title: Fearonly_pos_p4_A11_S255_mouse2


title: Fearonly_pos_p4_E4_S40_mouse2

status: Public on Jun 17 2020

type: SRA

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

country: USA

institute: Stanford

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: raw count tables

molecule: total RNA

organism: Mus musculus

extract_protocol:
Brain tissues were dissociated with Worthington Papain Digestion Kit
RNA libraries were prepared for sequencing using standard Illumina protocols
smart seq 2

tag: cell type

value: Primary brain cells  from muring mPFC


title: Fearonly_pos_p4_H9_S114_mouse2


title: Fearonly_pos_p4_K20_S194_mouse2


title: Fearonly_pos_p4_C21_S11_mouse2


title: Fearonly_neg_p5_P12_S69_mouse2


title: Fearonly_pos_p4_E8_S44_mouse2


title: Fearonly_pos_p4_N11_S254_mouse2


title: Fearonly_pos_p4_L17_S214_mouse2


title: Fearonly_pos_p4_M22_S242_mouse2


title: Fearonly_pos_p4_B5_S272_mouse2


title: Fearonly_pos_p4_D4_S17_mouse2


title: Fearonly_pos_p4_B17_S284_mouse2


title: Fearonly_neg_p5_P19_S76_mouse2


title: Fearonly_neg_p5_P8_S65_mouse2


title: Fearonly_pos_p4_I14_S142_mouse2


title: Fearonly_neg_p5_M17_S5_mouse2


title: Fearonly_pos_p4_H8_S113_mouse2


title: Fearonly_pos_p4_O14_S280_mouse2


title: Fearonly_neg_p5_M10_S298_mouse2


title: Fearonly_neg_p5_L1_S266_mouse2


title: Fearonly_pos_p4_L6_S203_mouse2


title: Fearonly_neg_p5_M1_S289_mouse2


title: Fearonly_pos_p4_E23_S59_mouse2


title: Fearonly_neg_p5_N4_S15_mouse2


title: Fearonly_pos_p4_H19_S124_mouse2


title: Fearonly_pos_p4_M21_S241_mouse2


title: Fearonly_pos_p4_I21_S149_mouse2


title: Fearonly_pos_p4_D22_S35_mouse2


title: Fearonly_pos_p4_G13_S95_mouse2


title: Fearonly_pos_p4_H18_S123_mouse2


title: Fearonly_pos_p4_M6_S226_mouse2


title: Fearonly_pos_p4_C19_S9_mouse2


title: Fearonly_pos_p4_N22_S265_mouse2


title: Fearonly_neg_p5_L21_S286_mouse2


title: Fearonly_neg_p5_I2_S198_mouse2


title: Fearonly_pos_p4_E12_S48_mouse2


title: Fearonly_neg_p5_L10_S275_mouse2


title: Fearonly_pos_p4_J19_S170_mouse2


title: Fearonly_pos_p4_F3_S62_mouse2


title: Fearonly_neg_p5_K10_S252_mouse2


title: Fearonly_neg_p5_N12_S23_mouse2


title: Fearonly_pos_p4_J15_S166_mouse2


title: Fearonly_pos_p4_P4_S293_mouse2


title: Fearonly_pos_p4_A13_S257_mouse2


title: Fearonly_pos_p4_D11_S24_mouse2


title: Fearonly_neg_p5_M14_S2_mouse2


title: Fearonly_pos_p4_H1_S106_mouse2


title: Fearonly_pos_p4_F11_S70_mouse2


title: Fearonly_pos_p4_H5_S110_mouse2


title: Homecage_pos_p8_J21_S64_mouse2


title: Fearonly_pos_p4_D5_S18_mouse2


title: Fearonly_pos_p4_F22_S81_mouse2


title: Fearonly_pos_p4_L14_S211_mouse2


title: Fearonly_pos_p4_J8_S159_mouse2


title: Fearonly_pos_p4_N5_S248_mouse2


title: Fearonly_pos_p4_E9_S45_mouse2


title: Fearonly_pos_p4_G21_S103_mouse2


title: Fearonly_pos_p4_C17_S7_mouse2


title: Fearonly_pos_p4_A22_S266_mouse2


title: Fearonly_neg_p5_L7_S272_mouse2


title: Fearonly_pos_p4_H15_S120_mouse2


title: Fearonly_pos_p4_C18_S8_mouse2


title: Fearonly_pos_p4_B23_S290_mouse2


title: Fearonly_pos_p4_N6_S249_mouse2


title: Fearonly_pos_p4_J14_S165_mouse2


title: Fearonly_pos_p4_E18_S54_mouse2


title: Fearonly_pos_p4_F15_S74_mouse2


title: Fearonly_pos_p4_I19_S147_mouse2


title: Fearonly_pos_p4_P11_S300_mouse2


title: Fearonly_pos_p4_E6_S42_mouse2


title: Fearonly_pos_p4_D14_S27_mouse2


title: Fearonly_pos_p4_L7_S204_mouse2


title: Fearonly_neg_p5_K15_S257_mouse2


title: Fearonly_pos_p4_L5_S202_mouse2


title: Fearonly_pos_p4_I18_S146_mouse2


title: Fearonly_pos_p4_M7_S227_mouse2


title: Fearonly_pos_p4_K6_S180_mouse2


title: Fearonly_pos_p4_M11_S231_mouse2


title: Fearonly_pos_p4_O17_S283_mouse2


title: Fearonly_pos_p4_D7_S20_mouse2


title: Fearonly_pos_p4_K11_S185_mouse2


title: Fearonly_pos_p4_C15_S5_mouse2


title: Fearonly_pos_p4_I3_S131_mouse2


title: Fearonly_pos_p4_O6_S272_mouse2


title: Fearonly_pos_p4_H11_S116_mouse2


title: Fearonly_pos_p4_B14_S281_mouse2


title: Fearonly_pos_p4_P8_S297_mouse2


title: Fearonly_pos_p4_O10_S276_mouse2


title: Fearonly_pos_p4_N23_S266_mouse2


title: Fearonly_pos_p4_B18_S285_mouse2


title: Fearonly_pos_p4_E16_S52_mouse2


title: Fearonly_pos_p4_D23_S36_mouse2


title: Fearonly_pos_p4_G18_S100_mouse2


title: Fearonly_pos_p4_G16_S98_mouse2


title: Fearonly_pos_p4_F2_S61_mouse2


title: Fearonly_pos_p4_B20_S287_mouse2


title: Fearonly_pos_p4_D18_S31_mouse2


title: Fearonly_pos_p4_I17_S145_mouse2


title: Fearonly_pos_p4_M18_S238_mouse2


title: Fearonly_pos_p4_G9_S91_mouse2


title: Fearonly_neg_p5_I1_S197_mouse2


title: Fearonly_pos_p4_O16_S282_mouse2


title: Fearonly_pos_p4_M5_S225_mouse2


title: Fearonly_pos_p4_L19_S216_mouse2


title: Fearonly_neg_p5_K16_S258_mouse2


title: Fearonly_pos_p4_G5_S87_mouse2


title: Fearonly_pos_p4_N15_S258_mouse2


title: Fearonly_pos_p4_O9_S275_mouse2


title: Fearonly_pos_p4_C6_S296_mouse2


title: Fearonly_pos_p4_G23_S105_mouse2


title: Fearonly_pos_p4_D20_S33_mouse2


title: Fearonly_neg_p5_P20_S77_mouse2


title: Fearonly_neg_p5_J23_S242_mouse2


title: Fearonly_pos_p4_P22_S11_mouse2


title: Fearonly_neg_p5_N22_S33_mouse2


title: Fearonly_pos_p4_K13_S187_mouse2


title: Fearonly_pos_p4_K18_S192_mouse2


title: Fearonly_pos_p4_H22_S127_mouse2


title: Fearonly_pos_p4_E17_S53_mouse2


title: Fearonly_pos_p4_N20_S263_mouse2


title: Fearonly_pos_p4_D6_S19_mouse2


title: Fearonly_pos_p4_G12_S94_mouse2


title: Context_pos_p6_G11_S217_mouse2


title: Fearonly_pos_p4_N14_S257_mouse2


title: Context_pos_p6_N6_S73_mouse2


title: Context_pos_p6_B17_S108_mouse2


title: Context_pos_p6_M5_S49_mouse2


title: Fearonly_pos_p4_B21_S288_mouse2


title: Context_pos_p6_M15_S59_mouse2


title: Context_pos_p6_K4_S2_mouse2


title: Context_pos_p6_O6_S96_mouse2


title: Context_neg_p7_A16_S16_mouse2


title: Context_neg_p7_J11_S218_mouse2


title: Context_pos_p6_K2_S300_mouse2


title: Context_neg_p7_O7_S29_mouse2


title: Fearonly_pos_p4_F12_S71_mouse2


title: Context_pos_p6_C7_S121_mouse2


title: Context_pos_p6_L9_S30_mouse2


title: Fearonly_pos_p4_L13_S210_mouse2


title: Context_neg_p7_L11_S264_mouse2


title: Context_pos_p6_O23_S113_mouse2


title: Context_pos_p6_I12_S264_mouse2


title: Context_pos_p6_D16_S153_mouse2


title: Context_pos_p6_O1_S91_mouse2


title: Context_pos_p6_I4_S256_mouse2


title: Context_pos_p6_G16_S222_mouse2


title: Context_pos_p6_K19_S17_mouse2


title: Context_pos_p6_N15_S82_mouse2


title: Context_pos_p6_L23_S44_mouse2


title: Context_pos_p6_P20_S133_mouse2


title: Context_pos_p6_A8_S76_mouse2


title: Context_pos_p6_I9_S261_mouse2


title: Context_pos_p6_B15_S106_mouse2


title: Context_neg_p7_B10_S33_mouse2


title: Context_pos_p6_M3_S47_mouse2


title: PANC-1_siImp1_rep3

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 --trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters  -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values for each sample

organism: Homo sapiens

source_name: pancreas cancer derived cell line

growth_protocol: PANC-1 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
1µg of total RNA served as input for rRNA depletion using RiboCop v1.2 (Lexogen). NEBNext Ultra Directional RNA Library kit (NEB) was used for library generation. Sequencing was performed on the Illumina NextSeq 500 platform

treatment_protocol: 96 hours upon transfection cells were harvested for RNA extraction.

tag: cell line

value: pancreas cancer derived cell line

tag: sirna

value: siRNA pool against IGF2BP1

tag: collection time

value: harvested 96h upon transfection


title: Context_pos_p6_E15_S175_mouse2


title: Context_neg_p7_F16_S131_mouse2


title: Context_pos_p6_H22_S251_mouse2


title: Context_pos_p6_H19_S248_mouse2


title: Context_pos_p6_O9_S99_mouse2


title: Context_pos_p6_O13_S103_mouse2


title: Context_pos_p6_G19_S225_mouse2


title: PANC-1_siImp1_rep2


title: Context_neg_p7_P4_S49_mouse2


title: Context_neg_p7_J21_S228_mouse2


title: PANC-1_siImp1_rep1


title: Context_neg_p7_L21_S274_mouse2


title: PANC-1_siC_rep3_control_for_siIGF2BP1

value: Control siRNA


title: Context_neg_p7_A14_S14_mouse2


title: PANC-1_siC_rep1_control_for_siIGF2BP1


title: PANC-1_siC_rep2_control_for_siIGF2BP1


title: MV3_siImp1_rep4

source_name: melanoma derived cell line

growth_protocol: MV3 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

treatment_protocol: 72 hours upon transfection cells were harvested for RNA extraction.

value: melanoma derived cell line

value: harvested 72h upon transfection


title: Context_neg_p7_E1_S93_mouse2


title: Context_neg_p7_E13_S105_mouse2


title: MV3_siImp1_rep3


title: Context_neg_p7_F23_S138_mouse2


title: MV3_siImp1_rep1


title: Context_neg_p7_B13_S36_mouse2


title: Context_neg_p7_A10_S10_mouse2


title: MV3_siImp1_rep2


title: MV3_siC_rep3


title: Context_pos_p6_H18_S247_mouse2


title: MV3_siC_rep2


title: MV3_siC_rep1


title: Context_pos_p6_J22_S297_mouse2


title: siImp1_rep3

source_name: lung cancer derived cell line

growth_protocol: A549 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
1µg of total RNA served as input for rRNA depletion using RiboCop v1.2 (Lexogen). NEBNext Ultra Directional RNA Library kit (NEB) was used for library generation. Sequencing was performed on the Illumina NextSeq 500 platform
total RNA-Seq

tag: passages


title: siImp1_rep2


title: Context_pos_p6_G1_S207_mouse2


title: siImp1_rep1


title: Context_pos_p6_K5_S3_mouse2


title: Context_pos_p6_N1_S68_mouse2


title: Context_neg_p7_A4_S4_mouse2


title: siC_rep2 (IGF2BP1)


title: Context_neg_p7_N22_S21_mouse2


title: Context_neg_p7_K7_S237_mouse2


title: siC_rep1 (IGF2BP1)


title: Context_pos_p6_I13_S265_mouse2


title: siC_rep3 (IGF2BP1)


title: Context_neg_p7_G5_S143_mouse2


title: Context_pos_p6_F12_S195_mouse2


title: MV3_siC_rep4


title: Context_pos_p6_L3_S24_mouse2


title: iBET-BD2_Rep2

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina bcl2fastq v2 software was used for basecalling.
Reads were trimmed to remove adapters using cutadapt 1.14
The SlamDunk pipeline v0.2.4 was used to align reads to the human genome (GRCh37.73) and the 3’ UTR of gene, and call T to C conversions and count the numbers of total and TC converted reads.
The DESeq2 package in R was used to normalise the T to C converted read counts using the size factors calculated from the total read counts.
Genome_build: hg19
Supplementary_files_format_and_content: Output from slamdunk pipeline containing the total and TC converted read counts, and CPM

molecule: polyA RNA

source_name: macrophage

growth_protocol: The AML cell lines were grown in RPMI-1640 supplemented with 20% FCS, streptomycin (100g/mL), penicillin (100 units/mL) and glutamax, under standard culture conditions (5% CO2, 37 °C).

extract_protocol:
All SLAM-seq assays were performed at 60% of the maximum cell density counted on a hemocytometer for suspension cells. 5-7h prior to each assay, growth medium was aspirated and replaced. Newly synthesized RNA was labeled for the last 60 minutes at the end of the treatment with the inhibitors at a final concentration of 100μM 4-Thiouridine.
Suspension cells were spun down and immediately snap-frozen, before RNA extraction using the RNeasy Plus Mini Kit (Qiagen). Total RNA was subjected to alkylation by iodoacetamide (Sigma, 10mM) for 15 minutes and RNA was re-purified by ethanol precipitation.
Libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep kit (Lexigen)

treatment_protocol: DMSO, I-BET151,iBET-BD1 and iBET-BD2 were dosed by direct addition to the culture media at 0.1%. Drugs were refreshed everythree days to ensure maximal activity.  I-BET151, iBET-BD1, and iBET-BD2 were used at a final concentration of 1000 nM

tag: inhibitor treatment

tag: replicate


title: Context_neg_p7_O12_S34_mouse2


title: Context_neg_p7_N15_S14_mouse2


title: I-BET151_Rep1


title: iBET-BD1_Rep2


title: iBET-BD2_Rep1


title: DMSO_Rep2

value: DMSO


title: iBET-BD1_Rep1


title: Context_pos_p6_F13_S196_mouse2


title: Context_pos_p6_P17_S130_mouse2


title: DMSO_Rep1


title: Context_neg_p7_M16_S292_mouse2


title: iBET-BD1_Rep3


title: iBET-BD2_Rep3


title: I-BET151_Rep3


title: Context_pos_p6_N8_S75_mouse2


title: Context_neg_p7_N2_S1_mouse2


title: I-BET151_PMA_Rep3

source_name: monocyte

tag: stimulation

value: PMA

tag: stimulation protocol

value: 2 hours of 40nM PMA after 30 minutes of pretreatment with BET inhibitor


title: I-BET151_Rep2


title: DMSO_Rep3


title: Context_pos_p6_I23_S275_mouse2


title: iBET-BD2_PMA_Rep3


title: Context_neg_p7_G18_S156_mouse2


title: DMSO_PMA_Rep3


title: Context_pos_p6_O3_S93_mouse2


title: Context_neg_p7_B21_S44_mouse2


title: I-BET151_noPMA_Rep3

value: no PMA


title: iBET-BD1_PMA_Rep3


title: iBET-BD2_noPMA_Rep3


title: iBET-BD1_noPMA_Rep3


title: Context_neg_p7_G19_S157_mouse2


title: Context_pos_p6_E13_S173_mouse2


title: Context_pos_p6_I18_S270_mouse2


title: Context_neg_p7_E6_S98_mouse2


title: Context_pos_p6_H20_S249_mouse2


title: I-BET151_PMA_Rep2


title: Context_pos_p6_D21_S158_mouse2


title: Context_pos_p6_C2_S116_mouse2


title: Context_neg_p7_O22_S44_mouse2


title: iBET-BD2_PMA_Rep2


title: iBET-BD1_PMA_Rep2


title: DMSO_PMA_Rep2


title: Context_neg_p7_L18_S271_mouse2


title: Context_pos_p6_J6_S281_mouse2


title: I-BET151_noPMA_Rep2


title: Context_pos_p6_M13_S57_mouse2


title: Context_neg_p7_P20_S65_mouse2


title: iBET-BD1_noPMA_Rep2


title: iBET-BD2_noPMA_Rep2


title: Context_pos_p6_J18_S293_mouse2


title: DMSO_noPMA_Rep2


title: Context_pos_p6_D23_S160_mouse2


title: I-BET151_PMA_Rep1


title: iBET-BD2_PMA_Rep1


title: Context_neg_p7_L8_S261_mouse2


title: DMSO_noPMA_Rep3


title: iBET-BD1_PMA_Rep1


title: Context_pos_p6_F6_S189_mouse2


title: DMSO_PMA_Rep1


title: Context_pos_p6_A13_S81_mouse2


title: I-BET151_noPMA_Rep1


title: Context_pos_p6_K20_S18_mouse2


title: Context_pos_p6_K12_S10_mouse2


title: iBET-BD1_noPMA_Rep1


title: unstim DMSO Rep3

source_name: erythroleukaemia


title: Context_pos_p6_F10_S193_mouse2


title: Context_neg_p7_L15_S268_mouse2


title: unstim I-BET151 Rep2


title: DMSO_noPMA_Rep1


title: unstim iBET-BD1 Rep2


title: unstim DMSO Rep2


title: Context_pos_p6_F22_S205_mouse2


title: Context_pos_p6_G3_S209_mouse2


title: Context_pos_p6_I7_S259_mouse2


title: Context_pos_p6_M23_S67_mouse2


title: Context_neg_p7_N1_S300_mouse2


title: Context_neg_p7_P12_S57_mouse2


title: unstim I-BET151 Rep1


title: Context_pos_p6_M21_S65_mouse2


title: unstim iBET-BD2 Rep1


title: unstim iBET-BD2 Rep2


title: unstim iBET-BD1 Rep1


title: Context_pos_p6_I14_S266_mouse2


title: iBET-BD2_noPMA_Rep1


title: Context_pos_p6_G8_S214_mouse2


title: unstim iBET-BD2 Rep3


title: unstim I-BET151 Rep3


title: Context_pos_p6_G6_S212_mouse2


title: Context_pos_p6_N3_S70_mouse2


title: unstim iBET-BD1 Rep3


title: Context_neg_p7_H16_S177_mouse2


title: Context_pos_p6_O10_S100_mouse2


title: Context_pos_p6_P2_S115_mouse2


title: unstim DMSO Rep1


title: DMSO IFN Rep2

value: IFNγ

value: 6 hours of 10ng/mL IFNγ after 1 hour of pretreatment with BET inhibitor


title: Context_pos_p6_L20_S41_mouse2


title: Context_pos_p6_J20_S295_mouse2


title: Context_neg_p7_G22_S160_mouse2


title: I-BET151 IFNg Rep1


title: Context_neg_p7_I7_S191_mouse2


title: iBET-BD1 IFNg Rep1


title: iBET-BD2 IFNg Rep1


title: Context_pos_p6_G7_S213_mouse2


title: DMSO IFNg Rep1


title: I-BET151 Rep3

value: no IFNγ


title: I-BET151 Rep2


title: I-BET151 Rep1


title: Context_neg_p7_D22_S91_mouse2


title: Context_neg_p7_M22_S298_mouse2


title: Context_neg_p7_N20_S19_mouse2


title: DMSO noIFNg Rep1


title: Context_neg_p7_D8_S77_mouse2


title: I-BET151 IFNg Rep3


title: iBET-BD2 IFNg Rep3


title: Context_neg_p7_N17_S16_mouse2


title: iBET-BD1 IFNg Rep3


title: Context_neg_p7_D13_S82_mouse2


title: DMSO IFN Rep3


title: Context_pos_p6_J4_S279_mouse2


title: DMSO noIFN Rep2


title: DMSO noIFN Rep3


title: Context_pos_p6_F8_S191_mouse2


title: I-BET151 IFNg Rep2


title: Context_pos_p6_I6_S258_mouse2


title: Context_neg_p7_L14_S267_mouse2


title: iBET-BD1 IFNg Rep2


title: Context_neg_p7_G16_S154_mouse2


title: iBET-BD2 IFNg Rep2


title: Context_pos_p6_C23_S137_mouse2


title: US-D3-BD2-R2

data_processing:
Illumina bcl2fastq v2 software was used for basecalling.
Reads were aligned to the human genome (GRCh37.73) using HISAT2
Reads were assigned to genes using htseq-count. Differential expression was calculated using edgeR.
Genome_build: Hg19
Supplementary_files_format_and_content: counts files as outputted from htseq-count

growth_protocol: Human CD4+ Tcells were grown in RPMI-1640 supplemented with 20% FCS, streptomycin (100g/mL), penicillin (100 units/mL) and glutamax, under standard culture conditions (5% CO2, 37 °C).

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit
Libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep kit (Lexigen)

treatment_protocol: DMSO, I-BET151,iBET-BD1 and iBET-BD2 were dosed by direct addition to the culture media at 0.1%.  I-BET151, iBET-BD1, and iBET-BD2 were used at a final concentration of 500nM, 500nM and 1000 nM respectively.


title: Context_pos_p6_P7_S120_mouse2


title: US-D3-BD2-R1


title: US-D3-BD1-R2


title: Context_pos_p6_H10_S239_mouse2


title: US-D3-BD1-R1


title: Context_neg_p7_C5_S51_mouse2


title: US-D3-DMSO-R2


title: Context_pos_p6_F18_S201_mouse2


title: Context_pos_p6_O18_S108_mouse2


title: Context_neg_p7_L17_S270_mouse2


title: US-D3-DMSO-R1


title: US-D1-BD2-R2


title: US-D1-BD2-R1


title: Context_neg_p7_D19_S88_mouse2


title: Context_neg_p7_I10_S194_mouse2


title: Context_neg_p7_I20_S204_mouse2


title: US-D1-BD1-R2


title: Context_neg_p7_G17_S155_mouse2


title: US-D1-BD1-R1


title: Context_neg_p7_G6_S144_mouse2


title: D3-BD1-R2

value: 4 hours of anti CD3/CD8 after 30 minutes of pretreatment


title: Context_pos_p6_D2_S139_mouse2


title: Context_pos_p6_O14_S104_mouse2


title: D3-BD2-R2


title: D3-BD2-R1


title: Context_pos_p6_B11_S102_mouse2


title: Context_neg_p7_C18_S64_mouse2


title: Context_pos_p6_K13_S11_mouse2


title: D3-DMSO-R2


title: D1-BD2-R2


title: Context_pos_p6_L17_S38_mouse2


title: Context_pos_p6_P14_S127_mouse2


title: D3-DMSO-R1


title: Context_pos_p6_F20_S203_mouse2


title: Context_pos_p6_L21_S42_mouse2


title: D3-BD1-R1


title: Context_pos_p6_P13_S126_mouse2


title: D1-BD2-R1


title: D1-BD1-R2


title: US-D1-DMSO-R2


title: D1-DMSO-R2


title: Context_pos_p6_A9_S77_mouse2


title: US-D1-DMSO-R1


title: D1-BD1-R1


title: D1-DMSO-R1


title: Context_pos_p6_O19_S109_mouse2


title: TCell-PolII-BD2-stim

library_source: genomic

data_processing:
Illumina bcl2fastq v2 software was used for basecalling
Reads were aligned to the human genome (GRCh37.73) using bwa mem
Duplicate reads and reads mapping to blacklist regions or the mitochondria were removed
Peak calling was performed using MACS2
Genome_build: Hg19
Supplementary_files_format_and_content: MAC2 peaks

molecule: genomic DNA

growth_protocol: The AML cell lines and human Tcells were grown in RPMI-1640 supplemented with 20% FCS, streptomycin (100g/mL), penicillin (100 units/mL) and glutamax, under standard culture conditions (5% CO2, 37 °C).

extract_protocol:
20 million cells were crosslinked for 15 mins with 1% formaldehyde. Crosslinked material was sonicated to ~200–1000 bp using the Covaris Ultrasonicator e220. Sonicated material was incubated overnight with each antibody, then incubated for 3 h with Protein A magnetic beads. Beads were washed with low and high salt wash buffers, LiCl buffer and TE, before being eluted and decrosslinked overnight. DNA was purified using Qiagen Minelute columns. All ChIP antibodies were used at ~10μg per IP
Sequencing libraries were prepared from eluted DNA using Rubicon ThruPLEX DNA- seq kit. Libraries were size selected between 200–500 bps

treatment_protocol: DMSO, I-BET151,iBET-BD1 and iBET-BD2 were dosed by direct addition to the culture media at 0.1%. Drugs were refreshed every three days to ensure maximal activity.  I-BET151, iBET-BD1, and iBET-BD2 were used at a final concentration of 1000 nM in AML cell lines, and at 500nM, 500nM and 1000 nM respectively for Tcells

tag: antibody


title: Context_pos_p6_M11_S55_mouse2


title: Context_neg_p7_B23_S46_mouse2


title: Context_pos_p6_N13_S80_mouse2


title: TCell-PolII-IBET-stim


title: TCell-BRD4-BD2-stim


title: TCell-PolII-DMSO-stim


title: Context_pos_p6_P11_S124_mouse2


title: TCell-BRD4-BD1-stim


title: Context_pos_p6_J14_S289_mouse2


title: Context_pos_p6_K16_S14_mouse2


title: Context_pos_p6_F11_S194_mouse2


title: TCell-BRD4-DMSO-stim


title: Context_pos_p6_I20_S272_mouse2


title: Context_pos_p6_N10_S77_mouse2


title: TCell-BRD3-BD1-stim

value: BRD3(Bethyl; A302-368A)


title: Context_pos_p6_N14_S81_mouse2


title: TCell-BRD3-BD2-stim


title: TCell-BRD3-DMSO-stim


title: Context_pos_p6_C15_S129_mouse2


title: Context_pos_p6_F23_S206_mouse2


title: TCell-BRD2-BD1-stim

value: BRD2(D89B4;Cell Signalling;5848S;lot 3)


title: Context_neg_p7_G9_S147_mouse2

value: Primary brain cells  from muring mPFC


title: TCell-BRD2-DMSO-stim


title: Context_pos_p6_O15_S105_mouse2


title: TCell-PolII-BD1-stim


title: K562-H3K27ac-DMSO-noIFNG

value: noIFNγ

value: anti-Histone H3 (acetyl K27) (Abcam;ab4729;lot GR3231937-1)


title: Context_pos_p6_P3_S116_mouse2


title: Context_pos_p6_B22_S113_mouse2


title: Context_pos_p6_P16_S129_mouse2


title: K562-BRD4-BD2-noIFNG-R2


title: Context_pos_p6_N22_S89_mouse2


title: TCell-BRD4-IBET-stim


title: Context_pos_p6_A22_S90_mouse2


title: Context_pos_p6_N19_S86_mouse2


title: K562-BRD4-BD1-noIFNG-R2


title: K562-BRD4-IBET-noIFNG-R2


title: TCell-BRD2-BD2-stim


title: Context_pos_p6_B23_S114_mouse2


title: Context_pos_p6_D14_S151_mouse2


title: K562-BRD4-DMSO-noIFNG


title: K562-BRD3-DMSO-noIFNG


title: Context_pos_p6_K18_S16_mouse2


title: Context_pos_p6_B14_S105_mouse2


title: Context_neg_p7_L6_S259_mouse2


title: K562-BRD4-BD2-IFNG


title: Context_pos_p6_P22_S135_mouse2


title: K562-BRD4-BD1-IFNG


title: K562-H3K27ac-DMSO-IFNG


title: K562-BRD4-IBET-IFNG


title: K562-BRD2-DMSO-noIFNG


title: Context_pos_p6_B19_S110_mouse2


title: Context_pos_p6_M16_S60_mouse2


title: K562-BRD4-DMSO-IFNG


title: Context_pos_p6_C20_S134_mouse2


title: K562-BRD3-BD1-IFNG


title: K562-BRD3-IBET-IFNG


title: K562-BRD4-DMSO-noIFNG-R2


title: Context_pos_p6_O17_S107_mouse2


title: K562-BRD3-DMSO-IFNG


title: K562-BRD2-BD1-IFNG


title: K562-BRD2-IBET-IFNG


title: K562-BRD2-BD2-IFNG


title: Context_pos_p6_F9_S192_mouse2


title: Context_pos_p6_I11_S263_mouse2


title: Context_pos_p6_M14_S58_mouse2


title: Context_pos_p6_N18_S85_mouse2


title: K562-BRD2-DMSO-IFNG


title: Context_neg_p7_N19_S18_mouse2


title: Context_pos_p6_G20_S226_mouse2


title: THP1-H3K27ac-DMSO-noPMA

value: noPMA


title: Context_pos_p6_A11_S79_mouse2


title: THP1-BRD4-BD1-noPMA-R2


title: THP1-BRD4-IBET-noPMA-R2


title: Context_pos_p6_C16_S130_mouse2


title: Context_pos_p6_N7_S74_mouse2


title: Context_pos_p6_F2_S185_mouse2


title: THP1-BRD4-DMSO-noPMA-R2


title: Context_pos_p6_H7_S236_mouse2


title: THP1-H3K27ac-DMSO-noPMA-R2


title: Context_pos_p6_F17_S200_mouse2


title: THP1-BRD4-BD2-noPMA-R2


title: THP1-BRD4-IBET-noPMA


title: THP1-BRD4-BD1-noPMA


title: Context_pos_p6_I22_S274_mouse2


title: Context_pos_p6_G12_S218_mouse2


title: Context_pos_p6_H5_S234_mouse2


title: Context_neg_p7_A20_S20_mouse2


title: THP1-BRD3-BD2-noPMA


title: Context_pos_p6_E1_S161_mouse2


title: Context_pos_p6_G23_S229_mouse2


title: THP1-BRD3-BD1-noPMA


title: THP1-BRD3-IBET-noPMA


title: THP1-BRD4-DMSO-noPMA


title: K562-BRD3-BD2-IFNG


title: THP1-BRD3-DMSO-noPMA


title: Context_pos_p6_A20_S88_mouse2


title: Context_neg_p7_L20_S273_mouse2


title: Context_pos_p6_P15_S128_mouse2


title: THP1-BRD2-BD2-noPMA


title: Context_pos_p6_N9_S76_mouse2


title: Context_pos_p6_D1_S138_mouse2


title: THP1-BRD2-BD1-noPMA


title: THP1-BRD2-IBET-noPMA


title: THP1-BRD4-BD2-noPMA


title: Context_neg_p7_I23_S207_mouse2


title: THP1-BRD2-DMSO-noPMA


title: THP1-H3K27ac-BD1-PMA


title: Context_neg_p7_K3_S233_mouse2


title: THP1-BRD4-BD2-PMA


title: Context_pos_p6_M7_S51_mouse2


title: Context_pos_p6_L22_S43_mouse2


title: THP1-H3K27ac-BD2-PMA


title: Context_neg_p7_L10_S263_mouse2


title: Context_neg_p7_I1_S185_mouse2


title: THP1-H3K27ac-DMSO-PMA


title: Context_neg_p7_N14_S13_mouse2


title: Context_pos_p6_E4_S164_mouse2


title: Context_neg_p7_E18_S110_mouse2


title: Context_pos_p6_M19_S63_mouse2


title: Context_neg_p7_M23_S299_mouse2


title: THP1-BRD4-BD2-PMA-R2


title: THP1-BRD4-DMSO-PMA-R2


title: THP1-BRD3-BD2-PMA


title: THP1-BRD2-BD2-PMA


title: THP1-BRD3-BD1-PMA


title: THP1-BRD4-BD1-PMA


title: Context_pos_p6_O20_S110_mouse2


title: Context_neg_p7_P15_S60_mouse2


title: THP1-BRD3-DMSO-PMA


title: Context_neg_p7_E23_S115_mouse2


title: Context_pos_p6_F14_S197_mouse2


title: THP1-BRD2-BD1-PMA


title: FC_pos_p10_L2_S227_mouse2


title: K562-input


title: THP1-input-R2


title: THP1-BRD2-DMSO-PMA


title: THP1-input


title: FC_pos_p10_E5_S69_mouse2


title: THP1-BRD4-DMSO-PMA


title: FC_neg_p3_A5_S181_mouse2


title: THP1-BRD4-BD1-PMA-R2


title: FC_pos_p10_A3_S275_mouse2


title: FC_pos_p10_G9_S119_mouse2


title: HUVEC.miRNA.hypo+oxP_7h.rep3

city: Kuopio

first: Minna

last: Kaikkonen-Määttä

country: Finland

institute: A. I. Virtanen Institute

data_processing:
For GRO-Seq and RNA-Seq, reads have been trimmed to remove 3' A-stretches from the library preparation and for all libraries the low quality reads were excluded (minimum 97% of bp over quality cutoff 10).
GRO-Seq reads have been aligned to hg19 with bowtie allowing up to two mismatches and only one alignment per read.
RNA-Seq data have been mapped to hg19 using STAR v2.5.4b with ENCODE standard options for long RNA-seq pipeline.
microRNA-Seq data have been mapped to hg19 using STAR v2.5.4b with ENCODE standard options for small RNA-seq pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraphs

source_name: human umbilical vein endothelial cells

growth_protocol: HUVECs and HAECs were cultured in Endothelial Cell Growth medium (EGM; Thermo Scientific) on fibronectin-gelatin coated surfaces (10 µg/ml, 0.05%; Sigma-Aldrich); HASMC were cultrured in Medium 231 (Cascade Biologics®) supplemented with Smooth Muscle Growth Supplement (SMGS). CD14+/Macrophages were cultured in Medium RPMI 1640, supplemented with 10 % FBS, 100μg/ml streptomycin,100 U/ml penicillin, and 2 mM glutamine, 1 % Na-pyruvate, 1 % NEAA and supplemented with rHu M-CSF (50ng/ml; ThermoFisher Scientific).

extract_protocol:
Small RNA-fraction (17-200 bases) was obtained by adding ethanol to the flow through from Zymo RNA Clean and Conc kit and passing the RNA through a new column.
The libraries were prepared by Exiqon (Vedbæk, Denmark) small RNAseq protocol
GRO-seq: Nuclei were extracted from 5-10 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol-LS.
RNA-seq, miRNA-seq: One hour after collection of GRO-Seq samples (reflecting the lag in nascent transcription and mature RNAs), cells were treated for 10 min with cycloheximide (0,1mg/mL), washed with PBS and scraped into lysis buffer [1x Mammalian Polysome Buffer (Epicentre, Madison, Wisconsin), 1% Triton X-100, 1 mM DTT, 250 U/ml SUPERase Inhibitor, 7.1 U/ml Turbo DNase (Thermo Fisher Scientific, Waltham, Massachusetts, U.S.A.) and 0.1 mg/ml Cycloheximide] on ice. To confim the complete lysis of the cells, they were drawn up and expelled 4 times through a sterile 22-25 gauge needle. The cleared lysate was further treated with 10% SDS, snap-frozen in liquid nitrogen and stored at -80°C. For RNA-Seq, larger mRNAs (>200 nt) was purified with Zymo RNA Clean and Conc kit (Zymo Research, Irvine, California, U.S.A.) and rRNAs were eliminated using the Ribo-Zero Gold rRNA Removal Kit (Illumina, San Diego, CA, U.S.A.). For miRNA-Seq, small RNA-fraction (17-200 bases) was obtained by adding ethanol to the flow through from Zymo RNA Clean and Conc kit and passing the RNA through a new column.
GRO-seq, RNA-seq: The RNA was fragmented (RNA fragmentation reagent, Thermofisher), dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). For GRO-Seq only immunopurification step was performed, where BrUTP-labeled run-on RNA was bound with anti-BrdUTP-coated agarose beads and precipitated overnight. FOr both GRO-Seq and RNA-Seq libraries, the RNA was polyadenylated, followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 11-16 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: Hypoxia was achieved in Ruskinn Invivo2 400 hypoxia workstation (1% O2 and 5% CO2). OxPAPC has been generated from 1-palmitoyl-2-archidonoyl-sn-glycero-3-phophocholine [PAPC, 10 mg/ml (Avanti Polar Lipids, Inc)]. PAPC was exposed to air for 40h, then dissolved in chloroform and stored at -70 °C. At the start of the oxPAPC stimulation, chloroform was evaporated with nitrogen gas and lipids were re-suspended in growth medium to achieve a concentration of 30 μg/ml.

tag: timepoint

value: 7 hours

tag: stimulus

value: Hypoxia+OxPAPC


title: HUVEC.miRNA.hypo+oxP_7h.rep2


title: HUVEC.miRNA.oxPAPC_7h.rep2

value: OxPAPC


title: HUVEC.miRNA.oxPAPC_7h.rep3


title: FC_pos_p10_D10_S51_mouse2


title: Context_pos_p6_O22_S112_mouse2


title: FC_pos_p1_P7_S92_mouse2


title: HUVEC.miRNA.hypoxia_7h.rep2

value: Hypoxia


title: FC_pos_p1_E8_S140_mouse2


title: HUVEC.miRNA.hypoxia_7h.rep3


title: FC_pos_p10_J7_S186_mouse2


title: HUVEC.miRNA.control.rep2

value: Control


title: HUVEC.miRNA.control.rep3


title: FC_pos_p10_K5_S207_mouse2


title: HAEC.miRNA.hypo+oxP_7h.rep2

source_name: primary human aortic endothelial cells


title: FC_pos_p1_K10_S280_mouse2


title: Context_pos_p6_H17_S246_mouse2


title: HAEC.miRNA.oxPAPC_7h.rep2


title: HAEC.miRNA.hypoxia_7h.rep2


title: FC_pos_p10_O9_S3_mouse2


title: FC_pos_p10_M6_S254_mouse2


title: HAEC.miRNA.control.rep2


title: FC_pos_p10_C8_S26_mouse2


title: FC_neg_p2_E15_S215_mouse2


title: FC_neg_p2_P2_S155_mouse2


title: RNAseq_Tex15KO_3

city: Edinburgh

first: Yuka

last: Kabayama

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

description: HWVTHAFXY_RNAseqAZpool_19s004407-1-1_Zoch_lane1Tex15301

data_processing:
For analysis of piRNA, adapter sequence 'AGATCGGAAGA' was removed from fastq file using cutadapt version 1.8.1 with option '-m 16 --trimmed-only'.
Processed reads were mapped with bowtie (1.2.1.1) to known miRNAs, non-coding RNAs, repeatmasker track (UCSC mm10), and mouse genome (UCSC mm10).
Up to 3 mismatches were allowed when reads are mapped to genomic retrotransposon sequences.
For analysis of differentially expressed TEs, single-end reads were mapped to consensus sequences from Repbase (24.01) using bowtie2 (2.3.4.3).
Mapped reads per TE were counted by home made scripts.
Differentially expressed TEs were analysed using DESeq2 (1.26.0).
Genome_build: UCSC mm10
Supplementary_files_format_and_content: the sequence, length, raw counts, and annotation of small RNAs as well as sample ID and condition.

source_name: RNAseq_Tex15KO_P20 testis

extract_protocol:
Total RNA was extracted from 1 testis using QIAGEN RNeasy Mini kit and following manufacture’s protocol including on-column DNase treatment.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

tag: strain

value: mixed B6CBAF1/Crl; C57BL/6N

tag: genotype

tag: developmental stage

tag: tissue

value: testis

tag: molecule subtype

value: rRNA depleted total RNA


title: FC_neg_p3_J13_S96_mouse2

tag: cell type


title: FC_pos_p10_N5_S276_mouse2


title: RNAseq_Tex15KO_1

description: HWVTHAFXY_RNAseqAZpool_19s004407-1-1_Zoch_lane1Tex15297


title: FC_pos_p1_O1_S63_mouse2


title: RNA-seq_P20_spocd1_KO_3

first: Ansgar

last: Zoch

department: MRC Centre for Regenerative Medicine

description:
rRNA depleted total RNA
Spocd1-/-

data_processing:
For analysis of small RNA, adapter sequence 'AGATCGGAAGA' was removed from fastq file using cutadapt version 1.16 with option '-m 16 --trimmed-only'.
Processed reads were mapped with bowtie (1.2.1.1) to known miRNAs, non-coding RNAs, repeatmasker track (UCSC mm10), and mouse genome (UCSC mm10).
Up to 3 mismatches were allowed when reads are mapped to genomic retrotransposon sequences.
For analysis of differentially expressed genes, paired-end reads were mapped to GRCm38 genome_tran (release 84) using HISAT2 '--no-mixed --no-discordant --qc-filter --trim5 3'.
Mapped reads per gene were counted with htseq-count (HTSeq 0.11.1) providing GTF file.
Differentially expressed genes were analysed using DESeq2.
For analysis of differentially expressed TEs, single- or paired-end reads were mapped to consensus sequences from Repbase using bowtie2 (2.3.4.3).
Mapped reads per TE were counted by home made pipeline.
Differentially expressed TEs were analysed using DESeq2.
Genome_build: UCSC mm10, GRCm38
Supplementary_files_format_and_content: The processed data file is the tab-delimited txt file that contains the sequence, length, count, annotation, sample ID, and condition of small RNAs identified in this study.

source_name: P20 testis


title: RNA-seq_P20_spocd1_KO_2

description:
rRNA depleted total RNA
Spocd1-/-


title: FC_pos_p10_J4_S183_mouse2


title: FC_pos_p10_O7_S1_mouse2


title: RNA-seq_P20_Miwi2_KO_2

description:
rRNA depleted total RNA
Miwi2^Tom/Tom


title: FC_pos_p10_A5_S277_mouse2


title: FC_pos_p10_M1_S249_mouse2


title: RNA-seq_P20_spocd1_KO_1

description:
rRNA depleted total RNA
Spocd1-/-


title: RNA-seq_P20_Miwi2_KO_1

description:
rRNA depleted total RNA
Miwi2^Tom/Tom


title: FC_pos_p10_N6_S277_mouse2


title: RNA-seq_P20_control_3

description:
rRNA depleted total RNA
wildtype

value: wildtype


title: FC_pos_p10_O6_S300_mouse2


title: FC_neg_p2_P15_S168_mouse2


title: Brain, MCAO_18M_F

city: Vestec

first: Lukas

last: Valihrach

address: Prumyslova 595

country: Czech Republic

institute: Institute of Biotechnology of the Czech Academy of Sciences

data_processing:
Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna (version 2) and the SILVA rRNA database (version 119). Reads were aligned against the reference Mouse genome version GRCm38 including ERCC spike-in sequences and count tables were generated to annotation version genecode.vM8 using htseq-count.
Normalized number of reads was generated by DESeq2 using default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized and DESeq2-normalized number of reads for each sample

growth_protocol: The mice were kept on a 12-hr light/dark cycle with access to food and water ad libitum.

extract_protocol:
Brain tissue samples were homogenized using the Tissue-Lyser (Qiagen). Total RNA was extracted with TRI Reagent (Sigma-Aldrich) according to the manufacturer´s protocol and treated with TURBO DNA-free kit (Thermo Fisher).
RNA libraries were prepared for sequencing using Lexogen QuantSeq 3'mRNA-Seq Library Prep Kit FWD for Illumina from 400 ng total RNA according to manufacturer´s protocol.

treatment_protocol: Prior to the induction of MCAO, mice were anaesthetized with 3% isoflurane (Abbot) and maintained in 2% isoflurane using a vaporizer (Tec-3, Cyprane Ltd.). A skin incision between the orbit and the external auditory meatus was made, and a 1-2 mm hole was drilled through the frontal bone 1 mm rostral to the fusion of the zygoma and the squamosal bone and about 3.5 mm ventrally to the dorsal surface of the brain. The middle cerebral artery (MCA) was exposed after the dura was opened and re-moved. The MCA was occluded by short coagulation with bipolar tweezers (SMT) at a proximal location, followed by transection of the vessel to ensure permanent occlusion. During the surgery, body temperature was maintained at 37±1°C using a heating pad. This MCAO model yields small infarct lesions in the parietal cortical region. Intact cortical tissue from 3 and 18 month-old mice was used as control.

tag: condition

value: MCAO

tag: biological replicate

value: F

tag: age

value: 18 months


title: FC_pos_p1_H10_S211_mouse2


title: FC_pos_p10_F5_S92_mouse2


title: FC_pos_p1_K22_S292_mouse2


title: Brain, MCAO_18M_E

value: E


title: RNA-seq_P20_control_1

description:
rRNA depleted total RNA
wildtype


title: Brain, MCAO_18M_C

value: C


title: FC_pos_p1_P9_S94_mouse2

value: Primary brain cells  from muring mPFC


title: RNA-seq_P20_control_2

description:
rRNA depleted total RNA
wildtype


title: FC_pos_p1_E7_S139_mouse2


title: FC_pos_p1_N21_S60_mouse2


title: FC_pos_p1_C6_S92_mouse2


title: Brain, MCAO_18M_D

value: D


title: Brain, MCAO_18M_B

value: B


title: Brain, MCAO_18M_A

value: A


title: Brain, MCAO_3M_E

value: 3 months


title: RNAseq_Tex15KO_2

description: HWVTHAFXY_RNAseqAZpool_19s004407-1-1_Zoch_lane1Tex15298


title: RNA-seq_P20_Miwi2_KO_3

description:
rRNA depleted total RNA
Miwi2^Tom/Tom


title: Brain, MCAO_3M_F


title: Brain, MCAO_3M_D


title: FC_pos_p10_D8_S49_mouse2


title: Brain, MCAO_3M_B


title: Brain, MCAO_3M_C


title: FC_pos_p1_O18_S80_mouse2


title: FC_pos_p1_O7_S69_mouse2


title: FC_pos_p1_B19_S82_mouse2


title: Brain, MCAO_3M_A


title: Brain, Ctrl_18M_F


title: FC_pos_p1_A23_S63_mouse2


title: FC_neg_p3_F19_S10_mouse2


title: Brain, Ctrl_18M_E


title: FC_neg_p3_I2_S62_mouse2


title: Brain, Ctrl_18M_D


title: Brain, Ctrl_18M_C


title: FC_pos_p1_F22_S177_mouse2


title: Brain, Ctrl_18M_B


title: FC_neg_p3_K14_S120_mouse2


title: Brain, Ctrl_18M_A


title: Brain, Ctrl_3M_E


title: FC_pos_p1_E16_S148_mouse2


title: FC_pos_p1_F23_S178_mouse2


title: Brain, Ctrl_3M_D


title: Brain, Ctrl_3M_F


title: FC_pos_p1_I7_S231_mouse2


title: FC_pos_p1_K5_S275_mouse2


title: FC_pos_p1_P6_S91_mouse2


title: Brain, Ctrl_3M_B


title: FC_pos_p1_G11_S189_mouse2


title: FC_pos_p1_O4_S66_mouse2


title: FC_pos_p1_G6_S184_mouse2


title: Brain, Ctrl_3M_C


title: Brain, Ctrl_3M_A


title: Triple Mutant Input H3Ac_ChIPSeq Rep2

city: Omaha

first: Adam

middle: R.

last: Karpf

state: Nebraska

address: 985950 Nebraska Medical Center

department: Eppley Institute for Research in Cancer

institute: University of Nebraska Medical Center

data_processing:
Adaptor sequences and low quality (Phred score < 20) ends were trimmed from sequences using Trim Galore software package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Resulting fastq files were aligned to the human genome (GRCm38/mm10) using the sequence aligner Bowtie2 (version 2.2.3).
Picard routine MarkDuplicates (http://broadinstitute.github.io/picard/) was used to remove sequence duplications.
Peak calling, of ChIP enriched regions the THOR peak caller software of each ChIP to corresponding input DNA sample was used to determine binding regions based on a FDR adjusted p-value (q-value) <0.05.
BigWig files were generated using the deeptools bamCoverage routine (https://deeptools.readthedocs.io/en/develop/).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated using the resulting bam files and deeptools bamCoverage routine (https://deeptools.readthedocs.io/en/develop/).

source_name: S. aureus infected orthopedic implant-associated tissue

extract_protocol: Soft tissues surrounding S. aureus-infected implants were removed, homogenized and stained for FACS. Live MDSCs from WT and triple mutant-infected animals were sorted and chromatin isolated from each sample.

value: MDSCs

value: 10-12 weeks

tag: infected with

value: triple mutant S. aureus

tag: chip antibody

value: none (input)

tag: s. aureus background strain and genotype

value: USA300 LAC13c


title: FC_pos_p10_L7_S232_mouse2


title: WT Input H3Ac_ChIPSeq Rep2

value: WT S. aureus


title: FC_neg_p3_B11_S210_mouse2


title: FC_pos_p1_N19_S58_mouse2


title: FC_pos_p1_G16_S194_mouse2


title: FC_neg_p3_K13_S119_mouse2


title: FC_pos_p1_E20_S152_mouse2


title: Triple Mutant Input H3Ac_ChIPSeq Rep1


title: WT H3Ac_ChIPSeq Rep2

value: Histone H3ac (pan-acetyl, pAb) antibody (Active motif Cat no. 61537)


title: Triple Mutant H3Ac_ChIPSeq Rep2


title: FC_pos_p1_I20_S244_mouse2


title: FC_neg_p3_D21_S266_mouse2


title: WT H3Ac_ChIPSeq Rep1


title: sRNAseq_Tex15KO_3

description: CCTMVANXX_T15_sRNA_19s002356-1-1_Schoepp_lane1C3

source_name: sRNAseq_Tex15KO_foetal testes

extract_protocol:
Total RNA was extracted from 6 foetal testes using the QIAzol reagent following the manufacturer’s instructions.
Size selected (15–40 nt) total RNA was applied for library preparation using NEBnext Multiplex Small RNA Library Prep Set for Illumina (NEB).

value: mixed B6CBAF1/Crl; C57BL/6N

value: testis

value: Small RNA (15–40 nt)


title: FC_pos_p1_F7_S162_mouse2


title: sRNAseq_Tex15KO_1

description: CCTMVANXX_T15_sRNA_19s002356-1-1_Schoepp_lane1C1


title: sRNAseq_control_3

description: CCTMVANXX_T15_sRNA_19s002356-1-1_Schoepp_lane1T3

source_name: sRNAseq_control_foetal testes


title: FC_neg_p3_H19_S56_mouse2


title: FC_pos_p1_J19_S266_mouse2


title: FC_pos_p1_P15_S100_mouse2


title: sRNAseq_control_1

description: CCTMVANXX_T15_sRNA_19s002356-1-1_Schoepp_lane1T1


title: FC_neg_p2_A17_S125_mouse2


title: FC_pos_p1_C8_S94_mouse2


title: sRNAseq_control_2

description: CCTMVANXX_T15_sRNA_19s002356-1-1_Schoepp_lane1T2


title: PIN5_16214_GGCTAC

city: Zaragoza

first: Janne

middle: M

last: Toivonen

address: Miguel servet 177

department: Departamento de Anatomía, Embriología y Genética Animal

country: Spain

institute: Universidad de Zaragoza

description:
raw_counts_chimira.txt
normalized_counts_chimira.txt

data_processing:
Sequencing and basecalling by Illumina HiSeq Control Software 2.2.58
Sequenced reads were trimmed for adaptor sequence (TGGAATTCTCGGGTGCCAAGGAACT) and the processed data files were produced using "Clean&Run" mode of Chimira (http://wwwdev.ebi.ac.uk/enright-dev/chimira/).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw (raw_counts_chimira.txt) or DESeq2-normalized (normalized_counts_chimira.txt) miRNA counts for each sample. In each case, the first column denotes the miRNA name, and columns 2-25 denote the count value for each miRNA in samples CC1-PIN6.

source_name: Cervical spinal cord

extract_protocol:
Cervical spinal cords were removed, submerged in RNAlater at 4 degrees celsius for 24 hours, and frozen in RNAlater at -80 degrees celsius. Total RNA was harvested using Qiazol reagent and Direct-zol column purification.
Sequencing libraries were prepared using TrueSeq Small RNA Library Preparation Kit (Illumina)

treatment_protocol: Tg501 mice were intracerebrally inoculated with caprine scrapie strain (Goat-Sc S2) at 50 days of age. Non-inoculated age-matched Tg501 animals were used as controls. The mice were sacrificed at preclinical stage (PC, preclinical control; PIN, preclinical inoculated) or at clinical stage (CC, clinical control,CIN; clinical inoculated).

value: postnatal day 100

tag: Stage

value: preclinical (prion-inoculated), 150 days post inoculation


title: FC_neg_p3_B4_S203_mouse2

value: Primary brain cells  from muring mPFC


title: PIN6_16214_CTTGTA


title: PIN4_16214_TAGCTT


title: FC_pos_p1_A7_S47_mouse2


title: FC_neg_p3_C3_S225_mouse2


title: PIN3_16214_GATCAG


title: FC_neg_p3_H22_S59_mouse2


title: FC_pos_p1_G12_S190_mouse2


title: sRNAseq_Tex15KO_2

description: CCTMVANXX_T15_sRNA_19s002356-1-1_Schoepp_lane1C2


title: PC5_16214_ACAGTG

value: preclinical (control)


title: WT Input H3Ac_ChIPSeq Rep1


title: PIN2_16214_ACTTGA


title: Triple Mutant H3Ac_ChIPSeq Rep1


title: FC_pos_p1_A9_S49_mouse2


title: PC6_16214_GCCAAT


title: FC_neg_p3_C16_S238_mouse2


title: PIN1_16214_CAGATC


title: FC_pos_p10_J2_S181_mouse2


title: FC_pos_p1_B16_S79_mouse2


title: PC4_16214_TGACCA


title: PC3_16214_TTAGGC


title: FC_pos_p1_J11_S258_mouse2


title: PC2_16214_CGATGT


title: PC1_16214_ATCACG


title: FC_pos_p1_E21_S153_mouse2


title: CIN5_16214_CATGGC

value: postnatal day 200

value: clinical (prion-inoculated), 150 days post inoculation


title: FC_pos_p1_C7_S93_mouse2


title: CIN4_16214_CAGGCG


title: FC_neg_p2_O21_S151_mouse2


title: CIN3_16214_CGTACG


title: FC_pos_p1_L7_S300_mouse2


title: FC_pos_p1_B22_S85_mouse2


title: FC_pos_p1_O11_S73_mouse2


title: CIN2_16214_GTTTCG


title: FC_pos_p1_H7_S208_mouse2


title: CIN1_16214_GTGGCC


title: CC7_16214_GTGAAA

value: clinical (control)


title: FC_pos_p1_J20_S267_mouse2


title: FC_pos_p10_G1_S111_mouse2


title: CC2_16214_AGTTCC


title: FC_neg_p2_I10_S2_mouse2


title: CC4_16214_CCGTCC


title: CC6_16214_GTCCGC


title: FC_neg_p2_B3_S134_mouse2


title: FC_neg_p3_A12_S188_mouse2


title: CC3_16214_ATGTCA


title: FC_pos_p1_B12_S75_mouse2


title: FC_pos_p1_I18_S242_mouse2


title: CC5_16214_GTAGAG


title: sRNA-seq_spocd1_KO_3

description:
Spocd1 KO 3
Small RNA (15–40 nt)

data_processing:
Adapter sequence 'AGATCGGAAGA' was removed from fastq file using cutadapt version 1.16 with option '-m 16 --trimmed-only'.
Reads were mapped with bowtie version 1.2.1.1 to non-coding RNAs, repeatmasker track (UCSC mm10), and mouse genome (UCSC mm10).
Genome_build: UCSC mm10
Supplementary_files_format_and_content: The processed data file is the tab-delimited txt file that contains the sequence, length, count, annotation, sample ID, and condition of small RNAs identified in this study.

source_name: E16.5 testes

extract_protocol:
Six fetal testes were pooled and total RNA was isolated using the QIAzol reagent following the manufacturer’s instructions.
Total RNA was size selected for 15–40 nt and applied for library preparation using NEBnext Multiplex Small RNA Library Prep Set for Illumina (NEB).


title: FC_pos_p1_P22_S107_mouse2


title: CC1_16214_AGTCAA


title: sRNA-seq_spocd1_KO_1

description:
Spocd1 KO 1
Small RNA (15–40 nt)


title: FC_pos_p1_I5_S229_mouse2


title: sRNA-seq_control_3

description:
Control 3
Small RNA (15–40 nt)

value: control


title: sRNA-seq_control_2

description:
Control 2
Small RNA (15–40 nt)


title: sRNA-seq_control_1

description:
Control 1
Small RNA (15–40 nt)


title: FC_pos_p1_I15_S239_mouse2


title: FC_pos_p1_I21_S245_mouse2


title: FC_neg_p3_N17_S192_mouse2


title: FC_pos_p1_L14_S7_mouse2


title: Mtg16 KO replicate 3

city: London

first: Vivian

last: Li

address: 1 Midland Road

institute: The Francis Crick Institute

description: RNA-Seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”.
The RSEM package (version 1.3.0) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 11th December 2017. The parameters used were “--star-output-genome-bam --forward-prob 0”.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al., 2014) within the R programming environment (version 3.3.1) (http://www.R-project.org/). An adjusted p-value of <= 0.1 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

source_name: Intestinal crypt epithelial cells

growth_protocol: Mouse intestinal epithelial crypts from WT or Mtg16 -/- mice were isolated after 30min incubation in cold PBS containing 2mM EDTA (Sato et al., 2009).

extract_protocol:
RNA was extracted using Qiagen's Rneasy mini kit according to manufacturer's instructions. RNA integrity was examined using Bioanalyzer 2100 RNA 6000 Nano kit from Agilent Technologies.
Libraries were generated using KAPA RNA HyperPrep with RiboErase (HMR) (KK8561). 200ng RNA input, 14 PCR cycles.

treatment_protocol: Isolated mouse crypts were resuspended in 1ml RLT buffer (Qiagen Rneasy mini kit) containing DTT, followed by two freezing/thawing cycles, to increase the yield of extracted RNA.

value: Intestinal crypt epithelial cells

tag: genotype/variation

value: Mtg16 KO

tag: treatment

value: CRISPR induced Mtg16 knock-out


title: Mtg16 KO replicate 2

description: RNA-Seq


title: Mtg16 KO replicate 1

description: RNA-Seq


title: FC_pos_p1_D11_S120_mouse2


title: FC_pos_p1_D23_S132_mouse2


title: sRNA-seq_spocd1_KO_2

description:
Spocd1 KO 2
Small RNA (15–40 nt)


title: FC_pos_p1_M23_S39_mouse2


title: Wild-type replicate 3

description: RNA-Seq

value: Wild-type


title: Wild-type replicate 1

description: RNA-Seq


title: FC_pos_p1_M20_S36_mouse2


title: Wild-type replicate 2

description: RNA-Seq


title: FC_pos_p1_I10_S234_mouse2


title: Kidney-1

city: Chengdu

first: Xu

last: Zhongxian

address: NO. 211, Huiming Road, Wenjiang District

country: China

institute: Sichuan Agricultural University

data_processing:
Small RNA library construction and sequencing using Illumina (Solexa) platform was conducted in ANNOROAD, Beijing, China
Fast-toolkit software (http://hannonlab.cshl.edu/fastx-toolkit/) was used to remove low-quality reads (the proportion of bases with a mass value below 30 exceeds 20%) from sequencing data and convert the fastq file to a fasta file.
Cutadapt software was used to remove the adapter and sequences less than 18 nt in length and greater than 30 nt. The remaining reads  were used for alignment and remove  tRNA, rRNA, rRNA, snRNA, snoRNA and Repease by bowtie software.
The clean data were mapped to the known miRNA database in miRBase (v21) (http://www.mirbase.org/) to identify mature miRNAs or pre-miRNAs. And the mature miRNAs were mapped to a chicken closely related species (Taeniopygia guttata) to predict novel miRNAs by mirdeep2.pl
Genome_build: miRNA database in miRBase (v21); FASTA files are included on series record with novel miRNA sequences.
Supplementary_files_format_and_content: TPM

organism: Gallus gallus

source_name: Kidney

extract_protocol: All samples were raised in poultry farm of Tibetan and were triplicate collected. Tissues were taken out of animals immediately after slaughtering when anaesthetized, wrapped in tin foil, snap-frozen in liquid nitrogen, and  transfered to  storage at -80°C until RNA extraction.

value: At the age of  300 days

value: Kidney

value: Tibetan chicken


title: Spleen-3

source_name: Spleen

value: Spleen


title: FC_neg_p2_K3_S41_mouse2


title: Kidney-2


title: FC_pos_p1_E15_S147_mouse2


title: Spleen-1


title: FC_pos_p1_J17_S264_mouse2


title: Ovary-3

source_name: Ovary

value: Ovary


title: FC_neg_p3_O14_S212_mouse2


title: FC_neg_p2_D16_S193_mouse2


title: Ovary-2


title: FC_pos_p10_A1_S273_mouse2


title: FC_pos_p10_E1_S65_mouse2


title: FC_pos_p1_N12_S51_mouse2


title: FC_pos_p1_N16_S55_mouse2


title: Liver-3

source_name: Liver

value: Liver


title: FC_pos_p10_H4_S137_mouse2


title: FC_pos_p1_D20_S129_mouse2


title: Liver-2


title: FC_pos_p1_A16_S56_mouse2


title: FC_pos_p1_G5_S183_mouse2


title: Brain-3

source_name: Brain

value: Brain


title: Liver-1


title: Spleen-2


title: Brain-2


title: Y12-3

source_name: Pectoral muscle

value: At the age of 12 years

value: Pectoral muscle


title: FC_pos_p1_K14_S284_mouse2

value: Primary brain cells  from muring mPFC


title: FC_pos_p1_O19_S81_mouse2


title: FC_pos_p1_F6_S161_mouse2


title: Kidney-3


title: FC_neg_p2_B7_S138_mouse2


title: FC_neg_p3_O21_S219_mouse2


title: FC_pos_p1_H16_S217_mouse2


title: Ovary-1


title: FC_neg_p3_K20_S126_mouse2


title: Brain-1


title: Y12-1


title: FC_pos_p1_C10_S96_mouse2


title: Y8-3

value: At the age of 8 years


title: Y5-3

value: At the age of 5 years


title: FC_pos_p1_L11_S4_mouse2


title: Y5-2


title: FC_pos_p1_C16_S102_mouse2


title: FC_neg_p2_G12_S258_mouse2


title: FC_neg_p3_M11_S163_mouse2


title: FC_pos_p10_J3_S182_mouse2


title: Y3-3

value: At the age of 3 years


title: Y12-2


title: FC_pos_p1_H18_S219_mouse2


title: Y5-1


title: FC_neg_p2_C4_S158_mouse2


title: Y8-2


title: D300-3


title: FC_pos_p1_D5_S114_mouse2


title: Y3-1


title: Y8-1


title: FC_pos_p1_M8_S24_mouse2


title: D300-1


title: FC_pos_p1_C22_S108_mouse2


title: FC_pos_p1_F12_S167_mouse2


title: FC_neg_p2_A9_S117_mouse2


title: FC_pos_p1_O2_S64_mouse2


title: D100-3

value: At the age of 100 days


title: D100-2


title: FC_pos_p1_B9_S72_mouse2


title: FC_pos_p1_C5_S91_mouse2


title: D36-3

value: At the age of 36 days


title: D36-2


title: FC_pos_p1_A22_S62_mouse2


title: Y3-2


title: FC_pos_p1_K21_S291_mouse2


title: D36-1


title: D1-3

value: At the age of 1 days


title: FC_neg_p3_B7_S206_mouse2


title: FC_neg_p3_N6_S181_mouse2


title: E20-3

value: Embryonic day 20


title: FC_pos_p1_P10_S95_mouse2


title: D1-2


title: FC_pos_p1_I8_S232_mouse2


title: D1-1


title: D300-2

value: At the age of  300 days


title: E20-2


title: D100-1


title: E18-3

value: Embryonic day 18


title: E20-1

value: Tibetan chicken


title: FC_neg_p3_C10_S232_mouse2


title: FC_pos_p1_F21_S176_mouse2


title: E18-1


title: FC_neg_p3_J17_S100_mouse2


title: E15-3

value: Embryonic day 15


title: FC_pos_p1_H8_S209_mouse2


title: FC_pos_p1_G14_S192_mouse2


title: FC_neg_p2_C15_S169_mouse2


title: FC_pos_p1_I6_S230_mouse2


title: E18-2


title: E15-2


title: E12-3

value: Embryonic day 12


title: FC_pos_p1_F4_S159_mouse2


title: FC_pos_p1_H15_S216_mouse2


title: E12-2


title: FC_pos_p1_F10_S165_mouse2


title: E12-1


title: E9-2

value: Embryonic day 9


title: E9-3


title: FC_pos_p1_L9_S2_mouse2


title: FC_pos_p1_B10_S73_mouse2


title: FC_neg_p2_M1_S85_mouse2


title: E9-1


title: E7-3

value: Embryonic day 7


title: E15-1


title: FC_pos_p1_C19_S105_mouse2


title: E7-1


title: FC_pos_p1_A21_S61_mouse2


title: E7-2


title: E5-3

value: Embryonic day 5


title: E5-2

value: Pectoral muscle


title: FC_neg_p3_E22_S290_mouse2

value: Primary brain cells  from muring mPFC


title: FC_neg_p2_C8_S162_mouse2


title: E5-1


title: MTF1-Null_Suloctidil_rep3_P-5_E05

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package which uses the statistical computing language R. The input data analyzed was taken from the FASTQ files. Each file was aligned to a pseudo-transcriptome input using the Bowtie algorithm. The data analysis output is a table of counts with each column representing a sample and each row representing a gene.
Supplementary_files_format_and_content: counts

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were cultured in DMEM media (GIBCO) supplemented with 10% FBS (Omega Scientific, Australia) and 1x penicillin/streptomycin/glutamine. Cells were plated at 15 x10^5 cells per well in 12-well plates and cultured for 48 hours and then exposed to test chemicals for 6 hours.

extract_protocol: After cells were lysed in 0.5 mL Trizol, total RNA was extracted from each lysate and prepared for gene expression analysis using the human 1500+ Tempo-Seq platform (BioSpyder, Inc, Carlsbad, CA).

treatment_protocol: Chemicals, purchased from Sigma-Aldrich, were ≥ 95% pure. All chemical stock solutions were made in DMSO. After a 48 hour incubation, MCF-7 cells were exposed for 6 hours to DMSO (0.05%) or one of the six test chemicals in DMSO (final concentration 0.05%) at a concentration of 1-100 uM. Media was removed and cells were lysed in 0.5 mL Trizol.

tag: chemical

value: Suloctidil

tag: dose (um)


title: MTF1-Null_Suloctidil_rep2_P-5_E04


title: FC_pos_p1_A13_S53_mouse2


title: FC_pos_p1_H19_S220_mouse2


title: MTF1-Null_Suloctidil_rep1_P-5_E03


title: MCF7-WT_Suloctidil_rep3_P-5_E02


title: FC_neg_p2_H17_S286_mouse2


title: FC_pos_p1_L19_S12_mouse2


title: MCF7-WT_Suloctidil_rep2_P-5_D12


title: FC_neg_p2_K6_S44_mouse2


title: FC_pos_p1_J12_S259_mouse2


title: FC_pos_p1_M17_S33_mouse2


title: MTF1-Null_Deoxycholic acid_rep3_P-5_D10

value: Deoxycholic acid


title: MCF7-WT_Suloctidil_rep1_P-5_D11


title: MTF1-Null_Deoxycholic acid_rep2_P-5_D09


title: FC_neg_p3_I4_S64_mouse2


title: FC_pos_p1_O10_S72_mouse2


title: MTF1-Null_Deoxycholic acid_rep1_P-5_D08


title: FC_neg_p2_I9_S1_mouse2


title: FC_neg_p2_L4_S65_mouse2


title: FC_pos_p1_A10_S50_mouse2


title: MCF7-WT_Deoxycholic acid_rep3_P-5_D07


title: MCF7-WT_Deoxycholic acid_rep1_P-5_D05


title: MCF7-WT_Deoxycholic acid_rep2_P-5_D06


title: FC_pos_p1_M9_S25_mouse2


title: FC_neg_p2_L19_S80_mouse2


title: MTF1-Null_Disulfiram_rep3_P-5_D04

value: Disulfiram


title: FC_pos_p1_F16_S171_mouse2


title: MTF1-Null_Disulfiram_rep2_P-5_D03


title: FC_neg_p2_L11_S72_mouse2


title: FC_pos_p1_G7_S185_mouse2


title: MTF1-Null_Disulfiram_rep1_P-5_D02


title: MCF7-WT_Disulfiram_rep3_P-5_C12


title: FC_pos_p1_G23_S201_mouse2


title: MCF7-WT_Disulfiram_rep2_P-5_C11


title: FC_pos_p1_J7_S254_mouse2


title: FC_neg_p3_I23_S83_mouse2


title: MCF7-WT_Disulfiram_rep1_P-5_C10


title: FC_neg_p3_F12_S3_mouse2


title: MTF1-Null_Phenoxybenzamine_rep1_P-5_C07

value: Phenoxybenzamine


title: MTF1-Null_Phenoxybenzamine_rep2_P-5_C08


title: FC_pos_p10_D7_S48_mouse2


title: MTF1-Null_Phenoxybenzamine_rep3_P-5_C09


title: MCF7-WT_Phenoxybenzamine_rep3_P-5_C06


title: MCF7-WT_Phenoxybenzamine_rep2_P-5_C05


title: FC_pos_p1_D13_S122_mouse2


title: MCF7-WT_Phenoxybenzamine_rep1_P-5_C04


title: FC_neg_p2_O10_S140_mouse2


title: FC_neg_p2_O16_S146_mouse2


title: FC_neg_p3_C2_S224_mouse2


title: FC_neg_p2_K21_S59_mouse2


title: FC_pos_p10_P8_S25_mouse2


title: FC_pos_p1_L4_S297_mouse2


title: MTF1-Null_Astemizole_rep1_P-5_B12

value: Astemizole


title: MCF7-WT_Astemizole_rep3_P-5_B11


title: MTF1-Null_Astemizole_rep2_P-5_C02


title: MCF7-WT_Astemizole_rep2_P-5_B10


title: MCF7-WT_Astemizole_rep1_P-5_B09


title: FC_neg_p3_D19_S264_mouse2


title: MTF1-Null_Alexidine_rep3_P-5_B08

value: Alexidine


title: FC_pos_p1_H9_S210_mouse2


title: MTF1-Null_Alexidine_rep2_P-5_B07


title: FC_neg_p3_J15_S98_mouse2


title: FC_pos_p1_M21_S37_mouse2


title: FC_neg_p3_O9_S207_mouse2


title: MTF1-Null_Alexidine_rep1_P-5_B06


title: MCF7-WT_Alexidine_rep3_P-5_B05


title: MCF7-WT_Alexidine_rep1_P-5_B03


title: FC_neg_p3_N19_S194_mouse2


title: MCF7-WT_Alexidine_rep2_P-5_B04


title: FC_neg_p2_N13_S120_mouse2


title: MTF1-Null_Astemizole_rep3_P-5_C03


title: FC_neg_p3_M12_S164_mouse2


title: MTF1-Null_ZnSO4_rep3_P-5_B02


title: FC_pos_p1_L22_S15_mouse2


title: FC_neg_p2_A22_S130_mouse2


title: FC_neg_p2_I23_S15_mouse2


title: FC_neg_p3_C19_S241_mouse2


title: MTF1-Null_ZnSO4_rep1_P-5_A11


title: MTF1-Null_ZnSO4_rep2_P-5_A12


title: FC_neg_p2_L15_S76_mouse2


title: FC_pos_p1_E9_S141_mouse2


title: FC_pos_p1_O17_S79_mouse2


title: MCF7-WT_ZnSO4_rep3_P-5_A10


title: FC_neg_p3_N15_S190_mouse2


title: MCF7-WT_ZnSO4_rep1_P-5_A08


title: MCF7-WT_ZnSO4_rep2_P-5_A09


title: FC_neg_p2_B10_S141_mouse2


title: FC_pos_p10_M2_S250_mouse2


title: MCF7-WT_Control_rep3_P-5_A04

value: Control


title: FC_neg_p2_P16_S169_mouse2


title: MTF1-Null_Control_rep1_P-5_A05


title: FC_pos_p1_K20_S290_mouse2


title: MCF7-WT_Control_rep2_P-5_A03


title: MCF7-WT_Control_rep1_P-5_A02


title: FC_neg_p3_I21_S81_mouse2


title: FC_neg_p2_L17_S78_mouse2


title: FC_pos_p1_B8_S71_mouse2


title: FC_neg_p3_C20_S242_mouse2


title: HUVEC.GRO.metOH_2h.rep1

description:
HUVEC.GRO.metOH_2h.rep1
Nascent transcripts, immunopurified

data_processing:
Library strategy: GRO-Seq
GRO-Seq reads have been trimmed to remove 3' A-stretches from the library preparation and for all libraries the low quality reads were excluded (minimum 97% of bp over quality cutoff 10).
GRO-Seq reads have been aligned to hg19 with bowtie allowing up to two mismatches and only one alignment per read.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraphs

source_name: human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were isolated from umbilical cords obtained from the maternity ward of the Kuopio University Hospital by the approval of the Kuopio University Hospital Ethics Committee. HUVECs were maintained in endothelial cell growth medium (EGM; 0.1% human epidermal growth factor, 0.1% hydrocortisone, 0.1% Gentamicin-Amphotericin-B, 0.4% bovine brain extract, 2% FBS; Lonza) on cell culture flasks coated with 10 g/ml fibronectin (Sigma, St. Louis, MO) and 0.05% gelatin in phosphate buffered saline (PBS). HUVECs were used at passage 5.

extract_protocol:
Cells were treated with medium containing 1% FBS. Cells washed twice with cold PBS and incubated on ice with 10mL of swelling buffer [10 mM Tris-HCl, 2 mM MgCl2, 3 mM CaCl2 and 2 U/ml SUPERase Inhibitor (Thermofisher, Carlsbad, CA, U.S.A.)] for 5 mins. Cells were scraped and centrifuged at 400xg for 10 min and resuspended in 50μL of swelling buffer supplemented with 10% glycerol. Next, 500μL of swelling buffer containing 10% glycerol and 1% Igepal was added drop by drop while gently vortexing. Nuclei was washed twice with lysis buffer (10 ml of swelling buffer containing 0.5% Igepal and 10% glycerol), and once with 1 ml of freezing buffer (50 mM Tris-HCl pH 8.3, 40% glycerol, 5 mM MgCl2 and 0.1 mM EDTA). Finally, nuclei were counted, centrifuged at 900xg for 6min to be further resuspended in to a concentration of 5 million nuclei per 100μL of freezing buffer, snap-frozen in liquid nitrogen and stored at -80°C until run-on reaction. The run-on reaction was performed as described in [M. Bouvy-Liivrand et al. Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture, Nucleic Acids Res. 23 (2017) 862–876.].
Library preparation were performed as described in [M. Bouvy-Liivrand et al. Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture, Nucleic Acids Res. 23 (2017) 862–876.]. Libraries were amplified using 13-15 cycles, size-selected (180-350 bp) from 10 % TBE gels (Life Technologies) and sequenced (single end 50 bases) using Illumina HiSeq 2000 at EMBL GeneCore (Heidelberg, Germany).
GRO-seq: Nuclei were extracted from 5-10 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol-LS.
GRO-seq: The RNA was fragmented (RNA fragmentation reagent, Thermofisher), dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Next, immunopurification step was performed, where BrUTP-labeled run-on RNA was bound with anti-BrdUTP-coated agarose beads and precipitated overnight. The RNA was polyadenylated, followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 11-16 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: HUVECs were treated with 3 µM OA-NO2 or vehicle (0.06% meOH) for 2 or 12 h in EGM medium.

tag: timepoint

value: 2 hours

tag: stimulus

value: methanol


title: HUVEC.GRO.nitroOA_2h.rep1

description:
HUVEC.GRO.nitroOA_2h.rep1
Nascent transcripts, immunopurified

value: nitro-oleic acid


title: HUVEC.GRO.metOH_12h.rep1

description:
HUVEC.GRO.metOH_12h.rep1
Nascent transcripts, immunopurified

value: 12 hours


title: FC_neg_p3_I22_S82_mouse2

extract_protocol:
Brain tissues were dissociated with Worthington Papain Digestion Kit
RNA libraries were prepared for sequencing using standard Illumina protocols
smart seq 2


title: FC_pos_p1_O5_S67_mouse2


title: HUVEC.GRO.nitroOA_12h.rep1

description:
HUVEC.GRO.nitroOA_12h.rep1
Nascent transcripts, immunopurified


title: FC_neg_p3_A22_S198_mouse2


title: MTF1-Null_Control_rep2_P-5_A06


title: HUVEC.RNA.oxPAPC_7h.rep2

extract_protocol:
Cells were treated for 10 min with cycloheximide (0,1mg/mL), washed with PBS and scraped into lysis buffer [1x Mammalian Polysome Buffer (Epicentre, Madison, Wisconsin), 1% Triton X-100, 1 mM DTT, 250 U/ml SUPERase Inhibitor, 7.1 U/ml Turbo DNase (Thermo Fisher Scientific, Waltham, Massachusetts, U.S.A.) and 0.1 mg/ml Cycloheximide] on ice. To confirm the complete lysis of the cells, they were drawn up and expelled 4 times through a sterile 22-25 gauge needle. The cleared lysate was further treated with 10% SDS, snap-frozen in liquid nitrogen and stored at -80°C. Larger mRNAs (>200 nt) was purified with Zymo RNA Clean and Conc kit (Zymo Research, Irvine, California, U.S.A.) and rRNAs were eliminated using the Ribo-Zero Gold rRNA Removal Kit (Illumina, San Diego, CA, U.S.A.). RNA was then fragmentated (RNA fragmentation reagent, Thermofisher) and dephosphorylated.
RNA fragments were poly-A tailed (PolyA polymerase, New England Biolabs, Ipswich, MA, USA) according to manufacturer's instructions, then, fragments were circularized and re-linearized.  The libraries were amplified by 11 to 16 cycles size selected (190–350 bp) and quantified (Qubit dsDNA HS Assay Kit on a Qubit fluorometer, Thermofisher, Carlsbad, CA, USA). Sequencing (single end 50 bases) with Illumina Hi-Seq2000 at EMBL GeneCore (Heidelberg, Germany).
GRO-seq: Nuclei were extracted from 5-10 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol-LS.
RNA-seq, miRNA-seq: One hour after collection of GRO-Seq samples (reflecting the lag in nascent transcription and mature RNAs), cells were treated for 10 min with cycloheximide (0,1mg/mL), washed with PBS and scraped into lysis buffer [1x Mammalian Polysome Buffer (Epicentre, Madison, Wisconsin), 1% Triton X-100, 1 mM DTT, 250 U/ml SUPERase Inhibitor, 7.1 U/ml Turbo DNase (Thermo Fisher Scientific, Waltham, Massachusetts, U.S.A.) and 0.1 mg/ml Cycloheximide] on ice. To confim the complete lysis of the cells, they were drawn up and expelled 4 times through a sterile 22-25 gauge needle. The cleared lysate was further treated with 10% SDS, snap-frozen in liquid nitrogen and stored at -80°C. For RNA-Seq, larger mRNAs (>200 nt) was purified with Zymo RNA Clean and Conc kit (Zymo Research, Irvine, California, U.S.A.) and rRNAs were eliminated using the Ribo-Zero Gold rRNA Removal Kit (Illumina, San Diego, CA, U.S.A.). For miRNA-Seq, small RNA-fraction (17-200 bases) was obtained by adding ethanol to the flow through from Zymo RNA Clean and Conc kit and passing the RNA through a new column.
GRO-seq, RNA-seq: The RNA was fragmented (RNA fragmentation reagent, Thermofisher), dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). For GRO-Seq only immunopurification step was performed, where BrUTP-labeled run-on RNA was bound with anti-BrdUTP-coated agarose beads and precipitated overnight. FOr both GRO-Seq and RNA-Seq libraries, the RNA was polyadenylated, followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 11-16 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

value: 7 hours

value: OxPAPC


title: FC_pos_p1_J4_S251_mouse2


title: MTF1-Null_Control_rep3_P-5_A07


title: FC_pos_p1_D22_S131_mouse2


title: HUVEC.RNA.oxPAPC_7h.rep1


title: FC_neg_p2_P10_S163_mouse2


title: FC_pos_p1_L21_S14_mouse2


title: HUVEC.RNA.control.rep2


title: FC_neg_p3_J19_S102_mouse2


title: HUVEC.RNA.oxPAPC_7h.rep3


title: HAEC.RNA.oxPAPC_7h.rep3

source_name: primary human aortic endothelial cells


title: HUVEC.RNA.control.rep1


title: FC_neg_p3_M8_S160_mouse2


title: FC_neg_p3_C11_S233_mouse2


title: HAEC.RNA.oxPAPC_7h.rep2


title: HUVEC.RNA.control.rep3


title: FC_pos_p1_G19_S197_mouse2


title: HAEC.RNA.control.rep2


title: FC_pos_p1_H4_S205_mouse2


title: FC_pos_p1_A17_S57_mouse2


title: FC_neg_p2_A10_S118_mouse2


title: CD14+.GRO.control.rep2

data_processing:
Library strategy: GRO-Seq
For GRO-Seq and RNA-Seq, reads have been trimmed to remove 3' A-stretches from the library preparation and for all libraries the low quality reads were excluded (minimum 97% of bp over quality cutoff 10).
GRO-Seq reads have been aligned to hg19 with bowtie allowing up to two mismatches and only one alignment per read.
RNA-Seq data have been mapped to hg19 using STAR v2.5.4b with ENCODE standard options for long RNA-seq pipeline.
microRNA-Seq data have been mapped to hg19 using STAR v2.5.4b with ENCODE standard options for small RNA-seq pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraphs

source_name: human macrophages

extract_protocol:
Cells were treated with medium containing 1% FBS. Cells washed twice with cold PBS and incubated on ice with 10mL of swelling buffer [10 mM Tris-HCl, 2 mM MgCl2, 3 mM CaCl2 and 2 U/ml SUPERase Inhibitor (Thermofisher, Carlsbad, CA, U.S.A.)] for 5 mins. Cells were scraped and centrifuged at 400xg for 10 min and resuspended in 50μL of swelling buffer supplemented with 10% glycerol. Next, 500μL of swelling buffer containing 10% glycerol and 1% Igepal was added drop by drop while gently vortexing. Nuclei was washed twice with lysis buffer (10 ml of swelling buffer containing 0.5% Igepal and 10% glycerol), and once with 1 ml of freezing buffer (50 mM Tris-HCl pH 8.3, 40% glycerol, 5 mM MgCl2 and 0.1 mM EDTA). Finally, nuclei were counted, centrifuged at 900xg for 6min to be further resuspended in to a concentration of 5 million nuclei per 100μL of freezing buffer, snap-frozen in liquid nitrogen and stored at -80°C until run-on reaction. The run-on reaction  was performed as described in [M. Bouvy-Liivrand et al. Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture, Nucleic Acids Res. 23 (2017) 862–876.].
Library preparation were performed as described in [M. Bouvy-Liivrand et al. Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture, Nucleic Acids Res. 23 (2017) 862–876.].  Libraries were amplified using 13-15 cycles, size-selected (180-350 bp) from 10 % TBE gels (Life Technologies) and sequenced (single end 50 bases) using Illumina HiSeq 2000 at EMBL GeneCore (Heidelberg, Germany).
GRO-seq: Nuclei were extracted from 5-10 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol-LS.
RNA-seq, miRNA-seq: One hour after collection of GRO-Seq samples (reflecting the lag in nascent transcription and mature RNAs), cells were treated for 10 min with cycloheximide (0,1mg/mL), washed with PBS and scraped into lysis buffer [1x Mammalian Polysome Buffer (Epicentre, Madison, Wisconsin), 1% Triton X-100, 1 mM DTT, 250 U/ml SUPERase Inhibitor, 7.1 U/ml Turbo DNase (Thermo Fisher Scientific, Waltham, Massachusetts, U.S.A.) and 0.1 mg/ml Cycloheximide] on ice. To confim the complete lysis of the cells, they were drawn up and expelled 4 times through a sterile 22-25 gauge needle. The cleared lysate was further treated with 10% SDS, snap-frozen in liquid nitrogen and stored at -80°C. For RNA-Seq, larger mRNAs (>200 nt) was purified with Zymo RNA Clean and Conc kit (Zymo Research, Irvine, California, U.S.A.) and rRNAs were eliminated using the Ribo-Zero Gold rRNA Removal Kit (Illumina, San Diego, CA, U.S.A.). For miRNA-Seq, small RNA-fraction (17-200 bases) was obtained by adding ethanol to the flow through from Zymo RNA Clean and Conc kit and passing the RNA through a new column.
GRO-seq, RNA-seq: The RNA was fragmented (RNA fragmentation reagent, Thermofisher), dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). For GRO-Seq only immunopurification step was performed, where BrUTP-labeled run-on RNA was bound with anti-BrdUTP-coated agarose beads and precipitated overnight. FOr both GRO-Seq and RNA-Seq libraries, the RNA was polyadenylated, followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 11-16 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

value: 6 hours


title: FC_neg_p3_F4_S295_mouse2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: raw count tables


title: FC_neg_p2_M13_S97_mouse2


title: HAEC.RNA.control.rep3


title: FC_pos_p1_N9_S48_mouse2


title: FC_neg_p2_L7_S68_mouse2


title: FC_neg_p2_G23_S269_mouse2


title: HASMC.GRO.oxPAPC_6h.rep1

source_name: human aortic smooth muscle cells


title: HAEC.RNA.control.rep1


title: HASMC.GRO.control.rep1


title: HASMC.GRO.control.rep2


title: HASMC.GRO.oxPAPC_6h.rep2


title: HUVEC.GRO.hypo+oxP_6h.rep3

value: Hypoxia+OxPAPC


title: FC_pos_p10_L4_S229_mouse2


title: HUVEC.GRO.hypo+oxP_6h.rep2


title: HAEC.RNA.oxPAPC_7h.rep1


title: HUVEC.GRO.hypo+oxP_6h.rep1


title: FC_pos_p1_J13_S260_mouse2


title: FC_pos_p10_O11_S5_mouse2


title: HUVEC.GRO.oxPAPC_6h.rep3


title: CD14+.GRO.oxPAPC_6h.rep1


title: FC_pos_p1_D8_S117_mouse2


title: FC_pos_p1_P12_S97_mouse2


title: HUVEC.GRO.oxPAPC_6h.rep2


title: HUVEC.GRO.oxPAPC_6h.rep1


title: FC_neg_p3_J2_S85_mouse2


title: CD14+.GRO.control.rep1


title: FC_neg_p3_C4_S226_mouse2


title: HUVEC.GRO.hypoxia_6h.rep2

value: Hypoxia


title: HUVEC.GRO.hypoxia_6h.rep3


title: FC_neg_p3_A1_S177_mouse2

value: Primary brain cells  from muring mPFC


title: HUVEC.GRO.hypoxia_6h.rep1


title: FC_neg_p3_E10_S278_mouse2


title: FC_neg_p2_H11_S280_mouse2


title: HUVEC.GRO.control.rep3


title: FC_neg_p3_D16_S261_mouse2


title: FC_neg_p2_B22_S153_mouse2


title: HUVEC.GRO.control.rep2


title: FC_neg_p2_P7_S160_mouse2


title: FC_pos_p1_J1_S248_mouse2


title: HAEC.GRO.hypo+oxP_6h.rep1


title: HAEC.GRO.hypo+oxP_6h.rep2


title: FC_neg_p3_D10_S255_mouse2


title: HAEC.GRO.oxPAPC_6h.rep2


title: FC_neg_p2_M6_S90_mouse2


title: HAEC.GRO.oxPAPC_6h.rep1


title: HAEC.GRO.hypoxia_6h.rep2


title: FC_neg_p2_J6_S21_mouse2


title: HAEC.GRO.hypoxia_6h.rep1


title: FC_neg_p2_K11_S49_mouse2


title: HAEC.GRO.control.rep2


title: HAEC.GRO.control.rep1


title: prostate_tissue-H+sf-replicate_RIB0034257

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Gene expression of prostate RP tissue specimen (prostate cancer, tumor free tissue)

data_processing:
Processing of primary sequencing data was done using the workflow management software UAP (https://github.com/yigbt/uap).
CASAVA 1.8.2 was used to demultiplex FASTQ files. Adapter sequences were clipped by utilizing Cutadapt v1.6.
For de novo transcript assembly, all reads were mapped to the human genome version GRCh37/hg19 with TopHat v.2.0.87 setting RNA library type to fr-secondstrand and all other parameters to default values. Transcripts were assembled using cufflinks v.2.2.18 with default parameters and library type specification fr-secondstrand. Assembled transcripts were compared to Gencode v17 (Ensembl 72) utilizing cuffmerge and cuffcompare with default parameters in order to generate a comprehensive transcript assembly of novel and known transcripts.
For gene expression quantification, reads were mapped to the human genome version GRCh37/hg19 using segemehl v.0.1.7. Segemehl was used in split read mode (option -S) with additional parameters -H 1 -D 0 to report all alignments with no indels or mutations in the initial seed and passing the default minimal alignment accuracy. We used segemehl for expression quantification, since it outperforms TopHat in terms of sensitivity and specificity. Read counts for known (Gencode v17) and novel transcripts contained in the comprehensive transcript assembly were determined using HTSeqCount v0.6.0 with parameters mode intersection-strict, stranded yes, idattr gene_id, and type exon.
Differential expression of genes between tumor and BPH samples was assessed using the R v3.2 package DeSeq2 v1.81.  Raw read counts were normalized, and variance stabilized (vst transformation). False discovery rate (FDR) was controlled by Benjamini-Hochberg adjustment.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Processed data files contain raw read counts (HTSeqCount v0.6.0 with parameters mode intersection-strict, stranded yes, idattr gene_id, and type exon) and gene identifiers according to the custom assembly (de-novo transcript assembly using cufflinks v.2.2.18 merged with Gencode v17).

source_name: prostate tissue

extract_protocol:
Stacks of consecutive cryosections were generated from frozen RP tissue samples and immediately transferred to 1ml Qiazol (Qiagen, Hilden, Germany). A pathologist evaluated HE-stained cryosections flanking the stacks concerning tumor and stroma cell content. Only PCa tissue stacks, which were flanked on either side by sections containing at least 50% tumor cells underwent RNA isolation. In case of insufficient RNA quantity, we combined multiple tissue stacks with suitable tumor cell content. We isolated total RNA using the miRNeasy Mini Kit on the QIAcube (Qiagen) followed by manual DNase I digestion. After determining the RNA concentration with a NanoDrop 1000 (Peqlab, Erlangen, Germany), we verified the RNA integrity on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). RNA samples with an RNA-Integrity-Number (RIN) of at least six passed for further processing.
We depleted 1 µg of total RNA of ribosomal RNA using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI) and processed 50 ng of rRNA-depleted RNA with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre). After ten cycles of PCR, to incorporate index barcodes for sample multiplexing and to amplify the cDNA libraries, we determined the quality and concentration of the amplified libraries using the Bioanalyzer 2100. 4 ng each of 8 samples were pooled and size-selected on 2% agarose gels using agarose gel electrophoresis. We gel-excised the sample ranging between 150 bp and 600 bp and purified it with the MinElute Gel Extraction Kit (Qiagen), according to manufacturer's instructions. To quantify the purified libraries we used the Bioanalyzer 2100. Then we loaded every purified and size-selected library pool onto an Illumina HiSeq2000 flow cell, distributing it among all lanes. Finally, we performed sequencing with 2 x 101-bp paired-end reads using SBS V3 chemistry on a HiSeq2000 (Illumina, Inc, San Diego, CA).

value: prostate

tag: diagnosis

value: prostate cancer

tag: gleason score

tag: risk group

value: H+sf

tag: gender

value: male


title: FC_pos_p10_P5_S22_mouse2

tag: cell type


title: prostate_tissue-H-df-replicate_RIB0034228

tag: tissue

value: H-df


title: FC_pos_p10_J10_S189_mouse2


title: FC_neg_p2_O19_S149_mouse2


title: prostate_tissue-H+df-replicate_RIB0034220

value: H+df


title: prostate_tissue-H-df-replicate_RIB0034903


title: FC_neg_p2_E17_S217_mouse2


title: FC_neg_p2_O18_S148_mouse2


title: FC_neg_p3_C7_S229_mouse2


title: FC_pos_p1_F11_S166_mouse2


title: FC_neg_p3_A15_S191_mouse2


title: prostate_tissue-H+sf-replicate_RIB0034402


title: prostate_tissue-H-df-replicate_RIB0034995


title: FC_pos_p10_F11_S98_mouse2


title: prostate_tissue-H-sf-replicate_RIB0034437

value: H-sf


title: prostate_tissue-H+df-replicate_RIB0034923


title: FC_pos_p10_K4_S206_mouse2


title: prostate_tissue-H-df-replicate_RIB0034427


title: FC_pos_p1_A3_S43_mouse2


title: FC_pos_p1_M15_S31_mouse2


title: FC_neg_p2_A7_S115_mouse2


title: prostate_tissue-H-sf-replicate_RIB0034482


title: FC_pos_p1_E4_S136_mouse2


title: prostate_tissue-H+sf-replicate_RIB0034394


title: prostate_tissue-H-sf-replicate_RIB0034262


title: FC_neg_p3_L20_S149_mouse2


title: FC_pos_p1_F5_S160_mouse2


title: prostate_tissue-H+sf-replicate_RIB0034844


title: prostate_tissue-H+df-replicate_RIB0034296


title: prostate_tissue-C-replicate_RIB0034294

description: Gene expression of prostate RP tissue specimen (benign prostate hyperplasia)

value: benign prostate hyperplasia

value: C


title: FC_neg_p3_O17_S215_mouse2


title: FC_pos_p1_O6_S68_mouse2


title: prostate_tissue-H+df-replicate_RIB0034831


title: prostate_tissue-V-replicate_RIB0034299

description: Gene expression of prostate RP tissue specimen (prostate cancer, tumor tissue)

value: V


title: prostate_tissue-H+st-replicate_RIB0034235

value: H+st


title: FC_neg_p2_D11_S188_mouse2


title: prostate_tissue-H-df-replicate_RIB0034316


title: prostate_tissue-H-dt-replicate_RIB0034239

value: H-dt


title: prostate_tissue-L-replicate_RIB0034258

value: L


title: FC_neg_p3_F14_S5_mouse2


title: FC_neg_p3_H1_S38_mouse2


title: prostate_tissue-C-replicate_RIB0034281


title: FC_pos_p1_E3_S135_mouse2


title: FC_neg_p2_G20_S266_mouse2


title: prostate_tissue-L-replicate_RIB0034271


title: FC_pos_p1_G10_S188_mouse2


title: FC_neg_p2_E7_S207_mouse2


title: prostate_tissue-Ms-replicate_RIB0034214

value: Ms


title: FC_neg_p3_D17_S262_mouse2


title: FC_neg_p2_E19_S219_mouse2


title: FC_neg_p2_N20_S127_mouse2


title: prostate_tissue-H-dt-replicate_RIB0034918


title: FC_neg_p3_B19_S218_mouse2


title: FC_pos_p1_H22_S223_mouse2


title: prostate_tissue-H+dt-replicate_RIB0034276

value: H+dt


title: prostate_tissue-C-replicate_RIB0034687


title: prostate_tissue-Md-replicate_RIB0034731

value: Md


title: prostate_tissue-L-replicate_RIB0034798


title: FC_pos_p1_J22_S269_mouse2

value: Primary brain cells  from muring mPFC


title: FC_neg_p3_B9_S208_mouse2


title: FC_pos_p10_D4_S45_mouse2


title: FC_neg_p2_J21_S36_mouse2


title: prostate_tissue-H-st-replicate_RIB0034224

value: prostate

value: H-st


title: prostate_tissue-Ms-replicate_RIB0034497

value: prostate cancer


title: FC_pos_p1_N23_S62_mouse2


title: prostate_tissue-H+st-replicate_RIB0034434

value: male


title: FC_neg_p3_P9_S230_mouse2


title: FC_pos_p1_P2_S87_mouse2


title: prostate_tissue-L-replicate_RIB0034489


title: FC_neg_p2_O3_S133_mouse2


title: FC_pos_p1_B21_S84_mouse2


title: FC_pos_p10_N11_S282_mouse2


title: FC_neg_p2_A21_S129_mouse2


title: FC_neg_p3_M20_S172_mouse2


title: prostate_tissue-V-replicate_RIB0034942


title: prostate_tissue-H-dt-replicate_RIB0034491


title: prostate_tissue-H-st-replicate_RIB0034471


title: prostate_tissue-V-replicate_RIB0034496


title: prostate_tissue-Ms-replicate_RIB0034702


title: prostate_tissue-H+dt-replicate_RIB0034913


title: prostate_tissue-H-dt-replicate_RIB0034986


title: FC_neg_p2_D19_S196_mouse2


title: FC_pos_p1_B6_S69_mouse2


title: prostate_tissue-Md-replicate_RIB0034448


title: prostate_tissue-H-st-replicate_RIB0034477


title: prostate_tissue-C-replicate_RIB0034454


title: FC_pos_p1_M19_S35_mouse2


title: prostate_tissue-V-replicate_RIB0034321


title: prostate_tissue-V-replicate_RIB0034457


title: prostate_tissue-V-replicate_RIB0034483


title: prostate_tissue-Md-replicate_RIB0034485


title: prostate_tissue-C-replicate_RIB0034345


title: prostate_tissue-C-replicate_RIB0034341


title: prostate_tissue-H-dt-replicate_RIB0034385


title: prostate_tissue-Ms-replicate_RIB0034372


title: prostate_tissue-L-replicate_RIB0034486


title: prostate_tissue-C-replicate_RIB0034350


title: prostate_tissue-L-replicate_RIB0034340


title: prostate_tissue-L-replicate_RIB0034383


title: prostate_tissue-L-replicate_RIB0034373


title: FC_neg_p2_J12_S27_mouse2


title: FC_neg_p2_E22_S222_mouse2


title: FC_pos_p1_E2_S134_mouse2


title: FC_neg_p3_O22_S220_mouse2


title: FC_pos_p1_L18_S11_mouse2


title: FC_pos_p1_O22_S84_mouse2


title: FC_pos_p10_K9_S211_mouse2


title: FC_neg_p2_A5_S113_mouse2


title: FC_neg_p2_K22_S60_mouse2


title: FC_pos_p1_D16_S125_mouse2


title: FC_pos_p10_E9_S73_mouse2


title: FC_pos_p1_H12_S213_mouse2


title: FC_pos_p1_I16_S240_mouse2


title: prostate_tissue-H+st-replicate_RIB0034303


title: FC_neg_p2_K15_S53_mouse2


title: FC_neg_p3_M19_S171_mouse2


title: prostate_tissue-H+dt-replicate_RIB0034370


title: FC_neg_p2_C20_S174_mouse2


title: FC_neg_p2_B11_S142_mouse2


title: FC_pos_p10_L8_S233_mouse2


title: FC_pos_p1_O9_S71_mouse2


title: prostate_tissue-C-replicate_RIB0034238


title: prostate_tissue-V-replicate_RIB0034227


title: prostate_tissue-H+st-replicate_RIB0034830


title: FC_pos_p1_H6_S207_mouse2


title: prostate_tissue-Ms-replicate_RIB0034207


title: prostate_tissue-V-replicate_RIB0034226


title: prostate_tissue-H+dt-replicate_RIB0034827


title: FC_pos_p1_H21_S222_mouse2


title: FC_neg_p3_N2_S177_mouse2


title: FC_neg_p2_F8_S231_mouse2


title: ANM_77 miRNA-Seq

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

description:
miRNA
P77

data_processing:
Basecalls performed using Perl package developed by NOVOGENE
Contaminant reads from the fq file were removed and get the final clean reads. And then summarize the length distribution of these clean reads. Normally, length of small RNA is between 18nt and 30nt. The length distribution analysis is helpful to see the compositions of small RNA sample. For example, miRNA is normally 21nt or 22nt, siRNA is 24nt, and piRNA is 30nt.
The data is processed by the following steps: 1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table); 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt; 7) Summarize the length distribution of the clean reads.
Genome_build: hg19
Supplementary_files_format_and_content: txt file

source_name: adjacent normal mucosa tissue

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life  technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tumor and adjacent mormal mucosa tissues excised from LSCC patients after surgery were stored with RNAlater  (Cat#AM7020，Life  technologies, Carlsbad, CA, US)  following the manufacturer’s instructions.

value: adjacent normal mucosa tissue

tag: tumor stage

value: Not Applicable

tag: tobacco smoking

tag: alcohol consumption


title: ANM_76 miRNA-Seq

description:
miRNA
P76


title: ANM_75 miRNA-Seq

description:
miRNA
P75


title: ANM_73 miRNA-Seq

description:
miRNA
P73


title: FC_pos_p1_O14_S76_mouse2


title: ANM_74 miRNA-Seq

description:
miRNA
P74


title: FC_pos_p1_M7_S23_mouse2


title: ANM_65 miRNA-Seq

description:
miRNA
P65


title: FC_pos_p1_E10_S142_mouse2


title: FC_pos_p10_L10_S235_mouse2


title: FC_pos_p1_L2_S295_mouse2


title: FC_pos_p1_J21_S268_mouse2


title: ANM_66 miRNA-Seq

description:
miRNA
P66


title: ANM_64 miRNA-Seq

description:
miRNA
P64


title: FC_pos_p10_B9_S4_mouse2


title: ANM_62 miRNA-Seq

description:
miRNA
P62


title: ANM_63 miRNA-Seq

description:
miRNA
P63


title: ANM_60 miRNA-Seq

description:
miRNA
P60


title: FC_neg_p2_H2_S271_mouse2


title: FC_neg_p2_I7_S299_mouse2


title: FC_pos_p1_A8_S48_mouse2


title: FC_pos_p1_D17_S126_mouse2


title: ANM_57 miRNA-Seq

description:
miRNA
P57


title: FC_neg_p2_O12_S142_mouse2


title: ANM_56 miRNA-Seq

description:
miRNA
P56


title: ANM_58 miRNA-Seq

description:
miRNA
P58


title: ANM_59 miRNA-Seq

description:
miRNA
P59


title: FC_pos_p1_B13_S76_mouse2


title: FC_pos_p1_G1_S179_mouse2


title: FC_neg_p3_B2_S201_mouse2


title: ANM_54 miRNA-Seq

description:
miRNA
P54


title: ANM_55 miRNA-Seq

description:
miRNA
P55


title: FC_neg_p2_H9_S278_mouse2


title: FC_pos_p1_J10_S257_mouse2


title: FC_pos_p1_L3_S296_mouse2


title: FC_neg_p3_G20_S34_mouse2


title: ANM_46 miRNA-Seq

description:
miRNA
P46


title: FC_pos_p1_C4_S90_mouse2


title: ANM_53 miRNA-Seq

description:
miRNA
P53


title: ANM_52 miRNA-Seq

description:
miRNA
P52


title: ANM_50 miRNA-Seq

description:
miRNA
P50


title: FC_neg_p3_P3_S224_mouse2


title: ANM_51 miRNA-Seq

description:
miRNA
P51


title: FC_neg_p3_L21_S150_mouse2


title: ANM_61 miRNA-Seq

description:
miRNA
P61


title: ANM_37 miRNA-Seq

description:
miRNA
P37


title: FC_neg_p3_H11_S48_mouse2


title: ANM_35 miRNA-Seq

description:
miRNA
P35


title: ANM_36 miRNA-Seq

description:
miRNA
P36


title: ANM_34 miRNA-Seq

description:
miRNA
P34


title: ANM_31 miRNA-Seq

description:
miRNA
P31


title: FC_pos_p1_J16_S263_mouse2


title: FC_neg_p2_K23_S61_mouse2


title: FC_pos_p1_N14_S53_mouse2


title: ANM_30 miRNA-Seq

description:
miRNA
P30


title: FC_neg_p3_K4_S110_mouse2


title: ANM_29 miRNA-Seq

description:
miRNA
P29


title: FC_neg_p3_H14_S51_mouse2


title: ANM_28 miRNA-Seq

description:
miRNA
P28


title: FC_neg_p2_A19_S127_mouse2


title: FC_neg_p2_P22_S175_mouse2


title: ANM_26 miRNA-Seq

description:
miRNA
P26


title: FC_pos_p1_B5_S68_mouse2


title: ANM_24 miRNA-Seq

description:
miRNA
P24


title: ANM_20 miRNA-Seq

description:
miRNA
P20


title: ANM_22 miRNA-Seq

description:
miRNA
P22


title: FC_neg_p2_K14_S52_mouse2


title: ANM_23 miRNA-Seq

description:
miRNA
P23


title: ANM_27 miRNA-Seq

description:
miRNA
P27


title: FC_neg_p3_G3_S17_mouse2


title: ANM_25 miRNA-Seq

description:
miRNA
P25


title: FC_neg_p2_P9_S162_mouse2


title: ANM_18 miRNA-Seq

description:
miRNA
P18


title: FC_neg_p3_N9_S184_mouse2


title: ANM_19 miRNA-Seq

description:
miRNA
P19


title: FC_neg_p3_D8_S253_mouse2


title: FC_neg_p3_K15_S121_mouse2


title: FC_neg_p2_N3_S110_mouse2


title: FC_pos_p1_D6_S115_mouse2


title: ANM_17 miRNA-Seq

description:
miRNA
P17


title: FC_neg_p3_L23_S152_mouse2


title: ANM_15 miRNA-Seq

description:
miRNA
P15


title: ANM_14 miRNA-Seq

description:
miRNA
P14


title: FC_pos_p1_L15_S8_mouse2


title: FC_neg_p2_I6_S298_mouse2


title: ANM_16 miRNA-Seq

description:
miRNA
P16


title: FC_neg_p3_M1_S153_mouse2


title: FC_pos_p1_I4_S228_mouse2


title: ANM_13 miRNA-Seq

description:
miRNA
P13


title: FC_neg_p3_D18_S263_mouse2


title: ANM_12 miRNA-Seq

description:
miRNA
P12


title: ANM_8 miRNA-Seq

description:
miRNA
P_8


title: ANM_11 miRNA-Seq

description:
miRNA
P11


title: FC_neg_p3_G15_S29_mouse2


title: FC_pos_p1_K2_S272_mouse2


title: FC_pos_p10_N8_S279_mouse2


title: ANM_9 miRNA-Seq

description:
miRNA
P_9


title: ANM_7 miRNA-Seq

description:
miRNA
P_7


title: FC_pos_p10_H1_S134_mouse2


title: FC_pos_p10_J5_S184_mouse2


title: ANM_5 miRNA-Seq

description:
miRNA
P_5


title: FC_pos_p10_I9_S165_mouse2


title: ANM_4 miRNA-Seq

description:
miRNA
P_4


title: ANM_6 miRNA-Seq

description:
miRNA
P_6


title: ANM_2 miRNA-Seq

description:
miRNA
P_2


title: FC_pos_p10_P10_S27_mouse2


title: FC_pos_p10_F8_S95_mouse2


title: ANM_10 miRNA-Seq

description:
miRNA
P10


title: ANM_3 miRNA-Seq

description:
miRNA
P_3


title: FC_neg_p3_O10_S208_mouse2


title: ANM_1 miRNA-Seq

description:
miRNA
P_1


title: FC_pos_p10_I8_S164_mouse2


title: LSCC_77 miRNA-Seq

description:
miRNA
C77

source_name: Laryngeal squamous cell carcinoma tissue

value: Yes

value: No


title: FC_neg_p3_J14_S97_mouse2


title: FC_pos_p10_E10_S74_mouse2


title: LSCC_75 miRNA-Seq

description:
miRNA
C75

value: Laryngeal squamous cell carcinoma tissue


title: LSCC_76 miRNA-Seq

description:
miRNA
C76


title: FC_pos_p10_A11_S283_mouse2


title: LSCC_74 miRNA-Seq

description:
miRNA
C74


title: LSCC_73 miRNA-Seq

description:
miRNA
C73


title: LSCC_65 miRNA-Seq

description:
miRNA
C65


title: FC_pos_p1_G17_S195_mouse2


title: LSCC_66 miRNA-Seq

description:
miRNA
C66


title: LSCC_64 miRNA-Seq

description:
miRNA
C64


title: FC_pos_p10_O8_S2_mouse2


title: FC_pos_p10_P12_S29_mouse2


title: FC_pos_p10_L1_S226_mouse2


title: LSCC_63 miRNA-Seq

description:
miRNA
C63


title: LSCC_62 miRNA-Seq

description:
miRNA
C62


title: FC_pos_p10_M8_S256_mouse2


title: FC_pos_p10_J6_S185_mouse2


title: LSCC_61 miRNA-Seq

description:
miRNA
C61


title: FC_pos_p1_K15_S285_mouse2


title: FC_pos_p1_H5_S206_mouse2


title: FC_pos_p1_C12_S98_mouse2


title: FC_pos_p10_K6_S208_mouse2


title: LSCC_59 miRNA-Seq

description:
miRNA
C59


title: LSCC_60 miRNA-Seq

description:
miRNA
C60


title: LSCC_58 miRNA-Seq

description:
miRNA
C58


title: FC_pos_p10_B3_S298_mouse2


title: LSCC_57 miRNA-Seq

description:
miRNA
C57


title: LSCC_56 miRNA-Seq

description:
miRNA
C56


title: FC_pos_p1_C11_S97_mouse2


title: FC_pos_p10_D6_S47_mouse2


title: FC_pos_p10_O4_S298_mouse2


title: FC_pos_p10_P3_S20_mouse2


title: LSCC_54 miRNA-Seq

description:
miRNA
C54


title: FC_pos_p10_E3_S67_mouse2


title: LSCC_52 miRNA-Seq

description:
miRNA
C52


title: FC_pos_p10_B6_S1_mouse2


title: LSCC_51 miRNA-Seq

description:
miRNA
C51


title: FC_pos_p10_P4_S21_mouse2


title: LSCC_53 miRNA-Seq

description:
miRNA
C53


title: FC_pos_p10_H11_S144_mouse2


title: LSCC_37 miRNA-Seq

description:
miRNA
C37


title: LSCC_36 miRNA-Seq

description:
miRNA
C36


title: LSCC_50 miRNA-Seq

description:
miRNA
C50


title: FC_neg_p2_E21_S221_mouse2


title: FC_pos_p10_C10_S28_mouse2


title: LSCC_46 miRNA-Seq

description:
miRNA
C46


title: LSCC_35 miRNA-Seq

description:
miRNA
C35


title: FC_pos_p1_C18_S104_mouse2


title: FC_neg_p2_K2_S40_mouse2


title: LSCC_34 miRNA-Seq

description:
miRNA
C34


title: FC_neg_p2_O15_S145_mouse2


title: LSCC_31 miRNA-Seq

description:
miRNA
C31


title: LSCC_55 miRNA-Seq

description:
miRNA
C55


title: FC_pos_p1_N6_S45_mouse2


title: LSCC_29 miRNA-Seq

description:
miRNA
C29


title: FC_pos_p1_D21_S130_mouse2


title: FC_pos_p10_D11_S52_mouse2


title: FC_neg_p3_I16_S76_mouse2


title: LSCC_28 miRNA-Seq

description:
miRNA
C28


title: FC_neg_p3_P13_S234_mouse2


title: LSCC_27 miRNA-Seq

description:
miRNA
C27


title: LSCC_26 miRNA-Seq

description:
miRNA
C26


title: FC_neg_p2_F20_S243_mouse2


title: LSCC_25 miRNA-Seq

description:
miRNA
C25


title: FC_pos_p1_P11_S96_mouse2


title: LSCC_24 miRNA-Seq

description:
miRNA
C24


title: FC_pos_p1_E19_S151_mouse2


title: FC_neg_p2_M18_S102_mouse2


title: LSCC_22 miRNA-Seq

description:
miRNA
C22


title: FC_pos_p10_A2_S274_mouse2


title: LSCC_20 miRNA-Seq

description:
miRNA
C20


title: FC_pos_p1_G4_S182_mouse2


title: LSCC_23 miRNA-Seq

description:
miRNA
C23


title: LSCC_30 miRNA-Seq

description:
miRNA
C30


title: LSCC_19 miRNA-Seq

description:
miRNA
C19


title: FC_neg_p3_B14_S213_mouse2


title: LSCC_15 miRNA-Seq

description:
miRNA
C15


title: FC_neg_p2_H14_S283_mouse2


title: FC_pos_p1_J5_S252_mouse2


title: FC_pos_p1_N5_S44_mouse2


title: FC_neg_p2_A3_S111_mouse2


title: LSCC_17 miRNA-Seq

description:
miRNA
C17


title: LSCC_16 miRNA-Seq

description:
miRNA
C16


title: LSCC_14 miRNA-Seq

description:
miRNA
C14


title: FC_neg_p3_N8_S183_mouse2


title: FC_neg_p2_L16_S77_mouse2


title: LSCC_11 miRNA-Seq

description:
miRNA
C11


title: LSCC_12 miRNA-Seq

description:
miRNA
C12


title: LSCC_13 miRNA-Seq

description:
miRNA
C13


title: LSCC_18 miRNA-Seq

description:
miRNA
C18


title: LSCC_10 miRNA-Seq

description:
miRNA
C10


title: LSCC_9 miRNA-Seq

description:
miRNA
C_9


title: FC_pos_p1_L8_S1_mouse2


title: FC_neg_p3_B21_S220_mouse2


title: FC_pos_p10_G10_S120_mouse2