title: Tenofovir40_rep1_r1

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

description: Tenofovir 40µM

data_processing:
Library strategy: ALE-seq
Trimmomatic (Bolger et al., 2014) was used to remove adapters and discard low-quality reads.
Paired end reads were mapped to the reference genomes using Bowtie2 (Langmead and Salzberg, 2013) with minor optimization.
The numbers of reads mapped throughout each annotated retrotransposon were counted by the featureCounts tool of the SubRead package (Lia et al. 2013).
IGV was used to visualize the sequencing data.
Genome_build: MSU7
Supplementary_files_format_and_content: For each genotype, the bigwig coverage file is provided, generated with samtools depth (Li et al 2009, Bioinformatics) from the the aligned reads.

organism: Oryza sativa Japonica Group

source_name: whole seedling

growth_protocol: Rice callus were induced by the method used for rice transformation as previously described (Nishimura et al., 2006). Briefly, seeds of Oryza sativa ssp. japonica cv. Nipponbare were surface-sterilized in 20% bleach for 15 min, rinsed three times with sterile water and placed on N6D media. Plates have been incubated at 27°C in dark and calli have been formed after 3-4 weeks and kept on plates for another 4 weeks before analysis.

extract_protocol:
Genomic DNA was extracted using a DNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instruction, and 100 ng was used for ALE-seq following the previously described protocol (Cho et al., 2019).
Libraries for ALEseq (https://doi.org/10.1038/s41477-018-0320-9) were prepared following the previously described protocol (Cho et al., 2019), with minor modifications. Briefly, an adapter, containing T7 promoter sequence at its 5’ end, was ligated to the end of extrachromosomal DNA, following by in vitro transcription with T7 RNA polymerase. The synthesised RNA was then reversed transcribed using the primer binding the transcripts at the LTR-TE conserved PBS site. the obtqained cDNA was amplified following the standard ALE-seq procedure.

treatment_protocol: In drug treated plants, Tenofovir (Cayman Chemical, N 13874), was dissolved in DMSO and added to the medium used for calli induction at 40 µM. Mock treated calli were trated with DMSO only. Plates have been incubated at 27°C in dark and for 8 weeks.

tag: ecotype

value: Nipponbare

value: callus

value: 8 weeks

value: wild-type

tag: treatment

value: Tenofovir 40uM


title: Leaf_rep1

status: Public on Jan 06 2023

type: SRA

country: United Kingdom

description: control leaves rep 1

library_source: genomic

molecule: genomic DNA

tag: tissue

value: leaves

tag: age

value: 2 months

tag: genotype

value: not treated


title: I14_C

city: Chengdu

first: Wei

last: Li

state: Sichuan

address: Department of Liver Surgery and Liver Transplantation Centre, West China Hospital, Sichuan University

country: China

description: C:tumor; F: adjacent liver; I: samples of the first surgery; II: samples from the recurrent surgery

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: hepatocellular carcinoma

growth_protocol: Clinical sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Clinical sample

tag: tumor type

value: primary

tag: sample type

value: tumor

tag: first or second surgery

value: first


title: II13_F

institute: Department of Liver Surgery and Liver Transplantation Centre, West China Hospital, Sichuan University

value: Recurrent

value: adjacent liver

value: second


title: I13_C


title: Tenofovir0_rep1_r1

description: Tenofovir 0µM rep 1

value: mock


title: Leaf_rep2

description: control leaves rep 2


title: Tenofovir0_rep1_r2

description: Tenofovir 0µM rep 2


title: I12_C


title: I10_C


title: I4_C


title: B-35_HBoV_24h

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

data_processing:
Basecalls performed using illumina's bcl2fastq
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to Ensembl GRCh38.p10 Release 89 genome assembly using STAR 2.5.3a with following parameters: '--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif'
Counts were generated by Rsubread 1.26.1
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: count file was generated by 'featureCounts' from Rsubread package. The numbers are raw counts.

extract_protocol:
PolyA, TruSeq RNA Kit
TruSeq RNA stranded

tag: subject id

value: Be

tag: subject status

value: healthy individual

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

value: stimulated with 2.4 µg/ml HBoV1-VLPs

tag: time


title: Fur-R88H 1.0% NaCl, replicate 2

city: Nashville

first: John

last: Loh

state: TN

address: A2320 MCN VUMC

department: Infectious Diseases

country: USA

institute: Vanderbilt University

data_processing:
RNA-seq data were trimmed to remove all bases below a quality of Q3, and adapter sequences were removed using FastQ quality control software (FaQCs).
Kallisto pseudocounting was applied to all annotated genes in the H. pylori B8 genome (GenBank accession no. NC_014256.1).
The EdgeR package for R was used to analyze count files. Data from individual samples were normalized within EdgeR and analyzed using the generalized linear model (GLM).
Fold change values were calculated by comparing the means of normalized pseudocounts for samples from each group (calculated by edgeR).
Assembly: H. pylori B8 genome (GenBank accession no. NC_014256.1).

organism: Helicobacter pylori

growth_protocol: H. pylori cells were cultured in medium containing either 0.5%  or 1.0% added NaCl for 15 h.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were sequenced on a NovaSeq 6000 with paired reads of 150-bp length, according to the manufacturer’s protocol.  Bcl2fastq2 conversion software (Illumina) was used to generate de-multiplexed Fastq files.
A total of 15 independent samples were analyzed; 8 RNA preparations from Fur-R88H expressing bacteria grown in media containing either 0.5% NaCl (4 independent samples) or 1.0% NaCl (4 independent samples), and 7 RNA preps from cultures of WT Fur expressing strains grown in media containing 0.5% NaCl (4 independent samples) or 1.0% NaCl (3 independent samples)

tag: strain

value: 1.0% NaCl


title: Fur-R88H 1.0% NaCl, replicate 1


title: Fur-R88H 1.0% NaCl, replicate 4


title: Fur-R88H 1.0% NaCl, replicate 3


title: B-33_HBoV_6h


title: Fur-R88H 0.5% NaCl, replicate 4

value: 0.5% NaCl


title: Fur-R88H 0.5% NaCl, replicate 3


title: Fur-R88H 0.5% NaCl, replicate 2


title: B-31_unst_0h

value: none; unstimulated


title: Fur-R88H 0.5% NaCl, replicate 1


title: B-32_unst_6h


title: B-30_HBoV_24h

value: An-G


title: B-28_HBoV-6h


title: I11_C


title: B-25_HBoV_24h

value: Re


title: WT Fur 0.5% NaCl, replicate 2

source_name: WT Fur

value: WT Fur


title: B-27_unst_6h


title: WT Fur 0.5% NaCl, replicate 3


title: WT Fur 0.5% NaCl, replicate 4


title: B-34_unst_24h


title: B-26_unst_0h


title: B-23_HBoV_6h


title: B-24_unst_24h


title: WT Fur 0.5% NaCl, replicate 1


title: WT Fur 1.0% NaCl, replicate 2


title: B-22_unst_6h


title: B-20_HBoV_24h

value: O


title: B-21_unst_0h


title: WT Fur 1.0% NaCl, replicate 3


title: WT Fur 1.0% NaCl, replicate 1


title: AAME3

city: Zhengzhou

first: liang

middle: nian

last: nian

address: 100 Science Avenue

institute: Zhengzhou University

data_processing:
Trim Smart-seq2 public primer sequence from the Reads
The reference genomes and the annotation file were downloaded from Brassicadb database (http://brassicadb.org). Bowtie v1.0.1 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: Brassica_juncea_v1.5(http://brassicadb.org)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Brassica rapa

source_name: anther

growth_protocol: B. rapa ♀×B. nigra ♂, haploid

extract_protocol:
Flower buds from meiosis and tetrad to maturity were collected and RNA was collected with Trizol reagent. Rna-seq library was constructed with 5 ~ 10 μg total RNA as template
RNA libraries were prepared for sequencing using standard Illumina protocols

value: young anther(pollen)

tag: Stage

value: ME(meiosis(sporogenesis))

tag: genomes

value: AA


title: AAMI2

value: anther(pollen)

value: MI(mitosis(gametogenesis))


title: AAME2


title: B-17_unst_6h


title: AAME1


title: AAMI1


title: BBCCMi3

first: Shen

last: xiaohan

description: Brassica carinata(B.oleracea var. alboglabra ♀×B.nigra ♂, ovule culture and colchicine treatment, tetraploid )

data_processing:
Trim Smart-seq2 public primer sequence from the Reads
The reference genomes and the annotation file were downloaded from Brassica Genomics Database (http://brassicadb.bio2db.com/). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2
Reads Count for each gene in each sample was counted by featureCounts v2.0.1, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: Brassica_carinata(http://brassicadb.bio2db.com/)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Brassica carinata

growth_protocol: B.oleracea var. alboglabra ♀×B.nigra ♂,haploid. ovule culture and colchicine treatment, tetraploid Brassica carinata

extract_protocol:
floral buds were collectedand,and RNA was harvested using Trizol reagent.5–10 μg total RNA was used as the template for constructing RNA-seq libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Mi(mitosis(gametogenesis))

value: BBCC


title: B-16_unst_0h

value: healthy individual


title: input

city: Shenzhen

first: JING

last: LUO

email: luoj17@lzu.edu.cn, luojing9520@163.com

address: No 7,Pengfei Road,Dapeng District

institute: Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

data_processing:
the MEA-seq sequences were aligned to mm9/hg19 by using bwa -aln (version 0.7.5a-r405) with default parameters
The uniq mapped fragment counts were normalized
The poisson test was used to calculate the significant difference between input and output data, then, the Benjaminiand Hochberg test was used to select the loci with q value which were lower than 0.01 as effective signals
Genome_build: mm9,hg19
Supplementary_files_format_and_content: MAE-seq enhancers text file

organism: blank sample

source_name: Randomly generated sequence

growth_protocol: Both mESCs and HEK293T were purchased from ATCC and cultured in accordance with ATCC's protocol.

extract_protocol:
The cells were transfected with lipo3000, and the cells were collected for flow screening after 48 hours.
DNA was extracted from the collected fluorescent cells. Components were added according to the TruePrep DNA Library Prep kit (Vazyme; Cat.TD202) and followed by one-step PCR (72℃ for 3min, 98℃ for 30s; followed by 5-15 cycles of 98℃ for 15s, 60℃ for 30s, 72℃ for 3min; 72℃ for 5mins). The product was recovered by 2% agarose gel electrophoresis for 35 min (120v, 130mA) and sent for high-throughput sequencing. Sequence after one-step PCR amplification is 5’-AATGATACGGCGACCACCGAGATCTACACIIIIIIIITCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-NNNNNN-CTGTCTCTTATACACATCTCCGAGCCCACGAGACIIIIIIIIATCTCGTATGCCGTCTTCTGCTTG-3’, IIIIIIII: Index 2 (i5), IIIIIIII: Index 1 (i7), -NNNNNN-: random sequence.
MAE-seq

value: input


title: B-15_HBoV_24h

value: Kr

value: peripheral blood mononuclear cells (PBMCs)

value: stimulated with 2.4 µg/ml HBoV1-VLPs


title: BBCCMi2


title: BBCCMi1


title: B-11_unst_0h

value: none; unstimulated


title: B-12_unst_6h


title: BCMi2

description: Brassica carinata(B.oleracea var. alboglabra ♀×B.nigra ♂, haploid)

value: BC


title: B-13_HBoV_6h


title: B-14_unst_24h


title: AAMI3


title: B-19_unst_24h


title: BCMi1


title: B-18_HBoV_6h


title: B-5_HBoV_24h

value: An


title: BCMe1

value: Me(meiosis(sporogenesis))


title: BBCCMe3


title: B-3_HBoV_6h


title: BBCCMe1


title: B-2_unst_6h


title: MEL72_5_10 µM enterolactone treated

city: Guwahati

first: Anil

middle: Mukund

last: Limaye

state: Assam

address: IIT Guwahati

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Guwahati

data_processing:
Quality control check - FastQC Version 0.11.5: It checks for read quality
Data Trimming Steps - Trimmomatic Version 0.36: Adapter trimming and filtering out low quality reads
Quality Control Check - FastQC Version 0.11.5: Re-assess the quality of filtered reads prior to successive mapping.
Read Alignment - STAR Aligner Version 2.7.6a: Mapping the reads against the reference genome.
Assembly: Ensemble Homo sapiens GRCh38 genome
Quantification of Reads - featureCounts v2.0.0: Quantification of mapped reads.
Annotation Reference File - Homo sapiens GRCh38 (gtf):
Supplementary files format and content: Raw_gene_counts_matrix

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were grown in a humidified chamber maintained at 37 °C and 5% CO2. The cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM), supplemented with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, and 100 μg/mL streptomycin (M1 medium).

extract_protocol:
Total RNA was isolated using RNA extraction reagent prepared in-house as per Chomczynski and Sacchi, with modifications
mRNA enrichment was performed using KAPA mRNA capture kit. Libraries were prepared according to instructions accompanying the KAPA RNA Hyper prep kit (Roche, Switzerland). mRNA was fragmented and reverse transcribed using oligo-dT primers to synthesize cDNA. The double-stranded cDNAs were end-repaired, polyadenylated, and ligated with adapter sequences. Sequencing was performed using Nextseq2K Platform in 150 paired-end reads length format.

treatment_protocol: MCF-7 cells were seeded at a density of 0.2 million cells/ well using M1 medium in 6-well plates. After 48 hours of seeding, the cells were given phenol red-free DMEM supplemented with 10% heat-inactivated charcoal-stripped fetal bovine serum, 100 units/mL penicillin, and 100 μg/mL streptomycin (M2 medium) for 24 h. Then the cells were treated with M2 medium containing 10 μM enterolactone or 0.1% DMSO (vehicle control) for 72 h. The treatment medium was replenished every 24 h.

value: Treated with 10 µM enterolactone for 72 hours

value: Breast cancer cell line

tag: cell line

value: Wild type


title: B-6_unst_0h

value: C


title: B-9_unst_24h


title: BCMe2

value: young anther(pollen)


title: BBCCMe2


title: B-10_HBoV_24h


title: MEL72_2_10 µM enterolactone treated


title: BCMe3


title: B-1_unst_0h


title: BCMi3

value: anther(pollen)


title: MEL72_4_10 µM enterolactone treated


title: HeLa 6hr ARID1a KD 2

city: Bristol

first: Felicity

last: Stubbs

address: Whitson St

institute: University of Bristol

data_processing:
Data was processed using RTA version 1.18.64, with default filter and quality settings. The reads were demultiplexed with CASAVA 1.8.4 (allowing no mismatches). Raw data from high throughput RNA sequencing was uploaded to Galaxy bioinformatics (www.galaxyproject.org).
Three lanes were uploaded for each RNA sample. For each condition an n of 3 were assessed.
A workflow was run for each lane, forward (dataset 1) and reverse strand (dataset 2).
The Cuff Diff parameters included were geometric library organization, pooled dispersion estimation, 0.05 False Discovery Rate, Min alignment count 10, multi-read correct, bias correction and cuff-links effective length correction.
For RNA-seq data differential gene expression was calculated as fragments per kilobase per million mapped reads (FPKM) values; summed fragments of each transcript with same gene ID. After Benjamini-Hochberg false discovery correction, genes with adjusted p values less than 0.05 were considered as differentially expressed genes. Suprahex analysis was used to aid visualization of regulation patterns in the data.
Assembly: Genome Hg19
Supplementary files format and content: Excel spreadsheet with FPKM

source_name: HeLa

growth_protocol: DMEM, 10% FCS.

extract_protocol:
Cells were collected in TRIzol (Ambion, Life Technologies, UK), and total RNA was purified using membrane columns (RNAeasy minikit, Qiagen, UK). An on-column DNase step (Qiagen, UK) was used to ensure the removal of genomic DNA. RNA was eluted in nuclease free water, and stored at -80oC.
Approx 500 ng of total RNA (16 samples) were prepared for sequencing using the Illumina Truseq Stranded Total RNA Kit (Manual part RS-122-9007DOC, part 15031048 Rev E, Oct 2013). Final average library size distribution (including adapters) was 335 bp.

treatment_protocol: 100nM Dex

value: HeLa

value: Cervical cancer cells

value: Dexamethasone

tag: time (hours)


title: HeLa 6hr Control siRNA 3

tag: treatment


title: MC72_2_DMSO treated_Vehicle control

value: Treated with 0.1% DMSO for 72 hours


title: HeLa 6hr ARID1a KD 3


title: HeLa 6hr ARID1a KD 1


title: HeLa 6hr Control siRNA 2


title: B-29_unst_24h

value: An-G

value: healthy individual


title: B-4_unst_24h

value: peripheral blood mononuclear cells (PBMCs)


title: HeLa 6hr Control siRNA 1


title: cKO-MZ-M2 (ATAC-seq)

city: Baltimore

first: Amit

middle: Kumar

last: Singh

state: Maryland

address: 251 Baview Blvd

department: Laboratory of Molecular Biology Immunology

institute: National Institute on Aging

data_processing:
Reads were analyzed using online server Galaxy RNA-seq pipeline (usegalaxy.org).
Adapter trimmed sequences were aligned to mouse genome (mm10) using HISAT2 or BOWTIE2
featureCounts or htseq-count were used for differential gene expression analysis using DESeq2
differentially open chromatin (DOC) was analyzed by DiffBind
Assembly: mm10
Supplementary files format and content: tab-delimited text file include normalized expression levels form for RNA-seq samples (both WT and cKO)
Supplementary files format and content: coverage normalized bigwig files for ATAC-seq samples

organism: Mus musculus

source_name: FACS Sorted MZ B cells

extract_protocol:
Total RNA from 1x10^6 isolated using Qiazol (Qiagen) kit according to manufacturer’s protocol. Genomic DNA tagmented by Tn5.
RNA-sequencing of total RNA was performed at the Johns Hopkins Deep Sequencing and Microarray Core facility using standard protocol for NextSeq 500 sequencer. Ribosomal RNA was depleted from 100ng of total RNA and barcoded library was made and 50bp single end reads were generated from each sample. ATAC-seq libraries were made from 100.000 cells as protocol described by Buenrostro et al. Nat. Methods 10, 1213–1218. Barcoded libraries were sequenced NextSeq 500 for at least 30 million single end reads per sample.

treatment_protocol: mouse splenic B cells were sorted for follicular (FO) and marzinal zone (MZ) B cells sorted using FACS. And total RNA or ATAC-seq libraries were prepared

value: FACS Sorted MZ B cells

value: Gtf2i fl/flxCD19cre+


title: cKO-MZ-M1 (ATAC-seq)


title: HeLa 3hr Control siRNA 3


title: cKO-FO-M2 (ATAC-seq)

source_name: FACS Sorted FO B cells

value: FACS Sorted FO B cells


title: HeLa 3hr ARID1a KD 3


title: HeLa 3hr ARID1a KD 2


title: cKO-FO-M1 (ATAC-seq)


title: HeLa 3hr Control siRNA 1


title: WT-MZ-M1 (ATAC-seq)

value: WT


title: WT-FO-M2 (ATAC-seq)


title: WT-MZ-M2 (ATAC-seq)


title: cKO-MZ-Rep2 (RNA-seq)

description:
Normalizedcounts RNA-seq
cKO-MZ-Rep2


title: WT-FO-M1 (ATAC-seq)


title: HeLa 1hr ARID1a KD 3


title: HeLa 3hr Control siRNA 2


title: HeLa 3hr ARID1a KD 1


title: cKO-MZ-Rep1 (RNA-seq)

description:
Normalizedcounts RNA-seq
cKO-MZ-Rep1


title: HeLa 1hr ARID1a KD 2


title: MC72_5_DMSO treated_Vehicle control


title: HeLa 1hr Control siRNA 2


title: HeLa 1hr ARID1a KD 1


title: cKO-FO-Rep2 (RNA-seq)

description:
Normalizedcounts RNA-seq
cKO-FO-Rep2


title: HeLa 1hr Control siRNA 3


title: MC72_1_DMSO treated_Vehicle control


title: cKO-FO-Rep1 (RNA-seq)

description:
Normalizedcounts RNA-seq
cKO-FO-Rep1


title: WT-MZ-Rep2 (RNA-seq)

description:
Normalizedcounts RNA-seq
WT-MZ-Rep2


title: HeLa 0hr ARID1a KD 3


title: HeLa 1hr Control siRNA 1


title: WT-MZ-Rep1 (RNA-seq)

description:
Normalizedcounts RNA-seq
WT-MZ-Rep1


title: WT-H3

city: Aurora

first: Andrés

last: Vázquez-Torres

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description: Barcode: CAGATC; Mean Q-score: 35.14

data_processing:
i7 Illumina universal adapter trimming from raw paired reads with Cutadapt version 2.10
Read mapping with Bowtie2 version 2.3.2 using CP001363.1 and CP001362.1
Duplicate read removal and sorting with Picard version 2.18.27
Count file generation with HTseq version 0.13.5
Statistical analysis performed with DEseq2 1.30.1 and edgeR 3.32.1 in R Studio running R version 4.0.4 via Fisher's exact test on the tagwise dispersion of counts for loci that had at least 80 reads total across all samples be analyzed
Assembly: CP001362.1, CP001363.1
Supplementary files format and content: Comma-delimited matrix file with raw counts for every loci from every sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: strain 14028s

growth_protocol: Salmonella strains were cultured overnight in LB broth and the subcultured 1:100 into MOPS media with 0.4% D-glucose until an OD600 of 0.25

extract_protocol:
RNA extration was performed via TRIzol reagent with a sodium acetate, glucogen and isopropyl alcohol precipitation. Extracts were washed twice with 70% ethanol, dried, and resuspended in DEPC-treated water. RNA solutions were treated with DNase I according to supplier's specifications (Promega). Reactions were terminated with phenol-choloroform-isoamyl alcohol and RNA was re-extracted as before. rRNA was removed using the MICROBExpress kit (Life Technologies).
1 µg of purified mRNA was fragmented with NEB Magnesium Fragmentation module and purified as previously stated. Libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for a target insert size of 300 bp. Sampels were barcoded with NEBNext Multiplex Oligos

treatment_protocol: Cultures were either left untreated or treated with 400 µM hydrogen peroxide for 30 minutes. 2 mL from each culture was pelleted for extraction.

value: 400 uM hydrogen peroxide

tag: culture media

value: MOPS Glucose

value: strain 14028s


title: WT-FO-Rep2 (RNA-seq)

description:
Normalizedcounts RNA-seq
WT-FO-Rep2


title: WT-H4

description: Barcode: ACTTGA; Mean Q-score: 35.13


title: WT-H2

description: Barcode: GCCAAT; Mean Q-score: 35.08


title: HeLa 0hr Control siRNA 3


title: greAB-H4

description: Barcode: CCGTCC; Mean Q-score: 35.07

source_name: strain AV19001 ∆greAB

value: strain AV19001 {delta}greAB

value: greAB


title: WT-FO-Rep1 (RNA-seq)

description:
Normalizedcounts RNA-seq
WT-FO-Rep1


title: HeLa 0hr ARID1a KD 1


title: greAB-H2

description: Barcode: AGTTCC; Mean Q-score: 35.14


title: greAB-H1

description: Barcode: AGTCAA; Mean Q-score: 34.96


title: WT-H1

description: Barcode: ACAGTG; Mean Q-score: 35.15


title: Spl_aGC_72hr

city: Dublin

first: Lydia

last: Lynch

address: Trinity Biomedical Sciences Institute 152-160 Pearse St

country: Ireland

institute: Trinity College Dublin

data_processing:
Raw BCL files were demultiplexed using Cell Ranger v3.0.2 mkfastq to generate fastq files with default parameters.
Fastq files were aligned to the mm10 genome (v1.2.0) and feature reads were quantified simultaneously using Cell Ranger count for feature barcoding to generate filtered barcode.tsv, feature.tsv and matrix.mtx files
Filtered barcode.tsv, feature.tsv and matrix.mtx files were read using Seurat v.4.0.5. Dead, apoptotic and poor quality cells were removed for quality control and the raw gene expression data was normalized using sctransform v.0.3.2 with default parameters.
Genome_build: mm10 genome (v1.2.0)
Supplementary_files_format_and_content: Filtered barcode.tsv, feature.tsv and matrix.mtx files for each sample from the Cell Ranger output.

source_name: Splenic iNKT cells 72-hours post-αGalCer

extract_protocol:
Adipose tissue was carefully dissected and dissociated in 1mg/mL Type II collagenase (Worthington) for 25 minutes at 37 degrees celcius. Digested tissue was filtered through a 70uM filter and centrifuged at 15,000rpm for 7 minutes. Spleens were manually disrupted and filtered through a 70uM filter and centrifged. Splenocytes were treated with ACK red blood cell lysis buffer (VWR) prior to further analysis. iNKT cells were FACS-sorted, gated on TCRB+ CD1d-PBS57 Tetramer+ CD19- F4/80- CD45+ live single cells. Single cell suspensions from the adipose tissue and spleens of mice 4 weeks post-αGalCer were tagged by TotalSeq-A Mouse hashtag antibody #2, #3 and #4 (Biolegend) before the three samples were pooled for sequencing. In the HTO sample data hashtag #2 labels adipose iNKT cells, hashtag #3 labels splenic iNKT cells without further stimulation, hashtag #4 labels splenic iNKT cells restimulated with 1μg αGalCer for 4 hours.
Cell suspensions were loaded onto a 10x Chromium controller to generate gel bead-in-emulsions (GEMs) according to the manufacturers instructions, and libraries were prepared according to standard protocols produced by 10X Genomics for sequencing using Chromium Single Cell 3' V3 chemistry. Libraries were sequenced using a NextSeq 500 sequencer (Illumina).

treatment_protocol: αGalCer was prepared for injection by dilution in sterile PBS (Sigma) and the final concentration of DMSO was adjusted to less than 10% vol/vol. Mice were injected IP with 1µg or 4ug of αGalCer or PBS vehicle, and sacrificed 4 hours, 72 hours or 4 weeks later.

tag: tissue

value: Spleen

tag: age

value: 8-12 weeks


title: HeLa 0hr ARID1a KD 2

value: HeLa

value: Cervical cancer cells


title: HeLa 0hr Control siRNA 2


title: D2

city: Yangzhou

first: Demin

last: Cai

address: Daxue South Road 88

institute: Yangzhou University

description: bio rep cotreatment of DON and LF 1

data_processing:
The sequence data in FASTQ format was analyzed using a standard BWA–Bowtie-Cufflinks workflow
Sequence reads were mapped to mm9 assembly with BWA and Bowtie software
The Cufflinks package was used for transcripts assembly, quantification of normalized gene and isoform expression, and analysis of different expressions
Genes were ranked using the Gene Set Enrichment Analysis (GSEA v.4.1) based on the shrunken limma log2 fold changes.The GSEA tool was used in a ‘pre-ranked’ model with default parameters.
Gene Ontology (GO) analysis was performed using DAVID Bioinformatics Resources.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Testis

extract_protocol:
The testis tissue RNA were isolated using Illumina Tru-Seq RNA Sample Prep Kit according to the instructions of the manufacturer.
The quality of libraries were validated with an Agilent Bioanalyzer, sequencing was performed on an Illumina HiSeq 2000 sequencer at BGI Tech

treatment_protocol: Mice in vehicle group were feed with basal diet; In DON group mice were fed basal diet supplemented with 12 mg/kg DON, which was orignated from DON contaminated corn.LF was dissolved in normal saline and mice were oral administrated with LF at  10mg per day. Mice in DON+LF group was co-treatment of DON and LF with same dose refered above.

value: Testis

value: ICR mouse


title: D1

description: Cotreatment of DON and LF

value: co-treatment of DON and LF with same dose refered above


title: C1

description: LF

value: Oral administration of LF at 10mg per day


title: C2

description: bio rep LF 1


title: AT_aGC_4hr

source_name: Adipose iNKT cells 4-hours post-αGalCer

value: Epididymal adipose tissue


title: B2

description: bio rep DON 1

value: Basal diet inclusion of DON at 12mg/kg


title: HeLa 0hr Control siRNA 1


title: GFP 6HR REP4

data_processing:
Data was processed using RTA version 1.18.64, with default filter and quality settings. The reads were demultiplexed with CASAVA 1.8.4 (allowing no mismatches). Raw data from high throughput RNA sequencing was uploaded to Galaxy bioinformatics (www.galaxyproject.org).
Three lanes were uploaded for each RNA sample. For each condition an n of 4 were assessed.
A workflow was run for each lane, forward (dataset 1) and reverse strand (dataset 2).
The Cuff Diff parameters included were geometric library organization, pooled dispersion estimation, 0.05 False Discovery Rate, Min alignment count 10, multi-read correct, bias correction and cuff-links effective length correction.
For RNA-seq data differential gene expression was calculated as fragments per kilobase per million mapped reads (FPKM) values; summed fragments of each transcript with same gene ID. After Benjamini-Hochberg false discovery correction, genes with adjusted p values less than 0.05 were considered as differentially expressed genes. Suprahex analysis was used to aid visualization of regulation patterns in the data.
Assembly: Genome Hg19
Supplementary files format and content: Excel spreadsheet with FPKM

value: Dexamethasone


title: GFP 6HR REP3


title: B1

description: DON


title: GFP 6HR REP2


title: A2

description: bio rep vehicle 1

value: basal diet and oral administration of normal saline


title: ovarian organoids_scRNA-seq

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
Read pairs with low sequencing quality (too long, too short, low sequencing score or with high single nucleotide frequency) were firstly removed in the reads quality filtering step.
The quality-filtered R1 reads were analyzed to identify the cell label sequence (CL), Molecular Identifier sequence (UMI), and poly-dT tail sequence, meanwhile the quality-filtered R2 reads were mapped to Genome Reference Consortium Mouse Build 38 patch release 4 (GRCm38.p4) using STAR (verison 2.5.2b) in reads annotation step.
Further adjustment was performed with the recursive substitution error correction (RSEC) and distribution-based error correction (DBEC) algorithms to remove artifact molecules due to amplification bias in molecules annotation step.
Putative cells were distinguished from background noise with second derivative analysis in putative cell determination step.
Putative cells information was combined together with RSEC/DBEC-adjusted molecules to generate a single-cell expression matrix. The pipeline output provided raw gene expression matrices corrected by RSEC and DBEC algorithms. Among all the matrices, UMI counts per cell corrected by DBEC algorithm were later used in the clustering analysis.
Raw gene expression matrices from two cartridges were read into R (version 3.6.0) separately and converted to Seurat objects using the Seurat R package (version 2.0). The gene expression matrix was then normalized to the total cellular UMI count.
Genome_build: mm10
Supplementary_files_format_and_content: Combined_SC192_RSEC_MolsPerCell.csv

source_name: ovarian organoids

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Double strand cDNA was firstly generated from Microbeads-captured single cell transcriptome following several steps including reverse transcription, second strand synthesis, end preparation, adapter ligation and whole transcriptome amplification. Then final cDNA library was generated from double strand full length cDNA by random priming amplification with BD Rhapsody cDNA Kit (BD Biosciences, 633773) and BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (BD Biosciences, 633774). Library was sequenced in a PE150 mode (Pair-End for 150bp read) on the TenX instrument (Illumina).

value: ovarian organoids

tag: genotype

value: wild type


title: greAB-H3

description: Barcode: ATGTCA; Mean Q-score: 34.98

value: 400 uM hydrogen peroxide

value: MOPS Glucose


title: AT_aGC_72hr

source_name: Adipose iNKT cells 72-hours post-αGalCer


title: GFP 6HR REP1


title: aGC_4wk

description: Adipose and splenic iNKT cells were sequenced together. Samples are labeled using hashtag antibodies. Adipose 4WK iNKT: hashtag antibody #2. Splenic 4WK iNKT cells without secondary activation: hashtag antibody #3. Reactivated Splenic 4WK iNKT cells: hashtag antibody #4.

source_name: Splenic and adipose iNKT cells 4-weeks post-αGalCer

value: Epididymal adipose tissue, Spleen


title: GFP 1HR REP4


title: A1

description: Vehicle


title: GFP 1HR REP3


title: GFP 1HR REP2


title: GFP 1HR REP1


title: CTERM 6HR REP4


title: TL47-95 kcal

type: genomic

city: Chiba

first: Masaaki

last: Sunaoshi

state: Chiba

address: 4-9-1 Anagawa, Inage-ku

department: Department of Radiation Effects Research, Institute for Radiological Science

country: Japan

institute: National Institutes for Quantum Science and Technology

description:
TL47-S30360-95 kcal
Thymocytes

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially in wash buffer.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and data extraction.

source_name: TL47-Radiation-induced thymic lymphoma in 95 kcal group

label_protocol: Alu I- and Rsa I-restricted DNA (400 ng) derived from ear and lymphoma were labeled by 60 µM Cyanine3-UTP and Cyanine5-UTP, respectively. Exo-Klenow fragment enzyme (Agilent Genomic DNA Enzymatic Labeling kit) was used to label these DNA.

growth_protocol: Mice were separated into different calorie-intake groups from 7 weeks of age. Mice were observed daily until moribund, when thymic enlargement and dyspnea symptoms were recognized, after which they were sacrificed by exsanguination under terminal isofluorane anesthesia and autopsied.

extract_protocol: Genomic DNA was extracted from 48 mice ears and lymphomas using Maxwell® 16 Instrument (Promega). After extraction, DNA was treated with RNase A (Sigma).

treatment_protocol: B6C3F1 male mice were exposed to 3.8 Gy X-rays at 1 week of age, and then separated into different calorie-intake groups (95 kcal/mouse/week or 65 kcal/mouse/week) from 7 weeks of age.

tag: Sex

value: Male

tag: calorie

value: 95 kcal/week

value: Thymic lymphoma

source_name: Ear obtained from the same individual

value: Ear


title: Cardiac left ventricle - WT_P20 - Rep1

type: RNA

city: Toulouse

first: Celine

last: GALES

address: 1 Avenue du Pr. Jean Poulhès

country: France

institute: INSERM

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 37042 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 34370 rows each corresponding to a unique ProbeName.

source_name: Cardiac left ventricle

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Mice were housed since birth in 12h light/12h dark period and fed a chow diet.

extract_protocol: Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. RNA amounts were determined by NanoDrop®ND-1000 and the RNA quality was assessed using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer.

value: WT

tag: gender

value: Cardiac left ventricle


title: CTERM 6HR REP3

value: HeLa

value: Cervical cancer cells


title: Cardiac left ventricle - Efnb1cKO_P20 - Rep6


title: Cardiac left ventricle - Efnb1cKO_P20 - Rep3


title: Cardiac left ventricle - WT_P20 - Rep6


title: TL46-95 kcal

description:
TL46-S30359-95 kcal
Thymocytes

source_name: TL46-Radiation-induced thymic lymphoma in 95 kcal group


title: TL39-65 kcal

description:
TL39-S29966-65 kcal
Thymocytes

source_name: TL39-Radiation-induced thymic lymphoma in 65 kcal group

value: 65 kcal/week


title: Cardiac left ventricle - Efnb1cKO_P60 - Rep4


title: TL42-65 kcal

description:
TL42-S30226-65 kcal
Thymocytes

source_name: TL42-Radiation-induced thymic lymphoma in 65 kcal group


title: TL48-65 kcal

description:
TL48-S30544-65 kcal
Thymocytes

source_name: TL48-Radiation-induced thymic lymphoma in 65 kcal group


title: TL45-95 kcal

description:
TL45-S30328-95 kcal
Thymocytes

source_name: TL45-Radiation-induced thymic lymphoma in 95 kcal group


title: TL40-95 kcal

description:
TL40-S30199-95 kcal
Thymocytes

source_name: TL40-Radiation-induced thymic lymphoma in 95 kcal group


title: Cardiac left ventricle - WT_P60 - Rep6


title: TL44-65 kcal

description:
TL44-S30276-65 kcal
Thymocytes

source_name: TL44-Radiation-induced thymic lymphoma in 65 kcal group


title: TL38-65 kcal

description:
TL38-S29950-65 kcal
Thymocytes

source_name: TL38-Radiation-induced thymic lymphoma in 65 kcal group


title: TL43-65 kcal

description:
TL43-S30245-65 kcal
Thymocytes

source_name: TL43-Radiation-induced thymic lymphoma in 65 kcal group


title: TL35-95 kcal

description:
TL35-S29845-95 kcal
Thymocytes

source_name: TL35-Radiation-induced thymic lymphoma in 95 kcal group


title: Cardiac left ventricle - WT_P60 - Rep4


title: Cardiac left ventricle - Efnb1cKO_P60 - Rep5


title: TL36-95 kcal

description:
TL36-S29860-95 kcal
Thymocytes

source_name: TL36-Radiation-induced thymic lymphoma in 95 kcal group


title: TL41-95 kcal

description:
TL41-S30224-95 kcal
Thymocytes

source_name: TL41-Radiation-induced thymic lymphoma in 95 kcal group


title: CTERM 6HR REP2

source_name: HeLa


title: Cardiac left ventricle - Efnb1cKO_P20 - Rep2


title: TL33-65 kcal

description:
TL33-S29612-65 kcal
Thymocytes

source_name: TL33-Radiation-induced thymic lymphoma in 65 kcal group


title: TL34-65 kcal

description:
TL34-S29815-65 kcal
Thymocytes

source_name: TL34-Radiation-induced thymic lymphoma in 65 kcal group


title: CTERM 6HR REP1


title: TL32-65 kcal

description:
TL32-S29599-65 kcal
Thymocytes

source_name: TL32-Radiation-induced thymic lymphoma in 65 kcal group

source_name: Ear obtained from the same individual


title: CTERM 1HR REP3


title: CTERM 1HR REP2


title: Cardiac left ventricle - WT_P20 - Rep2

source_name: Cardiac left ventricle


title: TL30-65 kcal

description:
TL30-S29574-65 kcal
Thymocytes

source_name: TL30-Radiation-induced thymic lymphoma in 65 kcal group


title: GFP 3HR REP4


title: CTERM 1HR REP1


title: TL31-65 kcal

description:
TL31-S29597-65 kcal
Thymocytes

source_name: TL31-Radiation-induced thymic lymphoma in 65 kcal group


title: TL29-95 kcal

description:
TL29-S29552-95 kcal
Thymocytes

source_name: TL29-Radiation-induced thymic lymphoma in 95 kcal group


title: TL27-95 kcal

description:
TL27-S29545-95 kcal
Thymocytes

source_name: TL27-Radiation-induced thymic lymphoma in 95 kcal group


title: CTERM 1HR REP4


title: Cardiac left ventricle - Efnb1cKO_P20 - Rep5


title: GFP 3HR REP3


title: TL24-95 kcal

description:
TL24-S29526-95 kcal
Thymocytes

source_name: TL24-Radiation-induced thymic lymphoma in 95 kcal group


title: GFP 3HR REP2


title: Cardiac left ventricle - WT_P20 - Rep5


title: Cardiac left ventricle - WT_P60 - Rep5


title: Cardiac left ventricle - WT_P20 - Rep4


title: Cardiac left ventricle - Efnb1cKO_P60 - Rep6


title: TL26-95 kcal

description:
TL26-S29542-95 kcal
Thymocytes

source_name: TL26-Radiation-induced thymic lymphoma in 95 kcal group


title: TL37-95 kcal

description:
TL37-S29884-95 kcal
Thymocytes

source_name: TL37-Radiation-induced thymic lymphoma in 95 kcal group


title: TL22-95 kcal

description:
TL22-S28874-95 kcal
Thymocytes

source_name: TL22-Radiation-induced thymic lymphoma in 95 kcal group


title: TL21-65 kcal

description:
TL21-S28873-65 kcal
Thymocytes

source_name: TL21-Radiation-induced thymic lymphoma in 65 kcal group


title: GFP 3HR REP1


title: TL28-95 kcal

description:
TL28-S29551-95 kcal
Thymocytes

source_name: TL28-Radiation-induced thymic lymphoma in 95 kcal group


title: Cardiac left ventricle - Efnb1cKO_P20 - Rep4


title: Cardiac left ventricle - WT_P60 - Rep3


title: TL17-95 kcal

description:
TL17-S15448-95 kcal
Thymocytes

source_name: TL17-Radiation-induced thymic lymphoma in 95 kcal group


title: TL23-65 kcal

description:
TL23-S28982-65 kcal
Thymocytes

source_name: TL23-Radiation-induced thymic lymphoma in 65 kcal group


title: TL25-95 kcal

description:
TL25-S29532-95 kcal
Thymocytes

source_name: TL25-Radiation-induced thymic lymphoma in 95 kcal group


title: TL19-95 kcal

description:
TL19-S28715-95 kcal
Thymocytes

source_name: TL19-Radiation-induced thymic lymphoma in 95 kcal group


title: Cardiac left ventricle - Efnb1cKO_P60 - Rep3


title: TL20-95 kcal

description:
TL20-S28814-95 kcal
Thymocytes

source_name: TL20-Radiation-induced thymic lymphoma in 95 kcal group


title: GFP 0HR REP4

source_name: HeLa


title: GFP 0HR REP3


title: GFP 0HR REP2


title: GFP 0HR REP1


title: CTERM 3HR REP4


title: TL15-95 kcal

description:
TL15-S13871-95 kcal
Thymocytes

source_name: TL15-Radiation-induced thymic lymphoma in 95 kcal group

source_name: Ear obtained from the same individual


title: TL14-65 kcal

description:
TL14-S13789-65 kcal
Thymocytes

source_name: TL14-Radiation-induced thymic lymphoma in 65 kcal group


title: TL16-65 kcal

description:
TL16-S13911-65 kcal
Thymocytes

source_name: TL16-Radiation-induced thymic lymphoma in 65 kcal group


title: Cardiac left ventricle - Efnb1cKO_P60 - Rep1

source_name: Cardiac left ventricle


title: Cardiac left ventricle - WT_P60 - Rep1


title: TL13-65 kcal

description:
TL13-S13690-65 kcal
Thymocytes

source_name: TL13-Radiation-induced thymic lymphoma in 65 kcal group


title: TL12-65 kcal

description:
TL12-S13656-65 kcal
Thymocytes

source_name: TL12-Radiation-induced thymic lymphoma in 65 kcal group


title: CTERM 3HR REP3


title: TL9-65 kcal

description:
TL9-S13133-65 kcal
Thymocytes

source_name: TL9-Radiation-induced thymic lymphoma in 65 kcal group


title: TL10-95 kcal

description:
TL10-S13302-95 kcal
Thymocytes

source_name: TL10-Radiation-induced thymic lymphoma in 95 kcal group


title: TL11-65 kcal

description:
TL11-S13335-65 kcal
Thymocytes

source_name: TL11-Radiation-induced thymic lymphoma in 65 kcal group


title: dCTCF_C60_1

city: Ithaca

first: Joel

last: Baines

state: NY

address: Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

data_processing:
library strategy: PRO-seq
Data was processed using Danko lab PRO-Seq pipeline, available here: https://github.com/Danko-Lab/utils/tree/master/proseq
BigWig files can views on IGV genome browser: www.broadinstitute.org/igv/
Assembly: concatenated Hg38, Dm3 and EBV (NC_007605.1) genomes
Supplementary files format and content: BigWig file containing strand specific single base pair position of the 3' read

source_name: B95-8 LCL

growth_protocol: LCLs were maintained RPMI 1640 medium supplemented with 15% fetal bovine serum and pen/strep in a 5% CO2 incubator at 37°C

extract_protocol:
Nuclei were isolated and nuclear run-on performed with biotinylated nucleotides. Biotinylated RNA transcripts were isolated using streptavidin coated magnetic beads.
Constructed as detailed in Mahat et al. 2016. "Base-pair-resolution genome-wide mapping of active RNA Polymerases using precision nuclear run-on (PRO-seq). Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086

treatment_protocol: LCLs were treated with DMSO (latency) or C60 to induce reactivation

value: B95-8 LCL

value: EBV transformed B-cell

tag: virus

value: B95-8 ΔCTCF EBV


title: TL4-95 kcal

description:
TL4-S12768-95 kcal
Thymocytes

source_name: TL4-Radiation-induced thymic lymphoma in 95 kcal group


title: Cardiac left ventricle - WT_P20 - Rep3


title: TL18-65 kcal

description:
TL18-S16758-65 kcal
Thymocytes

source_name: TL18-Radiation-induced thymic lymphoma in 65 kcal group


title: TL8-95 kcal

description:
TL8-S13120-95 kcal
Thymocytes

source_name: TL8-Radiation-induced thymic lymphoma in 95 kcal group


title: dCTCF_C60_2

tag: cell type


title: CTERM 3HR REP2

value: Dexamethasone


title: iPD9

city: Barcelona

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

country: Spain

institute: Fundacio Clinic/IDIBAPS

description: miRNA array serum Parkinson

hyb_protocol: In the discovery genome-wide miRNA expression analysis, serum miRNA samples were hybridized individually and blind to operator for 42 hours onto Affymetrix GeneChip miRNA 4.0 Array (Applied Biosystems #902411; product datasheet), which contains probes for more than 4,603 human miRNAs (2,578 mature miRNAs and 2,025 pre-miRNAs) following manufacturer instructions.

scan_protocol: Images were scanned using an Affymetrix GeneChip Scanner 3,000 7G following the manufacturer's recommendations. Files generated by the Affymetrix GeneChip Command Console (AGCC) were processed with the Expression Console software to determine the data quality.

data_processing:
Files generated by the Affymetrix GeneChip Command Console (AGCC) were processed with the Expression Console software to determine the data quality. Microarray raw data were analysed using Partek Genomic Suite v7.0 software applying the robust multi-array average (RMA) background correction model, which allows the relative comparison of miRNA abundance in different arrays.Only miRNAs with fluorescence detection values above 2.4 arbitrary units and a significant expression P-value below 0.05 compared to background were considered expressed in human serum samples
Normalized gene level expression values. Partek Genomic Suite v7.0 software applying the robust multi-array average (RMA) background correction model

label: biotin

source_name: serum

label_protocol: standard Affymetrix protocol

extract_protocol: A total of 5ml peripheral blood was collected in tubes without anticoagulant (BD Vacutainer) and centrifuged 10 minutes at 1500xg and 4°C. Serum was aliquoted into polypropylene CryoTubes (Greiner Bio-One) and kept at −80°C until use. Total miRNA enriched RNA was extracted using the miRNeasy Serum/Plasma Kit (QIAGEN #217184) following manufacturer recommendations. As a carrier for miRNA isolation, we added 2ul of diluted yeast tRNA (Invitrogen #AM7119) into 200ul of serum for a final concentration of 10ug/ml. RNA concentration was determined for all samples on a NanoDrop ND-3300 fluorospectrometer (Thermo Fisher Sci.), and miRNA quality was evaluated for a subset of randomly selected samples by electropherogram using an Bioanalizer Small RNA Kit (Agilent #5067-1548).

tag: group

value: iPD

value: H


title: dCTCF_DMSO_2

tag: time

value: DMSO


title: dCTCF_DMSO_1


title: TL2-65 kcal

description:
TL2-S12705-65 kcal
Thymocytes

source_name: TL2-Radiation-induced thymic lymphoma in 65 kcal group

tag: strain


title: WT_C60_2

value: B95-8 EBV


title: iPD8

description: miRNA array serum Parkinson

treatment_protocol: A total of 5ml peripheral blood was collected in tubes without anticoagulant (BD Vacutainer) and centrifuged 10 minutes at 1500xg and 4°C. Serum was aliquoted into polypropylene CryoTubes (Greiner Bio-One) and kept at −80°C until use.

value: M


title: CTERM 3HR REP1

source_name: HeLa


title: CTERM_0HR_REP4


title: H35R_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13

city: Bethesda

first: Massimiliano

last: Bissa

state: MD

address: 9000 Rockville Pike, bldg 41/ room c303

department: NCI/CCR

institute: National Institutes of Health

data_processing:
An average number of reads of 1x10 millions million reads/sample were acquired with a read length of 76 nucleotides and with a single-end read
Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina, Inc.)
FASTQ data were checked using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Annotation of the obtained sequences was performed using the following reference annotations: Organism Macaca mulatta; Reference genome Mmul 1; Annotation reference: miRbase 20.
mirDeep2 was used for quantification
Raw counts of miR-Seq were TPM-scaled and quantile normalized to generate the levels of miRs.
Genome_build: Organism Macaca mulatta / Reference genome Mmul 1 / Annotation reference: miRbase 20
Supplementary_files_format_and_content: TXT file containing normalized miRNA counts, tab-separated

organism: Macaca mulatta

source_name: Extracellular vesicles

growth_protocol: Forty juvenile (young, average age 3.45 years, 0.545 SD) and twenty-eight adult (old, average age 7.98 years and 2.60 SD) macaques were assigned to four groups based on their major histocompatibility status, age, and weight. Thirteen young and seventeen old macaques were immunized twice with DNA-SIV at weeks 0 and 4. At weeks 8 and 12 all 30 macaques were boosted with intramuscular inoculations of 108 Plaque Forming Units (PFU) of recombinant ALVAC (vCP2432). At week 12, vaccinated macaques also received 200 μg each of SIVmac251 – M766 and SIVsmE660 – CG7V gp120-gD proteins formulated in alum Alhydrogel. Plasma collected at baseline from 7 young animals and 1 week following vaccination (week 13) from all vaccinated animals was used for extracellular vesicles (EVs) isolation.

extract_protocol:
EVs isolated from plasma were processed by Exiqon, Inc. (Woburn, MA). The RNA was isolated from EVs by following a proprietary RNA isolation protocol optimized for serum/plasma (no carrier added). At the end of the isolation the total RNA was eluted in ultra-low volume.
The library preparation was done using the QIAseq miRNA Library Kit (Ref #331502, Qiagen). A total of 5 μl of total RNA isolated from EVs was converted into microRNA NGS libraries. Adapters containing UMIs were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (22 cycles) and the indices were added during PCR amplification. After amplification, the samples were purified. Library preparation quality control was performed using either Bioanalyzer 2100 or TapeStation 4200 (Agilent technologies, Santa Clara, CA). The libraries were pooled in equimolar ratios based on quality of the inserts and concentration measurements. The library pools were quantified using Qubit, then sequenced on a NextSeq500 sequencing instrument (Illumina, Inc.) according to the manufacturer’s instructions.

treatment_protocol: After collection plasma was isolated by centrifugation at 2100 rpm for 30 min at 20°C and then stored at -80°C. EVs were isolated from plasma as described previously(Thery, C.et al.. Isolation and characterization of exosomes from cell culture supernatants and biological fluids. Curr Protoc Cell Biol Chapter 3, Unit 3 22 (2006))  with minor modifications. Briefly, 1 mL of plasma was thawed in ice, centrifuged at 300 xg for 10 min at 4°C to remove possible remaining cells, then transferred to clean tube and centrifuged at 2000 xg for 10 min at 4°C to remove dead cells. Supernatants were collected and centrifuged at high-speed at 10,000 xg for 30 min at 4°C to remove any remaining cell debris. Following centrifugation, supernatants were transferred to ultracentrifuge tubes (Ref #326814, Beckman Coulter, Brea, CA), diluted with cold sterile phosphate-buffered saline (PBS, pH 7.4) and centrifuged at 25,000 rpm for 2 h at 4°C. Pellets containing EVs were resuspended in 350 µl of PBS and stored at -80°C.

tag: sample type

value: EVs

tag: time-point

tag: animal id

value: Young

tag: vaccination

tag: protocol

tag: study

value: Study 1

tag: time of acquisition


title: H35H_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13

tag: age


title: WT_C60_1

tag: cell line

tag: treatment


title: Cardiac left ventricle - Efnb1cKO_P20 - Rep1

tag: genotype

value: Male

tag: tissue


title: TL6-95 kcal

description:
TL6-S12789-95 kcal
Thymocytes

source_name: TL6-Radiation-induced thymic lymphoma in 95 kcal group

tag: Sex

tag: calorie

value: 95 kcal/week

value: Thymic lymphoma

source_name: Ear obtained from the same individual

value: Ear


title: CTERM_0HR_REP3

value: HeLa

tag: cell type

value: Cervical cancer cells


title: iPD4

description: miRNA array serum Parkinson

tag: group


title: TL5-95 kcal

description:
TL5-S12788-95 kcal
Thymocytes

source_name: TL5-Radiation-induced thymic lymphoma in 95 kcal group

tag: strain


title: TL7-95 kcal

description:
TL7-S13012-95 kcal
Thymocytes

source_name: TL7-Radiation-induced thymic lymphoma in 95 kcal group


title: TL1-95 kcal

description:
TL1-S12657-95 kcal
Thymocytes

source_name: TL1-Radiation-induced thymic lymphoma in 95 kcal group


title: WT_DMSO_2

value: B95-8 LCL

value: EBV transformed B-cell

tag: virus

tag: time


title: H28V_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13

tag: sample type

tag: time-point

tag: animal id


title: TL3-95 kcal

description:
TL3-S12767-95 kcal
Thymocytes

source_name: TL3-Radiation-induced thymic lymphoma in 95 kcal group


title: CTERM_0HR_REP2


title: CTERM_0HR_REP1


title: iPD2

description: miRNA array serum Parkinson


title: WT_DMSO_1


title: iPD6

description: miRNA array serum Parkinson


title: S2.3

city: Duarte

first: Charles

middle: David

last: Warden

state: CA

address: 1500 East Duarte Rd

department: Department of Molecular and Cellular Biology

institute: City of Hope

description: RNA-Seq data, Resistant+Sotorasib, replicate 2

data_processing:
Real Time Analysis (RTA, v1.18.64) was used for base calling, and bcl2fastq v2.18 was used to generate FASTQ files
Reads aligned using STAR (version 2.5), with --twopassMode Basic --outSAMstrandField intronMotif
Unique reads quantified using htseq-count (version 0.9.1), with database generated from TxDb.Hsapiens.UCSC. hg38.knownGene (Bioconductor annotations, downloaded 8/30/2018).
Genome_build: hg38
Supplementary_files_format_and_content: FPKM normalized expression (using aligned reads and TxDb annotations in R) and read counts (calculated using htseq-count)

molecule: polyA RNA

source_name: Resistant+Sotorasib, replicate 2

growth_protocol: lNSCLC cell lines H23 was obtained from American Type Culture Collection (ATCC) (Manassas, VA, USA). It was cultured in RPMI 1640 medium (Corning) supplemented with fetal bovine serum (FBS) (10%), L-glutamine (2 mM), penicillin/streptomycin (50 U/ml), sodium pyruvate (1 mM), and sodium bicarbonate (0.075%) at 37°C, 5% CO2

extract_protocol:
Total RNA isolation and on-column DNase digestion from cells were performed basing on the manufacturer’s protocol RNeasy Plus Mini Kit (Qiagen Cat #: 74134).
KAPA Stranded RNA-Seq Kit

treatment_protocol: H23 cell untreated (parent), H23 sotorasib treated (Parent Treated) and H23 cells resistant to 7.5µM treated with sotorasib (Resistant treated).  Treatment was initiated using a dose of 1µM sotorasib and eventually raised to 7.5µM.  The parental and resistant cells were seeded in fresh medium and treated with the 3.2 µM (IC50 concentration) of sotorasib for 3 days

value: Resistant+Sotorasib

value: 45 Days

tag: tin

tag: barcode

value: CAGATC

tag: lane


title: H24H_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13

tag: age

tag: vaccination

tag: protocol

tag: study

tag: time of acquisition


title: iPD13

description: miRNA array serum Parkinson

value: iPD

tag: Sex

value: H


title: iPD5

description: miRNA array serum Parkinson


title: H28T_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: S2.2

description: RNA-Seq data, Parent+Sotorasib, replicate 2

source_name: Parent+Sotorasib, replicate 2

value: Parent+Sotorasib

value: 3 Days

value: GCCAAT


title: PDX4 H1047R

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to hg19 whole genome using HISAT2 (Galaxy tool version2.1.0). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.2).  UCSC known transcripts were supplied in GTF format file.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UCSC genes and their FPKM values along with confidence intervals for each sample.

source_name: Patient-derived primary GBM cell line

growth_protocol: Patient-derived primary GBM cell lines were maintained in neurosphere media (DMEM/F12 (ThermoFisher, 11320082), supplemented with B27 (1X, ThermoFisher, 17504001), bFGF (20ng/mL, Peprotech, 100-18B), and EGF (20ng/mL, Peprotech, 100-47)).

extract_protocol:
tissue samples were harvested with the aid of a fluorescence microscope from end stage tumors, dissecting out the GFP-positive tumor tissue, minced into ~30mg pieces, snap frozen on dry ice, and stored at -80°C. Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, #74134) according to the manufacturer’s protocol. Samples were prepared in biological replicates, n ≥ 3 per genotype. RNA integrity (RIN ≥ 8.0) was confirmed using the High Sensitivity RNA Analysis Kit (AATI, DNF-472-0500) on a 12-Capillary Fragment Analyzer.
Illumina sequencing libraries with 6-bp single indices were constructed from 1 μg total RNA using the TruSeq Stranded mRNA LT kit (Illumina, RS-122-2101). The resulting library was validated using the Standard Sensitivity NGS Fragment Analysis Kit (AATI, DNF-473-0500) on a 12-Capillary Fragment Analyzer. Equal concentrations (2nM) of libraries were pooled and subjected to sequencing of approximately 20 million reads per sample using the Mid Output v2 kit (Illumina, FC-404-2001) on a Illumina NextSeq550 following the manufacturer’s instructions.

treatment_protocol: Cells were lentivirally infected with different PIK3CA mutants (or a mCherry control reporter). After 48 hours infection, cells were selected for by puromycin (1µg/mL, ThermoFisher, A1113803). 50,000 live cells were stereotaxically transplanted into the brains of 6 week old male ICR-SCID (Taconic, ICRSC-M) mouse brains (from bregma, cells were injected 1.0mm lateral, 2.0mm caudal, 2.5mm ventral).

tag: tissue

value: Patient-derived primary GBM cell line

tag: lentivirus infection

value: H1047R PIK3CA mutant


title: PDX3 H1047R


title: H28Y_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13

value: EVs

value: Young

value: Study 1


title: iPD12-2

description: miRNA array serum Parkinson

tag: group


title: H24G_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: S2.1

description: RNA-Seq data, Control, replicate 2

source_name: Control, replicate 2

value: Control

value: 0 Days

value: TGACCA


title: PDX2 H1047R


title: iPD11-2

description: miRNA array serum Parkinson

value: M


title: PDX1 H1047R


title: iPD10-2

description: miRNA array serum Parkinson


title: PDX4 C420R

value: C420R PIK3CA mutant


title: H22F_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: S1.3

description: RNA-Seq data, Resistant+Sotorasib, replicate 1

source_name: Resistant+Sotorasib, replicate 1

value: Resistant+Sotorasib

value: 45 Days

value: TTAGGC


title: H24D_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: iPD1

description: miRNA array serum Parkinson

value: iPD

value: H


title: H22E_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: PDX3 C420R


title: PDX2 C420R


title: S1.1

description: RNA-Seq data, Control, replicate 1

source_name: Control, replicate 1

value: ATCACG


title: H22D_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: P8

description: miRNA array serum Parkinson

value: DaT-negative L2NMCal


title: H21Y_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: PDX4 R88Q

value: Patient-derived primary GBM cell line

value: R88Q PIK3CA mutant


title: P7

description: miRNA array serum Parkinson


title: LP-1_500nM_JQ1_30min_GRO-seq_rep2

city: Cambridge

first: Barbara

middle: M

last: Bryant

state: MA

address: 215 First Street

institute: Constellation Pharmaceuticals

description: nascent RNA

data_processing:
Library strategy: GRO-seq
Reads from GRO-seq were mapped to the hg19 version of the human genome using BWA version 0.7.10. Duplicate reads were removed using samtools’ sort and rmdup functions.
GRO-seq data was normalized to reads per kilobase of measured interval, per million mappable bases. Normalized reads over the interval from +1 kb to +11 kb downstream of the TSS was used to define expression and log2 fold change expression.
IGVTools count was run with an extension of 100 and a window size of 25 bp to generate coverage signal in TDF and WIG formats. The WIG files were scaled to a mean of 1.0 assuming an effective genome size of 2,700,000,000 bases.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including normalized expression data and log fold change values for treated vs. untreated, Groseq signal in enhancers and wig files

growth_protocol: LP-1 cells were cultured at 37 ˚C under 5% CO2 in IMDM medium supplemented with 10% fetal bovine serum, 100U/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
Briefly, nuclei were isolated and nuclear run-on reactions were performed in the presence of ATP, GTP, CTP and BrdU.  RNA was isolated and base hydrolyzed to ~100 nt.  Nascent RNA was isolated using anti-BrdU antibodies conjugated to agarose beads.
Briefly, A poly A tail was added to each nascent RNA and used to prime first strand cDNA synthesis that added Illumina adaptors to one end of each nascent RNA.  First strand cDNA was circularized and digested to give linear cDNAs flanked by adaptor sequences.  Linear cDNAs were PCR amplified for 16 cycles. Libraries were size selected (175-400 bp) on a 2% agarose gel.

treatment_protocol: LP-1 cells were treated with DMSO or 0.5 μM JQ1 for 10 min, or with 0.5 μM JQ1 for 30 min.

tag: cell line

tag: cell type

value: multiple myeloma


title: LP-1_500nM_JQ1_10min_GRO-seq_rep2

description: nascent RNA


title: iPD3

description: miRNA array serum Parkinson


title: H02V_Young_DNA/DNA/ALVAC/ALVAC+gp120_week13

tag: sample type

value: EVs

value: Young


title: P6

description: miRNA array serum Parkinson


title: LP-1_DMSO_10min_GRO-seq_rep2

description: nascent RNA


title: H34F_Young_DNA/DNA/ALVAC/ALVAC+gp120_Baseline

tag: time-point

value: Baseline

value: Study 1


title: P5

description: miRNA array serum Parkinson


title: S1.2

description: RNA-Seq data, Parent+Sotorasib, replicate 1

source_name: Parent+Sotorasib, replicate 1

value: Parent+Sotorasib

tag: time

value: 3 Days

value: CGATGT


title: H30G_Young_DNA/DNA/ALVAC/ALVAC+gp120_Baseline

tag: animal id


title: PDX1 R88Q


title: PDX2 R88Q


title: P9

description: miRNA array serum Parkinson

source_name: serum

value: DaT-positive L2NMCered

value: M


title: LP-1_500nM_JQ1_30min_GRO-seq_rep1

description: nascent RNA


title: PDX4 mCherry

value: mCherry control reporter


title: H29N_Young_DNA/DNA/ALVAC/ALVAC+gp120_Baseline


title: LP-1_500nM_JQ1_10min_GRO-seq_rep1

description: nascent RNA


title: LP-1_DMSO_10min_GRO-seq_rep1

description: nascent RNA


title: P31

description: miRNA array serum Parkinson


title: P30

description: miRNA array serum Parkinson


title: P3

description: miRNA array serum Parkinson


title: LP-1_DMSO_4h_Input_ChIP-seq_rep2

description: ChIP antibody: none (input)

data_processing:
Reads from ChIP-seq were mapped to the hg19 version of the human genome using BWA version 0.7.10. Duplicate reads were removed using samtools’ sort and rmdup functions.
IGVTools count was run with an extension of 100 and a window size of 25 bp to generate coverage signal in WIG format. The WIG files were scaled to a mean of 1.0 assuming an effective genome size of 2,700,000,000 bases.
Genome_build: hg19
Supplementary_files_format_and_content: bed file with enhancers, tab-delimited text file including BRD4 ChIP-seq signal in enhancers and promoters and wig files

extract_protocol:
Cells were incubated in lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.2 % NP-40) for 1 hour at 4 ˚C.  Chromatin was digested at a concentration of 25 x106 cells/mL with 350 U/mL MNase (Roche,10107921001) for 20 minutes at RT in MNase reaction buffer (55 mM Tris-HCl pH 7.5, 0.05 mM EDTA, 2.5 mM MgAc2, 12.5 % glycerol, 25 mM KCl, 4 mM MgCl2, 1 mM CaCl2).  The digestion was stopped with 10 mM EDTA.  The chromatin was then sonicated with a 550 Sonic Dismembrator (Fisher Scientific) on power 4, using cycles of 0.7 seconds on and 1.4 seconds off for a total processing time of 3 minutes.  Lysates were centrifuged at 21,000 x g for 10 min at 4 ˚C.  5 x106 cell equivalents were used for each ChIP assay, diluted to 1 mL with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 1.2 mM EDTA, 1.1% Triton-X 100, 167 mM NaCl, 0.01 % SDS).  Chromatin was pre-cleared for 2 hours at 4 ˚C with Protein A Dynabeads (Life Technologies,10001D) in blocking buffer (1x PBS, 0.5 % BSA, 0.1% Tween-20).  Beads were captured and pre-cleared chromatin was incubated with antibodies overnight at 4 ˚C.  Samples were then incubated with Protein A Dynabeads in blocking buffer for 2 hours at 4 ˚C.  Beads were washed 3x with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate, 0.1 % SDS) and 1x with RIPA high salt buffer (10 mM Tris-HCl pH 8.0, 360 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate, 0.1 % SDS).  Bound chromatin was eluted with elution buffer (10 mM Tris-HCl, 1 % SDS, 300 mM NaCl, 10 mM EDTA pH 8.0).  Crosslinks were reversed by incubation at 65 ˚C for 6 hours.  Eluted chromatin was treated with 150 U/mL RNase A for 30 minutes at 37 ˚C and digested with 75 µg/mL proteinase K for 1 hour at 55 ˚C. ChIP DNA was purified with using a MinElute PCR Purification Kit (QIAGEN) and quantified with a Qubit fluorimeter (Life Technologies).
Library DNA fragments for BRD4, RNAPII, RNAPIISer2P ChIP and input DNA were ligated to Illumina adapters and size selected (200-250 bp) on a 2% agarose gel and PCR amplified for 18 cycles.  Libraries of H3K27ac ChIP and input DNA were constructed using an Ovation Ultralow DR Multiplex System Kit (NuGEN) using 15 cycles of amplification. Libraries were size selected (250-300 bp) on a 2% agarose gel.

treatment_protocol: LP-1 cells were treated with DMSO or 0.5 μM JQ1 for 4 hours.  Cells were fixed with 1% formaldehyde by the addition of 37% formaldehyde directly to the culture medium.  Cells were fixed for 10 minutes at room temperature (RT) and quenched with 0.125 M glycine, pH 7.9.


title: PDX3 mCherry


title: PDX3 R88Q


title: P28

description: miRNA array serum Parkinson


title: H24C_Young_DNA/DNA/ALVAC/ALVAC+gp120_Baseline


title: LP-1_500nM_CPI203_4h_H3K27ac_ChIP-seq

description: ChIP antibody: H3K27ac (Abcam, ab4729)


title: H22H_Young_DNA/DNA/ALVAC/ALVAC+gp120_Baseline


title: P27

description: miRNA array serum Parkinson


title: PDX1 mCherry


title: H22E_Young_DNA/DNA/ALVAC/ALVAC+gp120_Baseline


title: LP-1_DMSO_4h_H3K27ac_ChIP-seq

description: ChIP antibody: H3K27ac (Abcam, ab4729)


title: H02V_Young_DNA/DNA/ALVAC/ALVAC+gp120_Baseline


title: P25

description: miRNA array serum Parkinson


title: LP-1_DMSO_4h_RNA-seq_rep2

data_processing:
Reads from RNA-seq were mapped to the hg19 version of the human genome using TopHat v1.4.1 with parameters –p 2 --library-type fr-unstranded. The hg19 bowtie genome index was downloaded from ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/. Duplicate read pairs were removed prior to further processing.
Cufflinks was run against reference transcriptome Homo_sapiens.GRCh37.73.chr.gtf, obtained from ftp://ftp.ensembl.org/pub/release-73/gtf/homo_sapiens/Homo_sapiens.GRCh37.73.gtf.gz, with parameters --no-effective-length-correction and --library-type fr-unstranded. Failed expression estimate attempts were set to NA and ignored for the rest of the analyses. We worked with regularized log expression data, calculated by adding 1.0 to Cufflink’s RPKM expression estimates and taking the log base 2. Log fold change values were then calculated by taking the difference between regularized log expression values.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes regularized log expression data and log fold change values for treated vs. untreated

extract_protocol:
Cells were counted using a Countess Automated Cell Counter (Life Technologies).  Equal numbers of cells for each sample were used for total RNA isolation: Cells were harvested, lysed directly in 1 mL Trizol Reagent (Life Technologies) and incubated for 5 minutes at room temperature.  200 µL chloroform was added to each sample, and samples were shaken for 15 seconds, followed by a 3 minute incubation at room temperature. Samples were spun at 15,000 x g for 15 minutes at 4 ˚C.  The aqueous layer was removed and RNA was purified using an RNeasy Mini Kit (QIAGEN) with on-column DNase digestion. Equal amounts of ERCC RNA spike-in mix 1 (Life Technologies) were added to each sample, to give the same amount of synthetic spike-in RNA per cell equivalent across samples
500 ng of total RNA were used for library construction using the TruSeq RNA Sample Preparation Kit v2 (Illumina)

treatment_protocol: LP-1 cells were treated with DMSO or 0.5 μM JQ1 for 4 hours.


title: Tregs, Vein_3

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v12.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Genome_build: GRCm38

source_name: Live CD45+CD4+EGFP[Foxp3]+CD69+ T cells

extract_protocol:
FACS-sorted CD45+CD4+EGFP[Foxp3]+CD69+ Treg of IVC-ligated DEREG mice were directly collected in RNA extraction buffer (RLT-buffer supplemented with beta-Mercaptoethanol)
Quantity of total RNA was assessed by Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Full-length cDNA was prepared from 2 ng total RNA (RIN>8) using Takarabio's SmartSeq v4 Kit with a final cDNA amplification of 12 cycles. Barcoded sequencing libraries were prepared from 1ng full-length cDNA using Illumina's Nextera XT kit according to the manual. Quantity of final libaries was assessed by Qubit 2.0 and average size was determined on a Bioanalyzer 8Agilent) using a HS DNA chip.

treatment_protocol: Deep Vein Thrombosis induced by vena cava ligation (IVC; flow reduction model).Thrombus formation confirmed in live animals by ultrasound. Isolation of spleens, thrombi and vein walls at day 14 after thrombus induction.

tag: strain

value: vein wall tissue

value: CD69+ vein wall Treg

tag: exp


title: T112_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13

tag: age

value: Old


title: P23

description: miRNA array serum Parkinson

value: H


title: LP-1_DMSO_4h_RNA-seq_rep1


title: LP-1_500nM_JQ1_4h_RNA-seq_rep2


title: P21

description: miRNA array serum Parkinson

value: DaT-negative L2NMCal


title: Tregs, Vein_2


title: LP-1_500nM_JQ1_4h_RNA-seq_rep1


title: PDX2 mCherry

value: Patient-derived primary GBM cell line


title: R968_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13

tag: vaccination


title: P20

description: miRNA array serum Parkinson


title: R966_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13

tag: protocol


title: Tregs, Thrombus_4

value: thrombus

value: CD69+ thrombus Treg


title: Tregs, Vein_1


title: WT7St

description: WT_Stromal, sample 3

data_processing:
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat2, and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: mouse prostate cells

growth_protocol: All animals used in this study received humane care in compliance with the principles stated in the Guide for the Care and Use of Laboratory Animals, NIH Publication, 1996 edition, and the protocol was approved by the Institutional Animal Care Committee of University of Washington. The C57BL/6 and SCID/Beige mice were purchased from Charles River (Wilmington, MA). Lgr5-DTR-eGFP mice were originally generated by Genentech (PMID: 21927002) and were kindly provided by Dr. Noah Schroyer at the Baylor College of Medicine.

extract_protocol:
NucleoSpin RNA XS Kit (Macherey-Nagel, Bethlehem, PA) was used to purify RNAs from FACS-isolated mouse prostate basal, luminal and stromal cells. Reverse transcriptions were performed using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech Laboratories, Mountain View, CA).
CDNA libraries were prepared using Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA), and were sequenced using HiSeq 2500 sequencer.

treatment_protocol: Dissociated single mouse prostate cells were incubated with florescence conjugated antibodies at 4℃ for 30 minutes. FACS analyses and sorting were performed using the BD LSR II and Aria III (BD Biosciences, San Jose, CA), respectively.

tag: genotype/variation

value: wild type

tag: facs-isolated cells

value: Stromal


title: Tregs, Thrombus_3


title: R963_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13

source_name: Extracellular vesicles

value: EVs

tag: study

value: Study 1

tag: time of acquisition


title: Tregs, Vein_4

tag: tissue


title: WT6Lu

description: WT_Luminal, sample 3

value: Luminal


title: P2

description: miRNA array serum Parkinson

tag: group

tag: Sex


title: R962_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: WT6Ba

description: WT_Basal, sample 3

value: Basal


title: P24

description: miRNA array serum Parkinson


title: P18

description: miRNA array serum Parkinson

value: DaT-positive L2NMCered


title: Tregs, Thrombus_1

tag: cell type


title: R976_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13

tag: sample type


title: R960_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13

tag: time-point


title: P16

description: miRNA array serum Parkinson

value: M


title: WT5Ba

description: WT_Basal, sample 2


title: WT5Lu

description: WT_Luminal, sample 2


title: R958_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: Tregs, Spleen_4

value: spleen

value: CD69+ splenic Treg


title: P15

description: miRNA array serum Parkinson


title: R957_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: WT3St

description: WT_Stromal, sample 2


title: P14

description: miRNA array serum Parkinson


title: WT3Lu

description: WT_Luminal, sample 1


title: Tregs, Spleen_1


title: T127_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: Tregs, Thrombus_2


title: WT3Ba

description: WT_Basal, sample 1


title: P11

description: miRNA array serum Parkinson


title: MM6_01-24-17 (Mut)

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

source_name: Primary mouse rib chondrocytes

growth_protocol: Mouse rib primary chondrocytes were collected immidetely after isolation to retain the chondrocyte phenotypes

extract_protocol:
Cells were scraped in TRIzol reagent total RNA was isolated using phenol-chloroform extraction using Invitrogen PureLink RNA Mini Kit (#12183018A)
RNA sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina). This protocol provides strand specific data while
Simultaneously removing both cytoplasmic and mitochondrial rRNA. Libraries were sequenced on the HiSeq 2500 instruments and 50 million 50 base pair single end
Reads were produced per sample. Data was extracted, de-convoluted based on dual index reads and analyzed using CLC Genomics Workbench software (Qiagen).

treatment_protocol: Wild type (WT) and mutant (MUT) mouse primary rib chondrocytes were isolated following a sequential digestion by pronase (2 mg/ml in PBS) for 30 min at 37°C, collagenase D (3 mg/ml in DMEM) for 1.5 h at 37°C, and overnight at 37°C in collagenase D (1.5 mg/ml in DMEM). Collagenase D digestion was stopped next day by adding FBS. Chondrocytes were washed twice with PBS and cells were collected.

value: Jab1 chondrocyte-specific knockout Jab1flox/flox; Col2a1-Cre (cKO) mutants

value: E18.5 mouse rib tissue


title: MM5_01-24-17 (Mut)


title: WT2St

description: WT_Stromal, sample 1


title: T125_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13

value: Old


title: T126_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: P13

description: miRNA array serum Parkinson

value: H


title: Tregs, Spleen_3


title: P17

description: miRNA array serum Parkinson


title: P10

description: miRNA array serum Parkinson


title: T123_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: P1

description: miRNA array serum Parkinson


title: Tregs, Spleen_2


title: Lgr71St

description: Lgr_Stromal, sample 4


title: MM3_01-24-17(WT)

value: Wild-type primary chondrocytes


title: T128_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: Lgr5St

description: Lgr_Stromal, sample 3


title: Lgr7Lu

description: Lgr_Luminal, sample 3


title: LPD9

description: miRNA array serum Parkinson


title: LPD8

description: miRNA array serum Parkinson


title: T115_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: Lgr4St

description: Lgr_Stromal, sample 2


title: T114_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13


title: MM1A_01-30-17 (WT)


title: Lgr4Lu

description: Lgr_Luminal, sample 2


title: MM4_01-24-17 (Mut)


title: Lgr4Ba

description: Lgr_Basal, sample 3


title: 8/16 PB

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat (Galaxy tool version 2.1.0). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0).  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: prostate luminal cells

extract_protocol:
These libraries were prepared using SMART-Seq v4 Ultra-Low-Input RNA Kit & Illumina Nextera XT Library Prep Kit.
Total RNA samples were made into cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (using both random priming and poly d(T) priming). cDNA from the SMART kit were taken into the Illumina TruSeq DNA Sample Prep Kit for library construction. Completed libraries were sequenced on the Illumina HiSeq 2500.

treatment_protocol: We generated a transgenic mouse harboring mouse Csf-1 transgene driven by the rat probasin promoter. Luminal cells from the 4 month old transgenic mice and WT littermate controls were FACS isolated.

value: prostate luminal cells

value: over-expression of CSF1


title: LPD6

description: miRNA array serum Parkinson


title: Rec_T_B

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

institute: University of Birmingham

description: 3 days of recovery from stress with Tenofovir rep2

data_processing:
Trimmomatic (Bolger et al., 2014) was used to remove adapters and discard low-quality reads.
The cleaned reads were mapped to Arabidopsis reference genome (TAIR10 version) by TopHat2 (Kim et al., 2013).
Picard tools (available from http://broadinstitute.github.io/picard/) was used to discard duplicated reads.
Mapped reads from TopHat2 analysis were subsequently counted using htseq-count (Anders et al., 2015), and the raw count per gene was used to determine differentially expressed genes between control and Tenofovir-treated samples using DESeq (Anders and Huber, 2010) and default parameters. Genes with a significance p-value below 0.05 after Benjamini and Hochberg correction were considered to be differentially expressed
Genome_build: TAIR10
Supplementary_files_format_and_content: For each genotype, the bigwig coverage file is provided, generated with samtools depth (Li et al 2009, Bioinformatics) from the the aligned reads.

organism: Arabidopsis thaliana

source_name: HS3 T+

growth_protocol: Arabidopsis seedlings were grown in plates on ½ MS media (1% sucrose and 0.8% agar, pH5.7) at 20°C under 12h light conditions (12h light/12h dark)

extract_protocol:
Total RNA was isolated from seedlings using the RNeasy Plant Mini Kit (Qiagen), following the manufacturer's instructions. The RNA quality and integrity were assessed on the Agilent 2200 Tape Station.
Libraries for RNA expression analysis were prepared in tripicate from 1 µg of  high-integrity total RNA (RIN>8) using the TrueSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA)  following the manufacturer’s instructions. Libraries quality and fragment sizes were checked with a TapeStation 2200 (Agilent technologies, Santa Clara, CA) instrument.

treatment_protocol: In drug treated plants, Tenofovir (Cayman Chemical, N 13874), was dissolved in DMSO and added to the medium at 10 µM.  One-week old seedlings have been primed by cold treatment for 24°C and immediately transferred to normal growth conditions (Control plants or CS) or to 37°C for 24hr (Heat Stressed or HS) plants. Plants have been collected 24h after heat application (HS0). Tenofovir-treated and control Arabidopsis plants have been subsequently grown at 21°C for the remaining time, and samples have been collected 3 days after heat-stress.

tag: ecotype

value: seedling

value: 12 days

tag: genotype

value: wild-type

tag: treatment

value: Tenofovir 10uM

value: heat stress and recovery


title: LPD5

description: miRNA array serum Parkinson


title: Rec_T_C

description: 3 days of recovery from stress with Tenofovir rep3


title: 8/16 WT

tag: strain

value: wild type


title: T121_Old_DNA/DNA/ALVAC/ALVAC+gp120_week13

value: EVs

tag: animal id

tag: age

value: Study 1


title: 5/16 PB


title: Rec_T_A

description: 3 days of recovery from stress with Tenofovir rep1


title: LPD4

description: miRNA array serum Parkinson

value: M


title: 5/16 WT


title: LPD3

description: miRNA array serum Parkinson


title: LPD7

description: miRNA array serum Parkinson


title: Lgr2St

description: Lgr_Stromal, sample 1

value: Stromal


title: HS_T_B

description: heat stressed with Tenofovir rep2

source_name: HS0 T+

value: 9 days

value: heat stress


title: LPD2

description: miRNA array serum Parkinson


title: LPD13

description: miRNA array serum Parkinson


title: HS_T_A

description: heat stressed with Tenofovir rep1


title: Lgr2Ba

description: Lgr_Basal, sample 1

value: Basal


title: Lgr3Ba

description: Lgr_Basal, sample 2


title: Lgr3Lu

description: Lgr_Luminal, sample 1

value: Luminal


title: Lin-/CD24high/CD49flow/Sca-1+ luminal cells LX2096

description:
Lin-/CD24high/CD49flow/Sca-1+ luminal cells
Sca-1+Luminal

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat (Galaxy tool version 0.9) with parameters -r 100. UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0) with parameters -r 100.  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

growth_protocol: 8∼12-week-old C57BL/6 mouse prostate tissues were digested and dissociated into single cells.  Dissociated single cells were cultured in Biocoat™ Collage I-coated plates (Corning, Corning, NY) in Bfs medium (5% Nu-Serum, 5% FBS, 1 × Insulin/Selenium, 1 × L-Glutamine, 1 × Penicillin/Streptomycin, and 1 × 10−10M DHT in DMEM medium) at 37°C with 5% CO2. When the cell confluency reached around 90%, cells were trypsinized into single cells with 0.25% Trypsin-EDTA (Invitrogen, Carlsbad, CA). Cells were replated in Biocoat™ Collage I-coated plates (Corning, Corning, NY) for 30 min at 37°C/5% CO2. Unattached cells were discarded, and remaining cells were cultured in Bfs at 37°C/5% CO2 till 80%–90% confluency.

extract_protocol:
NucleoSpin RNA Kit from Macherey-Nagel, using manufacturer's protocol.
Total RNA samples were made into cDNA using the NuGEN Ovation® RNA‑Seq System V2 kit (using both random priming and poly d(T) priming). cDNA from the NuGEN kit were taken into the Illumina TruSeq DNA Sample Prep Kit for library construction. Completed libraries were sequenced on the Illumina HiSeq 2500.

treatment_protocol: Dissociated single mouse prostate cells were incubated with florescence conjugated antibodies at 4°C for 30 minutes. FACS analyses and sorting were performed by using the BD LSR II, BD LSR Fortessa, Aria I (BD Biosciences, San Jose, CA).


title: T5_F3

city: Legnaro

first: Giovanni Battista

last: Tornielli

state: Padova

address: Viale dell'Università, 16

department: DAFNAE

country: Italy

institute: University of Padova

data_processing:
base-calling and demultiplexing
adapter clipping and quality filtering with Trimmomatic 0.39
alignments were performed with TopHat
read counts with featureCounts
Differential expression analysis usignDESeq2 (v1.30)
Assembly: Vitis vinifera genome based on the pinot noir genome (Genoscope 12X; Jaillon et al. 2007)
Supplementary files format and content: raw_counts.txt

organism: Vitis vinifera

source_name: berry

extract_protocol:
Total RNA was extracted using perchlorate method
Illumina TruSeq Stranded mRNA Library

treatment_protocol: During the summer, in correspondence with the pre-veraison phase, it was induced for the plants of the second tunnel a gradual reduction of the water supply, up to one state of drought stress (30% of field capacity), followed by the application of a heat wave (+ 5 ° C) lasting one week. The samplings were carried out at T0 (27/06) on controls plants before the gradual cut of irrigation, at T1 (6/07) with overt water stress, immediately before the heat wave, at T2 (10/07) in the middle of the heat wave, at T3 (12/07) at the end of the heat wave, at T4 (21/07) one week after the end of stress, the "recovery" and at T5 (25/07) a technological maturation of the berry, the so called "harvest".

value: berry

tag: variety

value: Sauvignon Blanc

value: Flooded


title: Lin-/CD24high/CD49flow/Sca-1- luminal cells LX2095

description:
Lin-/CD24high/CD49flow/Sca-1- luminal cells
Luminal


title: CC_T_C

description: control with Tenofovir rep3

source_name: CS0 T+

value: seedling

value: not stressed


title: LPD11

description: miRNA array serum Parkinson


title: T5_F2


title: Lin-/CD24high/CD49flow/Sca-1+ luminal cells LX2094


title: T5_F1


title: CC_T_A

description: control with Tenofovir rep1

value: wild-type


title: Lin-/CD24-/CD49f- stromal cells LX2093

description:
Lin-/CD24-/CD49f- stromal cells
Stromal


title: 3/16 WT

value: prostate luminal cells

tag: genotype/variation


title: HS_T_C

description: heat stressed with Tenofovir rep3

value: Tenofovir 10uM


title: 3/16 PB

value: over-expression of CSF1


title: LPD10

description: miRNA array serum Parkinson

value: H


title: T5_FH3

value: drought+heat wave+spring flooding


title: Rec_0_C

description: 3 days of recovery from stress rep3

value: 12 days

value: mock

value: heat stress and recovery


title: LPD1

description: miRNA array serum Parkinson


title: Rec_0_B

description: 3 days of recovery from stress rep2


title: Lin-/CD24high/CD49flow/Sca-1- luminal cells LX2092


title: IPD08

description: miRNA array serum Parkinson

value: iPD

value: M


title: T5_FH1


title: T5_FH2


title: Rec_0_A

description: 3 days of recovery from stress rep1


title: iPD25

description: miRNA array serum Parkinson


title: Lin-/CD24high/CD49flow/Sca-1+ luminal cells LX2090


title: T5_H3

value: drought+heat wave


title: Lin-/CD24low/CD49fhigh basal cells LX2091

description:
Lin-/CD24low/CD49fhigh basal cells
Basal

value: Basal


title: CC_T_B

description: control with Tenofovir rep2

value: 9 days


title: HS_0_C

description: heat stressed rep3

value: heat stress


title: Lin-/CD24-/CD49f- stromal cells LX2089

description:
Lin-/CD24-/CD49f- stromal cells
Stromal

value: Stromal


title: iPD18

description: miRNA array serum Parkinson


title: IPD16

description: miRNA array serum Parkinson


title: T5_H2

value: berry

value: Sauvignon Blanc


title: T5_H1


title: Lin-/CD24high/CD49flow/Sca-1- luminal cells LX2088

value: Luminal


title: HS_0_A

description: heat stressed rep1

value: seedling

value: wild-type


title: Lin-/CD24low/CD49fhigh basal cells LX2087


title: T5_C3

value: Control


title: IPD12-2

description: miRNA array serum Parkinson


title: IPD11-1

description: miRNA array serum Parkinson

value: H


title: T5_C2


title: CC_0_B

description: control rep2

value: not stressed


title: Sentinel lymph node, OSNA S32

city: Coimbra

first: Henriqueta

middle: A. M. B. L. Coimbra

last: Silva

address: Azinhaga Santa Comba, Celas

department: Coimbra Institute for Clinical and Biomedical Research - Center of Investigation on Environment, Genetics and Oncobiology (iCBR-CIMAGO)

country: Portugal

institute: Faculty of Medicine, University of Coimbra

description: Sentinel lymph node, OSNA

data_processing:
Pre-base calling calibration, base calling and alignment arguments, including trim quality cutoff of 15, barcode filtering minimum number of reads set to 10 and wells files normalization, performed automatically and according to manufacturer's default pipeline for the Ion S5 System.
Raw count extraction were obtained by Torrent Suite ImmuneResponseRNA plugin (immuneResponseRNA v5.16.0.0)
Assembly: hg19
Supplementary files format and content: raw_counts_by_oncomine.csv refers to a comma-separated values (csv) file that includes the the raw counts values for each sample.
Supplementary files format and content: normalized_counts_DESeq2.txt refers to a tab-delimited text file that includes normalized counts values using the median of ratios method by DESeq2 R package (version 1.36.0) (Love et al., 2014) for each sample.
Supplementary files format and content: normalized_rlog_.txt refers to a tab-delimited text file that includes normalized counts values using regularized logarithm data transformation (rlog) by DESeq2 R package (version 1.36.0) (Love et al., 2014) for each sample.

source_name: Sentinel lymph node

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini kit (Quiagen). gDNA decontamination was confirmed. Reverse transcription was performed with 10.5 ng of total RNA using Ion TorrenTM NGS Reverse transcription kit (ThermoFisher Scientific)
The Oncomine Immune Response Research Assay – Chef Ready library preparation kit (Thermo Fisher Scientific, Carlsbad, CA, USA) was used for library construction. Automated library preparation, template preparation and subsequent chip loading were performed on the Ion Chef System using the Ion 530 Chef chip kit (ThermoFisher Scientific). For the sequencing step, 25 µl of libraries yielding 50pM were run using the Ion S5 System (ThermoFisher).

value: Sentinel lymph node


title: iPD10-1

description: miRNA array serum Parkinson


title: T5_C1


title: C9

description: miRNA array serum Parkinson


title: Sentinel lymph node, OSNA S30

description: Sentinel lymph node, OSNA


title: Sentinel lymph node, OSNA S29

description: Sentinel lymph node, OSNA


title: T4_F2

value: Flooded


title: Sentinel lymph node, OSNA S31

description: Sentinel lymph node, OSNA


title: CC_0_A

description: control rep1

value: mock


title: C7

description: miRNA array serum Parkinson

value: M


title: T4_F3


title: Sentinel lymph node, OSNA S28

description: Sentinel lymph node, OSNA


title: T4_F1