title: s04_160116_21722_KARPAS299_CRI_RNA

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

institute: University of Pennsylvania

data_processing:
Pair-ended RNA sequencing reads were aligned to human reference sequence (Feb. 2009, GRCh37/hg19).
Uniquely mapped reads were quantified by Subread (v1.5.0).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files including read counts per ensembl gene id.

source_name: Anaplastic large-cell lymphoma

growth_protocol: RNA was isolated using the RNeasy mini kit from Qiagen after treatment of the cells with Crizotinib or its vehicle (DMSO). Terminal deoxynucleotidyl transferase was used to add poly(A) tail to the end of the first-strand cDNA which were amplified by 20 cycles of PCR. Hundred nanograms of cDNA (0.5-3kb) were sheared into 80-130bp fragments. Adaptors were ligated to each end then the fragments were subjected to 10 cycles of PCR amplification. The libraries were sequenced on Illumina HiSeq 2000 (paired-end, long-read sequencing).

extract_protocol:
RNA was isolated using the RNeasy mini kit from Qiagen after treatment of the cells with Crizotinib or its vehicle (DMSO). Terminal deoxynucleotidyl transferase was used to add poly(A) tail to the end of the first-strand cDNA which were amplified by 20 cycles of PCR. The libraries were sequenced on Illumina HiSeq 2000 (paired-end, long-read sequencing).
Hundred nanograms of cDNA (0.5-3kb) were sheared into 80-130bp fragments. Adaptors were ligated to each end then the fragments were subjected to 10 cycles of PCR amplification.
The libraries were sequenced on Illumina HiSeq 2000 (paired-end, long-read sequencing).

tag: cell line

value: Crizotinib

tag: chromosomal translocation


title: fca10_H3K9ac

status: Public on Sep 08 2017

type: SRA

city: College Station

first: Jennifer

last: Goldsby

state: TX

address: 112 Cater-Mattil

department: Nutrition and Food Sciences

country: USA

institute: Texas A&M University

library_source: genomic

data_processing:
Illumina CASAVA v 1.8.2 used for basecalling
ChIP-seq : mapped to the reference rat genome (rn4) with commonly used BWA for Illumina (version 1.2.3) settings and only non-identical uniquely mapped reads were retained
ChIP-seq : The peak caller programme MACS (version 1.4.1) (5) was used to identify peaks with the following parameter settings: --bw=300 --keep-dup=1.
ChIP-seq : Islands were defined (using merge function of BEDTools (6)) as the genomic areas enriched with the ChIPed protein (peaks) in at least one sequenced sample, and reads were quantified using coverageBed function of BEDTools (6)
ChIP-seq : Regions showing differences in histone modification were identified using the edgeR package (8, 9) for the R software environment.  .  Read counts per gene were normalized using the scaling factor method of Anders and Huber (10).  Differential expression testing of genes was performed using likelihood ratio tests on the negative binomial GLMs estimated by edgeR (8, 9).  Regions with FDR < 0.1 and minimal threshold of one count per million mapped reads in at least four samples were selected as differentially enriched regions (DERs).
RNA: Reads were mapped with the STAR aligner using the default parameters and rn5 genome assembly
RNA: Read counts per gene were normalized using the scaling factor method of Anders and Huber  (10).  The read counts were modeled directly using negative binomial generalized linear models accounting for the differences in diet and subsequently fit with the R programming language (5) and Bioconductor package edgeR (8, 9). Differential expression was then tested using likelihood ratio tests involving the fitted models.   Genes with false discovery rate adjusted p-value (FDR) less than 0.1 were selected as differentially expressed transcripts (DE).
Genome_build: rn4
Supplementary_files_format_and_content: xls files include counts processed with Bedtools(number of reads that mapped to the specified locations).  EdgeR was used to determine FDR, and differential expression(in the form of fold change experimental over control)

molecule: genomic DNA

organism: Rattus norvegicus

source_name: colonocytes

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody for ChIP .  For RNA colonic crypts were homogenized on ice in lysis buffer (RNAqueous Isolation kit, Ambion)
generate multiplex libraries for whole-transcriptome analysis following Illumina’s TruSeq RNA v2 sample preparation protocol. Libraries from 24 individual rats per treatment were sequenced on an Illumina HiSeq 2000.   BioScientific NETflex (ChIPseq kit 5143-01, Barcodes kit 514120) multiplex libraries from ChIPed DNA (10 nM) were sequenced using a Illumina Hiseq 2000 DNA Sequencer.  Libraries from  biological replicates of pooled ChIPed samples per treatment were individully sequenced on an Illumina HiSeq 2000.
ChIP-seq with BioScientific NETflex (ChIPseq kit 5143-01, Barcodes kit 514120)and RNA-seq (Illumina’s TruSeq RNA v2 )

treatment_protocol: After 2 weeks of feeding weanling male rats with specified oil/fiber, 24 rats were injected with saline (control), and 43 rats were AOM (Sigma, St. Louis, MO) injected s.c. at 15 mg/kg body weight. Each rat subsequently received a second AOM or saline injection 1 week later and animals were terminated 10 weeks after the first AOM injection.

tag: chip antibody

value: H3K9ac (Abcam ab10812)

tag: carcinogen

value: AOM

tag: oil

value: fish oil

tag: fiber

value: cellulose


title: s03_160116_21721_KARPAS299_DMSO_RNA

department: Pathology

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment

value: DEMSO


title: 38hpi_E16

city: Cambridge

first: Daniel

middle: E.

last: Neafsey

state: MA

address: 415 Main St.

institute: Broad Institute

description:
AGGCAGAA_E16
38hpi.raw.tsv
38hpi.normalized.tsv

data_processing:
Illumina NextSeq standard basecalling platform
Well barcode demultiplexing. Custom python script. Separates wells in 384-well plate
Unique molecular identifier demultiplexing. Custom python script. Counts reads from same mRNA molecule as only 1
Transcript alignment with bwa aln v0.7.10 allowing 4 mismatches in seed sequence and rest of sequence.
Discard reads with polyA tails (> 20 As in a row)
Additional filtering: Filter reads for rRNA. Remove samples with fewer than 300 reads. Remove genes that were found in <20 samples.
Generate normalized abundances with edgeR v3.14.0
Genome_build: PlasmoDB Plasmodium falciparum 3D7 transcript v29
Supplementary_files_format_and_content: 38hpi.raw.tsv - 38hpi raw read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 42hpi.raw.tsv - 42hpi raw read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 46hpi.raw.tsv - 46hpi raw read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 38hpi.filtered.tsv - 38hpi filtered read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 42hpi.filtered.tsv - 42hpi filtered read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 46hpi.filtered.tsv - 46hpi filtered read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 38hpi.normalized.tsv - 38hpi normalized read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 42hpi.normalized.tsv - 42hpi normalized read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 46hpi.normalized.tsv - 46hpi normalized read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: all.normalized.tsv - all normalized read counts from all time points in matrix forrmat, where rows are samples and columns are genes

molecule: polyA RNA

organism: Plasmodium falciparum NF54

source_name: Single cell sorted Plasmodium infected human erythrocytes

growth_protocol: P.falciparum cell culture was performed as described previously (REF). Culture media consisted of RPMI-1640 supplemented with 25 mM HEPES, 100 μM hypoxanthine, 24 mM sodium bicarbonate, and gentamicin (all from Sigma-Aldrich). Serum media was generated by additional supplementation of 10% O+ human serum (The Interstate Companies) while serum-free medium was generated by additional supplementation of 0.39% fatty acid-free BSA, 30 μM oleic acid, and 30 μM palmitic acid (all from Sigma-Aldrich). To generate serum-free media supplemented with 20 μM LysoPC, LysoPC (Avanti Polar Lipids) was dissolved in ethanol and dried on culture dishes prior to culture addition. All cell cultures were maintained in a 5% CO2/1 % O2 and 95 % N2 gas mixture (Med-Tech Gases). All experiments used a clone of the Pf2004/164TdTomato P.falciparum line 14, which requires addition of 4 nM WR99210 (Jacobus Pharmaceuticals).

extract_protocol:
We used an optimized version of Single Cell RNA Barcoding and Sequencing 7 (SCRB-seq; Soumillon et al, 2014), further reducing the reverse transcriptase reaction volume. In brief, poly(A)+ mRNA from flow-sorted single Plasmodium infected erythrocytes were converted to cDNA, decorated with universal adapters, well barcodes, and unique molecular identifiers (UMIs), using a template-switching reverse transcriptase. Then, cDNA from multiple cells was pooled, amplified, and prepped for multiplexed sequencing using a transposon-based fragmentation method, enriching for 3’ ends and preserving strand information.
Nextera XT

treatment_protocol: Parasite cultures were sorbitol-synchronized (Sigma-Aldrich) as described previously 21 to a 4-hour cycle window using 4 consecutive treatments across two growth cycles. At 28-32 hour post invasion, parasites were washed in RPMI/mFA media and plated with or without LysoPC. At 4, 8, and 12 hours post induction, cells were stained with Vybrant DyeCycle Violet (Life Technologies) in HBSS (Thermo Fisher Scientific). Stained cells were pelleted and resuspended in phenol red-free PBS supplemented with 0.3% RNaseOUT (Life Technologies). Collection Twin.tec PCR 384-well plates (Eppendorf) were prepared by addition of cell lysis buffer to each well; lysis buffer consisted of nuclease-free water (Thermo Fisher Scientific) supplemented with 0.2% HF buffer (New England Biolabs). Single Vybrant Dye Cycle Violet-positive cells were sorted using a Beckman Coulter MoFlo Astrios EQ. At each time point, 48 cells from the non-induced culture (+LysoPC) and 336 cells from the induced culture (-LysoPC) were sorted into the collection plate and snap frozen on dry ice. Cultures were maintained for an additional two cycles for parasitemia and gametocytemia measurement. The media of both non-induced and induced cultures was replaced with RPMI/serum 12 hours post induction and daily thereafter.

tag: time point

tag: induced

value: Induced


title: Q22_ESSHG

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

department: Department of Pathology

institute: Stanford University

data_processing:
The paired-end sequence reads were aligned to the human genome (hg19) with Subread (version 1.5.0) using default settings
Reads were summarized using default settings of the featureCounts program for paired-end reads, and single nucleotide polymorphisms were identified using default settings of the exactSNP program within the Subread package
Variants were annotated with wANNOVAR web interface (http://wannovar.usc.edu)
Mutations were filtered for <0.1% presence in any population included in 1000 Genomes or ExAC studies, exonic location, and nonsynonymous or stopgain effect.
Genome_build: hg19
Supplementary_files_format_and_content: subread_counts.txt files contain reads summarized using default settings of the featureCounts program for paired-end reads

source_name: ESS high grade

extract_protocol:
Total RNA was extracted from frozen tissue specimens using the miRNeasy Mini Kit (Qiagen), including DNase treatment using RNase-free DNase Set (Qiagen). RNA quality was verified using Bio-Rad Experion system (Bio-Rad Laboratories).
Samples were prepared with the Illumina TruSeq RNA Sample Preparation Kit (Illumina). The insert sizes of the libraries were assessed using Agilent Technologies 2100 Bioanalyzer. Validated DNA libraries were pooled, clustered on the cBot cluster generation station (Illumina), and sequenced on a HiSeq 2000 platform (Illumina). Prepared libraries were sequenced using HiSeq 2000 (Illumina) operated in paired-end 2x100 bp mode. Reads were quality-filtered using a standard Illumina pipeline.

tag: tumor type

value: High grade


title: s02_160116_21720_SUDHL1_CRI_RNA


title: 38hpi_E15

description:
AGGCAGAA_E15
38hpi.raw.tsv
38hpi.normalized.tsv


title: s01_160116_21719_SUDHL1_DMSO_RNA


title: cps27_H3K9ac

value: saline

value: corn oil

value: pectin


title: fca9_H3K9ac


title: cps26_H3K9ac


title: 38hpi_E12

description:
AGGCAGAA_E12
38hpi.raw.tsv
38hpi.normalized.tsv


title: cpa16_H3K9ac


title: cpa15_H3K9ac


title: 38hpi_E11

description:
AGGCAGAA_E11
38hpi.raw.tsv
38hpi.normalized.tsv


title: cpa14_H3K9ac


title: DNMT3b_siRNA_BS_rep3

city: Gainesville

first: Xiefan

last: Fang

state: Florida

address: 1200 Newell Drive, ARB R1-148

department: Pediatrics

institute: University of Florida

data_processing:
The fastq files generated from MiSeq were uploaded to the UF Research Computing Galaxy instance developed by the University of Florida. The data were cleaned with the following steps: removed sequencing artifacts, trimmed 5’ or 3’ ends with low scores, removed adaptor contamination, and filtered low quality reads by the FastQC program. A reference genome with the amplicon sequences was built and bisulfite converted in silico with Bismark Bisulfite Mapper. The high quality sequence reads were aligned to the reference genome using Bowtie 2. Cytosine methylation counting was performed with the Bismark methylation extractor.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include percent methylation for each cytosine in the target gene promoters.

organism: Mus musculus

source_name: Embryonic cardiomyocyte

growth_protocol: Primary cardiomyocytes were isolated from mouse E13.5 embryonic ventricles. Briefly, hearts were dissected from embryos, and the ventricular tissue from each litter of embryos was pooled and digested with papain solution that contained 4 mg/ml papain, 1.1 mM EDTA, 5.5 mM L-cystein, and 67 mM b-mercaptoethanol dissolved in the Earle’s Balanced Salt Solution. Digestion was terminated with 1 mg/ml soybean trypsin inhibitor solution. Cells were suspended in DMEM supplemented with 10% inactivated fetal bovine serum, 2 mM L-glutamine, and antibiotic/antimycotic solution. Cells were placed in non-coated flasks for 1 h to allow differential attachment to occur. The non-attached cells, which are predominantly cardiomyocytes, were transferred to new flasks or plates coated with either 2% gelatin (for plastic) or 10 mg/ml fibronectin (for glass surface).

extract_protocol:
At 72 h after transfection, cells were released with Accutase (Innovative Cell Technologies, San Diego, CA) and dissociated with Accumax (Innovative Cell Technologies). To sort cardiomyocytes, dissociated cells were stained with anti-VCAM1 antibody conjugated with allophycocyanin (APC; BioLegend, San Diego, CA) and magnetically sorted using anti-APC microbeads and magnetic assisted cell sorting (MACS) columns (Miltenyi Biotec, Bergisch Gladbach, Germany). DNA was extracted with the Quick-gDNA™ MicroPrep kit (Zymo Research, Irvine, CA). Genomic DNA was treated with sodium metabisulfite for bisulfite conversion. Bisulfite specific PCR primers for fifteen target genes (two promoter regions per gene) were designed with Methyl Primer Express V1.0 (Thermo Fisher Scientific, Waltham, MA). Target gene regions were PCR-amplified from the bisulfite-converted DNA with ZymoTaq™ PreMix (Hot start DNA taq polymerase, ZYMO Research). The fifteen genes include Myh6, Myh7, Myh7b, Nppa, Nppb, Tnnc1, Tnni3, Tnnt2, Camta1, Camta2, Cdkn1A, Cdkn1B, Cdkn1C, Mef2c, and Mef2d. PCR products were cleaned with the ZR-96 DNA Clean & Concentrator™-5 kit (ZYMO Research). PCR products from the same genomic DNA sample were pooled at equal concentration ratio.
PCR products from the same genomic DNA were made into an indexed sequencing library with the Nextera XT DNA Library Preparation kit and the Nextera XT Index Kit (Illumina). Briefly, amplicon pools were tagmented, PCR-amplified with index primers, and cleaned with AMPure XP beads. The libraries were validated with an Agilent 2200 TapeStation high sensitivity DNA assay and quantitated by a KAPA Library Quantification kit (Illumina platforms; Kapa Biosystems) on a GeneAmp 7300 Real Time PCR (Thermo Fisher Scientific).

treatment_protocol: Cardiomyocytes were cultured for 48 h at 37°C to reach 70-80% confluency. Cells were transfected with either Qiagen FlexiTube GeneSolution (with 4 siRNAs) DNMT3a siRNA (#GS13435), DNMT3b siRNAs (#GS13436), or AllStars negative control siRNA (#1027281) at 0.012 pmol using lipofectamine RNAiMAX (n=3 per treatment).

tag: strain

tag: tissue

value: cardiomyocyte

tag: developmental stage

value: embrynoic day 13.5

value: DNMT3b siRNA


title: DNMT3b_siRNA_BS_rep1


title: DNMT3b_siRNA_BS_rep2


title: 38hpi_E10

description:
AGGCAGAA_E10
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_E17

description:
AGGCAGAA_E17
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_F21

description:
AGGCAGAA_F21
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_E1

description:
AGGCAGAA_E1
38hpi.raw.tsv
38hpi.normalized.tsv


title: DNMT3a_siRNA_BS_rep2

value: DNMT3a siRNA


title: 38hpi_D9

description:
AGGCAGAA_D9
38hpi.raw.tsv
38hpi.normalized.tsv


title: cps28_H3K9ac


title: DNMT3a_siRNA_BS_rep1


title: ccs19_H3K9ac


title: 38hpi_E13

description:
AGGCAGAA_E13
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_E14

description:
AGGCAGAA_E14
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_D7

description:
AGGCAGAA_D7
38hpi.raw.tsv
38hpi.normalized.tsv


title: ccs18_H3K9ac


title: negative_siRNA_BS_rep1

value: negative siRNA


title: 38hpi_D8

description:
AGGCAGAA_D8
38hpi.raw.tsv
38hpi.normalized.tsv


title: ccs17_H3K9ac


title: 38hpi_D6

description:
AGGCAGAA_D6
38hpi.raw.tsv
38hpi.normalized.tsv


title: negative_siRNA_BS_rep2


title: cca4_H3K9ac


title: cca3_H3K9ac


title: 38hpi_D5

description:
AGGCAGAA_D5
38hpi.raw.tsv
38hpi.normalized.tsv


title: cca2_H3K9ac


title: DNMT3a_siRNA_BS_rep3


title: 38hpi_D3

description:
AGGCAGAA_D3
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_D4

description:
AGGCAGAA_D4
38hpi.raw.tsv
38hpi.normalized.tsv


title: cpa13_H3K9ac


title: cca1_H3K9ac


title: fps_2805

value: not applicable


title: 38hpi_D23

description:
AGGCAGAA_D23
38hpi.raw.tsv
38hpi.normalized.tsv


title: fps_2804


title: 38hpi_D22

description:
AGGCAGAA_D22
38hpi.raw.tsv
38hpi.normalized.tsv


title: fcs_2706


title: negative_siRNA_BS_rep3


title: 38hpi_D21

description:
AGGCAGAA_D21
38hpi.raw.tsv
38hpi.normalized.tsv


title: fcs_2705


title: 38hpi_D20

description:
AGGCAGAA_D20
38hpi.raw.tsv
38hpi.normalized.tsv


title: fcs_2704


title: cps_2605


title: 38hpi_D2

description:
AGGCAGAA_D2
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_D19

description:
AGGCAGAA_D19
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_D18

description:
AGGCAGAA_D18
38hpi.raw.tsv
38hpi.normalized.tsv


title: cps_2604


title: 38hpi_D17

description:
AGGCAGAA_D17
38hpi.raw.tsv
38hpi.normalized.tsv


title: ccs_2506


title: 38hpi_D14

description:
AGGCAGAA_D14
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_D24

description:
AGGCAGAA_D24
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_D13

description:
AGGCAGAA_D13
38hpi.raw.tsv
38hpi.normalized.tsv


title: cps_2606


title: 38hpi_D15

description:
AGGCAGAA_D15
38hpi.raw.tsv
38hpi.normalized.tsv


title: ccs_2504


title: ccs_2505


title: fpa_2410


title: 38hpi_D11

description:
AGGCAGAA_D11
38hpi.raw.tsv
38hpi.normalized.tsv


title: fpa_2408


title: fca_2311


title: 38hpi_D12

description:
AGGCAGAA_D12
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_D10

description:
AGGCAGAA_D10
38hpi.raw.tsv
38hpi.normalized.tsv


title: fca_2306


title: 38hpi_D1

description:
AGGCAGAA_D1
38hpi.raw.tsv
38hpi.normalized.tsv


title: cpa_2210


title: cpa_2209


title: 38hpi_C8

description:
AGGCAGAA_C8
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_D16

description:
AGGCAGAA_D16
38hpi.raw.tsv
38hpi.normalized.tsv


title: cpa_2207


title: 38hpi_C6

description:
AGGCAGAA_C6
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_C7

description:
AGGCAGAA_C7
38hpi.raw.tsv
38hpi.normalized.tsv


title: cca_2111


title: cca_2108


title: fps_2806


title: cca_2109


title: fpa_2409


title: cca_2107


title: 38hpi_C5

description:
AGGCAGAA_C5
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_C23

description:
AGGCAGAA_C23
38hpi.raw.tsv
38hpi.normalized.tsv


title: cca_2106


title: 38hpi_C24

description:
AGGCAGAA_C24
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_MeDNA_24hr_Rep3

city: Lewiston

first: Andrew

middle: John

last: Kennedy

state: ME

address: 5 Andrews Rd, Dana 322

department: Chemistry

institute: Bates College

data_processing:
RNA-seq: Raw paired-end sequenced reads were quality controlled, filtered for read quality (FASTX toolkit, Galaxy)
RNA-seq: Aligned to the rat Rn5 genome sequence in Galaxy using Tophat v1.4.0 (with custom settings –p 8 –r 175)
RNA-seq: Gene expression differences between groups were calculated using DESeq2 via R plugin in Seqmonk software release v0.28.0 (Babraham Institute), using Ensembl release v70 gene and feature annotations
RNA-seq: For independent PolyA+ samples, transcript expression levels were determined by computing the fragments per kilobase of exon per million mapped reads (FPKM) and multiple comparisons were corrected using a false-discovery rate of 0.05
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: a single tab-delimited text file includes FPKM values for each sample; MBD-seq: One tab-delimited text file includes RPKM values for each sample over 500nt windows and another text file includes RPKM values for each gene
MBD-seq: Raw single-end sequenced reads were quality controlled, filtered for read quality (FASTX toolkit, Galaxy)
MBD-seq: Aligned to the rat genome (Rn5 assembly) in Galaxy using Bowtie
MBD-seq: CpG coverage and saturation analyses were performed using the program MEDIPS from the Bioconductor open source software package, and each sample was required to have > 90% signal saturation with a false positive rate of < 20% to pass quality control
MBD-seq: Differentially methylated genes (DMGs) were quantified using the EdgeR algorithm (FDR < 0.1)
MBD-seq: Differentially methylated regions (DMRs) were assessed by dividing the rat genome (rn5) into 500nt windows using the MEDIPS software package, which allows for the identification of DMRs in the context of CpG density, and these 500nt regions were quantified using the EdgeR algorithm (FDR < 0.3)

source_name: Hippocampus

extract_protocol:
DNA was extracted, RNase treated, and purified (DNeasy, Qiagen). Methylated DNA was captured using methyl-binding domain protein immunoprecipitation (MBD-IP; MethylMiner Kit, Invitrogen)
DNA sequencing was performed at Hudson Alpha using NEBNext reagents (New England Biolabs) according to manufacturer's recommendations with minor modifications (including the use of custom library adapters and indexes).

value: Sprague-Dawley

value: CA1 area of the hippocampus

tag: age


title: 38hpi_C3

description:
AGGCAGAA_C3
38hpi.raw.tsv
38hpi.normalized.tsv


title: fps_1802


title: Threat_MeDNA_24hr_Rep2


title: fps_1803


title: fps_1801


title: 38hpi_C22

description:
AGGCAGAA_C22
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_C21

description:
AGGCAGAA_C21
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_C9

description:
AGGCAGAA_C9
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_MeDNA_24hr_Rep1


title: fcs_1703


title: Threat_MeDNA_1hr_Rep3


title: fcs_1702


title: 38hpi_C20

description:
AGGCAGAA_C20
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_MeDNA_1hr_Rep2


title: 38hpi_C2

description:
AGGCAGAA_C2
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_C4

description:
AGGCAGAA_C4
38hpi.raw.tsv
38hpi.normalized.tsv


title: fcs_1701


title: 38hpi_C19

description:
AGGCAGAA_C19
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_MeDNA_1hr_Rep1


title: cps_1603


title: Place_MeDNA_24hr_Rep4


title: 38hpi_C17

description:
AGGCAGAA_C17
38hpi.raw.tsv
38hpi.normalized.tsv


title: Place_MeDNA_24hr_Rep3


title: 38hpi_C18

description:
AGGCAGAA_C18
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_C15

description:
AGGCAGAA_C15
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_C16

description:
AGGCAGAA_C16
38hpi.raw.tsv
38hpi.normalized.tsv


title: Place_MeDNA_24hr_Rep2


title: Place_MeDNA_24hr_Rep1


title: ccs_1502


title: cps_1601


title: Place_MeDNA_1hr_Rep4


title: ccs_1503


title: cps_1602


title: ccs_1501


title: Place_MeDNA_1hr_Rep3


title: fpa_1405

value: AOM


title: 38hpi_C12

description:
AGGCAGAA_C12
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_C13

description:
AGGCAGAA_C13
38hpi.raw.tsv
38hpi.normalized.tsv


title: Place_MeDNA_1hr_Rep2


title: 38hpi_C11

description:
AGGCAGAA_C11
38hpi.raw.tsv
38hpi.normalized.tsv


title: Place_MeDNA_1hr_Rep1


title: fpa_1403

value: fish oil


title: fpa_1402


title: Naive_MeDNA_24hr_Rep3


title: 38hpi_C10

description:
AGGCAGAA_C10
38hpi.raw.tsv
38hpi.normalized.tsv


title: fca_1305

value: cellulose


title: Naive_MeDNA_24hr_Rep2


title: 38hpi_B9

description:
AGGCAGAA_B9
38hpi.raw.tsv
38hpi.normalized.tsv


title: Naive_MeDNA_24hr_Rep1


title: fca_1303


title: fca_1302


title: Naive_MeDNA_1hr_Rep2


title: 38hpi_C14

description:
AGGCAGAA_C14
38hpi.raw.tsv
38hpi.normalized.tsv


title: Naive_MeDNA_1hr_Rep3


title: fca_1301


title: 38hpi_B8

description:
AGGCAGAA_B8
38hpi.raw.tsv
38hpi.normalized.tsv


title: Input_24hr_Rep3


title: 38hpi_B6

description:
AGGCAGAA_B6
38hpi.raw.tsv
38hpi.normalized.tsv


title: cpa_1205


title: Naive_MeDNA_1hr_Rep1


title: cpa_1204


title: 38hpi_B7

description:
AGGCAGAA_B7
38hpi.raw.tsv
38hpi.normalized.tsv


title: Input_24hr_Rep2


title: 38hpi_B5

description:
AGGCAGAA_B5
38hpi.raw.tsv
38hpi.normalized.tsv


title: cpa_1202


title: 38hpi_B4

description:
AGGCAGAA_B4
38hpi.raw.tsv
38hpi.normalized.tsv


title: cca_1103


title: Input_24hr_Rep1


title: Input_1hr_Rep3


title: Input_1hr_Rep2


title: 38hpi_B3

description:
AGGCAGAA_B3
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_C1

description:
AGGCAGAA_C1
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_B23

description:
AGGCAGAA_B23
38hpi.raw.tsv
38hpi.normalized.tsv


title: Input_1hr_Rep1


title: Threat_24hr_RNA_Rep6

extract_protocol:
RNA was extracted, DNase-treated, and purified (RNeasy, Qiagen).
2 µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 8.0), and was prepared for directional, PolyA+ RNA sequencing at Hudson Alpha using NEBNext reagents (New England Biolabs) according to manufacturer's recommendations with minor modifications (including the use of custom library adapters and indexes).


title: 38hpi_B21

description:
AGGCAGAA_B21
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_B20

description:
AGGCAGAA_B20
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_24hr_RNA_Rep5


title: 38hpi_B2

description:
AGGCAGAA_B2
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_24hr_RNA_Rep4


title: Threat_24hr_RNA_Rep3


title: 38hpi_B19

description:
AGGCAGAA_B19
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_24hr_RNA_Rep2


title: Threat_24hr_RNA_Rep1


title: 38hpi_B17

description:
AGGCAGAA_B17
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_1hr_RNA_Rep7


title: 38hpi_B16

description:
AGGCAGAA_B16
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_B15

description:
AGGCAGAA_B15
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_B13

description:
AGGCAGAA_B13
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_1hr_RNA_Rep4


title: 38hpi_B14

description:
AGGCAGAA_B14
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_1hr_RNA_Rep5


title: Threat_1hr_RNA_Rep8


title: 38hpi_B18

description:
AGGCAGAA_B18
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_1hr_RNA_Rep3


title: 38hpi_B12

description:
AGGCAGAA_B12
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_1hr_RNA_Rep6


title: 38hpi_B24

description:
AGGCAGAA_B24
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_B11

description:
AGGCAGAA_B11
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_1hr_RNA_Rep2


title: 38hpi_B22

description:
AGGCAGAA_B22
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_B10

description:
AGGCAGAA_B10
38hpi.raw.tsv
38hpi.normalized.tsv


title: Threat_1hr_RNA_Rep1


title: 38hpi_B1

description:
AGGCAGAA_B1
38hpi.raw.tsv
38hpi.normalized.tsv


title: Place_24hr_RNA_Rep5


title: 38hpi_A8

description:
AGGCAGAA_A8
38hpi.raw.tsv
38hpi.normalized.tsv


title: Place_24hr_RNA_Rep4


title: Place_24hr_RNA_Rep3


title: 38hpi_A7

description:
AGGCAGAA_A7
38hpi.raw.tsv
38hpi.normalized.tsv


title: Place_1hr_RNA_Rep6


title: Place_24hr_RNA_Rep2


title: 38hpi_A6

description:
AGGCAGAA_A6
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_A4

description:
AGGCAGAA_A4
38hpi.raw.tsv
38hpi.normalized.tsv


title: Place_1hr_RNA_Rep5


title: Place_1hr_RNA_Rep4


title: Place_1hr_RNA_Rep3


title: 38hpi_A3

description:
AGGCAGAA_A3
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_A21

description:
AGGCAGAA_A21
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_A22

description:
AGGCAGAA_A22
38hpi.raw.tsv
38hpi.normalized.tsv


title: Place_1hr_RNA_Rep1


title: Naive_RNA_Rep8


title: Place_1hr_RNA_Rep2


title: 38hpi_A24

description:
AGGCAGAA_A24
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_A23

description:
AGGCAGAA_A23
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_A2

description:
AGGCAGAA_A2
38hpi.raw.tsv
38hpi.normalized.tsv


title: control zebrafish embryos m6A miCLIP rep2

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

country: China

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

data_processing: library strategy: miCLIP-seq Reads were trimmed for adaptor sequence using fastx_clipper from FASTX-Toolkit (fastx_clipper -a AGATCGGAAGAGCACACG -n -Q 33). Low quality bases were filtered by fastq_filter.pl, a custom perl script from CLIP Tool Kit (CTK) and reads shorter than 24 nt would be discard. The forward reads were demultiplexed based on 5’ barcodes for individual replicates by fastq2collapse.pl to remove PCR amplified reads. The reverse reads were reversed complemented and processed like their forward mates. And then paired-end reads were mixed for downstream analysis. Random barcodes of remained reads were stripped by stripBarcode.pl. Then the barcode sequence was moved to header line for each read. Remained reads were mapped to the zebrafish genomes (version zv9) with BWA (v0.7.10). The CIMS pipeline (https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation) was used to collapse PCR duplicates based on their mapped coordinates and to determine the unique tag coverage (k) and the number of mutation (m) for each nucleotide. The filter for the dataset was k >= 15 and m/k <= 50% and only mutation positions within RRACH motif were identified as m6A for downstream analysis to exclude the potential m6Am modification. Genome_build: zv9 Supplementary_files_format_and_content: Single-nucleotide-resolution m6A sites identified by CIMS software.

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol: For miCLIP-seq, mRNA was isolate from the trunck region of zebrafish embryos at 28hpf and the RNA integrity was checked using an Agilent Bioanalyzer 2100. 10 ug of mRNA was first fragmented and immunoprecipitated with m6A antibody and thus obtained m6A containing RNA was subjected to cDNA library construction according to previously reported method [Linder et al. 2015; PMID: 26121403]. The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.

tag: cell type

value: normal zebrafish embryos cells

value: trunk

tag: enrichment antibody vendor

value: Abcam


title: 38hpi_A20

description:
AGGCAGAA_A20
38hpi.raw.tsv
38hpi.normalized.tsv

value: Induced


title: Naive_RNA_Rep9


title: 38hpi_A9

description:
AGGCAGAA_A9
38hpi.raw.tsv
38hpi.normalized.tsv


title: Naive_RNA_Rep7


title: 38hpi_A19

description:
AGGCAGAA_A19
38hpi.raw.tsv
38hpi.normalized.tsv


title: control zebrafish embryos m6A miCLIP rep1


title: 38hpi_A5

description:
AGGCAGAA_A5
38hpi.raw.tsv
38hpi.normalized.tsv


title: Place_24hr_RNA_Rep1


title: Naive_RNA_Rep6


title: 38hpi_A18

description:
AGGCAGAA_A18
38hpi.raw.tsv
38hpi.normalized.tsv


title: zebrafish embryos ythdf2 RIP rep1

data_processing:
Reads were aligned to the zv9 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.5.3p9
Genome_build: zv9
Supplementary_files_format_and_content: reads_count_HTSeq.xls: Reads count for each gene of all samples
Supplementary_files_format_and_content: ythdf2_binding_target.xls: ythdf2 binding targets identified by macs2 software

extract_protocol: For RIP-seq, RNA was isolate from ythdf2-Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.

tag: genotype/variation

value: normal

value: embryos cells


title: Naive_RNA_Rep5


title: 38hpi_A17

description:
AGGCAGAA_A17
38hpi.raw.tsv
38hpi.normalized.tsv


title: mettl3 morphant zebrafish embryos input rep2

data_processing:
Library strategy: MeRIP-seq
Reads were aligned to the zv9 genome assembly using TopHat v2.0.9
Genome_build: zv9
Supplementary_files_format_and_content: reads_count_HTSeq.xls: Reads count for each gene of all samples

extract_protocol: For MeRIP-seq, mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples, mRNA was sonicated and subjected to IP using m6A antibody (Synaptic Systems, 202003). The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp.


title: Naive_RNA_Rep2


title: Naive_RNA_Rep3


title: DNMT3b_siRNA_rep2

data_processing:
The fastq files generated from RNA-Seq were uploaded to the UF Research Computing Galaxy instance developed by the University of Florida. The data were cleaned with the following steps: removed sequencing artifacts, trimmed 5’ or 3’ ends with low scores, removed adaptor contamination, and filtered low quality reads by the FastQC program. The remaining high quality RNA-Seq reads were mapped to the mouse genome (mm10) with the Tophat2 tool. Counting of RNA-Seq reads were performed with HTSeq, with Ensembl Mus_GRCm38.79.gtf as the reference annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each gene annotated to Ensembl Mus_GRCm38.79.gtf.

growth_protocol: Primary cardiomyocytes were isolated from mouse E13.5 embryonic ventricles. Briefly, hearts were dissected from embryos, and the ventricular tissue from each litter of embryos was pooled and digested with papain solution that contained 4 mg/ml papain, 1.1 mM EDTA, 5.5 mM L-cystein, and 67 mM b-mercaptoethanol dissolved in the Earle’s Balanced Salt Solution. Digestion was terminated with 1 mg/ml soybean trypsin inhibitor solution. Cells were suspended in DMEM supplemented with 10% inactivated fetal bovine serum, 2 mM L-glutamine, and antibiotic/antimycotic solution. Cells were placed in non-coated flasks for 1 hr to allow differential attachment to occur. The non-attached cells, which are predominantly cardiomyocytes, were transferred to new flasks or plates coated with 2% gelatin (for plastic) or 10 mg/ml fibronectin (for glass surface).

extract_protocol:
At 72 h after transfection, cells were released with Accutase (Innovative Cell Technologies, San Diego, CA) and dissociated with Accumax (Innovative Cell Technologies). To sort cardiomyocytes, dissociated cells were stained with anti-VCAM1 antibody conjugated with allophycocyanin (APC; BioLegend, San Diego, CA) and magnetically sorted using anti-APC microbeads and magnetic assisted cell sorting (MACS) columns (Miltenyi Biotec, Bergisch Gladbach, Germany). Total RNA was isolated from the sorted cardiomyocytes with the RNAqueous®-Micro Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA). mRNA was isolated from total RNA using NEXTflex™ Poly(A) Beads (Bioo Scientific, Austin, TX). The mRNA was quantitated using the Qubit RNA assay and Qubit 2.0 Flourometer (Thermo Fisher Scientific), as well as a 2200 TapeStation (Pico mRNA; Agilent Technologies).
Sequencing libraries were prepared with the NEBNext® mRNA Library Prep Master Mix Set for Illumina (NEB, Ipswich, MA). Briefly, purified mRNA (50-250 ng) was fragmented to ~200 nucleotide mRNA prior to generating first and second strand cDNA. The resulting cDNA was prepared for sequencing by blunt end repair, dA-tailing, adaptor ligation using the NEBNext Multiplex Oligos for Illumina (NEB), size selection using Agencourt AMPure XP Beads (Beckman Coulter, Brea, CA), and PCR enrichment of adaptor ligated cDNA. Library quality was assessed using the Agilent 2200 TapeStation (high sensitivity DNA assay). The concentration of each library was quantitated by a KAPA Library Quantification kit (Illumina platforms; Kapa Biosystems, Woburn, MA) on a GeneAmp 7300 Real Time PCR (Thermo Fisher Scientific).

value: cardiomyocyte


title: 38hpi_A16

description:
AGGCAGAA_A16
38hpi.raw.tsv
38hpi.normalized.tsv


title: DNMT3b_siRNA_rep1

value: embrynoic day 13.5


title: DNMT3a_siRNA_rep1


title: 38hpi_A15

description:
AGGCAGAA_A15
38hpi.raw.tsv
38hpi.normalized.tsv


title: Naive_RNA_Rep1


title: mettl3 morphant zebrafish embryos m6A IP rep2

data_processing:
Library strategy: MeRIP-seq
Reads were aligned to the zv9 genome assembly using TopHat v2.0.9
Genome_build: zv9
Supplementary_files_format_and_content: m6A-peak_locus.xls: m6A peaks indentified by macs2 software
Supplementary_files_format_and_content: reads_count_HTSeq.xls: Reads count for each gene of all samples

value: Synaptic Systems


title: mettl3 morphant zebrafish embryos input rep1

extract_protocol: For MeRIP-seq, mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples, mRNA was sonicated and subjected to IP using m6A antibody (Synaptic Systems, 202003). The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 151 bp.


title: DNMT3a_siRNA_rep2

value: DNMT3a siRNA


title: zebrafish embryos ythdf2 RIP rep2


title: 38hpi_A13

description:
AGGCAGAA_A13
38hpi.raw.tsv
38hpi.normalized.tsv


title: DNMT3b_siRNA_rep3

value: DNMT3b siRNA


title: negative_siRNA_rep3

value: negative siRNA


title: 38hpi_A12

description:
AGGCAGAA_A12
38hpi.raw.tsv
38hpi.normalized.tsv


title: negative_siRNA_rep2


title: control zebrafish embryos input rep2


title: control zebrafish embryos input rep1


title: control zebrafish embryos m6A IP rep2


title: Naive_RNA_Rep4

value: Sprague-Dawley


title: DNMT3a_siRNA_rep3


title: 38hpi_A11

description:
AGGCAGAA_A11
38hpi.raw.tsv
38hpi.normalized.tsv


title: Small RNAs in Hibiscus syriacus (Root)

city: Seoul

first: Chanseok

last: Shin

address: 1, Gwanak-ro, Gwanak-gu

department: Agricultural Biotechnology

country: South Korea

institute: Seoul National University

description: Small RNA

data_processing:
Poor-quality small RNA reads and adapter sequences were eliminated using the FASTX toolkit, and the reads whose length was between 18 and 26 nt were selected for further analysis.
High-quality small RNAs (reads of ≥50) were mapped to the reference genome of Hibiscus syriacus and the perfectly mapped sequences were selected (≤42 times).
The filtered reads were analyzed to identify the putative miRNAs in the modified algorithm (Hwang et al., 2013; Meyers et al., 2008).
After identification, the miRNA candidates were classified to either the conserved miRNAs or novel miRNAs through a BLASTN search with miRBase.
The reads of miRNAs from each library were normalized to read per 10 million (RP10M).
Genome_build: MGA.V09 (https://hibiscus.kobic.re.kr/hibiscus.en/)
Supplementary_files_format_and_content: *fa: Fasta format; each data file contains sequence and raw reads. Header line definition: >X-Y, where X=rank in descending order (for example, 4 means that the read is the fourth largest read), and Y=abundance of raw read.

organism: Hibiscus syriacus

source_name: root

extract_protocol:
Total RNAs were extracted from Hibiscus syriacus tissue samples (leaf, root, flower, and ovary) using TRI Reagent solution (MRC), according to the manufacturer’s protocol. Both the flower and ovary were pretreated with CTAB buffer [2% CTAB, 2% polyvinylpyrrolidone K 30, 100 mM Tris (pH 8.0), 25 mM EDTA, 2 M NaCl, and 2% β-mercaptoethanol] followed by TRI Reagent extraction, as previously described (Peng et al., 2014).
A small RNA sequencing library was constructed using the Small RNA Sample Prep Kit (Illumina), according to the manufacturer’s instructions. As previously described (Hwang et al., 2013), 10 μg of total RNAs was resolved using 15% urea-PAGE, and size fractions of small RNAs between 18 and 30 nt were prepared. The prepared small RNAs were ligated to the 3′ and 5′ adapter, and cDNA was synthesized using RT-PCR. cDNAs were amplified using PCR and submitted for Illumina/Solexa sequencing.

value: root


title: Small RNAs in Hibiscus syriacus (Leaf)

description: Small RNA

source_name: leaf

value: leaf


title: Small RNAs in Hibiscus syriacus (Ovary)

description: Small RNA

source_name: ovary

value: ovary


title: 38hpi_A10

description:
AGGCAGAA_A10
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_A14

description:
AGGCAGAA_A14
38hpi.raw.tsv
38hpi.normalized.tsv


title: mettl3 morphant zebrafish embryos m6A IP rep1


title: Small RNAs in Hibiscus syriacus (Flower)

description: Small RNA

source_name: flower

value: flower


title: control zebrafish embryos m6A IP rep1


title: 38hpi_A1

description:
AGGCAGAA_A1
38hpi.raw.tsv
38hpi.normalized.tsv


title: Lgr6_Mouse2_SC_S191

status: Public on Sep 07 2017

city: Jerusalem

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

description: Lgr6 expressing cell sorted by FACS

data_processing:
bcl2fastq v2.17.1.14
kallisto v0.43.0
Sampling based read depth scaling
Filtering of poor quality cells
Genome_build: mm10
Supplementary_files_format_and_content: Gene by sample comma seperated matrices of pre/post quality control filtering of expression values quantified with Kallisto is provided as TPM and counts.

source_name: Lung tissue

growth_protocol: Lgr6-EGFP-IRES-CreERT2 mice were purchased from Jackson Laboratories. Lgr5-IRES-CreERT2 (Huch et al., 2013) mouse lines were kindly provided by Dr. Hans Clevers. 7-10 week old mice were used for most of experiments described in this study.

extract_protocol:
Agencourt RNA-Clean strepdavadin beads were used to precipitate nucleic acids, which were cleaned by washing with 70% ethanol.  RNA extraction step is done with Agilent Bravo Automated Liquid Handlin Platform.
We used a modified version of the SmartSeq2(SS2) protocol (Picelli et al., 2013), as previously described (Shekhar et al., 2016).  Library construction protocol: Reverse transcription of polyadenylated transcripts was done by using an oligo-dT primer. A reverse transcriptase was derived from the Moloney murine leukemia virus (MMLVRT) followed by a template switching reaction that relies on the terminal-transferase activity of the MMLVRT in the presence of a template switch oligonucleotide primer (TSO). The double-stranded RT-product was PCR amplified using Kapa Ready Mix to yield the whole transcriptome amplification (WTA) product. The WTA product was cleaned up with AMPure SPRI beads and 80% ethanol, and QCed with BioAnalyzer and qubit.  Each single-cell library was individually barcoded by PCR with index primers.
The barcoded single cells were pooled and sequenced on an Illumina NextSeq sequencer.

treatment_protocol: Lungs were dissociated with a collagenase/dispase solution as previously described (Lee et al., 2014). The cell pellet was resuspended in PBS with 10% FBS for further staining against antibodies for mouse flow cytometry: pan CD45-APC, CD31-APC, CD11b-APC, Ter119-APC (BD Biosciences), and EpCAM-PE-Cy7 (BioLegend).  4’, 6-diamidino-2-phenylindole (DAPI) (Sigma) was used to eliminate dead cells.  Cell sorting was performed with a FACS.

tag: sample type

value: Single Cell

tag: expression


title: Lgr6_Mouse2_SC_S192

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S190

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S187

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S189

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S186

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S184

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S182

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S185

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S183

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S179

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S178

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S180

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S181

description: Lgr6 expressing cell sorted by FACS


title: negative_siRNA_rep1


title: Lgr6_Mouse2_SC_S188

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S177

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S174

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S175

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S171

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S172

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S173

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S170

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S176

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S169

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S168

description: Lgr6 expressing cell sorted by FACS


title: CGH-3

first: Tong

last: Chen

address: No 16 Nan-xiao-jie Dong-zhi-men-nei

department: State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica

institute: China Academy of Chinese Medical Sciences

description: polyA-captured

data_processing:
Base-calling were performed using RTA and CASAVA.
The quality of sequencing data was estimated using FastQC (v0.11.3). Then adaptors and low quality bases were removed using Trimmomatic (v0.33).
Clean reads from all samples were pooled together and feeded to de novo RNA-seq assembly software Trinity (v2.0.6) with default parameters.
The expression of assembled transcripts and genes were quantified using RSEM (v1.2.19).
Genome_build: The FASTA file of assembled transcripts is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all unigenes in each treatment

organism: Isodon rubescens

source_name: leaf tissue

growth_protocol: The plant was grown in a controlled environment chamber, maintained at 25 °C under a 16 h light/8 h dark photoperiod.

extract_protocol:
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp).
Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The doublestrand cDNA is purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to thefragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify  the sample library. The library products are ready for sequencing via Illumina HiSeq TM 2000 or other sequencer when necessary.

treatment_protocol: The fresh leaves were harvested and immediately frozen in liquid nitrogen.


title: Lgr6_Mouse2_SC_S167

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S166

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S164

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S165

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S162

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S158

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S156

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S155

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S163

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S160

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S161

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S159

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S152

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S153

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S150

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S157

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S154

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S151

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S149

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S148

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S146

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S143

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S144

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S145

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S140

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S141

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S139

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S138

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S137

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S136

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S135

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S129

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S132

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S128

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S131

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S130

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S142

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S121

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S120

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S127

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S125

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S147

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S122

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S123

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S119

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S118

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S126

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S124

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S114

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S113

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S117

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S111

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S112

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S110

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S109

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S133

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S134

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S107

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S105

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S102

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S103

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S104

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S116

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S115

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S99

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S100

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S101

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S96

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S88

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S86

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S85

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S95

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S87

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S92

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S90

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S97

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S89

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S84

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S94

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S82

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S83

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S106

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S81

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S80

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_P_S98

description: Lgr6 expressing cell sorted by FACS

value: Pool


title: Lgr6_Mouse1_SC_S79

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse2_SC_S108

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S91

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S93

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S78

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S76

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S75

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S73

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S71

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S74

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S70

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S68

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S67

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S66

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S69

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S65

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S61

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S63

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S60

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S64

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S59

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S62

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S58

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S55

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S56

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S54

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S53

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S72

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S48

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S50

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S49

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S47

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S46

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S77

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S57

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S43

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S40

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S44

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S38

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S34

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S33

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S41

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S39

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S30

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S42

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S31

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S35

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S51

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S32

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S52

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S45

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S29

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S27

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S37

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S28

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S24

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S25

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S26

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S23

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S22

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S21

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S20

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S18

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S36

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S19

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S17

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S16

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S14

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S10

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S15

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S13

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S8

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S11

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S7

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S6

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S3

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S5

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S9

description: Lgr6 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S4

description: Lgr6 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S191

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S192

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S189

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S187

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S190

description: Lgr5 expressing cell sorted by FACS


title: Lgr6_Mouse1_P_S2

description: Lgr6 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S188

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S186

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S185

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S183

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S182

description: Lgr5 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S12

description: Lgr6 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S180

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S184

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S181

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S178

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S179

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S175

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S176

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S174

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S177

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S170

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S173

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S172

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S171

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S168

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S169

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S167

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S165

description: Lgr5 expressing cell sorted by FACS


title: Lgr6_Mouse1_SC_S1

description: Lgr6 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S162

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S161

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S166

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S163

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S159

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S157

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S158

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S156

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S155

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S154

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S150

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S151

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S153

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S149

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S146

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S143

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S145

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S147

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S144

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S148

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S142

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S140

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S138

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S164

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S141

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S160

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S139

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S137

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S136

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S134

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S135

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S152

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S133

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S131

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S132

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S128

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S127

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S126

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S130

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S122

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S123

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S125

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S114

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S115

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S119

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S121

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S116

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S120

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S112

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S110

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S129

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S109

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S107

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S106

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S113

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S105

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S104

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S108

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S103

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S102

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_P_S98

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S100

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S99

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S97

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S96

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S95

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S117

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S118

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S111

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S124

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S93

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S88

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S89

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S90

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S87

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S85

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S86

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S84

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S81

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S83

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S82

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S79

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse2_SC_S101

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S77

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S80

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S76

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S73

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S75

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S74

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S72

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S94

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S71

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S69

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S68

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S91

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S92

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S66

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S67

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S65

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S64

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S59

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S60

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S58

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S61

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S78

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S63

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S55

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S54

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S53

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S51

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S57

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S56

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S50

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S70

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S48

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S49

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S45

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S46

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S47

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S44

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S43

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S42

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S62

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S39

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S38

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S41

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S40

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S36

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S37

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S34

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S35

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S30

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S52

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S33

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S31

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S32

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S28

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S29

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S26

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S27

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S24

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S23

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S22

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S25

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S20

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S19

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S21

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S17

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S18

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S16

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S15

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S14

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S13

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S10

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S12

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S11

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S9

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S7

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S6

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_P_S2

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S3

description: Lgr5 expressing cell sorted by FACS


title: Lgr5_Mouse1_SC_S5

description: Lgr5 expressing cell sorted by FACS


title: high fat diet 3

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

data_processing:
Base calling was with Illumina GAP Pipeline Software v1.90
Sequences were aligned to mm9 reference genome using Tophat 2.0.8 with option -g with mm9 reference GTF
Novel transcripts were predicted with Cufflinks 2.1.1
Novel transcripts predictions were merged with mm9 reference genome using Cuffmerge 2.1.1 with option -G with mm9 reference GTF
Counts were generated using htseq-count v0.5.4p3
Genome_build: mm9
Supplementary_files_format_and_content: Raw count data for genes were normalized to the relative size of each library using R/Bioconductor package edgeR calcNormFactors function. Count data are provided in tab-delimited format

source_name: pancreatic islets

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen), followed by DNase treatment (Promega) and RNA precipitation to clean the RNA. Ribosomal RNA was removed using the Ribo-Zero Magnetic Gold kit (MRZG126, Illumina). sequence libraries were prepared using the Illumina TruSeq stranded mRNA LT kit without poly(A) selection (RS-122-2101).
Sequence libraries were prepared using the Illumina TruSeq stranded mRNA LT kit without poly(A) selection (RS-122-2101). Libraries were sequenced with the Illumina HiSeq2000 (2x100bp).

value: 14 weeks

value: pancreatic islets

tag: diet

value: high fat


title: Lgr5_Mouse1_SC_S1

description: Lgr5 expressing cell sorted by FACS


title: high fat diet 1


title: high fat diet 2


title: normal diet 2

value: normal


title: normal diet 3


title: normal diet 1


title: H3K23me1_wt_Rep2

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

data_processing:
Quality control was done with an in-house R script
Demultiplexing and adapter trimmng was done with reaper (EMBL-EBI)
Clean reads of the replicates were merged and mapped to Arabidopsis TAIR10 genome using Bowtie2
SAM file output from bowtie was converted to BAM format using SAMTOOLS (version 1.4) and imported into R.
Identical reads present more than 15 times were considered as PCR artifacts and filtered out using the filterDuplReads function from package HtSeqTools
ChIP-seq coverage was calculated using the coverage function from R
Normalization of the coverage to identical sequencing depth
Subsequent analysis were performed in R. The used gene models were from TAIR10 gff annotation file
Genome_build: TAIR10
Supplementary_files_format_and_content: BigWig files of coverage

organism: Arabidopsis thaliana

growth_protocol: Leaves number 5-6th were harvested from 5-week-old plants grown under short day conditions (8 h light).

extract_protocol:
Native Chromatin Immunoprecipitation (N-ChIP) was performed following a slightly modified procedure of (Mahrez et al. 2016).
Libraries were generated using the Ovation Ultralow Library System (NuGEN, San Carlos, USA) following the manufacturer's protocol using 1 ng of starting material previously sonicated for 25 cycles (30 sec ON, 30 sec OFF at high power) using a Bioruptor (Diagenode).
Sequencing was performed on an Illumina HiSeq2000 in 50-bp single-end mode.

tag: ecotype

value: Columbia

tag: genotype

value: WT

tag: antibody

value: anti-H3K23me1 cat. no. 39387 (ActiveMotif).

tag: biological replicate

tag: demultiplexbarcode

value: CACG


title: H3K23me1_kyp_Rep2

value: TCGA


title: H3K23me1_wt_Rep1

value: ATTT


title: H3K23me1_kyp_Rep1

value: GGAC


title: A5_12

city: BETHESDA

first: Jianfei

last: Hu

state: MD

address: 40 CONVENT DR

department: Vaccine Research Center

institute: NIH

data_processing:
Illumina bcl2fastq-2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 repeat-masked  genome using tophat v2.0.13 with parameters  -p 4 --coverage-search --library-type fr-unstranded
Gene transcript isoform expression level was calculated by cufflinks v2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: Gene transcript isoform expression file
gene.Ensembl.gtf.txt: Ensemble gene set file (based on Homo_sapiens.GRCh37.74.gtf)
gene.Merged.gtf.txt: Merged gene set file (predicted by cuffmerge with the reference annotation of Homo_sapiens.GRCh37.74.gtf)
geneExpr.Ensembl.txt: Gene Transcript isoform expression file based on Ensembl gene set
geneExpr.Merged.txt: Gene Transcript isoform expression file based on merged gene set

source_name: central memory (CM)_resting

extract_protocol:
Sorted cells were lysed and total RNA was extracted using RNAzol RT (Molecular Research Center Inc., Cincinnati, OH). Poly-adenylated RNA was purified using Dynabeads oligo (dT)25 (Invitrogen, Carlsbad, CA) and fragmented
cDNA was synthesized and Illumina-ready libraries were generated using a modified Illumina TruSeq mRNA Library preparation protocol (paired end HiSeq 2x100 reads)

tag: donor id

value: Donator 9

tag: t cell type

value: central memory (CM)

tag: status

value: resting

tag: sorting phenotype

value: CM (CD45RO+CD27+CCR7+)


title: A7_7

source_name: Transitional Memory (TM)_Activated

value: Transitional Memory (TM)

value: Activated

value: TM (CD45RO+CD27+CCR7-)


title: B7_5

value: Naive

value: Naive (CD45RO-CD27+)


title: B7_12

source_name: Effector Memory (EM)_Activated

value: Effector Memory (EM)

value: EM (CD45RO+CD27-)


title: H3_kyp_Rep1

value: Columbia

value: anti-H3 cat. no. H9289 (Sigma)

value: GCTG


title: H3_wt_Rep2

value: WT

value: CTGC


title: H3_kyp_Rep2

value: TGCT


title: Lgr5_Mouse1_SC_S8

description: Lgr5 expressing cell sorted by FACS

value: Single Cell


title: A3_7

value: Donator 9


title: A2_6

value: Donator 8


title: H3_wt_Rep1

value: AAAA


title: A3_5

value: Transitional Memory (TM)


title: Lgr5_Mouse1_SC_S4

description: Lgr5 expressing cell sorted by FACS


title: input_kyp_Rep2

value: TATC


title: A1_4

source_name: central memory (CM)_Activated

value: central memory (CM)

value: Activated

value: CM (CD45RO+CD27+CCR7+)


title: input_kyp_Rep1

value: GTCA


title: B8_7

source_name: Transitional Memory (TM)_resting

value: resting

value: TM (CD45RO+CD27+CCR7-)


title: B1_12

source_name: Effector Memory (EM)_resting

value: Effector Memory (EM)

value: EM (CD45RO+CD27-)


title: B3_2

value: Naive

value: Naive (CD45RO-CD27+)


title: B6_6


title: input_wt_Rep1

value: Columbia

value: WT

value: AGGG


title: B6_2

value: Donator 9


title: A6_4

value: Donator 7


title: ENAP1ox/ein2 4 hour C2H4 RNAseq, rep1

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

description: processed data file: ENAP1ox_ein2_air_vs_C2H4_gene_exp.diff

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome usingTopHat version 2.0.9 with default parameters
Differential expressed genes were calculated by Cuffdiff version 2.2.1
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, generated by Cuffdiff version 2.2.1

source_name: ENAP1ox/ein2 4 hour C2H4 RNAseq

growth_protocol: Arabidopsis seeds were  dark-grown at 24 ºC for 3 days

extract_protocol:
RNA was harvested using Trizol reagent from seedlings.
Libraries were prepared according to NEB instructions of the RNA Library Kit (NEB #E7420S/L)

treatment_protocol: Treated with air (hydrocarbon-free air (Zero grade air, AirGas)) or ethylene (hydrocarbon-free air with 10 parts per million  (ppm) ethylene) for 4 hours

tag: ecotype background

value: COL

tag: treated with

value: ethylene for 4 hours

tag: tissue

value: whole  seedling


title: ENAP1ox/ein2 4 hour air RNAseq, rep2

source_name: ENAP1ox/ein2 4 hour air RNAseq

tag: age

value: air for 4 hours


title: ENAP1ox/ein2 4 hour air RNAseq, rep1

tag: genotype/variation


title: A5_2

value: Transitional Memory (TM)

value: Activated


title: A1_7


title: A7_12

value: central memory (CM)

value: CM (CD45RO+CD27+CCR7+)


title: ein2 4 hour air RNAseq, rep2

description: processed data file: ein2_air_vs_C2H4_gene_exp.diff

source_name: ein2 4 hour air RNAseq


title: ein2 4 hour C2H4 RNAseq, rep1

source_name: ein2 4 hour C2H4 RNAseq


title: B8_5

value: resting

value: TM (CD45RO+CD27+CCR7-)


title: ein2 4 hour air RNAseq, rep1


title: input_wt_Rep2

value: CCAT


title: A5_4

value: Effector Memory (EM)

value: EM (CD45RO+CD27-)


title: A6_2

value: Naive

value: Naive (CD45RO-CD27+)


title: B3_12

value: Donator 6


title: ein2 4 hour C2H4 RNAseq, rep2


title: A1_6

value: Donator 8


title: ENAP1ox/ein2 4 hour C2H4 RNAseq, rep2

value: COL


title: B2_7


title: B1_5


title: A7_5


title: ein2_C2H4_ENAP1_input rep2

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bwa with default parameters
For each ENAP1 binding in each condition,mapped reads were pooled across ChIP-seq replicates as described (Gjoneska, Pfenning et al.Nature, 2015)
Peaks significantly enriched in ChIP-seq tags were identified by Model-based Analysis for ChIP-Seq (MACS2, version 2.1.0.20150603) following IDR pipeline (https://sites.google.com/site/anshulkundaje/projects/idr)
Genome_build: tair10
Supplementary_files_format_and_content: the  bdg and narrowPeak (after cutoff according IDR pipeline) files are generated using MACS2 (version 2.1.0.20150603) software.

source_name: whole seedling

extract_protocol:
ENAP1 proteins were extracted from seedlings and ENAP1-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB instructions of the ChIP-seq Library Kit (NEB #E6240S/L)

tag: developmental stage

value: whole seedling after ethylene treatment

tag: chip antibody

tag: treatment

value: ethylene treated for 4 hours


title: ein2_ENAP1_C2H4_ChIPseq_rep1

description:
macs2.optimal.C16_C12vsC11_C15.narrowPeak
C16_C12vsC11_C15_control_lambda.bdg
C16_C12vsC11_C15_treat_pileup.bdg

tag: ecotype

value: anti-green fluorescent protein (life technologies:A11122)


title: ein2_C2H4_ENAP1_input rep1


title: ein2_air_ENAP1_input rep2

value: whole seedling after air treatment

value: air treated for 4 hours


title: A3_4


title: ein2_air_ENAP1_input rep1


title: B7_2

value: Transitional Memory (TM)


title: A3_12

value: central memory (CM)

value: CM (CD45RO+CD27+CCR7+)


title: ein2_ENAP1_air_ChIPseq_rep1

description:
macs2.optimal.38_42vsC9_C13.narrowPeak
38_42vsC9_C13_control_lambda.bdg
38_42vsC9_C13_treat_pileup.bdg


title: COL_C2H4_ENAP1_input rep2


title: B6_4

value: Donator 7

value: resting


title: B7_7


title: A6_12

value: Donator 5

value: Effector Memory (EM)

value: Activated


title: COL_C2H4_ENAP1_input rep1


title: B3_7

value: TM (CD45RO+CD27+CCR7-)


title: COL_ENAP1_C2H4_ChIPseq_rep2

description:
macs2.optimal.C8_C4vsC3_C7.narrowPeak
C8_C4vsC3_C7_control_lambda.bdg
C8_C4vsC3_C7_treat_pileup.bdg


title: COL_ENAP1_C2H4_ChIPseq_rep1


title: A8_6


title: B3_6

value: Donator 6


title: B2_4

value: EM (CD45RO+CD27-)


title: COL_ENAP1_air_ChIPseq_rep2

description:
macs2.optimal.30_34vsC1_C5.narrowPeak
30_34vsC1_C5_control_lambda.bdg
30_34vsC1_C5_treat_pileup.bdg


title: COL_air_ENAP1_input rep2


title: COL_ENAP1_air_ChIPseq_rep1


title: A2_5

value: Donator 4


title: B8_12


title: A8_2


title: A7_4


title: A2_2

value: Naive

value: Naive (CD45RO-CD27+)


title: COL_ENAP1_C2H4_input

description: ethylene treated for 4 hours

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bwa with default parameters
Peaks significantly enriched in ChIP-seq tags were identified by Model-based Analysis for ChIP-Seq (MACS2, version 2.1.0.20150603) with -p 0.01
Genome_build: tair10
Supplementary_files_format_and_content: the txt files were generated using MACS2 (version 2.1.0.20150603) software.

extract_protocol:
ENAP1 proteins were extracted from seedlings and ENAP1-DNA complexes were isolated with antibody. For ChIP reChIP, ENAP1-DNA complexes were first isolated with antibody, then the EIN2-DNA complexes were furter isolated with EIN2 antibody.
Libraries were prepared according to NEB instructions of the ChIP-seq Library Kit (NEB #E6240S/L)

value: whole COL-0 seedling after air treatment


title: COL_ENAP1_ChIP_EIN2reChIP_C2H4

description: ethylene treated for 4 hours

value: anti-green fluorescent protein (life technologies:A11122) and EIN2 antibody


title: A6_6


title: ein2_ENAP1_air_ChIPseq_rep2

value: whole seedling after air treatment

value: anti-green fluorescent protein (life technologies:A11122)

value: air treated for 4 hours


title: COL_ENAP1_ChIPseq_C2H4

description: ethylene treated for 4 hours


title: COL_ENAP1_ChIP_EIN2reChIP_air

description: air treated for 4 hours


title: B1_7

value: Transitional Memory (TM)


title: COL_ENAP1_ChIPseq_air

description: air treated for 4 hours


title: B8_6

value: central memory (CM)

value: CM (CD45RO+CD27+CCR7+)


title: B1_2

value: Donator 3


title: A2_12

value: Effector Memory (EM)

value: resting


title: COL_ENAP1_air_input

description: air treated for 4 hours


title: COL_air_ENAP1_input rep1


title: A8_12

value: Activated

value: TM (CD45RO+CD27+CCR7-)


title: B6_7


title: B2_5


title: A2_7

value: Donator 5


title: A8_5


title: B7_6


title: A2_4

value: EM (CD45RO+CD27-)


title: A3_2


title: A7_6

value: Donator 2


title: A8_7

value: Naive

value: Naive (CD45RO-CD27+)


title: B8_4


title: B6_5


title: B6_12


title: A1_12


title: A7_2


title: A5_6


title: Liver_infected_rep2

city: Burlington

first: Diana

middle: Lea

last: Gerrard

state: VT

address: 89 Beaumont Ave C141C Given

department: Cellular molecular and biomedical sciences

institute: University of Vermont

data_processing:
FastX toolkit to filter adaptors, non-coding RNA, low quality reads, and raw reads with average lengths less than 20 bases
The Trinity program was employed for De novo transcriptome assembly. Parameters used were as follows: minimum contig length= 300 and minimum kmer coverage=2. The remaining contigs were further processed with Bowtie and RSEM
Genome_build: denovo
Supplementary_files_format_and_content: The De novo transcriptome assembly for bat (Trinity.fasta) was generated from pooled RNA-seq data from the different organ tissue

organism: Artibeus jamaicensis

source_name: Liver

extract_protocol:
Organ samples were homogenized using zirconia/silica beads and a mini-bead-beater and RNA was extracted using QiaShredder columns and RNeasy minikits.
RNA libraries were prepared for sequencing using the Kapa Biosystems stranded-RNA sample prep kit

treatment_protocol: Two Jamaican fruit bats were inoculated with 100 μl of sterile DPBS to act as negative controls, and two bats were inoculated with 100 μl containing 106 TCID50 Tacaribe virus.  Negative control bats were euthanized at the end of the experimental period (45 days p.i,), while TCRV inoculated bats were euthanized as they became moribund.  Kidney, liver, and spleen samples were collected in RNAlater and used for RNA extraction.

value: Liver

value: 100 ul containing 106 TCID50 Tacaribe virus


title: Liver_infected_rep1


title: Liver_control_rep1

value: 100 ul of sterile DPBS to act as negative controls


title: Liver_control_rep2


title: Kidney_infected_rep2

source_name: Kidney

value: Kidney


title: B3_5


title: B7_4

value: Donator 1


title: Kidney_infected_rep1


title: Kidney_control_rep2


title: Speen_infected_rep2

source_name: Spleen

value: Spleen


title: B2_2

value: Transitional Memory (TM)


title: Spleen_control_rep2


title: Spleen_infected_rep1


title: A6_7