title: Healthy non-stretched hiPS-derived cardiomyocytes, repl. 1


title: AC stretched hiPS-derived cardiomyocytes, repl. 1

status: Public on Dec 22 2018

type: SRA

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

library_source: transcriptomic

data_processing:
Filtering: removal of reads with adaptors; removal of reads in which unknown bases are more than 10%; removal of low quality reads (if the percentage of low quality bases is over 50% in a read).
Alignment: expression levels for all the genes from ENSEMBL 89 were quantified using RSEM 1.3.05 with STAR 2.5.3a (human genome GRCh38.89); we built the genome index for STAR alignment using "rsem-prepare-reference" with options '--star-sjdboverhang' set to 48, according to STAR guidelines. Alignment and quantification were performed with default parameters.
Normalization and filtering: all RNA-seq statistical analyses were performed in R environment (version 3.4.2) with Bioconductor 3.6. We excluded genes not annotated in Ensembl database and genes not having a count per million (CPM) of at least 0.5 in at least one sample. Data were normalized using edgeR Bioconductor package.
Genome_build: human genome GRCh38.89
Supplementary_files_format_and_content: tab-delimited text file including CPM (count per million) for each sample in each column.

molecule: total RNA

organism: Homo sapiens

source_name: Cardiomyocytes

growth_protocol: The cells were let attach and spread on Matrigel Reduced Growth Factor (MRGF)-coated polydimethylsiloxane (PDMS) membranes with patterned microgroves for 5 days before stretching experiments. During the stretching experiments cardiac basal medium was pre-warmed and supplemented with 25 mM HEPES to buffer the solution, given the absence of CO2 within the stretching device environment.

extract_protocol:
RNA was isolated with TRIzol Reagent followed by purification with RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: hiPS cell-derived cardiomyocytes

tag: patient status

value: arrhythmogenic cardiomyopathy (homozygous C-terminal frame-shift mutation in PKP2 gene c.2484C>T)

tag: stimulus

value: 10% uniaxial tensile strain at 1 Hz for 60 minutes


title: AC stretched hiPS-derived cardiomyocytes, repl. 2


title: Healthy non-stretched hiPS-derived cardiomyocytes, repl. 2

value: healthy

value: unstimulated


title: Healthy stretched hiPS-derived cardiomyocytes, repl. 2


title: AC non-stretched hiPS-derived cardiomyocytes, repl. 1


title: Mid-trimester placenta_rep3 (RNA-seq)

city: New Brunswick

first: Bingbing

last: Wang

state: New Jersey

address: 125 Paterson St Room 2143

country: USA

institute: Rutgers RWJMS

data_processing:
Torrent suite software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Output of the Cuffnorm software
Genome_build: hg18
Supplementary_files_format_and_content: Normalized counts in FPKM values.

source_name: Placenta

growth_protocol: Placental cytotrophoblast (CTB) were purified and maintained at 37C and 5% CO2 at least for 48 hr for spontaneous syncytialization prior to further analysis.

extract_protocol:
Total RNAs were extracted from 4 individual placentas at either mid-trimester or term pregnancy with use of Trizol method.
RNA libraries were prepared for sequencing using standard IonTorrent.

treatment_protocol: Not applicable.

tag: tissue

value: placenta

value: Cytotrophoblast

tag: Stage

value: Mid-trimester


title: merged_8

city: Boston

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

data_processing:
The resulted data were demultiplexed using Illumina CASAVA 1.8 and fastq files for each initial sample were generated
Tophat2 alignment of raw paired reads to UCSC human genome reference GRCh38
Cuffdids using the outputs from two previous steps with mm10 annotation
Genome_build: mm10

source_name: human cells

growth_protocol: purification and expansion of neoplastic cells: The cells were isolated from pre-invasive neoplastic lesions of patients with earliest stage of invasive cancer. Cells were expanded in complete RPMI with 10% FBS and 2% penicillin and streptomicin for 10 days.

extract_protocol:
RNA was extracted using Trizol according to the manufacture's instructions.Specifically, cells were lysed in 1 ml of Trizol, kept at RT for 5 minutes, followed by addition of 200 µl of CHCl3, shaked vigorously for 30", spun @5000 rpm for 2 minutes. The upper phase was recovered and an equal volume of i-PrOH was added, mixed, kept for 5 minutes, and precipitated for 15 minutes @10,000 rpm using Pellet-Paint (Novagen).
Library was prepared using Truseq pair-end Illumina kit. Briefly, 10-100 ng of total RNA was reconstituted in water, mixed with Ribosomal removal Buffer containing RNAClean XP beads, and depleted from rRNA. First strand was synthesized using RT, followed by a second strand synthesis, 3' ends were adenylated and ligated to the adaptors, followed by ligateion of the 5' adaptors; the library was purified and measured on DNA-concentration

treatment_protocol: Cells were harvested, centrifuged, rinsed once with medium, and counted. 5 million cells were used for RNA-extraction

tag: developmental stage

value: neoplasia


title: merged_7


title: P125_1-3_1

type: RNA

city: Tianjin

first: Yuanjie

last: Niu

address: Pingjiang Road 23

country: China

institute: Tianjin Institute of Urology

description: Gene expression of LNCaP-AI cells

hyb_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: LNCaP-AI cell line

label_protocol: Samples labeling were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

growth_protocol: The parental androgen dependent human prostate cancer cell line LNCaP were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). The cell line was maintained in RPMI-1640 medium (Gibco, Waltham, MA, USA) supplemented with 10% fetal bovine serum (Gibco), 100 ng/ml streptomycin and 100 U/ml penicillin (Gibco). For androgen deprivation，parental LNCaP cells were maintained in RPMI 1640 medium supplemented with 10% charcoal-stripped fetal bovine serum (BI, Cromwell, CT, USA). The LNCaP-AI line was generated following long-term culture of the parental LNCaP cells under androgen deprived conditions. Cells were incubated at 37 °C with 5% CO2.

extract_protocol: Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

treatment_protocol: The LNCaP cell line was maintained in RPMI-1640 medium (Gibco, Waltham, MA, USA) supplemented with 10% fetal bovine serum (Gibco), 100 ng/ml streptomycin and 100 U/ml penicillin (Gibco). For androgen deprivation，parental LNCaP cells were maintained in RPMI 1640 medium supplemented with 10% charcoal-stripped fetal bovine serum (BI, Cromwell, CT, USA). The LNCaP-AI line was generated following long-term culture of the parental LNCaP cells under androgen deprived conditions.

tag: cell line

value: LNCaP-AI

value: prostate cancer


title: LNCaP_RNA1-3

description: Gene expression of LNCaP cells

source_name: LNCaP cell line

value: LNCaP


title: P125_1-3_2

description: Gene expression of LNCaP-AI cells


title: LNCaP_RNA

description: Gene expression of LNCaP cells


title: LNCaP_RNA2-4

description: Gene expression of LNCaP cells


title: P125_1-3_3

description: Gene expression of LNCaP-AI cells


title: C4-2 cells_shRNA control for EZH2 knockdown

city: Houston

first: Guangyu

address: 6670 Bertner Ave

institute: Houston methodist research institute

description: FPKM.txt

data_processing:
Sequenced reads were mapped to hg19 whole genome using tophat2
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

molecule: polyA RNA

source_name: human prostatic carcinoma cell line

growth_protocol: C4-2 cells were cultured in RPMI-1640 (GenDEPOT) supplemented with 10% FBS (GenDEPOT).

extract_protocol:
Total RNA was isolated from cells to generate cDNA using the RNA MiniPrep kit (Direct-zol, R2052, ZYMO Research).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: C4-2 cells were re-plated in 6-well plates and allowed for adherence in the next 24 hours. The growth medium were then replaced with medium respectively supplemented with vehicle, GSK126, astemizole, and lentivirus constructed with scramble shRNA control, or the two different EZH2 shRNAs.

value: prostate cancer LNCaP-derived C4-2 cells

tag: treatment

value: shRNA control for EZH2 knockdown

tag: passages


title: C4-2 cells_EZH2 shRNA #1

description: FPKM.txt

value: EZH2 shRNA #1


title: C4-2 cells_EZH2 shRNA #2

description: FPKM.txt

value: EZH2 shRNA #2


title: C4-2 cells_astemizole

description: FPKM.txt

value: astemizole


title: C4-2 cells_GSK126

description: FPKM.txt


title: C4-2 cells_vehicle control for GSK126 and astemizole

description: FPKM.txt


title: Adult 1 ITGA6 enriched

city: La Jolla

first: Miles

middle: F

last: Wilkinson

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 4811

department: Reproductive Medicine

institute: University of California

data_processing:
De-multiplexing and FastQ file generation
Cell ranger based mapping and filtering
Seurat R package for QC filtering and normalization
pagoda2 and monocle for clustering and pseudotime trajectory
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix of genes, counts and cell barcodes

source_name: adult

extract_protocol:
Testis tissue was dissociated using two step enzymatic digestion with collagenase-IV and trypsin-EDTA. Single cell suspension was washed and enriched for ITGA6 expressing cells (MACS column) or was direclty used. Cells were diluted for loading on Chromium chip
Chromium Single Cell Kit [v2 chemistry]
10x single cell RNA sequencing

value: Testis

tag: age

value: 37 yr

tag: sample


title: neonatal day 7 unfractionated

source_name: neonatal

value: 7 days


title: Adult 2 ITGA6 enriched

value: 42 yr


title: neonatal day 2 unfractionated

value: 2 days


title: neonatal day 7 ITGA6 enriched


title: neonatal day 2 ITGA6 enriched


title: CTRB

city: New York

first: Genta

last: Ishikawa

state: NY

address: One Gustave L. Levy Place Box 1232

department: Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

description:
bone marrow sample of healthy individual from ALLCELLS®
Gene expression data from control subject

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

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

data_processing: Its concentrations were measured with NanoDrop (Thermo Scientific, Wilmington, DE, USA) and samples were run on the Illumina microarray Human HT-12_v4 Bead Chip gene expression array

label: biotin

source_name: Human bone marrow sample from a healthy subject

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

extract_protocol: RNA was extracted and purified with RNeasy Mini Kit (#79104 QIAGEN GmbH, Germany)

value: bone marrow

value: Healthy human control


title: ID 8

description:
essential thrombocythemia
Gene expression data from subject with essential thrombocythemia

source_name: Human bone marrow sample from a patient with essential thrombocythemia

value: Patient with essential thrombocythemia


title: C1


title: CTRD


title: ID 7-3

description:
essential thrombocythemia, the same patient as ID7 analyzed 1 year prior
Gene expression data from subject (obtained from the same subject for ET 3 (1) and ET 3 (2) but obtained 1 year prior) with essential thrombocythemia


title: D1


title: B1


title: E1


title: A1


title: ID 7-2

description:
essential thrombocythemia, 2nd measurement
Gene expression data from subject (obtained from the same subject and at the same time for ET 3 (1)) with essential thrombocythemia


title: CTRC


title: ID5 & 6

description:
primary myelofibrosis, bone marrows of ID 5 and 6 were mixed for RNA microarray analysis due to their low amount
Gene expression data from subject with primary myelofibrosis

source_name: Human bone marrow sample from a patient with primary myelofibrosis

value: Patient with primary myelofibrosis


title: ID 9


title: ID 7-1

description:
essential thrombocythemia, 1st measurement
Gene expression data from subject with essential thrombocythemia


title: Ago2_Plasma_sample_5_TAATCG

city: Phoenix

first: Kendall

last: Van Keuren-Jensen

state: AZ

address: 445 N. Fifth Street

institute: The Translational Genomics Research Institute

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of TGGAATTCTCGGGTGCCAAGG. Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
RNA-Seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns.
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

source_name: Plasma

extract_protocol:
RNA was isolated using MiRVana Paris (Ambion).
TruSeq Small RNA library prep kit (Illumina) was used.

value: Plasma

tag: condition

value: Healthy Control

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

tag: rna isolation kit

value: MiRVana Paris (Ambion)


title: Ago2_Plasma_sample_3_GACGAC


title: ID 3-2

description:
primary myelofibrosis, 2nd measurement
Gene expression data from subject with primary myelofibrosis


title: ID 3-1

description:
primary myelofibrosis, 1st measurement
Gene expression data from subject with primary myelofibrosis


title: Ago2_Plasma_TCATTC


title: ID 4-2

description:
primary myelofibrosis, 2nd measurement
Gene expression data from subject (obtained from the same subject and at the same time for PMF 1 (1))) with primary myelofibrosis


title: C57-W3,C57BL/6C mESC-folate-deficiency for 6 generations-replicate2-case3

city: taiyuan

first: Li

middle: jian

last: ting

state: shanxi province taiyuan city

institute: Shanxi Medical University

description: gene expression data from C57BL/6C mouse embryonic stem cell with folate deficiency for 6 generations

hyb_protocol: The labeled DNA was dissolved in a hybridization solution (2X GEx Hyb Buffer (HI-RPM), 25% formamide) and hybridized overnight at 45 °C.

scan_protocol: After the end of the hybridization, first wash in a liquid containing 0.2% SDS, 2 × SSC at 42 ° C for 5 min, then at 0.2 × SSC in room temperature to wash for 5 min. The slides are ready for scanning after drying.The chip was scanned with an Agilent G2565CA Microarray Scanner to obtain a hybrid image.

data_processing: Fluorescence signal value extractionThe feature extraction image analysis software is used to analyze the chip image and convert the image signal into a digital signal. Differential gene screeningImport raw data into GeneSpring GX software, normalize signal values using the percentile shift method

organism: Mus musculus

source_name: C57BL/6 mESC-folate-deficiency for 6 generations

label_protocol: Take 5ug cRNA, reverse transcription with CbcScriptII enzyme, Random Prime, reverse transcription product with PCRPurified by NucleoSpinExtract II Kit (MN). cDNA labeled with KLENOW enzymeTake the above reverse transcription product, use the Random Primer as a primer to carry out KLENOW enzyme labeling, and label the product with PCR.The NucleoSpinExtract II Kit (MN) was purified, purified and drained. Cy3-dCTP (GE Healthcare Cat. No.PA 53021).

growth_protocol: the  C57BL/6 mouse embryonic stem cells were cultured in mouse embryonic fibroblasts KM (MEFs),and change medium daily.

extract_protocol: cellular RNA extraction using Trizol  to extract total RNA  in cells,After the cell culture is finished,  use a pipette to remove the medium and add about 3 ml PBS to wash once.After absorbing the PBS, you can add the right amount of Trizol reagent, TrizolThe amount is usually 1 ml of Trizol per 10 cm 2 area; After the addition of Trizol, the cells were repeatedly pipetted with a pipette to allow the cells to fully lyse . JudgeThe criteria for the appropriate amount of Trizol addition can be judged based on the viscosity of the cell lysate. Just dissolved in the cell when it is solved, it can be found that there is a filament, which is the release of the genomic DNA of the cell.After a few times of blowing, the filament will disappear and the viscosity of the liquid will decrease. Total RNA was extracted by standard manipulation according to Trizol reagent.

treatment_protocol: the normal C57BL/6 mouse embryonic stem cells were cultured in normal medium with folate concentration 4 mg/ml  for consecutive generations,the case C57BL/6 mouse embryonic stem cells were cultured in folate-deficiency medium  for consecutive generations,

tag: strain

value: embryo stem cell

value: folate-deficient


title: ID 4-1


title: C57-Y3,C57BL/6C mESC-normal 6 generations-replicate 2-control3

description: gene expression data from C57BL/6C mouse embryonic stem cell with normal medium for 6 generations

source_name: C57BL/6 mESC-normal for 6 generations


title: C57-Y1,C57BL/6C mESC-normal 6 generations-control1


title: C57-W1,C57BL/6C mESC-folate-deficiency for 6 generations-case1


title: 8420_WT

status: Public on Dec 21 2018

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the mm10 genome was performed using the STAR aligner version 2.4.0k using the --outFilterIntronMotifs RemoveNoncanonical parameter
Gene expression was quantified using the HOMER analysis suite and differential gene expression was carried out using the edgeR package v3.6.8. FDR < 0.05 and log2 fold change greater than 0.8
Genome_build: mm10
Supplementary_files_format_and_content: raw counts (text file)
Supplementary_files_format_and_content: fpkm normalized table (text file)

source_name: Pancreatic tumors developed in LifrWT;KrasLSL-G12D/+;Trp53f/f;Rosa26LSL-Luc;Pdx1-Cre mice

growth_protocol: primary cells isolated directly from fresh pancreatic tumor without culture in dish

extract_protocol:
Clontech NucleoSpin® RNA II kit per manufacture protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Whole tumors were dissected from Lifrf/f;KrasLSL-G12D/+;Trp53f/f;Rosa26LSL-Luc;Pdx1-Cre or LifrWT;KrasLSL-G12D/+;Trp53f/f;Rosa26LSL-Luc;Pdx1-Cre mice at 44~49 days of age individually and dissociated into single cell suspension by enzyme digestion, and EpCAM+ pancreatic cancer cells were purified by FACS

value: FVB/NJ

value: pancreas

value: 44~49 days of age

tag: genotype


title: 8603_WT

tag: cell type

value: primary cells isolated directly from fresh pancreatic tumor


title: 8436_WT


title: 8397_KO

source_name: Pancreatic tumors developed in Lifrf/f;KrasLSL-G12D/+;Trp53f/f;Rosa26LSL-Luc;Pdx1-Cre mice


title: 8430_KO


title: 8490_KO


title: C57-W2,C57BL/6C mESC-folate-deficiency for 6 generations-replicate1-case2


title: 8433_KO


title: 8482_WT


title: C57-Y2,C57BL/6C mESC-normal 6 generations-replicate 1-control2


title: ID 2-1


title: KO Treg cells_rep1

city: Minneapolis

first: Hai-Bin

last: Ruan

state: MN

department: Integrative Biology and Physiology

institute: University of Minnesota

description: Tko - Tko1132

data_processing:
Sequencing reads were trimmed using Trimmomatic v0.33 enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Quality control checks on raw sequence data for each sample were performed with FastQC.
Read mapping was performed via bowtie2 (v2.2.4.0) using the UCSC mouse genome (mm10) as reference.
Gene quantification was done via Cuffquant for FPKM values and Feature Counts for raw read counts.
Differential gene expression was determined by EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: A .txt  file containing Edge tests.

source_name: Treg cells

extract_protocol:
Treg cells were isolated from female Foxp3YFP-Cre/wt Ogtfl/fl and Foxp3YFP-Cre/wt Ogtwt/fl mice using CD4 selection beads followed by sorting on YFP expression.
RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN, catalog no. 74034) and subjected to standard library construction and 2x50 paired-end sequencing on a HiSeq 2500 (Illumina) at the University of Minnesota Genomics Center.

value: Lymph nodes

value: Treg cells


title: ID 1-2


title: ID 1-1


title: ID 2-2


title: WT Treg cells_rep3

description: Twt - Twt1162


title: WT Treg cells_rep2

description: Twt - Twt1159


title: KO Treg cells_rep2

description: Tko - Tko1136


title: WT Treg cells_rep1

description: Twt - Twt1142


title: KO Treg cells_rep3

description: Tko - Tko1145


title: Ctrl2

city: Ann Arbor

first: xuyun

last: zhao

state: Michigan

address: 210 washtenaw ave

institute: Life Sciences Institute

data_processing:
The fastq files were performed quality control using FastQC
aligner STAR was used for alignment
HTSeq was used to count reads mapped to each gene feature
DESeq2 was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: excel file including normalized abundance measurements using DESeq2

source_name: liver

extract_protocol:
mouse liver was extracted, immediately frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Library Prep Kit v2 (Cat#RS-122-2001) 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: Ctrl and LKO mice was fed on NASH diet (D09100301, Research Diets) for 24 weeks

value: liver

value: 9 months

value: control


title: LKO1

value: LKO


title: LKO2


title: Ctrl3


title: Ctrl1


title: LKO3


title: Bent cotyledon mRNA-seq (SMARTer; 0.1 ng)

city: Wageningen

first: Michael

middle: D

last: Nodine

state: Gelderland

address: Radix West

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

description: Paired-end 50 base read mRNA-seq data from 0.1 ng total RNA isolated from Col-0 bent cotyledon staged embryos

data_processing:
cutadapt (v1.9.1) -m 18 -O 5 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA
cutadapt (v1.9.1) -m 18 -O 5 -g "A{100}" -G "A{100}"
cutadapt (v1.9.1) -m 18 -O 5 -g "T{100}" -G "T{100}"
kallisto quant (v0.43.1)
Genome_build: TAIR10
Supplementary_files_format_and_content: *kallisto.tsv files are tab-delimited files with transcript isoform names (target_id; column 1), transcript length (length; column 2), effective transcript length (eff_length; column 3), estimated counts (est_counts; column 4) and transcripts per million (tpm; column 5)

organism: Arabidopsis thaliana

source_name: Bent cotyledon staged embryos

growth_protocol: Controlled growth chamber at 20˚C-22˚C with a 16-h light/8-h dark cycle. Plants were four weeks old when tissue was harvested.

extract_protocol:
TRIzol reagent (Thermo Fisher Scientific)
mRNA-seq libraries were generated with the SMARTer Ultra Low Input RNA Kit for Sequencing - v3 from Clontech.

tag: ecotype

value: wild type

value: Bent cotyledon staged embryos

tag: number of embryos collected for total rna isolation

tag: amount of total rna

tag: ngs library preparation method

value: SMARTer Ultra Low Input RNA Kit for Sequencing - v3 (Clontech)


title: Bent cotyledon mRNA-seq (SMARTer; 0.05 ng)

description: Paired-end 50 base read mRNA-seq data from 0.05 ng total RNA isolated from Col-0 bent cotyledon staged embryos

tag: tissue


title: Bent cotyledon mRNA-seq (SMARTer; 1 ng)

description: Paired-end 50 base read mRNA-seq data from 1 ng total RNA isolated from Col-0 bent cotyledon staged embryos

value: 1 ng


title: Bent cotyledon mRNA-seq (SMARTer; 5 ng)

description: Paired-end 50 base read mRNA-seq data from 5 ng total RNA isolated from Col-0 bent cotyledon staged embryos

value: 5 ng


title: Bent cotyledon mRNA-seq (SMARTer; 0.5 ng)

description: Paired-end 50 base read mRNA-seq data from 0.5 ng total RNA isolated from Col-0 bent cotyledon staged embryos


title: BM CD141 high (18)

city: Lund

first: Kristina

last: Lundberg

address: Medicon Village building 406, Scheelevägen 8

department: Immunotechnology

country: Sweden

institute: Lund University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 2 minutes, then 45° for 5 minutes. Centrifuge at max speed for 1 minute and then transfer 200μl on to the array. Hybridize 18 hours at 45° at 60rpm. Fluidics washing using the program FS450_0001.

scan_protocol: Signals were scanned by Affymetrix GeneChip Scanner 3000 7G

data_processing: Microarray signals were normalized using the RMA algorithm in the Affymetrix® Expression Console software (Affymetrix®).

source_name: Bone Marrow

label_protocol: Labeled with the Encore Biotin Module Kit (NuGEN) according to manufacturer’s protocols

growth_protocol: not applicable

extract_protocol: Total RNA isolated from FACS-sorted cells was amplified using the Ovation Pico WTA System V2 (NuGen, San Carlos, CA)

treatment_protocol: not applicable

value: BM

value: DC

tag: cell population


title: BM Slan DC (21)

value: SlanDC


title: BM Slan DC (19)


title: Bent cotyledon mRNA-seq (Ovation; 0.05 ng)

extract_protocol:
TRIzol reagent (Thermo Fisher Scientific)
mRNA-seq libraries were generated using the Ovation PicoSL WTA System V2 kit from Nugen.

value: Ovation PicoSL WTA System V2 (Nugen)


title: PB CD1c (7)

source_name: Peripheral blood

value: PB


title: BM CD1c (27)


title: PB CD141 high (5)


title: BM CD141 high (28)


title: PB CD1c (10)


title: PB Slan DC (6)


title: PB CD141 high (11)


title: BM CD141 high (13)


title: BM Slan DC (26)


title: PB Slan DC (12)


title: PB CD1c (4)


title: PB CD141 high (8)


title: BM CD1c (14)


title: BM CD1c (17)


title: PB Slan DC (3)


title: BM CD1c (24)


title: PB CD1c (1)


title: BM CD141 high (22)


title: PB Slan DC (9)


title: Bent cotyledon mRNA-seq (Ovation; 0.1 ng)


title: Bent cotyledon mRNA-seq (Ovation; 1 ng)


title: PB CD141high (2)


title: Bent cotyledon mRNA-seq (0.1 ng; biorep 3)

description: Paired-end 50 base read mRNA-seq data from 0.1 ng total RNA isolated from third biological replicate of Col-0 bent cotyledon staged embryos

extract_protocol:
TRIzol reagent (Thermo Fisher Scientific)
mRNA-seq libraries were generated according to the Smart-Seq2 protocol (Picelli et al. 2013. Nature Methods).

value: Smart-seq2 (Picelli et al. 2013, Nature Methods)


title: Bent cotyledon mRNA-seq (Ovation; 5 ng)


title: Bent cotyledon mRNA-seq (0.1 ng; biorep 1)

description: Paired-end 50 base read mRNA-seq data from 0.1 ng total RNA isolated from first biological replicate of Col-0 bent cotyledon staged embryos


title: BM Slan DC (15)


title: Bent cotyledon mRNA-seq (0.1 ng; biorep 2)

description: Paired-end 50 base read mRNA-seq data from 0.1 ng total RNA isolated from second biological replicate of Col-0 bent cotyledon staged embryos


title: Bent cotyledon mRNA-seq (0.5 ng; biorep 2)

description: Paired-end 50 base read mRNA-seq data from 0.5 ng total RNA isolated from second biological replicate of Col-0 bent cotyledon staged embryos


title: Bent cotyledon mRNA-seq (0.5 ng; biorep 3)

description: Paired-end 50 base read mRNA-seq data from 0.5 ng total RNA isolated from third biological replicate of Col-0 bent cotyledon staged embryos


title: Bent cotyledon mRNA-seq (0.5 ng; biorep 1)

description: Paired-end 50 base read mRNA-seq data from 0.5 ng total RNA isolated from first biological replicate of Col-0 bent cotyledon staged embryos


title: Bent cotyledon mRNA-seq (1 ng; biorep 1)

description: Paired-end 50 base read mRNA-seq data from 1 ng total RNA isolated from first biological replicate of Col-0 bent cotyledon staged embryos


title: Bent cotyledon mRNA-seq (1 ng; biorep 2)

description: Paired-end 50 base read mRNA-seq data from 1 ng total RNA isolated from second biological replicate of Col-0 bent cotyledon staged embryos


title: Mature green mRNA-seq (biorep 1)

description: Paired-end 50 base read mRNA-seq data from first biological replicate of Col-0 mature green staged embryos

source_name: Mature green staged embryos

value: Mature green staged embryos

value: unknown


title: Mature green mRNA-seq (biorep 2)


title: Mature green mRNA-seq (biorep 3)


title: Bent cotyledon mRNA-seq (5 ng; biorep 3)

description: Paired-end 50 base read mRNA-seq data from 5 ng total RNA isolated from third biological replicate of Col-0 bent cotyledon staged embryos


title: Bent cotyledon mRNA-seq (1 ng; biorep 3)

description: Paired-end 50 base read mRNA-seq data from 1 ng total RNA isolated from third biological replicate of Col-0 bent cotyledon staged embryos


title: Late torpedo mRNA-seq (biorep 3)

description: Paired-end 50 base read mRNA-seq data from third biological replicate of Col-0 late torpedo staged embryos

source_name: Late torpedo staged embryos

value: Late torpedo staged embryos


title: Bent cotyledon mRNA-seq (5 ng; biorep 2)

description: Paired-end 50 base read mRNA-seq data from 5 ng total RNA isolated from second biological replicate of Col-0 bent cotyledon staged embryos


title: Bent cotyledon mRNA-seq (5 ng; biorep 1)

description: Paired-end 50 base read mRNA-seq data from 5 ng total RNA isolated from first biological replicate of Col-0 bent cotyledon staged embryos


title: Late torpedo mRNA-seq (biorep 1)

description: Paired-end 50 base read mRNA-seq data from first biological replicate of Col-0 late torpedo staged embryos


title: Early torpedo mRNA-seq (biorep 2)

description: Paired-end 50 base read mRNA-seq data from second biological replicate of Col-0 early torpedo staged embryos

source_name: Early torpedo staged embryos

value: Early torpedo staged embryos


title: Early torpedo mRNA-seq (biorep 3)

description: Paired-end 50 base read mRNA-seq data from third biological replicate of Col-0 early torpedo staged embryos


title: Late heart mRNA-seq (biorep 2)

description: Paired-end 50 base read mRNA-seq data from second biological replicate of Col-0 late heart staged embryos

source_name: Late heart staged embryos

value: Late heart staged embryos


title: Early torpedo mRNA-seq (biorep 1)

description: Paired-end 50 base read mRNA-seq data from first biological replicate of Col-0 early torpedo staged embryos


title: Late heart mRNA-seq (biorep 3)

description: Paired-end 50 base read mRNA-seq data from third biological replicate of Col-0 late heart staged embryos


title: Late heart mRNA-seq (biorep 1)

description: Paired-end 50 base read mRNA-seq data from first biological replicate of Col-0 late heart staged embryos


title: Early heart mRNA-seq (biorep 3)

description: Paired-end 50 base read mRNA-seq data from third biological replicate of Col-0 early heart staged embryos

source_name: Early heart staged embryos

value: Early heart staged embryos


title: Early heart mRNA-seq (biorep 1)

description: Paired-end 50 base read mRNA-seq data from first biological replicate of Col-0 early heart staged embryos

value: wild type


title: Globular mRNA-seq (biorep 2)

description: Paired-end 50 base read mRNA-seq data from second biological replicate of Col-0 globular staged embryos

source_name: Globular staged embryos

value: Globular staged embryos


title: Early heart mRNA-seq (biorep 2)

description: Paired-end 50 base read mRNA-seq data from second biological replicate of Col-0 early heart staged embryos


title: Globular mRNA-seq (biorep 3)

description: Paired-end 50 base read mRNA-seq data from third biological replicate of Col-0 globular staged embryos


title: Preglobular mRNA-seq (biorep 2)

description: Paired-end 50 base read mRNA-seq data from second biological replicate of Col-0 preglobular (i.e. 8-cell/16-cell) staged embryos

source_name: 8-cell/16-cell staged embryos

value: 8-cell/16-cell staged embryos


title: Preglobular mRNA-seq (biorep 1)

description: Paired-end 50 base read mRNA-seq data from first biological replicate of Col-0 preglobular (i.e. 8-cell/16-cell) staged embryos


title: AMK15_Normal_Treg#9

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) and human reference genome (hg38) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16 for mouse, v27 for human)
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: raw read counts

source_name: Treg

extract_protocol:
max of 1,000 Cells were double-sorted by Moflo into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X25bp reads.

value: CD4+ Treg

value: Colon


title: AMK11_Normal_Treg#6


title: AMK10_Normal_Treg#5


title: Preglobular mRNA-seq (biorep 3)

description: Paired-end 50 base read mRNA-seq data from third biological replicate of Col-0 preglobular (i.e. 8-cell/16-cell) staged embryos


title: AMK11_Tumor_Treg#8

tag: tumor stage

value: IIIB

value: Tumor


title: AMK13_Tumor_Treg#10

value: I


title: AMK8_Normal_Treg#4


title: AMK12_Tumor_Treg#9

value: IIA


title: AMK10_Tumor_Treg#7


title: AMK15_Tumor_Treg#12


title: AMK7_Tumor_Treg#4


title: Late torpedo mRNA-seq (biorep 2)

description: Paired-end 50 base read mRNA-seq data from second biological replicate of Col-0 late torpedo staged embryos


title: AMK6_Normal_Treg#2


title: AMK5_Normal_Treg#1


title: AMK6_Tumor_Treg#3


title: Globular mRNA-seq (biorep 1)

description: Paired-end 50 base read mRNA-seq data from first biological replicate of Col-0 globular staged embryos


title: Bent cotyledon mRNA-seq (Ovation; 0.5 ng)

description: Paired-end 50 base read mRNA-seq data from 0.5 ng total RNA isolated from Col-0 bent cotyledon staged embryos

value: Bent cotyledon staged embryos

value: Ovation PicoSL WTA System V2 (Nugen)


title: AMK5_Tumor_Treg#2


title: AMK14_Tumor_Treg#11


title: RNAseq_Mut

city: Marseille

first: Mathilde

last: Poplineau

address: 27 BOULEVARD LEI ROURE CS 30059

country: France

institute: INSERM

data_processing:
Reads were mapped to mm10 genome using subread-align (v1.5.0) with default parameters
Tag counts were obtained using featureCounts (v1.5.0) with default parameters
Counts were normalized by the size of each library (DESeq2, estimateSizeFactors function)
Genome_build: mm10

source_name: GMP (Granulocyte-Monocyte Progenitors)

growth_protocol: 416b cells (Cd34+) were grown in RPMI 10% FCS 1% P/S; GMPs (Lineage negative, C-kit+, Sca-1-, Cd34+, FcγR+) were purified from the different mouse models

extract_protocol:
For RNA-seq, total RNA were extracted with RNeasy Plus Mini kit (Qiagen). For ATAC-seq and ChIP-seq home-made protocols were used (see Materials and Methods)
ChIP-seq : MicroPlex Library Preparation Kit (Diagenode) ; ATAC-seq : Nextera DNA Library Prep Kit (Illumina) ; RNA-seq in GMPs : TruSeq Stranded Total RNA with Ribo Zero Gold kit (Illumina) ; RNA-seq in 416b : SMART-Seq v3 Ultra Low Input RNA kit for (Clontech)

treatment_protocol: 416b transduced by PLZF-Flag or empty vector

value: bone marrow

value: GMP (Granulocyte-Monocyte Progenitors)

value: Zbtb16 lu/lu


title: AMK9_Tumor_Treg#6


title: H3K27ac_ChIPSeq_old

library_source: genomic

data_processing:
basecalling was performed using Illumina CASAVA
Reads with Phred quality score less than 30 were filtered out
Replicate concurrency was verified by PCA plots, and sample replicates were merged into a single fastq file
Sequences were mapped to a hybride genome (concatenation of mouse and drosophila genome : mm10 and dm6) using Bowtie2 alignment tool (ref: PMID 22388286) with default parameters
Mapped sequences were filtered depending on the organism they belong to
For each mouse datasets, tag counts were normalized by the total number of drosophila mapped tags such that each file correspond to the same amount of drosophila reads.
bigwig files were generated from spiked in bam files using either a customed script or Deeptools 2.0 suite (bamCompare)
Peak callings were performed using MACS2 (in sharp mode for transcription factors; in broad mode for histone marks) using inputs as controls
Genome_build: mm10

molecule: genomic DNA


title: RNAseq_WT


title: Input_old


title: H3K27ac_ChIPSeq_young


title: H3K27me3_ChIPSeq_PLZF

source_name: 416b cell line

tag: cell line

value: bone marrow-derived progenitor cells

value: 416b cell line

tag: culture properties

value: suspension

value: PLZF-Flag


title: H3K27me3_ChIPSeq_Ctrl

value: Empty vector


title: Input-H3K27me3_Ctrl


title: H3K27ac_ChIPSeq_Mut


title: H3K4me1_ChIPSeq_WT

value: wild type


title: Input-histones_WT


title: H3K27me3_ChIPSeq_Mut


title: H3K4me1_ChIPSeq_Mut


title: H3K4me3_ChIPSeq_Mut


title: AMK7_Normal_Treg#3

value: CD4+ Treg


title: Input-histones_Mut


title: AMK3_Tumor_Treg#1


title: Input_young


title: H3K27ac_ChIPSeq_WT


title: H3K4me3_ChIPSeq_WT


title: H3K27me3_ChIPSeq_WT


title: Input-H3K27me3_PLZF


title: CON 18

city: Columbus

middle: Grace

last: Witcher

state: OH

address: 460 Medical Center Dr

department: Neuroscience

institute: Ohio State University

data_processing:
STAR aligner
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2-normalized count matrix

source_name: FAC-sorted microglia

extract_protocol:
Microglia were enriched using Percoll separation, labeled with anti-CD11b and CD45 antibodies, and fluorescence-activated cell sorted. RNA was extracted using the PicoPure RNA Isolation Kit (Applied Biosystems) according to manufacturer’s protocols.
RNAseq libraries were prepared using the Ovation SoLo RNAseq System with AnyDeplete rRNA to remove rRNA and other abundant transcripts according to the manufacturer’s recommendation (Nugen, San Carlos, CA).

tag: stress

value: CON


title: RSD 13

value: RSD


title: CON 17


title: RSD 10


title: RSD 11


title: RSD 7


title: RSD 2


title: CON 5


title: CON 1


title: Mcm4^C3/C3 homozygous female2

city: Ithaca

first: Jennifer

middle: K

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description:
compareFemales_gene_exp.diff: C3F_1
Chaos3MvF_gene_exp.diff: C3F_1
compareFemales_genes.read_group_tracking: C3F_1
Chaos3MvF_genes.read_group_tracking: C3F_1

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.1.1 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--library-type fr-firststrand) was used to quantify transcripts based on the mouse mm10 reference genome+transcriptome (UCSC).
cuffdiff v2.2.1 was used to call differentially expressed genes based on the mouse mm10 reference genome+transcriptome (UCSC).
Genome_build: mouse mm10 reference (UCSC)
Supplementary_files_format_and_content: Tab delimited text files are standard cuffdiff2 output files for gene-level analysis, including counts, FPKM values, and q-values for differential expression testing (corrected for multiple hypothesis testing). The '*gene_exp.diff' files contain average FPKM values for each set of replicates as well as results for statistical testing for differential expression. The '*genes.read_group_tracking' files contain raw mapped read counts and FPKM values for individual samples.

source_name: Placenta

growth_protocol: mice were raised in standard lab housing

extract_protocol:
Placentas from E13.5 embryos were isolated and total RNA extracted using an Ezna total RNA extraction kit (Omega)
Diretional RNA-seq libraries were prepared from 1 µg total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

value: Placenta

tag: age

tag: placental genotype

tag: maternal genotype

value: Mcm4^C3/C3 dam

tag: placental sex

value: female


title: Mcm4^C3/C3 homozygous female1

description:
compareFemales_gene_exp.diff: C3F_0
Chaos3MvF_gene_exp.diff: C3F_0
compareFemales_genes.read_group_tracking: C3F_0
Chaos3MvF_genes.read_group_tracking: C3F_0

tag: strain


title: Mcm4^C3/+ Mcm2^Gt/+ dam female3

description:
compareFemales_gene_exp.diff: C3M2DamF_2
compareFemales_genes.read_group_tracking: C3M2DamF_2

value: Mcm4^C3/C3 Mcm2^Gt/+

value: Mcm4^C3/+ Mcm2^Gt/+ dam


title: Mcm4^C3/+ Mcm2^Gt/+ dam male2

description:
compareMales_gene_exp.diff: C3M2DamM_1
compareMales_genes.read_group_tracking: C3M2DamM_1

value: male


title: Mcm4^C3/+ Mcm2^Gt/+ dam female4

description:
compareFemales_gene_exp.diff: C3M2DamF_3
compareFemales_genes.read_group_tracking: C3M2DamF_3


title: CON 19


title: Mcm4^C3/C3 homozygous male1

description:
compareMales_gene_exp.diff: C3M_0
Chaos3MvF_gene_exp.diff: C3M_0
compareMales_genes.read_group_tracking: C3M_0
Chaos3MvF_genes.read_group_tracking: C3M_0


title: Mcm4^C3/+ Mcm2^Gt/+ dam male1

description:
compareMales_gene_exp.diff: C3M2DamM_0
compareMales_genes.read_group_tracking: C3M2DamM_0


title: Mcm4^C3/C3 dam female1

description:
compareFemales_gene_exp.diff: C3DamF_0
compareFemales_genes.read_group_tracking: C3DamF_0


title: Mcm4^C3/+ Mcm2^Gt/+ dam female1

description:
compareFemales_gene_exp.diff: C3M2DamF_0
compareFemales_genes.read_group_tracking: C3M2DamF_0


title: Mcm4^C3/C3 dam male2

description:
compareMales_gene_exp.diff: C3DamM_1
compareMales_genes.read_group_tracking: C3DamM_1


title: Mcm4^C3/C3 dam male1

description:
compareMales_gene_exp.diff: C3DamM_0
compareMales_genes.read_group_tracking: C3DamM_0


title: Mcm4^C3/C3 dam female2

description:
compareFemales_gene_exp.diff: C3DamF_1
compareFemales_genes.read_group_tracking: C3DamF_1


title: Mcm4^C3/+ Mcm2^Gt/+ dam female2

description:
compareFemales_gene_exp.diff: C3M2DamF_1
compareFemales_genes.read_group_tracking: C3M2DamF_1


title: RSD 12


title: WT dam male1

description:
compareMales_gene_exp.diff: WTM_0
compareMales_genes.read_group_tracking: WTM_0

value: wild-type


title: WT dam female2

description:
compareFemales_gene_exp.diff: WTF_1
compareFemales_genes.read_group_tracking: WTF_1


title: WT dam female1

description:
compareFemales_gene_exp.diff: WTF_0
compareFemales_genes.read_group_tracking: WTF_0


title: AM_CT26_Spleen_CD8#2

value: CD8+ T cells

value: Foxp3-IRES-GFP (C57BL/6)

value: Spleen


title: AM_CT26_Spleen_CD8#3


title: RSD 8


title: CON 4


title: AM_CT26_Spleen_CD8#1


title: AM_CT26_Spleen_Treg#3


title: AM_CT26_Spleen_Tconv#3

source_name: Tconv

value: Tconv


title: AM_CT26_Spleen_Tconv#2


title: AM_CT26_Spleen_Tconv#1


title: WT dam male2

description:
compareMales_gene_exp.diff: WTM_1
compareMales_genes.read_group_tracking: WTM_1


title: AM_CT26_Tumor_Treg#3

value: Tumor


title: AM_CT26_Tumor_CD8#3


title: AM_CT26_Tumor_Tconv#3


title: AM_CT26_Tumor_Tconv#1


title: AM_CT26_Tumor_Treg#1


title: AM_CT26_Tumor_Tconv#2


title: Mcm4^C3/C3 homozygous male2

description:
compareMales_gene_exp.diff: C3M_1
Chaos3MvF_gene_exp.diff: C3M_1
compareMales_genes.read_group_tracking: C3M_1
Chaos3MvF_genes.read_group_tracking: C3M_1


title: AM_CT26_Spleen_Treg#1


title: Tu.Tc.MC38.CLEAN.D21#2


title: WT dam female3

description:
compareFemales_gene_exp.diff: WTF_2
compareFemales_genes.read_group_tracking: WTF_2


title: AM_CT26_Tumor_CD8#1


title: Tu.Tc.B16.CLEAN.D16#3


title: AM_CT26_Tumor_CD8#2


title: AM_CT26_Spleen_Treg#2


title: AM_CT26_Tumor_Treg#2


title: Tu.Tc.MC38.CLEAN.D21#3


title: Tu.Tc.B16.CLEAN.D16#2


title: Tu.Tc.B16.CLEAN.D16#1


title: Tu.CD8.MC38.CLEAN.D21#2


title: Tu.CD8.B16.CLEAN.D16#3


title: Tu.CD8.MC38.CLEAN.D21#1


title: Tu.CD8.B16.CLEAN.D16#2


title: Tu.CD8.B16.CLEAN.D16#1


title: TITR.MC38.CLEAN.D21#3


title: TITR.MC38.CLEAN.D21#2


title: TITR.B16.CLEAN.D16#3


title: Tu.Tc.MC38.CLEAN.D21#1


title: TITR.B16.CLEAN.D16#2


title: Sp.Treg.MC38.CLEAN.D21#2


title: TITR.B16.CLEAN.D16#1


title: Sp.Treg.MC38.CLEAN.D21#3


title: TITR.MC38.CLEAN.D21#1


title: Sp.Treg.MC38.CLEAN.D21#1


title: Sp.Treg.B16.CLEAN.D16#1


title: Sp.Treg.B16.CLEAN.D16#2


title: Sp.Tc.MC38.CLEAN.D21#1


title: Sp.Tc.B16.CLEAN.D16#3


title: Sp.Tc.B16.CLEAN.D16#1


title: Sp.CD8.MC38.CLEAN.D21#2


title: Tu.CD8.MC38.CLEAN.D21#3


title: Sp.CD8.MC38.CLEAN.D21#1


title: Sp.Treg.B16.CLEAN.D16#3


title: Sp.CD8.B16.CLEAN.D16#1


title: Sp.CD8.B16.CLEAN.D16#2


title: NoTumor.Sp.Tc#2


title: Sp.CD8.B16.CLEAN.D16#3


title: NoTumor.Sp.Tc#1


title: NoTumor.Sp.Treg#2


title: Sp.Tc.B16.CLEAN.D16#2


title: NoTumor.Sp.Treg#1


title: NoTumor.Sp.CD8#1


title: Sp.Tc.MC38.CLEAN.D21#2


title: Sp.Tc.MC38.CLEAN.D21#3


title: KPC 3

city: Philadelphia

first: Gregory

middle: L.

last: Beatty

state: PA

address: 3400 Civic Center Blvd, South Pavilion, Rm 8-107

department: Medicine

institute: University of Pennsylvania

data_processing:
Raw files were uploaded into Illumina's BaseSpace hub (basespace.illumina.com) and aligned to Mus musculus mm10 genome using the RNA-Seq Alignment App (version 1.0.0), in which STAR was selected to align sequences with maximum mismatches set to 14 as recommended by Lexogen.
Transcripts were assembled, and differential expression was determined using the BaseSpace Cufflinks Assembly & DE App (Version 2.1.0). Mus musculus mm10 was used as reference genome. For "Strandedness" option, "Not Strand Specific" was selected. "POLYA" option was enabled for all samples.
FPKM tables and CuffDiff results were downloaded and significantly expressed genes (q < 0.05) were used for analyses.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited files contain FPKM values for each sample.

source_name: Liver

extract_protocol:
The liver was dissected from KPC and PC mice, and total RNA was extracted from dissected tissues using TRIzol and a RNeasy mini kit (Qiagen) following manufacturer’s protocols, and RNA quality was assessed using a 2100 Bioanalyzer (Agilent).
Sequencing libraries were prepared using a QuantSeq 3’ mRNA-Seq library prep kit FWD for Illumina (Lexogen) following manufacturer’s protocol and analyzed on a NextSeq 500 sequencing system (Illumina).

tag: genotype

tag: gender

value: Female


title: KPC 2

value: Male


title: KPC 4


title: Control 5

value: LSL-Trp53R127H/+;Pdx-1-Cre (PC)


title: KPC 1


title: Control 3


title: Control 1


title: KPC 5


title: Control 2


title: heart ventricle muscle [TOF-14v]

city: Shanghai

first: Bo

last: Wang

address: 1678 Dongfang Road

institute: Shanghai Children's Medical Center

data_processing:
Raw data were processed through in-house python scripts. In this step. Clean data were obtained by removeing adapter sequences using cutadapt (v1.16), Reads with low quality (e.g. proportion of bases with sQ<=5 greater than 50%; proportion of N greater >10%; 5’adaptor contamination) were also removed.
The reads were mapped onto the human genome (hg38) using STAR (2.5.1a)
sRNA clusters were detected and quantified using SeqCluster pipeline
Genome_build: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/GRCh38.primary_assembly.genome.fa.gz
Supplementary_files_format_and_content: json file including all information of small RNA cluster, sequences, and quantification across samples generated from seqCluster pipeline

source_name: right ventricle from TOF human heart

extract_protocol:
Total RNA was extracted using the miRNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
A total amount of 3 μg total RNA for each sample was used for small RNA library construction. Sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, Beverly, MA, USA.) following manufacturer’s recommendations and index codes were ligated to attribute sequences to each sample.

value: heart, right ventricle

value: 6 month


title: Sp.CD8.MC38.CLEAN.D21#3

city: Boston

tag: cell type


title: Control 4


title: heart ventricle muscle [TOF-7v]


title: heart ventricle muscle [TOF-12v]

value: 4 month


title: heart ventricle muscle [TOF-4v]


title: heart ventricle muscle [TOF-13v]

value: 8 month


title: heart ventricle muscle [TOF-6v]


title: heart ventricle muscle [TOF-9v]

value: female


title: heart ventricle muscle [TOF-2v]


title: heart ventricle muscle [TOF-1v]


title: NoTumor.Sp.CD8#2


title: heart ventricle muscle [TOF-3v]

value: 1 year 2 month


title: Erythroblast_P38α ko_rep2

city: Indianapolis

first: ping

last: hu

address: 420 University Blvd

institute: IUPUI

description: Gene expression in P38α-/-bone marrow erthroblasts during recovery of anemia

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the agilent Gene Expression Hybridization kit (Agilent Technologies).Briefly, 600 ng cy3-labeled gragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Genome Oligo Microarrays 8X60K using Agilent's recommended hybridization chamber and oven.

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

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

source_name: Bone marrow erythroblasts, P38α-/-, anemia, replicate 2

label_protocol: For the linear T7-based amplification step, 10 ng of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent low input quick Amp labeling kit (Agilent Technologies) following the manufacturer's protocol.

extract_protocol: RNA was isolated using standard RNA extraction protocols (Trizol). The RNA were quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies)

treatment_protocol: P38α+/- and P38α-/- mice were subjected to to phenylhydrazine (PHZ) treatment to induce hemolytic anemia. During the recovety, Bone marrow erythroblasts were sorted from those mice.


title: Erythroblast_P38α ko_rep3

source_name: Bone marrow erythroblasts, P38α-/-, anemia, replicate 3


title: Erythroblast_P38α ko_rep1

source_name: Bone marrow erythroblasts, P38α-/-, anemia, replicate 1


title: Erythroblast_P38α hetero_rep3

description: Gene expression in P38α+/-bone marrow erthroblasts during recovery of anemia

source_name: Bone marrow erythroblasts, P38α+/-, anemia, replicate3


title: Erythroblast_P38α hetero_rep1

source_name: Bone marrow erythroblasts, P38α+/-, anemia, replicate 1


title: Erythroblast_P38α hetero_rep2

source_name: Bone marrow erythroblasts, P38α+/-, anemia, replicate 2


title: 11_wt-/mt-

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

description: Gene expression data from mouse germinal center B cells

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were normalized using RMA. Intensity values were log2 transformed

label: Biotin

source_name: murine BL cell line

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).

treatment_protocol: Isogenic murine BL cell line modified by CRISPR/Cas9 genome editing

tag: foxo1 status

value: wt-/mt-

value: Burkitt lymphoma (BL)


title: 5_wt-/mt+

value: wt-/mt+


title: 2_wt+/mt+

value: wt+/mt+


title: 7_wt+/mt-

value: wt+/mt-


title: 12_wt-/mt-


title: X900142_hpc

city: Evanston

first: Peng

last: Jiang

state: IL

address: 2205 Tech Drive, Hogan 2-160

department: Center for Sleep and Circadian Biology

institute: Northwestern University

hyb_protocol: Biotinylated cRNA samples were hybridized onto Affymetix GeneChip® Mouse Genome 430 2.0 Array according to the manufacturer’s guidelines.

scan_protocol: Arrays are scanned using a GeneChip Scanner according to the standard Affymetrix protocol.

data_processing: Affymetrix CEL files were processed using the R affy package. Raw data was normalized using robust multiarray averaging (RMA) with quantile normalization and log2-transformed. To mitigate the effects of high leverage points, outliers were identified on a transcript by transcript basis and set to missing. The outlier identification algorithm was as follows, if an expression value was greater than 2 interquartile ranges from the first or third quartiles, then it was identified as an outlier. If greater than 4% of the data were identified as outliers, only the most extreme outliers would be identified as such, totaling less than or equal to 4%. The influence of potential experimental covariates, such as animal cohorts, was carefully evaluated by computing ANOVA P-values of the covariate across all phenotypes and comparing the distribution of the P-values against theoretical quantiles from a uniform distribution in a q-q plot. For selected significant covariates, data was adjusted by fitting the data in a robust linear model and taking the intercept + residuals as the adjusted values. We also used principal component analysis to capture unknown source of variations in each tissue. For any principal component that is not associated with any genomic loci (LOD < 3), we further adjusted the data by treating those principal components as covariates.

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

growth_protocol: Male (C57BL/6J x 129S1/SvImJ) F2 mice were purchased from The Jackson Laboratory (Bar Harbor, ME) at 4 weeks of age, and were housed under a 12h:12h light/dark cycle at a room temperature of 23±2°C with food and water available ad libitum.

extract_protocol: trizol

treatment_protocol: Mice were phenotyped starting at 7 weeks of age for activies in the elevated plus maze, open field, fear conditioning, tail suspention, and forced swim tests. Behaviroal tests were completed in 2 weeks, and mice were surgically implanted with EEG/EMG electrodes at 10 weeks of age for sleep/wake recordings under undisrupted baseline conditions, after 6-hour of sleep deprivation (ZT2-8; ZT0, light-on), and after 1 hour of restraint stress (ZT5-6). Mice were then left undisturbed for 2 weeks. At 16 weeks of age, mice were sacrificed at ZT6-7, and brain tissues were collected and stored at -80 degrees until use.

value: C57BL/6J x 129S1/SvImJ

value: male

value: hippocampus

tag: ampdate

tag: hybdate

tag: rin


title: X900191_hpc

tag: tissue


title: X900154_hpc


title: X900158_hpc


title: 9_wt+/mt-


title: 8_wt+/mt-


title: X900155_hpc


title: X900137_hpc


title: 6_wt-/mt+


title: X900165_hpc


title: 10_wt-/mt-


title: X900149_hpc


title: X900127_hpc


title: 3_wt+/mt+


title: 1_wt+/mt+


title: X900135_hpc


title: X900161_hpc


title: 4_wt-/mt+


title: X900143_hpc


title: GMshC-D2

city: Oxford

first: Andrea

last: Pellagatti

state: Oxfordshire

address: John Radcliffe Hospital, Headley Way

department: RDM Clinical Laboratory Sciences

country: United Kingdom

institute: University of Oxford

data_processing:
Real time Analysis (RTA):  HiSeq 4000 - RTA version 2.7.7
Base-calling: bcl2fastq 2.19.1
Adapter Trimming: Reads were trimmed for Nextera, Smart-seq2, Illumina adapter sequences using skewer-v0.1.125.
Alignment: Trimmed read pairs were mapped to human genome hg38.ERCC using HISAT2 version 2.0.4.
Read Counts: Uniquely mapped read pairs were counted using featureCounts, subread-1.5.0, using exons annotated in ENSEMBL annotations, release 81.
Normalized Counts: Read counts were normalized to counts per million (CPM) and transcripts per million (TPM) to account for bias in sequencing depth and gene lengths.
Genome_build: hg38.ERCC
Supplementary_files_format_and_content: edgeR.txt: Differential expression data using edgeR for scramble control vs PRR14L knockdown comparision.
Supplementary_files_format_and_content: Full_gene_count_table.xlsx: Raw read counts for ENSEMBL annotated genes
Supplementary_files_format_and_content: CPM_gene_count_table.xlsx: Counts per million normalized counts ENSEMBL annotated
Supplementary_files_format_and_content: TPM_gene_count_table.xlsx: Transcripts per million (gene-length and sequencing depth normalized counts) ENSEMBL annotated genes

growth_protocol: CD34+ cells from healthy donors were obtained from Lonza. The cells were cultured in granulomonocytic differentiation media for 14 day as described previously. On day 7 of culture, 3000 transduced cells were plated on methylcellulose (MethoCult H4434 Classic, Stemcell Technologies) containing 0.65µg/ml puromycin according to the manufacturer’s protocol. Colonies were counted and collected after 14 days.

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies). Linear acrylamide was used as a carrier. The extracted RNA was treated with DNase (Invitrogen) and further purified using Agencourt RNA Clean XP beads (Beckman Coulter)
Library was constructed using Smart-seq2 protocol.

treatment_protocol: Recombinant lentiviruses (shRNA and Scramble control) were used to infect healthy CD34+ cells. Transduced cells were selected in puromycin (0.65µg/ml) and the cells were kept in selection medium throughout the experiment.

tag: genotype/variation

value: PRR14L knockdown


title: GMshC-D3


title: X900190_hpc


title: X900180_hpc


title: X900138_hpc


title: GMshC-D1


title: X900198_hpc


title: X900199_hpc


title: X900152_hpc


title: X900136_hpc


title: X900200_hpc


title: X900159_hpc


title: X900201_hpc


title: GMSCR5

value: Scramble control


title: GMSCR3


title: X900184_hpc


title: X900168_hpc


title: X900156_hpc


title: X900166_hpc


title: X900128_hpc


title: X900182_hpc


title: X900214_hpc


title: X900164_hpc


title: X900187_hpc


title: X900186_hpc


title: X900167_hpc


title: X900169_hpc


title: X900157_hpc


title: X900134_hpc


title: X900194_hpc


title: X900183_hpc


title: wing disc E_EHT, biological rep2

city: Ribeirao Preto

first: Flavia Cristina de

middle: Paula

last: Freitas

state: Sao Paulo

address: Avenida dos Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of Sao Paulo

description:
Drosophila_E_EHT_2
Gene expression data from EGFR early-hyperplastic tumor

hyb_protocol: A hybridization cocktail is prepared, including the fragmented target, and probe array controls. It is then hybridized to the probe array during a 16-hour incubation. The hybridization process is described in the respective sections for the different probe array types.

scan_protocol: GeneChips were scanned using Hewlett-Packard GeneArray Scanner 3000 7G

data_processing: Microarray data analysis was performed using functions in the library Limma of the R/Bioconductor package. Robust Multi-array Average (RMA) method was used to summarize probe set data and normalize raw data

organism: Drosophila melanogaster

source_name: Drosophila early-hyperplastic tumors (EGFR)

label_protocol: An in vitro transcription (IVT) reaction was done to produce biotin-labeled cRNA from the cDNA. The cRNA was fragmented before hybridization.

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

value: EGFR

tag: time point

value: at day 4

value: wing imaginal disc

tag: tissue subtype

value: early-hyperplastic tumors


title: X900181_hpc


title: wing disc E_Ctrl, biological rep2

description:
Drosophila_E_Ctrl_2
Gene expression data from EGFR wing disc, before tumor formation

source_name: Drosophila wing discs before tumor formation (EGFR Control)

value: at 12 hr

value: wing discs before tumor formation


title: wing disc E_EHT, biological rep3

description:
Drosophila_E_EHT_3
Gene expression data from EGFR early-hyperplastic tumor


title: wing disc E_EHT, biological rep1

description:
Drosophila_E_EHT_1
Gene expression data from EGFR early-hyperplastic tumor


title: wing disc E_Ctrl, biological rep4

description:
Drosophila_E_Ctrl_4
Gene expression data from EGFR wing disc, before tumor formation


title: wing disc E_Ctrl, biological rep3

description:
Drosophila_E_Ctrl_3
Gene expression data from EGFR wing disc, before tumor formation


title: wing disc E_EHT, biological rep4

description:
Drosophila_E_EHT_4
Gene expression data from EGFR early-hyperplastic tumor


title: wing disc EP_LNT, biological rep4

description:
Drosophila_EP_LNT_4
Gene expression data from EGFR+psqRNAi late-neoplastic tumor

source_name: Drosophila late-neoplastic tumors (EGFR+psqRNAi)

value: EGFR+psqRNAi

value: at day 11

value: late-neoplastic tumors


title: X900139_hpc


title: X900148_hpc


title: X900163_hpc


title: wing disc EP_LNT, biological rep3

description:
Drosophila_EP_LNT_3
Gene expression data from EGFR+psqRNAi late-neoplastic tumor


title: wing disc E_Ctrl, biological rep1

description:
Drosophila_E_Ctrl_1
Gene expression data from EGFR wing disc, before tumor formation


title: X900151_hpc


title: X900133_hpc


title: X900140_hpc


title: wing disc EP_LNT, biological rep1

description:
Drosophila_EP_LNT_1
Gene expression data from EGFR+psqRNAi late-neoplastic tumor


title: wing disc EP_LNT, biological rep2

description:
Drosophila_EP_LNT_2
Gene expression data from EGFR+psqRNAi late-neoplastic tumor


title: X900245_hth

value: hypothalamus


title: wing disc EP_EHT, biological rep3

description:
Drosophila_EP_EHT_3
Gene expression data from EGFR+psqRNAi early-hyperplastic tumor

source_name: Drosophila early-hyperplastic tumors (EGFR+psqRNAi)


title: wing disc EP_EHT, biological rep2

description:
Drosophila_EP_EHT_2
Gene expression data from EGFR+psqRNAi early-hyperplastic tumor


title: wing disc EP_EHT, biological rep1

description:
Drosophila_EP_EHT_1
Gene expression data from EGFR+psqRNAi early-hyperplastic tumor


title: X900246_hth


title: X900208_hpc


title: X900215_hpc


title: wing disc EP_Ctrl, biological rep3

description:
Drosophila_EP_Ctrl_3
Gene expression data from EGFR+psqRNAi wing disc, before tumor formation

source_name: Drosophila wing discs before tumor formation (EGFR+psqRNAi Control)


title: wing disc EP_Ctrl, biological rep4

description:
Drosophila_EP_Ctrl_4
Gene expression data from EGFR+psqRNAi wing disc, before tumor formation


title: FL

city: Xi'an

last: He

address: No. 620, West Chang'an Avenue, Chang'an District,

institute: Shaanxi Normal University

description: FL, hairless (fuzzless-lintless) seeds with minimal fiber development

data_processing:
RNA-Seq reads were mapped to the mitochondria genome of G. hirsutum using SOAPaligner/soap2 (http://soap.genomics.org.cn/) and Bowtie 2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) with strand specific mode.
We excluded possible genomic polymorphisms at the step of the RNA editing sites prediction. Only the DNA-RNA differences that had at least 5% editing efficiency, and more than five individual read supports were kept. RNA editing efficiency was counted by edited reads divided by total mapped reads
RPKM of each gene was caculated based on the length of the gene and reads count mapped to this gene
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Gossypium hirsutum

growth_protocol: cotton plants were grown in a fully automated greenhouse at 22°C under long-day conditions (a 16 h light / 8 h dark cycle).

extract_protocol:
Total RNA was extracted using an RNA Isolation Kit (Invitrogen™). The RNA was digested with RNase-Free DNase (Qiagen) and checked for integrity by capillary gel electrophoresis.
Total RNA was separated into two parts. One was enriched using an oligo-(dT) primer to quantify the transcription levels of nuclear-encoded genes. The other portion of total RNA was subjected to ribosomal RNA depletion using the Ribo-Zero rRNA removal kit (Epicentre, USA) before cDNA library construction. The mRNA was enriched by oligo-(dT), then reverse-transcribed into cDNA with the SuperscriptTM first-strand synthesis system (Invitrogen, Carlsbad, CA, USA). The mRNA extracted by the Ribo-Zero rRNA removal kit was then fragmented into segments approximately 200 nucleotides in length and reverse-transcribed using random hexamer primers. The library was then constructed and sequenced using an Illumina HiSeqTM 2500. The raw sequence data were filtered and produced 8 Gb bases of clean reads

value: ovule

value: day post anthesis 10

tag: cultivar


title: wing disc EP_Ctrl, biological rep2

description:
Drosophila_EP_Ctrl_2
Gene expression data from EGFR+psqRNAi wing disc, before tumor formation


title: X900131_hpc

value: C57BL/6J x 129S1/SvImJ


title: WT

description: WT, normal fiber development

value: fiber

tag: age

value: wild type


title: wing disc EP_EHT, biological rep4

description:
Drosophila_EP_EHT_4
Gene expression data from EGFR+psqRNAi early-hyperplastic tumor


title: X900205_hpc

value: male

value: hippocampus


title: X900247_hth


title: wing disc EP_Ctrl, biological rep1

description:
Drosophila_EP_Ctrl_1
Gene expression data from EGFR+psqRNAi wing disc, before tumor formation


title: X900174_hpc


title: X900171_hpc


title: X900239_hth


title: X900173_hpc


title: AML 745

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

source_name: mononuclear cells from peripheral blood or bone marrow

extract_protocol: The total RNA was purified with a TRIzol-based protocol.

treatment_protocol: Primary AML samples were enriched for mononuclear cells (myeloid blasts) by Ficoll density gradient centrifugation.

tag: diagnosis

value: acute myeloid leukemia (AML)

tag: ret grouping

value: intermediate


title: X900179_hpc


title: X900210_hpc


title: AML 692

value: mononuclear cells from peripheral blood or bone marrow


title: AML 682


title: X900193_hpc


title: AML 729


title: X900185_hpc


title: AML 739


title: X900176_hpc


title: AML 674

value: high


title: X900153_hpc


title: AML 660


title: X900189_hpc


title: AML 701


title: X900147_hpc


title: AML 667


title: AML 587


title: X900207_hpc


title: X900212_hpc


title: AML 637


title: AML 592


title: X900132_hpc


title: AML 717


title: X900150_hpc


title: X900202_hpc


title: X900172_hpc


title: X900130_hpc


title: AML 658


title: X900189_hth


title: X900173_hth


title: AML 659


title: AML 654


title: X900205_hth


title: AML 625


title: AML 614


title: X900193_hth


title: X900140_hth


title: X900180_hth


title: AML 602

value: low


title: AML 628


title: X900172_hth


title: AML 624


title: AML 327


title: X900184_hth


title: X900188_hpc


title: X900188_hth


title: AML 323


title: AML 619


title: X900215_hth


title: X900174_hth


title: X900156_hth


title: AML 643


title: X900204_hth


title: X900211_hth


title: AML 655


title: AML 472


title: AML 583


title: X900143_hth


title: AML 514


title: X900187_hth


title: X900207_hth


title: AML 553


title: X900208_hth


title: X900157_hth


title: X900185_hth


title: X900202_hth


title: X900190_hth


title: AML 550


title: AML 225


title: AML 517


title: AML 468


title: X900132_hth


title: AML 496


title: X900139_hth


title: AML 552


title: X900153_hth


title: AML 289


title: X900147_hth


title: AML 65


title: AML 341


title: AML 491


title: X900155_hth


title: X900149_hth


title: X900131_hth


title: AML 525


title: AML 138


title: AML 588


title: X900148_hth


title: AML 483


title: X900167_hth


title: AML 396


title: X900127_hth


title: X900159_hth


title: AML 577


title: X900145_hth


title: X900128_hth


title: AML 20


title: X900168_hth


title: AML 581


title: AML 437


title: AML 457


title: AML 513


title: AML 503


title: X900151_hth


title: X900242_hth


title: AML 391


title: X900165_hth


title: X900163_hth


title: X900164_hth


title: AML 348


title: X900137_hth


title: AML 363


title: X900209_hth


title: AML 450


title: X900243_hth


title: AML 456


title: AML 427


title: AML 584


title: X900158_hth


title: AML 531


title: X900150_hth


title: AML 286


title: AML 405


title: AML 582


title: AML 284


title: AML 351


title: X900136_hth


title: X900200_hth


title: X900181_hth


title: X900191_hth


title: X900235_hth


title: AML 493


title: X900236_hth


title: X900241_hth


title: AML 99


title: X900250_hth


title: AML 288


title: AML 275


title: X900238_hth


title: AML 433


title: AML 464


title: X900152_hth


title: AML 622


title: X900171_hth


title: X900198_hth


title: X900197_hth


title: X900161_hth


title: AML 782


title: AML 268


title: AML 833


title: X900135_hth


title: X900199_hth


title: X900248_hth


title: AML 829


title: AML 844


title: X900186_hth


title: AML 836


title: X900249_hth


title: AML 831


title: AML 834


title: AML 838


title: X900210_hth


title: X900141_hth


title: X900129_hth


title: X900214_hth


title: X900169_hth


title: AML 822


title: AML 432


title: AML 172


title: X900133_hth


title: X900200_thl

value: thalamus


title: X900210_thl


title: AML 175


title: X900201_thl


title: AML 171


title: AML 254


title: X900209_thl


title: AML 219


title: X900205_thl


title: AML 218


title: AML 758


title: X900156_thl


title: X900215_thl


title: AML 184


title: X900216_thl


title: X900189_thl


title: AML 223


title: X900235_thl


title: AML 7


title: X900214_thl


title: AML 151


title: AML 217


title: AML 120


title: AML 78


title: X900174_thl


title: X900183_thl


title: X900137_thl


title: AML 568


title: AML 399


title: X900176_thl


title: AML 444


title: X900208_thl


title: AML 365


title: AML 590


title: X900207_thl


title: X900204_thl


title: X900181_thl


title: X900190_thl


title: X900180_thl


title: AML 589


title: X900212_thl


title: X900206_thl


title: AML 346


title: AML 6


title: AML 250


title: AML 374


title: X900236_thl


title: AML 232


title: AML 236


title: X900248_thl


title: X900211_thl


title: X900239_thl


title: AML 234


title: AML 240


title: X900243_thl


title: X900134_thl


title: AML 2


title: AML 664


title: X900130_thl


title: X900244_thl


title: AML 222


title: AML 656


title: AML 311


title: X900138_thl


title: AML 459


title: AML 1


title: AML 307


title: X900128_thl


title: X900237_thl


title: X900136_thl


title: AML 309


title: AML 632


title: AML 693


title: X900146_thl


title: X900249_thl


title: AML 302


title: X900250_thl


title: X900135_thl


title: AML 228


title: X900238_thl


title: X900242_thl


title: X900247_thl


title: AML 337


title: X900148_thl


title: X900143_thl


title: X900245_thl


title: AML 340


title: X900129_thl


title: AML 212


title: AML 181


title: AML 342


title: AML 334


title: AML 197


title: X900142_thl


title: AML 335


title: X900157_thl


title: AML 331


title: X900152_thl


title: X900150_thl


title: AML 29


title: AML 55


title: X900147_thl


title: X900153_thl


title: AML 28


title: X900155_thl


title: AML 1020


title: X900159_thl


title: AML 207


title: AML 31


title: X900131_thl


title: AML 1018


title: X900241_thl


title: AML 1012


title: AML 1019


title: AML 39


title: X900166_thl


title: X900158_thl


title: X900145_thl


title: X900172_thl


title: AML 1008


title: AML 1011


title: AML 1005


title: X900168_thl


title: X900139_thl


title: AML 995


title: X900167_thl


title: X900141_thl


title: X900127_thl


title: X900140_thl


title: X900133_thl


title: AML 556


title: X900132_thl


title: X900161_thl


title: X900164_thl


title: AML 361


title: X900169_thl


title: AML 557


title: AML 559


title: X900165_thl


title: AML 347


title: AML 265


title: AML 549


title: AML 235


title: X900154_thl


title: X900151_thl


title: AML 266


title: AML 267


title: AML 259


title: AML 229


title: AML 535


title: X900149_thl


title: AML 238


title: X900246_thl


title: AML 193


title: AML 230


title: X900191_thl


title: AML 194


title: AML 198


title: X900249_ctx

value: cortex


title: X900185_thl


title: X900186_thl


title: X900198_ctx


title: AML 209


title: AML 174


title: X900152_ctx


title: X900187_thl


title: AML 173


title: X900197_thl


title: X900235_ctx


title: X900138_ctx


title: X900133_ctx


title: X900198_thl


title: X900186_ctx


title: AML 242


title: AML 101


title: AML 251


title: AML 261


title: AML 252


title: AML 249


title: AML 245


title: X900238_ctx


title: X900236_ctx


title: X900197_ctx


title: X900136_ctx


title: AML 66


title: AML 237


title: X900247_ctx


title: AML 91


title: X900244_ctx


title: X900134_ctx


title: X900245_ctx


title: AML 321


title: AML 927


title: AML 35


title: AML 48


title: AML 153


title: AML 18


title: AML 60


title: X900180_ctx


title: AML 51


title: AML 81


title: X900194_thl


title: AML 61


title: AML 10


title: X900128_ctx


title: X900246_ctx


title: X900193_thl


title: X900140_ctx


title: X900243_ctx


title: X900188_thl


title: X900132_ctx


title: AML 46


title: X900141_ctx


title: X900129_ctx


title: X900199_thl


title: X900127_ctx


title: AML 17


title: X900137_ctx


title: AML 314


title: AML 319


title: AML 320


title: AML 684


title: X900130_ctx


title: AML 313


title: AML 424


title: X900241_ctx


title: X900135_ctx


title: X900193_ctx


title: X900205_ctx


title: X900202_ctx


title: AML 515


title: AML 519


title: AML 495


title: AML 494


title: AML 481


title: AML 394


title: AML 465


title: X900181_ctx


title: AML 460


title: X900172_ctx


title: X900153_ctx


title: AML 454


title: AML 407


title: X900169_ctx


title: AML 248


title: X900200_ctx


title: AML 383


title: AML 408


title: AML 255


title: AML 233


title: X900167_ctx


title: X900173_ctx


title: X900204_ctx


title: X900174_ctx


title: X900215_ctx


title: AML 189


title: X900161_ctx


title: AML 98


title: AML 132


title: X900164_ctx


title: AML 469


title: X900208_ctx


title: X900184_ctx


title: AML 636


title: AML 192


title: X900163_ctx


title: X900142_ctx


title: X900189_ctx


title: X900145_ctx


title: AML 159


title: AML 566


title: AML 574


title: AML 631


title: X900216_ctx


title: X900166_ctx


title: AML 190


title: X900156_ctx


title: X900191_ctx


title: AML 668


title: X900143_ctx


title: AML 640


title: AML 512


title: X900212_ctx


title: X900165_ctx


title: AML 134


title: X900146_ctx


title: AML 205


title: AML 42


title: X900207_ctx


title: AML 52


title: X900211_ctx


title: AML 130


title: AML 30


title: X900183_ctx


title: X900154_ctx


title: X900187_ctx


title: AML 131


title: X900179_ctx


title: X900151_ctx


title: X900149_ctx


title: X900157_ctx


title: AML 57


title: AML 83


title: AML 33


title: AML 90


title: AML 107


title: X900209_ctx


title: AML 64


title: AML 63


title: X900155_ctx


title: X900206_ctx


title: X900171_ctx


title: X900158_ctx


title: X900150_ctx


title: AML 56


title: AML 72


title: AML 86


title: X900147_ctx


title: X900185_ctx


title: AML 88


title: X900159_ctx


title: AML 152


title: X900086_ctx


title: AML 149


title: AML 103


title: AML 128


title: X900210_ctx


title: AML 105


title: X900086_hpc


title: AML 47


title: X900122_hpc


title: X900117_thl


title: X900087_hpc


title: X900190_ctx


title: X900120_thl


title: X900121_thl


title: AML 167


title: AML 147


title: AML 119


title: AML 213


title: AML 168


title: AML 102


title: X900082_ctx


title: AML 164


title: AML 179


title: AML 203


title: X900082_thl


title: X900102_hpc


title: X900107_thl


title: X900194_ctx


title: X900105_thl


title: X900106_hpc


title: X900081_hpc


title: X900123_hpc


title: X900089_ctx


title: Breast_tumor_sample_L_foci_2

city: Brussels

first: David

last: Brown

address: Boulevard de Waterloo 127

country: Belgium

institute: Institut Jules Bordet

hyb_protocol: Hybridization was done according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, Rev. 5, Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner

data_processing: The probe level intensities were background adjusted using the Robust multi-array analysis (RMA) method followed by quantile normalization to a predefined distribution as impletemented in the R/Bioconductor package frma. Probe level annotations were obtained from Affymetrix’s website. In particular, we used release 31 of the NetAffx annotation files.

source_name: Breast tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, Rev. 5, Affymerrix)

extract_protocol: RNA was isolated by the Trizol method (Invitrogen) according to manufacturers’ instructions.

tag: er

tag: pgr

tag: grade


title: X900088_ctx

tag: strain

tag: gender


title: Breast_tumor_sample_K_foci_1


title: AML 195


title: X900117_ctx


title: Breast_tumor_sample_L_foci_1


title: Breast_tumor_sample_K_foci_2


title: Breast_tumor_sample_I_foci_2


title: X900104_ctx


title: Breast_tumor_sample_J_foci_2


title: Breast_tumor_sample_H_foci_1


title: X900087_ctx


title: Breast_tumor_sample_H_foci_2


title: X900124_thl


title: X900100_ctx


title: Breast_tumor_sample_J_foci_1


title: Breast_tumor_sample_I_foci_1


title: X900106_thl


title: DCLC_T_BDCA1+DC_D6_6

city: Paris

first: Sebastian

last: Amigorena

state: --- Select a state ---

address: 26 rue Ulm

department: Center of Immunotherapy

institute: Curie Institute

data_processing:
RNA purification was performed with Norgen kit (NorgenBioteck) and cDNA synthesis with SMARter kit for Illumina Sequencing-HV(Clontech). 50nt-length reads per samples were obtained.
Filtering out all the genes with less than 5 counts in more than 25% of the samples
normalizing method RUVr (R program package RUVSeq - Risso et al., Nat Biotech of 2014)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include filtered and normalized data

source_name: Tumor

extract_protocol:
RNA purification was performed with Norgen kit (NorgenBioteck) and cDNA synthesis with SMARter kit for Illumina Sequencing-HV(Clontech).
Sequencing was performed in Illumina HiSeq 2500, the average depth is 15 million reads of 50-nt-length reads per sample. Library (pair-ends fragments), sequencing and sequencing quality control were performed by the Institut Curie NGS plateform.

treatment_protocol: Primary LUADs and juxtatumor lung tissues were pushed through 40μm strainers (Corning). CD45+ cells were magnetically enriched using CD45 Microbeads (Miltenyi Biotech), stained as described in Figure S16 and sorted in RL buffer (NorgenBioteck).

value: lung adenocarcinoma (LUAD)

value: Tumor

value: F

tag: smoked

value: Y

tag: subset


title: DCLC_J_BDCA1+DC_D6_5

source_name: Juxtatumor

value: lung juxtatumor

value: Juxtatumor


title: DCLC_J_BDCA1-DC_D6_9


title: X900119_thl

value: C57BL/6J x 129S1/SvImJ

tag: ampdate

tag: hybdate


title: X900085_thl

tag: tissue

tag: rin


title: X900085_ctx


title: X900103_thl


title: Breast_tumor_sample_F_foci_1

data_processing: The probe level intensities were background adjusted using the Robust multi-array analysis (RMA) method followed by quantile normalization to a predefined distribution as implemented in the R/Bioconductor package fRMA. Probe level annotations were obtained from Affymetrix’s website. In particular, we used release 31 of the NetAffx annotation files.


title: DCLC_T_BDCA1-DC_D6_8


title: Breast_tumor_sample_F_foci_2


title: DCLC_T_BDCA1+DC_D5_6

value: M

value: N


title: Breast_tumor_sample_B_foci_1


title: Breast_tumor_sample_C_foci_1


title: X900081_thl

value: male


title: X900118_hpc

value: hippocampus


title: X900117_hpc


title: DCLC_J_BDCA1-DC_D5_7


title: X900101_thl


title: X900105_ctx


title: Breast_tumor_sample_B_foci_2


title: Breast_tumor_sample_G_foci_2


title: X900104_hpc


title: Breast_tumor_sample_C_foci_2


title: Breast_tumor_sample_G_foci_1


title: X900084_thl


title: DCLC_T_BDCA1-DC_D5_8


title: DCLC_T_BDCA1-DC_D4_8


title: DCLC_J_BDCA1+DC_D5_5


title: DCLC_J_BDCA1-DC_D4_7


title: X900101_ctx


title: X900103_ctx


title: DCLC_T_BDCA1+DC_D4_6


title: X900106_ctx


title: X900107_ctx


title: DCLC_J_BDCA1+DC_D4_5


title: DCLC_J_BDCA1-DC_D2_4


title: DCLC_T_BDCA1-DC_D2_5


title: TNY15_TG16_155T1

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

description: 3' adapter sequence:TTACATCGTATGCTGTCCTCTG

data_processing:
HiSeq 2500 standard base-calling
A published small RNAseq pipeline, "rnaworld", PMID: 22836126
Genome_build: hg19
Supplementary_files_format_and_content: Excel worksheet: microRNA read counts in all study samples

source_name: ex-vivo FNAB

extract_protocol:
TRIzol extraction followed by glycogen-fascilitated isopropanol precipitation
ligation & gel-based small RNA cDNA library (see PMID: 24489795)

tag: malignancy

value: female

tag: group

value: malignant

tag: barcode


title: TNY15_TG12_181N2

description: 3' adapter sequence:TAATATCGTATGCTGTCCTCTG

tag: age

value: benign


title: TNY15_TG14_185FL3

description: 3' adapter sequence:TATCATCGTATGCTGTCCTCTG

value: FL


title: TNY15_TG10_183N3

description: 3' adapter sequence:TTAAGTCGTATGCTGTCCTCTG


title: TNY15_TG13_185FL2

description: 3' adapter sequence:TAGAGTCGTATGCTGTCCTCTG


title: TNY15_TG11_185FL1

description: 3' adapter sequence:TAACGTCGTATGCTGTCCTCTG


title: TNY15_TG15_184FL2

description: 3' adapter sequence:TGATGTCGTATGCTGTCCTCTG


title: TNY15_TG9_142N1

description: 3' adapter sequence:TCTCCTCGTATGCTGTCCTCTG


title: X900105_hth

value: hypothalamus


title: TNY15_TG7_184FL1

description: 3' adapter sequence:TCGCGTCGTATGCTGTCCTCTG


title: TNY15_TG8_140N1

description: 3' adapter sequence:TCTAGTCGTATGCTGTCCTCTG


title: X900100_thl

value: thalamus


title: X900104_hth


title: X900102_thl


title: X900101_hth


title: X900118_thl


title: X900122_thl


title: X900088_thl


title: TNY15_TG6_184FL2

description: 3' adapter sequence:TCGATTCGTATGCTGTCCTCTG


title: X900122_ctx

value: cortex


title: X900104_thl


title: X900089_thl


title: TNY15_TG5_178N1

description: 3' adapter sequence:TCCTATCGTATGCTGTCCTCTG


title: X900087_hth


title: X900102_hth


title: X900102_ctx


title: X900082_hth


title: X900086_hth


title: TNY15_TG4_158T2

description: 3' adapter sequence:TCCGTTCGTATGCTGTCCTCTG


title: TNY15_TG3_158N3

description: 3' adapter sequence:TCCACTCGTATGCTGTCCTCTG


title: TNY15_TG1_198N2

description: 3' adapter sequence:TCACTTCGTATGCTGTCCTCTG


title: TNY15_TG24_BCPAP

description: 3' adapter sequence:TGCCATCGTATGCTGTCCTCTG

source_name: cell-line


title: TNY15_TG2_198FL3

description: 3' adapter sequence:TCATCTCGTATGCTGTCCTCTG


title: X900100_hth


title: TNY15_TG23_196T2

description: 3' adapter sequence:TGTTATCGTATGCTGTCCTCTG


title: TNY15_TG21_168N1

description: 3' adapter sequence:TTGACTCGTATGCTGTCCTCTG


title: X900118_ctx


title: TNY15_TG22_193FL3

description: 3' adapter sequence:TTGTATCGTATGCTGTCCTCTG


title: TNY14_TG16_184N3

description: 3' adapter sequence:TTACATCGTATGCTGTCCTCTG


title: TNY15_TG20_140N2

description: 3' adapter sequence:TTCATTCGTATGCTGTCCTCTG


title: TNY15_TG18_191FL3

description: 3' adapter sequence:TAGCCTCGTATGCTGTCCTCTG


title: TNY15_TG17_183N3

description: 3' adapter sequence:TACTCTCGTATGCTGTCCTCTG


title: TNY15_TG19_181N2

description: 3' adapter sequence:TTATTTCGTATGCTGTCCTCTG


title: TNY14_TG15_182FL3

description: 3' adapter sequence:TGATGTCGTATGCTGTCCTCTG


title: X900087_thl


title: X900085_hth


title: TNY14_TG14_158N1

description: 3' adapter sequence:TATCATCGTATGCTGTCCTCTG


title: TNY14_TG13_179T1

description: 3' adapter sequence:TAGAGTCGTATGCTGTCCTCTG


title: TNY14_TG12_175T1

description: 3' adapter sequence:TAATATCGTATGCTGTCCTCTG


title: X900120_ctx


title: X900081_hth


title: X900119_ctx


title: X900124_ctx


title: X900120_hth


title: X900117_hth


title: X900084_hth


title: X900124_hth


title: TNY14_TG10_184FL3

description: 3' adapter sequence:TTAAGTCGTATGCTGTCCTCTG


title: X900121_hth


title: X900118_hth


title: X900119_hth


title: X900103_hth


title: X900122_hth


title: X900103_hpc


title: TNY14_TG9_180N1

description: 3' adapter sequence:TCTCCTCGTATGCTGTCCTCTG


title: TNY14_TG8_179T3

description: 3' adapter sequence:TCTAGTCGTATGCTGTCCTCTG


title: X900120_hpc


title: TNY14_TG6_180T3

description: 3' adapter sequence:TCGATTCGTATGCTGTCCTCTG


title: X900121_hpc


title: X900084_hpc


title: TNY14_TG5_180N3

description: 3' adapter sequence:TCCTATCGTATGCTGTCCTCTG


title: TNY14_TG3_177T1

description: 3' adapter sequence:TCCACTCGTATGCTGTCCTCTG


title: TNY14_TG11_177T3

description: 3' adapter sequence:TAACGTCGTATGCTGTCCTCTG


title: TNY14_TG4_178T2

description: 3' adapter sequence:TCCGTTCGTATGCTGTCCTCTG


title: TNY14_TG2_178T1

description: 3' adapter sequence:TCATCTCGTATGCTGTCCTCTG


title: TNY14_TG1_179N1

description: 3' adapter sequence:TCACTTCGTATGCTGTCCTCTG


title: TNY14_TG24_BCPAP

description: 3' adapter sequence:TGCCATCGTATGCTGTCCTCTG


title: TNY14_TG7_184N1

description: 3' adapter sequence:TCGCGTCGTATGCTGTCCTCTG


title: TNY14_TG23_199T2

description: 3' adapter sequence:TGTTATCGTATGCTGTCCTCTG


title: X900088_hpc


title: TNY14_TG20_181N3

description: 3' adapter sequence:TTCATTCGTATGCTGTCCTCTG


title: TNY14_TG19_184N3

description: 3' adapter sequence:TTATTTCGTATGCTGTCCTCTG


title: TNY14_TG22_199T1

description: 3' adapter sequence:TTGTATCGTATGCTGTCCTCTG


title: TNY14_TG18_183T2

description: 3' adapter sequence:TAGCCTCGTATGCTGTCCTCTG


title: TNY14_TG17_180T1

description: 3' adapter sequence:TACTCTCGTATGCTGTCCTCTG


title: TNY13_TG16_170T1

description: 3' adapter sequence:TTACATCGTATGCTGTCCTCTG


title: TNY13_TG15_173N3

description: 3' adapter sequence:TGATGTCGTATGCTGTCCTCTG


title: 2500 ppm isoniazid for 14 days, biological rep3

city: Osaka

first: Ayako

last: Ohara

address: 1-98, Kasugade-naka 3-chome, Konohana-ku

country: Japan

institute: Sumitomo Chemical Co., Ltd.

description: Gene expression data from lung of mice fed diets containing 2500 ppm isoniazid for 14 days

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained with Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with a Genechip Scanner 3000 (Affymetrix) and the image files were obtained.

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

label_protocol: Biotin-labeled cRNA were prepared from 100 ng of total RNA using 3’IVT Express Kit (Affymetrix) following the manufacturer's protocol.

growth_protocol: Crlj:CD1(ICR) female mice aged 9 weeks were purchased, quarantined for 7 days and maintained at 22 - 26°C and a relative humidity range of 40 - 70% with frequent ventilation. A powdered diet and water were provided ad libitum.

extract_protocol: The lungs were stored in RNA stabilization solution (Ambion, Austin, TX) at –20°C. Total RNA samples were extracted from lung using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Animals were fed diets containing 0 (control), 5000 and 10000 ppm permethrin and 2500 ppm isoniazid (positive control for tumor induction) for periods of 7 and 14 days.

value: lung

value: age of 12 weeks


title: 10000 ppm permethrin for 14 days, biological rep2

description: Gene expression data from lung of mice fed diets containing 10000 ppm permethrin for 14 days


title: TNY13_TG14_79B

description: 3' adapter sequence:TATCATCGTATGCTGTCCTCTG


title: 2500 ppm isoniazid for 14 days, biological rep5

source_name: lung of mice fed diets containing 2500 ppm isoniazid for 14 days


title: 2500 ppm isoniazid for 14 days, biological rep1


title: 10000 ppm permethrin for 14 days, biological rep4

source_name: lung of mice fed diets containing 10000 ppm permethrin for 14 days


title: 2500 ppm isoniazid for 14 days, biological rep2


title: 10000 ppm permethrin for 14 days, biological rep3


title: 10000 ppm permethrin for 14 days, biological rep1


title: TNY14_TG21_142T1

description: 3' adapter sequence:TTGACTCGTATGCTGTCCTCTG


title: TNY13_TG13_77

description: 3' adapter sequence:TAGAGTCGTATGCTGTCCTCTG


title: 5000 ppm permethrin for 14 days, biological rep2

description: Gene expression data from lung of mice fed diets containing 5000 ppm permethrin for 14 days


title: 2500 ppm isoniazid for 14 days, biological rep4


title: TNY13_TG12_75A

description: 3' adapter sequence:TAATATCGTATGCTGTCCTCTG


title: TNY13_TG11_157N3

description: 3' adapter sequence:TAACGTCGTATGCTGTCCTCTG


title: 5000 ppm permethrin for 14 days, biological rep3

source_name: lung of mice fed diets containing 5000 ppm permethrin for 14 days


title: TNY13_TG10_157N2

description: 3' adapter sequence:TTAAGTCGTATGCTGTCCTCTG


title: 5000 ppm permethrin for 14 days, biological rep4


title: 0 (control) for 14 days, biological rep5

description: Gene expression data from lung of mice fed diets containing 0 (control) ppm chemical for 14 days


title: 5000 ppm permethrin for 14 days, biological rep1


title: 0 (control) for 14 days, biological rep3

source_name: lung of mice fed diets containing 0 (control) ppm chemical for 14 days


title: 0 (control) for 14 days, biological rep2


title: 2500 ppm isoniazid for 7 days, biological rep5

description: Gene expression data from lung of mice fed diets containing 2500 ppm isoniazid for 7 days

value: age of 11 weeks


title: 0 (control) for 14 days, biological rep4


title: 0 (control) for 14 days, biological rep1


title: TNY13_TG9_156FL3

description: 3' adapter sequence:TCTCCTCGTATGCTGTCCTCTG


title: TNY13_TG7_156FL1

description: 3' adapter sequence:TCGCGTCGTATGCTGTCCTCTG


title: TNY13_TG6_155T3

description: 3' adapter sequence:TCGATTCGTATGCTGTCCTCTG


title: TNY13_TG8_156FL2

description: 3' adapter sequence:TCTAGTCGTATGCTGTCCTCTG


title: TNY13_TG3_154N1

description: 3' adapter sequence:TCCACTCGTATGCTGTCCTCTG


title: TNY13_TG4_155T1

description: 3' adapter sequence:TCCGTTCGTATGCTGTCCTCTG


title: TNY13_TG5_155T2

description: 3' adapter sequence:TCCTATCGTATGCTGTCCTCTG


title: 2500 ppm isoniazid for 7 days, biological rep3

source_name: lung of mice fed diets containing 2500 ppm isoniazid for 7 days


title: TNY13_TG2_153FL3

description: 3' adapter sequence:TCATCTCGTATGCTGTCCTCTG

value: omitted


title: TNY13_TG24BCPUP

description: 3' adapter sequence:TGCCATCGTATGCTGTCCTCTG


title: 2500 ppm isoniazid for 7 days, biological rep2


title: 2500 ppm isoniazid for 7 days, biological rep4


title: TNY13_TG23_177N3

description: 3' adapter sequence:TGTTATCGTATGCTGTCCTCTG


title: TNY13_TG22_164T3

description: 3' adapter sequence:TTGTATCGTATGCTGTCCTCTG


title: 10000 ppm permethrin for 7 days, biological rep1

description: Gene expression data from lung of mice fed diets containing 10000 ppm permethrin for 7 days


title: 5000 ppm permethrin for 7 days, biological rep4

description: Gene expression data from lung of mice fed diets containing 5000 ppm permethrin for 7 days


title: TNY13_TG21_165N2

description: 3' adapter sequence:TTGACTCGTATGCTGTCCTCTG


title: TNY13_TG20_163FL2

description: 3' adapter sequence:TTCATTCGTATGCTGTCCTCTG


title: 5000 ppm permethrin for 7 days, biological rep3

source_name: lung of mice fed diets containing 5000 ppm permethrin for 7 days


title: TNY13_TG19_166N1

description: 3' adapter sequence:TTATTTCGTATGCTGTCCTCTG


title: 2500 ppm isoniazid for 7 days, biological rep1

description: Gene expression data from lung of mice fed diets containing 2500 ppm isoniazid for 7 days


title: TNY13_TG18_167N2

description: 3' adapter sequence:TAGCCTCGTATGCTGTCCTCTG


title: TNY13_TG1_153FL1

description: 3' adapter sequence:TCACTTCGTATGCTGTCCTCTG


title: 10000 ppm permethrin for 7 days, biological rep5

source_name: lung of mice fed diets containing 10000 ppm permethrin for 7 days


title: 10000 ppm permethrin for 7 days, biological rep3


title: TNY13_TG17_170T3

description: 3' adapter sequence:TACTCTCGTATGCTGTCCTCTG


title: 5000 ppm permethrin for 7 days, biological rep2


title: 10000 ppm permethrin for 7 days, biological rep2


title: 0 (control) for 7 days, biological rep5

description: Gene expression data from lung of mice fed diets containing 0 (control) ppm chemical for 7 days


title: TNY12_TG16_150N2

description: 3' adapter sequence:TTACATCGTATGCTGTCCTCTG


title: 10000 ppm permethrin for 7 days, biological rep4


title: 5000 ppm permethrin for 7 days, biological rep5


title: TNY12_TG15_150N1

description: 3' adapter sequence:TGATGTCGTATGCTGTCCTCTG


title: TNY12_TG14_149T1

description: 3' adapter sequence:TATCATCGTATGCTGTCCTCTG


title: 0 (control) for 7 days, biological rep4

source_name: lung of mice fed diets containing 0 (control) ppm chemical for 7 days


title: 0 (control) for 7 days, biological rep3


title: TNY12_TG11_147T2

description: 3' adapter sequence:TAACGTCGTATGCTGTCCTCTG


title: TNY12_TG12_147T3

description: 3' adapter sequence:TAATATCGTATGCTGTCCTCTG


title: 0 (control) for 7 days, biological rep1


title: TNY12_TG9_144N2

description: 3' adapter sequence:TCTCCTCGTATGCTGTCCTCTG


title: TNY12_TG8_144T2

description: 3' adapter sequence:TCTAGTCGTATGCTGTCCTCTG


title: TNY12_TG7_68

description: 3' adapter sequence:TCGCGTCGTATGCTGTCCTCTG