title: HFD rep2

city: Bunkyo-ku

first: Hironobu

last: Morinaga

state: Tokyo

address: 1-5-45 Yushima

department: Stem Cell Biology

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
Bcl2fastq (v2.17.1.14) was used to processed the original image data for base calling and preliminary quality analysis.
Data were filtered using the following specification by Cutadapt (version 1.9.1)…
(1) remove the adapter sequences  (2) remove the 5' or 3' end bases that contains N’s or of quality values below 20 (3) remove reads that are less than 75 bp long after trimming
Genome_build: Short-read alignment was performed using Hisat2 (v2.0.1) (Nat Methods. 2015 Apr; Kim D, et al.) with default parameters.
Supplementary_files_format_and_content: txt files include FPKM values

organism: Mus musculus

source_name: Hair follicle stem cells from HFD-fed mice

extract_protocol:
Total RNA was purified with an RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hair follicle stem cells

tag: treatment

value: High fat diet (HFD) for 4months


title: HEC_shNRSF_rep2

status: Public on Apr 14 2021

type: SRA

city: Shanghai

first: Yuanxiao

last: Tang

address: Dongchuan Road 800

country: China

institute: Shanghai Jiao Tong University

library_source: transcriptomic

data_processing:
Reads were sorted using index.
Reads were aligned to hg19 using TopHat.
The expression levels were calculated using the Cufflinks software.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_fpkm.txt: Tab-delimited text files include FPKM values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: HEC-1-B cells

growth_protocol: HEC-1-B were cultured in MEM (Hyclone), supplemented with 10% (v/v) FBS, 2 mM GlutaMAX (Gibco), 1 mM sodium pyruvate (Sigma), and 1% penicillin-streptomycin. HEK293T cells were cultured in DMEM/High glucose (Hyclone), supplemented with 10% (v/v) FBS. Cells were maintained at 37 °C in a 5% (v/v) CO2 incubator.

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol Reagent (Ambion).
RNA-Seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol.

treatment_protocol: The shGFP or shNRSF3 plasmid was transfected into HEK293T cells with the psPAX2 and pMD2.G helper plasmids (Addgene) using Lipofectamine 2000 to produce lentiviral particles. HEK293T cells or HEC-1-B cells were infected with the virus in the presence of 8 μg/mL polybrene (Sigma). Puromycin (Sigma) was added to a final concentration of 2 μg/mL to select the infected cells. Fresh puromycin-containing medium was changed every other day. Cells were collected for assays at 5 days post infection. For monoclones, HEC-1-B cells or HEK293T cells at ~80% confluency was transfected with Cas9 (0.6 μg) and sgRNA (1.2 μg) expressing plasmids by Lipofectamine 2000 in a 12-well plate. 2 days post transfection, puromycin was added to a final concentration of 2 μg/mL. Four days later, cells were changed to fresh medium without puromycin and cultured for another ten days. The cells were diluted and plated in 96-well plates with approximately one cell per well. Two weeks later, single cell clones were screened for target deletion by PCR.

tag: cell line

tag: cell type

value: endometrium

tag: disease

value: adenocarcinoma

tag: genotype/variation

value: shRNA for NRSF transfected


title: APL037

first: Niu

last: Qiao

address: 197 Rui Jin Er Road

department: National Research Center for Translational Medicine (Shanghai)

data_processing:
The HISAT2 was used to align the raw RNA-seq sequences to the hg19 human reference genome. Transcript counts table files were generated using the HTSeq htseq-count subprogram with the GENCODE annotation database and processed with the BAM files created using the Hisat2.
All gene expression data from the RNA-seq experiment were normalized using the variance-stabilizing transformation in the DESeq2. Differentially expressed genes (DEGs) were obtained using the DESeq2 R package. Genes and samples were clustered using the ward.D or the ward.D2 method, and distance was calculated on the basis of the Euclidean or Pearson’s correlation coefficient in the R gplots (version 3.0.1.1) package.
The raw sequence variants of the APL RNA-seq samples without WES samples (n = 144) were called in accordance with the GATK forum-recommended analysis pipeline. The driver mutation sites from the RNA-seq only samples were reported on sites available in the WES data. The detailed screening of the candidate driver gene mutations was carried out in accordance with our previously published procedures.
The FusionCatcher was used to find somatic fusion genes, such that at least 2 split and 3 spanning reads were in the analyzed RNA-seq data.
The IPA was applied to find out whether DEGs were controlled by the same upstream regulator or by the same pathway. The gene set enrichment analysis (GSEA) was performed using the GSEA (version 3.0) with MSigDB-hallmark (H) and MSigDB-curated gene sets. For GSEA, all measured genes with phenotype labels of high and low risks were used. The GO functional and the KEGG pathway analyses were used for enrichment analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression matrix

source_name: Bone marrow mononuclear cells, APL patients

extract_protocol:
Bone marrow mononuclear cells from 18 centers were isolated after Ficoll–Isopaque density gradient centrifugation. Genomic mRNA were extracted from the patients’ BM using the AllPrep PowerFecal RNA Kit in accordance with the manufacturer’s instructions. After additional enrichment by purification with Ficoll, BM blasts were over 80%.
The DNase I-treated total RNA preparations were qualitatively validated by Agilent RNA 6000 Nano Kit with the 2100 Bioanalyzer system, and libraries were prepared using the KAPA RNA HyperPrep kit in accordance with the manufacturer’s instructions (KAPA). High-throughput sequencing was performed on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s paired-end 2 × 150 bp protocol.

tag: tissue

value: Bone Marrow

tag: disease state

value: acute promyelocytic leukemia

tag: gender

value: Male

tag: age


title: APL036


title: symsym rep3

city: Heidelberg

first: Annika

last: Guse

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies

country: Germany

institute: Heidelberg University

description:
Sample 13
Aiptasia
processed data file: TMM_all_replicates.xlsx

data_processing:
Paired-end reads were mapped to the Aiptasia genome version GCF_001417965.1 using HISAT2 version 2.1.0 at default settings, except -X 2000 --no-discordant --no-unal --no-mixed.
Host-derived transcripts were quantified in Trinity v2.5.1 using salmon v0.10.2 at default settings.
Principal component analysis of gene expression across all samples was conducted using the perl script PtR supplied with Trinity based on raw expression counts. Based on principal component analysis, for further analysis, samples apoapo rep1, 3, 4, and aposym rep2, 3, 4, 5 were used in further analysis as the condition "aposymbiotic cells", and samples symsym rep1, 2, 3, and 4 were used as condition "symbiotic cells".
Differentially expressed genes between clustered symbiotic and aposymbiotic samples were detected using DEseq2 (log2-fold change > 2; false-discovery-rate < 0.01) from raw read counts.
Genome_build: GCF_001417965.1
Supplementary_files_format_and_content: TMM_all_replicates.xlsx file contains normalized TMM values for each gene for each replicate.

molecule: polyA RNA

organism: Exaiptasia diaphana

source_name: symbiotic cells from symbiotic Aiptasia larvae

growth_protocol: Aiptasia larvae were maintained at ~300 larvae per ml in glass beakers in 0.22 µm filter-sterilized artificial sea water (FASW) at 26ºC and exposed to a 12L:12D cycle. B. minutum were grown in cell culture flasks in 0.22 µm filter-sterilized 1X Daigo’s IMK medium (398-01333, Nihon Pharmaceutical Co. Ltd., Tokyo, Japan) on a 12h light:12h dark (12L:12D) cycle under 20–25 µmol m−2 s−1 of photosynthetically active radiation (PAR) at 26 °C.

extract_protocol:
Following collection of cells, these were lysed in 4.3 µl lysis buffer (0.2 % TritonX-100, 1U/µl Protector RNase inhibitor (3335399001, Sigma-Aldrich Co. LLC), 1.25 µM oligo-dT30VN, and 2.5 mM dNTP mix), and flash-frozen in liquid nitrogen.
Sequencing libraries were prepared following the SmartSeq2 protocol (Picelli et al., 2014). Briefly, full-length polyA+ mRNA was reverse transcribed using SuperScript II Reverse Transcriptase (18064014, Sigma-Aldrich Co. LLC), followed by pre-amplification of cDNA over 21 PCR cycles using KAPA HiFi Hotstart Ready Mix (07958935001, Roche Diagnostics International AG, Rotkreuz, Switzerland). cDNA libraries were then prepared for Illumina sequencing using the Nextera XT sequencing kit (FC-131-1096, Illumina, Inc., San Diego, CA, USA) and sequenced on NextSeq500 with 75 bp paired-end sequencing.

treatment_protocol: Following washing in calcium and magnesium-free artificial sea water (FMF-SW), ectodermal tissue was removed in 0.5 % Pronase and 1% sodium thio glycolate in CMF-SW. The endodermal tissue was macerated and the respective cells (symbiotic or aposymbiotic) were collected using a microcapillary needle.

tag: strain

value: CC7 x F003

value: endoderm

tag: symbiotic state of larvae

value: symbiotic

tag: symbiotic state of isolated cells

tag: age of larvae at start of infection

tag: duration of infection

tag: age at time of sampling

tag: number of cells per replicate


title: HFD rep1


title: HEC_wt_rep1

value: wild type


title: symsym rep2

description:
Sample 12
Aiptasia
processed data file: TMM_all_replicates.xlsx


title: Mg-Apo Rep1

description: Exaiptasia pallida (Aiptasia)

data_processing:
Paired-end reads were mapped to the Aiptasia genome version GCF_001417965.1 using HISAT2 version 2.1.0 at default settings, except -X 2000 --no-discordant --no-unal --no-mixed.
Host-derived transcripts were quantified in Trinity v2.5.1 using salmon v0.10.2 at default settings.
Differentially expressed genes between clustered different conditions were detected using DEseq2 (log2-fold change > 2; false-discovery-rate < 0.01) from raw read counts.
Genome_build: GCF_001417965.1
Supplementary_files_format_and_content: .xlsx file contains normalized TMM values for each gene for each replicate.

source_name: aposymbiotic cells from Aiptasia larvae infected with Microchlopopsis gaditana

growth_protocol: Aiptasia larvae were maintained at ~300 larvae per ml in glass beakers in 0.22 µm filter-sterilized artificial sea water (FASW) at 26ºC and exposed to a 12L:12D cycle. M. gaditana were grown in cell culture flasks in 0.22 µm filter-sterilized 1X Daigo’s IMK medium (398-01333, Nihon Pharmaceutical Co. Ltd., Tokyo, Japan) on a 12h light:12h dark (12L:12D) cycle under 20–25 µmol m−2 s−1 of photosynthetically active radiation (PAR) at 18 °C.

treatment_protocol: Following washing in calcium and magnesium-free artificial sea water (FMF-SW), ectodermal tissue was removed in 0.5 % Pronase and 1% sodium thio glycolate in CMF-SW. The endodermal tissue was macerated and the respective cells (aposymbiotic or containing M. gaditana) were collected using a microcapillary needle.

value: infected with M. gaditana

value: aposymbiotic


title: HEC_shNRSF_rep1


title: ND rep2

source_name: Hair follicle stem cells from ND-fed mice

value: Normal diet (ND)


title: ND rep1


title: symsym rep6

description:
Sample 16
Aiptasia
processed data file: TMM_all_replicates.xlsx


title: M46_rep1

value: HS5-1 NRSE -/- monocolon


title: APL034

value: Female


title: aposym rep5

description:
Sample 10
Aiptasia
processed data file: TMM_all_replicates.xlsx

source_name: aposymbiotic cells from symbiotic Aiptasia larvae


title: HEC_shGFP_rep1

value: shGFP transfected


title: pt15rep2

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

country: USA

institute: St. Jude Children's Research Hospital

data_processing:
Raw fastq files were assessed by FastQC (v0.11.5).
The adapters and low-quality sequence were trimmed by cutadapt (v-1.13).
The gene expression quantification analysis was performed by Salmon (v-0.9.1) based on the reference genome hg38 (GRCh38) with gene annotation from GENCODE (release 28).
The raw counts of reads mapped to each gene were extracted and used for subsequent analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM and raw counts values for each Sample

source_name: ductal breast cancer tissue

extract_protocol:
Total RNA was extracted from 11 ductal breast cancer tissues and 32 breast cancer cell line samples. Ribosomal RNA were further removed.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: ductal breast cancer

tag: subtype

tag: response

value: Responder

tag: progression-free survival indicator

tag: progression-free survival

value: 5.19 months


title: pt15rep1


title: APL032


title: aposym rep3

description:
Sample 8
Aiptasia
processed data file: TMM_all_replicates.xlsx


title: aposym rep2

description:
Sample 7
Aiptasia
processed data file: TMM_all_replicates.xlsx


title: APL031


title: pt14

value: 2.76 months


title: symsym rep1

description:
Sample 11
Aiptasia
processed data file: TMM_all_replicates.xlsx


title: aposym rep1

description:
Sample 6
Aiptasia
processed data file: TMM_all_replicates.xlsx


title: APL030

value: Bone Marrow


title: pt13

value: 4.47 months


title: APL029

value: acute promyelocytic leukemia


title: apoapo rep5

description:
Sample 5
Aiptasia
processed data file: TMM_all_replicates.xlsx

source_name: aposymbiotic cells from aposymbiotic Aiptasia larvae

value: CC7 x F003


title: APL035

value: Male


title: HEC_shGFP_rep2

tag: cell line

tag: cell type

value: endometrium

tag: disease

value: adenocarcinoma


title: apoapo rep4

description:
Sample 4
Aiptasia
processed data file: TMM_all_replicates.xlsx

tag: tissue

value: endoderm


title: APL033

tag: disease state

tag: gender


title: pt09

value: 6.51 months


title: APL028

tag: age


title: pt08

value: 11.41 months


title: apoapo rep3

description:
Sample 3
Aiptasia
processed data file: TMM_all_replicates.xlsx

tag: strain

tag: symbiotic state of larvae

value: aposymbiotic


title: pt07

value: TNBC

value: 20.28 months


title: apoapo rep2

description:
Sample 2
Aiptasia
processed data file: TMM_all_replicates.xlsx

tag: symbiotic state of isolated cells

tag: age of larvae at start of infection


title: pt06

value: ductal breast cancer

value: Non-responder

value: 1.08 months


title: APL025


title: pt05

value: 1.84 months


title: APL026

value: Bone Marrow

value: Female


title: APL024

value: acute promyelocytic leukemia


title: APL023


title: APL027


title: pt03

value: 2.53 months


title: pt04

value: Responder

value: 5.03 months


title: APL022

value: Male


title: scrambled1

city: Salzburg

first: Selma

middle: M

last: Soyal

address: Strubergasse 18

department: Institute of Pharmacology and Toxicology

country: Austria

institute: Paracelsus Private Medical University

data_processing:
FastQC quality check.
Trimmomatic adapter and low-quality ends trimming.
STAR reference genome and transcriptome mapping.
RSEM read count summary to genes.
edgeR normalization and differential expression calculation.
DEXSeq differential exon usage calculation.
Genome_build: hg38
Supplementary_files_format_and_content: GTF with PPARGC1A RefSeq isoforms missing in Ensembl v91 annotation.
Supplementary_files_format_and_content: Matrix table with raw read counts for protein-coding mRNAs for each sample.
Supplementary_files_format_and_content: Matrix table with normalized (edgeR) read counts for protein-coding mRNAs for each sample.
Supplementary_files_format_and_content: Matrix table with differential gene expression (edgeR) for protein-coding mRNAs for each comparison.
Supplementary_files_format_and_content: Matrix table with differential exon usage for protein-coding mRNAs for each comparison.

source_name: SH-SY5Y neuroblastoma cells

growth_protocol: SH-SY5Y cells were cultured in DME (D6046)/F12 1:1 (Sigma-Aldrich) supplemented with 0.21% NaHCO3, 10% fetal bovine serum (FBS, Gibco) and 1% penicillin/ streptomycin

extract_protocol:
RNA was extracted with QIAZOL Lysis Reagent and RNeasy Lipid Tissue Mini Kit (QIAGEN) . RNA concentration and integrity were measured using a Nanovue Spectrophotometer (GE Healthcare) and the QIAxcel Advanced Instrument (QIAGEN), respectively. DNase I-treated total RNA (1 µg/reaction) was reverse transcribed with the QuantiTect Reverse Transcription (RT) kit (QIAGEN), using a mix of random hexamer and oligo-dT primers, as described. cDNAs were amplified in duplicate by real-time PCR using Maxima SYBR Green (Thermo Scientific) or GoTaq™ qPCR Master Mix (Promega), the LightCyclerTM480 (Roche) or Rotor-GeneTMQ (QIAGEN) instruments.
Libraries were prepared with NEBNext Ultra II Directional Kit (New England Biolabs, Ipswich, MA, USA) In brief, 200 to 300 ng total RNA was used as input in the polyA enrichment module protocol. Enriched samples were fragmented and transcribed into cDNA. Following universal adapter ligation, samples were barcoded using dual indexing primers.

treatment_protocol: dCAS9-VPR (for CRISPR activation) was stably integrated into the genome of SH-SY5Y cells. Cells were subsequently transfected with single guide (sg) RNAs designed to target the CNS or Reference PPARGC1A promoters or scrambled sgRNAs designed not to target a human promoter.

value: clonal SH-SY5Y cell line expressing dCAS9-VPR for CRISPR activation

value: neuroblastoma cells

tag: treatment

value: dCAS9-VPR SH-SY5Y cells transiently transfected with scrambled sgRNAs not specific for a human promoter

tag: replicate


title: scrambled2


title: scrambled3


title: apoapo rep1

description:
Sample 1
Aiptasia
processed data file: TMM_all_replicates.xlsx

value: CC7 x F003

value: endoderm

value: aposymbiotic

tag: duration of infection

tag: age at time of sampling

tag: number of cells per replicate


title: APL021


title: 36

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

data_processing:
demultiplexing: bcl2fastq
quality control: FastQC
trimming off the 3' adapter sequences: UEA sRNA WorkbenchV3.2
filtering: UEA sRNA WorkbenchV3.2; parameters: 17-25 nt in length, minimum abundance of at least 6 supporting reads, tRNA and rRNA sequences excluded.
mapping: the filtered reads were mapped to Bos taurus UMD 3.1 genome and miRBase 21, using miRCat tool embeded in UEA sRNA WorkbenchV3.2. The following parameters were applied - default animal parameters, except for: minimum abundance (6), minimum length (17 nt) and maximum length (25 nt).
differential expression analysis: DESeq2 (a Bioconductor R-project package)
Genome_build: Bos taurus UMD 3.1
Supplementary_files_format_and_content: FASTA files after filtering and adaptor trimming, generated with the use of UEA sRNA Workbench V3.2. They include the number of reads of detected sequences.

organism: Bos taurus

source_name: mammary gland parenchyma

extract_protocol:
The quantity and quality of the obtained RNA were checked on a NanoDrop 2000 spectrophotometer (Thermo Scientific; Wilmington, USA) and on a TapeStation 2200 instrument (RNAScreen Tape, Agilent, Perlan Technologies, Poland).
microRNA libraries were prepared with the use of NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs; E7300L), according the standard protocol. Briefly, the first step was the 3’ adaptor ligation, followed by hybridization with the Reverse Transcription Primer and ligation with the 5’ adaptor. The RNA-adaptor ligation products were subjected to reverse transcription. Then, PCR amplification with 12 different indexed primers was performed to allow further multiplexing of the samples. The amplified samples were purified and size-selected on a Novex 6% TBE PAGE gel (Invitrogen). After the overnight elution from the gel, the libraries were precipitated and purified with ethanol (POCH). Next, they were subjected to a concentration measurement with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and a size assessment with a 2200 TapeStation instrument (Agilent). The libraries were stored at -20°C at 10nM concentration until further use.

treatment_protocol: Immediately after slaughter, tissue samples were frozen in liquid nitrogen and stored at -80°C

tag: type of infecting bacteria

value: healthy (control)

tag: sampled animal and mammary gland quarter (lf - left frontal, rf- right frontal, lb - left back, rb - right back)

tag: platform

value: HiScanSQ (Illumina)


title: 35

value: Coagulase-positive staphylococci (CoPS)


title: ref2

tag: cell line

tag: cell type

value: dCAS9-VPR SH-SY5Y cells transiently transfected with specific sgRNAs targeting the Reference-PPARGC1A promoter


title: APL020

tag: tissue

value: Bone Marrow

tag: disease state


title: 34


title: aposym rep4

description:
Sample 9
Aiptasia
processed data file: TMM_all_replicates.xlsx

value: symbiotic


title: ref1


title: cns3

value: dCAS9-VPR SH-SY5Y cells transiently transfected with specific single guide (sg) RNAs targeting the CNS-PPARGC1A promoter


title: APL019

value: acute promyelocytic leukemia

tag: gender

value: Female

tag: age


title: 33

value: Coagulase-negative staphylococci (CoNS)


title: APL018


title: ref3


title: 32


title: APL017

value: Male


title: cns2

value: clonal SH-SY5Y cell line expressing dCAS9-VPR for CRISPR activation


title: APL016


title: APL015


title: RNA-seq_wt_T_rep2

city: shanghai

first: meng

last: liu

address: 1239,SiPing Road

institute: TongJi University

description:
RNA-seq_wt_T_rep2
G7N-T_rep2

data_processing:
Low-quality and adaptor sequences were trimmed using cutadapt (v1.18) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20. RNA sequencing reads were aligned using hisat2 (v2.1.0) with strand specific mode (--rna-strandness RF) to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB). Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf 3D7 v32) using featureCounts (v1.6.1) with parameters: -M -p -B -C -s 2.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: Tab-delimited text file include raw read count values for each transcript across all samples.

organism: Plasmodium falciparum

growth_protocol: P. falciparum 3D7strain with 2% hematocrit was cultured in medium containing 10.44g/L RPMI-1640, 25mM HEPES, 10% Albumax I, 20μg/ml gentamicin, 0.1 mM hypoxanthine, a gas phase with 5% O2, 3% CO2 at 37 °C. Parasites were synchronized by 5% sorbitol and a 40%/70% Percoll gradient centrifugation.

extract_protocol:
Total RNA was extracted from highly synchronous parasites using Trizol based on the manufacturer's instructions of Direct-zol™ RNA MiniPrep (R2052).
The library was constructed by KAPA Stranded mRNA-Seq Kit (KK8421)
The library were sequenced on an Illumina HiSeq Xten systerm with PE150 strategy.

treatment_protocol: Infected RBC were collected by centrifugation(room tempereture, 2500 rpm, 5 min) and resuspened with Trizol(1 ml/200-300 μl RBC).

tag: development stage

value: Trophozoite

tag: strain

value: Pf 3D7

tag: genotype

value: wild type

tag: host

value: Homo sapiens


title: 31


title: RNA-seq_wt_T_rep1

description:
RNA-seq_wt_T_rep1
G7N-T_rep1


title: cns1

value: neuroblastoma cells

tag: treatment

tag: replicate


title: 30

value: healthy (control)


title: 29

value: HiScanSQ (Illumina)


title: Genomic DNA from pancretatic tissue_PNC034T

type: genomic

city: Shinjyuku-ku

first: Yae

last: Kanai

address: 35, Shinano-machi

institute: Keio University School of Medicine

description: Pamcreatic ductal adenocarcinoma

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450K Beadchip using standard Illumina protocol.

scan_protocol: Hybridization fluorescence signals were read by the iScan reader  using standard recommended Illumina scanner setting.

data_processing: GenomeStudio methylation software

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: High-molecular-weight DNA was extracted from fresh frozen tissue samples using phenol–chloroform, followed by dialysis.


title: Genomic DNA from pancretatic tissue_PNC032T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC044T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC033T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC029T

description: Pamcreatic ductal adenocarcinoma


title: 28

value: Coagulase-positive staphylococci (CoPS)


title: APL014


title: Genomic DNA from pancretatic tissue_PNC035T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC031T

description: Pamcreatic ductal adenocarcinoma


title: RNA-seq_wt_S_rep2

description:
RNA-seq_wt_S_rep2
G7N-S_rep2

value: Schizont


title: APL012

value: Bone Marrow


title: 27


title: Genomic DNA from pancretatic tissue_PNC025T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC028T

description: Pamcreatic ductal adenocarcinoma


title: APL011


title: 26


title: APL010


title: RNA-seq_wt_R_rep2

description:
RNA-seq_wt_R_rep2
G7N-R_rep2

value: Ring


title: 25


title: Genomic DNA from pancretatic tissue_PNC022T

description: Pamcreatic ductal adenocarcinoma


title: 24


title: Genomic DNA from pancretatic tissue_PNC015T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC018T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC026T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC012T

description: Pamcreatic ductal adenocarcinoma


title: RNA-seq_wt_R_rep1

description:
RNA-seq_wt_R_rep1
G7N-R_rep1


title: APL007


title: RNA-seq_wt_S_rep1

description:
RNA-seq_wt_S_rep1
G7N-S_rep1


title: Genomic DNA from pancretatic tissue_PNC008T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC019T

description: Pamcreatic ductal adenocarcinoma


title: APL009


title: Genomic DNA from pancretatic tissue_PNC016T

description: Pamcreatic ductal adenocarcinoma


title: RNA-seq_Pfhmgb1_RC_T_rep2

value: Pfhmgb1 Rescue


title: Genomic DNA from pancretatic tissue_PNC009T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC013T

description: Pamcreatic ductal adenocarcinoma


title: 23


title: APL006

value: acute promyelocytic leukemia


title: RNA-seq_Pfhmgb1_RC_S_rep1


title: APL008

value: Female


title: 20


title: Genomic DNA from pancretatic tissue_PNC004T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC005T

description: Pamcreatic ductal adenocarcinoma


title: APL005


title: RNA-seq_Pfhmgb1_RC_T_rep1


title: Genomic DNA from pancretatic tissue_PNC014T

description: Pamcreatic ductal adenocarcinoma


title: 22


title: RNA-seq_Pfhmgb1_RC_S_rep2


title: 21


title: 19


title: RNA-seq_Pfhmgb1_RC_R_rep2


title: APL004


title: RNA-seq_Pfhmgb1_RC_R_rep1


title: 18


title: 17


title: APL003


title: RNA-seq_Pfhmgb1_KO_T_rep2

value: Pfhmgb1 Knock Down


title: APL002


title: Genomic DNA from pancretatic tissue_PK05-32T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC003T

description: Pamcreatic ductal adenocarcinoma

value: Male


title: RNA-seq_Pfhmgb1_KO_T_rep1


title: MS-6

city: Planegg-Martinsried

first: Eduardo

last: Beltrán

state: Bayern

address: Großhaderner Str. 9

department: Institute of Clinical Neuroimmunology

institute: University Hospital, LMU Munich

description: 10x Chromium Single Cell 5' Solution

data_processing:
Cell Ranger software (10x Genomics, v.3.1.0) was used to demultiplex samples, process raw data, align reads to the GRCh38 human reference genome and summarize unique molecular identifier (UMI) counts. Filtered gene-barcode and hashing-barcode matrices that contained only barcodes with UMI counts that passed the threshold for cell detection were used for further analysis.
We processed the filtered UMI count matrices using the R package Seurat (version 3.0). Cell hashing raw counts were normalized using centered log ratio (CLR) transformation, where counts were divided by the geometric mean of an HTO across cells and log-transformed.
As a QC steps we filtered out: we discarded cells where the number of detected genes was <200 or >5,000 and/or 10% of the counts belonged to mitochondrial genes. After QC, only raw gene counts in high-quality singlets were submitted to: log-normalization; identification of high variable genes by using the MeanVarPlot method; scaling; and regression against the number of UMIs and mitochondrial RNA content per cell.
Integration was performed to remove bath effects and the integrated assay was used for principal component analysis and unsupervised clustering. After marker identification for each cluster, only cells where a TCR clonotype was detected, were used for upstream analysis of TCR repertoire. Single-cell TCR annotation was performed using the 10x cellranger vdj pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered feature-barcode counts

source_name: cerobrospinal fluid

tag: disease

value: Multiple sclerosis

tag: Sex

value: female


title: RNA-seq_Pfhmgb1_KO_S_rep2

value: Pf 3D7


title: MS-5

description: 10x Chromium Single Cell 5' Solution


title: MS-4

description: 10x Chromium Single Cell 5' Solution


title: RNA-seq_Pfhmgb1_KO_S_rep1


title: 14

tag: type of infecting bacteria


title: 16

tag: sampled animal and mammary gland quarter (lf - left frontal, rf- right frontal, lb - left back, rb - right back)


title: 15

tag: platform


title: Genomic DNA from pancretatic tissue_PK05-31T

description: Pamcreatic ductal adenocarcinoma


title: 13

value: Coagulase-negative staphylococci (CoNS)


title: RNA-seq_Pfhmgb1_KO_R_rep2

value: Homo sapiens


title: MS-1

description: 10x Chromium Single Cell 5' Solution

value: male


title: 11

value: healthy (control)


title: 12

value: HiScanSQ (Illumina)


title: Genomic DNA from pancretatic tissue_PK05-30T

description: Pamcreatic ductal adenocarcinoma


title: 10


title: SAßGal high, old donor #2

city: Piscataway

first: Ricardo

middle: Iván

last: Martínez Zamudio

state: New Jersey

address: 675 Hoes Lane West

department: Pharmacology

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

data_processing:
Base Calling was performed with RTA version 2.0
Alignment was performed with bowtie2 using the local option against the hg19 version of the human genome
Reads in exons were counted with SummarizeOverlaps, using exons from Homo_sapiens.GRCh37.75.gtf
Reads were filtered as follows: at least 3 samples have at least 5 reads per every gene
Read normalization was performed during differential analysis with DESeq2. For visualizations, we used rld-transformed reads.
Differentially expressed genes were clustered with WGCNA, with two gene modules being identified.
Genome_build: hg19
Supplementary_files_format_and_content: counts per exon; rld transform and log2 fold-change of differentially expressed genes
Supplementary_files_format_and_content: raw counts and rld transformed values per gene (SummarizeOverlaps and DESeq2 rld transform output)
Supplementary_files_format_and_content: rld transformed values and log2 fold change of differentially regulated genes (DESeq2 output)

source_name: CD8+ T Cells

growth_protocol: Blood was isolated from healthy donors in their 20`s and 60's, PBMCs isolated by density centrifugation and CD8+ T cells enriched by negative selection using a StemCell EasySep Human CD8+ T‐Cell Isolation Kit

extract_protocol:
Macherey-Nagel RNA-XS kit
Smarted Stranded V2 Kit (Takara)

treatment_protocol: Young and old donors were always processed in pairs to allow for direct comparison

tag: saßgal activity

value: High

value: CD8+ T Cells

value: old


title: 9

value: Coagulase-positive staphylococci (CoPS)


title: RNA-seq_Pfhmgb1_KO_R_rep1

value: Ring


title: SAßGal high, old donor #3

tag: cell type


title: Genomic DNA from pancretatic tissue_PK05-25T

description: Pamcreatic ductal adenocarcinoma


title: SAßGal high, old donor #1


title: ND 4d anagen

type: RNA

hyb_protocol: 1.69 ug of Cy3-labelled cDNA was hybridized to Agilent SurePrint G3 Mouse GE v2 8x60K Microarray for 17 hours at 65 oC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37oC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label: total RNA

source_name: Hair follicle stem cells, normal diet, anagen, 4 days

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 0.5 ug cDNA using Exo-Klenow fragment.

extract_protocol: Total RNA was purified with an RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.

value: Hair follicle stem cell

value: 2 month old


title: Genomic DNA from pancretatic tissue_PK05-24T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK05-26T

description: Pamcreatic ductal adenocarcinoma

value: Female


title: Genomic DNA from pancretatic tissue_PK05-21T

description: Pamcreatic ductal adenocarcinoma


title: 8


title: Agen anagen

source_name: Hair follicle stem cells, aged, anagen

value: 24 month old


title: Genomic DNA from pancretatic tissue_PK05-17T

description: Pamcreatic ductal adenocarcinoma

value: Male


title: HFD 4d anagen

source_name: Hair follicle stem cells, high fat diet, 4 days, anagen


title: SAßGal low, old donor #2

value: Low


title: SAßGal low, old donor #3


title: 6


title: Genomic DNA from pancretatic tissue_PK05-12T

description: Pamcreatic ductal adenocarcinoma


title: HFD 3M anagen

source_name: Hair follicle stem cells, high fat diet, anagen, 3 month

value: 5 month old


title: SAßGal low, old donor #1


title: Genomic DNA from pancretatic tissue_PK05-11T

description: Pamcreatic ductal adenocarcinoma


title: ND 3M anagen

source_name: Hair follicle stem cells, normal diet, anagen, 3 month


title: SAßGal high, young donor #3

value: young


title: MS-3

description: 10x Chromium Single Cell 5' Solution

value: Multiple sclerosis

value: female


title: MS-2

description: 10x Chromium Single Cell 5' Solution


title: 5


title: Genomic DNA from pancretatic tissue_PK05-15T

description: Pamcreatic ductal adenocarcinoma


title: SAßGal high, young donor #2


title: 3

value: Coagulase-negative staphylococci (CoNS)


title: Aged telogen-3

source_name: Hair follicle stem cells, aged, telogen, replicate 3

value: male


title: 4

value: HiScanSQ (Illumina)


title: Genomic DNA from pancretatic tissue_PK05-10T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK05-14T

description: Pamcreatic ductal adenocarcinoma


title: Aged telogen-1

source_name: Hair follicle stem cells, aged, telogen, replicate 1


title: SAßGal high, young donor #1

value: High

value: CD8+ T Cells


title: HFD 4d telogen-3

source_name: Hair follicle stem cells, high fat diet, telogen, 4 days, replicate 3


title: Genomic DNA from pancretatic tissue_PK05-07T

description: Pamcreatic ductal adenocarcinoma


title: Aged telogen-2

source_name: Hair follicle stem cells, aged, telogen, replicate 2


title: Genomic DNA from pancretatic tissue_PK05-05T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK05-04T

description: Pamcreatic ductal adenocarcinoma


title: 1


title: 2

value: Coagulase-positive staphylococci (CoPS)


title: SAßGal low, young donor #3


title: SAßGal low, young donor #2


title: SAßGal low, young donor #1


title: HFD 4d telogen-2

source_name: Hair follicle stem cells, high fat diet, telogen, 4 days, replicate 2


title: MDA-MB-468_Tm_18hrs_rep2

description: Treated by tunicamycin for 18 hours.

source_name: breast cancer cell line: MDA-MB-468

tag: cell line

tag: subtype

value: Basal A

tag: response

value: Resistant

value: Tunicamycin

tag: time


title: HFD 4d telogen-1

source_name: Hair follicle stem cells, high fat diet, telogen, 4 days, replicate 1

value: Hair follicle stem cell

tag: gender

tag: age

value: 2 month old


title: MDA-MB-468_24hrs_rep2

description: Treated by ricolinostat for 24 hours.

value: Ricolinostat


title: Genomic DNA from pancretatic tissue_PK05-03T

description: Pamcreatic ductal adenocarcinoma

value: Female


title: ND 4d telogen-3

source_name: Hair follicle stem cells, normal diet, telogen, 4 days, replicate 3


title: HFD 3M telogen-3

source_name: Hair follicle stem cells, High fat diet, telogen, 3 month, replicate 3

value: 5 month old


title: Gastric cancer and adjacent noncancerous tissues from patient 5

city: Guangzhou

first: Min

last: Deng

address: 78 Hengzhigang Road

institute: Affiliated Cancer Hospital & Institute of Guangzhou Medical University

description: Gastric tissue and  paired adjacent noncancerous tissue from patient5

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Agilent chip scanner (G2565CA) was used to scan the cleaned chip and obtain the hybrid picture

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used for background subtraction and LOWESS normalization.

source_name: Gastric cancer  tissue of patient5

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine¡¯s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted using Trizol reagent(Invitrogen,Camarillo,USA) following the manufacturer's instructions and purified with NucleoSpin? RNA clean-up (Macherey-nagel,Duren,Germany,Cat. No.740609.250). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1.2% formaldehyde denaturing gel electrophoresis.

tag: tissue

value: Cancer tissue of patient5

source_name: Adjacent noncancerous tissues

value: Paired adjacent noncancerous tissue of patient5


title: MDA-MB-468_Tm_18hrs_rep1

description: Treated by tunicamycin for 18 hours.


title: HFD 3M telogen-2

source_name: Hair follicle stem cells, High fat diet, telogen, 3 month, replicate 2


title: Gastric cancer and adjacent noncancerous tissues from patient 4

description: Gastric tissue and  paired adjacent noncancerous tissue from patient4

source_name: Gastric cancer  tissue of patient4

value: Cancer tissue of patient4

value: Male

value: Paired adjacent noncancerous tissue of patient4


title: ND 4d telogen-2

source_name: Hair follicle stem cells, normal diet, telogen, 4 days, replicate 2

value: male


title: 7

source_name: mammary gland parenchyma

value: Coagulase-negative staphylococci (CoNS)

value: HiScanSQ (Illumina)


title: ND 4d telogen-1

source_name: Hair follicle stem cells, normal diet, telogen, 4 days, replicate 1


title: Mock depletion mRNA-seq-3

city: Riverside

first: HAO

last: HU

state: California

address: 16 Round Table Dr.

institute: University of California, Riverside

data_processing:
All prepared libraries were pooled and sequenced on Illumina NovaSeq 6000 system (paired-end, 150 bp) at Novogene company (Beijing, China).
RNA-seq data were analyzed using the pRNASeqTools pipeline ("https://github.com/grubbybio/RNASeqTools"). The raw reads were mapped to the Arabidopsis genome (Araport 11) using STAR 2.7.3a (Dobin et al, 2013) with the parameters “--alignIntronMax 5000 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.1. Mapped reads counts were calculated by featureCounts 2.0.0 (Liao et al, 2014). Transcript levels were quantified in reads per kilobase per million total read counts.
NAD-RNAs were defined as RPKM with two-fold change and adjusted P-value < 0.05 in NAD-seq samples compared to mRNA-seq samples using DESeq2
Genome_build: Araport 11
Supplementary_files_format_and_content: text files with gene ID and raw counts

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Col-0 seeds were sowed on solid 1/2 Murashige and Skoog (MS) medium with 1% sucrose and 0.7% agar. Plates were kept in the dark at 4 ℃ for 3 days for seeds stratification and then transferred to growth room with 16 h/8 h light/dark photoperiod at 22 ℃ for 12 days. Seedlings were collected at 10 am - 11 am in the morning for this study.

extract_protocol:
Total RNAs were extracted from 12 days Col-0 seedlings by TRIzol reagent (Molecular Research Center) and treated with 1 unit/μg DNase I at 37 ℃ for 1 h. (Roche). After DNase I treatment, total RNAs were phenol/chloroform extracted and ethanol precipitated. Poly(A) RNAs were isolated from total RNAs using Oligo d(T)25 Magnetic Beads (New England Biolabs) following the manufacturer’s instructions. RNA concentration was determined by Nanodrop spectrophotometers.
10 μg mRNAs were subjected to Anti-m7G antibody treatment to remove the m7G-RNAs (Samples without adding Anti-m7G antibody as the Mock depletion). mRNAs in supernatants were acid phenol/chloroform extracted, ethanol precipitated and redissolved in DEPC H2O. Finally, redissolved mRNAs were separated to three aliquots. One aliquot contained ~150 ng mRNAs was subjected to mRNA-seq library construction, the other two aliquots contained ~3 μg mRNAs in each were made up to 100 μg by adding E. coli tRNA and further performed CuAAC- and SPAAC-NAD reaction. After CuAAC- or SPAAC-NAD reaction, RNAs were incubated at 25 ℃ for 1 h with 25 μl magnetic MyOne Streptavidin C1 beads, RNAs were finally eluted from beads by incubating with 20 μl H2O at 80 ℃ for 5 min. NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420, New England Biolabs) was used for subsequent mRNA-seq and NAD-seq libraries construction. Firstly, three RNAs batches were incubated with RT mix in the kits containing First Strand Synthesis Reaction Buffer and random primers at 94 ℃ for 6 min to fragment mRNAs. The remaining steps were performed according to the manufacturer’s instructions.

value: 12 days

tag: antibody

value: Mock antibody

tag: ecotype


title: Gastric cancer and adjacent noncancerous tissues from patient 1

description: Gastric tissue and  paired adjacent noncancerous tissue from patient1

source_name: Gastric cancer  tissue of patient1

value: Cancer tissue of patient1

value: Paired adjacent noncancerous tissue of patient1


title: Genomic DNA from pancretatic tissue_PK04-45T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK04-43T

description: Pamcreatic ductal adenocarcinoma


title: Gastric cancer and adjacent noncancerous tissues from patient 2

description: Gastric tissue and  paired adjacent noncancerous tissue from patient2

source_name: Gastric cancer  tissue of patient2

value: Cancer tissue of patient2

value: Paired adjacent noncancerous tissue of patient2


title: Genomic DNA from pancretatic tissue_PK05-01T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK04-44T

description: Pamcreatic ductal adenocarcinoma


title: Gastric cancer and adjacent noncancerous tissues from patient 3

description: Gastric tissue and  paired adjacent noncancerous tissue from patient3

source_name: Gastric cancer  tissue of patient3

value: Cancer tissue of patient3

value: Paired adjacent noncancerous tissue of patient3


title: MDA-MB-468_6hrs_rep2

description: Treated by ricolinostat for 6 hours.

value: Basal A

value: Resistant

tag: treatment

value: Ricolinostat


title: Mock depletion mRNA-seq-2


title: HFD 3M telogen-1

source_name: Hair follicle stem cells, High fat diet, telogen, 3 month, replicate 1

value: Hair follicle stem cell

value: 5 month old


title: MDA-MB-468_24hrs_rep1

description: Treated by ricolinostat for 24 hours.


title: ND 3M telogen-3

source_name: Hair follicle stem cells, normal diet, telogen, 3 month, replicate 3


title: MDA-MB-468_6hrs_rep1

description: Treated by ricolinostat for 6 hours.

source_name: breast cancer cell line: MDA-MB-468


title: MDA-MB-468_Vehicle_rep2

description: Treated by vehicle.

value: Vehicle


title: Genomic DNA from pancretatic tissue_PK04-46T

description: Pamcreatic ductal adenocarcinoma

value: Female


title: Genomic DNA from pancretatic tissue_PK04-41T

description: Pamcreatic ductal adenocarcinoma

value: Male


title: ND 3M telogen-2

source_name: Hair follicle stem cells, normal diet, telogen, 3 month, replicate 2

value: male


title: Mock depletion mRNA-seq-1

value: 12 days


title: Mock depletion CuAAC-NAD-seq-3

value: Mock antibody

value: CuAAC-NAD reaction


title: Genomic DNA from pancretatic tissue_PK04-37T

description: Pamcreatic ductal adenocarcinoma


title: a12_m47

library_source: genomic

data_processing:
Library strategy: QHR-4C
Reads were sorted  using index and barcode
Duplicated paired-end reads were removed by FastUniq (version 1.1) for QHR-4C
The unique reads were aligned to hg19 using Bowtie1
The  interaction were calculated using the r3Cseq program (version 1.20) in the R package for  QHR-4C
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph were generated using Python

source_name: HEC-1-B cells

growth_protocol: HEC-1-B were cultured in MEM (Hyclone) , supplemented with 10% (v/v) FBS, 2 mM GlutaMAX (Gibco), 1 mM sodium pyruvate (Sigma), and 1% penicillin-streptomycin.

extract_protocol:
Cell pellets were lysed twice with cold lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% Triton X-100, 5 mM EDTA, 0.5% NP-40, 1xprotease inhibitors) for nuclei. Then, Nuclear pellet was resuspended in 225 μl of water, 30 μl of 10x DpnII buffer, and 7.5 μl of 10% SDS and incubated at 37 °C for 1 h with constant shaking at 900 rpm. After quenching SDS by adding 37.5 μl of 20% Triton X-100 and incubating at 37 °C for 1 h with shaking at 900 rpm. The nuclei were then digested with 10 μl of DpnII (10 U/μl) in situ at 37 °C with shaking at 900 rpm overnight. After enzyme inactivation at 65 °C for 20 min, nuclei were centrifuged at 2500g for 5 min, resuspended and digested in 358 μl of water, 40 μl of 10x T4 ligation buffer, and 2 μl of T4 DNA ligase (400 unit/μl) overnight at 16 °C. The ligated product was then reverse crosslinked by adding 10 μl of proteinase K (10 mg/ml) and heating at 65 °C for 4 h, followed by adding 2 μl of RNase A (37 mg/ml) and heating at 37 °C for 45 min. DNA was then extracted using phenol-chloroform. 2 μl of glycogen (20 mg/ml) was added to facilitate DNA precipitation.
For 4C libraries, the precipitated DNA was dissolved in 50 μl water, and then sonicated using the Bioruptor system with low energy setting at a train of 30s on with 30s off for 12 cycles for DNA fragments ranging from 200 to 600 bp. With the fragmented DNA as template, a linearized amplification step was applied using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100 μl of PCR system for a total of 80 cycles. The PCR product was denatured at 95 °C for 5 min and immediately chilled on ice to obtain ssDNA. The ssDNA was enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions, and then ligated with annealed adapters in 45 μl of ligation system (20 μl of DNA-coated beads, 4.5 μl of 10x T4 ligation buffer, 10 μl of 30% PEG 8000, 1 μl of 50 μΜ adapter, 0.9 μl of T4 DNA ligase, 8.6 μl of water). The beads were then washed twice to remove the free adapters with the B/W buffer (5mM Tris-HCl, 1M NaCl, 0.5mM EDTA, Ph7.5). The DNA-coated beads were resuspended in 10 μl water. With the DNA on beads as template and a pair of primers, the QHR-4C libraries were generated by PCR amplification and purified with a PCR purification kit (Roche).

treatment_protocol: The shGFP or shNRSF plasmid was transfected into HEK293T cells with the psPAX2 and pMD2.G helper plasmids (Addgene) using Lipofectamine 3000 to produce lentiviral particles.HEC-1-B cells were  infected with the virus in the presence of 8 μg/mL polybrene (Sigma). Puromycin (Sigma) was added to a final concentration of 2 μg/mL to select the infected cells. Fresh puromycin-containing medium was changed every other day. Cells were collected for assays at 5 days post infection.For monoclones, HEC-1-B cells  at ~80% confluency was transfected with Cas9 (0.6 μg) and sgRNA (1.2 μg) expressing plasmids by Lipofectamine 3000 in a 12-well plate. 2 days post transfection, puromycin was added to a final concentration of 2 μg/mL. Four days later, cells were changed to fresh medium without puromycin and cultured for another ten days. The cells were diluted and plated in 96-well plates with approximately one cell per well. Two weeks later, single cell clones were screened for target deletion by PCR.

value: endometrium

tag: disease state

value: adenocarcinoma

tag: transfection

value: HS5-1 NRSE -/- monocolon


title: Genomic DNA from pancretatic tissue_PK04-36T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK04-40T

description: Pamcreatic ductal adenocarcinoma


title: a12_Hec1b_shNRSF

value: shRNA for NRSF transfected


title: Genomic DNA from pancretatic tissue_PK04-32T

description: Pamcreatic ductal adenocarcinoma


title: Mock depletion CuAAC-NAD-seq-2


title: MDA-MB-436_Tm_18hrs_rep1

description: Treated by tunicamycin for 18 hours.

source_name: breast cancer cell line: MDA-MB-436

value: Basal B

value: Tunicamycin


title: Genomic DNA from pancretatic tissue_PK04-33T

description: Pamcreatic ductal adenocarcinoma


title: ND 3M telogen-1

source_name: Hair follicle stem cells, normal diet, telogen, 3 month, replicate 1


title: Mock depletion SPAAC-NAD-seq-3

value: SPAAC-NAD reaction


title: Genomic DNA from pancretatic tissue_PK04-31T

description: Pamcreatic ductal adenocarcinoma


title: a12_Hec1b_shGFP

value: shGFP transfected


title: Genomic DNA from pancretatic tissue_PK05-06T

description: Pamcreatic ductal adenocarcinoma


title: Mock depletion SPAAC-NAD-seq-1


title: a12_Hec1b_wt

value: wild type


title: Genomic DNA from pancretatic tissue_PK04-34T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK04-30T

description: Pamcreatic ductal adenocarcinoma


title: HS51_m47

growth_protocol: HEC-1-B were cultured in MEM (Hyclone) , supplemented with 10% (v/v) FBS, 2 mM GlutaMAX (Gibco), 1 mM sodium pyruvate (Sigma), and 1% penicillin-streptomycin. HEK293T cells were cultured in DMEM/High glucose (Hyclone) , supplemented with 10% (v/v) FBSCells were maintained at 37 °C in a 5% (v/v) CO2 incubator.

treatment_protocol: The shGFP or shNRSF plasmid was transfected into HEK293T cells with the psPAX2 and pMD2.G helper plasmids (Addgene) using Lipofectamine 3000 to produce lentiviral particles. HEK293T cells or HEC-1-B cells were  infected with the virus in the presence of 8 μg/mL polybrene (Sigma). Puromycin (Sigma) was added to a final concentration of 2 μg/mL to select the infected cells. Fresh puromycin-containing medium was changed every other day. Cells were collected for assays at 5 days post infection.For monoclones, HEC-1-B cells or HEK293T cells at ~80% confluency was transfected with Cas9 (0.6 μg) and sgRNA (1.2 μg) expressing plasmids by Lipofectamine 3000 in a 12-well plate. 2 days post transfection, puromycin was added to a final concentration of 2 μg/mL. Four days later, cells were changed to fresh medium without puromycin and cultured for another ten days. The cells were diluted and plated in 96-well plates with approximately one cell per well. Two weeks later, single cell clones were screened for target deletion by PCR.


title: MDA-MB-436_24hrs_rep1

description: Treated by ricolinostat for 24 hours.

value: Resistant

value: Ricolinostat


title: m7G depletion SPAAC-NAD-seq-2

value: m7G-RNA antibody


title: Genomic DNA from pancretatic tissue_PK04-28T

description: Pamcreatic ductal adenocarcinoma

value: Male


title: HS51_Hec1b_wt


title: HS51_m46


title: Mock depletion SPAAC-NAD-seq-2


title: MDA-MB-436_Tm_18hrs_rep2

description: Treated by tunicamycin for 18 hours.


title: MDA-MB-436_Vehicle_rep2

description: Treated by vehicle.

value: Vehicle


title: m7G depletion SPAAC-NAD-seq-1

value: 12 days


title: HS51_Hec1b_shNRSF


title: MDA-MB-468_Vehicle_rep1

description: Treated by vehicle.

value: Basal A


title: m7G depletion CuAAC-NAD-seq-3

value: CuAAC-NAD reaction


title: MDA-MB-436_6hrs_rep2

description: Treated by ricolinostat for 6 hours.


title: m7G depletion SPAAC-NAD-seq-3


title: HS51_Hec1b_shGFP

value: endometrium


title: MDA-MB-436_Vehicle_rep1

description: Treated by vehicle.


title: MDA-MB-436_24hrs_rep2

description: Treated by ricolinostat for 24 hours.


title: Mock depletion CuAAC-NAD-seq-1

value: Mock antibody


title: SK-BR-3_Tm_18hrs_rep2

description: Treated by tunicamycin for 18 hours.

source_name: breast cancer cell line: SK-BR-3

value: Luminal

value: Sensitive


title: SK-BR-3_Tm_18hrs_rep1

description: Treated by tunicamycin for 18 hours.


title: m7G depletion CuAAC-NAD-seq-1


title: Genomic DNA from pancretatic tissue_PK04-23T

description: Pamcreatic ductal adenocarcinoma

value: Female


title: Genomic DNA from pancretatic tissue_PK04-24T

description: Pamcreatic ductal adenocarcinoma


title: H3K27ac_M26

description: HS5-1 NRSE -/- monocolon

data_processing:
Reads were sorted  using index
Reads were aligned to hg19 using bowtie2 for ChIP-Seq
The  peaks were called using the MACS for ChIP-Seq
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph were generated using Python

source_name: HEK293T cells

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-Seq libraries were prepared according to the manual of VAHTSTM Universal DNA Library Prep Kit for Illumina® V2 (ND606). Briefly, DNA was end-repaired using End Prep Mix 3, ligated with index-contained adapters using Rapid DNA ligase in Rapid Ligation buffer, amplificated using PCR Primers and Amplification Mix for libraries. The library fragments of ~350 bp (insert plus adaptor and PCR primer sequences) were isolated  with Agencourt® AMPure® XP (Beckman Coulter®). Library DNAs were sequenced on an Illumina HiSeq platform.

value: kidney

value: fetus

tag: chip antibody

value: H3K27ac(Abcam, ab4729)


title: SK-BR-3_24hrs_rep2

description: Treated by ricolinostat for 24 hours.


title: a12_m46

value: adenocarcinoma

value: HS5-1 NRSE -/- monocolon


title: H3K27ac_293T_wt

description: wild type


title: SK-BR-3_24hrs_rep1

description: Treated by ricolinostat for 24 hours.

value: Ricolinostat


title: SK-BR-3_6hrs_rep2

description: Treated by ricolinostat for 6 hours.


title: SK-BR-3_6hrs_rep1

description: Treated by ricolinostat for 6 hours.


title: MKN-28 cells, IgG RIP-seq

data_processing:
RIP-Seq high throughput sequencing and subsequent bioinformatics analysis were all done by Cloud-Seq Biotech (Shanghai, China). Briefly, raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina HiSeq4000 sequencer. Firstly, Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.3) software, high quality reads were generated. Then these high quality reads were aligned to human genome (UCSC hg19) using bowtie2 software  (v2.2.4) with default parameters. Peak calling was performed with MACS software (v1.4.3). Differentially enriched regions were identified by diffReps software (v1.55.4). The enriched peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
Genome_build: Genome_build: UCSC hg19
Supplementary_files_format_and_content: Peaks

source_name: Gastric cancer cell line

growth_protocol: Cells grown and maintained in RPMI 1640 medium (Gibco, USA) containing penicillin (100 units/ml) and streptomycin (100 µg/ml). Cultures were incubated in a humidified environment at 5% CO2 and 37°C.

extract_protocol:
RIP experiments were conducted using a PTBP1 antibody (Cell Signaling Technology) or IgG (Cell Signaling Technology) with the Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore, Bedford, MA, USA) according to the manufacturer’s instructions . Briefly, 100 μL MKN-28 cell extract was incubated with magnetic beads-antibody complex. The antibodies were used for RIP, and IgG served as a negative control. Total RNA was isolated with Trizol (Invitrogen), and ribosomal RNA was removed from total RNA using a Ribo-Zero™ rRNA Removal Kit (Illumina, USA). RNA-seq was performed using HiSeq4000 (Illumina, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gastric cancer

tag: rip antibody

value: Normal Rabbit IgG (Cell Signaling Technology)


title: m7G depletion CuAAC-NAD-seq-2

value: m7G-RNA antibody


title: MKN-28 cells, PTBP1 RIP-seq

value: PTBP1 antibody (Cell Signaling Technology)


title: H3K27ac_M36

description: HS5-1 NRSE -/- monocolon


title: Genomic DNA from pancretatic tissue_PK04-17T

description: Pamcreatic ductal adenocarcinoma

value: Male


title: SK-BR-3_Vehicle_rep2

description: Treated by vehicle.

value: Vehicle


title: Genomic DNA from pancretatic tissue_PK04-27T

description: Pamcreatic ductal adenocarcinoma


title: H3K4me3_293T_wt

description: wild type

value: H3K4me3 (Millipore, 17-614)


title: NRSF_M36

description: HS5-1 NRSE -/- monocolon

value: NRSF (Millipore, 17-641 )


title: NRSF_M26

description: HS5-1 NRSE -/- monocolon


title: SK-BR-3_Vehicle_rep1

description: Treated by vehicle.

value: Luminal


title: MDA-MB-453_Tm_18hrs_rep2

description: Treated by tunicamycin for 18 hours.

source_name: breast cancer cell line: MDA-MB-453

value: Sensitive

value: Tunicamycin


title: NRSF_293T_wt

description: wild type

value: kidney


title: MDA-MB-453_Tm_18hrs_rep1

description: Treated by tunicamycin for 18 hours.


title: Genomic DNA from pancretatic tissue_PK04-14T

description: Pamcreatic ductal adenocarcinoma

value: Female


title: H3K27ac_293T_shNRSF

description: shRNA for NRSF transfected

value: fetus

value: H3K27ac(Abcam, ab4729)


title: MDA-MB-453_24hrs_rep2

description: Treated by ricolinostat for 24 hours.


title: Genomic DNA from pancretatic tissue_PK04-15T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK04-13T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK04-11T

description: Pamcreatic ductal adenocarcinoma


title: MDA-MB-453_24hrs_rep1

description: Treated by ricolinostat for 24 hours.


title: H3K27ac_293T_shGFP

description: shGFP transfected


title: MDA-MB-453_6hrs_rep2

description: Treated by ricolinostat for 6 hours.


title: MDA-MB-436_6hrs_rep1

description: Treated by ricolinostat for 6 hours.

value: Basal B

value: Resistant


title: Genomic DNA from pancretatic tissue_PK04-10T

description: Pamcreatic ductal adenocarcinoma


title: MDA-MB-453_6hrs_rep1

description: Treated by ricolinostat for 6 hours.

value: Ricolinostat


title: Genomic DNA from pancretatic tissue_PK04-25T

description: Pamcreatic ductal adenocarcinoma


title: MDA-MB-453_Vehicle_rep2

description: Treated by vehicle.


title: Genomic DNA from pancretatic tissue_PK04-05T

description: Pamcreatic ductal adenocarcinoma


title: H3K4me3_293T_shGFP

description: shGFP transfected


title: MDA-MB-453_Vehicle_rep1

description: Treated by vehicle.


title: Genomic DNA from pancretatic tissue_PK04-08T

description: Pamcreatic ductal adenocarcinoma


title: H3K27ac_M47

description: HS5-1 NRSE -/- monocolon


title: TotalRNA-seq_siStau1_DAC_rep2

city: Daejeon

first: Ku

last: yongsuk

address: KAIST, 291, Daehak-ro, Yuseong-gu

department: Department of Chemical and Biomolecular Engineering

country: South Korea

institute: KAIST

data_processing:
bcl2fastq2 (Version 2.20) software used for basecalling.
Reads were aligned with the human genome (hg38) using Hisat2(ver.2.1.0) with the cufflink option.
Non-coding RNA was analyzed by counting raw transcript reads using the featurecount software. Each transcript was matched by a manually made ncRNA gtf reference file which was extracted from the ncRNA database. Raw counts were normalized and analyzed with the DESeq(ver.1.36.0) software which is capable of handling non-replicated RNA-seq data.
Mapped reads were assembled by two distinct methods. Initial transcript raw counts were assembled using the hg38 gtf file by the featurecount software. Count data with replicates were normalized and analyzed with the DESeq software. The same transcript raw counts were assembled using the cufflink software(ver.2.2.1). Each file was converted to abundance files by cuffquant(ver.2.2.1). Abundance files were normalized by FPKM and compared by the cuffdiff(ver.2.2.1) and cuffnorm(ver.2.2.1).
For Differential analysis, four types of treatment done to the HCT116 (siLuc_DAC, siLuc_DMSO, siStau1_DAC, siStau1_DMSO) was grouped and compared using both DESeq and cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

extract_protocol:
Staufen1 binding lncRNAs are enriched with Staufen1 antibody and extracted using Trizol reagent. TruSeq Stranded Total RNA Sample Prep Kit (Illumina, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries. Total RNA was harvested using Trizol reagent. TruSeq Stranded Total RNA Library Prep Gold (Cat#20020598) was used with Total RNA 400ng that was subjected to ribosomal RNA depletion, with Ribo-zero Gold reagent for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 500nM decitabine treated for 5days

value: Colorectal cancer cell line

tag: genotype/variation

value: Staufen1 siRNA

value: Decitabine treated


title: NRSF_293T_shNRSF

description: shRNA for NRSF transfected


title: Genomic DNA from pancretatic tissue_PK04-12T

description: Pamcreatic ductal adenocarcinoma

value: Male


title: TotalRNA-seq_siStau1_DAC_rep1


title: H3K27ac_HEC_wt

description: wild type


title: TotalRNA-seq_siStau1_DMSO_rep2

value: DMSO treated


title: TotalRNA-seq_siStau1_DMSO_rep1


title: Genomic DNA from pancretatic tissue_PK03-33T

description: Pamcreatic ductal adenocarcinoma


title: TotalRNA-seq_siLuc_DAC_rep2

value: Luciferase siRNA


title: Genomic DNA from pancretatic tissue_PK03-32T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK04-06T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK04-07T

description: Pamcreatic ductal adenocarcinoma


title: H3K27ac_M46

description: HS5-1 NRSE -/- monocolon


title: NRSF_M47

description: HS5-1 NRSE -/- monocolon

value: endometrium

value: adenocarcinoma

value: NRSF (Millipore, 17-641 )


title: H3K4me3_HEC_wt

description: wild type

value: H3K4me3 (Millipore, 17-614)


title: TotalRNA-seq_siLuc_DAC_rep1


title: TotalRNA-seq_siLuc_DMSO_rep2


title: Genomic DNA from pancretatic tissue_PK04-04T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK03-25T

description: Pamcreatic ductal adenocarcinoma


title: TotalRNA-seq_siLuc_DMSO_rep1


title: Genomic DNA from pancretatic tissue_PK03-28T

description: Pamcreatic ductal adenocarcinoma


title: J2CLIP-seq_siStau1_DAC

tag: molecule subtype

value: J2 antibody binding RNA


title: NRSF_HEC_wt

description: wild type


title: H3K27ac_HEC_shNRSF

description: shRNA for NRSF transfected


title: J2CLIP-seq_siLuc_DAC

tag: cell type


title: H3K27ac_HEC_shGFP

description: shGFP transfected


title: Genomic DNA from pancretatic tissue_PK03-29T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC044N

description: Non-cancerous pancreatic tissue

value: Female


title: Genomic DNA from pancretatic tissue_PK03-31T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PK03-27T

description: Pamcreatic ductal adenocarcinoma


title: J2CLIP-seq_siLuc_DMSO

tag: cell line


title: H3K4me3_HEC_shGFP

description: shGFP transfected


title: Young polyploid hepatocytes_rep2

city: Suita

first: Tomonori

last: Matsumoto

state: Osaka

address: 3-1 Yamadaoka

institute: Osaka University

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Raw gene counts for every gene

source_name: Hepatocytes

extract_protocol:
Primary hepatocytes were isolated by a two-step collagenase perfusion method, and sorted based on their reporter expressions and DNA content determined by Hoechst intensities. RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using SMART-Seq v4 Ultra Low Input RNA Kit (Takara, Cat#634894) according to the manufacturer's protocol.

tag: strain

value: Hepatocytes

tag: ploidy

value: polyploid

value: 3 months old


title: Genomic DNA from pancretatic tissue_PIP04-05T

description: Pamcreatic ductal adenocarcinoma


title: Young polyploid hepatocytes_rep3


title: NRSF_HEC_shNRSF

description: shRNA for NRSF transfected


title: Genomic DNA from pancretatic tissue_PNC033N

description: Non-cancerous pancreatic tissue


title: Kc167_M1BPKD1_ATACseq

city: bethesda

first: Elissa

last: Lei

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

data_processing:
The ATAC-seq data were processed based on the ATAC-seq Guidelines (https://informatics.fas.harvard.edu/atac-seq-guidelines.html). The raw paried-end fastq files are trimmed by 51 bp reads were trimmed using cutadapt v1.8.1 60 with arguments ‘--quality-cutoff 20’, ‘-a AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG -A AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG’, ‘--minimum-length 18’.
Then trimmed reads were mapped to the Flybase r6-24 dm6 genome assembly with Bowtie2 v2.3.5 with ‘--very-sensitive -X 2000’. chrM reads were removed using samtools v1.9.
Duplicates were removed with picard MarkDuplicates v2.20.2 (http://broadinstitute.github.io/picard/index.html). We filtered the unmapped reads, non-primary alignment and keep the proper pair reads and unique mapped reads (-f 2 -q 30) using samtools v1.9.
MACS2 v2.2.5 (https://github.com/taoliu/MACS) was used to call peaks for only properly paired alignments with ‘-f BAMPE, ‘--gsize=dm’, ‘-q 0.0001’.
Genome_build: Flybase r6-24 genome
Supplementary_files_format_and_content: Tab-delimited ATAC-seq peak files and bigwig files

organism: Drosophila melanogaster

growth_protocol: Kc167 cells-derived from Drosophila embryo, were routingly maintained in CCM3 (Thermo Scientific HyClone, Logan, UT). The cells were maintained in monolayer at 25°C.

extract_protocol: ATAC-seq was performed following protocol from Kaestner Lab (https://www.med.upenn.edu/kaestnerlab/assets/user-content/documents/ATAC-seq%20Protocol%20(Omni)%20-%20Kaestner%20Lab.pdf) with minor modification. 100,000 Kc cells were washed with 50 μl cold 1X PBS and followed and discard supernatant. Cell pellet was lysed with 50 μl cold lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin) and incubate for 10 min in ice. Then 500 μl of wash buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20) was added to lysate. Then nuclei were collected by centrifuging at 500 g for 10 min at 4°C and resuspended nuclei in transposition reaction mix [25 μl 2X TD buffer (Illumina), 16.5 μl PBS, 0.5 μl 10% Tween-20, 0.5 μl 1% Digitonin, 2.5 ul Tn5 enzyme (Illumina), 5 ul nuclease free water) and incubated for 45 min at 37°C at 1000 rpm (Eppendorf Thermomixer) for fragmentation. DNA was purified with Qiagen Minelute columns and libraries were amplified by adding 10 ul DNA to 25 ul of NEBNext HiFi 2x PCR mix (New England Biolabs) and 2.5 ul of 25 uM each of Ad1 and Ad2 primers using 11 PCR cycles. Libraries were purified with 1.2x AMPure XP beads. All samples were sequenced with NextSeq-550 (Illumina) using 50 bp paired-end sequencing.

treatment_protocol: 10 million Kc167 cells were transfected with 20 ug of dsRNA against M1BP and 12 µg of dsRNA against Cp190 by using Amexa cell line Nucleofector kit V (Lonza) and incubated 5 days at 25°C to obtain significant knockdown of M1BP and CP190.

value: Kc167 cells

tag: developmental stage

value: embryo

tag: Sex

value: female


title: Kc167_M1BPKD3_ATACseq


title: Genomic DNA from pancretatic tissue_PNC029N2

description: Non-cancerous pancreatic tissue

tag: gender

tag: age


title: NRSF_HEC_shGFP

description: shGFP transfected

tag: tissue


title: Genomic DNA from pancretatic tissue_PNC035N

description: Non-cancerous pancreatic tissue


title: Kc167_M1BPKD2_ATACseq


title: Young diploid hepatocytes_rep2

value: diploid


title: Kc167_Cp190KD3_ATACseq


title: Genomic DNA from pancretatic tissue_PNC034N

description: Non-cancerous pancreatic tissue


title: Kc167_Cp190KD2_ATACseq


title: Young diploid hepatocytes_rep1


title: Genomic DNA from pancretatic tissue_PNC029N

description: Non-cancerous pancreatic tissue


title: Aged polyploid hepatocytes_rep3

value: 27 months old


title: Kc167_Cp190KD1_ATACseq


title: Genomic DNA from pancretatic tissue_PNC031N

description: Non-cancerous pancreatic tissue


title: U2OS cells - DMSO - siMLL3.2

city: Wuhan

first: Jun-Yi

last: Zheng

address: No. 299 Of Bayi Road

institute: Wuhan Univisity

description: samples3,7_gene_FPKM_matrix.txt;samples3-8_gene_FPKM_matrix.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2-align-s version 2.2.0 with parameters -p 16
The gene expression level was calculated by Cufflinks (v 2.2.1).
Fragments Per Kilobase of exon model per Million mapped fragments(FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of Fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: U2OS cells

growth_protocol: U2OS cells were cultured in RPMI 1640 media supplemented with 10% FBS at 37℃ with 5% CO2

extract_protocol:
Cells were harvested and total RNA was extracted with EASYspin RNA Mini Kit (Aidlab RN07) according to the manufacturer’s manual.
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).

treatment_protocol: Cells were transfected with control or two different MLL3 siRNAs for 48 h. For samples 5-10, transfection was followed with treatment with DMSO or 20 nM Nutlin3a for 12 h.

value: transfected with siMLL3.2, treated with DMSO for 12 h


title: U2OS cells - Nutlin3A - siMLL3.2

value: transfected with siMLL3.2, treated with 20 nM Nutlin3a for 12 h


title: Genomic DNA from pancretatic tissue_PNC025N

description: Non-cancerous pancreatic tissue

value: Male


title: Young polyploid hepatocytes_rep1


title: Genomic DNA from pancretatic tissue_PIP04-12T

description: Pamcreatic ductal adenocarcinoma


title: U2OS cells - Nutlin3A - siMLL3.1

value: transfected with siMLL3.1, treated with 20 nM Nutlin3a for 12 h


title: NRSF_M46

description: HS5-1 NRSE -/- monocolon

value: endometrium

value: adenocarcinoma


title: NRSF_293T_shGFP

description: shGFP transfected

value: kidney

value: fetus

value: NRSF (Millipore, 17-641 )


title: Aged polyploid hepatocytes_rep2

value: Hepatocytes


title: Kc167_mock3_ATACseq

value: mock


title: Young diploid hepatocytes_rep3

value: 3 months old


title: U2OS cells - DMSO - siMLL3.1

value: transfected with siMLL3.1, treated with DMSO for 12 h


title: Kc167_mock2_ATACseq

value: Kc167 cells

value: embryo


title: Aged polyploid hepatocytes_rep1

value: polyploid


title: U2OS cells - Nutlin3A - siNC

value: transfected with siNC, treated with 20 nM Nutlin3a for 12 h


title: Genomic DNA from pancretatic tissue_PK03-21T

description: Pamcreatic ductal adenocarcinoma


title: Genomic DNA from pancretatic tissue_PNC032N

description: Non-cancerous pancreatic tissue

value: Female


title: Genomic DNA from pancretatic tissue_PNC027N

description: Non-cancerous pancreatic tissue


title: Kc167_mock1_ATACseq

value: female


title: U2OS cells - siMLL3.1

value: transfected with siMLL3.1


title: Genomic DNA from pancretatic tissue_PNC024N

description: Non-cancerous pancreatic tissue

value: Male


title: R5_jy121C: pnp-1(jy121) replicate 5

city: San Diego

first: Emily

last: Troemel

state: CA

address: 4202 Bonner Hall, 9500 Gilman #0349

department: Cell and Developmental Biology

institute: University of California, San Diego

data_processing:
Reads were aligned to WS235 using Rsubreads in R studio
Reads were counted using Featurecounts in Rstudio
Transcript abundance was quantified with limma-voom in Galaxy
Genome_build: Wormbase Release WS235
Supplementary_files_format_and_content: txt files of CPM for all genes excluding undetected and lowly expressed genes (CPM of less than one)

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: N2, pnp-1(jy90) and pnp-1(jy121) animals were grown for 56 hours post L1 at 20°C.

extract_protocol:
Total RNA was extracted using TriReagent (Sigma-Aldrich) and cleaned using RNAeasy (Qiagen) column purification. RNA quality was assesed using Tapestation analysis.
Paired-end sequencing libraries were constructed using TruSeq stranded mRNA TruSeq Stranded mRNA (Illumina) prep kit.

tag: genotype

value: whole animals

value: 56 hours post L1


title: Aged diploid hepatocytes_rep2

value: diploid

value: 27 months old


title: Aged diploid hepatocytes_rep1


title: Aged diploid hepatocytes_rep3


title: R4_jy121: pnp-1(jy121) replicate 4


title: U2OS cells - DMSO - siNC

description:
Samples 3-8 were used for idenfication of DEGs after p53 activation and MLL3 knockdown.
samples3,7_gene_FPKM_matrix.txt;samples3-8_gene_FPKM_matrix.txt

tag: treatment

value: transfected with siNC, treated with DMSO for 12 h


title: Genomic DNA from pancretatic tissue_PNC022N

description: Non-cancerous pancreatic tissue


title: U2OS cells - siNC-1

description:
Samples 1,2,3,7 were used for idenfication of DEGs after MLL3 knockdown.
samples1-2_gene_FPKM_matrix.txt

value: transfected with siNC


title: R2_jy121: pnp-1(jy121) replicate 2


title: MM2 - MEF Nf2 KO, rep2

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

data_processing:
Fastq files were process by trimming adapter, aligned with HISAT1, duplicates marked, quantified and FPKM-normalized.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM-normalized values were included as processed data in txt format.

source_name: mouse embryonic fibroblast

growth_protocol: MEF WT and  MEF Nf2 KO cells were maintained in culture in DMEM 1x supplemented with 10% FBS, 1% sodium pyruvate, and 1% nonessential amino acids

extract_protocol:
Total RNA was harvested using the RNeasy Mini kit (Qiagen) and sent to GENEWIZ for sample analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Both MEF WT and  MEF Nf2 KO cells were cultured in serum-free media for 24h prior to total RNA extraction

value: FVB

value: Mouse embryonic fibroblast

value: Nf2 KO

tag: age of embryos

value: approximately 14 days


title: U2OS cells - H3K4me1 - siMLL3.2

data_processing:
All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
ChIP-seq reads were aligned to the hg19 genome assembly using  with bowtie2-align-s version 2.3.5.1
Data were filtered using cutadapt version 1.18 with parameters -u 10 -u -15 -U 10 -U -15 -m 30
peaks were called using macs2 2.1.1.20160309 with the following setting -p 1E-10 --nomodel --keep-dup all --SPMR --extsize 147 --broad --broad-cutoff 1E-10
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using deeptools 3.1.3; Scores represent RPKM

extract_protocol:
Lysates were clarified from MNase digested nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606).

treatment_protocol: Cells were transfected with control or two different MLL3 siRNAs for 48 h

value: transfected with siMLL3.2

tag: chip-antibody


title: R3_jy121: pnp-1(jy121) replicate 3


title: MM2 - MEF Nf2 KO, rep3


title: U2OS cells - H3K4me1 - siMLL3.1


title: R1_jy121: pnp-1(jy121) replicate 1


title: U2OS cells - H3K4me1 - siNC


title: MM2 - MEF Nf2 KO, rep1


title: R5_jy90: pnp-1(jy90) replicate 5


title: MM1 - MEF WT (control), rep3

value: WT (control)


title: Genomic DNA from pancretatic tissue_PNC016N

description: Non-cancerous pancreatic tissue


title: U2OS cells - H3K27ac - siMLL3.2

value: H3K27ac (abcam, ab4729)


title: R4_jy90C: pnp-1(jy90) replicate 4


title: Genomic DNA from pancretatic tissue_PNC026N

description: Non-cancerous pancreatic tissue


title: MM1 - MEF WT (control), rep2


title: U2OS cells - H3K27ac - siMLL3.1


title: Genomic DNA from pancretatic tissue_PNC014N

description: Non-cancerous pancreatic tissue

value: Female


title: Genomic DNA from pancretatic tissue_PNC013N

description: Non-cancerous pancreatic tissue


title: R5_N2: N2 replicate 5

value: wild-type


title: Genomic DNA from pancretatic tissue_PNC009N

description: Non-cancerous pancreatic tissue


title: Sample 116_Plate 2_Human brain total RNA_Rep 2

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
Plate #2 control
HDACi_Human_Brain_48_S48

data_processing:
library strategy: TempO-Seq
Initial quality assessment was performed using negative controls (water only) and reference standards (human universal reference RNA and human brain total RNA) included on every TempO-Seq plate. We confirmed very little signal (< 0.3%) from samples with no cells/RNA. The BCL files were converted to FASTQ files and the reads were demultiplexed using bcl2fastq v. 2.20.0.42. The FASTQ files were processed using the “pete. star. Script_v3.0” (BioSpyder). The script uses star v.2.5 and the qCount function from QuasR to align the reads and to extract the feature counts specified in a Gene Transfer Format (GTF) file from the aligned reads, respectively.
Using R 3.4.1, the read counts of all samples were normalized as counts per million (CPM) (Law et al. 2014).
Supplementary_files_format_and_content: Text file with counts per million (CPM) for each gene

organism: blank sample

source_name: Plate 2_Human brain total RNA

growth_protocol: TK6 cells were cultured in suspension in a T75 flask in RPMI1640 medium supplemented with 10% v/v heat-inactivated horse serum, 2 mM L-glutamine, and 1 mM sodium pyruvate at 37ºC in 5% CO2. The cell density was maintained between 1x10^5 cells/mL and 1x10^6 cells/mL.

extract_protocol:
Total RNA was extracted using a Qiagen RNeasy Mini kit. Quality was assessed using High Sensitiy RNA ScreenTapes on an Agilent TapeStation. RNA integrity number (RIN) of all samples was above 7.5.
The Templated Oligo-Sequencing (TempO-Seq) Human Whole Transcriptome Assay kit (BioSpyder, Carlsbad, CA) was used to generate sequencing libraries using total RNA from TK6 cells following the manufacturer's protocol. An input of 100ng was used from each RNA sample.

treatment_protocol: Prior to exposure, cells were plated in 6-well plates with 5 mL of 3x10^5 cells/mL suspension in each well. Cells were exposed to each chemical prepared in their respective vehicle solvent (1% v/v). After 4 hours, cells were rinsed once with PBS and lysed in TempO-Seq lysis buffer. RNA was extracted using a Qiagen RNeasy Mini kit. The exposure was performed on three separate occasions to produce three replicates of each sample.

tag: sample type

value: Human brain total RNA


title: Genomic DNA from pancretatic tissue_PNC015N

description: Non-cancerous pancreatic tissue

data_processing: GenomeStudio methylation software

value: Male


title: NRSF_S_ChIP-nexus_rep2

city: Shanghai

first: Yuanxiao

last: Tang

address: Dongchuan Road 800

institute: Shanghai Jiao Tong University

data_processing:
Reads were sorted  using barcode and index
Reads were aligned to the hg19 genome or mm9 genome using Bowtie2
Peaks were called using MACS2
Genome_build: hg19, mm9
Supplementary_files_format_and_content: bedgraph were generated using Python

source_name: SK-N-SH cells

growth_protocol: HEC-1-B and SK-N-SH cells were cultured in MEM (Hyclone), supplemented with 10% (v/v) FBS, 2 mM GlutaMAX (Gibco), 1 mM sodium pyruvate (Sigma), and 1% penicillin-streptomycin. Cells were maintained at 37 °C in a 5% (v/v) CO2 incubator.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-nexus libraries were performed as described (He et al., 2015), with some modifications. Briefly, The chromatin-enriched magnetic beads were then washed with buffers, repaired with the end-repair enzyme mixture (NEB) and dA-tailed with Klenow exo- (NEB) in NEB buffer 2 containing 0.2 mM dATP. After ligating the Nexus adaptors to DNA with 2x Blunt/TA Ligase Master Mix (NEB, M0367S) for 1h at 25 ℃, dealt the mixtures with Klenow exo- and followed by ligation with T4 DNA polymerase (NEB). The blunt-ended DNAs were then treated with Lambda Exonuclease in its buffer (NEB). Subsequently, samples were then digested by RecJf exonuclease (NEB) and washed three times with the RIPA buffer. DNA was then eluted, reverse-crosslinked, purified with phenol: chloroform to get ssDNA.  The ssDNA was circularized with CircLigase (Epicentre), annealed with the Cut_oligo in FastDigest buffer (Thermo), and then digested with FastDigest BamHI (Thermo),  precipitated using ethanol and sodium acetate, resuspended with 20 μl of water.DNAs were amplified by Q5 polymerase (NEB) with Illumina universal primer and index primers.  The PCR products with the sizes of 150 bp to 300bp were extracted from 2% agarose gel using MinElute Gel Extraction Kit (Qiagen).ChIP-Seq libraries were prepared according to the manual of VAHTSTM Universal DNA Library Prep Kit for Illumina® V2 (ND606). Briefly, DNA was end-repaired using End Prep Mix 3, ligated with index-contained adapters using Rapid DNA ligase in Rapid Ligation buffer, amplificated using PCR Primers and Amplification Mix for libraries. The library fragments of ~350 bp (insert plus adaptor and PCR primer sequences) were isolated  with Agencourt® AMPure® XP (Beckman Coulter®). Library DNAs were sequenced on an Illumina HiSeq platform

treatment_protocol: Mouse tissues were dispersed by 0.00625% (w/v) (for brain) or 0.0125% (w/v) (for kidney) collagenase (Sigma) treatment in DMEM supplemented with 10% (v/v) FBS for 45 min at 37 °C with rotating at 700 rpm, or directly resuspended in DMEM supplemented with 10% (v/v) FBS by pipetting (for liver). Cells were then filtered through a 40 μm cell strainer (BD) to obtain single-cell suspension.

value: brain

tag: disease/strain

value: neuroblastoma

tag: chip antibody

value: Streptavidin (Invitrogen, 65001)

value: NRSF-biotag-overexpression


title: MM1 - MEF WT (control), rep1


title: R4_N2: N2 replicate 4

value: whole animals

value: 56 hours post L1


title: U2OS cells - input DNA - siMLL3

description: Input for sample 4, 5, 7, 8

value: transfected with siMLL3.1 or siMLL3.2


title: U2OS cells - H3K27ac - siNC

value: transfected with siNC


title: Sample 120_Plate 2_Negative control (H2O)_Rep 2

description:
Plate #2 control
HDACi_NC_35_S35

source_name: Plate 2_Negative control (H2O)

value: Water; negative control


title: R2_jy90: pnp-1(jy90) replicate 2


title: Sample 115_Plate 2_Human brain total RNA_Rep 1

description:
Plate #2 control
HDACi_Human_Brain_43_S43


title: U2OS cells - input DNA - siNC

description: Input for sample 3, 6


title: Sample 119_Plate 2_Negative control (H2O)_Rep 1

description:
Plate #2 control
HDACi_NC_27_S27


title: R1_jy90: pnp-1(jy90) replicate 1


title: Genomic DNA from pancretatic tissue_PNC012N

description: Non-cancerous pancreatic tissue

extract_protocol: High-molecular-weight DNA was extracted from fresh frozen tissue samples using phenol–chloroform, followed by dialysis.


title: Genomic DNA from pancretatic tissue_PNC018N

description: Non-cancerous pancreatic tissue


title: NRSF_S_ChIP-nexus_rep1


title: R3_N2C: N2 replicate 3


title: Sample 28_Plate 1_Negative control (H2O)_Rep 2

description:
Plate #1 control
HDACi_ctrl_neg_317_S29

source_name: Plate 1_Negative control (H2O)


title: Genomic DNA from pancretatic tissue_PNC005N

description: Non-cancerous pancreatic tissue


title: R2_N2: N2 replicate 2


title: Genomic DNA from pancretatic tissue_PK05-30N

description: Non-cancerous pancreatic tissue


title: Genomic DNA from pancretatic tissue_PK05-11N

description: Non-cancerous pancreatic tissue


title: input

status: Public on Apr 13 2021

city: San Francisco

first: Karishma

middle: Joanne Bhatia

last: Pratt

address: 513 Parnassus Ave, Med. Sci. Bldg S1364

department: Anatomy

institute: UCSF

description:
Hydroxymethylated DNA immunoprecipitation
MACS2_wtoverkopeaks.txt

data_processing:
Trimmomatic -trim reads
Bowtie2-mapping
MACS2 - peak calling/data normalization
Supplementary_files_format_and_content: peaks over wt .txt

source_name: hippocampal neuronal nuclei (in vivo)

extract_protocol:
fragment DNA, IP with 5hmC Ab, Protein A dynabead capture
NEB Ultra II  for paired end illumina sequencing

value: all samples, no Ab


title: Sample 23 - KO

value: CamKIIaCreERt2;Tet2 cKO


title: Genomic DNA from pancretatic tissue_PK05-16N

description: Non-cancerous pancreatic tissue


title: R1_N2: N2 replicate 1


title: Sample 20 - KO


title: Genomic DNA from pancretatic tissue_PNC003N

description: Non-cancerous pancreatic tissue


title: NRSF_H_ChIP-nexus_rep2

value: endometrium

tag: disease/disease state

value: adenocarcinoma

value: NRSF (Millipore, 17-641)

value: wild type


title: NRSF_H_ChIP-nexus_rep1


title: Sample 27_Plate 1_Negative control (H2O)_Rep 1

description:
Plate #1 control
HDACi_ctrl_neg_316_S28


title: Sample 16 - KO


title: Genomic DNA from pancretatic tissue_PK05-03N

description: Non-cancerous pancreatic tissue

value: Female


title: Sample 19 - WT

value: WT (Tet2 fl/fl)


title: Genomic DNA from pancretatic tissue_PK04-41N

description: Non-cancerous pancreatic tissue

value: Male


title: Sample 11 - WT


title: Sample 4 - WT


title: R3_jy90: pnp-1(jy90) replicate 3


title: PAs group rep1

first: ronggui

last: hu

state: China

address: Shanghai Institute of Biochemistry and Cell Biology

institute: Center for Excellence in Molecular Cell Science

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10  genome using HISAT2 v2.1.0 with default parameters.
Reads count were calculated using htseq-count software with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Count text files

extract_protocol:
Mice liver was removed and stored. Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Gynura segetum extract was concentrated to 2 g/mL for intragastrical administration to induce liver injury mice model. Mice were given normal saline or Gynura segetum (30 g/kg/d) for 3 weeks.

value: 6-8 weeks

value: Gynura segetum extract

value: liver


title: Control rep2

value: saline


title: PAs group rep2


title: Control rep1


title: Mouse_116_homo_dim (H5_Guang_GL9989-3)

city: Pittsburgh

first: guang

last: li

state: PA

address: 530 45th St. 8116 Rangos Research Center

institute: university of pittsburgh

description: H5_Guang_GL9989-3-ACTGAGCG-CTTAATAG_S232

data_processing:
The data were demultiplexed based on barcode sequences using Illumina sorfware  bcl2fastq
The fastq files were aligned to the reference sequences consisting of mouse genome, eGFP, and human Bag3 transcript sequences using STAR2.7.0f with the default parameters, and gene expression counts were calculated using STAR “–quantMode GeneCounts” parameter.
Supplementary_files_format_and_content: Gene_expression_counts_matrix.csv

source_name: mouse cardiomyocyte

growth_protocol: The transgenic PGKcre:BAG3P209L mice were generated through overxpression of a mutated BAG3.

extract_protocol:
Cardiomyocytes (CMs) were isolated from hearts using Langendorff system and picked up using hand pippete.
The mRNA in single CMs were isolatedy following the SMART-seq2 protocol.
The single cell libraries were made by following the SMART-seq 2 protocol. The cells with low amount of cDNA were excluded for library preparations. Different barcodes were used to label each single cell for multiplexing purpose when generating the libraries and demultiplexing during analysis.

tag: cell type

value: cardiomyocyte (CM)


title: Mouse_116_homo_dim (H7_Guang_GL9989-3)

description: H7_Guang_GL9989-3-CCTAAGAC-CTTAATAG_S234


title: Genomic DNA from pancretatic tissue_PK04-37N

description: Non-cancerous pancreatic tissue


title: Mouse_116_homo_dim (H6_Guang_GL9989-3)

description: H6_Guang_GL9989-3-AAGAGGCA-CTTAATAG_S233


title: Mouse_116_homo_bright (H1_Guang_GL9989-3)

description: H1_Guang_GL9989-3-ATGCGCAG-CTTAATAG_S228


title: Mouse_116_homo_bright (H3_Guang_GL9989-3)

description: H3_Guang_GL9989-3-TAGCGCTC-CTTAATAG_S230


title: Mouse_116_homo_dim (G5_Guang_GL9989-3)

description: G5_Guang_GL9989-3-GGACTCCT-CTTAATAG_S225


title: Mouse_116_homo_bright (H2_Guang_GL9989-3)

description: H2_Guang_GL9989-3-CTCTCTAC-CTTAATAG_S229


title: Mouse_116_homo_dim (G8_Guang_GL9989-3)

description: G8_Guang_GL9989-3-TAGGCATG-CTTAATAG_S227


title: Mouse_116_homo_dim (G6_Guang_GL9989-3)

description: G6_Guang_GL9989-3-TACGCTGC-CTTAATAG_S226


title: Mouse_116_homo_bright (G4_Guang_GL9989-3)

description: G4_Guang_GL9989-3-CGGAGCCT-CTTAATAG_S224


title: Mouse_116_homo_bright (G3_Guang_GL9989-3)

description: G3_Guang_GL9989-3-TCCTGAGC-CTTAATAG_S223


title: Mouse_116_homo_dim (F8_Guang_GL9989-3)

description: F8_Guang_GL9989-3-GGAGCTAC-CTTAATAG_S220


title: Mouse_116_homo_bright (H4_Guang_GL9989-3)

description: H4_Guang_GL9989-3-CGAGGCTG-CTTAATAG_S231


title: Mouse_116_homo_bright (G2_Guang_GL9989-3)

description: G2_Guang_GL9989-3-GCGTAGTA-CTTAATAG_S222


title: Genomic DNA from pancretatic tissue_PK04-46N

description: Non-cancerous pancreatic tissue


title: Sample 21 - KO


title: Mouse_116_homo_bright (F3_Guang_GL9989-3)

description: F3_Guang_GL9989-3-ACTCGCTA-CTTAATAG_S218


title: Mouse_116_homo_bright (G1_Guang_GL9989-3)

description: G1_Guang_GL9989-3-AGGCAGAA-CTTAATAG_S221


title: Genomic DNA from pancretatic tissue_PK04-32N

description: Non-cancerous pancreatic tissue


title: Genomic DNA from pancretatic tissue_PK04-27N

description: Non-cancerous pancreatic tissue


title: Mouse_116_homo_bright (F1_Guang_GL9989-3)

description: F1_Guang_GL9989-3-TCGACGTC-TACTCCTT_S216


title: Mouse_116_homo_bright (E1_Guang_GL9989-3)

description: E1_Guang_GL9989-3-CCTAAGAC-TACTCCTT_S210


title: Mouse_116_homo_bright (E2_Guang_GL9989-3)

description: E2_Guang_GL9989-3-GTAGAGGA-TACTCCTT_S211


title: Mouse_116_homo_dim (E8_Guang_GL9989-3)

description: E8_Guang_GL9989-3-ATCTCAGG-TACTCCTT_S215


title: Mouse_116_homo_bright (E3_Guang_GL9989-3)

description: E3_Guang_GL9989-3-CGATCAGT-TACTCCTT_S212


title: Mouse_116_homo_bright (F2_Guang_GL9989-3)

description: F2_Guang_GL9989-3-TAAGGCGA-CTTAATAG_S217


title: Mouse_116_homo_bright (F4_Guang_GL9989-3)

description: F4_Guang_GL9989-3-CGTACTAG-CTTAATAG_S219


title: Mouse_116_homo_dim (D5_Guang_GL9989-3)

description: D5_Guang_GL9989-3-ACTGAGCG-TACTCCTT_S208


title: Mouse_116_homo_bright (D4_Guang_GL9989-3)

description: D4_Guang_GL9989-3-CGAGGCTG-TACTCCTT_S207


title: Mouse_116_homo_dim (D6_Guang_GL9989-3)

description: D6_Guang_GL9989-3-AAGAGGCA-TACTCCTT_S209


title: Genomic DNA from pancretatic tissue_PK04-17N

description: Non-cancerous pancreatic tissue


title: Genomic DNA from pancretatic tissue_PK04-15N

description: Non-cancerous pancreatic tissue


title: Mouse_116_homo_bright (D2_Guang_GL9989-3)

description: D2_Guang_GL9989-3-CTCTCTAC-TACTCCTT_S205


title: Mouse_116_homo_dim (C8_Guang_GL9989-3)

description: C8_Guang_GL9989-3-TAGGCATG-TACTCCTT_S203


title: Mouse_116_homo_dim (E7_Guang_GL9989-3)

description: E7_Guang_GL9989-3-TGCAGCTA-TACTCCTT_S214


title: Mouse_116_homo_bright (D1_Guang_GL9989-3)

description: D1_Guang_GL9989-3-ATGCGCAG-TACTCCTT_S204


title: Mouse_116_homo_bright (D3_Guang_GL9989-3)

description: D3_Guang_GL9989-3-TAGCGCTC-TACTCCTT_S206


title: Mouse_116_homo_dim (C6_Guang_GL9989-3)

description: C6_Guang_GL9989-3-GGACTCCT-TACTCCTT_S201


title: Mouse_116_homo_dim (C5_Guang_GL9989-3)

description: C5_Guang_GL9989-3-CGGAGCCT-TACTCCTT_S200


title: Mouse_116_homo_dim (E6_Guang_GL9989-3)

description: E6_Guang_GL9989-3-GCTCATGA-TACTCCTT_S213


title: Mouse_116_homo_dim (C7_Guang_GL9989-3)

description: C7_Guang_GL9989-3-TACGCTGC-TACTCCTT_S202


title: Mouse_116_homo_bright (C3_Guang_GL9989-3)

description: C3_Guang_GL9989-3-GCGTAGTA-TACTCCTT_S198


title: Mouse_116_homo_bright (C1_Guang_GL9989-3)

description: C1_Guang_GL9989-3-AGGCAGAA-TACTCCTT_S197


title: Mouse_116_homo_bright (C4_Guang_GL9989-3)

description: C4_Guang_GL9989-3-TCCTGAGC-TACTCCTT_S199


title: Mouse_116_homo_dim (B8_Guang_GL9989-3)

description: B8_Guang_GL9989-3-GGAGCTAC-TACTCCTT_S196


title: Mouse_116_homo_dim (B5_Guang_GL9989-3)

description: B5_Guang_GL9989-3-ACTCGCTA-TACTCCTT_S194


title: Mouse_116_homo_bright (B4_Guang_GL9989-3)

description: B4_Guang_GL9989-3-TAAGGCGA-TACTCCTT_S193


title: Mouse_116_homo_bright (B3_Guang_GL9989-3)

description: B3_Guang_GL9989-3-TCGACGTC-TCTTACGC_S192


title: Mouse_116_homo_bright (B1_Guang_GL9989-3)

description: B1_Guang_GL9989-3-TGCAGCTA-TCTTACGC_S190


title: Mouse_116_homo_bright (B2_Guang_GL9989-3)

description: B2_Guang_GL9989-3-ATCTCAGG-TCTTACGC_S191


title: Mouse_116_homo_dim (A6_Guang_GL9989-3)

description: A6_Guang_GL9989-3-GCTCATGA-TCTTACGC_S189


title: Mouse_116_homo_bright (A4_Guang_GL9989-3)

description: A4_Guang_GL9989-3-GTAGAGGA-TCTTACGC_S187


title: Mouse_116_homo_dim (A5_Guang_GL9989-3)

description: A5_Guang_GL9989-3-CGATCAGT-TCTTACGC_S188


title: Mouse_116_homo_bright (A2_Guang_GL9989-3)

description: A2_Guang_GL9989-3-AAGAGGCA-TCTTACGC_S185


title: Mouse_116_homo_dim (H7_Guang_GL9989-2)

description: H7_Guang_GL9989-2-TAGCGCTC-TCTTACGC_S182


title: Mouse_116_homo_bright (A1_Guang_GL9989-3)

description: A1_Guang_GL9989-3-ACTGAGCG-TCTTACGC_S184


title: Mouse_116_homo_bright (A3_Guang_GL9989-3)

description: A3_Guang_GL9989-3-CCTAAGAC-TCTTACGC_S186


title: Mouse_116_homo_dim (H5_Guang_GL9989-2)

description: H5_Guang_GL9989-2-ATGCGCAG-TCTTACGC_S180


title: Mouse_116_homo_bright (H4_Guang_GL9989-2)

description: H4_Guang_GL9989-2-TAGGCATG-TCTTACGC_S179


title: Mouse_116_homo_bright (H2_Guang_GL9989-2)

description: H2_Guang_GL9989-2-TACGCTGC-TCTTACGC_S178


title: Mouse_116_homo_dim (G6_Guang_GL9989-2)

description: G6_Guang_GL9989-2-GCGTAGTA-TCTTACGC_S174


title: Mouse_116_homo_bright (H1_Guang_GL9989-2)

description: H1_Guang_GL9989-2-GGACTCCT-TCTTACGC_S177


title: Mouse_116_homo_dim (G5_Guang_GL9989-2)

description: G5_Guang_GL9989-2-AGGCAGAA-TCTTACGC_S173


title: Mouse_116_homo_dim (G7_Guang_GL9989-2)

description: G7_Guang_GL9989-2-TCCTGAGC-TCTTACGC_S175


title: Mouse_116_homo_dim (H8_Guang_GL9989-2)

description: H8_Guang_GL9989-2-CGAGGCTG-TCTTACGC_S183


title: Mouse_116_homo_bright (G4_Guang_GL9989-2)

description: G4_Guang_GL9989-2-GGAGCTAC-TCTTACGC_S172


title: Mouse_116_homo_dim (G8_Guang_GL9989-2)

description: G8_Guang_GL9989-2-CGGAGCCT-TCTTACGC_S176


title: Mouse_116_homo_dim (F8_Guang_GL9989-2)

description: F8_Guang_GL9989-2-ACTCGCTA-TCTTACGC_S170


title: Mouse_116_homo_dim (F7_Guang_GL9989-2)

description: F7_Guang_GL9989-2-TAAGGCGA-TCTTACGC_S169


title: Mouse_116_homo_dim (F5_Guang_GL9989-2)

description: F5_Guang_GL9989-2-ATCTCAGG-TATGCAGT_S167


title: Mouse_116_homo_dim (B6_Guang_GL9989-3)

description: B6_Guang_GL9989-3-CGTACTAG-TACTCCTT_S195


title: Mouse_116_homo_bright (F4_Guang_GL9989-2)

description: F4_Guang_GL9989-2-TGCAGCTA-TATGCAGT_S166


title: Mouse_116_homo_dim (H6_Guang_GL9989-2)

description: H6_Guang_GL9989-2-CTCTCTAC-TCTTACGC_S181


title: Mouse_116_homo_bright (F3_Guang_GL9989-2)

description: F3_Guang_GL9989-2-GCTCATGA-TATGCAGT_S165


title: Mouse_116_homo_bright (F1_Guang_GL9989-2)

description: F1_Guang_GL9989-2-GTAGAGGA-TATGCAGT_S163


title: Mouse_116_homo_bright (F2_Guang_GL9989-2)

description: F2_Guang_GL9989-2-CGATCAGT-TATGCAGT_S164


title: Mouse_116_homo_dim (E8_Guang_GL9989-2)

description: E8_Guang_GL9989-2-CCTAAGAC-TATGCAGT_S162


title: Mouse_116_homo_dim (E7_Guang_GL9989-2)

description: E7_Guang_GL9989-2-AAGAGGCA-TATGCAGT_S161