title: 259O


title: PANC1_6hr_100nM_rep1

status: Public on Jan 23 2018

type: SRA

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute

library_source: transcriptomic

data_processing:
Fastq raw sequencing files were preprocessed using cutadapt to remove sequencing adapters and low quality sequencing tails (options –q 10).
Trimmed files were aligned to the human genome (GRCh37/hg19) using tophat2 and using the UCSC gtf file provided by Illumina iGenomes as an annotation file (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
Gene counts were calculated using htseq-count and the same gtf file. Differential expression analysis was done using the R package edgeR.
Differentially expressed genes were estimated independently for both cell lines (MIA PaCa-2 and PANC-1) and for the different time points (6 and 24 h), and were then intersected to inspect the common genes.
Genome_build: hg19

molecule: polyA RNA

organism: Homo sapiens

source_name: ATCC Cell Lines

growth_protocol: PANC-1 (ATCC, cat #CRL-1469) and MIA PaCa-2 (ATCC, cat # CRL-142-) were maintained in DMEM (ThermoFisher, cat #11965092) supplemented with 10% (v/v) heat inactivated FBS (ThermoFisher) in a humidified atmosphere containing 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy® Plus Mini Kit (ThermoFisher, cat #74134) as per the manufacturer’s instructions.
RNA-seq libraries were  generated using the Illumina Truseq RNA HT (stranded mRNA) kit (Illumina, cat #RS-122-2103) as per the manufacturer’s instructions and sequenced using an Illumina NextSeq 500.

treatment_protocol: PANC-1 and MIA PaCa-2  cell lines were treated with 400 nM CM03 for 6 and 24 h. For gemcitabine treatment, cells were treated for 6 and 24 h with DMSO or 30 nM, 100 nM, 300 nM, 1 μM, 3 μM and 10 μM gemcitabine-HCL for PANC-1 and 30 nM, 300 nM and 3 μM gemcitabine-HCl for MIA PaCa-2

tag: cell type

tag: treatment

value: gemcitabine 100nM 6h


title: PANC1_6hr_10uM_rep2

value: gemcitabine 10uM 6h


title: PANC1_6hr_10uM_rep1


title: 250O

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

data_processing:
Transcript abundances were calculated with kallisto v0.43.0.
Genome_build: S. mediterranea dd_Smed_v6 transcriptome assembly
Supplementary_files_format_and_content: Tab-separated values file containing TPM expression values.

organism: Schmidtea mediterranea

source_name: whole animal

extract_protocol:
RNA was extracted with TRIzol® (Invitrogen) following the manufacturer's instructions. Quantification of RNA was assessed with a Nanodrop ND-1000 spectrophotometer (Thermo Scientific) and quality check was performed by capillary electrophoresis in an Agilent 2100 Bioanalyzer (Agilent Technologies)prior to library preparation.
cDNA libraries were prepared using the Illumina® TruSeq Stranded mRNA Library Prep Kit and sequenced as paired-end reads in an Illlumina® HiSeq 2000 sequencer. Quality check of the reads was performed with the FastQC suite.

tag: strain

value: asexual BCN-10 clonal line

tag: tissue

value: whole animal

value: gfp(RNAi) 1 week


title: PANC1_24hr_30nM_rep3

value: gemcitabine 30nM 24h


title: PANC1_24hr_3uM_rep2

value: gemcitabine 3uM 24h


title: PANC1_24hr_3uM_rep3


title: PANC1_24hr_30nM_rep1


title: PANC1_24hr_30nM_rep4


title: PANC1_24hr_30nM_rep2


title: 249O


title: PANC1_24hr_3uM_rep1


title: PANC1_24hr_1uM_rep2

value: gemcitabine 1uM 24h


title: Pt35_On_AD485758-6

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

department: LRI

country: USA

institute: Cleveland Clinic

data_processing:
Raw reads in the fastq format were aligned to Human Genome HG19 using the RNAseq STAR aligner version 2.4.0d.
Mapped reads for each sample were counted for each gene in annotation files TxDb.Hsapiens.UCSC.hg19.knownGene using the  GenomicFeatures read summarization program
Raw reads were normalized with regularized-logarithm transformation (rlog function with robust estimation)
Normalized FPKM (fragments per kilobase per million mapped reads) were obtained using the robust fpkm estimate function of DeSeq2 v1.12.4.
To refine subsets of immune cells that were present in each sample, cibersort was used to conduct immune de-convolution on the FPKM values of each patient
Genome_build: HG19
Gene IDs in the processed data files are NCBI Entrez Gene IDs.
Supplementary_files_format_and_content: Row and normalized feature count matrices
Supplementary_files_format_and_content: BMS038_118Sample.hg19KnownGene.raw.csv.gz: Raw feature counts matrix
Supplementary_files_format_and_content: BMS038_118Sample.hg19KnownGene.rld.csv.gz: Rlog-transformed values feature counts matrix
Supplementary_files_format_and_content: BMS038_118Sample.hg19KnownGene.fpkm.csv.gz: Normalized FPKM feature counts matrix

molecule: total RNA

source_name: tumor

extract_protocol:
RNA Later
RNASeq

tag: visit (pre or on treatment)

value: On

tag: response

value: PRCR

value: melanoma


title: PANC1_24hr_1uM_rep4


title: PANC1_24hr_300nM_rep3

value: gemcitabine 300nM 24h


title: PANC1_24hr_10uM_rep4

value: gemcitabine 10uM 24h


title: PANC1_24hr_300nM_rep2


title: Pt34_On_AD485757-6


title: Pt106_On_AD513626-6

value: PD


title: PANC1_24hr_1uM_rep1


title: PANC1_24hr_3uM_rep4


title: Pt34_Pre_AD466985-6

value: Pre


title: Pt44_On_AD167376-6


title: Pt44_Pre_AD467790-6


title: PANC1_24hr_10uM_rep2


title: PANC1_24hr_10uM_rep3


title: Pt106_Pre_AD502250-5


title: PANC1_24hr_300nM_rep4


title: PANC1_6hr_3uM_rep4

value: gemcitabine 3uM 6h


title: PANC1_24hr_10uM_rep1


title: Pt28_Pre_AD297619-6


title: Pt28_On_AD167375-7


title: PANC1_24hr_100nM_rep3

value: gemcitabine 100nM 24h


title: Pt26_Pre_AD467789-6

value: SD


title: PANC1_24hr_100nM_rep4


title: PANC1_24hr_300nM_rep1


title: Pt16_On_AD167378-6

value: UNK


title: Pt26_On_AD467915-5


title: Pt13_On_AD314067-6


title: PANC1_24hr_1uM_rep3


title: PANC1_24hr_100nM_rep2


title: Pt11_On_AD314068-6


title: Pt11_Pre_AD153352-6


title: Pt8_On_AD167380-7


title: Pt8_Pre_AD153354-6


title: Pt31_Pre_AD453872-5


title: PANC1_24hr_100nM_rep1


title: MIAPACA2_control_rep4

value: MIA PACA-2

value: untreated


title: Pt31_On_AD467932-6


title: Pt30_Pre_AD497503-5


title: MIAPACA2_control_rep2


title: Pt29_Pre_AD497504-5


title: Pt30_On_AD505620-6


title: Pt27_Pre_AD453873-5


title: Pt27_On_AD467934-5


title: Pt46_On_AD781834-6


title: MIAPACA2_6hr_3uM_rep4


title: MIAPACA2_6hr_3uM_rep3


title: Pt46_Pre_AD467096-6


title: Pt24_Pre_AD436687-5


title: Pt37_On_AD495183-5


title: MIAPACA2_6hr_3uM_rep2


title: Pt48_Pre_E9047561-7


title: MIAPACA2_6hr_3uM_rep1


title: Pt37_Pre_AD502452-5


title: MIAPACA2_control_rep1


title: Pt36_Pre_AD467095-6


title: Pt36_On_AD495182-6


title: Pt48_On_E9047631-6


title: MIAPACA2_6hr_30nM_rep4

value: gemcitabine 30nM 6h


title: Pt38_On_E9414881-5


title: MIAPACA2_6hr_30nM_rep3


title: Pt38_Pre_E9200719-6


title: MIAPACA2_control_rep3


title: MIAPACA2_6hr_30nM_rep2


title: Pt17_Pre_E9047563-6


title: Pt18_Pre_E9024732-6


title: Pt10_On_E9047632-6


title: Pt17_On_E9261162-5


title: MIAPACA2_6hr_30nM_rep1


title: MIAPACA2_6hr_300nM_rep4

value: gemcitabine 300nM 6h


title: Pt10_Pre_E9047565-6


title: Pt9_On_E9047644-7


title: Pt5_Pre_E9021022-6


title: Pt9_Pre_E9021024-6


title: Pt4_Pre_E9021023-6


title: Pt4_On_E9047643-7


title: MIAPACA2_6hr_300nM_rep1


title: Pt5_On_E9047635-6


title: RUVBL2 HepG2 A

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

description: Reanalysis of GSM2564085

library_source: genomic

data_processing:
Align bowtie2 --sensitive
samtools rmdup
samtools merge
bamCoverage --binSize 10 --extendReads 150 --normalizeUsingRPKM --centerReads
macs2 callpeak -q 0.001 --keep-dup all --shift 37 --nomodel --extsize 147 -g hs
peaks were filtered against blacklist (ENCODE) using bedtools and recursviely merged with other peaks within 500bp to yield final peak calls
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files = Reads per million  signal tracks
Supplementary_files_format_and_content: bed files = peaks called from merged replicates of bam files for INO80 subunits in HepG2
Supplementary_files_format_and_content: raw files ending in rmdup.dtags.bam  were aligned against dm3 to count the total number of non-duplicate uniquely mapping drosohpila reads in each IP sample and used for normalization - count values are in dtags_agg.csv

molecule: genomic DNA

growth_protocol: Cells were grown in DMEM + 10% FBS + penicillin + streptomycin at 37 degrees in 5% C02. Experiments were performed on cells less than 10 passages.

extract_protocol:
Cells were fixed in 0.3% formaldehyde for 30 minutes at 4 degrees prior to processing for ChIP using protocol from Raab et al 2015.
Kapa Hyperprep kit using Illumina Truseq barcoded adapters

value: liver cancer cell line

tag: cell line

tag: antibody

tag: vendor

value: bethyl

tag: catalog number

tag: lot


title: Pt3_On_E9047638-6

value: On


title: Pt32_On_E9414883-5


title: RUVBL1 HepG2 B

description: Reanalysis of GSM2564084


title: Pt3_Pre_E9024733-3

value: PRCR


title: MIAPACA2_24hr_3uM_rep4

value: gemcitabine 3uM 24h


title: MIAPACA2_24hr_3uM_rep3


title: Pt18_On_E9261163-5

value: melanoma


title: Pt109_On_AE527955-6


title: Pt103_Pre_AE134058-2


title: RUVBL1 HepG2 A

description: Reanalysis of GSM2564083


title: MIAPACA2_24hr_3uM_rep2


title: RUVBL2 HepG2 B

description: Reanalysis of GSM2564086


title: MIAPACA2_24hr_3uM_rep1


title: Pt92_On_AE148750-5


title: Pt92_Pre_AE134060-5


title: MCRS1 HepG2 B

description: Reanalysis of GSM2564080

value: protein-tech


title: MIAPACA2_6hr_300nM_rep2


title: MIAPACA2_6hr_300nM_rep3


title: Pt90_Pre_AD467873-6

value: PD


title: MIAPACA2_24hr_30nM_rep4

value: gemcitabine 30nM 24h


title: Pt80_On_AD467874-5


title: Input HepG2 B

description: Reanalysis of GSM2564076


title: Pt78_Pre_AD467018-5

value: Pre


title: Pt109_On_AE527955-5


title: MIAPACA2_24hr_30nM_rep2


title: MIAPACA2_24hr_30nM_rep3


title: Pt69_On_AD635730-6


title: Pt68_On_AD635729-6


title: Pt78_On_AE148748-6


title: Input HepG2 A

description: Reanalysis of GSM2564075


title: INO80 HepG2 C

description: Reanalysis of GSM2564072

value: abcam


title: MIAPACA2_24hr_30nM_rep1


title: Pt65_On_AD796996-5

value: SD


title: MIAPACA2_24hr_300nM_rep4

value: gemcitabine 300nM 24h


title: Pt103_On_AE134059-6


title: Pt65_Pre_AD793919-6


title: INO80 HepG2 B

description: Reanalysis of GSM2564071


title: Pt62_On_AD635728-5


title: Pt62_Pre_AD608303-5


title: MIAPACA2_24hr_300nM_rep3

value: MIA PACA-2


title: INO80 HepG2 A

description: Reanalysis of GSM2564070


title: MCRS1 HepG2 A

description: Reanalysis of GSM2564079


title: Pt98_On_AE086717-6


title: Pt98_Pre_AD733586-8


title: Pt87_On_AD495198-6


title: Pt84_On_AD495199-6


title: RRBS on normal crypts, patient #178

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Data were aligned to hg19 genome using Bismark v0.7.4
Reads were imported into R, extended to 200bp and coverage of each base was calculated using customized R scripts to generate the bedGragh files.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph with methylation levels

source_name: Colon

growth_protocol:
CRYPTS: All ACF subjects included in this study were enrolled in an ongoing clinical study at John Dempsey Hospital (UConn Health). All patients who met the Amsterdam criteria for familial adenomatous polyposis (FAP) or hereditary non-polyposis CRC (HNPCC) were excluded from this study. In order to control for the effects of age and smoking on DNA methylation, all selected subjects were non-smokers between the ages of 50 and 65. 10 ACF were biopsied from the distal colons of individual subjects. ACF were identified and biopsied during high-definition, magnifying chromoendoscopy using indigo carmine dye-spray. For each subject, a sample of normal-appearing mucosa was also obtained from the distal colon. Biopsies were immediately embedded in OCT freezing medium (Neg 50, ThermoFisher Scientific), flash-frozen, and stored at -80C. Frozen tissues were sectioned onto polyethylene naphthalate (PEN, ThermoFisher Scientific) membrane slides using a Leica CM1900 Cryostat. Frozen sections were stained with hematoxylin and eosin (H&E) and routine histologic analyses were performed. All biopsies collected from ACF subjects were histologically confirmed by a board-certified human gastrointestinal pathologist blinded.
CRC: Ten Stage II-IV CRCs resected from the distal colons of individual subjects were obtained from the City of Hope and University of Connecticut Health frozen tumor banks. In addition, 10 histologically-confirmed matched normal samples, collected from the margins on either side of the resected tumor, were obtained. Tissue sections were stained with H&E and reviewed by a board-certified pathologist to confirm the presence and histopathology of the lesions. This study was conducted with the written, informed consent of each subject, as well as Institutional Review Board approval from both the University of Connecticut Health and City of Hope (IRB Protocols IE-10-068OSJ-3 and 97134, respectively).

extract_protocol:
CRYPTS: Laser Capture Microdissection of ACF and matched normal biopsies: an ArcturusXT Laser Capture Microdissection system was used to isolate a minimum of 1 mm2 of tissue (~10.000 cells) from 12 μm-thick frozen serial sections.
CRC: RNA was isolated from laser-captured ACF samples using the Arcturus PicoPure Frozen RNA Isolation Kit (ThermoFisher) according to the manufacturers' instructions. RNA was isolated from cancer patient frozen tissues using the mirVana miRNA Isolation Kit (Ambion) according to the manufacturers' instructions
RRBS: Briefly, purified DNA was digested by overnight incubation with MspI at 37°C. Following restriction digest, DNA fragments were subjected to end repair and A-tailing, followed by linker ligation. Bisulfite conversion was done using the EZ DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s instructions

tag: disease state

value: Healthy individual

value: normal colonic crypt


title: MIAPACA2_24hr_300nM_rep1


title: MIAPACA2_24hr_300nM_rep2


title: Pt72_Pre_AD793922-5


title: RRBS on normal crypts, patient #515


title: RRBS on ACF, patient #2

value: aberrant crypt foci


title: PANC1-24hr_04cm03_4


title: Pt84_Pre_AD486532-5


title: Pt79_Pre_AD733587-5


title: Pt79_On_AD733628-6


title: PANC1-24hr_04cm03_2


title: Pt77_Pre_AD733591-7


title: Pt108_On_AE373243-6


title: Pt77_On_AD733629-8


title: RRBS on normal crypts, patient #245


title: RRBS on normal crypts, patient #2


title: Pt105_On_AE373241-6


title: PANC1-24hr_04cm03_3


title: Pt94_Pre_AD732850-6


title: Pt94_On_AE373242-6


title: PANC1-24hr_04cm03_1


title: RRBS on ACF, patient #190


title: Pt52_Pre_AD506075-6


title: Pt67_On_AD530366-6


title: Pt67_Pre_AD506074-6


title: RRBS on normal crypts, patient #190


title: PANC1-6hr_04cm03_3

value: CM03 6h


title: RRBS on normal crypts, patient #173


title: RRBS on ACF, patient #163


title: Pt52_On_AD530365-6


title: Pt47_On_AD530367-6


title: Pt47_Pre_AD506073-6


title: PANC1-6hr_04cm03_2


title: RRBS on ACF, patient #139


title: Pt93_On_AE070988-5


title: RRBS on normal crypts, patient #163


title: Pt101_Pre_AD486328-5


title: PANC1-6hr_04cm03_1


title: Pt101_On_AD681975-5


title: PANC1-0hr_ctrl_4

value: untreated


title: Pt89_On_AE070987-5

value: On


title: Pt89_Pre_AE070951-5


title: PANC1-6hr_04cm03_4


title: Pt85_On_AE070989-10


title: Pt85_Pre_AD486329-5


title: PANC1-0hr_ctrl_3


title: Pt81_On_AD681973-5


title: PANC1-0hr_ctrl_2


title: RRBS on adjacent normal colon, patient #60

value: Colon cancer stage II-IV

value: adjacent normal colon


title: Pt66_Pre_AD667850-6

value: melanoma


title: RRBS on CRC, patient #60

value: primary tumor


title: PANC1-0hr_ctrl_1


title: Pt49_On_AD681976-5

value: PRCR


title: Pt76_Pre_AD667852-6

value: UNK


title: RRBS on adjacent normal colon, patient #54


title: MIAPACA2-24h-4


title: RRBS on CRC, patient #54


title: MIAPACA2-24h-3


title: RRBS on adjacent normal colon, patient #51


title: RRBS on CRC, patient #51


title: Pt82_Pre_AD823914-8

value: Pre


title: MIAPACA2-24h-2


title: Pt59_Pre_AD823915-5


title: Pt58_On_AE045812-10


title: Pt39_Pre_AD485899-5

value: PD


title: Pt23_Pre_AD313075-5


title: MIAPACA2-6h-4


title: Pt2_On_AD174046-6

value: SD


title: Pt23_On_AD486568-8


title: RRBS on CRC, patient #50


title: RRBS on adjacent normal colon, patient #50


title: Pt2_Pre_AD101150-6


title: MIAPACA2-6h-3


title: Pt49_Pre_AD667851-6


title: RRBS on CRC, patient #16


title: RRBS on adjacent normal colon, patient #16


title: Pt82_On_AD125218-6


title: MIAPACA2-6h-2


title: MIAPACA2-6h-1


title: RRBS on CRC, patient #15


title: RRBS on adjacent normal colon, patient #15


title: MIAPACA2-Control-3


title: Pt1_Pre_AD101148-6


title: MIAPACA2-Control-4


title: MIAPACA2-Control-1


title: MIAPACA2-Control-2


title: MIAPACA2-24h-1


title: RRBS on ACF, patient #245


title: RRBS on ACF, patient #165


title: RRBS on normal crypts, patient #165


title: RRBS on ACF, patient #178


title: RRBS on ACF, patient #143


title: RRBS on normal crypts, patient #143


title: RRBS on normal crypts, patient #139


title: Pt1_On_AD174047-6


title: RRBS on ACF, patient #515


title: RRBS on ACF, patient #173


title: RRBS on adjacent normal colon, patient #42


title: RRBS on CRC, patient #8


title: iPAR-CLIP_L001

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

country: Germany

institute: University Medicine Greifswald

data_processing:
FastQC preprocessing
Adapter removal by Trimmomatic with ILLUMINACLIP options
Filtering for sequences shorter than 20bp
reads were aligned by TopHat2 --max-multihits 1; --min-intron-length 36
Genome_build: Homo sapiens version GRCh37.74
Supplementary_files_format_and_content: csvfiles (.csv) representing the Reads per million (RPM) for the 3'UTR and 5'UTR mRNAs. BED graph files (.bed) include the start positions of reads and mutations T to C of mapped reads.

extract_protocol:
The PAR-iCLIP was carried out according to the protocol described by: Huppertz, I., Attig, J., D'Ambrogio, A., Easton, L.E., Sibley, C.R., Sugimoto, Y., Tajnik, M., Konig, J. and Ule, J. (2014) iCLIP: protein-RNA interactions at nucleotide resolution, Methods, 65, 274–287. Briefly, MCF-7 cells (1 x 107) were seeded 48 h before they were incubated with 100 µM 4-thiouridine (4-SU) for 4 h. For cross-linking purposes, cells were treated with UV light (365 nm, 4000 mJ/cm²) directly before lysis.
The PAR-iCLIP was carried out according to the protocol described by: Huppertz, I., Attig, J., D'Ambrogio, A., Easton, L.E., Sibley, C.R., Sugimoto, Y., Tajnik, M., Konig, J. and Ule, J. (2014) iCLIP: protein-RNA interactions at nucleotide resolution, Methods, 65, 274–287. hnRNPA1, and the cross-linked RNA, was immunoprecipitated using 6 µg anti-hnRNPA1 antibody and 100 µL Dynabeads® protein G (Thermo Fisher Scientific). The RNA was radiolabeled and the hnRNPA1-RNA complexes were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and blotted onto nitrocellulose membranes. RNA was isolated from the membranes by digestion of the protein with proteinase K (Thermo Fisher Scientific) and reverse transcribed. The resulting cDNA was gel purified and amplified with primers containing the adapter sequences for subsequent next generation sequencing (NGS), which was carried out on a NextSeq500 platform (Illumina, San Diego, USA).

tag: stress

value: control


title: RRBS on adjacent normal colon, patient #41


title: RRBS on CRC, patient #41


title: RRBS on CRC, patient #32


title: RRBS on adjacent normal colon, patient #8


title: LALB_siAATF_3

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

country: Italy

institute: Italian National Cancer Institute "Regina Elena"

description: processed data file: fpkm_table_LALB_siAATF.txt

data_processing:
BaseSpace Illumina Cloud Environment was used for basecalling and demultiplexing.
RNA-seq was analyzed via the web pipeline RAP, which employs the Tuxedo suite for mapping (Tophat) and transcripts reconstruction (Cufflinks, Cuffdiff)
For spikein-normalized data, HTSeq count were normalized using spikein raw counts as scaling factors.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: ALL-B patient-derived cell line

extract_protocol:
total RNA was extracted using Qiazol (Invitrogen), purified from genomic DNA contamination through a DNase I (Qiagen) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen). Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies) and by Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.
RNA libraries for sequencing were generated in triplicate according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, Inc., San Diego, CA, US). Starting material was 500ng of total RNA.

value: B-Cell

value: LALB (ALL-B patient-derived cell line)


title: LALB_siAATF_1


title: LALB_CN_3


title: RNA-seq on ACF, patient #165_S2

description:
9179_165_S2_GGCTAC_L999_R1_001.fastq
Barcode: GGCTAC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to hg19 whole genome using tophat-v2.0.8b
Aligned reads was normalized by edgeR bioconductor package and outputed as normalized counts file
Genome_build: hg19
Supplementary_files_format_and_content: Normalized counts in linear scale

extract_protocol:
CRYPTS: Laser Capture Microdissection of ACF and matched normal biopsies: an ArcturusXT Laser Capture Microdissection system was used to isolate a minimum of 1 mm2 of tissue (~10.000 cells) from 12 μm-thick frozen serial sections.
CRC: RNA was isolated from laser-captured ACF samples using the Arcturus PicoPure Frozen RNA Isolation Kit (ThermoFisher) according to the manufacturers' instructions. RNA was isolated from cancer patient frozen tissues using the mirVana miRNA Isolation Kit (Ambion) according to the manufacturers' instructions
CRYPTS: For RNA extracted from ACF, depletion of rRNA was done using the RiboZero Magnetic Kit according to the “Protocol for Removal of rRNA from Small Amounts of Total RNA” (Clontech). Subsequently, dscDNA library preparation and amplification were done using the SMARTer Stranded RNA-Seq Kit (Clontech) according to the manufacturer's protocol.
CRC: Sequencing libraries were prepared from RNA isolated from cancer samples using the TruSeq Stranded Total Library Preparation Kit and the RiboZero Gold rRNA Removal Kit (Illumina).

value: Healthy

tag: technical replicates

value: techical replicate of 165S1


title: RNA-seq on ACF, patient #165_S1

description:
9178_165_S1_TAGCTT_L999_R1_001.fastq
Barcode: TAGCTT

value: aberrant crypt foci

value: techical replicate of 165S2


title: RNA-seq on normal crypts, patient #165

description:
9177_165_N_GATCAG_L999_R1_001.fastq
Barcode: GATCAG

value: normal colonic crypt


title: LALB_CN_2


title: LALB_CN_1


title: RNA-seq on ACF, patient #245

description:
9176_245_S_ACTTGA_L999_R1_001.fastq
Barcode: ACTTGA


title: RNA-seq on ACF, patient #178

description:
9174_178_S_GCCAAT_L999_R1_001.fastq
Barcode: GCCAAT


title: RNA-seq on normal crypts, patient #245

description:
9175_245_N_CAGATC_L999_R1_001.fastq
Barcode: CAGATC


title: RNA-seq on ACF, patient #139

description:
9172_139_S_TGACCA_L999_R1_001.fastq
Barcode: TGACCA


title: RNA-seq on normal crypts, patient #139

description:
9171_139_N_TTAGGC_L999_R1_001.fastq
Barcode: TTAGGC


title: RNA-seq on normal crypts, patient #178

description:
9173_178_N_ACAGTG_L999_R1_001.fastq
Barcode: ACAGTG


title: RRBS on adjacent normal colon, patient #32

value: Colon cancer stage II-IV


title: RNA-seq on adjacent normal colon, patient #60

description:
8710_60N_GTCCGC_L002_R1_001.fastq
Barcode: GTCCGC

value: adjacent normal colon


title: CDKO3

city: Houston

first: Pablo

middle: Riera

last: Freire

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Amplified mRNA

data_processing:
Sequencing reads were trimmed using Trimming Galore
Reads were aligned to the mm10 mouse reference genome using TopHat2
Aligned reads were assigned to Refseq annotated genes using the HTSeq suite
Identification of differentially expressed genes was performed with the DESeq2 program using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 output in a text tab-delimited format

organism: Mus musculus

source_name: Hematopoietic stem cells

extract_protocol:
Total RNA was extracted using Rneasy Micro columns from Qiagen
mRNA was amplified using a SMARTer Ultra Low Input v3 amplification kit from Clontech. Library was constructed using a Nextera XT kit from Illumina

tag: genotype

value: Nr4a1 fl/fl; Nr4a3-/-; Rosa26-ERt2

value: hematopoietic stem cells


title: RNA-seq on ACF, patient #515

description:
9170_51_S_CGATGT_L999_R1_001.fastq
Barcode: CGATGT


title: RNA-seq on normal crypts, patient #515

description:
9169_51_N_ATCACG_L999_R1_001.fastq
Barcode: ATCACG


title: LALB_siAATF_2


title: RNA-seq on CRC, patient #60

description:
8709_60T_CCGTCC_L002_R1_001.fastq
Barcode: CCGTCC

value: primary tumor


title: RNA-seq on adjacent normal colon, patient #54

description:
8707_54N_AGTTCC_L002_R1_001.fastq
Barcode: AGTTCC


title: RRBS on CRC, patient #42


title: Control 3

description: Amplified mRNA

value: Nr4a1 fl/fl; Nr4a3-/-


title: CDKO1

description: Amplified mRNA


title: RNA-seq on adjacent normal colon, patient #51

description:
8704_51N_CAGATC_L001_R1_001.fastq
Barcode: CAGATC


title: RNA-seq on CRC, patient #51

description:
8703_51T_GCCAAT_L001_R1_001.fastq
Barcode: GCCAAT


title: CDKO2

description: Amplified mRNA


title: input DNA LALB

data_processing:
The data has been analyzed thanks to the CAST pipeline at Cineca, that employs bowtie2 for mapping and MACS2 for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

source_name: B-Cell

extract_protocol:
Extract protocol not provided.
Chromatin immunoprecipitations were performed as previously described (Bruno et al, 2002) by using rabbit polyclonal antibodies ChIP grade, anti-Che-1 (Bethyl), and anti c-Myc and Dynabeads Protein G (Life Technologies). The quantity of the immunoprecipitated material was determined by Qubit 2.0 fluorometer (Life Technologies). 10 ng of the immunoprecipitated chromatin was used to prepare the libraries for sequencing following the manufacturer’s instructions including DNA and repairing, adaptor ligation, and amplification (Illumina). The libraries were then sequenced using the Illumina NextSeq 500 system.

value: LAL-B  (ALL-B patient-derived cell line)

value: B-cell

tag: chip antibody

value: none (input)


title: AATF_ChIPSeq_LALB

value: anti-Che-1 (Bethyl, A301-032A)


title: RNA-seq on adjacent normal colon, patient #50

description:
8701_50N_TGACCA_L001_R1_001.fastq
Barcode: TGACCA


title: Control 1

description: Amplified mRNA


title: RNA BZK Treated 2

city: Austin

first: Bryan

last: Davies

address: 2506 Speedway

institute: University of Texas at Austin

data_processing:
Base calls performed using Applied Biosciences 7900
Sequenced reads were trimmed for adaptor sequence, then mapped to 17978 whole genome using CLC genomic workbench version 9.0 RNAseq default settings.
The statistical test performed was a Baggerley’s test on proportion of counts in each group of samples to generate a p value associated with the weighted proportion fold change between experiment and control groups for each gene
Genome_build: CP000521
Supplementary_files_format_and_content: Tab deliminated file containing the feature ID, the corresponding weighted propotions fold change, the FDR corrected p-value, and the features annotation. The processed data file only contains features with a statistically significant increase in reads of 3.0 fold or more.

organism: Acinetobacter baumannii

source_name: Lysogeny-Bertani Broth Culture_BZK treated

growth_protocol: Samples were grown at 25oC with shaking in Lysogeny-Bertani Broth

extract_protocol:
Qiagen RNeasy Mini Kit
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®

treatment_protocol: Samples were treated or untreated with 5 μg/mL benzalkonium chloride for 45 minutes at 25oC with shaking prior to RNA extraction

tag: treated with

value: 5 μg/mL benzalkonium chloride for 45 m


title: RNA BZK Treated 1


title: RNA-seq on CRC, patient #8

description:
7288_8T_ATTCCT_L006_R1_001-39.fastq
Barcode: ATTCCT


title: RNA-seq on CRC, patient #50

description:
8700_50T_CGATGT_L001_R1_001.fastq
Barcode: CGATGT


title: RNA Control 2

source_name: Lysogeny-Bertani Broth Culture_control

value: none (untreated control)


title: WT_20FS3

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

data_processing:
Convert BAM files to FASTQ files using picard-toolds-1.108, SamToFastq.jar
Trimming of adapter and poor quality reads with trim_galore_v0.3.3
Align to genome and get methylation calls with bsmap-2.74
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing information for each sample: chrBase, chr, base, strand, coverage, FreqC (methylation), FreqT

source_name: Sperm

extract_protocol:
Genomic DNA was extracted from tissues and cell lines using DNeasy Blood & Tissue Kit (Qiagen) as per manufacturer protocols
Reduced represenation bisulfite sequencing (RRBS) libraries were prepared according to previously published prototols using gel-free technique (Boyle, P. Genome Biol., 2012).  Briefly, DNA was digested with MspI restriction enzyme, followed by size selection, gap filling and 3'-A-tailing.  Ligation of NEBNext methylated adaptors was performed, followed by bisulfite conversion and index PCR amplificaton.

treatment_protocol: BALB/c mice were placed on Control diets (CD), 10x supplemented (10FS) or 20x supplemented (20FS) diets for 6-12 months

value: wild type

value: BALB/c

tag: diet

value: 20x supplement diet

value: sperm


title: RNA-seq on adjacent normal colon, patient #8

description:
7287_8N_ACTGAT_L006_R1_001-39.fastq
Barcode: ACTGAT


title: RNA Control 1


title: RNA-seq on CRC, patient #54

description:
8706_54T_AGTCAA_L003_R1_001.fastq
Barcode: AGTCAA


title: RNA-seq on CRC, patient #16

description:
7286_16T_GAGTGG_L006_R1_001-39.fastq
Barcode: GAGTGG


title: WT_20FS1


title: Tn BZK Treated 2

data_processing:
library strategy: Tn-seq
Base calls performed using Applied Biosciences 7900
Sequenced reads were trimmed for adaptor sequence and first 15bp, then mapped to 17978 whole genome using CLC genomic workbench version 9.0 RNAseq default settings.
The statistical test performed was a Baggerley’s test on proportion of counts in each group of samples to generate a p value associated with the weighted proportion fold change between experiment and control groups for each gene
Genome_build: CP000521
Supplementary_files_format_and_content: Tab deliminated file containing the feature ID, the corresponding weighted propotions fold change, the FDR corrected p-value, and the features annotation. The processed data file only contains features with a statistically significant decrease in reads of 3.0 fold or more.

extract_protocol:
Qiagen DNeasy Blood & Tissue Kit
Custom built as described in Dong T. G., Ho B. T., Yoder-Himes D. R. & Mekalanos J. J. Identification of T6SS-dependent effector and immunity proteins by Tn-seq in Vibrio cholerae. Proc. Natl Acad. Sci. 110, 2623–2628 (2013).

treatment_protocol: Samples were treated or untreated with 5 μg/mL benzalkonium chloride and allowed to grow to saturation at 25oC with shaking prior to DNA extraction

value: 5 μg/mL benzalkonium chloride


title: Tn BZK Treated 1


title: WT_newCD4

value: Control diet


title: WT_newCD3


title: RNA-seq on CRC, patient #15

description:
7284_15T_GTTTCG_L007_R1_001-39.fastq
Barcode: GTTTCG

value: Colon cancer stage II-IV


title: RNA-seq on adjacent normal colon, patient #15

description:
7283_15N_GTGGCC_L007_R1_001-39.fastq
Barcode: GTGGCC

value: adjacent normal colon


title: WT_newCD2


title: Control 2

description: Amplified mRNA

tag: cell type

value: hematopoietic stem cells


title: WT_pooled polysome fractionation

city: Heidelberg

first: Michael

last: Brunner

address: Im Neuenheimer Feld 328

institute: BZH

description:
Sample 8
fractionated RNA

data_processing:
Reads were mapped to the NC10 and NC12 genome using Bowtie2 (v 2.1.0 and 2.2.5) and Tophat2 (v 2.0.13 and 2.0.14) softwares.
Dataset normalisation was done by library size.
HTSeq was used for read counting over genes.
BigWig coverage files were created by custom R scripts.
Splice site analysis was done by the Tophat2 junction output.
BigWig files were used to generate the data tracks of the NEUTRA database.
Genome_build: Neurospora crassa NC10 and NC12
Supplementary_files_format_and_content: [List_of_lincRNAs.txt] tab-delimited text file, list of identified lincRNAs with read counts from pooled polysome-RNA-seq
Supplementary_files_format_and_content: [BigWig files] Coverage on plus and minus strand
Supplementary_files_format_and_content: [W*.txt and w*.txt files] Read counts over genes, strand specific in samples 1-4, non-specific in 5-7

organism: Neurospora crassa

source_name: After a light to dark transfer, samples were harvested at 2 h intervals for 22 h

growth_protocol: Samples 1,2,3 and 4  were grown for 1 day in light at 25°C and transferred to darkness for 24 h before they were exposed to light (100 μE) and harvested after 0, 30, 60 and 120 min. Samples 5, 6 and 7 were grown in constant light for 48 h at 25°C. Sample 8 was grown for 1 day in light at 25°C, released to constant darkness for 22 h and individual samples of the pooled data were harvested at 2 h intervals.

extract_protocol:
RNA was prepared with peqGOLD TriFAST (peqLab, Erlangen, Germany).
For 1,2, 3 and 4; NEBNext Ultra Directional RNA prep Kit for Illumina (E7420) was used. For samples 5,6,7 and 8 RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The samples were pulverized in liquid nitrogen and approximately 0.25 g of the ground mycelia was used for each experiment. For sample 8, cycloheximide was added to the cultures prior to harvesting. Gradients containing 10-50-60% sucrose were used.

tag: strain

value: wildtype

tag: treatment

tag: growth protocol

value: Liquid culture

value: mycelia


title: Tn Control 2


title: Tn Control 1


title: Het_10FS5

value: heterozygote for targeted inactivation of the Mthfr

value: 10x supplement diet

tag: tissue


title: RNA-seq on CRC, patient #42

description:
5676_42T_ATTCCT_L002_R1_001.fastq
Barcode: ATTCCT

value: primary tumor


title: RNA-seq on CRC, patient #41

description:
5674_41T_GTGGCC_L002_R1_001.fastq
Barcode: GTGGCC


title: BL4C-anchor3-rep2

city: Shenzhen

first: Zhengyu

last: LIANG

state: Guangzhou

address: 1088 Xueyuan Avenue

department: Department of Biology

country: China

institute: Southern University of Science and Technology

data_processing:
Library strategy: 4C-seq
We used software ChIA-PET2 to process sequencing data, including linker trimming, reads alignment (BWA), paired-end tags formation and duplicates removal (parameters: -m 1 -k 2 -e 1 -A ACGCGATATCTTATC -B AGTCAGATAAGATAT).
Then the viewpoints interacted interactions were extracted from duplicates removed file *rmdup.bedpe and converted into bedgraph format.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedGraph format: Chromosome, Start, End, Interaction counts

source_name: human immortalised myelogenous leukemia line

growth_protocol: K562 cell line was cultured according to manufacturer's instructions

extract_protocol:
Cells were cross-linked with formaldehyde and then nucleuses were isolated for lysis. Then the chromatin was fragmented with restriction enzymes HaeIII and the proximal ends were ligated with biotin-labeled bridge linker in situ. A whole genome chromatin was extracted and sheared into 300-500 bp. Then the biotinylated junctions were captured by M-280 streptavidin magnetic beads.
The DNA libraries were prepared according to the standard Illumina library construction protocol, including end repair, A-tailing and Y-adaptor ligation (annealing: 5P- GATCGGAAGAGCACACGTCTGAACTCCAGTCAC and TACACTCTTTCCCTACACGACGCTCTTCCGATCT). Then two rounds of PCR were followed: 4C viewpoint primer and adaptor sequence of I7 (GTGACTGGAGTTCAGACGTGT) for the first round, I5 with 4C viewpoint and I7 with barcodes for the second round. Then the libraries were sequenced on Illumina sequencer Hiseq X Ten.

tag: cell line

tag: 4c viewpoint primer

value: ATTACCGTGTTTCTGGTGCTA


title: RNA-seq on adjacent normal colon, patient #41

description:
5673_41N_GGCTAC_L002_R1_001.fastq
Barcode: GGCTAC


title: BL4C-anchor2-rep2

value: GGCAACAAAAGCAATACTCCG


title: BL4C-anchor2-rep1


title: WT_20FS2

value: wild type


title: Het_10FS4

value: BALB/c


title: RNA-seq on CRC, patient #32

description:
5672_32T_TAGCTT_L002_R1_001.fastq
Barcode: TAGCTT


title: Het_10FS3


title: RNA-seq on adjacent normal colon, patient #16

description:
7285_16N_CGTACG_L006_R1_001-39.fastq
Barcode: CGTACG


title: RNA-seq on adjacent normal colon, patient #32

description:
5647_32N_ACAGTG_L002_R1_001.fastq
Barcode: ACAGTG


title: Het_10FS2


title: Het_10FS1


title: BL4C-anchor1-rep1

value: GACGGAGTATTGCTTTTGTTG


title: WT_newCD1

value: sperm


title: WT_10FS4


title: RNA-seq on adjacent normal colon, patient #42

description:
5675_42N_TGACCA_L002_R1_001.fastq
Barcode: TGACCA


title: WT_10FS5


title: WT_120 min light treatment

description: Sample 4

source_name: wild type, 24 h dark and then 120 min light exposure


title: WT_10FS3


title: BL4C-anchor3-rep1


title: BL02

data_processing:
Library strategy: BL-Hi-C
We used software ChIA-PET2 to process BL-Hi-C sequencing data, including linker trimming, reads alignment (BWA), paired-end tags formation and duplicates removal (two-step ligation parameters: -m 1 -k 2 -e 1 -A ACGCGATATCTTATC -B AGTCAGATAAGATAT; one-step ligation parameters: -m 2 -k 2-e 1 -A AGCTGAGGGATCCCTCAGCT -B AGCTGAGGGATCCCTCAGCT ).
genome build: GRCh37/hg19
processed data files format and content: bedpe format: Chromosome 1, Start 1, End 1, Chromosome 2, Start 2, End 2, ID, ., Strand 1, Strand 2

source_name: BL-Hi-C experiment of 500 K cells, rep1

growth_protocol: K562 cell line was cultured according to manufacturer's instructions.

extract_protocol:
BL-Hi-C: cells were cross-linked with formaldehyde and then nucleuses were isolated for lysis. Then the chromatin was fragmented with restriction enzymes (HaeIII, MboI or HindIII) and the proximal ends were ligated (one-step or two-step) with biotin-labeled bridge linker in situ. A whole genome chromatin was extracted and sheared into 300-500 bp. Then the biotinylated junctions were captured by M-280 streptavidin magnetic beads.
The BL-Hi-C libraries were prepared according to the standard Illumina library construction protocol and sequenced on the HiSeq2500/HiSeq X Ten.

tag: restriction enzyme

value: HaeIII

tag: proximity ligation

value: two-step ligation


title: BL01

source_name: BL-Hi-C experiment of 5 M cells, rep1


title: WT_10FS2


title: WT_30 min light treatment

description: Sample 2

source_name: wild type, 24 h dark and then 30 min light exposure


title: BL12

data_processing:
Library strategy: BL-Hi-C
We used software ChIA-PET2 to process BL-Hi-C sequencing data, including linker trimming, reads alignment (BWA), paired-end tags formation and duplicates removal (two-step ligation parameters: -m 1 -k 2 -e 1 -A ACGCGATATCTTATC -B AGTCAGATAAGATAT; one-step ligation parameters: -m 2 -k 2-e 1 -A AGCTGAGGGATCCCTCAGCT -B AGCTGAGGGATCCCTCAGCT ).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedpe format: Chromosome 1, Start 1, End 1, Chromosome 2, Start 2, End 2, ID, ., Strand 1, Strand 2

source_name: BL-Hi-C experiment with enzyme HaeIII, two-step ligation, rep1


title: BL11

source_name: BL-Hi-C experiment with enzyme HaeIII, one-step ligation, rep2

value: one-step ligation


title: WT_10FS1


title: BL10

source_name: BL-Hi-C experiment with enzyme HaeIII, one-step ligation, rep1


title: WT_constant dark

description: Sample 1

source_name: wild type, grown in dark for 24 h after a light to dark transfer


title: BL4C-anchor1-rep2


title: BL09

source_name: BL-Hi-C experiment with enzyme HindIII, two-step ligation, rep2

value: HindIII


title: Het_CD5

value: Control diet


title: BL08

source_name: BL-Hi-C experiment with enzyme HindIII, two-step ligation, rep1


title: Het_CD4


title: Type2 neuroblast 84hr after larva hatch replicate 3

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

description:
T2_84hALH_rep3
Processed data file: dm-type2-neuroblast-htseq.txt
Processed data file: dm-type2-neuroblast-tpm.txt

data_processing:
Illumina Casava and BCL2FASTQ1.8.3 were used for basecalling.
Sequenced reads were trimmed for NuGEN and Illumina adaptor sequences using cutadapt v1.7.1 with parameters --overlap=7 --minimum-length=30. Ribosomal RNA, mitochondrial and phiX sequences were filtered using bowtie2 v2.1.0 with default parameters. Remaining reads were then mapped to mm10 genome using STAR v2.4.0i with parameters --chimSegmentMin 15 --outFilterMismatchNmax 3.
Uniquely mapped reads were assigned to genes using HTSeq v0.6.1p1 with parameter -s no -m intersection-nonempty and using Illumina UCSC/dm3 annotation. FPKM for a gene was calculated by dividing assigned count by the sum of lengths of all exons belonging to the gene and then by total number of reads in million.
Genome_build: dm3 (BDGP Release 5)
Supplementary_files_format_and_content: dm-type2-neuroblast-htseq.txt: Tab-delimited file includes raw count values.
Supplementary_files_format_and_content: dm-type2-neuroblast-tpm.txt: Tab-delimited file includes TPM values.

organism: Drosophila melanogaster

source_name: CNS

growth_protocol: Newly hatched fly larvae were first synchronized with maximum 2 hour age difference and then grew at 25C until dissection.

extract_protocol:
30 fly larvae brain tissues were dissected at defined ages, digested with a mixture of pronase (1mg/ml) and dispase (1mg/ml) for 30 min at 25C, washed, triturated and 10 GFP labeled cells were sorted with a robotic sorter and stored at -80C in XB buffer from PicoPure kit (Life Technologies, KIT0204). Total RNA from around 100 pooled cells was extracted using PicoPure kit.
Extracted RNA was amplified using Ovation RNA-Seq System V2 (NuGEN, #7102). 1~1.5 ug of the amplified material was used for library construction using Encore NGS Multiplex System (NuGEN, #0314).

value: type II neuroblast

tag: age

value: 84hr after larva hatch

tag: num_cells (number of neuroblast cells in sample)

tag: ercc_mix (1 or 2)

tag: ercc_5 (10^-5 dilution of ercc in ul)


title: Het_CD3

tag: genotype


title: BL13

source_name: BL-Hi-C experiment with enzyme HaeIII, two-step ligation, rep2


title: BL06

source_name: BL-Hi-C experiment with enzyme MboI, two-step ligation, rep1

value: MboI


title: BL07

source_name: BL-Hi-C experiment with enzyme MboI, two-step ligation, rep2


title: Type2 neuroblast 84hr after larva hatch replicate 1

description:
T2_84hALH_rep1
Processed data file: dm-type2-neuroblast-htseq.txt
Processed data file: dm-type2-neuroblast-tpm.txt


title: Het_CD2

source_name: Sperm

value: heterozygote for targeted inactivation of the Mthfr


title: WT_60 min light treatment

description: Sample 3

source_name: wild type, 24 h dark and then 60 min light exposure

value: wildtype

value: Liquid culture

value: mycelia


title: Type2 neuroblast 50hr after larva hatch replicate 3

description:
T2_50hALH_rep3
Processed data file: dm-type2-neuroblast-htseq.txt
Processed data file: dm-type2-neuroblast-tpm.txt

value: 50hr after larva hatch


title: BL05

source_name: BL-Hi-C experiment of 500 K cells, rep2


title: Het_CD1


title: Type2 neuroblast 50hr after larva hatch replicate 1

description:
T2_50hALH_rep1
Processed data file: dm-type2-neuroblast-htseq.txt
Processed data file: dm-type2-neuroblast-tpm.txt


title: WT_CD4

value: wild type


title: BL03

source_name: BL-Hi-C experiment of 5 M cells, rep2


title: WT_CD3

value: BALB/c


title: Type2 neuroblast 36hr after larva hatch replicate 3

description:
T2_36hALH_rep3
Processed data file: dm-type2-neuroblast-htseq.txt
Processed data file: dm-type2-neuroblast-tpm.txt

value: 36hr after larva hatch


title: Type2 neuroblast 36hr after larva hatch replicate 1

description:
T2_36hALH_rep1
Processed data file: dm-type2-neuroblast-htseq.txt
Processed data file: dm-type2-neuroblast-tpm.txt


title: Type2 neuroblast 36hr after larva hatch replicate 2

description:
T2_36hALH_rep2
Processed data file: dm-type2-neuroblast-htseq.txt
Processed data file: dm-type2-neuroblast-tpm.txt


title: WT_CD2

value: sperm


title: WT_CD1


title: Wntup_3

city: Goettingen

first: Laura

middle: C

last: Zelarayan

state: Lower Saxony

address: Robert-Koch Strasse 40

department: Institute of Pharmacology and Toxicology

institute: University Medical Center, Goettingen

data_processing:
cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (SR; 1x50 bp; 51 cycles with single indexing; 6 GB ca. 30- 35 million reads per sample).
Sequence reads were aligned to the mouse reference assembly (UCSC version mm9) using Bowtie 2.0
For each gene, the number of mapped reads was counted using htseqcount and DESeq2 was used to analyze the differential expression
Genome_build: mm9
Supplementary_files_format_and_content: Excel file contains the output from DESeq2: variance stabilized counts of the raw data (normalization).

source_name: Cardiac ventricles

growth_protocol: mice were kept on a 12/12 light/dark facility with ad lib access to food.

extract_protocol:
RNA was isolated from mice cardiac tissue using NucleoSpin RNA kit from Macherey-Nagel (Cat no: 740955.10). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 12 weeks-old adult mice were administered with TX 30mg/Kg/day for 3 days and were sacrificed 3 weeks-post induction

value: 15 weeks-old

value: alphaMHC Cre recombinase positive, beta-catenin exon3 deleted-stabilized beta-catenin


title: Type2 neuroblast 24hr after larva hatch replicate 3

description:
T2_24hALH_rep3
Processed data file: dm-type2-neuroblast-htseq.txt
Processed data file: dm-type2-neuroblast-tpm.txt

value: 24hr after larva hatch


title: Type2 neuroblast 24hr after larva hatch replicate 2

description:
T2_24hALH_rep2
Processed data file: dm-type2-neuroblast-htseq.txt
Processed data file: dm-type2-neuroblast-tpm.txt


title: Wntup_2


title: Type2 neuroblast 24hr after larva hatch replicate 1

description:
T2_24hALH_rep1
Processed data file: dm-type2-neuroblast-htseq.txt
Processed data file: dm-type2-neuroblast-tpm.txt


title: L-DKO NKT Input

city: Durham

first: Yuan

last: Zhuang

state: NC

address: 207 Research Drive

department: Immunology

institute: Duke University

data_processing:
Reads were aligned to the mm9 genome using Bowtie software (version 1.1.2, parameters: --chunkmbs 128 --mm -m1 --best --strata -p4 -S -q)
Peaks were called using MACS (version 1.4.2, default parameters)
Peaks called by MACS were annotated by the NGS: Peak Annotation tool on Nebula (https://nebula.curie.fr/)
Genome_build: mm9
Supplementary_files_format_and_content: Bed and wig files were generated by MACS for visualization using the IGV tool
Supplementary_files_format_and_content: Scores in bed files represent peak scores assigned by MACS

source_name: sorted cells from thymus

extract_protocol:
Thymii were harvested from mice, and thymocytes were stained with appropriate antibodies for sorting. Following sort, Cells were fixed for 15 min in PBS containing 1.5 mM EGS(ethylene glycol-bis(succinic acid N-hydroxysuccinimide ester)), followed by incubation for 15 min with 1% formaldehyde. Formaldehyde was quenched by incubation for 10 min with 0.2 M glycine, and then washed twice with PBS and pellets were frozen in liquid nitrogen. Crosslinked cells were lysed, washed and sonicated for 22 cycles using a Biorupter Plus sonicator. Lysates were cleared with dilution buffer, and incubated overnight at 4°C with magnetic beads bound with 15 μg of anti-E2A antibody (V-18, Santa Cruz Biotechnology, Lot G0814) or 3 μl anti-H3K4me2 antibody (Millipore, 07-030, Lot 2430486). Beads were washed multiple times with appropriate buffers. Bound complexes were then eluted from beads by incubation for 30 min at 65 °C with shaking in elution buffer. Crosslinks were reversed by incubation overnight at 65°C. RNA and proteins were digested, followed by DNA purification using a ChIP DNA Clean and Concentrator kit (Zymoresearch).
Libraries were prepared with the NEBNext primer set which involved applying ChIP DNA to end repair, A-tailing, adapter ligation, PCR amplification. They were then cleaned and size selected by AMPure beads (Agencourt)

value: L-DKO mice (deficient in Id2 and Id3)

value: 3-5 weeks

value: thymus

value: Invariant Natural Killer T (iNKT) cells

tag: sorting strategy

value: CD1dTet+ TCRβ+

tag: molecule subtype

value: genomic DNA + crosslinked, bound protein


title: Type2 neuroblast 84hr after larva hatch replicate 2

description:
T2_84hALH_rep2
Processed data file: dm-type2-neuroblast-htseq.txt
Processed data file: dm-type2-neuroblast-tpm.txt

value: type II neuroblast

value: 84hr after larva hatch


title: Wntup_1


title: L-DKO NKT E2A

tag: chip antibody

value: anti-E2A antibody (V-18, Santa Cruz Biotechnology, Lot G0814)


title: L-DKO DP Input

tag: cell type

value: double-positive (DP) thymocyte

value: CD1dTet- CD4+ CD8+


title: Control_2

tag: strain

value: alphaMHC Cre recombinase positive, WT for beta-catenin


title: Control_3


title: Type2 neuroblast 50hr after larva hatch replicate 2

description:
T2_50hALH_rep2
Processed data file: dm-type2-neuroblast-htseq.txt
Processed data file: dm-type2-neuroblast-tpm.txt

value: 50hr after larva hatch


title: BL04

source_name: BL-Hi-C experiment of 5 M cells, rep3

value: HaeIII

value: two-step ligation


title: MM067

status: Public on Jan 22 2018

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

data_processing:
RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Reads are quality-checked with FastQC, and aligned to the human genome (NCBI37/mm9) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 20 multihits
Transcripts quantification and differential expression are calculated with Cufflinks 2.2.1, using the human GRCh37/hg19 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Tabulated text file with gene Cuffnorm FPKM values

source_name: Pancreatic cells

extract_protocol:
Cell sorting from fresh tumor and pancreas samples
Illumina Truseq RNA prep Kit
Libraries were then sequenced using Illumina HiSeq2000

tag: mouse model/genotype

value: Tumor cell

tag: treatment


title: MM064

value: Fibroblast


title: Control_1

value: 15 weeks-old


title: MM063


title: L-DKO DP E2A

value: L-DKO mice (deficient in Id2 and Id3)

value: 3-5 weeks

tag: tissue


title: MM061


title: MM059


title: MM058


title: MM056


title: WT_CD5

value: wild type

value: BALB/c

tag: diet

value: Control diet

value: sperm


title: MM055


title: MM051


title: MM043


title: MM041

value: mNPF


title: MM052


title: MM047


title: hnRNPF KD rep-1

first: Samuel

middle: Emerson

last: Harvey

state: TEXAS

department: Lester and Sue Smith Breast Center

data_processing:
Paired-end RNA-seq reads for each sample were mapped to the human genome (GRCh37) and transcriptome (Gencode v24 backmapped to GRCh37) using STAR v2.5.3a using the following command: STAR --runThreadN 16 --alignEndsType EndToEnd –outSAMtype BAM SortedByCoordinate --readFilesCommand zcat
Gene expression quantification and differential gene expression was conducted for all replicates cuffdiff v2.2.1 using the following command: cuffdiff -p 8 –max-bundle-frags 1000000000 --library-type fr-firststrand -o output_dir gencode.v24lift37.annotation.gtf
Alternative splicing quantification and differential analysis was conducted for all replicates using rMATS v3.2.5 using the following command: python RNASeq-MATS.py -gtf gencode.v24lift37.annotation.gtf -o output_dir  -t paired -len 100 -analysis U -libType fr-firststrand
Genome_build: GRCh37
Supplementary_files_format_and_content: Unfiltered FPKM values and log2FC are provided in cuffdiff outputted tab-delimited gene_exp.diff file titled shNS_and_shhnRNPF.cuffdiff.gene_diff.txt.gz. Unfiltered alternative splicing output from rMATS for skipped exons (SE) using only junction counts are provided in the tab-delimited file shNS_and_shhnRNPF.rmats.se.junction_count_only.txt.gz

source_name: HMLE cells

growth_protocol: The maintenance of immortalized human mammary epithelial cells HMLE was conducted as previously described (Brown et al., 2011)

extract_protocol:
Total RNA was extracted using standard Trizol extraction procedures
Stranded paired-end polyA-purified RNA sequencing libraries were prepared using Illumina TruSeq protocols

treatment_protocol: Cell lines stably expressing the relevant shRNA were generated using lentiviral vectors using standard infection protocols

value: Immortalized breast epithelial cells

tag: cell line

value: HMLE

value: hnRNPF shRNA treated


title: MM066


title: Control rep-2

value: Non-specific shRNA treated


title: HEC-1-A shMETTL3-input

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description: no IP (input RNA)

data_processing:
For m6A-seq, reads were aligned to the reference genome (hg38) using Tophat (v2.0.14, ref) with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks, the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. edgeR was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP sample in the current peak/window (a), median reads count of the IP sample in all 100 bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c) and median reads count of the input sample in all 100 bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c).
Genome_build: hg38
Supplementary_files_format_and_content: m6A peaks bed

source_name: HEC-1-A cell line

growth_protocol: Stable HEC-1-A was grown in McCoy’s 5A medium (Gibco, 16600) supplemented with 10% FBS (Gibco), 1% Penicillin-Streptomycin (Gibco, 15140), and 1ug/ml puromycin

extract_protocol:
Tissues were homogenized in Trizol reagent with a Tissure-Tearor. Total RNA were extracted using manufacturer’s instructions.Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen). RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols. Cell line total RNA was isolated from stable cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen). RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.
TruSeq Small RNA Sample Preparation Kit (Illumina)

treatment_protocol: we used CRISPR-Cas9 genome editing system from IDT to generate a METTL14+/- cell line in HEC-1-A, then transfected the METTL14+/- cell lines with a PiggyBac Transposon System (SBI) encoding FLAG-tagged wilytype METTL14 or Flag-tagged METTL14(R298P) to generate wt/mu METTL14 stable cell line; we used TRC Lentiviral Human shRNA systems encoding a control shRNA or shRNA targeting METTL3 to generate shControl or shMETTL3 stable HEC-1-A cell line

value: HEC-1-A knockdown METTL3 stable cell line

tag: antibody

value: no IP (input RNA)


title: HEC-1-A wtMETTL14-IP

description: RNA IP against m6A

value: HEC-1-A wild type METTL14 stable cell line

value: m6A-antibody (202003; Synaptic Systems)


title: MM060

value: Fibroblast


title: MM040


title: HEC-1-A shMETTL3-IP

description: RNA IP against m6A


title: HEC-1-A muMETTL14-IP

description: RNA IP against m6A

value: HEC-1-A mutant METTL14 (R298P) stable cell line


title: HEC-1-A muMETTL14-input

description: no IP (input RNA)


title: HEC-1-A shControl-IP

description: RNA IP against m6A

value: HEC-1-A knockdown control stable cell line


title: HEC-1-A wtMETTL14-input

description: no IP (input RNA)


title: 41-tumor-input

description: no IP (input RNA)

source_name: endometrial tissue samples

tag: disease

value: endometrial cancer


title: 42-tumor adjacent-IP

description: RNA IP against m6A


title: 41-tumor-IP

description: RNA IP against m6A


title: MM050


title: MM042


title: 35-tumor-input

description: no IP (input RNA)


title: 36-tumor adjacent-input

description: no IP (input RNA)


title: c+b2 control cell line add bFGF treatment

city: Wenzhou

first: Yuanhu

last: Xuan

address: Chashan High School District

department: Medical School

institute: wenzhou medical university

data_processing:
Mapping of single-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent ofbases with qualities of <13.
The clean reads were then aligned to human genome (version: GRCH38) using the MapSplice program (v2.1.6). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 15 --ins 6 --del 6 --non-canonical) to provide the largest information on the AS events.
We applied DEseq algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) Fold Change>1.5 or <0.667; ii) FDR<0.05. [3] Volcano Plot was drawn by the R based on the differentially gene analysis and the color was determined by the filtering criteria.
Genome_build: GRCH38
Supplementary_files_format_and_content: RPKM for each sample

source_name: human dermis fibroblast

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately.The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies)

value: dermis fibroblast

value: wild type


title: c+b1 control cell line add bFGF treatment


title: c+b3 control cell line add bFGF treatment


title: c2 control cell line


title: c1 control cell line


title: 1834-tumor-IP

description: RNA IP against m6A


title: c3 control cell line


title: 36-tumor adjacent-IP

description: RNA IP against m6A


title: 35-tumor-IP

description: RNA IP against m6A


title: 1820-tumor-input

description: no IP (input RNA)


title: 1642 tumor adjacent-input

description: no IP (input RNA)


title: 1642 tumor adjacent-ip

description: RNA IP against m6A


title: 1820-tumor adjacent-input

description: no IP (input RNA)


title: 1642 tumor-input

description: no IP (input RNA)


title: 1834-tumor adjacent-input

description: no IP (input RNA)


title: 1806-tumor-input

description: no IP (input RNA)


title: 1834-tumor adjacent-IP

description: RNA IP against m6A


title: 1820-tumor adjacent-IP

description: RNA IP against m6A


title: 1806-tumor adjacent-IP

description: RNA IP against m6A


title: 1820-tumor-IP

description: RNA IP against m6A


title: HEK293 Harr

first: Yiwen

last: Chen

state: Texas

address: 1400 Pressler St

department: Bioinformatics and computational biology

institute: UT MD Anderson Cancer Center

description: HEK293 Ribosome profiling treated with harringtonine

data_processing:
Library strategy: Ribosome profiling
Fastq reads were trimmed and mapped to human rRNA sequences using bowtie allowing 2 mismatches.
Unmapped reads were mapped to human genome GRCh38 with Ensembl gene annotation release 83 using STAR with parameters ‘--outSAMattributes All --outFilterMismatchNmax 2 --alignEndsType EndToEnd --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 20000 --outMultimapperOrder Random --outSAMmultNmax 1’
Reads with mapQ=0 or NH>5 were filtered out and only primary loci are counted.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Ensembl gene id, gene symbol, length and raw counts

molecule: cytoplasmic RNA

source_name: HEK293 cells

growth_protocol: HKE293 cells were grown in high-glucose DMEM supplemented with 10% fetal bovine serum, penicillin and streptomycin at 37℃ under an atmosphere of 5% CO2.

extract_protocol: For CHX treatment, HEK293 cells were treated with CHX (Sigma-Aldrich, final concentration 0.1mg/ml) for 1 minutes. For Harr treatment, the cells were firstly treated with Harr (LKT Laboratories, final concentation 2 μg/ml) for 2 minutes at 37℃ in the incubator and then proceed CHX treatment. In-dish cell lysis were performed using Mammalian Lysis Buffer (including CHX at a concentration of 0.1mg/ml). Then 600 μl of lysate were taken and 15 ul of RNase I (100 U/μl, Thermo Fisher Scientific) were added and the mixtures were incubated for 45min at room temperature followed by adding 15 μl SUPERaseIn RNase inhibitor (Thermo Fisher Scientific) to stop the reaction. Ribosome recovery were done by illustra MicroSpin S-400 HR Columns (GE Healthcare) and the Ribosomal Protected Fragments (PFFs) were purified by RNA Clean & Concentrator (Zymo Research). Ribosomal RNA was subtracted using Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat, Illumina). RPFs without ribosomal RNA were ran on a 15% Urea denaturing-PAGE gel, and the gel slides from 28nt~30nt were excised.


title: 1834-tumor-input

description: no IP (input RNA)


title: 1642 tumor-ip

description: RNA IP against m6A


title: iSLKr219_NoDox_CaptureHiC

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
Image processing, base calling, quality scoring (Phred), and sample demultiplexing were executed by HiSeq Control Software with Real Time Analysis (HCS 1.5/RTA 1.13) and CASAVA 1.8 software (Illumina; San Diego, CA).
Paired-end sequence data (FASTQ format) was processed to identify putative Capture Hi-C interaction products (di-tags) using the Capture Hi-C User Pipeline (HiCUP) (Babraham Bioinformatics; http://www.bioinformatics.babraham.ac.uk/projects/hicup/). By executing a series of Perl scripts, this performed identification of the Hi-C ligation junctions within the reads (BamHI or DpnII sites, depending on the experiment), read alignment, and removal of PCR duplicates and common Capture Hi-C artifacts. Subsequently, read pairs derived from the interacting fragments were output in SAM format. Within HiCUP, Bowtie 2 was used to align FASTQ data to the reference human (hg19) genome assembly and KSHV genome sequence (Human herpesvirus 8 strain JSC-1 clone BAC16, GenBank: GQ994935.1) and an in silico BamHI-digested reference genome. Hi-C output was then analyzed with HOMER (Hypergeometric Optimization of Motif EnRichment; http://homer.salk.edu/homer/interactions/) to generate a Capture Hi-C tag directory and for identification of significant interactions.
Genome_build: Human hg19 + HHV8/KSHV strain JSC-1 (GenBank: GQ994935.1)
Supplementary_files_format_and_content: Tab-delimited text files that contain information describing the coordinates of the interacting genomic regions, specifically the human chromosome number or KSHV genome, start location, and strand.

growth_protocol: TREx-(F3H3)-K-Rta BCBL-1 (TREx-K-Rta BCBL-1, which have tetracycline/doxycycline (Dox)-inducible expression of N-terminal Flagx3- and HAx3-tagged K-Rta, were cultured in complete RPMI 1640 (supplemented with 10% FBS) containing blasticidin (50 ug/ml) and hygromycin B (100 mg/ml). iSLK cells were maintained in DMEM medium containing 10% fetal bovine serum (FBS; complete DMEM), G418 (50 ug/ml), and hygromycin B (100 ug/ml) in the presence of 5% CO2. iSLK.r219 cells containing wild-type or mutant KSHV (BAC16) genomes were cultured in complete DMEM containing G418 (250 ug/ml), hygromycin (1000 ug/gml), and puromycin (1 ug/ml). All cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2 (v/v)

extract_protocol:
Chromatin prepared from KSHV-infected cells for the 3C procedure described above was used as input for Capture Hi-C. Briefly, infected TREx-K-Rta BCBL-1 or iSLK/r.219 cells (1 x 10^8) were fixed with formaldehyde, and the chromatin was digested with either BamHI or DpnII restriction enzyme and re-ligated under ultra-dilute conditions. DNA-protein crosslinks were reversed by incubation at 65°C overnight with 0.2% SDS. The DNA was then purified with the QIAquick PCR Purification Kit (Qiagen).
Capture Hi-C sequencing libraries enriched for KSHV genome re-ligation products were prepared from DNA samples obtained from chromosome conformation capture (3C) 3analysis of TREx-K-Rta BCBL-1 and iSLK.r219 cells. The DNA preparations were sheared to a mean fragment length of 250 bp using a Covaris E220 Focused-ultrasonicator (Covaris, Inc.) and sequencing libraries were then prepared from the DNA chimerae using the NEBNext DNA Library Prep Kit (New England BioLabs, Inc.). Target enrichment for KSHV genomic content was performed using a custom-designed KSHV genomic capture probe library and according to the manufacturer’s standard protocols (IDT, Coralville, Iowa). Briefly, in-solution hybrid capture was performed by hybridizing libraries (500 ng) with the KSHV genomic capture probe pool (3 pmol) in a mixture containing xGen 1X Hybridization Buffer, Cot-1 (5 µg), and xGen Universal Blocking Oligos at a temperature of 65°C for 4 hours. Hybridized targets were then bound to streptavidin-coupled magnetic beads (Dynabeads M-270 Streptavidin beads; Thermo Fisher Scientific) by incubation at 65°C for 45 minutes, and unbound DNA was removed by a series of high-stringency (65°C) and low-stringency (room temperature) washes. The KSHV genome-enriched Capture Hi-C library DNA was eluted and post-capture PCR enrichment performed with high-fidelity KAPA HiFi HotStart DNA Polymerase (Kapa Biosystems, Inc., Wilmington, MA) and purified with Agencourt AMPure XP magnetic beads. KSHV-enriched libraries were then validated with an Agilent 2100 Bioanalyzer, and quantitated with a Qubit fluorometer (Invitrogen) and by qPCR-based quantification (KAPA Library Quantification Kit).

treatment_protocol: TREx-(F3H3)-K-Rta BCBL-1 and iSLK.r219 cells were treated with doxyclyine for 24 hours in order to induce K-Rta expression, which consequently triggers KSHV reactivation.

value: human gingival endothelial cells

value: Stable doxycycline-inducible K-Rta expression and infected with rKSHV.219

tag: passages

tag: restriction enzyme for dna digestion

value: BamHI

tag: capture library

value: KSHV


title: BCBL1_TREx-KRta_NoDox_CaptureHiC

source_name: TREx-(F3H3)-K-Rta BCBL-1 cells

value: human primary effusion lymphoma

value: KSHV-positive human B cell lymphoma cells


title: 1806-tumor-IP

description: RNA IP against m6A


title: iSLKr219_Dox_CaptureHiC


title: Input DNA

description: FLAG-K-Rta narrow_Peaks.bed

data_processing:
Image processing, base calling, quality scoring (Phred), and sample demultiplexing were executed by HiSeq Control Software with Real Time Analysis (HCS 1.5/RTA 1.13) and CASAVA 1.8 software (Illumina; San Diego, CA).
FASTQ-formatted ChIP-Seq reads were aligned to the human hg19 reference genome and reference KSHV genome sequence (Human herpesvirus 8 strain JSC-1 clone BAC16, GenBank: GQ994935.1) with Bowtie 2.
Peak finding was performed using MACS2 (Model-based Analysis for ChIP-Seq) following the developer’s manual and default settings, including a minimum FDR (q-value) cutoff of 0.05.
Genome_build: Human hg19 + HHV8/KSHV strain JSC-1 (GenBank: GQ994935.1)
Supplementary_files_format_and_content: Tab-delimited text files that include information pertaining to the peaks identified, including location (chromosome,  start site, end site), length, summit, tags, -10*log10(pvalue), fold_enrichment, and FDR(%) and were prepared from the MACS2 output files.

growth_protocol: TREx-(F3H3)-K-Rta BCBL-1 ( TREx-K-Rta BCBL-1) cells, which have tetracycline/doxycycline (Dox)-inducible expression of N-terminal Flagx3- and HAx3-tagged K-Rta, were cultured in complete RPMI 1640 (supplemented with 10% FBS and L-Glutamine) containing blasticidin (50 mg/ml) and hygromycin B (100 mg/ml). The cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2 (v/v).

extract_protocol:
Following treatment with doxycycline, cells (1 x 10^8) were fixed with formaldehyde, lysed, and chromatin DNA was sonicated to an average size of ~300 bp using a Diagenode Bioruptor. Chromatin immunoprecipitation (ChIP) of K-Rta-associated chromatin was performed with anti-FLAG M2 monoclonal antibody (10 ug).  Subsequently, DNA was isolated with the QIAquick PCR Purification Kit (Qiagen) from the FLAG-K-RTa immunoprecipitates (ChIP DNA) and from input DNA controls.
ChIP-enriched and input DNA samples (1 ng) were used to generate indexed, Illumina-compatible libraries with the KAPA LTP Library Preparation Kit (Kapa Biosystems, KK8230) according to manufacturer’s recommendations for end repair and A-tailing, adapter ligation, size selection, and library amplification.

treatment_protocol: Expression of Flag- and HA-tagged K-Rta was induced by treatment of TREx-(F3H3)-K-Rta BCBL-1 cells with Dox (1 µg/ml) for 24 hours.


title: 1806-tumor adjacent-input

description: no IP (input RNA)


title: HEK293 RPF Rep2

source_name: Human embryonic kidney cell line


title: HEK293 RPF Rep1


title: GA3 (+EPA)_20°C

city: Düsseldorf

first: Heidrun

middle: Sigrid

last: Windisch

state: NRW

address: Universitätsstrasse 1

department: Cell Biology and Zoology

institute: Heinrich-Heine-University

data_processing:
Raw sequencing data were clipped and trimmed using Trimmomatic (Bolger, Lohse, & Usadel, 2014) to remove bias of sequencing adapters and low quality regions at the beginning and end of sequences.
Reads were mapped to the Daphnia magna genome assembly version 2.4 (NCBI BioProject accession No. PRJNA298946), containing 26.646 translations (open access since April 2016). Mapping was conducted using RSEM v.1.2.31 (Li & Dewey, 2011) connected to bowtie2 (Langdon, 2015) to generate FPKM outputs for transcript analysis.
MeV software v. 4.8.1 (Howe, Sinha, Schlauch, & Quackenbush, 2011) connected to edgeR (Robinson, McCarthy, & Smyth, 2010) was used for the analysis and clustering of differential gene expression. One-Way ANOVA was used on the basis of normalized FPKM values generated with RSEM (Li & Dewey, 2011) to identify differently expressed genes among all treatments.
The available annotation from the Daphnia magna genome was enriched through assignments from the artNOG (EggNOG 4.0) database. COG categories as well as functional descriptions were added to the existing annotation.
Genome_build: NCBI BioProject accession No. PRJNA298946
Supplementary_files_format_and_content: txt files were generated using RSEM. FPKM values were used for the analysis of DGE in MeV

organism: Daphnia magna

source_name: pool of 3 whole specimen

growth_protocol: Daphnia magna clone P132.85 originating from the pond Driehoek in Heusden (The Netherlands; N51°44'01", E5°08'17") were cultured at 20°C in aged, aerated and sterile-filtered (45 µm) tap water under dim light conditions. The animals were kept at a maximum density of 15 individuals per L under non-limiting food conditions by feeding them 2 mg carbon per L of Acutodesmus obliquus (formerly: Scenedesmus obliquus) during pre-culture every second day by transferring them into fresh glasses with food.

extract_protocol:
In total, 5 treatment groups were prepared for sequencing with 3 replicates each. Replicate sample pools consisted of 5 specimens to ensure appropriate amounts for RNA extraction and comparability. Total RNA was extracted using the NucleoSpin RNA extraction kit (Machery und Nagel, Düren/Germany) according to the manufacturer´s instructions. In addition, traces of remaining genomic DNA were removed using the Turbo DNA-free Kit (Invitrogen, Karlsruhe/Germany) in line with the manufacturer´s manual. The quality of the isolated RNA was monitored using capillary electrophoresis on a Bioanalyzer (Agilent Technologies, Santa Clara/USA). Only samples with OD280/OD260≤ 2.0,  OD280/OD230 ≤ 2.0 and RIN ≤ 8.0 were used for sequencing.
Clean-up of mRNA, cDNA library construction as well as sequencing was conducted at the University of Cologne’s Cologne Centre for Genomics (CCG)

treatment_protocol: Juvenile D. magna for experiments originated from mothers that carried the third clutch of parthenogenetic offspring. Neonates (within 8 h after release from the mothers’ brood pouch) were randomly distributed to jars containing 600 ml tap water, the respective food and if scheduled, supplements. In total we analysed 5 treatments with RNAseq: GA, GA+ EPA, CY, Cy + EPA, and CRY. All D. magna individuals were raised until they deposited the first clutch of eggs into their brood pouch (reaching maturity) before sampling. Daphnia were rinsed twice with deionized water before blotting them dry with lint-free tissue. Whole animal samples were shock-frozen in liquid nitrogen and stored at -80°C thereafter until further experimentation.

tag: developmental stage

value: mothers reproducing parthenogenetically, carrying the first clutch of eggs

value: GA +EPA

tag: temperature


title: 42-tumor adjacent-input

description: no IP (input RNA)

value: no IP (input RNA)


title: GA2 (+EPA)_20°C


title: CY2 (+EPA)_20°C

value: CY +EPA


title: GA2 (-EPA)_20°C

value: GA


title: GA4 (+EPA)_20°C


title: K-Rta-FLAG ChIP-Seq

description: FLAG-K-Rta narrow_Peaks.bed

value: FLAG M2 (Sigma, F1804)


title: GA3 (-EPA)_20°C


title: BCBL1_TREx-K-Rta_Dox_CaptureHiC


title: CY2 (-EPA)_20°C

value: CY


title: CY1 (-EPA)_20°C


title: CY3 (+EPA)_20°C


title: CRY2_20°C

value: CRY


title: Mock #3

city: Ithaca

first: Joel

middle: D

last: Baines

state: NY

address: 235 Hungerfordhill Rd

institute: Cornell University

data_processing:
Library strategy: PRO-seq
All processing steps were done using the Danko lab template for PRO-seq alignment/QC found at https://github.com/Danko-Lab/utils/tree/master/proseq with instructions at https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md
Pre-processing reads and sequence adapter trimming are done with cutadapt
Reads are mapped to the bwa index reference genome using bowtie
BAM files are converted to BigWig using Kentsource
BigWig can be viewed using IGV, and BAM files analyzed with DESeq2 statistics using SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/.  SeqMonk data is reported in Xcel files as supporting/supplemental information in the publication
Genome_build: hg 38 (Samples 1-12), and dm3 (Samples 7-12)
Supplementary_files_format_and_content: big wig

source_name: HEp-2 Cells

growth_protocol:
Hep-2 cells--grown at 37 degrees C in 5% CO2 in DMEM 10% Newborn calf serum supplemented with Penn/Strep
Drosophila S2 cells--grown at 20 degrees C on bench top in Schneider's Drosophila Medium with 10% FBS and Penn/Strep

extract_protocol:
Nuclei isolation followed by Nuclear Run-on in the presence of biotinylated nucleotides (A, U, G, C).  Biotinylated transcripts were isolated using streptavadin coated magnetic beads
Libraries were constructed following the protocol outlined by Mahat et al. 2016. "Base-pair-resolution genome-wide mapping of active RNA Polymerases using precision nuclear run-on (PRO-seq).  Nature Protocols. Aug 11(8):1455-76 doi:10.1038/nprot.2016.086

treatment_protocol: Hep-2 cells were infected with HSV-1 F strain at an MOI of 5.  S2 cells were left untreated before nuclei isolation, and spiked-in to isolated Hep-2 nuclei (1 drosophila nuclei/10,000 Hep-2 nuclei)

value: lung epithelial cells from a carcinoma

tag: infection

value: mock

tag: processing

value: nuclei isolation


title: CY1 (+EPA)_20°C


title: CRY1_20°C


title: Mock #2


title: CY3 (-EPA)_20°C


title: HSV-1 #2


title: HSV-1 #1


title: HSV-1 #3


title: Mock #1


title: CRY5_20°C


title: Mock w/Dro #3

organism:
Drosophila melanogaster
Homo sapiens

source_name: HEP-2 Cells and Drosophila S2 Cells

value: epithelial, late stage embryo


title: Mock w/Dro #1


title: Mock w/Dro #2


title: HSV-1 w/Dro #3


title: HSV-1 w/Dro #2


title: GA1 (-EPA)_20°C


title: HSV-1 w/Dro #1


title: Δjjj1Δpdr1_B

status: Public on Jan 21 2018

city: Memphis

first: Katherine

middle: S

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

data_processing:
Individual sample fragments were concatenated to form the whole sample fastq file.
Files were run through FASTQC to check data quality.  Any reads with a phred score<20 were trimmed.
Read counts for each sample were normalized using transcripts per kilobase million (TPM) method.
Genome_build: Reads were aligned to the C. glabrata CBS138 reference transcriptome using RNA-Star long method. Read counts for each sample were normalized using transcripts per kilobase million (TPM) method.
Supplementary_files_format_and_content: Processed data is in the form of an Excel matrix. Reads were aligned to the C. glabrata CBS138 reference genome for biological Samples A and B for the wild type and mutant strains. Normalized read counts aligned to each genomic feature are listed for each sample.

organism: Nakaseomyces glabratus

source_name: yeast

growth_protocol: Cultures were maintained on YPD agar plates.  To initiate cultures, a single colony was used to inoculate a 2-ml culture of YPD liquid medium, and this culture was grown to saturation overnight at 30 degrees Celsius.  An aliquot of the overnight cultures was then used to inoculate 20 ml YPD liquid culture to achieve a final OD(600)= 0.2.  These cultures were then grown at 30 degrees Celsius for 3 hours at which time cells were collected by centrifugation, supernatants removed, and cell pellets frozen at -80 degrees Celsius until RNA isolation.

extract_protocol:
RNA was isolated using the hot phenol method of RNA isolation.  RNA concentrations were determined using a Nanodrop spectrophotometer, and RNA integrity was verified using a Bioanalyzer 2100.
Barcoded libraries were prepared using the Lexogen mRNA Sense kit for Ion Torrent according to the manufacturer's standard protocol.

treatment_protocol: There was no treatment of cells beond the listed growth conditions

tag: fluconazole mic (mg/ml)

tag: genotype/variation

value: jjj1delta ::FRT/pdr1delta ::FRT


title: Δjjj1_B

value: jjj1delta ::FRT


title: wox11 replication2

city: Wuhan

first: Saifeng

last: Cheng

state: Hubei

address: No.1,Shizishan Street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

data_processing:
Illumina software Hiseq Control/RTA used for basecalling.
Sequence reads were filtered using Trimmomatic (http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-0.35.zip).
Clean data were mapped against the MSU 7.0 rice genome with corresponding annotation by Tophat2.0 (http://tophat.cbcb.umd.edu/) using default parameters.
Data were analyzed for differentially expressed genes using Cufflinks (http://cole-trapnelllab.github.io/cufflinks/releases/v2.2.1/). Genes with an expression change fold >2 with P <0.05 were defined as differentially expressed.
Genome_build: MSU 7.0
Supplementary_files_format_and_content: xls files include FPKM values for each Sample

organism: Oryza sativa Japonica Group

source_name: Hwayoung shoot apex

growth_protocol: Seeds with indicated genotypes were surface-sterilized and germinated in media containing 0.3% phytagel supplemented with 2% (w/v) sucrose at 28 °C (in light) and 24 °C (in dark) with a 14 h light/10 h dark cycle for 5 days, then the shoot apex were taken  with a scalpel under a dissecting microscope.

extract_protocol:
Shoot apex were taken in liquid nitrogen. TRIzol-based RNA extraction method was conducted (Invitrogen, 10296-010). 1 to 4 µg of total RNA were used for library construction using the TruSeq RNA Sample Preparation Kit from Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 2-3 mm shoot apex from 5-day-old shoot

tag: genotype

value: wox11 mutant


title: jmj705 replication1

value: jmj705 mutant


title: jmj705 replication2


title: Δjjj1_A


title: wox11 replication1


title: SM1_A

description: parent clinical isolate

value: parent clinical isolate


title: HY replication1

value: wild type


title: SM1_B

description: parent clinical isolate


title: HY replication2


title: DMSO

status: Public on Jan 20 2018

city: Kyoto

first: Masamichi

last: Ishiai

state: Kyoto

address: Yoshidakonoe-cho, Sakyo-ku

department: Radiation Biology Center

country: Japan

institute: Kyoto University

data_processing:
Basecalls performed using illumina package bcl2fastq v1.8.4.
Low quality (score <20) bases were trimmed from both ends of the reads. Trimmed reads shorter than 40nt or containing many (>20%) low-quality (score <20) bases were discarded. Read pairs were retained for the subsequent analysis only if both ends passed.
The filter-passed reads were aligned to the human genome hg19 using TopHat2 with --no-novel-juncs option.
The reads mapped in a proper pair were extracted using SAMtools with -f 3 option.
The mapped reads were counted for each known gene using HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: The number of mapped reads for genes. Each column represents as follow; control, the number of mapped reads under DMSO condition; case, the number of mapped reads under APH condition; gene_id, Ensembl gene ID; gene_name, HUGO gene symbol; seqnames, chromosome number; start, transcription start site; end, transcription termination site; width, transcript length.

source_name: U2OS cells exoressing FANCD2- 3x FLAG

growth_protocol: Cells were cultured in DMEM supplemented woth 10% FCS in 5% CO2 at 37 degree.

extract_protocol:
Total RNA was isolated by using Rneasy Kit (QIAGEN).
RNA libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold rRNA Removal Kit (Illumina) according to the instructions. Libraries were sequenced on the Illumina Hiseq following the manufacturer's protocols (100 bp paried-end run).

treatment_protocol: Cells are treated at 0.4 micro M (for APH), or untreated (for DMSO) for 24 hours.

value: non treated (solvent control)


title: input DNA

city: Basel

first: Renato

last: Paro

address: Mattenstrasse 35

department: Department of Biosystems Science and Engineering (D-BSSE)

country: Switzerland

institute: Swiss Federal Institute of Technology Zurich (ETHZ)

description: ChIP-Seq input from S2-DRSC cells

data_processing:
base-calling with RTA 1.17.21.3
demultiplexing: configureBclToFastq.pl --with-failed-reads --fastq-cluster-count 50000000 --output-dir ../../../Unaligned_7 --sample-sheet ./SampleSheet_7_C4DK2ACXX.csv --use-bases-mask Y51,I6n --no-eamss
Genome-alignment to dm3-BDGPR5 with Bowtie 0.12.7 using -n 1 -l 20 -m 100 --best
bam file conversion using Samtools 0.1.9
Peak calling using MACS 1.4 and default parameters
Genome_build: dm3-BDGP Release 5
Supplementary_files_format_and_content: BED file containing peaks called

source_name: S2-DRSC cell line

growth_protocol: S2 cells were grown under standard conditions in S2 media supplemented with 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and Su(H)-DNA complexes were isolated with antibody.
Sequencing libraries were prepared with the NEB Next ChIP-Seq Library Prep Kit according to NEB’s instructions (New England Biolabs, Ipswich, MA, USA). After adapter ligation, library fragments of 250-350 bp were isolated and PCR amplified with 18 cycles. Library fragments were purified, loaded on an Illumina flow cell for cluster generation and sequenced on the HiSeq 2000 (TruSeq cBot-HS v3 and TruSeq SBS Kit v3) following the manufacturer’s protocols (Illumina, San Diego, CA, USA)

tag: strain

value: DRSC

tag: chip antibody


title: APH

tag: treatment

value: APH treated


title: Su(H)_ChIPSeq

description: ChIP-Seq for endogenous Su(H) in S2-DRSC cells

value: goat anti-Su(H) pAb (Santa Cruz Biotechnology, catalog# sc-15813, lot# I1704)


title: Primary human melanocytes, scrambled siRNA-treated

city: Seoul

first: Sang Ho

last: Oh

address: 50-1 Yonsei-ro

department: Dermatology

country: South Korea

institute: Yonsei University College of Medicine

description:
PHM_scrambled_siRNA
Gene expression data from primary human melanocytes treated with scrambled siRNA.

data_processing:
Reads were quality trimmed and filtered using the NGS QC toolkit v2.3 to remove reads containing low-quality bases.
After preprocessing, the RNA sequenced reads were mapped to the human genome using RSEM with bowtie2 v2.0.0-beta7.
FPKM (fragments per kilobase of exon per million fragments mapped) for RNA-Seq were calculated using RSEM.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Wig files were generated using RSEM.

growth_protocol: Melanocytes were incubated (37°C, humidified 5% CO2) in MGM-4 growth media (Lonza, Walkerville, MD, USA), using cells from passages 3-8 for experimentation.

extract_protocol:
Total cellular RNA was isolated using an RNeasy Plus Mini Kit (QIAGEN, Valencia, USA).
An RNA sequencing library was prepared using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA).

treatment_protocol: To suppress Keap1, primary human melanocytes were transfected (TransIT-TKO reagent; Mirus Bio, Madison, WI, USA) as specified by the manufacturer with 10 nM of siRNA (Bioneer Corp, Daejeon, South Korea). An equivalent amount of scrambled siRNA was used as a negative control.

tag: gender

value: Male

tag: age

value: 12 years

tag: tissue

value: Foreskin

tag: cell type

value: Melanocytes

value: Scrambled siRNA


title: H9 Input

city: Irvine

first: Peter

middle: J

last: Donovan

address: Gross Hall, Rm 3006, 845 Health Sciences Road

institute: University of California, Irvine

data_processing:
Reads were mapped with Bowtie 0.12.8 using -v 2, -S, -k 1 -m 1 parameters to report only uniquely mapped reads with at most 2 mismatches.
SAM files outputed from Bowtie were converted to bam using Samtools version 0.1.19.
TCF7L1 ChIP BAM files were randomly downsampled (using Samtools -view -b -s) so they contain fewer reads than Input, as suggested by ENCODE.  Samtools was also used to remove PCR duplicates (using the rmdup parameter).
Genome_build: hg19

source_name: H9 human ES cells

growth_protocol: H9 human embryonic stem cells were grown under feeder-free conditions on Geltrex (life technologies) with mTeSR1 medium (StemCell Technologies). The cells were harvested for ChIP once they reached ~90% confluence.

extract_protocol:
Nuclei were isolated and treated with micrococcal nuclease (2,000 U/ul) for 25 minutes at 37 degrees to digest chromatin. Nuclie were briefly sonicated, clarifed and then TCF7L1-DNA complexes were isolated by immunoprecipitation.
Illumina sequencing libraries were constructed using the Bioo Scientific NEXTflex Rapid DNA-Seq kit and NEXTflex DNA barcodes (Bioo Scientific Corporation, Austin TX).  Ten nanograms of input DNA was taken into end repair, adenylation and adapter ligation reactions.  The adapter ligated product was cleaned up without  library size selection using Agencourt AMPure XP beads (Beckman Coulter, Inc. Brea, CA).  The cleaned ligated DNA was amplified by 15 PCR cycles to enrich for adapter ligated products.  The amplified PCR product was cleaned by AMPure XP beads and the library was size selected using the Blue Pippin 2% agarose gel with broad range settings (206bp – 561bp) (Sage Science, Inc. Beverly, MA).  The libraries were quantified by Kapa qPCR  (Kapa Biosystems, Inc. Wilmington, MA).   The libraries were denatured and diluted to 13pM for onboard clustering on the Illumina HiSeq 2500 (Illumina Inc., San Diego, CA) using rapid run mode and SR50 chemistry.  The HiSeq 2500 real time analysis software was version 1.17.21.3 and the HiSeq control software version was 2.0.10.0.

value: H9 human embryonic stem cells (passage 44)

tag: cell state

value: Undifferentiated

tag: antibody

value: TCF7L1 (Santa Cruz, sc-8635)


title: H9 TCF7L1 ChIp-seq Replicate 2


title: H9 TCF7L1 ChIP-seq Replicate 1


title: Δjjj1Δpdr1_A

value: jjj1delta ::FRT/pdr1delta ::FRT


title: Pancreatic cancer-associated fibroblasts, 2

city: La Jolla

first: Paul

middle: A

last: Insel

address: 9500 Gilman Drive

department: Pharmacology

institute: UC San Diego

description: Monolayer of cells at low passage (~P5)

data_processing:
FASTQ files were checked for quality via FASTQC
Alignment to Human genome via STAR, on the Illumina Basespace platform
Quantitation of Normalized gene expression in FPKM via Cufflinks
Normalized gene abundance estimation in CPM via EdgeR
Genome_build: Human, hg38, Refseq
Supplementary_files_format_and_content: Tab-delimited files containing gene expression in FPKM

source_name: Pancreas

growth_protocol: Cells were cultured in 4.5g/L glucose Dulbecco’s Modified Eagle’s Medium (DMEM), 30% fetal bovine serum (FBS), 1ug/ml fetuin, 20ng/ml EGF, 2mM glutamate, 1mM sodium pyruvate, non-essential amino acids (AAs), 100 I.U./ml penicillin (pen), 100µg/ml streptomycin (strep), 0.25µg/ml amphotericin B

extract_protocol:
RNA was isolated via the Qiagen Rneasy mini Kit, with digestion on-column using DNase-1
Illumina Truseq Stranded mRNA

treatment_protocol: Untreated cells at low passage (~P5) were used for profiling


title: Pancreatic cancer-associated fibroblasts, 3

description: Monolayer of cells at low passage (~P5)


title: Pancreatic cancer-associated fibroblasts, 5

description: Monolayer of cells at low passage (~P5)


title: APH/WCL

data_processing:
Basecalls performed using Illumina CASAVA v1.8.
Adapter sequences were trimmed using cutadapt v1.1 with -n 2 option.
Reads with many (>80%) low-quality (score <20) bases were discarded. Low quality (score <20) bases were trimmed from both ends of the reads. Reads shorter than 20nt were discarded.
The filter-passed reads were aligned to the human genome hg19 using bowtie v0.12.7 with --maxins 600 --seedlen 20 --all options.
Peak calling was performed using MACS v1.4.2 with the threshold of p-value < 1e-5. The detected peaks were annotated using SnpEff v3.2.
Genome_build: hg19
Supplementary_files_format_and_content: wig files including fragment pileup were created using MACS v1.4.2 with a option -w.

source_name: U2OS cells expressing FANCD2-3xFLAG

growth_protocol: U2OS cells were cultured in DMEM supplemented with 10% FCS in 5% CO2 at 37 degree.

extract_protocol:
Lysates were clarified from sonicated nuclei and FANCD2-DNA complexes were isolated with antibody.
After franmentation to 200 bp using covaris, DNA libraries were prepared using the NEBNext ChIP-Seq library prep reagent set for Illumina (NEB #E6200) and the NEBNext multiplex oligos for Illumina (NEB #E7335 and #E7500) according to the instructions. Adapter ligated DNA was PCR amplified for 15 cycles. Libraries were sequenced on the Illumina Genome Analyzer IIx following the manufacturer's protocols (75 bp paried-end run).

value: whole cell lysate (wcl:input control)


title: Pancreatic Stellate Cells

description: Monolayer of cells at low passage (~P5)

value: Pancreatic Stellate Cells


title: DMSO/WCL

value: DMSO control


title: Dnmt3a WT rep2

status: Public on Jan 19 2018

city: Research Triangle Park

last: Wade

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

description:
Dnmt3a_WT.mapped_depth.bigWig
Dnmt3a_WT.pctMeth.bigWig

data_processing:
Raw sequenced reads were filtered to retain only read pairs with average base quality score of at least 20 for each read.  Sequenced reads were trimmed to remove the final base from the 3' end.
Reads were mapped against mm9 reference genome with Bismark v0.14.0 (parameters: -X 10000 --non_bs_mm -n 2 -l 50 -e 70 --chunkmbs 1024), using Bowtie v0.12.8 as the underlying alignment tool. PE150 reads unmapped at full length were trimmed to PE75 and re-submitted to Bismark with the previously described parameters.
All mapped hits from the same animal were concatenated, then duplicates removed with the Bismark deduplication script (deduplicate_bismark_alignment_output.pl).
Mapped reads were then processed as follows:  1. Separated by source strand (plus or minus).  2. Clipped positions with positional methylation bias (identified using bismark_methylation_extractor, --mbias_only option).  3.  Trimmed redundant mapped bases from overlapping mapped reads in a read pair to avoid bias in quantification of methylation status.
Data from replicate animals were combined with MergeSamFiles.jar from the Picard suite (v1.119).
The CpG context of genomic cytosines was considered confirmed if at least 95% of mapped bases at the N+1 position were 'G' with a total depth of at least 5; both the plus and minus strand data were required to pass these criteria. Assessment of cytosine context was performed after merging all animals in the study.
Percent methylation at each genomic cytosine was calculated as methylated cytosine bases / total cytosine bases; reciprocal CpG sites (i.e. plus and minus strand) were combined for these calculations. Sites for which the CpG context of the reference cystosine could not be confirmed were excluded.
Mapped reads were converted to aggregate coverage by BEDtools v2.24.0 genomeCoverageBed (to generate bedGraph files) and then UCSC command-line utilities bedGraphToBigWig (to generate bigWig files).
DMRs were identified via MOABS v1.3.2 using default parameters except ‘--minNominalDif=0.2’.
Genome_build: mm9
Supplementary_files_format_and_content: Aggregate coverage by mapped reads (merged for all 3 replicates, both strands); format = bigWig.
Supplementary_files_format_and_content: Percent methylation at single-base resolution; calculations are done with merged replicate animals & combined strand information. Format = bigWig.
Supplementary_files_format_and_content: Differentially methylated regions (DMRs) between null and WT. Format = BED.

source_name: naïve splenic B cells

growth_protocol: Animals were housed in a specific pathogen-free environment at the National Institute of Environmental Health Sciences (NIEHS). All animal experiments were approved by the NIEHS Institutional Animal Care and Use Committee and were performed according to NIH guidelines for the care and use of laboratory animals.

extract_protocol:
Spleen was harvested, and B220+IgD++GL7- B cells were sorted to a purity of 98-99%. Using the Trizol reagent, genomic DNA was extracted from the organic phase and further purified by performing Phenol-chloroform extractions.
For each sample, 1500 ng intact genomic DNA and 1.5 ng unmethylated lambda DNA (Promega) were fragmented using a Covaris S220 Focused-ultrasonicator. Sequencing libraries were prepared using the NEXTflex Bisulfite-Seq Kit (BIOO Scientific) with a starting input of 1000 ng and using agarose gel size selection. Bisulfite conversion was performed using an EpiTect Bisulfite Kit (Qiagen). Bisulfite converted DNA product was PCR amplified for 10 cycles using KAPA HiFi Uracil+ Ready Mix (Kapa Biosystems). After library construction, all six libraries were equally multiplexed and sequenced using the Illumina NextSeq500 platform in paired-end format for 76 or 151 cycles at the NIEHS Epigenomics Core Laboratory.

value: B6;129 (mixed background of C57BL/6 and 129)

tag: Sex

value: male

value: 2-4 months

value: spleen

value: naive B cells

tag: markers

tag: stimulus