title: passage control_rep2

type: genomic

city: Suzhou

first: Jianxiang

last: Li

state: Jiangsu

address: No. 199 Renai Road

department: Department of Toxicology, School of Public Health, Medicine College

institute: Soochow university

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: iScan

data_processing: minfi R package

label: Cy3, Cy5

source_name: passage control,BEAS-2B

label_protocol: Standard Illumina Protocol

growth_protocol: Human bronchial epithelium BEAS-2B cells were obtained from American Type Culture Collection (ATCC) (Manassas, VA, USA). Cells were cultured in Dulbecco’s modified Eagle medium (DMEM; Hyclone CM; Fisher Scientific) supplemented with 10% FBS.

extract_protocol: The total DNA was extracted using the DNA extraction kit (Tiangen, China) and modified using the EpiTect Bisulfite Kit (Qiagen, Germany). according to the manufacturer’s protocol.

treatment_protocol: BEAS-2B cells were continuously exposed to a sub-cytotoxic concentration (10 μg/ml, according to the cell viability analysis) of SWCNTs in medium and passaged 2-3 days for 60 days (approximately 20 passages). After chronic SWCNTs exposure, the cells were cultured in standard medium without SWCNTs for at least 60 days before further experiments. The sham-exposed passage control group without SWCNTs was subcultured under the same culture conditions.

tag: cell line

tag: treatment

value: control


title: post-exposure_rep2

status: Public on Jun 26 2020

country: China

molecule: genomic DNA

organism: Homo sapiens

value: SWCNT


title: passage control_rep3


title: dilp_fatbody_day50_3

type: SRA

city: Cologne

first: Carina

middle: Marianne

last: Weigelt

address: Joseph-Stelzmann-Str 9b

country: Germany

institute: Max Planck Institute for Biology of Ageing

description: CircCoordinates.tsv,CircRNACount.tsv,LinearCount.tsv,bbTest.linear.Fat_body_50.tsv,isoforms.fpkm_tracking.tsv

library_source: transcriptomic

data_processing:
Primary data analysis is done by Illumina’s real-time analysis software (RTA)
raw reads were mapped using STAR version 2.5.2b(circRNA)
circRNAs were detected using DCC version 0.4.4.
differential circRNA expression was analyzed using R’s ibb package
raw reads were mapped using HISAT version 2.0.4 (isoform expression)
transcripts were assembled using StringTie version 1.3.0
differential isoform expression was analyzed using cufflinks/cuffdiff version 2.2.1
Genome_build: BDGP6 Ensembl build 90
Supplementary_files_format_and_content: tab separated tables were generated representing circRNA coordinates, circRNA counts, linearRNA counts, differential circRNA statistics and isoform fpkm table

molecule: total RNA

organism: Drosophila melanogaster

source_name: manually dissected fruit fly tissues

growth_protocol: Female flies were kept at 25°C and 65% humidity on standard sugar-yeast-agar food. Fly tissues were dissected manually with fine forceps in PBS and frozen in dry ice.

extract_protocol:
Total RNA extraction with Trizol and DNase treatment. For samples 73-78: Polysome-bound RNA was enriched.
RNA libraries were prepared for sequencing using standard Illumina protocols based on rRNA depleted RNA samples

treatment_protocol: Dissected tissues: brain, thorax (without gut), gut (without crop, but including maphigian tubules), fat body (without gut and without ovaries)

tag: rna

value: Total RNA

tag: age

value: Day 50

tag: genotype

tag: tissue

value: fat body


title: passage control_rep1


title: post-exposure_rep1


title: post-exposure_rep3


title: oeNORS-1

city: Indianapolis

first: Mircea

last: Ivan

state: IN

address: 980 W Walnut Street

country: USA

institute: Indiana University School of Medicine

data_processing:
Sequencing and base-calling were performed with Torrent_Suite 4.0.2
Reads were aligned using STAR (v2.3.0)
Read coutns for each gene was created using bamutils count from the ngsutils and Gencode v19 as the annotation
Genome_build: hg19
Supplementary_files_format_and_content: read counts

source_name: breast cancer cell line

growth_protocol: MCF-7 cells were tested mycoplasma-free and maintained at 37°C in 5% CO2 with DMEM/High glucose medium supplemented with 10% (v/v) FBS and antibiotics

extract_protocol:
For RNA extraction, cells were lysed using QIAzol Lysis Reagent (QIAGEN) and total RNA was isolated using the RNeasy kit (QIAGEN) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For knockdown study, MCF-7 cells was transfected with lincNORS siRNA or control siRNA. After overnight incubation, medium was changed to growth media and the cells were further cultured for 24 hours under 1%O2 condition before RNA harvesting; For overexpression study, MCF-7 cells stably expressing lincNORS or pcDNA vector was cultured under normoxia (21% O2) condition for 24 hours beofore RNA harvesting.

tag: transfection

tag: culture condition

value: normoxia:21% O2


title: PX_4wk_58_Inc_YES_BG_114

city: Boston

first: Aref

last: Ebrahimi

state: MA

address: 1 Joslin Pl

department: Islet Cell and Regenerative Biology

institute: Harvard Medical School - Joslin

description: 4-5 Week Lewis Rat

data_processing:
fastqc
subread-buildindex
subread-align
featureCounts
limma
Genome_build: voom
Supplementary_files_format_and_content: Rnor6 ENSEMBLE v93

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Islets of Langerhans

extract_protocol:
miRNeasy Qiagen
Wafergreen Directional

tag: strain

value: Lewis Rats

tag: average bg pre-sac


title: HFD616_liver

city: Oxford

first: Rui

last: Gao

address: Old Road

department: Oxford Centre for Diabetes, Endocrinology and Metabolism

country: United Kingdom

institute: Churchill Hospital

data_processing:
The sequencing raw reads were filtered for low-quality, adaptor-polluted, high content of unknown base reads by SOAPnuke (v1.5.2).
We used Trinity (v2.0.6) to perform de novo assembly, and Tgicl (v2.0.6) on cluster transcripts to remove redundancy and get unigenes. The high-quality clean reads were then mapped to the mouse reference genome (GRCm38) via HISAT2 (v2.0.4) 25 and full-length transcriptome database via Bowtie2 (v2.2.5)
The gene expression levels were then quantified by RSEM (v1.1.12) and were normalized by the method of fragments per kilobase of exon model per million reads mapped (FPKM).
The DEseq2 (fold change≥2 and adjusted P-value≤0.05) package was applied to identify differentially expressed genes (DEGs) between HFD and CD groups at each time point.
Ingenuity Pathway Analysis (IPA, Qiagen, Redwood City, CA, USA, www.qiagen.com/ingenuity) was conducted to determine enriched canonical pathways, upstream regulators, mechanistic networks, and diseases and functions. Kyoto Encyclopedia Genes and Genomes (KEGG) analyses of DEGs were also performed according to the gene annotations provided by DAVID online tool (v6.8).
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Matrix table with fragments per kilobase per million (FPKM) for every gene and every sample

organism: Mus musculus

source_name: high-fat diet mice liver

growth_protocol: Four-week-old C57BL/6N male mice were purchased from GemPharmatech Co., Ltd. and were maintained at 22°C on a 12 h light/dark cycle with ad libitum access to food.

extract_protocol:
Islets extraction: After clamped with a hemostat at the duodenal opening, the bile duct was cannulated and perfused with 2 mL collagenase P (Roche Diagnostics, Germany, 1 mg/mL in Hanks' balanced salt solution (HBSS)). Pancreatic tissue was digested at 37 °C for 10 min. The reaction was stopped by adding cold HBSS with 10% fetal bovine serum (FBS), followed by 10 seconds of vigorous shaking. Islets were separated onto a gradient composed of HBSS and Histopaque (11191 and 10771, Sigma Aldrich, USA) layers and were hand-picked for 2 times under a dissection microscope to minimize acinar cells. The purity of islets for RNA-sequencing was evaluated by the expression of Amy1a (a marker of acinar cells) and Krt19 (a marker of ductal cells). In our transcriptome dataset, Amy1a and Krt19 showed no statistical difference at mRNA level from any time points, which indicates the contaminants were fairly minimized. Liver extraction: The same region of the liver were removed and flash frozen in liquid nitrogen. Total RNA was isolated from handpicked islets and homogenized liver tissue using TRIzol reagent (Invitrogen, CA, USA) in accordance with the manufacturer’s instructions. The quality and quantity of extracted RNA were measured by on-chip electrophoresis utilizing the Agilent RNA 6000 Nano Kit and Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). Samples exhibited 1.9≤A260/A280 ≤ 2.2, RNA integrity number>8.0 and 28S/18S>1.0 were selected for library preparation.
The total RNA was purified by enriching poly (A) mRNA with magnetic oligo (dT) beads. After reverse transcription by using the random hexamer (N6) primers, double-stranded cDNA fragments were synthesized and subjected to end repair and adapter ligation. The cDNA libraries were then constructed by PCR amplification, and finally sequenced on BGISEQ-500 sequencing platform by the Beijing Genomics Institute (Shenzhen, China).

treatment_protocol: Mice were fed either CD (LabDiet 5001, 13.5% fat) or HFD (Research Diets D12492, 60% fat) for 4−24 weeks.

value: liver

tag: diet

value: high-fat diet

tag: weeks on diet

value: 24 weeks


title: LSH-AID-late-chase-24h

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

description: Enrich EdU-labeled DNA, add hairpin, and BS-seq

library_source: genomic

data_processing:
Basecalls performed by Annoroad Gene Technology Co. Ltd.
Raw reads from Illumina platforms were processed by HBS-Tools. In brief, preprocessing of raw reads, including bad quality bases trimming, sequencing adaptor, and hairpin adaptor removal were performed with the module of ‘hbs_process’. And then each preprocessed read pair was aligned pairwise using Smith-Waterman algorithm and only aligned parts were kept to recover the original genomic sequence. The recovered original sequences were then mapped to the genome assembly, with which the methylation information was extracted into the result SAM output. The original sequence recovery and mapping was performed with the module ‘hbs_mapper’ of HBS-Tools.  The aligned SAM files, that contain both strands of the hairpin read, were then de-duplicated based on the following criteria: the two strands were firstly concatenated with the one with higher-methylation as head and the lower as tail, and strand pairs with the same concatenated sequence were regarded as duplication and only one copy was retained.  Based on the de-duplicated aligned reads (in SAM file), reads of each pair were discriminated as parent (higher) or daughter (lower) strand according to the No. of methylated CpGs, with equally methylated reads randomly distributed to parent or daughter. Read pairs with no methylated CpGs on both strands were discarded. Then, methylation maintenance events were called based on parent/daughter read pairs, among which maintained methylation, un-maintained methylation, maintained un-methylation and de novo methylation were designated as MM, MU, UU, UM, respectively. All events were summed up for each genomic CpG site by chromosome coordinates, so now we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site.
Genome_build: hg19
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are provided as gzipped text files, that contain methylation mainenance events called for covered CpG sites. All events were summed up for each genomic CpG site by chromosome coordinates, so we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site. Maintenance events are also asigned into individual arm of the replication fork. Upper arm indicates parental Waston and daughter Crick strand, and lower arm indicates parental Crick and daughter Watson strand. All coloumns are indicated by the first row of the files.

source_name: IAA-treated LSH-AID HeLa cells, release 6 hr, EdU labeled and chase 24 hr

growth_protocol:
HeLa-S3 Cells were cultured at 37 °C with 5% CO2. Culture medium contains DMEM High Glucose (HyClone, SH30022), 10% FBS (BI, 04-010-1ACS) and 1X Penicillin-Streptomycin (Gibco, 15140122). Cells were passed every two days. Detached from plates with 0.25% Trypsin at 37 °C for 2 to 3 min. The sub-cultivation is about 1:5 to 1:6.
Mouse embryonic stem cells were cultured on gelatin coated dishes in ES culture medium containing DMEM (ThermoFisher 11995), supplemented with 15% fetal bovine serum (Hyclone 30070.03), 1% None essential amino acids (Merck M7145), 1% L-glutamine (BBI Life Sciences E607004), 0.1% β-mercaptoethanol (Gibco 21985023), 0.01 % LIF (107 U/ml), and 1% Penicillin-Streptomycin (Gibco, 15140122).

extract_protocol:
Harvest cells and extract DNA with phenol-chloroform.
Fragment DNA with sonication (Covaris M200) or restrictive enzyme AluI (NEB, R0137). Size select DNA fragments ranging from 100 bp to 200 bp with AMPure beads (1.05X to 2.8X) (Beckman, A63881). Click it reaction to conjugate biotin to EdU labeled DNA: (Tris pH7.5 buffer 15 mM; Biotin azide (Sigma, 762024) 400 uM; CuSO4 (Sigma, 209198)/THPTA (Sigma, 762342) mix (1:5) (100 uM: 500 uM); Sodium ascorbate (freshly prepared, Sigma, A4034) 5 mM). Reaction at 34 °C for 20 min. DNA was purified with MinElute PCR purification kit (Qiagen, 28004). The click it reaction system is modified from (1) (2). End repair (NEB, E6050), dA-tailing (NEB, E6053) and adaptor ligation (NEB, E6056). Hairpin adapter and methylated sequencing adapter were pre-mix at the molar ratio of 3:1 before adapter ligation. After ligation, 1.4X AMPure beads were added to remove un-ligated adapters. Dissolve adapter ligated DNA in 1X TE buffer. Incubate DNA with M280 streptavidin beads (Thermo Fisher, 11205D) in 1X Binding & Washing buffer (5 mM Tris-Cl (pH 7.5), 1M NaCl, 0.5 mM EDTA (pH 8.0)) for 20 min. Wash with 1X Binding & Washing buffer containing 0.5% IGEPAL CA-630 (Sigma, I3021) for 6 times, and then wash with ddH2O once. Dissolve beads in 40 ul ddH2O. Perform bisulfite conversion (Qiagen, 59104) with DNA on beads. PCR amplification (KAPA KR0413) with bisulfite converted DNA. PCR product was running on a 2% agarose-gel and the larger band ranging from 300 bp to 400 bp was hairpin-ligated sample. Recover this band with gel-extraction kit (TIANGEN, DP208). Clean up with AMPure beads (0.9X). Dissolve DNA in 0.1X TE buffer. The HAMMER-seq library is ready for Next Generation Sequencing.

treatment_protocol: HeLa-S3 cells were synchronized at G1/S entrance with thymidine/aphidicolin double block (2 mM thymidine (Sigma, T1895) for 18 h; remove thymidine and continue to culture for 9 h; 1ug/ml aphidicolin (Abcam, 38966-21-1) for another 14 h). Remove aphidicolin. Pulse labeling with 20 uM EdU (Thermo Fisher, E10187) for 4 min. Remove EdU and chase with 20 uM thymidine for a series of desired time length (0 min to 24 h).

tag: strain background

value: Adult female

value: HeLa-S3 with LSH-AID

tag: cell type

value: epithelial adenocarcinoma

tag: genotype/variation

value: LSH-AID

value: cervix

tag: developmental stage

value: 31 years


title: dilp_fatbody_day50_2


title: HFD616_islet

source_name: high-fat diet mice islets

value: islets


title: LSH-AID-late-chase-2h

source_name: IAA-treated LSH-AID HeLa cells, release 6 hr, EdU labeled and chase 2 hr


title: Sham_4wk_50_Inc_YES_BG_99

description: 4-5 Week Lewis Rat


title: dilp_fatbody_day50_1


title: HFD614_liver


title: Sham_4wk_49_Inc_YES_BG_94

description: 4-5 Week Lewis Rat


title: LSH-AID-late-chase-30m

source_name: IAA-treated LSH-AID HeLa cells, release 6 hr, EdU labeled and chase 30 min


title: wt_fatbody_day50_3

value: wDah (wildtype)


title: HFD614_islet


title: Sham_4wk_48_Inc_YES_BG_82

description: 4-5 Week Lewis Rat


title: HFD611_liver


title: wt_fatbody_day50_2


title: LSH-AID-late-chase-5m

source_name: IAA-treated LSH-AID HeLa cells, release 6 hr, EdU labeled and chase 5 min


title: LSH-AID-late-chase-0

source_name: IAA-treated LSH-AID HeLa cells, release 6 hr, EdU labeled and chase 0 min


title: Sham_4wk_47_Inc_YES_BG_92

description: 4-5 Week Lewis Rat


title: Sham_4wk_46_Inc_YES_BG_97

description: 4-5 Week Lewis Rat


title: HFD611_islet


title: dilp_fatbody_day30_3

description: CircCoordinates.tsv,CircRNACount.tsv,LinearCount.tsv,bbTest.linear.Fat_body_30.tsv,isoforms.fpkm_tracking.tsv

value: Day 30


title: dilp_fatbody_day30_2

value: Total RNA


title: PX_4wk_44_Inc_YES_BG_101

description: 4-5 Week Lewis Rat


title: HFD518_liver

value: 20 weeks


title: LSH-AID-chase-2h

source_name: EdU labeled IAA-treated LSH-AID HeLa cells with chasing 2 hr


title: LSH-AID-chase-24h

source_name: EdU labeled IAA-treated LSH-AID HeLa cells with chasing 24 hr


title: PX_4wk_57_Inc_YES_BG_140

description: 4-5 Week Lewis Rat


title: HFD518_islet


title: LSH-AID-chase-30m

source_name: EdU labeled IAA-treated LSH-AID HeLa cells with chasing 30 min


title: dilp_fatbody_day30_1

value: fat body


title: pcDNA3-2

value: pcDNA3 only

value: normoxia:21% O2


title: HFD517_liver

value: liver


title: PX_4wk_41_Inc_YES_BG_156

description: 4-5 Week Lewis Rat

value: Lewis Rats


title: LSH-AID-chase-5m

source_name: EdU labeled IAA-treated LSH-AID HeLa cells with chasing 5 min


title: PX_4wk_38_Inc_YES_BG_119

description: 4-5 Week Lewis Rat


title: PX_4wk_37_Inc_YES_BG_110

description: 4-5 Week Lewis Rat


title: wt_fatbody_day30_2


title: wt_fatbody_day30_3


title: LSH-AID-chase-0

source_name: EdU labeled IAA-treated LSH-AID HeLa cells with chasing 0 min


title: HFD516_liver

value: high-fat diet


title: dilp_fatbody_day10_3

description: CircCoordinates.tsv,CircRNACount.tsv,LinearCount.tsv,bbTest.linear.Fat_body_10.tsv,isoforms.fpkm_tracking.tsv

value: Day 10


title: PX_4wk_36_Inc_YES_BG_121

description: 4-5 Week Lewis Rat


title: Sham_4wk_24_Inc_YES_BG_97

description: 4-5 Week Lewis Rat


title: Sham_4wk_22_Inc_YES_BG_104

description: 4-5 Week Lewis Rat


title: dilp_fatbody_day10_2


title: HFD516_islet


title: dilp_fatbody_day10_1


title: Sham_4wk_21_Inc_YES_BG_96

description: 4-5 Week Lewis Rat


title: HFD511_liver


title: HFD511_islet


title: HFD418_liver

value: 16 weeks


title: wt_fatbody_day10_3


title: HFD418_islet


title: wt_fatbody_day30_1


title: wt_fatbody_day50_1

value: Day 50


title: WT-late-chase-2h, replicate2

source_name: WT HeLa cells release 6 hr, EdU labeled and chased 2 hr, replicate2

value: Adult female

value: epithelial adenocarcinoma

value: WT


title: WT-late-chase-24h, replicate2

source_name: WT HeLa cells release 6 hr, EdU labeled and chased 24 hr, replicate2

value: cervix

value: 31 years


title: wt_fatbody_day10_2

source_name: manually dissected fruit fly tissues

value: wDah (wildtype)


title: Cells treated with MPA

city: West Haven

first: Guste

last: Urbonaite

state: CT

address: 300 Heffernan Drive, ISTC, Rm 117

department: Molecular and Cellular Biology

institute: Yale University

data_processing:
Paired end reads were combined after trimming of adapters on R1 and subjected to fastq quality control and trimming
Cell barcodes were extracted from reads and attached to read name. This was done using the DropSeq alignment protocol
Reads were aligned to S. cerevisiae genome for MPA experiments, or aligned to the cerevisiae and bayanus genomes for the species mixing experiments
Aligned reads had gene and exon information added to produce digital gene expression data
MPA experiment data was integrated and analyzed using the seurat standard integration protocol
Genome_build: S. cerevisiae genome (R64-1-1), or S. bayanus genome (unassembled CBS 7001)
Supplementary_files_format_and_content: .dge files are in txt format and contain digital gene expression data of individual genes per cell

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cells

growth_protocol: Cells were grown for 18 hrs in CSM 2% glucose in MPA, Guanine, DMSO, or Guanine+MPA for MPA experiments. Cells were grown in CSM 2% glucose for species mixing S. bayanus and S. cerevisiae

extract_protocol:
DropSeq
Nextera XT standard illumina primers
Single cell RNA seq

treatment_protocol: Treated with 10 uM DMSO, MPA, Guanine, of Guanine and MPA. Species mixing experiment cells were not treated

tag: growth period

value: 18 hrs


title: Cells treated with Guanine and MPA


title: HFD517_islet

value: islets

value: 20 weeks


title: wt_fatbody_day10_1

value: Total RNA

value: fat body


title: HFD416_liver

value: liver


title: Cells treated with Guanine


title: HFD416_islet


title: Cells treated with DMSO


title: HFD414_liver


title: WT-late-chase-5m, replicate2

source_name: WT HeLa cells release 6 hr, EdU labeled and chased 5 min, replicate2

tag: cell line


title: WT-late-chase-0, replicate2

source_name: WT HeLa cells release 6 hr, EdU labeled and chased 0 min, replicate2


title: HFD414_islet


title: dilp_gut_day50_2

description: CircCoordinates.tsv,CircRNACount.tsv,LinearCount.tsv,bbTest.linear.Gut_50.tsv,isoforms.fpkm_tracking.tsv

value: gut


title: dilp_gut_day50_1


title: HFD411_liver

source_name: high-fat diet mice liver

value: high-fat diet


title: WT-late-chase-24h, replicate1

source_name: WT HeLa cells release 6 hr, EdU labeled and chased 24 hr, replicate1


title: HFD318_liver

value: 12 weeks


title: wt_gut_day50_2


title: wt_gut_day50_3


title: HFD411_islet

source_name: high-fat diet mice islets

value: 16 weeks


title: WT-late-chase-2h, replicate1

source_name: WT HeLa cells release 6 hr, EdU labeled and chased 2 hr, replicate1


title: wt_gut_day50_1

value: Day 50


title: WT-late-chase-30m, replicate1

source_name: WT HeLa cells release 6 hr, EdU labeled and chased 30 min, replicate1

value: Adult female


title: HFD316_liver


title: HFD318_islet


title: WT-late-chase-5m, replicate1

source_name: WT HeLa cells release 6 hr, EdU labeled and chased 5 min, replicate1

value: epithelial adenocarcinoma


title: WT-late-chase-0, replicate1

source_name: WT HeLa cells release 6 hr, EdU labeled and chased 0 min, replicate1

value: WT


title: WT-late-chase-30m, replicate2

source_name: WT HeLa cells release 6 hr, EdU labeled and chased 30 min, replicate2

value: cervix


title: dilp_gut_day50_3


title: dilp_gut_day30_2

description: CircCoordinates.tsv,CircRNACount.tsv,LinearCount.tsv,bbTest.linear.Gut_30.tsv,isoforms.fpkm_tracking.tsv

value: Day 30


title: HFD316_islet


title: Peritonelal mesothelial cells Crocidolite 1

type: RNA

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

hyb_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.9, May 2017).

scan_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.9, May 2017, Agilent C Scanner Settings).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 074036_D_F_20180103) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Peritoneal Mesothelial Cells, Fischer 344

extract_protocol: Total RNA was extracted using RNeasy Mini(QIAGEN).

treatment_protocol: The collection of mesothelial cells was from rat mesentery. The mesentery incubated with Dispase at 37 degrees centigrade for 30 min. The suspension was then passed through a 100 micrometer-pore nylon mesh to remove undigested fragments, and centrifuged at 300 x g for 5 min. The collected cells were used for cRNA synthesis.

value: Mesothelial cells from mesentery

value: Fischer 344


title: Peritonelal mesothelial cells Crocidolite 2

label_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.9, May 2017).


title: Peritonelal mesothelial cells NT 1


title: Peritonelal mesothelial cells NT 3


title: PH003

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Genomics Cell Ranger software.
ADTs and HTOs for each cell were normalized using a centered log ratio (CLR) transformation across cells.
Samples were demultiplexed based on HTOs using the HTODemux function in Seurat.
Genome_build: GRCh38
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome and feature-barcode matrices.

source_name: bone marrow

extract_protocol:
Frozen BM specimens were rapidly thawed and transferred into 50 mL conical tubes. 20 mL Pre-warmed RPMI 1640 (Corning) supplemented with 5% Fetal Bovine Serum (FBS) (Sigma Aldrich) and 2-Mercaptoethanol (2-ME, 55nM) (Thermo Fisher Scientific) was added drop-wise to tubes. Cell suspensions were subjected to centrifugation at 400 x g for 5 min at 4°C and supernatant was discarded. Pellets were re-suspended in 5mL RPMI 1640 with 5% FBS and 2-ME, and filtered using a 70 μm nylon mesh (Thermo Fisher Scientific) with residual cell clumps discarded. After centrifuging at 400 x g at 4°C for 5 min, the supernatant was discarded, and the cell pellet was re-suspended in PBS (Corning) with 2% FCS and placed on ice prior to staining for FACS. Single-cell BM suspensions were re-suspended in PBS with 2% FCS and Human TruStain FcX Blocking Solution (BioLegend) and incubated on ice for 10 mins. Cell suspensions were centrifuged at 400 x g at 4°C for 5 min, and supernatant discarded. Cell pellets were re-suspended in PBS with 2% FCS, FITC-conjugated anti-human CD45 (1:200, BD Pharmingen), APC-conjugated anti-human CD19 (1:200 concentration, BioLegend) and PE-conjugated anti-human CD10 (1:200, BioLegend), and incubated on ice for 30 mins. Following incubation, cell suspensions were subjected to two wash cycles involving re-suspension of cell pellets in 3 mL PBS with 2% FCS, followed by centrifuging at 400 x g at 4°C for 5 min, followed by supernatant removal. Finally, samples were re-suspended in 300 mL of PBS with 2% FCS per 2 x 106 cells, supplemented with DAPI (0.5 mg/mL) for live/dead staining. Cell sorting was performed using the SY3200™ highly automated parallel sorting (HAPS) cell sorter (Sony).
Single Cell 3’ Reagent Kits: Chromium™ Single Cell 3’ Library & Gel Bead Kit v3, PN-1000075; Single Cell 3’ Chip Kit v3 PN-1000073 and i7 Multiplex Kit PN-120262 (10x Genomics). Samples were tagged with cell hashing oligo-tagged antibodies (BioLegend) according to manufacturer’s instructions. CITE-Seq antibodies were stained according to manufacturer’s instructions (https://cite-seq.com/protocol/), with the exception of PBS supplemented with 2% FBS as the washing and staining buffer.
CITE-seq

tag: Stage

value: Diagnosis/Remission/Relapse

value: ratio of 1:5 CD19+:CD19-CD45+ bone marrow cells

value: 16 years

tag: Sex

value: male


title: Peritonelal mesothelial cells Crocidolite 3


title: dilp_gut_day30_1

tag: rna

value: Total RNA

tag: age


title: WT-chase-24h, replicate

source_name: EdU labeled WT HeLa cells with chasing 24 hr, replicate

tag: tissue

value: 31 years


title: PH002

value: 8 years

value: female


title: MLL001

value: 2 months


title: wt_gut_day30_3

tag: genotype

value: wDah (wildtype)

value: gut


title: HFD315_islet

value: islets

value: high-fat diet

value: 12 weeks


title: HFD315_liver

value: liver


title: dilp_gut_day30_3

value: Day 30


title: WT-chase-30m, replicate

source_name: EdU labeled WT HeLa cells with chasing 30 min, replicate

value: Adult female

value: epithelial adenocarcinoma

value: WT

value: cervix


title: HFD313_liver


title: WT-chase-5m, replicate

source_name: EdU labeled WT HeLa cells with chasing 5 min, replicate


title: ETV003

value: Diagnosis/Remission/Relapse

value: ratio of 1:5 CD19+:CD19-CD45+ bone marrow cells

value: 9 years


title: VCaP SI-2

city: SACRAMENTO

first: Cameron

middle: Michelle

last: Armstrong

state: CA

address: 4645 2nd Ave.Research Bldg. III, Ste. 1300

institute: UC Davis Medical Ctr.

data_processing: read counts and fpkm

source_name: Prostate Tumor

growth_protocol: VCaP cells were maintained in DMEM media

extract_protocol: RNA was extracted using Trizol and resuspended in water

treatment_protocol: VCaP cells were treated overnight with DMSO control or 5µM SI-1 or SI-2

tag: tumor stage

value: CRPC

tag: treatment

value: VCaP


title: eHi-C hiPSC-ATCC ACS-1026

city: Cleveland

first: Xiaoxiao

last: Liu

state: Ohio

address: 10900 Euclid Ave

department: Genetics and Genomes Sciences

institute: Case Western Reserve University

data_processing:
The paired-end Hi-C reads were mapped to human genome hg19 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed. Easy Hi-C reads were mapped to hg19 using BOWTIE. Because nearly all the mappable reads start with HindIII sequence AGCTT, we trimmed the first 5 bases from every read, took the next 36 bases, and added the 6-base sequence AAGCTT to the 5’ of every read before mapping using the whole 42 bases.
For Hi-C, we focus on cis-interactions and therefore only kept Hi-C paired-end reads which both ends are mapped to the same chromosome. Out of all the intra-chromosome paired-end reads, we also discard the reads with both ends mapped to the same HindIII fragments. Since cut-and-ligation events are expected to generate reads within 500bp upstream of HindIII cutting sites due to the size selection (“+” strand reads should be within 500bp upstream of a HindIII site, and “-“ strand reads should be within 500bp downstream a HindIII site), we only keep reads pairs with both ends satisfying this criteria. For eHi-C library, the only type of invalid cis- pairs are self-circles with two ends within the same HindIII fragment facing each other
We next split all these reads into three classes based on their strand orientations (“same-strand”, “inward”, or “outward”), and generated the resulting lists of fragment pairs (with Hi-C read counts) from each class of reads.
There are total ~840k fragments in human genome. They are assembled into ~335k anchors after short fragments (<5kb) are merged into neighboring anchors. For every anchor, we first count Hi-C/eHi-C reads from the anchor to every fragment within 2Mb range.
We estimated a background frequency between any two fragments based on the average reads count of all fragment pairs that have similar lengths, similar gap distance, GC content, and visibility. The fragment-to-fragment data can be then converted to anchor-to-anchor data by adding the read counts and background frequencies together based on the assignment of fragments to anchors. P values of the enrichment of Hi-C reads over the background frequency can be calculated using a negative binomial model. The statistical method has been described in previous publication (Jin, F. et al. Nature 2013, 503:290-294)
Genome_build: hg19
Supplementary_files_format_and_content: For each Hi-C and easy Hi-C data set, the fragment-to-fragment frequency are provided in the txt file. For each Chip-Seq replicate, peak-calling results are provided in the bed file.

source_name: Bone Marrow Cd34+ Cells,  ATCC ACS-1026

growth_protocol: Fibroblasts were grown in DMEM medium supplemented with 10% FBS (Hyclone), Glutamax (Thermo Fisher Scientific) and NEAA (Thermo Fisher Scientific) and subcultured at a ratio of 1:3 when they reach 90% confluence. H1 cells were cultured on the hESC-qualified Matrigel (Corning, #354277) coated plates in mTeSR1 medium (StemCell Technologies, #05850). iPS cells were cultured on Matrigel with a daily change of E8 medium and passaged by collagenase. To generate iPSC-derived NPCs, detached iPSC colonies were suspended in embryoid body (EB) medium (DMEM:F12 with 20% KOSR, 2?M dorsomorphin and 2 ?M A 83-01) for 7 days. Floating EBs were attached on Matrigel and cultured in NPC medium (DMEM/F12, N2 supplement, NEAA and 2 uM cyclopamine). After 14 days, neural tube-like rosettes were mechanically picked and dissociated into single NPCs by Accutase. NPCs were maintained as monolayer in NPC medium with medium change every two days. For neuronal differentiation, NPCs were plated on Matrigel and cultured in Neurobasal medium supplemented with 2%B27, 2 mM L-glutamine, 10 ng/ml BDNF and 10 ng/ml GDNF.

extract_protocol:
For Hi-C, nuclei were extraced after fixing using a cell lysis buffer. For ChIP-seq, nuclei were extracted and chromatins were fragmented by sonication. The TF/histone-DNA complexes were isolated by antibody.     Total RNA was isolated from samples by RNeasy Mini Kit (Qiagen) according to the manufacturer?s instructions.
For eHi-C, briefly, the cells and tissues were first fixed with 1% formaldehyde and then quenched with 150mM glycine. The fixed samples were lysed using a cell lysis buffer or a tissue specific buffer. And nuclei were isolated and then digested with HindIII. After that, in situ proximity ligation was done by  ligating the digested chromatin in a large volume. Ligation products were then reverse-linked with proteinase K and purified using phenol-chloroform. The purified DNA was then digested with DpnII and then self ligated using T4 DNA ligase. After purification, the DNA products were then re-linearized with HindIII followed by DNA purification. The resulting DNA were used for library construction. First, the DNA were end-repaired using End-it kit (Epicentre). Second, the end repaired DNA was A-tailed by Klenow fragment (3??5? exo?; NEB). Then, a customized Illumina truseq Adapter was ligated and the resulting DNA was then PCR amplified. The final libraries were quantified and sequenced on Illumina Hiseq platform.
All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit.  Random indexes were introduced for eHi-C libraries to remove PCR duplication. Generally, PCR amplification was done with 7-9 cycles. All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.

value: foreskin fibroblasts

tag: restrictive enzyme

value: HindIII


title: WT-chase-0, replicate

source_name: EdU labeled WT HeLa cells with chasing 0 min, replicate

value: 31 years


title: HFD313_islet

tag: strain

value: islets

tag: diet


title: VCaP SI-1


title: VCaP DMSO

value: DMSO


title: wt_gut_day30_1

source_name: manually dissected fruit fly tissues

value: Total RNA

value: wDah (wildtype)

value: gut


title: wt_gut_day30_2

value: Day 30


title: WT-chase-2h, replicate

source_name: EdU labeled WT HeLa cells with chasing 2 hr, replicate

tag: strain background

value: Adult female

value: epithelial adenocarcinoma


title: Peritonelal mesothelial cells NT 2

value: Mesothelial cells from mesentery

value: Fischer 344


title: dilp_gut_day10_3

description: CircCoordinates.tsv,CircRNACount.tsv,LinearCount.tsv,bbTest.linear.Gut_10.tsv,isoforms.fpkm_tracking.tsv

value: Day 10


title: HFD213_liver

source_name: high-fat diet mice liver

value: liver

value: high-fat diet

tag: weeks on diet

value: 8 weeks


title: 10h-IAA-6hR-rescue, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
UHRF1-AID-10hIAA+6hRescue.rep2

data_processing:
Basecalls performed by Annoroad Gene Technology Co. Ltd.
Raw reads from Illumina platforms were processed by HBS-Tools. In brief, preprocessing of raw reads, including bad quality bases trimming, sequencing adaptor, and hairpin adaptor removal were performed with the module of ‘hbs_process’. And then each preprocessed read pair was aligned pairwise using Smith-Waterman algorithm and only aligned parts were kept to recover the original genomic sequence. The recovered original sequences were then mapped to the genome assembly, with which the methylation information was extracted into the result SAM output. The original sequence recovery and mapping was performed with the module ‘hbs_mapper’ of HBS-Tools.  The aligned SAM files, that contain both strands of the hairpin read, were then de-duplicated based on the following criteria: the two strands were firstly concatenated with the one with higher-methylation as head and the lower as tail, and strand pairs with the same concatenated sequence were regarded as duplication and only one copy was retained.  Based on the de-duplicated aligned reads (in SAM file), reads of each pair were discriminated as parent (higher) or daughter (lower) strand according to the No. of methylated CpGs, with equally methylated reads randomly distributed to parent or daughter. Read pairs with no methylated CpGs on both strands were discarded. Then, methylation maintenance events were called based on parent/daughter read pairs, among which maintained methylation, un-maintained methylation, maintained un-methylation and de novo methylation were designated as MM, MU, UU, UM, respectively. All events were summed up for each genomic CpG site by chromosome coordinates, so now we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: Processed data files are provided as gzipped text files, that contain methylation mainenance events called for covered CpG sites. All events were summed up for each genomic CpG site by chromosome coordinates, so we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site. Maintenance events are also asigned into individual arm of the replication fork. Upper arm indicates parental Waston and daughter Crick strand, and lower arm indicates parental Crick and daughter Watson strand. All coloumns are indicated by the first row of the files.

source_name: 10 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release 6 h (rescue), replicate

growth_protocol:
HeLa-S3 Cells were cultured at 37 °C with 5% CO2. Culture medium contains DMEM High Glucose (HyClone, SH30022), 10% FBS (BI, 04-010-1ACS) and 1X Penicillin-Streptomycin (Gibco, 15140122). Cells were passed every two days. Detached from plates with 0.25% Trypsin at 37 °C for 2 to 3 min. The sub-cultivation is about 1:5 to 1:6.
Mouse embryonic stem cells were cultured on gelatin coated dishes in ES culture medium containing DMEM (ThermoFisher 11995), supplemented with 15% fetal bovine serum (Hyclone 30070.03), 1% None essential amino acids (Merck􀀂M7145), 1% L-glutamine (BBI Life Sciences􀀂E607004), 0.1% β-mercaptoethanol (Gibco 21985023), 0.01 % LIF (107 U/ml), and 1% Penicillin-Streptomycin (Gibco, 15140122).

value: HeLa-S3 with UHRF1-AID

tag: cell type

tag: genotype/variation

value: cervix


title: HFD213_islet

source_name: high-fat diet mice islets


title: 10h-IAA-4hR-rescue, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
UHRF1-AID-10hIAA+4hRescue.rep2

source_name: 10 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release 4 h (rescue), replicate

tag: developmental stage

value: 31 years


title: HFD212_liver


title: HFD217_islet

value: islets


title: dilp_gut_day10_2


title: HFD217_liver


title: DNMT1-H170V-chase-24h

data_processing:
Basecalls performed by Annoroad Gene Technology Co. Ltd.
Raw reads from Illumina platforms were processed by HBS-Tools. In brief, preprocessing of raw reads, including bad quality bases trimming, sequencing adaptor, and hairpin adaptor removal were performed with the module of ‘hbs_process’. And then each preprocessed read pair was aligned pairwise using Smith-Waterman algorithm and only aligned parts were kept to recover the original genomic sequence. The recovered original sequences were then mapped to the genome assembly, with which the methylation information was extracted into the result SAM output. The original sequence recovery and mapping was performed with the module ‘hbs_mapper’ of HBS-Tools.  The aligned SAM files, that contain both strands of the hairpin read, were then de-duplicated based on the following criteria: the two strands were firstly concatenated with the one with higher-methylation as head and the lower as tail, and strand pairs with the same concatenated sequence were regarded as duplication and only one copy was retained.  Based on the de-duplicated aligned reads (in SAM file), reads of each pair were discriminated as parent (higher) or daughter (lower) strand according to the No. of methylated CpGs, with equally methylated reads randomly distributed to parent or daughter. Read pairs with no methylated CpGs on both strands were discarded. Then, methylation maintenance events were called based on parent/daughter read pairs, among which maintained methylation, un-maintained methylation, maintained un-methylation and de novo methylation were designated as MM, MU, UU, UM, respectively. All events were summed up for each genomic CpG site by chromosome coordinates, so now we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are provided as gzipped text files, that contain methylation mainenance events called for covered CpG sites. All events were summed up for each genomic CpG site by chromosome coordinates, so we have 4 numbers indicating 4 kinds of events of MM/MU/UU/UM for each CpG site. Maintenance events are also asigned into individual arm of the replication fork. Upper arm indicates parental Waston and daughter Crick strand, and lower arm indicates parental Crick and daughter Watson strand. All coloumns are indicated by the first row of the files.

source_name: EdU labeled IAA-treated DNMT1-H170V HeLa cells with chasing 24 hr

growth_protocol: HeLa-S3 Cells were cultured at 37 °C with 5% CO2. Culture medium contains DMEM High Glucose (HyClone, SH30022), 10% FBS (BI, 04-010-1ACS) and 1X Penicillin-Streptomycin (Gibco, 15140122). Cells were passed every two days. Detached from plates with 0.25% Trypsin at 37 °C for 2 to 3 min. The sub-cultivation is about 1:5 to 1:6.

tag: gender

value: female

value: adult

tag: cell line

value: HeLa-S3 with DNMT1-H170V


title: wt_gut_day10_3

value: Total RNA

value: wDah (wildtype)

value: gut


title: DNMT1-H170V-chase-2h

source_name: EdU labeled IAA-treated DNMT1-H170V HeLa cells with chasing 2 hr

value: epithelial adenocarcinoma


title: 10h-IAA-14hR-rescue, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
UHRF1-AID-10hIAA+14hRescue.rep2

source_name: 10 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release 14 h (rescue), replicate

value: Adult female


title: wt_gut_day10_1


title: eHi-C hiPSC-ATCC ACS-1019

source_name: Foreskin Fibroblast Sendai Virus Reprogrammed, ATCC® ACS-1019

value: foreskin fibroblasts

value: HindIII


title: eHi-C hiPSC-ATCC ACS-1011

description:
anchor_2_anchor.loop.iPS.txt.gz
hiPSC_1011.frag_loop.txt.gz

source_name: Foreskin Fibroblast Retroviral Reprogrammed, ATCC® ACS-1011


title: DNMT1-H170V-chase-30m

source_name: EdU labeled IAA-treated DNMT1-H170V HeLa cells with chasing 30 min


title: HFD212_islet


title: DNMT1-H170V-chase-5m

source_name: EdU labeled IAA-treated DNMT1-H170V HeLa cells with chasing 5 min


title: 10h-IAA-2hR-rescue, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
UHRF1-AID-10hIAA+2hRescue.rep2

source_name: 10 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release 2 h (rescue), replicate


title: dilp_thorax_day50_3

description: CircCoordinates.tsv,CircRNACount.tsv,LinearCount.tsv,bbTest.linear.Thorax_50.tsv,isoforms.fpkm_tracking.tsv

value: Day 50

value: thorax


title: HFD211_islet

value: high-fat diet

value: 8 weeks


title: HFD211_liver

value: liver


title: dilp_thorax_day50_2


title: RescueTo24h-noIAA, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
UHRF1-AID-0hIAA+24hRelease.rep2

source_name: no IAA treatment of UHRF1-AID HeLa cells, release 24 h, replicate.

value: HeLa-S3 with UHRF1-AID

value: cervix

value: 31 years


title: DNMT3A3B-DKO-chase-24h

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
B3A3B-AluI-24hC-0112_L2_A022.R1.clean.fastq.gz

source_name: EdU labeled DNMT3A/3B double KO HeLa cells with chasing 24 h

value: HeLa-S3 with DNMT3A/3B double KO

value: DNMT3A/3B DKO


title: dilp_gut_day10_1

value: Total RNA

value: Day 10


title: wt_gut_day10_2

value: wDah (wildtype)

value: gut


title: HFD118_liver

value: 4 weeks


title: DNMT1-H170V-chase-0

source_name: EdU labeled IAA-treated DNMT1-H170V HeLa cells with chasing 0 min

value: female

value: adult

value: HeLa-S3 with DNMT1-H170V

value: epithelial adenocarcinoma


title: wt_thorax_day50_3

source_name: manually dissected fruit fly tissues

value: Day 50

value: thorax


title: dilp_thorax_day50_1


title: CHAF1A-AID-chase-24h

source_name: EdU labeled IAA-treated CHAF1A-AID HeLa cells with chasing 24 hr

value: HeLa-S3 with CHAF1A-AID


title: LSH-AID-late-chase-24h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
LSH-late-c24h-rep

source_name: IAA-treated LSH-AID HeLa cells, release 6 hr, EdU labeled and chase 24 hr, replicate

value: Adult female

value: HeLa-S3 with LSH-AID

value: LSH-AID


title: DNMT3A3B-DKO-chase-0, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
DNMT3A3B-DKO-c0-rep

source_name: EdU labeled DNMT3A/3B double KO HeLa cells with chasing 0 min, replicate

value: HeLa-S3 with DNMT3A/3B double KO

value: cervix

value: 31 years


title: wt_thorax_day50_2

value: Total RNA


title: HFD118_islet

source_name: high-fat diet mice islets

value: islets

value: high-fat diet


title: 10h-IAA-0hR-rescue, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
UHRF1-AID-10hIAA+0hRescue.rep2

source_name: 10 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release 0 h (rescue), replicate

value: HeLa-S3 with UHRF1-AID


title: LSH-AID-late-chase-2h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
LSH-late-c2h-rep

source_name: IAA-treated LSH-AID HeLa cells, release 6 hr, EdU labeled and chase 2 hr, replicate


title: CHAF1A-AID-chase-30m

description: Enrich EdU-labeled DNA, add hairpin, and BS-seq

source_name: EdU labeled IAA-treated CHAF1A-AID HeLa cells with chasing 30 min

value: female


title: wt_thorax_day50_1

value: wDah (wildtype)


title: HFD114_islet

value: 4 weeks


title: dilp_thorax_day30_3

description: CircCoordinates.tsv,CircRNACount.tsv,LinearCount.tsv,bbTest.linear.Thorax_30.tsv,isoforms.fpkm_tracking.tsv

value: Day 30


title: LSH-AID-late-chase-30m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
LSH-late-c30m-rep

source_name: IAA-treated LSH-AID HeLa cells, release 6 hr, EdU labeled and chase 30 min, replicate

value: epithelial adenocarcinoma


title: CHAF1A-AID-chase-5m

source_name: EdU labeled IAA-treated CHAF1A-AID HeLa cells with chasing 5 min

value: adult


title: HFD114_liver

source_name: high-fat diet mice liver

value: liver


title: LSH-AID-late-chase-5m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
LSH-late-c5m-rep

source_name: IAA-treated LSH-AID HeLa cells, release 6 hr, EdU labeled and chase 5 min, replicate

value: Adult female


title: dilp_thorax_day30_2

value: thorax


title: HFD113_islet


title: CHAF1A-AID-chase-0

source_name: EdU labeled IAA-treated CHAF1A-AID HeLa cells with chasing 0 min

value: HeLa-S3 with CHAF1A-AID


title: dilp_thorax_day30_1


title: LSH-AID-late-chase-0, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
LSH-late-c0-rep

source_name: IAA-treated LSH-AID HeLa cells, release 6 hr, EdU labeled and chase 0 min, replicate

value: HeLa-S3 with LSH-AID

value: LSH-AID


title: H3K9me3-ChIPseq-WT-HeLa

source_name: WT HeLa cells

value: WT

value: cervix

value: 31 years

tag: antibody

value: ab8898, Abcam


title: HFD112_liver

value: high-fat diet


title: CHAF1A-AID-chase-2h

source_name: EdU labeled IAA-treated CHAF1A-AID HeLa cells with chasing 2 hr

value: female


title: HFD112_islet

value: islets


title: LSH-AID-chase-24h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
LSH-early-c24h-rep

source_name: EdU labeled IAA-treated LSH-AID HeLa cells with chasing 24 hr, replicate


title: wt_thorax_day30_3

source_name: manually dissected fruit fly tissues

tag: rna

value: Total RNA

value: wDah (wildtype)


title: LSH-AID-chase-2h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
LSH-early-c2h-rep

source_name: EdU labeled IAA-treated LSH-AID HeLa cells with chasing 2 hr, replicate

value: epithelial adenocarcinoma


title: H3K9me2-ChIPseq-WT-HeLa

value: adult

value: ab1220, Abcam


title: wt_thorax_day30_2

tag: age

value: Day 30


title: CD608_liver

source_name: chow diet mice liver

tag: tissue

value: liver

value: chow diet

value: 24 weeks


title: wt_thorax_day30_1

tag: genotype

value: thorax


title: CD608_islet

source_name: chow diet mice islets


title: HFD113_liver

value: 4 weeks


title: input-of-ChIPseq-WT-HeLa

value: WT

value: cervix


title: 10h-IAA-14hR-rescue

source_name: 10 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release 14 h (rescue)

value: HeLa-S3 with UHRF1-AID

value: 31 years


title: dilp_thorax_day10_3

description: CircCoordinates.tsv,CircRNACount.tsv,LinearCount.tsv,bbTest.linear.Thorax_10.tsv,isoforms.fpkm_tracking.tsv

value: Day 10


title: LSH-AID-chase-5m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
LSH-early-c5m-rep

source_name: EdU labeled IAA-treated LSH-AID HeLa cells with chasing 5 min, replicate

value: Adult female

value: HeLa-S3 with LSH-AID

value: LSH-AID


title: 10h-IAA-6hR-rescue

source_name: 10 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release 6 h (rescue)

value: female

value: epithelial adenocarcinoma


title: 10h-IAA-4hR-rescue

source_name: 10 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release 4 h (rescue)

value: adult


title: LSH-AID-chase-30m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
LSH-early-c30m-rep

source_name: EdU labeled IAA-treated LSH-AID HeLa cells with chasing 30 min, replicate


title: CD606_liver


title: LSH-AID-chase-0, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
LSH-early-c0-rep

source_name: EdU labeled IAA-treated LSH-AID HeLa cells with chasing 0 min, replicate


title: dilp_thorax_day10_2

value: Total RNA


title: CD605_liver

value: liver


title: 10h-IAA-2hR-rescue

source_name: 10 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release 2 h (rescue)


title: CD606_islet

value: islets

value: chow diet


title: CD601_liver

value: 24 weeks


title: RescueTo24h-24hIAA

source_name: 24 hr IAA treatment of UHRF1-AID HeLa cells, no time to rescue.


title: RescueTo24h-14hIAA

source_name: 14 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release to 24 h


title: CD601_islet


title: wt_thorax_day10_2

value: wDah (wildtype)

value: thorax


title: RescueTo24h-10hIAA

source_name: 10 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release to 24 h

value: cervix


title: wt_thorax_day10_1


title: CD507_liver

value: 20 weeks


title: RescueTo24h-6hIAA

source_name: 6 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release to 24 h

value: HeLa-S3 with UHRF1-AID

value: 31 years


title: CHAF1A-AID-chase-24h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
CHAF1A-c24h-rep

source_name: EdU labeled IAA-treated CHAF1A-AID HeLa cells with chasing 24 hr, replicate

value: Adult female

value: HeLa-S3 with CHAF1A-AID


title: dilp_brain_day50_3

description: CircCoordinates.tsv,CircRNACount.tsv,LinearCount.tsv,bbTest.linear.Brain_50.tsv,isoforms.fpkm_tracking.tsv

value: Day 50

value: brain


title: CD507_islet


title: dilp_brain_day50_2


title: dilp_brain_day50_1


title: RescueTo24h-2hIAA

source_name: 2 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release to 24 h

value: female

value: epithelial adenocarcinoma


title: wt_brain_day50_3

source_name: manually dissected fruit fly tissues

value: Total RNA


title: CHAF1A-AID-chase-2h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
CHAF1A-c2h-rep

source_name: EdU labeled IAA-treated CHAF1A-AID HeLa cells with chasing 2 hr, replicate


title: CD505_liver

source_name: chow diet mice liver

value: liver


title: RescueTo24h-30minIAA

source_name: 30 min IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release to 24 h

value: adult


title: dilp_thorax_day10_1

value: Day 10


title: wt_thorax_day10_3


title: 10h-IAA-0hR-rescue

source_name: 10 hr IAA treatment of UHRF1-AID HeLa cells, withdraw IAA, then release 0 h (rescue)


title: RescueTo24h-noIAA

source_name: no IAA treatment of UHRF1-AID HeLa cells, release 24 h


title: CD605_islet

source_name: chow diet mice islets

value: islets

value: chow diet

value: 24 weeks


title: CHAF1A-AID-chase-5m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
CHAF1A-c5m-rep

source_name: EdU labeled IAA-treated CHAF1A-AID HeLa cells with chasing 5 min, replicate

value: cervix


title: wt_brain_day50_2

value: wDah (wildtype)


title: HeLa-WGBS

description: WGBS

source_name: WGBS of WT HeLa-S3 cells

value: WT


title: CD502_liver

value: 20 weeks


title: wt_brain_day50_1


title: dilp_brain_day30_3

description: CircCoordinates.tsv,CircRNACount.tsv,LinearCount.tsv,bbTest.linear.Brain_30.tsv,isoforms.fpkm_tracking.tsv

value: Day 30


title: CD502_islet


title: CHAF1A-AID-chase-0, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
CHAF1A-c0-rep

source_name: EdU labeled IAA-treated CHAF1A-AID HeLa cells with chasing 0 min, replicate

value: Adult female

value: HeLa-S3 with CHAF1A-AID

value: 31 years


title: CD501_liver


title: UHRF1-TTDmut-chase-2h

description: Enrich EdU-labeled DNA, add hairpin, and BS-seq

source_name: EdU labeled IAA-treated UHRF1-TTDmut HeLa cells with chasing 2 hr

value: female

value: HeLa-S3 with UHRF1-TTDmut (Y188V/Y191V)


title: dilp_brain_day30_2

value: Total RNA

value: brain


title: dilp_brain_day30_1


title: UHRF1-TTDmut-chase-5m

source_name: EdU labeled IAA-treated UHRF1-TTDmut HeLa cells with chasing 5 min

value: adult

value: epithelial adenocarcinoma


title: CHAF1A-AID-chase-30m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
CHAF1A-c30m-rep

source_name: EdU labeled IAA-treated CHAF1A-AID HeLa cells with chasing 30 min, replicate


title: CD501_islet

value: islets


title: CD505_islet

value: chow diet


title: CD407_liver

value: liver

value: 16 weeks


title: CD407_islet


title: UHRF1-TTDmut-chase-0

source_name: EdU labeled IAA-treated UHRF1-TTDmut HeLa cells with chasing 0 min

value: cervix


title: UHRF1-TTDmut-chase-30m

source_name: EdU labeled IAA-treated UHRF1-TTDmut HeLa cells with chasing 30 min


title: wt_brain_day30_3

value: wDah (wildtype)


title: wt_brain_day30_1


title: wt_brain_day30_2


title: CD405_liver


title: dilp_brain_day10_3

description: CircCoordinates.tsv,CircRNACount.tsv,LinearCount.tsv,bbTest.linear.Brain_10.tsv,isoforms.fpkm_tracking.tsv

value: Day 10


title: UHRF1-TTDmut-chase-24h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
UHRF1-TTD-c24h.rep

source_name: EdU labeled IAA-treated UHRF1-TTDmut HeLa cells with chasing 24 hr, replicate


title: dilp_brain_day10_2


title: CD405_islet


title: UHRF1-TTDmut-chase-2h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
UHRF1-TTD-c2h.rep

source_name: EdU labeled IAA-treated UHRF1-TTDmut HeLa cells with chasing 2 hr, replicate


title: CD403_liver


title: UHRF1-TTDmut-chase-30m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
UHRF1-TTD-c30m.rep

source_name: EdU labeled IAA-treated UHRF1-TTDmut HeLa cells with chasing 30 min, replicate


title: CD403_islet


title: UHRF1-TTDmut-chase-24h

source_name: EdU labeled IAA-treated UHRF1-TTDmut HeLa cells with chasing 24 hr


title: dilp_brain_day10_1

source_name: manually dissected fruit fly tissues


title: wt_brain_day10_3


title: UHRF1-TTDmut-chase-0, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
UHRF1-TTD-c0.rep

source_name: EdU labeled IAA-treated UHRF1-TTDmut HeLa cells with chasing 0 min, replicate


title: CD401_liver

source_name: chow diet mice liver


title: CD401_islet


title: UHRF1-AID-chase-24h

source_name: EdU labeled IAA-treated UHRF1-AID HeLa cells with chasing 24 hr

value: HeLa-S3 with UHRF1-AID


title: CD308_liver

value: 12 weeks


title: wt_brain_day10_2


title: UHRF1-AID-chase-2h

source_name: EdU labeled IAA-treated UHRF1-AID HeLa cells with chasing 2 hr


title: DNMT1-H170V-chase-2h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
DNMT1-H170V-c2h.rep

source_name: EdU labeled IAA-treated DNMT1-H170V HeLa cells with chasing 2 hr, replicate

value: Adult female

value: HeLa-S3 with DNMT1-H170V


title: wt_brain_day10_1


title: CD308_islet

source_name: chow diet mice islets


title: UHRF1-AID-chase-30m

source_name: EdU labeled IAA-treated UHRF1-AID HeLa cells with chasing 30 min

value: female

value: 31 years


title: DNMT1-H170V-chase-30m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
DNMT1-H170V-c30m.rep

source_name: EdU labeled IAA-treated DNMT1-H170V HeLa cells with chasing 30 min, replicate


title: CD307_liver


title: UHRF1-AID-chase-5m

source_name: EdU labeled IAA-treated UHRF1-AID HeLa cells with chasing 5 min


title: DNMT1-H170V-chase-5m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
DNMT1-H170V-c5m.rep

source_name: EdU labeled IAA-treated DNMT1-H170V HeLa cells with chasing 5 min, replicate


title: UHRF1-TTDmut-chase-5m, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
UHRF1-TTD-c5m.rep

source_name: EdU labeled IAA-treated UHRF1-TTDmut HeLa cells with chasing 5 min, replicate

value: HeLa-S3 with UHRF1-TTDmut (Y188V/Y191V)


title: CD306_liver


title: MDAMB231.SREBF1ko.g2

city: Cambridge

first: Xin

last: Jin

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

description: 20190925_MDAMB231_SREBF1_k4_2_XJ7389_S30

data_processing:
Basecalling and sample demultiplexing were performed in Illumina NovaSeq Control Software.
Read mapping and gene-level counting were performed using RSEM (https://deweylab.github.io/RSEM/).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files that contain estimated count values.

source_name: in vitro_MDAMB231.SREBF1ko

growth_protocol: Cell lines were maintained in RPMI1640 + 10% Fetal Bovine Serum + Penicillin/Streptomycin

extract_protocol:
RNA extraction was performed using Rneasy Plus Mini Kit (QIAGEN). RNA was quantified using RNA 6000 Pico Kit on a 2100 Bioanalyzer (Agilent).
RNA-Seq libraries were prepared using KAPA mRNA Hyper Prep Kit from 100 ng RNA input according to manufacturer’s instructions (Roche). The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and qPCR using the KAPA Library Quantification Kit (Roche). Uniquely indexed libraries were pooled in equimolar ratios and sequenced on Illumina NovaSeq6000 runs with paired-end 50bp reads.

treatment_protocol: Cell lines were infected with lenti-Cas9-Blast and selected in 5 ug/mL Blasticidin until non-infected controls were completely killed. Cas9-expressing cells were then infected with CRISPR guides targeting candidate genes or non-targeting guides. Post infection, cells were selected in 2 ug/mL Puromycin until non-infected controls were killed. Cells were recovered in RPMI1640 media for 48 hours and subjected to harvest and RNA extraction. Western Blot confirmed that the majority of cells were knocked out with the candidate genes at this time point.

tag: cell line background

value: brain metastatic breast cell line

tag: perturbagen


title: WT-chase-24h

source_name: EdU labeled WT HeLa cells with chasing 24 hr

value: WT

tag: timepoint


title: CD306_islet

tag: strain


title: WT-chase-10h

source_name: EdU labeled WT HeLa cells with chasing 10 hr

value: epithelial adenocarcinoma


title: MDAMB231.wildtype.g1

source_name: in vitro_MDAMB231.wildtype


title: CD304_liver

tag: diet


title: WT-chase-6h

source_name: EdU labeled WT HeLa cells with chasing 6 hr

tag: strain background


title: DNMT1-H170V-chase-24h, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
DNMT1-H170V-c24h.rep

source_name: EdU labeled IAA-treated DNMT1-H170V HeLa cells with chasing 24 hr, replicate


title: WT-chase-2h

source_name: EdU labeled WT HeLa cells with chasing 2 hr


title: CD304_islet

value: islets

tag: weeks on diet


title: JIMT1.SREBF1ko.g2

source_name: in vitro_JIMT1.SREBF1ko

tag: cell type


title: CD208_liver

source_name: chow diet mice liver

value: chow diet

value: 8 weeks


title: JIMT1.SREBF1ko.g1


title: UHRF1-AID-chase-0

source_name: EdU labeled IAA-treated UHRF1-AID HeLa cells with chasing 0 min

value: adult

tag: genotype/variation


title: MDAMB231.wildtype.g2


title: WT-chase-30m

source_name: EdU labeled WT HeLa cells with chasing 30 min

value: cervix

tag: developmental stage


title: CD208_islet

source_name: chow diet mice islets


title: DNMT1-H170V-chase-0, replicate

description:
Enrich EdU-labeled DNA, add hairpin, and BS-seq
DNMT1-H170V-c0.rep

source_name: EdU labeled IAA-treated DNMT1-H170V HeLa cells with chasing 0 min, replicate


title: JIMT1.SCAPko.g2

source_name: in vitro_JIMT1.SCAPko


title: CD307_islet


title: CD207_liver

value: liver


title: JIMT1.SCAPko.g1


title: CD34+ SCs, Melanoma-infiltrated LN, biological rep 7

city: Auckland

first: Jennifer

last: Eom

address: 3A Symonds Street

country: New Zealand

institute: University of Auckland

description: Gene expression data from CD34+ stromal cells, isolated from human melanoma infiltrated lymph node tissue

hyb_protocol: 5 ug of fragmented and labelled ds-cDNA were hybridized for 16 hr at 45C on GeneChip Clariom S Human Array. GeneChips were washed and stained using the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalised with the Robust Multichip Average (RMA) algorithm using the rma package in R. Default parameters were used without background correction.

label: biotin

source_name: FACS isolated CD34+ stromal cells from melanoma infiltrated human lymph node

label_protocol: Maximum of 12 cycles of pre-IVT amplification was performed. Fragmented ds-cDNA was biotinylated, according to GeneChip® Pico Reagent Kit UserGuide (Affymetrix).

extract_protocol: Total RNA extraction was performed using RNeasy Micro Kit (Qiagen), following manufacturer's instructions.

treatment_protocol: Melanoma and normal lymph node tissues were digested into single cell suspension using Liberase DH (Roche) and DNAseI (Sigma-Adrich). Lymph node stromal cells were then labelled with a selection of fluorophore conjugated antibodies, and isolated using fluroescence activated cell sorting (FACS).

value: Lymph node

tag: tumour

value: Melanoma


title: FRCs, Melanoma-infiltrated LN, biological rep 6

description: Gene expression data from CD34- stromal cells (FRCs), isolated from human melanoma infiltrated lymph node tissue

source_name: FACS isolated CD34- stromal cells (FRCs) from melanoma infiltrated human lymph node


title: FRCs, Melanoma-infiltrated LN, biological rep 7


title: CD34+ SCs, Melanoma-infiltrated LN, biological rep 6


title: CD34+ SCs, Melanoma-infiltrated LN, biological rep 5


title: FRCs, Melanoma-infiltrated LN, biological rep 5


title: CD34+ SCs, Melanoma-infiltrated LN, biological rep 4


title: WT-chase-10m

source_name: EdU labeled WT HeLa cells with chasing 10 min

tag: cell line


title: FRCs, Melanoma-infiltrated LN, biological rep 4


title: CD207_islet


title: WT-chase-5m

source_name: EdU labeled WT HeLa cells with chasing 5 min


title: JIMT1.PMVKko.g2

source_name: in vitro_JIMT1.PMVKko


title: FRCs, Melanoma-infiltrated LN, biological rep 3


title: CD205_liver


title: WT-chase-0

source_name: EdU labeled WT HeLa cells with chasing 0 min


title: T02

city: zhenjiang

first: wu

last: feng

state: jiangsu

address: xuefu road 301

institute: jiangsu university

description: processed data file: all.gene_fpkm.xls

data_processing:
Raw reads were pre-processed to obtain the clean reads by removing reads containing ploy-N, reads containing adapter and low-quality reads from raw data were filtered with FASTQ-Quality-Filter tool.
HISAT2 generate a database of splice junctions based on the gene model annotation ﬁle, which was used to align the paired-end clean reads to the reference genome of Pyrus_bretschneideri_chromosome_V121121.fa.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Then, the number of fragments per kilobase of transcript per Million fragments mapped (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Prunus persica Genome v2.0.a1
Supplementary_files_format_and_content: ctab.txt files and xls file

organism: Prunus persica

source_name: tissues in wound

growth_protocol: Incubator 28℃, 95% RH.

extract_protocol:
The sample was ground in liquid nitrogen. RNA of peaches was extracted with UNlQ-10 Column Trizol Total RNA Extraction Reagent (Sangon Biotech, Shanghai, China) according to the instruction of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 30 μL of Pichia membranaefaciens suspension was pipetted into each wound (T02), and 30 μL of sterilized water was used as the control (T01).

tag: treatment

value: Pichia membranaefaciens

tag: time point

value: 3 days after treatment

value: wound tissue


title: WT-chase-20m

source_name: EdU labeled WT HeLa cells with chasing 20 min

value: Adult female


title: CD205_islet


title: JIMT1.wildtype.g1

source_name: in vitro_JIMT1.wildtype


title: CD203_liver


title: JIMT1.wildtype.g2


title: T01

description: processed data file: all.gene_fpkm.xls

value: Control


title: CD203_islet


title: HCC1954.SREBF1ko.g1

source_name: in vitro_HCC1954.SREBF1ko


title: CD106_liver

value: 4 weeks


title: FRCs, Melanoma-infiltrated LN, biological rep 2


title: K1 KO+ K1F201A H355A rep2

city: Houston

first: Guangsheng

last: Pei

state: Texas

address: 7000 Fanin

institute: UTHealth

description:
cervix, epithelial
K1KO-K1F201AH355A2_S16
processed data file: RPKM_TPM_Matrix.xlsx

data_processing:
Raw mRNA sequence reads were pre-processed using Cutadapt (v1.15) to remove bases with quality scores < 20 and adapter sequences, followed by alignment of clean RNA-seq reads to GRCh38.83 with STAR (v2.5.3a). Uniquely-mapped reads overlapping genes were counted by HTseq-count with default parameter using annotation from ENSEMBL v83. Gene normalized reads count RPKM and TPM value were calculated by RSEM (v1.3.0).
Genome_build: RNA-seq: GRCh38.83
Supplementary_files_format_and_content: RPKM_TPM_Matrix.xlsx: Merged file: tab-delimited table files include FPKM and TPM values for each sample.

source_name: HeLa cells

growth_protocol: All the cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum.

extract_protocol:
Cells were collected and total RNA was extracted using an RNeasy Mini Kit (QIAGEN; #74104) according to the manufacturer’s instructions.
The library was prepared using an Illumina TruSeq Stranded Total RNA Library Prep Kit.
RNA-seq was performed using the Illumina NextSeq 550 system with the 75 bp pair-ended running mode.

value: HeLa

tag: Sex

value: Female


title: CD34+ SCs, Melanoma-infiltrated LN, biological rep 2

tag: tissue


title: CD106_islet


title: K1 KO+ K1H355A rep2

description:
cervix, epithelial
K1KO-K1H355A2_S14
processed data file: RPKM_TPM_Matrix.xlsx

value: K1 KO+ K1H355A


title: HCC1954.wildtype.g1

source_name: in vitro_HCC1954.wildtype

value: brain metastatic breast cell line


title: CD34+ SCs, Melanoma-infiltrated LN, biological rep 3


title: FRCs, Melanoma-infiltrated LN, biological rep 1


title: CD104_liver

source_name: chow diet mice liver

value: chow diet


title: K1 KO+ K1H355A rep1

description:
cervix, epithelial
K1KO-K1H355A1_S13
processed data file: RPKM_TPM_Matrix.xlsx


title: JIMT1.PMVKko.g1


title: HCC1954.wildtype.g2


title: PMSCs_rep5

city: Nanchang

first: Jixiong

last: Xu

state: Jiangxi Province

address: No.17 Yongwaizheng St.

department: Department of Endocrinology and Metabolism

institute: The first hospital of nanchang university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PMSCs (1 × 10^6 in 2 mL PBS, per rat) were injected intravenously via the tail vein once per week for 3 weeks.

value: Sprague Dawley

tag: disease state

value: Diabetic nephropathy (DN)

value: Human placenta-derived mesenchymal stem cells

value: kindey; Renal cortex


title: PMSCs_rep4


title: PMSCs_rep6


title: CD104_islet

value: islets


title: CD103_liver

value: liver


title: K1 KO+ K1F201A rep2

description:
cervix, epithelial
K1KO-K1F201A2_S12
processed data file: RPKM_TPM_Matrix.xlsx

value: K1 KO+ K1F201A


title: PMSCs_rep3


title: HCC1806.SREBF1ko.g2

source_name: in vitro_HCC1806.SREBF1ko

tag: cell line background


title: PMSCs_rep1


title: HCC1954.SREBF1ko.g2

tag: perturbagen


title: K1 KO+ K1F201A H355A rep1

description:
cervix, epithelial
K1KO-K1F201AH355A1_S15
processed data file: RPKM_TPM_Matrix.xlsx


title: CD34+ SCs, Melanoma-infiltrated LN, biological rep 1

value: Lymph node

value: Melanoma


title: PMSCs_rep2


title: K1 KO+ K1F201A rep1

description:
cervix, epithelial
K1KO-K1F201A1_S11
processed data file: RPKM_TPM_Matrix.xlsx


title: HCC1806.SREBF1ko.g1


title: CD103_islet

source_name: chow diet mice islets


title: K1 KO+ K1WT rep2

description:
cervix, epithelial
K1KO-K1WT2_S10
processed data file: RPKM_TPM_Matrix.xlsx

value: K1 KO+ K1WT


title: HCC1806.SCAPko.g2

source_name: in vitro_HCC1806.SCAPko


title: DN_rep6


title: K1 KO+ K1WT rep1

description:
cervix, epithelial
K1KO-K1WT1_S9
processed data file: RPKM_TPM_Matrix.xlsx


title: CD101_islet


title: CD101_liver


title: DKO rep2

description:
cervix, epithelial
HelaK1K2DKO2_S8
processed data file: RPKM_TPM_Matrix.xlsx

value: DKO


title: DN_rep5


title: DN_rep4


title: 39.5°C-input

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Sequencing reads were mapped to the mouse genome mm10 by bowtie2
PCR duplicates were removed using picard MarkDuplicates
The uniquely mapped reads were used to call peak with MACS2 using a p value cutoff 0.01
ChIPseeker was used for peak annotation
Deeptools was used to generate coverage track file (bigWig) to visualize using IGV tools

source_name: Spleen+Lymph nodes

extract_protocol:
The ChIP assay was performed using Active Motif’s ChIP assay kit (53035) according to manufacturer’s instructions with slight modifications.
ChIP-seq DNA library was constructed for deep sequencing by BGI Genomics.

treatment_protocol: Naïve CD4+ T cells were activated and cultured under IL-6 plus TGF-β1 condition at 37°C and 39.5°C for 24 hours

value: Th17 cells

tag: antibody

value: input

value: Spleen+Lymph nodes

tag: age

value: 24 hours in vitro

tag: genotype

value: wild type


title: DKO rep1

description:
cervix, epithelial
HelaK1K2DKO1_S7
processed data file: RPKM_TPM_Matrix.xlsx

value: HeLa

value: Female


title: HCC1806.PMVKko.g1

source_name: in vitro_HCC1806.PMVKko

value: brain metastatic breast cell line


title: HCC1806.wildtype.g1

source_name: in vitro_HCC1806.wildtype


title: 37°C-input

tag: strain


title: DN_rep3

tag: strain background

value: Sprague Dawley

value: Diabetic nephropathy (DN)


title: FOXK2-KO rep2

description:
cervix, epithelial
HelaK2KO2_S6
processed data file: RPKM_TPM_Matrix.xlsx


title: DN_rep2

value: kindey; Renal cortex


title: HCC1806.wildtype.g2

tag: cell type


title: FOXK2-KO rep1

description:
cervix, epithelial
HelaK2KO1_S5
processed data file: RPKM_TPM_Matrix.xlsx

tag: genotype/variation


title: 39.5°C-Smad4


title: DN_rep1


title: FOXK1-KO rep2

description:
cervix, epithelial
HelaK1KO2_S4
processed data file: RPKM_TPM_Matrix.xlsx


title: Input_BlCa_3

first: Henry

last: Long

address: 450 Brookline ave

institute: Dana Farber Cancer Institute

description: Input DNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bw files were generated using MACS2 within the chilin pipeline.
Supplementary_files_format_and_content: bed files

source_name: FFPE micropapillary carcinoma

extract_protocol:
FFPE blocks were histologically examined and accordingly sectioned, macrodissected or cored. Samples were deparaffinized, rehydrated and homogenized by heating at 65C in 1% SDS detergent buffer overnight. Next samples were sonicated and solubilized chromatin was immunoprecipitated following a low-input protocol.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) or SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio USA Inc), amplified for 14 cycles.

tag: tissue type

value: bladder

tag: biopsy year

tag: storage years

tag: sample collection

value: full section

tag: chip antibody


title: 37°C-Smad4

tag: treatment


title: WT rep2

description:
cervix, epithelial
HelaWT2_S2
processed data file: RPKM_TPM_Matrix.xlsx

tag: cell line

value: WT

tag: Sex


title: FOXK1-KO rep1

description:
cervix, epithelial
HelaK1KO1_S3
processed data file: RPKM_TPM_Matrix.xlsx


title: HCC1806.PMVKko.g2

tag: cell line background


title: Neonatal rat ventricular cardiomyocytes  - CPEB4 siRNA rep1

city: Heidelberg

first: Christoph

last: Sandmann

address: Im Neuenheimer Feld 669

institute: Heidelberg University Hospital

description: Ribosomal footprints - RNA

data_processing:
Library strategy: Ribo-Seq
Adapter removal was performed with Flexbar using standard filtering parameters. Reads with more than 1 uncalled base were not included in the output.
Reads aligning to a custom bowtie2 library including rat rRNA, tRNA, mtRNA, snRNA and other ncRNA were discarded.
All remaining reads were then aligned in genomic coordinates with STAR 2.7.
ORF prediction was performed using RP-BP, keeping reads that uniquely mapped to one genomic position. Fragment lenghts that showed a 3-nt periodicity, as determined by the statistical graphical models implemented in RP-BP, were kept. Final reads were quantified with HTSeq 0.12.
Count normalization and differential gene expression analysis was performed using the R package edegeR 3.11.
Genome_build: Rnor_6.0 (Ensembl)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample and Excel table with diffential gene expression analysis including Ensembl gene ID and gene name, log2FC, p-value, FDR and normalized gene counts for every gene and every sample.

source_name: Neonatal rat ventricular cardiomyocytes

growth_protocol: Ventricular cardiomyocytes from 1 to 2 day old Wistar rats neonatal hearts (NRCMs) were prepared by trypsin digestion and percoll gradient separation. mTORC1 was pharmacologically inhibited with 250 nM Torin1 for 24h.

extract_protocol:
Polysome fractionations from NRCMs were isolated in a sucrose gradient. The absorbance was monitored at 254 nm to record the polysome profile. The collected fractions were treated with RNaseI and mixed with Qiazol to recover ribosomal footprints.
Ribo-Seq  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cpeb4 expression was silenced using siRNA for 72h.

value: Wistar

tag: tissue

value: ventricular cardiomyocytes

tag: knockdown

value: CPEB4 siRNA

value: 1-2 days


title: Neonatal rat ventricular cardiomyocytes  - CPEB4 siRNA rep2

description: Ribosomal footprints - RNA

tag: age


title: HCC1806.SCAPko.g1

tag: perturbagen


title: Neonatal rat ventricular cardiomyocytes  - Control siRNA rep2

description: Ribosomal footprints - RNA

tag: strain

value: Control siRNA


title: WT rep1

description:
cervix, epithelial
HelaWT1_S1
processed data file: RPKM_TPM_Matrix.xlsx


title: BlCa_1

description: Immunoprecipitated DNA

source_name: FFPE urothelial cell carcinoma


title: BlCa_3

description: Immunoprecipitated DNA

value: cores


title: Neonatal rat ventricular cardiomyocytes  - Control siRNA rep1

description: Ribosomal footprints - RNA


title: R2795

city: Leiden

first: Tim

middle: Marijn

last: van Leeuwe

address: Sylviusweg 72

country: Netherlands

institute: Leiden University

data_processing:
Filtered reads were mapped to the NRRL3 transcriptome annotation version 20140311 using Salmon v.0.14.1
Differential gene expression was assessed via pairwise comparisons using DESeq2 v1.24.0 using the design ~ mutation
Supplementary_files_format_and_content: tab-delimited text files include read values for each gene in each Sample

organism: Aspergillus niger

source_name: mycelial biomass

growth_protocol: Controlled batch cultivations for A. niger strains N402 and the ΔkexB strain were performed in 6.6L BioFlo bioreactors (New Brunswick Scientific), as previously described (Jørgensen et al., 2010). A batch of 21 L MM containing 0.75% D-glucose was made by adding 1 L filter-sterilized (0.2 µm pore) glucose (15.75% w/v) solution to a freshly autoclaved volume of 20 L MM (no carbon source) as described above. Allowing 1 day of dissolving and a check for contamination, 5 L MM 0.75% glucose was added to each bioreactor directly after autoclaving. Temperature, acidity and stir speed were set to and kept at 30°C, pH 3 and 250 rpm, respectively. The pH was controlled by addition of titrants (2M NaOH and 1M HCl). Sparger aeration of 1 L/min was left on to allow oxygen saturation of the medium prior to inoculation. Next, aeration was set to headspace only and 1.5 mL 10% w/v Yeast Extract was added to the medium to promote homogeneous germination for the to-be-added spores. Subsequently, a total of 5x109 (106 sp/mL) spores were added to the medium using a concentrated spore solution. Germination time of approximately 4-5h was maintained, preceding the addition of polypropyleneglycol P2000 anti-foam agent, increasing agitation to 750 rpm and changing aeration from headspace to sparger only (1 L/min). Oxygen, base and acid consumption were monitored and samples were taken at regular intervals to obtain biomass, culture filtrate and microscopy samples. Biomass was harvested by applying a vacuum over Whatman™ Glass Microfiber Filter (GF/C™) (diameter 47 mm, CAT No.1822-047, Buckinghamshire, UK). Samples were all quickly frozen in liquid nitrogen prior to storage at -80°C. Biomass accumulation through time was gravimetrically determined by lyophilizing designated samples from the corresponding broth culture mass.

extract_protocol:
RNA was isolated from mycelial biomass samples obtained from batch cultivated A. niger strains N402 and the ΔkexB strain, using TRIzol (Invitrogen). RNA was purified afterwards with NucleoSpin RNA Clean-up kit (Macherey-Nagel) with DNase treatment. Concentration and quality of the RNA was determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific) and by gel-electrophoresis, respectively
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: deltakexB

tag: percentage of maximum biomass

tag: biological replicate


title: R2794

value: wild type


title: R2796


title: Pax2a-High_TFC_1

status: Public on Jun 25 2020

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

data_processing:
Mapping using HISAT2 against GRCz11with default parameters
Counts per gene generated using FeatureCounts with default parameters
Genome_build: Zebrafish GRCz11
Supplementary_files_format_and_content: read counts as tsv file

organism: Danio rerio

source_name: Thyroid Follicular Cells (TFCs)

extract_protocol:
Enzymatic Dissociation
Ribozyme depletion, adapter ligation, followed by llumina NextSeq500

value: 5 mpf

tag: genotype/variation

value: Tg(tg:nls-EGFP), pax2a:mKO2-Knock-in

tag: population

value: pax2a-High (mKO2-High)


title: Pax2a-Low_TFC_2

value: pax2a-Low (mKO2-Low)


title: Pax2a-Low_TFC_1


title: Pax2a-High_TFC_3


title: Pax2a-High_TFC_2


title: Pax2a-Low_TFC_3


title: Input_BlCa_1

description: Input DNA

tag: tissue type

tag: biopsy year

tag: storage years


title: human unselected 40S 1

city: Canberra

first: Susan

last: Wagner

state: ACT

address: 131 Garran Road

department: The John Curtin School of Medical Research

country: Australia

institute: Australian National University

description: Raw data were originally paired-end but only read 1 was analysed and is provided here.

data_processing:
Library strategy: TCP-seq
Illumina CASAVA 1.8 for base calling
adapter trimming (fastx_clipper of FASTX Toolkit 0.0.13), filtering by alignment to rRNA (bowtie 1.2.2) and ncRNA, tRNA (bowtie2 2.2.6)
alignment to transcriptome Ensembl GRCh38.80 and genome GRCh38 with TopHat 2.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: human_metagene_FP5end_AUG_-80+30_FPlength.ods; counts of footprint 5’ ends positioned from -80 nt to +30 nt relative to the AUG start codon (over rows) respecting the footprint length (18 – 98 nt over columns)
Supplementary_files_format_and_content: human_metagene_FP5end_STOP_-80+30_FPlength.ods; counts of footprint 5’ ends positioned from -80 nt to +30 nt relative to the STOP codon (over rows) respecting the footprint length (18 – 98 nt over columns)
Supplementary_files_format_and_content: human_metagene_coverage_CAP_-40+40.csv; footprint coverage from -40 nt to +40 nt relative to the transcript start
Supplementary_files_format_and_content: human_genewise_FPcount_transcript_area.csv; footprint count per transcript area
Supplementary_files_format_and_content: human_genewise_mean_CI_FP5end_FP3end_AUG_-50+50.ods; distribution (mean and 95 percentiles) of footprint 5’end and 3’end positions relative to the AUG start codon of start codon associated footprints without 5’extension (footprint 5’end from -12 to -14 nt)
Supplementary_files_format_and_content: human_coverage_ATF4_ENST00000396680_-50.csv; coverage for the 5’UTR and the beginning of the CDS for ATF4 (starting at -50 nt from the transcript start)

source_name: HEK293T cells

growth_protocol: 3.5 Mio cell seeded into one Ø 15 cm dish, 48 h growth, around 80 % confluency at harvest; growth at 37ºC, 5 % CO2, in DMEM + 10% FBS (20 ml per dish)

extract_protocol:
in-plate cell lysis with detergent, RNase I digestion to generate ribosomal footprints, 40S/80S separation (followed by Co-IP if indicated), hot acid phenol RNA extraction
according to Ingolia et al., 2010, Methods Enzymol (different RNA fragment size selection, different set of rRNA depletion oligos)

treatment_protocol: incubation of the cell culture with 0.3 % w/v formaldehyde for 5 min in a cold room

tag: antibody

value: no

tag: protocol

value: RNA 40S footprint


title: PC9 DTP rep3

first: Meng

last: Nie

address: Haidian  District

institute: Tsinghua  University

data_processing:
Sequencing quality was evaluated by FastQC v.0.11.8.
FASTQ files were aligned to hg38 (GRCh38) using STAR v.2.6.1b (default parameters).
Gene level counts were computed using featureCounts v.1.6.3 with the same human genome reference used for mapping (Gencode v.27).
Differential expression analysis was performed with DESeq2 v.1.22.2 in R, and a threshold of fold change > 2 and adjusted P value <0.05 was used to call differentially expressed genes.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

growth_protocol: PC9 was maintained in RPMI-1640 medium supplemented with penicillin–streptomycin, and 10% fetal bovine serum (FBS) at 37 °C in a humidified atmosphere containing 5% CO2 and 95% air. All cells were routinely screened for the absence of Mycoplasma contamination and were validated by short tandem repeat (STR) DNA fingerprinting.

extract_protocol:
Total RNA from approximately 1 million Osimertinib-tolerant cells or parental PC9 cells was isolated by Trizol (Life Technologies) following the manufacturer’s instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Drug-tolerant persister (DTP) cells were generated through continuous treatment with 2 μM of Osimertinib for 9 days

value: lung

tag: treatment

value: 2μM Osimertinib 9d

tag: cell type

value: non-small cell lung cancer


title: PC9 Parental rep3

tag: tissue

value: DMSO 9d


title: R2793


title: PC9 Parental rep2


title: human eIF3b bound 40S 1

data_processing:
Library strategy: SelTCP-seq
Illumina CASAVA 1.8 for base calling
adapter trimming (fastx_clipper of FASTX Toolkit 0.0.13), filtering by alignment to rRNA (bowtie 1.2.2) and ncRNA, tRNA (bowtie2 2.2.6)
alignment to transcriptome Ensembl GRCh38.80 and genome GRCh38 with TopHat 2.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: human_metagene_FP5end_AUG_-80+30_FPlength.ods; counts of footprint 5’ ends positioned from -80 nt to +30 nt relative to the AUG start codon (over rows) respecting the footprint length (18 – 98 nt over columns)
Supplementary_files_format_and_content: human_metagene_FP5end_STOP_-80+30_FPlength.ods; counts of footprint 5’ ends positioned from -80 nt to +30 nt relative to the STOP codon (over rows) respecting the footprint length (18 – 98 nt over columns)
Supplementary_files_format_and_content: human_metagene_coverage_CAP_-40+40.csv; footprint coverage from -40 nt to +40 nt relative to the transcript start
Supplementary_files_format_and_content: human_genewise_FPcount_transcript_area.csv; footprint count per transcript area
Supplementary_files_format_and_content: human_genewise_mean_CI_FP5end_FP3end_AUG_-50+50.ods; distribution (mean and 95 percentiles) of footprint 5’end and 3’end positions relative to the AUG start codon of start codon associated footprints without 5’extension (footprint 5’end from -12 to -14 nt)
Supplementary_files_format_and_content: human_coverage_ATF4_ENST00000396680_-50.csv; coverage for the 5’UTR and the beginning of the CDS for ATF4 (starting at -50 nt from the transcript start)

value: yes (goat polyclonal anit-eIF3b, sc16377)

tag: cell line


title: H4-ChIP_1

city: Wuhan

first: Weiwu

last: Zeng

state: Hubei

address: Bayi Road

department: College of Chemistry and Molecular Sciences

institute: Wuhan University

data_processing:
Raw fastq reads were deduplicated with FastUniq, trimmed by Trim Galore(v0.5.0) to remove adapters and low quality bases, and mapped to the human reference genome GRCh38.p7 using Bowtie2(v 2.3.4.2). Reads with mapping quality less than 10 were discarded by SAMtools(v0.1.19). HOMER was employed for peak calling.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak file, including peak coordiante, fold change, etc.

source_name: thyroid carcinoma

extract_protocol:
Nuclei were obtained with lysis buffer and subjected to sonication. DNA-histone complexes were isolated with antibody.
Libraries were prepared according to the protocol of VAHTSTM Universal DNA Library Prep Kit for Illumina® V3.

treatment_protocol: Nuclei were treated with NaCNBH3 and subsequently the binding buffer of Genejet PCR purification kit.

value: thyroid carcinoma

tag: chip antibody


title: Normal_2

city: Shanghai

first: Caiyan

last: Zhang

address: 399, Wanyuan Road

institute: Children's Hospital of Fudan University

description: miRNA expression in PBMCs from healthy volunteer

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US)

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.)

source_name: PBMCs, healthy volunteer, replicate 2

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

growth_protocol: Freshly drawn peripheral blood from healthy volunteers and T1DM patients was sent to suffer from microarray analysis.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: disease state

value: healthy

value: peripheral blood mononuclear cells (PBMCs)

tag: gender

value: female

tag: age

value: 9 y


title: T1DM_4

description: miRNA expression in PBMCs from T1DM patient

source_name: PBMCs, T1DM, replicate 4

value: type 1 diabetes mellitus

value: 4 y


title: Normal_3

source_name: PBMCs, healthy volunteer, replicate 3


title: PC9 DTP rep1

city: Beijing


title: input-DNA_1


title: T1DM_3

source_name: PBMCs, T1DM, replicate 3


title: T1DM_2

source_name: PBMCs, T1DM, replicate 2


title: Normal_4

source_name: PBMCs, healthy volunteer, replicate 4


title: human unselected 80S 1

value: RNA 80S footprint


title: Normal_1

source_name: PBMCs, healthy volunteer, replicate 1

value: male


title: T1DM_1

source_name: PBMCs, T1DM, replicate 1


title: Sample 67_Preglobular_Rep3_Technical3_MethylC-Seq

city: Vienna

first: Ranjith

last: Papareddy

address: Dr Bohr Gasse 3

country: Austria

institute: Gregor Mendel Institute

description:
Single-end 100 base read MethylC-seq data from Preglobular Biological replicate3 Technical replicate 3
Preglobular_Rep3_Technical3_MethylC-Seq

data_processing:
Small RNA-seq Analysis: Adaptor trimming with Cutadapt parameters "cutadapt -a AGATCGGAAGA  -m 18 -M 30 --trimmed-only". End to End alignment with zero mismatched and upto 100 multimappers  against TAIR10  Arabidopsis thaliana genome with STAR "STAR --outFilterMultimapNmax 100 --outSAMtype SAM --outFilterMismatchNmax 0 --alignEndsType EndToEnd --outReadsUnmapped Fastx --alignIntronMax 1 --outSAMprimaryFlag AllBestScore".  Multi mapping reads rescued with rich-get-richer algorithem " readmapIO.py  ". Resulting bedfiles sorted, collapsed and normalized to totoal genome matching reads.
MethylC-Seq Analysis: Adaptor trimming with  trimeGalore (a wraper up trimmerer from Cutadapt) along with quality trimming, 6nt from 3' and 5' end were remove to exclude random hexamers used in preamplification step of methylome library preperation. After quality filtering and adaptor trimming, bisulfite-converted reads were aligned against the TAIR10 genome  using Bismark (bismark --non_directional -q --score-min L,0,-0.4) and deduplicated with function deduplicate_bismark -s --bam. Aligned BAM files with unique mapping reads and clonal deduplated were used as  input for the Methylpy software (https://bitbucket.org/schultzmattd/methylpy) to extract weighted methylation rate at each covered Cytosine site. Bisulfite conversion rates were calculated using the unmethylated chloroplast genome or spiked-in unmethylated Lambda phage DNA controls (European Nucleotide Archive Accession Number J02459, Promega catalog number D1521)
Genome_build: TAIR10
Supplementary_files_format_and_content: sRNA-Seq: Bed files contain tab-separated values of chromosomes (column 1), start (column 2) and stop (column 3) coordinates of smallRNAs followed by normalize RPM score (column 4), strand (column 5), sequence (column 6) and small RNA size (column 7)
Supplementary_files_format_and_content: MethylC-seq:  All Cytosin containing tab-separated values of chromosomes (column 1), start position(column 2)  of cytosine followed by strand  (column 3), Trinucleotide context  (column 4), count of reads supporting methylation (column 5) and total reads  (column 6); In addition ,Bigwig files containing chromosomes (column 1), start (column 2) and stop (column 3) and weighted methylation rate (column 4)

organism: Arabidopsis thaliana

growth_protocol: Controlled growth chamber at 20˚C-22˚C with a 16-h light/8-h dark cycle. Plants were four weeks old when tissue was harvested.

extract_protocol:
samples 1 to 28 : Total RNA extracted with TRIzol reagent (Thermo Fisher Scientific) and size selected for 18-30nt RNA molecules with denaturing urea gel; Samples 29 to 69 : genomic DNA extracted with Quick-DNATM Micro prep Kit (Zymo D3020)
Samples 1 to 28 : Size selected RNA was used to synthesise cDNA with NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (cat. no E7300; New England Biolabs) according to the manufacturer’s recommendations. Various numbers of PCR cycles were used to amplify cDNAs: 18, 20, 22, and 24 PCR cycles for globular; 14, 16, 18, and 20 PCR cycles for early heart and 3 weeks old leaf samples. Final PCR amplicons were initially run on a 90% (v/v) formamide/8% (w/v) acrylamide gel for 30 min at 5W, followed by 30W for ≥2 h, and stained with SYBR Gold (1:10,000; Thermo Fisher Scientific). Intensity of PCR amplicons between 137-bp and 147-bp  Fluorescence intensities of amplicons were examined across the PCR cycles, 137-bp to 149-bp corresponding to 18- nucleotide to 30- nucleotide sRNAs with adapters respectively was inspected under UV transilluminator. Amplicons with  non-saturated signals from PCR cycles were gel-purified. Gel purified small RNA libraries are resuspenden in 15 μL of Elution Buffer (Qiagen). Finally small RNA libraries quality checked for expected size range with Agilent High sensitivity NGS fragment Kit (DNF-474-1000) were sequenced on a HiSeq 2500 instrument (Illumina) in 50 base single-end mode.
Samples 29 to 69 : Genomic DNA subjected to genomic DNA  bisulfite treatment for 200 minutes with EZ DNA Methylation-DirectTM Kit (Zymo D5020).preamplified for two cycles with primers (5′-CCCTACACGACGCTCTTCCGATCTNNNNNN-3′) containing random hexamers and purified using the Zymo DNA Clean and Concentrator kit. Adaptor primers (5′-CAGACGTGTGCTCTTCCGATCTNNNNNN-3′) were added to preamplified products and then amplified for 12 PCR cycles with indexing primers for Illumina sequencing. Methylome libraries were purified using Beckman Coulter AMPureXP DNA beads.
samples 1 to 28 : smallRNA-seq; samples 29 to 69: MethylC-Seq

tag: genotype acronym

tag: genotype

value: wild type

value: Preglobular (8/16 cell) embryo

tag: treatment nucleic acids prior to library construction

value: Bisulfite treated

tag: amount of total rna used for library construction


title: Sample 68_Preglobular_Rep3_Technical4_MethylC-Seq

description:
Single-end 100 base read MethylC-seq data from Preglobular Biological replicate3 Technical replicate 4
Preglobular_Rep3_Technical4_MethylC-Seq


title: Sample 61_Preglobular_Rep2_Technical5_MethylC-Seq

description:
Single-end 100 base read MethylC-seq data from Preglobular Biological replicate2 Technical replicate 5
Preglobular_Rep2_Technical5_MethylC-Seq