title: 53480

city: Leipzig

first: Torsten

last: Thalheim

address: Härtelstr. 16 – 18

department: Interdisciplinary Centre for Bioinformatics

country: Germany

institute: Leipzig University

description:
Mouse9
940_53480

data_processing:
The sequenced reads underwent a quality trimming using cutadapt to ensure a minimum read length of 40 bases and a Phred quality score above 20.
The high-quality reads were mapped to the mouse reference genome NCBI37/mm9 (GRCh37/hg19) using the software tool segemehl 0.2.0 with parameter settings “-s -t 8”.
Histone modification peaks were identified by applying MACS 1.4.2 with the H3pan data as control and the following parameter settings: “--nomodel -w --space = 30 --bw 300 --pvalue 1e-5 --shiftsize 200".
The histone modification peak lists were summarized for each genotype and treatment. A peak is accepted, if it is detected in both replicates or in one replicate with a high reliability (MACS fold enrichment > 5.0). Finally, a peak is assigned to be within the promoter region of genes ((TSS) ± 1000 bases) and the gene bodies. If the overlap with a promoter or body region is at least 5%, the respective gene-associated histone is considered as modified.
X- and Y-chromosome is excluded from the analysis.
Histone 3 lysine K9 peaks located in blacklisted regions (R-package GreyListChIP) are marked.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Processed data is stored in comma separated value format and provides modification profiles of mouse genes. The list includes those genes that show a modification in at least one of the lysines K4, K9, K27 or K36 of histone 3 only, while the modification data considering lysines K4, K27 and K36 have been processed with ChIP-seq data provided in GEO under accession number GSE128842. If the lysine is modified, the respective value is '1', otherwise '0' (unmodified). In the respective columns ([Plus|Plus_irr|Minus|Minus_irr]_H3K[4|9|27|36]me3), Plus/Minus refers to the non-irradiated samples and Plus_irr/Minus_irr refers to the irradiated samples. Furthermore Plus/Minus identifies the genotype, though Plus is associated with VC-/-Msh2LoxP/LoxP (Msh2+/+) and Minus is associated with VC+/?Msh2LoxP/LoxP (Msh2-/-). In addition, beside the gene's name, the following data is provided: ensID: Ensembl transcription ID, chr: chromosome, strand, txStart, txEnd: start and end position GreyListChIP_black (in genelist_mm9_H3K9modified.csv only): The region txStart to txEnd is blacklisted in R-package GreyListChIP. The file genelist_mm9_modification.csv comprises entire modification data including any modification identified in one of the lysines K4, K9, K27 and K36. The file genelist_mm9_H3K9modified.csv is a reduced version of genelist_mm9_modification.csv and provides only those regions, that show are histone H3 lysine K9 modied. In addition, this file provides data on blacklisted regions.

source_name: jejunum

growth_protocol: The mouse strains B6.SJL-Tg(Villin-Cre)997Gum/J and B6.Cg-Msh2tm2.1Rak/J mice 4 were obtained from The Jackson Laboratory (Bar Harbor, USA). By crossing both, the conditional Msh2 allele has been placed under the control of the Villin-Cre transgene. Mice were genotyped as described  {Kucherlapati, 2010 5090 /id}. VC+/?Msh2LoxP/LoxP (Msh2-/-) and VC-/-Msh2flox/flox (Msh2+/+) mice were 113 bred under specific pathogen-free conditions. A mouse duplet consisted of one Msh2-/- and one 114 Msh2+/+ mouse from one litter.

extract_protocol:
Samples were dissected, shock frozen without delay, and stored in liquid nitrogen until further use. Chromatin was prepared from up to 50 mg tissue using SDS Shearing Buffer and the truChlP Tissue Chromatin Shearing Kit (Covaris, Brighton, UK). ChIPs were run on the IP-Star compact system using the Auto iDeal ChIP-seq kit for histones (Diagenode, Seraing, Belgium).
Library preparations were performed according to the TrueSeq LT PCR free or TruSeq Nano DNA Kit instructions (Illumina, San Diego, USA). Sequencing was performed on the Illumina HiSeq 4000 with 76 bp paired-end sequencings.

treatment_protocol: 3 month old mice were placed in the radiation unit (X-ray generator, Gulmay D3225, round tube 170 mm, radiation level at 2.5 cm: 1.068 Gy/min). One pair of mice of each genotype was irradiated with a total dose of 0.5 Gy, while the other pair was left non-radiated. All mice were killed after 28 days.

value: radiation

value: jejunum

value: 4 months

tag: chip antibody


title: B71

status: Public on Mar 07 2020

type: RNA

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

department: Surgery

country: USA

institute: Stanford University

description: Recruited progenitors

data_processing: Cycle Theshold (CT) values from PCR on Fluidigm C1

label: FAM

molecule: total RNA

organism: Mus musculus

source_name: Dorsal wound

label_protocol: FACS as lin-, GFP+

growth_protocol: Primary harvest

extract_protocol: Primary harvest

treatment_protocol: Cells 1-48 are WT mice, Cells 49-96 are EKO mice on each chip

tag: genotype

value: EKO


title: RIP-seq control rep1

type: SRA

city: Beijing

first: Jingrui

last: Li

state: Beijing

address: Medicine Building

country: China

institute: Tsinghua University

description: Random RNA

library_source: transcriptomic

data_processing:
The adapter or low quality reads were removed by Trimmomatic( Bolger, 2014) .Clean reads were aligned to the Arabidopsis reference genome (TAIR10) by using TopHat version 2.0.10(Trapnell,2009) with default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: The processed files contain three columns transcript_id, transcript location and expression level respectively. The abundance of transcripts expression is estimated by FPKM.

organism: Arabidopsis thaliana

source_name: 3-week-old plants

growth_protocol: Plants were grown on 1/2 MS medium with 30 g/L sucrose in long-day (LD, 16-hour light, 22°C / 8-hour dark, 18°C) condition. The Myc-tagged CLF can rescue the defective phenotype of clf-28, which shows a normal phenotype as Col-0.

extract_protocol:
Briefly, 2 g of crosslinked plant materials were ground into fine powder and suspended in Chromatin Extraction Buffer. The nuclear pellets were collected by centrifugation and washed for 4-5 times with NRBT Buffer. The pellet was resuspended in 150 μL Lysis Buffer and sonicated for 10 minutes. The supernatant was diluted with ChIP Dilution Buffer. Anti-Myc antibody and protein-A beads were added and incubated for 3 hours. Then, the beads were collected and washed with RIP Washing Buffer for 3 times. The CLF-RNA complex was eluted by RIP Elution Buffer. After de-crosslinking, the CLF-associated RNA was purified by TRIzol.
Libraries were prepared according to NEBNext Ultra II RNA Library Prep Kit. Briefly, the CLF-associated RNA was fragmented by alkaline hydrolysis. Then, the first-strand cDNA was synthesized by using Random primers. After the synthesis of the second-strand cDNA, the end-repaired reagents were used to yield a protruding 3- ‘A’ base for ligation of Illumina’s adaptors. After ligation, the libraries were amplified and ~200 bp PCR products were collected for sequencing.

tag: ecotype

value: Columbia

tag: cultivar

value: wild type


title: vehicle5

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

data_processing:
CASAVA v1.8.2 was used to demultiplex pooled samples and convert BCL to FASTQ.
Multiple fastq files were combined into one file for the forward reads and one file for the reverse reads.
RNA-Seq data were aligned to the mouse genome build mm9 by STAR-2.5.2a.
Data were normalized at the gene-level, using a resampling strategy PORT (v0.8.2-beta), the code is available at https://github.com/itmat/Normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

source_name: vehicle, aorta thoracica

growth_protocol: Mice were housed in groups on a 12 hour light, 12 hour dark schedule. feed type : regular chow; diet availability : ad libitum; diet supplements : none; water supply type : bottle; water type : tap

extract_protocol:
Aorta were homogenized using magnetic beads and a TissueLyzer. RNA was extracted using Trizol and Qiagen Rneasy Mini kit.
Library construction was carried out using TruSeq RNA Sample Prep kit Set B. In line controls were not used, and samples were barcoded using kit adapters. Library construction was carried out over three days. Selection strategy: polyA; PCR cycles: 13

treatment_protocol: Mice were treated with 100 uL of celecoxib (30 mg/Kg), rofecoxib (10 mg/Kg), or vehicle (PEG-400) by gavage and were sacrified 6hrs later.

tag: strain

tag: developmental stage

value: adult

tag: Sex

value: male

tag: age

value: 10 to 12 week

tag: genetic alteration

value: wildtype

tag: agent

tag: dose

tag: collection time

tag: tissue

value: aorta


title: ovary, KO_hCG6h

city: Urbana

first: CheMyong

middle: Jay

last: Ko

state: Illinois

address: 2001 S. Lincoln Ave.

department: Comparative Biosciences

institute: University of Illinois at Urbana Champaign

data_processing:
Basecalling and demultiplexing done by Cell Ranger mkfastq v2.1.1
Custom reference made with Gencode's M20 mouse genome and gene models using cellranger mkref v.3.0.1
Alignment to custom reference done with cellranger count v3.0.1 and argument --expect-cells=3000
The resulting filtered count matrix for each sample t was imported into R (v3.6.1), and analyzed with Seurat (v3.1.0) and Monocle (2.10.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: tar archive of cellranger's filtered_feature_bc_matrix output including barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz files.

source_name: Ovary

extract_protocol:
After collagenase-assisted tissue dissociation, single-cell suspensions were converted into individually barcoded cDNA libraries with the Single-Cell 3’ Chromium kit version 3 from 10X Genomics.
RNA libraries were prepared using Ilumina's Single-Cell Gene Expression Kit v3 and sequenced on a 2x150nt lane in a NovaSeq S4 flowcell.
Single-cell RNA-seq
Illumina NovaSeq S4 flowcell

treatment_protocol: Wild type (Pgr flox/flox) and Esr2-driven Pgr conditional knockout (Esr2 iCre/wt Pgr flox/flox; Esr2-PgrKO) mice were injected with PMSG at the age of 25 days after birth. On day 27, mice were injected with hCG to induce the superovulation. At 6h after hCG injection, 8 ovaries were collected from 4-different mice in each group.

value: ovary

value: post natal day 27

value: Esr2 iCre/wt Pgr flox/flox (Esr2-PgrKO)


title: A26

description: Recruited progenitors

value: WT


title: 43579

description:
Mouse4
813_43579

library_source: genomic

molecule: genomic DNA

tag: treatment


title: rofecoxib2

source_name: rofecoxib, aorta thoracica

value: NSAID rofecoxib

value: 10 mg/kg


title: rofecoxib3


title: celecoxib1

source_name: celecoxib, aorta thoracica

value: NSAID celecoxib

value: 30 mg/kg


title: ovary, WT_hCG6h


title: control_rep8.4792

data_processing:
CASAVA v1.8.2 was used to demultiplex pooled samples and convert BCL to FASTQ.
Multiple fastq files were combined into one file for the forward reads and one file for the reverse reads.
RNA-Seq data were aligned to the mouse genome build mm9 by STAR-2.5.1b.
Data were normalized at the gene-level, using a resampling strategy PORT (v0.8.1-beta), the code is available at https://github.com/itmat/Normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

source_name: control, aorta thoracica

treatment_protocol: Mice were fed regular chow for 3 weeks containing celecoxib (100 mg/kg/day), rofecoxib (50 mg/kg/day) or with no added NSAID.

tag: genotype/variation

tag: duration of dosing

value: 3 weeks


title: rofecoxib5


title: celecoxib5


title: A31

description: Recruited progenitors


title: A25

description: Recruited progenitors


title: A22

description: Recruited progenitors


title: 53490

description:
Mouse7
399_53490

value: radiation

value: jejunum

value: 4 months


title: 44748

description:
Mouse3
811_44748


title: 53470

description:
Mouse8
812_53470


title: 43584

description:
Mouse2
345_43584


title: control_rep6.4790

value: adult


title: control_rep7.4791

value: male


title: 44768

description:
Mouse5
347_44768


title: control_rep5.4789

value: 10 to 12 week


title: A21

description: Recruited progenitors


title: A24

description: Recruited progenitors


title: control_rep3.4786

value: wildtype


title: A20

description: Recruited progenitors


title: 43560

description:
Mouse1
343_43560


title: control_rep4.4787

value: aorta


title: control_rep2.4784


title: A19

description: Recruited progenitors


title: 89698

description:
Mouse16
952_89698

data_processing:
Raw counts were normalized to the total number of reads resulting in one reads per million (RPM) value per gene. These RPM values were normalized to the genes length (RPKM- reads per kilobase million).
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Processed data is stored in tab separated value format and provides RPKM values per gene. In addition, beside the gene's name, the following data is provided: gene_stable_ID: Ensembl gene ID, transcript_stable_id: Ensembl transcription ID, RefSeq_ID: Reference Sequence ID, chr: chromosome, strand, txStart, txEnd: start and end position.

growth_protocol: The mouse strains B6.SJL-Tg(Villin-Cre)997Gum/J and B6.Cg-Msh2tm2.1Rak/J mice were obtained from The Jackson Laboratory (Bar Harbor, USA). By crossing both, the conditional Msh2 allele has been placed under the control of the Villin-Cre transgene. Mice were genotyped as described (Kucherlapati,M.H et al. Gastroenterology 2010, 138,993-1002). VC+/?Msh2LoxP/LoxP (Msh2-/-), VC+/?Msh2LoxP/+ (Msh2+/-), and VC-/-Msh2LoxP/LoxP (Msh2+/+) mice were bred under specific pathogen-free conditions.

extract_protocol:
Whole tissue from jejunum was homogenized with the Tissue Lyser (20s at 15 Hz). RNA was prepared following manufacturer’s recommendations (Qiagen QIA AllPrep kit) including a DNase I digest.
Library preparation was performed with the TrueSeq RNA Sample preparation kit (Illumina) according to the manufacturer's instructions and sequenced on an Illumina HiSeq 4000 sequencer with 75bp paired-end, strand-specific, random priming.

treatment_protocol: Three month old mice were placed in the radiation unit (X-ray generator, Gulmay D3225, round tube 170 mm, radiation level at 2.5 cm: 1.068 Gy/min) and irradiated with a total dose of 0.5 Gy. All mice were killed 28 days after radiation.


title: 89700

description:
Mouse17
947_89700


title: A18

description: Recruited progenitors


title: A23

description: Recruited progenitors


title: control_rep1.4783


title: rofecoxib_rep8.4731

value: 50 mg/kg/day


title: 89696

description:
Mouse15
831_89696


title: A16

description: Recruited progenitors


title: 89692

description:
Mouse13
816_89692


title: rofecoxib_rep7.4730


title: A15

description: Recruited progenitors


title: rofecoxib_rep6.4729


title: 89690

description:
Mouse12
814_89690


title: rofecoxib_rep5.4728


title: 89688

description:
Mouse7
399_89688


title: rofecoxib_rep4.4725


title: A13

description: Recruited progenitors


title: A17

description: Recruited progenitors


title: A12

description: Recruited progenitors


title: 89694

description:
Mouse14
833_89694


title: rofecoxib_rep3.4724


title: A11

description: Recruited progenitors


title: rofecoxib_rep2.4723


title: A14

description: Recruited progenitors


title: A10

description: Recruited progenitors


title: 89682

description:
Mouse6
344_89682


title: 89686

description:
Mouse2
345_89686


title: rofecoxib_rep1.4722


title: 89680

description:
Mouse1
343_89680


title: celecoxib_rep8.4721

value: 100 mg/kg/day


title: A09

description: Recruited progenitors


title: A08

description: Recruited progenitors


title: celecoxib_rep7.4720


title: 89678

description:
Mouse10
402_89678


title: A07

description: Recruited progenitors


title: celecoxib_rep6.4719


title: ZNF281kd.2 rep2

first: Chenguang

last: Zhang

address: No.10 You An street, Fengtai district

department: Biochemistry and Molecular Biology

institute: Capital Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) . After that, Ericscript (v0.5.5) [4] and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included
The expression level of gene was calculated by RSEM (v1.2.12)
Genome_build: GRCh38.p11(hg38)
Supplementary_files_format_and_content: xls

organism: Homo sapiens

source_name: HLE HCC_ZNF281kd.2

growth_protocol: The Cells were maintained in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Gibco, New York, NY, USA) and 1% Penicillin/Streptavidin (KeyGene, MD, USA) in Corning (New York, NY, USA) dishes at 37℃ in a humidified incubator with 5% CO2

extract_protocol: Total RNAs from  HLE cells were extracted using aan RNeasy Mini Kit (Yishan, Shanghai, China) according to the manufacturer’s protocol.

treatment_protocol: The HLE cells were transfected with lentivirus that harbor control shRNA, two ZNF281 kockdown shRNAs ZNF281 kd.1 and ZNF281 kd.2, at a multiplicity of infection (MOI) of 10 and the medium was refreshed after 12 h; the infection efficiency was assessed by fluorescence microscopy 96 h after infection.  After the selection in 2mg/ml puromycine for 7 days, cell lines with constitutive ZNF281 depletion were established, which were named as Con, ZNF281.kd1, ZNF281.kd2, respectively.

tag: cell line

value: HLE

tag: cell type

value: hepatocellular carcinoma (HCC) cell line

value: ZNF281 kd.2 shRNA


title: A06

description: Recruited progenitors

tag: genotype

value: WT


title: celecoxib_rep5.4718

value: NSAID celecoxib


title: fine_roots_senescence_first_stage_rep3

city: Poznan

first: Katarzyna

last: Marzec-Schmidt

address: Umultowska 89

department: General Botany

country: Poland

institute: Adam Mickiewicz University

description: Gene expression data from Gene expression data from brown roots in the first stage of senescence.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized to an Affymetrix GeneChip Poplar Genome Array (A-AFFY-131) according to the provided Affymetrix protocol.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Thermo Fisher Scientific, USA)

data_processing: The raw image data from a total of three A-AFFY-131 arrays were normalized with Robust Multi-Array Average (RMA). The normalized data were statistically analyzed using GeneSpringGX7 13.1 (Agilent Technologies Inc., USA) software. Data were subjected to a one-way ANOVA with a Benjamini Hochberg corrected p-value cut-off = 0.05. The analysis was limited to genes with statistically significant differences in expression level and a fold difference equal to or larger than 2 between LC and LS1/LS2 in leaf samples and between RC and RS1/RS2 in fine root samples.

label: biotin

organism: Populus trichocarpa

source_name: first stage of senescence: roots which had changed in colour from white to brown

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Affymetrix GeneChip Poplar Genome Array, A-AFFY-131).

growth_protocol: All experiments were performed on seed-grown Populus trichocarpa (Torr. & Gray). Seeds were germinated on 0.8% agar medium in a growth chamber. After developing of first roots, seedlings were transfered into multi-pot trays filled with sterile garden substrate mixed with perlite and kept in phytotron chamber (16h/8h, 18℃/14℃). After  1.5 months of growth, plants were planted into rhizotrons filled with natural soil with shoots extending from the top into the air. Plants were  grown in plastic tunel. Waterlogging was avoided by installing a drainage hole in the bottom of each rhizotron that permitted soil aeration and drainage of excess water.

extract_protocol: Total RNA was extracted from three biological replicates of each stage of  senescence of fine roots and leaves using an RNeasy Plant Mini kit (Qiagen, USA).

treatment_protocol: Samples of fine roots and leaves were collected three times during a growing season. The first collection was considered as a control leaf (LC) and fine roots (RC) samples and was collected in early summer (July 7 - 15), when leaves and the root system were fully developed and functional. The second group of leaf and root samples were harvested in early autumn (October 1 - 7) when chlorophyll levels in leaves had decreased by approximately 40% (LS1) and when fine roots had changed in colour from white to brown (RS1). The third group of samples were harvested in the middle of autumn (November 2 - 9), when chlorophyll levels in leaves decreased by approximately 65% (LS2) and fine roots were dark brown or black colour (RS2). No special treatment was used in the experiment.

value: fine roots


title: Steer 456

city: Seoul-si

first: Sang Weon

state: Seoul-si

address: 1, Gwanak-ro, Gwanak-gu, Seoul-si

department: College of Agriculture and Life Science

country: South Korea

institute: Seoul National University

data_processing:
Quality of RNA-seq reads was checked using FastQC
The reads passed the quality control were mapped to Bovine Taurus genome (UMD3.1) from UCSC using Tophat2 (v2.0.2)
The reads were counted using HTseq (v0.5.3p3)
Trimmed mean of M values (TMM) were calculated using a protocol from Robinson et al., Genome Biology, 2010.
Genome_build: UMD3.1
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

organism: Bos taurus

source_name: longissimus dorsi muscle

extract_protocol:
longissimus dorsi muscles were removed, flash frozen on liquid nitrogen and dry ice. Total RNAs were isolated using Trizol (invitrogen) and a RNeasy RNA purification kit with DNase treatment (Qiagen). mRNA was isolated from the total RNA using oligo-dT beads and were reverse transcribed into double strand cDNA fragments. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using  Illumina NextSeq 500 protocols

tag: breed

value: Hanwoo (Korean cattle)

value: longissimus dorsi muscle

value: post natal day 950

tag: sex type

value: Steer


title: Steer 458

value: post natal day 930


title: 89684

description:
Mouse11
346_89684

tag: strain

value: radiation

value: jejunum

value: 4 months


title: A05

description: Recruited progenitors


title: Steer 439

value: post natal day 996


title: fine_roots_control_rep3

description: Gene expression data from Gene expression data from white roots without senescence symptoms.

source_name: control white roots without senescence symptoms


title: ZNF281kd.1 rep2

source_name: HLE HCC_ZNF281kd.1

value: ZNF281 kd.1 shRNA


title: A04

description: Recruited progenitors


title: celecoxib_rep3.4716

tag: developmental stage

value: adult

value: male

value: 10 to 12 week

value: wildtype

value: 100 mg/kg/day

value: 3 weeks

value: aorta


title: fine_roots_senescence_second_stage_rep2

description: Gene expression data from roots in the second stage of senescence.

source_name: second stage of senescence: roots which had changed in colour from brown to dark brown or almost black, shrinkage was also visible in most fine roots

value: fine roots


title: celecoxib_rep2.4715

tag: Sex

value: NSAID celecoxib


title: ZNF281kd.1 rep1

value: HLE

value: hepatocellular carcinoma (HCC) cell line


title: Bull 22

value: Hanwoo (Korean cattle)

value: longissimus dorsi muscle

tag: age

value: post natal day 746

value: Bull


title: Con rep2

source_name: HLE HCC_control

value: control


title: leaf_control_rep3

description: Gene expression data from green leaves with no sign of senescence.

source_name: control green leaves without senescence symptoms

value: leaf


title: A02

description: Recruited progenitors

value: WT


title: A03

description: Recruited progenitors


title: celecoxib_rep4.4717

value: adult

value: male


title: Bull 20


title: fine_roots_senescence_second_stage_rep3


title: leaf_senescence_second_stage_rep1

description: Gene expression data from yellow leaves in the second stage of senescence.

source_name: second stage of senescence: yellow leaves in which chlorophyll level had decreased by approximately 60%


title: fine_roots_senescence_first_stage_rep2


title: leaf_senescence_second_stage_rep2


title: fine_roots_senescence_second_stage_rep1


title: Bull 23


title: leaf_senescence_first_stage_rep1

description: Gene expression data from yellowing leaves in the first stage of senescence.

source_name: first stage of senescence: yellowing leaves in which chlorophyll level had decreased by approximately 40%


title: fine_roots_control_rep2


title: leaf_control_rep1

description: Gene expressions data from green leaves with no sign of senescence.


title: ZNF281kd.2 rep1

value: ZNF281 kd.2 shRNA


title: fine_roots_senescence_first_stage_rep1

description: Gene expression data from brown roots in the first stage of senescence.


title: fine_roots_control_rep1

description: Gene expression data from white roots without senescence symptoms.


title: leaf_senescence_first_stage_rep2


title: leaf_control_rep2


title: A01

description: Recruited progenitors

source_name: Dorsal wound


title: leaf_senescence_second_stage_rep3


title: leaf_senescence_first_stage_rep3


title: bfPAM16min

status: Public on Mar 06 2020

city: Wuhan

first: chen

last: peng

address: College of Life Sciences, Wuhan University

department: College of Life Sciences

institute: Wuhan University

description: bfPAMMerged.xlsx

data_processing:
The clean data was generated by trimming low quality bases at both ends of read and remove short fragments, this work was completed by sequencing company
For PAM depletion assay, we used custom Python or R scripts to get the result
For guide-seq, the sequencing data was processed by corresponding software named guideseq,the human genome version used in the analysis is hg19;
For deep-seq, the data was handled by CRISPRessoPooled
Genome_build: hg19
Supplementary_files_format_and_content: txt files include DNA sequences for each sample

organism: synthetic construct

source_name: PCR fragments; gene EGFP

extract_protocol:
Cells were collected after 48h post-transfection for genomic DNA extraction using FastPure Cell/Tissue DNA Isolation Mini Kit(Vazyme)
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V2 (Vazyme)

value: wild type


title: bfPAM0min

description: bfPAMMerged.xlsx


title: bfPAM8min

description: bfPAMMerged.xlsx


title: cePAM16min

description: cePAMMerged.xlsx


title: celecoxib_rep1.4712

value: 10 to 12 week

value: wildtype

value: 100 mg/kg/day

value: 3 weeks


title: cePAM8min

description: cePAMMerged.xlsx


title: bfPAM32min

description: bfPAMMerged.xlsx


title: cePAM32min

description: cePAMMerged.xlsx


title: bfPAM10min

description: bfPAMMerged.xlsx


title: bfPAM4min

description: bfPAMMerged.xlsx


title: cePAM6min

description: cePAMMerged.xlsx


title: cePAM4min

description: cePAMMerged.xlsx


title: Con rep1

value: HLE


title: cePAM2min

description: cePAMMerged.xlsx


title: bfPAM6min

description: bfPAMMerged.xlsx


title: cePAM1min

description: cePAMMerged.xlsx


title: AsPAM32min

description: AsPAMMerged.xlsx


title: cePAM0min

description: cePAMMerged.xlsx


title: AsPAM8min

description: AsPAMMerged.xlsx


title: AsPAM10min

description: AsPAMMerged.xlsx


title: AsPAM4min

description: AsPAMMerged.xlsx


title: AsPAM2min

description: AsPAMMerged.xlsx


title: AsPAM16min

description: AsPAMMerged.xlsx


title: AsPAM1min

description: AsPAMMerged.xlsx


title: AsPAM6min

description: AsPAMMerged.xlsx


title: bfPAM2min

description: bfPAMMerged.xlsx


title: AsPAM0min

description: AsPAMMerged.xlsx


title: lbPAM32min

description: LbPAMMerged.xlsx


title: cePAM10min

description: cePAMMerged.xlsx


title: lbPAM10min

description: LbPAMMerged.xlsx


title: lbPAM2min

description: LbPAMMerged.xlsx


title: lbPAM6min

description: LbPAMMerged.xlsx


title: lbPAM4min

description: LbPAMMerged.xlsx


title: lbPAM8min

description: LbPAMMerged.xlsx


title: lbPAM0min

description: LbPAMMerged.xlsx


title: lbPAM16min

description: LbPAMMerged.xlsx


title: lbPAM1min

description: LbPAMMerged.xlsx


title: EOC100: Female high grade serous ovarian cancer, primary tumor

city: Omaha

first: Adam

middle: R

last: Karpf

state: NE

address: S 42nd &, Emile St

institute: UNMC

data_processing:
Used Cutadapt (version 1.4) in conjuction with Trim Galore (version 0.4) to remove linker sequences from fastq files.
Aligned sequence tags to the human genome (hg19) using Bismark Bisulfite Mapper software (version 0.12.1).
Resulting CpG context file was reduced to only those CpGs that had at least a total of 10 sequences (methylated and/or unmethylated) that was used to represent a final determination of percent methylation. Final CpGs analyzed were only those that were present across all samples (n-7).
Genome_build: Human hg19 (GRCh37)
Supplementary_files_format_and_content: Processed tab delimited text files contain the following columns and headers. Column 1: chromosome (chr), Column 2: chromosome base location (location). Column 3: CpG percent methylation (percent_meth). Column 4: Number of sequences that were determined to be methylated at that CpG (num_meth_CpG). Column 5: Number of sequences that were determined to be unmethylated at that CpG (num_unmeth_CpG).

extract_protocol:
Isolated genomic DNA using the Puregene Tissue Kit (Qiagen), which includes RNAse treatment
Samples FTE19, OSE19, EOC59 and EOC83 performed Agilent SureSelect Methyl-Seq procedures according to manufacturers recommendation. For FTE11, OSE11, and EOC12 used Zymo Pico Methyl-Seq Library Prep Kit starting with 1000ng of DNA incorporating the Agilent SureSelect human baits to capture the reduced genome representation.

tag: grade

tag: histotype

value: carcinosarcoma

tag: patient age

tag: gender

value: female


title: EOC91: Female high grade serous ovarian cancer, primary tumor

value: serous

tag: tissue


title: EOC59: Female high grade serous ovarian cancer, primary tumor


title: EOC83: Female high grade serous ovarian cancer, primary tumor

value: mixed


title: OSE19: Epithelial layer by mechanical scraping of resected ovaries


title: FTE19: Epithelial layer by mechanical scraping of resected fimbriae fallopian tubes


title: Sample20: Slanneg_N

city: La Jolla

first: Huy

middle: Q

last: Dinh

address: 9420 Athena Circle

department: Division of Inflammation Biology

institute: La Jolla Institute

data_processing:
Read quality was QC using FastQC 0.11.7
Read mapping was done by Rsubread 1.30.5
Read count was calculated using FeatureCount 1.22.2 and edgeR 1.30.5
Genes with at least 2 samples with CPM>1 were kept for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: read_count.txt: tab-delimited text files includes read count for each samples (Column names: Gene ID, 12 samples as described in the SAMPLES section)

source_name: Blood

extract_protocol:
Intermedidate and nonclassical monocytes were FACS sorted from healthy human PBMC
Universal Plus mRNA-Seq (Nugen)

value: Blood

tag: disease state

value: Healthy


title: Sample13: Int


title: Sample19: SlanposCD61neg_N


title: Sample12: Slanneg_N


title: Sample11: SlanposCD61neg_N


title: Sample9: Int


title: Sample15: SlanposCD61neg_N


title: Sample14: SlanposCD61_N


title: Sample10: SlanposCD61_N


title: Sample16: Slanneg_N


title: 4C_K562_HS5_WT_rep1

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
Library strategy: 4C-seq
Sequenced reads were trimmed for adaptor sequence and the bait sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1). The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3).
Genome_build: hg19 for human, mm9 for mouse
Supplementary_files_format_and_content: bedGraph files: the reads per million (RPM) value in 4C-seq experiments.

source_name: K562 cells

growth_protocol: Human endometrial HEC-1-B cells (ATCC) were cultured in MEM medium (Hyclone), supplemented with 10% (v/v) FBS (Gibco), 2 mM glutamine (Gibco), 1 mM sodium pyruvate (Sigma), and 1× penicillin-streptomycin (Gibco). Human K562 cells (ATCC) were cultured in DMEM medium (Hyclone) supplemented with 10% (v/v) FBS and 1× penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% (v/v) of CO2, and were passaged every three days.

extract_protocol:
After cross-linking with 2% formaldehyde, cells were lysed twice with cold lysis buffer, digested with DpnII, ligated with T4 DNA ligase.
4C libraries were generated by PCR.

value: K562 cells

tag: affected genomic coordinate


title: 4C_K562_HS5_WT_rep2


title: 4C_K562_HS2_WT_rep2


title: 4C_K562_HS5_REV-FWD_rep3

value: RF2 insertion


title: 4C_K562_HS5_REV-FWD_rep4


title: 4C_K562_HS5_REV-FWD_mut_rep1

value: RF2 mutation


title: bfPAM1min

description: bfPAMMerged.xlsx


title: 4C_K562_HS5_REV-FWD_mut_rep2


title: Sample17: Int


title: Sample18: SlanposCD61_N


title: 4C_K562_HS5_REV-FWD_rep2


title: 4C_K562_HS2_WT_rep1


title: 4C_K562_HS2_REV-FWD_rep2


title: 4C_K562_HS2_REV-FWD_rep1


title: 4C_K562_HBG2_REV-FWD_mut_rep2


title: 4C_K562_HBG2_REV-FWD_rep2


title: 4C_K562_HBG2_WT_rep1


title: 4C_K562_HBG2_REV-FWD_mut_rep1


title: 4C_K562_HS2_REV-FWD_mut_rep2


title: 4C_K562_3HS1_REV-FWD_mut_rep2


title: 4C_K562_HBG2_WT_rep2


title: 4C_K562_HS2_REV-FWD_mut_rep1


title: 4C_K562_HS5_REV-FWD_rep1


title: 4C_K562_3HS1_REV-FWD_rep2


title: 4C_HEC-1-B_insert_WT_rep4

source_name: HEC-1-B cells

value: HEC-1-B cells


title: 4C_K562_3HS1_WT_rep1


title: 4C_K562_3HS1_REV-FWD_mut_rep1


title: 4C_K562_3HS1_REV-FWD_rep1


title: 4C_HEC-1-B_insert_WT_rep3


title: 4C_HEC-1-B_insert_WT_rep2


title: 4C_HEC-1-B_insert_WT_rep1


title: 4C_HEC-1-B_insert_FWD-REV_rep1

value: RF insertion


title: 4C_HEC-1-B_insert_FWD-REV_mut_rep2

value: RF mutation


title: 4C_HEC-1-B_HS7_REV-FWD_mut_rep2


title: 4C_HEC-1-B_HS7_WT_rep1


title: 4C_HEC-1-B_HS7_REV-FWD_rep2


title: 4C_HEC-1-B_insert_FWD-REV_mut_rep1


title: 4C_HEC-1-B_HS7_REV3_rep2

value: R3 insertion


title: 4C_HEC-1-B_HS7_WT_rep2

value: wildtype


title: 4C_HEC-1-B_HS7_REV-FWD_rep1


title: 4C_HEC-1-B_HS7_REV3_rep1


title: 4C_HEC-1-B_HS7_REV3_mut_rep2

value: R3 mutation


title: 4C_K562_HBG2_REV-FWD_rep1


title: 4C_K562_3HS1_WT_rep2


title: Detritusphere of decaying root rep1

city: Urrbrae

first: YI

last: ZHOU

address: Waite Campus

country: Australia

institute: The University of Adelaide

data_processing:
Library strategy: DNA metagenome
The sequenced reads were removed if they met any one of the following criteria: (1) with ≥ 20% low quality bases, (2) with adapter contamination (15 bases overlapped by reads and adapter with maximal 3 base mismatches allowed), (3) with N base (also removing paired reads), and (4) with low complexity (reads with 10 consecutive reads of the same base).
MEGAHIT was used to assemble all the clean reads with the “meta-large” parameters set up in the software.
Using the assembled contigs with a length of > 300 bp, gene prediction was carried out on MetaGeneMark software with default parameters
Using the CD-HIT software with 95% sequence identity, the redundant predicted metagenomic genes were removed to generate the non-redundant gene catalogue.
The clean reads for each sample were aligned to the non-redundant genes using SoapAligner software with 90% identity to generate the gene abundance table
Genome_build: FASTA file with gene sequences is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include the number of matched reads for each non-redundant gene in each sample

organism: soil metagenome

source_name: soil

extract_protocol:
The total DNA were extracted using a PowerSoil DNA isolation kit (Mo Bio, Carlsbad, CA, USA) based on the manufacturer’s instructions.
DNA libraries were prepared for sequencing using standard Illumina HiSeq 2000 protocols

tag: host plant

value: no

tag: growing condition

value: with decaying root

tag: replicate


title: Detritusphere of decaying root rep2


title: Detritusphere of decaying root rep3


title: Chickpea rhizosphere under decaying root rep2

value: chickpea


title: 4C_HEC-1-B_HS7_2FWD_rep4

tag: cell type

tag: genotype

value: FF insertion


title: 4C_HEC-1-B_HS7_REV1_mut_rep1

value: R1 mutation


title: 4C_HEC-1-B_HS7_2REV-2FWD_rep1

value: RRFF insertion


title: 4C_HEC-1-B_HS7_REV-FWD_mut_rep1


title: 4C_HEC-1-B_HS7_REV1_rep2

value: R1 insertion


title: 4C_HEC-1-B_HS7_REV3_mut_rep1


title: 4C_HEC-1-B_HS7_REV1_rep1


title: Chickpea rhizosphere under decaying root rep1


title: 4C_HEC-1-B_HS7_2FWD_rep3


title: Chickpea rhizosphere under no decaying root rep1

value: with no decaying root


title: 4C_HEC-1-B_HS7_2FWD_rep2


title: Wheat rhizosphere under no decaying root rep3

value: wheat


title: 4C_HEC-1-B_HS7_REV1_mut_rep2


title: 4C_HEC-1-B_HS7_2FWD_rep1


title: 4C_HEC-1-B_HS7_2FWD_mut_rep1

value: FF mutation


title: Chickpea rhizosphere under decaying root rep3


title: Wheat rhizosphere under decaying root rep3


title: 4C_HEC-1-B_HS5-1_WT_rep9


title: Wheat rhizosphere under decaying root rep2


title: 4C_HEC-1-B_HS5-1_WT_rep10


title: Chickpea rhizosphere under no decaying root rep3


title: Wheat rhizosphere under no decaying root rep1


title: Wheat rhizosphere under decaying root rep1


title: 4C_HEC-1-B_HS5-1_WT_rep8


title: Bulk soil rep3


title: 4C_HEC-1-B_HS5-1_WT_rep7


title: Chickpea rhizosphere under no decaying root rep2


title: Bulk soil rep2


title: 4C_HEC-1-B_HS5-1_WT_rep6


title: Bulk soil rep1


title: 4C_HEC-1-B_HS5-1_WT_rep3


title: 4C_HEC-1-B_HS5-1_WT_rep4


title: 4C_HEC-1-B_HS5-1_WT_rep5


title: 4C_HEC-1-B_HS7_2FWD_mut_rep2


title: 4C_HEC-1-B_HS5-1_WT_rep2


title: Wheat rhizosphere under no decaying root rep2


title: 4C_HEC-1-B_HS5-1_ac1CBSdel_rep4

value: ac1 CBS deletion


title: 4C_HEC-1-B_HS5-1_WT_rep1

value: HEC-1-B cells


title: 4C_HEC-1-B_HS5-1_ac1CBSdel_rep3


title: 4C_K562_HS5_FWD2_rep2

data_processing:
Duplicated paired-end reads were removed by FastUniq (version 1.1) program, and only the unique reads were used for analyses using the Bowtie and r3Cseq program.
Reads were aligned to the reference mouse genome (NCBI37/mm9) or Homo sapien genome(UCSC hg19) using the Bowtie program (version 1.2.2)
File format is  transformed to BAM using samtools version 1.9
The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3)
Genome_build: UCSC hg19
Supplementary_files_format_and_content: zipped bedGraph files include RPM values for each Sample

source_name: K562 cell

extract_protocol:
P0 mouse brain was dissected, and the tissue from cerebral cortex was digested with 0.013% of collagenase in Neurobasal Medium (Gibco) at 37℃ for 3 min. The collagenase was neutralized by adding excess amount of Neurobasal Medium. Single-cell suspension was made by gentle pipetting, and then filtered through 100-μm cell strainers (BD Biosciences). For HEC-1-B cells, trypsin was added to the culture dish and the single cells were suspended in the culture medium. Single cells were then picked under the microscope by using a micro capillary pipette into the thin-walled PCR tube containing 2 µl of cell lysis buffer, 1 µl of oligo-dT primer and 1 µl of dNTP mix.
The cells were then digested overnight at 37 °C with DpnII while shaking at 900 rpm. After inactivation of DpnII at 65 °C for 20 min, proximity ligation was carried out for 24 hr at 16 °C with T4 DNA ligase in 0.1 ml 1 × T4 ligation buffer. The ligated product was then reverse cross-linked and DNA was extracted using phenol-chloroform. Glycogen was added to facilitate DNA precipitation. The precipitated DNA was then dissolved in 50 ml water, and sonicated using the Biorupter system (with low energy setting at a train of 30-second sonication with 30 second intervals for 12 cycles) to obtain DNA fragments ranging from 200 to 600 bp.The captured fragments were linear-amplified using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100ul of PCR system for a total of 60 cycles. This primer should be neither too close to the DpnII site to facilitate the nested PCR at the final amplification step, nor too far away from the DpnII site to maximize the product amount. The amplification products were denatured by incubating at 95 °C for 5 min, and immediately chilled on ice to obtain ssDNA. The ssDNA was then enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions.  The ssDNA on-beads was then ligated in 15 µl with 0.1 µM of adapters (Supplementary Table 1) at 16 °C for 24 hr. The adapters were generated by annealing two complementary primers matching Illumina P7 sequences. After ligation, free adapters were removed by washing the beads twice with the B/W Buffer (5 mM Tris-HCl, 1 M NaCl, 0.5 mM EDTA, pH 7.5). Finally, the QHR-4C libraries were generated by one-step PCR amplification (94 °C, 2 min; 94 °C, 10 sec, 60 °C, 15 sec, 72 °C, 1 min for 19 cycles; and a final extension at 72 °C, 5 min) with captured ssDNA on beads as the template and a pair of PCR primers. The forward primer matches the Illumina P5 and the viewpoint sequence adjacent to the viewpoint DpnII site with barcodes, and the reverse primer matches Illumina P7 with indexes. The PCR products were purified with a PCR purification kit (Qiagen).
4C-seq

tag: line


title: 4C_K562_HS5_FWD2_rep1


title: 4C_K562_HS2_WT_rep4

value: WT


title: 4C_K562_HS5_FWD2_mut_rep1

value: FWD2_mut -/-


title: 4C_K562_HS5_FWD2_mut_rep2


title: 4C_K562_HS2_WT_rep2


title: 4C_HEC-1-B_HS5-1_ac1CBSdel_rep2


title: 4C_HEC-1-B_HS5-1_a12CBSdel_rep4

value: a12 CBS deletion


title: 4C_HEC-1-B_HS5-1_a12CBSdel_rep3


title: 4C_K562_HS2_FWD2_rep1


title: 4C_K562_HS2_FWD2_rep2


title: 4C_HEC-1-B_bac2_WT_rep2

value: wildtype


title: 4C_HEC-1-B_bac2_WT_rep1


title: 4C_K562_HBG2_WT_rep4


title: 4C_K562_HS2_FWD2_mut_rep2


title: 4C_K562_HS2_FWD2_mut_rep1


title: 4C_K562_HBG2_FWD2_rep2


title: 4C_HEC-1-B_a6_WT_rep6


title: 4C_K562_HBG2_FWD2_mut_rep1


title: 4C_HEC-1-B_HS5-1_a12CBSdel_rep2


title: 4C_K562_3HS1_WT_rep2


title: 4C_HEC-1-B_a6_REV-FWD_rep1

value: RF insertion


title: 4C_HEC-1-B_a6_WT_rep2


title: 4C_K562_HBG2_FWD2_mut_rep2


title: 4C_K562_HBG2_FWD2_rep1


title: 4C_K562_3HS1_FWD2_mut_rep2


title: 4C_HEC-1-B_HS5-1_a12CBSdel_rep1


title: 4C_HEC-1-B_a6_WT_rep3


title: 4C_HEC-1-B_a6_REV2_rep2

value: R2 insertion


title: 4C_HEC-1-B_a6_REV-FWD_mut_rep1

value: RF mutation


title: 4C_HEC-1-B_a5_FWD_rep1

source_name: HEC-1-B cell

value: FWD

value: FWD -/-


title: 4C_HEC-1-B_a6_WT_rep4


title: 4C_K562_3HS1_WT_rep1


title: 4C_HEC-1-B_a6_REV2_rep1


title: 4C_K562_3HS1_FWD2_rep2


title: 4C_HEC-1-B_a5_2FWD_rep2


title: 4C_K562_3HS1_FWD2_rep1


title: 4C_HEC-1-B_a6_REV-FWD_mut_rep2


title: 4C_K562_3HS1_FWD2_mut_rep1


title: 4C_K562_HBG2_WT_rep3


title: 4C_HEC-1-B_a5_FWD_rep2


title: 4C_HEC-1-B_a3_2FWD_rep1


title: 4C_HEC-1-B_a6_WT_rep5


title: 4C_HEC-1-B_a3_2FWD_mut_rep2

value: 3FWD_mut -/-


title: 4C_HEC-1-B_a5_FWD_mut_rep2

value: FWD_mut -/-


title: 4C_HEC-1-B_a6_REV2_mut_rep2

value: R2 mutation


title: 4C_HEC-1-B_a6_REV1_rep1

value: R1 insertion


title: 4C_HEC-1-B_a5_FWD_mut_rep1


title: 4C_HEC-1-B_a6_REV1_rep2


title: Resting rep 4 [miRNA]

city: Newcastle

first: Ebrahim

last: Mahmoudi

state: NSW

address: Callaghan

institute: University of Newcastle

data_processing:
Sequencing reads were mapped to the reference genome hg38 using the Bowtie2 (v2.2.6) short read aligner. Using the miRBase mature miRNA reference annotation, reads mapping to mature miRNAs were then counted using htseq-count and differential expression was quantified using EdgeR package.
Genome_build: hg38
Supplementary_files_format_and_content: read counts

source_name: Neuroblastoma cell line

extract_protocol: RNA libraries were prepared for sequencing using Illumina TruSeq Small RNA Library Prep kit according to the manufacturer’s protocol

tag: condition

value: Resting


title: 4C_HEC-1-B_a5_2FWD_rep1


title: 4C_HEC-1-B_a6_WT_rep1


title: 4C_HEC-1-B_a6_REV1_mut_rep2

value: R1 mutation


title: 4C_HEC-1-B_a6_REV1_mut_rep1


title: 4C_HEC-1-B_a6_FWD_rep2

value: F insertion


title: 4C_HEC-1-B_a3_2FWD_rep2


title: 4C_HEC-1-B_a3_2FWD_mut_rep1

value: 2FWD_mut -/-


title: 4C_HEC-1-B_a6_FWD_mut_rep2

value: HEC-1-B cells

value: F mutation


title: 4C_HEC-1-B_a6_FWD_rep1


title: 4C_HEC-1-B_a6_FWD_mut_rep1


title: 4C_HEC-1-B_a6_2REV-2FWD_rep2

value: RRFF insertion


title: 4C_HEC-1-B_a2_FWD_mut_rep2


title: 4C_HEC-1-B_a2_FWD_rep2


title: Resting rep 4 [mRNA]

data_processing:
Sequencing reads were aligned to the human reference genome hg38 using TopHat (v2.0.9). Reads aligning to features were counted using htseq-count (v0.7.2) and differential expression analysis was performed using the Bioconductor package EdgeR.
Genome_build: hg38
Supplementary_files_format_and_content: read counts

molecule: polyA RNA

extract_protocol: RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Library Prep kit according to the manufacturer’s protocol

treatment_protocol: Total RNA were rRNA depleted using Ribo-Zero before library preperation.


title: 4C_HEC-1-B_a2_FWD_rep1


title: 4C_HEC-1-B_a2_FWD_mut_rep1


title: Resting rep 2 [mRNA]


title: Resting rep 3 [miRNA]


title: Resting rep 2 [miRNA]


title: Resting rep 1 [miRNA]


title: 4C_HEC-1-B_a6_2REV-2FWD_rep1


title: 4C_HEC-1-B_2FWD_2REV-2FWD_rep2


title: 4C_HEC-1-B_2REV_2REV-2FWD_rep2


title: 4C_HEC-1-B_a6_2REV-2FWD_mut_rep2

value: RRFF mutation


title: 4C_HEC-1-B_a6_2FWD_rep2

value: FF insertion


title: 4C_HEC-1-B_a6_2REV-2FWD_mut_rep1


title: 4C_HEC-1-B_a6_2FWD_mut_rep2

value: FF mutation


title: 4C_HEC-1-B_a6_2FWD_mut_rep1


title: 4C_HEC-1-B_2FWD_2REV-2FWD_mut_rep1


title: Depolarized rep 4 [mRNA]

value: Depolarized


title: Depolarized rep 4 [miRNA]


title: 4C_HEC-1-B_2FWD_2FWD-2REV_rep2

value: FFRR insertion


title: Depolarized rep 2 [mRNA]


title: Depolarized rep 3 [mRNA]


title: Depolarized rep 1 [mRNA]


title: Depolarized rep 2 [miRNA]


title: Depolarized rep 3 [miRNA]


title: 4C_HEC-1-B_a6_2FWD_rep1


title: Depolarized rep 1 [miRNA]


title: 4C_HEC-1-B_2REV_2REV-2FWD_mut_rep1


title: Resting rep 3 [circRNA]

data_processing:
We used CIRCexplorer pipeline to predict back-splice junction candidates
Genome_build: hg19
Supplementary_files_format_and_content: reads matrix.txt

extract_protocol: RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Library Prep kit according to the manufacturer’s protocol

treatment_protocol: Total RNA were treated with Rnase R before library preperation.

value: neuroblastoma cells

tag: treatment

value: control


title: Resting rep 3 [mRNA]


title: 4C_HEC-1-B_2REV_2REV-2FWD_mut_rep2


title: Resting rep 1 [circRNA]


title: 4C_HEC-1-B_2FWD_2REV-2FWD_rep1


title: Resting rep 1 [mRNA]


title: 697_shE2A-N_RNAseq_1

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the HG19 human genome assembly using bowtie version 1.12 with with parameters "-n 2 -m 1 -l 36 --best". RNA-seq reads were alined to the HG19 human genome sequence using TopHat with the default parameters.
Potential PCR duplicates in ChIP-seq reads were removed using samtools rmdup command.
Tiled data files (TDF) were generated by igvtools with parameters "-z 5 -w 10 -e 200" for ChIP-seq ; bigWig files were generated by Homer software with makeUCSCfile with defauld parameters for RNA-seq .
The gene expression profiling was analyzed by HOMER software
Genome_build: HG19
Supplementary_files_format_and_content: Tiled data files (TDF) and bigWig for gene track visilization; tab-delimited text files include MACS peak calling output and analyzed RPKM values for each RNA-seq samples.

source_name: pre-B leukemic 697 cells

growth_protocol: The human pre-B leukemia 697 cell line was grown in RPMI1640 (Sigma) supplemented with 10% fetal bovine serum at 37 °C.

extract_protocol:
Total RNAs were extrated using Quick-RNA Miniprep kit (Zymo Research) . Chromatin lysates were prepared by sonication and protein-DNA complexes were isolated with indicated antibodies followed by purification with PCR purification kit (Qiagen).
Multiplexing libraries were prepared for sequencing using Illumina standard protocol.

treatment_protocol: The cells were treated with indicated shRNAs before RNA extraction or without treatment for ChIP-seq analysis.

tag: cell line

value: pre-B leukemic cell line 697

value: parental 697 treated with shE2A-N_#1 (TRCN0000017535)


title: 697_shScr_RNAseq_2

value: parental 697 treated with shScramble_#2


title: 4C_HEC-1-B_2REV_2REV-2FWD_rep1


title: shS6K2 cells with sh4: TRNC0000010540, replicate 1 [shS6K2.sh4.1]

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against hg19 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts and FPKM values using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene as estimated by RSEM

source_name: shS6K2 cells with sh4: TRNC0000010540

extract_protocol:
Cells were lysed in Tri-Reagent (Sigma-Aldrich, #T9424-100ml) and RNA was extracted using the Direct-zol MiniPrep Kit (Zymo Research, #R2050) with in column DNAse I treatment.
Total RNA (200ng) was used to prepare 3’ QuantSeq mRNASeq libraries (Lexogen, #KO152x96)

value: NRAS-mutant melanoma cells

tag: genotype/varaition

value: shS6K2; S6K2 knockdown

tag: hairpin


title: 697_shScr_RNAseq_1

value: parental 697 treated with shScramble_#1


title: 4C_HEC-1-B_2FWD_2FWD-2REV_rep1


title: 4C_HEC-1-B_2FWD_2FWD-2REV_mut_rep1

value: FFRR mutation


title: 4C_HEC-1-B_2FWD_2FWD-2REV_mut_rep2

value: HEC-1-B cells


title: 697_shRUNX1_RNAseq_2

value: parental 697 treated with shRUNX1_#2 (TRCN0000338427)


title: shS6K2 cells with sh1: TRNC0000000729, replicate 3 [shS6K2.sh1.3]

source_name: shS6K2 cells with sh1: TRNC0000000729


title: Resting rep 2 [circRNA]


title: shS6K2 cells with sh1: TRNC0000000729, replicate 2 [shS6K2.sh1.2]


title: 697_shRUNX1_RNAseq_1

value: parental 697 treated with shRUNX1_#1 (TRCN0000338490)


title: 697_H3K27ac_ChIPSeq

value: parental 697

tag: chip antibody

value: anti-H3K27ac (ab4729, Abcam)


title: Depolarized rep 2 [circRNA]

value: depolarized


title: 697_shPBX1-C_RNAseq_2

value: parental 697 treated with shPBX1-C_#2 (TRCN0000274085)


title: Depolarized rep 1 [circRNA]


title: 697_shE2A-N_RNAseq_2

value: parental 697 treated with shE2A-N_#2 (TRCN0000017534)


title: shS6K2 cells with sh4: TRNC0000010540, replicate 3 [shS6K2.sh4.3]


title: 697_shPBX1-C_RNAseq_1

value: parental 697 treated with shPBX1-C_#1 (TRCN0000274137)


title: shS6K1 cells with sh5: TRNC0000003162, replicate 3 [shS6K1.sh5.3]

source_name: shS6K1 cells with sh5: TRNC0000003162

value: shS6K1; S6K1 knockdown


title: shS6K2 cells with sh4: TRNC0000010540, replicate 2 [shS6K2.sh4.2]


title: 697_RUNX1_ChIPSeq

value: pre-B leukemic cell line 697

value: anti-RUNX1 (ab23980, Abcam)


title: RNA-seq: SA2-AID clone 2 auxin

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Straße 40

department: Institut für Pathologie

institute: Universitätsmedizin Göttingen

data_processing:
Raw reads were mapped to the human reference genome (hg19) using default settings of the STAR aligner.
Quantification of unique counts was performed using featureCounts. These counts were further normalized via the RUVs function of RUVseq to estimate factors of unwanted variation using those genes in the replicates for which the covariates of interest remain constant and correct for unwanted variation.
Differential gene expression was estimated using DESeq2. Genes with an FDR < 0.05 and an absolute (log2) fold-change of > 0.6 were deemed as differentially-expressed.
Gene ontology and networks were generated through Metascape.
Genome_build: hg19
Supplementary_files_format_and_content: Microsoft excel spreadsheets show differentially expressed genes after SA1/SA2 degradation.

source_name: HCT116 cells

growth_protocol: SA1-AID and SA2-AID cells were cultured in McCoy's 5A medium supplemented with 10% FBS and PSG. For all auxin degradation experiments using SA1-AID and SA2-AID cells auxin or the solvent ethanol as control were added for 12 hours.

extract_protocol:
Trizol purification of total cell RNA
RNA-seq libraries were prepared according to the Illumina TruSeq stranded mRNA protocol starting from 200ng total RNA. One microliter of library was loaded on an Agilent Technologies 2100 Bioanalyzer using a DNA 1000 assay to determine the library concentration and for quality check. The libraryes were sequenced according to the Illumina TruSeq Rapid v2 protocol on the HiSeq2500 for a single read 50bp in length and a 8bp dual index read.

treatment_protocol: mAIDmClover neomycin cassette (plasmid pMK289 obtained from Addgene) was inserted at the 3' end of the SA1 and SA2 genes, 500-800nt homology arms were inserted left and right to the cassette present in the pMK289 plasmid. A gRNA targeting the 3' end of the SA1 or SA2 gene in front of the stop codon was cloned into a Cas9 expression construct (Addgene p48193). Both, the gRNA/Cas9 plasmid as well as the plasmid carrying homology arms and mAID-mClover neomycin cassette were transfected into HCT116 CMV-OsTIR1 cells using FuGene HD (Promega). After 6 days selection with 700 µg/ml G418 the cells were FACS-sorted for mClover expression and seeded into 96 well plates to grow single clones. To induce protein degradation 500 µM indole-3-acetic acid (auxin, IAA) dissolved in ethanol was added to the cells.

value: HCT116 CMV-OsTIR1

tag: library id

value: auxin


title: shS6K2 cells with sh1: TRNC0000000729, replicate 1 [shS6K2.sh1.1]

value: NRAS-mutant melanoma cells

value: shS6K2; S6K2 knockdown


title: RNA-seq: SA2-AID clone 1 auxin


title: shS6K1 cells with sh5: TRNC0000003162, replicate 2 [shS6K1.sh5.2]


title: shS6K1 cells with sh5: TRNC0000003162, replicate 1 [shS6K1.sh5.1]


title: shS6K1 cells with sh1: TRCN0000003158 + sh4:TRNC0000003161, replicate 2 [shS6K1.sh1.2]


title: RNA-seq: SA2-AID clone 1 noauxin

value: no auxin


title: RNA-seq: SA1-AID clone 3 auxin


title: RNA-seq: SA1-AID clone 3 noauxin


title: RNA-seq: SA1-AID clone 2 auxin


title: shS6K1 cells with sh1: TRCN0000003158 + sh4:TRNC0000003161, replicate 1 [shS6K1.sh1.1]


title: WT cells with pLKO.1 vector, replicate 2 [ctr.2]

source_name: WT cells with pLKO.1 vector

value: WT

value: pLKO.1 vector


title: WT cells with pLKO.1 vector, replicate 1 [ctr.1]


title: WT cells with pLKO.1 vector, replicate 3 [ctr.3]


title: RNA-seq: SA1-AID clone 2 noauxin


title: ChIP-seq: SA2-AID clone 1 input

data_processing:
ChIP-seq data was aligned to hg19 using Bowtie under default settings.
Peak calling was carried out using MACS2, setting a q-value to 0.06 or 0.005. All data were normalized against the corresponding input control using the '-c' option of MACS 2.0.
Genome_build: hg19
Supplementary_files_format_and_content: Signal tracks (wig files) were generated with the "bamCoverage" function of deepTools 3.1.3 and were normalized to sequencing depth. Bigwig files were created from wig files using the wigToBigWig command line tool from UCSC Genome Browser Utilities.

extract_protocol:
ChIP-Seq for EGFP was performed as described (Cabianca, Casa et al. 2012) with some adaptations. Approximately 5*107-1*108 cells were crosslinked by replacing the medium with the same volume 1% formaldehyde in PBS  for 10’ at RT. After quenching with 0.125M Glycine (final concentration), cells were washed three times with PBS, harvested using a silicon scraper. Lysis of the cells was carried out by incubating the cells in LB1 buffer (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0,5% NP-40, 0,25% Triton X-100) for 5’, followed by centrifugation at 1,350g for 5 min and incubation with LB2 buffer (10 mM Tris-HCl, pH= 8.0, 200 mM NaCl, 1 mM EDTA, 0,5 mM EGTA) for 10’. Nuclei were pelleted down by centrifugation of the cells at 1,350g for 5 min and were resuspended in LB3 buffer (10 mM Tris-HCl, ph=8,0, 100 mM NaCl, 1 mM EDTA, 0,5 mM EGTA, 0,1% Na-Deoxycholate, 0,5% N-lauroylsarcosine). All lysis buffer contained 1x protease inhibitors. This protocol ensures the removal of cytoplasmic proteins from the lysates. Sonication was performed using a Diagenode bioruptor (15 min, 5-7 cycles, 30” each). Sonicated lysates were cleared by the addition of Triton X-100 to a final concentration of 1% and by centrifugation at maximum speed for 10 min at 4°C. 50 µl of the sonicated lysates were reserved for input and the remaining material stored at – 80°C until use. To prepare the antibody-loaded beads, 100 µl of Dynabeads were washed three times with blocking solution (1x PBS, 0,5% BSA) and incubated overnight with 10 µg of the required antibodies. For each ChIP 100 µg  chromatin was incubated overnight at 4°C with the antibody-bound beads. Beads were washed 6X with RIPA buffer (50 mM Hepes-KOH, pH= 7,6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0,7% Na-Deoxycholate), 1X with TE/50mM NaCl. The DNA was eluted from the beads by incubation with 250 µl of elution buffer (1x TE , 2% SDS) for 15 min at 65°C. Crosslinking of the ChIP and input samples was reversed by incubation at 65°C overnight, proteins were digested  by incubation with 8 µl of 10 mg/ml of Proteinase K at 55°C for 1 hour and RNA degraded by incubation with 8µl of 10 mg/ml  at 37°C for 30 min. DNA was purified then purified using phenol-chloroform extraction followed by ethanol precipitation. The DNA was then resuspended in 25 µL TE and used sequencing. The samples were prepared as Chip Seq Multiplex samples using the NEXTFlex ChIP-Seq kit from BioO Scientific and sequenced them according to the Illumina TruSeq v3 protocol on the HiSeq2000 for a single read 50bp in length and a 7bp index read. The data were de-multiplexed and mapped against GRCh38/hg19 as indicated below.
NGS libraries have been prepped from the ChIP DNA using the NEXTFlex ChIP-seq kit from BioO Scientific and sequenced according to the Illumina TruSeq Rapid v2 protocol on the HiSeq2500 for a single read 50bp in length and a 8bp dual index read.

treatment_protocol: The mAIDmClover neomycin cassette (plasmid pMK289 obtained from Addgene) was inserted at the 3' end of the STAG1 and STAG2 genes, 500-800nt homology arms were inserted left and right to the cassette present in the pMK289 plasmid. A gRNA targeting the 3' end of the SA1 or SA2 gene in front of the stop codon was cloned into a Cas9 expression construct (Addgene p48193). Both, the gRNA/Cas9 plasmid as well as the plasmid carrying homology arms and mAID-mClover neomycin cassette were transfected into HCT116 CMV-OsTIR1 cells using FuGene HD (Promega). After 6 days selection with 700 µg/ml G418 the cells were FACS-sorted for mClover expression and seeded into 96 well plates to grow single clones. To induce protein degradation 500 µM indole-3-acetic acid (auxin, IAA) dissolved in ethanol was added to the cells.


title: ChIP-seq: SA2-AID clone 1 rep 2 EGFP


title: TI006-Virus-UV-48h-3

city: Cambridge

first: Frederic

last: Sorgeloos

address: Addenbrookes Hospital, Hills Road

department: Pathology

country: United Kingdom

institute: University of Cambridge

data_processing:
Sequence reads were inspected with FastQC v0.11.7
Adapters and low quality sequences were removed using Trimmomatic version 0.33 using the following parameters: ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Sequence reads were inspected with FastQC v0.11.7
Transcript level quantification for each sample was obtained using the kallisto (v0.44.0) against the human transcriptome GRCh38.p12 (Ensembl release v92; accessed 22/03/2018) and genes with average transcripts per million less than 1 in both control and virus infection conditions were excluded from downstream analysis.
Read counts were then normalized using the trimmed mean of M-values normalization method and log2 count per million (CPM) were obtained using calcNormFactors and voom functions of edgeR and limma (Law et al., 2014, Gentleman et al., 2004) packages, respectively.
Student’s t-tests were then applied for each transcript and p-values were adjusted for false discoveries due to simultaneous hypotheses testing by applying the Benjamini–Hochberg procedure (FDR).
Genome_build: GRCh38.p12 (Ensembl release v92, accessed 22/03/2018)
Supplementary_files_format_and_content: Tab-delimited text files including the read counts for each transcript in each sample.

source_name: ileum organoid TI006

growth_protocol: Human intestinal organoids were generated from biopsy samples collected from the terminal ileum. Organoids were maintained in proliferation media then differentiated as monolayers in differentiation media for 4 to 5 days before infection.

extract_protocol:
Total cellular RNA was extracted using Trizol (Invitrogen) and genomic DNA was removed by DNase I digestion (TURBO DNA-free™ Kit, Ambion, AM1907).
Libraries were prepared for sequencing from 300 ng of total RNA using a TruSeq stranded mRNA kit (Illumina Technologies) according to the manufacturer's instructions. RNA integrity was assessed via an Agilent 2200 TapeStation system using RNA ScreenTape reagents (Agilent Technologies).

treatment_protocol: GII.4 norovirus clinical samples were serially filtered using 5um, 0.8um, 0.4um and 0.2um microfilters. For the generation of UV-inactivated virus, samples were placed in 24-well plates to a fluid depth of 10mm and exposed to 4000 mJ from a Stratalinker UV source for 12mins at 4C. Mock, filtered virus samples or UV-treated samples were then inoculated onto differentiated monolayers for 2h. The virus inoculum was then removed and monolayers were washed twice with differentiation media in the presence of GCDCA. Virus replication was measured after 2 days of infection by RT-qPCR.

value: ileum organoid TI006

value: UV-treated HuNoV GII.4 48h


title: ChIP-seq: SA1-AID clone 1 input


title: TI006-Virus-UV-48h-2


title: ChIP-seq: SA2-AID clone 1 rep 1 EGFP


title: RNA-seq: SA2-AID clone 2 noauxin


title: TI006-Virus-48h-2

value: HuNoV GII.4 infection 48h


title: ChIP-seq: SA1-AID clone 1 rep 1 EGFP


title: TI006-Virus-48h-3


title: shS6K1 cells with sh1: TRCN0000003158 + sh4:TRNC0000003161, replicate 3 [shS6K1.sh1.3]


title: TI006-Mock-48h-3

value: Mock 48h


title: TI006-Virus-48h-1


title: OC_29

city: Chengdu

first: Shentao

last: Zhou

address: Chengdu

institute: West China Second University Hospital

data_processing:
For small RNA-Seq, adpters were removed by Cutadapt. Clean reads were mapped to GENCODE.V24 (https://www.gencodegenes.org/) by STAR software. Small RNA was annonated to microRNA.subset.of.GENCODE.V24.gtf
We mapped reads to GENCODE.V24 (https://www.gencodegenes.org/) and annotated to microRNA.subset.of.GENCODE.V24.gtf. Therefore, the output data were ENSGnnn-level data. We have transformed the Entriz ID to gene symbol in the Patent-miRNA-expression-profile.txt.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample.

source_name: ovarian cancer

extract_protocol:
Total RNA was extracted using the High Pure RNA paraffin kit (Roche Applied Science, Indianapolis, IN). And for small RNA sequencing, small RNA was isolated from total RNA by gel electrophoresis.
The libraries were sequenced on the Illumina HiSeq platform.

value: primary ovary tumor

tag: age

tag: Stage

value: IA


title: TI006-Mock-48h-1

tag: tissue


title: OC_31

value: IC


title: TI365-Virus-UV-48h-3

source_name: ileum organoid TI365

value: ileum organoid TI365


title: TI006-Mock-48h-2


title: OC_27


title: OC_28

value: I


title: OC_26


title: OC_25


title: TI365-Virus-UV-48h-2


title: OC_24


title: ChIP-seq: SA1-AID clone 1 rep 2 EGFP


title: TI365-Virus-48h-3


title: TI365-Virus-UV-48h-1


title: TI006-Virus-UV-48h-1


title: TI365-Virus-48h-2


title: TI365-Virus-48h-1


title: TI365-Mock-48h-3


title: OC_32


title: OC_21

source_name: healthy

value: Fallopian Tube

value: III


title: OC_20

value: IB


title: TI365-Mock-48h-1


title: OC_18


title: OC_30


title: TI365-Mock-48h-2


title: OC_16


title: OC_15


title: OC_14


title: OC_17

value: IV


title: C-733

city: London

first: Haider

middle: Muhammad

last: Hassan

state: Ontario

address: 800 Commissioners Road

department: Biochemistry and Oncology

country: Canada

institute: Western University

data_processing:
Sequenced reads were trimmed for adaptor sequence
The paired-end RNA-sequencing FASTQ files were aligned to the mm9 genome using STAR aligner
FPKM was calculated using cufflinks in STAR aligner
The p-value and FDR/ q-value was calculated
Overlap between the HCC and pre-tumor samples was performed using bash commands ("Grep" based commands, with "-i" ,"-w", "-m1"). A p-value and q-value/FDR cutoff of 0.05, as well  as, fold change cutoff of 1.5 fold was used for the generation of gene lists for overlap analysis.
Genome_build: mm10

source_name: Liver isolated from male control mice

growth_protocol: Tdg fl/fl mice (Control) were bred with UBC-cre/ERT2 mice to generate Tdg fl/fl; UBC-cre/ERT2+ (Tdg cKO)mice. These mice were then bred with the Tdgf/- mice to generate the Tdg fl/-; UBC-Cre/ERT2+ experimental genotype.

extract_protocol:
We isolated whole livers from male TDG knockout livers (4-month post tamoxifen injection) and HCC (22 - 24 months post tamoxifen injection), along with their age/sex matched controls. The liver was kept in RNAzol and at -80 degrees celsius until RNA extraction. The RNA extraction was performed using the manufacturer guidelines.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: The control and Tdg cKO mice were treated with tamoxifen over a 5 day course at 8 weeks of age. Then the mice were allowed to age for 4 months prior to extraction of the livers for high throughput RNA sequencing (pre-tumor). The animals were also aged until late-onset HCC development. Then the HCC samples and their respective age/sex matched control livers were harvested and also subjected to high throughput RNA sequencing. Only the male mice livers were analyzed via high throughput sequencing.

tag: strain

tag: Sex

value: male

value: Liver

tag: age of mice post tam injection

value: 4 months


title: KO-706


title: KO-711


title: KO-725


title: OC_22


title: T3_HCC

source_name: HCC isolated from male TdgcKO mice that had been aged from 22 - 24 months

value: Hepatocellular carcinoma (Mouse 676)

value: 22 - 24 months


title: C-732


title: OC_11


title: OC_12

value: IIIC


title: OC_23


title: T2_HCC

value: Hepatocellular carcinoma (Mouse 666)


title: Control 3 liver

value: 22 months


title: OC_9

value: primary ovary tumor


title: OC_10


title: OC_8

value: IIIB


title: C-813


title: Control 1 liver


title: OC_7


title: lbDNMT1off5

source_name: HEK 293 cells

value: embryonic kidney

value: HEK 293

value: wild type


title: lbB2moff8


title: OC_5

value: Fallopian Tube


title: OC_6

value: III


title: ceDNMT1off5


title: Control 2 liver


title: OC_4

value: IC


title: LbGUIDE seqPOLQ target2


title: OVCAR3_DAC

description: gene expression microarray

hyb_protocol: Hybridization protocol was performed using Affymetrix HG 1.0ST array analysis at the University at Buffalo Center of Excellence in Bioinformatics and Life Sciences according to manufactures protocol.

scan_protocol: Scan protocol was performed using Affymetrix HG 1.0ST array analysis at the University at Buffalo Center of Excellence in Bioinformatics and Life Sciences according to manufactures protocol.

data_processing: Microarray probe cell intensity data (.cel) were normalized using the Affymetrix Expression Console(version 1.3.0.187) software running the RMA workflow. We used a regularized t test analysis of control versus treatment comparisons using a Bayesian approach to estimate the within treatment variation among replicates, using Cyber-T software.

source_name: OVCAR3 cell line

label_protocol: Label protocol was performed using Affymetrix HG 1.0ST array analysis at the University at Buffalo Center of Excellence in Bioinformatics and Life Sciences according to manufactures protocol.

extract_protocol: Total RNA was purified using TRIzol (Invitrogen).

tag: grade

tag: histotype

tag: patient age

tag: methylation status

value: OVCAR3 cell line

tag: gender

value: female


title: OVCAR3_P22

description: gene expression microarray


title: OC_3

value: I


title: OVCAR3_P25

description: gene expression microarray


title: IOSE_p16

description: gene expression microarray

source_name: IOSE cell line

value: IOSE cell line


title: IOSE_P20

description: gene expression microarray


title: IOSE_DAC1

description: gene expression microarray


title: OVCAR3_P23

description: gene expression microarray


title: IOSE_DAC2

description: gene expression microarray


title: OVCAR3_DAC2

description: gene expression microarray


title: LbGUIDE seqIL12A1

data_processing:
The clean data was generated by trimming low quality bases at both ends of read and remove short fragments, this work was completed by sequencing company
For PAM depletion assay, we used custom Python or R scripts to get the result
For guide-seq, the sequencing data was processed by corresponding software named guideseq,the human genome version used in the analysis is hg19;
For deep-seq, the data was handled by CRISPRessoPooled
Genome_build: hg19
Supplementary_files_format_and_content: txt files include DNA sequences for each sample

extract_protocol:
Cells were collected after 48h post-transfection for genomic DNA extraction using FastPure Cell/Tissue DNA Isolation Mini Kit(Vazyme)
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V2 (Vazyme)

tag: genotype


title: OVCAR3_DAC3

description: gene expression microarray


title: IOSE_P18

description: gene expression microarray


title: OC_13

value: IV


title: IOSE_DAC3

description: gene expression microarray


title: OC_2

value: IIIA


title: Hypo_EOC_100: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

source_name: Fresh-frozen high grade serous ovarian cancer sample from patient undergoing surgical resection at Roswell Park Cancer Institute

value: carcinosarcoma

value: Hypo


title: Hyper_EOC_150: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: serous

value: Hyper


title: OC_1

value: primary ovary tumor

value: IA


title: Hyper_EOC_152: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: mixed


title: TgCPEB4∆4-3 ELUTED

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA algorithm (Irizarry et al., 2003)

source_name: Cortex/Striatum, 6 week-old

label_protocol: 5 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2). Amplification was performed for 21 cycles. 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: All mice were housed in animal facility. Mice were housed four per cage with food and water available ad libitum and maintained in a temperature-controlled environment on a 12/12 h light-dark cycle with light onset at 08:00. Animal housing and maintenance protocols followed the guidelines. Animal experiments were performed under approved protocols.

extract_protocol: The cortex and striatum together were quickly dissected, homogenized and total RNA (Input) was extracted using the Maxwell® 16 LEV simplyRNA Tissue Kit (Promega). The poly(A) RNA fraction was purified by poly(U) chromatography (Poly(U)-agarose, Sigma). Differential elution with 25% or 90% formamide yielded two fractions of mRNAs enriched for short (WASH) or long (ELUTED) poly(A)-tails, respectively. The RNA of the two poly(A) fractions was precipitated with isopropanol and purified by Phenol:Chloroform protocol.

tag: group

value: ELUTED

tag: replicate

value: Cortex/Striatum

value: 6 week-old

tag: rna fraction

value: Enriched in long poly(A)-tail RNA


title: LbGUIDE seqCCR5

value: embryonic kidney

tag: cell line

value: HEK 293

value: wild type


title: TgCPEB4∆4-3 WASH

value: WASH

value: Enriched in short poly(A)-tail RNA


title: enAsHF1GUIDE seqPOLQ target2


title: CTCF-AID_rna_d6_washout_rep2

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
fastq: Illumina's HiSeq Control Software
RNA-seq reads were aligned against the mouse mm10 genome assembly using STAR (Dobin et al., 2013). The processed data was created using HTseq (Anders et al., 2015) and used for differential expression analysis by edgeR (Robinson et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: The processed file include all sample data of the number of read counts in each gene that were calculated using HTseq (Anders et al., 2015).

source_name: embryonic stem cells

growth_protocol: Cells were grown in DMEM supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 15% KnockOut Serum Replacement (ThermoFisher, 10828028), Glutamax (Gibco, 35050), 0.1 mM non-essential amino acid, 0.1mM beta-mercaptoethanol, and 500 U/ml LIF at 37°C and 5% CO2

extract_protocol: RNA-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 protocols (Illumina, San Diego, CA).

treatment_protocol: To deplete CTCF, 1 ul 500 mM auxin per 1 ml medium was added, and medium with auxin was changed every 24 hours. Cells were harvested 24, 48 or 96 hours after stating auxin treatment. Neural progenitor cell differentiation treatment was performed with or without auxin treatment, and harvested on day 2, 4, 6 and 2 days after washing out auxin from day 4 and day 6 samples.

value: F123 mouse ES cell


title: Hyper_EOC_99: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: female


title: enAsHF1GUIDE seqIL12A


title: TgCPEB4∆4-3 INPUT

value: INPUT

value: total RNA


title: CTCF-AID_rna_d6_washout_rep1


title: CTCF-AID_rna_d6_auxin_rep1


title: LbGUIDE seqDNMT1


title: CTCF-AID_rna_d6_auxin_rep2


title: enAsHF1GUIDE seqDNMT1


title: CTCF-AID_rna_d6_ctl_rep2


title: enAsHF1GUIDE seqCCR5


title: CTCF-AID_rna_d6_ctl_rep1


title: CeGUIDE seqPOLQ target2


title: enAsHF1GUIDE seqHEKsite1


title: Hypo_EOC_97: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: carcinosarcoma

value: Hypo


title: CTCF-AID_rna_d4_washout_rep2


title: Hypo_EOC_89: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: serous


title: TgCPEB4∆4-2 ELUTED


title: CeGUIDE seqHEK site1


title: Hyper_EOC_87: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: Hyper


title: TgCPEB4∆4-2 WASH


title: Hypo_EOC_96: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: Hypo_EOC_91: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: TgCPEB4∆4-2 INPUT


title: Hyper_EOC_82: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: CTCF-AID_rna_d4_washout_rep1


title: TgCPEB4∆4-1 WASH


title: TgCPEB4∆4-1 ELUTED

value: ELUTED


title: CeGUIDE seqDNMT


title: CTRL-3 WASH

value: CTRL

value: Cortex/Striatum


title: CTRL-3 ELUTED

value: 6 week-old

value: Enriched in long poly(A)-tail RNA


title: TgCPEB4∆4-1 INPUT


title: Hyper_EOC_83: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: mixed


title: CTCF-AID_rna_d4_auxin_rep2


title: Hypo_EOC_72: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: mucinous


title: Hypo_EOC_67: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: CTRL-3 INPUT


title: CTRL-2 ELUTED


title: Cas9GUIDE seqPOLQtarget2

value: embryonic kidney

value: HEK 293

value: wild type


title: CTCF-AID_rna_d4_ctl_rep2

value: F123 mouse ES cell


title: CTRL-2 WASH

value: WASH

value: Enriched in short poly(A)-tail RNA


title: Hyper_EOC_68: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: female


title: CTCF-AID_rna_d4_ctl_rep1


title: CTCF-AID_rna_d2_auxin_rep1


title: BhCas12b v4GUIDE seqDNMT1


title: CeGUIDE seqCCR5


title: BhCas12b V4guide seqCCR5


title: Hypo_EOC_63: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: clear cell

value: Hypo


title: CTCF-AID_rna_d2_ctl_rep2


title: CTRL-2 INPUT

value: INPUT

value: total RNA


title: Hyper_EOC_66: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: serous

value: Hyper


title: Hypo_EOC_60: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: CTCF-AID_rna_d2_auxin_rep2


title: BhCas12b v4GUIDE seqHEK site1


title: AsGUIDEseqPOLQ target2


title: CTRL-1 ELUTED

value: CTRL

value: ELUTED

value: Cortex/Striatum

value: 6 week-old


title: Hyper_EOC_58: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: immature teratoma


title: Hypo_EOC_57: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: Hyper_EOC_54: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: CTRL-1 INPUT


title: Hyper_EOC_59: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: CPEB4KO-2 ELUTED

value: CPEB4 KO

value: Enriched in long poly(A)-tail RNA


title: CTRL-1 WASH


title: CTCF-AID_rna_d4_auxin_rep1

value: F123 mouse ES cell


title: CTCF-AID_rna_d2_ctl_rep1


title: AsGUIDEseqIL12A

value: embryonic kidney

value: HEK 293

value: wild type


title: BhCas12b v4GUIDE seqIL12A


title: CPEB4KO-2 WASH

value: WASH

value: Enriched in short poly(A)-tail RNA


title: AsGUIDEseqHEK site1


title: AsGUIDEseqDNMT1


title: Cas9GUIDE seqIL12A


title: AsGUIDEseqCCR5


title: CPEB4KO-2 INPUT

value: INPUT


title: lbPOLQtarget


title: lbPOLQoff3


title: lbPOLQoff6


title: Hyper_EOC_51: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: clear cell

value: female


title: Hyper_EOC_48: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: granulosa cell

value: Hyper


title: CPEB4KO-1 INPUT

value: total RNA


title: Hypo_EOC_52: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: serous

value: Hypo


title: Hypo_EOC_53: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: lbPOLQoff2


title: Input_ChIP_CTCF-AID_NPC_d6_washout_rep2

data_processing:
fastq: Illumina's HiSeq Control Software
Each fastq file was mapped to mouse genom (mm10) with BWA -aln (Li and Durbin, 2009) and PCR duplicates were removed using Picard MarkDuplicate. The bigWig files were created using deepTools (Ramírez et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (bigWig) were created using deepTools (Ramírez et al., 2016).

source_name: neural precursor cells

extract_protocol:
ChIP and input library preparation for histone modifications (H3K4me1, H3K4me3, H3K27ac) were carried out as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol” in https://www.encodeproject.org/documents/), and ChIP and input library preparation for CTCF were also performed as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol for MicroChIP” in https://www.encodeproject.org/documents/).
ChIP-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 or HiSeq2500 protocols (Illumina, San Diego, CA).

treatment_protocol: To deplete CTCF, 1 ul 500 mM auxin per 1 ml medium was added, and medium with auxin was changed every 24 hours. Cells were harvested 24 or 48 hours after stating auxin treatment. Neural cell differentiation treatment was performed with or without auxin treatment, and the neural precursor cells were harvested on day 4, 6 or 2 days after washing out auxin from the day 4, 6 sample.

value: F123 mouse neural precursor cell

tag: chip antibody


title: Hyper_EOC_45: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: endometroid


title: CPEB4KO-1 ELUTED

value: CPEB4 KO

value: ELUTED

value: Cortex/Striatum

tag: age

value: 6 week-old

value: Enriched in long poly(A)-tail RNA


title: CPEB4GT/+,2 ELUTED

value: CPEB4 GT/+


title: Input_ChIP_CTCF-AID_NPC_d6_washout_rep1


title: CPEB4GT/+,2 INPUT


title: CPEB4GT/+,2 WASH

value: WASH

value: Enriched in short poly(A)-tail RNA


title: Hypo_EOC_44: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: CPEB4GT/+,1 WASH


title: Hypo_EOC_43: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: CPEB4GT/+,1 ELUTED


title: lbPOLQoff1

value: embryonic kidney

value: HEK 293

value: wild type


title: Input_ChIP_CTCF-AID_NPC_d6_auxin_rep2


title: lbPOLQoff5


title: CPEB4KO-1 WASH


title: Hypo_EOC_38: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: mixed

value: female


title: lbIL12Atarget


title: Hyper_EOC_41: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: mucinous

value: Hyper


title: WT-2 ELUTED

value: WT


title: CPEB4GT/+,1 INPUT

value: INPUT

value: total RNA


title: lbIL12Aoff8


title: Input_ChIP_CTCF-AID_NPC_d6_auxin_rep1

value: F123 mouse neural precursor cell


title: Hyper_EOC_32: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: serous


title: Input_ChIP_CTCF-AID_NPC_d6_ctl_rep2


title: Input_ChIP_CTCF-AID_NPC_d6_ctl_rep1


title: lbIL12Aoff7


title: lbIL12Aoff6


title: Hypo_EOC_39: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: Hypo


title: Input_ChIP_CTCF-AID_NPC_d4_washout_rep1


title: Input_ChIP_CTCF-AID_NPC_d4_washout_rep2


title: lbIL12Aoff4


title: Hypo_EOC_13: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: WT-2 INPUT

value: Cortex/Striatum

value: 6 week-old


title: WT-1 ELUTED

value: ELUTED

value: Enriched in long poly(A)-tail RNA


title: WT-1 WASH

value: WASH

value: Enriched in short poly(A)-tail RNA


title: Input_ChIP_CTCF-AID_NPC_d4_auxin_rep2


title: lbIL12Aoff3

value: embryonic kidney

value: HEK 293

value: wild type


title: Input_ChIP_CTCF-AID_NPC_d4_ctl_rep2


title: Input_ChIP_CTCF-AID_NPC_d4_auxin_rep1


title: lbIL12Aoff5


title: lbIL12Aoff2


title: lbIL12Aoff1


title: Hypo_EOC_7: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: female


title: Input_ChIP_CTCF-AID_NPC_d4_ctl_rep1


title: Input_ChIP_CTCF-AID_NPC_d2_auxin_rep2


title: Hyper_EOC_8: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: carcinosarcoma

value: Hyper


title: Hyper_EOC_05: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: WT-2 WASH

value: WT


title: lbHBBoff8


title: Hyper_EOC_11: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: Rabbit IgG RIP - HD mice

source_name: Striatum, 7-8 months

label_protocol: Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 27 cycles. 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

extract_protocol: mRNA-protein complexes from total striatum were crosslinked with formaldehyde in PBS and homogenized in lysis buffer. Lysates were precleared with unconjugated dynabeads (Life Technologies) and immunoprecipitated with anti-CPEB1, anti-CPEB4 or rabbit IgG. RNAs were extracted using the TRIzol reagent (Invitrogen), purified using Agencourt RNAClean XP bead suspension (Beckman Coulter) and amplified using WTA2 (Sigma-Aldrich).

value: HD

tag: condition

value: IgG RIP


title: Hypo_EOC_1: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: serous

tag: tissue


title: Input_ChIP_CTCF-AID_NPC_d2_auxin_rep1

value: F123 mouse neural precursor cell


title: Hypo_EOC_2: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray

value: Hypo


title: CPEB4 RIP - HD mice

value: CPEB4 RIP


title: Hyper_EOC_12: Female high grade serous ovarian cancer, primary tumor

description: gene expression microarray


title: lbHBBtarget


title: Input_ChIP_CTCF-AID_NPC_d2_ctl_rep2


title: Input_ChIP_CTCF-AID_NPC_d2_ctl_rep1


title: Rabbit IgG RIP - WT mice


title: P60 MIA_MG-REP 3

city: Boston

first: Tsuneya

last: Ikezu

state: MA

address: 72 East Concord St

department: BUSM - Department of Pharmacology and Experimental Therapeutics

institute: Boston University School of Medicine

data_processing:
The Bioconductor Rsubread package in the R programming language was used to align reads to the mouse genome and obtain feature counts
“buildindex” was used with the mm10 Musculus reference genome
Rsubread function “Align” was used with the “seed- and-vote" paradigm for read mapping, generating .bam files for read summarization.
For read summarization, an annotation file (.gtf) from UCSC genome browser (https://genome.ucsc.edu) was used, with the Rsubread function “featureCounts,” in which reads are assigned to genomic features of interest once they are mapped to the reference genome
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values

source_name: CD11b+ Microglia

extract_protocol:
Microglia were isolated using MACS CD11b+ beads, immediately lysed in Qiazol (Qiagen) and frozen at -80C. RNA was extracted using the miRNeasy kit
Truseq (Illumina) non-stranded cDNA libraries were constructed from Poly A-enriched mRNA

tag: strain

value: Whole brain

tag: cell type

value: CD11b+ Microglia

tag: maternal treatment

value: MIA

tag: post-natal treatment

value: CSF1R inhibitor PLX5622 (MG-REP)


title: lbHBBoff6

value: embryonic kidney


title: P60 MIA_MG-REP 2


title: Normal_2: Female bulk normal ovary

description: gene expression microarray

source_name: Female bulk normal ovary

tag: grade

tag: histotype

value: bulk normal ovary


title: lbHBBoff5

value: HEK 293

value: wild type


title: CPEB4 RIP - WT mice


title: Input_ChIP_CTCF-AID_auxin_48hr_rep2

value: F123 mouse ES cell


title: P60 MIA_MG-REP 1


title: Normal_1: Female bulk normal ovary

description: gene expression microarray

tag: patient age

tag: methylation status

value: female


title: Normal_8: Female bulk normal ovary

description: gene expression microarray

tag: gender


title: INPUT - WT mice

tag: genotype

value: WT


title: CPEB1 RIP - HD mice

value: HD

value: CPEB1 RIP


title: lbHBBoff4


title: INPUT - HD mice


title: P60 Saline_MG-REP 3

value: saline


title: Input_ChIP_CTCF-AID_auxin_48hr_rep1


title: lbHBBoff7


title: P60 Saline_MG-REP 2


title: Input_ChIP_CTCF-AID_auxin_24hr_rep2


title: P60 Saline_MG-REP 1


title: CPEB1 RIP - WT mice


title: lbHBBoff1


title: P60 MIA_CTRL 3

value: control


title: Input_ChIP_CTCF-AID_auxin_0hr_rep2


title: lbHBBoff3


title: lbDNMT1target


title: Input_ChIP_CTCF-AID_auxin_0hr_rep1


title: P60 MIA_CTRL 1


title: lbHBBoff2


title: OSE5: Epithelial layer by mechanical scraping of resected ovaries

type: genomic

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Rnbeads Version 1.0.0

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: Isolated genomic DNA using the Puregene Tissue Kit (Qiagen), which includes RNAse treatment

value: Female

tag: tumor histology

tag: Stage


title: lbDNMT1off7

tag: cell line


title: H3K27me3_ChIP_CTCF-AID_NPC_d4_auxin_rep1

value: F123 mouse neural precursor cell

tag: chip antibody

value: H3K27me3 (Active Motif, 61017)


title: P60 MIA_CTRL 2

value: Whole brain

value: CD11b+ Microglia

tag: age


title: lbDNMT1off8


title: H3K27me3_ChIP_CTCF-AID_NPC_d4_auxin_rep2


title: Input_ChIP_CTCF-AID_auxin_24hr_rep1


title: P60 Saline_CTRL 2


title: lbDNMT1off6


title: H3K27me3_ChIP_CTCF-AID_NPC_d4_ctl_rep2


title: OSE4: Epithelial layer by mechanical scraping of resected ovaries


title: lbDNMT1off4


title: P60 Saline_CTRL 1


title: P60 Saline_CTRL 3


title: lbDNMT1off3.


title: OSE21: Epithelial layer by mechanical scraping of resected ovaries


title: OSE22: Epithelial layer by mechanical scraping of resected ovaries


title: H3K27me3_ChIP_CTCF-AID_auxin_0hr_rep2


title: H3K27me3_ChIP_CTCF-AID_NPC_d4_ctl_rep1


title: lbDNMT1off2


title: lbDNMT1off1


title: P20 MIA 1

value: MIA


title: P20 MIA 2


title: P20 Saline 3


title: lbB2Mtarget

value: embryonic kidney


title: OSE20: Epithelial layer by mechanical scraping of resected ovaries


title: P20 MIA 3


title: H3K27me3_ChIP_CTCF-AID_auxin_0hr_rep1


title: OSE18: Epithelial layer by mechanical scraping of resected ovaries


title: H3K4me3_ChIP_CTCF-AID_NPC_d6_auxin_rep1

value: H3K4me3 (Millipore, 04-745)


title: OSE19: Epithelial layer by mechanical scraping of resected ovaries


title: lbB2Moff7

value: HEK 293


title: H3K4me3_ChIP_CTCF-AID_NPC_d6_ctl_rep2


title: OSE11: Epithelial layer by mechanical scraping of resected ovaries


title: H3K4me3_ChIP_CTCF-AID_NPC_d6_auxin_rep2


title: lbB2Moff6

value: wild type


title: P20 Saline 1


title: P20 Saline 2


title: H3K4me3_ChIP_CTCF-AID_NPC_d6_ctl_rep1


title: P7 MIA 3


title: lbB2Moff5


title: lbB2Moff4


title: P7 MIA 2


title: lbB2Moff3


title: P7 MIA 1


title: H3K4me3_ChIP_CTCF-AID_NPC_d4_auxin_rep2


title: lbB2Moff2


title: H3K4me3_ChIP_CTCF-AID_NPC_d4_auxin_rep1


title: H3K4me3_ChIP_CTCF-AID_NPC_d4_ctl_rep2


title: H3K4me3_ChIP_CTCF-AID_NPC_d4_ctl_rep1


title: P7 Saline 2


title: P7 Saline 3


title: lbB2Moff1


title: NO1: bulk normal ovary

source_name: bulk normal ovary

value: bulk normal ovary


title: H3K4me3_ChIP_CTCF-AID_NPC_d2_auxin_rep2


title: FTE22: Epithelial layer by mechanical scraping of resected fimbriae fallopian tubes


title: CeVEGFAtarget


title: P7 Saline 1


title: WT-1 INPUT

tag: group

value: INPUT

tag: replicate

value: Cortex/Striatum

value: 6 week-old

tag: rna fraction

value: total RNA


title: H3K4me3_ChIP_CTCF-AID_NPC_d2_auxin_rep1


title: E17 MIA 3

tag: strain

tag: tissue

tag: cell type


title: H3K4me3_ChIP_CTCF-AID_NPC_d2_ctl_rep2


title: CeTRBCtarget


title: cePOLQtarget


title: E17 MIA 2

tag: maternal treatment


title: H3K4me3_ChIP_CTCF-AID_NPC_d2_ctl_rep1


title: cePOLQoff6


title: E17 MIA 1


title: cePOLQoff5


title: FTE20: Epithelial layer by mechanical scraping of resected fimbriae fallopian tubes

tag: grade


title: FTE18: Epithelial layer by mechanical scraping of resected fimbriae fallopian tubes

tag: patient age


title: FTE17: Epithelial layer by mechanical scraping of resected fimbriae fallopian tubes


title: H3K4me3_ChIP_CTCF-AID_auxin_48hr_rep1

value: F123 mouse ES cell


title: cePOLQoff3


title: H3K4me3_ChIP_CTCF-AID_auxin_48hr_rep2


title: H3K4me3_ChIP_CTCF-AID_auxin_24hr_rep2


title: H3K4me3_ChIP_CTCF-AID_auxin_24hr_rep1


title: E17 Saline 3

value: saline


title: cePOLQoff1


title: E17 Saline 1


title: EOC99: Female high grade serous ovarian cancer, primary tumor

value: Female

value: serous

value: IIIB


title: EOC96: Female high grade serous ovarian cancer, primary tumor

value: IIIC


title: FTE12: Epithelial layer by mechanical scraping of resected fimbriae fallopian tubes


title: Activin

city: Athens

first: Anastasia

last: Kotanidou

address: 45 Ipsilantou Str

department: 1st Department of Critical Care Medicine and Pulmonary Services

country: Greece

institute: Evangelismos Hospital, National and Kapodistrian University of Athens

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequences and low quality base calls using cutadapt, and mapped to mm9 genome build using tophat2.
Normalized counts were calculated using R Bioconductor Package metaseqR.
BigWig files were generated using samtools, bedtools and UCSC kent tools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files were generated to visualize RNA-seq signal distribution along mouse mm9 genes in UCSC/IGV genome browser. Txt file contains genomic coordinates, strand information, Ensembl gene id, gene name, gene biotype, gc content and normalized exon counts for each  ensembl  gene, for each aligned sample.

growth_protocol: CD4+CD62L+ naive T cells were isolated by magnetic beads or sorted on a BD FACSAria II sorter from the spleens and lymph nodes of C57BL/6 mice and activated with plate-bound anti-CD3 (1μg/ml) and soluble anti-CD28 ( 1μg/ml) in 96-well plates, for 3-4 days. For Th17 cell differentiation, 10E5 naive T cells were supplemented with recombinant IL-6 (20ng/ml), IL-1 (20ng/ml) and IL-23 (20ng/ml) in the presence of PBS (control) or activin-A (100ng/ml).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD4+ T cells

value: 8-12 weeks old

tag: treatment

value: Activin


title: H3K4me3_ChIP_CTCF-AID_auxin_0hr_rep2

value: H3K4me3 (Millipore, 04-745)


title: cePOLQoff2

value: embryonic kidney

value: HEK 293


title: NO2: bulk normal ovary

tag: gender

value: bulk normal ovary


title: ceIL12Atarget

tag: genotype

value: wild type


title: Control

value: Control


title: FTE21: Epithelial layer by mechanical scraping of resected fimbriae fallopian tubes

tag: tumor histology


title: ceIL12Aoff8


title: H3K4me3_ChIP_CTCF-AID_auxin_0hr_rep1


title: EOC83: Female high grade serous ovarian cancer, primary tumor

value: mixed

tag: Stage


title: H3K4me1_ChIP_CTCF-AID_NPC_d6_auxin_rep2

tag: cell line

value: F123 mouse neural precursor cell

value: H3K4me1 (abcam, ab8895)


title: FTE11: Epithelial layer by mechanical scraping of resected fimbriae fallopian tubes


title: E17 Saline 2

value: Whole brain

value: CD11b+ Microglia

value: saline


title: FTE19: Epithelial layer by mechanical scraping of resected fimbriae fallopian tubes

value: Female


title: ceIL12Aoff7


title: EOC91: Female high grade serous ovarian cancer, primary tumor

value: serous

value: IIIC


title: ceIL12Aoff6


title: H3K4me1_ChIP_CTCF-AID_NPC_d6_auxin_rep1

tag: chip antibody


title: H3K4me1_ChIP_CTCF-AID_NPC_d6_ctl_rep1