title: D4_a

city: Guangzhou

first: Yu-Jing

last: Zhang

address: No.2 Zhongshan Road #58

institute: Sun Yat-sen University

description:
mRNA_expression
lncRNA_expression

data_processing:
Purified total RNA was subjected to rRNA removal, fragmentation, first and second-strand cDNA synthesis, end repair, poly-A tail addition, ligation, enrichment and other steps to construct sequencing sample library. High-throughput RNA paired-end sequencing was then performed using the Illumina Hiseq Xten platform (Illumina, lnc., CA, USA). The unqualified reads, with low overall or end quality and containing sequencing primers, etc. were removed from the raw reads to obtain clean reads, from which rat ribosomal RNAs were further filtered. The Spliced Mapping algorithm in Hisat2 (version: 2.0.4) was applied to map the above processed reads to the rat reference genome (ftp://ftp.ensembl.org/pub/release-100/fasta/rattus_norvegicus/dna/).
With use of the Stringtie software (version: 1.3.0), the mapped reads were assembled to construct the transcripts, which were then matched to the reference databases (NOCODE and Ensembl) using the GffCompare (version: 0.9.8) software to obtain annotation. The unmatched transcripts were performed the potential novel lncRNA prediction with the criteria as follows: (1) transcript length >= 200 bp AND exon >= 2, (2) the predicted ORF < 300 bp, (3) Coding Potential Calculator (CPC) score < 0 AND Coding-Non-Coding Index (CNCI) score < 0 AND with no significant difference using Pfam comparison. The Perl script was then applied to locate the position of the above novel lncRNAs on the chromosomes and to make annotation.
With use of Stringtie software, the Fragment numbers of each gene were counted, which were then normalized by TMM (trimmed mean of M values) method. Finally the FPKM value of each known or newly predicted lncRNA was counted using perl script, where the lncRNA ID starting with NON is the known lncRNA in the NONCODE database, the ID starting with ENS is the known lncRNA in the Ensembl database, and the ID starting with MSTRG is the newly predicted lncRNA. The edgeR package was then used to analyze the differentially expressed genes between samples (Control vs D4 and Control vs D7). The screening criteria for differentially expressed genes are as follows: (1) q-value (the corrected p-value) < 0.05, (2) the absolute value of fold change >= 2.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include count number and FPKM values of each sample

organism: Rattus norvegicus

source_name: sciatic nerve

extract_protocol: none provided by the submitter

value: 4 days post sciatic nerve crush


title: D7_b

status: Public on Apr 30 2021

type: SRA

country: China

description:
mRNA_expression
lncRNA_expression

library_source: transcriptomic

molecule: total RNA

tag: treatment

value: 7 days post sciatic nerve crush


title: D7_a

description:
mRNA_expression
lncRNA_expression


title: 7000AA_MSCB-151

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:
Primary data analysis was carried out with the standard Illumina pipeline following the manufacturer's protocol. Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
MARS-Seq libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the mouse or human genome reference.
Gene quantification was performed using UMI information to correct for amplification biases.
Genome_build: human: GRCh38. Gencode release 26.  Mouse: GRCm38. Gencode release M15.
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as UMI counts for each cell (columns).

molecule: polyA RNA

organism: Mus musculus

source_name: bladder

extract_protocol:
Short-term cultured pancreatic islet cells were isolated from a healthy pancreas donor. The culturing process favor the enrichment of pancreatic islet cells while large eliminating endothelial and immune cell types. Primary bladder epithelial cells were isolated by FACS (CD45-, CD140a-, CD31-, Ter119-) from a healthy mouse.
To construct single cell libraries from polyA-tailed RNA, we applied massively parallel single-cell RNA sequencing (MARS-Seq; Jaitin et al., Science 2014). This methodology generates paired-end reads where read 1 contains the transcript sequence and read 2 the cell and UMI barcodes (bases 1 to 6 and 7 to 14, respectively). Briefly, single cells were FACS-sorted into 384-well plates, containing lysis buffer and reverse-transcription (RT) primers. The RT primers contained the single cell barcodes and unique molecular identifiers (UMIs) for subsequent de-multiplexing and correction for amplification biases, respectively.

tag: cell type

value: primary bladder epithelial cell


title: Con_a

description:
mRNA_expression
lncRNA_expression

value: normal control


title: 7000AA_MSCB-150


title: 7000AA_MSCB-149


title: 7000AA_MSCB-147


title: Flower florets (FP) repeat3  (bisulfite-seq)

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

library_source: genomic

data_processing:
In the first step we created methylated reference genome for bismark alignment using bismark_genome_preparation with default parameters. Then bismark software was used using the pair-end reads (FASTQ) using default parameters to get the bam alignment files. Then we extract the methylation information we use Bismark_methylation_extractor -p --no_overlap --comprehensive --report --bedGraph --CX_context --scaffolds --cytosine_report.
All the ID information in BEDGRAPH files can be verified in following websites:  http://forestry.fafu.edu.cn/db/PhePacBio/download.php
Supplementary_files_format_and_content: BEDGRAPH

molecule: genomic DNA

organism: Phyllostachys edulis

source_name: Flower florets (FP)

growth_protocol: The leaf of flower moso bamboo (P. edulis) were collected from the GUANGXI province

extract_protocol: In total, we collected data from five samples including leaves from three-week bamboo (TW), one-year bamboo (OY), flower in next year bamboo (FLNY), flowering bamboo (FL) and Flower florets (FP) for Bisulfite sequencing (BS-seq). EZ DNA Methylation-Gold kit (ZYMO) was used for bisulfite conversion. These samples covered the phase transition from vegetative to reproductive growth in moso bamboo .

treatment_protocol: no treatment

tag: developmental stage

value: reproductive growth

tag: tissue

value: flower florets


title: D4_b

description:
mRNA_expression
lncRNA_expression


title: Flower florets (FP) repeat1  (bisulfite-seq)


title: 7000AA_MSCB-146


title: 7000AA_MSCB-156


title: 7000AA_MSCB-145


title: Flower leaf (FL) repeat3  (bisulfite-seq)

source_name: Flower leaf (FL)

value: leaf


title: Flower leaf (FL) repeat2  (bisulfite-seq)


title: 7000AA_MSCB-144


title: Flower in the Next year (FLNY) repeat3  (bisulfite-seq)

source_name: Flower in the Next year (FLNY)


title: 7000AA_MSCB-142


title: 7000AA_MSCB-153


title: Flower in the Next year (FLNY) repeat2  (bisulfite-seq)


title: 7000AA_MSCB-152


title: Flower in the Next year (FLNY) repeat1  (bisulfite-seq)


title: 7000AA_MSCB-139


title: One year (OY) repeat3  (bisulfite-seq)

source_name: One year (OY)

value: vegetative growth


title: 7000AA_MSCB-141


title: One year (OY) repeat2  (bisulfite-seq)


title: 7000AA_MSCB-140


title: 7000AA_MSCB-138


title: Flower florets (FP) repeat2  (bisulfite-seq)


title: 7000AA_MSCB-137


title: Three week seedling (TW) repeat3  (bisulfite-seq)

source_name: Three week seedling (TW)


title: 7000AA_MSCB-148


title: One year (OY) repeat1  (bisulfite-seq)


title: 7000AA_MSCB-136


title: Flower leaf (FL) repeat1  (bisulfite-seq)


title: 7000AA_MSCB-143


title: 7000AA_MSCB-134


title: Three week seedling (TW) repeat1  (bisulfite-seq)


title: 7000AA_MSCB-133


title: 7000AA_MSCB-131


title: 7000AA_MSCB-130


title: Macrophage_M2_Untreated_8

city: Oxford

first: Chris

last: O'Callaghan

state: Oxfordshire

address: Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Samples were demultiplexed and sequences converted to FASTQ format using bcl2fastq.
Adapter sequences were trimmed using PEAT-1.2.4 before mapping to the hg19 reference genome using STAR 2.6 with default parameters.
Alignments were filtered using samtools 1.9 to retain only uniquely aligned, properly-paired reads.
Gene-level read counts were obtained using featureCounts (from Rsubread 1.32.4) in R, and raw counts were TMM normalised and analysed with edgeR 3.30.3.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix containing raw gene-level read counts for all samples.

organism: Homo sapiens

source_name: Peripheral blood monocyte derived macrophages

growth_protocol: CD14+ monocytes were purified from peripheral blood by MACS and differentiated to macrophages over 7 days in R10 supplemented with 50 ng/ml M-CSF. After 7 days, adherent macrophages were polarised to the M1 or M2 state by 24 hours treatment with 50 ng/ml IFN-γ and 10 ng/ml LPS or 20 ng/ml IL-4 and 20 ng/ml IL-13, respectively.

extract_protocol:
Adherent macrophages were lysed directly with TRIzol reagent and total RNA was extracted using the Qiagen RNeasy Micro kit (Qiagen, Hilden Germany).
PolyA-selected, strand-specific RNA-seq libraries were prepared for BGI DNBSEQ-G400 or Illumina HiSeq 4000 sequencing according to standard protocols.

treatment_protocol: M2 macrophages were treated with 500 μM succinate only, or in combination with either a SUCNR1/GPR91 antagonist (NF-56-EJ40, 1 μM) or a Gq inhibitor (YM-254890, 1 μM).

value: Untreated

tag: polarisation

tag: donor


title: 7000AA_MSCB-129


title: Macrophage_M2_Untreated_6


title: Macrophage_M2_Untreated_5


title: 7000AA_MSCB-128


title: Late L3 larvae (SPLiT-Seq)

city: Beijing

first: Guangshuo

last: Ou

address: Tsinghua University Haidian District

department: School of Life Science

institute: Tsinghua university

data_processing:
Quality control of sequencing reads was done by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Any read with >1 low-quality base (Phred <=10) was discarded. We used zUMIs(Parekh S et al., 2018) to determine UBC (unique barcodes) and UMI for every barcoded read (Read 2). The cDNA reads (Read 1) were then mapped to a WS263 genome using STAR. Each original barcoded cDNA molecule is amplified before tagmentation and subsequent PCR, so we used zUMIs to collapse UMIs of aligned reads that were within 1 nt mismatch of another UMI, assuming the two aligned reads were also from the same UBC. For each gene, both intronic and exonic UMI counts were used. Since the poly(dT)15 and random hexamer RT primer in the same well have different round 1 barcodes, we combined those transcriptome-pairs according to the equivalent sequence. We then generated a matrix of gene counts for each cell (N x K matrix, with N cells and K genes). Transcriptomes with greater than 1000,000 expressed gene counts were discarded, yielding 5054 transcriptomes used for downstream analysis.
Genome_build: WS263
Supplementary_files_format_and_content: CSV. The cell vs. gene counts expression matrix

organism: Caenorhabditis elegans

source_name: late L3 larvae

growth_protocol: Worms were cultivated at 20 °C on nematode growth medium (NGM) agar plates seeded with the Escherichia coli OP50

extract_protocol:
The RNA extraction follows SPLiT-seq protocol
SPLiT-seq experiments were performed as described previously (Rosenberg et al., 2018), with a few adaptations according to cell type and population size: (1) 15 μm strainers were used to generate single-cell suspension; (2) fixed worm cells were pellet by centrifuging at 800g for 5 min at 4˚C; (3) cells were counted on a hemocytometer and diluted to 1,000 cells/μL; (4) cells were split into 4 wells for the first round of barcoding (Table S1), each containing barcoded well-specific reverse transcription primers（poly(dT)15 and random hexamer）. Cells were split into 96 wells in round 2 and 48 wells in round 3 well-specific barcoding (Table S1). (5) For tagmentation, the TruePrep DNA Library Prep Kit (Vazyme, #TD501) was used.

tag: strain

tag: development stage

value: late L3 larvae

tag: genotype


title: Macrophage_M1_Untreated_8


title: Macrophage_M1_Untreated_7


title: Con_b

description:
mRNA_expression
lncRNA_expression


title: 7000AA_MSCB-127


title: 7000AA_MSCB-126


title: Macrophage_M1_Untreated_6


title: Macrophage_M1_Untreated_5


title: Three week seedling (TW) repeat2  (bisulfite-seq)


title: 7000AA_MSCB-135


title: N5

city: Wenzhou

first: yuesheng

last: zhu

state: Zhejiang

address: Lucheng District

department: Department of Gastroenterology

institute: Second Affiliated Hospital, Wenzhou Medical University

description:
All_genes_fpkm_expression.txt
CRC5VSN5_Gene_differential_expression.txt

data_processing:
Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowtie2 and topaht2 to map reads to the genome of GRCh38. The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and Ballgown was used to estimate the expression levels of all transcripts.
LncRNA identification: First, transcripts that overlapped with known mRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC and CNCI to predict transcripts with coding potential. All transcripts with CPC score < -1 and CNCI score < 0 were removed. The remaining transcripts were considered as lncRNAs.
StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM. The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: GRCh38
Supplementary_files_format_and_content: All_genes_fpkm_expression.txt: Tab-delimited text file includes FPKM values for each Sample.
Supplementary_files_format_and_content: *_Gene_differential_expression.txt: Tab-delimited text files

source_name: Colorectal mucosa

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (LC Bio Technology CO.,Ltd. Hangzhou, China) following the vendor's recommended protocol.

value: adjacent normal mucosa epithelium


title: 7000AA_MSCB-124


title: 7000AA_MSCB-125


title: N4

description:
All_genes_fpkm_expression.txt
CRC4VSN4_Gene_differential_expression.txt


title: N3

description:
All_genes_fpkm_expression.txt
CRC3VSN3_Gene_differential_expression.txt


title: 7000AA_MSCB-132


title: Macrophage_M2_Untreated_7


title: N2

description:
All_genes_fpkm_expression.txt
CRC2VSN2_Gene_differential_expression.txt


title: 7000AA_MSCB-121


title: N1

description:
All_genes_fpkm_expression.txt
CRC1VSN1_Gene_differential_expression.txt


title: 7000AA_MSCB-123


title: 7000AA_MSCB-122


title: 7000AA_MSCB-120


title: 7000AA_MSCB-119


title: 7000AA_MSCB-118


title: 7000AA_MSCB-117


title: CRC3

value: colorectal cancer mucosa epithelium

tag: tumor stage

value: TNM stage 4


title: CRC2

value: TNM stage 2


title: CRC1


title: 7000AA_MSCB-116


title: 7000AA_MSCB-114


title: 7000AA_MSCB-115


title: 7000AA_MSCB-112


title: 7000AA_MSCB-113


title: EOC1023_pOme_RNA_seq2

city: Helsinki

first: Elina

middle: A

last: Pietilä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

data_processing:
Read pairs were trimmed using Trimmomatic (version 0.33)
the first 12 and last 5 bases were cropped due to uneven per base sequence content
leading bases with a quality score lower than 20 and any trailing bases with a quality score lower than 30 were removed
the reads were scanned with a 3-base wide sliding window, cutting when the average quality per base dropped below 20
resulting sequences shorter than 20bp were discarded. Trimmed reads were aligned to the reference genome (GRCh38.d1.vd1) using STAR (version 2.5.2b), allowing up to 10 mismatches, and all alignments for a read were output
Genome_build: GRCh38.d1.vd1
Supplementary_files_format_and_content: Matrix table with effective counts

source_name: Tumor tissue from treatment-naïve patient

growth_protocol: Cells were not cultured

extract_protocol:
Total RNA was extracted from fresh patient tissues and ascites-derived cells by using RNeasy kit from QIAGEN (Qiagen, Hilden, Germany) with DNase I treatment. RNA quality and concentration were tested with Bioanalyzer 2100 (Agilent CA, USA). All samples fulfilled the criteria of RNA integrity number (RIN) > 7 and concentration > 50 ng/µl.
Sequencing libraries were constructed in Beijing Genomics Institute (Beijing, China) using a modified protocol similar to the TrueSeq Stranded Total RNA with RiboZeroKit (Illumina Inc.)

treatment_protocol: The post-chemotherapy samples were collected from patients after chemotherapy treatment.

tag: disease state

value: high-grade serous ovarian carcinoma

tag: anatomical location

value: Omentum

tag: treatment strategy

value: Neoadjuvant chemotherapy


title: 7000AA_MSCB-108


title: EOC868_pPer_RNA_seq2

value: Peritoneum


title: EOC551_pOva_RNA_seq2

value: Primary


title: EOC60_pPer_RNA_seq2


title: 7000AA_MSCB-110

value: primary bladder epithelial cell


title: 7000AA_MSCB-109


title: 7000AA_MSCB-107


title: 7000AA_MSCB-106


title: EOC1133_pPer_RNA_seq2


title: CRC5

value: TNM stage 1


title: EOC889_iOme_RNA_seq2

source_name: Tumor tissue from post-chemotherapy patient


title: 7000AA_MSCB-105


title: EOC868_iOme_RNA_seq2


title: EOC868_iOva_RNA_seq2


title: CRC4


title: EOC1133_iOme_RNA_seq2


title: EOC551_iOme_RNA_seq2


title: 7000AA_MSCB-104


title: EOC60_iMes_RNA_seq2

value: Mesentery


title: 7000AA_MSCB-103


title: SiRNF31-3

city: Shenzhen

first: Juntao

last: Xu

state: Guangdong

address: Yuehai Subdistrict, Nanshan District

institute: Philrivers

data_processing:
Illumina hiseq4000 used for basecalling.
Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed by quality, reads were filtered by quality and mapped to GRCh37 using the HISAT2 software
mapping QC by samtools and picard software
Quantification was done by using Cufflinks to produce gene-level expression values (FPKMs)
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: breast cancer cell

growth_protocol: cells were cultured in DMEM with 10% FBS.

extract_protocol:
The total RNA was extracted from cells by the qiagen RNA exaction kit
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# 0801-0303).

treatment_protocol: cells were treated with 50nM siRNF31 or siControl

tag: passage

value: 15-18 passage

tag: cell line


title: 7000AA_MSCB-101


title: SiRNF31-2


title: 7000AA_MSCB-102


title: 7000AA_MSCB-100


title: 7000AA_MSCB-111


title: EOC664_iOme_RNA_seq2


title: 7000AA_MSCB-097


title: 7000AA_MSCB-099


title: NC3

value: scramble siRNA


title: 7000AA_MSCB-096


title: NC1


title: MST_3

treatment_protocol: cells were treated with vehicle or 3 uM MST1/2 inhibitor for 6 hours

value: MST1/2 inhibitor


title: 7000AA_MSCB-095


title: MST_2


title: MST_1


title: NC2


title: 7000AA_MSCB-092


title: NC_1

value: vehicle


title: NC_2


title: NC_3


title: 7000AA_MSCB-094


title: 7000AA_MSCB-093


title: 7000AA_MSCB-091


title: SiRNF31-1


title: E1_Recovery-HSATIIIKD-rep1

city: 吹田市山田丘１－３

first: KENSUKE

last: NINOMIYA

state: 大阪府

department: Graduate school of Frontier Biosciences

country: Japan

institute: Osaka university

data_processing:
Sequencer image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Sequencing read quality was examined by FastQC software.
The clean reads (pass Illumina quality filter and adapter trimmed by Trimmomatic) were aligned to Ensembl reference genome using HISAT2 software (v2.1.0).
The m6A-RIP-enriched regions (peaks) were detected by exomePeak software.
Genome_build: human hg19
Supplementary_files_format_and_content: An exel file including m6A peaks for each sample

source_name: HeLa cell

growth_protocol: HeLa cells were culturedat 37 °C in 5% CO2 in Dulbecco’s modified eagle’s medium containing 10% fetal bovine serum and penicillin and streptomycin

extract_protocol:
Total RNAs were prepared using TRI Reagent (Molecular Research Center, Inc.), according to the manufacturer’s manual. The mRNAs were isolated Seq-Star poly(A) mRNA Isolation Kit (Arraystar) and chemically fragmented to around 100-nt sizes.
m6A RIP was performed to enrich m6A methylated mRNA fragments with anti-N6-methyadenosine (m6A) antibody (Synaptic Systems, 202003). The RNA-seq libraries for both the m6A immunoprecipitated RNAs and the input RNAs were prepared with a KAPA Stranded mRNA-seq Kit.
The barcoded libraries were denatured to single-stranded DNAs, captured on Illumina flow cells, amplified in situ as sequencing clusters, and sequenced for 300 cycles on Illumina HiSeq 4000 system per the manufacturer’s instructions.

treatment_protocol: HeLa cells were transfected with HSATIII antisense oligonucleotide (ASO) or control sense oligonucleotide (SO) using Nucleofector technology. For thermal stress induction, the cells were incubated at 42 °C in an incubator with 5% CO2, with or without recovery at  37 °C.

value: HeLa

tag: rna population

value: poly(A) RNA

value: 42 C 2 hours and 37 C 1hour

tag: genotype/variation

value: HSATIII knockdown

tag: sample type

value: IP sample


title: E2_Recovery-HSATIIIKD-IP-rep2

tag: treatment


title: 7000AA_MSCB-090

tag: cell type


title: 7000AA_MSCB-088


title: 7000AA_MSCB-089


title: 7000AA_MSCB-087


title: E2_Recovery-HSATIIIKD-input rep2

value: Input sample


title: D2_Recovery-control-IP-rep2

value: Control


title: E1_Recovery-HSATIIIKD-input rep1


title: 7000AA_MSCB-086


title: D2_Recovery-control-input rep2


title: 7000AA_MSCB-085


title: D1_Recovery-control-input rep1


title: 7000AA_MSCB-084


title: D1_Recovery-control-IP-rep1


title: 7000AA_MSCB-098


title: C2_HS-HSATIIIKD-input rep2

value: 42 C 2 hours


title: C2_HS-HSATIIIKD-IP-rep2


title: 7000AA_MSCB-081


title: 7000AA_MSCB-082


title: 7000AA_MSCB-080


title: 7000AA_MSCB-079


title: 7000AA_MSCB-078


title: 7000AA_MSCB-077


title: C1_HS-HSATIIIKD-rep1


title: C1_HS-HSATIIIKD-input rep1


title: B2_HS-control-input rep2


title: B2_HS-control-IP-rep2


title: B1_HS-control-input rep1


title: 7000AA_MSCB-076


title: B1_HS-control-IP-rep1


title: 7000AA_MSCB-075


title: A2_37-IP-rep2


title: 7000AA_MSCB-073


title: 7000AA_MSCB-083


title: A1_37-IP-rep1


title: A2_37-input rep2


title: 7000AA_MSCB-071


title: 7000AA_MSCB-072


title: 7000AA_MSCB-070


title: A1_37-input rep1


title: Breast_cancer_44R

city: Guadalajara

first: Carlos

middle: Alfredo

last: Barrón Gallardo

state: Jalisco

address: Sierra Mojada 950

country: Mexico

institute: Universidad de Guadalajara

data_processing:
Flexbar 3.5.0 was used for removing adapters.
Then mapped to GRCh38 human genome using Kallisto 0.46.1.
Differential expression analysis was performed by using DESeq2
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include counts and TPM values of every gene for each sample

source_name: Breast Cancer

extract_protocol:
Breast cancer biopsies were taken and immediately submerged into RNA-later. RNA was extracted using Rneasy Plus Mini Kit from Qiagen (Cat No./ID: 74136). Total RNA (200ng) was purified with oligo-dT beads and then was fragmented. RNAseq was performed in the HiSeq4000-Sequencer for paired-end sequencing (HiSeq® 4000 SBS Kit, Illumina) with recommended read lengths 150bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment response

value: Resistant

tag: age

tag: molecular subtype

value: HER 2

tag: histological type

value: Invasive ductal carcinoma

tag: histological grade

value: SBRII


title: Breast_cancer_41S

value: Carboplatin-Paclitaxel weekly 4 cycles + Epirubicin-Cyclophosphamide 4 cycles + Trastuzumab 6 concomitant cycles

value: Sensitive

value: Luminal B


title: Breast_cancer_40R

value: Epirubicin-Cyclophosphamide + Paclitaxel weekly 4 cycles

value: Triple Negative

value: SBRIII


title: 7000AA_MSCB-069

value: primary bladder epithelial cell


title: Breast_cancer_39S

value: Epirubicin-Cyclophosphamide 4 cycles + Docetaxel 4 cycles


title: 7000AA_MSCB-068


title: Breast_cancer_32S

value: Doxorubicin-Cyclophosphamide 4 cycles + Docetaxel 4 cycles

value: SBR III


title: 7000AA_MSCB-067


title: Breast_cancer_28R

value: Carboplatin-Paclitaxel weekly 4 cycles + Epirubicin-Cyclophosphamide 4 cycles + Trastuzumab 8 concomitant cycles


title: Breast_cancer_30S

value: Carboplatin-Paclitaxel weekly 4 cycles + Epirubicin-Cyclophosphamide 3 cycles


title: 7000AA_MSCB-065


title: 7000AA_MSCB-066


title: 7000AA_MSCB-064


title: Breast_cancer_27R

value: Epirubicin-cyclophosphamide 4 cycles, docetaxel 4 ciclo and trastuzumab 3 cycles


title: 7000AA_MSCB-074


title: 7000AA_MSCB-063


title: 7000AA_MSCB-062


title: Breast_cancer_25R

value: Resistant


title: Breast_cancer_24S

value: HER 2


title: 7000AA_MSCB-061


title: 7000AA_MSCB-060


title: Breast_cancer_22R

value: Epirubicina-Cyclophosphamide 4 cycles + Docetaxel 4 cycles

value: LUMINAL A

value: Invasive ductal carcinoma


title: Breast_cancer_21S

value: Sensitive


title: 7000AA_MSCB-059


title: 7000AA_MSCB-058


title: Breast_cancer_20S

value: Luminal B


title: Breast_cancer_12R

value: SBRII


title: 7000AA_MSCB-057


title: 7000AA_MSCB-056


title: Breast_cancer_11R

value: Epirubicin-Cyclophosphamide 6 cycles

value: Triple Negative


title: Breast_cancer_9S

value: Carboplatin-Paclitaxel weekly 4 cycles + Epirubicin-Cyclophosphamide 4 cycles


title: Breast_cancer_7S

value: Doxorubicin-Cyclophosphamide 4 cycles + Docetaxel 4 cycles + trastuzumab 3 concomitant cycles

value: SBR II


title: 7000AA_MSCB-055

value: primary bladder epithelial cell


title: 7000AA_MSCB-054


title: 7000AA_MSCB-053


title: Breast_cancer_8R

value: Doxorubicin-Cyclophosphamide 2 cycles


title: 7000AA_MSCB-050


title: Breast_cancer_5R

value: SBRIII


title: Breast_cancer_3R

value: Epirubicin-Cyclophosphamide 4 cycles + Docetaxel 4 ciclo + Trastuzumab 3 concomitant cycles


title: 7000AA_MSCB-049


title: 7000AA_MSCB-052


title: Breast_cancer_2R

value: Epirubicin-Cyclophosphamide 4 cycles + Docetaxel 1 cycle

value: Resistant


title: Breast_cancer_6R

value: Epirubicin-Cyclophosphamide 4 cycles + Docetaxel 4 cycles

value: SBRI


title: 7000AA_MSCB-051


title: 7000AA_MSCB-048


title: 7000AA_MSCB-047


title: S18_SET1BHypoxiaInput

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

description: input control

data_processing:
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3) and reads were aligned to Genome Reference Consortium GRCh37 (hg19) using BWA (0.7.5a-r405). Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19)
Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19) and reads mapping to Duke Encode black list regions (http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability) were excluded using BEDTools (2.17.0)
Duplicate reads were marked for exclusion using Picard tools (1.106) (http://picard.sourceforge.net/).
ChIP-seq peaks were identified using T-PIC (Tree shape Peak Identification for ChIP-Seq) and MACS (Model-based analysis of ChIP-Seq) in control mode
Peaks detected by both peak callers were filtered quantitatively using the total count under the peak to include only peaks that were above the 99.99th percentile of random background regions selected from the ENCODE DNASE II cluster (p-value < 0.0001).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigwig and bed files of called peaks

source_name: Hela cells_SET1B_CRISPR

growth_protocol: Wildtype HeLa cells, SET1B KO or HIF1beta KO cells were grown on 15 cm dishes in complete DMEM media

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody for H3K4me3.
Libraries were constructed according to Illumina protocols
ChIP-seq. Each sample was sequenced over two lanes, using 75bp paired-end reads

treatment_protocol: Cells were incubated in  21% or 1 oxygen for 6 hr

value: HeLa

tag: genotype

tag: ambient o2

tag: treatment time

value: 6 hours

tag: chip antibody


title: 7000AA_MSCB-045


title: 7000AA_MSCB-046


title: S15_HIF1BNormoxiaInput

description: input control

source_name: Hela cells_HIF1b_CRISPR


title: S17_SET1BNormoxiaInput

description: input control


title: S16_HIF1BHypoxiaInput

description: input control


title: 7000AA_MSCB-044


title: S14_ControlHypoxiaInput

description: input control

source_name: Hela cells_control_CRISPR

value: control


title: S12_SET1BHypoxiaChIP2

description: ChIP

value: H3K4me3 (cell signaling) rabbit mAb  #9751


title: 7000AA_MSCB-043

source_name: bladder


title: S13_ControlNormoxiaInput

description: input control


title: S11_SET1BNormoxiaChIP2

description: ChIP


title: S10_HIF1BHypoxiaChIP2

description: ChIP


title: 7000AA_MSCB-042


title: 7000AA_MSCB-040


title: 7000AA_MSCB-041


title: S06_SET1BHypoxiaChIP

description: ChIP


title: 7000AA_MSCB-039


title: S09_HIF1BNormoxiaChIP2

description: ChIP


title: S07_ControlNormoxiaChIP2

description: ChIP


title: 7000AA_MSCB-035


title: 7000AA_MSCB-036


title: S05_SET1BNormoxiaChIP

description: ChIP


title: 7000AA_MSCB-038


title: 7000AA_MSCB-037


title: S02_ControlHypoxiaChIP

description: ChIP


title: (repeated) Caco-2-2 [TMG126_1000052_S29]

city: Suita

first: Hiroyuki

last: Mizuguchi

state: Osaka

address: 1-6, Yamadaoka

department: Graduate School of Pharmaceutical Sciences

institute: Osaka University

description:
additional reads for enough sequence coverage
TMG126_1000052_S29_L005

data_processing:
Illumina Real-Time Analysis (RTA) v2.7.7 software used for basecalling.
Sequenced reads were mapped to GRCh38 whole genome using STAR aligner.
After filtering out duplicate reads, RNA quantification and normarization with Trimmed mean of M-values (TMM ) or Transcripts per million (TPM )  were done by using Strand NGS 3.4 (Strand Life Sciences).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with TMM or TPM-normalized gene counts for every gene and every sample

growth_protocol: Caco-2 cells were obtained from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany. Caco-2 cells were maintained at 37℃, 8% CO2 and 95% relative humidity in a cell culture dish supplemented with DMEM + 3.7 g/L NaHCO3 (Biochrom AG), MEM-NEAA (Thermo Fisher Scientific), L-Glutamine (Biochrom AG), penicillin-streptomycin (Thermo Fisher Scientific) and 10% FBS (Gibco, Themo Fisher Scientific). The passage number of the Caco-2 cells was between 60 and 90. Total RNA was extracted and purified by using an RNeasy Mini kit (QIAGEN) according to manufacturer’s standard protocol. RNA quality was evaluated in the same way as the biopsy samples using the BioAnalyzer (Agilent Technologies).  The human iPS cell line, YOW-iPS cell, was maintained on a feeder layer of mitomycin C-treated MEF (mouse embryonic fibroblasts, Millipore) with ReproStem medium (ReproCELL) supplemented with 10 ng/ml fibroblast growth factor 2 (FGF2, KATAYAMA CHEMICAL INDUSTRIES).Intestinal differentiation of human iPS cells was performed according to our previous report. Before the initiation of intestinal differentiation, human iPS cells were dissociated into clumps by using dispase (Roche) and plated onto the BD Matrigel Matrix Growth Factor Reduced (BD Biosciences)-coated apical chamber of BD Falcon cell culture inserts (6-well plate, 1.0 μm pore size, 1.6×106 pores/cm, PET Membrane). These cells were cultured in the MEF-conditioned medium for 2-3 days. For the definitive endoderm differentiation, human iPS cells were cultured for 4 days in RPMI1640 medium (Sigma-Aldrich) containing 100 ng/ml Activin A (R&D Systems), 1×GlutaMAX (Thermo Fisher Scientific), penicillin-streptomycin, and 1×B27 Supplement Minus Vitamin A (Thermo Fisher Scientific). During the definitive endoderm differentiation, the mesendoderm cells (day 2) were transduced with 3,000 vector particles (VP)/cell of FOXA2-expressing adenovirus (Ad) vector (Ad-FOXA2) for 1.5 hr to promote definitive endoderm differentiation.  For the induction of intestinal progenitor cells, the definitive endoderm cells were cultured for 4 days in the intestinal differentiation medium [DMEM, high glucose (FUJIFILM Wako) containing 5 μM 6-bromoindirubin-3'-oxime (BIO; Calbiochem), 1×MEM Non-Essential Amino Acids Solution (Thermo Fisher Scientific), penicillin-streptomycin, 1×GlutaMAX, and 100 μM β-mercaptoethanol] supplemented with 10 μM N-[(3,5-difluorophenyl) acetyl]-L-alanyl-2-phenyl-1, 1-dimethylethyl ester-glycine (DAPT; Peptide Institute), and 10% Knockout Serum Replacement (Thermo Fisher Scientific).  For the induction of intestinal epithelial cell monolayers, the intestinal progenitor cells were cultured for 11 days in intestinal differentiation medium supplemented with 1 μM BIO and 2.5 μM DAPT, and then cultured for 15 days in the Wnt-3A-conditioned intestinal differentiation medium supplemented with 0.1 μM BIO, 1 μM DAPT, 250 ng/ml EGF, and 10 μM SB431542. During the intestinal differentiation, the intestinal progenitor cells (day 8) were transduced with 3,000 VP/cell of Ad-CDX2 (caudal-related homeobox transcription factor 2) for 1.5 hr to promote intestinal differentiation.

extract_protocol:
RNA was harvested using QIAzol reagent.Illumina TruSeq stranded totalRNA (#20020596) was used with 300 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colon-cancer cell line


title: S03_HIF1BNormoxiaChIP

description: ChIP


title: 7000AA_MSCB-033


title: S01_ControlNormoxiaChIP

description: ChIP


title: 7000AA_MSCB-028


title: 7000AA_MSCB-031


title: S08_ControlHypoxiaChIP2

description: ChIP


title: 7000AA_MSCB-030


title: (repeated) Duodenum-2 [TMG126_1000035_S47]

description:
additional reads for enough sequence coverage
TMG126_1000035_S47_L008

source_name: Duodenum

tag: disease state

value: Crohn’s Disease (CD) or Ulcerative colitis (UC)

tag: sampling region

value: non-inflammatory area

tag: age (year)

tag: Sex

value: male

tag: race

value: Japanese


title: (repeated) Ileum-7 [TMG126_1000049_S41]

description:
additional reads for enough sequence coverage
TMG126_1000049_S41_L007

source_name: Ileum

value: female


title: (repeated) Ileum-5 [TMG126_1000045_S35]

description:
additional reads for enough sequence coverage
TMG126_1000045_S35_L006


title: 7000AA_MSCB-034

value: primary bladder epithelial cell


title: undifferentiated iPS cell-3 [TMG126_27_S18]

source_name: iPS-cell (YOW)

tag: cell line

value: YOW

value: undifferentiated iPS-cells


title: 7000AA_MSCB-027


title: S04_HIF1BHypoxiaChIP

description: ChIP


title: undifferentiated iPS cell-2 [TMG126_26_S12]


title: undifferentiated iPS cell-1 [TMG126_25_S6]


title: 7000AA_MSCB-024


title: 7000AA_MSCB-023


title: 7000AA_MSCB-026


title: 7000AA_MSCB-021


title: Caco-2-3 [TMG126_53_S24]

description:
obtained from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany.
TMG126_53_S24_L004


title: Caco-2-1 [TMG126_51_S22]

description:
obtained from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany.
TMG126_51_S22_L004


title: Caco-2-2 [TMG126_52_S23]

description:
obtained from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany.
TMG126_52_S23_L004


title: 7000AA_MSCB-029


title: 7000AA_MSCB-022


title: 7000AA_MSCB-016


title: 7000AA_MSCB-018


title: 7000AA_MSCB-019


title: 7000AA_MSCB-015


title: 7000AA_MSCB-013


title: 7000AA_MSCB-025


title: 7000AA_MSCB-014


title: 7000AA_MSCB-010


title: 7000AA_MSCB-009


title: 7000AA_MSCB-020


title: 7000AA_MSCB-008


title: 7000AA_MSCB-005


title: 7000AA_MSCB-007


title: 7000AA_MSCB-006


title: 7000AA_MSCB-004


title: 7000AA_MSCB-002


title: 7000AA_MSCB-001


title: 7000AA_MSCB-003


title: 6999AA_MSCB-192


title: 7000AA_MSCB-017


title: 6999AA_MSCB-191


title: 6999AA_MSCB-188


title: 6999AA_MSCB-190


title: 7000AA_MSCB-012


title: 7000AA_MSCB-011


title: lv+ctrl+lps

city: tianjin

first: chun

last: dang

address: Tianjin Anshan Road

institute: Tianjin Medical University General Hospital

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM value for gene and transcript level

source_name: Control-LPS

growth_protocol: Cells are cultured using DMEM basic medium

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: NSC-34 cells treated with 1mg/ml lipopolysaccharide (LPS) 6h NSC-34 cells were transfected lentiviral to generate pgc1α overexpression cell (LV- PGC-1α) and negative control cells (LV-Ctrl).

value: Neuronal cell line

tag: genotype/variation

value: negative control cells (LV-Ctrl)

tag: treatment

value: lipopolysaccharide (LPS) 6h


title: 6999AA_MSCB-187

tag: cell type


title: lv-pgc

source_name: PGC

value: pgc1alpha overexpression cell (LV- PGC-1[alpha])


title: 6999AA_MSCB-186


title: 6999AA_MSCB-184


title: lv-ctrl

source_name: Control


title: 6999AA_MSCB-183


title: 6999AA_MSCB-180


title: 6999AA_MSCB-189


title: 6999AA_MSCB-182


title: 6999AA_MSCB-181


title: 6999AA_MSCB-178


title: 6999AA_MSCB-177


title: 6999AA_MSCB-185


title: 6999AA_MSCB-176


title: 6999AA_MSCB-175


title: 6999AA_MSCB-174


title: 6999AA_MSCB-179


title: lv+pgc+lps

source_name: PGC-LPS


title: 6999AA_MSCB-173


title: 6999AA_MSCB-172


title: 6999AA_MSCB-171


title: 21 days differentiated Caco-2 cells incubated with C. difficile Toxin B for ~4 hours, biological replicate 2

type: RNA

city: Wageningen

first: Nicole

last: de Wit

address: Bornse Weilanden 9

department: Food & Biobased Research

country: Netherlands

institute: Wageningen UR

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm using the Affymetrix® Expression Console™ Software.

label: biotin

source_name: 21 days differentiated Caco-2 cells

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: ATCC derived Caco-2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco-Invitrogen, Bleiswijk, The Netherlands) with 4.5 g/L glucose, 0.58 g/L glutamine, no pyruvate, supplemented with 10% heat inactivated FBS (Hyclone Perbio, Etten-Leur, The Netherlands) and used with passage numbers between 30 and 60. For transwell assays, 0.33x105 cells were grown on ThinCert transwells with 33.6 mm2 membranes and 0.4 μm pores in 24-well suspension culture plates. Cells were grown for 21 days at 5% CO2 and 37°C and apical (150 μl) and basolateral (700 μl) medium were replaced three times per week.

extract_protocol: Total RNA was prepared from the Caco-2 cells using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Twenty-one days differentiated Caco-2 cells were exposed to 0.25ug/ml Toxin A (ToxA), 0.25ug/ml Toxin B (ToxB), 0.25ug/ml Toxin A + 0.25ug/ml Toxin B (ToxAB) or 0.25ug/ml Toxoid A + 0.25ug/ml Toxoid B (ToxoidAB) and DMEM control (MEDIUM) samples for ~4 hours. The cell medium was replaced the day before the exposure experiments. Medium was removed from the apical and basal compartments and samples were added to the apical compartment while fresh DMEM+10%FBS medium was added to the basal compartment. In each experiment, the toxin, toxoid and control samples were exposed to Caco-2 cells in triplicate and three independent exposure experiments were performed (=3 independent biological replicates). After ~4 hours incubation, the Caco-2 cells were lysed with 200 μL TRIzol and the triplicates in each experiment were pooled for RNA isolation.

value: ToxB

tag: tumor origin

value: Caucasian colon adenocarcinoma

tag: passage nr

tag: days of differentiation on tranwells


title: 21 days differentiated Caco-2 cells incubated with DMEM (=control) for ~4 hours, biological replicate 3

value: Medium


title: 21 days differentiated Caco-2 cells incubated with C. difficile Toxin B for ~4 hours, biological replicate 3


title: 21 days differentiated Caco-2 cells incubated with C. difficile Toxin B for ~4 hours, biological replicate 1


title: 6999AA_MSCB-170


title: 21 days differentiated Caco-2 cells incubated with C. difficile Toxoid AB for ~4 hours, biological replicate 1

value: ToxoidAB


title: 21 days differentiated Caco-2 cells incubated with C. difficile Toxin A for ~4 hours, biological replicate 2

value: ToxA


title: 21 days differentiated Caco-2 cells incubated with C. difficile Toxin AB for ~4 hours, biological replicate 1

value: ToxAB


title: 21 days differentiated Caco-2 cells incubated with C. difficile Toxin A for ~4 hours, biological replicate 3


title: 6999AA_MSCB-168


title: 21 days differentiated Caco-2 cells incubated with C. difficile Toxin AB for ~4 hours, biological replicate 2


title: 21 days differentiated Caco-2 cells incubated with C. difficile Toxoid AB for ~4 hours, biological replicate 2


title: 21 days differentiated Caco-2 cells incubated with C. difficile Toxin AB for ~4 hours, biological replicate 3


title: 21 days differentiated Caco-2 cells incubated with C. difficile Toxoid AB for ~4 hours, biological replicate 3


title: 21 days differentiated Caco-2 cells incubated with DMEM (=control) for ~4 hours, biological replicate 2


title: 21 days differentiated Caco-2 cells incubated with C. difficile Toxin A for ~4 hours, biological replicate 1


title: in vivo_d14_hirafl/fl input

city: New York

first: Shahin

last: Rafii

state: New York

address: 413 East 69th Street

country: USA

institute: Weill Cornell Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
Raw reads (fastq files) from ChIP-seq was aligned to mouse genome mm9 using bwa. Duplicate reads and reads aligning to more than one location were excluded. After QC and alignment, bam files were obtained.
Bam files are converted to bed files using bedtools
Peaks are called using SICER V1.1, using the following parameters.
SICER was used to identify the peaks for H3.3 (HA) by comparing to the input control sample using a FDR < 0.01, fragment size of 150bp, window size 200bp, gap size 600bp.  For identification of significantly decreased or increased H3K9me3, H3K27me3, H3K27ac peak regions, bed files for BKO_H3K9me3, BKO_input, DKO_H3K9me3 and DKO_input were used. The parameters used are FDR < 0.01, fragment size of 150bp, window size 200bp, and gap size of 600bp. For H3K4me3 peak calling, gap size 200 bp is used. The peak region bed files were annotated to the nearest TSS using HOMER annotatepeaks.pl function.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated automatically during the process of peak calling using SICER. This wig files represents the peak islands-filtered reads normalized according to the totalnumber of reads.

source_name: LKS cells

growth_protocol: For in vitro cultured WT or H3.3DKO LKS cells, Lin- cells were enriched from mouse bone marrow using miltenyi beads. 0.1 million Lin- cells were coculture onto E4-HUVECs within one well of 12 well plate, using Stemspan medium supplemented with sKitL (20ng/ml), Flt3 (10 ng/ml) and TPO (10 ng/ml). 3-5 days later, 0,5 microgram/ml of 4-OH tamoxifen is added into the medium only once. 4 days later, the LKS cells were sorted on BD FacsAriaII.

extract_protocol:
The nucleosome was extracted using TruChip Chromatin Shearing Reagent Kit (Covaris, 520127). DNA was sheared using Covaris E220/S220 for 20 min in cold circulating water. ChIP was done using the ChIP-IT high sensitivity kit (Active Motif, 53040). For all the rest of the ChIP-seq experiments, which are Mnase based native ChIP, nuclei are extracted using NP40 detergent at the final concentration of 0.6%. The Di-nucleosomes and mono-nucleosomes are generated by enzymatic digestion using diluted MNase.
for H3.3 ChIP-seq in cocultured LKS cells, DNA was eluted and library was prepared using ThruPLEX DNA-seq Kit Dual Index (Rubicon Genomics, R400523). For all the rest of the ChIP-seq experiments, DNA library was prepared using Kapa Hyper Kit (KK8504) according to the product manual. Adaptor was from KAPA Single-Indexted Adaptor Kit (KAPA 8700 08005699001). DNA was purified using the DNA purification kit AMPure XP 60 mL (A63800, Beckman Coulter). 13 cycles of PCR amplication cycles are used.

treatment_protocol: for in vivo BKO or DKO LKS cells, age and gender matched mice were treated with tamoxifen at 100 mg/kg body weight,for 4 doses.Tamoxifen effectiveness was assessed by peripheral blood drawing and tail genotyping. Lin- cells were isolated from mouse bone marrow by miltenyi beads enrichment, LKS cells were sorted out on BD FACS AriaII at day 14 and day 56 post tamoxifen injection.

value: sorted as cKit+Sca1+Lin- cells

tag: passages

value: primary

tag: strain


title: in vivo_d14_hiraKO input


title: 21 days differentiated Caco-2 cells incubated with DMEM (=control) for ~4 hours, biological replicate 1

value: male


title: in vivo_d14_hiraKO H3K27me3

value: H3K27me3 Diagnode C15410069 ChIP


title: 6999AA_MSCB-167

value: primary bladder epithelial cell


title: 6999AA_MSCB-166


title: in vivo_d14_hirafl/fl H3K27me3


title: in vivo_d14_hirafl/fl H3K9me3

value: H3K9me3 Active Motif 39161 ChIP


title: 6999AA_MSCB-165


title: 6999AA_MSCB-164


title: 6999AA_MSCB-169


title: in vivo_d14_hiraKO H3K9me3


title: 6999AA_MSCB-162


title: 6999AA_MSCB-163


title: 6999AA_MSCB-160


title: 6999AA_MSCB-161


title: 6999AA_MSCB-158


title: 6999AA_MSCB-157


title: 6999AA_MSCB-159


title: in vivo_d56_DKO_H3K27me3


title: in vivo_d56_DKO_H3K4me3

value: H3K4me3 Cell Signaling Technologies 9727S ChIP


title: in vivo_d56_DKO_H3K9me3


title: in vivo_d56_BKO_H3K27ac

value: H3K27ac Abcam ab4729 ChIP


title: in vivo_d56_BKO_H3K4me3


title: in vivo_d56_BKO_H3K27me3


title: in vivo_d14_DKO_H3K27ac


title: in vivo_d56_BKO_H3K9me3


title: in vivo d56_DKO_input


title: 6999AA_MSCB-155


title: in vivo d14_DKO_input


title: 6999AA_MSCB-153


title: 6999AA_MSCB-152


title: in vivo_d56_DKO_H3K27ac


title: in vivo_d14_DKO_H3K9me3


title: 6999AA_MSCB-151


title: in vivo_d14_DKO_H3K4me3


title: 6999AA_MSCB-150


title: 7000AA_MSCB-032


title: 6999AA_MSCB-149


title: in vivo d14_BKO_input


title: in vivo d56_BKO_input


title: 6999AA_MSCB-148


title: 6999AA_MSCB-156


title: 6999AA_MSCB-146


title: 6999AA_MSCB-154


title: 6999AA_MSCB-147


title: in vivo_d14_BKO_H3K4me3


title: 6999AA_MSCB-144


title: in vitro_DKO_input

value: cultured for 9 days


title: in vitro_DKO_H3K27me3


title: in vitro_DKO_H3K9me3


title: 6999AA_MSCB-143


title: in vitro_DKO_H3K27ac


title: 6999AA_MSCB-145


title: in vivo_d14_DKO_H3K27me3


title: in vitro_DKO_H3K4me3


title: in vivo_d14_BKO_H3K9me3


title: 6999AA_MSCB-141


title: 6999AA_MSCB-142


title: 6999AA_MSCB-140


title: in vitro_WT_input


title: in vivo_d14_BKO_H3K27ac


title: 6999AA_MSCB-137


title: 6999AA_MSCB-139


title: in vivo_d14_BKO_H3K27me3


title: 6999AA_MSCB-138


title: in vitro_WT_H3K9me3


title: in vitro_WT_H3K4me3


title: in vitro_WT_H3K27me3


title: in vitro_WT_H3K27ac


title: 6999AA_MSCB-132


title: 6999AA_MSCB-135


title: 6999AA_MSCB-133


title: 6999AA_MSCB-131


title: 6999AA_MSCB-134


title: in vitro_H3.3

value: HA Bon Opus Biosciences (BA020061) 12CA5 Chip, western blot


title: 6999AA_MSCB-130


title: 6999AA_MSCB-128


title: 6999AA_MSCB-127


title: 6999AA_MSCB-126


title: 6999AA_MSCB-125


title: 6999AA_MSCB-124


title: 6999AA_MSCB-123


title: Input 1

city: Headington

first: Eui Jung

last: Moon

address: Old Road Campus Research Building, Roosevelt Drive

department: Department of Oncology

description:
Endogenous MAFF was knocked down using shRNA targeting MAFF. Then V5-tagged MAFF with mutations on shRNA target sites were overexpressed.
Input
MAFF_peaks_V5_2021.csv

data_processing:
Alignment was performed with Bowtie2.
Peak calling performed with MACS.
MEME was used for motif search using ChIP seq data.
Genome_build: hg19
Supplementary_files_format_and_content: MAFF_peaks_V5_2021.csv: Comma-separated text file.

growth_protocol: MDA-MB-231 cells were maintained in DMEM media with 10% FBS at 37°C, 21% O2 and 5% CO2.

extract_protocol:
2x10^7 cell were crosslinked with 1% formaldehyde in CiA fixation buffer (50mM HEPES pH8, 1mM EDTA, 0.5mM EGTA, 100mM NaCl) for 10min. Then glycine was added to a final concentration of 125mM to stop the fixation. To collect nuclei cells were resuspended in CiA NP-Rinse 1 (50mM HEPES pH8, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-10) and incubated in ice for 10min. Cells were washed with CiA NP-Rinse 2 (10mM Tris pH8, 1mM EDTA, 0.5mM EDTA, 200mM NaCl) and dissolved in Covaris shearing buffer (0.1% SDS, 1mM EDTA, 10mM Tris-HCl pH8). Cells were sonicated using Covaris S220 (Intensity 4, Duty Factor 5%, Cycle/Burst 200) for 420sec.
Libraries were prepared using NEBNext Ultra II DNA Library Prep kit for Illumina (NEB #E7103) and NEBNext Multiplex Oligos for Illumina (NEB #E7730S). To control the quality of DNA libraries, the size and purity of samples were confirmed by Bioanalyzer.

treatment_protocol: V5-tagged MAFF was overexpressed in MDA-MB-231 cells with stable MAFF knockdown using shRNA. Cells were crosslinked with 1% formalin and ChIP procedure was performed.

value: breast cancer cell line

tag: hormone receptor

value: Triple negative

value: endogenous MAFF knocked out, V5-tagged MAFF overexpressed


title: V5-MAFF ChIP 2

description:
Endogenous MAFF was knocked down using shRNA targeting MAFF. Then V5-tagged MAFF with mutations on shRNA target sites were overexpressed.
ChIPed DNA
MAFF_peaks_V5_2021.csv


title: 6999AA_MSCB-122


title: 6999AA_MSCB-136


title: V5-MAFF ChIP 1


title: 6999AA_MSCB-121


title: 6999AA_MSCB-120


title: 6999AA_MSCB-119


title: 6999AA_MSCB-129


title: BM2

city: RENNES

first: vonick

last: sibut

address: avenue du Prof Leon BERNARD

country: France

data_processing:
Illumina software used for basecalling.
FastQC control quality
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using STAR with parameters :                     --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
The read counts were called using Subread
Differential gene expression analysis was performed using DESeq2 in R Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample ...

extract_protocol:
Bone marrow tissues from 4 healthy donors were collected and enzymatically dissociated. After depletion of hematopoietic cells (Dynal, Dynabeads CD45) stromal cells where sorted by FACS based on their phenotype and RNA extraction (Macherey-Nagel, NucleoSpin RNA XS) was performed. Quality control was performed using the Agilent RNA 6000 Pico Kit.
RNA libraries were prepared (with 10ng of total RNA)  for sequencing using standard Illumina protocols

tag: individual

value: healthy donor

tag: tissue

value: Bone Marrow

tag: cell population

value: CD45[neg] /CD11b[neg] /CD235a[neg] /CD31[neg] /CD271[pos] /CD49a[pos]


title: BM1


title: BM4


title: BM3


title: Normal_tissue2

city: Chengdu

first: Tingting

last: Song

address: The Incubation Building, Tianfu Life Science and Technology Park, 38 Keyuan South Road, Chengdu City, Sichuan Province.

institute: 四川大学华西医院

data_processing:
Basecalls performed using CASAVA version 1.4
HiC-seq reads were aligned to the Gch38 genome assembly using BWA 0.7.10-r7789 with the following configurations: align type: aln, other default parameters.
Data were filtered using the following specifications: reads containing adapter, reads containing ploy-N, Q20, Q30, GC content.
Genome_build: Gch38
Supplementary_files_format_and_content: bed files
Supplementary_files_format_and_content: matrix files
Supplementary_files_format_and_content: biases files

source_name: normal tissue

extract_protocol:
Disrupt the frozen tissue(20-40 mg ) either by coarsely chopping it with a razor blade on a petri dish placed on dry ice or by grinding it with a mortar and pestle in liquid nitrogen. Then Transfer the disrupted tissue samples to a 1.5 mL microcentrifuge tube which contain 1 ml 1X PBS and 40.5µl 37% formaldehyde, then vortexing the tube for 30s to mix and rotating tube at room temperature for 20 min. Pipeting off and discard the supernatant and washing the pellet with 300 µl wash buffer, after the second wash, added to pellet (99 µl Wash Buffer;1 µl 40 mM Calcium Chloride ;25 µl 1 mg/mL Collagenase), then incubate it for 1 hour at 37°C in an agitating thermal mixer (1250 rpm). After incubation, add 6.3 µl 20% SDS to the sample, then pipet up and down to break up any large clumps, after briefly vortex to resuspend, transfer the SUPERNATANT to a new 1.5 mL microcentrifuge tube.
the sample was fixed with formaldehyde, and the intracellular protein was cross-linked with DNA, the cross-linked cells were lysed and digested with DpnII, filled with biotin-14-dATP, proximately ligated with T4 DNA ligase and reverse crosslinked with 5M sodium chloride. Then the genome DNA was purified, sheared and size-selected. Biotin pull-down was performed to enrich target DNA fragments, followed by standard Illumina library construction, lastly using a TapeStation or Bioanalyzer to verify the size distribution of your size-selected library.Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: lung

value: untreated


title: Input 2

tag: chip antibody


title: 6999AA_MSCB-115

first: Gustavo

last: Rodriguez-Esteban

data_processing:
Primary data analysis was carried out with the standard Illumina pipeline following the manufacturer's protocol. Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
MARS-Seq libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the mouse or human genome reference.
Gene quantification was performed using UMI information to correct for amplification biases.
Genome_build: human: GRCh38. Gencode release 26.  Mouse: GRCm38. Gencode release M15.
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as UMI counts for each cell (columns).

extract_protocol:
Short-term cultured pancreatic islet cells were isolated from a healthy pancreas donor. The culturing process favor the enrichment of pancreatic islet cells while large eliminating endothelial and immune cell types. Primary bladder epithelial cells were isolated by FACS (CD45-, CD140a-, CD31-, Ter119-) from a healthy mouse.
To construct single cell libraries from polyA-tailed RNA, we applied massively parallel single-cell RNA sequencing (MARS-Seq; Jaitin et al., Science 2014). This methodology generates paired-end reads where read 1 contains the transcript sequence and read 2 the cell and UMI barcodes (bases 1 to 6 and 7 to 14, respectively). Briefly, single cells were FACS-sorted into 384-well plates, containing lysis buffer and reverse-transcription (RT) primers. The RT primers contained the single cell barcodes and unique molecular identifiers (UMIs) for subsequent de-multiplexing and correction for amplification biases, respectively.


title: Normal_tissue1


title: 6999AA_MSCB-114


title: 6999AA_MSCB-116


title: 6999AA_MSCB-112


title: LUAD_tissue2

source_name: cancer tissue

value: lung adenocarcinoma

tag: tumor stage

value: stage III


title: LUAD_tissue1


title: FL_FDC3

data_processing:
Illumina software used for basecalling.
FastQC control quality
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using STAR with parameters :                     --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
The read counts were called using Subread
Differential gene expression analysis was performed for all populations (dn, FDC, FRC, FL_DN, FL_FDC and FL_FRC) cells using DESeq2 in R Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample ...

growth_protocol: not applicable

extract_protocol:
Tonsil tissues from 6 healthy donors and LN from 4 FL patients were collected and enzymatically dissociated. After depletion of hematopoietic cells (Dynal, Dynabeads CD45) three stromal cell subsets (FRC, FDC, DN) where sorted by FACS based on their phenotype and RNA extraction (Macherey-Nagel, NucleoSpin RNA XS) was performed. Quality control was performed using the Agilent RNA 6000 Pico Kit.
RNA libraries were prepared (with 10ng of total RNA)  for sequencing using standard Illumina protocols

treatment_protocol: not applicable

value: FL patient

value: Follicular Lymphoma

tag: phenotype

value: Follicular dendritic cells


title: 6999AA_MSCB-111

value: primary bladder epithelial cell


title: FL_DN4

value: Double negative cells


title: FL_FDC2


title: FL_FRC4

value: Fibroblastic reticular cells CD49a+


title: 6999AA_MSCB-110


title: FL_FRC3


title: FL_DN3


title: 6999AA_MSCB-109


title: 6999AA_MSCB-108


title: 6999AA_MSCB-107


title: 6999AA_MSCB-118


title: 6999AA_MSCB-106


title: 6999AA_MSCB-117


title: FL_DN2


title: 6999AA_MSCB-113


title: FL_FRC1


title: 6999AA_MSCB-105


title: 6999AA_MSCB-104


title: FL_FDC1


title: 6999AA_MSCB-103


title: 6999AA_MSCB-102


title: FRC3

value: Tonsil


title: FRC5


title: FL_DN1


title: 6999AA_MSCB-101


title: FRC2


title: 6999AA_MSCB-099


title: 6999AA_MSCB-100


title: 6999AA_MSCB-098


title: FRC1


title: 6999AA_MSCB-097


title: FDC4

value: FDC


title: 6999AA_MSCB-096


title: 6999AA_MSCB-095


title: FDC3


title: FL_FRC2


title: 6999AA_MSCB-094


title: FDC1


title: 6999AA_MSCB-093


title: 6999AA_MSCB-092


title: DN4

value: DN


title: DN3


title: 6999AA_MSCB-091


title: DN2


title: 6999AA_MSCB-090


title: FRC4


title: DN1


title: 6999AA_MSCB-088


title: MDAsiSCRHyp3

description: RNA seq data

data_processing:
Raw FASTQ files obtained in the ChIP-seq experiments were uploaded to DNAnexus and processed using DNAnexus pipeline for ChIP-seq analysis.  Basespace’s RNA express pipeline (RNA Express Legacy; version: 1.0.0), using the STAR aligner and DESEQ2 to call differentially expressed genes.
The quality of ChIP-seq libraries was confirmed by the number and percentage of mapped and confidently mapped reads. Peak calling was performed using DNAnex with us settings for peak enrichment >20, peak-to-background enrichment >3, a minimum ratio between uniquely and repetitively mapped reads of 3:1, a kernel bandwith of 30.0, and enabling FDR calculation.
Distribution and conservation analysis of the ChIP-seq peaks was performed using Galaxy.
For RNA seq, raw FASTQ sequence files obtained from the RNA-seq experiments were analyzed in Basespace’s RNA express pipeline (RNA Express Legacy; version: 1.0.0), using the STAR aligner and DESEQ2 to call differentially expressed genes.
Genome_build: hg19

source_name: a human breast cancer cell line

growth_protocol: MDA-MB-231 cells were grown in DMEM media with 10% FBS and 1% antibiotics

extract_protocol:
For ChIP-seq, after fixation with 37% formaldehyde, nuclei was collected by sonication (Bioruptor, Diagenode). DNA-MAFF bound was immunoprecipitated with a MAFF-specific antibody. For RNA-seq, RNA was collected using a Rneasy kit (Qiagen)
For ChIP-seq, libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix set for Illumina (NEB #E6240) and NEBNext Multiplex Oligos for Illumina (NEB #E7730S). For RNA-seq, libraries were prepared using Illumina's TruSeq RNA library prep kit v2.
ChIP seq and RNA seq

treatment_protocol: For ChIP-seq, cells were grown under normoxia or hypoxia (0.5% O2) for 24hours. For RNA-seq, cells were knocked down with siSCR or siMAFF and grown under normoxia or hypoxia (0.5% O2) for 24hours.

tag: origin

value: mammary gland/breast; derived from metastatic site:pleural effusion

tag: disease

value: adenocarcinoma

tag: antibody or sirna

value: ONTARGET plus SMARTpool siRNAs


title: MDAsiSCRHyp2

description: RNA seq data


title: 6999AA_MSCB-087


title: MDAsiSCRHyp1

description: RNA seq data


title: MDAsiSCR3

description: RNA seq data


title: 6999AA_MSCB-086


title: 6999AA_MSCB-084


title: 6999AA_MSCB-083


title: MDAsiSCR2

description: RNA seq data


title: 6999AA_MSCB-085


title: MDAsiSCR1

description: RNA seq data


title: 6999AA_MSCB-082


title: MDAsiMAFFHyp3

description: RNA seq data


title: MDAsiMAFF

description: RNA seq data


title: MDAsiMAFFHyp2

description: RNA seq data


title: FDC2

value: healthy donor


title: 6999AA_MSCB-081


title: MDAsiMAFFHyp1

description: RNA seq data


title: 6999AA_MSCB-080


title: 6999AA_MSCB-079


title: MDAsiMAFF2

description: RNA seq data


title: RA patients 2124-JS-0034_23

city: Winnipeg

first: Vidyanand

last: Anaparti

state: MB

address: 715 McDermot Avenue

country: Canada

institute: University of Manitoba

description: RA patients

data_processing:
Bowtie 2 was used for mapping and sequence alignment against hg19 version of reference genome and Bismark was used to calculate beta scores indicating methylation level at each CpG locus across the target region after performing batch normalization. Only CpGs with a minimum depth coverage >15x were included and sites containing missing values were excluded. Filtered beta values were log2 transformed and differential methylation at each CpG site was calculated (RA – HC). Benjamini-Hochberg correction was used to perform multiple correction (FDR > 5%) and differentially methylated loci (DMLs) with FDR-corrected P-values < 0.05 were considered as significant. To annotate and determine the genomic distribution of identified DMLs, we utilized diffReps script region_analysis.pl.
Genome_build: hg19
Supplementary_files_format_and_content: beta

source_name: Whole blood

extract_protocol:
Venous blood was collected into Paxgene® Blood DNA tubes (Qiagen Inc, Canada), and processed using QIAamp DNA Blood Maxi Kit (Qiagen Inc, Canada) per the manufacturer’s instructions to isolate genomic DNA. Quality and concentration of isolated DNA was determined by Nanodrop and Qubit high sensitivity double-stranded DNA assays.
CATCH-Seq target enrichment technology (Ubiquity Genomics, Huntsville, AL) was used to perform bisulfite sequencing of coding and non-coding regions encompassing ~3.8Mb around the MHC locus located within chromosome 6 (chr6:29530000-33500000). Library creation, bisulfite treatment, and Illumina sequencing for each DNA sample and beta value estimation for each CpG across the MHC region were performed by Ubiquity Genomics Inc according to their standardized methodologies. Briefly, DNA samples were sheared, end-repaired, hybridized to streptavidin-coated Dyna beads and ligated to uniquely barcoded custom methylated/non-methylated adapters. For target enrichment, pooled DNA samples bound to streptavidin-coated Dyna beads were captured with biotinylated probes generated from human BAC library. Following capture, target enriched library was bisulfite (EpiTect Bisulfite Kit, Qiagen) treated, amplified by PCR, and sequenced using an Illumina HiSeq2500.

tag: condition

value: RA


title: MDAsiMAFF3

description: RNA seq data


title: RA patients 2124-JS-0034_24

description: RA patients


title: MAFF ChIP-seq Hypoxia

description: MAFF ChIP-seq after hypoxia treatment

value: MAFF antibody (MilliporeSigma #M8194)


title: 6999AA_MSCB-078

city: Barcelona

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

tag: cell type


title: 6999AA_MSCB-089


title: 6999AA_MSCB-074


title: MAFF ChIP-seq Input normoxia

description: Input sample after normoxia treatment


title: MAFF ChIP-seq normoxia

description: MAFF ChIP-seq after normoxia treatment


title: 6999AA_MSCB-073


title: 6999AA_MSCB-070


title: RA patients 2124-JS-0034_19

description: RA patients


title: 6999AA_MSCB-072


title: 6999AA_MSCB-067


title: RA patients 2124-JS-0034_21

description: RA patients


title: 6999AA_MSCB-066


title: 6999AA_MSCB-071


title: RA patients 2124-JS-0034_20

description: RA patients


title: 6999AA_MSCB-075


title: RA patients 2124-JS-0034_22

description: RA patients


title: MAFF ChIP-seq Input Hypoxia

description: Input sample after hypoxia treatment


title: 6999AA_MSCB-076


title: 6999AA_MSCB-077


title: 6999AA_MSCB-068


title: RA patients 2124-JS-0034_18

description: RA patients


title: 6999AA_MSCB-069


title: RA patients 2124-JS-0034_16

description: RA patients


title: 6999AA_MSCB-065


title: RA patients 2124-JS-0034_17

description: RA patients


title: RA patients 2124-JS-0034_15

description: RA patients


title: 6999AA_MSCB-061


title: 6999AA_MSCB-063


title: 6999AA_MSCB-064


title: RA patients 2124-JS-0034_14

description: RA patients


title: 6999AA_MSCB-060


title: RA patients ubp5_s8

description: RA patients


title: RA patients ubp5_s6

description: RA patients


title: 6999AA_MSCB-058


title: 6999AA_MSCB-057


title: RA patients 2124-JS-0034_13

description: RA patients


title: RA patients ubp5_s9

description: RA patients


title: 6999AA_MSCB-062


title: RA patients ubp5_s7

description: RA patients


title: Controls (ACPA-/FDR) 2124-JS-0034_12

description: Controls (ACPA-/FDR)

value: control


title: Controls (ACPA-/FDR) 2124-JS-0034_11

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-053


title: 6999AA_MSCB-054


title: Controls (ACPA-/FDR) 2124-JS-0034_8

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-059


title: 6999AA_MSCB-056


title: 6999AA_MSCB-052


title: Controls (ACPA-/FDR) 2124-JS-0034_7

description: Controls (ACPA-/FDR)


title: Controls (ACPA-/FDR) 2124-JS-0034_6

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-050


title: 6999AA_MSCB-055


title: RA patients ubp5_s10

description: RA patients


title: Controls (ACPA-/FDR) 2124-JS-0034_10

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-051


title: Controls (ACPA-/FDR) 2124-JS-0034_9

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-049


title: Controls (ACPA-/FDR) 2124-JS-0034_5

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-047


title: 6999AA_MSCB-048


title: Controls (ACPA-/FDR) ubp5_s3

description: Controls (ACPA-/FDR)


title: Controls (ACPA-/FDR) 2124-JS-0034_3

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-041


title: Controls (ACPA-/FDR) 2124-JS-0034_1

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-046


title: Controls (ACPA-/FDR) 2124-JS-0034_4

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-042


title: 6999AA_MSCB-043


title: 6999AA_MSCB-044


title: Controls (ACPA-/FDR) ubp5_s5

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-039


title: Controls (ACPA-/FDR) ubp5_s2

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-040


title: Controls (ACPA-/FDR) 2124-JS-0034_2

description: Controls (ACPA-/FDR)


title: Controls (ACPA-/FDR) ubp5_s1

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-038


title: 6999AA_MSCB-036


title: 6999AA_MSCB-037


title: 6999AA_MSCB-035


title: 1578AA_MSCB-188

source_name: pancreas

value: pancreatic islet cell


title: 1578AA_MSCB-189


title: 1578AA_MSCB-190


title: 1578AA_MSCB-191


title: 6999AA_MSCB-034


title: 1578AA_MSCB-187


title: 1578AA_MSCB-192


title: 6999AA_MSCB-033


title: 1578AA_MSCB-186


title: 6999AA_MSCB-045


title: Controls (ACPA-/FDR) ubp5_s4

description: Controls (ACPA-/FDR)


title: 6999AA_MSCB-032


title: 1578AA_MSCB-185


title: 1578AA_MSCB-183


title: 6999AA_MSCB-031


title: 1578AA_MSCB-184


title: 1578AA_MSCB-182


title: 6999AA_MSCB-027


title: 1578AA_MSCB-179


title: 6999AA_MSCB-028


title: 6999AA_MSCB-026


title: 1578AA_MSCB-178


title: 6999AA_MSCB-024


title: 1578AA_MSCB-176


title: 6999AA_MSCB-021


title: 6999AA_MSCB-022


title: 6999AA_MSCB-023


title: 1578AA_MSCB-177


title: 6999AA_MSCB-020


title: 6999AA_MSCB-019


title: 1578AA_MSCB-171


title: 1578AA_MSCB-172


title: 6999AA_MSCB-018


title: 6999AA_MSCB-029


title: 1578AA_MSCB-181


title: 6999AA_MSCB-017


title: 1578AA_MSCB-170


title: 1578AA_MSCB-180


title: 1578AA_MSCB-169


title: 6999AA_MSCB-025


title: 6999AA_MSCB-030


title: 6999AA_MSCB-016


title: 6999AA_MSCB-015


title: 6999AA_MSCB-013


title: 6999AA_MSCB-014


title: 1578AA_MSCB-168


title: 1578AA_MSCB-175


title: 1578AA_MSCB-165


title: 6999AA_MSCB-012


title: 6999AA_MSCB-011


title: 1578AA_MSCB-174


title: 1578AA_MSCB-167


title: 1578AA_MSCB-166


title: 6999AA_MSCB-010


title: 1578AA_MSCB-163


title: 1578AA_MSCB-162


title: 1578AA_MSCB-164


title: 6999AA_MSCB-009


title: 1578AA_MSCB-173


title: 6999AA_MSCB-008


title: 6999AA_MSCB-007


title: 1578AA_MSCB-161


title: 6999AA_MSCB-006


title: 1578AA_MSCB-160


title: 1578AA_MSCB-159


title: 6999AA_MSCB-005


title: 1578AA_MSCB-158


title: 6999AA_MSCB-003


title: 1578AA_MSCB-156


title: 6999AA_MSCB-004


title: 1578AA_MSCB-155


title: 6999AA_MSCB-002


title: 6999AA_MSCB-001


title: 6998AA_MSCB-192


title: 1578AA_MSCB-153


title: 6998AA_MSCB-191


title: 1578AA_MSCB-152


title: 6998AA_MSCB-190


title: 1578AA_MSCB-151


title: 6998AA_MSCB-189


title: 1578AA_MSCB-150


title: 6998AA_MSCB-188


title: 6998AA_MSCB-186


title: 1578AA_MSCB-147


title: 6998AA_MSCB-185


title: 6998AA_MSCB-187


title: 1578AA_MSCB-149


title: 6998AA_MSCB-184


title: 1578AA_MSCB-145


title: 6998AA_MSCB-183


title: 1578AA_MSCB-144


title: 6998AA_MSCB-182


title: 1578AA_MSCB-142


title: 6998AA_MSCB-180


title: 1578AA_MSCB-143


title: 1578AA_MSCB-157


title: 1578AA_MSCB-154


title: 6998AA_MSCB-181


title: 1578AA_MSCB-141


title: 1578AA_MSCB-140


title: 6998AA_MSCB-179


title: 1578AA_MSCB-139


title: 6998AA_MSCB-176


title: 6998AA_MSCB-177


title: 1578AA_MSCB-138


title: 1578AA_MSCB-136


title: 1578AA_MSCB-137


title: 1578AA_MSCB-148


title: 1578AA_MSCB-146


title: 1578AA_MSCB-135


title: 1578AA_MSCB-134


title: 6998AA_MSCB-173


title: 6998AA_MSCB-172


title: 6998AA_MSCB-171


title: 6998AA_MSCB-170


title: 1578AA_MSCB-132


title: 1578AA_MSCB-131


title: 1578AA_MSCB-130


title: 6998AA_MSCB-166


title: 1578AA_MSCB-127


title: 6998AA_MSCB-167


title: 1578AA_MSCB-128


title: 6998AA_MSCB-178


title: 6998AA_MSCB-168


title: 6998AA_MSCB-175


title: 6998AA_MSCB-164


title: 6998AA_MSCB-163


title: 6998AA_MSCB-162


title: 6998AA_MSCB-174


title: 6998AA_MSCB-161


title: 1578AA_MSCB-122


title: 1578AA_MSCB-126


title: 1578AA_MSCB-125


title: 1578AA_MSCB-123


title: 6998AA_MSCB-159


title: 1578AA_MSCB-124


title: 1578AA_MSCB-133


title: 1578AA_MSCB-120


title: 1578AA_MSCB-119


title: 6998AA_MSCB-169


title: 6998AA_MSCB-157


title: 6998AA_MSCB-158


title: 1578AA_MSCB-118


title: 6998AA_MSCB-156


title: 6998AA_MSCB-165


title: 6998AA_MSCB-155


title: 1578AA_MSCB-116


title: 1578AA_MSCB-117


title: 6998AA_MSCB-154


title: 1578AA_MSCB-115


title: 6998AA_MSCB-153


title: 1578AA_MSCB-114


title: 6998AA_MSCB-152


title: 1578AA_MSCB-129


title: 6998AA_MSCB-151


title: 1578AA_MSCB-113


title: 1578AA_MSCB-112


title: 6998AA_MSCB-150


title: 6998AA_MSCB-160


title: 1578AA_MSCB-121


title: 1578AA_MSCB-110


title: 1578AA_MSCB-111


title: 6998AA_MSCB-148


title: 1578AA_MSCB-109


title: 6998AA_MSCB-146


title: 1578AA_MSCB-107


title: 6998AA_MSCB-145


title: 1578AA_MSCB-108


title: 6998AA_MSCB-144


title: 1578AA_MSCB-106


title: 1578AA_MSCB-105


title: 6998AA_MSCB-143


title: 1578AA_MSCB-104


title: 1578AA_MSCB-103


title: 6998AA_MSCB-140


title: 1578AA_MSCB-102


title: 1578AA_MSCB-101


title: 6998AA_MSCB-139


title: 6998AA_MSCB-141


title: 1578AA_MSCB-100


title: 6998AA_MSCB-138


title: 1578AA_MSCB-098


title: 1578AA_MSCB-097


title: 6998AA_MSCB-136


title: 6998AA_MSCB-137


title: 6998AA_MSCB-149


title: 1578AA_MSCB-099


title: 6998AA_MSCB-147


title: 6998AA_MSCB-135


title: 6998AA_MSCB-133


title: 6998AA_MSCB-134


title: 1578AA_MSCB-094


title: 6998AA_MSCB-132


title: 1578AA_MSCB-095


title: 1578AA_MSCB-093


title: 6998AA_MSCB-142


title: 6998AA_MSCB-130


title: 6998AA_MSCB-129


title: 1578AA_MSCB-091


title: 1578AA_MSCB-092


title: 1578AA_MSCB-090


title: 6998AA_MSCB-128


title: 6998AA_MSCB-131


title: 1578AA_MSCB-088


title: 6998AA_MSCB-126


title: 1578AA_MSCB-089


title: 1578AA_MSCB-087


title: 6998AA_MSCB-125


title: 1578AA_MSCB-086


title: 6998AA_MSCB-127


title: 6998AA_MSCB-124


title: 1578AA_MSCB-084


title: 6998AA_MSCB-121


title: 1578AA_MSCB-085


title: 6998AA_MSCB-120


title: 1578AA_MSCB-081


title: 6998AA_MSCB-122


title: 6998AA_MSCB-123


title: 1578AA_MSCB-096


title: 1578AA_MSCB-082


title: 1578AA_MSCB-080


title: 1578AA_MSCB-079


title: 6998AA_MSCB-117


title: 1578AA_MSCB-077


title: 1578AA_MSCB-078


title: 6998AA_MSCB-118


title: 6998AA_MSCB-116


title: 1578AA_MSCB-076


title: 6998AA_MSCB-115


title: 1578AA_MSCB-075


title: 6998AA_MSCB-114


title: 1578AA_MSCB-074


title: 6998AA_MSCB-113


title: 1578AA_MSCB-073


title: 6998AA_MSCB-111


title: 6998AA_MSCB-112


title: 1578AA_MSCB-083


title: 1578AA_MSCB-071


title: 6998AA_MSCB-109


title: 6998AA_MSCB-110


title: 1578AA_MSCB-070


title: 6998AA_MSCB-108


title: 6998AA_MSCB-119


title: 1578AA_MSCB-069


title: 1578AA_MSCB-067


title: 1578AA_MSCB-068


title: 6998AA_MSCB-106


title: 6998AA_MSCB-107


title: 6998AA_MSCB-105


title: 1578AA_MSCB-066


title: 6998AA_MSCB-104


title: 1578AA_MSCB-065


title: 1578AA_MSCB-063


title: 6998AA_MSCB-102


title: 6998AA_MSCB-101


title: 1578AA_MSCB-064


title: 6998AA_MSCB-103


title: 1578AA_MSCB-061


title: 1578AA_MSCB-062


title: 6998AA_MSCB-100


title: 1578AA_MSCB-072


title: 1578AA_MSCB-060


title: 1578AA_MSCB-059


title: 6998AA_MSCB-098


title: 6998AA_MSCB-097


title: 6998AA_MSCB-099


title: 1578AA_MSCB-058


title: 6998AA_MSCB-096


title: 6998AA_MSCB-094


title: 1578AA_MSCB-056


title: 1578AA_MSCB-055


title: 6998AA_MSCB-093


title: 6998AA_MSCB-095


title: 6998AA_MSCB-092


title: 1578AA_MSCB-054


title: 1578AA_MSCB-053


title: 1578AA_MSCB-052


title: 6998AA_MSCB-090


title: 6998AA_MSCB-089


title: 1578AA_MSCB-051


title: 6998AA_MSCB-091


title: 1578AA_MSCB-050


title: 6998AA_MSCB-087


title: 1578AA_MSCB-047


title: 6998AA_MSCB-088


title: 1578AA_MSCB-048


title: 6998AA_MSCB-086


title: 6998AA_MSCB-085


title: 1578AA_MSCB-046


title: 1578AA_MSCB-049


title: 1578AA_MSCB-044


title: 6998AA_MSCB-083


title: 1578AA_MSCB-045


title: 6998AA_MSCB-084


title: 1578AA_MSCB-057


title: 6998AA_MSCB-082


title: 1578AA_MSCB-043


title: 6998AA_MSCB-080


title: 6998AA_MSCB-079


title: 6998AA_MSCB-081


title: 1578AA_MSCB-040


title: 6998AA_MSCB-078


title: 1578AA_MSCB-039


title: 1578AA_MSCB-041


title: 1578AA_MSCB-042


title: 6998AA_MSCB-077


title: 1578AA_MSCB-038


title: 1578AA_MSCB-037


title: 6998AA_MSCB-074


title: 6998AA_MSCB-075


title: 1578AA_MSCB-036


title: 1578AA_MSCB-035


title: 1578AA_MSCB-034


title: 6998AA_MSCB-072


title: 1578AA_MSCB-033


title: 6998AA_MSCB-071


title: 6998AA_MSCB-070


title: 1578AA_MSCB-032


title: 1578AA_MSCB-031


title: 6998AA_MSCB-069


title: 1578AA_MSCB-030


title: 6998AA_MSCB-068


title: 6998AA_MSCB-067


title: 1578AA_MSCB-028


title: 1578AA_MSCB-029


title: 1578AA_MSCB-027


title: 1578AA_MSCB-026


title: 6998AA_MSCB-066


title: 6998AA_MSCB-076


title: 1578AA_MSCB-025


title: 6998AA_MSCB-064


title: 6998AA_MSCB-062


title: 1578AA_MSCB-024


title: 6998AA_MSCB-065


title: 1578AA_MSCB-023


title: 6998AA_MSCB-063


title: 6998AA_MSCB-061


title: 6998AA_MSCB-073


title: 6998AA_MSCB-060


title: 1578AA_MSCB-021


title: 1578AA_MSCB-019


title: 1578AA_MSCB-020


title: 6998AA_MSCB-057


title: 1578AA_MSCB-018


title: 1578AA_MSCB-017


title: 6998AA_MSCB-053


title: 1578AA_MSCB-014


title: 1578AA_MSCB-015


title: 6998AA_MSCB-056


title: 1578AA_MSCB-013


title: 6998AA_MSCB-051


title: 6998AA_MSCB-050


title: 1578AA_MSCB-010


title: 1578AA_MSCB-011


title: 1578AA_MSCB-012


title: 6998AA_MSCB-049


title: 6998AA_MSCB-048


title: 1578AA_MSCB-009


title: 6998AA_MSCB-047


title: 6998AA_MSCB-046


title: 6998AA_MSCB-058


title: 1578AA_MSCB-022


title: 1578AA_MSCB-008


title: 6998AA_MSCB-059


title: 6998AA_MSCB-045


title: 1578AA_MSCB-007


title: 1578AA_MSCB-006


title: 6998AA_MSCB-055


title: 1578AA_MSCB-005


title: 6998AA_MSCB-054


title: 6998AA_MSCB-043


title: 1578AA_MSCB-016


title: 1578AA_MSCB-004


title: 6998AA_MSCB-052


title: 6998AA_MSCB-042


title: 1578AA_MSCB-003


title: 6998AA_MSCB-041


title: Macrophage_M2_Succinate+YM-254890_4

first: Chris

last: O'Callaghan

data_processing:
Samples were demultiplexed and sequences converted to FASTQ format using bcl2fastq.
Adapter sequences were trimmed using PEAT-1.2.4 before mapping to the hg19 reference genome using STAR 2.6 with default parameters.
Alignments were filtered using samtools 1.9 to retain only uniquely aligned, properly-paired reads.
Gene-level read counts were obtained using featureCounts (from Rsubread 1.32.4) in R, and raw counts were TMM normalised and analysed with edgeR 3.30.3.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix containing raw gene-level read counts for all samples.

source_name: Peripheral blood monocyte derived macrophages

extract_protocol:
Adherent macrophages were lysed directly with TRIzol reagent and total RNA was extracted using the Qiagen RNeasy Micro kit (Qiagen, Hilden Germany).
PolyA-selected, strand-specific RNA-seq libraries were prepared for BGI DNBSEQ-G400 or Illumina HiSeq 4000 sequencing according to standard protocols.

tag: treatment

tag: polarisation

tag: donor


title: Macrophage_M2_Succinate+YM-254890_3


title: 1578AA_MSCB-002


title: Macrophage_M2_Succinate+YM-254890_2


title: Macrophage_M2_Succinate+YM-254890_1


title: 6998AA_MSCB-040


title: Macrophage_M2_Succinate+NF-56-EJ40_4


title: 1578AA_MSCB-001


title: 6998AA_MSCB-039


title: 1577AA_MSCB-192


title: Macrophage_M2_Succinate+NF-56-EJ40_3


title: 6998AA_MSCB-038


title: 6998AA_MSCB-044


title: Macrophage_M2_Succinate+NF-56-EJ40_2


title: Macrophage_M2_Succinate+NF-56-EJ40_1


title: 1577AA_MSCB-191


title: Macrophage_M2_Succinate_4

value: Succinate


title: Macrophage_M2_Succinate_3


title: 6998AA_MSCB-037


title: Macrophage_M2_Succinate_2


title: Macrophage_M2_Succinate_1


title: 1577AA_MSCB-189


title: 6998AA_MSCB-036


title: Macrophage_M2_DMSO_4

value: Control (DMSO)


title: Macrophage_M2_DMSO_3


title: 6998AA_MSCB-035


title: 1577AA_MSCB-188


title: Macrophage_M2_DMSO_2


title: Macrophage_M2_DMSO_1


title: 6998AA_MSCB-034


title: Macrophage_M2_H2O_4

value: Control (H2O)


title: 6998AA_MSCB-033

value: primary bladder epithelial cell


title: 6998AA_MSCB-032


title: Macrophage_M2_H2O_3


title: 1577AA_MSCB-186


title: Macrophage_M2_H2O_1


title: 1577AA_MSCB-185


title: flower_leaf_nanopore_data

city: Guangzhou

first: zeyu

last: zhang

state: Guangzhou

address: Kaiyuan streat 190

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
In Nanopore sequencing file, FAST5 was converted into a single file with the command of command multi_to_single_fast5 from ont_fast5_api (https://github.com/nanoporetech/ont_fast5_api). Then the script of read_fast5_basecaller.py from Albacore 1.2.x (Oxford Nanopore Technologies Ltd.) was used to do base calling for each FAST5 file for subsequent analysis. Then Tombo software (https://nanoporetech.github.io/tombo) was used for data processing and extraction of methylation file. In brief, moso bamboo genomic index file was generated using resquiggle command from Tombo. Then 5mC methylations were identified using Tombo detect_modifications alternative_model. Finally, the coordinate of methylated site was extracted using tomb text_output browser_files --statistics-filename --file-types dampened_fraction --browser-file.
Genome_build: P.heterocycla-v1.0 (http://forestry.fafu.edu.cn/bioinfor/db/ASmiR/EtractSeq/phe/)

source_name: Phyllostachys edulis

growth_protocol: The materials were collected from the botanical garden of bamboo at Guangxi Zhuang Autonomous Region in June.

extract_protocol:
Genomic DNA was isolated with Plant Genomic DNA Kit (Tiangen, Cat. #DP305-02, China).
Oxford Nanopore Technologies, SQK-LSK108

treatment_protocol: No treatment

tag: age

value: Last year (flower)


title: 1577AA_MSCB-184


title: 6998AA_MSCB-030

source_name: bladder


title: 6998AA_MSCB-031


title: Cast

city: Vienna

first: Juan

last: Garcia

address: Althanstraße 14

country: Austria

institute: University of Vienna

data_processing:
The sequencing single reads were trimmed for adaptor sequence, and filtered for low-complexity and low-quality sequence.
Reads shorter than 50 bp or with quality mean < 30 were removed using Prinseq-lite-0.20.3.
Full length ribosomal genes were reconstructed from short reads in each sample with Emirge with parameters -f ./silva/SSURef_111_candidate_db.fasta -b ./silva/SSURef_111_candidate_db_btindex --phred33 -j 0.97
Contigs were built out of short-read using the Velvet de novo assembler. The minimun contig length was 500 bp
Prokka 1.11 was used for the  annotation of coding regions and RNA genes present on the contigs with parameters --kingdom Bacteria --usegenus --hmms /home/software/prokka-1.11/db/hmm/Pfam-A.hmm --metagenome --evalue 1e-08. Gene abundance was calculated based on the Prokka annotation
Genome_build: Prokka v. 1.11
Supplementary_files_format_and_content: .txt file reports abundance measurements

organism: seawater metagenome

source_name: CTD Cast, Natural Sample

growth_protocol: In the dark, in situ temperature (~3ºC)

extract_protocol:
Water samples were filtered onto 0.2µm pore size polycarbonate filters, flash frozen in liquid nitrogen and preserved at -80ºC. RNA was extracted using the mirVana™ miRNA Isolation Kit, purified and concentrated with the RNeasy MinElute Cleanup Kit. cDNA libraries were generated using the Ovation RNA-Seq System V2 Kit. Sequencing libraries were constructed using Illumina’s Truseq RNA Sample Prep kit v2 according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: depth

tag: latitude

tag: longitude

value: CTD Cast, Natural Sample


title: TD3 T72

source_name: Thiosulfate + DOM, T=72

treatment_protocol: Thiosulfate + Glucose(10µM)

value: Thiosulfate + DOM

tag: time


title: 1577AA_MSCB-183

institute: Centro Nacional de Análisis Genómico


title: 1577AA_MSCB-190


title: 6998AA_MSCB-029


title: C3 T72

source_name: Control, T=72

treatment_protocol: control

value: Control


title: TD1 T1

source_name: Thiosulfate + DOM, T=1


title: 1577AA_MSCB-182


title: 6998AA_MSCB-028


title: T1 T1

source_name: Thiosulfate, T=1

treatment_protocol: Thiosulfate (1µM)

value: Thiosulfate


title: 1577AA_MSCB-187


title: C1 T1

source_name: Control, T=1


title: 6998AA_MSCB-027


title: Macrophage_M2_H2O_2

city: Oxford

address: Roosevelt Drive


title: 6998AA_MSCB-026


title: 1577AA_MSCB-180


title: 1577AA_MSCB-179


title: 1577AA_MSCB-178


title: T3 T72

source_name: Thiosulfate, T=72


title: 6998AA_MSCB-024


title: 1577AA_MSCB-177


title: three_week_leaf_nanopore_data

value: three week


title: F2 forskolin2

city: Los Angeles

first: William

last: Lowry

state: CA

address: 621 Charles Young Drive

department: MCDB

institute: UCLA

data_processing:
Data was sequenced on HiSeq3000 using a single-read 50bp read run
Data quality check with Illumina SAV
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
Partek flow and Ingenuity Pathway Analysis (IPA) were used for bioinformatics methods and data analysis, respectively. Trimming of bases was performed based on From 5' end, the bases to be trimmed was 5.
Partek E/M was used to quantify reads to an annotation model. After obtaining transcript counts, the counts were normalized by CPM (counts per million), 1.0E-4.
p<.01, FDR<.01, and |FC|>2 for all differential gene expression results
Genome_build: USCS STAR - 2.6 1d
Supplementary_files_format_and_content: normalized expression of all genes

source_name: Total epidermis

growth_protocol: 7 week-old C57BL/6 male mice were dorsally shaved and subjected to topical treatment

extract_protocol:
Total epidermis was isolated from whole skin tissue via dissection and overnight trypsinization. Cell suspension was then treated with Trizol and subjected to RNA extraction using the Qiagen RNeasy Micro Kit.
Libraries for RNA-Seq were prepared with Illumina stranded mRNA seq

treatment_protocol: Compounds were resuspneded in DMSO and PLO lotion vehicle at 5 times the IC50 according to manufacturer datasheet

value: Epidermal

tag: strain

value: 10um forskolin

tag: genotype

value: wildtype

tag: Sex

value: male

value: post natal day 49


title: C1.2 control

value: untreated


title: F1 forskolin1

value: 10uM forskolin


title: cAMP1 cyclicAMP1

value: 1.325mM cAMP


title: LCL161_LT_1 (vitro)

city: Boston

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

description: BMDMs treated in vitro with LCL161 and LTα1β2 for 24h

data_processing:
FASTQs were aligned using STAR (v2.7.3a) against the GRCm38 genome with ENSEMBL 97 exon annotations.
Gene-level counts were obtained from the alignments using the R package "Rsubread" (v1.32.4).
Count normalization and differential expression analysis was performed with the R package "DESeq2" (v1.26.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated text file of raw (unnormalized) gene-level counts for each sample

source_name: Bone Marrow Derived Macrophages

extract_protocol:
Total RNA was prepared from treated BMDMs using a Qiagen RNeasy kit according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Bone Marrow Derived Macrophages (BMDMs)


title: LT_2 (vitro)

description: BMDMs treated in vitro with LTα1β2 for 24h

value: Lymphotoxin


title: LCL161_LT_2 (vitro)

description: BMDMs treated in vitro withLCL161 and LTα1β2 for 24h


title: 1577AA_MSCB-181

value: pancreatic islet cell


title: LT_1 (vitro)


title: Vehicle_2 (vitro)

description: BMDMs treated in vitro with Vehicle for 24h

value: Vehicle


title: cAMP2 cyclicAMP2


title: 1577AA_MSCB-176


title: 1577AA_MSCB-175


title: 6998AA_MSCB-021

value: primary bladder epithelial cell


title: 1577AA_MSCB-174


title: pol2-S430A 90' 50 mM HU

city: Madrid

first: Mohammed

last: Al Mamun

state: Madrid

address: Calle Ramiro de Maeztu, 9

department: Cell and Molecular Biology

institute: CIB-CSIC

data_processing:
DNA libraries were sequenced on Illumina HiSeq2500 platform using single-end sequencing strategy.
Fastq files were aligned against S288C yeast reference genome using Bowtie 2 version 2.3.5.1
sort and index the resultant bam (converted from sam) files using samtools version 1.9
read coverage were mapped in 100 bp windows using bedtools version 2.29.0
ratios were made between replication time points against corresponding G1s using Repliscope version 1.1.0
Genome_build: S288C
Supplementary_files_format_and_content: bed formatted binwise coverage with score field
Supplementary_files_format_and_content: bigwig files containing ration between replication time points against the G1 sample

organism: Saccharomyces cerevisiae

growth_protocol: All strains are RAD5+ derivatives from W303 and are listed in Table S1. For 10-fold serial dilution assays cells were grown on YPDA for 48 hours at 30ºC, unless otherwise stated. α-factor was used to a final concentration of 5 µg/ml to arrest cells in G1. Release into S-phase in the presence of HU was performed at the concentrations and for the times indicated in the figures.

extract_protocol: CGS analysis was performed as previously reported (Frattini et al., 2017).

value: treated with hydroxyurea


title: pol2-S430A 120' 50 mM HU

treatment_protocol: CGS analysis was performed as previously reported (Frattini et al., 2017).


title: 6998AA_MSCB-025


title: pol2-S430A 60' 50 mM HU


title: pol2-S430A 30' 50 mM HU


title: 6998AA_MSCB-020


title: 1577AA_MSCB-173


title: 6998AA_MSCB-023


title: 1577AA_MSCB-172


title: 6998AA_MSCB-019


title: 6998AA_MSCB-018


title: 6998AA_MSCB-017


title: wild type 90' 50 mM HU

source_name: wild type 90' 50 mM HU


title: wild type 30' 50 mM HU

source_name: wild type 30' 50 mM HU


title: wild type 120' 50 mM HU

source_name: wild type 120' 50 mM HU


title: 1577AA_MSCB-170


title: wild type G1

source_name: wild type G1

value: treated with αFactor


title: 6998AA_MSCB-016


title: 6998AA_MSCB-022


title: rad53 pol2D ppol2-S430D exo1D 90' 25 mM HU


title: Vehicle_1 (vitro)


title: wild type 60' 50 mM HU

source_name: wild type 60' 50 mM HU


title: rad53 pol2D ppol2-S430D exo1D 60' 25 mM HU


title: 1577AA_MSCB-169

source_name: pancreas


title: 6998AA_MSCB-015


title: rad53 pol2D ppol2-S430D exo1D G1

source_name: rad53 pol2D ppol2-S430D exo1D G1


title: rad53 pol2D ppol2-S430D exo1D  30' 25 mM HU


title: 1577AA_MSCB-168


title: 6998AA_MSCB-014

source_name: bladder


title: rad53 pol2D pPOL2 exo1D 60' 25 mM HU

source_name: rad53 pol2D pPOL2 exo1D 60' 25 mM HU


title: rad53 pol2D pPOL2 exo1D 90' 25 mM HU

source_name: rad53 pol2D pPOL2 exo1D 90' 25 mM HU


title: 1577AA_MSCB-167


title: 6998AA_MSCB-013


title: pol2-S430A G1

source_name: pol2-S430A G1


title: rad53 pol2D pPOL2 exo1D 30' 25 mM HU

source_name: rad53 pol2D pPOL2 exo1D 30' 25 mM HU


title: 1577AA_MSCB-171


title: 1577AA_MSCB-166


title: 6998AA_MSCB-012


title: rad53 pol2D ppol2-S430D 90' 25 mM HU

source_name: rad53 pol2D ppol2-S430D 90' 25 mM HU


title: 1577AA_MSCB-165


title: rad53 pol2D ppol2-S430D 60' 25 mM HU

source_name: rad53 pol2D ppol2-S430D 60' 25 mM HU


title: rad53 pol2D ppol2-S430D 30' 25 mM HU

source_name: rad53 pol2D ppol2-S430D 30' 25 mM HU


title: 1577AA_MSCB-164


title: rad53 pol2D pPOL2 90' 25 mM HU

source_name: rad53 pol2D pPOL2 90' 25 mM HU


title: 6998AA_MSCB-010


title: rad53 pol2D pPOL2 60' 25 mM HU

source_name: rad53 pol2D pPOL2 60' 25 mM HU


title: rad53 pol2D pPOL2 G1

source_name: rad53 pol2D pPOL2 G1


title: rad53 pol2D pPOL2 30' 25 mM HU

source_name: rad53 pol2D pPOL2 30' 25 mM HU


title: 1577AA_MSCB-163


title: 6998AA_MSCB-009


title: rad53 pol2exo- exo1D 90' 10 mM HU

source_name: rad53 pol2exo- exo1D 90' 10 mM HU


title: 1577AA_MSCB-161


title: 6998AA_MSCB-008


title: 1577AA_MSCB-162


title: rad53 pol2D pPOL2 exo1D G1

source_name: rad53 pol2D pPOL2 exo1D G1


title: rad53 pol2exo- exo1D 120' 10 mM HU

source_name: rad53 pol2exo- exo1D 120' 10 mM HU


title: rad53 pol2exo- exo1D 60' 10 mM HU

source_name: rad53 pol2exo- exo1D 60' 10 mM HU


title: 6998AA_MSCB-007


title: 1577AA_MSCB-160

source_name: pancreas


title: rad53 exo1D 120' 10 mM HU

source_name: rad53 exo1D 120' 10 mM HU


title: 6998AA_MSCB-006

source_name: bladder


title: 1577AA_MSCB-159


title: rad53 pol2exo- exo1D 30' 10 mM HU

source_name: rad53 pol2exo- exo1D 30' 10 mM HU


title: 6998AA_MSCB-011


title: 6998AA_MSCB-005


title: rad53 exo1D 90' 10 mM HU

source_name: rad53 exo1D 90' 10 mM HU


title: rad53 pol2D ppol2-S430D G1

source_name: rad53 pol2D ppol2-S430D G1


title: 1577AA_MSCB-158


title: 6998AA_MSCB-004


title: rad53 exo1D 30' 10 mM HU

source_name: rad53 exo1D 30' 10 mM HU


title: 1577AA_MSCB-157


title: 6998AA_MSCB-003


title: rad53 exo1D 60' 10 mM HU

source_name: rad53 exo1D 60' 10 mM HU


title: rad53 exo1D G1

source_name: rad53 exo1D G1


title: rad53 pol2exo- 120' 10 mM HU

source_name: rad53 pol2exo- 120' 10 mM HU


title: rad53 pol2exo- 90' 10 mM HU

source_name: rad53 pol2exo- 90' 10 mM HU


title: 1577AA_MSCB-156


title: 6998AA_MSCB-002


title: 1577AA_MSCB-155


title: rad53 pol2exo- exo1D G1

source_name: rad53 pol2exo- exo1D G1


title: rad53 pol2exo- 30' 10 mM HU

source_name: rad53 pol2exo- 30' 10 mM HU


title: 6998AA_MSCB-001


title: rad53 pol2exo- 60' 10 mM HU

source_name: rad53 pol2exo- 60' 10 mM HU


title: rad53 120' 10 mM HU


title: rad53 pol2exo- G1

source_name: rad53 pol2exo- G1


title: 1577AA_MSCB-154


title: rad53 90' 10 mM HU

source_name: rad53 90' 10 mM HU


title: rad53 60' 10 mM HU

source_name: rad53 60' 10 mM HU


title: 1577AA_MSCB-153

source_name: pancreas


title: rad53 30' 10 mM HU

source_name: rad53 30' 10 mM HU


title: MUV056-10X

first: Li

last: Jiang

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description: Frozen nucleus sample

data_processing:
Illumina bcl2fastq 2.20 is used for demultiplexing
Sequenced reads were mapped to hg38 whole genome using cellranger (3.0.2) and default setting
UMI were calculated using cellranger (3.0.2) and default setting
Genome_build: hg38
Supplementary_files_format_and_content: Three Cell Ranger output files including barcodes, gene names, and count matrix for each sample

source_name: Human ependymoma cells

extract_protocol:
10X protocol
Illumina, Nextera XT Library Prep kit,

tag: tissue type

value: Human ependymoma

tag: age at diagnosis

tag: gender


title: 1577AA_MSCB-152


title: MUV006-10X

description: Frozen nucleus sample

value: female


title: 1577AA_MSCB-151


title: MUV051-10X

description: Frozen nucleus sample


title: MUV043/R4-10X

description: Frozen nucleus sample


title: MUV013-10X

description: Frozen nucleus sample


title: 1577AA_MSCB-150