title: Unstimulated Fibroblast 6 hours rep 1

source_name: Unstimulated Fibroblast 6 hours rep 1

tag: cell type


title: D319N ERK2, rep 1

status: Public on Jan 11 2019

type: RNA

city: Peoria

first: Sejeong

last: Shin

state: Illinois

address: 1 illini drive

country: USA

institute: University of Illinois at Chicago

description: BB

hyb_protocol: Following fragmentation,  60 uL of cDNA were hybridized for 16 hr at 45 C on GeneChip Human Transcriptome 2.0 Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing:
The data were analyzed with using Affymetrix Expression Console ver 1.4 using Analysis algorithm RMA.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HTA-2_0
program-name = Expression Console
program-version = 1.4.1.46

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: MCF10A D319N ERK2

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ug total RNA using amplification kit WT PLUS, Lot # 4224182, followed by labeling 5.5 ug cDNA using kit WT PLUS, Lot # 4224182.

growth_protocol: MCF-10A cells are grown on standard tissue culture plastic in a 5% CO2 humidified incubator at 37 °C. The growth medium is composed of DMEM/F12 supplemented with 5% donor horse serum, 20 ng/ml epidermal growth factor (EGF), 10 μg/ml insulin, 0.5 μg/ml hydrocortisone, 100 ng/ml cholera toxin

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen)

treatment_protocol: Vector control, D319N ERK2, and Y261A ERK2 expression was induced by doxycycline in Tet-on MCF10A cell systems.

tag: cell line

value: breast epithelial cells

tag: genotype/variation

value: expressing D319N ERK2


title: Unstimulated Fibroblast 6 hours rep 2

city: örebro

first: isak

last: demirel

address: campus usö

country: Sweden

institute: örebro University

description: Gene expression after 6 hours of unstimulated human fibroblasts

hyb_protocol: Labelled samples were hybridized onto G4851C SurePrint G3 Human Gene Expression v3 8x60K Microarray glass slides (Agilent)

scan_protocol: Microarrays were scanned with a G2565 CA array laser scanner (Agilent) followed by image analysis and data extraction with Feature Extraction Software version 10.7.3.1 (Agilent).

data_processing: 75th percentile shift normalization and baseline adjusted

source_name: Unstimulated Fibroblast 6 hours rep 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the low input quick amp labeling kit,one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Primary human renal fibroblasts were derived from a healthy woman and cultured in Dulbecco's modified eagle medium (DMEM) containing 10% foetal bovine serum (FBS), 2 mM L-glutamine, 1mM non-essential amino acids, 50 U/mL penicillin and 50 ml/mL streptomycin at 37°C in a 5% CO2 atmosphere. The cells were serum starved overnight in DMEM containing 2 mM L-glutamine, 1mM non-essential amino acids and 50 µg/ml Gentamicin (Sigma-Aldrich, St. Louis, MO, USA). During experiments, the medium was replaced with DMEM containing 1% FBS, 1 mM non-essential amino acids and 2 mM L-glutamine.

extract_protocol: Total RNA was isolated from the primary renal fibroblasts using the RNeasy Mini Kit (Qiagen Technologies) according to manufacturer instructions. RNA quality and integrity was analysed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) according to manufacturer instructions.

treatment_protocol: The renal fibroblasts were stimulated with CFT073 at a multiplicity of infection (MOI) of 10 for 6 hours and incubated at 37ºC with 5% CO2.

value: Primary human renal fibroblasts

tag: treatment

value: control


title: MCF-7-TNR_CTLsi.1 RNA-SEQ

type: SRA

city: Spokane

first: Bin

last: Shan

state: Washington

address: 412 E Spokane Falls Blvd

department: Biomedical Sciences

institute: Washington State University

library_source: transcriptomic

data_processing:
FASTQ files were trimmed using systemPipeR Bioconductor package,
rsem-calculate-expression --star --star-gzipped-read-file --output-genome-bam -p 48 --paired-end
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: MCF-7-TNR_CTLsi.1.results.tsv: Tab-separated value text file includes TPM and FPKM values.
Supplementary_files_format_and_content: MCF-7-TNR_CTLsi.2.results.tsv: Tab-separated value text file includes TPM and FPKM values.
Supplementary_files_format_and_content: MCF-7-TNR_HOTAIRsi.1.results.tsv: Tab-separated value text file includes TPM and FPKM values.
Supplementary_files_format_and_content: MCF-7-TNR_HOTAIRsi.2.results.tsv: Tab-separated value text file includes TPM and FPKM values.

source_name: Breast Cancer Cell Line

growth_protocol: MCF-7-TNR cells were cultured in DMEM with 10% FBS.

extract_protocol:
Total cell RNA was extracted when cells were ~80% confluent using TRIZOL.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit/Ribo-Zero Gold kit.

treatment_protocol: HOTAIR-specific siRNA or control siRNA was transfected into MCF-7-TNR cells using RNAiMAX.

value: Breast cancer cell line

tag: sirna

value: CTLsi


title: MCF-7-TNR_CTLsi.2 RNA-SEQ


title: Adipocytes_shNF1_Rosi_2

city: Philadelphia

first: Chunjie

last: Jiang

state: PA

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

data_processing:
ChIP-seq reads were aligned to human reference genome (hg19) using Bowtie2. Only unique mapped reads were considered for further analysis. Aligned reads from biological replicates were pooled together and peak calling was performed by HOMER with normalized tag count >=6, p value < 0.00001 and fold change >= 4 for each patient. After that peaks from each patient were merged together using BEDTools, and then resized to 200 bp.
RNA-seq reads were aligned to human reference genome (hg19) using Hisat2 with default parameters. Only unique mapped reads were considered for further analysis. Normalized expression value, fragments per kilobase of exon per million reads mapped (FPKM), was calculated for each gene using StringTie
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using HORMER V4.9; Normalized abundance measurement was generated using StringTie.

source_name: Adipocytes

growth_protocol: hASCs at passage P3-P4 were cultured in DMEM medium. Confluent hASCs were then transferred into adipogenic medium for 14 days. Then, cells were further cultured in maintenance medium another 7 days.

extract_protocol:
Total RNA was extracted by using Qiagen RNeasey Mini kit. Ribosomal RNA was depleted by Ribo-Zero gold kit.
DNA was isolated using phenol/chloroform extraction and NaCl/EtOH precipitated with 20 μg glycogen carrier.
RNA libraries were prepared for sequencing using TruSeq RNA Sample Prep Kit. ChIP-seq library was prepared for sequencing according to the amplification protocol from Illumina.

treatment_protocol: hASC-derived adipocytes were treated with rosiglitazone for 48h beginning at day 21

value: hASC-derived adipocytes


title: MCF-7-TNR_HOTAIRsi.1 RNA-SEQ

value: HOTAIRsi


title: P2_Adipose_PPARg_ChIP

library_source: genomic

molecule: genomic DNA

source_name: Adipose tissue

tag: tissue

value: Adipose

tag: chip antibody

value: PPARg(Santa Cruz Biotechnology, Cat# sc-7196)


title: P3_Adipose_PPARg_ChIP


title: TPM_Sample_B7_20160407000

city: Iowa City

first: John

last: Engelhardt

state: Iowa

address: 51 Newton Rd, 1-111 BSB

department: Developmental and Cellular Biology

institute: University of Iowa

description:
Sample_B7_20160407000
B7_20160407000_S58_L006

data_processing:
TPM quantification via RSEM
Transcripts were collated by gene via summing transcript expression
Remove cells with <60% cellular RNA relative to exogenous RNAspike-in
multiply mRNAs by 1e6 then divide by the sum RNAspike-in TPM
Normalize to upper quartile TPM, removing samples whose upper quartile value was zero.
Remove genes with less than 1% of cells expressing at >=5 normalized TPM
Genome_build: human mRNA (Ensembl V87) with added Ambion RNAspike sequences
Supplementary_files_format_and_content: tab-delimited text file containing normalized TPM values for each included sample

source_name: Human 4

growth_protocol: After receipt of islets from the integrated islet distribution program (IIDP), islets were cultured overnight in RPMI supplemented with 10mM glucose, 10% FBS, and 1% Penn/Strep prior to scRNAseq.

extract_protocol:
Fluidigm C1 microfluidics chip
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject id

value: individual 4

tag: ethnicity

value: White

value: Pancreatic islet

tag: age

tag: gender

value: female

tag: bmi


title: P1_Adipose_PPARg_ChIP


title: TPM_Sample_H4_20160407000

description:
Sample_H4_20160407000
H4_20160407000_S44_L006


title: TPM_Sample_F1_20160407000

description:
Sample_F1_20160407000
F1_20160407000_S27_L006


title: TPM_Sample_C11_20160407000

description:
Sample_C11_20160407000
C11_20160407000_S80_L006


title: TPM_Sample_F11_20160407000

description:
Sample_F11_20160407000
F11_20160407000_S82_L006


title: TPM_Sample_B6_20160407000

description:
Sample_B6_20160407000
B6_20160407000_S52_L006


title: P3_Adipocytes_PPARg_ChIP

tag: agent


title: P4_Adipocytes_PPARg_ChIP


title: Adipocytes_Scramble_DMSO_3


title: P2_Adipocytes_PPARg_ChIP


title: TPM_Sample_C7_20160407000

description:
Sample_C7_20160407000
C7_20160407000_S59_L006


title: TPM_Sample_A1_20160407000

description:
Sample_A1_20160407000
A1_20160407000_S23_L006


title: TPM_Sample_E3_20160407000

description:
Sample_E3_20160407000
E3_20160407000_S36_L006


title: TPM_Sample_F4_20160407000

description:
Sample_F4_20160407000
F4_20160407000_S42_L006


title: TPM_Sample_B8_20160407000

description:
Sample_B8_20160407000
B8_20160407000_S63_L006


title: P5_Adipocytes_PPARg_ChIP


title: P5_Adipocytes_Rosi_1

value: rosiglitazone


title: P5_Adipocytes_Rosi_2


title: TPM_Sample_H11_20160407000

description:
Sample_H11_20160407000
H11_20160407000_S84_L006


title: TPM_Sample_F12_20160407000

description:
Sample_F12_20160407000
F12_20160407000_S90_L006


title: TPM_Sample_D8_20160407000

description:
Sample_D8_20160407000
D8_20160407000_S65_L006


title: P5_Adipocytes_DMSO_1

value: DMSO


title: P5_Adipocytes_DMSO_2


title: P5_Adipocytes_DMSO_3


title: P5_Adipocytes_Rosi_3


title: P1_Adipocytes_PPARg_ChIP


title: TPM_Sample_G5_20160407000

description:
Sample_G5_20160407000
G5_20160407000_S50_L006


title: P4_Adipocytes_Rosi_3


title: P4_Adipocytes_Rosi_2


title: TPM_Sample_E4_20160407000

description:
Sample_E4_20160407000
E4_20160407000_S41_L006


title: TPM_Sample_D11_20160407000

description:
Sample_D11_20160407000
D11_20160407000_S81_L006


title: P4_Adipocytes_DMSO_2


title: P4_Adipocytes_Rosi_1


title: P4_Adipocytes_DMSO_3


title: TPM_Sample_H1_20160407000

description:
Sample_H1_20160407000
H1_20160407000_S29_L006


title: TPM_Sample_B12_20160407000

description:
Sample_B12_20160407000
B12_20160407000_S86_L006


title: P4_Adipocytes_DMSO_1


title: TPM_Sample_D4_20160407000

description:
Sample_D4_20160407000
D4_20160407000_S40_L006


title: P3_Adipocytes_Rosi_3


title: P3_Adipocytes_Rosi_2


title: TPM_Sample_C8_20160407000

description:
Sample_C8_20160407000
C8_20160407000_S64_L006


title: P3_Adipocytes_Rosi_1


title: TPM_Sample_E6_20160407000

description:
Sample_E6_20160407000
E6_20160407000_S55_L006


title: TPM_Sample_D6_20160407000

description:
Sample_D6_20160407000
D6_20160407000_S54_L006


title: TPM_Sample_C12_20160407000

description:
Sample_C12_20160407000
C12_20160407000_S87_L006


title: P3_Adipocytes_DMSO_3


title: P3_Adipocytes_DMSO_1


title: P3_Adipocytes_DMSO_2


title: TPM_Sample_E10_20160407000

description:
Sample_E10_20160407000
E10_20160407000_S77_L006


title: TPM_Sample_D12_20160407000

description:
Sample_D12_20160407000
D12_20160407000_S88_L006


title: P2_Adipocytes_Rosi_2


title: TPM_Sample_E1_20160407000

description:
Sample_E1_20160407000
E1_20160407000_S26_L006


title: P2_Adipocytes_Rosi_1


title: TPM_Sample_G7_20160407000

description:
Sample_G7_20160407000
G7_20160407000_S61_L006


title: TPM_Sample_A10_20160407000

description:
Sample_A10_20160407000
A10_20160407000_S74_L006


title: P2_Adipocytes_Rosi_3


title: TPM_Sample_F8_20160407000

description:
Sample_F8_20160407000
F8_20160407000_S67_L006


title: P2_Adipocytes_DMSO_2


title: TPM_Sample_G9_20160407000

description:
Sample_G9_20160407000
G9_20160407000_S72_L006


title: P1_Adipocytes_Rosi_3


title: TPM_Sample_H7_20160407000

description:
Sample_H7_20160407000
H7_20160407000_S62_L006


title: P2_Adipocytes_DMSO_1


title: P1_Adipocytes_Rosi_2


title: P1_Adipocytes_DMSO_2


title: P1_Adipocytes_DMSO_3


title: TPM_Sample_E5_20160407000

description:
Sample_E5_20160407000
E5_20160407000_S48_L006


title: TPM_Sample_E9_20160407000

description:
Sample_E9_20160407000
E9_20160407000_S70_L006


title: P1_Adipocytes_DMSO_1


title: TPM_Sample_E7_20160407000

description:
Sample_E7_20160407000
E7_20160407000_S60_L006


title: TPM_Sample_E12_20160407000

description:
Sample_E12_20160407000
E12_20160407000_S89_L006


title: TPM_Sample_E2_20160407000

description:
Sample_E2_20160407000
E2_20160407000_S31_L006


title: KAP1 TI

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

description: processed data file: Kap1hES_TKD_100.bed

data_processing:
Raw fastq were quality checked with FastQC (version 0.11.5), followed by adapter and base quality trimming with TrimGalore (version 0.2.7). Reads post-QC were aligned using bowtie2 (v2.3.3, --end-to-end).
Potential PCR duplicates were removed with Picard tools (“MarkDuplicates” function).
Peak were called on mapped data using MACS v.2.1.0 with broad peak option using only uniquely aligned reads (MAPQ>10).
For KAP1 ChIP, peaks were filtered for score > 100.
Genome_build: hg19 (GRCh37) and mm10 (GRCm38)
Supplementary_files_format_and_content: *.bed: bed files contain unfiltered raw peaks.

source_name: TKD hES

growth_protocol: H1 ESCs (WA01, WiCell) were maintained in mTesRI (StemCell Technologies) on hES-qualified Matrigel (BD Biosciences). For transduction, hES were detached using TryPLE Express (Invitrogen), split at 40,000 cells/cm2 and maintained at least 12 hrs with ROCK inhibitor (Y-27632) to increase viability.

extract_protocol:
ES cell samples were washed 2x (in KO medium), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde at RT), quenched with glycine at 125mM, incubated 5' on ice, washed 3x (cold PBS) and pelleted at 10e7 cells per eppendorf. Pellets were lysed according to Covaris protocol: pellets were resuspended in ice cold buffer 1 (50mM HEPES-KOH pH7.4, 140mM NaCl, 1mM EDTA, 0.5mM EGTA, 10% glycerol, 0.5% NP40, 0.25% TX100, antiproteases), then in ice cold buffer 2 (10mM Tris pH8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, antiproteases) then washed 3 times and resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to TC12 glass tubes (Covaris: 520056) and sonicated (Covaris settings: 20% duty cycle, intensity 5, 200cyles/ burst, 15, 30 or 60 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification and quality control on a Bioanalyzer (Agilent 2100). Samples were also checked for the absence of single-stranded DNA by Exonuclease I treatment and the 60' sonicated samples were used for further chromatin immunoprecipitation.
Paired-end libraries were prepared and sequenced in 100bp reads runs according to Illumina instructions.

value: Embryonic stem cells (ESCs)

value: knockdown for DNA methyltransferases DNMT1, DNMT3A, DNMT3B


title: KAP1 Chip

value: AbCam (ab10483)


title: TPM_Sample_C10_20160407000

description:
Sample_C10_20160407000
C10_20160407000_S75_L006


title: TPM_Sample_A9_20160407000

description:
Sample_A9_20160407000
A9_20160407000_S68_L006


title: P2_Adipocytes_DMSO_3


title: TPM_Sample_C5_20160407000

description:
Sample_C5_20160407000
C5_20160407000_S46_L006


title: KO3

city: Mitaka

first: Jun-ichi

last: Suehiro

state: Tokyo

address: 6-20-2, Shinkawa

department: Department of Pharmacology and Toxicology

country: Japan

institute: Kyorin University School of Medicine

data_processing:
Over 50 million sequence reads per sample were trimmed for removing adapters and low-quality sequences with Trimmomatic v0.33 and mapped against Mus musculus genome (UCSC version mm9) using TopHat v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKM) values and differentially expressed genes (DEGs) were determined with Cuffnorm and Cuffdiff v.2.2.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values generated by Cuffnorm v.2.2.1

organism: Mus musculus

source_name: TAK1 conditional knockout_liver

extract_protocol:
mRNA derived from mouse liver was isolated using RNA extracting spin column (Qiagen)
RNA libraries were prepared with TruSeq Sample Prep v2 kit and sequenced using a paired-end protocol on a HiSeq 2500 (Illumina) according to manufarcture's instruction.

tag: strain background

value: liver

tag: treated with

value: tamoxifen


title: TPM_Sample_H5_20160407000

description:
Sample_H5_20160407000
H5_20160407000_S51_L006


title: Cont3


title: TPM_Sample_C6_20160407000

description:
Sample_C6_20160407000
C6_20160407000_S53_L006


title: Cont2


title: P1_Adipocytes_Rosi_1


title: Cont1


title: TPM_Sample_B4_20160407000

description:
Sample_B4_20160407000
B4_20160407000_S38_L006


title: TPM_Sample_D3_20160407000

description:
Sample_D3_20160407000
D3_20160407000_S35_L006


title: TPM_Sample_D9_20160407000

description:
Sample_D9_20160407000
D9_20160407000_S69_L006


title: TPM_Sample_C3_20160407000

description:
Sample_C3_20160407000
C3_20160407000_S34_L006


title: Sample_Plate8_B7

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

data_processing:
Sequencing and mapping were controlled for quality using standard tools provided in the FastQC software.
Raw reads were mapped to the reference mouse genome (Ensembl v74 GRCm38/mm10) using tophat 2.0.11. Read counts per gene were calculated for each sample using HTseq version 0.6.1 (only genes with the “gene_biotype” type “protein coding” were considered for quantification).
Low expressed genes were removed (i.e. genes with a total number of less than 5 counts across all samples). The total number of remaining genes was 10,238. Read counts per gene were further normalised across all samples using DESeq2 variance stabilised transformation (VST). VST counts were log2 transformed with an offset of 1.
Genome_build: Ensembl v74 GRCm38/mm10
Supplementary_files_format_and_content: raw_gene_counts_not_filtered.txt: tab separated file with raw gene expression counts for each gene and sample (only genes with the “gene_biotype” type “protein coding”); log2_filtered_gene_counts_VST: Read counts per gene normalised across all samples using DESeq2 variance stabilised transformation (VST) and log2 transformed with an offset of 1.

source_name: Bone marrow derived macrophage

growth_protocol: Bone marrow-derived macrophages (BMDMs) were isolated and characterized as described previously (Lai et al. 2014; Behmoaras et al. 2015). Bone marrow cells were allowed to differentiate in Dulbecco’s modified Eagle’s medium (DMEM) (Thermo Fisher Scientific, Waltham, MA) containing 25 mM HEPES buffer (Sigma), 25% L929-conditioned medium, 25% fetal bovine serum (Labtech), penicillin (100 units/ml; Thermo Fisher Scientific) and streptomycin (100 μg/ml; Thermo Fisher Scientific), and cultured for 5 days in Petri dishes (Nunc).

extract_protocol:
Total RNA was extracted from BMDMs using Trizol (Invitrogen) and RNeasy mini kit (Qiagen) according to manufacturer's instructions, with an additional purification step by on-column DNase treatment using the RNase-free DNase Kit (Qiagen) to ensure elimination of any genomic DNA. The integrity and quantity of total RNA was determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies).
500 ng of total RNA was used to generate RNA-seq libraries using TruSeq RNA sample preparation kit (Illumina) according to the manufacturer's instructions. Briefly, RNA was purified and fragmented using poly-T oligo-attached magnetic beads using two rounds of purification followed by the first and second cDNA strand synthesis. Next, cDNA 3' ends were adenylated and adapters ligated followed by 15 cycles of library amplification. Finally, the libraries were size selected using AMPure XP Beads (Beckman Coulter) purified and their quality was checked using Agilent 2100 Bioanalyzer. Samples were randomized to avoid batch effects and multiplexed libraries were run on a single lane (6 samples/lane) of the HiSeq 2500 platform (Illumina) to generate 100bp paired-end reads

tag: strain

value: Crl:CFW(SW)-US_P08 (CFW)

value: 16 weeks

tag: batch

tag: lane

tag: Sex

value: M


title: TPM_Sample_G4_20160407000

description:
Sample_G4_20160407000
G4_20160407000_S43_L006


title: KO2

tag: genotype/variation


title: KO1


title: TPM_Sample_D1_20160407000

description:
Sample_D1_20160407000
D1_20160407000_S25_L006


title: TPM_Sample_D10_20160407000

description:
Sample_D10_20160407000
D10_20160407000_S76_L006


title: Sample_Plate8_B5

value: F


title: TPM_Sample_F9_20160407000

description:
Sample_F9_20160407000
F9_20160407000_S71_L006


title: TPM_Sample_H9_20160407000

description:
Sample_H9_20160407000
H9_20160407000_S73_L006


title: TPM_G5A

description:
G5A
G5A_S173_L005

source_name: Human 3

value: individual 3

value: Black/African American


title: Sample_Plate8_B1


title: TPM_B6A

description:
B6A
B6A_S114_L005


title: Sample_Plate8_B6


title: Sample_Plate8_B4


title: Sample_Plate8_B3


title: TPM_C7A

description:
C7A
C7A_S127_L005


title: TPM_B11A

description:
B11A
B11A_S119_L005


title: Sample_Plate8_B9


title: TPM_E7A

description:
E7A
E7A_S151_L005


title: Sample_Plate8_B11


title: Sample_Plate8_B12


title: Sample_Plate8_B10


title: TPM_F2A

description:
F2A
F2A_S158_L005


title: TPM_C4A

description:
C4A
C4A_S124_L005


title: Sample_Plate8_A9


title: TPM_D4A

description:
D4A
D4A_S136_L005


title: Sample_Plate8_A8


title: TPM_H5A

description:
H5A
H5A_S185_L005


title: Sample_Plate8_A7


title: Sample_Plate8_B2


title: TPM_C1A

description:
C1A
C1A_S121_L005


title: Sample_Plate8_A6


title: TPM_C11A

description:
C11A
C11A_S131_L005


title: TPM_G10A

description:
G10A
G10A_S178_L005


title: Sample_Plate8_A2


title: Sample_Plate8_A4


title: Sample_Plate8_A3


title: Sample_Plate8_A1


title: TPM_A6A

description:
A6A
A6A_S102_L005


title: TPM_B4A

description:
B4A
B4A_S112_L005


title: TPM_F12A

description:
F12A
F12A_S168_L005


title: TPM_A12A

description:
A12A
A12A_S108_L005


title: Sample_Plate8_A12


title: Sample_Plate8_A11


title: TPM_A11A

description:
A11A
A11A_S107_L005


title: TPM_D5A

description:
D5A
D5A_S137_L005


title: Sample_Plate8_A10


title: Sample_Plate7_B7


title: Sample_Plate7_B8


title: TPM_G3A

description:
G3A
G3A_S171_L005


title: Sample_Plate7_B6


title: TPM_D8A

description:
D8A
D8A_S140_L005


title: TPM_D7A

description:
D7A
D7A_S139_L005


title: Sample_Plate8_A5


title: TPM_H6A

description:
H6A
H6A_S186_L005


title: Sample_Plate7_B5


title: TPM_E9A

description:
E9A
E9A_S153_L005


title: TPM_F5A

description:
F5A
F5A_S161_L005


title: Sample_Plate7_B4


title: Sample_Plate7_B3


title: Sample_Plate7_B2


title: TPM_A8A

description:
A8A
A8A_S104_L005


title: TPM_A2A

description:
A2A
A2A_S98_L005


title: TPM_H10A

description:
H10A
H10A_S190_L005


title: Sample_Plate7_B1


title: Sample_Plate7_B12


title: TPM_H11A

description:
H11A
H11A_S191_L005


title: Sample_Plate7_B9


title: Sample_Plate7_B10


title: Sample_Plate7_B11


title: Sample_Plate7_A9


title: TPM_D1A

description:
D1A
D1A_S133_L005


title: TPM_E12A

description:
E12A
E12A_S156_L005


title: TPM_B8A

description:
B8A
B8A_S116_L005


title: Sample_Plate7_A7


title: TPM_H1A

description:
H1A
H1A_S181_L005


title: TPM_D6A

description:
D6A
D6A_S138_L005


title: Sample_Plate7_A4


title: Sample_Plate7_A5


title: TPM_E3A

description:
E3A
E3A_S147_L005


title: Sample_Plate7_A3


title: TPM_F4A

description:
F4A
F4A_S160_L005


title: TPM_E1A

description:
E1A
E1A_S145_L005


title: Sample_Plate7_A2


title: TPM_F6A

description:
F6A
F6A_S162_L005


title: TPM_E2A

description:
E2A
E2A_S146_L005


title: TPM_C6A

description:
C6A
C6A_S126_L005


title: Sample_Plate7_A10


title: Sample_Plate7_A6


title: Sample_Plate7_A8


title: TPM_G1A

description:
G1A
G1A_S169_L005


title: Sample_Plate7_A1


title: TPM_A9A

description:
A9A
A9A_S105_L005


title: TPM_D3A

description:
D3A
D3A_S135_L005


title: Sample_Plate4_B8


title: TPM_B2A

description:
B2A
B2A_S110_L005


title: Sample_Plate4_B9


title: TPM_B7A

description:
B7A
B7A_S115_L005


title: Sample_Plate7_A12


title: Sample_Plate4_B7


title: TPM_F10A

description:
F10A
F10A_S166_L005


title: Sample_Plate4_B6


title: TPM_B1A

description:
B1A
B1A_S109_L005


title: TPM_C8A

description:
C8A
C8A_S128_L005


title: Sample_Plate4_B5


title: Sample_Plate4_B4


title: TPM_B5A

description:
B5A
B5A_S113_L005


title: TPM_B3A

description:
B3A
B3A_S111_L005


title: Sample_Plate4_B3


title: Sample_Plate4_B2


title: TPM_G4A

description:
G4A
G4A_S172_L005


title: TPM_C10A

description:
C10A
C10A_S130_L005


title: Sample_Plate4_B1


title: Sample_Plate4_B12


title: TPM_E6A

description:
E6A
E6A_S150_L005


title: Sample_Plate4_A9


title: Sample_Plate4_B11


title: TPM_C9A

description:
C9A
C9A_S129_L005


title: Sample_Plate4_A8


title: TPM_D11A

description:
D11A
D11A_S143_L005


title: Sample_Plate4_A7


title: TPM_E8A

description:
E8A
E8A_S152_L005


title: Sample_Plate4_A6


title: TPM_D12A

description:
D12A
D12A_S144_L005


title: Sample_Plate4_A5


title: ms_rel_f_3

city: Moscow

first: Natalia

last: Baulina

address: Ostrovityanov 1

department: Molecular biology and medical biotechnology

country: Russia

institute: Pirogov Russian National Research Medical University

data_processing:
Each library was indexed in order to multiplex four samples per sequencing run on the Illumina MiSeq platform using MiSeq 50 cycle Reagent Kits v2. A minimum of 15 million 50bp sequencing reads were collected from each sample
Illumina Casava1.7 software used for basecalling
The Illumina adapter sequences as well as low quality nucleotides were trimmed from the raw fastq files using Trimmomatic
The trimmed reads were aligned and annotated to miRBase version 21 using Bowtie2
The cpm tables represent only those miRNAs that achieved at least one read in at least one sample after applying "Filter low expression tags" step when preprocessing the data.
Differential expression analysis was conducted using the limma package
Genome_build: miRBase version 21
Supplementary_files_format_and_content: CPM

source_name: peripheral blood mononuclear cells

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll-Hypaque density gradient method within 3 h of sampling. RNA was isolated using miRNeasy Mini Kit.
Small RNA libraries were constructed using TruSeq® Small RNA Library Prep Kit, following manufacturer instructions. Individual libraries were constructed using 1µg of total RNA isolated from each sample. Samples were individually barcoded and sequenced in multiplexed pools each containing 4 samples using the 36 bp fragment protocol on Illumina MiSeq platform

treatment_protocol: All patients were treatment-naïve

tag: disease state

value: relapsing multiple sclerosis

tag: cell type

value: PBMCs


title: ms_rel_f_1


title: ms_rem_f_4

value: remitting multiple sclerosis


title: Sample_Plate4_A4


title: ms_rel_f_4

value: female


title: ms_rem_f_3


title: ms_rem_f_1


title: TPM_E11A

description:
E11A
E11A_S155_L005

tag: tissue

value: Pancreatic islet


title: Sample_Plate4_A3


title: TPM_B10A

description:
B10A
B10A_S118_L005


title: ctrl_f_4

value: healthy control


title: TPM_F3A

description:
F3A
F3A_S159_L005


title: ms_rel_f_2


title: ms_rem_f_2


title: ctrl_f_2


title: TPM_G8A

description:
G8A
G8A_S176_L005


title: ctrl_f_3


title: Sample_Plate4_A1


title: Sample_Plate4_B10


title: TPM_A5A

description:
A5A
A5A_S101_L005


title: TPM_C3A

description:
C3A
C3A_S123_L005


title: ctrl_f_1


title: ms_rel_m_4

description: cpm_male.txt  (Note: ms_rel_m_4 was excluded from the final processed data after examining all the samples for outliers using the multi-dimensional scaling procedure at the preprocessing stage.)

value: male


title: ms_rel_m_3


title: TPM_C2A

description:
C2A
C2A_S122_L005


title: TPM_A3A

description:
A3A
A3A_S99_L005


title: ms_rel_m_2


title: Sample_Plate4_A2


title: Sample_Plate4_A12


title: ms_rel_m_1


title: ms_rem_m_3


title: TPM_G4

description:
Sample_G4
G4_TCCTGAGC-CTAAGCCT_L004

source_name: Human 2

value: individual 2

value: Hispanic/Latino


title: ms_rem_m_2


title: Sample_Plate4_A11


title: Sample_Plate4_A10


title: Sample_Plate3_B9


title: ms_rem_m_4


title: ctrl_m_4


title: TPM_E2

description:
Sample_E2
E2_CGTACTAG-ACTGCATA_L004


title: ms_rem_m_1


title: ctrl_m_3


title: Sample_Plate3_B8


title: ctrl_m_2


title: ctrl_m_1


title: TPM_Sample_C2_20160407000

description:
Sample_C2_20160407000
C2_20160407000_S30_L006

value: individual 4

value: White


title: TPM_A5

description:
Sample_A5
A5_GGACTCCT-CTCTCTAT_L004


title: Sample_Plate3_B6

value: Crl:CFW(SW)-US_P08 (CFW)


title: TPM_C12A

description:
C12A
C12A_S132_L005


title: Sample_Plate3_B5

value: 16 weeks


title: TPM_C8

description:
Sample_C8
C8_CAGAGAGG-AGAGTAGA_L004


title: Stem_B1b8_rep1

city: Bozeman

first: Michael

last: Giroux

state: Montana

address: 119 Plant Bioscience Building

department: Plant Sciences

institute: Montana State University

description:
8-B1b-1
processed data file: RNA_SEQ_edited_7.19.xlsx

data_processing:
The sequence data were analyzed using ArrayStar (DNASTAR, Madison, Wisconsin), with the parameters set as: match setting at 100% for a minimum 50 bp, and all other settings left as default. The resultant data were presented as reads per kilobase of transcript for million mapped reads (RPKM) (Mortazavi et al., 2008) and normalized to Act-2, an actin like protein which was similarly expressed in both genotypes, and previously reported as a reliably expressed gene for normalization (Tenea et al., 2011). The data was analyzed globally against the available rice genome.  Specific wheat genes of interest were also analyzed. Genes central to either carbon or nitrogen metabolism were identified based on expression profiling done in rice by Hirose (2006) and adapted in Schlosser (2014) to identify the most prevalent form of the gene in green tissue during development. Wheat genome orthologs were identified using NCBI BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and used for expression analysis.
Genome_build: Not provided
Supplementary_files_format_and_content: 9.30.2016_Select_Genes_Default.astar
Supplementary_files_format_and_content: RNA_SEQ_edited_7.19.xlsx: Excel file

organism: Triticum aestivum

source_name: Wheat stem tissue

growth_protocol: Plants were grown under field conditions near Bozeman, MT (latitude 45.6N, longitude 111.00W). Plants were irrigated with 5cm of water on week pre- and post-anthesis.

extract_protocol:
Total RNA was extracted in accordance with the QIAGEN RNeasy Plant Mini kit and quantified using an Agilent Bioanalyzer.
Libraries were prepared according to Illumina's TruSeq Stranded mRNA Library prep.

treatment_protocol: Plants either carried the mutant semi-dwarfing allele, Rht-B1b, or the wildtype tall allele, Rht-B1a.

tag: cultivar/background

value: Fortuna (spring wheat)

value: 14 days past anthesis

value: stem


title: hsa-miR-9-5p rep 2

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

description: RNA-seq read counts combined from two sequencing runs

data_processing:
Raw sequence reads were mapped to the human RefSeq transcriptome with Bowtie and then normalized by computing the gene expression count per million reads, followed by trimmed median normalization. A floor value of 5 was set for low readings (<5).
Genome_build: NCBI RefSeq
Supplementary_files_format_and_content: Tab-delimited text files containing normalized read count values for individual samples

source_name: HeLa cells

extract_protocol:
Total RNA was extracted from the cell lysate using the mirVana kit (Life Technologies)
RNA libraries were prepared for sequencing using NEBNext mRNA Library Prep kit. Ribosome RNA was removed from total RNA by rRNA-specific biotin-labeled DNA oligo probes.

treatment_protocol: Individual miRNAs were transfected into cells 24 h prior to RNA extraction

value: Cervical cancer cell line


title: hsa-miR-9-3p rep 2


title: Negative Control rep 2


title: TPM_E1

description:
Sample_E1
E1_TAAGGCGA-ACTGCATA_L004

tag: subject id


title: Stem_B1b8_rep2

description:
8-B1b-2
processed data file: RNA_SEQ_edited_7.19.xlsx


title: Sample_Plate3_B3

value: F


title: Stem_Fortuna7_rep1

description:
7-Fortuna-1
processed data file: RNA_SEQ_edited_7.19.xlsx


title: TPM_D1

description:
Sample_D1
D1_TAAGGCGA-GTAAGGAG_L004

tag: ethnicity


title: Sample_Plate3_B4

tag: age


title: Negative Control rep 1


title: Sample_Plate3_B2

value: M


title: TPM_E12

description:
Sample_E12
E12_GTAGAGGA-ACTGCATA_L004

tag: gender


title: hsa-miR-9-3p rep 1


title: hsa-miR-34a-5p rep 2


title: Sample_Plate3_B7


title: Sample_Plate3_B1


title: Stem_B1b5_rep2

description:
5-B1b-2
processed data file: RNA_SEQ_edited_7.19.xlsx


title: TPM_E4

description:
Sample_E4
E4_TCCTGAGC-ACTGCATA_L004

tag: bmi


title: Stem_B1b5_rep1

description:
5-B1b-1
processed data file: RNA_SEQ_edited_7.19.xlsx


title: hsa-miR-34a-5p rep 1


title: TPM_E11

description:
Sample_E11
E11_AAGAGGCA-ACTGCATA_L004


title: TPM_H10

description:
Sample_H10
H10_CGAGGCTG-GCGTAAGA_L004


title: Sample_Plate3_B12


title: Stem_Fortuna4_rep2

description:
4-Fortuna-2
processed data file: RNA_SEQ_edited_7.19.xlsx


title: hsa-miR-9-5p rep 1


title: Stem_Fortuna7_rep2

description:
7-Fortuna-2
processed data file: RNA_SEQ_edited_7.19.xlsx


title: TPM_G8

description:
Sample_G8
G8_CAGAGAGG-CTAAGCCT_L004


title: hsa-miR-31-5p rep 2


title: Stem_Fortuna4_rep1

description:
4-Fortuna-1
processed data file: RNA_SEQ_edited_7.19.xlsx


title: Sample_Plate3_B11


title: Stem_B1b2_rep2

description:
2-B1b-2
processed data file: RNA_SEQ_edited_7.19.xlsx


title: Sample_Plate3_A9


title: TPM_E8

description:
Sample_E8
E8_CAGAGAGG-ACTGCATA_L004


title: Stem_B1b2_rep1

description:
2-B1b-1
processed data file: RNA_SEQ_edited_7.19.xlsx


title: hsa-miR-21-5p rep 2


title: TPM_F10

description:
Sample_F10
F10_CGAGGCTG-AAGGAGTA_L004


title: Sample_Plate3_B10


title: Stem_Fortuna1_rep2

description:
1-Fortuna-2
processed data file: RNA_SEQ_edited_7.19.xlsx


title: hsa-miR-31-5p rep 1


title: Sample_Plate3_A8


title: hsa-miR-210-3p rep 1


title: TPM_C4

description:
Sample_C4
C4_TCCTGAGC-AGAGTAGA_L004


title: Sample_Plate3_A6


title: TPM_D2

description:
Sample_D2
D2_CGTACTAG-GTAAGGAG_L004


title: TPM_C11

description:
Sample_C11
C11_AAGAGGCA-AGAGTAGA_L004


title: Sample_Plate3_A7


title: Leaf_B1b17_rep8

description:
17-B1b-2
processed data file: RNA_SEQ_edited_7.19.xlsx

source_name: Wheat flag leaf

value: leaf


title: hsa-miR-206 rep 2


title: hsa-miR-210-3p rep 2


title: TPM_F1

description:
Sample_F1
F1_TAAGGCGA-AAGGAGTA_L004


title: hsa-miR-206 rep 1


title: TPM_B6

description:
Sample_B6
B6_TAGGCATG-TATCCTCT_L004


title: Leaf_Fortuna16_rep6

description:
16-Fortuna-2
processed data file: RNA_SEQ_edited_7.19.xlsx


title: Leaf_B1b17_rep7

description:
17-B1b-1
processed data file: RNA_SEQ_edited_7.19.xlsx


title: hsa-miR-21-5p rep 1


title: Sample_Plate3_A5


title: TPM_A12

description:
Sample_A12
A12_GTAGAGGA-CTCTCTAT_L004


title: Stem_Fortuna1_rep1

description:
1-Fortuna-1
processed data file: RNA_SEQ_edited_7.19.xlsx


title: Sample_Plate3_A1


title: TPM_E6

description:
Sample_E6
E6_TAGGCATG-ACTGCATA_L004


title: Leaf_Fortuna16_rep5

description:
16-Fortuna-1
processed data file: RNA_SEQ_edited_7.19.xlsx


title: hsa-miR-200c-3p rep 1


title: Sample_Plate3_A2


title: Sample_Plate3_A12


title: Sample_Plate3_A11


title: hsa-miR-200c-3p rep 2


title: TPM_C9

description:
Sample_C9
C9_GCTACGCT-AGAGTAGA_L004


title: Leaf_B1b14_rep4

description:
14-B1b-2
processed data file: RNA_SEQ_edited_7.19.xlsx


title: hsa-miR-200a-3p rep 2

description: RNA-seq read counts combined from two sequencing runs


title: Leaf_B1b14_rep3

description:
14-B1b-1
processed data file: RNA_SEQ_edited_7.19.xlsx


title: hsa-miR-200b-3p rep 1


title: Leaf_Fortuna13_rep4

description:
13-Fortuna-2
processed data file: RNA_SEQ_edited_7.19.xlsx


title: TPM_G10

description:
Sample_G10
G10_CGAGGCTG-CTAAGCCT_L004


title: TPM_D11

description:
Sample_D11
D11_AAGAGGCA-GTAAGGAG_L004


title: hsa-miR-200b-3p rep 2


title: Sample_Plate3_A10


title: Leaf_Fortuna13_rep3

description:
13-Fortuna-1
processed data file: RNA_SEQ_edited_7.19.xlsx


title: Sample_Plate2_B9


title: hsa-miR-200a-3p rep 1


title: Leaf_B1b11_rep2

description:
11-B1b-2
processed data file: RNA_SEQ_edited_7.19.xlsx


title: TPM_G12

description:
Sample_G12
G12_GTAGAGGA-CTAAGCCT_L004


title: hsa-miR-193b-3p rep 2


title: TPM_C10

description:
Sample_C10
C10_CGAGGCTG-AGAGTAGA_L004


title: Sample_Plate2_B8


title: Leaf_B1b11_rep1

description:
11-B1b-1
processed data file: RNA_SEQ_edited_7.19.xlsx


title: Sample_Plate2_B7


title: TPM_E3

description:
Sample_E3
E3_AGGCAGAA-ACTGCATA_L004


title: Sample_Plate2_B6


title: Leaf_Fortuna10_rep2

description:
10-Fortuna-2
processed data file: RNA_SEQ_edited_7.19.xlsx


title: hsa-miR-17-5p rep 2


title: TPM_E9

description:
Sample_E9
E9_GCTACGCT-ACTGCATA_L004


title: hsa-miR-193b-3p rep 1


title: Sample_Plate2_B5


title: Leaf_Fortuna10_rep1

description:
10-Fortuna-1
processed data file: RNA_SEQ_edited_7.19.xlsx


title: hsa-miR-17-5p rep 1


title: hsa-miR-16-5p rep 2


title: Scrambled shRNA 1

city: Frankfurt

first: Daniela

last: Krause

address: Paul-Ehrlich-Straße 42-44

country: Germany

institute: Georg-Speyer-Haus

description:
ReadCounts_DeSeqRes.csv
p329sCML09

data_processing:
CASAVA 1.8
Data were analyzed for differential expression using DESeq2 (version 1.18.1)
Supplementary_files_format_and_content: comma separated file contains raw read counts for each gene and sample as well as results from differential analysis using DESeq2.

source_name: Bone marrow Lineage- BCR-ABL1+ shRNA+

extract_protocol:
Lineage- BCR-ABL1-RFP+ shRNA-Venus+ DAPI- cells from bone marrow of CML mice were sorted directly into TRIzol.
500 ng were used as start Material for library construction. The TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Cat. No. RS-122-2201) and TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Cat. No. RS-122-2301) were used according to manuf. Recommendations
TruSeq total stranded RNA Seq approach

tag: genotype

value: scrambled control

value: Bone marrow


title: TPM_C12

description:
Sample_C12
C12_GTAGAGGA-AGAGTAGA_L004

value: Pancreatic islet


title: TPM_F7

description:
Sample_F7
F7_CTCTCTAC-AAGGAGTA_L004

value: male


title: Sample_Plate2_B4


title: 445 BC TI rep1

description:
processed data file: mES_445_peaks.bed
processed data file: ZFP445_BC_1.bed

source_name: Embryonic stem cells (Black6/Cast)

growth_protocol: Naive murine embryonic stem cells were cultured in N2B27 medium with 1x MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1x penicillin/streptomycin, 25µg/mL Bovine serum albumin, leukaemia inhibitory factor (LIF), and 2i containing 1µM MEK inhibitor PD 0325901 (Axon 1408) and 3µM GSK3 inhibitor CHIR 99021 (Axon 1386). Cells were grown on 0.1% gelatin-coated plates and split every two days. Cells were transduced, selected with 4μg/mL puromycin and collected after 5 days.

extract_protocol:
Cells were harvested, washed with Episerf (LifeTechnologies, #10732), fixed in 10mL per 1x10^7 cells (10 min in 1% formaldehyde), quenched with TrisHCl in 50mL (at 250 mM final), washed with PBS, and pelleted. Each pellet containing 1x10^7 cells was lysed, resuspended in 1 mL of sonication buffer on ice (10 mM Tris at pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.25% NLS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 20 min, 5% duty cycle, 140W, 200 cycles). Sonication was assessed by reverse cross-linking (65°C, RNase A at 1μg/μL, overnight), followed by DNA extraction. Fragment size (between 200-400bp) was checked on a Bioanalyzer (Agilent 2100). Immunoprecipitations were performed with chromatin from 1x10^7 cells with Dynabeads (ThermoFisher) in IP buffer (16.25 mM Tris at pH 8.1, 137.5 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1.25% Triton X-100, and protease inhibitors) overnight. Chromatin was reversed cross-linked (65°C, Proteinase K at 400ng/μL, overnight) and DNA was further extracted for analysis.
Single-end libraries were prepared and sequenced in 100bp reads runs according to Illumina instructions.

tag: strain/background

value: Embryonic stem cells (ESCs)

value: overexpressing HA-tagged ZFP445

tag: chip antibody


title: hsa-miR-16-5p rep 1


title: Sample_Plate2_B3

tag: strain


title: TPM_D5

description:
Sample_D5
D5_GGACTCCT-GTAAGGAG_L004

value: individual 2

value: Hispanic/Latino


title: TPM_H1

description:
Sample_H1
H1_TAAGGCGA-GCGTAAGA_L004


title: hsa-miR-15a-5p rep 2


title: Sample_Plate2_B1

value: Crl:CFW(SW)-US_P08 (CFW)

tag: batch


title: TPM_A4

description:
Sample_A4
A4_TCCTGAGC-CTCTCTAT_L004


title: Sample_Plate2_B2

value: 16 weeks

tag: lane


title: hsa-miR-15a-5p rep 1


title: Sample_Plate2_B12

tag: Sex


title: hsa-miR-155-5p rep 2


title: hsa-miR-155-5p rep 1


title: Sample_Plate2_B10


title: TPM_F11

description:
Sample_F11
F11_AAGAGGCA-AAGGAGTA_L004


title: hsa-miR-146a-5p rep 2


title: TPM_B11

description:
Sample_B11
B11_AAGAGGCA-TATCCTCT_L004


title: 445 BC ChIP rep1

tag: genotype/variation

value: HA (Covance, MMS-101P)


title: TPM_A11

description:
Sample_A11
A11_AAGAGGCA-CTCTCTAT_L004


title: hsa-miR-146a-5p rep 1


title: Sample_Plate2_A9


title: Sample_Plate2_A7


title: TPM_C2

description:
Sample_C2
C2_CGTACTAG-AGAGTAGA_L004


title: TPM_H7

description:
Sample_H7
H7_CTCTCTAC-GCGTAAGA_L004


title: hsa-miR-145-5p rep 1


title: hsa-miR-145-5p rep 2


title: Sample_Plate2_A6


title: hsa-miR-142-3p rep 2


title: Sample_Plate2_B11


title: Sample_Plate2_A5


title: hsa-miR-142-3p rep 1


title: Sample_Plate2_A4


title: TPM_F9

description:
Sample_F9
F9_GCTACGCT-AAGGAGTA_L004


title: hsa-miR-133b rep 2


title: Sample_Plate2_A3


title: Sample_Plate2_A8


title: TPM_C1

description:
Sample_C1
C1_TAAGGCGA-AGAGTAGA_L004


title: TPM_D12

description:
Sample_D12
D12_GTAGAGGA-GTAAGGAG_L004


title: shCTL 24h replicate 1

city: Granada

first: Concepción

last: Marañón

address: Avda Ilustración 114

country: Spain

institute: Genyo Centre

description: replicate

hyb_protocol: Standard Illumina Human-HT12 Version 4

scan_protocol: Standard Illumina Genome Studio

data_processing: The data were background corrected and normalized using the neqc function from the Limma package

source_name: Gen2.2 cell line

label_protocol: Illumina TotalPrep RNA Amplification Kit

growth_protocol: Cells were mantained in RPMI 1640 supplemented with 10% FBS

extract_protocol: RNA was extracted high pure RNA isolation kit from Roche, in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cultured cells at log phase

tag: phenotype

value: shCTL

tag: stimulus

tag: time


title: shSIDT1 24h replicate 1

description: replicate


title: TPM_B3

description:
Sample_B3
B3_AGGCAGAA-TATCCTCT_L004

tag: tissue


title: Sample_Plate2_A2


title: shSIDT1 24h replicate 2

description: replicate


title: hsa-miR-133b rep 1

tag: cell type


title: TPM_H11

description:
Sample_H11
H11_AAGAGGCA-GCGTAAGA_L004

tag: subject id

tag: ethnicity


title: hsa-miR-126-5p rep 2


title: TPM_G6

description:
Sample_G6
G6_TAGGCATG-CTAAGCCT_L004

tag: age

tag: gender


title: hsa-miR-126-3p rep 1


title: TPM_H3

description:
Sample_H3
H3_AGGCAGAA-GCGTAAGA_L004

tag: bmi


title: Sample_Plate2_A1


title: shCTL 24h replicate 2

description: replicate


title: hsa-miR-126-5p rep 1


title: TPM_H12

description:
Sample_H12
H12_GTAGAGGA-GCGTAAGA_L004


title: hsa-miR-126-3p rep 2


title: TPM_F5

description:
Sample_F5
F5_GGACTCCT-AAGGAGTA_L004


title: Gen2.2 24h replicate 1

description: replicate

value: WT


title: shSIDT1 6h replicate 2

description: replicate


title: Gen2.2 24h replicate 3

description: replicate


title: shSIDT1 6h replicate 3

description: replicate


title: TPM_E10

description:
Sample_E10
E10_CGAGGCTG-ACTGCATA_L004


title: shSIDT1 6h replicate 1

description: replicate


title: Gen2.2 24h replicate 2

description: replicate


title: Sample_Plate2_A11


title: hsa-miR-10a-5p rep 2

value: Cervical cancer cell line


title: Sample_Plate2_A10


title: shCTL 6h replicate 2

description: replicate


title: shCTL 6h replicate 1

description: replicate


title: shCTL 6h replicate 3

description: replicate


title: Sample_Plate1_A5

value: F


title: TPM_D4

description:
Sample_D4
D4_TCCTGAGC-GTAAGGAG_L004


title: Gen2.2 6h replicate 3

description: replicate


title: Sample_Plate1_A3


title: TPM_D8

description:
Sample_D8
D8_CAGAGAGG-GTAAGGAG_L004


title: Sample_Plate2_A12

value: M


title: Sample_Plate1_A6


title: hsa-miR-124-3p rep 2


title: hsa-miR-124-3p rep 1


title: Sample_Plate1_A4


title: TPM_F3

description:
Sample_F3
F3_AGGCAGAA-AAGGAGTA_L004


title: TPM_F12

description:
Sample_F12
F12_GTAGAGGA-AAGGAGTA_L004


title: hsa-miR-107 rep 2


title: hsa-miR-10a-5p rep 1


title: hsa-miR-107 rep 1


title: TPM_D3

description:
Sample_D3
D3_AGGCAGAA-GTAAGGAG_L004


title: TPM_G1

description:
Sample_G1
G1_TAAGGCGA-CTAAGCCT_L004


title: Sample_Plate1_A1


title: hsa-let-7c-5p rep 1


title: TPM_G7

description:
Sample_G7
G7_CTCTCTAC-CTAAGCCT_L004


title: Sample_Plate10_B9


title: TPM_H4

description:
Sample_H4
H4_TCCTGAGC-GCGTAAGA_L004


title: Sample_Plate10_B8


title: Sample_Plate1_A2


title: TPM_A1

description:
Sample_A1
A1_TAAGGCGA-CTCTCTAT_L004


title: Sample_Plate10_B7


title: Sample_Plate10_B6


title: TPM_B1

description:
Sample_B1
B1_TAAGGCGA-TATCCTCT_L004


title: hsa-let-7c-5p rep 2


title: Sample_Plate10_B5


title: Sample_Plate10_B4


title: Gen2.2 6h replicate 2

description: replicate


title: shCTL 2h replicate 3

description: replicate


title: shCTL 2h replicate 1

description: replicate


title: shSIDT1 2h replicate 2

description: replicate


title: Gen2.2 6h replicate 1

description: replicate


title: Gen2.2 2h replicate 2

description: replicate


title: shCTL 2h replicate 2

description: replicate


title: Gen2.2 2h replicate 1

description: replicate


title: compensated cirrhotic liver tissue transcriptome LM 57

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v3) in R.3.2.1

label: biotin

source_name: liver tissue

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA from sorted cells was obtained using the RNeasy Micro Kit (Qiagen). Total RNA was retro-transcribed using a high capacity complementary DNA reverse-transcription kit (Applied Biosystems, Foster City, CA).

value: whole liver tissue


title: shSIDT1 NS replicate 1

description: replicate


title: shSIDT1 2h replicate 1

description: replicate


title: shSIDT1 NS replicate 3

description: replicate


title: compensated cirrhotic liver tissue transcriptome LM47


title: shSIDT1 2h replicate 3

description: replicate


title: Gen2.2 2h replicate 3

description: replicate


title: shSIDT1 NS replicate 2

description: replicate


title: TPM_D7

description:
Sample_D7
D7_CTCTCTAC-GTAAGGAG_L004


title: Sample_Plate10_B3


title: compensated cirrhotic liver tissue transcriptome LM 30


title: TPM_E5

description:
Sample_E5
E5_GGACTCCT-ACTGCATA_L004


title: Sample_Plate10_B2


title: TPM_C3

description:
Sample_C3
C3_AGGCAGAA-AGAGTAGA_L004


title: TPM_A3

description:
Sample_A3
A3_AGGCAGAA-CTCTCTAT_L004


title: Sample_Plate10_B1


title: TPM_F8

description:
Sample_F8
F8_CAGAGAGG-AAGGAGTA_L004


title: TPM_C6

description:
Sample_C6
C6_TAGGCATG-AGAGTAGA_L004


title: Iliopsoas muscle_Severe_3

city: Kitakyushu

first: Takahiro

last: Umehara

address: 1-1 Iseigaoka Yahatanishiku

institute: University of Occupational and Environmental Health

data_processing:
StrandNGS 3.0.1 used for base-calling, alignment, filtering, peak-calling, generation of normalized abundance measurements.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 using COBWeb.
Reads Per Kilobase of exon model per Million mapped reads  (RPKM) were calculated using a protocol from A. Mortazavi et al., Nature Methods, 2008.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

organism: Rattus norvegicus

source_name: Iliopsoas muscle

extract_protocol:
Iliopsoas muscle of rat was immediately dissected and immersed in Ambion RNAlater (Thermo Fisher Scientific, Waltham, MA, USA) and kept overnight at 4°C. Total RNA was extracted using RNeasy Protect Mini kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer's instructions. RNA integrity was assessed by on-chip capillary electrophoresis using an Agilent RNA 6000 Nano kit and Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). NGS was performed using 2000 ng of total RNA. Three libraries were generated for each of the four conditions (Control, mild, moderate and severe hypothermia) (TruSeq Stranded mRNA LT Sample Prep Kit, Illumina, San Diego, California, USA), and sequenced on an Illumina Miseq (MiSeq Reagent Kit v3 (150 cycles)).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: condition

value: severe hypothermia

value: Iliopsoas muscle

value: Male

value: Wistar


title: Sample_Plate10_B12


title: TPM_F4

description:
Sample_F4
F4_TCCTGAGC-AAGGAGTA_L004

value: Pancreatic islet

value: male


title: Sample_Plate10_B11


title: Iliopsoas muscle_Severe_2


title: Iliopsoas muscle_Severe_1


title: TPM_H6

description:
Sample_H6
H6_TAGGCATG-GCGTAAGA_L004

value: individual 2


title: Iliopsoas muscle_Moderate_3

value: moderate hypothermia


title: P5_Adipose_2

value: Adipose


title: Sample_Plate10_A9

value: Crl:CFW(SW)-US_P08 (CFW)

value: 16 weeks


title: P5_Adipose_1


title: Liver progenitor cell organoids transcriptome HB6

value: Liver progenitor cells


title: shCTL NS replicate 2

description: replicate

value: shCTL


title: compensated cirrhotic liver tissue transcriptome LM 29


title: shCTL NS replicate 3

description: replicate


title: Liver progenitor cell organoids transcriptome HB9


title: Gen2.2 NS replicate 3

description: replicate

value: WT


title: Sample_Plate10_A8

value: F


title: TPM_H2

description:
Sample_H2
H2_CGTACTAG-GCGTAAGA_L004

value: Hispanic/Latino


title: Liver progenitor cell organoids transcriptome 521


title: Liver progenitor cell organoids transcriptome 995


title: Iliopsoas muscle_Moderate_1


title: shCTL NS replicate 1

description: replicate


title: Gen2.2 NS replicate 1

description: replicate


title: Gen2.2 NS replicate 2

description: replicate


title: Iliopsoas muscle_Moderate_2


title: ZFP57 TI

description: processed data file: hES_57_vs_hES_TI_peaks_macs100

source_name: H1 hESCs

extract_protocol:
Cells were harvested, washed 2x (in KO medium), fixed in 10mL per 1x10^7 cells (10 min in 1% formaldehyde), quenched with TrisHCl in 50mL (at 250 mM final), washed with PBS, and pelleted. Each pellet containing 1x10^7 cells was lysed, resuspended in 1 mL of sonication buffer on ice (10 mM Tris at pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.25% NLS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 20 min, 5% duty cycle, 140W, 200 cycles). Sonication was assessed by reverse cross-linking (65°C, RNase A at 1μg/μL, overnight), followed by DNA extraction. Fragment size (between 200-400bp) was checked on a Bioanalyzer (Agilent 2100). Immunoprecipitations were performed with chromatin from 1x10^7 cells with Dynabeads (ThermoFisher) in IP buffer (16.25 mM Tris at pH 8.1, 137.5 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1.25% Triton X-100, and protease inhibitors) overnight. Chromatin was reversed cross-linked (65°C, Proteinase K at 400ng/μL, overnight) and DNA was further extracted for analysis.
Single-end libraries were prepared and sequenced in 100bp reads runs according to Illumina instructions.

tag: cell line

value: Embryonic stem cells (ESCs)

value: overexpressing HA-tagged ZFP57

tag: chip antibody


title: P4_Adipose_1

source_name: Adipose tissue


title: Sample_Plate10_B10

tag: strain

tag: batch

value: M


title: Iliopsoas muscle_Mild_5

value: mild hypothermia

value: Iliopsoas muscle

value: Male


title: P4_Adipose_2


title: Sample_Plate10_A7

tag: lane

tag: Sex


title: Sample_Plate10_A6


title: TPM_B5

description:
Sample_B5
B5_GGACTCCT-TATCCTCT_L004

value: Pancreatic islet

value: male


title: ZFP57 Chip

tag: genotype/variation

value: HA (Covance, MMS-101P)


title: Sample_Plate10_A4


title: Sample_Plate10_A5


title: P3_Adipose_1

value: Adipose


title: P2_Adipose_2


title: Iliopsoas muscle_Mild_1

value: Wistar


title: Iliopsoas muscle_Mild_4


title: Sample_Plate10_A3

value: Crl:CFW(SW)-US_P08 (CFW)

value: 16 weeks


title: Iliopsoas muscle_Control_3

value: control


title: P2_Adipose_1


title: Sample_Plate10_A2


title: P3_Adipose_2


title: Iliopsoas muscle_Control_2


title: P1_Adipose_2


title: Iliopsoas muscle_Control_1


title: P1_Adipose_1


title: DT40-ASF_Clone 47

city: Indore

first: Amit

middle: Kumar

last: Singh

state: Madhya Pradesh

address: SB-215, School Building, IIT Indore, Khandwa Road, Simrol, Indore

department: Biosciences and Bio-medical Engineering

country: India

institute: Indian Institute of Technology, Indore

description: Reconstituted cells

data_processing:
The rawdata generated was checked for the quality with FastQC1. The first step is to pre process the data that includes removing the adapter sequences and removing the low quality bases. Preprocessing of the data is done with the Genotypic's proprietary script.
Tophat-2.0.133 was used for the analysis. TopHat is a fast splice junction mapper for RNA-Seqreads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra-high-throughput short  read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
Cufflinks-2.2.1 4 assembles transcripts, estimates their abundances, and tests for differentialexpression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in librarypreparation protocols.
Cufflinks-2.2.1 4 includes a script called cuffmerge that can be used to merge several Cufflinksassemblies together. The main purpose of this script is to make it easier to make an assembly GTF  file suitable for use with Cuffdiff.
Cufflinks-2.2.1 4 includes a program, "Cuffdiff", which is used to find significant changes in transcript expression. Merged GTF file produced by Cuffmerge was used as input in Cuffdiff. Merged GTF file for each set of DGE is also provided.
Genome build: Gallus_gallus-4.0 (galGal4)
Supplementary_files_format_and_content: GT_SO_5954_Expression_Report.xlsx

organism: Gallus gallus

source_name: DT40 chicken B-cells

growth_protocol: DT40-ASF cells were cultured in RPMI 1640 medium supplement with 10% FBS, 1% chicken serum, 50 μM 2-mercaptoethanol, 2 mM glutamine, 100 μg/ml penicillin G, and 50 μg/mL streptomycin at 39.5°C in 5% CO2.

extract_protocol: Sureselect strand specific mRNA library preparation for illumina platform sequencing. Libraries for RNA sequencing were prepared by Illumina compatible SureSelect strand-specific RNA Library prep kit (Agilent) at the Genotypic Technology Pvt. Ltd., Bangalore, India. mRNA enrichment was performed from 1 µg of Qubit quantified total RNA. The enriched mRNA was fragmented for 4 min at 94°C in the presence of divalent cations. Synthesis of the first strand cDNA was performed in the presence of actinomycin-D (Gibco) and purified using HighPrep magnetic beads (Magbio Genomics Inc.). Purified ss cDNA was used for second strand synthesis followed by the end repair using second strand synthesis containing end repair mix. The end-repaired cDNA was purified by using HighPrep magnetic beads. Adapters were ligated to the cDNA molecules after 3’ adenylation. The adaptor-ligated DNA was purified with HighPrep beads and then amplified for 10 cycles of PCR using Illumina-compatible indexing primers provided in the SureSelect strand-specific RNA library prep kit. The final PCR product was purified with HighPrep beads, followed by library quality control check. The sequencing library was initially quantified by Qubit fluorometer (Thermo Fisher Scientific) and its fragment size distribution was analyzed on the Agilent TapeStation system. Finally, the sequencing library was quantified accurately by quantitative PCR using the Kapa Library Quantification Kit (Kapa Biosystems). The PCR quantified libraries were then pooled in equimolar amounts to create a final multiplexed library pool for sequencing on an Illumina sequencer for 75 base paired-end chemistry.

value: B cell line DT40

tag: genotype

value: SRSF1-3 knock in


title: Sample_Plate10_A12

value: F


title: DT40-ASF_Untransfected

description: Reconstituted cells


title: DT40-ASF_Clone 41

description: Reconstituted cells


title: Sample_Plate10_A11


title: Sample_Plate10_A10


title: Tcf7-GFP+ P14 cells_tumor_Donor3

status: Public on Jan 10 2019

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

institute: University of Lausanne

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3) (Martin et al., 2011) and filtered for low complexity with seq crumbs (v. 0.1.8).
Reads were aligned against Mus musculus (version GRCm38) genome using STAR (v. 2.4.2a) (Dobin et al., 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1) (Anders et al., 2015) using M. musculus (Ensembl v. GRCm38.82) gene annotation.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include htseq gene counts for each sample.

source_name: Tcf7-GFP+ P14 cells_Tumor

extract_protocol:
Flow sorted cells were lysed and stored in Trizol before extraction of total cellular RNA using the Direct-zol™ RNA MiniPrep kit (Zymo Research).
RNA-seq libraries were prepared using SMART-Seq v4 Ultra Low Input RNA reagents (# 634888, Clontech) according to the protocol provided with the reagents beginning with 5ng of total RNA and using 9 cycles of PCR.  150 pg of the resulting cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (# 15032354, Illumina).

treatment_protocol: P14 cells from the spleen of naive mice were enriched using the EasySep Mouse CD8+ T Cell Isolation Kit (StemCell Technologies).  P14 cells, flow sorted based on the expression of CD8 and Tcf7-GFP, were kept as Naive control samples or were transferred into mice. Tumor infiltrating lympohcytes were obtained using a tumor dissociation kit (Miltenyi) followed by CD8 enrichement using a EasySep Mouse CD8+ T Cell Isolation Kit (StemCell Technologies) and flow sorting Tcf7-GFP+ and Tcf7-GFP- P14 cells based on the expresssion of CD45.2+ CD45.1- CD8+ Tcf7-GFP+/-.

tag: strain background

value: CD8 T cells expressing a P14 TCR and a Tcf7-GFP reporter

value: B6;D2-Tg(TcrLCMV)327Sdz/JDvsJ   B6-Tg(Tcf7-GFP)WHe

tag: cell subtype

value: Tcf7-GFP+ P14 cells


title: Tcf7-GFP+ P14 cells_tumor_Donor4

tag: cell type


title: Tcf7-GFP- P14 cells_tumor_Donor3

source_name: Tcf7-GFP- P14 cells_tumor

value: Tcf7-GFP- P14 cells


title: Naive P14 cells_Spleen_Donor2

source_name: Naive P14 cells_Spleen

value: Naive P14 cells


title: Tcf7-GFP- P14 cells_tumor_Donor2


title: Tcf7-GFP- P14 cells_tumor_Donor4


title: Naive P14 cells_Spleen_Donor3


title: Tcf7-GFP+ P14 cells_tumor_Donor1


title: Naive P14 cells_Spleen_Donor1


title: Dystrophic dog

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Serum samples of 3 dystrophic dogs were mixed to avoid detection of individual differences in miRNA expression.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Canis lupus familiaris

source_name: Serum from dystrophic dog

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

extract_protocol: RNA samples were extracted from serum using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

tag: phenotype

value: Affected

value: 2 months

value: Male


title: Normal dog

description: Serum samples of 3 normal dogs were mixed to avoid detection of individual differences in miRNA expression.

source_name: Serum from normal dog

value: Normal


title: Sample_Plate10_A1

source_name: Bone marrow derived macrophage


title: Tcf7-GFP- P14 cells_tumor_Donor1


title: x01_ABA_L12_rep02

city: Köln

first: Matthias

middle: Leonhard

last: Berens

address: Carl-von-Linné-Weg 10

institute: Max Planck Institute for Plant Breeding Research

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the Arabidopsis genome using splice-aware read aligner TopHat (version 2.0.10) with the parameters -p 10 -a 10 -g 10 --library-type fr-firststrand -G TAIR10_GFF3_genes.gff and transformed into a count per gene per library by using HTSeq (version 0.6.1) with the parameters -s reverse -f bam -t exon.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

organism: Arabidopsis thaliana

source_name: Fully-expanded true leave 12 of 28 to 35 day-old plants

growth_protocol: Arabidopsis plants were grown in a chamber at 22°C with a 10 h light period and 60% relative humidity for 3 weeks and then in another chamber at 22°C with a 12 h light period and 60% relative humidity.

extract_protocol:
Total RNAs were extracted using TRIzol (Invitrogen), followed by Dnase I (Roche) treatment.
RNA libraries were prepared from 1 μg of total RNA. Poly A enrichment and library preparation were performed with NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: 4 to 5 week old plants were foilar sprayed with either mock (0.5 % EtOH, 0.02% Tween20) or ABA (500 µM ABA, Sigma A1049, 500 µM in 0.5 % EtOH, 0.02% Tween20) solution. Old leaves (L7) and young leaves (L12) were harvested 48h after the spray treatment and samples were frozen in liquid nitrogen

tag: treatment

value: ABA

tag: leaf age

value: True leave 12 (L12)

tag: replicate


title: x01_ABA_L12_rep03


title: RNA profiles of skin tissues form IRF1 wild type mouse following radiation 2

city: suzhou

first: zhang

middle: shu

last: yu

state: Jinagsu

address: 199 Ren'ai Rd

department: Radiation Medicine

country: China

institute: soochow University

description: skin tissue of IRF1 wild-type mouse 2 with 35 Gy radiation

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse lncRNA Microrray V3 (4*180K,Design ID:084388) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 14.9(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: skin tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: IRF1 knockout (IRF-/-) mice and wild-type mice were kept in SPF-level animal houses where rats can drink and eat freely.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: The C57B L/6 IRF1 knockout (IRF-/-) mice were obtained from The Jackson Laboratory (stock number: 002762). IRF1 knockout (IRF-/-) mice and wild-type mice were anesthetized with an intraperitoneal injection of chloral hydrate (360 mg/kg), and the hair on hind limb of the mice was shaved using a razor. Mice were immobilized with adhesive tape on a plastic plate to minimize motion during radiation exposure. A 3-cm-thick piece of lead was used to shield the animals and localize the radiation field on hind leg. Irradiation was administered to the treatment area with 35 Gy at a dose rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems) as reported

tag: exposure

value: 35 Gy radiation

tag: tissue

value: skin

value: IRF1 wild-type

tag: age

value: 8 weeks old

value: male


title: RNA profiles of skin tissues form IRF1 wild type mouse following radiation 1

description: skin tissue of IRF1 wild-type mouse 1 with 35 Gy radiation


title: RNA profiles of skin tissues form IRF1 KO mouse following radiation 3

description: skin tissue of IRF1 KO-3 with 35 Gy radiation

value: IRF1 KO


title: RNA profiles of skin tissues form IRF1 KO mouse following radiation 4

description: skin tissue of IRF1 KO-4 with 35 Gy radiation


title: RNA profiles of skin tissues form IRF1 wild type mouse following radiation 4

description: skin tissue of IRF1 wild-type mouse 4 with 35 Gy radiation


title: x01_ABA_L12_rep01


title: hskm cells_miR20b-transfected_subject3

city: Stockholm

first: Mutsumi

last: Katayama

address: Solnavägen 9

department: Physiology and Pharmacology

institute: Karolinska Institutet

hyb_protocol: Biotin-labelled cDNA was then hybridized to GeneChip® Human Gene 2.0 ST microarrays at 45°C for 17 h and microarrays were washed on the Fluidic Station FS450 according to the specific manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner GCS3000 7G.

data_processing: Expression Console software was used. Analysis method: med-polish (rma-bg, quant-norm, sketch=-1, bioc=true, lowprecision=false, usepm=true, target=0, doavg=false)

source_name: primary human skeletal muscle cell (Subject 3), miR-20b transfected

label_protocol: GeneChip™ WT PLUS Reagent Kit (Thermo Fisher) was used according to the manufacturer's protocol.

extract_protocol: Extraction of total RNA was performed with miRNeasy kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Primary human skeletal muscle cells were transfected with miR-20b or miRNA-negative control.

value: primary human skeletal muscle cells

tag: transfected mirna

tag: subject


title: x01_ABA_L07_rep03

source_name: Fully-expanded true leave 7 of 28 to 35 day-old plants

value: True leave 7 (L07)


title: hskm cells_negative control-transfected_subject3

source_name: primary human skeletal muscle cell (Subject 3), miRNA-negative control transfected

value: miRNA-negative control


title: x01_ABA_L07_rep01


title: hskm cells_miR20b-transfected_subject1

source_name: primary human skeletal muscle cell (Subject 1), miR-20b transfected


title: x01_Mock_L12_rep03

value: Mock


title: x01_Mock_L12_rep01


title: x01_Mock_L07_rep03


title: hskm cells_miR20b-transfected_subject2

source_name: primary human skeletal muscle cell (Subject 2), miR-20b transfected


title: x01_Mock_L07_rep02


title: x01_ABA_L07_rep02


title: x01_Mock_L07_rep01


title: x01_Mock_L12_rep02


title: RNA profiles of skin tissues form IRF1 KO mouse following radiation 1

description: skin tissue of IRF1 KO-1 with 35 Gy radiation

tag: strain


title: hskm cells_negative control-transfected_subject1

source_name: primary human skeletal muscle cell (Subject 1), miRNA-negative control transfected


title: RNA profiles of skin tissues form IRF1 wild type mouse following radiation 3

description: skin tissue of IRF1 wild-type mouse 3 with 35 Gy radiation


title: RNA profiles of skin tissues form IRF1 KO mouse following radiation 2

description: skin tissue of IRF1 KO-2 with 35 Gy radiation


title: Passage10 (bulk RNA-seq)

city: BETHESDA

first: Shutong

last: Liu

state: Maryland

address: 9000 Rockville Pike

department: Clinical Center

institute: National Institutes of Health

data_processing:
bcl2fastq2 Conversion Software v2.19.1 to process raw data to FASTQ files
STAR - 2.4.1d for alligment
Partek E/M to generate gene counts
Genome_build: hg19-RefSeq Transcripts 2016-5-2
Supplementary_files_format_and_content: gene counts

source_name: human bone marrow

growth_protocol: One vial of frozen Passage 2 BMSCs was thawed and plated in T75 flasks following the SOP. During the serial culture, cells were seeded at 5000 cells per cm2 and harvested at 70-80% confluence. From passage 3 to 8, cells were passaged after 5 days of culture, and culture media was changed on day 3; from passage 9 to 10, the cells were passaged after 8 days of culture, and culture media was changed on day 3 and 6. Cells from each passage were cryopreserved in a solution containing 90% FBS and 10% DMSO for further studies.

extract_protocol:
Total RNA extractions were performed on samples from passages 2, 3, 4, 6, 8, 9, and 10 using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA was quantified using Nanodrop 8000 (Thermo Scientific, Wilmington, DE). Total RNA quality was evaluated following isolation using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples with an RNA Integrity Number (RIN) value ≥ 8 were used for bulk cell RNA-Seq and MicroArray for gene expression analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: healthy donor

value: Bone marrow stromal cells (BMSCs)

tag: passage


title: P09_Ctrl56-37576853_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl56_S56

data_processing:
BCL files generated by Illumina NextSeq were converted to standard FASTQ files following Illumina’s protocol (basespace.illumina.com).
STAR - 2.4.1d for alligment
Partek E/M to generate gene counts
Genome_build: hg19-RefSeq Transcripts 2016-5-2
Supplementary_files_format_and_content: gene counts

extract_protocol:
Frozen cells from different passages were thawed and plated in T75 flasks for 5-7 days. Once they reached 70-80% confluence, cells were collected for single cell separation. Fluidigm C1 Single-Cell Auto Prep Array for mRNA-Seq (10-17um) and Fluidigm C1 system were used for cell capture following the Fluidigm protocol, then reverse transcription and cDNA amplification were performed using the SMARTer PCR cDNA Synthesis kit (Clontech, version 1) on the C1 unit.
Single-cell cDNA from validation cells were harvested for library preparation. Nextera XT DNA sample preparation kits and Index kits were used for library preparation following the manufacturer’s protocol. Single-cell cDNA libraries from each passage were pooled and cleaned up, then cDNA size distribution was examined by 2100 Bioanalyzer. This was followed by quantification and normalization with the KAPA Library Quantification Kit and BioRad CFX96 qPCR machine (BioRad). Single cell mRNA sequencing was performed on NextSeq 500 by using the NextSeq High Output v2 kit (300 cycles). PhiX Control v3 (Illumina) was used as a quality control for sequencing runs.


title: Passage8 (bulk RNA-seq)


title: Passage9 (bulk RNA-seq)


title: Passage4 (bulk RNA-seq)


title: Passage6 (bulk RNA-seq)


title: Passage2 (bulk RNA-seq)


title: P09_Ctrl55-37579836_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl55_S55


title: P09_Ctrl54-37576848_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl54_S54


title: P09_Ctrl53-37580854_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl53_S53


title: P09_Ctrl52-37593704_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl52_S52


title: P09_Ctrl46-37577802_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl46_S46


title: P09_Ctrl45-37575827_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl45_S45


title: P09_Ctrl49-37580850_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl49_S49


title: P09_Ctrl50-37578855_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl50_S50


title: P09_Ctrl48-37575831_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl48_S48


title: P09_Ctrl43-37580836_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl41_S41


title: P09_Ctrl51-37578856_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl51_S51


title: P09_Ctrl42-37573840_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl42_S42


title: P09_Ctrl40-37574817_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl40_S40


title: hskm cells_negative control-transfected_subject2

source_name: primary human skeletal muscle cell (Subject 2), miRNA-negative control transfected


title: P09_Ctrl41-37593693_single_cell_passage_09


title: P09_Ctrl36-37593685_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl36_S36


title: P09_Ctrl37-37594697_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl37_S37


title: P09_Ctrl35-37577794_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl35_S35


title: P09_Ctrl38-37579821_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl38_S38


title: P09_Ctrl34-37594693_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl34_S34


title: P09_Ctrl32-37577790_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl32_S32


title: P09_Ctrl47-37574829_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl47_S47


title: P09_Ctrl31-37579812_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl31_S31


title: P09_Ctrl30-37577785_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl30_S30


title: P09_Ctrl28-37573826_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl28_S28


title: P09_Ctrl29-37594685_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl29_S29


title: P09_Ctrl26-37575800_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl26_S26


title: P09_Ctrl25-37573819_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl25_S25


title: P09_Ctrl24-37578827_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl24_S24


title: P09_Ctrl27-37579809_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl27_S27


title: P09_Ctrl44-37593697_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl44_S44


title: P09_Ctrl39-37580834_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl39_S39


title: P09_Ctrl22-37577775_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl22_S22


title: P09_Ctrl23-37579803_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl23_S23


title: P09_Ctrl33-37593681_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl33_S33


title: P09_Ctrl10-37577764_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl10_S10


title: P09_Ctrl12-37579795_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl12_S12


title: P09_Ctrl18-37578825_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl18_S18


title: P09_Ctrl09-37575789_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl09_S9


title: P09_Ctrl15-37578821_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl15_S15


title: P09_Ctrl16-37575792_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl16_S16


title: P09_Ctrl21-37579802_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl21_S21


title: P09_Ctrl19-37594676_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl19_S19


title: P09_Ctrl14-37578820_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl14_S14


title: P09_Ctrl11-37593657_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl11_S11


title: P09_Ctrl17-37594674_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl17_S17


title: P09_Ctrl13-37573811_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl13_S13


title: P09_Ctrl20-37576824_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl20_S20


title: P09_Ctrl07-37579789_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl07_S7


title: Tcf7-GFP+ P14 cells_tumor_Donor2

value: CD8 T cells expressing a P14 TCR and a Tcf7-GFP reporter

tag: genotype/variation

value: B6;D2-Tg(TcrLCMV)327Sdz/JDvsJ   B6-Tg(Tcf7-GFP)WHe

value: Tcf7-GFP+ P14 cells


title: P09_Ctrl08-37579791_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl08_S8


title: P09_Ctrl06-37593653_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl06_S6


title: P09_Ctrl04-37573805_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl04_S4


title: P09_Ctrl05-37579788_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl05_S5


title: P8_Ctrl44-36930980_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl44_S44


title: P8_Ctrl45-36931983_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl45_S45


title: P8_Ctrl43-36932980_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl43_S43


title: P09_Ctrl01-37576811_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl01_S1


title: P8_Ctrl47-36930982_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl47_S47


title: P8_Ctrl46-36927981_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl46_S46


title: P09_Ctrl03-37574782_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl03_S3


title: P09_Ctrl02-37573802_single_cell_passage_09

description:
processed data file: single_cell_passage_09_processed.txt
P09_Ctrl02_S2


title: P8_Ctrl48-36929975_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl48_S48


title: P8_Ctrl41-36923115_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl41_S41


title: P8_Ctrl40-36932978_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl40_S40


title: P8_Ctrl38-36923111_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl38_S38


title: P8_Ctrl39-36923113_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl39_S39


title: P8_Ctrl35-36928995_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl35_S35


title: P8_Ctrl36-36929969_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl36_S36


title: P8_Ctrl33-36932976_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl33_S33


title: P8_Ctrl30-36928994_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl30_S30


title: P8_Ctrl25-36927972_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl25_S25


title: P8_Ctrl31-36934994_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl31_S31


title: P8_Ctrl29-36923110_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl29_S29


title: P8_Ctrl32-36930976_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl32_S32


title: P8_Ctrl24-36928992_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl24_S24


title: P8_Ctrl34-36927975_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl34_S34


title: P8_Ctrl28-36928993_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl28_S28


title: P8_Ctrl27-36932975_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl27_S27


title: P8_Ctrl23-36923109_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl23_S23


title: P8_Ctrl42-36930979_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl42_S42


title: P8_Ctrl22-36928991_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl22_S22


title: P8_Ctrl26-36932974_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl26_S26


title: P8_Ctrl15-36922105_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl15_S15


title: P8_Ctrl16-36933993_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl16_S16


title: P8_Ctrl19-36927970_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl19_S19


title: P8_Ctrl14-36932970_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl14_S14


title: P8_Ctrl18-36932971_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl18_S18


title: P8_Ctrl17-36927969_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl17_S17


title: P8_Ctrl21-36929966_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl21_S21


title: P8_Ctrl13-36930973_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl13_S13


title: P8_Ctrl37-36929970_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl37_S37


title: P8_Ctrl12-36929964_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl12_S12


title: P8_Ctrl10-36929963_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl10_S10


title: P8_Ctrl08-36934990_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl08_S8


title: P8_Ctrl07-36922103_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl07_S7


title: P8_Ctrl06-36930969_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl06_S6


title: P8_Ctrl02-36928985_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl02_S2


title: P6_Ctrl48_35457428_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl48_S48


title: P8_Ctrl04-36930966_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl04_S4


title: P8_Ctrl03-36933987_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl03_S3


title: P6_Ctrl47_35454432_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl47_S47


title: P8_Ctrl20-36922106_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl20_S20


title: P8_Ctrl05-36922101_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl05_S5


title: P6_Ctrl44_35453436_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl44_S44


title: P6_Ctrl45_35459428_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl45_S45


title: P6_Ctrl46_35455435_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl46_S46


title: P6_Ctrl43_35453435_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl43_S43


title: P8_Ctrl01-36927963_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl01_S1


title: P6_Ctrl41_35457426_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl41_S41


title: P6_Ctrl42_35444489_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl42_S42


title: P6_Ctrl40_35456427_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl40_S40


title: P6_Ctrl37_35438485_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl37_S37


title: P6_Ctrl38_35457424_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl38_S38


title: P6_Ctrl36_35444486_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl36_S36


title: P6_Ctrl35_35438483_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl35_S35


title: P6_Ctrl34_35436480_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl34_S34


title: P8_Ctrl11-36933991_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl11_S11


title: P6_Ctrl31_35436478_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl31_S31


title: P6_Ctrl32_35455426_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl32_S32


title: P8_Ctrl09-36929961_single_cell_passage_08

description:
processed data file: single_cell_passage_08_processed.txt
P8_Ctrl09_S9


title: P6_Ctrl30_35406646_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl30_S30


title: P6_Ctrl29_35455425_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl29_S29


title: P6_Ctrl39_35453434_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl39_S39


title: P6_Ctrl28_35441493_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl28_S28


title: P6_Ctrl27_35444482_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl27_S27


title: P6_Ctrl25_35458424_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl25_S25


title: P6_Ctrl13_35452449_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl13_S13


title: P6_Ctrl18_35459426_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl18_S18


title: P6_Ctrl33_35435490_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl33_S33


title: P6_Ctrl21_35442485_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl21_S21


title: P6_Ctrl19_35453430_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl19_S19


title: P6_Ctrl16_35456424_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl16_S16


title: P6_Ctrl24_35441491_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl24_S24


title: P6_Ctrl22_35406645_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl22_S22


title: P6_Ctrl11_35441490_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl11_S11


title: P6_Ctrl15_35457423_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl15_S15


title: P6_Ctrl10_35452448_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl10_S10


title: P6_Ctrl14_35444481_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl14_S14


title: P6_Ctrl09_35452447_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl09_S9


title: P6_Ctrl08_35442483_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl08_S8


title: P6_Ctrl12_35433554_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl12_S12


title: P6_Ctrl20_35442484_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl20_S20


title: P6_Ctrl17_35406644_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl17_S17


title: P6_Ctrl06_35437482_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl06_S6


title: P6_Ctrl07_35406642_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl07_S7


title: P6_Ctrl04_35437481_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl04_S4


title: P6_Ctrl05_35436474_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl05_S5


title: P6_Ctrl03_35457422_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl03_S3


title: P6_Ctrl02_35433553_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl02_S2


title: P6_Ctrl26_35441492_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl26_S26


title: P04_Ctrl48_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl48_S49


title: P6_Ctrl23_35435486_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl23_S23


title: P04_Ctrl47_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl47_S50


title: P04_Ctrl46_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl46_S51


title: P04_Ctrl45_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl45_S52


title: P04_Ctrl44_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl44_S53


title: P04_Ctrl39_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl39_S58


title: P04_Ctrl38_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl38_S59


title: P04_Ctrl42_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl42_S55


title: P04_Ctrl41_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl41_S56


title: P04_Ctrl37_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl37_S60


title: P04_Ctrl36_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl36_S61


title: P04_Ctrl33_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl33_S64


title: P04_Ctrl35_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl35_S62


title: P6_Ctrl01_35453429_single_cell_passage_06

description:
processed data file: single_cell_passage_06_processed.txt
P6_Ctrl01_S1


title: P04_Ctrl26_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl26_S71


title: P04_Ctrl25_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl25_S72


title: P04_Ctrl23_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl23_S74


title: P04_Ctrl43_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl43_S54


title: P04_Ctrl34_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl34_S63


title: P04_Ctrl29_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl29_S68


title: P04_Ctrl27_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl27_S70


title: P04_Ctrl24_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl24_S73


title: P04_Ctrl22_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl22_S75


title: P04_Ctrl20_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl20_S77