title: sRNA_Seq_E14_d9.3_DNMT1KO

data_processing:
small RNASeq: Raw FastQ data were trimmed with Trim Galore (v0.3.5, default parameters) and mapped to the mouse NCBIM37 genome assembly using Bowtie2 (version 2.2.9). Data were quantitated at gene level using the read count enrichment over genes correcting for reads per million and read length  in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: NCBIM37
Supplementary_files_format_and_content: Quantitated RNA-Seq data file is tab delimited and contains the following 89 columns: (1) gene name; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-89) RPKM values of each sample

extract_protocol:
RNA was isolated using TriReagent (Sigma) and treated with DNAseI (Ambion DNA-free DNA Cat #1311027) using manufacturers instructions
smallRNASeq: 10-1000ng RNA was used for library preparation using Illumina small RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions. Libraries were indexed using Illumina smallRNA Indexes and 50 bp single-end or paired-end sequencing was performed on Illumina HiSeq 2000 or Miseq instruments using TruSeq reagents (Illumina, San Diego, CA, USA), according to manufacturer’s instructions.


title: WD without culture replicate 2

status: Public on Nov 01 2017

type: SRA

city: Dresden

first: Natalie

middle: Anne

last: Dye

address: Pfotenhauerstrasse 108

country: Germany

institute: MPI-CBG

description:
Sample name: no_culture_2
Column header name in gene_fpkms_by_replicate.txt: no_culture_1

library_source: transcriptomic

data_processing:
Reads were trimmed with cutadapt
Trimmed Reads were mapped using tophat2
Abundance estimation was performed using cufflinks
Genome_build: BDGP5
Supplementary_files_format_and_content: FPKM for each replicate

molecule: total RNA

organism: Drosophila melanogaster

source_name: 96hr wing discs (WD)

growth_protocol: Wild type OregonR flies were grown at low density at 25C on standard food containing cornmeal, molasses agar and yeast extract. Larvae were collected for dissection at 96hr after egg laying, washed thoroughly with water and surface sterilized with 70% ethanol. Hormone free media for culture was as follows: Grace's media (Sigma G9771) prepared without Sodium Bicarbonate but with 5mM BisTris; pH adjusted to 6.7; + 5% fetal bovine serum (Invitrogen 10270098) + Penicillin/Streptomycin (Sigma P4333, diluted to 1X in media). Hormone was added just prior to the start of the experiment. 20-hydroxyecdysone (Sigma H5142) was added as a 1000x dilution from an ethanol stock solution (final 20nM in media). Bovine insulin (Sigma I6634) was added as a 2000x dilution from an acidified water stock solution (final 5ug/ml in media). Discs were dissected in hormone-free media, and then immediately transferred to the media for culture. Dissections were performed within 45min, and the middle of that window was considered to be time 0hr. Discs were cultured in a volume of 500ul/~15 discs at 25C. No_culture discs were taken from the initial timepoint (96hr AEL) and frozen in liquid nitrogen within 30min of dissection.

extract_protocol:
RNA was isolated using a Qiagen RNeasy Mini kit. Samples were lysed by vortexing for 20-30sec in Buffer RLT + 2-mercaptoethanol on ice. Manufacturer's instructions were followed. Ethanol precipitation was subsequantly performed to achieve greater purification. mRNA was isolated from 1ug of total RNA using poly-dT enrichment with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Final elution was in 15ul of 2x first strand cDNA synthesis buffer.
NEBNext Ultra Directional RNA Library Prep Kit was used after chemical fragmentation of the sample at 94C for 15min. Custom adaptors were used for ligation and then depleted using an XP bead purification (Beckman Coulter) with a ratio of 1:1. Indexing was achieved during PCR enrichment using amplification primers carrying the index sequence. Two more XP bead purifications were done, and then the samples were quantified with Qubit dsDNA HS Assay Kit (Invitrogen).

treatment_protocol: At the given times specified for each sample, discs were removed from the culture vessel in a volume of 10-15ul and transferred to a microfuge tube. Samples were rapidly frozen in liquid nitrogen and stored at -80C until all replicates were collected.

tag: strain

value: OregonR

tag: hormone for culture

tag: length of culture

tag: tissue

value: WD


title: ESC_H3K27me3_WT_Rep2

city: Baltimore

first: Yixian

last: Zheng

state: MD

address: 3520 San Martin Drive

department: Embryology

country: USA

institute: Carnegie Institution for Science

library_source: genomic

data_processing:
All RNA-seq samples were sequenced on an Illumina Hi-Seq 2000 using paired-end 100-bp mode. The resulting paired-end reads were trimmed to 75-bp paired-end reads as the last 25 bp had low sequencing quality. Then the reads were then mapped to the mouse genome mm9 using Tophat 2.1.0 (Kim et al., 2013a), and we used the Gencode gtf file (vM1) as known transcripts (-G option). We used htseq-count (Anders et al., 2015) to count reads on genes defined by the Gencode gtf file. Only genes in the “lincrna” and “protein coding” types were considered.
Chip-seq libraries were sequenced on an IlluminaHi-seq 2000 with single-end 50-bp mode. The reads were mapped to the mm9 genome using Bowtie 1.1.2 (Langmead et al., 2009) with "-v 2 -m 1" option. Bedgraph files for genome browser view were generated using custom script.
For HiC data, trimming, mapping, pair-matching and filtering were done using the HiCUP software (Wingett et al., 2015), The interaction read number beween each two 20-Kb windows are counted.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file showing counts of RNA-seq reads on each gene
Supplementary_files_format_and_content: gzipped bedgraoh file showing ChIP-seq read density (RPKM)
Supplementary_files_format_and_content: tab-delimited text file showing interaction read counts between each two 20-Kb windows.

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: The derivation of wild-type and lamin-TKO mESCs were described in our previous publication (Kim et al., 2013b). WT and TKO mESCs were cultured using the same method as described (Kim et al., 2013b) for Hi-C, ChIP-seq, and RNA-seq experiments. For FISH, mESC stocks, which were prepared from the mESCs expanded on feeder cells, were thawed and grown using 0.1% gelatin-coated plates in the absence of feeder cells with KO-DMEM medium (Invitrogen) containing 15% fetal bovine serum (FBS, Invitrogen), 100 μM β-mercaptoethanol (Invitrogen), 2 mM Glutamax, 0.1 mM nonessential amino acids, 50 μg/ml penicillin/streptomycin, and 1,000 units/ml LIF (Millipore). When the cells became ~70% confluent, they were passaged to a new plate and incubated for 30 min at 37°C in 5% CO2 to allow the attachment of the residue feeder cells to the bottom of the plate.

extract_protocol:
4 x 106 TKO or WT mESCs were harvested and fixed as described in the Hi-C method section. The crosslinked cells were resuspended in Nucleus/Chromatin Preparation (NCP) buffer I [10 mMHepes, pH 6.5, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100 and 1x protease inhibitors (Roche)] and incubated at 4oC for 10 min with gentle rotation. The suspension was centrifuged at 2,000g for 5 min. The pellets were resuspended in NCP buffer II (10 mM Hepes, pH 6.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 1x protease inhibitors), followed by centrifugation. The pellets were resuspended in SDS lysis buffer (10 mM Tris, pH 8.0, 1 mM EDTA, 1% SDS and 1x protease inhibitors). The suspension was sonicated with a Bioruptor sonicator (Diagenode) to break chromatin DNA into about 200 bp in size. The sonicated DNA was diluted 10-fold with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris, pH 8.1, and 167 mM NaCl). To precipitate chromatin, 40 μl protein A-Dynabeads (Life Technologies, 10001D) resuspended in 0.5 ml ChIP binding buffer (0.01% Tween-20 in 1x PBS) were incubated with 4 mg of antibodies for each IP at 4oC for 6 h. After washing with ChIP binding buffer, the beads were incubated with diluted sonicated chromatin DNA suspension overnight, continuously rotating. The beads were sequentially washed with low salt wash buffer (20 mM Tris pH 8.1, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, and 150 mM NaCl), high salt wash buffer (20 mM Tris pH 8.1, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, and 500 mM NaCl), LiCl buffer (10 mM Tris, pH8.0, 250 mM LiCl, 1% IGEPA CA630 (NP40), 1% Sodium deoxycholate, and 1 mM EDTA), and TE buffer. To reverse crosslinking, the beads were incubated with elution buffer (10 mM Tris, pH 8.0, 1% SDS, 1 mM EDTA and 0.2 mg/μl Proteinase K) at 65oC overnight. Supernatant was collected, extracted with Phenol:Chloroform (1:1), and precipitated with ethanol. The pellets were washed with 75% ethanol, air-dried and resuspended in 10 mM Tris (pH 8.0). DNA concentration was determined with a Quant-iTDS DNA kit (Life Tech, Q-33120).
1 ~ 400 ng of DNA were used to prepare ChIP-seq libraries with a TruSeq DNA prep kit (Illumina) according to the manufacturer’s recommendation

tag: cell type

value: ESC

tag: genotype

value: wildtpye

tag: chip antibody

value: Millipore, 07-449


title: WGBS_Seq_E14_d11.2_DNMT1KO

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
WGBS: Trimmed sequences were mapped to the mouse NCBIM37 genome using Bismark (Krueger and Andrews, 2011) (v0.12.3); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and custom R scripts.
Genome_build: NCBIM37
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

extract_protocol:
DNA was isolated from samples using Qiaamp kit from Qiagen
WGBS-Seq was performed as described previously (Ficz et al., 2013) with 12 cycles of PCR amplification using Kapa Uracil Polymerase (Kapa Biosystems)

tag: background strain

value: Dnmt1 KO


title: WGBS_Seq_E14_d11.2_control

value: Wildtype


title: ESC_H3K27me3_TKO_Rep3

value: lamin-B1/B2/A triple knockout


title: WD in insulin_9h replicate 1

description:
Sample name: insulin_9h_1
Column header name in gene_fpkms_by_replicate.txt: insulin_9h_0

value: 5ug/ml bovine insulin


title: ESC_H3K27Ac_WT_Rep2

value: Abcam, ab4729


title: ESC_H3K27Ac_WT_Rep1


title: WGBS_Seq_E14_d11.1_DNMT1KO


title: WD in ecdysone_9h replicate 3

description:
Sample name: ecdysone_9h_3
Column header name in gene_fpkms_by_replicate.txt: ecdysone_9h_2

value: 20nM 20-hydroxyecdysone


title: ESC_H3K27me3_TKO_Rep2


title: ESC_H3K27me3_TKO_Rep4


title: WD in insulin_4h replicate 2

description:
Sample name: insulin_4h_2
Column header name in gene_fpkms_by_replicate.txt: insulin_4h_1


title: ESC_H3K27me3_TKO_Rep1


title: ESC_H3K27Ac_TKO_Rep2


title: ESC_H3K27Ac_WT_Rep3


title: sRNA_Seq_E14_d9.3_control


title: ESC_HiC_WT_Rep1

extract_protocol:
WT or TKO mESCs were cultured in feeder-free condition as described (Kim et al., 2011). Five to eight million feeder-free mESCs were harvested and resuspended in 10 ml basal culture medium [10% FBS, 100 µM beta-mercaptoethanol (Life Technologies), 2 mM L-glutamine, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, and 50 µg/ml penicillin/streptomycin in GMEM (Life Technologies)]. Cells were fixed with 1% formaldehyde for 10 min at room temperature. After fixation, formaldehyde was quenched by adding 125 mM glycine. The cells were incubated at RT for 5 min, followed by an additional incubation on ice for 15 min. The cells were centrifuged at 1,000g for 10 min, and the cell pellets were washed with ice-cold 1x PBS.The crosslinked cell pellet was resuspended and lysed in Hi-C lysis buffer [10mMTris, pH8.0; 10 mM NaCl; 0.2% IGEPAL CA-630 (NP-40);1xprotease inhibitor cocktail (Roche, 04693132001)], rotating at 4oC for 30 min. The lysed cells were centrifuged at 1,000 g for 5 min. The pellet was washed with 1ml ice-cold 1.2x NEBuffer 3.1 (NEB, B7203S), and then resuspended in 0.4 ml 1.2x NEBuffer 3.1. To remove uncrosslinked proteins, 6 μl 20% SDS were added, followed by incubation at 65oC for 10 min. 40 μl 20% Triton X-100 were added to quench SDS and mixed carefully by inverting several times. The suspension was incubated at 37oC for 10 min. To digest the crosslinked chromatin, 30 μl 50 units/μl BglII enzyme (NEB, R0144M) were added to the suspension. The enzyme reactant was incubated overnight at 37oC.To mark the cohesive ends generated by BglII with biotin, 1.5 μl 10 mM dATP, 1.5 μl 10 mM dGTP, 1.5 μl 10 mM dTTP (Qiagen), 3.0 μl 5 mM biotin-16-dCTP (Axxora, JBS-NU-809-BIO16) and 10 μl 5 units/μl Klenow (NEB, M0210L) were added. The mixture was incubated at 37oC for 45 min, and then placed on ice. The blunted chromatin DNA was ligated by adding 750 μl 10x T4 ligase buffer (NEB, B0202S), 75 μl 10 mg/ml BSA (NEB), 6151.5 μl distilled water, and 30 μl 30 units/μl T4 DNA ligase (Thermo Scientific, EL0013). A total of 7.5 ml ligation mixture was incubated overnight at 16oC.To reverse crosslinking, 25 μl 20 mg/ml proteinase K (Life Technologies, 25530-049) was added and incubated overnight at 65oC. After cooling at RT, 10 ml phenol (pH 8.0) were added to the suspension, and vigorously mixed by vortexing for 2 min. The suspension was centrifuged for 5 min at 3,500 rpm with a standard tabletop centrifuge. The aqueous phase was mixed with 10 ml phenol:chloroform (1:1). After centrifugation, the supernatant was transferred to a 50 ml Oak Ridge centrifuge tube (Nalgene) and the total volume was brought to 10 ml with 1x TE (pH 8.0). To precipitate the ligated DNA, 1 ml 3M sodium acetate, 5 μl 15 mg/ml GlycoBlue (Life Tech, AM9515), and 10 ml isopropanol were added, and mixed by inverting. The mixture was incubated at -80oC for at least 1 h. The suspension was centrifuged at 38,000 g, 4oC for 30 min. The precipitated pellet was resuspended in 450 μl 1x TE (pH 8) and the suspension was transferred to an 1.5 ml Eppendorf tube. DNA was extracted with 500 μl phenol:chloroform (1:1). After phenol:chloroform extraction, 40 μl 3M sodium acetate, 1 μl GlycoBlue, and 1 ml 100% ethanol were added to the supernatant, and incubated at -80oC for 30 min. To precipitate DNA, the suspension was centrifuged at 18,000 g for 20 min. The pellet was washed with 70% ethanol and then air dried completely. The dried pellet was resuspended in 45 μl 10 mM Tris (pH 8.0). DNA concentration was determined using a Quant-iTdsDNA assay kit (Life Tech, 33120).  5 g DNA was used for the next step.5 g DNA was mixed with 10 μl 10x NEBuffer 2.1, 12.5 μl 10 mM dNTP mix (Qiagen, 201900), 1.6 μl 3 units/μl T4 DNA polymerase (NEB, M0203S), and the total reaction volume was brought to 100 μl with distilled water. The mixture was incubated at 12oC for 2 h. The 3’-5’ exonuclease activity of the T4 DNA polymerase degraded the un-ligated biotinylated DNA. The reaction was stopped by adding 2 μl 0.5 M EDTA. DNA was purified with a QIAquick PCR purification kit (Qiagen), eluting with 50 μl 10 mM Tris (pH 8.0).  To bind biotinylated DNA to streptavidin beads, 30 μl Dynabeads MyOne Streptavidin C1 (Life Technologies, 65501) were washed and resuspended in 50 μl 2x binding buffer (10 mM Tris, pH 8.0, 0.1 mM EDTA, 2 M NaCl), 50 μl biotinylated DNA was added, and the mixture was incubated at RT for 30 min, constantly mixing with an Intelli mixer (Cole Parmer, UX-51202-22) or an equivalent. After washing with 1x binding buffer (10 mM Tris, pH 8.0, 0.1 mM EDTA, 1 M NaCl) and 1x NEBuffer 4.1, the beads were resuspended in 50 μl 1x NEBuffer 4.1. To trim biotinylated DNA into small fragments, 1μl 10 units/μl AluI (NEB, R01317S) was added and incubated at 37oC for 60 min. After AluI digestion, the beads were subsequently washed with 1x binding buffer and 10 mM Tris (pH 8.0), and resuspended in 16 μl 10 mM Tris (pH 8.0).
To ligate paired-end Illumina sequencing adaptors to the AluI digested DNA fragments, beads were processed with NEBNext® DNA Library Prep Reagent Set (NEB, E6000S) as follows: For dA-tailing, the beads in 16 μl 10 mM Tris (pH 8.0) were mixed with 2.5 μl 10x NEBuffer 2, 5.0 μl dATP, 1.5 μl Klenow (all included in the NEB kit), and incubated at 37oC for 30 min; constant agitation is not required hereafter. dA-tailed beads were washed with 1x binding buffer, and resuspended in 5.0 μl 10 mM Tris (pH 8.0). To ligate sequencing adaptors, the beads in 5.0 μl 10 mM Tris (pH 8.0) were mixed with 12.5 μl ligation reaction buffer, 5.0 μl NEBNext adaptor, and 2.5 μl Quick T4 ligase (all included in the NEB kit), and incubated at 20oC for 15 min. To cleave the hairpin loop of NEBNext adaptors, 1.5 μl USER enzyme (included in the NEB kit) were added and incubated at 37oC for 15 min. The beads were washed with 1x binding buffer and resuspended in 10 μl of 10 mM Tris (pH 8.0). To amplify adaptor ligated DNA, the beads in 10 μl of 10 mM Tris (pH 8.0) were mixed with 1.25 μl Universal PCR primer, 12.5 μl PCR master mix (included in the NEB kit), 1.25 μl of NEBNext Indexed primer (NEB, E7500S), and the PCR was performed with the following program (98oC 30 sec, 8 cycles of [98oC 10 sec, 65oC 30 sec, 72oC 30 sec], and 72oC 5min). PCR amplified Hi-C library DNA was purified with AMPure XP magnetic beads (Beckman Coulter). The quality of Hi-C library DNA was assessed with a Bioanalyzer (Agilent, 2100). Successful Hi-C library DNA ranged from 200 bp to 1 kb in size with a clear single peak at about 600 bp.


title: sRNA_Seq_E14_d9.2_DNMT1KO


title: sRNA_Seq_E14_d9.2_control


title: ESC_H3K27Ac_TKO_Rep3


title: ESC_HiC_TKO_Rep1


title: ESC_RNASeq_WT_Rep2

molecule: polyA RNA

extract_protocol:
Total RNA was extracted from ESCs using an RNeasy Plus mini kit (Qiagen)
Poly A+ RNA was purified from the total RNA and processed according to manufacturer’s recommendations to generate paired-end libraries for an Illumina HiSeq 2000 sequencer


title: sRNA_Seq_E14_d9.1_DNMT1KO


title: WD in ecdysone_9h replicate 2

description:
Sample name: ecdysone_9h_2
Column header name in gene_fpkms_by_replicate.txt: ecdysone_9h_1


title: ESC_RNASeq_WT_Rep1


title: sRNA_Seq_E14_d9.1_control


title: sRNA_Seq_E14_d6.1_DNMT1KO


title: WD in ecdysone_9h replicate 1

description:
Sample name: ecdysone_9h_1
Column header name in gene_fpkms_by_replicate.txt: ecdysone_9h_0


title: sRNA_Seq_E14_d6.1_control


title: ESC_RNASeq_TKO_Rep1


title: WD in ecdysone_4h replicate 3

description:
Sample name: ecdysone_4h_3
Column header name in gene_fpkms_by_replicate.txt: ecdysone_4h_2


title: sRNA_Seq_E14_d6.3_control


title: ESC_H3K27Ac_TKO_Rep1


title: sRNA_Seq_E14_d3.3_control


title: sRNA_Seq_E14_d6.2_DNMT1KO


title: WD in ecdysone_4h replicate 2

description:
Sample name: ecdysone_4h_2
Column header name in gene_fpkms_by_replicate.txt: ecdysone_4h_1


title: 141_Wapl-control

city: Vienna

first: Johanna

last: Gassler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute for Molecular Biotechnology

data_processing:
Base calling was performed by VBCF NGS unit
Mapping: iterative mapping (see Imakaev et al, 2012) using bowtie2 with increased stringency parameters: --score-min -L 0.6,0.2--very-  sensitive
Read filtering was performed as in Flyamer et al., 2017:
Summary of filtering: If two reads map to the same strand, and each side of the read is within 500 bp of any side of the other read, we retain only one copy of the read. We separate the genome into 500 bp bins. If any two bins are interacting more than once, only one interaction is counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide 4 resolutions) using read start as a read position and stored in the Cool file format. No normalization was applied to the data.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 10kb, 40kb, and 100kb resolutions stored in the Cool file format.

source_name: zygote pronucleus

extract_protocol:
snHi-C protocol according to Flyamer et al., 2017
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) following the standard DNA sample preparation protocol.

tag: strain background

value: mixed (mainly C57BL/6J)

tag: genotype/variation

value: Waplfl(m)/+(p)

tag: sex/reassigned-sex

value: both


title: WD in ecdysone_4h replicate 1

description:
Sample name: ecdysone_4h_1
Column header name in gene_fpkms_by_replicate.txt: ecdysone_4h_0


title: IgG_16wkHFD_reps_1_2_3

city: Bethesda

first: Anthony

middle: Robert

last: Soltis

address: 4301 Jones Bridge Road

department: Anatomy, Physiology and Genetics

institute: Uniformed Services University

data_processing:
For ChIP-Seq studies: We aligned raw reads using Bowtie (version 0.12.7) with parameters -n 2 -q -m 1 and performed peak calling using MACS (version 1.4.0rc2) against an IgG control. We considered significant MACS peaks to be those possessing a p-value <1e-6 and an FDR <10%. We also performed differential peak analyses between conditions of the same histone mark. We used MACS-called peaks on replicate-pooled samples and used BEDTools to merge significant peak regions from each condition into one set of common genomic loci. We then extracted raw read counts in these regions from each individual replicate ChIP-seq sample and used DESeq2 to perform the differential enrichment analyses on the read counts. We considered regions possessing an FDR-corrected p-value <0.05 as significant.
genome build: mm9
processed data files format and content: For ChIP-Seq studies: We generated bigWig files either from alignment BAM files with BEDTools functions or from MACS; *.bed files contain MACS-called peak regions from pooled replicate runs and were post-filtered from MACS-generated file for peaks with FDR < 10%; *.xls files contain peak regions from pooled replicate runs and were post-filtered from MACS-generated file for peaks with FDR < 10%; *_union_MACS_peaks-read_counts.txt files contain read counts in union MACS peak regions for all replicates across all conditions; *_gene_promoter_read_counts.txt files contain read counts of histone mark in gene promoter regions (+/- 2 kb of TSS); *_DESeq2_output.txt contain DESeq2 output results between chow diet and 16 week high-fat diet conditions for regions described in file name with columns "region", "baseMean", "log2FoldChange" (HFD/ND), "l2fcSE", "pvalue", and "padj".

source_name: Liver

extract_protocol:
We euthanized all mice at 24 weeks after an overnight fast and froze the livers prior to removal using clamps cooled in liquid nitrogen. The frozen livers were then pulverized into a powder using a CryoPREP impactor (Covaris). We prepared aliquots of pulverized liver for all samples and used these for subsequent library construction.
Histone modification ChIP experiments were performed using the MAGnify Chromatin Immunoprecipitation System kit (Life Technologies, Carlsbad, CA) with an antibody against H3K27ac (ab4729, Abcam, Cambridge, MA). ChIP-Seq libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England Biolabs, Ipswich, MA) and sequenced on an Illumina Hi-Seq 2000 machine.

treatment_protocol: We fed the mice a standard chow diet (Prolab Isopro RMH 3000, Purina) for 24 weeks or a high-fat diet (S3282, Bioserve) starting at 8 weeks for 16 week high-fat diet.

value: liver

tag: diet

value: 16 week high-fat diet

tag: age

value: 24 weeks

value: IgG

value: wild type


title: WD in insulin_4h replicate 1

description:
Sample name: insulin_4h_1
Column header name in gene_fpkms_by_replicate.txt: insulin_4h_0

value: OregonR

value: WD


title: 144_Wapl-control


title: sRNA_Seq_E14_d6.2_control

value: ESC


title: ESC_RNASeq_TKO_Rep2


title: 143_Wapl-control


title: H3K27Ac_16wkHFD_rep3

description:
processed data file available on series record: H3K27Ac_all_reps_CD_16wkHFD_union_MACS_peaks_read_counts.txt
processed data file available on series record: H3K27Ac_CD_vs_16wkHFD_union_MACS_peaks_DESeq2_output.txt
processed data file available on series record: H3K27Ac_16wkHFD_reps_1_2_3_vs_IgG_pval_1e-6_MACS_peaks.filtered_fdr_10.0.bed
processed data file available on series record: H3K27Ac_16wkHFD_reps_1_2_3_vs_IgG_pval_1e-6_MACS_peaks.filtered_fdr_10.0.xls
processed data file available on series record: H3K27Ac_all_reps_CD_16wkHFD_gene_promoter_read_counts.txt
processed data file available on series record: H3K27Ac_CD_vs_16wkHFD_gene_promoters_DESeq2_output.txt

value: H3K27Ac (Abcam, ab4729)


title: 142_Wapl-control


title: 139_Wapl-control

value: maternal


title: sRNA_Seq_E14_d3.1_DNMT1KO

value: Dnmt1 KO


title: H3K27Ac_16wkHFD_rep2


title: H3K27Ac_16wkHFD_rep1


title: sRNA_Seq_E14_d6.3_DNMT1KO


title: sRNA_Seq_E14_d1.3_DNMT1KO


title: sRNA_Seq_E14_d3.3_DNMT1KO


title: 140_Wapl-control


title: sRNA_Seq_E14_d3.2_DNMT1KO


title: sRNA_Seq_E14_d3.2_control

value: Wildtype


title: 138_Wapl-control


title: 135_Wapl-control


title: 137_Wapl-control

value: paternal


title: H3K27Ac_CD_rep1

description:
processed data file available on series record: H3K27Ac_all_reps_CD_16wkHFD_union_MACS_peaks_read_counts.txt
processed data file available on series record: H3K27Ac_CD_vs_16wkHFD_union_MACS_peaks_DESeq2_output.txt
processed data file available on series record: H3K27Ac_CD_reps_1_2_3_vs_IgG_pval_1e-6_MACS_peaks.filtered_fdr_10.0.bed
processed data file available on series record: H3K27Ac_CD_reps_1_2_3_vs_IgG_pval_1e-6_MACS_peaks.filtered_fdr_10.0.xls
processed data file available on series record: H3K27Ac_all_reps_CD_16wkHFD_gene_promoter_read_counts.txt
processed data file available on series record: H3K27Ac_CD_vs_16wkHFD_gene_promoters_DESeq2_output.txt

value: chow diet


title: sRNA_Seq_E14_d3.1_control


title: WD in insulin_4h replicate 3

description:
Sample name: insulin_4h_3
Column header name in gene_fpkms_by_replicate.txt: insulin_4h_2

value: 5ug/ml bovine insulin


title: H3K4me1_16wkHFD_rep2

description:
processed data file available on series record: H3K4me1_all_reps_CD_16wkHFD_union_MACS_peaks_read_counts.txt
processed data file available on series record: H3K4me1_CD_vs_16wkHFD_union_MACS_peaks_DESeq2_output.txt
processed data file available on series record: H3K4me1_16wkHFD_reps_1_2_3_vs_IgG_pval_1e-6_MACS_peaks.filtered_fdr_10.0.bed
processed data file available on series record: H3K4me1_16wkHFD_reps_1_2_3_vs_IgG_pval_1e-6_MACS_peaks.filtered_fdr_10.0.xls

extract_protocol:
We euthanized all mice at 24 weeks after an overnight fast and froze the livers prior to removal using clamps cooled in liquid nitrogen. The frozen livers were then pulverized into a powder using a CryoPREP impactor (Covaris). We prepared aliquots of pulverized liver for all samples and used these for subsequent library construction.
Histone modification ChIP experiments were performed using the MAGnify Chromatin Immunoprecipitation System kit (Life Technologies, Carlsbad, CA) with an antibody against H3K4me1 (Millipore, 17-676). ChIP-Seq libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England Biolabs, Ipswich, MA) and sequenced on an Illumina Hi-Seq 2000 machine.

value: H3K4me1 (Millipore, 17-676)


title: sRNA_Seq_E14_d1.2_control


title: 136_Wapl-control

value: mixed (mainly C57BL/6J)

value: Waplfl(m)/+(p)


title: H3K4me1_CD_rep3

description:
processed data file available on series record: H3K4me1_all_reps_CD_16wkHFD_union_MACS_peaks_read_counts.txt
processed data file available on series record: H3K4me1_CD_vs_16wkHFD_union_MACS_peaks_DESeq2_output.txt
processed data file available on series record: H3K4me1_CD_reps_1_2_3_vs_IgG_pval_1e-6_MACS_peaks.filtered_fdr_10.0.bed
processed data file available on series record: H3K4me1_CD_reps_1_2_3_vs_IgG_pval_1e-6_MACS_peaks.filtered_fdr_10.0.xls

value: liver


title: IgG_CD_reps_1_2_3

value: 24 weeks


title: H3K27Ac_CD_rep2


title: H3K27Ac_CD_rep3


title: sRNA_Seq_E14_d1.3_control


title: 127_Wapl-KO

value: Wapldelta(m)/+(p)


title: 134_Wapl-control


title: sRNA_Seq_E14_d1.2_DNMT1KO


title: H3K4me1_16wkHFD_rep3

value: 16 week high-fat diet

value: wild type


title: 125_Wapl-KO


title: 132_Wapl-KO


title: 133_Wapl-KO


title: 131_Wapl-KO


title: H3K4me1_16wkHFD_rep1


title: sRNA_Seq_E14_d1.1_control


title: 124_Scc1-control

value: mixed (B6, 129, Sv)


title: sRNA_Seq_E14_d11.2_DNMT1KO

value: ESC


title: 130_Wapl-KO

value: bad


title: sRNA_Seq_E14_d11.3_DNMT1KO


title: sRNA_Seq_E14_d11.3_control


title: 129_Wapl-KO

value: both


title: mRNAseq_16wkHFD_rep1

description:
processed data file available on series record: mRNA_CD_vs_16wkHFD_normalized_counts.txt
processed data file available on series record: mRNA_CD_vs_16wkHFD_DESeq2_results.txt

data_processing:
For mRNA-Seq studies: Raw sequencing reads were aligned to known mouse RefSeq gene transcripts obtained from the UCSC table browser (accessed on January 25, 2012) and the mouse genome (build mm9) with the splice junction-aware short-read alignment tool TopHat (version 1.4.0). We restricted TopHat to only align to known transcript splice junctions. Gene-level read counts were quantified using the python package HTSeq. We used the Bioconductor package conditional quantile normalization (CQN, version 1.6.0) to remove systematic biases due to GC-content and gene length coverage and used DESeq2 (version 1.0.18) to perform differential expression analyses. We considered a gene to be differentially expressed if it possessed an absolute log2 fold-change between conditions ≥ 0.5, an FDR-adjusted p-value (q-value) ≤ 0.05, and was expressed in at least one tested condition (i.e. ≥ 0.1 FPKM).
genome build: mm9
processed data files format and content: For mRNA-Seq studies: All bigWig files were generated from alignment BAM files using BEDTools functions; *_gene_counts.txt files were generated with HTSeq count on BAM files against mouse RefSeq gene models with columns "gene" and "count"; *_normalized_counts.txt files contain conditional quantile normalization (CQN) and DESeq2 normalized counts for all replicates across all conditions; *_DESeq2_results.txt contain DESeq2 output results between chow diet and 16 week high-fat diet conditions with columns "gene", "baseMean", "log2FoldChange" (HFD/ND), "l2fcSE", "pvalue", and "padj".

extract_protocol:
We euthanized all mice at 24 weeks after an overnight fast and froze the livers prior to removal using clamps cooled in liquid nitrogen. The frozen livers were then pulverized into a powder using a CryoPREP impactor (Covaris). We prepared aliquots of pulverized liver for all samples and used these for subsequent library construction.
We extracted total RNA from the pulverized frozen livers of mice using the miRNeasy Mini kit (Qiagen). We prepared mRNA-Seq libraries using the TruSeq RNA Sample Prep Kit v1 (Illumina) and size-selected using 2% agarose gel electrophoresis for 180 +/- 25 base-pairs of insert. We multiplexed mRNA-Seq libraries and paired-end sequenced samples for 40-50 base-pairs on an Illumina Hi-Seq 2000 machine.


title: sRNA_Seq_PGC_E14_5_F


title: sRNA_Seq_E14_d11.2_control


title: 128_Wapl-KO


title: H3K4me3_CD_rep2

description:
processed data file available on series record: H3K4me3_reps_1_2_vs_IgG_pval_1e-6_MACS_peaks.filtered_fdr_10.0.bed
processed data file available on series record: H3K4me3_reps_1_2_vs_IgG_pval_1e-6_MACS_peaks.filtered_fdr_10.0.xls

extract_protocol:
We euthanized all mice at 24 weeks after an overnight fast and froze the livers prior to removal using clamps cooled in liquid nitrogen. The frozen livers were then pulverized into a powder using a CryoPREP impactor (Covaris). We prepared aliquots of pulverized liver for all samples and used these for subsequent library construction.
Histone modification ChIP experiments were performed using the MAGnify Chromatin Immunoprecipitation System kit (Life Technologies, Carlsbad, CA) with an antibody against H3K4me3 (Millipore, 17-614). ChIP-Seq libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England Biolabs, Ipswich, MA) and sequenced on an Illumina Hi-Seq 2000 machine.

value: H3K4me3 (Millipore, 17-614)


title: H3K4me1_CD_rep1


title: sRNA_Seq_E14_d1.1_DNMT1KO

value: Dnmt1 KO


title: sRNA_Seq_E14_d11.1_DNMT1KO


title: H3K4me3_CD_rep1


title: 121_Scc1-control

value: maternal


title: mRNAseq_16wkHFD_rep3


title: mRNAseq_CD_rep2

value: chow diet


title: 120_Scc1-KO

value: paternal


title: mRNAseq_CD_rep1


title: sRNA_Seq_E14_none_1_control


title: sRNA_Seq_PGC_E14_5_M


title: 118_Scc1-KO


title: 119_Scc1-KO


title: H3K4me1_CD_rep2

value: H3K4me1 (Millipore, 17-676)


title: mRNAseq_16wkHFD_rep2


title: 123_Scc1-control


title: 126_Wapl-KO

value: mixed (mainly C57BL/6J)


title: sRNA_Seq_E14_Ago2_4_control


title: 122_Scc1-control


title: sRNA_Seq_E14_Ago2_3_control


title: mRNAseq_CD_rep3


title: 116_Scc1-KO


title: sRNA_Seq_E14_d11.1_control

value: Wildtype


title: sRNA_Seq_PGC_E13_5_M


title: sRNA_Seq_E14_none_1_DNMT1KO


title: sRNA_Seq_PGC_E13_5_F


title: 113_Scc1-KO


title: 117_Scc1-KO


title: sRNA_Seq_E14_Ago2_3_DNMT1KO


title: sRNA_Seq_E14_Ago2_4_DNMT1KO


title: 110_Scc1-KO


title: 111_Scc1-KO


title: 112_Scc1-KO


title: 115_Scc1-KO


title: 114_Scc1-KO


title: 108_Scc1-control


title: sRNA_Seq_E14_d9.2_DNMT1KO_R1


title: sRNA_Seq_E14_Ago2_2_control


title: sRNA_Seq_E14_Ago2_2_DNMT1KO


title: sRNA_Seq_E14_d9.2_control_R1


title: 107_Scc1-control


title: 106_Scc1-control


title: sRNA_Seq_E14_d9.3_DNMT1KO_R1


title: sRNA_Seq_E14_Ago2_1_control


title: sRNA_Seq_E14_Ago2_1_DNMT1KO


title: sRNA_Seq_E14_d9.3_control_R1


title: 109_Scc1-KO


title: sRNA_Seq_E14_d3.3_DNMT1KO_R1


title: sRNA_Seq_E14_d6.3_control_R1


title: sRNA_Seq_E14_d6.3_DNMT1KO_R1


title: 105_Scc1-control


title: sRNA_Seq_E14_d6.2_DNMT1KO_R1


title: sRNA_Seq_E14_d9.1_control_R1


title: sRNA_Seq_E14_d3.3_control_R1


title: sRNA_Seq_E14_d6.1_control_R1


title: sRNA_Seq_E14_d6.2_control_R1


title: sRNA_Seq_E14_d3.2_DNMT1KO_R1


title: sRNA_Seq_E14_d3.2_control_R1


title: sRNA_Seq_E14_d1.2_DNMT1KO_R1


title: sRNA_Seq_E14_d6.1_DNMT1KO_R1


title: sRNA_Seq_E14_d3.1_DNMT1KO_R1


title: sRNA_Seq_E14_d1.3_control_R1


title: sRNA_Seq_E14_d1.3_DNMT1KO_R1


title: sRNA_Seq_E14_d11.2_WT_R1


title: sRNA_Seq_E14_d3.1_control_R1


title: sRNA_Seq_E14_d1.1_DNMT1KO_R1


title: sRNA_Seq_E14_d11.2_DNMT1KO_R1


title: sRNA_Seq_E14_d9.1_DNMT1KO_R1


title: sRNA_Seq_E14_d1.1_control_R1


title: sRNA_Seq_E14_d11.3_WT_R1


title: sRNA_Seq_E14_d11.3_DNMT1KO_R1


title: sRNA_Seq_E14_d11.1_WT_R1


title: sRNA_Seq_E14_d1.2_control_R1


title: sRNA_Seq_PGC_E14_5_M_R1


title: sRNA_Seq_PGC_E13_5_M_R1


title: sRNA_Seq_PGC_E13_5_F_R1


title: RNA_Seq_E14_DICERKO_R1

data_processing:
RNASeq: Raw FastQ data were trimmed with Trim Galore (v0.3.5, default parameters) and mapped to the mouse NCBIM37 genome assembly using TopHat v2.0.11, guided by gene models from Ensembl v61. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) applying transcript length correction.
Genome_build: NCBIM37
Supplementary_files_format_and_content: Quantitated RNA-Seq data file is tab delimited and contains the following 41 columns: (1) gene name; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-41) RPKM values for each sample

extract_protocol:
RNA was isolated using TriReagent (Sigma) and treated with DNAseI (Ambion DNA-free DNA Cat #1311027) using manufacturers instructions
Total RNA libraries (ribozero) were made using 200ng-1μg RNA at the Sanger Institute Illumina bespoke pipeline

value: Dicer KO


title: RNA_Seq_E14_d25.2_DNMT1KO_R1


title: RNA_Seq_E14_d25.1_DNMT1KO_R1


title: RNA_Seq_E14_d25.2_control_R1


title: RNA_Seq_E14_d25.1_control_R1


title: RNA_Seq_E14_d17.2_DNMT1KO_R1


title: RNA_Seq_E14_d17.2_control_R1


title: RNA_Seq_E14_d17.1_control_R1


title: RNA_Seq_E14_d1.3_DNMT1KO_R1


title: RNA_Seq_E14_d17.1_DNMT1KO_R1


title: RNA_Seq_E14_d1.3_control_R1


title: sRNA_Seq_E14_d11.1_DNMT1KO_R1


title: RNA_Seq_E14_d11.1_control_R1


title: RNA_Seq_E14_d9.2_DNMT1KO_R1


title: RNA_Seq_E14_d11.2_control_R1


title: RNA_Seq_E14_d9.2_control_R1


title: RNA_Seq_E14_d9.1_DNMT1KO_R1


title: RNA_Seq_E14_d9.1_control_R1


title: RNA_Seq_E14_d6.2_control_R1


title: RNA_Seq_E14_d6.1_DNMT1KO_R1


title: RNA_Seq_E14_d6.1_control_R1


title: RNA_Seq_E14_d1.2_DNMT1KO_R1


title: RNA_Seq_E14_d1.2_control_R1


title: RNA_Seq_E14_d1.1_DNMT1KO_R1


title: RNA_Seq_E14_d3.1_DNMT1KO_R1


title: RNA_Seq_E14_d0.1_DNMT1KO_R1


title: RNA_Seq_E14_d11.1_DNMT1KO_R1


title: ChIP-seq_H3K9me3_d8.2_DNMT1KO

data_processing:
ChIP-Seq: Trimmed sequences were mapped to the mouse NCBIM37 genome using Bowtie2 (v.2.2.9); Read counts over 2kb tiles were normalised per million reads and log2 transformed.
Genome_build: NCBIM37
Supplementary_files_format_and_content: Quantitated ChIPseq data file is tab delimited and contains the following 32 columns: (1) Probe, (2) Chromosome; (3) Start; (4) End; (13-32) log2 readcount for each sample

extract_protocol: ChIP-Seq: Cells were cross-linked with 1% methanol-free formaldehyde in fresh medium for 10 minutes. Cross-linking reaction was quenched with glycine at a final concentration of 0.2M. Cells were then washed twice with ice-cold PBS and harvested. Cell pellets were then resuspended in LB1 buffer (50 mM Hepes–KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, protease inhibitors) for 10 minutes at 4°C, pelleted and resuspended in LB2 buffer (10 mM Tris–HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, protease inhibitors) for 10 minutes at 4°C. Cells were pelleted, resuspended in LB3 buffer (10 mM Tris–HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na–Deoxycholate; 0.5% N-lauroylsarcosine, protease inhibitors) and sonicated using Misonix Sonicator 3000. After addition of Triton-X to a final concentration of 1%, the lysate was centrifuged at 20,000g for 10 minutes to pellet debris. Sonicate chromatin was then added to the bead-antibody complexes and incubated overnight at 4°C. Bead-antibody were prepared as follows: Protein G-coupled Dynabeads were incubated overnight with primary antibodies (anti-H3K9me2; Abcam ab1220) in PBS added with 5 mg/ml BSA. Beads were washed extensively with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCL), once with 1x TE buffer and eluted in 200ul of buffer containing 1% SDS and 0.1M NaHCO3. Cross-linking was reversed by incubation at 65°C overnight, followed by RNase A treatment at 37°C for 1 hour and Proteinase K treatment at 55°C for 2 hours. DNA was then extracted using Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions. Eluted DNA was then used to perform ChIP-Seq library preparation using the MicroPlex Library Preparation Kit v2 (Diagenode)

value: anti-H3K9me3; Active Motif, MABI 0319


title: ChIP-seq_Input_control

value: none (input)


title: ChIP-seq_H3K9me3_d8.2_control


title: ChIP-seq_H3K9me3_d8.1_control


title: RNA_Seq_E14_d11.2_DNMT1KO_R1


title: RNA_Seq_E14_d3.2_DNMT1KO_R1


title: ChIP-seq_H3K9me2_d8.2_control

value: anti-H3K9me2; Abcam ab1220


title: ChIP-seq_H3K9me3_d4.1_DNMT1KO


title: ChIP-seq_H3K9me2_d8.2_DNMT1KO


title: RNA_Seq_E14_d3.2_control_R1


title: ChIP-seq_H3K9me2_d8.1_DNMT1KO


title: ChIP-seq_H3K9me2_d8.1_control


title: ChIP-seq_H3K9me3_d4.1_control


title: RNA_Seq_E14_d3.1_control_R1


title: ChIP-seq_H3K9me2_d4.1_control


title: ChIP-seq_H3K9me2_d4.1_DNMT1KO


title: ChIP-seq_H3K27me3_d8.2_control

value: anti-H3K27me3; Active Motif, 39157


title: RNA_Seq_E14_d1.1_control_R1


title: ChIP-seq_H3K27me3_d8.1_DNMT1KO

value: anti-H3K27me3; Active Motif, 39156


title: RNA_Seq_E14_d0.2_DNMT1KO_R1

value: ESC


title: ChIP-seq_H3K27me3_d4.1_control

value: anti-H3K27me3; Active Motif, 39155


title: RNA_Seq_E14_d0.2_control_R1


title: ChIP-seq_H3K9me3_d8.1_DNMT1KO


title: ChIP-seq_H3K27me3_d4.1_DNMT1KO


title: RNA_Seq_E14_d0.1_control_R1


title: ChIP-seq_H3K27me3_d8.2_DNMT1KO

value: anti-H3K27me3; Active Motif, 39158


title: SAM22154295 WT negative

city: South San Francisco

first: Janina

last: Reeder

address: 1 DNA Way

institute: Genentech

description: SAM22154295 WT negative

data_processing:
Sequencing reads were mapped to the reference mouse genome (GRCm38), using the GSNAP short read aligner (Thomas D Wu, 2010).
Expression was measured in reads per kilobase per million total reads (RPKM) by normalizing the number of reads aligning to coding sequence in a given gene to the total length of the coding sequence and the total number of reads. Analysis of processed RNAseq data (normalized and variance-stabilized by voom) was performed using R (v3.2.2) and Bioconductor (v3.2).
Differential expression filtering was performed with the limma package using single-term linear models and cut-off thresholds of absolute log fold change greater than 2 and adjusted (Benjamini-Hochberg) p-value less than 0.001. Clustering was performed on data for these sets differentially expressed genes by complete agglomerative iteration on euclidean distances of log-transformed, scaled and centered data.
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data files were created for each sample using the Bioconductor package, HTSeqGenie. The tab-delimited text files contain 4 columns: entrez gene IDs, gene exonic counts, gene length, and RPKM values

source_name: WT negative

growth_protocol: B cells were isolated from spleen of at least 8-week old mice according to the Miltenyi Biotec murine B-cell isolation kit. Briefly: spleen were harvested from euthanized mice and made into single-cell suspensions in RPMI. After spinning at 1300 rpm for 5 minutes, media was aspirated and 1 mL of red blood cell lysis solution (Sigma) was used to resuspend the cells for 1 minute. After washing with MACS buffer, cells were counted and isolated according to the protocol. Following isolation, cells were counted and either immediately plated in complete B-cell medium (DMEM:H12*10e6 cells/mL, with 200 μL/well in 48-well plates, or stained with CFSE (eBioscience) at a concentration of 2 μM for 8 minutes in sterile PBS in the dark, then washed 3 times with cold complete medium and plated.

extract_protocol:
Cells were then harvested, spun down at 450 g for 5 minutes, and resuspended in 350 μL of buffer RLT with added beta-mercaptoethanol. Triplicate samples were pooled for RNA purification. RNA purification was performed using the RNEasy kit with on-column DNAse digestion (Qiagen).
0.5μg of total RNA was used as an input material for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). Size of the libraries was confirmed using Fragment Analyzer (Advanced Analytical Technologies) and their concentration was determined by qPCR based method using Library quantification kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30M of single end 50 base pair reads.

treatment_protocol: Cells were stimulated in triplicate in 2*10e6 cells/mL for 4 hours with either 10 μg/mL anti-IgM F(ab)2 or 20 μg/mL LPS, or no stimulation.

value: C57BL/6 N

value: WT

value: Splenic B-cells

tag: treatment

value: resting


title: SAM22154293 WT negative 3

description: SAM22154293 WT negative 3


title: SAM22154294 WT negative 2

description: SAM22154294 WT negative 2


title: SAM22154290 WT IgM 3

description: SAM22154290 WT IgM 3 10 ug/mL anti-IgM F(ab)2

source_name: WT IgM

value: stimulated with anti-IgM F(ab)2

tag: dose

value: 10 ug/mL anti-IgM F(ab)2


title: SAM22154291 WT IgM 2

description: SAM22154291 WT IgM 2 10 ug/mL anti-IgM F(ab)2


title: SAM22154292 WT IgM

description: SAM22154292 WT IgM 10 ug/mL anti-IgM F(ab)2


title: SAM22154289 WT LPS

description: SAM22154289 WT LPS 20 ug/mL LPS from K12 E.coli

source_name: WT LPS

value: stimulated with LPS from K12 E.coli

value: 20 ug/mL LPS


title: SAM22154286 Ubiquilin-1 KO negative

description: SAM22154286 Ubiquilin-1 KO negative

source_name: Ubiquilin-1 KO negative

value: Ubiquilin-1 KO


title: SAM22154285 Ubiquilin-1 KO negative 2

description: SAM22154285 Ubiquilin-1 KO negative 2


title: SAM22154287 WT LPS 3

description: SAM22154287 WT LPS 3 20 ug/mL LPS from K12 E.coli


title: SAM22154288 WT LPS 2

description: SAM22154288 WT LPS 2 20 ug/mL LPS from K12 E.coli


title: SAM22154284 Ubiquilin-1 KO negative 3

description: SAM22154284 Ubiquilin-1 KO negative 3


title: ChIP-seq_H3K27me3_d8.1_control

value: Wildtype


title: SAM22154283 Ubiquilin-1 KO IgM

description: SAM22154283 Ubiquilin-1 KO IgM 10 ug/mL anti-IgM F(ab)2

source_name: Ubiquilin-1 KO IgM


title: SAM22154281 Ubiquilin-1 KO IgM 3

description: SAM22154281 Ubiquilin-1 KO IgM 3 10 ug/mL anti-IgM F(ab)2


title: SAM22154282 Ubiquilin-1 KO IgM 2

description: SAM22154282 Ubiquilin-1 KO IgM 2 10 ug/mL anti-IgM F(ab)2


title: SAM22154280 Ubiquilin-1 KO LPS

description: SAM22154280 Ubiquilin-1 KO LPS 20 ug/mL LPS from K12 E.coli

source_name: Ubiquilin-1 KO LPS


title: DRC high-fluorescence cells

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

description:
DRC cells, FACS-sorted, high-fluorescence cells, 5 days-old multicellular aggregate.
JC3_DRC_positive

data_processing:
Demultiplexing
FastQ quality trimming: cut-off value of 20 (FastX)
Fastq to fasta conversion (FastX)
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.3)
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Coverage calculation and normalisation by total number of aligned reads and multiplied by 1 mio (READemption 0.3.3)
Genome_build: NC_009641 from NCBI [ASM1046v1]
Supplementary_files_format_and_content: Raw and normalized coverage files (wig)

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: Staphylococcus aureus strain Newman multicellular aggregates

growth_protocol: Staphylococcus aureus multicellular aggregates grown in TSBMg medim at 37ºC during 5 days.

extract_protocol:
Total RNA was extracted using hot-phenol method with some modifications.
Library preparation and deep-sequencing was performed by Vertis Biotechnology AG, using standard Illumina protocols

treatment_protocol: BRC and DRC bacterial cells were collected from the multicellular aggregates 5 days after culture and 25000000 cells were sorted per population in: BRC+ (high-fluorescence), BRC- (low-fluorescence), DRC+ or DRC- using FACS.

value: DRC cells

tag: fluorescence of facs-sorted cells

value: high


title: BRC low-fluorescence cells

description:
BRC cells, FACS-sorted, low-fluorescence cells, 5 days-old multicellular aggregate.
JC2_BRC_negative

value: BRC cells

value: low


title: DRC low-fluorescence cells

description:
DRC cells, FACS-sorted, low-fluorescence cells, 5 days-old multicellular aggregate.
JC4_DRC_negative


title: BRC high-fluorescence cells

description:
BRC cells, FACS-sorted, high-fluorescence cells, 5 days-old multicellular aggregate.
JC1_BRC_positive


title: NT_2

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

description: root-specific overexpression

data_processing:
Single-end seq were generated and raw seq reads were trimmed to removed adaptor seq, and those with a quality lower than Q20 were removed using the clc quality trim software (CLCBIO).
Duplicate paired short reads were removed using FastUniq.
All reads were assembled with the clc_ref_assmble 6 (version 4.06) program, using annotated gene and noncoding RNA seq from the rapdb (http://rapdb.dna.affrc.go.jp).
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: abundance measurements

organism: Oryza sativa

source_name: ILMI (nontransgenic rice)

growth_protocol: Rice was germinated on MS (Murashige and Skoog) media at 28C for 4 days, and transplanted into soil pots (4x4x6 cm; 3 plants per pot) and grown in a greenhouse.

extract_protocol:
Total RNA was extracted from the roots of 2-week-old ROX plants and NT rice seedlings grown under normal growth conditions using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
A modified TruSeq method was used to construct a strand-specific RNA-seq library with different index primers and libraries were sequenced in the Illumina HiSeq 2500 system in MACROGEN. Cutoff criteria to eliminate genes that showed no significant difference were more than 2 fold up- and down-regulation in ROX plants compared to NT (Ilmi).

value: roots

tag: developmental stage

value: 2-week-old at vegetative stage


title: SAM22154278 Ubiquilin-1 KO LPS 3

description: SAM22154278 Ubiquilin-1 KO LPS 3 20 ug/mL LPS from K12 E.coli

tag: strain


title: ROX6_2

description: root-specific overexpression

source_name: Rcc3-OsERF48#6 (root specific promoter transgenic rice)


title: Linc-smad7_3

city: Yangling

first: Chengchuang

last: Song

address: xinong road

department: College of Animal Science and Technology

country: China

institute: Northwest A&F University

data_processing:
Illumina Casava1.8 software used for basecalling.
The genome build number used for read alignment is: mm10.  Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq  R package (1.12.0),|log2foldchang|>1 && qvalue<0.005
Read alignment software: HISAT, 2.0.4. the default parameters.
Go term was performed using the GOSeq，topGO,hmmscan (Release2.12),corrected P-Value<0.05
KEGG enrichment was performed using the KOBAS (v2.0), corrected P-Value<0.05
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

source_name: L7, tibialis anterior muscle, CTX-induced muscle injury in vivo

growth_protocol: Six skeletal muscle samples of mouse  from the Fourth Military Medical University, Xi’An, P.R. China. Tissue samples were snap-frozen in liquid nitrogen and stored at –80°C freezer until use.

extract_protocol:
Total RNA was extracted from every sample using the TRIzol reagent (Takara, Japan) following the manufacturer's procedure. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA) .RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample  preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library  Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index  codes were added to attribute sequences to each sample. Briefly, mRNA was purified from  total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out  using divalent cations under elevated temperature in NEBNext First Strand Synthesis  Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer  and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was  subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs  were converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to  prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp  in length, the library fragments were purified with AMPure XP system (Beckman Coulter,  Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected,  adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then  PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers  and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and  library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cardiotoxin (CTX, Whiga, Shanghai), 5_week_old mice were injected with 50 µl of CTX (10 µΜ) into the tibialis anterior (TA) muscles. Plasmids were prepared by preincubating 6.25 µg pcDNA3.1 with EntransterTM-in vivo reagent (Engreen Biosystem Co,Ltd) in a final volume of 50 µl in 10% Glucose solution for 30 min. The mixture were injected the TA muscles on on days 1/2, 2 and 4. TA muscles were harvested on day 7.

value: Linc-smad7 overexpression

value: skeletal muscle


title: ROX6_1

description: root-specific overexpression


title: SAM22154279 Ubiquilin-1 KO LPS 2

description: SAM22154279 Ubiquilin-1 KO LPS 2 20 ug/mL LPS from K12 E.coli

value: C57BL/6 N


title: NT_4

description: root-specific overexpression


title: NT_1

description: root-specific overexpression


title: Linc-smad7_1


title: Control_3

source_name: Control, tibialis anterior muscle, CTX-induced muscle injury in vivo

value: control


title: Linc-smad7_2


title: ROX2_2

description: root-specific overexpression

source_name: Rcc3-OsERF48#2 (root specific promoter transgenic rice)


title: RNA_Seq_E14_d6.2_DNMT1KO_R1

value: ESC

value: Dnmt1 KO


title: Control_2


title: Control_1


title: NT_3

description: root-specific overexpression


title: ESC-ASC.r2 (RNA-Seq)

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
Paired-end RNA-seq reads were mapped to the mouse reference genome (GRCm38/mm10) with TopHat2 (https://ccb.jhu.edu/software/tophat) allowing for one mismatch. The alignments were guided by Ensembl gene models (Ensembl release 86).  Read counts for either the full transcript or the first exon only were obtained with featureCounts (http://bioinf.wehi.edu.au/featureCounts). Transcript or first exon counts were normalized, and the statistical significance of differential expression between samples was assessed using the R Bioconductor DESeq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Transcript and exon counts normalized by DESeq2 size factors were subsequently normalized by their length/1000. RNA-seq data from early mouse embryos were obtained from the European Nucleotide Archive (accession number: ERP007120), and identically processed.
Paired-end reads were further aligned to the mouse reference genome (GRCm38/mm10) with bowtie (options: “-M 1 – v2 —best – strata”). RepeatMasker annotations of transposable elements on the mouse reference genome were obtained from the UCSC genome browser table (GRCm38/mm10). Counts for all TE copies and Ensembl transcripts were obtained using featureCounts, and TE counts were subsequently processed by DESeq2 as described above, with the exception that TE counts were normalized by the total number of transcript counts instead of DESeq2 size factors.
The top 90% expressed genes (log2(normalized counts)) in the whole RNAseq dataset were used for clustering analysis. Pearson correlation analysis was performed by the R cor function with (1- Pearson correlation coefficient) as a distance metric. UHC analysis was performed by the R hclust function with the “ward” method and Euclidean distance metric. t-SNE analysis was performed using the R Rtsne function omitting an initial PCA step. PCA analysis was performed with the R prcomp function on centered and scaled log2(normalized counts) expression values. GSEA analysis was performed by the javaGSEA programme developed by the Broad Institute.
Processed data files represent count files obtained by featureCounts on ENSEMBL 86 transcripts with parameterss "-O" "--minOverlap" "10" "-p" "-C" "-M" "-B" "-t"
Genome_build: GRCm38/mm10

growth_protocol: Embryonic stem cells were cultured in different culture medium in vitro.

extract_protocol:
The RNA-seq libraries for this paper were constructed by using NEBNext Ultra Directional RNA Library Prep Kit from Illumina. After isolation of total RNA from bulk amount of mouse stem cells using RNeasy Micro Kit (QIAGEN), approximately 500ng total RNA was used to enrich mRNA with polyA tails by using NEBNext Magnetic Oligo d(T)25 beads.
After RNA fragmentation and random priming, the first strand cDNAs and second strand cDNAs were synthesized, which was followed by end repair, dA-tailing, adapter ligation and PCR enrichment. The RNA-seq libraries were sequenced on HiSeq4000 platform.

value: wild type

value: ASC converted from ESC.2iL


title: ESC-ASC.r1 (RNA-Seq)


title: ESC.r1 (RNA-Seq)

value: Naive ESC cultured in 2iL containing medium


title: ESC.r3 (RNA-Seq)

value: Naive ESC cultured in 2iL containing medium.


title: ESC.r2 (RNA-Seq)


title: ROX2_1

description: root-specific overexpression


title: EpiSC.r1 (RNA-Seq)

value: Epiblast stem cells (EpiSC)


title: EpiSC.r3 (RNA-Seq)


title: EpiSC.r2 (RNA-Seq)


title: EpiLC.r3 (RNA-Seq)

value: Epiblast-like cells (EpiLC)


title: EpiLC.r2 (RNA-Seq)


title: EpiLC.r1 (RNA-Seq)


title: AFSC.r1 (RNA-Seq)

value: Primed pluripotent stem cells cultured in Activin A and FGF2 (AFSC)


title: EpiSC.r2 (BS-Seq)

data_processing:
PBAT-reads were quality-trimmed with TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore), and 4 nt random primer sequences at the 5’ end and 1 nt at the 3’ end of all reads were removed. PBAT-reads were then mapped to the computationally bisulfite-converted mouse reference genome (GRCm38/mm10) by using Bismark (version: 0.16.3; parameter settings: ‘bismark --pbat -N 1 -L 40’). Potential PCR duplicates were removed using the deduplicate bismark command.
Post-alignment analysis was performed by using the MethPipe package. First, aligned sequences were converted to MethPipe format using the to-mr command. Methylation levels and coverage for each symmetric CpG site were calculated by the methcounts and symmetric-cpgs commands. Average CpG methylation levels of annotated genomic regions, i.e. promoters, exons, repeats, imprint control regions, CGIs, enhancers and 2 kb genomic tiles, were calculated with the MethPipe roimethstat program. Only high-confidence genomic regions with at least 40 CpG observations from reads in the region were used in further analyses.
2 kb tiles were calculated for all chromosomes with a 1 kb offset. Coordinates of promoters (-1000 bp and +100 bp from the transcription start site (TSS)), exons, introns and intergenic regions were retrieved from Ensembl (Mouse Release 86). CGI annotations were obtained from the UCSC Table Browser. Imprint control regions annotations were obtained from Tomizawa et al (2011). Tissue-specific enhancer coordinates (+/- 1000 bp from peak; mm9 coordinates were converted to mm10 by the UCSC liftOver tool) were retrieved from the Mouse Encode Project46. Hypermethylated regions and Hypomethylated regions were calculated by the hmr command from the MethPipe package.
Unsupervised hierarchical clustering of 2 kb tile methylation was performed using the R hclust command with the “ward” method. Correlation matrix was calculated by the R corrplot package. Profile plot was created by the R seqplots package. Gene ontology analysis was performed by GREAT and DAVID Bioinformatics Resource 6.8.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: The methpipe CpG.meth files are tab delimited and contain methylation level at each CpG site in the following format: <chromosome> <C lcoation> <strand> <sequence context> <methylation level> <coverage>

source_name: Epiblast stem cells

extract_protocol:
Genomic DNA (two biological replicates per condition) was extracted by QIAamp DNA Micro Kit (Qiagen).
100 ng of genomic DNA was subjected to 3.5 hours bisulfite treatment using the Methylcode Bisulfite Conversion Kit (Invitrogen). To monitor the bisulfite conversion efficiency, unmethylated Lambda DNA (0.5ng, Promega) was spiked-in before conversion. Single-stranded BS-converted DNA was subjected to the post-bisulfite adaptor tagging (PBAT) protocol as described previously. PBAT libraries were subjected to single-end 150 bp sequencing on HiSeq 4000 sequencing system (Illumina).

value: embryonic stem cells


title: ESC-ASC.r3 (RNA-Seq)


title: AFSC.r3 (RNA-Seq)


title: AFSC.r2 (RNA-Seq)


title: ASC.r2 (RNA-Seq)

value: Advanced pluripotent stem cell (ASC) derived from AFSC


title: ASC.r3 (RNA-Seq)


title: ASC.r2 (BS-Seq)

source_name: advanced pluripotent stem cell


title: EpiSC.r1 (BS-Seq)


title: ASC.r1 (RNA-Seq)

source_name: embryonic stem cells


title: ESC.r1 (BS-Seq)


title: ESC.r2 (BS-Seq)


title: M_3_Kidney_TTAGGC

city: Wanju-Gun

first: woncheoul

last: park

state: Iseo-Myeon

address: 1500 kongjwipatjwi-Ro

department: Animal genomics and Bioinformatics

institute: National Institute of Animal Science

data_processing:
Quality of RNA-seq reads from all of the kidney tissues were checked using FastQC.
Reads passed the quality control were mapped to Gallus gallus genome (Galgal4) from ENSEMBL using Hisat2 (v2.0.4).
The reads were counted using featurecount tool
The reads were nomalized using FPKM by Cufflinks
DEGs were detacted by both tools such as Cuffdiff(Cufflinks) and GLM(edgeR)
Genome_build: Galgal4
Supplementary_files_format_and_content: tab-delimited text files include raw counts of genes for each sample.

organism: Gallus gallus

source_name: kidney tissue

extract_protocol:
RNA extraction using Isol
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Preparation Guide

value: kidney

tag: breed

value: broiler

tag: calcium intake


title: M_2_Kidney_GTGAAA

tag: tissue


title: M_4_Kidney_GATCAG


title: H_1_Kidney_CGATGT


title: L_3_Kidney_CGTACG


title: H_3_Kidney_ATGTCA


title: Copper Replete Rep 1

city: Seattle

first: Serdar

last: Turkarslan

state: WA

address: 401 Terry Ave

institute: Institute for Systems Biology

data_processing:
reads were checked for technical artifacts using the FastQC software (Andrews 2010) following Illumina default quality filtering steps.
Reads were further trimmed based on base quality scores and cleaned up for adapter contamination using
trimmed based on base quality scores and cleaned up for adapter contamination using Trimmomatic (Bolger et al., 2014).
Alignment of reads to reference Nitrosopumilus maritimus (Genome Assembly ASM18465 v1.25) was performed by using STAR RNA-seq aligner software (Dobin et al., 2013) with modification of recommended parameters where appropriate.
Read counts were collected by using HTSeq package (Anders et al., 2015) followed by normalization and analysis by using DESeq2 R package (Love et al., 2014).
Genome_build: Nitrosopumilus maritimus (Genome Assembly ASM18465 v1.25)
Supplementary_files_format_and_content: Processed files are read counts that were collected by using HTSeq package (Anders et al., 2015).

organism: Nitrosopumilus maritimus SCM1

source_name: cells grown with copper perturbations

growth_protocol: Cell were grown in trace-metal depleted media using Chelex-100 resin in the presence of 1 µM 1,4,8,11-tetraazacyclotetradecane- 1,4,8,11-tetraacetic acid (TETA) to control metal speciation.

extract_protocol:
RNA isolated by mechanical shaking (5 min) with sterile glass beads using the RNeasy Qiagen kit (Qiagen) according to the manufacturer’s protocol. Residual DNA was depleted from RNA samples using the RNAqueous-4PCR kit according to the manufacturer’s instructions and ribosomal RNAs depleted of using  Illumina RiboZero rRNA removal kit (Illumina, San Diego, CA).
Samples were prepared with TrueSeq Stranded mRNA HT library preparation kit (Illumina, San Diego, CA) and sequenced using Illumina HiSeq 2000 sequencing machine with approximately 10-15 million reads per sample.

treatment_protocol: Cultures were acclimated to either Cu-replete conditions (50 nM Cu), Cu-limited (5 nM Cu) or Cu-toxic (750 nM Cu) conditions limited (5 nM Cu) or Cu-toxic (750 nM Cu) conditions

tag: perturbation

value: Copper replete

tag: cu-concentration

value: 50 nM


title: H_2_Kidney_CTTGTA


title: L_4_Kidney_ATTCCT


title: M_1_Kidney_CCGTCC


title: Copper Replete Rep 3


title: Copper Toxic Rep 3

value: Copper toxic


title: Copper Limited Rep 1

value: Copper limited

value: 5 nM


title: Copper Toxic Rep 1


title: L_1_Kidney_TAGCTT


title: Sample_Matthews_SGM25

city: Toronto

first: Stephen

last: Matthews

state: Ontario

address: 1 King's College Circle

country: Canada

institute: University of Toronto

data_processing:
Sequenced reads were aligned to cavPor3 genome assembly using TOPHAT2 and default settings
Gene read counts were generated using Genomic Alignemnts (version 1.6.3) and outliers removed using Cook's distance with default cutoffs.
Count data were normalized by residuals using RUVSeq (version 3.12.1)
Differential gene expression was assessed using EdgeR's (version 3.12.1) genral linear model likelihood ratio test and FDR-corrected p< 0.05 was considered significant.
Genome_build: cavPor3
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample- EdgeR output

organism: Cavia porcellus

source_name: F2_Beta_paraventricular nucleus

extract_protocol:
Brains were removed, flash frozen on dry ice. Paranvetricular nucleus was extracted via micro-punch. RNA was harvested using AllPrep RNA/DNA/microRNA Universal Extraction Kit (Qiagen Cat#80224).TruSeq RNA Library Preparation Kit V2 (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: generation

tag: in utero treatment

value: Beta

value: post natal day 40

value: paraventricular nucleus


title: Sample_Matthews_SGM30


title: Sample_Matthews_SGM27

source_name: F2_Control_paraventricular nucleus

value: Control


title: Sample_Matthews_SGM26


title: Sample_Matthews_SGM23


title: ASC.r1 (BS-Seq)

tag: cell type

value: wild type


title: Sample_Matthews_SGM29


title: Sample_Matthews_SGM28


title: Sample_Matthews_SGM24


title: Sample_Matthews_SGM22


title: MGC803-TREM2 rep2 RNA-seq

city: HANGZHOU

first: YULONG

last: ZHENG

state: ZHEJIANG

address: 79 Qingchun Road

department: Department of Medical Oncology

institute: the First Affiliated Hospital, School of Medicine, Zhejiang University

description:
8T-2
Overexpression of TREM2
Processed data file: processed_data_file.rpkm.txt

data_processing:
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, P-value of genes were set <0.05 to detect differential expressed ones.
Genome_build: hg38
Supplementary_files_format_and_content: processed_data_file.rpkm.txt: Tab_delimited text file includes raw counts and normalized results (RPKM).

organism: Homo sapiens

source_name: human gastric cancer cell

growth_protocol: Indicated cells were maintained in DMEM plus 10% FBS.

extract_protocol:
Total RNA was extracted using TriZol.
Next-generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).

treatment_protocol: MGC-803 cells were transfected with vector control or vector expressing TREM2. Stable cell lines were selected by treatment with G418 for two weeks.

tag: cell line

value: gastric cancer cell line

tag: transfection

value: vector expressing Trem2


title: Sample_Matthews_SGM21


title: Matthews_47_SGM_5_TechRep

source_name: F3_Control_paraventricular nucleus


title: Matthews_48_SGM_9_TechRep


title: MGC803-TREM2 rep1 RNA-seq

description:
8T-1
Overexpression of TREM2
Processed data file: processed_data_file.rpkm.txt


title: Matthews_49_SGM_21

source_name: F3_Beta_paraventricular nucleus


title: Matthews_50_SGM_22


title: Copper Toxic Rep 2


title: Sample_Matthews_SGM20

source_name: F1_Beta_paraventricular nucleus


title: MGC803-Vector rep2 RNA-seq

description:
88-2
Empty vector control
Processed data file: processed_data_file.rpkm.txt

value: vector control


title: MGC803-Vector rep1 RNA-seq

description:
88-1
Empty vector control
Processed data file: processed_data_file.rpkm.txt


title: Sample_Matthews_SGM17


title: Sample_Matthews_SGM16


title: Sample_Matthews_SGM15

source_name: F1_Control_paraventricular nucleus


title: Sample_Matthews_SGM18


title: Sample_Matthews_SGM14


title: Sample_Matthews_SGM13


title: Sample_Matthews_SGM12


title: Sample_Matthews_SGM19


title: Copper Limited Rep 3


title: Sample_Matthews_SGM8


title: Sample_Matthews_SGM10


title: Sample_Matthews_SGM11


title: Sample_Matthews_SGM5


title: Sample_Matthews_SGM6


title: Sample_Matthews_SGM9


title: Sample_Matthews_SGM3


title: Sample_Matthews_SGM4


title: Sample_Matthews_SGM1


title: Sample_Matthews_SGM7


title: Gibeaux201611_XenopusHybrid_TETSs39

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

institute: Ulsan National Institute of Science and Technology

description:
Xenopus tropicalis
TETSs39

data_processing:
Mapped paired-reads to primary transcripts with bwa mem (0.7.10)
Filtered out reads mapped on multiple targets (i.e. reads mapped on both species)
Count reads per transcripts, and transferred it to human orthologs (humanized)
Genome_build: X. laevis JGIv18 primary transcripts + X. tropicalis JGIv90 primary transcripts (available at http://www.xenbase.org)
Supplementary_files_format_and_content: count.txt - RPKM for each samples based on Xenopus transcripts
Supplementary_files_format_and_content: count.humanized.txt - RPKM for each samples based on human orthologs (the expression of X. laevis and X. tropicalis orthologs and X. laevis homeologs are combined)

organism: Xenopus tropicalis

source_name: 7 hpf whole embryo

growth_protocol: Embryos at 7 hpf were collected

extract_protocol:
Embryos were homogenize mechanically in TRIzol (Thermo Fisher Scientific, Waltham, MA) using up to a 30-gauge needle and processed according to supplier instructions. After resuspension in nuclease-free H2O, RNAs were cleaned up using RNeasy kit (Qiagen Inc.) with on-column DNA digestion, following supplier protocol.  mRNA enrichment was performed on total RNA using polyA selection with the Invitrogen Dynabeads mRNA Direct kit.
The library preparation was done on the Apollo324™ with PrepX™ RNAseq Library Prep Kits (WaferGen Biosystems, Fremont, CA), and 13 cycles of PCR amplification was used for index addition and library fragment enrichment.

value: 7 hpf


title: Gibeaux201611_XenopusHybrid_TELSs40

description:
Xenopus laevis (sperm) x Xenopus tropicalis (egg) hybrid
TELSs40

organism: Xenopus tropicalis x Xenopus laevis


title: Gibeaux201611_XenopusHybrid_TETSs37

description:
Xenopus tropicalis
TETSs37


title: Gibeaux201611_XenopusHybrid_TETSs38

description:
Xenopus tropicalis
TETSs38


title: Mutant-2

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Clean reads were obtained by removing contaminating reads, adapter sequences, poly-A tails and other artifacts.
Sequences reads were mapped to the Ginkgo biloba genome database downloaded from (http://gigadb.org/dataset/100209, Rui et al. 2016) using HISAT v2.0.4 software with default parameters.
The read counts for each gene was calculated by HTSeq v0.6.1, and then gene expression levels were estimated using FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) values.
Genome_build: http://gigadb.org/dataset/100209
Supplementary_files_format_and_content: The tab-delimited text files files include genes read count and fpkm values for each sample (.txt)

organism: Ginkgo biloba

source_name: Yellow-green stripe leaves

growth_protocol: Healthy leaves were collected from Ginkgo biloba growing under natural conditions at Yangzhou University, Yangzhou, China (32.39°N, 119.42°E).

extract_protocol:
The leaves of mutant and normal green leaves from the developmental stage (May) were used for RNA isolation. Total RNAs were extracted using TaKaRa MiniBEST plant RNA extraction kit (TaKaRa Bio Inc., Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

value: leaf color mutant

tag: development stages

value: Rapid development stage (May)

value: Yellow-green stripe leaves


title: Gibeaux201611_XenopusHybrid_TELSs41

description:
Xenopus laevis (sperm) x Xenopus tropicalis (egg) hybrid
TELSs41


title: Mutant-1


title: Microdissected cTAL, Single-tubule RNA-Seq, transcriptome 02

status: Public on Oct 31 2017

first: Lihe

last: Chen

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
Sequenced reads were mapped to Ensembl mouse gene set (GRCm38.p5) using STAR v2.5.1b
Transcript abundances in TPM were caculated by  RSEM/1.2.31
Single-cell RNA-seq data analysis were carried out using Seurat package
Genome_build: GRCm38.p5 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

growth_protocol: Male mice were grown and maintained in the Animal Facility of the NHLBI. 2 month-old mice were used in the experiments.

extract_protocol:
Cells at 500-700 cells/ul were loaded to C1 IFC, single cell was captured in each champer. After cell lysis, reverse transcription, and PCR on the C1 system, cDNAs were harvested from each IFC outlet. For single-tubule RNA-Seq, the CCDs and cTALs were manually dissected in ice-cold Burg solution under a Wild M8 dissection stereomicroscope equipped with on-stage cooling. After washes in ice-cold PBS (2 times), the microdissected tubules were transferred to Trizol reagent for RNA extraction and cDNA generation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

value: Kidney


title: Microdissected cTAL, Single-tubule RNA-Seq, transcriptome 03


title: Microdissected cTAL, Single-tubule RNA-Seq, transcriptome 06


title: Microdissected cTAL, Single-tubule RNA-Seq, transcriptome 07


title: Microdissected cTAL, Single-tubule RNA-Seq, transcriptome 08


title: Microdissected cTAL, Single-tubule RNA-Seq, transcriptome 05


title: Microdissected cTAL, Single-tubule RNA-Seq, transcriptome 01


title: Sample_Matthews_SGM2

tag: age


title: Microdissected CCD, Single-tubule RNA-Seq, transcriptome 11


title: Microdissected CCD, Single-tubule RNA-Seq, transcriptome 08


title: Microdissected CCD, Single-tubule RNA-Seq, transcriptome 05


title: Microdissected CCD, Single-tubule RNA-Seq, transcriptome 10


title: Microdissected CCD, Single-tubule RNA-Seq, transcriptome 06


title: Microdissected CCD, Single-tubule RNA-Seq, transcriptome 03


title: Microdissected CCD, Single-tubule RNA-Seq, transcriptome 07


title: Microdissected CCD, Single-tubule RNA-Seq, transcriptome 02


title: Microdissected CCD, Single-tubule RNA-Seq, transcriptome 04


title: Microdissected CCD, Single-tubule RNA-Seq, transcriptome 01


title: Microdissected cTAL, Single-tubule RNA-Seq, transcriptome 04


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 19

data_processing:
Sequenced reads were mapped to Ensembl mouse gene set (GRCm38.p5) using STAR v2.5.1b
Transcript abundances in TPM were caculated by  RSEM/1.2.31
Single-cell RNA-seq data analysis were carried out using Seurat package
GRCm38.p5 (Ensembl)
Genome_build: tab-delimited text files include TPM values for each cell

source_name: Kidney

extract_protocol:
Cells at 500-700 cells/ul were loaded to C1 IFC, single cell was captured in each champer. After cell lysis, reverse transcription, and PCR on the C1 system, cDNAs were harvested from each IFC outlet.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male mice were grown and maintained in the Animal Facility of the NHLBI. 2 month-old mice were used in the experiments.

tag: facs antibody

value: c-Kit


title: Gibeaux201611_XenopusHybrid_TELSs42

description:
Xenopus laevis (sperm) x Xenopus tropicalis (egg) hybrid
TELSs42

tag: developmental stage


title: Bulk RNA-Seq c-Kit rep2

tag: strain


title: Microdissected CCD, Single-tubule RNA-Seq, transcriptome 09


title: Bulk RNA-Seq DBA rep1

value: DBA


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 17


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 18


title: Green leaf-1

source_name: Green leaves

value: normal control

value: Green leaves


title: Bulk RNA-Seq DBA rep2


title: Green leaf-2


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 15


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 14


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 16


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 12


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 09

value: DBA + c-Kit


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 11


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 10


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 08


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 06


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 05


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 04


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 01


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 03


title: Principal cell, single-cell RNA-Seq, transcriptome 74


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 02


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 07


title: Principal cell, single-cell RNA-Seq, transcriptome 73


title: Bulk RNA-Seq c-Kit rep1


title: Principal cell, single-cell RNA-Seq, transcriptome 72


title: Principal cell, single-cell RNA-Seq, transcriptome 71


title: Principal cell, single-cell RNA-Seq, transcriptome 67


title: Principal cell, single-cell RNA-Seq, transcriptome 70


title: Principal cell, single-cell RNA-Seq, transcriptome 66


title: Principal cell, single-cell RNA-Seq, transcriptome 65


title: Principal cell, single-cell RNA-Seq, transcriptome 69


title: Principal cell, single-cell RNA-Seq, transcriptome 64


title: Proximal tubule cell, single-cell RNA-Seq, transcriptome 13


title: Principal cell, single-cell RNA-Seq, transcriptome 63


title: Principal cell, single-cell RNA-Seq, transcriptome 61


title: Principal cell, single-cell RNA-Seq, transcriptome 59


title: Principal cell, single-cell RNA-Seq, transcriptome 62


title: Principal cell, single-cell RNA-Seq, transcriptome 57


title: Principal cell, single-cell RNA-Seq, transcriptome 58


title: Principal cell, single-cell RNA-Seq, transcriptome 56


title: Principal cell, single-cell RNA-Seq, transcriptome 55


title: Principal cell, single-cell RNA-Seq, transcriptome 53


title: Principal cell, single-cell RNA-Seq, transcriptome 51


title: Principal cell, single-cell RNA-Seq, transcriptome 50


title: Principal cell, single-cell RNA-Seq, transcriptome 47


title: Principal cell, single-cell RNA-Seq, transcriptome 49


title: Principal cell, single-cell RNA-Seq, transcriptome 46


title: Principal cell, single-cell RNA-Seq, transcriptome 48


title: Principal cell, single-cell RNA-Seq, transcriptome 54


title: Principal cell, single-cell RNA-Seq, transcriptome 45


title: Principal cell, single-cell RNA-Seq, transcriptome 68


title: Principal cell, single-cell RNA-Seq, transcriptome 43


title: Principal cell, single-cell RNA-Seq, transcriptome 44


title: Principal cell, single-cell RNA-Seq, transcriptome 42


title: Principal cell, single-cell RNA-Seq, transcriptome 39


title: Principal cell, single-cell RNA-Seq, transcriptome 40


title: Principal cell, single-cell RNA-Seq, transcriptome 37


title: Principal cell, single-cell RNA-Seq, transcriptome 35


title: Principal cell, single-cell RNA-Seq, transcriptome 38


title: Principal cell, single-cell RNA-Seq, transcriptome 41


title: Principal cell, single-cell RNA-Seq, transcriptome 36


title: Principal cell, single-cell RNA-Seq, transcriptome 60


title: Principal cell, single-cell RNA-Seq, transcriptome 34


title: Principal cell, single-cell RNA-Seq, transcriptome 33


title: Principal cell, single-cell RNA-Seq, transcriptome 31


title: Principal cell, single-cell RNA-Seq, transcriptome 32


title: Principal cell, single-cell RNA-Seq, transcriptome 30


title: Principal cell, single-cell RNA-Seq, transcriptome 52


title: Principal cell, single-cell RNA-Seq, transcriptome 27


title: Principal cell, single-cell RNA-Seq, transcriptome 28


title: Principal cell, single-cell RNA-Seq, transcriptome 29


title: Principal cell, single-cell RNA-Seq, transcriptome 26


title: Principal cell, single-cell RNA-Seq, transcriptome 20


title: Principal cell, single-cell RNA-Seq, transcriptome 25


title: Principal cell, single-cell RNA-Seq, transcriptome 23


title: Principal cell, single-cell RNA-Seq, transcriptome 22


title: Principal cell, single-cell RNA-Seq, transcriptome 21


title: Principal cell, single-cell RNA-Seq, transcriptome 17


title: Principal cell, single-cell RNA-Seq, transcriptome 18


title: Principal cell, single-cell RNA-Seq, transcriptome 14


title: Principal cell, single-cell RNA-Seq, transcriptome 24


title: Principal cell, single-cell RNA-Seq, transcriptome 16


title: Principal cell, single-cell RNA-Seq, transcriptome 13


title: Principal cell, single-cell RNA-Seq, transcriptome 11


title: Principal cell, single-cell RNA-Seq, transcriptome 10


title: Principal cell, single-cell RNA-Seq, transcriptome 15


title: Principal cell, single-cell RNA-Seq, transcriptome 09


title: Principal cell, single-cell RNA-Seq, transcriptome 08


title: Principal cell, single-cell RNA-Seq, transcriptome 07


title: Principal cell, single-cell RNA-Seq, transcriptome 04


title: Principal cell, single-cell RNA-Seq, transcriptome 05


title: Principal cell, single-cell RNA-Seq, transcriptome 03


title: Principal cell, single-cell RNA-Seq, transcriptome 06


title: Principal cell, single-cell RNA-Seq, transcriptome 01


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 31


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 30


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 32


title: Principal cell, single-cell RNA-Seq, transcriptome 19


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 28


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 29


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 27


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 25


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 24


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 23


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 22


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 19


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 20


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 16


title: Principal cell, single-cell RNA-Seq, transcriptome 12


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 26


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 15


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 18


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 14


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 13


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 12


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 17


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 10


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 07


title: Principal cell, single-cell RNA-Seq, transcriptome 02


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 08


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 11


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 06


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 03


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 04


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 05


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 21


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 02


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 01


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 21

value: PNA


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 23


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 20


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 22


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 17


title: Non-epithelial cell, single-cell RNA-Seq, transcriptome 09


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 14


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 12


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 15


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 16


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 13


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 10


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 07


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 09


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 18


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 11


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 05


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 02


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 04


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 03


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 01


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 87


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 84


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 83


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 79


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 85


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 19


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 08


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 76


title: Type B intercalated cell, single-cell RNA-Seq, transcriptome 06


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 75


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 73


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 72


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 71


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 70


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 67


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 74


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 63


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 86


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 61


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 64


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 62


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 60


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 66


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 65


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 81


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 80


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 82


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 77


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 59


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 58


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 78


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 57


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 56


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 55


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 69


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 68


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 54


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 53


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 51


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 48


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 45


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 52


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 49


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 46


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 47


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 41


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 39


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 44


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 43


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 40


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 42


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 37


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 38


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 35


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 36


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 32


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 34


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 33


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 31


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 30


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 25


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 26


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 50


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 28


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 27


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 24


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 23


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 22


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 21


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 20


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 18


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 17


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 16


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 19


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 15


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 13


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 14


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 11


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 10


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 12


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 09


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 08


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 07


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 29


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 06


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 05


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 02


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 04


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 01


title: Type A intercalated cell, single-cell RNA-Seq, transcriptome 03


title: FFPE-2

city: Goyang

first: Young-Ki

last: Bae

state: Gyeonggi

address: 323 Ilsan-ro

department: Research Institute

institute: National Cancer Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to danRer10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: danRer10
Supplementary_files_format_and_content: FFPE-1.txt and FFPE-2.txt report quantile-normalized abundance measurements.
Supplementary_files_format_and_content: WT.txt report quantile-normalized abundance measurements.  Column WT1 reports quantile-normalized abundance measurements after quantile-  normalization had done between WT and FFPE-1.  Column WT2 reports quantile-normalized abundance measurements after quantile-  normalization had done between WT and FFPE-2.

organism: Danio rerio

source_name: tumor 2 induced by rb1 TALENs

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: tumor tissues 2 induced by rb1 TALENs

value: 5 month post fertilization


title: WT

source_name: whole brain

value: AB

value: whole brain


title: FFPE-1

source_name: tumor 1 induced by rb1 TALENs

value: tumor tissues 1 induced by rb1 TALENs