mice are littermates obtained by crossing Mef2bFl/+; Cg1cre/+ with Mef2bD83Vstop/+; Cg1+/+ mice.

value: Mef2bFl/+; Cg1cre/+


title: D737H


title: GC_Bcells_HET_317


title: GC_Bcells_D83V_312

description: Mouse genotype is Mef2bD83Vstop/+; Cg1cre/+. Mice are littermates obtained by crossing Mef2bFl/+; Cg1cre/+ with Mef2bD83Vstop/+; Cg1+/+ mice.

value: Mef2bD83Vstop/+; Cg1cre/+


title: GC_Bcells_D83V_327


title: GC_Bcells_D83V_328


title: GC_Bcells_WT_333

description: Mouse genotype is Mef2b+/+; Cg1cre/+. Mice are littermates obtained by crossing Mef2bFl/+; Cg1cre/+ with Mef2bD83Vstop/+; Cg1+/+ mice.

value: Mef2b+/+; Cg1cre/+


title: GC_Bcells_WT_326


title: GC_Bcells_HET_318


title: GC_Bcells_WT_304


title: GC_Bcells_KO_109

description: Mouse genotype is Mef2bFl/Fl; Cg1cre/+. Mice are littermates obtained by crossing Mef2bFl/+; Cg1cre/+ with Mef2bFl/+; Cg1+/+ mice.

value: Mef2bFl/Fl; Cg1cre/+


title: GC_Bcells_KO_98


title: GC_Bcells_KO_99


title: GC_Bcells_KO_103


title: GC_Bcells_HET_101

description: Mouse genotype is Mef2bFl/+; Cg1cre/+. Mice are littermates obtained by crossing Mef2bFl/+; Cg1cre/+ with Mef2bFl/+; Cg1+/+ mice.


title: GC_Bcells_D83V_319


title: GC_Bcells_HET_316


title: GC_Bcells_HET_87


title: GC_Bcells_HET_100


title: GC_Bcells_WT_334


title: GC_Bcells_WT_140

description: Mouse genotype is Mef2b+/+; Cg1cre/+. Mice are littermates obtained by crossing Mef2bFl/+; Cg1cre/+ with Mef2bFl/+; Cg1+/+ mice.


title: GC_Bcells_WT_87


title: P9-3_S9

city: Helsinki

first: Virpi

last: Talman

address: P.O. Box 56 (Viikinkaari 5E)

department: Faculty of Pharmacy

country: Finland

institute: University of Helsinki

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic.
Trimmed reads were mapped to GRCm38.p5 whole genome using STAR aligner (2.5.0c) with parameters  --runThreadN 20 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterType BySJout --outFilterMismatchNmax 999 --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --quantMode GeneCounts --twopassMode Basic
Counts per gene were calculated using featureCounts software. Paramters used: -s 2 -T 20 -t exon -g gene_id . Annotation file: gencode.vM12.primary_assembly.annotation.gtf
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric mean, estimation of samples-wise factors to correct for library size variability (for example), estimation of dispersion (i.e. variance, scatter) of gene-wise values between conditions, negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance) results to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Genome_build: GRCm38.p5 from GENCODE Mus musculus Release M12
Supplementary_files_format_and_content: featureCount reads per gene have been collected into single tab-delimited text file, RNAseq_raw_counts.txt.  This data matrix has NOT been normalized or filtered in any way.

source_name: Ventricular tissue

growth_protocol: The unweaned mouse pups were grown in standard conditions.

extract_protocol:
RNA from tissue samples is extracted using Precellys soft-tissue beads and TriZol. First, TriZol is pipetted on the frozen tissue sample. The tissue is transferred in TriZol to Precellys soft-tissue bead tube and homogenized in Precellys 24 Lysis & Homogenization (Bertil Technologies) machine. Chloroform is added to the homogenized sample and after the upper aqueous phase and lower organic phase have separated, the aqueous phase containing RNA is collected. The RNA is then precipitated using isopropanol and washed using 75 % ethanol. The formed RNA pellet is resuspended in RNase free water after which the RNA is purified using RNeasy® Mini Kit (Qiagen).
SureSelect Strand-Specific RNA Library Prep Kit is used for RNA-sequencing library preparation for next generation sequencing. Before the cDNA synthesis the total RNA is treated with Ribo-Zero treatment that removes the ribosomal RNA from the total RNA (1µg). The ribosomal depleted RNA is purified with RNeasy mini Elute columns (Qiagen) and fragmented to generate inserts around 300bp. The first-strand cDNA is synthesized and purified after which the second strand cDNA is synthesized and end repaired in one reaction. The created double-stranded cDNA is purified with AMPure XP beads. The double-stranded cDNA’s 3’end is adenylated and adaptors are ligated. After AMPure XP beads purification adaptor-ligated cDNA library is amplified and purified with AMPure XP beads

treatment_protocol: Mice were decapitated, hearts were excised and rinsed in PBS, whereafter ventricular tissue samples were snap-frozen in liquid nitrogen.

tag: postnatal age (days)


title: P23-3_S12


title: P23-2_S11


title: P9-2_S8


title: P4-3_S6


title: P4-1_S4


title: P1-3_S3


title: P1-1_S1


title: P1-2_S2


title: CTRL Drop-seq

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

description: Raw data not provided for this record

data_processing:
Bcl2fastq ver 2.0 was used for the base calling
Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation (Macosko et al; 2015), the reads were demultiplexed for the cell barcode and UMI. The genes mapped to mm9 whole genome using STAR genome aligner - with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts

source_name: microglia isolated from saline control mice

extract_protocol: Single cell RNA seq using Dropseq - 3' bead based enrichment technique, using SMART synthesis (Macosko et al; 2015)

value: microglia isolated from control mice

value: CTRL


title: LPS Drop-seq

description: Raw data not provided for this record

source_name: microglia isolated from LPS-injected mice

value: LPS


title: GC_Bcells_WT_146


title: P23-1_S10


title: P9-1_S7


title: P4-2_S5


title: Healthy donor2_xenograft_Saline_Control_Recipient mouse 2

city: Hamilton

first: Mickie

last: Bhatia

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

scan_protocol: GeneChips were scanned using  Affymetrix® Scanner 3000 7G.

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm and batch corrected to account for technical variation of isolation of human cells from patients versus xenografts using Partek Genomics Suite 6.6 software.

source_name: Xenografted human CB

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

treatment_protocol: Xenografted animals were treated with subcutaneous injections of AraC (50 mg/kg/day) or saline control for 5 consecutive days

value: Purified xenografted human cells

value: Xenograft purified cells

tag: leukemic engraftment capacity

value: not specified


title: Healthy donor1_xenograft_Saline_Control

source_name: Xenografted human MPB

label_protocol: In accordance with manufacturer's protocols


title: Healthy donor2_xenograft_Saline_Control_Recipient mouse 1


title: AML7 xenograft_Saline_Control_Recipient mouse 2

source_name: Xenografted human AML

value: Purified xenografted human leukemic cells


title: Healthy donor2_xenograft_AraC_Post induction_Recipient mouse 2


title: AML5 xenograft_Saline_Control


title: Healthy donor2_xenograft_AraC_Post induction_Recipient mouse 1


title: AML2 xenograft_AraC_Post induction


title: AML7 xenograft_AraC_Post induction_Recipient mouse 1


title: AML7 xenograft_AraC_Post induction_Recipient mouse 2


title: AML5 xenograft_AraC_Post induction


title: AML7 xenograft_Saline_Control_Recipient mouse 1


title: AML3_Blast Diagnosis

source_name: human AML

value: Human leukemic blast cells

value: PB

value: Engrafter


title: AML2 xenograft_Saline_Control


title: AML15_Blast_Post induction


title: AML11_Blast_Post induction

value: BM


title: AML17_Blast_Diagnosis


title: AML16_Blast_Post induction


title: AML17_Blast_Post induction


title: AML7_Blast_Diagnosis


title: AML11_Blast_Diagnosis


title: Healthy donor1_ xenograft_AraC_Post induction


title: AML16_Blast_Diagnosis


title: AML22_Blast_Relapse


title: AML23_Blast_Diagnosis


title: AML24_Blast_Relapse


title: AML24_Blast_Diagnosis


title: AML23_Blast_Relapse


title: MB370_rep2

city: Bethesda

first: Fred

middle: P.

last: Davis

address: 9000 Rockville Pike

department: NIAMS

institute: NIH

data_processing:
We trimmed RNA-seq reads (5nt from the 5’ end of the forward read, using seqtk option “trim -b 5”; https://github.com/lh3/seqtk) to remove non-transcript sequences introduced by the NuGen Ovation kit and then pseudo-aligned these to the Drosophila transcriptome (ENSEMBL release 91, BDGP6) using kallisto (Bray et al., 2016) to estimate transcript abundances. We also included sequences for the synthetic ERCC spike-in species and TAPIN reporter in the transcriptome index.
After pseudo-alignment, we removed ERCC, TAPIN reporter, and ribosomal RNA entries and renormalized the transcript abundance matrix to units of transcripts per million (TPM).
Genome_build: dm6. ENSEMBL BDGP.r91
Supplementary_files_format_and_content: abundance measurements

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Kenyon cell subtype alphap.betap.ap_m

growth_protocol: Split-GAL4 driver lines were used to express the INTACT reporter (UNC84-2XGFP) in defined cell populations

extract_protocol:
Fly heads were first isolated with a customized sieve. 400 frozen heads were added to 6 mL of 20 mM sodium acetate pH 8.5, 2.5 mM MgCl2, 250 mM sucrose, 0.5% NP-40, 0.6 mM spermidine, 0.2 mM spermine, 1 mM DTT, 1× complete protease inhibitor, 0.5 mg/mL torula RNA, 0.6 mg/mL carboxyl coated Dynabeads and 1.6 mg anti-GFP antibody. Homogenization was carried out on ice by 50 tractions in a Dounce homogenizer using the tight pestle followed by filtration over either a 10 or 20 μm cup filter (Partec: 0400422314, 040042315). Released chromatin and broken nuclei were adsorbed to carboxyl coated magnetic beads for 30 minutes at 4°C with constant rotation. Unbound antibody was removed by incubating the sample on ice for 20 minutes with 100 mL of washed UNOsphere SUPra resin (Bio-Rad: 1560218). After the resin was removed on a 10 μm cup filter and the carboxyl beads on a magnet stand, the nuclei-containing supernatant was mixed with an equal volume of 500 mM sodium acetate pH 8.5, 250 mM sucrose, 6 mM EGTA, 6 mM EDTA, 0.6 mM spermidine, 0.2 mM spermidine, 1 mM DTT, 1× complete protease inhibitor, 0.25 mg/mL torula RNA and 30 mL Protein A Dynabeads (ThermoFisher: 10002D). A 2-hour incubation on ice with occasional agitation was used to recover tagged nuclei. Bead-bound nuclei were then recovered on a magnet stand and washed twice with 250 mM sodium acetate pH 8.5, 250 mM sucrose and 0.1% NP-40. Nuclei were then released at 37°C for 1 hour by incubation in 50 μL of 10 mM Tris pH 7.5, 2.5 mM MgCl2, 0.5 mM CaCl2, 250 mM sucrose, 0.1% NP-40, 1 mg/mL torula RNA, 40 units RNAsin (Promega: N2515), 2 units DNAseI (NEB: M0303L), 320 units IdeZ protease (NEB: P0770S). The sample was diluted to 100 μL with 10 mM Tris pH 7.5, 2.5 mM MgCl2, 0.5 mM CaCl2, 250 mM sucrose and 0.1% NP-40, EGTA was added to 1 mM and the suspension was rapidly triturated 100 times. After returning the sample to a magnet stand, 90 μL of buffer containing released nuclei was removed and added to 1.5 μL of Protein G Dynabeads that were previously resuspended in 10 μL of 10 mM Tris pH 7.5, 2.5 mM MgCl2, 0.5 mM CaCl2, 250 mM sucrose and 0.1% NP-40. The second binding reaction was run for 1 – 3 hours on ice with occasional agitation, followed by 2× 250 μL washes in 10 mM Tris pH 7.5, 2.5 mM MgCl2, 0.5 mM CaCl2, 250 mM sucrose and 0.1% NP-40. Prior to the last wash a 5 μL aliquot was removed for quantitation and the remainder of the sample was solubilized in Arcturus Picopure RNA extraction buffer.
Nuclear RNA was DNAseI treated and purified using the Arcturus PicoPure system exactly as instructed by the supplier. Purified RNA was mixed with a 1:100,000 dilution of ERCC standard RNA (ThermoFisher: 4456740) and amplified using the Nugen Ovation v2 system (Nugen: 7102-32). cDNA was then blunted, ligated to barcoded linkers (Nugen: 0319-32, 0320-32) and sequenced in paired-end mode on an Illumina HiSeq2500 to 125 nt read lengths.

tag: genetic driver

value: Kenyon cell subtype alphap.betap.ap_m


title: MB594_rep1

source_name: Kenyon cell subtype alpha.beta.c

value: Kenyon cell subtype alpha.beta.c


title: MB370_rep1


title: MB185_rep2

source_name: Kenyon cell subtype alpha.beta.s

value: Kenyon cell subtype alpha.beta.s


title: MB185_rep1


title: MB418_rep1

source_name: Kenyon cell subtype alphap.betap.m

value: Kenyon cell subtype alphap.betap.m


title: MB131_rep2

source_name: Kenyon cell subtype gamma.m_d

value: Kenyon cell subtype gamma.m_d


title: MB371_rep2

source_name: Kenyon cell subtype alpha.beta.p

value: Kenyon cell subtype alpha.beta.p


title: MB607_rep1

source_name: Kenyon cell subtype gamma.d

value: Kenyon cell subtype gamma.d


title: MB371_rep1


title: MB607_rep2


title: AML21_Blast_Relapse

value: Non-engrafter


title: AML15_Blast_Diagnosis


title: Lung-ILC2

city: San Francisco

first: Roberto

last: Ricardo-Gonzalez

address: 513 Parnassus Ave, HSE-1001

institute: University of California San Francisco

data_processing:
10x data for scRNA samples are run through cellranger software to produce the fastqfiles.
The fastq files are processed throgh the cellranger count to get differential expression counts.
Genome_build: The data is aligned to mm10 genome
Supplementary_files_format_and_content: The processed data files are cellranger count matrix files.

source_name: Lung ILC2

extract_protocol: We use the ChromiumTM Single Cell 3 Reagent Kits v2 per the manufacturer instructions.

treatment_protocol: Il5(Red5), Arg1(Yarg), and Il13(Smart13) reporter alleles on wild-type C57BL/6 background were used to prepare single cell suspensions from bone marrow (BM), lung, adipose tissue (fat), and small intestinal lamina propria (gut) as previously described (von Moltke J et al, Nature 2016; Van Dyken SJ et al, Immunity 2014; Molofsky AB et al, J. Exp Med 2013). For skin single cell suspensions, pooled ear/back or back tissue was minced in RPMI-1640 with 10% FBS, then transferred to C tubes (Miltenyi Biotec), containing 5ml of RPMI-1640 supplemented with Collagenase XI (2mg/ml; Sigma C9407), Hyaluronidase (0.5mg/ml; Sigma H3506), and DNAse I (0.1mg/ml; Sigma 10104159001).  Samples were shaken at 200-250 rpm for 90min at 37¡ C, then dispersed using an automated tissue dissociator (GentleMACS; Miltenyi Biotec) running program C.  Single-cell suspensions were passed through a 70um filter and washed twice with RPMI containing 10% FBS. Cells were sorted as Lin-CD45+Red5+ for Lung, Gut, Skin and Fat. For BM, ILC2s were sorted as Lin-CD45+Yarg+.

value: Lung


title: Skin-ILC2

source_name: Skin ILC2

value: Skin


title: BM-ILC2

source_name: Bone marrow ILC2

value: Bone marrow


title: AML21_Blast_Diagnosis


title: MB418_rep2


title: MB131_rep1


title: Fat-ILC2

source_name: Fat ILC2

value: Visceral adipose tissue


title: AML22_Blast_Diagnosis

value: not specified


title: Gut-ILC2

source_name: Gut ILC2

value: Small intestine lamina propia


title: MB594_rep2


title: Sk_I_KO5

data_processing:
Sequence alignment and splice junction estimation was performed using STAR_2.4.2a (Dobin et al., 2013)
Mappings were restricted to those that were uniquely assigned to the mouse transcriptome, as provided by Ensembl (Flicek, et al., 2014) and aggregated on a per-gene basis
Variance and differential expression assessed using DESeq2 (Anders and Huber, 2010)
No filtering was applied to the data set.
Genome_build: Mus musculus Ensembl GRCm38.78
Supplementary_files_format_and_content: gene-level normalized counts

source_name: Skin TKO ILC2

extract_protocol:
Total RNA was isolated from sorted tissue ILC2s using the RNeasy Plus Micro Kit (Qiagen) with on-column DNAase treatment.
Nugen Ovation

tag: gender

value: male

tag: genotype

value: TKO


title: Sk_I_KO4


title: Sk_I_KO2


title: Sk_I_WT6

source_name: Skin WT ILC2

value: WT


title: Sk_I_KO1


title: Sk_I_WT5


title: Sk_I_KO3


title: L_I_KO4

source_name: Lung TKO ILC2


title: Sk_I_WT2


title: L_I_KO1


title: L_I_WT4

source_name: Lung WT ILC2


title: Sk_I_WT3


title: L_I_WT1


title: G_I_WT5

source_name: Small intestine WT ILC2


title: G_I_WT6


title: G_I_KO5

source_name: Small intestine TKO ILC2


title: G_I_KO2


title: G_I_KO1


title: L_I_KO2


title: L_I_WT5


title: Sk_I_WT1


title: Sk_I_WT4


title: G_I_WT4


title: L_I_WT2


title: L_I_KO5


title: F_I_KO4

source_name: Fat TKO ILC2


title: F_I_KO2


title: F_I_KO3


title: L_I_WT3


title: G_I_WT3


title: G_I_WT1


title: G_I_WT2


title: F_I_KO1


title: F_I_WTB2

source_name: Fat WT ILC2


title: F_I_WTB1


title: F_I_WTA4


title: F_I_WTA1


title: BM_I_KO3

source_name: Bone marrow TKO ILC2


title: Vastus_lateralis_muscle_male_9_trained_pre

city: São Paulo

first: Carlos

last: Ugrinowitsch

state: SP

address: Av. Prof. Mello Moraes, 65. Cidade Universitária, Butantã.

department: Departamento de Esporte

country: Brazil

institute: Escola de Educação Física e Esporte - USP

description: Sample name: IND_9_T_3

hyb_protocol: Direct hybridization assay for whole genome expression (Human HT-12 v4 Expression BeadChip, Illumina, CA, USA).

scan_protocol: Microarray scanning was done using iScan array scanner following standard Illumina protocol.

data_processing: Detection p-values were calculated with function detectionPValues() from limma 3.32.10. Function neqc() from limma was used to perform normexp background correction using negative control probes, and quantile normalization using negative and positive control probes. After normalization, intensities were log2 transformed and control probes were removed.

source_name: Vastus lateralis muscle

label_protocol: The amount of (normalized) RNA was determined by RiboGreen quantitation (Quant-iT RiboGreen RNA Assay Kit, Thermo Fisher Scientific, Rockville, MD, USA) before input into the Ambion Illumina Total Prep Kit (Thermo Fisher Scientific, Rockville , MD, USA) for amplification, cRNA synthesis and biotinylation. The cRNA generated was quantified and normalized by the RiboGreen fluorescence method.

extract_protocol: Tissues were homogenized with 1mL TRIzol (Life Technologies, Burlington, ON, Canada) using Lysing Matrix D tubes (MP Biomedicals, Solon, OH, USA), with FastPrep-24 Tissue and Cell Homogenizer (MP Biomedicals) during 40s at 6m/s. 200μL of chloroform (Sigma-Aldrich) was added, the tubes vigorously agitated for 15s and rested for 5min. Samples were centrifuged at 12000 g, 4ºC for 10min and the aqueous phase containing RNA was collected and transferred to a RNeasy minispin column. The RNA was purified according to the Total RNA Kit 1 (Omega Bio-Tek, Norcross, GA, USA) manufacturer instructions.

value: Vastus lateralis muscle

tag: Sex

value: trained

value: pre


title: F_I_WTA3


title: F_I_WTA2


title: BM_I_KO2


title: Vastus_lateralis_muscle_male_10_trained_pre

description: Sample name: IND_10_T_3


title: Vastus_lateralis_muscle_male_9_untrained_pos

description: Sample name: IND_9_T_2

value: untrained

value: pos


title: BM_I_KO1


title: Vastus_lateralis_muscle_male_7_trained_pos

description: Sample name: IND_7_T_4


title: Vastus_lateralis_muscle_male_10_untrained_pre

description: Sample name: IND_10_T_1


title: Vastus_lateralis_muscle_male_8_untrained_pre

description: Sample name: IND_8_T_1


title: Vastus_lateralis_muscle_male_9_trained_pos

description: Sample name: IND_9_T_4


title: Vastus_lateralis_muscle_male_8_trained_pre

description: Sample name: IND_8_T_3


title: Vastus_lateralis_muscle_male_9_untrained_pre

description: Sample name: IND_9_T_1


title: Vastus_lateralis_muscle_male_10_untrained_pos

description: Sample name: IND_10_T_2


title: Vastus_lateralis_muscle_male_10_trained_pos

description: Sample name: IND_10_T_4


title: Vastus_lateralis_muscle_male_8_trained_pos

description: Sample name: IND_8_T_4


title: Vastus_lateralis_muscle_male_8_untrained_pos

description: Sample name: IND_8_T_2


title: Vastus_lateralis_muscle_male_7_trained_pre

description: Sample name: IND_7_T_3


title: Vastus_lateralis_muscle_male_6_trained_pos

description: Sample name: IND_6_T_4


title: Vastus_lateralis_muscle_male_6_untrained_pos

description: Sample name: IND_6_T_2


title: Vastus_lateralis_muscle_male_6_trained_pre

description: Sample name: IND_6_T_3


title: Vastus_lateralis_muscle_male_7_untrained_pos

description: Sample name: IND_7_T_2


title: Vastus_lateralis_muscle_male_7_untrained_pre

description: Sample name: IND_7_T_1


title: BM_I_WT3

source_name: Bone marrow WT ILC2


title: BM_I_WT1


title: BM_I_WT2


title: JJ_TG_141055

city: Salamanca

first: Norma C.

last: Gutiérrez

state: Salamanca

address: Campus Miguel de Unamuno

department: Hematologia

institute: Centro de Investigación del Cáncer de Salamanca

data_processing:
Illumina 3' adaptors were trimmed using cutadapt version 1.4
FASTQ files were aligned to the Homo sapiens genome hg19 using Tophat version 2.0.11
Gene counts were obtained using the HTSeq algorithm version 0.6.1p1 in the intersection-strict mode.
Gene count normalization was carried out using DESeq2 version 1.12.4
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample. Supplementary files: tab-delimited matrix tables which include normalized gene count values for each cell line

source_name: JJN3 cell line

growth_protocol: All cell lines were cultured in RPMI 1640 medium supplemented with 10% (JJN3) or 20% KMS12M) fetal bovine serum and antibiotics (Gibco). Cells were routinely checked for the presence of mycoplasma with MycoAlert  kit  (Lonza  GmBH)  and  only  mycoplasma-free  cells were used in the experiments.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini kit (Qiagen). The RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries were constructed following a TrueSeq Strand-Specific RNA Sequencing Library protocol (Illumina).

treatment_protocol: KMS12-BM and JJN3 cells untreated or treated with amiloride or TG003 (0.1 mM, 0.4mM and 0.4 mM, respectively) for 24 h was isolated and prepared for RNA-seq

tag: disease

value: plasma cell leukemia

tag: treated with


title: BM_TG_141064

source_name: KMS12-BM cell line

value: multiple myeloma


title: BM_TG_141058


title: JJ_TG_141049


title: JJ_TG_141061


title: Vastus_lateralis_muscle_male_5_untrained_pos

description: Sample name: IND_5_T_2


title: Vastus_lateralis_muscle_male_5_untrained_pre

description: Sample name: IND_5_T_1


title: Vastus_lateralis_muscle_male_5_trained_pre

description: Sample name: IND_5_T_3


title: Vastus_lateralis_muscle_male_4_trained_pre

description: Sample name: IND_4_T_3


title: Vastus_lateralis_muscle_male_5_trained_pos

description: Sample name: IND_5_T_4


title: Vastus_lateralis_muscle_male_2_untrained_pos

description: Sample name: IND_2_T_2


title: Vastus_lateralis_muscle_male_2_trained_pos

description: Sample name: IND_2_T_4


title: Vastus_lateralis_muscle_male_2_trained_pre

description: Sample name: IND_2_T_3


title: Vastus_lateralis_muscle_male_4_untrained_pre

description: Sample name: IND_4_T_1


title: Vastus_lateralis_muscle_male_1_untrained_pre

description: Sample name: IND_1_T_1


title: Vastus_lateralis_muscle_male_1_untrained_pos

description: Sample name: IND_1_T_2


title: Vastus_lateralis_muscle_male_3_trained_pre

description: Sample name: IND_3_T_3


title: Vastus_lateralis_muscle_male_3_untrained_pos

description: Sample name: IND_3_T_2


title: Vastus_lateralis_muscle_male_1_trained_pre

description: Sample name: IND_1_T_3


title: Vastus_lateralis_muscle_male_3_untrained_pre

description: Sample name: IND_3_T_1


title: Vastus_lateralis_muscle_male_6_untrained_pre

description: Sample name: IND_6_T_1


title: Vastus_lateralis_muscle_male_2_untrained_pre

description: Sample name: IND_2_T_1


title: Vastus_lateralis_muscle_male_4_untrained_pos

description: Sample name: IND_4_T_2


title: Vastus_lateralis_muscle_male_3_trained_pos

description: Sample name: IND_3_T_4


title: BM_TG_141052


title: shIFIT1-II 6h_A9132

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

scan_protocol: Standard Illumina scanning protocol with Illumina HiScan-SQ

data_processing: Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that did not have detection p-value < 0.1 in at least 2 arrays were removed from the dataset.  After filtering probes, quantile normalization was applied across all arrays.

source_name: THP-1 cell line

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: THP1 monocytes were propagated in RPMI media with 10% FBS, 10 mM HEPES, and Betamercaptoethanol in 5% CO2 at 37oC.

extract_protocol: RNA was isolated with an RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol and eluted in RNase free TE buffer

treatment_protocol: Wild type THP1 and IFIT1 shRNA cells (3.5x105 per well) were transfected with NT siRNA and IFIT1 siRNA respectively in 24-well plates, and differentiated with 10 ng/ml PMA for 72 hours. Cells were stimulated with 100 ng/ml LPS for 0h, 1h, 2h, 4h, 6h and 24h

tag: sirna

tag: shRNA

value: LPS

tag: treatment time

tag: experiment

value: II


title: shIFIT1-II 24h_A9133

tag: treatment


title: shIFIT1-II 2h_A9130


title: shIFIT1-II 4h_A9131


title: THP1-II 6h_A9126

value: NT


title: AML14362_PB

source_name: human AML

value: mononuclear cells

value: PB

value: Non-engrafter


title: shIFIT1-I 2h_A9106

value: I


title: AML28_PB


title: THP1-II 24h_A9127


title: shIFIT1-I 1h_A9105


title: THP1-I 2h_A9100


title: THP1-I 6h_A9102


title: THP1-I 0h_A9098


title: THP1-II 0h_A9122