title: QscR-1_HLR15

description:
qscR_RNA_seq_analyzed.XLSX
HLR15

extract_protocol:
To examine the effect of MvfR,RhlR and QscR on the transcriptome, 2 ml of mid-log-phase (OD600= 0.6) bacterial cultures (PAO1 and ∆MvfR/∆RhlR or ∆QscR strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the TruSeq RNA sample prep kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina). Bacterial RNA-seq reads were mapped to the P. auruginosa genome by using STAR (version 2.6), with two mismatches allowed. Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using R package DESeq2.  The each sample in RNA-seq assay was repeated twice.
TruSeq RNA sample prep kit protocol (Illumina)

value: qscR mutant


title: H3K4me3_WT_ChIPSeq

status: Public on Jul 16 2019

type: SRA

city: Beijing

first: Xiaozhong

last: Peng

address: No.5, Dongdan Santiao, Dongcheng District

department: Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

country: China

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

library_source: genomic

data_processing:
The 150-nt sequence reads generated by Illumina sequencing were mapped to the genome using the Burrows-Wheeler Aligner algorithm with default settings.Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the mouse genome (mm10) were used in the subsequent analysis
For identifying intervals over input control, the MACS cutoff for the false discovery rate after controlling for significance was P=1×10 –7.
The two main peak callers used at this study are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig. Files with extension *.bw. Binary files that can be opened in or uploaded to genome browsers and show the fragment density for 32-nt bins along the genome (“signal map”)

molecule: genomic DNA

organism: Mus musculus

source_name: dorsal cortex

extract_protocol:
Lysates were clarified from sonicated nuclei of E14.5 dorsal cortex and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions

tag: strain

tag: tissue

value: dorsal cortex

tag: age

tag: genotype

value: WT

tag: chip antibody


title: QscR-2_HLR16

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
qscR_RNA_seq_analyzed.XLSX
HLR16

library_source: transcriptomic

data_processing:
Bacterial RNA-seq reads were mapped to the P. auruginosa genome by using STAR (2.6), with two mismatches allowed
Only the uniquely mapped reads were kept for the subsequent analyses.
The gene differential expression analysis was performed using DESeq2 R package
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: xls file containing comparisons between MvfR, RhlR and QscR mutant and wild-type, respectively

molecule: total RNA

organism: Pseudomonas aeruginosa PAO1

source_name: liquid culture in LB (Luria-Bertani)  medium

treatment_protocol: grow until mid-log phase in LB


title: Epididymal_adipose_fibroblasts_2

city: South San Francisco

first: Shannon

last: Turley

state: California

address: 1 DNA Way, Building 15, MS 231b

department: Cancer Immunology

country: USA

institute: Genentech

data_processing: Reads were aligned to the GRCm38 genome using Salmon. The Salmon index was created using the parameter, k = 25. Gene models were from our internal database. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

molecule: polyA RNA

extract_protocol: RNA was isolated from TRIZOL as described (Painter et al., 2011).

tag: group

value: EpiAdipose

tag: region

tag: pdgfra

value: PDGFRApos

tag: gfp

value: GFPneg


title: ZEN_high_u rep3

city: Tulln

first: Bertrand

last: Grenier

address: Technopark 1

department: Research Center

country: Austria

institute: BIOMIN

description:
99; 5307-011
processed data file: data_ref_5307_Pool1_Uterus.xlsx

data_processing:
Raw data were de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina)
Total reads were adapter trimmed using Cutadapt and quality filtered (Q-Score > 30) using the FastQC tool v0.10.1
Trimmed and quality filtered reads were aligned to reference microRNA sequences in miRBase release 21 (www.mirbase.org) using bowtie2 v2.2.6. Subsequently, reads were mapped against the Sus scrofa genome assembly Sscrofa10.2 as well as Ensembl small non-coding RNA reference databases
Reads were normalized to the total read count per library to generate tags per million (TPM) values
EdgeR was used for differential expression analysis based on TPM values. The p-values obtained were adjusted for multiple testing using Benjamini-Hochberg false discovery rate (FDR).
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: abundance measurements & expression analysis

organism: Sus scrofa

extract_protocol:
Approximately 30 mg of tissue were disrupted via a bead-beating step, and the total RNA, including RNA from approximately 18 nucleotides upwards, was extracted and purified with the miRNeasy Mini Kit (Qiagen).
1 µg of total RNA was used for construction of small RNA sequencing libraries with the NEBNext Multiplex Small RNA Library preparation set for Illumina (New England Biolabs Inc.). Adapter ligated total RNA was reverse transcribed into cDNA, which served as template for PCR amplification (15 cycles) using Illumina´s SR Primer and Index Primers 1-18. Barcoded DNA libraries were purified using the QIAQuick PCR purification protocol (Qiagen) and quantified by DNA 1000 high sensitivity chip (Agilent Technologies). Purified samples were pooled at equimolar (50 nM) concentration. Size selection was performed using gel purification to select for insert sizes between 18 and 50 nucleotides.

treatment_protocol: Small pieces of the uterus and the mid-jejunum were dissected, placed into 1 mL of RNAlater (Ambion Inc.), stored overnight at 4 °C, and transferred to -80 °C until transcriptomics analysis

value: post weaned day 28

tag: treatment

value: 4.58 mg/kg ZEN (ZEN medium) for 28 days

value: uterus

tag: molecule subtype

value: small RNA


title: Epididymal_adipose_fibroblasts_1


title: Epididymal_adipose_fibroblasts_3


title: ZEN_low_u rep3

description:
45_A; 5307-012
processed data file: data_ref_5307_Pool1_Uterus.xlsx

value: 0.17 mg/kg ZEN (ZEN medium) for 28 days


title: Inguinal_adipose_fibroblasts_3

value: IngAdipose


title: Control_u rep4

description:
8; 5307-009
processed data file: data_ref_5307_Pool1_Uterus.xlsx

value: uncontaminated feed (Control) for 28 days


title: RhlR-1_HLR5

description:
rhlR_RNA_seq_analyzed.XLSX
HLR5

value: rhlR mutant


title: RhlR-2_HLR6

description:
rhlR_RNA_seq_analyzed.XLSX
HLR6


title: Control_u rep3

description:
117; 5307-008
processed data file: data_ref_5307_Pool1_Uterus.xlsx


title: E16.5_376_5_KO

description:
E16.5_featureCounts.txt
E16.5_condition.DESeq2_results_allgenes

data_processing:
Read mapping statistics were obtained from STAR (v2.5.2b)
Fragment assignment statistics obtained from featureCounts in the Subread software packages
Differential gene expression analysis was performed through DESeq2 (v1.14.1)
Genome_build: mm10
Supplementary_files_format_and_content: The output of featureCounts program reports read counts for each gene in each library in a tab-delimited file;The CSV file reports the Gene ID, Gene Symbol with normalized fragment counts for each sample, normalized sum of fragment counts for each group of samples under comparison and the statistics obtained from DESeq2 for each gene.

extract_protocol:
RNA was isolated from E14.5 and E16.5 dorsal cortices with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80°C.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ash2l cKO


title: E16.5_378_2_KO


title: Epididymal_adipose_mesothelial_cells_2

value: PDGFRAneg


title: E16.5_378_1_WT


title: Epididymal_adipose_mesothelial_cells_3


title: CK-1_HLR12

description:
qscR_RNA_seq_analyzed.XLSX
HLR12

extract_protocol:
2 ml of mid-log-phase (OD600= 0.6) bacterial cultures (PAO1 and ∆rpoN strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the TruSeq RNA sample prep kit protocol (Illumina).
TruSeq RNA sample prep kit protocol (Illumina)


title: ZEN_medium_u rep2

description:
2; 5307-007
processed data file: data_ref_5307_Pool1_Uterus.xlsx

value: 1.46 mg/kg ZEN (ZEN medium) for 28 days


title: MvfR-2_HLR4

description:
mvfR_RNA_seq_analyzed.XLSX
HLR4

value: mvfR mutant


title: WT_3

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential gene expression analysis was performed through DESeq2 (v1.16.1)
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.

source_name: primary neurosphere derived from dorsal cortex

growth_protocol: NPCs were isolated from E14.5 mice by dissection of the lateral walls of the lateral ventricles and digested into single cell suspension with Accutase (Sigma). Cells were cultured in DMEM/F12 proliferation medium supplemented with 2% B27 supplement, 20 ng/ml EGF, 20 ng/ml bFGF and 0.2% BSA for proliferation.

extract_protocol:
Neurosphere RNA isolated from the 6th day culturing NPCs dissected from E14.5 mice.
A total amount of 3 µg RNAper sample was used as input material for the RNAsample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: MvfR-1_HLR3

description:
mvfR_RNA_seq_analyzed.XLSX
HLR3


title: ZEN_low_u rep1

description:
136_B; 5307-006
processed data file: data_ref_5307_Pool1_Uterus.xlsx


title: E16.5_354_2_KO

value: dorsal cortex


title: E16.5_376_8_WT

value: WT


title: Epididymal_adipose_mesothelial_cells_1

value: EpiAdipose


title: CK-2_HLR2

description:
mvfR_RNA_seq_analyzed.XLSX
HLR2


title: ZEN_high_u rep2

description:
85; 5307-005
processed data file: data_ref_5307_Pool1_Uterus.xlsx


title: Control_u rep2

description:
116_A; 5307-004
processed data file: data_ref_5307_Pool1_Uterus.xlsx


title: ZEN_low_u rep2

description:
50_A; 5307-010
processed data file: data_ref_5307_Pool1_Uterus.xlsx


title: Bone_associated_fibroblasts_1

value: Bone

value: bone

value: PDGFRApos


title: E14.5_355_4_KO

description:
E14.5_featureCounts.txt
E14.5_condition.DESeq2_results_allgenes


title: Bone_associated_fibroblasts_2

value: GFPneg


title: CK-1_HLR1

description:
mvfR_RNA_seq_analyzed.XLSX
HLR1


title: E16.5_354_4_WT


title: E14.5_355_2_WT


title: Control_u rep1

description:
71; 5307-003
processed data file: data_ref_5307_Pool1_Uterus.xlsx

value: post weaned day 28

value: uterus


title: E14.5_351_4_KO


title: Brown_adipose_fibroblasts_3

value: BrnAdipose


title: ZEN_high_u rep1

description:
43; 5307-002
processed data file: data_ref_5307_Pool1_Uterus.xlsx

value: 4.58 mg/kg ZEN (ZEN medium) for 28 days

value: small RNA


title: Dam_SG_SetDB1-KO_3

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

description:
control sample for Su(var)3-9_SG_SetDB1-KO
Su(var)3-9_SetDB1-KO_Females_SG_at_FDR_0.05_probability_track.wig

data_processing:
The reads obtained were mapped to BDGP R6/dm5 Drosophila genome assembly using MOSAIK software with following parameters: -m all -mmp 0.1 -act 20 -a single
For further analysis, only the reads that started with GATC sequence were retained. The number of reads for each genomic fragment between the neighboring GATC sites (GATC fragments) was summed up.
The data were filtered for reproducibility: all GATC fragments were sorted according to the total read count in two biological samples. This list was binned into groups of 200 fragments having similar read counts. For each GATC fragment, a difference in read counts was calculated between the replicates. Those fragments that showed the difference above 2 standard deviations in the particular group were filtered out.
Genome_build: BDGP R6/dm5
Supplementary_files_format_and_content: wig files containing scores for each GATC fragment of the genome. Score represents -Log10(P), where P is significance level assessed with exact Fisher’s test for each GATC region in the genome. Positive values were ascribed to GATC fragments enriched in Dam-X sample, while negative values to those enriched in Dam-alone sample.

organism: Drosophila melanogaster

source_name: salivary glands

growth_protocol: The flies were kept at 23°C

extract_protocol:
50 egg chambers were dissected for each sample.
DNA was isolated using phenol-chloroform method. 300ng of genomic DNA was digested by DpnI endonuclease. Digested DNA was ligated with double-stranded DNA adapters and then digested with DpnII endonuclease. Next, methylated fragments were selectively amplified using adapter-specific primer. Before the preparation of libraries for Illumina DamID-seq, the adapters used in DamID procedure were cut with DpnII enzyme. No further fragmentation was performed.

value: SetDB1 mutant

tag: developmental stage


title: Dam_SG_SetDB1-KO_2


title: E14.5_351_1_WT


title: ZEN_medium_u rep1

description:
115_A; 5307-001
processed data file: data_ref_5307_Pool1_Uterus.xlsx


title: Dam_SG_SetDB1-KO_1


title: Bone_associated_fibroblasts_3


title: Brown_adipose_fibroblasts_2


title: Brown_adipose_fibroblasts_1


title: Su(var)3-9_SG_SetDB1-KO_3

description: Su(var)3-9_SetDB1-KO_Females_SG_at_FDR_0.05_probability_track.wig


title: E14.5_248_2_KO

value: Ash2l cKO


title: ZS97_RNAPII_Rep2

city: Wuhan

first: Shuangqi

last: Wang

state: Hubei

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

data_processing:
ChIA-PET data was processed with updated ChIA-PET Tool software,a JAVA-based package for automatic processing of ChIA-PET sequence data, including linker filtering, read mapping, redundancy removal, protein binding sites and chromatin interaction identification.
Genome_build: MH63
Supplementary_files_format_and_content: Tab-delimited bed file for interactions

organism: Oryza sativa Indica Group

source_name: young leaf

growth_protocol: Two rice varieties, ZS97 and MH63 (the parents of one of the most widely cultivated rice hybrids in China, Shanyou 63. The germinating seeds were collected by soaking dry seeds in water for 72 h at 37 °C. The germinated seeds were grown in a phytotron with the day/night cycle set at 14 h/10 h and a temperature of 32 °C/28 °C. Young leaves of 2-week-old seedlings were collected and immediately cross-linked.

extract_protocol: Rice long-read ChIA-PET libraries were constructed with a modified ChIA-PET method, rice tissues were dual cross-linked with formaldehyde and ethylene glycol bis (succinimidylsuccinate) (Thermo Fisher Scientific, 21565).

tag: cultivar

value: Zhenshan 97

tag: data type

value: ChIA-PET

tag: antibody


title: HC_24h replicate2

city: Qingdao

first: Jian

last: Xu

state: Shandong province

address: No.189 Songling Rd, LaoShan District

department: BEGC

institute: QIBEBT-CAS

description:
nuclear RNA
HC24-FPKM.txt

data_processing:
To ensure quality, the raw data (2×90bpPE reads) was modified by following 2 steps: first the adapter pollutions in reads were deleted, and then because the sequence qualities of Illumina reads degrade quickly toward the 3’ end, all reads were trimmed from the 3’ end until the 3’-end-most position with Phred-equivalent score was 20 or greater. These filtered Illumina reads with 75bp length were aligned to the N.oceanica draft genome with Tophat (version 2.0.4, allowed no more than two segment-mismatches) and reads mapped to more than one location were excluded. Thirdly, the short read mapping results from TopHat was used for the following differential gene expression analysis with Cufflinks (version 2.0.2).
Genome_build: de novo assembly of Nannochloropsis oceanica IMET1, please access to our website: http://www.bioenergychina.org/fg/d.wang_genomes/ .
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of two replicates

organism: Nannochloropsis oceanica

source_name: whole cells

growth_protocol: Nannochloropsis oceanica IMET1 was inoculated into modified f/2 liquid medium, which was prepared as follows:35 g/l sea salt, 1 g/l NaNO3, 67 mg/1 NaH2PO4*H2O, 3.65 mg/l FeCl3*6H2O, 4.37 mg/l Na2EDTA*2H2O, trace metal mix (0.0196 mg/l CuSO4*5H2O, 0.0126 mg/l NaMoO4*2H2O, 0.044 mg/l ZnSO4*7H2O, 0.01mg/l CoCl2, 0.36 mg/l MnCl2*4H2O) and vitamin mix(5 mg/l VB12, 5 mg/l Biotin and 1 mg/l Thiamine HCl). The cells were grown in liquid cultures under continuous light (approximately 80±5 µmol photons m-2 s-1) at 25℃ and aerated by bubbling with a mixture of 5% CO2 in air or 0.01% CO2.

extract_protocol: Algal total RNAs under the above conditions were extracted using Trizol reagents (Invitrogen). For RNA-Seq, the poly (A) containing mRNA molecules were purified using Sera-mag Magnetic Oligo(dT) Beads (Thermo Scientific) and was fragmented into 200- to 300-bp fragments by incubation in RNA Fragmentation Reagent (Ambion)according to the manufacturer’s instructions. The fragmented mRNA was then purified away from the fragmentation buffer by Agencourt®RNAClean beads (Beckman Coulter). The purified, fragmented mRNA was then converted into double-stranded cDNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) by priming with random hexamers. Strand nonspecific transcriptome libraries were prepared using NEBNext® mRNA Library Prep Reagent Set(New England Biolabs) and sequenced for 2×90bprun(paired-end, PE) using Illumina HiSeq2000.

treatment_protocol: Nannochloropsis oceanica IMET1 cells were grown in liquid cultures under continuous light (approximately 80±5 µmol photons m-2 s-1) at 25℃ and aerated by bubbling with a mixture of 5% CO2 in air. Mid-logarithmic phase algal cells were collected and washed three times with axenic seawater. Equal numbers of cells were re-inoculated in fresh medium and cultured under 5% CO2 for preadaption for one hour, and then two samples (from biological replicates) were collected as 0h samples. After the preadaption for one hour, half of them were sequentially grown under 5% in air (High carbon or HC) and other half of them were grown under 0.01% CO2   (Very low carbon or VLC) with 80±5 µmol m-2 s-1 light intensity, respectively. Cell aliquots were collected for RNA isolation after being transferred to the designated conditions for 3h, 6h, 12h and 24h. Three biological replicates of algal cultures were established under each of the above “VLC” and “HC” conditions, respectively. Two biological replicates were randomly selected to prepare mRNA-Seq library. In total, 18 samples collected at 5 time points (0h, 3h, 6h, 12h, and 24h) were used for mRNA-Seq library preparation and then submitted to Illumina HiSeq 2000 for sequencing.


title: Su(var)3-9_SG_SetDB1-KO_1


title: E14.5_248_6_WT


title: ZS97_RNAPII_Rep1


title: ZS97_H3K9me2_Rep2


title: Su(var)3-9_SG_SetDB1-KO_2


title: Dam_juv-Ovary_SetDB1-KO_2

description:
control sample for Su(var)3-9_juv-Ovary_SetDB1-KO
Su(var)3-9_ovaries_SetDB-KO_at_FDR_0.05_probability_track.wig

source_name: ovaries

value: adult


title: ZS97_H3K9me2_Rep1


title: HC_24h replicate1

description:
nuclear RNA
HC24-FPKM.txt


title: VLC_24h replicate1

description:
nuclear RNA
VLC24-FPKM.txt


title: MH63_RNAPII_Rep2

value: Minghui 63


title: Su(var)3-9_juv-Ovary_SetDB1-KO_2

description: Su(var)3-9_ovaries_SetDB-KO_at_FDR_0.05_probability_track.wig


title: HC_12h replicate2

description:
nuclear RNA
HC12-FPKM.txt


title: ZS97_H3K4me3_Rep1


title: ZS97_H3K4me3_Rep2


title: KU-treated 9 days activated NK cells biological replicate 2

type: RNA

city: Stanford

first: Maite

last: Alvarez

address: CCSR 269 Campus Drive Room 2210

institute: Stanford University

hyb_protocol: A total of 20 μg of biotinylated cRNA was fragmented and hybridized to Affymetrix murine Mouse Gene 2.0ST (ThermoFisher Scientific Inc.)

scan_protocol: Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running Affymetix GeneChip Command Console (AGCC) Software at the Protein and Nucleic Acid Facility (Stanford University).

data_processing: The microarray data were analyzed using the Affymetrix Transcriptome Analysis Console. Microarray probe intensity values (CEL files) were background-corrected, summarized and normalized using the Robust Multi-array Average (RMA16) algorithm 32 and subsequently filtered on raw intensity for data in the upper 20-100th percentile using the Expression Suite Software version 1.1 (ThermoFisher Scientific Inc.).

label: biotin

source_name: Ex vivo bone marrow derived IL-2 activated NK cells

label_protocol: RNA (150–300 ng) was used for generating biotinylated cRNA through single-round amplification using the MessageAmpIII RNA Amplification kit following the manufacturer’s recommendations (Ambion, ThermoFisher Scientific Inc.).

growth_protocol: Single-cell suspensions from bone marrow (BM) of mice were T-cell-depleted using CD90 positive selection kit (StemCell Technology, Vancouver) according to manufacturer’s instructions and cultured in RPMI complete media at 37°C with 5% CO2 and with 1000 IU/mL of IL-2. . Activated lymphocyte adherent killer cells were collected at multiple time points (day 0: control, day 4: acute and day 9: chronic). IL-2 was added again after 4 days of activation in the case of longer activation times

extract_protocol: RNA from freshly isolated NK cells or activated adherent NK cells was extracted using RNeasy Mini kit (Qiagen) with on-column DNase step (Qiagen) per the manufacturer’s instructions.

treatment_protocol: On day 4 of activation, cells were treated with 7.5 μM of KU55933 (Calbiochem EMD Millipore, Hayward, CA) or vehicle control.

tag: cell type

value: NK

tag: days of activation

tag: ku treatment

value: YES


title: VLC_24h replicate2

description:
nuclear RNA
VLC24-FPKM.txt

tag: strain


title: Su(var)3-9_juv-Ovary_SetDB1-KO_1


title: 9 days activated NK cells biological replicate 2

value: NO


title: KU-treated 9 days activated NK cells biological replicate 1


title: MH63_RNAPII_Rep1


title: MH63_H3K9me2_Rep2


title: HC_12h replicate1

description:
nuclear RNA
HC12-FPKM.txt


title: MH63_H3K9me2_Rep1


title: Dam_juv-Ovary_1

description:
control sample for Su(var)3-9_juv-Ovary
Su(var)3-9_Juv_ovaries_at_FDR_0.05_probability_track.wig

value: yw


title: Dam_juv-Ovary_2


title: VLC_12h replicate1

description:
nuclear RNA
VLC12-FPKM.txt


title: VLC_12h replicate2

description:
nuclear RNA
VLC12-FPKM.txt


title: Su(var)3-9_juv-Ovary_2

description: Su(var)3-9_Juv_ovaries_at_FDR_0.05_probability_track.wig


title: MH63_H3K4me3_Rep2


title: Dam_juv-Ovary_SetDB1-KO_1


title: 4 days activated NK cells biological replicate 1


title: 4 days activated NK cells biological replicate 2


title: 9 days activated NK cells biological replicate 1


title: Su(var)3-9_juv-Ovary_1


title: HC_6h replicate2

description:
nuclear RNA
HC6-FPKM.txt


title: GPRC5AKO#2_rep3

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

data_processing:
Sequence data were mapped on the mouse genome (hg38) using Tophat v2.0.22(Linux).
For TMM, gene counts were performed with featureCounts v1.4.6(Linux).
Differential comparison was performed with R program v3.4.2, package TCC v1.18.0 and package edgeR v3.20.1. tmm normalization was done by iDEGES/edgeR.
Genome_build: hg38

organism: Homo sapiens

growth_protocol: Cultured in Ham's F-12K medium supplemented with 7% fetal bovine serum and antibiotic. Cells were cultured at 37 degree under 5% CO2 conditions.

extract_protocol:
Total RNA was extracted with ISOGEN (Nippongene, Japan) and RNeasy spin column kit (Qiagen, USA) followed by treatment with DNase I (Qiagen, USA). RNA samples with RNA integrity number (RIN) greater than 8 were normalized to 100 ng/μl before further analyses.
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego CA) according to the manufacturer's instructions and subsequently validated for an average size of about 300-310 bp using a Bioanalyzer and the Agilent DNA1000 kit for the construction of sequencing libraries.

tag: cell line background

value: prostatic adenocarcinoma cell line

tag: cell form

value: epithelial-like

tag: genotype/variation

value: GPRC5A knockout


title: GPRC5AKO#2_rep2


title: HC_6h replicate1

description:
nuclear RNA
HC6-FPKM.txt


title: VLC_6h replicate2

description:
nuclear RNA
VLC6-FPKM.txt


title: Naïve NK cells biological replicate 2


title: VLC_6h replicate1

description:
nuclear RNA
VLC6-FPKM.txt


title: GPRC5AKO#2_rep1


title: HC_3h replicate2

description:
nuclear RNA
HC3-FPKM.txt


title: HC_3h replicate1

description:
nuclear RNA
HC3-FPKM.txt


title: VLC_3h replicate2

description:
nuclear RNA
VLC3-FPKM.txt


title: MH63_H3K4me3_Rep1


title: Hippocampus  SAHA and Tadalafil, Biological replica 1

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

description: B6.Cg-Tg(APPswe)E1-2Dbo/J  mice 16-18 month-old

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix MoGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with Bioconductor software using RMA algorithm.

source_name: Mouse hippocampi after chronic treatment with SAHA and Tadalafil

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Hippocampus of mouse treated with different solutions during four weeks. The mouse underwent fear conditioning and Morris water maze test during week 3 and 4 of the treatment. Mice were sacrficed 24 hours after the end of the treatment.

extract_protocol: The RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: Mice were sacrificed by cervical dislocation, brain was extracted and the hippocampus was dissected and kept in dry ice immediately. Tissue was stored at -80 C until RNA extraction.

tag: tissue

value: hippocampus

tag: age

value: 16-18 month-old


title: Naïve NK cells biological replicate 1


title: GPRC5AKO#1_rep2


title: GPRC5AKO#1_rep3


title: GPRC5AKO#1_rep1


title: PC3_Control_rep3

value: pMSCV-luc transfected cell


title: 40-HPC

city: Golden

first: Teresa

middle: Hinkle

last: Sanders

state: CO

address: 1510 Quail Court

institute: University of Colorado, Boulder

description:
Total RNA (ribo-depleted)
HPC_counts.txt
1429-TS-7

data_processing:
Quality control on raw reads was performed with FastQC (version 0.10.1) and adaptor trimming and removal of trimmed reads shorter than 20 bp was performed with Trimmomatic (Bolger et al., 2014).
Trimmed reads were mapped to the Rattus norvegicus rn5 genome.
Samtools (version 0.1.19 –96b5f2294a) were used to sort SAM files and de-duplicate reads.
Bowtie2 was used to align reads (Langmead and Salzberg, 2012).
The subread featureCounts function was used to obtain counts. EdgeR was used for normalization and calculation of fold changes (Robinson et al., 2010).
Genome_build: rn5
Supplementary_files_format_and_content: excel, counts

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
RNA was harvested using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)
Stranded mRNA-seq was done by Vanderbilt Sequencing core facility using the TruSeq Stranded mRNA-Seq library prep kit to make sequencing libraries, which are typically sequenced on Illumina instruments with 100 bp paired end reads length.

value: control


title: 36-HPC

description:
Total RNA (ribo-depleted)
HPC_counts.txt
1429-TS-3

value: stimulated with implanted vagus nerve stimulation devices for 30 minutes on 4 consecutive days


title: 42-HPC

description:
Total RNA (ribo-depleted)
HPC_counts.txt
1429-TS-9


title: 37-HPC

description:
Total RNA (ribo-depleted)
HPC_counts.txt
1429-TS-4


title: 12-HPC

description:
Total RNA (ribo-depleted)
HPC_counts.txt
1429-TS-2


title: 38-HPC

description:
Total RNA (ribo-depleted)
HPC_counts.txt
1429-TS-5


title: Hippocampus CM695, Biological replica 3

source_name: Mouse hippocampi after chronic treatment with CM695


title: Hippocampus CM695, Biological replica 2


title: 0h replicate2

description:
nuclear RNA
0h-FPKM.txt


title: Hippocampus  SAHA and Tadalafil, Biological replica 3


title: Hippocampus CM414, Biological replica 3

source_name: Mouse hippocampi after chronic treatment with CM414


title: Hippocampus CM695, Biological replica 1


title: Hippocampus  SAHA and Tadalafil, Biological replica 2


title: Hippocampus CM414, Biological replica 1


title: Hippocampus CM414, Biological replica 2


title: 67-AC

description:
Stranded mRNA (polyAselected)
CTX_counts.txt
1136-TS-8

source_name: cortex

value: cortex


title: Hippocampus vehicle, Biological replica 3

source_name: Mouse hippocampi after chronic treatment with saline


title: 0h replicate1

description:
nuclear RNA
0h-FPKM.txt


title: 39-HPC

description:
Total RNA (ribo-depleted)
HPC_counts.txt
1429-TS-6


title: VLC_3h replicate1

description:
nuclear RNA
VLC3-FPKM.txt


title: PC3_Control_rep1


title: 66-AC

description:
Stranded mRNA (polyAselected)
CTX_counts.txt
1136-TS-7


title: PC3_Control_rep2


title: 63-AC

description:
Stranded mRNA (polyAselected)
CTX_counts.txt
1136-TS-4


title: 64-AC

description:
Stranded mRNA (polyAselected)
CTX_counts.txt
1136-TS-5


title: 65-AC

description:
Stranded mRNA (polyAselected)
CTX_counts.txt
1136-TS-6


title: 62-AC

description:
Stranded mRNA (polyAselected)
CTX_counts.txt
1136-TS-3


title: ZT18_HF.NOB

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

description: GeneReadCount.xlsx

data_processing:
RNA-seq data were aligned to mouse reference genome (mm10) using Tophat2 v2.0.12
The abundance of genes was quantified by Cufflinks v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Excel file included read count for each gene

source_name: Calf muscle

growth_protocol: We collected  samples from  24-26 month old male C57BL/6 following the 5-6 month of high fat diet treatment with or without Nobiletin compound.

extract_protocol:
Total RNA was extracted used the TRizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tissues were removed at ZT6 and ZT18, snap frozen in liquid nitrogen, and RNA was extracted using Trizol reagent.

tag: diet

value: high fat (HF)

tag: drug treatment

value: Nobiletin

value: skeletal muscle

value: 24-26 month

tag: Sex

value: male

tag: time point


title: ZT6_HF

description: GeneReadCount.xlsx


title: ZT18_RD

description: GeneReadCount.xlsx

value: RD (regular diet)


title: ZT18_HF

description: GeneReadCount.xlsx


title: ZT6_HF.NOB

description: GeneReadCount.xlsx


title: ZT6_RD

description: GeneReadCount.xlsx


title: 60-AC

description:
Stranded mRNA (polyAselected)
CTX_counts.txt
1136-TS-1

tag: treatment


title: 61-AC

description:
Stranded mRNA (polyAselected)
CTX_counts.txt
1136-TS-2


title: Hippocampus vehicle, Biological replica 2


title: A375R Dabrafenib-resistant, biological rep2

city: Genoa

first: Adriana

middle: Agnese

last: Amaro

address: Largo Rosanna Benzi 10

department: Molecular Pathology

country: Italy

institute: IRCCS Ospedale Policlinico SAN MARTINO - IST - NATIONAL CANCER RESEARCH INSTITUTE

hyb_protocol: Following biotinylation, these fragments were hybridized for 20 hr at 45°C on Affymetrix miRNA 3.1 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for miRNA Array strips.

scan_protocol: GeneChip were finally scanned using GeneAtlas Scanner.

data_processing: Affymetrix Expression Console.  Data were preprocessed following the RMA procedure using quantile normalization

source_name: melanoma cell line derived from Lymph Node Metastasis

label_protocol: 130-1000 ng of total of RNA was biotin labeled using the FlashTag™ HSR RNA labeling kit for Affymetrix GeneChip™ miRNA 3.1 Array Strip hybidization.

growth_protocol: A375 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 50 m/ml gentamicin (Complete Medium, CM). The A375R cell line was maintained in CM supplemented with 1.5 mM dabrafenib

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) and mirVana miRNA isolation kit (Ambion) following the manufacturers protocol. RNA quantity and quality were determined using a Nanodrop-1000 spectrophotometer (Nanodrop Technology) and Agilent 2100 Bioanalyzer.

treatment_protocol: A375 and A375R cells were removed from culture, seeded into 10-cm dishes, and maintained in CM for 48 h. The cells were then detached with a solution of EDTA in PBS, washed in PBS and frozen in a RNA-later®/PBS solution.

tag: cell line

tag: sample type

value: derived from A375 cells chronically treated with dabrafenib

tag: phenotype

value: Dabrafenib Resistant cell line


title: A375 Parental, biological rep2

value: BRAFV600E parental cells sensitive to BRAF inhibitors

value: Parental cell line


title: A375R Dabrafenib-resistant, biological rep3


title: A375 Parental, biological rep3


title: A549-siMYMLR#2-rep3

status: Public on Jul 15 2019

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

description: compared with A549-sicontrol-rep8

hyb_protocol: 300 ng of Cy5-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) and Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K v2 Microarrays (G4851B) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: SurePrint G3 Human GE 8x60K v2 Microarray with 60k distinct probes was scanned using an Agilent DNA microarray scanner (G2539A, Agilent Technologies). Images were quantified using Agilent Scan Control Software (version 10.7.1.1. or 10.10.1.1).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Scan Control Software (version 10.7.1.1. or 10.10.1.1).

source_name: A549 cells were treated with siMYMLR#2, replicate 3

label_protocol: Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a SurePrint G3 Human GE 8x60K v2 Microarray kit (Agilent Technologies) with 60k distinct probes.

growth_protocol: A549 cells were cultured with 10% (v/v) FCS-containing RPMI 1640 at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 100 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

treatment_protocol: A549 cells were transfected with siRNAs and incubated for 72h before harvest

tag: sirna

value: mixture of 20 cell ines


title: Hippocampus vehicle, Biological replica 1

value: hippocampus


title: A549-siMYMLR#1-rep3

description: compared with A549-sicontrol-rep4

source_name: A549 cells were treated with siMYMLR#1, replicate 3


title: A549-siMYC-rep1

description: compared with A549-sicontrol-rep3

source_name: A549 cells were treated with siMYC, replicate 1

value: siMYC


title: Mito_vs_ContMito

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol.

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

organism: Acinetobacter sp. 5-2Ac.02

source_name: Culture

label_protocol: Two-color microarray-based prokaryote analysis Fair Play III Labeling v1.3 (Agilent)

growth_protocol: The culture was growth in LB medium to an exponential-phase about OD600=0.5

extract_protocol: For RNA purification it was used the High Pure RNA Isolation Kit (Roche, Germany).

treatment_protocol: Then was added: i) 10μM of mitomycin C (SOS response); ii) mix of acyl-homoserine lactones composed by N-(butyl, heptanoyl, hexanoyl, b-ketocaproyl, octanoyl and tetradecanoyl)-DL-homoserine lactones at a final concentration of 1mM; iii) 3-oxo-dodecanoyl-HSL (3-oxo-C12-HSL) at a final concentration of 10 μM to the culture (Quorum network).  After one hour in the presence of the compounds, 1ml of each culture was used to RNA extraction.

tag: replicate

value: Mito M1.3

value: 10μM of mitomycin C (SOS response)

value: ContMito C1.2

value: Control (no treatment)


title: AHLs_vs_ContAHLs

value: AHLs A1.1

value: Mix of acyl-homoserine lactones composed by N-(butyl, heptanoyl, hexanoyl, b-ketocaproyl, octanoyl and tetradecanoyl)-DL-homoserine lactones at a final concentration of 1mM

value: ContAHLs C4.1


title: A549-siMYC-rep2

description: compared with A549-sicontrol-rep4

source_name: A549 cells were treated with siMYC, replicate 2


title: A549-siMYMLR#1-rep2

description: compared with A549-sicontrol-rep2

source_name: A549 cells were treated with siMYMLR#1, replicate 2


title: A375 Parental, biological rep1


title: A549-siPCBP2-rep3

description: compared with A549-sicontrol-rep5

source_name: A549 cells were treated with siPCBP2, replicate 3


title: A549-siPCBP2-rep2

description: compared with A549-sicontrol-rep4

source_name: A549 cells were treated with siPCBP2, replicate 2


title: A375R Dabrafenib-resistant, biological rep1


title: Oxo_vs_ContOxo

value: Oxo O1.3

value: 3-oxo-dodecanoyl-HSL (3-oxo-C12-HSL) at a final concentration of 10 μM to the culture

value: ContOxo C7.1


title: A549-siPCBP2-rep1

description: compared with A549-sicontrol-rep3

source_name: A549 cells were treated with siPCBP2, replicate 1


title: A549-siMYMLR#1-rep1

description: compared with A549-sicontrol-rep1

source_name: A549 cells were treated with siMYMLR#1, replicate 1


title: A549-sicontrol-rep7

source_name: A549 cells were treated with sicontrol, replicate 7

value: sicontrol


title: A549-sicontrol-rep6

source_name: A549 cells were treated with sicontrol, replicate 6


title: Fetal blood

type: genomic

city: hangzhou

first: yixi

last: sun

state: zhejiang

address: XUESHI ROAD 1

institute: Zhejiang University

hyb_protocol: According to the instructions of Affymetrix CytoScan HD Array

data_processing:
All data were visualized  and analyzed with the Chromosome Analysis Suite  (ChAS) software (Affymetrix, USA).
affymetrix-array-type = CytoScanHD_Array
affymetrix-algorithm-param-ArraySet = CytoScanHD_Array
program-name = C:\Program Files\Affymetrix\ChAS\apt-copynumber-cyto-ssa.exe

source_name: Fetal blood

extract_protocol: Genomic DNA samples were extracted with the GentraPuregene  Kit (Qiagen, Germany).

treatment_protocol: After fetal blood sampling,we immediately performed Affymetrix CytoScan HD Array detection or stored it in 4°C

tag: subject status

value: X-linked hydrocephalus (XLH)

tag: gender

value: male

tag: developmental stage

value: fetus

value: blood


title: A549-sicontrol-rep4

source_name: A549 cells were treated with sicontrol, replicate 4

value: mixture of 20 cell ines


title: A549-siMYMLR#2-rep1

description: compared with A549-sicontrol-rep6

source_name: A549 cells were treated with siMYMLR#2, replicate 1


title: A549-sicontrol-rep8

source_name: A549 cells were treated with sicontrol, replicate 8


title: A549-siMYC-rep3

description: compared with A549-sicontrol-rep5

source_name: A549 cells were treated with siMYC, replicate 3

value: siMYC


title: A549-sicontrol-rep5

source_name: A549 cells were treated with sicontrol, replicate 5


title: A549-siMYMLR#2-rep2

description: compared with A549-sicontrol-rep7

source_name: A549 cells were treated with siMYMLR#2, replicate 2


title: ContMito_vs_Mito

value: ContMito C2.2

value: Mito M2.3


title: ContOxo_vs_Oxo

value: ContOxo C8.3

value: Oxo O2.3


title: A549-sicontrol-rep1

source_name: A549 cells were treated with sicontrol, replicate 1


title: ContAHLs_vs_AHLs

source_name: Culture

value: ContAHLs C5.3

value: Control (no treatment)

value: AHLs A2.1


title: A549-sicontrol-rep3

source_name: A549 cells were treated with sicontrol, replicate 3


title: L16_1288_Cyno_5_Thyroid

city: Cambridge

first: Sahin

last: Naqvi

state: MA

address: 455 Main St

institute: Whitehead Institute

description:
cyno.salmon.tximport.counts.txt
cyno.salmon.tximport.tpm.txt
cyno.stringtie.gtf
cyno.tx2geneid.txt

data_processing:
Image analysis and base calling was done using the standard Illumina pipeline for HiSeq2500
Libraries from the non-human mammals were mapped to their respective reference genomes using STAR v2.5.0 with the following parameters: --outFilterMultimapNmax 50 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.15
StringTie v1.3.3b with the --rf parameter was run on each resulting .bam file to assemble novel isoforms relative to the reference transcriptome annotation
The sets of novel and existing transcript annotations from each library were then compiled into a single set of annotations for each species using the --merge option in StringTie v1.3.3b
Abundances for these sets of transcripts for each species were then quantified using salmon v0.9.1 with the following parameters/flags: --seqBias, --gcBias, --useVBOpt
The tximport R package (with countsFromAbundance = “lengthScaledTPM”) was used to sum transcript-level counts and transcripts per million (TPM) values from salmon to the gene level for all transcripts with the following class codes: c, j, e, o, =, u
Genome_build: cyno, macFas5; dog, canFam3; mouse, mm10; rat, rn6
Supplementary_files_format_and_content: Transcript annotations for each species are provided as .gtf files. Assignments of transcripts (Ensembl ID for known, Stringtie ID for novel) to genes (Ensembl ID) along with transcript class codes are provided as tab-delimited .txt files. Gene-level TPM and counts are provided as tab-delimited .txt files

organism: Macaca fascicularis

source_name: Thyroid

growth_protocol: standard lab/breeding colony conditions

extract_protocol:
Tissues were isolated from freshly sacrificed animals (< 1 hour from time of death to tissue fixation), washed in cold PBS, and stored in RNALater (Ambion) per the manufacturer’s instructions. Each sample was then homogenized in a bead-mill in Trizol and total RNA was isolated by and treated with DNAse on a Qiagen miRNEasy column
Libraries were prepared using the TruSeq mRNA library kit (Illumina) according to manufacturer’s instructions with the following modifications: After prep, libraries were size-selected using 2% agarose gels on the PippinHT system (Sage Science) with a capture window of 300-600 bases. The size-selected material was then subjected to one additional cycle of PCR with fresh reagents and P5/P7 primers (Illumina) to ensure all library fragments were fully double-stranded. This step significantly reduced the percentage of smaller fragments co-purifying in the final gel size-selection. After PCR, libraries were size-selected a second time on the PippinHT with the same settings

treatment_protocol: RNALater (Ambion)

tag: organism common name

value: Cyno

tag: strain

value: Mauritius colony (Novaprim Group)

tag: individual

value: 80 months

tag: rna integry number (rin)

tag: library prep batch


title: L16_1072_Cyno_6_Adrenal

source_name: Adrenal

tag: age

value: 107 months


title: L16_1364_Cyno_6_Colon

source_name: Colon


title: L16_1611_Cyno_5_Testis

source_name: Testis


title: L16_1504_Cyno_6_Skin

source_name: Skin


title: L16_1596_Cyno_6_Pituitary

source_name: Pituitary


title: L16_1533_Cyno_5_Testis


title: L16_1431_Cyno_6_Liver

source_name: Liver


title: L16_1255_Cyno_6_Heart

source_name: Heart


title: L16_1527_Cyno_6_Brain

source_name: Brain


title: L16_1333_Cyno_6_Lung

source_name: Lung


title: A549-sicontrol-rep2

source_name: A549 cells were treated with sicontrol, replicate 2

value: sicontrol


title: L16_1347_Cyno_5_Testis


title: L16_1115_Cyno_5_Pituitary


title: L16_1373_Cyno_6_Muscle

source_name: Muscle


title: L16_1443_Cyno_5_Skin


title: L16_1315_Cyno_6_Thyroid


title: L16_1256_Cyno_6_Spleen

source_name: Spleen


title: L16_1401_Cyno_5_Testis


title: L16_1065_Cyno_5_Testis


title: L16_1388_Cyno_5_Muscle


title: L16_1144_Cyno_5_Testis


title: L16_1449_Cyno_5_Testis


title: L16_1304_Cyno_5_Lung


title: L16_1299_Cyno_5_Testis


title: L16_1607_Cyno_5_Liver


title: L16_1394_Cyno_5_Heart


title: L16_1498_Cyno_5_Colon


title: L16_1149_Cyno_5_Brain


title: L16_1340_Cyno_5_Adrenal


title: L16_1262_Cyno_4_Colon

value: 106 months


title: L16_1283_Cyno_4_Muscle


title: L16_1084_Cyno_4_Pituitary


title: L16_1292_Cyno_4_Adrenal


title: L16_1506_Cyno_4_Liver


title: L16_1148_Cyno_4_Heart


title: L16_1141_Cyno_4_Spleen


title: L16_1602_Cyno_4_Adipose

source_name: Adipose


title: L16_1126_Cyno_3_Thyroid

value: 75 months


title: L16_1495_Cyno_3_Spleen


title: L16_1125_Cyno_3_Muscle


title: L16_1286_Cyno_3_Pituitary


title: L16_1525_Cyno_3_Liver


title: L16_1059_Cyno_4_Skin


title: L16_1083_Cyno_3_Heart


title: L16_1306_Cyno_3_Brain


title: L16_1296_Cyno_3_Skin


title: L16_1057_Cyno_4_Brain


title: L16_1130_Cyno_3_Lung


title: L16_1146_Cyno_4_Thyroid


title: L16_1344_Cyno_2_Thyroid

value: 108 months


title: L16_1280_Cyno_2_Spleen


title: L16_1290_Cyno_2_Pituitary


title: L16_1386_Cyno_2_Skin


title: L16_1346_Cyno_3_Adrenal


title: L16_1049_Cyno_4_Lung


title: L16_1142_Cyno_2_Muscle


title: L16_1604_Cyno_2_Lung


title: L16_1501_Cyno_3_Colon


title: L16_1133_Cyno_3_Adipose


title: L16_1438_Cyno_2_Heart


title: L16_1154_Cyno_2_Liver


title: L16_1086_Cyno_2_Colon


title: L16_1372_Cyno_1_Muscle

value: 72 months


title: L16_1405_Cyno_1_Thyroid


title: L16_1120_Cyno_1_Spleen


title: L16_1313_Cyno_2_Adrenal


title: L16_1526_Cyno_1_Pituitary


title: L16_1076_Cyno_1_Colon


title: L16_1496_Cyno_1_Heart


title: L16_1055_Cyno_1_Adrenal


title: L16_1062_Cyno_1_Liver


title: L16_1321_Cyno_1_Adipose


title: L16_1069_Cyno_1_Skin


title: L16_1345_Cyno_1_Lung


title: L16_1222_Cyno_2_Adipose


title: L16_1530_Dog_8_Skin

description:
dog.salmon.tximport.counts.txt
dog.salmon.tximport.tpm.txt
dog.stringtie.gtf
dog.tx2geneid.txt

organism: Canis lupus familiaris

value: Dog

value: Beagle (Ridglan farms)

value: 20 months


title: L16_1606_Dog_9_Adipose

value: 22 months


title: L16_1493_Dog_8_Thyroid


title: L16_1177_Dog_8_Muscle


title: L16_1305_Dog_8_Liver


title: L16_1494_Dog_8_Lung


title: L16_1360_Dog_10_Adipose


title: L16_1324_Dog_8_Heart


title: L16_1529_Dog_8_Colon


title: L16_1310_Dog_7_Pituitary

value: 21 months


title: L16_1293_Cyno_2_Brain


title: L16_1362_Dog_7_Brain


title: L16_1598_Dog_6_Thyroid


title: L16_1610_Dog_6_Spleen


title: L16_1127_Dog_4_Adrenal


title: L16_1390_Dog_6_Muscle


title: L16_1603_Cyno_1_Brain


title: L16_1303_Dog_6_Liver


title: L16_1145_Dog_8_Spleen


title: L16_1051_Dog_6_Skin


title: L16_1593_Dog_6_Heart


title: L16_1121_Dog_6_Adrenal


title: L16_1503_Dog_5_Brain


title: L16_1152_Dog_6_Lung


title: L16_1377_Dog_4_Spleen


title: L16_1513_Dog_6_Colon


title: L16_1327_Dog_5_Pituitary


title: L16_1170_Dog_4_Heart


title: L16_1409_Dog_4_Colon


title: L16_1138_Dog_4_Pituitary


title: L16_1330_Dog_4_Liver


title: L16_1447_Dog_4_Lung


title: L16_1143_Dog_4_Brain


title: L16_1066_Dog_4_Adipose


title: L16_1398_Dog_3_Thyroid

value: 47 months


title: L16_1337_Dog_3_Skin


title: L16_1499_Dog_4_Skin


title: L16_1328_Dog_4_Muscle


title: L16_1435_Dog_3_Spleen


title: L16_1514_Dog_3_Pituitary


title: L16_1368_Dog_3_Lung


title: L16_1320_Dog_3_Muscle


title: L16_1608_Dog_3_Liver


title: L16_1510_Dog_3_Heart


title: L16_1070_Dog_3_Colon


title: L16_1258_Dog_3_Brain


title: L16_1528_Dog_3_Adrenal


title: L16_1171_Dog_2_Thyroid


title: L16_1358_Dog_3_Adipose


title: L16_1534_Dog_2_Testis


title: L16_1348_Dog_2_Testis


title: L16_1300_Dog_2_Testis


title: L16_1123_Dog_2_Testis


title: L16_1271_Dog_2_Spleen


title: L16_1289_Dog_2_Muscle


title: L16_1147_Dog_2_Brain


title: L16_1444_Dog_2_Adipose


title: L16_1402_Dog_2_Testis


title: L16_1509_Dog_1_Thyroid


title: L16_1150_Dog_2_Pituitary


title: L16_1429_Dog_2_Liver


title: L16_1380_Dog_2_Adrenal


title: L16_1058_Dog_1_Pituitary


title: L16_1274_Dog_1_Skin


title: L16_1297_Dog_2_Lung


title: L16_1612_Dog_2_Testis


title: L16_1450_Dog_2_Testis


title: L16_1132_Dog_1_Muscle


title: L16_1383_Dog_1_Adrenal


title: L16_1381_Dog_1_Colon


title: L16_1295_Dog_1_Liver


title: L16_1151_Dog_1_Brain


title: L16_1064_Dog_2_Testis


title: L16_1139_Dog_1_Adipose


title: L16_1056_Dog_2_Skin


title: L16_1446_Dog_1_Spleen


title: Pol II_EC_cell847

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts. For spliting single cell, we cut the first 21 bp of the read1 and the first 27 bp of the read2.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Cells with less than 3,000 non-duplicated were excluded.
Bed files were generated from bam files using bedtools (v2.25.0) bamToBed.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bed files. Each single cell bed file contain non-duplicated alignments as is in the bam file.

source_name: Pol II_EC_cell

extract_protocol:
Following CoBATCH protocol.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Organs were digested with 0.06 Collagenase II  + 0.08% Trypsin and 0.09% Collagenase II + 0.12% Trypsin  at 37 °C.

tag: tissue

value: heart

tag: chip antibody

value: RNA PolII, abcam, ab5408, Lot:GR205997-15


title: Pol II_EC_cell850


title: Pol II_EC_cell849


title: Pol II_EC_cell848


title: Pol II_EC_cell852


title: Pol II_EC_cell846


title: Pol II_EC_cell842


title: Pol II_EC_cell851


title: L16_1088_Dog_1_Heart


title: Pol II_EC_cell844


title: cNK1

city: hefei

first: baohui

last: wang

state: anhui

address: No.443 huangshan road

department: Institue of Immunology

institute: University of Science and Technology of China

data_processing:
A cDNA library constructed by technology from the pooled RNA from brain samples of mouse was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome (ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: spleen

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq RNA Sample Preparation v2 (Cat. RS-122-2001,RS-122-2002) (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing ( 2 x 150 bp) on an Illumina NovaseqTM 6000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.

tag: tisssue

value: spleen

tag: genotype

value: wild type


title: DN NK1


title: DN NK2


title: DN NK3


title: cNK3


title: Pol II_EC_cell840


title: cNK2


title: Pol II_EC_cell838


title: Pol II_EC_cell839


title: Pol II_EC_cell843


title: Pol II_EC_cell845


title: Pol II_EC_cell841


title: Pol II_EC_cell834


title: Pol II_EC_cell835


title: Pol II_EC_cell832


title: Pol II_EC_cell831


title: Pol II_EC_cell833


title: Pol II_EC_cell830


title: Pol II_EC_cell829


title: Pol II_EC_cell828


title: Pol II_EC_cell826


title: Pol II_EC_cell827


title: Pol II_EC_cell824


title: Pol II_EC_cell825


title: Pol II_EC_cell823


title: Pol II_EC_cell837


title: Pol II_EC_cell822


title: Pol II_EC_cell819


title: Pol II_EC_cell812


title: Pol II_EC_cell811


title: Pol II_EC_cell814


title: Pol II_EC_cell816


title: Pol II_EC_cell836


title: Pol II_EC_cell808


title: Pol II_EC_cell815


title: Pol II_EC_cell820


title: Pol II_EC_cell807


title: Pol II_EC_cell809


title: Pol II_EC_cell817


title: Pol II_EC_cell806


title: Pol II_EC_cell804


title: Pol II_EC_cell803


title: Pol II_EC_cell805


title: Pol II_EC_cell821


title: Pol II_EC_cell813


title: Pol II_EC_cell802


title: Pol II_EC_cell801


title: Pol II_EC_cell800


title: Pol II_EC_cell797


title: Pol II_EC_cell799


title: Pol II_EC_cell798


title: Pol II_EC_cell818


title: Pol II_EC_cell796


title: Pol II_EC_cell794


title: Pol II_EC_cell793


title: Pol II_EC_cell810


title: Pol II_EC_cell787


title: Pol II_EC_cell790


title: Pol II_EC_cell789


title: Pol II_EC_cell785


title: Pol II_EC_cell786


title: Pol II_EC_cell788


title: Pol II_EC_cell791


title: Pol II_EC_cell795


title: Pol II_EC_cell792


title: Pol II_EC_cell775


title: Pol II_EC_cell782


title: Pol II_EC_cell778


title: Pol II_EC_cell770


title: Pol II_EC_cell771


title: Pol II_EC_cell769


title: Pol II_EC_cell766


title: Pol II_EC_cell761


title: Pol II_EC_cell768


title: Pol II_EC_cell772


title: Pol II_EC_cell773


title: Pol II_EC_cell760


title: Pol II_EC_cell781


title: Pol II_EC_cell757


title: Pol II_EC_cell765


title: Pol II_EC_cell758


title: Pol II_EC_cell763


title: Pol II_EC_cell764


title: Pol II_EC_cell779


title: Pol II_EC_cell774


title: Pol II_EC_cell759


title: Pol II_EC_cell783


title: Pol II_EC_cell756


title: Pol II_EC_cell780


title: Pol II_EC_cell762


title: Pol II_EC_cell777


title: Pol II_EC_cell784


title: Pol II_EC_cell776


title: Pol II_EC_cell767


title: Pol II_EC_cell755


title: Pol II_EC_cell754


title: Pol II_EC_cell753


title: Pol II_EC_cell743


title: Pol II_EC_cell740


title: Pol II_EC_cell750


title: Pol II_EC_cell746


title: Pol II_EC_cell742


title: Pol II_EC_cell741


title: Pol II_EC_cell752


title: Pol II_EC_cell747


title: Pol II_EC_cell749


title: Pol II_EC_cell748


title: Pol II_EC_cell751


title: Pol II_EC_cell739


title: Pol II_EC_cell737


title: Pol II_EC_cell725


title: Pol II_EC_cell731


title: Pol II_EC_cell728


title: Pol II_EC_cell729


title: Pol II_EC_cell736


title: Pol II_EC_cell730


title: Pol II_EC_cell726


title: Pol II_EC_cell735


title: Pol II_EC_cell738


title: Pol II_EC_cell732


title: Pol II_EC_cell727


title: Pol II_EC_cell745


title: Pol II_EC_cell744


title: Pol II_EC_cell733


title: Pol II_EC_cell734


title: Pol II_EC_cell724


title: Pol II_EC_cell723


title: Pol II_EC_cell720


title: Pol II_EC_cell716


title: Pol II_EC_cell713


title: Pol II_EC_cell715


title: Pol II_EC_cell719


title: Pol II_EC_cell709


title: Pol II_EC_cell717


title: Pol II_EC_cell710


title: Pol II_EC_cell711


title: Pol II_EC_cell712


title: Pol II_EC_cell705


title: Pol II_EC_cell706


title: Pol II_EC_cell702


title: Pol II_EC_cell696


title: Pol II_EC_cell701


title: Pol II_EC_cell695


title: Pol II_EC_cell699


title: Pol II_EC_cell708


title: Pol II_EC_cell697


title: Pol II_EC_cell700


title: Pol II_EC_cell703


title: Pol II_EC_cell722


title: Pol II_EC_cell693


title: Pol II_EC_cell698


title: Pol II_EC_cell721


title: Pol II_EC_cell704


title: Pol II_EC_cell718


title: Pol II_EC_cell714


title: Pol II_EC_cell692


title: Pol II_EC_cell707


title: Pol II_EC_cell691


title: Pol II_EC_cell690


title: Pol II_EC_cell688


title: Pol II_EC_cell686


title: Pol II_EC_cell685


title: Pol II_EC_cell684


title: Pol II_EC_cell689


title: Pol II_EC_cell683


title: Pol II_EC_cell687


title: Pol II_EC_cell681


title: Pol II_EC_cell694


title: Pol II_EC_cell677


title: Pol II_EC_cell680


title: Pol II_EC_cell679


title: Pol II_EC_cell675


title: Pol II_EC_cell678


title: Pol II_EC_cell674


title: Pol II_EC_cell673


title: Pol II_EC_cell671


title: Pol II_EC_cell682


title: Pol II_EC_cell668


title: Pol II_EC_cell670


title: Pol II_EC_cell662


title: Pol II_EC_cell667


title: Pol II_EC_cell666


title: Pol II_EC_cell664


title: Pol II_EC_cell676


title: Pol II_EC_cell669


title: Pol II_EC_cell665


title: Pol II_EC_cell663


title: Pol II_EC_cell661


title: Pol II_EC_cell654


title: Pol II_EC_cell660


title: Pol II_EC_cell658


title: Pol II_EC_cell657


title: Pol II_EC_cell655


title: Pol II_EC_cell656


title: Pol II_EC_cell672


title: Pol II_EC_cell653


title: Pol II_EC_cell652


title: Pol II_EC_cell648


title: Pol II_EC_cell651


title: Pol II_EC_cell645


title: Pol II_EC_cell650


title: Pol II_EC_cell643


title: Pol II_EC_cell640


title: Pol II_EC_cell639


title: Pol II_EC_cell659


title: Pol II_EC_cell637


title: Pol II_EC_cell642


title: Pol II_EC_cell634


title: Pol II_EC_cell644


title: Pol II_EC_cell632


title: Pol II_EC_cell649


title: Pol II_EC_cell647


title: Pol II_EC_cell636


title: Pol II_EC_cell631


title: Pol II_EC_cell627


title: Pol II_EC_cell646


title: Pol II_EC_cell630


title: Pol II_EC_cell626


title: Pol II_EC_cell628


title: Pol II_EC_cell625


title: Pol II_EC_cell623


title: Pol II_EC_cell624


title: Pol II_EC_cell641


title: Pol II_EC_cell620


title: Pol II_EC_cell619


title: Pol II_EC_cell622


title: Pol II_EC_cell621


title: Pol II_EC_cell618


title: Pol II_EC_cell616


title: Pol II_EC_cell617


title: Pol II_EC_cell613


title: Pol II_EC_cell615


title: Pol II_EC_cell614


title: Pol II_EC_cell611


title: Pol II_EC_cell610


title: Pol II_EC_cell607


title: Pol II_EC_cell629


title: Pol II_EC_cell612


title: Pol II_EC_cell605


title: Pol II_EC_cell609


title: Pol II_EC_cell603


title: Pol II_EC_cell604


title: Pol II_EC_cell602


title: Pol II_EC_cell608


title: Pol II_EC_cell606


title: Pol II_EC_cell599


title: Pol II_EC_cell600


title: Pol II_EC_cell595


title: Pol II_EC_cell596


title: Pol II_EC_cell597


title: Pol II_EC_cell593


title: Pol II_EC_cell591


title: Pol II_EC_cell589


title: Pol II_EC_cell592


title: Pol II_EC_cell590


title: Pol II_EC_cell601


title: Pol II_EC_cell587


title: Pol II_EC_cell588


title: Pol II_EC_cell584


title: Pol II_EC_cell585


title: Pol II_EC_cell583


title: Pol II_EC_cell582


title: Pol II_EC_cell586


title: Pol II_EC_cell581


title: Pol II_EC_cell598


title: Pol II_EC_cell575


title: Pol II_EC_cell578


title: Pol II_EC_cell576


title: Pol II_EC_cell580


title: Pol II_EC_cell594


title: Pol II_EC_cell573


title: Pol II_EC_cell579


title: Pol II_EC_cell574


title: Pol II_EC_cell572


title: Pol II_EC_cell571


title: Pol II_EC_cell570


title: Pol II_EC_cell569


title: Pol II_EC_cell567


title: Pol II_EC_cell566


title: Pol II_EC_cell564


title: Pol II_EC_cell559


title: Pol II_EC_cell558


title: Pol II_EC_cell561


title: Pol II_EC_cell563


title: Pol II_EC_cell562


title: Pol II_EC_cell556


title: Pol II_EC_cell557


title: Pol II_EC_cell560


title: Pol II_EC_cell577


title: Pol II_EC_cell553


title: Pol II_EC_cell548


title: Pol II_EC_cell547


title: Pol II_EC_cell549


title: Pol II_EC_cell550


title: Pol II_EC_cell552


title: Pol II_EC_cell555


title: Pol II_EC_cell545


title: Pol II_EC_cell554


title: Pol II_EC_cell568


title: Pol II_EC_cell543


title: Pol II_EC_cell565


title: Pol II_EC_cell544


title: Pol II_EC_cell542


title: Pol II_EC_cell551


title: Pol II_EC_cell540


title: Pol II_EC_cell539


title: Pol II_EC_cell538


title: Pol II_EC_cell633


title: Pol II_EC_cell535


title: Pol II_EC_cell546


title: Pol II_EC_cell537


title: Pol II_EC_cell533


title: Pol II_EC_cell534


title: Pol II_EC_cell536


title: Pol II_EC_cell528


title: Pol II_EC_cell530


title: Pol II_EC_cell531


title: Pol II_EC_cell527


title: Pol II_EC_cell523


title: Pol II_EC_cell521


title: Pol II_EC_cell526


title: Pol II_EC_cell525


title: Pol II_EC_cell541


title: Pol II_EC_cell520


title: Pol II_EC_cell519


title: Pol II_EC_cell524


title: Pol II_EC_cell529


title: Pol II_EC_cell522


title: Pol II_EC_cell518


title: Pol II_EC_cell516


title: Pol II_EC_cell515


title: Pol II_EC_cell517


title: Pol II_EC_cell514


title: Pol II_EC_cell513


title: Pol II_EC_cell532


title: Pol II_EC_cell512


title: Pol II_EC_cell511


title: Pol II_EC_cell510


title: Pol II_EC_cell508


title: Pol II_EC_cell507


title: Pol II_EC_cell506


title: Pol II_EC_cell505


title: Pol II_EC_cell504


title: Pol II_EC_cell503


title: Pol II_EC_cell502


title: Pol II_EC_cell500


title: Pol II_EC_cell496


title: Pol II_EC_cell497


title: Pol II_EC_cell494


title: Pol II_EC_cell499


title: Pol II_EC_cell491


title: Pol II_EC_cell495


title: Pol II_EC_cell490


title: Pol II_EC_cell488


title: Pol II_EC_cell487


title: Pol II_EC_cell489


title: Pol II_EC_cell485


title: Pol II_EC_cell509


title: Pol II_EC_cell484


title: Pol II_EC_cell486


title: Pol II_EC_cell483


title: Pol II_EC_cell481


title: Pol II_EC_cell501


title: Pol II_EC_cell498


title: Pol II_EC_cell492


title: Pol II_EC_cell493


title: Pol II_EC_cell478


title: Pol II_EC_cell477


title: Pol II_EC_cell475


title: Pol II_EC_cell474


title: Pol II_EC_cell472


title: Pol II_EC_cell473


title: Pol II_EC_cell471


title: Pol II_EC_cell470


title: Pol II_EC_cell467


title: Pol II_EC_cell466


title: Pol II_EC_cell635


title: Pol II_EC_cell468


title: Pol II_EC_cell465


title: Pol II_EC_cell638


title: Pol II_EC_cell480


title: Pol II_EC_cell462


title: Pol II_EC_cell479


title: Pol II_EC_cell463


title: Pol II_EC_cell464


title: Pol II_EC_cell461


title: Pol II_EC_cell460


title: Pol II_EC_cell457


title: Pol II_EC_cell454


title: Pol II_EC_cell455


title: Pol II_EC_cell453


title: Pol II_EC_cell456


title: Pol II_EC_cell452


title: Pol II_EC_cell458


title: Pol II_EC_cell451


title: Pol II_EC_cell482


title: Pol II_EC_cell449


title: Pol II_EC_cell450


title: Pol II_EC_cell447


title: Pol II_EC_cell446


title: Pol II_EC_cell444


title: Pol II_EC_cell445


title: Pol II_EC_cell459


title: Pol II_EC_cell442


title: Pol II_EC_cell441


title: Pol II_EC_cell443


title: Pol II_EC_cell440


title: Pol II_EC_cell439


title: Pol II_EC_cell438


title: Pol II_EC_cell436


title: Pol II_EC_cell437


title: Pol II_EC_cell434


title: Pol II_EC_cell433


title: Pol II_EC_cell435


title: Pol II_EC_cell448


title: Pol II_EC_cell431


title: Pol II_EC_cell432


title: Pol II_EC_cell429


title: Pol II_EC_cell425


title: Pol II_EC_cell424


title: Pol II_EC_cell428


title: Pol II_EC_cell430


title: Pol II_EC_cell426


title: Pol II_EC_cell421


title: Pol II_EC_cell422


title: Pol II_EC_cell423


title: Pol II_EC_cell415


title: Pol II_EC_cell420


title: Pol II_EC_cell417


title: Pol II_EC_cell416


title: Pol II_EC_cell413


title: Pol II_EC_cell414


title: Pol II_EC_cell412


title: Pol II_EC_cell411


title: Pol II_EC_cell410


title: Pol II_EC_cell409


title: Pol II_EC_cell408


title: Pol II_EC_cell406


title: Pol II_EC_cell427


title: Pol II_EC_cell419


title: Pol II_EC_cell405


title: Pol II_EC_cell403


title: Pol II_EC_cell404


title: Pol II_EC_cell398


title: Pol II_EC_cell401


title: Pol II_EC_cell400


title: Pol II_EC_cell399


title: Pol II_EC_cell418


title: Pol II_EC_cell396


title: Pol II_EC_cell395


title: Pol II_EC_cell393


title: Pol II_EC_cell391


title: Pol II_EC_cell392


title: Pol II_EC_cell390


title: Pol II_EC_cell389


title: Pol II_EC_cell386


title: Pol II_EC_cell388


title: Pol II_EC_cell382


title: Pol II_EC_cell387


title: Pol II_EC_cell402


title: Pol II_EC_cell394


title: Pol II_EC_cell384


title: Pol II_EC_cell381


title: Pol II_EC_cell383


title: Pol II_EC_cell380


title: Pol II_EC_cell385


title: Pol II_EC_cell379


title: Pol II_EC_cell377


title: Pol II_EC_cell407


title: Pol II_EC_cell373


title: Pol II_EC_cell378


title: Pol II_EC_cell372


title: Pol II_EC_cell397


title: Pol II_EC_cell376


title: Pol II_EC_cell374


title: Pol II_EC_cell371


title: Pol II_EC_cell469


title: Pol II_EC_cell369


title: Pol II_EC_cell370


title: Pol II_EC_cell368


title: Pol II_EC_cell367


title: Pol II_EC_cell366


title: Pol II_EC_cell365


title: Pol II_EC_cell364


title: Pol II_EC_cell362


title: Pol II_EC_cell361


title: Pol II_EC_cell363


title: Pol II_EC_cell359


title: Pol II_EC_cell358


title: Pol II_EC_cell375


title: Pol II_EC_cell357


title: Pol II_EC_cell356


title: Pol II_EC_cell355


title: Pol II_EC_cell360


title: Pol II_EC_cell354


title: Pol II_EC_cell476


title: Pol II_EC_cell353


title: Pol II_EC_cell352


title: Pol II_EC_cell351


title: Pol II_EC_cell348


title: Pol II_EC_cell349


title: Pol II_EC_cell350


title: Pol II_EC_cell346


title: Pol II_EC_cell347


title: Pol II_EC_cell344


title: Pol II_EC_cell343


title: Pol II_EC_cell341


title: Pol II_EC_cell345


title: Pol II_EC_cell338


title: Pol II_EC_cell337


title: Pol II_EC_cell339


title: Pol II_EC_cell335


title: Pol II_EC_cell333


title: Pol II_EC_cell334


title: Pol II_EC_cell331


title: Pol II_EC_cell332


title: Pol II_EC_cell330


title: Pol II_EC_cell329


title: Pol II_EC_cell323


title: Pol II_EC_cell327


title: Pol II_EC_cell328


title: Pol II_EC_cell324


title: Pol II_EC_cell318


title: Pol II_EC_cell326


title: Pol II_EC_cell322


title: Pol II_EC_cell340


title: Pol II_EC_cell321


title: Pol II_EC_cell316


title: Pol II_EC_cell325


title: Pol II_EC_cell315


title: Pol II_EC_cell314


title: Pol II_EC_cell319


title: Pol II_EC_cell313


title: Pol II_EC_cell312


title: Pol II_EC_cell342


title: Pol II_EC_cell320


title: Pol II_EC_cell317


title: Pol II_EC_cell311


title: Pol II_EC_cell309


title: Pol II_EC_cell336


title: Pol II_EC_cell310


title: Pol II_EC_cell306


title: Pol II_EC_cell307


title: Pol II_EC_cell303


title: Pol II_EC_cell304


title: Pol II_EC_cell302


title: Pol II_EC_cell305


title: Pol II_EC_cell296


title: Pol II_EC_cell295


title: Pol II_EC_cell297


title: Pol II_EC_cell291


title: Pol II_EC_cell293


title: Pol II_EC_cell292


title: Pol II_EC_cell308


title: Pol II_EC_cell294


title: Pol II_EC_cell298


title: Pol II_EC_cell300


title: Pol II_EC_cell288


title: Pol II_EC_cell286


title: Pol II_EC_cell287


title: Pol II_EC_cell284


title: Pol II_EC_cell280


title: Pol II_EC_cell283


title: Pol II_EC_cell282


title: Pol II_EC_cell279


title: Pol II_EC_cell299


title: Pol II_EC_cell275


title: Pol II_EC_cell277


title: Pol II_EC_cell274


title: Pol II_EC_cell273


title: Pol II_EC_cell278


title: Pol II_EC_cell272


title: Pol II_EC_cell290


title: Pol II_EC_cell271


title: Pol II_EC_cell267


title: Pol II_EC_cell269


title: Pol II_EC_cell268


title: Pol II_EC_cell281


title: Pol II_EC_cell270


title: Pol II_EC_cell265


title: Pol II_EC_cell264


title: Pol II_EC_cell266


title: Pol II_EC_cell301


title: Pol II_EC_cell262


title: Pol II_EC_cell263


title: Pol II_EC_cell261


title: Pol II_EC_cell285


title: Pol II_EC_cell276


title: Pol II_EC_cell259


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title: Pol II_EC_cell289


title: Pol II_EC_cell255


title: Pol II_EC_cell258


title: Pol II_EC_cell253


title: Pol II_EC_cell251


title: Pol II_EC_cell249


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title: Pol II_EC_cell248


title: Pol II_EC_cell260


title: Pol II_EC_cell246


title: Pol II_EC_cell245


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title: Pol II_EC_cell194


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title: Pol II_EC_cell176


title: Pol II_EC_cell202


title: Pol II_EC_cell186


title: Pol II_EC_cell182


title: Pol II_EC_cell169


title: Pol II_EC_cell172


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title: Pol II_EC_cell193


title: Pol II_EC_cell167


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title: Pol II_EC_cell184


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title: Pol II_EC_cell181


title: Pol II_EC_cell163


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title: Pol II_EC_cell160


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title: Pol II_EC_cell151


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title: Pol II_EC_cell154


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title: Pol II_EC_cell153


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title: Pol II_EC_cell149


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title: Pol II_EC_cell109


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title: Pol II_EC_cell92


title: Pol II_EC_cell99


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title: Pol II_EC_cell94


title: Pol II_EC_cell84


title: Pol II_EC_cell80


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title: Pol II_EC_cell79


title: Pol II_EC_cell81


title: Pol II_EC_cell77


title: Pol II_EC_cell76


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title: Pol II_EC_cell75


title: Pol II_EC_cell67


title: Pol II_EC_cell68


title: Pol II_EC_cell69


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title: Pol II_EC_cell72


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title: Pol II_EC_cell65


title: Pol II_EC_cell62


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title: Pol II_EC_cell57


title: Pol II_EC_cell60


title: Pol II_EC_cell55


title: Pol II_EC_cell56


title: Pol II_EC_cell54


title: Pol II_EC_cell53


title: Pol II_EC_cell52


title: Pol II_EC_cell51


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title: Pol II_EC_cell44


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title: Pol II_EC_cell25


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title: Pol II_EC_cell24


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title: Pol II_EC_cell3


title: Pol II_EC_cell5


title: Pol II_EC_cell4


title: Pol II_EC_cell2


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title: H3K36me3_EC_cell_388

value: H3K36me3, Cell Signaling Technology, 4909


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title: H3K36me3_EC_cell_366


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title: H3K36me3_EC_cell_358


title: H3K36me3_EC_cell_357


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title: H3K36me3_EC_cell_351


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title: H3K36me3_EC_cell_276


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title: H3K36me3_EC_cell_75


title: H3K36me3_EC_cell_78


title: H3K36me3_EC_cell_72


title: H3K36me3_EC_cell_71


title: H3K36me3_EC_cell_73


title: H3K36me3_EC_cell_69


title: H3K36me3_EC_cell_68


title: H3K36me3_EC_cell_67


title: H3K36me3_EC_cell_66


title: H3K36me3_EC_cell_65


title: H3K36me3_EC_cell_70


title: H3K36me3_EC_cell_64


title: H3K36me3_EC_cell_82


title: H3K36me3_EC_cell_61


title: H3K36me3_EC_cell_62


title: H3K36me3_EC_cell_63


title: H3K36me3_EC_cell_58


title: H3K36me3_EC_cell_59


title: H3K36me3_EC_cell_60


title: H3K36me3_EC_cell_56


title: H3K36me3_EC_cell_51


title: H3K36me3_EC_cell_50


title: H3K36me3_EC_cell_52


title: H3K36me3_EC_cell_54


title: H3K36me3_EC_cell_49


title: H3K36me3_EC_cell_55


title: H3K36me3_EC_cell_53


title: H3K36me3_EC_cell_47


title: H3K36me3_EC_cell_46


title: H3K36me3_EC_cell_45


title: H3K36me3_EC_cell_42


title: H3K36me3_EC_cell_43


title: H3K36me3_EC_cell_41


title: H3K36me3_EC_cell_40


title: H3K36me3_EC_cell_39


title: H3K36me3_EC_cell_36


title: H3K36me3_EC_cell_37


title: H3K36me3_EC_cell_38


title: H3K36me3_EC_cell_35


title: H3K36me3_EC_cell_34


title: H3K36me3_EC_cell_57


title: H3K36me3_EC_cell_30


title: H3K36me3_EC_cell_28


title: H3K36me3_EC_cell_33


title: H3K36me3_EC_cell_31


title: H3K36me3_EC_cell_29


title: H3K36me3_EC_cell_27


title: H3K36me3_EC_cell_26


title: H3K36me3_EC_cell_48


title: H3K36me3_EC_cell_23


title: H3K36me3_EC_cell_24


title: H3K36me3_EC_cell_22


title: H3K36me3_EC_cell_20


title: H3K36me3_EC_cell_25


title: H3K36me3_EC_cell_21


title: H3K36me3_EC_cell_18


title: H3K36me3_EC_cell_19


title: H3K36me3_EC_cell_16


title: H3K36me3_EC_cell_44


title: H3K36me3_EC_cell_15


title: H3K36me3_EC_cell_12


title: H3K36me3_EC_cell_11


title: H3K36me3_EC_cell_14


title: H3K36me3_EC_cell_10


title: H3K36me3_EC_cell_13


title: H3K36me3_EC_cell_9


title: H3K36me3_EC_cell_32


title: H3K36me3_EC_cell_7


title: H3K36me3_EC_cell_6


title: H3K36me3_EC_cell_3


title: H3K36me3_EC_cell_1


title: H3K36me3_EC_cell_5


title: EZH2_100_rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad"
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bigwig files. Bigwig files of replicates data show reproducbility.

growth_protocol: Mouse embryonic stem cells were cultured in DMEM/F12 and neurobasal with 2i or 15% fetal bovine serum

extract_protocol:
The ESC was dissociated by 0.1% Trypsin digestion, and aliquot of cell numbers were directly used for in-situ ChIP
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

tag: cell type

value: cultured mESC (V6.5)

tag: cell state

value: Fixed by formaldehyde

value: EZH2, CST, 5246S, Lot:7


title: H3K36me3_EC_cell_17


title: H3K36me3_EC_cell_4


title: P300_2K


title: P300_100_rep2


title: H3K36me3_EC_cell_8


title: P300_100_rep1


title: EZH2_2K


title: CBP_100_rep1


title: EZH2_100_rep1


title: CBP_100_rep2


title: IgG_2K_ESC_rep1


title: H3K4me3_10K_ESC_ROC_rep1


title: H3K4me3_10K_ESC_ROC_rep2


title: H3K36me3_EC_cell_2


title: IgG_10K_ESC_rep1

value: native, cultured mESC (V6.5)

value: IgG, AB clonal, WH086883, Lot:AC005


title: H3K27me3_2K_ESC


title: H3K27me3_100_ESC_rep1


title: H3K27me3_100_ESC_rep2


title: H3K27ac_2K_ESC_rep2


title: IgG_10K_ESC_rep2


title: H3K27ac_100_ESC_rep2


title: H3K27ac_2K_ESC_rep1


title: H3K4me3_100_ESC_ROC_rep1


title: H3K27ac_100_ESC_rep1


title: H3K4me3_10K_ESC_rep1


title: CBP_2K


title: H3K4me3_100_ESC_rep4


title: H3K4me3_100_ESC_rep3


title: H3K4me3_10K_ESC_rep2


title: NKX2-5_E9.25_heart_rep2

extract_protocol:
The hearts of E9.25 embryo was isolated and directly used for in situ ChIP
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

value: E9.25 heart


title: H3K4me3_100_ESC_rep1


title: H3K4me3_100_ESC_rep2


title: IgG_E9.25_heart_rep1


title: IgG_E7.75_embryo

extract_protocol:
E6.5, E7.0 and E7.75 embryo were directly isolated form uterus and used for in-situ ChIP
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

value: IgG, AB clonal, WH086883, AC005


title: IgG_E9.25_heart_rep2


title: IgG_2K_ESC_rep2


title: IgG_E7.0_embryo


title: H3K4me3_100_ESC_ROC_rep2


title: NKX2-5_E9.25_heart_rep1


title: H3K27ac_E7.75_embryo_rep2


title: H3K27ac_E7.75_embryo_rep1


title: H3K27ac_E7.0_embryo_rep1


title: H3K4me3_E7.0_embryo_rep2


title: H3K27ac_E6.5_embryo_rep2


title: H3K4me3_E7.75_embryo_rep2


title: H3K27ac_E6.5_embryo_rep1


title: H3K4me3_E7.75_embryo_rep1


title: H3K4me3_E6.5_embryo_rep2


title: H3K4me3_E7.0_embryo_rep1


title: H3K4me3_E6.5_embryo_rep1


title: IgG_E6.5_embryo


title: H3K4me3_0.5M_ESC

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad"
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bigwig files.

source_name: cultured mESC (V6.5)

tag: strain background


title: H3K4me3_1M_ESC


title: H3K27ac_native_ESC_cell_2150

extract_protocol:
folloing CoBATCH protocol
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: The ESC was dissociated by 0.1% Trypsin digestion, and aliquot of cell numbers were directly used for in-situ ChIP

tag: cell type/status


title: H3K27ac_native_ESC_cell_2158


title: H3K27ac_native_ESC_cell_2154


title: H3K27ac_native_ESC_cell_2152


title: H3K27ac_native_ESC_cell_2148


title: H3K27ac_native_ESC_cell_2160


title: H3K27ac_native_ESC_cell_2155


title: H3K27ac_native_ESC_cell_2159


title: H3K27ac_native_ESC_cell_2147


title: H3K27ac_E7.0_embryo_rep2


title: H3K27ac_native_ESC_cell_2157


title: H3K27ac_native_ESC_cell_2149


title: H3K27ac_native_ESC_cell_2146


title: H3K27ac_native_ESC_cell_2145


title: H3K27ac_native_ESC_cell_2144


title: H3K27ac_native_ESC_cell_2141


title: H3K27ac_native_ESC_cell_2143


title: H3K27ac_native_ESC_cell_2142


title: H3K27ac_native_ESC_cell_2139


title: H3K27ac_native_ESC_cell_2138


title: H3K27ac_native_ESC_cell_2136


title: H3K27ac_native_ESC_cell_2161


title: H3K27ac_native_ESC_cell_2156


title: H3K27ac_native_ESC_cell_2140


title: H3K27ac_native_ESC_cell_2153


title: H3K27ac_native_ESC_cell_2151


title: H3K27ac_native_ESC_cell_2135


title: H3K27ac_native_ESC_cell_2130


title: H3K27ac_native_ESC_cell_2129


title: H3K27ac_native_ESC_cell_2134


title: H3K27ac_native_ESC_cell_2128


title: H3K27ac_native_ESC_cell_2127


title: H3K27ac_native_ESC_cell_2132


title: H3K27ac_native_ESC_cell_2126


title: H3K27ac_native_ESC_cell_2122


title: H3K27ac_native_ESC_cell_2121


title: H3K27ac_native_ESC_cell_2120


title: H3K27ac_native_ESC_cell_2124


title: H3K27ac_native_ESC_cell_2137


title: H3K27ac_native_ESC_cell_2118


title: H3K27ac_native_ESC_cell_2125


title: H3K27ac_native_ESC_cell_2131


title: H3K27ac_native_ESC_cell_2123


title: H3K27ac_native_ESC_cell_2114


title: H3K27ac_native_ESC_cell_2116


title: H3K27ac_native_ESC_cell_2115


title: H3K27ac_native_ESC_cell_2113


title: H3K27ac_native_ESC_cell_2119


title: H3K27ac_native_ESC_cell_2111


title: H3K27ac_native_ESC_cell_2112


title: H3K27ac_native_ESC_cell_2110


title: H3K27ac_native_ESC_cell_2108


title: H3K27ac_native_ESC_cell_2109


title: H3K27ac_native_ESC_cell_2133


title: H3K27ac_native_ESC_cell_2107


title: H3K27ac_native_ESC_cell_2105


title: H3K27ac_native_ESC_cell_2106


title: H3K27ac_native_ESC_cell_2104


title: H3K27ac_native_ESC_cell_2100


title: H3K27ac_native_ESC_cell_2102


title: H3K27ac_native_ESC_cell_2101


title: H3K27ac_native_ESC_cell_2099


title: H3K27ac_native_ESC_cell_2097


title: H3K27ac_native_ESC_cell_2094


title: H3K27ac_native_ESC_cell_2095


title: H3K27ac_native_ESC_cell_2093


title: H3K27ac_native_ESC_cell_2096


title: H3K27ac_native_ESC_cell_2098


title: H3K27ac_native_ESC_cell_2091


title: H3K27ac_native_ESC_cell_2090


title: H3K27ac_native_ESC_cell_2086


title: H3K27ac_native_ESC_cell_2117


title: H3K27ac_native_ESC_cell_2092


title: H3K27ac_native_ESC_cell_2088


title: H3K27ac_native_ESC_cell_2087


title: H3K27ac_native_ESC_cell_2085


title: H3K27ac_native_ESC_cell_2081


title: H3K27ac_native_ESC_cell_2082


title: H3K27ac_native_ESC_cell_2083


title: H3K27ac_native_ESC_cell_2080


title: H3K27ac_native_ESC_cell_2079


title: H3K27ac_native_ESC_cell_2078


title: H3K27ac_native_ESC_cell_2103


title: H3K27ac_native_ESC_cell_2089


title: H3K27ac_native_ESC_cell_2084


title: H3K27ac_native_ESC_cell_2076


title: H3K27ac_native_ESC_cell_2073


title: H3K27ac_native_ESC_cell_2077


title: H3K27ac_native_ESC_cell_2072


title: H3K27ac_native_ESC_cell_2070


title: H3K27ac_native_ESC_cell_2074


title: H3K27ac_native_ESC_cell_2069


title: H3K27ac_native_ESC_cell_2067


title: H3K27ac_native_ESC_cell_2064


title: H3K27ac_native_ESC_cell_2062


title: H3K27ac_native_ESC_cell_2061


title: H3K27ac_native_ESC_cell_2065


title: H3K27ac_native_ESC_cell_2063


title: H3K27ac_native_ESC_cell_2053


title: H3K27ac_native_ESC_cell_2056


title: H3K27ac_native_ESC_cell_2057


title: H3K27ac_native_ESC_cell_2055


title: H3K27ac_native_ESC_cell_2058


title: H3K27ac_native_ESC_cell_2052


title: H3K27ac_native_ESC_cell_2054


title: H3K27ac_native_ESC_cell_2059


title: H3K27ac_native_ESC_cell_2051


title: H3K27ac_native_ESC_cell_2050


title: H3K27ac_native_ESC_cell_2049


title: H3K27ac_native_ESC_cell_2071


title: H3K27ac_native_ESC_cell_2075


title: H3K27ac_native_ESC_cell_2048


title: H3K27ac_native_ESC_cell_2047


title: H3K27ac_native_ESC_cell_2046


title: H3K27ac_native_ESC_cell_2043


title: H3K27ac_native_ESC_cell_2045


title: H3K27ac_native_ESC_cell_2044


title: H3K27ac_native_ESC_cell_2068


title: H3K27ac_native_ESC_cell_2060


title: H3K27ac_native_ESC_cell_2042


title: H3K27ac_native_ESC_cell_2041


title: H3K27ac_native_ESC_cell_2066


title: H3K27ac_native_ESC_cell_2040


title: H3K27ac_native_ESC_cell_2039


title: H3K27ac_native_ESC_cell_2035


title: H3K27ac_native_ESC_cell_2038


title: H3K27ac_native_ESC_cell_2037


title: H3K27ac_native_ESC_cell_2036


title: H3K27ac_native_ESC_cell_2032


title: H3K27ac_native_ESC_cell_2033


title: H3K27ac_native_ESC_cell_2029


title: H3K27ac_native_ESC_cell_2026