title: Col_0_bio2


title: NT_rep1

status: Public on Jun 21 2020

type: SRA

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

country: China

institute: City University of Hong Kong

library_source: transcriptomic

data_processing:
Basecalling is performed by Illumina RTA software in sequencer
Demultiplexing is performed by Illumina bcl2fastq 2.17 software based on index information
RNA-seq reads were mapped to both 129S1/SvImJ and CAST/EiJ transcriptome reference sequences using Bowtie2 (version 2.1.0)
RNA-seq reads at SNP/indel sites were counted using samtools (version 0.1.19) depth command.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text file includes read counts at SNP/indel sites for both alleles.

molecule: total RNA

organism: Mus musculus musculus x Mus musculus castaneus

extract_protocol:
Total RNA was extracted and processed to remove rRNA by NEBNext rRNA depletion kit (NEB).
RNA-seq library preparation using NEBNext UltraTM II directional RNA library prep kit for Illumina (NEB).

tag: strain background

value: 129S1/SvImJ x CAST/EiJ

tag: cell type

value: mouse embryonic fibroblasts (MEF)

tag: treatment

tag: biological replicate

value: rep 1


title: LM_seq_293T_WT_rep1

description: MGISEQ-2000 platform

data_processing:
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
LM-Seq reads were aligned to the hg19 genome assembly using HISAT2 version 2.1.0 with default parameters.
Sam files were converted to bam files by using samtools version 1.9.
Gene expression was quantified using gFold version 1.1.4(Feng et al., Bioinformatics, 2012.).
Gene expression matrix merges using a customer script.
Data visualization by using the R ggplot package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample and one tab-delimited text file include gene expression matrix for all samples.

molecule: polyA RNA

organism: Homo sapiens

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in DMEM (Life Technologies) supplemented with 10% FBS (Life Technologies) and 1% penicillin-streptomycin (Life Technologies) at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated using MiniBEST Universal RNA Extraction Kit (TAKARA) following manufacturer’s instruction.
RNA-seq library was prepared using LM-seq library prep protocol (Hou, Z., et al. (2015). "A cost-effective RNA sequencing protocol for large-scale gene expression studies." Sci Rep 5: 9570.)

treatment_protocol: For RNA seq, transfections were performed in 6-well plates. 500,000 cells were seeded in each well one day before transfection. 1.5 μg of gRNA expressing plasmid and 1.5 μg of BASU-dCasRx constructs were co-transfected with 9 μg of PEI in each well. Forty-eight hours following transfection, the cells were harvested for total RNA extraction.

tag: cell line

value: human embryonic kidney (HEK) 293T cells

tag: transfection

value: control (WT)


title: Col_0_bio1

city: Beijing

first: Lei

last: Wang

address: Nanxincun 20, Xiangshan, Haidian District

department: Key Laboratory of Plant Molecular Physiology

institute: insitute of botany, chinese academy of sciences

data_processing:
150 nt paired-end high throughput sequencing was performed on an Illumina Hiseq X ten.
Low quality sequencing reads were removed. Clean reads were mapped to the Arabidopsis reference genome (TAIR10, www.arabidopsis.org) with Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml) software, and differential expressed genes (DEGs) was identified using edgeR in the R package (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) if FoldChange > 2 and FDR < 0.05 between case group sample and control group sample. GO and KEGG pathway enrichment analysis was performed using TopGO in the R package (http://bioconductor.org/).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: WT_whole seedling

growth_protocol: Plants were grown under LD conditions at 22ºC for 10 days and harvest at ZT15.

extract_protocol:
Total RNA was extracted with Trizol reagent (Ambion) and treated with DNase I (Thermo Fisher).
Sequencing libraries were prepared following the protocol of the Directional RNA library Prep Kit (NEB).

tag: genotype/variation

value: Wild type

tag: age

tag: medium

value: MS+3% sucrose

tag: time point

tag: tissue

value: whole seedling


title: Taf15_sh44_5a_rep1

value: TAF15 knockdown + 5-aza treatment


title: toc1-21 prr5-1_bio3

source_name: toc1-21 prr5-1_whole seedling


title: CD11b+ MDSC from spleen, biological rep3

type: RNA

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description:
Cd11b_spleen_3
Gene expression profile of CD11b+ cells from spleen of mice 9 days after s.c. challenge with 5E5 C26GM tumor cells.

hyb_protocol: According to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004.

data_processing: RMA of .CEL files using Bioconductor affy library and Brainarray custom CDF Mouse4302_Mm_ENTREZG_21.0.0. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization.

label: biotin

organism: Mus musculus

source_name: CD11b+ cells from spleen of mice 9 days after s.c. challenged with 5E5 C26GM tumor cells

growth_protocol: Balb/c mice were challenged with 5E5 C26GM cells sc. 9 days later, CD11b+ cells were magnetically isolated (Miltenyi) from RBC lysed splenocytes or collagenase (Sigma) treated tumors. CD11b+ cells purity was higher than 95% as per flow cytometry analysis.

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer guidelines, with minor modifications. Extraction was followed by Qiagen RNeasy column clean-up according to manufacturer instructions.

tag: strain/background

value: BALB/c

value: Spleen

value: CD11b+ MDSC

tag: experimental condition

value: Tumor-bearing


title: CD11b+ MDSC from spleen, biological rep4

description:
Cd11b_spleen_4
Gene expression profile of CD11b+ cells from spleen of mice 9 days after s.c. challenge with 5E5 C26GM tumor cells.

scan_protocol: According to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004.


title: CD11b+ MDSC from spleen, biological rep2

description:
Cd11b_spleen_2
Gene expression profile of CD11b+ cells from spleen of mice 9 days after s.c. challenge with 5E5 C26GM tumor cells.

label_protocol: According to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004.


title: CD11b+ MDSC from spleen, biological rep1

description:
Cd11b_spleen_1
Gene expression profile of CD11b+ cells from spleen of mice 9 days after s.c. challenge with 5E5 C26GM tumor cells.


title: CBMS1_Day7Diff_ESC_single_MidS_53

status: Public on Jun 20 2020

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description: 80kb resolution data

library_source: genomic

data_processing:
Sequence reads were trimmed to remove adapter sequences using the cutadapt program before mapping. For WGA samples, we performed a two-step adapter trimming, first removing the Illumina adapter based on the index of each NGS library and then removing the SEQXE adapter. As the SEQXE adapter sequence was not available, we empirically estimated it as the sequence that repeatedly appeared near the 5’ end.
Trimmed reads were mapped into mm9 and CBMS1-specific (CBA/MsM) diploid genome based on mm9 genomeby using bwa (ver: 0.7.10-r789, command: bwa aln => bwa samse). CBMS1-specific diploid genome was constructed as described in Sakata et al. Development (2017) with minor modifications using CBA or MsM strain genomic reads. Duplicated reads mapped into mm9 were removed by using picard tool and the reads overlapped with mm9 black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. The mapped reads with MAQP>10 were used for the further analysis. For the diploid genome mapping, we defined MAPQ>16 as the allele specific reads and used the liftover tool (UCSC Genome Browser) to convert to the mm9 genome coordinates. After this, duplicate reads identified as an identical chromosome start position and strand information were filtered out.
Single-cell data (CBMS1, differentiated CBMS1, EpiSC un-resolved at 80-kb): first, we counted the reads in non-overlapping 80-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the merged G1 control. Binarization was performed using the Mappability corrected 25per-S (25% S-phase) , Mid-S (50% S-phase), 75per-S (75% S-phase) reads described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy"; options for Mid-S, 75per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"; 1-somy, unreplicated; 2-somy, replicated]. In the processed data files, replicated bin was shown as 1, unrelicated bin was shown as -1, and no-data was shown as 0. “Repliscore” was calculated as a percentage of replicated bins in the total number of replicated and unreplicated bins.
Single-cell haplotype-resolved chrX data (d0, d2, d7): after the specific filtering steps for haplotype-resolved data, we counted the reads in non-overlapping 400-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the filtered merged G1 control. Binarization was performed as described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy" ; options for Mid-S, 75per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"].
For paired-end reads, only "R1" (Fwd) reads were used for the analysis.
Binarized 40kb data: Sample_Name_40k_100S_MAP_2HMM2_eps0.01.binary.bedGraph
Genome_build: mm9
Supplementary_files_format_and_content:  We provide three types of processed data files. One is the binarized data (scRepliseq_data_884cells_G1_Sphase_binary_data_80kb.txt). Second is the sample information data (scRepliseq_data_sample_Info.txt). Third is the haplotype-resolved Mid-S binarized data of chrX (scRepliseq_d0_33_CBA_XX_chrX_only_400kb.txt, scRepliseq_d0_33_MsM_XX_chrX_only_400kb.txt, scRepliseq_d2_27_CBA_XX_chrX_only_400kb.txt, scRepliseq_d2_27_MsM_XX_chrX_only_400kb.txt, scRepliseq_d7_36_XX_Xa_chrX_only_400kb.txt, scRepliseq_d7_36_XX_Xi_chrX_only_400kb.txt). We also provide README file for the description of each processed file.
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

source_name: Day7 Differentiated CBMS1 ESC

growth_protocol: CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013). EpiSCs (female) and their culture protocol have been described and were grown in Activin/FGF medium as described (Tesar et al. 2007).

extract_protocol:
For single cells samples, cells were sorted with a Sony SH800 cell sorter using the single-cell mode. Sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu).
NGS libraries were constructed with a NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions, with slight modifications based on the previous study (Kadota et al., Sci. Rep. 2017). For a multi-plex NGS run, a SeqCap adapter kit A/B (Roche, 07141530001/ 07141548001) and NEXTflex DNA barcode (Bio Scientific, NOVA) were used. The samples were subjected to NGS on an Illumina Hiseq 1500 system (80-bp length, single-read).

treatment_protocol: For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).

tag: strain

value: CBA/MsM

value: day7differentiated ESCs

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

value: FALSE

tag: cell cycle phase

value: MidS


title: CBMS1_Day7Diff_ESC_single_MidS_60

description: 80kb resolution data

tag: cell type


title: CBMS1_Day7Diff_ESC_single_MidS_62

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_57

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_61

description: 80kb resolution data

value: TRUE


title: CBMS1_Day7Diff_ESC_single_MidS_52

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_58

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_59

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_54

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_51

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_55

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_49

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_56

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_47

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_44

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_43

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_46

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_17

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_15

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_14

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_16

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_13

description: 80kb resolution data


title: Liver_γ-conglutin_7day_rep2

city: Guadalajara

first: Carmen

middle: Magdalena

last: Gurrola-Díaz

state: Jalisco

address: Sierra Mojada 950

department: Departamento de Biología Molecular y Genómica

country: Mexico

institute: Universidad de Guadalajara

hyb_protocol: Equivalent amounts of labelled cDNA were hybridized on printed arrays using UniHyb solution (TeleChem International Inc., USA) for 14 h, 42 °C.

scan_protocol: Array images were acquired and quantified in a GenePix 4100-A reader using GenePix software (Molecular Devices, USA).

data_processing: The genArise free software package was used to analyze the microarray data (Computing Unit of Cellular Physiology Institute of UNAM, http://www.ifc.unam.mx/genarise/). This software is a tool for dual-color microarray data implemented in the R language. It contains specific functions to perform an analysis of DNA microarrays data to detect genes that are significantly differentially expressed under different conditions by calculating an intensity-dependent Z-score.

organism: Rattus norvegicus

source_name: liver, γ-conglutin-treated, seven day treatment

label_protocol: High-quality total RNA was retrotranscribed using dUTP-Alexa555 or dUTP-Alexa647 fluorophores with the First-Strand cDNA Synthesis kit (ThermoFisher Scientific, USA). Incorporated fluorophores were analyzed by measuring the absorbance at 555 nm and 650 nm for Alexa555 and Alexa647, respectively.

growth_protocol: Male Wistar rats were caged, fed a standard rodent chow diet and water ad libitum, and maintained under a 24 ± 2 °C temperature, 55 ± 5% humidity, and 12 h-dark/light cycles.

extract_protocol: The liver was removed, washed in sterile saline, excised, and homogenized in RLT buffer. Later, total RNA was extracted using RNeasy Mini Kit (QIAGEN, USA) following manufacturer instructions.

treatment_protocol: Adult animals were fasted overnight (12 h) and chemically-induced to diabetes by a single intraperitoneal injection of STZ (65 mg/kg BW). Diabetes (glycaemia levels > 200 mg/dl) was confirmed 72 h after tue induction, and diabetic animals were randomly allocated into one of two groups of five rats each, as follows: 1) STZ-Ctrl, diabetic rats receiving only vehicle (0.9% w/v NaCl) or 2) STZ-Cγ, rats induced to diabetes and treated with γ-conglutin (120 mg/kg BW) dissolved in 0.9% NaCl. Treatment was administered for seven consecutive days.

value: Wistar

value: Liver

tag: developmental stage

value: Adult

tag: treatment

value: γ-conglutin

source_name: liver, vehicle-treated (control), seven day treatment

value: control


title: CBMS1_Day7Diff_ESC_single_G1_12

description: 80kb resolution data


title: Liver_γ-conglutin_7day_rep1


title: CBMS1_Day7Diff_ESC_single_MidS_50

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_48

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_11

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_45

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_10

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_08

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_09

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_32

description: 80kb resolution data

value: XX

value: MsM

value: CBA


title: CBMS1_Day7Diff_ESC_single_G1_06

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_28

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_05

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_30

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_26

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_27

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_31

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_33

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_04

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_29

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_24

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_25

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_23

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_20

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_22

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_18

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_21

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_19

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_17

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_16

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_14

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_15

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_07

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_13

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_12

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_11

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_08

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_10

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_04

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_03

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_07

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_02

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_65perS_11

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_65perS_12

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_05

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_65perS_06

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_65perS_10

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_65perS_09

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_65perS_08

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_65perS_05

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_65perS_07

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_65perS_02

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_65perS_04

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_65perS_03

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_55perS_12

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_65perS_01

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_55perS_11

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_55perS_09

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_55perS_10

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_55perS_08

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_09

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_55perS_07

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_55perS_06

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_55perS_05

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_06

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_75perS_01

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_55perS_04

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_55perS_02

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_55perS_03

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_50perS_21

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_50perS_18

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_50perS_23

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_50perS_20

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_50perS_19

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_50perS_22

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_50perS_16

description: 80kb resolution data


title: MBS cell line 4

city: New York

first: Jeetayu

last: Biswas

state: NY

address: 417 East 68th St

department: Molecular Pharmacology

country: USA

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Sequencing was performed by Novogene Inc., basecalling was performed using Illumina CASAVA 1.8
Sequenced reads were trimmed with cutadapt 1.12 and then aligned to the genome with STAR 020201
Alignments were processsed with samtools 1.3.1 and duplicate reads were removed using picard 2.8.2
Identification of RNA editing sites was determined using the protocol described in Rahman et al, Nature Protocols 2018, publicly available at: [https://github.com/rosbashlab/HyperTRIBE/]
Identification of CLIP peaks was determined using the CIMS protocol described in Zhang and Darnell, Nature  Biotechnology, 2011
Genome_build: mm10, hg38, both were modified to contain the MS2 stem loop array as a separate contig
Supplementary_files_format_and_content: Editing sites shared between replicates with 5% threshold provided as bedgraph files

source_name: Mouse embryo

extract_protocol:
CLIP protocol from (Cho et al., 2012) was used with the following adaptations  15cm dishes of MEFs (at ~70% confluency) were washed with ice cold DPBS, after aspiration and addition of 12mL ice cold DPBS, cells were irradiated with 300mJ/cm of 254nm UV light (BioRad GS Gene Linker). After irridation, each 15cm dish was scraped and collected into a 15mL falcon tube. Cells were pelleted at 500g for 5 minutes and then the pellets were stored at -80 until use. For Immunoprecipitations, a 1:1 mix of monoclonal Anti-GFP antibodies (Sigma Aldrich / Roche 11814460001) were used with protein G dynabeads (4ug of antibodies with 50uL of beads, Thermo Fisher Scientific). All washes were performed using a magnetic stand.
CLIP library construction protocol from (Cho et al., 2012) was used. Briefly, RNAse A was used to cleave the RNA prior to 3' adapter ligation. After purification and gel extraction of crosslinked fragments, 5' end adapter ligation was performed. Generation of cDNA, purification, amplification and size selection of amplfied cDNA libraries was performed as per Cho et al, 2012 and then sequenced on NextSeq500 in high output mode.

value: MEF

value: Fibroblast

tag: clip antibody

value: anti-GFP

tag: experiment

value: CLIP


title: CBMS1_Day7Diff_ESC_single_50perS_17

description: 80kb resolution data

value: CBA/MsM

value: day7differentiated ESCs


title: REH cells 25uM ML141 24 hours 3

city: London

first: Owen

last: Williams

address: 30 Guilford Street

department: Cancer section

country: United Kingdom

institute: UCL GOS ICH

data_processing:
All tools in the analysis were invoked through the Galaxy Project for NGS analysis, as follows:
Fastq was demultiplexed and generated using Illumina bcl2fastq v2.19 before pre-processing (trimmomatic) to remove adapter read-through and poor quality sequences.
Pre-processed data were then aligned to the genome (UCSC hg38) with Bowtie 2 and deduplicated using Picard.
Reads-per-transcript were counted by FeatureCounts, before differential expresson analysis by SARTools, a DESeq2 wrapper.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file including average count values for each sample.

source_name: REH cells 25uM ML141 24 hours

growth_protocol: REH cells (B precursor ALL cell line) (DSMZ, Braunschweig, Germany) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 100 units/ml penicillin and 100 ug/ml streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted with RNeasy Plus Mini Kit according to manufacturers instructions
Indexed RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA v2 protocols

treatment_protocol: REH cells were treated for 24 hours with DMSO or 25uM ML141

tag: cell line

value: REH

value: Pre-B Acute Lymphoblastic Leukemia (ALL) cell line


title: REH cells 25uM ML141 24 hours 2


title: HepG2

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 16
Trimmed reads were mapped against the human genome (hg38 UCSC) using Bowtie2 (v 2.3.2) with parameters  -p 6 -N 1 --un-gz
alignments were sorted using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -1 -t miRNA -g ID and miRBase annotations (v 21, GRCh 38)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including CPM values

source_name: small RNA-Seq of HepG2 cells

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
Small RNA-seq libraries and sequencing was performed by Novogene (Hong Kong)

treatment_protocol: 48 hours upon seeding cells were harvested for RNA extraction.

value: liver cancer derived cell line

tag: genotype/variation

value: parental cell line

tag: passages

value: harvested 48h upon seeding


title: CBMS1_Day7Diff_ESC_single_50perS_15

description: 80kb resolution data

value: Single cell

value: FALSE


title: REH cells DMSO 24 hours 3

source_name: REH cells DMSO 24 hours

value: DMSO


title: CBMS1_Day7Diff_ESC_single_50perS_13

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_50perS_14

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_55perS_01

description: 80kb resolution data

value: TRUE


title: RAW GfI1-1 at T0, biological rep2

city: Xinxiang

first: Qianqian

last: Zheng

address: 601 Jinsui Road

institute: Xinxiang Medical University

description: Gene expression data from RAW GfI1-1 at T0

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix GeneChip® Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: RAW GfI1-1 at T0

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: RAW264.7 macrophages were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing  Downloaded from www.jlr.org by guest, on November 2, 20196  10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 µg/ml streptomycin.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: without treatment

value: RAW GfI1-1


title: Bone marrow-derived stromal cells

city: Charlottesville

first: Basel

last: Al-Barghouthi

state: VA

institute: University of Virginia

description: Pooled cells from 5 mice, aged 87,90 92,92, and 79 days for 1 male sample and 4 female samples, respectively.

data_processing:
The library was sequenced on the Illumina NextSeq500 and the raw sequencing data was processed using CellRanger toolkit (version 2.0.1).
The reads were mapped to mm10 mouse reference genome assembly using STAR (version 2.5.1b)
Genome_build: mm10
Supplementary_files_format_and_content: The cellranger pipeline outputs feature-barcode matrices. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). Matrices are filtered by the cellranger pipeline to include only detected cellular barcodes. Each matrix is stored in the Market Exchange Format (MEX) for sparse matrices. Also included are gzipped TSV files with feature and barcode sequences corresponding to row and column indices respectively.

source_name: Bone marrow-derived stromal cells cultured from femoral bone marrow

growth_protocol: Previously frozen bone marrow were thawed at 37C, resuspended into 5mls bone marrow growth media (Alpha MEM, 10% FBS, 1% Pen/Strep, 0.01% Glutamax), pelleted in a Sorvall tabletop centrifuge at 1000rpm for 5 minutes at room temperature and then subjected to red blood cell lysis. Cells were pelleted again,resuspended into 1ml bone marrow growth media, plated into one well per sample of a 48 well tissue culture plate and placed into a 37C, 5% CO 2 incubator undisturbed for 3 days post- plating at which time the media was aspirated, cells were washed with 1ml DPBS one time and bone marrow growth media was replaced at 300ul volume. Repeated wash process through day  5 post-plating. At day 6 post-plating, cells were washed in same manner however bone marrow growth media was replaced with 300 ul bone marrow differentiation media (Alpha MEM, 10% FBS, 1% Penicillin Streptomycin, 0.01% Glutamax, 50mg/ml Ascorbic Acid, 1M B-glycerophosphate, 100uM Dexamethasome). Cultures were then washed in same manner every other day for following 10 days.

extract_protocol:
The left femurs of 5 Diversity Outbred mice (4 females, 1 male) were isolated and cleaned thoroughly of all muscle tissue followed by removal of the distal epiphysis. For each femur, marrow was exuded by centrifugation at 2000g for 30 seconds into a sterile tube containing 35ul freezing media (90% FBS, 10% DMSO). The marrow was then triterated 6 times on ice after addition of 150ul ice cold freezing media and again after further addition of 1ml ice cold freezing media until no visible clumps remained prior to being placed into a Mr. Frosty Freezing Container (Thermo Scientific) and stored overnight at -80C. Samples were transferred the following day to liquid nitrogen for long term storage.
Day 10 mineralized bone marrow cultures were washed twice with DPBS followed by addition of 0.5ml 60mM EDTA for a 15-minute room temperature incubation. The cultures were aspirated and solution replaced for a second incubation. Cultures were then washed with 0.5ml HBSS followed by a 37C shaking incubation containing 0.5ml 8mg/ml collagenase in HBSS/4mM CaCl 2 for 10 minutes after which cultures were triterated 10 times, incubated at 37C for 20 minutes and transferred to 1.5ml tubes. Cells were then pelleted in Sorvall tabletop centrifuge at 500g for 5 minutes at room temperature, resuspended into 0.5ml 0.25% trypsin and incubated for 15 minutes at 37C followed by triteration and incubation for an additional 15 minutes after which 0.5ml media was added, cells were re-triterated, re-pelleted, resuspended into 0.5ml bone marrow differentiation media (Alpha MEM, 10% FBS, 1% Penicillin Streptomycin, 0.01% Glutamax, 50mg/ml Ascorbic Acid, 1M B-glycerophosphate, 100uM Dexamethasome) and counted.
The samples were pooled and concentrated to 800 cells/ul in sterile PBS supplemented with 0.1% BSA. The single cell suspension was loaded into a 10xChromium Controller (10X Genomics, Pleasanton, CA, USA), aiming to capture 8,000 cells, with the Single Cell 3’ v2 reagent kit, according to the manufacturer’s protocol. Following Gem capturing and lysis, cDNA was amplified (13 cycles) and the manufacturer’s protocol was followed to generate sequencing library.

value: Cultured bone marrow-derived stromal cells

value: Diversity Outbred (J:DO)


title: REH cells DMSO 24 hours 2


title: RAW WT at T0, biological rep2

description: Gene expression data from RAW WT at T0

source_name: RAW WT at T0

value: RAW WT


title: RAW GfI1-1 at T0, biological rep3


title: RAW GfI1-1 at T0, biological rep1


title: RAW WT at T0, biological rep3

description: Gene expression data from RAW WT at T0


title: RAW GfI1-1 at T0, biological rep4


title: REH cells 25uM ML141 24 hours 1


title: CBMS1_Day7Diff_ESC_single_50perS_12

description: 80kb resolution data

value: XX

value: MsM

value: CBA


title: CBMS1_Day7Diff_ESC_single_50perS_10

description: 80kb resolution data

value: CBA/MsM

value: day7differentiated ESCs


title: Cell line without MBS 4

value: MEF

tag: tissue

value: Fibroblast

value: anti-GFP

value: CLIP


title: REH cells DMSO 24 hours 1

value: REH

value: Pre-B Acute Lymphoblastic Leukemia (ALL) cell line


title: CBMS1_Day7Diff_ESC_single_50perS_11

description: 80kb resolution data

value: Single cell


title: RAW WT at T0, biological rep1

description: Gene expression data from RAW WT at T0


title: CBMS1_Day7Diff_ESC_single_50perS_09

description: 80kb resolution data

value: TRUE


title: CBMS1_Day7Diff_ESC_single_50perS_08

description: 80kb resolution data

value: FALSE


title: CBMS1_Day7Diff_ESC_single_50perS_07

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_50perS_06

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_50perS_05

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_50perS_04

description: 80kb resolution data


title: O-183N surrounded HCC

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: liver tissue

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: Liver tissue was obtained by surgical resection.

extract_protocol: Total RNA from liver biopsy was extracted commercially available kit (miReasy mini kit (Qiagen)).

treatment_protocol: Liver tissue sample was obtained before anti-viral treatment.

tag: disease state

value: surrounded HCC

tag: age

tag: Sex

value: M

tag: bmi

value: no data

tag: viral infection

value: HCV


title: O-184N surrounded HCC

value: NBNC


title: O-186N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_50perS_02

description: 80kb resolution data

tag: strain

tag: sample state

tag: xx or xo chromosomes in single cell samples

value: XX

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

value: MsM

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

value: CBA


title: CBMS1_Day7Diff_ESC_single_50perS_03

description: 80kb resolution data

value: CBA/MsM

tag: cell type

value: day7differentiated ESCs

tag: repliscore of 40–70%

tag: cell cycle phase


title: O-185N surrounded HCC


title: O-182N surrounded HCC


title: O-187N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_50perS_01

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_45perS_12

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_45perS_10

description: 80kb resolution data


title: O-177N surrounded HCC

value: F


title: CBMS1_Day7Diff_ESC_single_45perS_11

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_45perS_09

description: 80kb resolution data


title: O-181N surrounded HCC


title: O-175N surrounded HCC


title: O-180N surrounded HCC


title: O-179N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_45perS_08

description: 80kb resolution data


title: O-178N surrounded HCC

value: HBV


title: O-174N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_45perS_07

description: 80kb resolution data


title: O-176N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_45perS_06

description: 80kb resolution data


title: O-172N surrounded HCC


title: O-173N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_45perS_05

description: 80kb resolution data


title: O-171N surrounded HCC


title: O-170N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_45perS_04

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_45perS_03

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_35perS_12

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_45perS_01

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_45perS_02

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_35perS_11

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_35perS_10

description: 80kb resolution data


title: O-167N surrounded HCC


title: O-168N surrounded HCC


title: O-169N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_35perS_08

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_35perS_09

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_35perS_06

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_35perS_05

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_35perS_07

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_35perS_04

description: 80kb resolution data


title: O-164N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_35perS_03

description: 80kb resolution data


title: O-166N surrounded HCC


title: O-158N surrounded HCC


title: O-157N surrounded HCC


title: O-165N surrounded HCC


title: O-159N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_35perS_02

description: 80kb resolution data


title: O-161N surrounded HCC


title: O-162N surrounded HCC


title: O-160N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_35perS_01

description: 80kb resolution data


title: O-156N surrounded HCC


title: O-155N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_34

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_31

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_35

description: 80kb resolution data


title: O-163N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_33

description: 80kb resolution data


title: O-146N surrounded HCC


title: O-150N surrounded HCC


title: O-153N surrounded HCC


title: O-152N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_32

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_29

description: 80kb resolution data


title: O-151N surrounded HCC


title: O-147N surrounded HCC


title: O-148N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_28

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_26

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_25

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_24

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_23

description: 80kb resolution data


title: O-144N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_30

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_22

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_27

description: 80kb resolution data


title: O-149N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_20

description: 80kb resolution data


title: O-141N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_21

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_18

description: 80kb resolution data


title: O-140N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_19

description: 80kb resolution data


title: O-145N surrounded HCC


title: O-139N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_17

description: 80kb resolution data


title: O-137N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_16

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_15

description: 80kb resolution data


title: O-143N surrounded HCC


title: O-134N surrounded HCC


title: O-133N surrounded HCC


title: O-142N surrounded HCC


title: O-135N surrounded HCC


title: O-132N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_14

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_13

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_12

description: 80kb resolution data


title: O-131N surrounded HCC


title: O-138N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_11

description: 80kb resolution data


title: O-130N surrounded HCC


title: O-129N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_10

description: 80kb resolution data


title: O-136N surrounded HCC


title: O-127N surrounded HCC


title: O-126N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_09

description: 80kb resolution data


title: O-125N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_08

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_07

description: 80kb resolution data


title: O-124N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_06

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_05

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_03

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_04

description: 80kb resolution data


title: O-123N surrounded HCC


title: O-122N surrounded HCC


title: CBMS1_Day7Diff_ESC_single_25perS_01

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_25perS_02

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_75perS_12

description: 80kb resolution data

source_name: Day5 Differentiated CBMS1 ESC

value: day5 differentiated ESCs


title: O-121N surrounded HCC


title: CBMS1_Day5Diff_ESC_single_75perS_11

description: 80kb resolution data


title: O-115N surrounded HCC-2


title: O-115N surrounded HCC


title: O-113N surrounded HCC


title: O-112N surrounded HCC


title: CBMS1_Day5Diff_ESC_single_75perS_10

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_75perS_09

description: 80kb resolution data


title: O-111N surrounded HCC


title: CBMS1_Day5Diff_ESC_single_75perS_08

description: 80kb resolution data


title: O-109N surrounded HCC


title: O-110N surrounded HCC


title: O-108N surrounded HCC


title: O-106N surrounded HCC


title: O-105N surrounded HCC


title: CBMS1_Day5Diff_ESC_single_75perS_06

description: 80kb resolution data


title: O-104N surrounded HCC


title: O-103N surrounded HCC


title: O-100N surrounded HCC


title: CBMS1_Day5Diff_ESC_single_55perS_08

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_35perS_11

description: 80kb resolution data


title: O-092N surrounded HCC


title: CBMS1_Day5Diff_ESC_single_75perS_07

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_35perS_12

description: 80kb resolution data


title: O-093N surrounded HCC


title: CBMS1_Day5Diff_ESC_single_45perS_09

description: 80kb resolution data


title: O-089N surrounded HCC


title: O-090N surrounded HCC


title: CBMS1_Day5Diff_ESC_single_25perS_10

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_65perS_10

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_65perS_09

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_25perS_08

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_25perS_09

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_25perS_07

description: 80kb resolution data


title: O-088N surrounded HCC


title: O-086N surrounded HCC


title: O-087N surrounded HCC


title: CBMS1_Day5Diff_ESC_single_55perS_07

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_65perS_08

description: 80kb resolution data


title: O-011N surrounded HCC


title: O-098N surrounded HCC


title: O-009N surrounded HCC


title: CBMS1_Day5Diff_ESC_single_25perS_11

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_35perS_10

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_G1_10

description: 80kb resolution data

source_name: Day2 Differentiated CBMS1 ESC

value: day2 differentiated ESCs


title: CBMS1_Day2Diff_ESC_single_G1_11

description: 80kb resolution data

source_name: Day3 Differentiated CBMS1 ESC

value: day3 differentiated ESCs

value: Single cell


title: O-010N surrounded HCC


title: CBMS1_Day2Diff_ESC_single_G1_07

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_G1_09

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_75perS_16

description: 80kb resolution data

value: FALSE


title: CBMS1_Day2Diff_ESC_single_75perS_15

description: 80kb resolution data


title: O-008N surrounded HCC

value: surrounded HCC


title: CBMS1_Day2Diff_ESC_single_75perS_12

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_75perS_14

description: 80kb resolution data


title: O-004N surrounded HCC

value: M


title: CBMS1_Day2Diff_ESC_single_75perS_13

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_75perS_11

description: 80kb resolution data


title: O-006N surrounded HCC

value: no data


title: O-002N surrounded HCC

value: HCV


title: O-007N surrounded HCC


title: O-005N surrounded HCC


title: O-003N surrounded HCC


title: CBMS1_Day2Diff_ESC_single_65perS_20

description: 80kb resolution data


title: O-001N surrounded HCC


title: CBMS1_Day2Diff_ESC_single_65perS_19

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_65perS_21

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_G1_08

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_65perS_17

description: 80kb resolution data


title: O-183T HCC

value: HCC


title: O-182T HCC

value: NBNC


title: O-186T HCC


title: O-184T HCC


title: O-185T HCC


title: O-187T HCC


title: O-179T HCC


title: CBMS1_Day2Diff_ESC_single_65perS_16

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_65perS_15

description: 80kb resolution data


title: O-181T HCC


title: O-177T HCC


title: O-178T HCC


title: CBMS1_Day2Diff_ESC_single_65perS_14

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_55perS_19

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_65perS_18

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_55perS_18

description: 80kb resolution data

value: XX

value: TRUE


title: CBMS1_Day2Diff_ESC_single_55perS_16

description: 80kb resolution data

value: CBA/MsM


title: CBMS1_Day2Diff_ESC_single_55perS_17

description: 80kb resolution data


title: O-180T HCC


title: CBMS1_Day2Diff_ESC_single_55perS_15

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_55perS_14

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_55perS_13

description: 80kb resolution data


title: O-171T HCC


title: O-170T HCC


title: CBMS1_Day2Diff_ESC_single_55perS_12

description: 80kb resolution data


title: O-174T HCC


title: O-175T HCC


title: O-173T HCC


title: CBMS1_Day2Diff_ESC_single_45perS_20

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_45perS_21

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_45perS_19

description: 80kb resolution data


title: O-169T HCC


title: CBMS1_Day2Diff_ESC_single_45perS_18

description: 80kb resolution data


title: O-168T HCC


title: O-166T HCC


title: O-176T HCC


title: CBMS1_Day2Diff_ESC_single_45perS_17

description: 80kb resolution data


title: O-165T HCC


title: CBMS1_Day2Diff_ESC_single_45perS_16

description: 80kb resolution data


title: O-167T HCC


title: CBMS1_Day2Diff_ESC_single_45perS_15

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_45perS_14

description: 80kb resolution data


title: O-163T HCC


title: CBMS1_Day2Diff_ESC_single_45perS_13

description: 80kb resolution data


title: O-172T HCC


title: O-164T HCC


title: O-162T HCC


title: O-161T HCC


title: CBMS1_Day2Diff_ESC_single_45perS_12

description: 80kb resolution data


title: O-158T HCC


title: O-159T HCC


title: O-160T HCC


title: O-156T HCC


title: CBMS1_Day2Diff_ESC_single_35perS_21

description: 80kb resolution data


title: O-155T HCC


title: CBMS1_Day2Diff_ESC_single_35perS_18

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_35perS_20

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_35perS_19

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_35perS_17

description: 80kb resolution data


title: O-153T HCC


title: CBMS1_Day2Diff_ESC_single_35perS_16

description: 80kb resolution data


title: O-152T HCC


title: CBMS1_Day2Diff_ESC_single_35perS_15

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_35perS_14

description: 80kb resolution data


title: O-150T HCC


title: O-151T HCC


title: CBMS1_Day2Diff_ESC_single_35perS_13

description: 80kb resolution data


title: O-148T HCC


title: CBMS1_Day2Diff_ESC_single_25perS_20

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_25perS_19

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_25perS_18

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_25perS_21

description: 80kb resolution data


title: O-149T HCC


title: CBMS1_Day2Diff_ESC_single_25perS_16

description: 80kb resolution data


title: O-147T HCC


title: CBMS1_Day2Diff_ESC_single_25perS_15

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_25perS_17

description: 80kb resolution data


title: O-145T HCC


title: O-157T HCC


title: CBMS1_Day2Diff_ESC_single_25perS_14

description: 80kb resolution data


title: O-144T HCC


title: O-146T HCC


title: O-141T HCC


title: O-142T HCC


title: O-139T HCC


title: O-137T HCC


title: O-138T HCC


title: O-135T HCC


title: O-143T HCC


title: O-136T HCC


title: CBMS1_Day2Diff_ESC_single_25perS_13

description: 80kb resolution data


title: CBMS1_ESC_single_G1_13

description: 80kb resolution data

source_name: CBMS1 ESC

value: embryonic stem cell


title: CBMS1_ESC_single_G1_14

description: 80kb resolution data


title: CBMS1_ESC_single_MidS_53

description: 80kb resolution data

value: MidS


title: CBMS1_ESC_single_G1_15

description: 80kb resolution data


title: CBMS1_ESC_single_MidS_52

description: 80kb resolution data


title: CBMS1_ESC_single_MidS_54

description: 80kb resolution data


title: CBMS1_ESC_single_G1_16

description: 80kb resolution data


title: CBMS1_ESC_single_75perS_39

description: 80kb resolution data


title: CBMS1_ESC_single_75perS_38

description: 80kb resolution data


title: CBMS1_ESC_single_75perS_37

description: 80kb resolution data


title: O-134T HCC


title: O-132T HCC


title: O-133T HCC

value: HBV


title: CBMS1_ESC_single_25perS_46

description: 80kb resolution data


title: CBMS1_ESC_single_25perS_47

description: 80kb resolution data


title: O-130T HCC

value: F


title: O-140T HCC


title: O-129T HCC


title: O-127T HCC


title: O-131T HCC


title: O-126T HCC


title: O-124T HCC


title: O-122T HCC


title: EpiSC_p5_single_G1_02

description: 80kb resolution data

source_name: EpiSC

value: epiblast stem cell


title: O-125T HCC


title: EpiSC_p5_single_G1_01

description: 80kb resolution data


title: EpiSC_p5_single_75perS_12

description: 80kb resolution data


title: EpiSC_p5_single_G1_04

description: 80kb resolution data


title: CBMS1_ESC_single_75perS_36

description: 80kb resolution data


title: O-121T HCC


title: O-115T HCC


title: EpiSC_p5_single_75perS_09

description: 80kb resolution data


title: EpiSC_p5_single_75perS_10

description: 80kb resolution data


title: O-111T HCC


title: EpiSC_p5_single_75perS_11

description: 80kb resolution data


title: O-113T HCC


title: O-112T HCC


title: O-110T HCC


title: EpiSC_p5_single_75perS_08

description: 80kb resolution data


title: O-109T HCC


title: EpiSC_p5_single_75perS_07

description: 80kb resolution data


title: EpiSC_p5_single_75perS_06

description: 80kb resolution data


title: O-106T HCC


title: O-108T HCC


title: O-115- HCC2T


title: EpiSC_p5_single_75perS_04

description: 80kb resolution data


title: EpiSC_p5_single_75perS_05

description: 80kb resolution data


title: EpiSC_p5_single_G1_03

description: 80kb resolution data


title: EpiSC_p5_single_75perS_03

description: 80kb resolution data


title: EpiSC_p5_single_75perS_02

description: 80kb resolution data


title: O-105T HCC


title: EpiSC_p5_single_75perS_01

description: 80kb resolution data


title: O-104T HCC


title: EpiSC_p5_single_65perS_09

description: 80kb resolution data


title: O-100T HCC


title: O-103T HCC


title: O-098T HCC


title: EpiSC_p5_single_65perS_10

description: 80kb resolution data


title: EpiSC_p5_single_65perS_08

description: 80kb resolution data


title: EpiSC_p5_single_65perS_07

description: 80kb resolution data


title: EpiSC_p5_single_65perS_05

description: 80kb resolution data


title: EpiSC_p5_single_65perS_06

description: 80kb resolution data


title: EpiSC_p5_single_65perS_04

description: 80kb resolution data


title: EpiSC_p5_single_65perS_03

description: 80kb resolution data


title: O-087T HCC


title: O-092T HCC


title: O-093T HCC


title: O-090T HCC


title: EpiSC_p5_single_65perS_02

description: 80kb resolution data


title: O-011T HCC


title: O-089T HCC


title: EpiSC_p5_single_65perS_01

description: 80kb resolution data


title: O-086T HCC


title: EpiSC_p5_single_55perS_13

description: 80kb resolution data


title: O-010T HCC


title: EpiSC_p5_single_55perS_12

description: 80kb resolution data


title: EpiSC_p5_single_55perS_10

description: 80kb resolution data


title: EpiSC_p5_single_55perS_09

description: 80kb resolution data


title: EpiSC_p5_single_55perS_08

description: 80kb resolution data


title: O-009T HCC


title: EpiSC_p5_single_55perS_07

description: 80kb resolution data


title: O-007T HCC


title: O-008T HCC


title: EpiSC_p5_single_55perS_06

description: 80kb resolution data


title: O-088T HCC


title: O-004T HCC


title: O-006T HCC


title: O-003T HCC


title: O-123T HCC


title: O-005T HCC


title: O-002T HCC


title: EpiSC_p5_single_55perS_04

description: 80kb resolution data


title: O-001T HCC


title: EpiSC_p5_single_55perS_02

description: 80kb resolution data


title: EpiSC_p5_single_55perS_11

description: 80kb resolution data


title: EpiSC_p5_single_55perS_03

description: 80kb resolution data


title: EpiSC_p5_single_55perS_01

description: 80kb resolution data


title: EpiSC_p5_single_45perS_12

description: 80kb resolution data


title: EpiSC_p5_single_45perS_11

description: 80kb resolution data


title: OCH-457  chronic hepatitis C

growth_protocol: Liver tissue was obtained by liver biopsy.

value: chronic hepatitis C


title: OCH-460  chronic hepatitis C


title: OCH-459  chronic hepatitis C


title: OCH-458  chronic hepatitis C


title: EpiSC_p5_single_45perS_10

description: 80kb resolution data

value: Single cell


title: EpiSC_p5_single_45perS_09

description: 80kb resolution data


title: EpiSC_p5_single_45perS_07

description: 80kb resolution data


title: EpiSC_p5_single_45perS_06

description: 80kb resolution data

value: FALSE


title: EpiSC_p5_single_55perS_05

description: 80kb resolution data


title: OCH-454  chronic hepatitis C


title: OCH-453  chronic hepatitis C


title: OCH-452  chronic hepatitis C


title: OCH-456  chronic hepatitis C


title: EpiSC_p5_single_45perS_04

description: 80kb resolution data


title: OCH-451  chronic hepatitis C


title: OCH-450  chronic hepatitis C


title: EpiSC_p5_single_45perS_03

description: 80kb resolution data


title: OCH-449  chronic hepatitis C


title: EpiSC_p5_single_45perS_01

description: 80kb resolution data


title: OCH-447  chronic hepatitis C


title: OCH-448  chronic hepatitis C


title: EpiSC_p5_single_45perS_08

description: 80kb resolution data


title: EpiSC_p5_single_35perS_13

description: 80kb resolution data


title: OCH-445  chronic hepatitis C


title: OCH-446  chronic hepatitis C


title: EpiSC_p5_single_45perS_05

description: 80kb resolution data


title: EpiSC_p5_single_35perS_12

description: 80kb resolution data


title: EpiSC_p5_single_35perS_11

description: 80kb resolution data


title: OCH-455  chronic hepatitis C


title: EpiSC_p5_single_35perS_10

description: 80kb resolution data


title: EpiSC_p5_single_35perS_09

description: 80kb resolution data


title: EpiSC_p5_single_35perS_08

description: 80kb resolution data


title: EpiSC_p5_single_35perS_07

description: 80kb resolution data


title: EpiSC_p5_single_35perS_05

description: 80kb resolution data


title: EpiSC_p5_single_35perS_14

description: 80kb resolution data


title: EpiSC_p5_single_35perS_06

description: 80kb resolution data


title: EpiSC_p5_single_45perS_02

description: 80kb resolution data


title: EpiSC_p5_single_35perS_04

description: 80kb resolution data


title: EpiSC_p5_single_35perS_03

description: 80kb resolution data


title: EpiSC_p5_single_35perS_02

description: 80kb resolution data


title: EpiSC_p5_single_35perS_01

description: 80kb resolution data


title: OCH-440  chronic hepatitis C


title: OCH-439  chronic hepatitis C


title: EpiSC_p5_single_25perS_12

description: 80kb resolution data


title: OCH-438  chronic hepatitis C


title: EpiSC_p5_single_25perS_13

description: 80kb resolution data


title: EpiSC_p5_single_25perS_11

description: 80kb resolution data


title: OCH-437  chronic hepatitis C


title: OCH-441  chronic hepatitis C


title: EpiSC_p5_single_25perS_09

description: 80kb resolution data


title: EpiSC_p5_single_25perS_08

description: 80kb resolution data


title: EpiSC_p5_single_25perS_07

description: 80kb resolution data


title: EpiSC_p5_single_25perS_10

description: 80kb resolution data


title: EpiSC_p5_single_25perS_06

description: 80kb resolution data


title: OCH-443  chronic hepatitis C


title: EpiSC_p5_single_25perS_05

description: 80kb resolution data


title: EpiSC_p5_single_25perS_03

description: 80kb resolution data


title: OCH-444  chronic hepatitis C


title: EpiSC_p5_single_25perS_02

description: 80kb resolution data


title: OCH-422  chronic hepatitis C


title: EpiSC_p5_single_25perS_04

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_79

description: 80kb resolution data

value: day7differentiated ESCs


title: OCH-417  chronic hepatitis C

value: M


title: OCH-425  chronic hepatitis C


title: OCH-427  chronic hepatitis C


title: OCH-423  chronic hepatitis C


title: OCH-424  chronic hepatitis C


title: OCH-426  chronic hepatitis C


title: OCH-418  chronic hepatitis C


title: OCH-421  chronic hepatitis C


title: CBMS1_Day7Diff_ESC_single_MidS_77

description: 80kb resolution data


title: OCH-429  chronic hepatitis C


title: OCH-430  chronic hepatitis C


title: OCH-431  chronic hepatitis C


title: CBMS1_Day7Diff_ESC_single_MidS_78

description: 80kb resolution data


title: EpiSC_p5_single_25perS_01

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_80

description: 80kb resolution data


title: OCH-436  chronic hepatitis C


title: OCH-434  chronic hepatitis C


title: OCH-433  chronic hepatitis C


title: CBMS1_Day7Diff_ESC_single_MidS_76

description: 80kb resolution data


title: OCH-432  chronic hepatitis C


title: OCH-428  chronic hepatitis C


title: CBMS1_Day7Diff_ESC_single_MidS_70

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_75

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_72

description: 80kb resolution data


title: OCH-442  chronic hepatitis C


title: OCH-416  chronic hepatitis C


title: OCH-419  chronic hepatitis C


title: OCH-435  chronic hepatitis C


title: CBMS1_Day7Diff_ESC_single_MidS_74

description: 80kb resolution data


title: OCH-420  chronic hepatitis C


title: OCH-414  chronic hepatitis C


title: OCH-415  chronic hepatitis C


title: OCH-408  chronic hepatitis C


title: OCH-413  chronic hepatitis C


title: OCH-409  chronic hepatitis C


title: OCH-406  chronic hepatitis C


title: OCH-410  chronic hepatitis C


title: OCH-412  chronic hepatitis C


title: CBMS1_Day7Diff_ESC_single_MidS_71

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_67

description: 80kb resolution data


title: OCH-407  chronic hepatitis C


title: OCH-411  chronic hepatitis C


title: CBMS1_Day7Diff_ESC_single_MidS_73

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_68

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_66

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_65

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_69

description: 80kb resolution data


title: OCH-404  chronic hepatitis C


title: OCH-403  chronic hepatitis C


title: CBMS1_Day7Diff_ESC_single_MidS_64

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_MidS_63

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_22

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_21

description: 80kb resolution data


title: OCH-402  chronic hepatitis C


title: OCH-405  chronic hepatitis C


title: OCH-399  chronic hepatitis C


title: CBMS1_Day7Diff_ESC_single_G1_20

description: 80kb resolution data


title: CBMS1_Day7Diff_ESC_single_G1_18

description: 80kb resolution data


title: OCH-400  chronic hepatitis C


title: CBMS1_Day7Diff_ESC_single_G1_19

description: 80kb resolution data


title: OCH-401  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_G1_07

description: 80kb resolution data

source_name: Day6 Differentiated CBMS1 ESC

value: day6 differentiated ESCs


title: OCH-396  chronic hepatitis C

value: HCV


title: OCH-395  chronic hepatitis C


title: OCH-397  chronic hepatitis C


title: OCH-398  chronic hepatitis C


title: OCH-393  chronic hepatitis C


title: OCH-394  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_G1_03

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_G1_02

description: 80kb resolution data


title: OCH-392  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_G1_01

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_75perS_08

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_75perS_09

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_75perS_10

description: 80kb resolution data


title: OCH-391  chronic hepatitis C


title: OCH-389  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_G1_06

description: 80kb resolution data


title: OCH-388  chronic hepatitis C


title: OCH-387  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_G1_05

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_G1_04

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_75perS_06

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_75perS_07

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_75perS_05

description: 80kb resolution data


title: OCH-386  chronic hepatitis C


title: OCH-385  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_75perS_03

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_75perS_04

description: 80kb resolution data


title: OCH-384  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_75perS_02

description: 80kb resolution data


title: OCH-390  chronic hepatitis C


title: OCH-378  chronic hepatitis C


title: OCH-379  chronic hepatitis C


title: OCH-382  chronic hepatitis C


title: OCH-380  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_65perS_07

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_65perS_06

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_65perS_05

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_65perS_04

description: 80kb resolution data


title: OCH-383  chronic hepatitis C


title: OCH-375  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_75perS_01

description: 80kb resolution data


title: OCH-376  chronic hepatitis C


title: OCH-374  chronic hepatitis C


title: OCH-377  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_65perS_01

description: 80kb resolution data


title: OCH-373  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_65perS_02

description: 80kb resolution data


title: OCH-371  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_65perS_03

description: 80kb resolution data


title: OCH-372  chronic hepatitis C


title: OCH-381  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_55perS_12

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_55perS_10

description: 80kb resolution data


title: OCH-370  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_65perS_08

description: 80kb resolution data


title: OCH-369  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_55perS_09

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_55perS_07

description: 80kb resolution data


title: OCH-367  chronic hepatitis C


title: OCH-366  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_55perS_11

description: 80kb resolution data


title: OCH-365  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_55perS_06

description: 80kb resolution data


title: OCH-368  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_55perS_05

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_55perS_04

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_55perS_03

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_55perS_02

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_55perS_01

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_45perS_11

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_45perS_12

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_45perS_10

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_45perS_09

description: 80kb resolution data


title: OCH-358  chronic hepatitis C


title: OCH-357  chronic hepatitis C


title: OCH-356  chronic hepatitis C


title: OCH-364  chronic hepatitis C


title: OCH-355  chronic hepatitis C


title: OCH-359  chronic hepatitis C


title: OCH-360  chronic hepatitis C


title: OCH-363  chronic hepatitis C


title: OCH-362  chronic hepatitis C


title: OCH-361  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_45perS_07

description: 80kb resolution data


title: OCH-354  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_45perS_08

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_45perS_06

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_45perS_05

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_45perS_04

description: 80kb resolution data


title: OCH-352  chronic hepatitis C


title: OCH-353  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_45perS_03

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_45perS_01

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_35perS_11

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_45perS_02

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_35perS_10

description: 80kb resolution data


title: OCH-350  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_35perS_09

description: 80kb resolution data


title: OCH-346  chronic hepatitis C


title: OCH-347  chronic hepatitis C


title: OCH-349  chronic hepatitis C


title: OCH-348  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_35perS_06

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_35perS_08

description: 80kb resolution data


title: OCH-344  chronic hepatitis C


title: OCH-342  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_35perS_04

description: 80kb resolution data


title: OCH-343  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_35perS_03

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_55perS_08

description: 80kb resolution data


title: OCH-345  chronic hepatitis C


title: OCH-339  chronic hepatitis C


title: OCH-338  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_35perS_02

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_35perS_07

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_25perS_11

description: 80kb resolution data


title: OCH-336  chronic hepatitis C


title: OCH-340  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_35perS_01

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_25perS_10

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_25perS_08

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_25perS_09

description: 80kb resolution data


title: OCH-332  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_25perS_07

description: 80kb resolution data


title: OCH-335  chronic hepatitis C


title: OCH-331  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_35perS_05

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_25perS_06

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_25perS_05

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_25perS_04

description: 80kb resolution data


title: OCH-330  chronic hepatitis C


title: OCH-337  chronic hepatitis C


title: OCH-329  chronic hepatitis C


title: OCH-328  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_25perS_02

description: 80kb resolution data


title: OCH-327  chronic hepatitis C


title: OCH-325  chronic hepatitis C


title: OCH-326  chronic hepatitis C


title: CBMS1_Day6Diff_ESC_single_25perS_01

description: 80kb resolution data


title: OCH-333  chronic hepatitis C


title: OCH-334  chronic hepatitis C


title: CBMS1_Day5Diff_ESC_single_G1_06

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_G1_05

description: 80kb resolution data


title: OCH-324  chronic hepatitis C


title: CBMS1_Day5Diff_ESC_single_G1_03

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_G1_04

description: 80kb resolution data


title: CBMS1_Day6Diff_ESC_single_25perS_03

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_G1_01

description: 80kb resolution data


title: OCH-323  chronic hepatitis C


title: CBMS1_Day5Diff_ESC_single_G1_02

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_75perS_05

description: 80kb resolution data

value: day5 differentiated ESCs


title: OCH-322  chronic hepatitis C


title: OCH-321  chronic hepatitis C


title: OCH-319  chronic hepatitis C


title: CBMS1_Day5Diff_ESC_single_75perS_03

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_75perS_04

description: 80kb resolution data


title: OCH-318  chronic hepatitis C


title: CBMS1_Day5Diff_ESC_single_75perS_02

description: 80kb resolution data


title: OCH-320  chronic hepatitis C


title: OCH-317  chronic hepatitis C


title: Inducible MBS reporter cell line 6

description:
SJ_TRIBE_48hrDox_both_rep_5%.bedgraph
SJ_TRIBE_ConcatDox_both_rep_5%.bedgraph

source_name: Bone

extract_protocol:
For TRIBE cells were FACS sorted directly into Trizol reagent. NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (Cat# E7765S) was used with at least 10ng of total RNA for the construction of sequencing libraries.
TRIBE RNA libraries were prepared for sequencing using standard NEB NextSeq protocols

value: Bone

tag: transfection

value: MCP ADAR

tag: treatment

value: 48 hour doxycycline induction

tag: experiment

value: TRIBE


title: OCH-316  chronic hepatitis C


title: CBMS1_Day5Diff_ESC_single_65perS_07

description: 80kb resolution data

value: CBA/MsM


title: OCH-315  chronic hepatitis C


title: OCH-351  chronic hepatitis C


title: Inducible MBS reporter cell line 5

tag: tissue

value: mCherry ADAR


title: OCH-314  chronic hepatitis C

tag: disease state


title: CBMS1_Day5Diff_ESC_single_65perS_06

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_65perS_05

description: 80kb resolution data


title: Inducible MBS reporter cell line 4

description:
SJ_TRIBE_24hrDox_both_rep_5%.bedgraph
SJ_TRIBE_ConcatDox_both_rep_5%.bedgraph

value: 24 hour doxycycline induction


title: CBMS1_Day5Diff_ESC_single_65perS_04

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_65perS_03

description: 80kb resolution data


title: Inducible MBS reporter cell line 3

value: untransfected

value: No doxycycline induction


title: Inducible MBS reporter cell line 2


title: CBMS1_Day5Diff_ESC_single_65perS_02

description: 80kb resolution data

value: TRUE


title: OCH-312  chronic hepatitis C

value: chronic hepatitis C

tag: age

value: F


title: OCH-313  chronic hepatitis C

tag: Sex


title: CBMS1_Day5Diff_ESC_single_55perS_05

description: 80kb resolution data

value: Single cell


title: Inducible MBS reporter cell line 1


title: CBMS1_Day5Diff_ESC_single_55perS_03

description: 80kb resolution data

value: FALSE


title: CBMS1_Day5Diff_ESC_single_55perS_06

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_55perS_04

description: 80kb resolution data


title: OCH-311  chronic hepatitis C

tag: bmi


title: CBMS1_Day5Diff_ESC_single_75perS_01

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_55perS_02

description: 80kb resolution data


title: gH2AX_U2OS_AsiS1_IP

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

country: France

institute: IGH

description: ChIP-Seq of γH2AX of AsiS1-induced cells.

data_processing:
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2.
Reads were aligned to the hg19 genome assembly using Bowtie 2 (version 2.1.0) for ChIP-Seq and DRIP-Seq data, and STAR for RNA-Seq data.
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al. (2016).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bigwig files correspond to signal 10 bp step without any further smoothing.

source_name: ChIP-Seq of γH2AX of AsiS1 cells

growth_protocol: Cells were cultured in DMEM containing 10% FCS and Penicillin/Streptomycin.

extract_protocol:
Cells were lysed in the sonication buffer (50mM Hepes pH8, 140mM NaCl, 1mM EDTA, 1% Triton, 0,1% sodium deoxycholate, 0.5% SDS). Chromatin was treated with protease K followed by Phenol/chloroform extraction and ethanol precipitation.
NeoPrep Illumina system for automatic NGS library preparation using TruSeq Nano DNA Library Prep Kit for NeoPrep (Illumina)_Sequencer:HiSeq 4000 (1x51 nt).

treatment_protocol: Cells were treated with 2 microgram/ml of Doxycycline for 72 hr before the ChIP experiments.

tag: cell line

tag: genotype/variation

value: shASF

value: untreated

tag: antibody

value: Abgent ; AJ1351a


title: CBMS1_Day5Diff_ESC_single_55perS_01

description: 80kb resolution data

tag: strain

value: day5 differentiated ESCs

tag: sample state

tag: xx or xo chromosomes in single cell samples


title: OCH-309  chronic hepatitis C

tag: viral infection

value: HCV


title: gH2AX_U2OS_Ctrl_IP

description: ChIP-Seq of γH2AX in WT cells.

source_name: ChIP-Seq of γH2AX in WT cells

value: WT


title: CBMS1_Day5Diff_ESC_single_45perS_08

description: 80kb resolution data

tag: cell type

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%


title: CBMS1_Day5Diff_ESC_single_45perS_07

description: 80kb resolution data

tag: cell cycle phase


title: CBMS1_Day5Diff_ESC_single_45perS_06

description: 80kb resolution data


title: OCH-307  chronic hepatitis C

value: M


title: CBMS1_Day5Diff_ESC_single_65perS_01

description: 80kb resolution data

value: CBA/MsM


title: OCH-308  chronic hepatitis C


title: gH2AX_U2OS_Ctrl_Inp

description: Input of wild type control cells.

source_name: Input of Wild type

tag: treatment


title: CBMS1_Day5Diff_ESC_single_45perS_05

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_45perS_04

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_45perS_03

description: 80kb resolution data


title: OCH-310  chronic hepatitis C

tag: disease state


title: RNA-seq_TOP1

description:
RNA-Seq in shTOP1 cells
PolyA RNA

source_name: RNA-Seq in shTOP1 cells

value: HeLa


title: CBMS1_Day5Diff_ESC_single_45perS_02

description: 80kb resolution data


title: OCH-306  chronic hepatitis C

tag: age


title: CBMS1_Day5Diff_ESC_single_45perS_01

description: 80kb resolution data


title: RNA-seq_HeLa

description:
RNA-Seq in wild type control cells
PolyA RNA

source_name: RNA-Seq in Wild Type cells


title: CBMS1_Day5Diff_ESC_single_35perS_09

description: 80kb resolution data


title: gH2AX_U2OS_AsiS1_Inp

description: Input for AsiS1-induced cells.

source_name: Input for AsiS1 cells


title: RNA-seq_ASF

description:
RNA-Seq in shASF cells
PolyA RNA

source_name: RNA-Seq in shASF cells


title: OCH-304  chronic hepatitis C

tag: Sex


title: OCH-305  chronic hepatitis C

tag: bmi


title: CBMS1_Day5Diff_ESC_single_35perS_06

description: 80kb resolution data


title: prpa_TOP1_IP_2_1

description: ChIP-Seq of pRPA in shTOP1 cells.

source_name: ChIP-Seq of pRPA in shTOP1 cells

tag: cell line

value: Bethyl Laboratories #A-300246A


title: CBMS1_Day5Diff_ESC_single_35perS_07

description: 80kb resolution data


title: OCH-302  chronic hepatitis C


title: CBMS1_Day5Diff_ESC_single_35perS_03

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_35perS_05

description: 80kb resolution data


title: OCH-301  chronic hepatitis C


title: CBMS1_Day5Diff_ESC_single_35perS_02

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_35perS_01

description: 80kb resolution data


title: OCH-300  chronic hepatitis C


title: prpa_HeLa_IP_2_1

description: ChIP-Seq of pRPA in HeLa cells.

source_name: ChIP-Seq of pRPA in HeLa cells

tag: genotype/variation


title: CBMS1_Day5Diff_ESC_single_35perS_08

description: 80kb resolution data


title: OCH-299  chronic hepatitis C

source_name: liver tissue


title: prpa_HeLa_INP_2_1

description: Input of wild type control cells.

tag: antibody


title: CBMS1_Day5Diff_ESC_single_25perS_06

description: 80kb resolution data

source_name: Day5 Differentiated CBMS1 ESC

tag: strain


title: OCH-303  chronic hepatitis C


title: prpa_ASF_IP_2_1

description: ChIP-Seq of pRPA in shASF cells.

source_name: ChIP-Seq of pRPA in shASF cells


title: CBMS1_Day5Diff_ESC_single_25perS_05

description: 80kb resolution data

tag: sample state


title: CBMS1_Day5Diff_ESC_single_25perS_04

description: 80kb resolution data

tag: xx or xo chromosomes in single cell samples


title: CBMS1_Day5Diff_ESC_single_25perS_03

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_25perS_02

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_25perS_01

description: 80kb resolution data


title: CBMS1_Day5Diff_ESC_single_35perS_04

description: 80kb resolution data


title: prpa_ASF_INP_2_1

description: Input of shASF cells.

source_name: Input of shASF cells


title: CBMS1_Day4Diff_ESC_single_G1_07

description: 80kb resolution data

source_name: Day4 Differentiated CBMS1 ESC

value: day4 differentiated ESCs


title: prpa_TOP1_INP_2_1

description: Input of shTOP1 cells.

source_name: Input of shTOP1 cells


title: CBMS1_Day4Diff_ESC_single_G1_06

description: 80kb resolution data


title: OCH-298  chronic hepatitis C

tag: viral infection


title: OCH-297  chronic hepatitis C


title: gh2ax_HeLa_IP_2_1

description: ChIP-Seq of γH2AX in WT cells.


title: OCH-296  chronic hepatitis C


title: CBMS1_Day4Diff_ESC_single_G1_03

description: 80kb resolution data

tag: cell type


title: CBMS1_Day4Diff_ESC_single_G1_04

description: 80kb resolution data

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)


title: gh2ax_HeLa_INP_2_1

description: Input of wild type control cells.


title: CBMS1_Day4Diff_ESC_single_G1_02

description: 80kb resolution data

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)


title: OCH-295  chronic hepatitis C


title: CBMS1_Day4Diff_ESC_single_G1_01

description: 80kb resolution data

tag: repliscore of 40–70%


title: OCH-293  chronic hepatitis C


title: CBMS1_Day4Diff_ESC_single_75perS_07

description: 80kb resolution data

tag: cell cycle phase


title: gh2ax_TOP1_IP_2_1

description: ChIP-Seq of γH2AX in shTOP1 cells.

source_name: ChIP-Seq of γH2AX in shTOP1 cells

tag: treatment


title: gh2ax_ASF_IP_2_1

description: ChIP-Seq of γH2AX in shASF cells.

source_name: ChIP-Seq of γH2AX in shASF cells


title: CBMS1_Day4Diff_ESC_single_75perS_06

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_75perS_05

description: 80kb resolution data


title: OCH-292  chronic hepatitis C

tag: disease state


title: CBMS1_Day4Diff_ESC_single_75perS_04

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_G1_05

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_75perS_03

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_75perS_02

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_75perS_01

description: 80kb resolution data


title: OCH-291  chronic hepatitis C

tag: age


title: drip_HeLa_INP_2_1

description: Input of wild type control cells.

data_processing:
Library strategy: DRIP-Seq
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2.
Reads were aligned to the hg19 genome assembly using Bowtie 2 (version 2.1.0) for ChIP-Seq and DRIP-Seq data, and STAR for RNA-Seq data.
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al. (2016).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bigwig files correspond to signal 10 bp step without any further smoothing.


title: OCH-294  chronic hepatitis C

tag: Sex


title: drip_HeLa_IP_2_1

description: DRIP-Seq wild type control cells.

source_name: DRIP-Seq Wild Type


title: CBMS1_Day4Diff_ESC_single_65perS_10

description: 80kb resolution data


title: OCH-290  chronic hepatitis C

tag: bmi


title: OCH-289  chronic hepatitis C


title: drip_ASF_IP_2_1

description: DRIP-Seq shASF cells.

source_name: DRIP-Seq shASF cells

tag: cell line


title: CBMS1_Day4Diff_ESC_single_65perS_09

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_65perS_08

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_75perS_08

description: 80kb resolution data


title: drip_TOP1_IP_2_1

description: DRIP-Seq shTOP1 cells.

source_name: DRIP-Seq shTOP1 cells

tag: genotype/variation


title: OCH-288  chronic hepatitis C


title: drip_ASF_INP_2_1

description: Input of shASF cells.

tag: antibody


title: CBMS1_Day4Diff_ESC_single_65perS_06

description: 80kb resolution data

tag: strain


title: OCH-287  chronic hepatitis C


title: OCH-341  chronic hepatitis C


title: CBMS1_Day4Diff_ESC_single_65perS_05

description: 80kb resolution data

tag: sample state


title: drip_TOP1_INP_2_1

description: Input of shTOP1 cells.


title: CBMS1_Day4Diff_ESC_single_65perS_07

description: 80kb resolution data

tag: xx or xo chromosomes in single cell samples


title: CBMS1_Day4Diff_ESC_single_65perS_04

description: 80kb resolution data


title: drip_TOP1_IP_1_1

description: DRIP-Seq shTOP1 cells.


title: CBMS1_Day4Diff_ESC_single_65perS_03

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_65perS_02

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_65perS_01

description: 80kb resolution data


title: OCH-285  chronic hepatitis C

tag: viral infection


title: OCH-286  chronic hepatitis C


title: drip_ASF_IP_1_1

description: DRIP-Seq shASF cells.


title: drip_HeLa_IP_1_1

description: DRIP-Seq wild type control cells.


title: CBMS1_Day4Diff_ESC_single_55perS_08

description: 80kb resolution data

tag: cell type


title: CBMS1_Day4Diff_ESC_single_55perS_07

description: 80kb resolution data

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)


title: drip_HeLa_INP_1_1

description: Input of wild type control cells.

source_name: Input of Wild type


title: CBMS1_Day4Diff_ESC_single_55perS_06

description: 80kb resolution data

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)


title: OCH-284  chronic hepatitis C


title: CBMS1_Day4Diff_ESC_single_55perS_04

description: 80kb resolution data

tag: repliscore of 40–70%


title: CBMS1_Day4Diff_ESC_single_55perS_05

description: 80kb resolution data

tag: cell cycle phase


title: Cell line without MBS 3

source_name: Mouse embryo

value: MEF

tag: tissue

value: Fibroblast

tag: transfection

value: GFP

tag: experiment

value: TRIBE


title: Cell line without MBS 2

value: MCP ADAR


title: CBMS1_Day4Diff_ESC_single_55perS_03

description: 80kb resolution data

value: Single cell

value: FALSE


title: CBMS1_Day4Diff_ESC_single_55perS_02

description: 80kb resolution data


title: OCH-283  chronic hepatitis C

tag: disease state

value: chronic hepatitis C

tag: age

tag: Sex

value: F


title: OCH-282  chronic hepatitis C

tag: bmi


title: Cell line without MBS 1

value: mCherry ADAR


title: CBMS1_Day4Diff_ESC_single_45perS_07

description: 80kb resolution data

value: TRUE


title: CBMS1_Day4Diff_ESC_single_55perS_01

description: 80kb resolution data


title: OCH-280  chronic hepatitis C

value: HCV


title: MBS cell line 3


title: CBMS1_Day4Diff_ESC_single_45perS_06

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_45perS_05

description: 80kb resolution data


title: MBS cell line 2


title: CBMS1_Day4Diff_ESC_single_45perS_02

description: 80kb resolution data


title: M44

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38.84 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample

source_name: hindlimb muscles

extract_protocol:
hindlimb muscles were washed with PBS, minced, and digested in  Ham's F10 Nutrient mix(Gibco) containing type II collagenase (2 mg/ml), dispase II(2.4U/ml), CaCl2(2.5mM,Sigma) for 1 hr at 37°C.Digested tissue was successively filtered through 70-μm and 40-μm cell strainers (BD Biosciences) and then centrifuged with 500g for 5min. The cell pellet was resuspended with PBS. Tomato+ cells were sorted by Bio-Rad S3e and then single cells were picked with fluorescence microscope.
Libraries were prepared according to Nextera® XT DNA Library Prep Kit for Illumina  (Cat# FC-131-1096)

value: hindlimb muscles

value: adult

tag: genotype

tag: treatment

value: Injection of Tamoxifen 2mg/mice once a day for 3 days


title: CBMS1_Day4Diff_ESC_single_45perS_01

description: 80kb resolution data

tag: strain

value: CBA/MsM

tag: sample state


title: CBMS1_Day4Diff_ESC_single_45perS_03

description: 80kb resolution data

value: day4 differentiated ESCs

tag: xx or xo chromosomes in single cell samples


title: OCH-279  chronic hepatitis C

tag: viral infection


title: OCH-276  chronic hepatitis C


title: M43


title: CBMS1_Day4Diff_ESC_single_35perS_08

description: 80kb resolution data

tag: cell type

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)


title: CBMS1_Day4Diff_ESC_single_35perS_04

description: 80kb resolution data

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%


title: OCH-278  chronic hepatitis C

value: M


title: CBMS1_Day4Diff_ESC_single_35perS_07

description: 80kb resolution data

tag: cell cycle phase


title: CBMS1_Day4Diff_ESC_single_35perS_06

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_35perS_03

description: 80kb resolution data


title: M42

tag: tissue


title: CBMS1_Day4Diff_ESC_single_35perS_05

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_35perS_02

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_45perS_04

description: 80kb resolution data


title: OCH-275  chronic hepatitis C


title: OCH-281  chronic hepatitis C


title: OCH-274  chronic hepatitis C


title: CBMS1_Day4Diff_ESC_single_35perS_01

description: 80kb resolution data


title: M41


title: OCH-273  chronic hepatitis C


title: MBS cell line 1

value: MEF

value: Fibroblast

tag: transfection

tag: experiment


title: OCH-272  chronic hepatitis C

tag: disease state

tag: age


title: OCH-277  chronic hepatitis C

tag: Sex

tag: bmi


title: CBMS1_Day4Diff_ESC_single_25perS_11

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_25perS_10

description: 80kb resolution data


title: M40

tag: genotype

tag: treatment


title: CBMS1_Day4Diff_ESC_single_25perS_09

description: 80kb resolution data

tag: strain

tag: sample state


title: OCH-271  chronic hepatitis C

tag: viral infection


title: M39


title: M37


title: OCH-270  chronic hepatitis C


title: CBMS1_Day4Diff_ESC_single_25perS_05

description: 80kb resolution data

tag: cell type

tag: xx or xo chromosomes in single cell samples


title: CBMS1_Day4Diff_ESC_single_25perS_04

description: 80kb resolution data

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)


title: CBMS1_Day4Diff_ESC_single_25perS_03

description: 80kb resolution data

tag: repliscore of 40–70%

tag: cell cycle phase


title: CBMS1_Day4Diff_ESC_single_25perS_02

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_G1_06

description: 80kb resolution data

source_name: Day3 Differentiated CBMS1 ESC

value: day3 differentiated ESCs


title: CBMS1_Day4Diff_ESC_single_25perS_07

description: 80kb resolution data


title: M35

tag: tissue


title: M36


title: OCH-267  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_G1_04

description: 80kb resolution data


title: OCH-269  chronic hepatitis C


title: CBMS1_Day4Diff_ESC_single_25perS_01

description: 80kb resolution data


title: OCH-268  chronic hepatitis C


title: M34


title: OCH-266  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_G1_03

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_G1_02

description: 80kb resolution data


title: CBMS1_Day4Diff_ESC_single_25perS_08

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_G1_01

description: 80kb resolution data


title: M33


title: M38


title: OCH-265  chronic hepatitis C


title: CBMS1_Day4Diff_ESC_single_25perS_06

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_75perS_10

description: 80kb resolution data


title: M32


title: OCH-264  chronic hepatitis C


title: OCH-263  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_G1_05

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_75perS_08

description: 80kb resolution data


title: M30


title: M31


title: CBMS1_Day3Diff_ESC_single_75perS_06

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_75perS_07

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_75perS_02

description: 80kb resolution data


title: M28


title: CBMS1_Day3Diff_ESC_single_75perS_03

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_75perS_05

description: 80kb resolution data


title: M29


title: M27


title: CBMS1_Day3Diff_ESC_single_75perS_04

description: 80kb resolution data


title: OCH-262  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_65perS_07

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_75perS_01

description: 80kb resolution data


title: OCH-259  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_65perS_09

description: 80kb resolution data


title: M26


title: CBMS1_Day3Diff_ESC_single_75perS_09

description: 80kb resolution data


title: OCH-258  chronic hepatitis C


title: OCH-261  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_65perS_06

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_65perS_04

description: 80kb resolution data


title: OCH-257  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_65perS_08

description: 80kb resolution data


title: M25


title: M24


title: OCH-256  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_65perS_05

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_65perS_02

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_65perS_03

description: 80kb resolution data


title: OCH-260  chronic hepatitis C


title: M23


title: CBMS1_Day3Diff_ESC_single_65perS_01

description: 80kb resolution data


title: M22


title: OCH-255  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_55perS_07

description: 80kb resolution data


title: M21


title: OCH-254  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_55perS_08

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_55perS_05

description: 80kb resolution data


title: OCH-253  chronic hepatitis C


title: M20


title: CBMS1_Day3Diff_ESC_single_55perS_06

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_55perS_04

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_55perS_03

description: 80kb resolution data


title: OCH-251  chronic hepatitis C


title: OCH-252  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_55perS_01

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_55perS_02

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_45perS_05

description: 80kb resolution data


title: M19


title: M18


title: CBMS1_Day3Diff_ESC_single_45perS_04

description: 80kb resolution data


title: M17


title: CBMS1_Day3Diff_ESC_single_45perS_03

description: 80kb resolution data


title: OCH-249  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_45perS_02

description: 80kb resolution data


title: OCH-250  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_45perS_01

description: 80kb resolution data


title: M16


title: CBMS1_Day3Diff_ESC_single_35perS_09

description: 80kb resolution data


title: OCH-248  chronic hepatitis C