title: niPSC p0 - primary naïve colonies

status: Public on Dec 31 2018

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

country: Italy

institute: University of Padua

data_processing:
Expression levels for all the genes from ENSEMBL 87 were quantified using RSEM 1.3.0 with STAR 2.5.2b
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Tab delimited file with RSEM output with 7 columns: gene_id, transcript_id, length, effective_length, expected_count, TPM, FPKM

source_name: BJ fibroblasts

extract_protocol:
Total RNA
The library was made using TruSeq Stranded mRNA Library Kit according to the manufacturer's protocol from total RNA.

value: BJ fibroblasts

tag: cell type

value: naive induced pluripotent stem cells

tag: passage

tag: medium

value: RSeT

value: naive pluripotency


title: Td I1-22

status: Public on Jan 01 2019

type: RNA

city: Chiyoda-ku

first: Kazuyuki

last: Ishihara

state: Tokyo

address: Misakicho 2-1-14

department: Microbiolgy

country: Japan

institute: Tokyo Dental College

hyb_protocol: 1. Fragmentation of Cy3 labeled cRNA was carried out at 60°C for 30 min.  2. Stop fragmentation.  3. Hybridization was performed at 65°C for 17 h with agitation in Hybrioven.

scan_protocol: Scanned by Agilent Technologies Microarray Scanner

data_processing: Normalization: Shift to 75 percentile  Baseline Transformation: median of control samples  GeneSpring 13.1.1 software.

molecule: total RNA

organism: Treponema denticola

source_name: Td I-1

label_protocol: Cy3 label with Input Quick-Amp WT Labeling Kit (Agilent Technologies, Santa Clara, CA)

growth_protocol: T. denticola ATCC 35405 or I-1 were inoculated into 100 mL 10% TYGVS and incubated at 37°C under anaerobic conditions for 2 d (to an absorbance at 660 nm of approximately 0.4-0.6).

extract_protocol: TRIzol reagent (Invitorogen, Carlsbad, CA)

treatment_protocol: Td 35405: T. denticola ATCC 35405 grown in medium containing 10% serum  Td I-1: T. denticola I-1 grown in medium containing containing 10% serum

tag: strain

tag: genotype/variation

value: dppA inactivated mutant


title: Td 405-11K

value: Wild type and type strain of the species


title: Td I1-19


title: Td 405-2


title: BJ fibroblasts

type: SRA

library_source: transcriptomic

organism: Homo sapiens

source_name: foreskin

tag: tissue

value: foreskin

value: fibroblast

value: DMEM/FBS

value: newborn


title: IMR90_FIBROBL [RRBS]

library_source: genomic

data_processing:
Sequence reads were trimmed using Trim Galore! Software to remove adapter sequences and low-quality end bases
Sequence reads were trimmed with a custom python script provided by NuGEN Technical Support to remove any read that does not contain an MspI site signature (YGG) at the 5’-end
Reads alignment on genome reference sequence and methylation calling was performed with bismark
Genome_build: hg19
Supplementary_files_format_and_content: Methylation levels on genome locations in UCSC bedGraph fromat

molecule: genomic DNA

source_name: IMR90 fibroblasts

growth_protocol: Fibroblasts were expanded under standard conditions, in DMEM/FBS medium. Naïve iPSCs were cultured in RSeT medium on a feeder layer of MEFs under hypoxic conditions. H9 Reset NK2 cells were expanded in t2iL+Go medium on feeder cells. Primed iPSCs (HPD00) were expanded in mTeSR on Matrigel-coated plates.

extract_protocol: RRBS libraries were produced using the Ovation RRBS Methyl-Seq System (NuGEN) starting from 100ng of genomic DNA extracted with the Quick-DNA Miniprep Plus kit (Zymo Research) according to manufacturer’s specifications

value: IMR90 Fibroblast


title: Progressive 41

city: London

first: Vitor

middle: H

last: Teixeira

address: 5 University Street

department: Medicine

country: United Kingdom

institute: University College London

hyb_protocol: Thermofisher/Affymetrix Human Clariom D GeneChip as per manufacturer's instructions [Fluidics Station 450]

scan_protocol: Affymetrix Scanner 3000 7G as per manufacturer's instructions

data_processing: Processing was performed using R and Bioconductor. Raw data in CEL format were read using the read.celfiles method from the oligo package, and normalised using RMA.

label: biotin

source_name: Human preinvasive lung squamous cell carcinoma lesions

label_protocol: Thermofisher/Affymetrix WT Pico Kit Biotin labelling module as per manufacturer's instructions

extract_protocol: Laser-capture micro-dissection (LCM) was used to selectively isolate CIS cells for molecular analysis, reducing the extent of contamination by stromal cells. RNA was extracted using the High Pure FFPE RNA Kit (Roche Applied Science, West Sussex, UK) according to manufacturer’s protocol. Quantification was carried out using the Quant-iT RNA assay kit and the Qubit® 2.0 fluorometer (Life Technologies, Paisley, UK).

value: Preinvasive lung squamous cell carcinoma lesions

tag: lesion outcome

value: progression


title: BJ_FIBROBL [RRBS]


title: H9_Reset_NK2 [RRBS]

source_name: naive PSC line previously sequenced in Takashima et al. 2014  - Cell

value: embryonic stem cells


title: HFF_FIBROBL [RRBS]

source_name: HFF fibroblasts

value: HFF Fibroblast


title: HPD08 [RRBS]

source_name: novel naive iPSC lines derived from IMR90 fibroblasts

value: lung


title: HPD03 [RRBS]

source_name: novel naive iPSC lines derived from BJ fibroblasts


title: HPD06 [RRBS]

source_name: novel naive iPSC lines derived from HFF fibroblasts


title: HPD07

source_name: WI38 Fibroblast

value: WI38 Fibroblast


title: HPD00 [RRBS]

source_name: primed iPSC line derived from BJ fibroblasts

value: BJ fibroblasts

value: primed pluripotent stem cells

value: mTeSR

value: primed pluripotency


title: HPD08

source_name: IMR90 Fibroblast

value: naive induced pluripotent stem cells

value: RSeT

value: naive pluripotency


title: Progressive 40


title: Progressive 39


title: Progressive 38


title: Progressive 37


title: Progressive 34


title: IMR90 Fibroblasts

source_name: lung

value: fibroblast


title: WI38 Fibroblast

value: DMEM/FBS


title: Progressive 36


title: HPD03


title: HPD00


title: HPD04


title: HPD05


title: H9 Reset NK2

source_name: embryonic stem cells


title: Progressive 35


title: HPD04 [RRBS]


title: MODEK_control_24hrs_3

city: Edinburgh

first: José

middle: Roberto

last: Bermúdez-Barrientos

state: Lothian

address: Charlotte Auerbach Rd

department: Institute of Immunology & Infection

institute: The University of Edinburgh

description: small RNAs

data_processing:
Raw reads were then cleaned and trimmed to remove 3’ adapter using reaper (DOI:10.1016/j.ymeth.2013.06.027) with the following parameters: geom no-bc, mr-tabu 14/2/1, 3p-global 12/2/1, -3p-prefix 8/2/1, -3p-head-to-tail 1, -nnn-check 3/5, -polya 5 -qqq-check 35/10, -tri 35.
Only reads between 18-30 nucleotides were kept, this size filtering was done with a R script and ShortRead package
Only reads that mapped perfectly to the mixed mouse and Heligmosomoides reference (see below) were considered for differential expression analysis, the sequence alignment was done with Bowtie 1.2.2
A count matrix was build with the sequences found in all libraries as rows and the times that sequence was detected in each library (columns).
Genome_build: Mus musculus genome GRCm38.p6 and Heligmosomoides bakeri genome were concatenated and used as a single reference, mouse ribosomal gene BK000964.8123.12852 (silva database) was included in this reference
Supplementary_files_format_and_content: processed data files are fastq files of sRNA-Seq libraries without the adapter and with read lengths 16 – 50 nt
Supplementary_files_format_and_content: reads_matrix.txt: Text individual sequences matrix counts used for differential expression analysis
Supplementary_files_format_and_content: reads_org_map.txt: Text mapping information for each individual sequence. Sequences may map to Heligmosomoides (Hp), mouse (Mm) or both genomes (both)

organism: Mus musculus

source_name: MODE-K cells

growth_protocol: MODE-K cells were maintained as previously described (https://doi.org/10.1016/0022-1759(93)90329-6).

extract_protocol:
Cells were then washed twice in PBS before RNA extraction with a miRNeasy mini kit (Qiagen), according to manufacturer’s instructions. The RNA Integrity Number (RIN) was tested with the Agilent RNA 6000 Pico Kit on a Agilent 2100 Bioanalyzer. Three biological replicates were included for each of the samples.
Small RNA sequencing: Total RNA was treated with RNA 5' Polyphosphatase (Epicenter) following manufacturer's instructions, before library preparation. Libraries for small RNA sequencing were prepared using the CleanTag small RNA library prep kit according to manufacturer’s instruction. For all samples, 1:2 dilutions of both adapters were used with 18 amplification cycles (TriLink BioTechnologies).
Libraries of the length between 140-170bp were size selected and sequenced on an Illumina HiSeq high output v4 50bp SE in Edinburgh Genomics at the University of Edinburgh (Edinburgh, UK).

treatment_protocol: Uptake experiments were carried out with 2.5ug EVs per 50,000 cells for 4 and 24 hrs time points, in a 37oC, 5% CO2 incubator.

tag: treatment

value: no treatment

tag: incubation time

value: 24 hours


title: HPD01 [RRBS]


title: Td 405-1A

value: Wild type and type strain of the species


title: MODEK_control_24hrs_2

description: small RNAs


title: HPD06

source_name: HFF-1 fibroblasts

value: HFF-1 fibroblasts


title: MODEK_control_4hrs_2

description: small RNAs

value: 4 hours


title: MODEK_control_24hrs_1

description: small RNAs


title: MODEK_control_4hrs_1

description: small RNAs


title: HPD01

source_name: BJ fibroblasts


title: 45d WT rep2

city: Shanghai

first: Xiaofen

last: Wu

address: 345 Lingling Rd

department: Shanghai Institute of Organic Chemistry

country: China

institute: Chinese Academy of Sciences

description: M_DESeq normalized-CountSet.txt

data_processing:
Sequencing reads were mapped to UCSC dm6(for sample 27-35) or flybase dm6_r6.05(for sample 1-26, 36-47) with STAR by default parameter.
Read counts for each gene were calculated by HTSeq-count.
Count files were used as input to DESeq for normalization and differential expression analysis.
Genome_build: dm6
Supplementary_files_format_and_content: Processed file with an extension ".csv" is differential expression called using DESeq, with an extension ".txt" is normalized count performed using DESeq.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: fly muscle

growth_protocol: Flies were cultured in standard or antibiotic (500μg/ml ampicillin, 50μg/ml tetracycline, and 200μg/ml rifamycin) media  at 25ºC with 60% humidity. The control (WT) line used was 5905 (FlyBase ID FBst0005905, w1118). The given genotype flies were collected at the day of eclosion and transferred to new vials every other day during aging process.

extract_protocol:
Muscles were removed at the given age, RNA was harvested using Trizol reagent, and polyA tail RNAs were selected.
NEBNext Ultra RNA library Prep Kit for Illumina (NEB, E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: post eclosion day 45

tag: genotype

tag: culture condition

value: Conventional culture

tag: Sex

value: male


title: small RNA-seq of nrpd1a x wild type seeds

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

country: USA

institute: The University of Texas at Austin

data_processing:
Basecalls performed using CASAVA version 1.8
Small RNA sequences were trimmed for 3’ adapters, collapsed into unique sequences and mapped to A. thaliana genome (TAIR10, November 2010 release) using CASHX with perfect match option (http://carringtonlab.org/resources/cashx).
The sequences from chloroplast, mitochondrial, tRNAs, rRNAs, snoRNAs, and snRNAs were excluded from the analysis.
Small RNA reads were normalized by dividing the total number of reads of a library by 10 millions.
Multiple-hit read was assigned equally to each locus and divided by the number of hits in the genome.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample. FIELD #1: chromosome; #2: start; #3: end; #4: strand; #5: small_RNA_length; #6: normalized_read_count

organism: Arabidopsis thaliana

source_name: whole seeds

growth_protocol: All plants were grown under an illumination cycle of 16-h day and 8-h night at 22oC (day) and 20oC (night).

extract_protocol:
Total RNA was extracted using Plant RNA Reagent (Invitrogen, http://www.invitrogen.com/).
Small RNA libraries were prepared as previously described.  In brief, an aliquot of 10 µg of total RNA was resolved in a 15% urea-polyacrylamide gel, and the fraction of 18-30-nt small RNAs was recovered.  For nrpd1a and rdr2 mutants and their crosses, whole seeds dissected from ~20 siliques were used for each library. For manually dissected seed, the embryo, endosperm and seed coat dissected from ~50 siliques were used for each library.  Purified small RNAs were ligated to 5’ and 3’ RNA oligo adapters and reverse transcribed to produce first-strand cDNAs.

treatment_protocol: Flowers in the floral stage 12C were manually emasculated and pollinated at 24 hours after emasculation.  Seeds were collected at designated days after pollination (DAP) for RNA extraction, GUS staining and functional assays.  Wild-type (Col-0) seeds at the linear cotyledon stage (6 DAP)  were manually dissected into embryo, endosperm and seed coat.  Embryos were rinsed three times with 0.3 M Sorbitol before RNA extraction.

tag: ecotype

tag: cross

value: nrpd1a x wild type

value: whole seeds

tag: Stage

value: 6 Days After Pollination


title: small RNA-seq of rdr2 x wild type

value: rdr2 x wild type


title: small RNA-seq of wild type x rdr2 seeds

value: wild type x rdr2


title: 45d WT rep1

description: M_DESeq normalized-CountSet.txt


title: small RNA-seq of wild type x nrpd1a seeds

value: wild type x nrpd1a


title: small RNA-seq of nrpd1a x nrpd1a seeds

value: nrpd1a x nrpd1a


title: 45d WT rep3

description: M_DESeq normalized-CountSet.txt


title: small RNA-seq of rdr2 x rdr2 seeds

value: rdr2 x rdr2


title: 30d WT rep2

description: M_DESeq normalized-CountSet.txt

value: post eclosion day 30


title: 30d WT rep1

description: M_DESeq normalized-CountSet.txt


title: 3d WT rep2

description: M_DESeq normalized-CountSet.txt

value: post eclosion day 3


title: 30d WT rep3

description: M_DESeq normalized-CountSet.txt


title: 15d WT rep3

description: M_DESeq normalized-CountSet.txt

value: post eclosion day 15


title: 3d WT rep3

description: M_DESeq normalized-CountSet.txt


title: MODEK_control_4hrs_3

description: small RNAs

value: no treatment


title: 15d WT rep1

description: M_DESeq normalized-CountSet.txt


title: 3d WT rep1

description: M_DESeq normalized-CountSet.txt


title: daw-3'UTR -/-; foxo-/- rep1

description: T_daw3UTRfoxo_vs_5905_female_muscle.csv, T_DESeq normalized-CountSet_Symbol.txt

value: female


title: daw-3'UTR -/-; foxo-/- rep3


title: daw-3'UTR -/- rep3

description: T_daw3UTR_vs_5905_female_muscle.csv,    T_DESeq normalized-CountSet_Symbol.txt


title: daw-3'UTR -/-; foxo-/- rep2


title: daw-3'UTR -/- rep1


title: Atg8a-/- rep2

description: T_Atg8a_vs_5905_female_muscle.csv,         T_DESeq normalized-CountSet_Symbol.txt


title: Atg8a-/- rep3


title: Atg8a-/- rep1


title: WT rep3

description: T_DESeq normalized-CountSet_Symbol.txt


title: daw-3'UTR -/- rep2


title: small RNA-seq of wild type x wild type seeds

value: wild type x wild type


title: 15d WT rep2

description: M_DESeq normalized-CountSet.txt


title: WT rep2

description: T_DESeq normalized-CountSet_Symbol.txt


title: 30d_Rip rep2

source_name: whole fly

value: pBID-UAS-HA-Ago1/+; GS-tubulin-GAL4/+

value: female and male


title: 30d_Rip rep1

value: Conventional culture


title: 3d_Input rep2


title: Ax foxo-/- rep3

value: Axenic culture


title: 30d_Input rep2


title: 3d_Rip rep1


title: WT rep1

description: T_DESeq normalized-CountSet_Symbol.txt


title: 3d_Rip rep2


title: 3d_Input rep1


title: 30d_Input rep1


title: Ax foxo-/- rep1


title: daw-/+; miR-252 -/-, foxo-/- rep3

description: WGC_dawmiR252foxo_vs_5905_female_muscle.csv, WGC_DESeq normalized-CountSet.txt


title: daw-/+; miR-252 -/-, foxo-/- rep2


title: Ax WT rep3


title: Ax foxo-/- rep2


title: Ax WT rep2


title: Ax WT rep1


title: daw-/+; miR-252 -/-, foxo-/- rep1


title: foxo-/- muscle rep2

description: WGC_foxo_vs_5905_female_muscle.csv, WGC_DESeq normalized-CountSet.txt


title: miR-252 -/-, foxo-/- rep2

description: WGC_miR252foxo_vs_5905_female_muscle.csv, WGC_DESeq normalized-CountSet.txt


title: foxo-/- muscle rep1


title: miR-252 -/-, foxo-/- rep1


title: foxo-/- muscle rep3


title: miR-252 -/- rep3

description: WGC_miR252_vs_5905_female_muscle.csv, WGC_DESeq normalized-CountSet.txt


title: miR-252 -/- rep2


title: miR-252 -/-, foxo-/- rep3


title: WT rep6

description: WGC_DESeq normalized-CountSet.txt


title: miR-252 -/- rep1


title: WT rep5

description: WGC_DESeq normalized-CountSet.txt


title: WT rep4

description: WGC_DESeq normalized-CountSet.txt


title: VSMC_CA_rep2

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using hisat2 software.
Reads were counted by Htseq-count.
Differentially expressed genes were calculated by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is HTseq reads count.

source_name: vascular smooth muscle cells, Cadasil

growth_protocol: Human VSMCs were cultured in N2B27 medium (Wang et al., 2018a) supplemented with 10 ng/mL PDGF-BB (Peprotech). Human VECs were cultured in EGM-2 medium (Lonza).

extract_protocol:
Total RNA extraction and cDNA synthesis were performed using TRIzol reagent (Invitrogen) .
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: ES-derived vascular smooth muscle cells

value: Cadasil


title: VSMC_CA_rep1


title: VSMC_WT1_rep1

source_name: vascular smooth muscle cells, WT

value: WT


title: VSMC_WT2_rep2


title: VSMC_WT2_rep1


title: VSMC_WT1_rep2


title: EC_CA_rep2

source_name: vascular endothelial cells, Cadasil

value: ES-derived vascular endothelial cells


title: EC_WT2_rep2

source_name: vascular endothelial cells, WT


title: EC_WT1_rep2


title: EC_CA_rep1


title: MODEK_vesicles_24hrs_3

description: small RNAs

organism:
Mus musculus
Heligmosomoides polygyrus bakeri

value: 2.5ug H. bakeri EVs per 50,000 cells

value: 24 hours


title: MODEK_vesicles_4hrs_2

description: small RNAs

value: 4 hours


title: MODEK_vesicles_24hrs_1

description: small RNAs


title: MODEK_vesicles_4hrs_1

description: small RNAs


title: EC_WT2_rep1


title: MODEK_vesicles_24hrs_2

description: small RNAs


title: MODEK_vesicles_4hrs_3

description: small RNAs


title: small RNA-seq of endosperm

source_name: endosperm

value: endosperm

value: 6 Days After Pollination


title: EC_WT1_rep1


title: small RNA-seq of embryo

source_name: embryo

value: embryo


title: small RNA-seq of seed coat

source_name: seed coat

value: seed coat


title: SAMPLE 3_CON3

city: SHANGHAI

first: Xinjie

state: SHANGHAI

address: RUIJIN ER ROAD

institute: Shanghai Institute of Hematology

description: SAMPLE 3

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00‐0331‐220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00‐0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00‐00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The Kasumi-1 cells were cultured in RPMI 1640 plus 10% FBS (GIBCO).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596‐018，Life technologies,Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase‐Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The Kasumi-1 cells were treated with/ without 20 nM HHT for 24h.

tag: cell line

value: acute myeloid leukemia with the t(8;21) translocation

value: vehicle for 24h


title: Lrp5/6 dKO rep2

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

data_processing:
FastQC version 0.11.5 was used to identify features of the raw data that may indicate quality problems
Low quality bases were removed using Trimmomatic
Reads were mapped to the mouse reference genome (mm9) with Tophat2 version 2.1.1. and post-processed with RSEM version 1.2.31. Default parameter settings were used for alignment
The uniquely mapped reads were assigned to genes using Htseq
The fold change and p-value of all the detected genes were estimated by DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: txt format. Read counts for each gene and TPM for each gene

source_name: CD34-Flt3- Lin-ScaI+C-Kithigh cells

growth_protocol: CD34-Flt3- LSK were isolated by cell sorting from WT or Lrp5/6 double deficient mice

extract_protocol:
Total RNA was extracted from 6K CD34-Flt3- Lin-ScaI+C-Kithigh cells using the RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s protocol.
Libraries are constructed according to the standard protocol for Smart-seq2

treatment_protocol: CD34-Flt3- LSK cells were sorted with a BD AriaII directly into Trizol reagent

value: Bone marrow

value: 8 weeks

value: Vav-cre;Lrp5 fl/fl Lrp6 fl/fl


title: SAMPLE 1_CON1

description: SAMPLE 1

tag: cell type


title: SAMPLE 2_CON2

description: SAMPLE 2


title: SAMPLE 5_H2

description: SAMPLE 5

source_name: Kasumi-1_20 nM HHT for 24h

value: 20 nM HHT for 24h


title: Lrp5/6 dKO rep1


title: Lrp5/6 dKO rep3


title: SAMPLE 4_H1

description: SAMPLE 4


title: WT rep2


title: WT rep1


title: hda19_short_day (RNA-seq)-rep2

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

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 TAIR10 whole genome using STAR-2.5.2b with parameters  --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 20  --alignSoftClipAtReferenceEnds No --readFilesCommand zcat-m 10 --best --strata
Fragments  Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cuflink2.0.0 cuffdiff with parameters -p 16 -N
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using deeptools bamCoverage with parameters --binSize 10 -p 30 --normalizeUsing RPKM --outFileFormat bigwig

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with a 8 h light/16 h dark photoperiod at 22ºC

extract_protocol:
Total RNA was extracted from 1 g samples of 18-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen)
libraries were prepared for mRNA-seq

value: seedlings

value: short day


title: SAMPLE 6_H3

description: SAMPLE 6


title: hda19_short_day (RNA-seq)-rep1


title: hdc1_short_day (RNA-seq)-rep2


title: hda6_short_day (RNA-seq)-rep1


title: hdc1_short_day (RNA-seq)-rep1


title: WT_short_day (RNA-seq)-rep2

value: wild type


title: WT_short_day (RNA-seq)-rep1


title: LD2 mRNA

status: Public on Dec 30 2018

city: Hangzhou

first: Minjie

last: Huang

address: NO.388 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Illumina RTA software used for basecalling.
After filtering out adaptor sequences and removing low quality reads from raw data, the clean reads were aligned to the reference genome(Sus scrofa10.2) using Tophat v2.0.13
Gene expression level was calculated by Reads Per Kilobase per Million reads (RPKM)
Illumina RTA software used for basecalling.
After removing adapter sequences, reads containing poly-N and low quality reads, all clean reads were mapped to Rfam12.1(rfam.xfam.org), pirnabank (pirnabank.ibab.ac.in), miRBase 21 (www.miRBase.org) and Mireap to annotate  rRNA, tRNA, snRNA, snoRNA, piRNA, mature miRNAs and porcine novel miRNA
The miRNA expression levels were calculated by RPM (Reads Per Million) values
Genome_build: Sus scrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each mRNA sample and tab-delimited text files include RPM values for each miRNA sample

organism: Sus scrofa

source_name: liver

extract_protocol:
Approximately 1 µg RNA per sample were used to construct the complementary (cDNA) library with NEBNext® Ultra™ RNA Library Prep Kit for Illumina®(NEB, USA) according to the manufacturer's instructions.  Approximately 1 µg RNA of total RNA were used to prepare a small RNA library according to instructions of NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Illumina, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Landrace

value: liver

tag: group

value: control


title: JH2 miRNA

value: Jinhua

value: experiment


title: JH1 miRNA


title: LD2 miRNA


title: JH3 mRNA


title: LD3 miRNA


title: JH3 miRNA


title: JH2 mRNA


title: LD1 miRNA


title: LD1 mRNA


title: JH1 mRNA


title: suvh1/3;sdj1/3 rep1 (RNA-seq)

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using HISAT2 v2.0.4(--phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000 )
The mapped reads were counted at exon level using featureCounts
The differentially expressed genes were identified using edgeR
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with a 16 h light/8 h dark photoperiod at 22ºC

extract_protocol:
Total RNA was extracted from 1 g samples of 12-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen)
libraries were prepared for mRNA-seq


title: suvh1/3;sdj1/3 rep2 (RNA-seq)


title: sdj1/2/3 rep1 (RNA-seq)


title: sdj1/2/3 rep2 (RNA-seq)


title: suvh1/3 rep2 (RNA-seq)


title: suvh1/3 rep1 (RNA-seq)


title: hda6_short_day (RNA-seq)-rep2


title: WT rep2 (RNA-seq)


title: WT rep1 (RNA-seq)


title: LD3 mRNA


title: Single cell C87

status: Public on Dec 29 2018

city: Minneapolis

first: Sunny

last: Chan

state: MN

address: 2231 6th St SE

department: Pediatrics

institute: University of Minnesota

description:
423 single cell.txt
C87

data_processing:
Basecalls with CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences in Galaxy
Reads mapped to mm10 using Tophat 0.7 in Galaxy
Gene expression estimation (FPKM values) using Cufflinks 2.2.1.0 in Galaxy
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing FPKM expression estimates calculated by Cufflinks

source_name: Pluripotent stem cell derivatives

growth_protocol: Mesp1-inducible mouse embryonic stem cells were growth as embryoid bodies in EB differentiation for 4 days.  On day 4, cells were dissociated and live cells (PI-) were sorted by FACS.  Single cells were then captured using the Fluidigm C1 microfluidic system.

extract_protocol:
Per Fluidigm C1 manual
Per Fluidigm C1 manual

treatment_protocol: Doxycycline (500 ng/ml) was added from day 2.25 to day 3.25 to induce Mesp1.

tag: strain

value: Mesp1-induced mesoderm

value: Mesp1 induction from D2.25-D3.25


title: Single cell C84

description:
423 single cell.txt
C84


title: Single cell C92

description:
423 single cell.txt
C92


title: Single cell C93

description:
423 single cell.txt
C93


title: Single cell C89

description:
423 single cell.txt
C89


title: Single cell C90

description:
423 single cell.txt
C90


title: Single cell C95

description:
423 single cell.txt
C95


title: Single cell C81

description:
423 single cell.txt
C81


title: Single cell C80

description:
423 single cell.txt
C80


title: Single cell C76

description:
423 single cell.txt
C76


title: Single cell C77

description:
423 single cell.txt
C77


title: Single cell C75

description:
423 single cell.txt
C75


title: Single cell C70

description:
423 single cell.txt
C70


title: Single cell C67

description:
423 single cell.txt
C67


title: Single cell C62

description:
423 single cell.txt
C62


title: Single cell C69

description:
423 single cell.txt
C69


title: Single cell C79

description:
423 single cell.txt
C79


title: Single cell C59

description:
423 single cell.txt
C59


title: Single cell C65

description:
423 single cell.txt
C65


title: Single cell C52

description:
423 single cell.txt
C52


title: Single cell C51

description:
423 single cell.txt
C51


title: Single cell C48

description:
423 single cell.txt
C48


title: Single cell C56

description:
423 single cell.txt
C56


title: Single cell C45

description:
423 single cell.txt
C45


title: Single cell C46

description:
423 single cell.txt
C46


title: Single cell C39

description:
423 single cell.txt
C39


title: Single cell C43

description:
423 single cell.txt
C43


title: Single cell C42

description:
423 single cell.txt
C42


title: Single cell C38

description:
423 single cell.txt
C38


title: Single cell C32

description:
423 single cell.txt
C32


title: Single cell C31

description:
423 single cell.txt
C31


title: Single cell C33

description:
423 single cell.txt
C33


title: Single cell C36

description:
423 single cell.txt
C36


title: Evolved bV --> bV line 2

city: Paterna

first: Juan

middle: Vicente

last: Bou

state: Valencia

address: Carrer del Catedratic Agustin Escardino Benlloch, 9

department: Genetics

country: Spain

institute: University of Valencia

description:
bV2
(+) ssRNA genome

data_processing:
Quality of the FastQ files was evaluated with FastQC 0.11.7 (www.bioinformatics.babraham.ac.uk/projects/fastqc).
First 10 nucleotides and last two nucleotides of each read were cut with Cutadapt (cutadapt.readthedocs.io).
Reads were trimmed with FASTQ Quality Filter (hannonlab.cshl.edu/fastx_toolkit) and Prinseq-lite 0.20.4 (Schmieder and Edwards, 2011) by quality (Q30), length (200 nucleotides) and sequencing artefacts (duplications, Ns).
The pipeline ViVan 0.43 (Isakov et al., 2015) was used for mapping and SNP calling.
Genome_build: CVB3 Nancy strain (GenBank accession JX312064.1)
Supplementary_files_format_and_content: *_mutation_frequency.xlsx: Excel files with the results of the SNP calling and mutation frequency for every position evaluated of the viral genome (11-7389).

organism: Coxsackievirus B3 (strain Nancy)

source_name: coxsackievirus b3

growth_protocol: Coxsackievirus B3 was cultured in HeLa-H1 cells (ATCC, CRL-1958) in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 2% fetal bovine serum (FBS), non-essential amino acids, 10 units/mL penicillin, 10 µg/mL streptomycin and 250 ng/mL amphotericin B under standard culturing conditions (37°C and 5% CO2).

extract_protocol:
100 µL of supernatant from transfer 20 of each lineage, as well as from the founder virus, were used to extract viral RNA using the Quick-RNA viral kit (ZymoResearch) following manufacturer’s instructions.
TruSeq DNA PCR free library preparation kit (Illumina) following manufacturer’s instructions.

treatment_protocol: S: supernatant of 10000 x g centrifugation. V: Pellet of 10000 x g centrifugation. bV: Vesicles treated with 0.17% Triton X-100 at 4°C 15 minutes.

tag: passages

tag: sample type

value: Broken vesicles


title: Single cell C53

description:
423 single cell.txt
C53


title: Single cell C12

description:
423 single cell.txt
C12


title: Single cell C19

description:
423 single cell.txt
C19


title: Single cell C18

description:
423 single cell.txt
C18


title: Single cell C22

description:
423 single cell.txt
C22


title: Evolved V --> V, line 2

description:
V2
(+) ssRNA genome

value: Vesicles


title: Single cell C13

description:
423 single cell.txt
C13


title: Single cell C15

description:
423 single cell.txt
C15


title: Founder

description:
founder
(+) ssRNA genome

value: Founder


title: Single cell C04

description:
423 single cell.txt
C04


title: Evolved V --> V, line 1

description:
V1
(+) ssRNA genome


title: Single cell C08

description:
423 single cell.txt
C08


title: Evolved S --> S, line 2

description:
S2
(+) ssRNA genome

value: Free viral particles


title: Single cell C02

description:
423 single cell.txt
C02


title: Evolved S --> S, line 1

description:
S1
(+) ssRNA genome


title: Single cell C09

description:
423 single cell.txt
C09


title: Single cell C07

description:
423 single cell.txt
C07


title: Single cell C05

description:
423 single cell.txt
C05


title: Single cell C23

description:
423 single cell.txt
C23


title: Evolved bV --> bV line 1

description:
bV1
(+) ssRNA genome


title: 181102_snm3C_H8_AD008_indexed

status: Public on Dec 26 2018

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Raw reads were trimmed first 25bp and last 3bp of both read1 and read2 to remove random primer sequence and adaptase low complexity tails. For the alignment, Bismark is used24. C to T converted and G to A converted reference genomes are prepared for mm10 and hg38 using bismark_genome_preparation. Each read end is mapped separately using Bismark with Bowtie1 with read1 as complementary (always G to A converted) and read2 (always C to T converted) as original strand. After first alignment, unmapped reads are retained and splitted into 3 pieces by 40bp, 32bp, and 40bp after removing 5bp of both ends results in having 6 reads (read1 and read2). Six reads derived from unmapped reads are mapped separately using Bismark Bowtie1. All aligned reads are merged into BAM using picard that is query name sorted. The fragments with all the mapped reads aligned to the same positions are considered as duplicates and removed and DNA methylation tracks are generated. For each fragment, the outermost aligned reads are chosen for the chromatin conformation map generation.
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)

source_name: NMuMG

growth_protocol: Mouse ES cells (E14TG2a) were purchased from American Type Culture Collection (ATCC CRL-1821). ES cells were grown in DMEM media (Corning 10-013-CV) supplemented with 10% HyClone FBS (Fisher SH3007003E), 1X MEM Non-essential amino acids (ThermoFisher 11140050), 1X Glutamax supplement (ThermoFisher 35050061), 1X ß-mercaptoethanol (Millipore ES-007-E), 100U/mL Penicillin-Streptomycin (ThermoFisher 15140122), and 1000U/mL Leukemia Inhibitory Factor (Millipore ESG1107). ES cells were cultured in feeder free conditions on 0.5% gelatin coated plates. GM12878 cells were obtained from Coriell Institute for Medical Research. GM12878 cells were grown in RPMI-1640 medium (ThermoFisher 11875093) supplemented with 15% Fetal Bovine Serum (Corning 35-010-CV) and 100U/mL Penicillin-Streptomycin (ThermoFisher 15140122). NMuMg cells (RBRC-RCB2868) were obtained from the RIKEN BioResource Center. NMuMg cells were grown in DMEM (Corning 10-013-CV) with 10% Fetal Bovine Serum (Corning 35-010-CV), 10ug/mL Insulin (ThermoFisher 12585014), and 100U/mL Penicillin-Streptomycin (ThermoFisher 15140122). All cell lines were routinely tested for mycoplasma contamination and tested negative.

extract_protocol: in situ Hi-C was performed as previously described using the MboI restriction enzyme. in situ 3C experiments were performed based on the previously described in situ Hi-C protocol with minor modifications. Briefly, prior to fixation, adherent cells were trypsinized, counted, and collected by centrifugation, and suspension cells were counted and collected by centrifugation. Cells were resuspended in culture media at a concentration of 1x106 cells per mL of media and fixed in 1% formaldehyde for 10 minutes at room temperature with shaking. For standard species mixture experiments, equal numbers of mouse and human cells were combined into a single tube prior to fixation. For the 1:10 dilution species mixture experiment, cells were resuspended at a concentration of 1x105 cells per mL of media prior to fixation. For the species mixture experiments where samples were mixed after fixation, each cell type was fixed independently as described above and combined at later stages in the protocol. in situ Hi-C samples were digested with the MboI restriction enzyme and processed as described previously. For in situ 3C experiments, samples were digested with DpnII enzyme overnight at 37ºC with gentle mixing. The following day, the sample was incubated at 62ºC for 10 minutes to inactivate the restriction enzyme. The typical biotin fill in step in the Hi-C protocol is omitted. The sample is then ligated for 4 hours at room temperature with T4 DNA ligase in the same manner as in in situ Hi-C experiments. The sample is then stained with Hoechst (0.1ug/uL) for the final 30 minutes of the ligation step. The sample is then passed through a 40 uM nylon cell strainer (Corning 431750) into a FACS tube prior to sorting. As a quality control step, 10% of the sample is taken for conventional library preparation and sequenced using shallow sequencing on a MiSeq. Libraries for bulk and single-cell methylomes were generated using snmC-seq2. A detailed step-by-step bench protocol for snmC-seq2 is provided as Supplement Methods in Luo et al. (2018) 23. Bulk methylome libraries were prepared manually using individual tubes. Single-cell methylome libraries were prepared using a Tecan Evo 100 robotic platform as described in Luo et al. (2018) 23. Sequencing libraries were sequenced using Illumina MiSeq and HiSeq 4000 instruments in PE150 mode.

value: Male

tag: genome build

tag: library strategy


title: 181102_snm3C_H8_AD007_indexed


title: 181102_snm3C_H7_AD010_indexed


title: 181102_snm3C_H7_AD012_indexed


title: 181102_snm3C_H9_AD012_indexed


title: 181102_snm3C_G8_AD012_indexed


title: 181102_snm3C_G8_AD008_indexed


title: 181102_snm3C_G8_AD007_indexed


title: 181102_snm3C_F7_AD010_indexed


title: 181102_snm3C_E9_AD007_indexed


title: 181102_snm3C_F8_AD007_indexed


title: 181102_snm3C_D9_AD012_indexed


title: 181102_snm3C_F9_AD010_indexed


title: 181102_snm3C_F7_AD007_indexed


title: 181102_snm3C_F9_AD008_indexed


title: 181102_snm3C_E7_AD007_indexed


title: 181102_snm3C_E8_AD010_indexed


title: 181102_snm3C_D8_AD010_indexed


title: Single cell C01

description:
423 single cell.txt
C01

tag: treatment


title: 181102_snm3C_D7_AD010_indexed


title: 181102_snm3C_D7_AD007_indexed


title: 181102_snm3C_C9_AD008_indexed


title: 181102_snm3C_D8_AD012_indexed


title: 181102_snm3C_H7_AD008_indexed


title: 181102_snm3C_C8_AD010_indexed


title: 181102_snm3C_C7_AD012_indexed


title: 181102_snm3C_G8_AD010_indexed


title: 181102_snm3C_C7_AD010_indexed


title: 181102_snm3C_B9_AD008_indexed


title: 181102_snm3C_C7_AD008_indexed


title: 181102_snm3C_B7_AD007_indexed


title: 181102_snm3C_B7_AD012_indexed


title: 181102_snm3C_D9_AD007_indexed


title: 181102_snm3C_B9_AD007_indexed


title: 181102_snm3C_C9_AD010_indexed


title: 181102_snm3C_A9_AD008_indexed


title: 181102_snm3C_A9_AD007_indexed


title: 181102_snm3C_H12_AD008_indexed


title: 181102_snm3C_A8_AD010_indexed


title: 181102_snm3C_H10_AD007_indexed


title: 181102_snm3C_A7_AD007_indexed


title: 181102_snm3C_G11_AD008_indexed


title: 181102_snm3C_G12_AD010_indexed


title: 181102_snm3C_G12_AD007_indexed


title: 181102_snm3C_G11_AD010_indexed


title: 181102_snm3C_G11_AD012_indexed


title: 181102_snm3C_G10_AD008_indexed


title: 181102_snm3C_F12_AD012_indexed


title: 181102_snm3C_G10_AD007_indexed


title: 181102_snm3C_G10_AD012_indexed


title: 181102_snm3C_F11_AD012_indexed


title: 181102_snm3C_F11_AD007_indexed


title: 181102_snm3C_F11_AD010_indexed


title: 181102_snm3C_F11_AD008_indexed


title: 181102_snm3C_F10_AD012_indexed


title: 181102_snm3C_A9_AD012_indexed


title: 181102_snm3C_F10_AD007_indexed


title: 181102_snm3C_F10_AD010_indexed


title: 181102_snm3C_E12_AD012_indexed


title: 181102_snm3C_E12_AD007_indexed


title: 181102_snm3C_G11_AD007_indexed


title: 181102_snm3C_A8_AD012_indexed


title: 181102_snm3C_H11_AD010_indexed


title: 181102_snm3C_E12_AD008_indexed


title: 181102_snm3C_F12_AD008_indexed


title: 181102_snm3C_E10_AD010_indexed


title: 181102_snm3C_D12_AD007_indexed


title: 181102_snm3C_E11_AD008_indexed


title: 181102_snm3C_D12_AD012_indexed


title: 181102_snm3C_D11_AD012_indexed


title: 181102_snm3C_E11_AD010_indexed


title: 181102_snm3C_D10_AD007_indexed


title: 181102_snm3C_D10_AD012_indexed


title: 181102_snm3C_D10_AD010_indexed


title: 181102_snm3C_C12_AD012_indexed


title: 181102_snm3C_D11_AD010_indexed


title: 181102_snm3C_C12_AD008_indexed


title: 181102_snm3C_D11_AD007_indexed


title: 181102_snm3C_C11_AD012_indexed


title: 181102_snm3C_B12_AD010_indexed


title: 181102_snm3C_E11_AD012_indexed


title: 181102_snm3C_C12_AD007_indexed


title: 181102_snm3C_C10_AD007_indexed


title: 181102_snm3C_B12_AD012_indexed


title: 181102_snm3C_C10_AD012_indexed


title: 181102_snm3C_B12_AD008_indexed


title: 181102_snm3C_B11_AD010_indexed


title: 181102_snm3C_B10_AD010_indexed


title: 181102_snm3C_B10_AD012_indexed


title: 181102_snm3C_B10_AD007_indexed


title: 181102_snm3C_D11_AD008_indexed


title: 181102_snm3C_A12_AD010_indexed


title: 181102_snm3C_A12_AD008_indexed


title: 181102_snm3C_B11_AD007_indexed


title: 181102_snm3C_A11_AD008_indexed


title: 181102_snm3C_H6_AD001_indexed

source_name: Mouse Embryonic Stem Cell Line E14


title: 181102_snm3C_H5_AD001_indexed


title: 181102_snm3C_H5_AD002_indexed


title: 181102_snm3C_B12_AD007_indexed


title: 181102_snm3C_A11_AD012_indexed


title: 181102_snm3C_H4_AD004_indexed


title: 181102_snm3C_H4_AD006_indexed


title: 181102_snm3C_G6_AD004_indexed


title: 181102_snm3C_G5_AD006_indexed


title: 181102_snm3C_G5_AD002_indexed


title: 181102_snm3C_G5_AD001_indexed


title: 181102_snm3C_G4_AD006_indexed


title: 181102_snm3C_G6_AD002_indexed


title: 181102_snm3C_F4_AD006_indexed


title: 181102_snm3C_F6_AD002_indexed


title: 181102_snm3C_G4_AD001_indexed


title: 181102_snm3C_F6_AD001_indexed


title: 181102_snm3C_F5_AD004_indexed


title: 181102_snm3C_F6_AD004_indexed


title: 181102_snm3C_G4_AD004_indexed


title: 181102_snm3C_H6_AD006_indexed


title: 181102_snm3C_E6_AD006_indexed


title: 181102_snm3C_E4_AD001_indexed


title: 181102_snm3C_E5_AD001_indexed


title: 181102_snm3C_F4_AD002_indexed


title: 181102_snm3C_E4_AD004_indexed


title: 181102_snm3C_E6_AD002_indexed


title: 181102_snm3C_F4_AD004_indexed


title: 181102_snm3C_D6_AD006_indexed


title: 181102_snm3C_D6_AD004_indexed


title: 181102_snm3C_D5_AD006_indexed


title: 181102_snm3C_D6_AD001_indexed


title: 181102_snm3C_D5_AD001_indexed


title: 181102_snm3C_C6_AD002_indexed


title: 181102_snm3C_C6_AD004_indexed


title: 181102_snm3C_C4_AD004_indexed


title: 181102_snm3C_B6_AD002_indexed


title: 181102_snm3C_B5_AD004_indexed


title: 181102_snm3C_B5_AD001_indexed


title: 181102_snm3C_B4_AD004_indexed


title: 181102_snm3C_B4_AD002_indexed


title: 181102_snm3C_B5_AD006_indexed


title: 181102_snm3C_A6_AD006_indexed


title: 181102_snm3C_B6_AD001_indexed


title: 181102_snm3C_B4_AD001_indexed


title: 181102_snm3C_H10_AD001_indexed


title: 181102_snm3C_A4_AD001_indexed


title: 181102_snm3C_A6_AD004_indexed


title: 181102_snm3C_H10_AD006_indexed


title: 181102_snm3C_H12_AD006_indexed


title: 181102_snm3C_A4_AD006_indexed


title: 181102_snm3C_D4_AD004_indexed


title: 181102_snm3C_H11_AD006_indexed


title: 181102_snm3C_D4_AD002_indexed


title: 181102_snm3C_G12_AD004_indexed


title: 181102_snm3C_C6_AD001_indexed


title: 181102_snm3C_C5_AD004_indexed


title: 181102_snm3C_G12_AD001_indexed


title: 181102_snm3C_C5_AD001_indexed


title: 181102_snm3C_C4_AD001_indexed


title: 181102_snm3C_D4_AD006_indexed


title: 181102_snm3C_G11_AD001_indexed


title: 181102_snm3C_G11_AD004_indexed


title: 181102_snm3C_G10_AD006_indexed


title: 181102_snm3C_G10_AD004_indexed


title: 181102_snm3C_F11_AD006_indexed


title: 181102_snm3C_F12_AD002_indexed


title: 181102_snm3C_F11_AD004_indexed


title: 181102_snm3C_F12_AD001_indexed


title: 181102_snm3C_G10_AD001_indexed


title: 181102_snm3C_G12_AD006_indexed


title: 181102_snm3C_F11_AD002_indexed


title: 181102_snm3C_G12_AD002_indexed


title: 181102_snm3C_F10_AD002_indexed


title: 181102_snm3C_F10_AD004_indexed


title: 181102_snm3C_E12_AD002_indexed


title: 181102_snm3C_F10_AD006_indexed


title: 181102_snm3C_F10_AD001_indexed


title: 181102_snm3C_E11_AD006_indexed


title: 181102_snm3C_E12_AD006_indexed


title: 181102_snm3C_D12_AD006_indexed


title: 181102_snm3C_D12_AD002_indexed


title: 181102_snm3C_E10_AD004_indexed


title: 181102_snm3C_D11_AD004_indexed


title: 181102_snm3C_F11_AD001_indexed


title: 181102_snm3C_G11_AD006_indexed


title: 181102_snm3C_E11_AD004_indexed


title: 181102_snm3C_D10_AD006_indexed


title: 181102_snm3C_D10_AD001_indexed


title: 181102_snm3C_D11_AD002_indexed


title: 181102_snm3C_C12_AD006_indexed


title: 181102_snm3C_C12_AD002_indexed


title: 181102_snm3C_D10_AD002_indexed


title: 181102_snm3C_C11_AD004_indexed


title: 181102_snm3C_C11_AD006_indexed


title: 181102_snm3C_C10_AD006_indexed


title: 181102_snm3C_B10_AD006_indexed


title: 181102_snm3C_B12_AD002_indexed


title: 181102_snm3C_B12_AD004_indexed


title: 181102_snm3C_C10_AD004_indexed


title: 181102_snm3C_C10_AD002_indexed


title: 181102_snm3C_B11_AD002_indexed


title: 181102_snm3C_B10_AD004_indexed


title: 181102_snm3C_B10_AD002_indexed


title: 181102_snm3C_H9_AD001_indexed


title: 181102_snm3C_A12_AD001_indexed


title: 181102_snm3C_A11_AD001_indexed


title: 181102_snm3C_H9_AD004_indexed


title: 181102_snm3C_A12_AD006_indexed


title: 181102_snm3C_H8_AD002_indexed


title: 181102_snm3C_H9_AD002_indexed


title: 181102_snm3C_H8_AD006_indexed


title: 181102_snm3C_H7_AD001_indexed


title: 181102_snm3C_H7_AD006_indexed


title: 181102_snm3C_G9_AD004_indexed


title: 181102_snm3C_G8_AD001_indexed


title: 181102_snm3C_H7_AD002_indexed


title: 181102_snm3C_H7_AD004_indexed


title: 181102_snm3C_G9_AD006_indexed


title: 181102_snm3C_G9_AD001_indexed


title: 181102_snm3C_F9_AD004_indexed


title: 181102_snm3C_F8_AD004_indexed


title: 181102_snm3C_G7_AD001_indexed


title: 181102_snm3C_F8_AD002_indexed


title: 181102_snm3C_E8_AD006_indexed


title: 181102_snm3C_E7_AD006_indexed


title: 181102_snm3C_F8_AD001_indexed


title: 181102_snm3C_F7_AD006_indexed


title: 181102_snm3C_E8_AD001_indexed


title: 181102_snm3C_E8_AD002_indexed


title: 181102_snm3C_F7_AD002_indexed


title: 181102_snm3C_D9_AD004_indexed


title: 181102_snm3C_D8_AD004_indexed


title: 181102_snm3C_D8_AD002_indexed


title: 181102_snm3C_D9_AD001_indexed


title: 181102_snm3C_E7_AD004_indexed


title: 181102_snm3C_D7_AD004_indexed


title: 181102_snm3C_E7_AD002_indexed


title: 181102_snm3C_D7_AD006_indexed


title: 181102_snm3C_D8_AD001_indexed


title: 181102_snm3C_C9_AD001_indexed


title: 181102_snm3C_C8_AD006_indexed


title: 181102_snm3C_C9_AD002_indexed


title: 181102_snm3C_C8_AD004_indexed


title: 181102_snm3C_G7_AD002_indexed


title: 181102_snm3C_C8_AD001_indexed


title: 181102_snm3C_C7_AD006_indexed


title: 181102_snm3C_C8_AD002_indexed


title: 181102_snm3C_B9_AD006_indexed


title: 181102_snm3C_C7_AD004_indexed


title: 181102_snm3C_B7_AD002_indexed


title: 181102_snm3C_A9_AD004_indexed


title: 181102_snm3C_A9_AD006_indexed


title: 181102_snm3C_A9_AD002_indexed


title: 181102_snm3C_A7_AD004_indexed


title: 181102_snm3C_A8_AD002_indexed


title: 181102_snm3C_D9_AD006_indexed


title: 181102_snm3C_A7_AD002_indexed


title: 181102_snm3C_A9_AD001_indexed


title: 181102_snm3C_H2_AD006_indexed


title: 181102_snm3C_G2_AD001_indexed


title: 181102_snm3C_A7_AD001_indexed


title: 181102_snm3C_G3_AD004_indexed


title: 181102_snm3C_F3_AD002_indexed


title: 181102_snm3C_F2_AD004_indexed


title: 181102_snm3C_F2_AD006_indexed


title: 181102_snm3C_F2_AD001_indexed


title: 181102_snm3C_F1_AD001_indexed


title: 181102_snm3C_H2_AD002_indexed


title: 181102_snm3C_E3_AD002_indexed


title: 181102_snm3C_F2_AD002_indexed


title: 181102_snm3C_B7_AD001_indexed


title: 181102_snm3C_E3_AD006_indexed


title: 181102_snm3C_E2_AD001_indexed


title: 181102_snm3C_B7_AD004_indexed


title: 181102_snm3C_F1_AD004_indexed


title: 181102_snm3C_E1_AD006_indexed


title: 181102_snm3C_E2_AD004_indexed


title: 181102_snm3C_E1_AD001_indexed


title: 181102_snm3C_E1_AD004_indexed


title: 181102_snm3C_E1_AD002_indexed


title: 181102_snm3C_D3_AD001_indexed


title: 181102_snm3C_D3_AD002_indexed


title: 181102_snm3C_D2_AD006_indexed


title: 181102_snm3C_C3_AD004_indexed


title: 181102_snm3C_D2_AD002_indexed


title: 181102_snm3C_D1_AD002_indexed


title: 181102_snm3C_C1_AD004_indexed


title: 181102_snm3C_C2_AD001_indexed


title: 181102_snm3C_B3_AD006_indexed


title: 181102_snm3C_B3_AD001_indexed


title: 181102_snm3C_B1_AD006_indexed


title: 181102_snm3C_A2_AD006_indexed


title: 181102_snm3C_A2_AD004_indexed


title: 181102_snm3C_A3_AD002_indexed


title: 181102_snm3C_A1_AD004_indexed


title: 181102_snm3C_H6_AD012_indexed


title: 181102_snm3C_H6_AD007_indexed


title: 181102_snm3C_A3_AD001_indexed


title: 181102_snm3C_H5_AD007_indexed


title: 181102_snm3C_H6_AD008_indexed


title: 181102_snm3C_H5_AD010_indexed


title: 181102_snm3C_H4_AD010_indexed


title: 181102_snm3C_H4_AD012_indexed


title: 181102_snm3C_H4_AD007_indexed


title: 181102_snm3C_G6_AD010_indexed


title: 181102_snm3C_G6_AD012_indexed


title: 181102_snm3C_G6_AD008_indexed


title: 181102_snm3C_G5_AD012_indexed


title: 181102_snm3C_B2_AD002_indexed


title: 181102_snm3C_H5_AD012_indexed


title: 181102_snm3C_B2_AD006_indexed


title: 181102_snm3C_G5_AD010_indexed


title: 181102_snm3C_G5_AD007_indexed


title: 181102_snm3C_G4_AD010_indexed


title: 181102_snm3C_G4_AD007_indexed


title: 181102_snm3C_G4_AD008_indexed


title: 181102_snm3C_F6_AD010_indexed


title: 181102_snm3C_F5_AD012_indexed


title: 181102_snm3C_F6_AD008_indexed


title: 181102_snm3C_F5_AD010_indexed


title: 181102_snm3C_F6_AD007_indexed


title: 181102_snm3C_F5_AD008_indexed


title: 181102_snm3C_G6_AD007_indexed


title: 181102_snm3C_F4_AD012_indexed


title: 181102_snm3C_G5_AD008_indexed


title: 181102_snm3C_F4_AD008_indexed


title: 181102_snm3C_F4_AD007_indexed


title: 181102_snm3C_E6_AD010_indexed


title: 181102_snm3C_E6_AD008_indexed


title: 181102_snm3C_E5_AD010_indexed


title: 181102_snm3C_E5_AD007_indexed


title: 181102_snm3C_E5_AD008_indexed


title: 181102_snm3C_E4_AD010_indexed


title: 181102_snm3C_E6_AD007_indexed


title: 181102_snm3C_E5_AD012_indexed


title: 181102_snm3C_D6_AD010_indexed


title: 181102_snm3C_F4_AD010_indexed


title: 181102_snm3C_D6_AD007_indexed


title: 181102_snm3C_E6_AD012_indexed


title: 181102_snm3C_D5_AD010_indexed


title: 181102_snm3C_D5_AD012_indexed


title: 181102_snm3C_E4_AD007_indexed


title: 181102_snm3C_D6_AD008_indexed


title: 181102_snm3C_D5_AD008_indexed


title: 181102_snm3C_H5_AD008_indexed


title: 181102_snm3C_D5_AD007_indexed


title: 181102_snm3C_D4_AD008_indexed


title: 181102_snm3C_D4_AD012_indexed


title: 181102_snm3C_D4_AD010_indexed


title: 181102_snm3C_C6_AD012_indexed


title: 181102_snm3C_C6_AD010_indexed


title: 181102_snm3C_D4_AD007_indexed


title: 181102_snm3C_C6_AD008_indexed


title: 181102_snm3C_C6_AD007_indexed


title: 181102_snm3C_C4_AD012_indexed


title: 181102_snm3C_C5_AD007_indexed


title: 181102_snm3C_C5_AD010_indexed


title: 181102_snm3C_C4_AD010_indexed


title: 181102_snm3C_C4_AD008_indexed


title: 181102_snm3C_C4_AD007_indexed


title: 181102_snm3C_B6_AD007_indexed


title: 181102_snm3C_B6_AD010_indexed


title: 181102_snm3C_C5_AD012_indexed


title: 181102_snm3C_C5_AD008_indexed


title: 181102_snm3C_B4_AD008_indexed


title: 181102_snm3C_B5_AD007_indexed


title: 181102_snm3C_B4_AD007_indexed


title: 181102_snm3C_B5_AD008_indexed


title: 181102_snm3C_A6_AD012_indexed


title: 181102_snm3C_A6_AD007_indexed


title: 181102_snm3C_A6_AD008_indexed


title: 181102_snm3C_A6_AD010_indexed


title: 181102_snm3C_A5_AD008_indexed


title: 181102_snm3C_A4_AD010_indexed


title: 181102_snm3C_A4_AD012_indexed


title: 181102_snm3C_A4_AD008_indexed


title: 181102_snm3C_H3_AD008_indexed


title: 181102_snm3C_B5_AD010_indexed


title: 181102_snm3C_H3_AD007_indexed


title: 181102_snm3C_H2_AD012_indexed


title: 181102_snm3C_H3_AD012_indexed


title: 181102_snm3C_H2_AD007_indexed


title: 181102_snm3C_H1_AD012_indexed


title: 181102_snm3C_H2_AD008_indexed


title: 181102_snm3C_B4_AD012_indexed


title: 181102_snm3C_A5_AD010_indexed


title: 181102_snm3C_H1_AD007_indexed


title: 181102_snm3C_H1_AD008_indexed


title: 181102_snm3C_H1_AD010_indexed


title: 181102_snm3C_G3_AD012_indexed


title: 181102_snm3C_C2_AD002_indexed


title: 181102_snm3C_G3_AD007_indexed


title: 181102_snm3C_G2_AD012_indexed


title: 181102_snm3C_G3_AD010_indexed


title: 181102_snm3C_G1_AD012_indexed


title: 181102_snm3C_G2_AD007_indexed


title: 181102_snm3C_G1_AD008_indexed


title: 181102_snm3C_F2_AD012_indexed


title: 181102_snm3C_H2_AD010_indexed


title: 181102_snm3C_F2_AD010_indexed


title: 181102_snm3C_G2_AD008_indexed


title: 181102_snm3C_F2_AD007_indexed


title: 181102_snm3C_F3_AD007_indexed


title: 181102_snm3C_F2_AD008_indexed


title: 181102_snm3C_F1_AD012_indexed


title: 181102_snm3C_F1_AD008_indexed


title: 181102_snm3C_E3_AD012_indexed


title: 181102_snm3C_E3_AD010_indexed


title: 181102_snm3C_F1_AD007_indexed


title: 181102_snm3C_E3_AD008_indexed


title: 181102_snm3C_E3_AD007_indexed


title: 181102_snm3C_E2_AD012_indexed


title: 181102_snm3C_E2_AD007_indexed


title: 181102_snm3C_E1_AD012_indexed


title: 181102_snm3C_E1_AD007_indexed


title: 181102_snm3C_D3_AD012_indexed


title: 181102_snm3C_D3_AD010_indexed


title: 181102_snm3C_D3_AD007_indexed


title: 181102_snm3C_D3_AD008_indexed


title: 181102_snm3C_D2_AD007_indexed


title: 181102_snm3C_D2_AD010_indexed


title: 181102_snm3C_D2_AD008_indexed


title: 181102_snm3C_D1_AD008_indexed


title: 181102_snm3C_D1_AD010_indexed


title: 181102_snm3C_C3_AD012_indexed


title: 181102_snm3C_C2_AD012_indexed


title: 181102_snm3C_C2_AD010_indexed


title: 181102_snm3C_C3_AD008_indexed


title: 181102_snm3C_C2_AD008_indexed


title: 181102_snm3C_D1_AD007_indexed


title: 181102_snm3C_C3_AD007_indexed


title: 181102_snm3C_D1_AD012_indexed


title: 181102_snm3C_B3_AD012_indexed


title: 181102_snm3C_C1_AD008_indexed


title: 181102_snm3C_B3_AD007_indexed


title: 181102_snm3C_C1_AD012_indexed


title: 181102_snm3C_B2_AD008_indexed


title: 181102_snm3C_C1_AD010_indexed


title: 181102_snm3C_B3_AD004_indexed


title: 181102_snm3C_B3_AD008_indexed


title: 181102_snm3C_C2_AD007_indexed


title: 181102_snm3C_B2_AD007_indexed


title: 181102_snm3C_B1_AD012_indexed


title: 181102_snm3C_B1_AD010_indexed


title: 181102_snm3C_B1_AD008_indexed


title: 181102_snm3C_A3_AD012_indexed


title: 181102_snm3C_H4_AD008_indexed


title: 181102_snm3C_G7_AD006_indexed

organism:
Homo sapiens
Mus musculus

source_name: E14 GM12878 multiplet


title: 181102_snm3C_F9_AD002_indexed


title: 181102_snm3C_C9_AD004_indexed


title: 181102_snm3C_H6_AD004_indexed


title: 181102_snm3C_B8_AD002_indexed


title: 181102_snm3C_B11_AD004_indexed


title: 181102_snm3C_B10_AD001_indexed


title: 181102_snm3C_A1_AD010_indexed


title: 181102_snm3C_A2_AD010_indexed


title: 181102_snm3C_A3_AD007_indexed


title: 3C_mESC


title: Hi-C_mESC

value: Hi-C


title: 181102_snm3C_C10_AD001_indexed


title: 181102_snm3C_A1_AD008_indexed


title: 181102_snm3C_D11_AD001_indexed


title: 181102_snm3C_A3_AD008_indexed


title: 181102_snm3C_G1_AD002_indexed


title: 181102_snm3C_G2_AD006_indexed


title: 181102_snm3C_A11_AD002_indexed


title: 181102_snm3C_F3_AD006_indexed


title: 181102_snm3C_C3_AD006_indexed


title: 181102_snm3C_D2_AD004_indexed


title: m3C_mESC

value: Bulk m3C


title: 181102_snm3C_C9_AD006_indexed


title: 181102_snm3C_D8_AD006_indexed


title: 181102_snm3C_C1_AD001_indexed


title: 181102_snm3C_B7_AD006_indexed


title: 181102_snm3C_C1_AD002_indexed


title: 181102_snm3C_E12_AD004_indexed


title: 181102_snm3C_B2_AD004_indexed


title: 181102_snm3C_H3_AD002_indexed


title: 181102_snm3C_H2_AD001_indexed


title: 181102_snm3C_B1_AD004_indexed


title: 181102_snm3C_E3_AD004_indexed


title: 181102_snm3C_B2_AD001_indexed


title: 181102_snm3C_C2_AD004_indexed


title: 10705X1 (SKBr3)

status: Public on Nov 30 2018

city: Salt Lake City

first: Alana

last: Welm

address: 2000 Circle of Hope

institute: University of Utah

data_processing:
fastq files to the human genome reference (hg19) using novoalignver 2.08.01
Counts and FPKM from USEQ HCI package : https://healthcare.utah.edu/huntsmancancerinstitute/research/shared-resources/center-managed/bioinformatics/software-useq.php
The gene annotation is taken from Ensembl Homo Sapiens GRCh37
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes counts  and FPKM values for each Sample

growth_protocol: Tumor fragments (solid tumors) or cell suspensions (PE or ascites, with matrigel) implanted into cleared mammary fat pads of NOD/SCID or NSG mice. Estrogen was supplemented in ER+ cases. See DeRose and Gligorich et al 2013 for detailed methods

extract_protocol:
PDX tumor was removed, flash frozen on dry ice, and RNA was harvested using Qiagen kit . 1 ug of total RNA for the construction of sequencing libraries.
Library protocol =Illumina TruSeq Stranded mRNA Library Preparation Kit with poly(A) selection , HiSeq 101 Cycle Paired-End Sequencing v4

tag: tissue

value: breast cancer

tag: index taga

value: Index 3 TTAGGC

tag: hci - reference sample name


title: 10705X3 (Lap/lapatinib resist)

source_name: Lap/lapatinib resist

value: Index 13 AGTCAA

value: Lap


title: 10705X4 (Her/Lap resist - sequential)

source_name: Her/Lap resist - sequential

value: Index 21 GTTTCG

value: Her/Lap


title: 10705X5 (Lap/Her resist - sequential)

source_name: Lap/Her resist - sequential

value: Index 9 GATCAG

value: Lap/Her


title: 10705X2 (Her/trastuz resist)

source_name: Her/trastuz resist

value: Index 7 CAGATC

value: Her


title: flg22_seedlings_24h_rep1

status: Public on Dec 11 2018

city: heraklion

first: Anastasia

last: Dimopoulou

state: Crete

address: Nikolaou Plastira 100

department: IMBB

country: Greece

institute: FORTH

description: Gene expression after 24hr in flg22.

hyb_protocol: Hybridization was performed on a 4 x 44K tomato array (Agilent Technologies G2519F-022270) following the standard procedure of the Gene Expression Hybridization Kit.

scan_protocol: Scanning was performed by an Agilent Technologies Scanner G2505C.

data_processing: Raw data was extracted using the GE2_107_Sep09 protocol of the Agilent Feature Extraction Software. Data normalization was performed by the implementation of normalizeBetweenArrays function of the limma package in R (Smyth, G. K., and Speed, T. P. , 2003: Normalization of cDNA microarray data. Methods 31, 265-273), using the quantile method.

organism: Solanum lycopersicum

label_protocol: Samples from treated S. lycopersicum seedlings were labeled with Cy3, using standard Agilent labeling protocols.

growth_protocol: Fifteen days after germination on agar plates containing 1× Murashige and Skoog (MS) medium (Duchefa), under controlled conditions, tomato seedlings were transferred to liquid MS (2 seedlings/2mL of medium in wells of 24-well-plates).

extract_protocol: Total RNA was extracted from each sample using TRI reagent (Ambion) according to the manufacturer’s instructions. The concentration and purity of RNA were estimated using a P330 nanophotometer (IMPLEN). DNase-treated RNA (RNase-free DNase; New England Biolabs) was reverse-transcribed into cDNA using Superscript II reverse transcriptase and oligo-dT as primers (Invitrogen).

treatment_protocol: Three hours after transfer, the medium was supplied with flg22 peptide (Eurogentec) to a final concentration of 1μΜ or with MBI600 CFCF to 1/5 v/v volume. Plantlets were collected in different time points after treatment (6 and 24h), frozen in liquid nitrogen and stored at −80°C. Two independent experiments were performed. Each experiment included 2 biological replicates per treatment and each replicate was a pool of two seedlings.

value: Whole seedlings

tag: age

value: 15 days

tag: time point


title: untreated_seedlings_6h_rep2

description: Gene expression after 6hr in water.

source_name: untreated, 6h

value: untreated


title: Spleen_Treg_intact

status: Public on Dec 01 2018

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

hyb_protocol: Expression Hybridization Kit (Agilent)

scan_protocol: DNA Microarray Scanner (2505C, Agilent), Gene Expression Wash Pack (Agilent)

data_processing: Feature Extraction ver 10.7.1.1 (Agielnt)

source_name: Tregs from intact spleen

label_protocol: One-Color RNA Spike-In Kit, Low Input Quick Amp Labeling Kit (Agilent)

extract_protocol: For brain tissue, total RNA was isolated using QIAzol Lysis Reagent (QIAGEN) from the day 14 post-ischemic or sham brains of WT or DEREG mice (slice 3 on the ischemic side). For CD4+ T cells, total RNA was isolated using a TRIzolTM LS reagent (Invitrogen) from the CD4+ T cells in WT ischemic mice brain or in untreated mice spleen.

value: Spleen

tag: cell

value: Treg


title: untreated_seedlings_24h_rep1

description: Gene expression after 24hr in water.

source_name: untreated, 24h


title: untreated_seedlings_6h_rep1

description: Gene expression after 6hr in water.


title: flg22_seedlings_24h_rep2

description: Gene expression after 24hr in flg22.


title: flg22_seedlings_6h_rep1

description: Gene expression after 6hr in flg22.

source_name: flg22, 6h


title: HepG2_miR-493-5p

status: Public on Dec 05 2018

city: Wako

first: Luc

last: Gailhouste

state: Saitama

address: 408 Main Research Building, 2-1 Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

description:
Gene expression after miR-493-5p overexpression versus control
4-G2_493

hyb_protocol: Agilent one-color gene expression hyb/wash protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The raw data were processed using Agilent’s Feature Extraction Software version 10.7.3.1 to analyze the array and calculate the intensities of the measured spots.

source_name: HepG2, miR-493-5p mimic, 72 hours

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol. Cyanine-3 (Cy3)

growth_protocol: Human Hep3B and HepG2 cells were purchased from the American Type Culture Collection and maintained in DMEM (Gibco) supplemented with penicillin (50 IU/mL; Gibco), streptomycin (50 µg/mL; Gibco), and 10 % fetal bovine serum (FBS; Thermo Scientific).

extract_protocol: mRNA and miRNA were purified using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. Total RNA was quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific), and the integrity of the RNA was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: For characterization of miR-493-5p targets, total RNAs were collected from Hep3B and HepG2 cells 72 hours after cell transfection using miR-493-5p and negative control miRNA mimics (100 nM).

value: hepatocellular carcinoma

tag: genotype

value: miR-493-5p overexpression


title: mbi600_seedlings_24h_rep1

description: Gene expression after 24hr in MBI600 CFCF.

value: MBI600 CFCF


title: mbi600_seedlings_6h_rep2

description: Gene expression after 6hr in MBI600 CFCF.


title: untreated_seedlings_24h_rep2

description: Gene expression after 24hr in water.


title: flg22_seedlings_6h_rep2

description: Gene expression after 6hr in flg22.


title: Spleen_nonTreg_inatct

source_name: non Tregs from intact spleen

treatment_protocol: For brain tissue, total RNA was isolated using QIAzol Lysis Reagent (QIAGEN) from the day 14 post-ischemic or sham brains of WT or DEREG mice (slice 3 on the ischemic side). For CD4+ T cells, total RNA was isolated using a TRIzolTM LS reagent (Invitrogen) from the CD4+ T cells in WT ischemic mice brain or in untreated mice spleen.

value: non Treg


title: Hep3B_control

description:
Gene expression after miR-493-5p overexpression versus control
1-3B_Ctrl

source_name: Hep3B, negative control miRNA mimic, 72 hours

tag: cell line

value: control


title: Brain_Treg_ischemia

source_name: Tregs from ischemic brain at day14 after stroke onset

value: Brain


title: mbi600_seedlings_6h_rep1


title: mbi600_seedlings_24h_rep2


title: HepG2_control

description:
Gene expression after miR-493-5p overexpression versus control
3-G2_Ctrl

source_name: HepG2, negative control miRNA mimic, 72 hours

tag: cell type


title: Brain_nonTreg_ischemia

source_name: non Tregs from ischemic brain at day14 after stroke onset


title: Hep3B_miR-493-5p

description:
Gene expression after miR-493-5p overexpression versus control
2-3B_493

source_name: Hep3B, miR-493-5p mimic, 72 hours


title: keratinocytes_gapmeR-2_rep3

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from keratinocytes with WAKMAR2 depletion.

hyb_protocol: The samples were hybridized to a Clariom S Human Array Plate according to standard Affymetrix GeneTitan protocol.

scan_protocol: The array plate was scanned using the Affymetrix GeneTitan Scanner.

data_processing: Generated CEL files were analyzed using Affymetrix Expression Console v. 3.1.0.5 and the RMA method

source_name: keratinocytes transfected with gapmeR-2

label_protocol: Total RNA was labeled using the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s (Affymetrix) instructions.

growth_protocol: Human adult epidermal keratinocytes were purchased from Cascade Biologics and cultured in EpiLife® serum-free keratinocyte growth medium including Human Keratinocyte Growth Supplement (Cascade Biologics) at 37°C in 5% CO2.

extract_protocol: 24 hours after transfection, the total RNA was extracted with miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The third passage keratinocytes at 60-70% confluence were transfected with 20nM WAKMAR2-specific GapmeR or GapmeR negative control (Exiqon) using Lipofectamine 2000 (Invitrogen).

value: skin


title: keratinocytes_gapmeR-2_rep2


title: CRISPR_c58_WT

status: Public on Nov 29 2018

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description:
PolyA RNA
Quantified_RNAseq_report_KO.txt

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Reads were trimmed for quality using Trim Galore using default parameters to remove the standard Illumina adapter sequence.
Reads were mapped to the mouse GRCm38 genome assembly using HiSat2.
BAM files were imported to Seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: Quantified_RNAseq_report_KO.txt file is tab delimited and contains the following columns: (1) gene name (Ensembl) ; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) ID (Ensembl) (7) Description (Ensembl) ; (8-14) log2 RPM value.

source_name: Embryonic Stem Cell

growth_protocol: Embryonic stem cells were cultured in serum/LIF feeder free conditions as previously described (Ficz et al., Cell Stem Cell 13, 351–359).

extract_protocol:
RNA was isolated using TriReagent (Sigma) and treated with DNaseI (Ambion DNA-free DNA Cat #1311027) using manufacturer's instructions.
PolyA RNA libraries were made using 200ng-1μg RNA at the Sanger Institute Illumina bespoke pipeline.

treatment_protocol: CRISPR genome editing of Dppa2 (clone 5, c05; clone 12, c12), Dppa4 (clone 23, c23; clone 29, c29), both Dppa2 and Dppa4 (clone 43, c43) or nontargetting control (clone 57, c57; clone 58, c58) was performed as previously described (Ran et al. Nature Protocols 2013 Vol 8 p2281-2308). Clones were seeded by flow cytometry and expanded for several passages prior to RNA isolation.

value: Embryonic stem cells

tag: strain/background

tag: crispr editing

value: Nontargetting control (c58)


title: CRISPR_c29_Dppa4_KO

value: Dppa4 KO (c29)


title: CRISPR_c43_DKO

value: Dppa2 Dppa24 DKO (c43)


title: CRISPR_c57_WT

value: Nontargetting control (c57)


title: CRISPR_c12_Dppa2_KO

value: Dppa2 KO (c12)


title: CRISPR_c23_Dppa4_KO

value: Dppa4 KO (c23)


title: CRISPR_c05_Dppa2_KO

value: Dppa2 KO (c05)


title: Dppa4_siRNA_rep3C

description:
PolyA RNA
processed data file: Quantified_RNAseq_report_siRNA.txt

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Reads were trimmed for quality using Trim Galore (v.0.4.5) using default parameters to remove the standard Illumina adapter sequence.
Reads were mapped to the mouse GRCm38 genome assembly using HISAT2 (v2.0.5).
BAM files were imported to Seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: Quantified_RNAseq_report_siRNA.txt file is tab delimited and contains the following columns: (1) gene name (Ensembl) ; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) ID (Ensembl) (7) Description (Ensembl) ; (8-16) log2 RPM value.

treatment_protocol: Embryonic stem cells were transfected with control, Dppa2 or Dppa4 siRNA at 0hrs and 48 hours. At 96 hours (4 days), cells were collected for RNA isolation.

tag: sirna


title: Dppa2_siRNA_rep3B


title: Dppa4_siRNA_rep3B


title: Dppa2_siRNA_rep3C


title: Dppa4_siRNA_rep3A


title: control_siRNA_rep3B

value: Control


title: keratinocytes_gapmeR-2_rep1


title: keratinocytes_gapmeR-ctr_rep3

description: Gene expression data from keratinocytes transfected with GapmeR negative control.

source_name: keratinocytes transfected with gapmeR-ctr


title: control_siRNA_rep3A


title: keratinocytes_gapmeR-ctr_rep2


title: Dppa2_siRNA_rep3A


title: control_siRNA_rep3C


title: Zscan4c_12b_neg

description:
PolyA RNA
processed data file: Quantified_RNAseq_report.txt

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Reads were trimmed for quality using Trim Galore (v0.4.5) using default parameters to remove the standard Illumina adapter sequence.
Reads were mapped to the mouse GRCm38 genome assembly using HISAT2 (v2.0.5).
BAM files were imported to Seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: Quantified_RNAseq_report.txt file is tab delimited and contains the following columns: (1) gene name (Ensembl) ; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) ID (Ensembl) (7) Description (Ensembl) ; (8-81) log2 RPM value.

extract_protocol:
RNA was isolated using Qiagen RNA-DNA allprep columns or TriReagent (Sigma) and treated with DNaseI (Ambion DNA-free DNA Cat #1311027) using manufacturer's instructions.
PolyA RNA libraries were made using 200ng-1μg RNA at the Sanger Institute Illumina bespoke pipeline.

treatment_protocol: Embryonic stem cells were transfected with constructs containing candidate gene of interest fused to GFP for 48 hours. Cells were then sorted based on GFP expression (neg vs. pos). Number between gene name and neg/pos represents experimental replicate.

tag: candidate gene

tag: gfp

value: negative


title: keratinocytes_gapmeR-ctr_rep1


title: Zscan4c_12b_pos

value: positive


title: usp3_4_pos


title: usp3_4_neg


title: Zscan4c_12a_neg


title: Zscan4c_12a_pos


title: usp3_5_neg


title: usp3_3_pos


title: Zscan4c_11_pos


title: usp3_5_pos


title: Trp63_8b_neg


title: Trp63_8b_pos


title: Zscan4c_11_neg


title: usp3_3_neg


title: Trp63_6_neg


title: tox3_8_neg


title: Trp63_6_pos


title: Trp63_8a_neg


title: Trp63_8a_pos


title: tox3_4_pos


title: tox3_4_neg


title: tox3_3_pos


title: Sp110_neg


title: Sp110_12a_pos


title: Sp110_12b_neg


title: Sp110_4_pos


title: Sp110_12a_neg


title: Irf1_4_pos


title: Irf1_12_pos


title: tox3_3_neg


title: Irf1_6_pos


title: Irf1_6_neg


title: Hdac9_12_neg


title: Hdac9_8_neg


title: Sp110_pos


title: Irf1_4_neg


title: Irf1_12_neg


title: Hdac9_8_pos


title: Hdac9_12_pos


title: gata3_6_neg


title: tox3_8_pos


title: Hdac9_8a_neg


title: Hdac9_8a_pos


title: gata3_6_pos


title: Gata3_12_pos


title: Sp110_4_neg


title: Sp110_12b_pos


title: Gata3_12_neg


title: Gata3_11_neg


title: Gata3_11_pos


title: eya1_6_neg


title: eya1_4_pos


title: eya1_5_neg


title: eya1_5_pos


title: eya1_6_pos


title: Dppa4_12_neg


title: Dppa4_12_pos


title: eya1_4_neg


title: Dppa4_11a_pos


title: Dppa4_11b_neg


title: Bahd1_8a_neg


title: Bahd1_pos


title: Dppa2_11a_pos


title: Bahd1_8a_pos


title: Bahd1_neg


title: Bahd1_6_neg


title: Dppa2_11b_neg


title: mouseskinCPDcon1

status: Public on Nov 24 2018

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

description: Replicate 1

data_processing:
Library strategy: XR-seq
Adaptor trimming
Filtering reads based on length
Random sampling
Alignment
Read filtering based on nucleotide composition
Strand separation
Gene coverage count
Remove mismatches and gaps and duplicates
Genome_build: rDNA and DHFR
Supplementary_files_format_and_content: wig files

source_name: mouse skin fibroblast cells

growth_protocol: NHF1, CSB, XPC, GM12878 and wild-type mouse skin fibroblast cells were grown in DMEM (Life Technologies, Gaithersburg, MD) supplemented with 10% fetal bovine serum (Gemini, Woodland, CA). Cells were maintained in an incubator at 37°C under 5% CO2.

extract_protocol:
Cells were lysed gently and small molecular weight DNA, consisting mostly of excised 26-27 mers, was separated from chromosomal high molecular weight DNA by centrifugation.
Briefly, the excised oligomers are immunoprecipitated with anti-TFIIH (anti-XPB and anti-p62) antibodies because the excision product is released in a relatively stable complex with TFIIH, which also protects the excision product from degradation by non-specific nucleases. This is followed by extraction of the excised oligomers and ligation to adaptors and a second immunoprecipitation with anti-CPD antibodies. Then photolyase repairs the CPD damage. This is followed by PCR amplification with index primers and NGS sequencing on HiSeq platform.

treatment_protocol: Cells were grown to about 80% confluence in 150mm dishes. Media was removed, cells were washed with PBS, irradiated with 20 J/m2 of UV, and then warm, fresh media was added and cells were incubated for 3hr at 37°C (MSF), 1hr at 37°C (NHF1, XPC, CSB). GM12878 were treated with cisplatin 2hr at 37°C. Cells were then harvested and processed using the XR-seq procedure.

value: skin fibroblasts

tag: genotype/variation

value: wild type

value: UV


title: Dppa2_12_neg


title: Dppa2_11b_pos


title: mouseskinCPDcon2

description: Replicate 2


title: Dppa4_11b_pos


title: Dppa4_11a_neg


title: Dppa2_12_pos


title: Dppa2_11a_neg


title: H3K9me2_bio3

status: Public on Nov 22 2018

city: Heidelberg

first: Marina

last: Lusic

address: Im Neuenheimer Feld 400

country: Germany

institute: Heidelberg University Hospital

data_processing:
All fastq reads were trimmed and their adaptors were removed with bbduk (part of bbtools) using parameters ktrim=r k=25 mink=6 hdist=1 rcomp=t qout=33 minlength=30 qtrim=t trimq=12.
Trimmed reads were mapped to reference human genome version hg10 with bbmap using parameters minid=0.98.
All bam the files for the same ChIP antibody were merged together and peaks were called with macs2 with parameters macs2 callpeak --broad --broad-cutoff 0.1 -p 1e-9 -g 2.7e9 -B, against corresponding merged inputs.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph for H3K9me2 signal

source_name: primary CD4+ T cells

extract_protocol:
20x10^6 CD4+ T cells were washed 1 time in PBS prior to crosslinking with 1% Formaldehyde for 10 minutes at room temperature, followed by termination of the reaction with 125mM glycine on ice. Cell pellet was washed 2 times with PBS at 4C and was lysed in 0.5% NP-40 buffer (10mM Tris-Cl pH7.4, 10 mM NaCl, 3 mM MgCl2, 1 mM PMSF and Protease Inhibitors). For histone ChIPs, obtained nuclei were washed once in the same buffer without NP-40. Nuclei were resuspended in 0.5% NP-40 buffer supplemented with 0.15 % SDS and 1.5 mM CaCl2. Nuclei were incubated at 37 C for 10 minutes prior to addition of Micrococcal Nuclease (16 units of the enzyme), and the reaction was stopped after 7 minutes with 3 mM EGTA. DNA was additionally sheared by sonication (Covaris or Bioruptor, Diagenode) to an average size of DNA fragments below 500 bps. Extracts were then diluted up to 0.01% SDS, 1% Triton-X, 20mM Tris pH 8, 150mM NaCl 2 mM EDTA. Extracts were precleared by 1 hr incubation with protein A/G Magna ChIP beads at 4C and diluted with 5x IP buffer to a final concentration of 140 mM NaCl and 1 % NP-40. Lysate corresponding to 3-4 x 106 million of cells was then incubated with 2-4 µg of the indicated antibody overnight at 40 C, followed by a 2.5 hr incubation with Magna ChIP Protein A/G Magnetic Beads (Millipore). Beads were then washed thoroughly with RIPA150, with LiCl – containing buffer and with TE buffer, RNAse treated for 1 hr at 370C, and Proteinase K treated for 2 hours at 560C. Decrosslinking of protein–DNA complexes was performed by an overnight incubation at 650C. Additional 1 hr of Proteinase K digestion was performed at 560C and DNA was then extracted using Agencourt AMPure XP beads (Beckman Coulter) and quantified by real time PCR. The following antibodies were used ChIP: H3K27ac (ab4729), H3K4me3 (ab8580) H3K36me3 (ab9050) IgG Rabbit (ab46540).
ChIP-Seq: Approximately 10 ng of corresponding inputs and ChIP-ed DNA from primary CD4 T cells: H3K27Ac, H3K4me3, H3K36me3, H4K20me1 and H3K9me2 Ips was prepared for the sequencing using NEBNext® Ultra™ II DNA Library Prep Kit

value: primary CD4+ T cells

tag: antibody

value: Anti-Histone H3 (di methyl K9) antibody [mAbcam 1220] - ChIP Grade (ab1220)

tag: date of sequencing


title: H4K20me1_bio2

data_processing:
All fastq reads were trimmed and their adaptors were removed with bbduk (part of bbtools) using parameters ktrim=r k=25 mink=6 hdist=1 rcomp=t qout=33 minlength=30 qtrim=t trimq=12.
Trimmed reads were mapped to reference human genome version hg10 with bbmap using parameters minid=0.98.
All bam the files for the same ChIP antibody were merged together and peaks were called with macs2 with parameters macs2 callpeak --broad --broad-cutoff 0.1 -p 1e-9 -g 2.7e9 -B, against corresponding merged inputs.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph for input, Peak files

value: Anti-Histone H4 (mono methyl K20) antibody - ChIP Grade (ab9051)


title: H4K20me1_bio1


title: H3K9me2_bio1


title: H3K9me2_bio2


title: Bahd1_6_pos

value: Embryonic stem cells


title: H3K4me3_bio3


title: H3K4me3_bio1


title: H3K4me3_bio2


title: H3K36me3_bio1


title: H3K36me3_bio2


title: H3K27ac_bio1_1


title: H3K27ac_bio2_1


title: H3K27ac_bio2_2


title: H3K27ac_bio1_2


title: Input 5

description: Input.bedGraph


title: Input 3

description: Input.bedGraph


title: Input 2

description: Input.bedGraph


title: Input 4

description: Input.bedGraph


title: Input 1

description: Input.bedGraph


title: IGRA positive at t6, biological rep 5

city: Mexico

first: Martha

last: Torres

state: Mexico City

address: Calzada de Tlalpan 4502

department: Microbiology

country: Mexico

institute: Instituo Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

description:
IGRApos_T6-5
Gene expression data from individual TST positive IGRA positive once prophylactic treatment with isoniazid was concluded (6 months later).

hyb_protocol: Samples were hybridized with the human 1.0 ST chip of the Affymetrix platform using the hybridization Kit (Affymetrix).

scan_protocol: The microarrays were scanned at a resolution of 5 μm using the Agilent scanner.

data_processing: Raw data were background-corrected using Robust Multiarray Average (RMA) and normalized using Quantile Normalization by Bioconductor affy package of the R (CRAN) software (https://bioconductor.org/biocLite.R). Differential expression was determined using statistical linear models with arbitrary coefficients and contrasts of interest were analyzed using the bioconductor library limma. Corrections for multiple comparisons were applied using the false discovery rate (FDR).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was isolated using a PAXgene kit for RNA (Qiagen, PreAnalytix GmbH) according to the manufacturer’s instructions.

treatment_protocol:
Storage protocol: Three milliliters of whole blood were collected using a PAXgene blood RNA kit (PreAnalytix by Qiagen, Hombrechtikon, UK) at the following time points: pretreatment (0) and at one month (1), and 6 months after the initiation of treatment (6). Whole blood samples were preserved in PAXgene at -70°C until RNA extraction and used for microarray.
Volunteers who were in contact with TB cases and without clinical or radiological evidence of TB disease, healthy, asymptomatic, aged 18 years or older and reactive to the TST (>10 mm) and with or without IGRA positive result received INH (5 mg per kg of body weight, up to 300 mg per day, for 6 months).

tag: tissue

value: Whole blood

tag: tst

value: Positive

tag: igra

tag: sampling time

value: 6 month isoniazid treatment


title: IGRA positive at t6, biological rep 8

description:
IGRApos_T6-8
Gene expression data from individual TST positive IGRA positive once prophylactic treatment with isoniazid was concluded (6 months later).


title: IGRA positive at t6, biological rep 2

description:
IGRApos_T6-2
Gene expression data from individual TST positive IGRA positive once prophylactic treatment with isoniazid was concluded (6 months later).


title: IGRA positive at t1, biological rep 4

description:
IGRApos_T1-4
Gene expression data from individual TST positive IGRA positive after 1 month of prophylactic treatment with isoniazid.

value: 1 month isoniazid treatment


title: IGRA positive at t6, biological rep 6

description:
IGRApos_T6-6
Gene expression data from individual TST positive IGRA positive once prophylactic treatment with isoniazid was concluded (6 months later).


title: IGRA positive at t1, biological rep 7

description:
IGRApos_T1-7
Gene expression data from individual TST positive IGRA positive after 1 month of prophylactic treatment with isoniazid.


title: IGRA positive at t1, biological rep 5

description:
IGRApos_T1-5
Gene expression data from individual TST positive IGRA positive after 1 month of prophylactic treatment with isoniazid.


title: IGRA positive at t6, biological rep 7

description:
IGRApos_T6-7
Gene expression data from individual TST positive IGRA positive once prophylactic treatment with isoniazid was concluded (6 months later).


title: IGRA positive at t6, biological rep 3

description:
IGRApos_T6-3
Gene expression data from individual TST positive IGRA positive once prophylactic treatment with isoniazid was concluded (6 months later).


title: IGRA positive at t1, biological rep 2

description:
IGRApos_T1-2
Gene expression data from individual TST positive IGRA positive after 1 month of prophylactic treatment with isoniazid.


title: IGRA positive at t1, biological rep 8

description:
IGRApos_T1-8
Gene expression data from individual TST positive IGRA positive after 1 month of prophylactic treatment with isoniazid.


title: IGRA positive at t1, biological rep 1

description:
IGRApos_T1-1
Gene expression data from individual TST positive IGRA positive after 1 month of prophylactic treatment with isoniazid.


title: IGRA positive at t6, biological rep 4

description:
IGRApos_T6-4
Gene expression data from individual TST positive IGRA positive once prophylactic treatment with isoniazid was concluded (6 months later).


title: IGRA positive at t0, biological rep 7

description:
IGRApos_T0-7
Gene expression data from individual TST positive IGRA positive before prophylactic treatment with isoniazid.

value: Before isoniazid treatment


title: IGRA positive at t1, biological rep 3

description:
IGRApos_T1-3
Gene expression data from individual TST positive IGRA positive after 1 month of prophylactic treatment with isoniazid.


title: IGRA positive at t1, biological rep 6

description:
IGRApos_T1-6
Gene expression data from individual TST positive IGRA positive after 1 month of prophylactic treatment with isoniazid.


title: IGRA positive at t0, biological rep 2

description:
IGRApos_T0-2
Gene expression data from individual TST positive IGRA positive before prophylactic treatment with isoniazid.


title: IGRA positive at t0, biological rep 6

description:
IGRApos_T0-6
Gene expression data from individual TST positive IGRA positive before prophylactic treatment with isoniazid.


title: IGRA negative at t6, biological rep 6

description:
IGRAneg_T6-6
Gene expression data from individual TST positive IGRA negative once prophylactic treatment with isoniazid was concluded (6 months later).

value: Negative


title: IGRA positive at t0, biological rep 5

description:
IGRApos_T0-5
Gene expression data from individual TST positive IGRA positive before prophylactic treatment with isoniazid.


title: IGRA positive at t0, biological rep 4

description:
IGRApos_T0-4
Gene expression data from individual TST positive IGRA positive before prophylactic treatment with isoniazid.


title: IGRA positive at t0, biological rep 3

description:
IGRApos_T0-3
Gene expression data from individual TST positive IGRA positive before prophylactic treatment with isoniazid.


title: IGRA negative at t6, biological rep 3

description:
IGRAneg_T6-3
Gene expression data from individual TST positive IGRA negative once prophylactic treatment with isoniazid was concluded (6 months later).


title: IGRA positive at t0, biological rep 8

description:
IGRApos_T0-8
Gene expression data from individual TST positive IGRA positive before prophylactic treatment with isoniazid.


title: IGRA negative at t6, biological rep 4

description:
IGRAneg_T6-4
Gene expression data from individual TST positive IGRA negative once prophylactic treatment with isoniazid was concluded (6 months later).


title: IGRA negative at t6, biological rep 2

description:
IGRAneg_T6-2
Gene expression data from individual TST positive IGRA negative once prophylactic treatment with isoniazid was concluded (6 months later).


title: IGRA positive at t6, biological rep 1

description:
IGRApos_T6-1
Gene expression data from individual TST positive IGRA positive once prophylactic treatment with isoniazid was concluded (6 months later).


title: IGRA negative at t6, biological rep 5

description:
IGRAneg_T6-5
Gene expression data from individual TST positive IGRA negative once prophylactic treatment with isoniazid was concluded (6 months later).


title: IGRA negative at t6, biological rep 1

description:
IGRAneg_T6-1
Gene expression data from individual TST positive IGRA negative once prophylactic treatment with isoniazid was concluded (6 months later).


title: IGRA negative at t1, biological rep 4

description:
IGRAneg_T1-4
Gene expression data from individual TST positive IGRA negative after 1 month of prophylactic treatment with isoniazid.


title: IGRA negative at t1, biological rep 2

description:
IGRAneg_T1-2
Gene expression data from individual TST positive IGRA negative after 1 month of prophylactic treatment with isoniazid.


title: IGRA negative at t1, biological rep 1

description:
IGRAneg_T1-1
Gene expression data from individual TST positive IGRA negative after 1 month of prophylactic treatment with isoniazid.


title: IGRA negative at t1, biological rep 5

description:
IGRAneg_T1-5
Gene expression data from individual TST positive IGRA negative after 1 month of prophylactic treatment with isoniazid.


title: IGRA negative at t0, biological rep 4

description:
IGRAneg_T0-4
Gene expression data from individual TST positive IGRA negative before prophylactic treatment with isoniazid.


title: IGRA negative at t1, biological rep 3

description:
IGRAneg_T1-3
Gene expression data from individual TST positive IGRA negative after 1 month of prophylactic treatment with isoniazid.


title: IGRA negative at t0, biological rep 5

description:
IGRAneg_T0-5
Gene expression data from individual TST positive IGRA negative before prophylactic treatment with isoniazid.


title: IGRA negative at t0, biological rep 3

description:
IGRAneg_T0-3
Gene expression data from individual TST positive IGRA negative before prophylactic treatment with isoniazid.


title: tn010-t

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

data_processing:
Basecalls performed using Ion Torrent Suite 4.0
XmaI-RRBS reads were aligned to the hg19 genome assembly using Bismark v0.12.2 with bowtie2 v2.2.3 with settings --non_directional -L 24 --rdg 0,3 --rfg 0,3.
Data were filtered to remove artificial methylation using custom script
Methylation state called using bismark_methylation_extractor
Genome_build: hg19
Supplementary_files_format_and_content: .cov files were generated using bismark_methylation_extractor

source_name: Breast

extract_protocol:
Phenol:chloroform protocol after proteinase K treatment
XmaI-RRBS protocol as in: Tanas AS, Borisova ME, Kuznetsova EB et al. Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-reduced representation bisulfite sequencing. Epigenomics. 9 (6), 833-847 (2017).

tag: sample type

value: Tissue

value: Breast Cancer

tag: mtypehe

value: hiHER

tag: etype

value: TN

tag: gtype

value: nos duct

tag: age

tag: t

tag: n

tag: m


title: IGRA negative at t1, biological rep 6

description:
IGRAneg_T1-6
Gene expression data from individual TST positive IGRA negative after 1 month of prophylactic treatment with isoniazid.


title: tms077-t

value: hiLumAB

value: LumB

value: duct


title: IGRA negative at t0, biological rep 1

description:
IGRAneg_T0-1
Gene expression data from individual TST positive IGRA negative before prophylactic treatment with isoniazid.


title: tms078-t

value: modHER


title: tms089-t


title: tms053-t


title: tms048-t

value: hiHET


title: tms088-t


title: tms096-t


title: mcf7-cl-2018

value: Cell line

value: CL


title: tms094-t


title: tn006-t


title: tms090-t

value: modLumB


title: IGRA negative at t0, biological rep 2

description:
IGRAneg_T0-2
Gene expression data from individual TST positive IGRA negative before prophylactic treatment with isoniazid.

value: Whole blood

value: Positive


title: tn016-t


title: tms047-t

value: lobul


title: IGRA positive at t0, biological rep 1

description:
IGRApos_T0-1
Gene expression data from individual TST positive IGRA positive before prophylactic treatment with isoniazid.

value: Before isoniazid treatment


title: tn023-t

value: Tissue

value: modTNBC


title: tms044-t

value: Breast Cancer


title: tms035-t


title: tms042-t


title: tms050-t


title: tms032-t


title: tms031-t


title: tms030-t


title: tms046-t


title: tms013-t

value: hiHER


title: g155-t

value: LumA


title: tms018-t


title: g093-t


title: nb002-b

value: Normal Breast

value: NORM


title: g101-t

value: TN

value: duct


title: g077-t


title: tms023-t

value: hiLumAB

value: LumB


title: nb006-b


title: tms006-t

value: modHER

value: UN


title: tms017-t


title: g148-t


title: tms010-t


title: tms014-t

value: hiHET


title: g021-t

value: mix


title: tms021-t

value: modLumB


title: g124-t


title: g014-t


title: ZR-cl

value: Cell line

value: CL


title: tms033-t

value: Tissue


title: g009-t

value: Breast Cancer


title: t47d-cl


title: r052-t

value: hiHER


title: tms025-t


title: nb004-b


title: tms029-t


title: r051-t

value: muc


title: r045-t


title: r042-t

value: modTNBC


title: r043-t


title: r041-t


title: r036-t

value: LumA


title: r037-t


title: r022-t

value: TN


title: r038-t

value: lobul


title: r021-t

value: duct


title: r039-t


title: r010-t

value: LumB


title: r040-t

value: hiLumAB


title: r014-t


title: r009-t


title: r002-t


title: r029-t

value: meta


title: r003-t


title: ob020-t

value: modHER


title: ob014-t


title: ob013-t


title: ob006R-t

value: neuro


title: ob006L-t


title: r005-t


title: ob004-t


title: nii029-t

value: hiHET


title: nii025-t


title: nii017-t


title: nii005-t


title: nii013-t


title: r011-t


title: nb003-b

value: Normal Breast

value: NORM


title: HBL-cl

value: Tissue

value: CL


title: g166-t

value: Breast Cancer

value: hiHER


title: g165-t


title: g164-t


title: g162-t


title: g158-t


title: g157-t

value: modLumB


title: g156-t

value: LumA


title: g163-t


title: g154-t

value: modTNBC

value: TN


title: g153-t

value: duct


title: g152-t


title: g144-t


title: g150-t

value: LumB


title: g142-t


title: g133-t

value: hiLumAB


title: g151-t


title: g128-t

value: lobul


title: g127-t


title: g097-t


title: nb005-b


title: g081-t


title: g068-t


title: g067-t

value: meta


title: g159-t


title: g025-t


title: g020-t

value: mpc


title: g023-t


title: g016_A-t

value: modHER


title: BT-cl

value: Cell line


title: nb001-b

value: Normal Breast

value: NORM


title: mcf7-cl

value: CL


title: g015-t

value: Tissue

value: Breast Cancer

value: hiHET


title: shRad21_vivo_v2_3

status: Public on Nov 21 2018

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

description:
GFP+ KSL cells from mice that were transplanted with lentivirally infected KSL cells (shRNA-Rad21), 3 month after transplantation
raw_counts.tsv

data_processing:
Reads/sequence information was extracted using bcl2fastq v1.8.4 (Illumina).
Read quality check; FastQC (v0.11.3)
Read quality trimming; PRINSEQ (v0.20.3); -min_len 20 -trim_tail_right 10 -trim_qual_right 20 -trim_qual_left 20 -ns_max_n 1
Removal of reads with rRNA origin; SortMeRNA (v2.0); used RFAM 5s|5.8s and Silva 18s|28s as reference databases for filtering
Read alignment of preprocessed data on mouse genome; tophat2 (v2.0.11); default parameters
Read alignment quantification based on the mm10 Ensembl annotation GRCm38.81; HTSeq-count (v0.6.1); --stranded=no
Count normalization and call of differential expressed genes; DESeq2 (v1.16.1)
Genome_build: mm10
Supplementary_files_format_and_content: Unique raw read counts obtained by HTSeq-count for each gene and sample in tab-separated value (TSV) format

source_name: total RNA

extract_protocol:
Total RNA of cells was extracted using MagMAX™-96 Total RNA Isolation Kit (Ambion) according to the manufacturer’s protocol.
in vitro samples: TruSeq RNA v2 (Illumina); in vivo: SMART-Seq v4 Ultra Low Input RNA Kit (Takara) + Nextera XT DNA library preparation kit (Illumina); all libraries processed following the manufacturer‘s description

tag: strain

tag: construct

value: shRNA Rad21 knockdown

tag: cell type

value: hematopoietic stem/progenitor cells from bone marrow

tag: experiment type

value: in vivo


title: shRad21_vivo_v2_2


title: shLuci_vivo_v2_3

description:
GFP+ KSL cells from mice that were transplanted with lentivirally infected KSL cells (control shRNA), 3 month after transplantation
raw_counts.tsv

value: control-shRNA Luciferase


title: shRad21_vivo_v2_1


title: shRad21_vitro_v2_3

description:
GFP+CD48-Sca-1+ cells purified from cultured LSK cells, 3 days after isolation and lentiviral infection with an shRNA targeting Rad21
raw_counts.tsv

value: in vitro


title: shRad21_vitro_v2_1


title: shLuci_vivo_v2_1


title: shLuci_vivo_v2_2


title: shRad21_vitro_v2_2


title: shLuci_vitro_v2_2

description:
GFP+CD48-Sca-1+ cells purified from cultured LSK cells, 3 days after isolation and lentiviral infection with a control shRNA
raw_counts.tsv


title: shLuci_vitro_v2_3


title: g060-t

value: duct