title: extra-cellular RNAs from HeLa cells

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

description:
all RNAs below 200 nt
167713_CGTACGATCCCCCCCC_HVKFJBGXJ_1_20210722B_20210722

data_processing:
base-calling was performed by VBCF sequencing facility
Read 3' end adapter trimming and quality filtering was performed by Cutadapt with the following parameters (-q 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC )
Small RNA seq reads were aligned to the Hg38 or mm10 genome for libraries originating from HeLa and MEF cells, respectively, by using Bowtie2 with the following parameters (-D 15 -R 2 -N 0  -L 10 -i S,1,1.15 )
for tRNA expression and coverage data, trimmed reads were aligned to the collapsed tRNA reference genome using Bowtie2 with the following parameters (--no-unal --no-1mm-upfront -D 15 -R 2 -N 0  -L 10 -i S,1,1.15)
Biotype extraction was performed by featureCounts software by using the following parameters (-a annotation.gtf -M -O  -g 'transcript_type') and the comprehensive gene and tRNA annotation gtf files awailable from Gencode webpage
tRNA coverage data was extracted from sorted BAM files using Samtools with the apropriate parameters (Samtools depth -a)
Genome_build: mm10 and Hg38
Supplementary_files_format_and_content: tsv files containing number of reads mapping to specific tRNA clusters
Supplementary_files_format_and_content: tsv files containing coverage per position information for every tRNA cluster

growth_protocol: HeLa cultured in a humidified 5% CO2 incubator at 37°C in standard DMEM supplemented with antibiotic/antimycotics, 2 mM L-glutamine and 10% fetal bovine serum. MEF were cultured in the same medium, additionally supplemented with non-essential amino acids.

extract_protocol:
0.2 mL of cell culture medium conditioned by cells growing in a 6-well dish format (2.5 mL each well total) was collected. were Aliquots were centrifuged for one hour at 16.000x g at 4°C. Total RNA was isolated from 0.2 mL of cell culture medium using TRIzol. Samples were incubated at room temperature for five minutes and extracted with 0.2 mL chloroform, followed by precipitation with isopropanol (over-night) and centrifugation for > 20 minutes at 16.000x g at 4°C. RNA pellets were washed once with 75% ethanol, re-suspended in RNase-free water.
Libraries were prepared according to NEBNext small RNA cloning protocol (E7580S)

treatment_protocol: 70% confluent cells were treated with sodium arsenite (0.75 mM) for one hour, followed by washout and recovery in fresh medium for 24 hours

tag: cell line/type

value: HeLa cells

tag: molecule subtype

value: small RNAs


title: A549-ACE2 cells infected with VIC SARS-CoV-2 strain at 2hpi, Replicate2

status: Public on Dec 31 2021

type: SRA

city: Oxford

first: Jeffrey

middle: Y

last: Lee

address: Dorothy Hodgkin Road

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Basecalling was done on the Illumina NextSeq sequencer with the Illumina Real Time Analysis software version 2.11.3
Sequenced reads were demultiplexed and adapter trimmed.
Reads were aligned to GRCh38 and SARS-CoV-2 reference sequence using STAR.
Gene counts were calculated using HTSeq-count.
Gene count normalisation and differential expression analysis were performed using the R package DESeq2.
Genome_build: GRCh38, NC_045512.2
Supplementary_files_format_and_content: Tab delimited file of DESeq2 normalised count and differential gene expression

molecule: total RNA

organism: Homo sapiens

source_name: A549 cells expressing ACE2

growth_protocol: A549-ACE2 (Klein et al., 2020) cells were maintained in standard DMEM supplemented with 10% fetal bovine serum, 2mM L-glutamine, 100 U/mL penicillin and 10μg/mL streptomycin and non-essential amino acids. The cells were maintained at 37°C and 5% CO2 in a standard culture incubator.

extract_protocol:
Infected cells were harvested in RLT buffer and RNA extracted using the Qiagen RNAeasy kit, following manufacturer instructions.
Sequencing libraries were prepared using the Illumina Total RNA Prep with Ribo-Zero Plus library kit (Cat# 20040525) according to manufacturer’s guidelines.

treatment_protocol: SARS-CoV-2 strains: Victoria 01/20 (BVIC01) (Caly et al., 2020) (Provided by PHE Porton Down after supply from the Doherty Centre Melbourne, Australia) and B.1.1.7 (Tegally et al., 2020) (20I/501Y.V1.HMPP1) (provided by PHE Porton Down). Cells were infected at an MOI of 1 for 2h followed by extensive washing in PBS. Residual cell surface associated virus was removed by trypsin treatment of the cell monolayer for 2mins followed by neutralisation of the trypsin using serum containing media. Infected cells were then maintained for defined periods up to 24h.

tag: infection

value: Infected with SARS-CoV-2

tag: sars-cov-2 strain

value: VIC

tag: hours post infection


title: Ctrl2_S2_L001

city: Houston

first: Qiang

last: Wang

state: Texas

address: 6550 FANNIN STREET

country: USA

institute: HOUSTON METHODIST RESEARCH INSTITUTE

description: DMSO 5

data_processing:
data filtering: fastp 0.20.0
read alignment: kallisto 0.46.2
gene abundance: DESeq2
Genome_build: human genome genecode release 34
Supplementary_files_format_and_content: FPM

source_name: Human MM cell line MM.1S

growth_protocol: MM.1S MM cells were cultured in RPMI1640 medium containing 10% fetal bovine serum and 100 U penicillin / 0.1 mg/ml streptomycin.

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2 x 106 MM.1S MM cells were pulsed with DMSO or Cfz for 1 hours and then cultured with fresh growth medium containing DMSO or 10 µM ATRA for 12 h.

tag: tissue

value: Human Multiple Myeloma cell line

tag: cell line

tag: treatment

value: DMSO


title: Ctrl1_S1_L002

description: DMSO 2


title: A549-ACE2 cells Mock infection control, Replicate2

value: Uninfected


title: Ctrl3_S3_L001

description: DMSO 9


title: A549-ACE2 cells infected with VIC SARS-CoV-2 strain at 8hpi, Replicate1


title: Ctrl1_S1_L001

description: DMSO 1


title: Cfz_S7_L004

description: Cfz 4

value: Cfz


title: Cfz_S7_L003

description: Cfz 3


title: Cfz_S7_L001

description: Cfz 1


title: Ctrl1_S1_L004

description: DMSO 4


title: ATRA3_S6_L004

description: ATRA 12

value: ATRA


title: Ctrl1_S1_L003

description: DMSO 3


title: ATRA3_S6_L002

description: ATRA 10


title: ATRA3_S6_L003

description: ATRA 11


title: ATRA3_S6_L001

description: ATRA 9


title: ATRA2_S5_L002

description: ATRA 6


title: ATRA2_S5_L003

description: ATRA 7


title: ATRA2_S5_L001

description: ATRA 5


title: ATRA1_S4_L002

description: ATRA 2


title: ATRA1_S4_L004

description: ATRA 4


title: ATRA1_S4_L001

description: ATRA 1


title: ATRA-Cfz_S8_L004

description: ATRA-Cfz 4

value: ATRA+Cfz


title: ATRA-Cfz_S8_L003

description: ATRA-Cfz 3


title: Sorghum leaves-drought degradome

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Cut the first 20 nucleotides in the remaining reads
Sort and remove repetitive sequences
Calculate the counts of unique sequences
Supplementary_files_format_and_content: sequences and count values

molecule: polyA RNA

organism: Sorghum bicolor

source_name: Sorghum leaves

growth_protocol: Sorghum (Sorghum bicolor (L.) Moench) seeds were sown in pots (0.2 m diameter × 0.45 m tall) filled with pure, fine sand soil and grown in growth chambers (Conviron Ltd., Winnipeg, Canada) at 28°/20°C (day/night) with a photoperiod of 14 h/10 h (day/night). After germination, sorghum seedlings were thinned to one plant per pot.

extract_protocol:
Total RNA was extracted from leaves of control, drought or heat, drought and heat-exposed sorghum using the Trizol reagent
Degradome libraries were constructed using poly-A+ RNA, which was ligated to a 5’adapter containing a MmeI site at its 3’-end. The ligated products were used for cDNA production and amplified by PCR for five cycles. The PCR products were digested with MmeI and the resulting fragments ligated to a second double-stranded oligonucleotide, purified and amplified for another ten PCR cycles. The PCR product has been purified and sequenced.

treatment_protocol: To impose heat stress,  30 days after sowing, sorghum seedlings grown at 28°/20°C (day/night) were transferred to another growth chamber maintained at 38°/30°C (day/night) for 50 days. Drought stress was imposed by withholding irrigation for one week on 73-day-old (after sowing) plants grown at 28°/20°C (day/night).  Drought and heat combination was imposed by withholding irrigation for one week on 73-day-old (after sowing) plants grown at 38°/30°C (day/night). At the end of stress treatment, leaf samples from control, drought or heat, drought and heat-stressed plants were harvested

value: leaves

value: drought


title: ATRA-Cfz_S8_L001

description: ATRA-Cfz 1


title: Sorghum leaves-control degradome

value: control


title: Cfz_S7_L002

description: Cfz 2


title: ATRA2_S5_L004

description: ATRA 8


title: ATRA1_S4_L003

description: ATRA 3


title: ATRA-Cfz_S8_L002

description: ATRA-Cfz 2


title: BMDM, control, biological rep3

type: RNA

city: Heidelberg

first: Tsunaki

last: Hongu

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Junior Research Group Metastatic Niches

country: Germany

institute: German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)

description: Gene expression of untreated BMDMs

hyb_protocol: 15 μg of fragmented and labeled ds-cDNA were hybridized for 17 hr at 45°C on Affymetrix/Applied Biosystems™ GeneChip® Mouse Genome U430 2.0 Arrays.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: The data were normalized using quantile normalization with R using function normalize.quantiles from Bioconductor package preprocessCore

label: biotin

organism: Mus musculus

source_name: Untreated BMDMs

label_protocol: The Applied Biosystems™ Gene Chip 3’ IVT PLUS Reagent Kit is used to generate labeled single-stranded cRNA from input amounts of 100 ng total RNA. Label: Biotin.

growth_protocol: Bone marrow cells isolated from BALB/c mice were cultured in DMEM (ThermoFisher Scientific) with 10% FBS, 20 μg/ml M-CSF (Peprotech), 50 U/ml penicillin (Sigma-Aldrich) and 50 μg/ml streptomycin (Sigma-Aldrich) for 7 days. Differentiated BMDMs were further cultured in DMEM containing 1% FBS and 20 μg/ml M-CSF overnight.

extract_protocol: RNA extraction was performed using the QIAGEN RNeasy Mini Kit according to the manufacturer’s protocol.

treatment_protocol: BMDMs were treated with 3 μM TAK-242 (TLR4i, Merck) or vehicle control (0.1% DMSO in final) for 1 hr, and stimulated with 2 μg/ml recombinant Tenascin-C (TNC, Merck) for 6 hrs.

tag: mouse strain

value: BALB/c

tag: cell type

value: BMDMs

value: Untreated


title: ECs, shControl MDA-LM2 metastatic lung, biological rep3

description: Gene expression of sorted mouse lung endothelial cells from NSG mice, 3 weeks after intravenous injection of MDA-MB-231-LM2 breast cancer cells expressing control shRNA

source_name: Endothelial cells sorted from metastatic lung of NSG mice, 3 weeks after i.v. injection of MDA-MB-231-LM2 cells expressing control shRNA

label_protocol: The Affymetrix/ Applied Biosystems™ 3’ IVT Pico Reagent Kit is used to generate labeled ds-cDNA from input amounts of 2 ng total RNA. Label: Biotin

value: NSG

value: Lung endothelial cells

tag: time point

value: 3 weeks after i.v. injection

tag: injected cancer cells


title: BMDM, treated with TNC and TLR4i, biological rep1

description: Gene expression of BMDMs treated with recombinant TNC and TAK-242 (TLR4i)

source_name: BMDMs treated with TNC and TLR4i

value: TNC with TAK-242


title: ECs, shTNC MDA-LM2 metastatic lung, biological rep3

description: Gene expression of sorted mouse lung endothelial cells from NSG mice, 3 weeks after intravenous injection of MDA-MB-231-LM2 breast cancer cells expressing shRNA for TNC

source_name: Endothelial cells sorted from metastatic lung of NSG mice, 3 weeks after i.v. injection of MDA-MB-231-LM2 cells expressing shRNA for TNC


title: ECs, shTNC MDA-LM2 metastatic lung, biological rep2

value: MDA-MB-231-LM2 cells expressing shRNA for TNC


title: BMDM, control, biological rep1

description: Gene expression of untreated BMDMs


title: ECs, MDA-LM2 metastatic lung, clodronate-lipo-treated, biological rep3

description: Gene expression of sorted mouse lung endothelial cells from NSG mice treated with clodronate-liposomes, 3 weeks after intravenous injection of MDA-MB-231-LM2 breast cancer cells

hyb_protocol: 6.6 ug of fragmented and labeled ds-cDNA were hybridized for 17 hr at 45°C on Affymetrix/Applied Biosystems™ GeneChip® Mouse Genome U430 2.0 Arrays.

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

source_name: Endothelial cells sorted from metastatic lung of NSG mice treated with clodronate-liposomes, 3 weeks after i.v. injection of MDA-MB-231-LM2 cells

label_protocol: The Affymetrix/ Applied Biosystems™ 3’ IVT Pico Reagent Kit is used to generate labeled ds-cDNA from input amounts of 1 ng total RNA. Label: Biotin

extract_protocol: RNA extraction was performed using the Arcturus PicoPure Extraction Kit (ThermoFisher Scientific) according to the manufacturer’s protocol.

value: Clodronate-liposomes


title: BMDM, treated with TNC, biological rep3

description: Gene expression of BMDMs treated with recombinant TNC

source_name: BMDMs treated with TNC

value: TNC with vehicle


title: sst1_1_ins_30dpf_03_D06

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

data_processing:
Trimming using trim_galore using default parameters
Mapping using HISAT2 against GRCz11with default parameters
Counts per gene generated using FeatureCounts with default parameters
Genome_build: Zebrafish GRCz11
Supplementary_files_format_and_content: read counts as csv file

organism: Danio rerio

extract_protocol:
Enzymatic Dissociation
Smart-Seq2, followed by llumina NextSeq

tag: genotype/variation

value: Tg(ins:BB1.0L), TgBAC(sst1.1:memEGFP)

tag: developmental stage

tag: growth

value: Normal

value: pancreas


title: BMDM, treated with TNC and TLR4i, biological rep3


title: ECs, MDA-LM2 metastatic lung, B20-treated, biological rep3

description: Gene expression of sorted mouse lung endothelial cells from NSG mice treated with anti-VEGFA antibody, 3 weeks after intravenous injection of MDA-MB-231-LM2 breast cancer cells

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore.

source_name: Endothelial cells sorted from metastatic lung of NSG mice treated with anti-VEGFA antibody, 3 weeks after i.v. injection of MDA-MB-231-LM2 cells

value: Anti-VEGFA antibody


title: ECs, MDA-LM2 metastatic lung, IgG-treated, biological rep3

description: Gene expression of sorted mouse lung endothelial cells from NSG mice treated with control IgG, 3 weeks after intravenous injection of MDA-MB-231-LM2 breast cancer cells

source_name: Endothelial cells sorted from metastatic lung of NSG mice treated with control IgG, 3 weeks after i.v. injection of MDA-MB-231-LM2 cells

value: Control IgG


title: BMDM, treated with TNC, biological rep2


title: ECs, shControl MDA-LM2 metastatic lung, biological rep2

value: MDA-MB-231-LM2 cells expressing control shRNA


title: ECs, MDA-LM2 metastatic lung, clodronate-lipo-treated, biological rep1


title: ECs, MDA-LM2 metastatic lung, PBS-lipo-treated, biological rep2

description: Gene expression of sorted mouse lung endothelial cells from NSG mice treated with control PBS-liposomes, 3 weeks after intravenous injection of MDA-MB-231-LM2 breast cancer cells

source_name: Endothelial cells sorted from metastatic lung of NSG mice treated with control PBS-liposomes, 3 weeks after i.v. injection of MDA-MB-231-LM2 cells

value: Control PBS-liposomes


title: ECs, MDA-LM2 metastatic lung, PBS-lipo-treated, biological rep3


title: BMDM, treated with TNC and TLR4i, biological rep2

value: BALB/c


title: BMDM, treated with TNC, biological rep1

value: BMDMs


title: BMDM, control, biological rep2

description: Gene expression of untreated BMDMs

value: Untreated


title: ECs, MDA-LM2 metastatic lung, B20-treated, biological rep2

value: NSG


title: ECs, shControl MDA-LM2 metastatic lung, biological rep1

value: Lung endothelial cells


title: ECs, MDA-LM2 metastatic lung, IgG-treated, biological rep1

value: 3 weeks after i.v. injection


title: ECs, healthy lung, IgG-treated, biological rep2

description: Gene expression of sorted mouse lung endothelial cells from healthy NSG mice treated with control IgG

source_name: Endothelial cells sorted from healthy lung of NSG mice treated with control IgG

value: Healthy


title: ECs, MDA-LM2 metastatic lung, IgG-treated, biological rep2


title: ECs, MDA-LM2 metastatic lung, PBS-lipo-treated, biological rep1


title: ECs, MDA-LM2 metastatic lung, B20-treated, biological rep1


title: ECs, MDA-LM2 metastatic lung, clodronate-lipo-treated, biological rep2


title: ECs, healthy lung, IgG-treated, biological rep3


title: ECs, MDA-LM2 metastatic lung, rat IgG-treated, biological rep1

label_protocol: The Affymetrix/ Applied Biosystems™ 3’ IVT Pico Reagent Kit is used to generate labeled ds-cDNA from input amounts of 500 pg total RNA. Label: Biotin


title: ECs, MDA-LM2 metastatic lung, DC101-treated, biological rep1

description: Gene expression of sorted mouse lung endothelial cells from NSG mice treated with anti-VEGFR2 antibody, 3 weeks after intravenous injection of MDA-MB-231-LM2 breast cancer cells

source_name: Endothelial cells sorted from metastatic lung of NSG mice treated with anti-VEGFR2 antibody, 3 weeks after i.v. injection of MDA-MB-231-LM2 cells

value: Anti-VEGFR2 antibody


title: ECs, MDA-LM2 metastatic lung, DC101-treated, biological rep3


title: ECs, MDA-LM2 metastatic lung, DC101-treated, biological rep2


title: ECs, healthy lung, IgG-treated, biological rep1


title: ECs, MDA-LM2 metastatic lung at week3, biological rep2

description: Gene expression of sorted mouse lung endothelial cells from NSG mice 3 weeks after intravenous injection of MDA-MB-231-LM2 breast cancer cells

source_name: Endothelial cells sorted from lung of NSG mice 3 weeks after i.v. injection of MDA-MB-231-LM2 cells


title: ECs, MDA-LM2 metastatic lung at week2, biological rep3

description: Gene expression of sorted mouse lung endothelial cells from NSG mice 2 weeks after intravenous injection of MDA-MB-231-LM2 breast cancer cells

source_name: Endothelial cells sorted from lung of NSG mice 2 weeks after i.v. injection of MDA-MB-231-LM2 cells

value: 2 weeks after i.v. injection


title: ECs, healthy lung, rat IgG-treated, biological rep3


title: ECs, MDA-LM2 metastatic lung at week3, biological rep1


title: ECs, healthy lung, rat IgG-treated, biological rep2


title: ECs, healthy lung, biological rep1

description: Gene expression of sorted mouse lung endothelial cells from healthy NSG mice

source_name: Endothelial cells sorted from lung of healthy NSG mice


title: ECs, MDA-LM2 metastatic lung, rat IgG-treated, biological rep3


title: ECs, healthy lung, biological rep2


title: ECs, MDA-LM2 metastatic lung, rat IgG-treated, biological rep2


title: ECs, MDA-LM2 metastatic lung at week1, biological rep1

description: Gene expression of sorted mouse lung endothelial cells from NSG mice 1 week after intravenous injection of MDA-MB-231-LM2 breast cancer cells

source_name: Endothelial cells sorted from lung of NSG mice 1 week after i.v. injection of MDA-MB-231-LM2 cells

value: 1 week after i.v. injection


title: ECs, healthy lung, rat IgG-treated, biological rep1


title: ECs, healthy lung, biological rep3


title: ECs, MDA-LM2 metastatic lung at week2, biological rep1


title: ECs, MDA-LM2 metastatic lung at week1, biological rep3


title: ECs, shTNC MDA-LM2 metastatic lung, biological rep1

value: MDA-MB-231-LM2 cells expressing shRNA for TNC


title: ECs, MDA-LM2 metastatic lung at week1, biological rep2


title: mdx quad at 6 weeks, biological rep3

city: Binghamton

first: Kanneboyina

last: Nagaraju

state: NY

address: PO Box 6000

department: Pharmaceutical Sciences

institute: Binghamton University-SUNY

description: Gene expression data from BL10 and mdx quadricep muscle at 6 weeks

hyb_protocol: Affymetrix Mouse Genome 430 v2 Array according to standard Affymetrix protocol.

scan_protocol: Hewlett Packard G2500A Gene Array Scanner

data_processing: Data analysis was performed using GeneSpring GX software by normalizing signal intensity values with the PLIER algorithm.

source_name: quadricep muscle at 6 weeks

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

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

value: quadriceps

tag: genotype

value: mdx

tag: age

value: 6 weeks


title: control quad at 5 days, biological rep1

description: Gene expression data from BL10 and mdx quadricep muscle at 5 days

source_name: quadricep muscle at 5 days

value: 5 days


title: ECs, MDA-LM2 metastatic lung at week3, biological rep3


title: mdx quad at 6 weeks, biological rep2


title: mdx quad at 5 days, biological rep1


title: control quad at 5 days, biological rep2


title: control quad at 3 weeks, biological rep1

description: Gene expression data from BL10 and mdx quadricep muscle at 3 weeks

source_name: quadricep muscle at 3 weeks

value: 3 weeks


title: control quad at 2 weeks, biological rep2

description: Gene expression data from BL10 and mdx quadricep muscle at 2 weeks

source_name: quadricep muscle at 2 weeks

value: 2 weeks


title: mdx quad at 2 weeks, biological rep1


title: mdx quad at 6 weeks, biological rep1


title: control quad at 6 weeks, biological rep2


title: Heart_M48N_rep5

city: Gold Coast

first: Kevin

middle: John

last: Ashton

state: QLD

address: University Drive

department: Health Sciences & Medicine

country: Australia

institute: Bond University

description: replicate 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumia scanning protocol

data_processing: Data were variance stabilized and robust spline normalized using the 'lumi' package in R/Bioconductor

source_name: ventricular myocardium, 48wk age, normoxia

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit from Ambion

growth_protocol: All studies were performed in accordance with the guidelines of the Animal Ethics Committee of Griffith University, which is accredited by the Queensland Government, Department of Primary Industries and Fisheries under the guidelines of The Animal Care and Protection Act 2001, Section 757. Male C57Bl/6 mice were purchased from the Animal Resource Centre (Western Australia, Australia) at 7 weeks of age, and group housed in individually ventilated cages (Tecniplast, Buguggiate VA, Italy) under standard laboratory conditions (21±1°C, 40-60%, rel. humidity, 12h:12h light/dark cycle with lights on at 7AM). Animals had access to standard rodent diet (Harlan-Teklad, Indianapolis, Indiana) and water ad libitum. Animals were maintained until 8, 16, 32 or 48 weeks of age.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control (RIN) was performed with Agilent Bioanalyzer

treatment_protocol: Mice were anesthetized with sodium pentobarbital and hearts excised and perfused in a Langendorff mode. After 20 min stabilization, hearts were subjected to either 25 min of global normothermic ischemia and 45 minutes of aerobic reperfusion, or time-matched normoxic perfusion. Hearts were collected in RNAlater and the left ventricular tissue dissected from the heart.

tag: strain

tag: Sex

value: male

value: 48 weeks

value: left ventricular myocardium

tag: treatment protocol

value: normoxia

tag: rin


title: control quad at 6 weeks, biological rep1


title: mdx quad at 5 days, biological rep2


title: ECs, MDA-LM2 metastatic lung at week2, biological rep2

value: NSG

value: Lung endothelial cells


title: Heart_M48N_rep6

description: replicate 6


title: Heart_M48N_rep3

description: replicate 3


title: mdx quad at 3 weeks, biological rep2


title: mdx quad at 5 days, biological rep3


title: control quad at 6 weeks, biological rep3


title: control quad at 5 days, biological rep3


title: Heart_M32N_rep6

description: replicate 6

source_name: ventricular myocardium, 32wk age, normoxia

value: 32 weeks


title: control quad at 3 weeks, biological rep2


title: mdx quad at 2 weeks, biological rep2


title: mdx quad at 3 weeks, biological rep3


title: control quad at 3 weeks, biological rep3


title: control quad at 2 weeks, biological rep1


title: mdx quad at 2 weeks, biological rep3


title: Heart_M32N_rep1

description: replicate 1


title: Heart_M32N_rep2

description: replicate 2


title: Heart_M32N_rep4

description: replicate 4


title: mdx quad at 3 weeks, biological rep1


title: control quad at 2 weeks, biological rep3


title: Heart_M48N_rep1

description: replicate 1


title: Heart_M32N_rep5

description: replicate 5


title: Heart_M32N_rep3

description: replicate 3


title: Heart_M16N_rep4

description: replicate 4

source_name: ventricular myocardium, 16wk age, normoxia

value: 16 weeks


title: Heart_M16N_rep6

description: replicate 6


title: Heart_M48N_rep4

description: replicate 4


title: Heart_M48N_rep2

description: replicate 2


title: Heart_M16N_rep5

description: replicate 5


title: Heart_M16N_rep1

description: replicate 1


title: Heart_M8N_rep6

description: replicate 6

source_name: ventricular myocardium, 8wk age, normoxia

value: 8 weeks


title: Heart_M8N_rep2

description: replicate 2


title: Heart_M16N_rep2

description: replicate 2


title: Heart_M8N_rep1

description: replicate 1


title: Heart_M48IR_rep5

description: replicate 5

source_name: ventricular myocardium, 48wk age, ischemia-reperfused

value: ischemia-reperfused


title: Heart_M48IR_rep3

description: replicate 3


title: Heart_M16N_rep3

description: replicate 3


title: Heart_M32IR_rep5

description: replicate 5

source_name: ventricular myocardium, 32wk age, ischemia-reperfused


title: Heart_M48IR_rep1

description: replicate 1


title: Heart_M8N_rep3

description: replicate 3


title: Heart_M8N_rep4

description: replicate 4


title: Heart_M48IR_rep6

description: replicate 6


title: Heart_M48IR_rep4

description: replicate 4


title: Heart_M8N_rep5

description: replicate 5


title: Heart_M48IR_rep2

description: replicate 2


title: Heart_M32IR_rep6

description: replicate 6


title: Heart_M32IR_rep4

description: replicate 4


title: Heart_M32IR_rep3

description: replicate 3


title: Heart_M16IR_rep6

description: replicate 6

source_name: ventricular myocardium, 16wk age, ischemia-reperfused


title: Heart_M32IR_rep1

description: replicate 1


title: Heart_M16IR_rep5

description: replicate 5


title: Input-2

city: Corvallis

first: Walter

middle: K

last: Vogel

state: OR

address: 1601 SW Jefferson Street

department: College of Pharmacy

institute: Oregon State University

description: Sample 7

library_source: genomic

data_processing:
base-calling: samples: BCL11B_ChIP-seq, BCL11B-PA_ChIP-seq, Input_BCL11B, Input-2; software: Illumina pipline; software version: 1.4.
base-calling: samples: Ikaros_ChIP-seq, Input-4; software: Illumina pipline; software version: 1.3.
base-calling: sample: Mi2beta_ChIP-seq; software: Illumina pipline; software version: 1.6.
alignment: as 36 base reads, BWA read quality trimming "-q 15"; software: BWA; software version: 0.6.2.
post alignment output quality filter:  MAPQ ≥ 20; software: samtools; software version: 0.1.18.
peak calling: q-value ≤0.05; software: MACS; software version: 2.0.10.20130306.
Genome_build: mm10: BCL11B_ChIP-seq, Input_BCL11B
Genome_build: mm10-female: Ikaros_ChIP-seq, Input-4, Mi2beta_ChIP-seq, Input-2
Supplementary_files_format_and_content: bigWig reports normalized abundance density (reads per million)
Supplementary_files_format_and_content: bigBed reports peak calls

molecule: genomic DNA

source_name: Primary thymocytes

growth_protocol: Primary mouse thymocytes were isolated from 5-8 week old mouse thymi and cultured in RPMI-1640 media supplemented with 5% fetal bovine serum and 100 units/ml penicillin-streptomycin.

extract_protocol: ChIP-seq and input libraries were prepared following Illumina's protocol with some modifications. The precipitated DNA was blunted, phosphorylated, and ligated to single-end adapter dimers, and then amplified by PCR [30 sec at 98°C; (10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C) x 14 cycles; 5 min at 72°C]. Excess PCR primers and adapter dimers were removed using AMPure beads (Agencourt Biosciences Corporation). DNA library size selection was performed by excising the 250-350 bp region from a 2% agarose gel followed by purification using a QIAquick Gel Extraction Kit (Qiagen).

treatment_protocol: Primary mouse thymocytes were cultured for 5 hr prior to crosslinking with 1% formaldehyde for 10 min at room temperature. Excess formaldehyde was scavenged by the addition of glycine to a final concentration of 125 mM. Crosslinked chromatin was prepared from crude nuclear extracts by micrococcal nuclease treatment (5 gel units/million cells), which was conducted for 15 min at 37°C in 10 mM Tris, pH 7.9, 10 mM NaCl, 4 mM CaCl2, 2% NP-40, and protease inhibitors, and stopped by the addition of 5 mM EDTA. After adding SDS to 0.1% and adjusting the NaCl to 150 mM, chromatin was further sheared by sonication, 15 cycles of 15 sec each (Branson 450 Digital Sonifier equipped with a stepped micotip and operated at 20% power), to an average fragment length of 180 bp. Genomic DNA was prepared from fragmented chromatin directly (input samples) or after immunoprecipitation (ChIP-seq samples), by reversing the chemical crosslinking at 65°C for 12 hr.

value: thymocytes

value: thymus

tag: chip antibody

value: none, input control


title: Mi2beta_ChIP-seq

description: Sample 6

tag: tissue

tag: chip antibody vendor

value: non-commercial, REF:Ramirez-Carrozzi, V. R., Nazarian, A. A., Li, C. C., Gore, S. L., Sridharan, R., Imbalzano, A. N., & Smale, S. T. (2006). Genes & development, 20(3), 282–296. doi:10.1101/gad.1383206, PMID:16452502


title: Input-4

description: Sample 5

tag: treatment


title: Heart_M32IR_rep2

description: replicate 2


title: Heart_M16IR_rep2

description: replicate 2


title: BCL11B_ChIP-seq

description: Sample 1

value: C57BL/6 x ICR

value: goat polyclonal anti-BCL11B

value: non-commercial, Leid Group

value: Primary thymocytes were cultured for 4 h before treating with vehicle (DMSO) or for 1 h prior to crosslinking.


title: Heart_M16IR_rep1

description: replicate 1

value: male


title: Input_BCL11B

description: Sample 3


title: Heart_M16IR_rep4

description: replicate 4

value: left ventricular myocardium


title: Heart_M8IR_rep1

description: replicate 1

source_name: ventricular myocardium, 8wk age, ischemia-reperfused


title: Heart_M8IR_rep5

description: replicate 5


title: Heart_M8IR_rep6

description: replicate 6


title: Heart_M8IR_rep4

description: replicate 4


title: Heart_M8IR_rep3

description: replicate 3


title: Heart_M16IR_rep3

description: replicate 3


title: BCL11B-PA_ChIP-seq

description: Sample 2

value: Primary thymocytes were cultured for 4 h before treating with a mixture consisting of 100 nM phorbol 12,13-dibutyrate and 500 nM A23187 in DMSO for 1 h prior to crosslinking.


title: Heart_M8IR_rep2

description: replicate 2


title: Ikaros_ChIP-seq

description: Sample 4

value: rabbit anti-Ikaros

value: non-commercial, REF:Kleinmann, E., Geimer Le Lay, A.-S., Sellars, M., Kastner, P., & Chan, S. (2008). Molecular and cellular biology, 28(24), 7465–7475. doi:10.1128/MCB.00715-08, PMID:18852286


title: 5C2

city: Lille

first: Lefebvre

last: Philippe

address: Bld Pr Jules Leclerc

country: France

institute: Inserm

description: RMA expression value derived from Expression Console software

hyb_protocol: Following fragmentation, 5,5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip® Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: The data were analyzed with Genespring 13,0 using global scaling as normalization method.

source_name: colon

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

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

value: colon

tag: age (years)

tag: ast (u/l)

tag: alt (u/l)

tag: triglycerides (mg/dl)

tag: total cholesterol (mg/dl)

tag: ogtt t0 (mmol/l)

tag: ogtt t120 (mmol/l)

tag: hba1c (mmol/mol)

tag: bmi (kg/m2)


title: 9C2


title: 6C2


title: 8C2


title: 10C2


title: 7C2


title: 3C2


title: 22C


title: 4C2


title: 21C


title: 19C


title: 20C


title: 17C


title: 18C


title: 14C


title: 16C


title: 8B


title: 11C


title: 7B


title: 13C


title: 9A


title: 12C


title: 4B


title: 10B


title: 5B


title: 2B


title: 6B


title: WT_CJ_G2_2

city: New York

first: Shan

last: Zha

address: 1130 Saint Nicholas Ave.

institute: Columbia University

description: G2 arrested, Coding Join junctions formed during V(D)J recombination

data_processing:
Library strategy: HTGTS
Basecalls performed using Illumina RTA version 1.18.54
Miseq reads was first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm10 genome (mm10pr) using Bowtie2. To specifically study the DNA repair junctions on the pMX-INV substrate we added the substrate sequence as an additional chromosome on top of the mm10 genome during the alignment process. The best-path searching algorithm (related to YAHA; ref. 50) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads are then filtered to exclude mispriming events, germ-line (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. To plot all of the S-region junctions, including those in the repeats but unequivocally mapped to an individual switch region, we combined the ones filtered by a mappability filter but unequivocally mapped to S regions with “good” reads passing both the mappability (both deduplicated) filters (please see ref. 28 for simulation and details on plotting). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait and prey-break site. Blunt junctions are considered to have no MHs or insertions.
Mutation rate was calculated by custom Excel integrated VBA script. Mutations were determined by comparing the actual bait sequence of each IgH junction with the germ-line bait sequence based on the IgH sequence from 129/Sv strain (NCBI gene accession no. AJ851868.3). Only true mismatches (no insertion or deletion within 7 nt) were counted as a mutation.
Genome_build: mm10pr (To specifically study the DNA repair junctions on the pMX-INV substrate we added the substrate sequence as an additional chromosome on top of the mm10 genome during the alignment process.)
Supplementary_files_format_and_content: Analysis pipeline .tlx output files and .xlsx files generated from tab-delimited text files after analysis for reads distribution and mutation rates and .xlsx files of combined analyses

source_name: B cells

growth_protocol: V-abl immortalized B cells from mice were cultured in DMEM medium

extract_protocol:
Samples were collected at specified time points for harvested for genomic DNA
To study RAG-generated breaks, 20 mg of genomic DNA from v-abl transformed B cells with stable integration of the pMX-INV substrate was used as input. Sonicated DNA was linearly amplified with biotinylated primer (/5BiosA/CAACCACTACCTGAGCACC) and nested amplified with (5’ CAAAGACCCCAACGAGAAGC3’) primers. Germline sequence was removed with BstBI (NEB) digestion. To study endonuclease-generated breaks, v-abl-transformed B cells were transiently infected with a retrovirus encoding I-PpoI-ER fusion followed by IRES human CD8, 20 hours after infection, half of the cells were arrested in G1 via STI571 (3 µM; Novartis Pharmaceuticals) for 24 hours, and treated with 500nM 4OHT to induce I-PpoI nuclear translocation for 24 hours. The other half was arrested in the S/G2 phase with CDK1 inhibitor (10 mM RO3306) for 16 hours, and 500nM 4OHT to induce I-PpoI cutting for 24 hours. Cells were collected at the end from both conditions for genomic DNA. Here, sonicated DNA was linearly amplified with biotinylated primer (/5BiosG/ACTTAGAACTGGCGCTGAC) and nested amplified with (5’ AACCCCAAAGCATCGCGAAG3’) primers. Germline sequence was removed with I-PpoI (Promega) digestion. To specifically study the DNA repair junctions on the pMX-INV substrate we added the substrate sequence as an additional chromosome on top of the mm10 genome during the alignment process.
high-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v

treatment_protocol: To investigate the repair events in RAG generated breaks, we treat v-abl-transformed B cells with the substrate with STI571 (3 µM; Novartis Pharmaceuticals) for 48 or 72 hours, or first for 24 hours and then switch to CDK1 inhibitor (10 uM RO3306) containing medium for 48 hours. Samples were collected at these time points for cell cycle analysis and harvested for genomic DNA.

tag: cell type

value: v-abl transformed B-cell

tag: genotype

value: WT

tag: sample type

value: CJ

tag: strain

tag: cell cycle phase


title: PKKO_CJ_G1

description: G1 arrested, Coding Join junctions formed during V(D)J recombination

value: DNA-PKcs -/-


title: PKKO_PpoI_G1

description: G1 arrested, PpoI-endonuclease cleavage site junctions

value: PpoI


title: PKKO_CJ_G2_2


title: 15C

tag: tissue

tag: Sex


title: PKKO_CJ_G2_1


title: 3B


title: 8A


title: CtIPA_PKKO_PpoI_G1

value: CtIP A/A DNA-PKcs -/-


title: CtIPA_PKKO_CJ_G1


title: PKKO_PpoI_G2

description: G2 arrested, PpoI-endonuclease cleavage site junctions


title: 5A


title: 10A


title: 1A


title: 4A


title: 3A


title: Hair, Patient2

city: isehara

first: Akira

last: Oka

state: Kanagawa

address: 143 Shimokasuya

country: Japan

institute: Tokai university

description: Gene expression data from patient scalp hair

hyb_protocol: The resultant single-strand cDNA was hybridized to the GeneChip Human Gene 2.0 ST Array.

scan_protocol: The arrays were washed, stained and scanned using the Affymetrix 450 Fluidics Station and GeneChip Scanner 3000 7G (Thermo Fisher Scientific) according to the manufacturer’s recommendations.

data_processing: Expression values were generated using Expression Console software (version 1.3 Thermo Fisher Scientific) with default robust multichip analysis parameters and evaluated by Genespring GX (version 12, Agilent Technologies).

source_name: adult patient hair

label_protocol: 10 ng of total RNA from human hair follicle was processed for use on the microarray using the GeneChip WT pico Reagent Kit (Thermo Fisher Scientific) according to the manufacturer's instructions. The resultant single-strand cDNA was fragmented and labeled with biotin.

extract_protocol: Total RNA was isolated using ISOGEN (Nippon Gene, Tokyo, Japan) in accordance with the manufacturer protocol and was treated twice with TURBO DNase (Ambion) to eliminate contaminating DNA. RNA was quantified using a NanoDrop 2000 (Thermo Fisher Scientific) and the quality of the extracted RNA was evaluated using a Bioanalyzer 2100 (Agilent Technologies).

tag: condition

value: AA

value: scalp hair


title: Hair, Control

description: Gene expression data from control scalp hair

source_name: adult normal hair

value: control


title: 6A

tag: age (years)


title: Hair, Patient4


title: 2A

tag: ast (u/l)


title: CtIPA_PKKO_CJ_G2_2


title: CtIPA_CJ_G2_1

value: CtIP A/A


title: CtIPA_PKKO_PpoI_G2


title: WT_PpoI_G2


title: CtIPA_CJ_G2_2


title: WT_CJ_G1


title: CtIPA_CJ_G1


title: Ri PA_2

city: Hangzhou

first: Meng

last: Funing

state: Zhejiang

address: Yuhangtang Road 866

department: College of life sciences

institute: Zhejiang University

description: OsPEP1 RNAi transgenic line1 treated with 1 μM PEP1

data_processing:
Illumina Casava1.7 software used for basecalling.
raw counts
Genome_build: FASTA files provide transcript sequences
Supplementary_files_format_and_content: raw counts

organism: Oryza sativa

source_name: OsPEP1 RNAi transgenic line1 treated with 1 µM PEP1

growth_protocol: Normal growth in the greenhourse for 7 days after sowing

extract_protocol:
The root tissues were obtained and the flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated with or without  1 μM PEP1

tag: cultivar

value: Root

tag: age

value: 7-day-old seedling

value: OsPEP1 RNAi

tag: treatment


title: Ri PB_3

description: OsPEP1 RNAi transgenic line1 treated with ethonal

source_name: OsPEP1 RNAi transgenic line1 treated with ethanol

value: ethanol


title: WT_CJ_G2_1


title: Ri PB_1


title: Ri PA_1


title: Ri PB_2


title: CtIPA_PKKO_CJ_G2_1


title: WT PA_3

description: wild type treated with 1 μM PEP1

source_name: wild type treated with 1 µM PEP1

value: wildtype


title: WT PB_3

description: wild type treated with ethonal

source_name: wild type treated with ethanol


title: WT PA_1

description: wild type treated with 1 μM PEP1


title: WT_PpoI_G1


title: WT PA_2

description: wild type treated with 1 μM PEP1


title: WT PB_2

description: wild type treated with ethonal


title: Resident fibroblast transfected with stealth SOX9 siRNA [S170]

city: Cincinnati

first: Anil

last: Jegga

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics

institute: Cincinnati Children's

description:
Sox9-3_S170_L007_R1_001
Sox9_vs_Control.all.gene.result.txt

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8.
fastq sequences were aligned to mm10 using Tophat.
Number of read counts was calculated for each Entrez gene.
Differential expression analysis was performed using DEseq.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Sox9_vs_Control.all.gene.result.txt: Tab-delimited text file

source_name: Lung resident fibroblasts

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Lung resident fibroblasts from IPF patients

tag: sirna

value: SOX9 siRNA


title: Resident fibroblast transfected with stealth SOX9 siRNA [S131]

description:
Sox9-1_S131_L006_R1_001
Sox9_vs_Control.all.gene.result.txt


title: Ri PA_3


title: Resident fibroblast transfected with stealth SOX9 siRNA [S169]

description:
Sox9-2_S169_L007_R1_001
Sox9_vs_Control.all.gene.result.txt


title: Resident fibroblast transfected with stealth control siRNA [S129]

description:
Control2_S129_L006_R1_001
Sox9_vs_Control.all.gene.result.txt

value: control siRNA


title: Resident fibroblast transfected with stealth control siRNA [S130]

description:
Control3_S130_L006_R1_001
Sox9_vs_Control.all.gene.result.txt


title: WT PB_1

description: wild type treated with ethonal


title: Resident fibroblast transfected with stealth control siRNA [S128]

description:
Control1_S128_L006_R1_001
Sox9_vs_Control.all.gene.result.txt


title: In_vivo_TS895_neratinib_R3

first: Colin

last: Tang

address: 1300 York Ave.

institute: Weill Cornell Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the TKOv3 library sequences with bowtie.
Sequenced reads aligned to GRCh38 with salmon. Differential expression analysis was performed with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited .txt file

source_name: Glioblastoma

growth_protocol: Cells were cultured in DMEM + 10% FBS

extract_protocol: CRISPR screen sequencing libraries were made with nested PCRs of the sgRNA region.

treatment_protocol: Inhibitors or DMSO were added to the cultured cells and treated for indicated times.

tag: cell line

value: neratinib 40mg/kg

tag: timepoint

value: 3 hr


title: In_vivo_TS895_neratinib_R2


title: In_vivo_TS895_vehicle_R3

value: vehicle


title: In_vivo_TS895_vehicle_R2


title: In_vivo_TS895_neratinib_R1


title: SF268_GCN2cr3_N675_3D_R1

value: neratinib 675 nM

value: 72 hr


title: SF268_GCN2cr3_N675_3D_R2


title: SF268_GCN2cr3_N675_6H_R2

value: 6 hr


title: In_vivo_TS895_vehicle_R1


title: SF268_GCN2cr3_N675_6H_R1


title: SF268_GCN2cr3_N675_D0_R1

value: untreated

value: 0 hr


title: SF268_LC9B_N675_6H_R1


title: SF268_LC9B_N675_D0_R2


title: SF268_LC9B_N675_6H_R2


title: X91iPSC Biological replicate 2

city: Copenhagen

first: Joshua

middle: M

last: Brickman

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)

description:
Gene expression after establishing POUV rescue-cell line
Sorted Nanog-eGFP+ c-Kit+ iPSCs generated by inducing Nanog-eGFP MEF with retroviral Xenopus Xlpou91 (X91) mouse Sox2 mouse Klf4 mouse Cmyc, Biological replicate 2

hyb_protocol: Fragmentation was performed on 600 ng of cRNA from each sample  and the fragmented cRNA was then hybridized to Agilent Mouse 8X60K slides (Grid_GenomicBuild: mm9:NCBI37:Jul2007) for 17h at 65 ºC. Processed slides were then washed with Agilent wash buffers

scan_protocol: scanned on an Agilent Scanner (Agilent Technologies, G2600D SG12524268)

data_processing: The data were analyzed using the NIA Array Analysis Tool (http://lgsun.grc.nia.nih.gov/ANOVA/bin/login.cgi)

label_protocol: High quality total RNA (RNA integrity number = 10) was labeled with Cyanine 3 CTP and purified using Qiagen’s RNeasy Mini Spin Columns. The quantity of purified Cy3 labelled cRNA was measured using aNanodrop spectrophotometer.

growth_protocol: iPSCs were cultured on the irradiated feeders and in defined iPSC induction medium composed of DMEM high glucose (ThermoFisher), 20% KnockOut Serum Replacement (ThermoFisher), 0.1 mM non-essential amino acids (Sigma), 2 mM L-glutamine (ThermoFisher), 0.1 mM β –mercaptoethanol (Sigma), LIF (homemade), 20 µg/mL Vitamin C (L-ascorbic acid, Sigma), 0.5 µM Alk5 inhibitor (A83-01, Tocris).

extract_protocol: RNA preparations were performed using the RNeasyTM Mini Kit (Qiagen)

treatment_protocol: Nanog-eGFP/129 MEF cells were infected with ectopic retrovirus carrying Oct4 or POU5 homologue gene together with other retrovirus carrying Sox2, Klf4 and cMyc. The infection was done at day 0 and day 1 under MEF medium. On day 3, MEF medium was replaced with defined iPSC induction medium. On day 4, induced cells were seeded onto irradiated feeders. Medium was changed daily from day 6 to day 10 and every two-day from day 12 onward. Nanog-eGFP positive iPSC clones were picked and expanded under defined iPSC induction medium. iPSC clones were stained with c-Kit-APC. Nanog-eGFP+c-Kit+ cells were sorted and collected for RNA extraction and DNA microarray.

tag: iPSc cell line

value: Nanog-eGFP iPSC (Nanog-eGFP/129)

tag: cells generated by


title: SF268_LC9B_N675_3D_R1


title: mOct4iPSC Biological replicate 1

description:
Gene expression after establishing POUV rescue-cell line
Sorted Nanog-eGFP+ c-Kit+ iPSCs generated by inducing Nanog-eGFP MEF with retroviral mouse Oct4 (mOct4) mouse Sox2 mouse Klf4 mouse Cmyc, Biological replicate 1


title: X25iPSC Biological replicate 2

description:
Gene expression after establishing POUV rescue-cell line
Sorted Nanog-eGFP+ c-Kit+ iPSCs generated by inducing Nanog-eGFP MEF with retroviral Xenopus Xlpou25 (X25) mouse Sox2 mouse Klf4 mouse Cmyc, Biological replicate 2


title: mOct4iPSC Biological replicate 2

description:
Gene expression after establishing POUV rescue-cell line
Sorted Nanog-eGFP+ c-Kit+ iPSCs generated by inducing Nanog-eGFP MEF with retroviral mouse Oct4 (mOct4) mouse Sox2 mouse Klf4 mouse Cmyc, Biological replicate 2


title: X91iPSC Biological replicate 1

description:
Gene expression after establishing POUV rescue-cell line
Sorted Nanog-eGFP+ c-Kit+ iPSCs generated by inducing Nanog-eGFP MEF with retroviral Xenopus Xlpou91 (X91) mouse Sox2 mouse Klf4 mouse Cmyc, Biological replicate 1


title: SF268_LC9B_N675_D0_R1


title: X25iPSC Biological replicate 1

description:
Gene expression after establishing POUV rescue-cell line
Sorted Nanog-eGFP+ c-Kit+ iPSCs generated by inducing Nanog-eGFP MEF with retroviral Xenopus Xlpou25 (X25) mouse Sox2 mouse Klf4 mouse Cmyc, Biological replicate 1


title: Circular RNAseq Sample 20 A75OR2

city: Singapore

first: Azhar

middle: B

last: Ali

address: 14 Medical Drive MD6 #11-01

department: CSI Singapore

country: Singapore

institute: National University of Singapore

description: Circular RNA-seq

data_processing:
Raw data or FASTQ  formats were firstly processed through  in-house perlscripts. At the same time, Q20, Q30 and GC content of the data were calculated.
Reads were mapped to reference genome using hisat2. The circular RNA were detected and identified using find_circ and CIRI2. Circos software was used to construct the circos figure.
The raw count were first normalized using TPM. Differential expression analysis was performed using DESeq2 R package.
GO enrichment analysis were performed using GEOseq R package. KOBAS software was used to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathway.
Genome_build: hg38
Supplementary_files_format_and_content: txt file recoding FPKM values

source_name: NCI-H1975 lung cancer cell line

growth_protocol: All the cells were cultured with RPMI supplemented with 10% fetal bovine serum. The cells were passage every 3 to 4 days.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Kit. Downstream processing of obtaining pure circular RNA was carried out by NovogeneAIT Genomics  Singapore.
Circular RNA-seq library were prepared by sequencing provider, Novogene IT.

treatment_protocol: Plasmid transfected cells were treated with 50µg/ml G418 selection antibody. Gefitinib resistant cell (GR) was treated with  1µM Gefitinib. Osimertinib resistant cell (OR) was treated with 1µM Osimertinib

value: Lung cancer cell line

tag: mutation

value: EGFR mutant

tag: passage


title: Circular RNAseq Sample 21 A75OR3

description: Circular RNA-seq


title: Circular RNAseq Sample 17 A75P2

description: Circular RNA-seq


title: Circular RNAseq Sample 19 A75OR1

description: Circular RNA-seq


title: SF268_LC9B_N675_3D_R2


title: Circular RNAseq Sample 16 A75P1

description: Circular RNA-seq


title: Circular RNAseq Sample 15 A75F3

description: Circular RNA-seq

value: EGFR mutant, FASN transfected


title: Circular RNAseq Sample 14 A75F2

description: Circular RNA-seq


title: Circular RNAseq Sample 13 A75F1

description: Circular RNA-seq


title: Circular RNAseq Sample 11 A75BB2

description: Circular RNA-seq

value: EGFR mutant, pCMV6 transfected


title: Circular RNAseq Sample 10 A75BB1

description: Circular RNA-seq


title: Circular RNAseq Sample 12 A75BB3

description: Circular RNA-seq


title: Circular RNAseq Sample 6 PP3

description: Circular RNA-seq

source_name: PC-9 lung cancer cell line


title: Circular RNAseq Sample 6 PGR3

description: Circular RNA-seq


title: Circular RNAseq Sample 6 PGR2

description: Circular RNA-seq


title: Circular RNAseq Sample 6 PGR1

description: Circular RNA-seq


title: Circular RNAseq Sample 3 N3

description: Circular RNA-seq

source_name: NL20 bronchial epithelial cell line

value: Immortalized nontumorigenic human bronchial epithelial cell line


title: Circular RNAseq Sample 4 PP1

description: Circular RNA-seq


title: Circular RNAseq Sample 2 N2

description: Circular RNA-seq


title: Circular RNAseq Sample 5 PP2

description: Circular RNA-seq


title: SF268_GCN2cr3_N675_D0_R2


title: Circular RNAseq Sample 18 A75P3

description: Circular RNA-seq


title: Circular RNAseq Sample 1 N1

description: Circular RNA-seq


title: MM1R com-2

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
Illumina bcl2fastq v2.18.0.12 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.6.0.a with default parameters
The HTSeq software (v.0.6.0) was applied to generate the count matrix, with default parameters. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR 3.28.1.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MM1R combo

growth_protocol: ATCC-formulated RPMI-1640 (ATCC, Rockville, MD) with 10% fetal bovine serum (FBS, Omega Scientific, Tarzana, CA) and 1% penicillin/streptomycin (Fisher Scientific, Chino, CA) at 370C with 5% CO2.

extract_protocol: Total RNA was extracted from cultured cells using the miRNeasy kit

treatment_protocol: Human multiple myeloma cell lines MM1.S  and MM1.R  were treated with 0.1 μM TAK-981, or 1 μM Dexamethasone or combo (0.1 μM TAK-981 and 1 μM Dexamethasone) for 48 h in duplicate

tag: cell line background

tag: cell type

value: human multiple myeloma cancer cell line

value: B lymphoblast

tag: cell phenotype

value: glucocorticoid resistant

value: combo (0.1μM TAK-981 and 1μM Dexamethasone) for 48 h


title: MM1R TAK-1

source_name: MM1R TAK

value: 0.1μM TAK-981 for 48 h


title: MM1R TAK-2


title: MM1S Dex-2

source_name: MM1S Dex

value: glucocorticoid sensitive

value: 1μM Dexamethasone for 48 h


title: MM1S com-2

source_name: MM1S combo


title: MM1R Veh-1

source_name: MM1R Veh

value: vehicle control


title: MM1S Dex-1


title: MM1R com-1


title: MM1R Dex-1

source_name: MM1R Dex


title: MM1S TAK-1

source_name: MM1S TAK


title: MM1S Veh-1

source_name: MM1S Veh


title: MM1R Veh-2


title: MM1R Dex-2


title: MM1S Veh-2


title: MM1S TAK-2


title: CT-05-05-10-2-0-ATAC

city: NY

first: Markus

last: Siegelin

address: 630 west 168th street

department: Pathology & Cell Biology

description: ATAC sequencing (Active Motif; cat# 53150)

data_processing:
ATACseq reads were aligned to the hg38 genome using Basepair software (alignment using Bowtie2) to generate bam files
from bam files were removed duplicates and convert into bigwig files
ATAC-seq peak calling  with MACS2
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: KNS42 pediatric glioblastoma cell line

extract_protocol:
DNA was extracted and purified using the ATACseq kit (Active Motif; cat# 53150)
next generation sequencing (NGS) from Genewiz, New Jersey

treatment_protocol: empty DMEM+1.5%FBS+primocin + a. Glucose (5mM), Glutamine (1mM) or b.Glucose (0.5mM), Glutamine (0.5mM), Lactate (0mM) or Glucose (0.5mM), Glutamine (0.5mM), Lactate (10mM) or d. Glucose (0.5mM), Glutamine (0.5mM), Lactate (15mM)

tag: growing media conditions


title: 05050H3K9ac-0

description: CHIP sequencing

data_processing:
ChIP-seq reads were aligned to the hg38 genome (Bowtie2).
BAM to BEDGRAPH (MACS2)
BEDGRAPH to BIGWIG
Genome_build: GRCh38
Supplementary_files_format_and_content: BIGWIG

extract_protocol:
DNA was extracted using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005 from Cell Signalling.
next generation sequencing (NGS) from Genewiz, New Jersey

value: pediatric glioblastoma cell line

value: Glucose (0.5mM), Glutamine (0.5mM), Lactate (10mM)

tag: chip antibody

value: H3K27ac (Cell Signalling, 8173)


title: MM1S com-1


title: 050510H3K9ac-0

description: CHIP sequencing

value: H3K9ac (Cell Signalling, )


title: CT-05-05-0-1-0

value: Glucose (0.5mM), Glutamine (0.5mM), Lactate (0mM)


title: 050510H3K27ac-0

description: CHIP sequencing


title: 510H3K27ac-0

description: CHIP sequencing

value: Glucose (5mM), Glutamine (1mM)


title: 510H3K9ac-0

description:
CHIP sequencing
Sample removed from analysis, therefore no processed data provided.


title: AshNC [ATAC-seq]

city: Shanghai

first: Ping

last: He

address: No. 280, South Chongqing Road.

institute: Shanghai Jiao Tong University, School of Medicine

description: atac-AshNC

data_processing:
Basecalls performed using CASAVA version 1.4
ATAC-seq reads were aligned to the hg19 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg19
Supplementary_files_format_and_content: peak text files

source_name: MCF10A_Control; shNC

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

tag: genotype/variaton

value: Control; shNC


title: BshNC [ATAC-seq]

description: atac-BshNC


title: 05050H3K27ac-0

description: CHIP sequencing


title: CA5

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

description: High risk HPV infection was determined by Digene HPV Genotyping Kits

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 hg19 whole genome using TopHat v2.0.11
The mapped reads were counted in lncRNAs regions with the annotation in LNCipedia database (version 3.0) (http://www.lncipedia.org).
Genome_build: HG19, GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw reads values of the known lncRNAs

source_name: Cancer

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

tag: tissue

value: Cervix

value: HPV-positive  tissue


title: CA6


title: AshG8d [ATAC-seq]

source_name: MCF10A_SNHG8d knockdown

value: SNHG8d knockdown


title: BshG8d [ATAC-seq]


title: CA4


title: CIN4

source_name: CIN 2-3

value: HPV-negative tissue


title: N6

source_name: Normal


title: CIN5


title: CA2


title: CIN6


title: CA3


title: N4


title: CA1


title: N2


title: CIN1


title: N1


title: CECR2 sg2-2

city: New Haven

first: Qin

last: Yan

state: CT

address: Department of Pathology, PO Box 208023

institute: Yale School of Medicine

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were mapped to hg38 whole genome using bowtie2  with parameters –local, keeping only alignments with MAPQ>=10
Reads Per Gene were calculated using FeatureCount of subread package.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include gene expression values normalized with DESeq2 variance stabilizing transformation (VST) for each Sample

source_name: breast cancer cell line

extract_protocol:
RNA was extracted by Qiagen RNeasy Plus Mini Kit
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA Library Preparation protocol

value: MDA-MB-231 derived LM2 breast cancer cell line

value: epithelial

tag: genotype/variation

value: CECR1 deletion 2


title: CIN2


title: CECR2 sg2-1


title: CIN3


title: Control-2

value: control knockout


title: YHP2

city: Wuhan

first: jinhua

address: Jiefang Avenue 1095

institute: Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Sequencing reads that contained adapters or low quality were pre-filtered before mapping. Filtered reads were mapped to the hg19 genome using Tophat 2 software (Version 2.0.11)
relative expression levels (reads per kilobase per million mapped reads, RPKM) were calculated using uniquely mapped reads by Cufflinks software (Version 2.2.1)
Genes with at least one sample RPKM > 2 were selected as the expressed genes in the following analysis.
Differential expression was defined as fold change > 1.25 or < 0.8 between paired samples (EC from the same cord but treated with YP and OP respectively) in EC from all three cords.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Endothelium

growth_protocol: Primary HUVECs were isolated from segments of fresh human umbilical cords within 4 h following birth. Briefly, the inner wall of the segments of umbilical cords by were digested by 0.1% collagenase II (Worthington, USA) for 13 minutes at 37°C, as described (Jaffe, Nachman, Becker, & Minick, 1973). Cells were precipitated and re-suspended in Medium 199 supplemented with 20% Fetal Bovine Serum (FBS), low serum growth supplement (LSGS) (Gibco, USA), 1% Penicillin-streptomycin in a humid incubator at 37°C in 5% CO2

extract_protocol:
Total cellular RNA was extracted with HI Pure RNA Extract Kit (Magen, China). The integrity, purification and quality of RNA were checked by Nanodrop 2000 (Thermo, USA) and agarose gel analysis (Biowest, Spain).
Library constructions were performed using Illumina Truseq RNA Sample Preparation v2 Kit.

treatment_protocol: HUVECs were cultivated to determine the population doubling level (PDL). At PDL 28, cells were switched to the medium containing 20% PFE (in place of 20% FBS), cultured for 48 hours, and then trypsinized and divided into 2 groups (one paired samples). One group was continuously cultivated in a 20% PFE-containing medium, while the other group was changed to the medium containing 20% PFY for 5 days. HUVECs isolated respectively from 3 individual cords were used for biological validations.

value: umbilical veins

tag: population doubling level


title: A549 cells siRNA_KMT9a treated biological replicate 3

city: Freiburg

first: Eric

last: Metzger

address: Breisacherstr. 66

institute: Uniklinik-Freiburg

description:
A549_Counts.txt
3_A549_siRNA_KMT9a

data_processing:
We aligned these reads to the hg19 build of the human genome using STAR
The aligned reads were counted with the homer software (analyzeRNA) and edgeR
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file are text files that include the raw read count for a specific transcript (indicated by the NM accession number)

source_name: A549 cells

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).

value: Lung Carcinoma Cells

tag: genotype

value: WT

tag: passages


title: A549 cells siRNA_KMT9a treated biological replicate 2

description:
A549_Counts.txt
2_A549_siRNA_KMT9a

tag: cell line


title: A549 cells siRNA_KMT9a treated biological replicate 1

description:
A549_Counts.txt
1_A549_siRNA_KMT9a


title: EHP1


title: A549 cells siRNA_Control, biological replicate 1

description:
A549_Counts.txt
1_A549_siRNA_Ctrl


title: YHP3


title: Control-1


title: EHP2


title: CECR2 sg1-2

value: CECR1 deletion 1


title: YHP1


title: Inf0

city: Jouy-en-Josas

first: Helene

last: Bierne

address: Domaine de Vilvert, bat 442, INRA Micalis

department: Micalis Institute

institute: INRAE - University PARIS SACLAY

description:
MBD enrichment
methylated DNA

data_processing:
Basecalls performed using CASAVA version 1.8
reads were filtered with custom Python scripts
MDB-seq reads were aligned to the hg19 genome assembly using bowtie with default parameters
reads were assigned to genomic windows of 200 bp using Repitools
counts were normalized with edgeR per effective library size
Genome_build: hg19
Supplementary_files_format_and_content: WIG files, counts per 200 bp genomic window which were used for statistical analysis

source_name: Human hepatocytes HepG2

growth_protocol: GFP-expressing Listeria monocytogenes EGDe strain  was grown in brain-heart infusion (BHI) at 37°C. Human HepG2 hepatocytes (ATCC HB-8065) were grown as recommanded by ATCC.

extract_protocol:
After FACS selection, genomic DNA from infected and uninfected cells was purified using a conventional proteinase K/organic extraction method. Methylated DNA was captured using the MethylCap kit (Diagenode AF-100-0048), Belgium), followed by high throughput sequencing  at Nxt-Dx (Belgium).
The methylated fragments were eluted in a single-step using High-Elution buffer. End repair, <A> base addition and adaptor ligation steps were performed following ‘multiplexed paired end ChIP protocol’ (Illumina, San Diego, California, USA) and Apollo 324™ automated DNA library preparation platform system IntegenX™ (CA, USA). Libraries were amplified by PCR. Fragments of 300 bp +/- 50 bp from the amplified libraries were excised after separating on a 2% agarose gel (Low Range Ultra agarose Biorad 161-3107). DNA from excised gel pieces was eluted using Qiagen Gel Extraction Kit (Qiagen). Purified libraries were quality checked for concentration with smear analysis using Agilent 2100 (Agilent Technologies, Santa Clara, California, USA).deep sequencing using HiSeq2000 (Illumina) to generate 50 bp-long paired-end reads.

treatment_protocol: Cells were uninfected or infected with GFP-Listeria at multiplicity of infection of 1. After 1h infection, extracellular bacteria were killed by adding gentamicin and cells were incubated for 3 days with 25 μg/ml gentamicin containing media.

tag: infection


title: Inf1

description:
MBD enrichment
methylated DNA

value: GFP-expressing Listeria monocytogenes EGDe


title: N3


title: N5


title: A549 cells siRNA_Control, biological replicate 3

description:
A549_Counts.txt
3_A549_siRNA_Ctrl


title: A549 cells siRNA_Control, biological replicate 2

description:
A549_Counts.txt
2_A549_siRNA_Ctrl


title: Cont0

description:
MBD enrichment
methylated DNA

value: control


title: 36_contralateral

city: Barcelona

first: Laura

last: Ramiro

state: Barcelona

address: Passeig De La Vall D'hebrón 119-129, Edificio Mediterránea, Laboratorio 120

country: Spain

institute: Vall d'Hebron Institute of Research

hyb_protocol: cDNA was hybridized in GeneChip Human Exon 1.0 ST arrays Affymetrix microarrays for 16 hours with rotation

scan_protocol: Microarrays were scanned in a GeneChip scanner 3000 7G

data_processing: images were processed with the GeneChip Command Console software (Affymetrix) to obtain .CEL files containing gene expression intensities. Data quality was assessed with the arrayQualityMetrics R package before further analyses were conducted without the exclusion of any sample.

label: Biotin

source_name: Brain homogenate

label_protocol: Total RNA was amplified and transformed to biotinylated sense-strand DNA with the GeneChip® WT PLUS Reagent Kit

growth_protocol: Brain samples were obtained from deceased ischemic stroke patients and snap-frozen in liquid nitrogen and stored at -80ºC

extract_protocol: Total RNA was isolated from frozen brain samples using the Fatty Tissue RNA Purification kit (Norgen Biotek Corp., Canada)

treatment_protocol: Brain pieces from the infarct core (IC) and the healthy contralateral (CL) areas were gathered within the first hours after death, snap-frozen in liquid nitrogen and stored at -80ºC

tag: gender

value: Female

value: Healthy contralateral brain

tag: age

tag: disease state

value: ischemic stroke


title: 36_infarct_core

value: Infarcted core Brain


title: 35_infarct_core

value: Male


title: IL-1β high+CoPP

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
MapSplice mapping to reference genome
count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Interlukin-1β (40ng/ml) and CoPP treated NP cells

growth_protocol: The cells extracted from the human intervertebral disc tissue were  resuspended in DMEM/F12 containing 10% FBS (Gibco), 100 U/mL penicillin, 100 μg/mL streptomycin, and 1%  L-glutamine. The viability of the suspended cells was over 90% when assessed using cell counting kit-8 (Dojindo,  Tokyo, Japan). Cells were incubated at 37 °C in 5% CO2 and the medium was changed every 3 days. Cells at the  second passage were used for subsequent experimental procedures.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Ion Proton protocols

treatment_protocol: When the NP cells reached conflence, the cells were  trypsinized with 0.25% trypsin/ethylenediaminetetraacetic acid (Gibco) and seeded into 6/24-well plates at  150,000/10,000 cells/well in the same medium.  We incubated the  cells with 10 μM CoPP (Frontier scientifi, Logan, UT, USA) for 1 h before activation with 10 ng/mL or 40 ng/mL  IL-1β (Peprotech,  Rocky Hill, NJ, USA) for 24h.

value: primary nucleus pulposus cells

tag: treatment

value: Interlukin-1β (40ng/ml) and CoPP

tag: passage


title: CoPP

source_name: CoPP treated NP cells

value: CoPP


title: 35_contralateral


title: IL-1β low+CoPP

source_name: Interlukin-1β (10ng/ml) and CoPP treated NP cells

value: Interlukin-1β (10ng/ml) and CoPP


title: IL-1β high

source_name: Interlukin-1β (40ng/ml) treated NP cells

value: Interlukin-1β (40ng/ml)


title: 33_contralateral


title: 33_infarct_core


title: 22_contralateral


title: 32_infarct_core


title: IL-1β low

source_name: Interlukin-1β (10ng/ml) treated NP cells

value: Interlukin-1β (10ng/ml)


title: 16_infarct_core


title: 32_contralateral


title: Control

source_name: Control NP cells


title: BMDM_4sU_LPS_PolyA_rep1

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

data_processing:
library strategy: 4sU-seq
NGS data quality was assessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
TrueSeq adapter sequences and low-quality reads were trimmed using Trimmomatic version 0.39 (http://www.usadellab.org/cms/?page=trimmomatic).
Paired-end reads from 4sU-seq were mapped to the murine genome build GRCm38.p6 (Ensembl) using HISAT2 version 2.2.1 (https://github.com/DaehwanKimLab/hisat2).
Transcripts were de-novo assembled using StringTie version 2.1.7b (https://github.com/gpertea/stringtie) and transcript annotation provided by Ensembl (GRCm38.p6) with the following settings: --rf -f 0.1 -c 2 -A –B –m 50. Transcripts assembled from all three replicates of LPS and LPS plus Dex treated macrophages were merged using StringTie with the following parameters: -m 50 -T 0.01 -F 0.01 and compared to annotated transcripts (GRCm38.p6) with gffcompare (https://github.com/gpertea/gffcompare).
Alignments were converted to bigwig files, merging 10 bp per bin and scaled according to the DESeq normalization factor using ‘bamCoverage’ from the Deeptools package version 3.5.0 (https://github.com/deeptools/deepTools). Mean BigWig files per treatment were generated with deepTools version 3.5.0.
For differential expression analysis fragments overlapping assembled transcripts or 1kb around reproducible GR binding sites were counted with featureCounts version 2.0.1 (https://doi.org/10.1093/bioinformatics/btt656) with the following parameters: -p -Q 20 -B -d 50 -D 1000 -s 0 -C -T 14.
FeatureCounts were supplied as input for DESeq2 version 1.32.0 (doi: 10.1186/s13059-014-0550-8). For the GR-enhancer expression analysis, size factors computed by DESeq2 were replaced by the sizeFactors estimated from all assembled transcript differential expression analysis.
Transcripts were annotated to the closest TSS using UCSC gene annotation (TxDb.Mmusculus.UCSC.mm10.knownGene) and the ChiPpeakAnno R package v3.24.1. (doi: 10.1186/1471-2105-11-237).
Genome_build: mm10, GRC38.p6
Supplementary_files_format_and_content: BigWig (.bw) files containing individual scaled or mean coverage (scaled mean for all three replicates per treatment) summarized at 10bp resolution for visualization in the genome browser. Tab-delimited text (.txt) files contain results from the differential expression analysis including raw counts, mean expression, log2-fold-changes and p-values, as well as transcript annotation. Gene transfer format (.gtf) file containing all assembled poly-adenylated transcripts (Column names: chromosome, source program, feature, feature start, feature end, score (. - NA), strand, frame (. - NA), attributes as list separated by semicolon).

source_name: bone marrow-derived macrophages

growth_protocol: Primary bone marrow-derived macrophages (BMDMs) were isolated from bone marrow of 5-8 weeks old male C57BL6/J mice. The bone marrow was flushed from humerus, tibia and femur with RPMI, erythrocytes lysed with AKC lysis buffer (1 M NH4Cl, 1 M KHCO3, 0.5 M EDTA). Cells were further purified by Ficoll gradient (Ficoll-Paque Premium; GE Healthcare #17-5442-02) and differentiated within 7 days in DMEM (4.5 g/l glucose, Sigma) supplemented with 20% FBS (Sigma), 1% penicillin/streptomycin (Sigma) and 30% L929 cell supernatant. The medium was changed after 3 days. After 7 days the differentiated macrophages were dissociated using Versene (ThermoFischer Scientific #15040066) at RT and seeded at 20 million cells/15-cm plate in serum-free conditions (macrophage-SFM medium (ThermoFisher Scientific #12065074)) for treatment.

extract_protocol:
4-thiouridine labelling and purification of nascent transcripts was performed according to the protocol published by Raedle at al. (doi: 10.3791/50195 ). In detail, RNA from Trizol-lysed and 4sU-labelled macrophages was isolated by chloroform-phenol extraction according to standard protocols. Shortly, 2 ml of chloroform was added to 10 ml of cell lysate, mixed vigorously and incubated for 2-3 mins at 20°C. After centrifugation (15 mins, 13,000xg at 4°C), the upper aqueous phase is transferred to a new 15-ml polypropylene tube. The RNA is precipitated with 0.5 volumes of RNA precipitation buffer (1.2M NaCl, 0.8 M sodium citrate) and 0.5 volumes of isopropanol and washed twice with 75% ethanol (centrifugation for 10 mins at 13,000xg and 4°C). The RNA was resolved in RNase-free water and the concentration measure using a Nanodrop1000 (ThermoFisher Scientific). For Thiol-specific biotinylation of the nascent (4sU-incorporated) RNA, 80 mg of total RNA were incubated with 1 mg/ml EZ-Link Biotin-HPDP (solubilized in DMF, Pierce, Cat.No: 21341) in biotinylation buffer (10 mM Tris pH=7.4, 1 mM EDTA) for 1.5 hrs. Subsequently, the total RNA was purified by chloroform-phenol extraction and precipitated with isopropanol in high salt conditions. The total RNA is diluted to 1 mg/ml and denatured (10 min 65°C). Streptavidin pulldown using streptavidin-coated magnetic beads (Miltenyi Biotec, Cat. No: 130-074-101) and mMACS columns (Miltenyi Biotec, Cat.No: 130-074-101) was performed to capture the fraction of nascent (biotinylated) RNAs. Shortly, columns are pre-equilibrated in washing buffer (100 mM Tris pH=7.4, 10 mM EDTA, 1M NaCl, 0.1% Tween-20), 100 ml streptavidin beads added to 100 ml 1 mg/ml biotinylated RNA and loaded to the column. Beads are washed three-times in pre-warmed (65°C) washing buffer and three-times in washing buffer at 20°C. RNA is eluted twice with 100 ml of 100 mM DTT into 400 ml of magnetic Agencourt RNA clean XP beads (Beckman Coulter, Cat.No: A63987). The nascent RNA is purified using Agencourt RNA clean XP beads as follows: 5 mins incubation at 20°C, 5 min incubation on the magnetic rack at 20°C, removal of the supernatant, 1x wash with 1 ml 70% ethanol, 5 min incubation on the magnetic rack at 20°C, removal of ethanol, air-dry Agencourt beads for approximately 10 mins at 20°C, elution in 30 ml RNase-free water.
The concentration of the nascent RNA was quantified using the Qubit2.0 (ThermoFisher Scientific) and the RNA quality judged by Bioanalyzer (Bioanalyzer2100, Agilent Technologies) using the RNA 6000Nano Reagents (Agilent Technologies, Cat.No: 5067-1511). Depletion of rRNAs (Ribo-Zero Gold rRNA Removal Kit (Illumina)) and library preparation was performed starting with 400 ng of nascent RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, total RNA) or the TrueSeq Stranded mRNA Library Prep Kit (Illumina, PolyA-RNA). Amplified cDNA libraries were further purified using Agencourt RNAClean XP Beads (Beckman Coulter) and quality control of biotinylated RNA and cDNA libraries were performed using Agilent Bioanalyzer2100 with the RNA 6000Nano Reagents (Agilent Technologies, Cat.No: 5067-1511) or High Sensitivity DNA Reagents (Agilent Technologies, Cat.No: 5067-4626).
RNAseq (total and PolyA)

treatment_protocol: BMDMs are pre-treated with either 1 mM dexamethasone (Dex, Sigma, Cat.No: D4902) or vehicle (Ethanol) for 30 mins followed by 2 h of 100 ng/ml LPS treatment (LPS E.COLI O111:B4, Sigma, Cat.No: LPS25). After 1 h of LPS treatment, 200 mM of 4-thiouridine (4sU, Carbosynth, Cat.No: 13957-31-8) was added for the labelling of nascent transcripts.

tag: cell type

value: bone marrow-derived macrophages

tag: strain

tag: Sex

value: male

value: 2h 100 ng/ml LPS, 1h 200 mM 4sU

tag: library type

value: PolyA-RNAseq


title: BMDM_4sU_DexLPS_PolyA_rep3

value: 2.5h 1mM Dex, 2h 100 ng/ml LPS, 1h 200 mM 4sU


title: BMDM_4sU_DexLPS_PolyA_rep1


title: BMDM_4sU_LPS_PolyA_rep2


title: BMDM_4sU_DexLPS_total_rep2

description:
macro_2hDex90minLPS_4sUtotal_mean.bw
BMDM_4sU_total_LPSDexvsLPS_unfiltered_GEO.txt

value: total RNAseq


title: BMDM_4sU_LPS_PolyA_rep3


title: BMDM_4sU_DexLPS_PolyA_rep2


title: 22_infarct_core


title: BMDM_4sU_DexLPS_total_rep1


title: BMDM_4sU_DexLPS_total_rep3


title: BMDM_4sU_LPS_total_rep3

description:
macro_90minLPS_4sUtotal_mean.bw
BMDM_4sU_total_LPSDexvsLPS_unfiltered_GEO.txt


title: 16_contralateral

value: Female


title: BMDM_4sU_LPS_total_rep2


title: WT_IL4_rep2

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
Second mate was used for sample demultiplexing. Only R1 was submitted.
Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained using in-house scripts based on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10

source_name: peritoneal cavity macrophages

growth_protocol: Peritoneal cavity macrophages (PCMs) were obtained from WT and LysM-Cre x Gls1 fl/fl mice.

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and amount was assessed by Nanodrop (Ozyme)
Library construction were conducted as described previously (Jha et al., Immunity 2015)

treatment_protocol: Peritoneal cavity macrophages (PCMs) were obtained from Gls1 fl/fl mice and LysM-Cre x Gls1 fl/fl mice.  Mice were i.p injected with saline or  with IL-4 complexed to anti-IL-4  mAb. Then, 36  hours later, PCMs were collected by lavage with 5ml of PBS and stained  with CD64 (Brilliant Violet 421 conjugated), ICAM-2 (Alexa Fluor 647  conjugated) and CD115 (PE conjugated) before cell sorting.

value: peritoneal cavity macrophages

tag: condition

value: WT


title: WT_Basal_rep2

value: Basal


title: WT_Basal_rep1


title: WT_IL4_rep3


title: KO_IL4_rep3


title: KO_IL4_rep2


title: KO_Basal_rep1


title: KO_Basal_rep2


title: KO_IL4_rep1


title: MP9

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Genome_build: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary_files_format_and_content: Tab-delimited text file includes raw count table for each sample

source_name: Myc;p53-/- ovarian EPO-GEMM tumor

growth_protocol: 8-12 week old WT C57BL/6 female mice were anesthetized with isofluorane and the surgical site (pelvic region) scrubbed with a povidone-iodine scrub (Betadine) and rinsed with 70% alcohol. After opening the peritoneal cavity, the left ovary and oviduct were exteriorized. 25 μl of a plasmid mix (see table below) was injected into the ovary using a 27.5 gauge syringe and tweezer electrodes were tightly placed around the injection bubble. Two poring pulses of electrical current (50V) given for 30 ms lengths at 450 ms intervals and five transfer pulses (60V, 50 ms length, 450 ms intervals) were then applied using an in vivo electroporator (NEPAGENE NEPA21 Type II electroporator). After electroporation, the peritoneal cavity was rinsed with 0.5ml of pre-warmed saline. After the procedure the peritoneal cavity was sutured and the skin closed with skin staples. The mice were kept at 37˚C until they awoke and post-surgery pain management was done with injections of buprenorphine for the three following days. Tumor formation was assessed by ultrasound imaging. Mice were sacrificed at end point, and RNA collected from whole tumor tissue. Genome editing in EPO-GEMM tumors was confirmed by Sanger sequencing.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

tag: tissue

value: ovarian tumor

value: Myc;p53-/- EPO-GEMM

value: non-treated


title: MP10


title: MP8


title: WT 2

source_name: WT ovary

value: ovary


title: MP2


title: MP5


title: MP3


title: MP7


title: MP1


title: WT_IL4_rep1


title: MP6


title: WT 3


title: BMDM_4sU_LPS_total_rep1


title: MP4


title: WT 1


title: P3451_278

city: Badalona

first: Elisabetta

last: Mereu

address: Ctra de Can Ruti, Camí de les Escoles, s/n

institute: Josep Carreras Leukemia Research Institute

description:
full-lenght RNA-seq
P3451.tsv

data_processing:
Reads were then demultiplexed according to the cell barcodes
Sequenced reads were filtered for low-complexity or low-quality sequence.
High quality reads were mapped according to the GEM pipeline
Genome_build: Mouse: Gencode release 21, assembly GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing gene expression values as read counts

extract_protocol:
Cells were sorted into 96-well plates containing the lysis buffer. Reverse transcription was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN, template-switching oligonucleotides and betaine. The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems), ISPCR primer and 22 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitvity DNA Kit (Agilent Technologies). 140 pg of the amplified cDNA were fragmented using Nextera® XT (Illumina) and amplified with indexed Nextera® PCR primers. Products were purified twice with Agencourt Ampure XP beads and quantified again using a Bioanalyzer High Sensitvity DNA Kit. Sequencing of Nextera® libraries from 384 cells was carried out in one lane on a Illumina HiSeq2500 v4.
Full-length single-cell RNA sequencing libraries were prepared using the Smart-seq2 protocol
single cell RNA-seq (scRNA-seq)

tag: protocol

value: Glioblastoma


title: P3451_287

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_280

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_282

description:
full-lenght RNA-seq
P3451.tsv

source_name: empty


title: P3451_279

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_285

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_283

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_277

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_284

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_281

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_276

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_270

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_271

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_274

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_273

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_288

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_269

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_268

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_267

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_272

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_286

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_265

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_264

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_266

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_262

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_275

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_256

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_258

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_257

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_255

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_260

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_259

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_251

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_252

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_254

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_253

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_248

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_263

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_249

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_250

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_246

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_241

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_242

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_245

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_240

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_261

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_239

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_243

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_237

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_247

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_238

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_235

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_236

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_234

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_232

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_227

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_230

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_231

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_233

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_229

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_225

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_222

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_228

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_244

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_224

description:
full-lenght RNA-seq
P3451.tsv


title: EHP3

value: umbilical veins

tag: population doubling level


title: P3451_220

description:
full-lenght RNA-seq
P3451.tsv


title: Cont1

description:
MBD enrichment
methylated DNA

value: control


title: P3451_221

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_219

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_215

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_217

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_216

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_214

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_213

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_218

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_212

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_211

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_210

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_209

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_208

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_226

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_204

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_223

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_206

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_207

description:
full-lenght RNA-seq
P3451.tsv


title: CECR2 sg1-1

value: MDA-MB-231 derived LM2 breast cancer cell line

value: epithelial

tag: genotype/variation

value: CECR1 deletion 1


title: P3451_202

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_203

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_197

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_198

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_200

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_195

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_193

description:
full-lenght RNA-seq
P3451.tsv


title: P3451_201

description:
full-lenght RNA-seq
P3451.tsv


title: P3406_384

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_382

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_383

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_379

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_380

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_378

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_377

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_374

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_375

description:
full-lenght RNA-seq
P3406.tsv


title: P3451_205

description:
full-lenght RNA-seq
P3451.tsv


title: P3406_373

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_376

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_381

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_372

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_371

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_370

description:
full-lenght RNA-seq
P3406.tsv


title: P3451_199

description:
full-lenght RNA-seq
P3451.tsv


title: P3406_365

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_366

description:
full-lenght RNA-seq
P3406.tsv


title: P3451_196

description:
full-lenght RNA-seq
P3451.tsv


title: P3406_369

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_360

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_359

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_364

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_355

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_357

description:
full-lenght RNA-seq
P3406.tsv


title: P3451_194

description:
full-lenght RNA-seq
P3451.tsv


title: P3406_363

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_361

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_353

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_356

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_350

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_345

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_346

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_354

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_358

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_341

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_340

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_368

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_352

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_351

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_367

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_349

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_348

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_333

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_330

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_332

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_327

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_362

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_326

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_343

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_342

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_322

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_339

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_336

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_337

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_320

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_338

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_347

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_335

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_321

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_316

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_334

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_319

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_318

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_331

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_329

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_328

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_311

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_317

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_323

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_324

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_325

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_310

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_314

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_315

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_308

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_313

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_306

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_299

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_307

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_300

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_298

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_296

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_295

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_305

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_303

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_309

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_302

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_304

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_312

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_297

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_294

description:
full-lenght RNA-seq
P3406.tsv


title: P3406_292

description:
full-lenght RNA-seq
P3406.tsv


title: P3405_286

description:
full-lenght RNA-seq
P3405.tsv


title: P3406_293

description:
full-lenght RNA-seq
P3406.tsv


title: P3405_288

description:
full-lenght RNA-seq
P3405.tsv


title: P3405_287

description:
full-lenght RNA-seq
P3405.tsv


title: P3406_291

description:
full-lenght RNA-seq
P3406.tsv


title: P3405_285

description:
full-lenght RNA-seq
P3405.tsv


title: P3406_301

description:
full-lenght RNA-seq
P3406.tsv


title: P3405_283

description:
full-lenght RNA-seq
P3405.tsv


title: P3405_282

description:
full-lenght RNA-seq
P3405.tsv


title: P3405_284

description:
full-lenght RNA-seq
P3405.tsv


title: P3405_281

description:
full-lenght RNA-seq
P3405.tsv


title: P3405_277

description:
full-lenght RNA-seq
P3405.tsv


title: P3405_279

description:
full-lenght RNA-seq
P3405.tsv


title: P3405_278

description:
full-lenght RNA-seq
P3405.tsv


title: P3405_276

description:
full-lenght RNA-seq
P3405.tsv


title: P3405_274

description:
full-lenght RNA-seq
P3405.tsv


title: P3405_272

description:
full-lenght RNA-seq
P3405.tsv