title: NMuMG Vp16-TRF1ΔN 24h TGFβ

city: Barcelona

first: Rocco

last: Mazzolini

address: Carrer Dr. Aiguader, 88

country: Spain

institute: PRBB-IMIM

description: Barcode: GGCTAC

data_processing:
[Quality check] FastQC
[Mapping] STAR
[Counting number of reads mapping each gene] HTSeq
[Differential expression analysis] DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: normalized_log2_htseq_counts.txt, raw_htseq_counts.txt

growth_protocol: NMuMG cells were maintained in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Invitrogen) and insulin (10 mg/ml) at 37ºC in 5% CO2.

extract_protocol:
RNA was isolated with Gene Elute Mammal Total RNA Miniprep Kit (Sigma)
mRNA library were prepared with the rRNA depletion protocol

treatment_protocol: TGFβ (5 ng/ml) was used to induce EMT

tag: cell line

value: NMuMG cell line

tag: expressing

value: overexpressing mutated human TRF1 protein fused with Vp16 transcription activation domain

tag: agent

value: TGFβ


title: Tet2 hetero ko bio2 rep2

status: Public on Mar 28 2019

type: SRA

city: Shanghai

first: Shaorong

last: Gao

address: Siping Road NO.1239

country: China

institute: Tongji University

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 reference genome using tophat(v1.3.3) default commands.
Differential gene expression was detemined using R package edgeR,genes with absolute value of log2 fold change less than 1 or p-value more than 0.05 were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM files and Counts files of gene were generated using cufflinks(v1.2.0) and htseq-count(v0.6.0) default commands

molecule: total RNA

organism: Mus musculus

source_name: Tet2+/- TSC cell line 2

growth_protocol: TSCs were cultured on 70% FCM+25 ng/ml F4H (25 ng/ml fibroblast growth factor 4 (FGF4); Peprotech and 1.0 μg/ml heparin; Sigma).

extract_protocol:
Total RNA was isolated from cell pellets by Trizol reagent
RNA-Seq library were generated using KAPA Strandard mRNA-Seq Kits according to the manufacturer’s recommendations (Cat No. KK8440 box1 and KK8420 box2). Briefly, the mRNA was enriched using oligo(dT) magnetic beads and sheared to create short fragments of approximately 300 bp. cDNA was synthesized using random hexamer primers and purified using 1.8X Agencourt AMPure XP beads (Beckman). Finally, the sequencing primers linked to the cDNA fragments (approximately 300 bp) were isolated by gel electrophoresis and enriched by PCR amplification to construct the library. The sequencing was performed at the Sequencing Center in National Institute of Biology, Beijing using the HiSeq 2500 system developed by Illumina. Paired-end 100-bp sequencing was applied.

tag: strain


title: Tet2 homo ko bio2 rep2

source_name: Tet2-/- TSC cell line 2


title: NMuMG Vp16-TRF1ΔN 0h TGFβ

description: Barcode: TAGCTT

value: control


title: Tet2 hetero ko bio1 rep2

source_name: Tet2+/- TSC cell line 1


title: NMuMG TRF1ΔN 0h TGFβ

description: Barcode: ATCACG

value: overexpressing mutated human TRF1 protein


title: NMuMG TRF1ΔN 24h TGFβ

description: Barcode: ACTTGA


title: WT bio1 rep1

source_name: WT TSC cell line RO-7


title: SSEA1-GFP-_A15day_colony1

status: Public on Mar 30 2019

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: Bulk RNA-Seq data

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
The sequenced short reads were trimmed by Trimmomatic 0.3.3 and mapped to the human reference genome mm9 using TopHat 2.0.14 and Bowtie 2.2.5.
RPKM counts for each gene were obtained using the RPKMforgenes software.
Genome_build: The sequence reads were mapped to mm9 reference genes, downloaded on 30th Sept 2015
Supplementary_files_format_and_content: Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012). The processed data file contains Genename, Refseq, RPKM, and Rawcount columns (from left to right), and the expression level was represented by RPKM.

source_name: Rex1 GFPd2 ESC

growth_protocol: mESCs Rex1 GFPd2 were cultured on 0.1% gelatin-coated dishes in basal medium (GMEM supplemented with 10% Knockout™ Serum Replacement, 1% fetal bovine serum , 0.1 mM MEM non-essential amino acids, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, penicillin/streptomycin) and were differentiated on 0.1% gelatin-coated dishes in differentiation medium (DM) (alpha minimal essential medium MEM; supplemented with 10% fetal bovine serum and 50 nM 2-mercaptoethanol).

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (QIAGEN).
The sequencing libraries were constructed using KAPA stranded mRNA-seq Kit (KAPA Biosystems) from 20 ng or higher amount of total RNA

treatment_protocol: After 2 days differentiation in DM, SSEA1/GFP double negative cells were sorted and differentiated in DM without or with AICAR  until 15days. We also picked up naïve-like GFP+ colonies or sorted GFP+ cells. Those GFP+ cells were expanded on gelatin-coated plates in basal maintenance medium with Lif+2i and passaged every 3-4 days.

tag: cell type

value: ESC

tag: treatment protocol

value: Lif+2i (Meki Gsk3i, Lif)

tag: Stage

value: undifferentiated

tag: gfp expression

value: positive

tag: sorting

value: maintenance after reversion


title: IAA-0h-2

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

country: USA

institute: NIH

library_source: genomic

data_processing:
The illumine Run Time Analysis software (RTA 2.4.6) was used for processing image files.
The Illumina Bcl2fastq 2.17 was used for demultiplex and converting binary base calls and qualities to FASTQ format.
The sequencing reads were trimmed (adapters and low-quality bases) using Trimmomatic (version 0.30).
The trimmed reads were aligned to mouse genome (MM9, NCBI Build 37) using Bowtie2 software.
The mapping and QC statistics were calculated using Bam tools and Picard.
Genome_build: MM9
Supplementary_files_format_and_content: BigWig

molecule: genomic DNA

source_name: Lsh cko MEF

growth_protocol: MEF cells were cultured in DMEM media supplemented with 15% heat-inactivated fetal bovine serum (FBS), 100μg/ml streptomycin, and 100μg/ml penicillin in a 5% CO2 environment at 37°C

extract_protocol:
Nucleosomal DNA was prepared using EZ nucleosomal DNA prep kit (Zymo research). Nucleosome digestion was performed at varying doses and a maximal amount of 0.5 U Micrococcal Nuclease for 5 min at 25°C.
Libraries of nucleosome fragments were prepared and adapted for deep sequencing using the standard Illumina protocol and sequenced them on NextSeq using NextSeq High V2 chemistry and set up as 1x76bp single end run

treatment_protocol: Primary  MEF cells were derived from the body of E13.5 C57Bl/6 mouse embryos and genotyping was performed to select Lsh WT and Lsh KO.

tag: cell types

value: mouse embryonic fibroblasts

tag: genotype/variation

value: Lsh cko

tag: h3k4me1 chip antibody

value: Micrococcal nuclease


title: IAA-7h


title: UtxF1_BM_RNAseq_rep4

status: Public on Apr 01 2019

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: processed data file: Utx_F1_RNAseq_GEO.txt

data_processing:
RNA-seq data was quantified using kallisto version 0.43.0 with default parameters and with Ensembl build 85 transcripts as the set of target sequences.  Transcripts per million for individual transcripts from a single gene were summed to get one value per gene.
genome build: mm10
processed data files format and content: single tab-delimited .txt file with TPM values for each sample for each Ensembl (build 85) gene model.

source_name: bone marrow

extract_protocol:
Spine, pelvice bones, and long bones of the leg were collected and macerated.  Cells were washed, filtered, viably frozen, and stored in liquid nitrogen.  Cells were thawed in a water bath, and RNA was extracted from 2-6 million cells using an RNEasy Plus Mini kit (Qiagen).
Libraries were prepared using the Illumina TruSeq RNA library prep kit (Illumina #RS-122-2001) according to the manufacturer's instructions.  Sequencing was done on an Illumina HiSeq2500 with 40 bp paired-end reads, with mulitplexing (4 samples per lane). Barcode: GATCAG

value: bone marrow

tag: chip antibody

tag: condition

value: sarcoma Utx F1


title: IAA-3D


title: pMEF_KO6

source_name: KO MEF

value: KO


title: GC-OHT-NC


title: IAA-24


title: pMEF_WT5

source_name: WT MEF

value: WT


title: WT bio1 rep2


title: GC-OHT-2D


title: Tet2 homo ko bio2 rep1


title: IAA-0h


title: Tet2 hetero ko bio2 rep1


title: Input DNA (H3K27acetylation in A549 ChIP-seq 2)

city: New York

first: Hideo

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option
H3K27Ac peaks were called using MACS (v1.4.2) at p-value threshould of 1E-05 with no-ChIP input sample as control.
Genome_build: hg19

organism: Homo sapiens

source_name: Non-small cell lung cancer cells

growth_protocol: A549 and MSR-A549 cells were cultured in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using Rubicon Genomics Thruplex-DNAseq sample preparation kits from 2 ng immunoprecipitated DNA according to manufacturer’s protocol. The finished double strand DNA (dsDNA) libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with single-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: To establish MSR-A549 cells, A549 cells were cultured in the presence of 5 μM MMB and 1 μM selumetinib or in DMEM supplemented with 10% FBS alternately for 2 months. MSR-A549 cells were maintained with 5 μM momelotinib and 1 μM selumetinib continuously.

tag: drugs treated

value: DMSO

tag: chip-antibody

value: H3K27 acetylation (Abcam, ab4729)


title: Input DNA (H3K27acetylation in A549 ChIP-seq 1)


title: H3K27acetylation in MSR-A549 ChIP-seq 2

value: 5uM momelotinib and 1uM selumetinib


title: Input DNA (H3K27acetylation in MSR-A549 ChIP-seq 2)


title: H3K27acetylation in MSR-A549 ChIP-seq 1


title: Input DNA (H3K27acetylation in MSR-A549 ChIP-seq 1)


title: H3K27acetylation in A549 ChIP-seq 1


title: MSR-A549 cells with JQ1 treatment 2

data_processing:
Sequenced reads were mapped to a UCSC RefGene transcriptome version obtained in Feb 2016 and hg19 genome using tophat 2.1.0 with Bowtie2.1.0, Samtools 1.1 and -G and default parameters.
Transcripts quantification and differential expression were calculated with Cufflinks 2.2.1
Genome_build: hg19 UCSC RefGene (Feb 2016)
Supplementary_files_format_and_content: FPKM

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen, Cat.# 74106) and PerfectPure RNA cultured cell Enzyme Set DNase (5 PRIME, Cat.# 2900315) according to the manufacturer’s protocol.
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and qRT-PCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with single-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: To establish MSR-A549 cells, A549 cells were cultured in the presence of 5 μM MMB and 1 μM selumetinib or in DMEM supplemented with 10% FBS alternately for 2 months. MSR-A549 cells were maintained with 5 μM momelotinib and 1 μM selumetinib continuously. Then MSR-A549 cells were treated with 200nM JQ1 for 24 hours. MSR-A549 withdrawal cells were established from MSR-A549 cells cultured without MMB and selumetinib treatment for 10 days.

value: 5uM momelotinib, 1uM selumetinib and 200nM JQ1


title: MSR-A549 cells drugs withdrawal 3


title: MSR-A549 cells drugs withdrawal 2


title: MSR-A549 cells with JQ1 treatment 1


title: MSR-A549 cells with JQ1 treatment 3


title: H3K27acetylation in A549 ChIP-seq 2


title: A549 cells parental 3


title: MSR-A549 cells 2


title: MSR-A549 cells drugs withdrawal 1


title: TAZ_shRNA2_B

city: Toronto

first: Ayesh

last: Seneviratne

state: Ontario

address: 610 University Avenue, 7th, PMH, 7-510

country: Canada

institute: University of Toronto

data_processing:
Reads adapters were removed using Trim Galore v. 0.4.0 and reads were aligned against hg19 using Tophat v. 2.0.11. Read counts per gene were obtained through htseq-count v.0.6.1p2 in the mode “intersection_nonempty”.
After removing genes whose cpm (counts per million reads) were less than 0.5, edgeR R package v.3.8.6 was used to normalize the data using the TMM (trimmed mean of M values) method and to estimate differential expression by applying a generalized linear model between the control TEX samples and the TEX cells isolated after MTCH2 knockdown.
Raw gene counts are loaded and sample-normalized using DESeq v.1.18.0
False Discovery Rate, calculated by Benjamini-Hochberg method (useful for hits selection)
Two-condition differential expression was done with the edgeR R package, v.3.8.6
Genome_build: hg19 (RefSeq gene models)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and comparision between groups

source_name: AML_TAZ shRNA

growth_protocol: OCI-AML2 leukemic cells were cultured in IMDM with 10% FCS, 100  units/mL streptomycin, 100 µg/mL penicillin.

extract_protocol:
RNeasy Plus Mini Kit. Quality of total RNA samples were checked on an Agilent Bioanalyzer 2100 RNA Nano chip following Agilent Technologies’ recommendation. Concentration was measured by Qubit RNA HS Assay ona Qubit fluorometer (ThermoFisher)
RNA library preparation was performed following the NEB NEBNext Ultra Directional Library Preparation protocol

treatment_protocol: shRNA knockdown was performed with lentiviral infections. 2 mL of virus was added to 5 mL of media containing 5.0 x 106 cells and protamine sulfate (5 µg/mL) followed by overnight incubation (37C, 5% CO2). The following day, cells were centrifuged and washed, and re-suspended in 25 mL fresh medium with appropriate puromycin concentration (2.0 ug/ml) and subjected to selection for 3 days.

value: Engineered leukemic stem cell line

tag: tissue

value: Blood

value: TAZ shRNA


title: TAZ_shRNA1_A

tag: cell line


title: TAZ_shRNA2_A


title: Control_shRNA_B

source_name: AML_Scramble shRNA

value: Scramble shRNA


title: TAZ_shRNA1_B


title: A549 cells parental 1


title: Control_shRNA_A


title: A549 cells parental 2


title: 00031

status: Public on Mar 27 2019

city: Ji'nan

first: Huang

last: Guangyong

address: Cultural West Road,No.44

institute: Shandong University

description:
Processed data file: mRNA Expression Profiling.xlsx
Processed data file: LncRNA Expression Profiling.xlsx

data_processing:
Basecalls performed using CASAVA version 1.8.
RNA-seq reads were mapped to human genome (UCSC hg19) by hisat2 (v2.04) software with default parameters.
Cuffdiff2 software (v2.2.1) was used to perform differentially expressed gene analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *xlsx: Excel files include FPKMs.

source_name: Mononuclear cells, healthy control

extract_protocol:
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

tag: disease status

value: Healthy

value: Peripheral blood

tag: gender

value: Male

tag: age


title: 00032


title: 00030


title: 00018


title: Primed1_1

description: Bulk RNA-Seq data

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
The sequenced short reads were trimmed by Trimmomatic 0.3.3 and mapped to the human reference genome hg19 using TopHat 2.0.14 and Bowtie 2.2.5.
RPKM counts for each gene were obtained using the RPKMforgenes software.
Genome_build: The sequence reads were mapped to hg19 reference genes, downloaded on 25th April 2014
Supplementary_files_format_and_content: Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012). The processed data file contains Genename, Refseq, RPKM, and Rawcount columns (from left to right), and the expression level was represented by RPKM.

growth_protocol: Human ESCs (H9) which carried a PB-EOS-GFP/puroR reporter were cultured on MEF feeder cells in primate ES cell medium supplemented with 4 ng/mL bFGF. Cells were passaged every 5-7 days and medium was changed every day.

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (QIAGEN).
The sequencing libraries were constructed using KAPA stranded mRNA-seq Kit (KAPA Biosystems) from 20 ng or higher amount of total RNA and were sequenced in 100 cycle Single-Read mode of HiSeq2500.

treatment_protocol: Human ES cells (H9-EOS) were dissociated by TrypLE (Invitrogen) or Trypsin (Invitrogen) and re-plated (on MEF feeder) in primate medium  supplemented with bFGF and Y-27632 10 μM for the first 1 day, then medium was changed for Ndiff 227 with t2iL (PD0325901: 1 μM; CHIR99021: 1 μM; Lif: 1000 U/mL)+Gö6983 (5 μM)+Y-27632 and AICAR (1mM) for 2 weeks, t2iLGö+Y27632+AICAR (0.5 mM) for next 1 week. Then medium was changed for t2iLGö+puromycin (1 μg/mL) for 1 week selection. Reset cells were passaged every 3-5 days in t2iLGö. Medium was changed every day.

tag: cell type

value: ESC

value: no treatment

value: undifferentiated


title: 00029

value: Female


title: 00034

source_name: Mononuclear cells, DCM patient

value: Dilated cardiomyopathy (DCM)


title: 00035


title: MSR-A549 cells 1


title: 00003


title: 00033


title: 00004


title: 00005


title: 00002


title: 00013


title: LN229/EGFRvIII/shTRIM59-1# [WGC090198]

status: Public on Mar 26 2019

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

institute: Shanghai Jiao Tong University

description: Overexpression of EGFRvIII and treatment with a TRIM59 shRNA-1#

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Trapnell et al., Nat Biotechnol, 2010. In short, A fragment corresponds to a single cDNA molecule, which can be represented by a pair of reads from each end. Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. FPKM is conceptually analogous to the reads per kilobase per million reads sequenced (RPKM) measure, but it explicitly accommodates sequencing data with one, two, or – if needed for future sequencing platforms – higher numbers of reads from single source molecules.
Genome_build: mm8
Supplementary_files_format_and_content: FPKM values for each Sample ...

molecule: polyA RNA

source_name: GBM cells

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
mRNA library construction was performed using the TruSeq Stranded mRNA Sample Preparation Kit (cat#RS-122-2101, Illumina) according to the manufacturer's instructions.

value: GBM

value: tumor cells

value: glioma cells


title: RNF2-BAP1KO-INPUT-rep2

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Illumina v1.8 software used for basecalling.
Raw reads were aligned to the mouse reference (GRCm38-mm10) using GSNAP (with parameters -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap). Reads were filtered to include only uniquely mapped reads.
ChIP-seq peaks were called for each dataset with matched input using MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files

source_name: Embryonic stem cells

extract_protocol:
ES cells were treated with 100 nM 4-OHT and 10 μM emricasan (Cayman Chemical) for 4 days. For RNF2 ChIP, nuclear extracts were prepared from 2×10^7 cells using the truChIP High Cell Chromatin Shearing Kit (Covaris). Chromatin was sheared to 200-700 bp with a Covaris E220 sonicator (settings: duty cycle 5%, peak incident power 140 W, cycles per burst 200, processing time 12 min, temperature 4oC, degassing mode continuous, volume 1.0 ml in TC12x12 AFA tubes). Bap1C91A/- and Bap1-FLAG tag cells were crosslinked in 2 mM disuccinimidyl glutarate (Thermo Fisher Scientific) at room temperature for 30 min prior to nuclear extracts following the process above. Sheered nuclear extracts were centrifuged at 16000xg for 5 min, and then the soluble fractions were supplemented with 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20mM Tris-HCl pH 8.1 and 1× protease inhibitor cocktail (Sigma). Next, anti-RNF2 (Abcamab3832), anti-BAP1 (Genentech, PRO424270), or anti-FLAG (M8823 Millipore) antibodies were added that had been pre-coupled to protein A-Dynabeads (Life Technologies).
Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100 Bioanalyzer. Barcoded libraries were sequenced 50 bp single end on HiSeq 2500 (Illumina).

tag: background strain

tag: genotype

value: BAP1 knockout


title: LN229/EGFRvIII/shTRIM59-2# [WGC090199]

description: Overexpression of EGFRvIII and treatment with a TRIM59 shRNA-2#


title: LN229/EGFRvIII/shTRIM59-2# [WGC090199R]


title: RNF2-BAP1KO-rep2

value: anti-RNF2 (Abcam, ab3832)


title: LN229/EGFRvIII/shTRIM59-1# [WGC090198R]


title: RNF2-RNF2KO

description: Since RNF2-RNF2KO is a control, when compared with input, it didn't have any peaks called.

value: RNF2 knockout


title: LM_DLY_RNA seq

city: Zhengzhou

first: Jing

last: Wang

address: Huayuan Road No.116

institute: Institute of Animal Husbandry and Veterinary Science

description: Sample C

data_processing:
The clean data was obtained by removing the poor-quality bases and adapter sequences from the raw sequencing data.
The TopHat2 software (Kim et al., 2013) was used to map the clean data to the porcine reference genome (Sscrofa10.2, ftp://ftp.ncbi.nlm.nih.gov/ genomes/Sus_scrofa/).
Then Cufflinks (Trapnell et al., 2010) was used to perform the transcript assembly and abundance estimation. The Findcirc software was used to predict the circRNAs (Memczak et al., 2013).
The expression profile of circRNAs was reflected by the fragments per kilo base per million reads (FPKMs). The DESeq software package (http://bioconductor.org/ packages/release/bioc/html/DESeq.html) was applied to detect differentially expressed circRNAs (DECs) with P≤ 0.05.
The functions of the DECs were determined through the Gene Ontology (GO) term and KEGG pathway annotation with the DAVID tool, using the porcine genome as background (Huang da et al., 2009).
Genome_build: Sscrofa10.2, ftp://ftp.ncbi.nlm.nih.gov/ genomes/Sus_scrofa/
Supplementary_files_format_and_content: baseMean values from DESeq. The FASTA file of the identified circRNAs is available on the series record.

organism: Sus scrofa

source_name: longissimus muscle

growth_protocol: Three HN and LW male pigs aged 300 days were obtained from the Henan Xing Rui Agricultural and Animal Husbandry Technology Co., LTD in the Henan province of China. All of the pigs were fed on a standard diet and watered ad libitum under normal condition.

extract_protocol:
LM were removed from HN and DLY pigs, frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The ribosomal RNA (rRNA) was removed using Ribo-ZeroTM kit (Epicentre, Madison, WY, USA) from the DNA-free RNA. Then, the DNA and rRNA-free RNA was used to prepare the library using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs lnc., Beverly, MA), and then sequenced by HiSeq 2500 (Illumina, San Diego, CA, USA).

value: 300 days

tag: breed

value: Duroc x (Landrace x Yorkshire)

value: longissimus muscle

value: male


title: RNF2-RNF2KO-INPUT


title: LM_HN_RNA seq

description: Sample A

value: Huainan


title: 00028

value: Healthy

value: Peripheral blood

value: Male


title: 00019


title: MSR-A549 cells 3

value: 5uM momelotinib and 1uM selumetinib


title: 00016


title: RNF2-WT-INPUT

extract_protocol:
ES cells were treated with 100 nM 4-OHT and 10 μM emricasan (Cayman Chemical) for 4 days. For RNF2 ChIP, nuclear extracts were prepared from 2×10^7 cells using the truChIP High Cell Chromatin Shearing Kit (Covaris). Chromatin was sheared to 200-700 bp with a Covaris E220 sonicator (settings: duty cycle 5%, peak incident power 140 W, cycles per burst 200, processing time 12 min, temperature 4oC, degassing mode continuous, volume 1.0 ml in TC12x12 AFA tubes). Bap1C91A/- and Bap1-FLAG tag cells were crosslinked in 2 mM disuccinimidyl glutarate (Thermo Fisher Scientific) at room temperature for 30 min prior to nuclear extracts following the process above. Sheered nuclear extracts were centrifuged at 16000×g for 5 min, and then the soluble fractions were supplemented with 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20mM Tris-HCl pH 8.1 and 1× protease inhibitor cocktail (Sigma). Next, anti-RNF2 (Abcamab3832), anti-BAP1 (Genentech, PRO424270), or anti-FLAG (M8823 Millipore) antibodies were added that had been pre-coupled to protein A-Dynabeads (Life Technologies).
Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100 Bioanalyzer. Barcoded libraries were sequenced 50 bp single end on HiSeq 2500 (Illumina).

value: ESC


title: BAP1-C91A

value: anti-BAP1 (Genentech, PRO424270)


title: RNF2-WT


title: BAP1-C91A-INPUT


title: RNF2-BAP1KO-INPUT


title: RNF2-BAP1KO


title: Capsella grandiflora D (Cg D) x Capsella grandiflora C (Cg C)  Run 2

city: Sentul

first: Marcelinus

middle: Rocky

last: Hatorangan

state: Jawa Barat

address: Cijayanti, Babakan Madang

department: Biotechnology

country: Indonesia

institute: PT SMART, Tbk.

description: Sequenced twice, run2

data_processing:
additional adapter cleanup: trimmomatic PE ILLUMINACLIP:adapter.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
All C. grandiflora and C. rubella genome and RNA reads were aligned to the C. rubella genome v1.0 (Phytozome) using Stampy. C. grandiflora bisulfite converted DNA were mapped to C. grandiflora genome using Bismark while C. orientalis bisulfite converted DNA were mapped to C. rubella genome using Bismark. Bowtie2 alignment option were used on Bismark.
Genome SNP calling was done using Freebayes with -i -X -u --min-coverage 20 --min-alternate-total 10 -q 30 option
Nucleotide counting for RNA-seq was done by running a loop of igvtools.jar count -w 1
Genome_build: C. rubella genome v1.0 (Phytozome) and C. grandiflora v1.1 (Phytozome)
Supplementary_files_format_and_content: Aligned reads

organism: Capsella grandiflora

source_name: Capsella grandiflora DxC hybrid endosperm

growth_protocol: All seeds were surface sterilized using 5 % Sodium Hypochloride solution under the fume hood. After sterilization seeds were plated on MS media containing 1% sucrose. After stratification for two days in the dark at 4°C seedlings were grown in a growth room under long-day photoperiod (16 hrs light and 8 hrs darkness) at 22°C light and 20°C darkness temperature and a light intensity of 110 µE. All seedlings were transferred to pots and plants were grown in a growth chamber at 60 % humidity and daily cycles of 16 hrs light at 21°C and 8hrs darkness at 18°C. ts were grown in a growth cabinet under long day photoperiods (16 h light and 8 h dark) at 22°C. After 10 days, seedlings were transferred to soil and plants were grown in a growth chamber at 60% humidity and daily cycles of 16 h light at 22°C and 8 h darkness at 18°C.

extract_protocol:
For DNA-seq, 300 mg young fresh leaves were used as DNA source. For RNA-seq, dissected endosperm of 300-500 seeds per replicate was used. Endosperm were harvested at 6 DAP and stored at -20oC in RNAlater® (Sigma-Aldrich, St Louis, USA). RNA extraction was done using RNAqueous® Kit with Plant RNA Isolation Aid (Life Technologies, Carlsbad, USA). For methylation analysis, bisulfite coversion was performed on leaves DNA using Epitect Bisulfite Kit (Qiagen) following the manufacturer's instructions.
The DNA-sequencing libraries were prepared using TruSeq® DNA Sample Preparation Kit (Illumina, San Diego, USA). The RNA-sequencing libraries were prepared using TruSeq® RNA Sample Preparation Kit v2 (Illumina). The Epitect Bisulfite Converted DNA libraries were prepared using TruSeq® DNA Sample Preparation Kit. All process were done according to the manufacturer's instructions.

treatment_protocol: For all crosses, designated female partners were emasculated, and the pistils were hand-pollinated 2 days after emasculation.

value: 6 DAP seed endosperm


title: Capsella grandiflora B (Cg B)

data_processing:
Library strategy: DNA-seq
additional adapter cleanup: trimmomatic PE ILLUMINACLIP:adapter.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
All C. grandiflora and C. rubella genome and RNA reads were aligned to the C. rubella genome v1.0 (Phytozome) using Stampy. C. grandiflora bisulfite converted DNA were mapped to C. grandiflora genome using Bismark while C. orientalis bisulfite converted DNA were mapped to C. rubella genome using Bismark. Bowtie2 alignment option were used on Bismark.
Genome SNP calling was done using Freebayes with -i -X -u --min-coverage 20 --min-alternate-total 10 -q 30 option
Nucleotide counting for RNA-seq was done by running a loop of igvtools.jar count -w 1
Genome_build: C. rubella genome v1.0 (Phytozome) and C. grandiflora v1.1 (Phytozome)
Supplementary_files_format_and_content: Aligned reads

source_name: Capsella grandiflora B leaves

value: leaves


title: Capsella grandiflora A (Cg A)

source_name: Capsella grandiflora A leaves


title: Capsella orientalis B (Co B)

organism: Capsella orientalis

source_name: Capsella orientalis B leaves


title: Capsella orientalis A (Co A)

source_name: Capsella orientalis A leaves


title: Capsella grandiflora B (Cg B) x Capsella grandiflora A (Cg A)

source_name: Capsella grandiflora BxA hybrid endosperm


title: RNF2-WT-INPUT-rep2

value: Wild type


title: Capsella grandiflora A (Cg A) x Capsella grandiflora B (Cg B)

source_name: Capsella grandiflora AxB hybrid endosperm


title: Capsella grandiflora D (Cg D) x Capsella grandiflora C (Cg C) Run 1

description: Sequenced twice, run1


title: Capsella grandiflora C (Cg C) x Capsella grandiflora D (Cg D) Run1

description: Sequenced twice, run1

source_name: Capsella grandiflora CxD hybrid endosperm


title: Capsella grandiflora D (Cg D)

source_name: Capsella grandiflora D leaves


title: Capsella orientalis (CoB) bisulfite


title: Capsella grandiflora C (Cg C)

source_name: Capsella grandiflora C leaves


title: Capsella grandiflora (CgA) bisulfite


title: Capsella orientalis B (Co B) x Capsella orientalis A (Co A)  Run 1 2

description: Sequenced twice, run1

source_name: Capsella orientalis BxA hybrid endosperm


title: Capsella orientalis A (Co A) x Capsella orientalis B (Co B)  Run 2 1

description: Sequenced twice, run2

source_name: Capsella orientalis AxB hybrid endosperm


title: Capsella orientalis B (Co B) x Capsella orientalis A (Co A)  Run 2 2

description: Sequenced twice, run2


title: Capsella orientalis A (Co A) x Capsella orientalis B (Co B)  Run 1 2

description: Sequenced twice, run1


title: Capsella orientalis B (Co B) x Capsella orientalis A (Co A)  Run 1 1

description: Sequenced twice, run1


title: softcolrBM_rep2_RNAseq

status: Public on Mar 25 2019

city: Stanford

first: Jessica

middle: Kay

last: Chang

address: 300 Pasteur Drive, Alway Building M311

institute: Stanford University

data_processing:
Adapter sequences and low quality bases were trimmed using fastx_clipper (fastx_toolkit v 0.13.2) for single end reads and trim_galore v 0.3.3 for paired end libraries.  Reads were subsequently mapped to the v9.0 genome via Tophat v2.0.13 with very-sensitive parameters.
Multimapped or unmapped reads were filtered using samtools v 1.1.
Count data was summarized via HTSeq (python v2.7).  Adjustments for sequencing depth (and prior to clustering, variance stabilization through rlog transformation) were performed using DESeq2 (R v3.2.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file containing normalized count data (adjusted by size factor via DESeq2).

growth_protocol: MCF10A cells were passaged in tissue culture dishes for no more than 20 passages.

extract_protocol:
RNA was harvested using TRIZOL reagent with the GenCatch Total RNA Extraction Kit (Epoch).
Libraries were constructucted using the TruSeq RNA Library Prep Kit v2.

treatment_protocol: MCF10A cells were encapsulated for 7 days in hydrogels of specified stiffness and col-1 density.

tag: hydrogel condition

value: soft col-1 and rBM

value: Spontaneously immortalized mammary epithelial cells

tag: passages


title: stiffcol_rep2_RNAseq

value: stiff col-1


title: Capsella orientalis A (Co A) x Capsella orientalis B (Co B) Run 1 1

description: Sequenced twice, run1

source_name: Capsella orientalis  AxB hybrid endosperm


title: softcolrBM_rep1_RNAseq


title: stiffIPN_rep2_RNAseq

value: stiff alginate and rBM


title: RNF2-WT-rep2

value: anti-RNF2 (Abcam, ab3832)


title: softIPN_rep1_RNAseq

value: soft alginate and reconstituted basement membrane (rBM)


title: Capsella orientalis (CoA) bisulfite


title: softIPN_rep2_RNAseq


title: Capsella grandiflora C (Cg C) x Capsella grandiflora D (Cg D)  Run 2

description: Sequenced twice, run2


title: stiffIPN_rep1_RNAseq


title: TBS014-95_S191_L002

status: Public on Mar 23 2019

first: Michael

last: Sikora

address: 450 Serra Mall

description:
processed data file:
count_matrix.txt
normalized_count_matrix.txt

data_processing:
Paired end, non-strand-specific mature RNA-seq reads were trimmed using fastq-mcf from ea-utils in order to remove low quality bases and adapter sequences, with default parameters and a quality threshold of 20.
The trimmed reads were then aligned to the human reference genome (ENSEMBL release 75), with the ERCC sequences appended using TopHat.
Duplicate reads were then removed using the MarkDuplicates tool from Picard Tools
Gene count quantification was assigned with HTSeqon a flattened gtf file generated by dexseq_prepare.py from DEXseq
Genome_build: hg19
Supplementary_files_format_and_content: count_matrix and normalized_count_matrix are matrices with expression values for each gene in each cell. count_matrix is the raw counts for reads aligning to each gene. normalized_count_matrix is identically structured, but values are post-normalization.

source_name: CD8+ T cell_Conventional

extract_protocol:
Single cells were directly sorted into lysis buffer for cDNA library prep
optimized Smart-seq2 protocol

treatment_protocol: PBMCs from Mtb exposed patients were stimulated ex vivo with Mtb lysate for 12 hours. Activated CD8+ T cells were selected and single cell sorted based on the upregulation of activation markers, including CD154 and CD137.

tag: tissue source

value: PBMCs from Mtb exposed patients

value: Activated CD8+ T cells

tag: cell subtype

value: Conventional


title: TBS014-94_S190_L002


title: TBS014-91_S187_L002


title: Capsella orientalis A (Co A) x Capsella orientalis B (Co B)  Run 2 2

description: Sequenced twice, run2


title: Capsella orientalis B (Co B) x Capsella orientalis A (Co A)  Run 2 1

description: Sequenced twice, run2


title: TBS014-88_S184_L002


title: TBS014-86_S182_L002


title: TBS014-93_S189_L002


title: TBS014-85_S181_L002


title: TBS014-83_S179_L002


title: TBS014-84_S180_L002


title: stiffcol_rep1_RNAseq


title: TBS014-81_S177_L002


title: TBS014-82_S178_L002


title: TBS014-80_S176_L002


title: TBS014-92_S188_L002


title: TBS014-79_S175_L002


title: TBS014-77_S173_L002


title: TBS014-78_S174_L002


title: TBS014-76_S172_L002


title: TBS014-74_S170_L002


title: TBS014-75_S171_L002


title: TBS014-73_S169_L002


title: TBS014-89_S185_L002


title: TBS014-69_S165_L002


title: TBS014-71_S167_L002


title: TBS014-72_S168_L002


title: TBS014-68_S164_L002


title: TBS014-70_S166_L002


title: TBS014-65_S161_L002


title: TBS014-90_S186_L002


title: TBS014-63_S159_L002


title: TBS014-66_S162_L002


title: TBS014-61_S157_L002


title: TBS014-60_S156_L002


title: TBS014-59_S155_L002


title: TBS014-57_S153_L002


title: TBS014-54_S150_L002


title: TBS014-56_S152_L002


title: TBS014-55_S151_L002


title: TBS014-58_S154_L002


title: TBS014-64_S160_L002


title: TBS014-53_S149_L002


title: TBS014-51_S147_L002


title: TBS014-50_S146_L002


title: TBS014-49_S145_L002


title: TBS014-48_S144_L002


title: TBS014-52_S148_L002


title: TBS014-67_S163_L002


title: TBS014-44_S140_L002


title: TBS014-41_S137_L002


title: TBS014-43_S139_L002


title: TBS014-45_S141_L002


title: TBS014-38_S134_L002


title: TBS014-40_S136_L002


title: TBS014-62_S158_L002


title: TBS014-42_S138_L002


title: TBS014-34_S130_L002


title: TBS014-33_S129_L002


title: TBS014-35_S131_L002


title: TBS014-36_S132_L002


title: TBS014-32_S128_L002


title: TBS014-31_S127_L002


title: TBS014-30_S126_L002


title: TBS014-28_S124_L002


title: TBS014-37_S133_L002


title: TBS014-27_S123_L002


title: TBS014-26_S122_L002


title: TBS014-46_S142_L002


title: TBS014-47_S143_L002


title: TBS014-21_S117_L002


title: TBS014-25_S121_L002


title: TBS014-24_S120_L002


title: TBS014-23_S119_L002


title: TBS014-39_S135_L002


title: TBS014-22_S118_L002


title: TBS014-14_S110_L002


title: TBS014-15_S111_L002


title: TBS014-16_S112_L002


title: TBS014-19_S115_L002


title: TBS014-20_S116_L002


title: TBS014-11_S107_L002


title: TBS014-17_S113_L002


title: TBS014-18_S114_L002


title: TBS014-13_S109_L002


title: TBS014-10_S106_L002


title: TBS014-09_S105_L002


title: TBS014-08_S104_L002


title: TBS014-29_S125_L002


title: TBS014-07_S103_L002


title: TBS014-06_S102_L002


title: TBS014-05_S101_L002


title: TBS014-01_S97_L002


title: TBS014-02_S98_L002


title: TBS014-03_S99_L002


title: TBS013-93_S93_L001


title: TBS014-04_S100_L002


title: TBS013-92_S92_L001


title: TBS013-88_S88_L001


title: TBS013-86_S86_L001


title: TBS013-91_S91_L001


title: TBS013-90_S90_L001


title: TBS013-85_S85_L001


title: TBS013-89_S89_L001


title: TBS013-82_S82_L001


title: TBS013-84_S84_L001


title: TBS013-81_S81_L001


title: TBS013-83_S83_L001


title: TBS013-74_S74_L001


title: TBS013-78_S78_L001


title: TBS013-73_S73_L001


title: TBS013-70_S70_L001


title: TBS013-69_S69_L001


title: TBS013-68_S68_L001


title: TBS013-67_S67_L001


title: TBS013-71_S71_L001


title: TBS013-66_S66_L001


title: TBS013-64_S64_L001


title: TBS013-63_S63_L001


title: TBS013-60_S60_L001


title: TBS013-58_S58_L001


title: TBS013-57_S57_L001


title: TBS013-80_S80_L001


title: TBS013-65_S65_L001


title: TBS013-56_S56_L001


title: TBS013-75_S75_L001


title: TBS013-62_S62_L001


title: TBS013-76_S76_L001


title: TBS013-55_S55_L001


title: TBS013-54_S54_L001


title: TBS013-53_S53_L001


title: TBS013-52_S52_L001


title: TBS013-51_S51_L001


title: TBS013-59_S59_L001


title: TBS013-48_S48_L001


title: TBS013-46_S46_L001


title: TBS013-45_S45_L001


title: TBS013-47_S47_L001


title: TBS013-61_S61_L001


title: TBS013-42_S42_L001


title: TBS013-41_S41_L001


title: TBS013-40_S40_L001


title: TBS013-38_S38_L001


title: TBS013-44_S44_L001


title: TBS013-39_S39_L001


title: TBS013-50_S50_L001


title: TBS013-33_S33_L001


title: TBS013-31_S31_L001


title: TBS013-49_S49_L001


title: TBS013-32_S32_L001


title: TBS013-34_S34_L001


title: TBS013-36_S36_L001


title: TBS013-35_S35_L001


title: TBS013-28_S28_L001


title: TBS013-27_S27_L001


title: TBS013-43_S43_L001


title: TBS013-29_S29_L001


title: TBS013-25_S25_L001


title: TBS013-24_S24_L001


title: TBS013-26_S26_L001


title: TBS013-22_S22_L001


title: TBS013-21_S21_L001


title: TBS013-20_S20_L001


title: TBS013-18_S18_L001


title: TBS013-17_S17_L001


title: TBS013-23_S23_L001


title: TBS013-37_S37_L001


title: TBS013-15_S15_L001


title: TBS013-14_S14_L001


title: TBS013-12_S12_L001


title: TBS013-09_S9_L001


title: TBS013-11_S11_L001


title: TBS013-08_S8_L001


title: TBS014-96_S192_L002


title: TBS013-10_S10_L001


title: TBS013-03_S3_L001


title: TBS013-13_S13_L001


title: TBS013-05_S5_L001


title: TBS013-06_S6_L001


title: TBS013-07_S7_L001


title: TBS013-02_S2_L001


title: TBS012-93_S189_L002

source_name: CD8+ T cell_MAIT

value: MAIT


title: TBS012-84_S180_L002

source_name: CD8+ T cell_MAIT-CNTRL

value: MAIT-CNTRL


title: TBS012-94_S190_L002


title: TBS013-30_S30_L001


title: TBS013-16_S16_L001


title: TBS012-83_S179_L002


title: TBS012-86_S182_L002


title: TBS012-82_S178_L002


title: TBS012-85_S181_L002


title: TBS012-78_S174_L002


title: TBS012-77_S173_L002


title: TBS012-79_S175_L002


title: TBS012-80_S176_L002


title: TBS012-76_S172_L002


title: TBS012-74_S170_L002


title: TBS013-04_S4_L001


title: TBS012-70_S166_L002


title: TBS012-65_S161_L002


title: TBS013-19_S19_L001


title: TBS012-67_S163_L002


title: TBS012-71_S167_L002


title: TBS012-63_S159_L002


title: TBS012-62_S158_L002


title: TBS012-61_S157_L002


title: TBS012-73_S169_L002


title: TBS012-66_S162_L002


title: TBS012-69_S165_L002


title: TBS012-60_S156_L002


title: TBS012-58_S154_L002


title: TBS012-57_S153_L002


title: TBS012-55_S151_L002


title: TBS012-54_S150_L002


title: TBS012-64_S160_L002


title: TBS012-59_S155_L002


title: TBS012-75_S171_L002


title: TBS012-52_S148_L002


title: TBS012-51_S147_L002


title: TBS012-50_S146_L002


title: TBS012-53_S149_L002


title: TBS012-72_S168_L002


title: TBS012-48_S144_L002


title: TBS012-49_S145_L002


title: TBS012-47_S143_L002


title: TBS012-42_S138_L002

source_name: CD8+ T cell_iNKT-CNTRL

value: iNKT-CNTRL


title: TBS012-40_S136_L002


title: TBS012-39_S135_L002


title: TBS012-56_S152_L002


title: TBS012-41_S137_L002


title: TBS012-35_S131_L002


title: TBS012-33_S129_L002


title: TBS012-32_S128_L002


title: TBS012-38_S134_L002


title: TBS012-29_S125_L002


title: TBS012-43_S139_L002


title: TBS012-31_S127_L002


title: TBS012-36_S132_L002


title: TBS012-37_S133_L002


title: TBS012-25_S121_L002


title: TBS012-30_S126_L002


title: TBS012-28_S124_L002


title: TBS012-24_S120_L002


title: TBS012-23_S119_L002


title: TBS012-19_S115_L002


title: TBS012-20_S116_L002


title: TBS012-46_S142_L002


title: TBS012-17_S113_L002


title: TBS012-68_S164_L002


title: TBS012-16_S112_L002


title: TBS012-15_S111_L002


title: TBS012-14_S110_L002


title: TBS012-13_S109_L002

source_name: CD8+ T cell_iNKT

value: iNKT


title: TBS013-72_S72_L001


title: TBS012-11_S107_L002


title: TBS012-12_S108_L002


title: TBS012-09_S105_L002


title: TBS012-27_S123_L002


title: TBS012-06_S102_L002


title: TBS012-07_S103_L002


title: TBS012-03_S99_L002


title: TBS012-05_S101_L002


title: TBS012-02_S98_L002


title: TBS011-87_S87_L001


title: TBS012-21_S117_L002


title: TBS012-22_S118_L002


title: TBS011-85_S85_L001


title: TBS011-86_S86_L001


title: TBS012-04_S100_L002


title: TBS011-83_S83_L001


title: TBS011-84_S84_L001


title: TBS011-82_S82_L001


title: TBS011-81_S81_L001


title: TBS011-80_S80_L001


title: TBS011-79_S79_L001


title: TBS011-76_S76_L001


title: TBS011-77_S77_L001


title: TBS012-10_S106_L002


title: TBS011-78_S78_L001


title: TBS012-08_S104_L002


title: TBS011-75_S75_L001


title: TBS011-74_S74_L001


title: TBS011-71_S71_L001


title: TBS011-73_S73_L001


title: TBS011-70_S70_L001


title: TBS011-72_S72_L001


title: TBS011-69_S69_L001


title: TBS012-01_S97_L002


title: TBS011-66_S66_L001


title: TBS011-63_S63_L001


title: TBS011-64_S64_L001


title: TBS011-62_S62_L001


title: TBS011-65_S65_L001


title: TBS011-67_S67_L001


title: TBS011-68_S68_L001


title: TBS011-61_S61_L001


title: TBS011-59_S59_L001


title: TBS011-55_S55_L001


title: TBS011-54_S54_L001


title: TBS011-53_S53_L001


title: TBS011-52_S52_L001


title: TBS011-58_S58_L001


title: TBS011-56_S56_L001


title: TBS011-50_S50_L001


title: TBS011-57_S57_L001


title: TBS011-49_S49_L001


title: TBS011-48_S48_L001


title: TBS011-47_S47_L001


title: TBS011-51_S51_L001


title: TBS011-46_S46_L001


title: TBS011-45_S45_L001


title: TBS011-42_S42_L001


title: TBS011-41_S41_L001


title: TBS011-43_S43_L001


title: TBS011-40_S40_L001


title: TBS011-39_S39_L001


title: TBS011-60_S60_L001


title: TBS011-38_S38_L001


title: TBS011-31_S31_L001


title: TBS011-35_S35_L001


title: TBS011-34_S34_L001


title: TBS011-37_S37_L001


title: TBS011-33_S33_L001


title: TBS011-30_S30_L001


title: TBS011-36_S36_L001


title: TBS011-27_S27_L001


title: TBS011-26_S26_L001


title: TBS011-25_S25_L001


title: TBS011-29_S29_L001


title: TBS011-28_S28_L001


title: TBS011-23_S23_L001


title: TBS011-22_S22_L001


title: TBS011-21_S21_L001


title: TBS011-24_S24_L001


title: TBS011-44_S44_L001


title: TBS011-20_S20_L001


title: TBS011-17_S17_L001


title: TBS011-19_S19_L001


title: TBS011-14_S14_L001


title: TBS011-16_S16_L001


title: TBS011-15_S15_L001


title: TBS011-12_S12_L001


title: TBS011-18_S18_L001


title: TBS011-11_S11_L001


title: TBS011-32_S32_L001


title: TBS011-10_S10_L001


title: TBS011-13_S13_L001


title: TBS011-09_S9_L001


title: TBS011-08_S8_L001


title: TBS011-05_S5_L001


title: TBS011-07_S7_L001


title: TBS011-04_S4_L001


title: TBS011-03_S3_L001


title: TBS011-02_S2_L001


title: TBS011-01_S1_L001


title: TBS010-93_S189_L002


title: TBS010-91_S187_L002


title: TBS010-92_S188_L002


title: TBS010-85_S181_L002


title: TBS010-84_S180_L002


title: TBS010-83_S179_L002


title: TBS010-80_S176_L002


title: TBS010-82_S178_L002


title: TBS010-79_S175_L002


title: TBS010-78_S174_L002


title: TBS010-77_S173_L002


title: TBS010-73_S169_L002


title: TBS010-76_S172_L002


title: TBS010-70_S166_L002


title: TBS010-72_S168_L002


title: TBS011-06_S6_L001


title: TBS010-71_S167_L002


title: TBS010-69_S165_L002


title: TBS010-67_S163_L002


title: TBS010-65_S161_L002


title: TBS010-66_S162_L002


title: TBS010-68_S164_L002


title: TBS010-64_S160_L002


title: TBS010-58_S154_L002


title: TBS010-59_S155_L002


title: TBS010-90_S186_L002


title: TBS010-57_S153_L002


title: TBS010-56_S152_L002


title: TBS010-54_S150_L002


title: TBS010-81_S177_L002


title: TBS010-53_S149_L002


title: TBS010-89_S185_L002


title: TBS010-52_S148_L002


title: TBS010-48_S144_L002


title: TBS010-49_S145_L002


title: TBS010-50_S146_L002


title: TBS010-47_S143_L002


title: TBS010-51_S147_L002


title: TBS010-41_S137_L002


title: TBS010-44_S140_L002


title: TBS010-45_S141_L002


title: TBS010-46_S142_L002


title: TBS010-43_S139_L002


title: TBS010-42_S138_L002


title: TBS010-60_S156_L002


title: TBS010-61_S157_L002


title: TBS010-29_S125_L002

source_name: CD8+ T cell_Conventional_CNTRL


title: TBS010-35_S131_L002


title: TBS010-34_S130_L002


title: TBS010-36_S132_L002


title: TBS010-55_S151_L002


title: TBS010-25_S121_L002


title: TBS010-31_S127_L002


title: TBS010-23_S119_L002


title: TBS010-37_S133_L002


title: TBS010-30_S126_L002


title: TBS010-20_S116_L002


title: TBS010-22_S118_L002


title: TBS010-19_S115_L002


title: TBS010-16_S112_L002


title: TBS010-21_S117_L002


title: TBS010-13_S109_L002


title: TBS010-17_S113_L002


title: TBS010-04_S100_L002


title: TBS010-09_S105_L002


title: TBS010-08_S104_L002


title: TBS009-87_S87_L001


title: TBS009-84_S84_L001


title: TBS010-01_S97_L002


title: TBS010-07_S103_L002


title: TBS009-85_S85_L001


title: TBS009-83_S83_L001


title: TBS009-82_S82_L001


title: TBS009-79_S79_L001


title: TBS009-75_S75_L001


title: TBS009-74_S74_L001


title: TBS009-78_S78_L001


title: TBS009-81_S81_L001


title: TBS009-80_S80_L001


title: TBS009-73_S73_L001


title: TBS009-77_S77_L001


title: TBS009-76_S76_L001


title: TBS009-72_S72_L001


title: TBS009-71_S71_L001


title: TBS010-05_S101_L002


title: TBS009-64_S64_L001


title: TBS009-68_S68_L001


title: TBS009-67_S67_L001


title: TBS009-65_S65_L001


title: TBS009-62_S62_L001


title: TBS009-60_S60_L001


title: TBS009-86_S86_L001


title: TBS009-59_S59_L001


title: TBS009-58_S58_L001


title: TBS009-61_S61_L001


title: TBS009-63_S63_L001


title: TBS009-55_S55_L001


title: TBS009-56_S56_L001


title: TBS009-54_S54_L001


title: TBS009-57_S57_L001


title: TBS009-53_S53_L001


title: TBS009-69_S69_L001


title: TBS009-50_S50_L001


title: TBS009-47_S47_L001


title: TBS009-43_S43_L001


title: TBS009-44_S44_L001


title: TBS009-42_S42_L001


title: TBS009-46_S46_L001


title: TBS009-49_S49_L001


title: TBS009-39_S39_L001


title: TBS009-36_S36_L001


title: TBS009-40_S40_L001


title: TBS009-34_S34_L001


title: TBS009-41_S41_L001


title: TBS009-35_S35_L001


title: TBS009-37_S37_L001


title: TBS009-32_S32_L001


title: TBS009-25_S25_L001


title: TBS009-26_S26_L001


title: TBS009-30_S30_L001


title: TBS009-27_S27_L001


title: TBS009-29_S29_L001


title: TBS009-28_S28_L001


title: TBS009-70_S70_L001


title: TBS009-31_S31_L001


title: TBS009-52_S52_L001


title: TBS009-24_S24_L001


title: TBS009-21_S21_L001


title: TBS009-20_S20_L001


title: TBS009-22_S22_L001


title: TBS009-19_S19_L001


title: TBS009-16_S16_L001


title: TBS009-18_S18_L001


title: TBS009-51_S51_L001


title: TBS009-33_S33_L001


title: TBS009-14_S14_L001


title: TBS009-15_S15_L001


title: TBS009-13_S13_L001


title: TBS009-10_S10_L001


title: TBS009-12_S12_L001


title: TBS009-03_S3_L001


title: TBS009-06_S6_L001


title: TBS009-02_S2_L001


title: TBS009-07_S7_L001


title: TBS009-11_S11_L001


title: TBS008-93_S189_L002


title: TBS008-92_S188_L002


title: TBS008-90_S186_L002


title: TBS008-91_S187_L002


title: TBS008-88_S184_L002


title: TBS008-86_S182_L002


title: TBS008-83_S179_L002


title: TBS008-81_S177_L002


title: TBS008-84_S180_L002


title: TBS009-17_S17_L001


title: TBS008-78_S174_L002


title: TBS008-76_S172_L002


title: TBS008-77_S173_L002


title: TBS008-73_S169_L002


title: TBS008-75_S171_L002


title: TBS009-04_S4_L001


title: TBS008-74_S170_L002


title: TBS008-69_S165_L002


title: TBS008-72_S168_L002


title: TBS008-68_S164_L002


title: TBS008-70_S166_L002


title: TBS008-71_S167_L002


title: TBS008-89_S185_L002


title: TBS008-87_S183_L002


title: TBS008-65_S161_L002


title: TBS008-61_S157_L002


title: TBS008-66_S162_L002


title: TBS008-63_S159_L002


title: TBS008-80_S176_L002


title: TBS008-62_S158_L002


title: TBS008-60_S156_L002


title: TBS008-57_S153_L002


title: TBS008-59_S155_L002


title: TBS008-55_S151_L002


title: TBS008-56_S152_L002


title: TBS008-54_S150_L002


title: TBS008-52_S148_L002


title: TBS008-51_S147_L002


title: TBS008-47_S143_L002


title: TBS008-50_S146_L002


title: TBS008-48_S144_L002


title: TBS008-67_S163_L002


title: TBS008-49_S145_L002


title: TBS008-64_S160_L002


title: TBS008-46_S142_L002


title: TBS008-45_S141_L002


title: TBS008-43_S139_L002


title: TBS008-41_S137_L002


title: TBS008-40_S136_L002


title: TBS008-39_S135_L002


title: TBS008-58_S154_L002


title: TBS008-38_S134_L002


title: TBS008-42_S138_L002


title: TBS008-36_S132_L002


title: TBS008-35_S131_L002


title: TBS008-34_S130_L002


title: TBS008-33_S129_L002


title: TBS008-32_S128_L002


title: TBS008-27_S123_L002


title: TBS008-28_S124_L002


title: TBS008-26_S122_L002


title: TBS008-29_S125_L002


title: TBS008-30_S126_L002


title: TBS008-24_S120_L002


title: TBS008-44_S140_L002


title: TBS008-21_S117_L002


title: TBS008-20_S116_L002


title: TBS008-37_S133_L002


title: TBS008-18_S114_L002


title: TBS008-19_S115_L002


title: TBS008-08_S104_L002


title: TBS008-14_S110_L002


title: TBS008-17_S113_L002


title: TBS008-13_S109_L002


title: TBS008-12_S108_L002


title: TBS008-15_S111_L002


title: TBS008-06_S102_L002


title: TBS008-11_S107_L002


title: TBS008-07_S103_L002


title: TBS008-05_S101_L002


title: TBS008-23_S119_L002


title: TBS008-53_S149_L002


title: TBS007-94_S94_L001


title: TBS008-01_S97_L002


title: TBS008-02_S98_L002


title: TBS008-03_S99_L002


title: TBS008-22_S118_L002


title: TBS007-92_S92_L001


title: TBS008-16_S112_L002


title: TBS007-93_S93_L001


title: TBS007-90_S90_L001


title: TBS007-91_S91_L001


title: TBS007-89_S89_L001


title: TBS007-86_S86_L001


title: TBS007-85_S85_L001


title: TBS008-10_S106_L002


title: TBS008-09_S105_L002


title: TBS007-80_S80_L001


title: TBS007-84_S84_L001


title: TBS007-82_S82_L001


title: TBS007-78_S78_L001


title: TBS007-81_S81_L001


title: TBS008-04_S100_L002


title: TBS007-76_S76_L001


title: TBS007-83_S83_L001


title: TBS007-73_S73_L001


title: TBS007-75_S75_L001


title: TBS007-72_S72_L001


title: TBS007-74_S74_L001


title: TBS007-77_S77_L001


title: TBS007-71_S71_L001


title: TBS007-70_S70_L001


title: TBS007-69_S69_L001


title: TBS007-68_S68_L001


title: TBS007-67_S67_L001


title: TBS007-64_S64_L001


title: TBS007-63_S63_L001


title: TBS007-59_S59_L001


title: TBS007-61_S61_L001


title: TBS007-57_S57_L001


title: TBS007-65_S65_L001


title: TBS007-58_S58_L001


title: TBS007-56_S56_L001


title: TBS007-53_S53_L001


title: TBS007-55_S55_L001


title: TBS007-49_S49_L001


title: TBS007-50_S50_L001


title: TBS007-52_S52_L001


title: TBS007-48_S48_L001


title: TBS007-66_S66_L001


title: TBS007-60_S60_L001


title: TBS007-43_S43_L001


title: TBS007-44_S44_L001


title: TBS008-25_S121_L002


title: TBS007-41_S41_L001


title: TBS007-39_S39_L001


title: TBS007-38_S38_L001


title: TBS007-54_S54_L001


title: TBS007-37_S37_L001


title: TBS007-42_S42_L001


title: TBS007-36_S36_L001


title: TBS007-34_S34_L001


title: TBS007-33_S33_L001


title: TBS007-35_S35_L001


title: TBS007-31_S31_L001


title: TBS007-30_S30_L001


title: TBS007-32_S32_L001


title: TBS007-47_S47_L001


title: TBS007-27_S27_L001


title: TBS007-29_S29_L001


title: TBS007-26_S26_L001


title: TBS007-45_S45_L001


title: TBS007-46_S46_L001


title: TBS007-21_S21_L001


title: TBS007-20_S20_L001


title: TBS007-22_S22_L001


title: TBS007-25_S25_L001


title: TBS007-18_S18_L001


title: TBS007-24_S24_L001


title: TBS007-19_S19_L001


title: TBS007-40_S40_L001


title: TBS007-14_S14_L001


title: TBS007-16_S16_L001


title: TBS007-13_S13_L001


title: TBS007-15_S15_L001


title: TBS007-11_S11_L001


title: TBS007-10_S10_L001


title: TBS007-07_S7_L001


title: TBS007-05_S5_L001


title: TBS007-08_S8_L001


title: TBS007-09_S9_L001


title: TBS007-03_S3_L001


title: TBS007-02_S2_L001


title: TBS007-01_S1_L001


title: TBS006-9_S69_L002


title: TBS006-60_S120_L002


title: TBS007-17_S17_L001


title: TBS006-5_S65_L002


title: TBS006-7_S67_L002


title: TBS006-6_S66_L002


title: TBS006-58_S118_L002


title: TBS006-57_S117_L002


title: TBS006-8_S68_L002


title: TBS007-12_S12_L001


title: TBS006-56_S116_L002


title: TBS006-54_S114_L002


title: TBS006-50_S110_L002


title: TBS006-59_S119_L002


title: TBS006-51_S111_L002


title: TBS006-42_S102_L002


title: TBS006-4_S64_L002


title: TBS006-3_S63_L002


title: TBS006-43_S103_L002


title: TBS007-28_S28_L001


title: TBS006-41_S101_L002


title: TBS007-06_S6_L001


title: TBS006-38_S98_L002


title: TBS006-39_S99_L002


title: TBS006-52_S112_L002


title: TBS006-37_S97_L002


title: TBS006-55_S115_L002


title: TBS006-35_S95_L002


title: TBS006-32_S92_L002


title: TBS006-34_S94_L002


title: TBS006-33_S93_L002


title: TBS006-30_S90_L002


title: TBS006-36_S96_L002


title: TBS006-31_S91_L002


title: TBS006-29_S89_L002


title: TBS006-53_S113_L002


title: TBS006-28_S88_L002


title: TBS006-40_S100_L002


title: TBS006-23_S83_L002


title: TBS006-21_S81_L002


title: TBS006-17_S77_L002


title: TBS006-20_S80_L002


title: TBS006-16_S76_L002


title: TBS006-19_S79_L002


title: TBS006-15_S75_L002


title: TBS006-22_S82_L002


title: TBS006-14_S74_L002


title: TBS006-13_S73_L002


title: TBS006-26_S86_L002


title: TBS006-18_S78_L002


title: TBS006-25_S85_L002


title: TBS006-12_S72_L002


title: TBS006-10_S70_L002


title: TBS005-7_S7_L001


title: TBS005-8_S8_L001


title: TBS005-60_S60_L001


title: TBS005-9_S9_L001


title: TBS005-5_S5_L001


title: TBS005-6_S6_L001


title: TBS006-2_S62_L002


title: TBS006-11_S71_L002


title: TBS005-57_S57_L001


title: TBS005-59_S59_L001


title: TBS005-58_S58_L001


title: TBS006-27_S87_L002


title: TBS005-53_S53_L001


title: TBS005-55_S55_L001


title: TBS005-56_S56_L001


title: TBS005-51_S51_L001


title: TBS005-50_S50_L001


title: TBS005-4_S4_L001


title: TBS005-47_S47_L001


title: TBS005-44_S44_L001


title: TBS005-49_S49_L001


title: TBS005-48_S48_L001


title: TBS005-45_S45_L001


title: TBS005-41_S41_L001


title: TBS005-43_S43_L001


title: TBS005-46_S46_L001


title: TBS005-40_S40_L001


title: TBS005-29_S29_L001


title: TBS005-37_S37_L001


title: TBS005-2_S2_L001


title: TBS005-30_S30_L001


title: TBS005-32_S32_L001


title: TBS005-38_S38_L001


title: TBS005-3_S3_L001


title: TBS005-26_S26_L001


title: TBS005-28_S28_L001


title: TBS005-27_S27_L001


title: TBS005-25_S25_L001


title: TBS005-54_S54_L001


title: TBS005-52_S52_L001


title: TBS005-24_S24_L001


title: TBS005-22_S22_L001


title: TBS006-1_S61_L002


title: TBS005-19_S19_L001


title: TBS005-20_S20_L001


title: TBS005-1_S1_L001


title: TBS005-17_S17_L001


title: TBS005-21_S21_L001


title: TBS004-8_S68_L002


title: TBS005-15_S15_L001


title: TBS004-60_S120_L002


title: TBS005-12_S12_L001


title: TBS005-16_S16_L001


title: TBS004-6_S66_L002


title: TBS005-10_S10_L001


title: TBS004-59_S119_L002


title: TBS004-58_S118_L002


title: TBS005-14_S14_L001


title: TBS004-9_S69_L002


title: TBS005-11_S11_L001


title: TBS004-57_S117_L002


title: TBS004-56_S116_L002


title: TBS005-13_S13_L001


title: TBS004-5_S65_L002


title: TBS004-55_S115_L002


title: TBS004-54_S114_L002


title: TBS005-23_S23_L001


title: TBS004-53_S113_L002


title: TBS004-7_S67_L002


title: TBS005-18_S18_L001


title: TBS004-51_S111_L002


title: TBS004-52_S112_L002


title: TBS004-49_S109_L002


title: TBS004-48_S108_L002


title: TBS004-4_S64_L002


title: TBS007-51_S51_L001


title: TBS004-47_S107_L002


title: TBS004-50_S110_L002


title: TBS004-46_S106_L002


title: TBS004-29_S89_L002


title: TBS004-3_S63_L002


title: TBS004-44_S104_L002


title: TBS004-39_S99_L002


title: TBS004-40_S100_L002


title: TBS004-41_S101_L002


title: TBS004-28_S88_L002


title: TBS004-42_S102_L002


title: TBS004-45_S105_L002


title: TBS004-37_S97_L002


title: TBS004-30_S90_L002


title: TBS004-2_S62_L002


title: TBS004-26_S86_L002


title: TBS004-38_S98_L002


title: TBS004-25_S85_L002


title: TBS004-43_S103_L002


title: TBS004-24_S84_L002


title: TBS004-27_S87_L002


title: TBS004-23_S83_L002


title: TBS004-22_S82_L002


title: TBS004-20_S80_L002


title: TBS004-1_S61_L002


title: TBS004-21_S81_L002


title: TBS004-19_S79_L002


title: TBS004-16_S76_L002


title: TBS004-15_S75_L002


title: TBS004-14_S74_L002


title: TBS004-17_S77_L002


title: TBS004-13_S73_L002


title: TBS004-11_S71_L002


title: TBS003-56_S56_L001


title: TBS003-6_S6_L001


title: TBS003-58_S58_L001


title: TBS003-57_S57_L001


title: TBS004-10_S70_L002


title: TBS003-8_S8_L001


title: TBS003-59_S59_L001


title: TBS004-12_S72_L002


title: TBS003-7_S7_L001


title: TBS003-53_S53_L001


title: TBS003-9_S9_L001


title: TBS003-54_S54_L001


title: TBS003-55_S55_L001


title: TBS003-51_S51_L001


title: TBS003-52_S52_L001


title: TBS003-4_S4_L001


title: TBS003-49_S49_L001


title: TBS003-48_S48_L001


title: TBS004-18_S78_L002


title: TBS003-45_S45_L001


title: TBS003-46_S46_L001


title: TBS003-47_S47_L001


title: TBS003-43_S43_L001


title: TBS003-41_S41_L001


title: TBS003-40_S40_L001


title: TBS003-5_S5_L001


title: TBS003-36_S36_L001


title: TBS003-60_S60_L001


title: TBS003-38_S38_L001


title: TBS003-3_S3_L001


title: TBS003-50_S50_L001


title: TBS003-27_S27_L001


title: TBS003-34_S34_L001


title: TBS003-29_S29_L001


title: TBS003-2_S2_L001


title: TBS003-26_S26_L001


title: TBS003-39_S39_L001


title: TBS003-31_S31_L001


title: TBS003-32_S32_L001


title: TBS003-35_S35_L001


title: TBS003-30_S30_L001


title: TBS003-28_S28_L001


title: TBS003-25_S25_L001


title: TBS003-23_S23_L001


title: TBS003-22_S22_L001


title: TBS003-21_S21_L001


title: TBS003-1_S1_L001


title: TBS003-20_S20_L001


title: TBS003-19_S19_L001


title: TBS003-42_S42_L001


title: TBS003-17_S17_L001


title: TBS003-33_S33_L001


title: TBS003-37_S37_L001


title: TBS003-16_S16_L001


title: TBS003-14_S14_L001


title: TBS003-12_S12_L001


title: TBS003-24_S24_L001


title: TBS002-Lipid_S1_L001


title: TBS002-39_S39_L001


title: TBS002-6_S6_L001


title: TBS002-34_S34_L001


title: TBS002-7_S7_L001


title: TBS002-8_S8_L001


title: TBS002-9_S9_L001


title: TBS003-10_S10_L001


title: TBS003-11_S11_L001


title: TBS002-29_S29_L001


title: TBS002-31_S31_L001


title: TBS002-3_S3_L001


title: TBS002-30_S30_L001


title: TBS002-27_S27_L001


title: TBS003-18_S18_L001


title: TBS002-2_S2_L001


title: TBS002-28_S28_L001


title: TBS002-26_S26_L001


title: TBS002-25_S25_L001


title: TBS002-24_S24_L001


title: TBS002-23_S23_L001


title: TBS003-13_S13_L001


title: TBS002-16_S16_L001


title: TBS003-15_S15_L001


title: TBS002-22_S22_L001


title: TBS002-15_S15_L001


title: TBS002-35_S35_L001


title: TBS002-13_S13_L001


title: TBS002-14_S14_L001


title: TBS002-33_S33_L001


title: TBS002-12_S12_L001


title: BM.CM.6

status: Public on Mar 21 2019

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

description: Sample 47

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17
Alignment of reads was done using topHat (v2.1.0)
For each gene all reads were counted that aligned to exonic regions using featureCounts (v1.4.3-p1) with Mus_musculus.GRCm38.78.gtf annotation from Ensembl
Differentially expression analysis was done in R edgeR (v2.13.0), taking the sort number as batch factor in the model. Groups (cell type per organ) were compared in contrasts and the glmTreat function was used to get genes with at least 1.5 fold change different between groups and an FDR-adjusted p-value < 0.05 was considered significant. Furthermore, only genes were considered significant if the average RPKM was at least 4 in at least one group of each contrast.
Genome_build: mm10
Supplementary_files_format_and_content: Raw read count per gene

source_name: Bone marrow

extract_protocol:
NucleoSpin RNA XS kit
NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: Central memory T cell

tag: sort number


title: BM.RM.6

description: Sample 46

value: Tissue resident memory T cell


title: BM.EM.6

description: Sample 45

value: Effector memory T cell


title: TBS002-10_S10_L001


title: Sp.EM.6

description: Sample 41

source_name: Spleen


title: Sp.RM.6

description: Sample 42


title: Sp.NV.6

description: Sample 44

value: Naive T cell


title: 8 h post light shift RNA-seq

city: Singapore

first: Siti Radiah

last: Binte Safie

address: 5 Science Drive 2

department: Microbiology and Immunology

country: Singapore

institute: National University Of Singapore

description: Sample 2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low-quality sequence in Partek Flow, then mapped to the Dunaliella tertiolecta transcriptome database GSE70876_Dt_v10.fa.gz
Transcripts Per Million (TPM) were calculated.
Genome_build: Dt_v10 (GEO accession no. GSE70876)
Supplementary_files_format_and_content: tab-delimited text files include gene annotation, TPM values under (Total Reads, normalised column) and fold-change of genes

organism: Dunaliella tertiolecta UTEX 'LB 999'

source_name: cultured cells

growth_protocol: Dunaliella tertiolecta strain UTEX LB-999 was obtained from the UTEX Culture Collection of Algae (University of Texas at Austin, TX). D. tertiolecta cells were grown in chemostat culture in ATCC-1174 DA liquid medium (American Type Culture Collection at Manassas, Virginia) containing 0.5M NaCl incubated in a photobioreactor at 25°C, under constant light intensity of 40 umol photons m-2 s-1.

extract_protocol:
Total RNA  was extracted at 4 h and 8 h after light shift using an RNeasyÂ® Plant Mini Kit (Qiagen, Valencia, CA, USA), according to manufacturer's protocol.
RNA libraries were prepared for sequencing using Illumina's TruSeq Stranded mRNA Library Prep Kit protocols.

treatment_protocol: Light intensity was increased to 400 umol photons m-2 s-1 when culture reached steady state

tag: strain

value: UTEX LB-999


title: Sp.CM.6

description: Sample 43


title: BM.NV.6

description: Sample 48


title: Sp.NV.5

description: Sample 36


title: Sp.CM.5

description: Sample 35


title: 4 h post light shift RNA-seq

description: Sample 1


title: BM.EM.5

description: Sample 37


title: BM.NV.5

description: Sample 40


title: BM.RM.5

description: Sample 38


title: Sp.RM.5

description: Sample 34


title: Sp.NV.4

description: Sample 28


title: BM.NV.4

description: Sample 32


title: BM.EM.4

description: Sample 29


title: Sp.EM.5

description: Sample 33


title: BM.CM.4

description: Sample 31


title: Sp.CM.4

description: Sample 27


title: Sp.RM.4

description: Sample 26


title: Sp.EM.4

description: Sample 25


title: Sample_LncCPR-KO-day8-3

city: houston

last: Soibam

address: one main street

institute: university of houston-Downtown

data_processing:
RNA-Seq reads were aligned to the mouse genome using tophat (6) with parameters: -p 8 --read-mismatches 2 --b2-L 20 -g 5. Reads, which mapped to multiple locations of the genome, were discarded before downstream analysis. An annotated list of known transcripts (mm9 UCSC refseq genes) was used for final set of transcriptome. The abundance and number of raw fragments aligned to each gene were computed using cufflinks. The abundance of each gene was expressed as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Genome_build: mm9
Supplementary_files_format_and_content: fpkm txt file - gene expression

source_name: LncCPR-KO mouse ES cells

growth_protocol: Cells were maintained at 37°C with 5% CO2 and 95% humidity and were grown in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM; ThermoFisher Scientific, Waltham, MA, USA) with 15% stem cell grade fetal bovine serum (FBS; Atlanta Biologicals, Inc., Flowery Branch, GA, USA), 1% antibiotic/antimitotic (ThermoFisher Scientific), 100 mM b-mercaptoethanol, and 2mM L-glutamine (ThermoFisher Scientific) and were supplemented with 1000 U/ml of leukemia inhibitory factor (LIF) to maintain pluripotency. Standard ESC culturing techniques were maintained.  For differentiation, one million cells were seeded in a gelatin-coated 10cM dish and grown with LIF for 48 hours to 70% confluency. Cells were trypsinized, counted, and resuspended in fresh media without LIF at a concentration of 20,000 cells/mL for differentiating the cells via embryoid bodies by using the hang-drop method.

extract_protocol:
total RNA was isolated from undifferentiated and whole embryoid bodies at day 3, 5, 8, 10, or 12 post-hang drop by using the RNeasy kit from Qiagen (Qiagen N.V., Venlo, Netherlands).
For the time-series transcriptome profiling, a total of 1 μg of total RNA from AB2.2 and AB2.2-LncCPR-/- cells was used for generating next-generation sequencing libraries with Illumina’s HiSeq3000 platform. Libraries were prepared by using the ScriptSeq Complete Gold kit from Epicentre (Cat. No. SCL24EP) according to the manufacturer’s recommended procedure for low-input starting material.

treatment_protocol: for CRISPR/Cas9 knockout, Ab2.2 cells were transfected with 2 constructs containing Cas9, GFP and a gRNA specific to upstream and downstream regions of the lncCPR gene for generating a knockout line. Transfected cells were single cell sorted and grown until enough cells were present for genotyping. Those with the desired knockout region were then expanded for characterization.

tag: genotype/variation

value: LncCPR-KO

tag: time point

value: day 8


title: Sample_LncCPR-KO-day8-1


title: Sample_LncCPR-KO-day8-2


title: Sample_LncCPR-KO-day5-1

value: day 5


title: Sample_LncCPR-KO-day5-3


title: BM.CM.5

description: Sample 39


title: Sample_LncCPR-KO-day5-2


title: Sample_LncCPR-KO-day12-2

value: day 12


title: Sample_LncCPR-KO-day12-3


title: Sample_LncCPR-KO-day3-2

value: day 3


title: Sample_LncCPR-KO-day12-1


title: Sample_LncCPR-KO-day10-2

value: day 10


title: Sample_Ab2-2-day8-3

source_name: mouse ES cells

value: control


title: Sample_LncCPR-KO-day0-2

value: day 0


title: Sample_LncCPR-KO-day10-1


title: Sample_LncCPR-KO-day0-3


title: Sample_LncCPR-KO-day10-3


title: Sample_LncCPR-KO-day0-1


title: Sample_Ab2-2-day8-2


title: Sample_Ab2-2-day5-2


title: Sample_Ab2-2-day5-1


title: Sample_Ab2-2-day3-2


title: Sample_Ab2-2-day5-3


title: Sample_Ab2-2-day3-3


title: Sample_Ab2-2-day8-1


title: Sample_Ab2-2-day3-1


title: Sample_Ab2-2-day12-3


title: Sample_Ab2-2-day12-2


title: Sample_Ab2-2-day12-1


title: Sample_LncCPR-KO-day3-1


title: Sample_Ab2-2-day10-3


title: Sample_Ab2-2-day0-3


title: Sample_Ab2-2-day10-2


title: Sample_Ab2-2-day0-2


title: Sample_Ab2-2-day10-1


title: Sample_LncCPR-KO-day3-3


title: mock_input_A

status: Public on Mar 20 2019

city: Portland

first: Joshi

last: Alumkal

state: OR

address: 3303 SW Bond Ave. CH14R

institute: Knight Cancer Institute

data_processing:
Sequences in raw .fastq files trimmed to 100bp.
Confirmed sequencing quality with FastQC utility.
Aligned .fastq files using bwa utility witn bwa-mem algorithm.
Converted to sorted .bam files ising samtools view and samtools sort utilities
Sequencing quality further confirmed using samtools stats utility.
For later analysis, translated out output .bam to sorted .bed files using bedtools utility.
Called peaks using epic peak caller.
Genome_build: hg38 release 85
Supplementary_files_format_and_content: .bed (called ChIP-seq peaks)
Supplementary_files_format_and_content: counts

source_name: Cell Line

growth_protocol: PC3 cells were grown in RPMI1640 + 10% FBS (Premium Select grade, Atlanta Biologicals).

extract_protocol:
ChIP experiments were performed with formaldehyde cross-linked cells using anti-BRD4 antibody (Bethyl #A301-985A). Input and ChIP samples were processed using Diagenode iDeal ChIP-seq for Transcription Factors Kit.
Illumina TruSeq ChIP Sample Prep Kit, using 10 ng of input material.
RNA: Trizol/CHCl3; ChIP: formaldedhyde cross-linking followed by Diagenode iDeal ChIP-seq for Transcription Factors Kit. Also see SAMPLES section.
RNA-seq: Agilent SureSelect Strand-Specific mRNA Library Preparation Protocol; ChIP-seq: Illumina TruSeq ChIP Sample Prep Kit. Also see SAMPLES section.

treatment_protocol: DMSO was diluted 1:2000 to 0.05% in appropriate cell culture media. Serves as vehicle control for JQ1 treatment. Samples for ChIP-seq were treated for 12 hours.

tag: tissue

value: prostate

value: prostate cancer cell line


title: RV1_05

growth_protocol: 22RV1 cells were grown in RPMI1640 + 10% FBS (Premium Select grade, Atlanta Biologicals).

extract_protocol:
Total RNA was extracted with Trizol (Life Technologies) per manufacturer's protocol.
Agilent SureSelect Strand-Specific mRNA Library Preparation Protocol (Version  A.2, September 2013, Agilent Technologies).
RNA: Trizol/CHCl3; ChIP: formaldedhyde cross-linking followed by Diagenode iDeal ChIP-seq for Transcription Factors Kit. Also see SAMPLES section.
RNA-seq: Agilent SureSelect Strand-Specific mRNA Library Preparation Protocol; ChIP-seq: Illumina TruSeq ChIP Sample Prep Kit. Also see SAMPLES section.

treatment_protocol: DMSO stock of 1 mM JQ1 was diluted 1:2000 to 500 nM final concentration in appropriate cell culture media. Samples for RNA-seq were treated for 24 hours.


title: RV1_0

treatment_protocol: DMSO was diluted 1:2000 to 0.05% in appropriate cell culture media. Serves as vehicle control for JQ1 treatment. Samples for RNA-seq were treated for 24 hours.


title: V16D_05

growth_protocol: V16D cells were grown in RPMI1640 + 10% FBS (Premium Select grade, Atlanta Biologicals).


title: mock_input_B


title: mock_BRD4_B


title: mock_BRD4_A


title: JQ1_input_A

treatment_protocol: DMSO stock of 1 mM JQ1 was diluted 1:2000 to 500 nM final concentration in appropriate cell culture media. Samples for ChIP-seq were treated for 12 hours.


title: V16D_0


title: PC3_0


title: JQ1_input_B


title: PC3_05


title: JQ1_BRD4_A


title: myc3_500

growth_protocol: LNCaP cells were grown in RPMI1640 + 10% FBS (Premium Select grade, Atlanta Biologicals).


title: NCI_H660_05

growth_protocol: NCI-H660 cells were grown in in RPMI 1640 + 5% FBS, 10 µg/mL transferrin (Sigma-Aldrich #T2252), 30 nM sodium selenite (Sigma-Aldrich #S9133), 10 nM β-estradiol (Sigma-Aldrich #E8875), 2 mM L-Glutamine (Gibco #25030-164), 5 µg/mL insulin (Sigma-Aldrich #I9278), and 10 nM hydrocortisone (Sigma-Aldrich #H4001).


title: myc3_0


title: NCI_H660_0


title: MR49F_05

growth_protocol: MR49F cells were grown in RPMI + 10% FBS and 10µM Enzalutamide (MedchemExpress #HY-70002).


title: Sample_Ab2-2-day0-1


title: MR49F_0


title: MR42D_05

growth_protocol: MR42D cells were grown in RPMI + 10% FBS and 10µM Enzalutamide (MedchemExpress #HY-70002).


title: MR42D_0


title: LNCaP_0


title: LNCaP_05


title: JQ1_BRD4_B


title: EV2_500


title: EV2_0


title: C42B_0

growth_protocol: C4-2B cells were grown in RPMI1640 + 10% FBS (Premium Select grade, Atlanta Biologicals).


title: LN95_0

growth_protocol: LNCaP-95 cells were grown in phenol-red-free RPMI-1640 + 10% charcoal/dextran-treated FBS.


title: abl_0

growth_protocol: Abl cells were grown in RPMI with 10% charcoal/dextran-treated FBS (Atlanta Biologicals).


title: SS_3h_B

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description: SS_3h_B PAs exposure for 3h

data_processing:
bcl2fastq software used for basecalling.
3' adapter (end1:TGGAATTCTCGGGTGCCAAGG;end2:GATCGTCGGACTGTAGAACTCTGAAC) trimmed with fastx_clipper,remove 3 bases of 5'.
discovering novel miRNAs using miRDeep2,then predicting miRNA target gene using miRanda and targetscan.
mapped using bowtie -v 1
detecting different expression miRNA (TPM value) using edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: txt format,the expressed genes TPM & reads of miRNA

growth_protocol: PANC-1 cells were cultured as monolayers in Dulbecco's Modified Eagle Medium (Gibco, USA) containing 10% fetal bovine serum (Hyclone, USA).Cells were incubated and maintained in a chamber with 95% air and 5% CO2 at 37℃.

extract_protocol:
Following treatment of PANC-1 cells with or without Proanthocyanidins the cells were harvested, washed with cold PBS, and lysed with ice-cold Trizol reagent.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to illumina NextSeq 500 system for 151 nt pair-end sequencing and 75 nt pair-end sequencing by ABlife. Inc (Wuhan, China).

treatment_protocol: PANC-1 cells were harvested at the indicated time post Proanthocyanidins (20μg/ml) or DMSO exposure.

tag: cell line

value: pancreatic cancer cells

tag: treated with

value: PAs for 3h


title: M12_EV_05

growth_protocol: M12 cells were grown in RPMI 1640 + 5% FBS, 0.01 µM dexamethasone (MP Biomedicals #ICN19456125), 10 ng/ml EGF (Corning #CB40052), and 10 mL/L ITS (Corning #25-800-CR).


title: abl_05


title: C42B_05


title: SC_12h_B

description: SC_12h_B DMSO exposure for 12h

value: DMSO for 12h


title: SS_12h_B

description: SS_12h_B PAs exposure for 12h

value: PAs for 12h


title: SC_0h_A

description: SC_0h_A Treatment with DMSO for 0h

value: DMSO for 0h


title: SC_12h_A

description: SC_12h_A DMSO exposure for 12h


title: SS_24h_A

description: SS_24h_A PAs exposure for 24h

value: PAs for 24h


title: SS_3h_A

description: SS_3h_A PAs exposure for  3h

value: PAs for  3h


title: SC_24h_B

description: SC_24h_B DMSO exposure for 24h

value: DMSO for 24h


title: SS_12h_A

description: SS_12h_A PAs exposure for 12h


title: M12_EV_0


title: SC_0h_B

description: SC_0h_B Treatment with DMSO for 0h


title: 3day adrenalectomy 4

city: Research Triangle Part

first: Jonathan

middle: T

last: Busada

state: NC

address: 111 TW Alexandar Drive

institute: NIEHS

data_processing:
Raw reads were first cleaned for adapter sequences using Trim Galore with default parameters;
RNA-SEQ reads (~60M per sample) were aligned to the UCSC mm9 reference genome using STAR
The quantification results from FeatureCounts were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Genome_build: mm9
Supplementary_files_format_and_content: excel table; log2 transformed and normalized abundance measurements by DESeq2

source_name: Stomachs

extract_protocol:
Stomach were collected after treatment and RNA extracted with Trizol and purified with with Qiagen Rneasy Kit
Libraries were constructed with the use of the Illumina TruSeq library construction kit V2 (Cat #RS-122-2001) according to manufacturer's protocol. Libaries were pooled and sequenced on the Illumina NextSeq500 sequencer

treatment_protocol: Mice were euthanized 3 days after sham surgery or adrenalectomy

tag: background

tag: gender

value: Female

value: Stomachs

tag: timepoint

value: 3 days post adrenalectomy

value: wild-type


title: 3day adrenalectomy 3


title: SC_3h_B

description: SC_3h_B DMSO exposure for 3h

tag: cell type

value: DMSO for 3h


title: SC_3h_A

description: SC_3h_A DMSO exposure for 3h


title: 3day adrenalectomy 1

tag: genotype


title: 3day sham 4

value: 3 days post sham surgery


title: 3day adrenalectomy 2


title: LN95_05


title: 3day sham 3


title: 3day sham 2


title: 3day sham 1


title: SS_24h_B

description: SS_24h_B PAs exposure for 24h


title: SC_24h_A

description: SC_24h_A DMSO exposure for 24h


title: Spaceflight, Root Rep. 3 [BS]

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

description:
bisulfite converted
ROOTFT.vs.ROOTGC.full CG
ROOTFT.vs.ROOTGC.full CHG
ROOTFT.vs.ROOTGC.full CHH
ROOTFT-winavg CG
ROOTFT-winavg CHG
ROOTFT-winavg CHH
ROOTFT.vs.ROOTGC.genes01.full CG
ROOTFT.vs.ROOTGC.genes01.full CHG
ROOTFT.vs.ROOTGC.genes01.full CHH
ROOTFT.vs.ROOTGC.genes02.full CG
ROOTFT.vs.ROOTGC.genes02.full CHG
ROOTFT.vs.ROOTGC.genes02.full CHH
ROOTFT.vs.ROOTGC.genes03.full CG
ROOTFT.vs.ROOTGC.genes03.full CHG
ROOTFT.vs.ROOTGC.genes03.full CHH
ROOTFT.vs.ROOTGC.genes04.full CG
ROOTFT.vs.ROOTGC.genes04.full CHG
ROOTFT.vs.ROOTGC.genes04.full CHH
ROOTFT.vs.ROOTGC.genes05.full CG
ROOTFT.vs.ROOTGC.genes05.full CHG
ROOTFT.vs.ROOTGC.genes05.full CHH

data_processing:
The fastq files containing short reads from whole-genome bisulfite sequencing were trimmed to remove low-quality bases using trimmomatic (version 0.36). Fastq files before and after trimming were analyzed for quality control with FastQC (version 0.11.4). The fraction of reads removed because of low quality was never more than 0.01%.  Total number of reads after trimming for each sample ranged from 22,446,135 to 39,065,215.
A second filtering step was performed to remove reads showing evidence of incomplete conversion, using the cscall tool (http://compbio.ufl.edu/software/cscall/). The fraction of reads removed in this step ranged between 0.05% and 0.08%.
The remaining reads were aligned to the Arabidopsis genome using bsmap (http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-232) version 2.87. The percentage of aligned reads ranged from 87.57% and 90.52%.
Methylation calling was performed with cscall using the ws_0.v7.allPlusChlMito-CG index. A site was included in the analysis if it reached a coverage of 20 in at least 2 out of the three replicates of each sample. Differential methylation was determined using the mcomp program, part of the MOABS suite (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-2-r38), version 1.3.4. Sites for which the P-value of the difference between test and control methylation rates was below 0.01 were considered significant. Sites with a methylation difference above 0.3 were classified as Strongly hyper/hypo methylated(++ or  --), otherwise they were classified as hyper/hypo methylated (+ or -).
Genome_build: Arabidopsis thaliana WS reference genome (Mott et al. Nature 2011)
Supplementary_files_format_and_content: .xls spreadsheets containing methylation levels in a 100 bp sliding window across the genome and differential methylation between the spaceflight vs. ground control comparisons.

organism: Arabidopsis thaliana

source_name: solid 0.5x MS media plates; grown on the ISS, 11 day old plant harvested into KFT containing RNAlater fixative

growth_protocol: Dry, sterilized Arabidopsis seeds of wild-type cultivar Wassilewskija  were planted aseptically on the surface of 10 cm2 solid media plates comprised of 0.5% Phytagel/0.5× MS media, and then immediately wrapped in light-tight black cloth (Duvetyne, SeattleFabrics.com) and transported to KSC (Kennedy Space Center), FL, USA. The wrapped plates were stored at temperatures between 4 and 10°C and remained dormant until removal from cold stowage and exposure to light at the initiation of the APEX03-2 experiment on the ISS (International Space Station). Plates were integrated and grown in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS. The 10 cm2 Petri plates were housed perpendicular (“vertical”) to the overhead LED lighting of the VPS. Plants received between 100–135 μmoles/m2/s PAR inside the VPS. The plants were grown for eleven days after germination, which was initiated by unwrapping the plates and exposing them to light in the VPS. The ground control plates were grown inside the VPS ground unit within the ISSES (International Space Station Environment Simulator) chamber at KSC with a 48-h delay. The ISSES chamber replicated the temperature, CO2 levels and lighting that had been experienced by the spaceflight plants in the previous 48 h. After eleven days, seedlings were harvested by an astronaut into a KFT (Kennedy Fixation Tube) containing RNAlater. Once the plants were placed in the KFTs, the KFT was actuated with RNAlater to chemically fix the sample. At 24 hours post-harvest, KFTs were then transferred to MELFI (Minus Eight Laboratory Freezer for ISS) and were kept at -32°C. Following SpaceX-3 splashdown in the Pacific Ocean, the KFTs were transferred to the Cold Stowage charter plane at the Long Beach Airport, placed into an insulated shipper with dry ice, and flown to Johnson Space Center (JSC). The KFTs were then transferred via FedEx ground to the Kennedy Space Center. The KFTs were removed from dry ice and transferred to a -80°C freezer on May 22, 2014. The PIs retrieved the plant samples from the KFTs on May 29, 2014 and transferred the samples back to the University of Florida.

extract_protocol:
Seedlings stored in RNAlater were recovered from the -80°C freezer. Each tube containing the seedlings from a single plate was allowed to thaw at 4°C overnight. After completely thawing the samples to room temperature, the seedlings were observed under the microscope. The preserved seedlings from the spaceflight and ground control harvests were dissected into distinct plant parts: leaf, hypocotyl, and root. Three plants were allocated for RNA analysis and the remaining plants from a plate (between 10 and 12) were allocated for DNA extraction and subsequent whole genome bisulfite sequencing. DNA was extracted using a modified phenol/chloroform protocol as previously described (LeFrois et al. 2016) from three biological replicates of root and leaf samples from spaceflight and ground controls. This DNA material was then submitted to the Interdisciplinary Center for Biotechnology at the University of Florida for bisulfite conversion and Next-Generation sequencing.
Genomic-wide bisulfite sequencing was performed using a similar procedure as described by Wang et al. (2013) with several modifications. In summary, genomic DNA was extracted from leaves and roots of spaceflight and ground control samples using a modified phenol/chloroform extraction method (LeFrois et al. 2016). Between 700-1700 ng of genomic DNA was processed for sequencing library construction. The average size of the genomic DNA for this type of samples was 5 Kb as observed on a DNA12000 BioAnalyzer chip (Agilent). DNA was transferred into 6x16 mm glass microtubes with AFA fiber and pre-slit snap caps (Cat# 520045, Covaris, Inc.). As it is required by the Illumina sequencing procedure, the DNA was sheared into average fragments size of ~400 bp, using the Covaris S220 ultrasonic disruptor, and following the recommended settings by the manufacturer. Short DNA fragments (<100 bp) were removed using AMPure magnetic beads (Cat# A63881, Beckman Coulter) at a 1:1 bead to sample ratio.  At this point we obtained a yield of 300-750 ng of clean, fragmented DNA. Between 100-250 ng of this material was used for Illumina sequencing library construction using the NEBnext Ultra DNA Illumina construction kit (Cat# E7370S, NEB) in conjunction with Illumina-specific methylated and barcoded adaptors (Cat# E7535S, NEB) from the same source. This particular library construction kit was chosen because it contains reagents that have been optimized for relatively low-input DNA in the library construction process. At the end of the end-repair, 3'-adenylation, and adaptor-ligation steps, 75-150 ng of clean, adaptor-ligated DNA fragments (Illumina library) were recovered in Tris-HCl, pH 8.0. It should be noted that the libraries were not PCR-amplified at this stage, as it would normally be done in the most typical Illumina library construction protocol. Libraries were quantitated using a QUBIT fluorometer (Life Technologies).Illumina libraries (containing methylated adaptors) were subjected to sodium bisulfite treatment using the EZ DNA Methylation Direct kit (ZYMO Research, Cat #D5020) according to the manufacturer's instructions. The resulting libraries were enriched by a 13-15 cycle amplification using an uracil-insensitive polymerase (EpiMark hot start Taq polymerase, NEB, Cat#M0490S). The amplified library products were separated on a 2% agarose gel from which library fragments in the 250-500 bp range were excised (QIAquick gel extraction kit, Cat# 28704, QIAGEN) and AMPure purified (Cat# A63881, Beckman Coulter). Gel staining was done with SYBR safe (Life Technologies) and visualized on a blue light transilluminator (Life Technologies) in order to avoid UV damage of DNA. The final libraries were quantitated by the QUBIT fluorometer, and by qPCR with the Kapa SYBR Fast qPCR reagents (Cat# KK4824, Kapa Biosystems) with monitoring on an ABI7900HT real-time PCR system (LifeTechnologies). The average library size was 350 bp. In preparation for sequencing on the HiSeq3000 Illumina sequencer, barcoded libraries were normalized to 2.5 nM and pooled (equimolarly). Up to 6 samples were pooled for sequencing on a single HiSeq3000 flow cell lane, using a 2x101 cycle multiplex, paired-end configuration. Typically, the PhiX library is used for a spike-in (at 20%) in order to correct for the low base diversity of bisulfite-converted genomic libraries. Alternatively, bisulfite-converted libraries were sequenced alongside RNA-seq libraries (60%:40% ratio of RNA-seq vs Bisulfite-converted libraries), without a PhiX spike-in. Library pools were processed according the Illumina protocol (HiSeq3000) for clustering on the cBOT machine. The final pool concentration for clustering was 0.25 nM, following denaturation, neutralization, and mixing with the ExAmp reagent. A typical sequencing run in the HiSeq3000 produced 600-650 million paired-end reads per lane. For genome-wide bisulfite sequencing 50-100 million reads provided sufficient depth for analysis of methylation. In Arabidopsis (and possibly other plants), this output is required in part due to the fact that up to 50% of the reads map to chloroplast DNA. Assuming the lowest end of reads/lane output in the HiSeq3000, a 36-sample project would need 6 lanes.

treatment_protocol: The two treatments involved in this experiment were spaceflight and ground control. Spaceflight plants were grown for 11 days aboard the ISS in the VPS hardware. Ground control plants were grown for 11 days in the VPS hardware in the ISSES chamber at KSC, which replicates the temperature, CO2 levels and lighting that had been experienced by the spaceflight plants in the previous 48h.

tag: cultivar

value: WS

tag: material type

value: Leaves

tag: organism part

tag: age

value: 11 days old plants

tag: biosource type

value: RNAlater fixed_sample


title: Ground Control, Leaf Rep. 1 [BS]

description:
bisulfite converted
LEAFFT.vs.LEAFGC.full CG
LEAFFT.vs.LEAFGC.full CHG
LEAFFT.vs.LEAFGC.full CHH
LEAFGC-winavg CG
LEAFGC-winavg CHG
LEAFGC-winavg CHH
LEAFFT.vs.LEAFGC.genes01.full CG
LEAFFT.vs.LEAFGC.genes01.full CHG
LEAFFT.vs.LEAFGC.genes01.full CHH
LEAFFT.vs.LEAFGC.genes02.full CG
LEAFFT.vs.LEAFGC.genes02.full CHG
LEAFFT.vs.LEAFGC.genes02.full CHH
LEAFFT.vs.LEAFGC.genes03.full CG
LEAFFT.vs.LEAFGC.genes03.full CHG
LEAFFT.vs.LEAFGC.genes03.full CHH
LEAFFT.vs.LEAFGC.genes04.full CG
LEAFFT.vs.LEAFGC.genes04.full CHG
LEAFFT.vs.LEAFGC.genes04.full CHH
LEAFFT.vs.LEAFGC.genes05.full CG
LEAFFT.vs.LEAFGC.genes05.full CHG
LEAFFT.vs.LEAFGC.genes05.full CHH

source_name: solid 0.5x MS media plates; grown on the ground, 11 day old plant harvested into KFT containing RNAlater fixative

value: Roots

value: Whole roots


title: Ground Control, Root Rep. 1 [BS]

description:
bisulfite converted
ROOTFT.vs.ROOTGC.full CG
ROOTFT.vs.ROOTGC.full CHG
ROOTFT.vs.ROOTGC.full CHH
ROOTGC-winavg CG
ROOTGC-winavg CHG
ROOTGC-winavg CHH
ROOTFT.vs.ROOTGC.genes01.full CG
ROOTFT.vs.ROOTGC.genes01.full CHG
ROOTFT.vs.ROOTGC.genes01.full CHH
ROOTFT.vs.ROOTGC.genes02.full CG
ROOTFT.vs.ROOTGC.genes02.full CHG
ROOTFT.vs.ROOTGC.genes02.full CHH
ROOTFT.vs.ROOTGC.genes03.full CG
ROOTFT.vs.ROOTGC.genes03.full CHG
ROOTFT.vs.ROOTGC.genes03.full CHH
ROOTFT.vs.ROOTGC.genes04.full CG
ROOTFT.vs.ROOTGC.genes04.full CHG
ROOTFT.vs.ROOTGC.genes04.full CHH
ROOTFT.vs.ROOTGC.genes05.full CG
ROOTFT.vs.ROOTGC.genes05.full CHG
ROOTFT.vs.ROOTGC.genes05.full CHH


title: Ground Control, Leaf Rep. 2 [BS]


title: Ground Control, Root Rep. 2 [BS]


title: Spaceflight, Leaf Rep. 3 [BS]

description:
bisulfite converted
LEAFFT.vs.LEAFGC.full CG
LEAFFT.vs.LEAFGC.full CHG
LEAFFT.vs.LEAFGC.full CHH
LEAFFT-winavg CG
LEAFFT-winavg CHG
LEAFFT-winavg CHH
LEAFFT.vs.LEAFGC.genes01.full CG
LEAFFT.vs.LEAFGC.genes01.full CHG
LEAFFT.vs.LEAFGC.genes01.full CHH
LEAFFT.vs.LEAFGC.genes02.full CG
LEAFFT.vs.LEAFGC.genes02.full CHG
LEAFFT.vs.LEAFGC.genes02.full CHH
LEAFFT.vs.LEAFGC.genes03.full CG
LEAFFT.vs.LEAFGC.genes03.full CHG
LEAFFT.vs.LEAFGC.genes03.full CHH
LEAFFT.vs.LEAFGC.genes04.full CG
LEAFFT.vs.LEAFGC.genes04.full CHG
LEAFFT.vs.LEAFGC.genes04.full CHH
LEAFFT.vs.LEAFGC.genes05.full CG
LEAFFT.vs.LEAFGC.genes05.full CHG
LEAFFT.vs.LEAFGC.genes05.full CHH


title: Spaceflight, Leaf Rep. 1 [BS]


title: Spaceflight, Root Rep. 1 [BS]


title: Ground Control, Root Rep. 3 [BS]


title: Spaceflight, Leaf Rep. 2 [BS]


title: Spaceflight, Root Rep. 2 [BS]