title: 17_Dicer/Brd4 mutant timecourse_RNAseq_2

description:
17_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt


title: 1263-1

status: Public on Nov 13 2021

type: SRA

city: Fuzhou

first: Liman

last: Qiu

address: Xihong Road 312, Fuzhou 350025, Fujian, P. R. China.

country: China

institute: Mengchao Hepatobiliary Hospital of Fujian Medical University

library_source: transcriptomic

data_processing:
The sequencing reads that meet any of the following criteria were removed: (1) containing adaptor sequence; (2) with >10% ambiguous bases (N) of total read length; (3) containing >20% low quality bases (base quality ≤ 20) of total read length
Qualified reads were aligned to ribosomal rRNA sequences download from RNAcentral database to remove possible rRNA inference.
The unmapped reads were aligned to UCSC human genome reference (GRCh37/hg) using TopHat2
All the reads that could not align to the genome were extracted to identify the potential back-spliced junction reads by TopHat-Fusion. The identified potential candidate reads that could be mapped to the same chromosome but in reverse order were further considered as the candidate back-spliced junction reads
After removing any circular RNA with less than two unique back-spliced reads in one tissue sample, the expression levels for each circular RNA were calculated, according to reads Per Million mapped reads (RPM) using all the junction reads within the circular RNA region
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: HCC tumor tissue

extract_protocol:
Total RNA from HCC tumor and peritumor tissue samples were extracted using TransZol reagents. rRNAs were removed by a Ribo-Zero Magnetic kit, and linear RNA was digested by RNase R before construction of the RNA-seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient diagnosis

value: hepatocellular carcinoma (HCC)

tag: subject id

tag: gender

value: Male

tag: age

tag: tissue

value: liver

tag: tissue region

value: tumor


title: 216-MRD4_2

city: Rotterdam

first: Paul

last: Hengeveld

address: Dr Molewaterplein 40

department: Immunology

country: Netherlands

institute: Erasmus MC

description: B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of serial dilutations and post-treatment samples from CLL patients enrolled in the CLL11 trial

library_source: genomic

data_processing:
Raw FASTQ files were uploaded to the ARResT/Interrogate immunoprofiler for annotation and initial exploratory analysis. The full productive IGH repertoire for each sample was downloaded in .csv format and processed in R (R Core Team, 2020) during further analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited tekst file containing: sample,QC.status,scenario,rearrangements,raw.count,w.junction.count,w.junction.percent,artefacts.count,artefacts.percent,usable.count,usable.percent,w.most.pop.cln.s..count,w.most.pop.cln.s..percent,uniq.usable.seq.count,clonotypes.count,diversity..norm.ed..count,effective.species.count,R1.Q.mean.stdev.count,R2.Q.mean.stdev.count,joined.normally.count,joined.normally.percent,joined.loosely.count,joined.loosely.percent,total.joined.count,total.joined.percent,saved.from.unjoined.count,saved.from.unjoined.percent,low.quality..ee.nt...0.01..count,low.quality..ee.nt...0.01..percent,short...50nt..count,short...50nt..percent,annotated.count,annotated.percent,w.TR.receptor.count,w.TR.receptor.percent,w.B.chain.count,w.B.chain.percent,w.VJ.Vb..Db..Jb.count,w.VJ.Vb..Db..Jb.percent,w.VJ.Vb..Db..Jb.cln

molecule: genomic DNA

source_name: PBMCs

extract_protocol:
gDNA was available from the CLL11 trial. 1-27 ug DNA was amplified through multiplex PCR of IGHV-IGHD-IGHJ gene rearrangements following the EC-NGS leader primer protocol. After amplification, PCR products were purified on Agencourt AMPURE beads (Beckman Coulter, Brea, CA, USA) and eluted using H2O. The purified product was checked for primer dimers using the Agilent Tapestation (Agilent,Santa Clara, CA, USA).
The intitial multiplex PCR already attached the indexes to the PCR products, so library construction was simply pooling the purified PCR product in equilmolar fashion.

tag: sequencing run number

tag: rearrangement/patient number

value: PBMCs

tag: sample type

value: Serial dilution


title: 16_Dicer/Brd4 mutant timecourse_RNAseq_1

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

country: USA

institute: Cold Spring Harbor Laboratory

description:
16_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt

data_processing:
RNA-seq: Reads were trimmed for adapters and quality with Trimmomatic. Mapping to the mm10 genome was performed with the STAR aligner with --winAnchorMultimapNmax and --outFilterMultimapNmax set to 100 in order to allow reads to multimap for downstream analysis. The analysis of differential expression of both genes and repetitive elements was performed with TEtranscripts and DESeq2. Gene set enrichment analysis was performed with GSEA. Intersections between RNA-seq data sets and ChIP-seq datasets were performed with custom scripts. For strand-specific analysis, trimmed reads were mapped with bowtie2 with default settings and -k 5 to allow for multimapping. Normalized, strand-specific coverage was generated using deepTools.
small RNA: Raw reads were first trimmed with Cutadapt to clip Illumina 3’ adapters, while retaining the 4nt-long degenerate sequences at the 5’ and 3’ end of each insert. Reads with an insert size between 12-60 nt were subsequently filtered using Gordon Assaf’s FASTX-Toolkit to discard low-quality reads with Phred scores less than 20 in 10% or more nucleotides. PCR duplicates were removed using PRINSEQ (derep option 1) and degenerate sequences were extracted and appended to the name of each read using UMI-tools. Preprocessed reads were first aligned to calibrator sequences and then either to Mus musculus mm10 UCSC genome using Bowtie2, which assigns multi-mapping reads in an unbiased way. Aligned reads were filtered for 0-2 mismatches using Samtools and BamTools. For ERV and GSAT (major satellite) analysis, aligned reads were intersected with RepeatMasker annotation (http://www.repeatmasker.org) using BEDtools. Read counts were normalized to total calibrator per library.
ChIP-seq: Reads were trimmed for adapters and quality with Trimmomatic. Bowties was used for mapping with default settings and –dovetail, -X 600, and -k 5. The resulting SAM files were converted, sorted, and indexed with SAMtools. Normalized coverage was calculated for library size for each sample and a relative normalized coverage was calculated for IP over input using deepTools. Peaks were called with default settings with MACS2. Differential peaks were called with default settings with MAnorm. Peaks were assigned to underlying or nearby features and a functional enrichment analysis of these features was performed with ChIP-Enrich.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq/sRNA-seq: counts table contains all features (genes and repetitve elements) as rows with individual samples as the columns.; ChIP-seq: peak files generated by MACS2 contain all relevant peak location, magnitude, and significance information

organism: Mus musculus

source_name: Dicer/Brd4 mutant timecourse_RNAseq

growth_protocol: Mouse embryonic stem cells, including Dicer1 flx/flx lines, were grown in 2i conditions. The 2i medium consists of : 250 mL Neurobasal medium (Gibco 21103-049), 250 mL DMEM/F12 (Gibco 11320-033), 2.5 mL N2 supplement (Gibco 17502-048), 5 mL B27 supplement (Gibco 17504-044), 5 mL GlutaMAX (Gibco 35050-061) and 3.3 mL 7.5% BSA Fraction V (Gibco 15260-037). Just prior to adding the media to the cells, the following additional supplements were added: PD0325901 to 1 M (Stemgent 04-0006), CHIR99021 to 3 M (Stemgent 04-0004), 2-Mercaptoethanol to 100 M (Gibco 21985-023), and Mouse LIF to 103 units/mL (EMD Millipore ESG1106). Culture dishes were coated with gelatin (1X Attachment Factor – ThermoFisher S006100) for a minimum 15 minutes, gelatin was removed, and dishes were allowed to dry before cells were plated. Cells were split with TrypLE Express Enzyme (Gibco 12605-010) for 5 minutes at 37 degrees Celsius. Cells were collected in enough media for a 10-fold dilution of the TrypLE Express and pipetted up and down a minimum of 10 times to achieve a single cell suspension. Cells were then spun for 5 minutes at 150 x g and resuspended in media for counting and plating. Cells were frozen in freezing media: 10% DMSO (Sigma D2650), 50% ES-FBS (Gibco 16141-002), and 40% cells in media. Inducible Dicer1 knockout cells were treated with hydroxytamoxifen (OHT – Sigma H7904) at a final concentration of 1 M.

extract_protocol:
RNA was isolated with TRIzol as described and DNase treated. When total RNA was sequenced, 1 microgram RNA was first depleted for ribosomal RNA using the rRNA Depletion Kit (NEB E6310). Total RNA libraries were then prepared using the NEBNext Ultra II Directional Kit (NEB E7760). Libraries were quantified with the KAPA Illumina Quantification Kit (KAPA KK4824).
For ChIP the following primary antibodies were used: H3K9me3 (Abcam, ab1769916), H3K9me2 (Cell Signaling Technology, 4658s), BRD4 (Active Motif, 39910), and H3 (Cell Signaling Technology, 4620s).
Illumina stranded

tag: strain background

tag: cell type

value: mouse embryonic stem cells

tag: extraction

value: Trizol


title: 216-MRD3_2


title: 14_Elp3 mutant_RNAseq_1

description:
14_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt

source_name: Elp3 mutant_RNAseq


title: 216-MRD2_2


title: 10_Brd4 mutant_RNAseq_1

description:
10_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt

source_name: Brd4 mutant_RNAseq


title: 12_Brd4 mutant_RNAseq_3

description:
12_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt


title: RIPK3-KO-3

city: Suzhou

first: xiaoliang

last: yu

state: Jiangsu

address: Chongwen Road

institute: Suzhou Institute of Systems Medicine

data_processing:
RTA2 software used for basecalling.
Trimmomatic was used to remove illumina sequencing adapters within raw reads of every sample, trim low quality bases of both read ends
Clean reads were mapped to mouse mm10 reference genome with STAR
The alignment bam files were used as htseq-sount（command of python package HTSeq）
DESeq2 was used to identify DEGs (p<=0.05, FC>=2) based on raw reads counts.
Genome_build: mouse mm10
Supplementary_files_format_and_content: ISMRNA-Expression Browser.xlsx

source_name: small intestine

extract_protocol:
Small intestine were removed, stored in RNAlater buffer, and RNA was harvested using TRIzol（Cat no. 15596018, invitrogen, Thermo Fisher Scientific）. Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat)(Illumina, MRZG12324) and NEBNext Ultra Directional RNA Libra（NEB, E7420L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were constructed using a TruSeq Stranded mRNA Sample Prep Kit (RS-122-2001, Illumina) according to the manufacturer’s guideline.

tag: strain

value: small intestine

value: post natal week 8

tag: genotype


title: 344-MRD3_2


title: RIPK3-KO-2


title: 11_Brd4 mutant_RNAseq_2

description:
11_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt


title: 1421-MRD5_2


title: RIPK3-KO-1


title: 1421-MRD4_2


title: 13_Brd4 mutant_RNAseq_4

description:
13_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt


title: WT Striatum E14.5 [201123B_ZZZ_S2]

city: Shanghai

first: Zihao

last: Su

address: 138 Yi Xue Yuan Road

institute: Fudan University

data_processing:
The libraries were sequenced using an Illumina NovaSeq 6000 sequencer with a sequencing depth of at least 25,000 read pairs per nucleus with a paired-end 50-bp reading strategy.
The Cell Ranger ATAC 1.2.0 pipeline and the mm10 reference genome were downloaded from the 10X Genomics website (https://support.10xgenomics.com/single-cell-atac/software/downloads/latest).
Raw sequencing data were converted to fastq format using cell rangeratac mkfastq.6806 cells.
Cells with pct_reads_in_peaks >40, peak_region_fragments >3,000 and <80,000, TSS.enrichment >2.5, blacklist_ratio <0.01, and nucleosome_signal <4 were also filtered out.
Peak calling, peak annotation, clustering visualization, TF motif enrichment analysis, and differential accessibility analysis were performed with the Signac package (https://satijalab.org/signac/index.html).
Genome_build: mm10
Supplementary_files_format_and_content: bed

source_name: E14.5 Striatum

extract_protocol:
Nuclei were isolated and washed according to the instructions supplied by 10X Genomics [Nuclei Isolation for Single Cell ATAC Sequencing (CG000169)].
Following the 10X Genomics instructions for the sc-ATAC solution, the Chromium Chip E Single Cell Kit (Product Code 1000156) and the Chromium Single Cell ATAC Library & Gel Bead Kit (Product Code 1000110), the nuclei in the bulk sample were partitioned into nanoliter-scale gel beads-in-emulsion; a pool of ~750,000 109 barcodes was sampled to separately and uniquely index the transposed DNA of each individual nucleus, and libraries were generated (by CapitalBio Technology, Beijing).

value: C57BL/6J and CD1

value: Striatum

tag: developmental stage

value: Embryonic day E14.5


title: WT Striatum E14.5 [201123B_ZZZ_S1]


title: 1421-MRD3_2


title: 344-MRD1_1


title: 2_wild type_RNAseq_2

description:
2_Aligned.sortedByCoord.out.bam.C
processed data file: RNAseq_summary_count_table.txt

source_name: wild type_RNAseq


title: 9_Dicer timecourse_RNAseq_3

description:
9_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt

source_name: Dicer timecourse_RNAseq


title: 1_wild type_RNAseq_1

description:
1_Aligned.sortedByCoord.out.bam.C
processed data file: RNAseq_summary_count_table.txt


title: 1421-MRD2_2


title: 344-MRD0_1


title: 7_Dicer timecourse_RNAseq_1

description:
7_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt


title: 6_Dicer clone_RNAseq_3

description:
6_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt

source_name: Dicer clone_RNAseq


title: 3_wild type_RNAseq_3

description:
3_Aligned.sortedByCoord.out.bam.C
processed data file: RNAseq_summary_count_table.txt


title: 4_Dicer clone_RNAseq_1

description:
4_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt


title: 8_Dicer timecourse_RNAseq_2

description:
8_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt


title: 216-MRD5_1


title: 5_Dicer clone_RNAseq_2

description:
5_Aligned.sortedByCoord.out.bam.T
processed data file: RNAseq_summary_count_table.txt


title: CMML_2096

city: Miami

first: Qin

last: Yang

state: FL

address: 1501 NW 10th Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

data_processing:
Read were trimmed using CUTADAPT
Trimmed reads were mapped to hg19 using star
gene expression data were analyzed using QoRTs
differentail expressed genes  were calculated using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: raw count matrix

source_name: CMML patient classical monocytes

extract_protocol:
Isolation protocol: Peripheral blood mononuclear cells (PBMC) were sorted using density centrifugation Pancoll (Pan-Biotech, Dutscher, Brumath, France) and CD14+ monocytes through negative selection with magnetic beads and the AutoMacs system (Miltenyi Biotech, Paris, France). For the 10 age-matched healthy monocytes, CD14+/CD16- were sorted by flow cytometry
Total DNA AND RNA were extracted using RNA/DNA/Protein Purification Plus Kit (Cat. 47700) (Norgen Biotek Corp.)
libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: TET2 mutation

tag: cell marker

value: monocyte


title: CMML_1612


title: 8R WT con veh

city: Chapel Hill

first: Abrar

middle: E

last: Al-Shaer

state: NC

address: 135 Dauer Dr

department: Nutrition

institute: University of North Carolina Chapel Hill

data_processing:
NovaSeq 6000 used for sequencing/base calling
Quality of sequencing files ran through FASTQC
FASTQ files aligned to the Mus musculus UCSC MM10 reference genome using Bowtie2
Gene counts were generated via the subread featureCounts package
DESeq2 was used for normalization and statistical analysis of the gene counts file output from the featureCounts program
Genome_build: UCSC MM10
Supplementary_files_format_and_content: CSV data table with DESeq2 output (statistics + normalized gene counts)

molecule: polyA RNA

source_name: Whole liver

extract_protocol:
mRNA from whole livers was extracted
Total RNA-Seq library construction was performed from the RNA samples using the TruSeq Stranded RNA Sample Preparation Kit and bar-coded with individual tags following the manufacturer’s instructions (Illumina, Inc. San Diego, CA)
Total RNA-Seq mRNA, 35 million reads per sample, 2 lanes per sample, paired-end run

treatment_protocol: Mice received intraperitoneal injections in the lower left visceral fat pad of either 300ng resolvin E1 or an ethanol vehicle control.

value: ChemR23 Wildtype

tag: dietary group

value: Lean (10% kcal from fat)

tag: treatment

value: Vehicle control (ethanol+PBS)

value: Whole liver


title: CMML_1378


title: CMML_1483


title: 9L KO con veh

value: ChemR23 knockout


title: CMML_1776


title: 8RL WT con veh


title: CMML_1357


title: 216-MRD4_1


title: 7R WT HF RvE1

value: High Fat (60% kcal from fat)

value: Resolvin E1 300ng


title: 9RL KO con veh


title: CMML_1859


title: 216-MRD3_1

value: PBMCs

value: Serial dilution


title: CMML_1982


title: CMML_2179


title: CMML_1795


title: CMML_2177


title: CMML_1925


title: 216-MRD2_1


title: CMML_1515


title: CMML_1755


title: 6R WT HF veh


title: CMML_1894


title: 7L WT HF RvE1


title: 7-2L WT HF RvE1


title: 1421-MRD5_1


title: 216-MRD0_1


title: 6L WT HF veh


title: 216-MRD1_1


title: CMML_2187


title: cPT-QC_run1

source_name: thymus, tonsil and PBMCs

value: cPT-QC

value: thymus, tonsil and PBMCs

value: quality control


title: CMML_1844


title: 31R KO HF veh


title: 1421-MRD4_1


title: 1421-MRD3_1


title: CMML_2206


title: 7RL WT HF RvE1


title: CMML_2005


title: CMML_1626


title: 31N KO HF veh


title: CMML_2178


title: CMML_2237


title: CMML_1913


title: 1421-MRD2_1


title: CMML_1788


title: 6RL WT HF veh


title: CMML_1381


title: CMML_1468


title: CMML_1397


title: rat TA3 rep3

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

data_processing:
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: read counts, fpkm

organism: Rattus norvegicus

source_name: hepatitis stage liver

growth_protocol: model group and TA group were induced liver fibrosis  by CCl4,normal group were given same dose normal saline

extract_protocol:
Total RNA was extracted from liver tissues with Trizol reagent
NEBNext UltraTM RNA Library Prep Kit（NEB #E7490）,AMPure XP system

treatment_protocol: TA group were treated with TA

tag: Sex

value: male

value: liver

value: rat TA3


title: 30RL WT HF RvE1


title: 1421-MRD0_1


title: rat TA2 rep2

value: rat TA2


title: 30R WT HF RvE1


title: 30L WT HF RvE1


title: rat model rep3

value: rat model


title: rat TA1 rep1

value: rat TA1


title: 344-MRD5_1


title: CMML_1587

value: TET2 mutation

value: monocyte


title: 344-MRD4_1


title: rat model rep2


title: 344-MRD3_1


title: 27-2R WT HF veh

value: ChemR23 Wildtype

value: Vehicle control (ethanol+PBS)

value: Whole liver


title: rat model rep1


title: 27-2L WT HF veh

value: High Fat (60% kcal from fat)


title: CMML_1551


title: rat wt rep3

source_name: normal control liver

value: rat wt


title: 31L KO HF veh

value: ChemR23 knockout


title: NG2

city: Hangzhou

first: Bo

last: Xie

address: Westlake Road, 38

institute: Hangzhou Third People's Hospital, Affiliated Dermatology Hospital of Zhejiang University School of Medicine

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Vitiligo melanocytes

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human vitiligo melanocytes cell line

value: untreated


title: CMML_1565


title: CMML_2214

value: TET2 WT


title: 26L WT con veh

value: Lean (10% kcal from fat)


title: 27RL WT HF veh


title: NG1


title: 1421-MRD1_1

value: PBMCs

value: Serial dilution


title: 26R WT con veh


title: 23RL KO HF RvE1

value: Resolvin E1 300ng


title: CMML_1504


title: rat wt rep1

value: male

value: liver


title: 344-MRD2_1


title: CMML_2272


title: 23L KO HF veh


title: CMML_1796


title: HCQ1

value: Hydroxychloroquine for 24 hours


title: CMML_1974

value: monocyte


title: CMML_2172

value: TET2 mutation


title: hL-Cre

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

description: LMNA-Cre

data_processing:
High-throughput sequencing was performed on the NOVA SEQ system (Illumina).
Trimmed reads were obtained by removing adapter sequences, and reads with low complexity or of low quality were removed.
The types and proportions of SNVs are analyzed using customized shell scripts
Genome_build: hg38
Supplementary_files_format_and_content: comma-delimited csv file includes SNV percentage of each Sample

extract_protocol:
Genomic DNAs were extracted from the HEK293 cells by using TIANamp Genomic DNA Kit (TIANGEN)
Amplification primers containing Illumina forward and reverse adapters were used for a first round of PCR (PCR 1) amplifying the genomic region of interest. Unique Illumina barcoding primer pairs were  added to each sample in a secondary PCR reaction (PCR 2).
AMP-seq

tag: cell line

value: hL-Cre


title: hL-Flpo

description: LMNA-Flpo

value: hL-Flpo


title: hL-CoCo

description: LMNA-CoCo

value: hL-CoCo


title: 22L WT HF veh

value: ChemR23 Wildtype

value: High Fat (60% kcal from fat)

value: Vehicle control (ethanol+PBS)

tag: tissue

value: Whole liver


title: rat wt rep2

value: rat wt


title: HCQ2

value: human vitiligo melanocytes cell line


title: CMML_2111

value: TET2 WT


title: CMML_2264


title: 21L WT con veh

value: Lean (10% kcal from fat)


title: 23-2L KO HF RvE1

value: ChemR23 knockout

value: Resolvin E1 300ng


title: 21R WT con veh


title: 20R KO con veh


title: TP53-Cre


title: CMML_1631


title: 20L KO con veh


title: TP53-CoCo


title: patient 37 tumor, region 1

type: RNA

city: Houston

first: Shawna

middle: Marie

last: Hubert

state: Texas

address: 1515 Holcombe Blvd

department: Thoracic/Head and Neck Medical Oncology

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: The fragmented and labeled sscDNA (5.2 µg) was then hybridized to the respective mouse or human GeneChip Clariom D arrays at 45ºC for 16h.

scan_protocol: The samples were washed and stained using the ThermoFisher proprietary reagents in the GeneChip Fluidics Station 450 (FS450) and scanned in the GeneChip Scanner 3000 7G (ThermoFisher Scientific).

data_processing: The in-house clariom.s.human microarray data were analyzed using Bioconductor packages Oligo61, pd.clariom.s.human, and limma62 following standard workflow.

label: biotin

source_name: lung tumor

label_protocol: Biotinylated sense-tstrand DNA targets were prepared form total RNA using the Clariom S. Assay by ThermoFisher and following the manufacturers protocol

extract_protocol: none provided by the submitter

value: tumor

tag: histologic subtype

value: LUAD


title: CMML_2261

value: monocyte


title: DMD-Flpo

description: DMD-Flpo

value: DMD-Flpo


title: patient 36 tumor, region 2

value: LUSC


title: 20-2L KO con veh


title: CMML_2265


title: patient 35 tumor, region 1

value: SCLC


title: patient 36 tumor, region 1


title: 60708 CTRL_10

source_name: Age-matched control classical monocytes

value: control


title: patient 37 tumor, region 2

value: LCNEC


title: 19R WT con veh

value: ChemR23 Wildtype


title: DMD-Cre

description: DMD-Cre

value: DMD-Cre


title: TP53-Flpo


title: patient 34 tumor, region 1


title: 60599 CTRL_09


title: patient 34 tumor, region 2


title: DMD-CoCo

description: DMD-CoCo

value: DMD-CoCo


title: 15-2L KO HF RvE1

value: High Fat (60% kcal from fat)

value: Whole liver


title: 15R KO HF RvE1


title: 61188 CTRL_08


title: 68692 CTRL_07


title: 14RL KO con veh

value: Vehicle control (ethanol+PBS)


title: patient 33 tumor, region 2


title: patient 33 tumor, region 1


title: CC_Cas9-2

data_processing:
High-throughput sequencing was performed on the llumina NovaSeq .
Trimmed reads were obtained by removing adapter sequences, and reads with low complexity or of low quality were removed.
quality filtered reads were mapped to the human reference genome using Salmon 0.14.1
Genome_build: hg38
Supplementary_files_format_and_content: comma-delimited csv file includes Raw reads counts of each Sample

extract_protocol:
The livers of indicated HEK293 cells were trypsinized and collected, and total mRNA was extracted using TRIzol reagent
The TruSeq RNA Sample Preparation kit (Illumina) was used to construct RNA-seq libraries


title: CC_Cas9-3


title: 694 CTRL_06


title: 14-2L KO con veh

value: Lean (10% kcal from fat)


title: CC_Cas9-1


title: CMML_2063

value: TET2 WT


title: CC_Cas9_Flpo-3


title: CC_Cas9_Flpo-2


title: 12RL KO HF RvE1

value: ChemR23 knockout

value: Resolvin E1 300ng


title: 12L KO HF RvE1


title: 12-2L KO HF RvE1


title: 997 CTRL_05


title: 68451 CTRL_03


title: CC_Cas9_Cre-3


title: CC_Cas9_Flpo-1


title: 10R KO HF veh


title: 1745 CTRL_02


title: 970 CTRL_01


title: 10RL KO HF veh


title: 6706 CTRL_04


title: 10-2L KO HF veh


title: TNBC.01

city: Winston-Salem

first: Jeff

last: Chou

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

data_processing:
Raw bcl and fastq data were demultiplexed, mapped to the GRCh38 human reference genome, and post-processed using Cell Ranger (10X Genomics) mkfastq pipelines and QC algorithms.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files in MM matrix format (*.mtx), genes and barcode IDs (*.tsv)

source_name: breast tumor tissue

extract_protocol:
Fresh tumor tissue inspected by a surgical pathologist was minced by razor blade into ~1 mm pieces and digested for 1 hr at 37˚C with the Human Dissociation Kit (Miltenyi Biotec, Auburn, CA) as per manufacturer’s instruction with the aid of gentleMACS Octo Dissociator fitted with a heating collar (Miltenyi Biotec). Digested tissue was passed through a 70 µm strainer, washed and resuspended in RPMI plus 10% fetal bovine serum (FBS), then underlaid with Histopaque-1077 (Sigma-Aldrich) and centrifuged at 400 x g for 30 min. The resulting buffy coat was harvested and washed in RPMI plus 10% FBS, resuspended in the same media, and counted. Approximately 1 million cells were frozen in 90% FBS/10% DMSO, and gently thawed and tested for viability just prior to library construction.
A single-cell cDNA library was constructed from thawed cells exhibiting >80% viability using the 10X Genomics Chromium Controller maintained by the Wake Forest Baptist Comprehensive Cancer Center’s Cancer Genomics Shared Resource. The library was prepared using the standard protocol from 10X Genomics and their V2 chemistry. The library was sequenced on an Illumina NextSeq 500 with paired-end sequencing and dual indexing. Cells were sequenced to an average read depth of 173,842 mapped reads per cell.

tag: tissue type

value: primary tumor

tag: clinical subtype

tag: clinical stage

value: stage III

tag: gender

value: female


title: Mutant1_1 (rep1)

status: Public on Nov 12 2021

city: Yangzhou

first: Liexiang

last: Huangfu

address: daxue road

institute: Yangzhou 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 Oryza_sativa.IRGSP-1.0 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using Cuffdiff.
Genome_build: Oryza_sativa.IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Oryza sativa

source_name: leaf

extract_protocol:
Rice leaves were sampled at 85 days after sowing, and than removed in ultra low temperature freezer. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Nevogene protocols

value: leaf

tag: age

value: 85 days after sowing

value: OsCOMT mutant


title: Mutant2_1 (rep2)


title: Mutant3_1 (rep3)


title: Lipo3

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

data_processing:
Illumina bcl2fastq conversion software used for basecalling.
reads were aligned using the STAR (2.5.2b) software.
raw read counts were obtained using htseq-count (HTSeq-0.6.1p12)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files of raw count values for each Sample

source_name: esophageal cells

growth_protocol: A normal esophageal squamous cells line, EPC2 (kind gift from Anil Rustgi, University of Pennsylvania).  EPC2 cells were maintained in Keratinocyte-SFM (KSFM) medium supplemented with Bovine Pituitary Extract (BPE) and human recombinant Epidermal Growth (ThermoFisher Scientific, Waltham, MA).  Trypsin was purchased from Sigma-Aldrich, St. Louis, MO.  The cell line was maintained in BEBM at 37°C in 5% carbon dioxide. The cells used in this study were within 5 passages after receipt (~1 month of culturing). Culture medium was replaced every alternate day. Each experiment was conducted in triplicate and repeated a minimum of three times. Contemporary mock untreated cells and control lipofectamine treated cells were run in each experiment.

extract_protocol:
Total RNA was prepared using Trizol, RNAzol (Molecular Research Center, Cincinnati, OH).
Sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation Kit (A cat#FC-122-2101, B cat#FC122-2102)

treatment_protocol: Cells were transfected with FOXF1 plasmid or empty vector by using Lipofectamine 2000 (Life Technologies, Carlsbad, CA).

value: esophageal epithelial cell line EPC2

value: Lipo

value: control


title: WT_1_100 (rep1)

value: WT


title: CC_Cas9_Cre-1


title: WT_2_100 (rep2)


title: OE_1_100 (rep1)

value: OsCOMT overexpression


title: Lipo2


title: OE_2_100  (rep2)


title: Lipo1


title: Fox3

value: transfected with FOXF1 plasmid

value: Forkhead box F1 overexpression


title: CC_Cas9_Cre-2


title: ATI in GP5d cells, cycle 0

city: Helsinki

first: Teemu

last: Kivioja

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
Library strategy: ATI/SELEX
The motifs were matched to the sequences using program MOODS (version 1.9.3). The matching was done separately for each strand using p-value thresholds 1e-6 and and strand- and sample-specific nucleotide frequencies.
The number of motif  matches for each motif in the sequences was counted so that only the best match per sequence was taken into account.
Fold changes between the motif match counts between ATI cycles 4 and 0 (input) were estimated using the function PsiLFC in R package lfc.
Supplementary_files_format_and_content: tab delimited text file, the columns are, name (name of the TF),   pfm (name of the motif used in the mathing),  count (motif match count in ATI cycle 4 sequences), input.count (motif match count in ATI cycle 0 sequences), effect (log2 fold change of motif matches between ATI cycles 4 and 0)

molecule: other

organism: synthetic construct

source_name: synthetic

extract_protocol:
The synthetized DNA oligos with illumina adapter sequences were enriched after incubating with the protein extract from specific cell lines, and then amplified for sequencing.
The DNA oligos are designed to include the illumina sequencing adapters for sequencing, no library consctruction steps are needed.
ATI/SELEX (See Bei Wei et al. Nature Biotechnology, 2018)

tag: cell type

value: GP5d colon cancer cells


title: ATI in GP5d cells, cycle 4


title: OE_3_100  (rep3)


title: Ctrl3

value: Ctrl


title: WT_3_100 (rep3)


title: Fox2


title: Ctrl1


title: STARR-seq random enhancer input library

data_processing:
Library strategy: STARR-seq
150 bases long STARR-seq RNA and input DNA paired-end reads were combined using the FLASH program (version 1.2.11, options --min-overlap=130--max-overlap=134 -x 0.25 -z -t 4) and only combined sequences of length 170 were chosen
Duplicate reads were removed by sorting the sequences four times based on 45 bases long non-overlapping subsequences from base 6 to 165 and taking only one sequence per identical subsequence at each sort step.
The motifs were matched to sequences using program MOODS (version 1.9.3). The matching was done separately for each strand using p-value thresholds 1e-6 and and strand- and sample-specific nucleotide frequencies.
The number of motif  matches for each motif in the sequences was counted so that overlapping matches in different strands were counted only once.
Fold changes between the motif match counts in RNA and  input DNA were estimated using the function PsiLFC in R package lfc.
Supplementary_files_format_and_content: tab delimited text files, the columns are: name (name of the TF),  pfm (motif used in the sequenc matching),  total.count (count of motif matches in STARR-seq RNA), input.total.count (count of motif matches in input DNA),  effect (log2 fold change between STARR-seq RNA and input DNA estimated by lfc)

source_name: STARR-seq random enhancer input library

growth_protocol: GP5d cells were cultured in DMEM and HepG2 cells in MEM media with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency. For each random enhaner STARR-seq experiment, a total of 250 million GP5d cells per replicate were transfected.

extract_protocol:
Total RNA was isolated Qiagen RNeasy maxi kit after 24 hours of transfection followed by polyA(+) purification using direct mRNA purfication beads (ThermoFisher).
STARR-seq reporter and input library was constructed with minor modifications as described in Arnold et al. Science 2013. First strand cDNA synthesis was done with 2.5-5 ug of polyA(+) RNA and with Superscript III (Invitrogen, #18080-044) using a reporter-RNA specific primer. This was followed by RNase A treatment for 1 h at 37˚C and purification. cDNA amplification was performed with reporter-specific nested cDNA primers corresponding to the respective STARR-seq reporter construct using KAPA HiFi PCR Master mix (Roche) in the same number of reactions as done for the reverse transcription. The final PCR reactions to produce Illumina-compatible sequencing libraries were prepared from the entire amplified cDNA using KAPA HiFi PCR Master mix (Roche) as descriubed in Arnold et al. Science 2013. All purifications were done using AMPure XP beads as per manufacturer’s instruction unless otherwise mentioned.
Illumina sequencing strategy adapted for random enhancer pCpG-free STARR-seq construct  using custom adapters, sequencing and index primers.

treatment_protocol: The cells were transfected with random enhancer STARR-seq library using transfex (ATCC) in GP5d cells and transfectin (Biorad) in HepG2 cells using one ug of library per one million cells.

tag: input

value: STARR-seq random enhancer input


title: Fox1

tag: genotype


title: LPS_2 (LncRNA)

city: shenyang

first: wei

last: xu

state: Liaoning province

address: NO.36  of sanhao street

department: Department of Pediatrics

institute: shengjing hospital of China medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2 v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default
Cuffdiff (V.2.1.1) was applied to compute fragments per kilobase of exon per million fragments mapped (FPKMs) of both lncRNAs and coding genes in each sample. FPKMs were computed according to the length of the fragments, as well as reads count mapped to the fragment. The FPKM of transcripts in every gene group was added up to calculate the gene FPKM.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: lung tissue

extract_protocol:
Lung tissue was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.  Illumina Hiseq 4000 platform and a total amount of 3 μg total RNA per sample  were used to construct the sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: BALB/c

value: lung

value: LPS-induced acute lung injury


title: NS_1 (LncRNA)

value: normal


title: LPS_1 (LncRNA)


title: NS_2 (LncRNA)


title: patient 31 tumor, region 2

value: tumor

value: LUAD


title: NS_3 (LncRNA)


title: patient 35 tumor, region 2


title: Non-Tg [SAM24360950]

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Single-cell RNA sequencing data were processed with an in-house analysis pipeline as described (https://www.sciencedirect.com/science/article/pii/S2211124719317656). Reads were demultiplexed based on perfect matches to expected cell barcodes. Transcript reads were aligned to the mouse reference genome (GRCm38) using GSNAP (2013-10-10) (Wu and Nacu, 2010). Only uniquely mapping reads were considered for downstream analysis. Transcript counts for a given gene were based on the number of unique UMIs (up to one mismatch) for reads overlapping exons in sense orientation. Cell barcodes from empty droplets were filtered by requiring a minimum number of detected transcripts. Sample quality was further assessed based on the distribution of per-cell statistics, such as total number of reads, percentage of reads mapping uniquely to the reference genome, percentage of mapped reads overlapping exons, number of detected transcripts (UMIs), number of detected genes, and percentage of mitochondrial transcripts.
For each sample the R1 file provides the barcode representing the cell and the R2 file provides the insert sequence
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

source_name: Hippocampus

extract_protocol:
Mice were perfused with PBS. Hippocampi and fibria were dissected out and dissociated with papain-containing Miltenyi kit (130-092-628). Live single cells were enriched by FACS, and single cell suspensions were subjected to 10X Genomics procedure (Chromium™Single Cell 3’ Reagent Kit v2 (10X Genomics PN-120237) for single cell RNA extraction and RT.
Library was contructed with Chromium™Single Cell 3’ Reagent Kit v2 (10X Genomics PN-120237) following manufacturer's user guide. cDNA amplification was done with 10 cycle PCR, and sample index PCR was done with 12 cycles. Libraries were sequenced by HiSeq4000 (Illumina) following 10X Genomics sequencing specification.

value: 15 months

tag: group

value: old Non-Tg

value: female


title: patient 29 tumor, region 4

value: NSCLC-NOS


title: PS2APP [SAM24356162]

value: 7 months

value: young PS2APP


title: PS2APP [SAM24359110]


title: PS2APP [SAM24359431]


title: PS2APP [SAM24364374]

value: old PS2APP


title: Non-Tg [SAM24359109]

value: young Non-Tg


title: Non-Tg [SAM24361188]


title: PS2APP [SAM24361189]


title: patient 29 tumor, region 1

value: LCNEC


title: Non-Tg [SAM24364373]


title: patient 26 tumor, region 1


title: patient 31 tumor, region 1

value: SCLC


title: patient 29 tumor, region 2

value: LUSC


title: patient 30 tumor, region 1


title: PS2APP [SAM24360951]


title: Non-Tg [SAM24356161]


title: patient 26 tumor, region 2


title: patient 30 tumor, region 2


title: Ctrl2

value: esophageal epithelial cell line EPC2

value: Ctrl

value: control


title: Non-Tg [SAM24359430]


title: MAYO_BM_7

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

data_processing:
Salmon (v.0.91) was used to perform quasi-mapping of sequencing reads, with seqBias and gcBias corrections enabled, using a 31bp k-mer index of the GRCh38.p10 (GENCODE v.27) human reference transcripts, to estimate transcript abundance for each sample
Tximport package was used to import transcript abundance estimates from quant.sf files, generated by Salmon read mapping into R statistical programming environment for gene expression quantification. Transcript abundance estimates were collapsed to gene level gene expression counts. TXI data objects for MAYO and PITT-RCSI RNA-Seq cohort, containing unprocessed Salmon read counts, transcript per million (TPM) and gene length values were combined for subsequent downstream analysis.
Genes with little to no expression across all 90 samples were filtered if gene TPM < 0.5 in at least 10% of all samples (N=90)
Filtered gene level counts were normalized with edgeR calcNormFactors() and cpm() function, where counts per million (CPM): CPM = C * 106/N (counts (C) scaled by the library depth in million units). A log2 transformation was applied to CPM: log2(CPM +1), where 1 is a pseudocount added to prevent negative value counts. Filtered log2 CPM and TPM genes were annotated using biomaRt R package to identify protein coding genes using the ENSEMBL GRCh38 p.10 database.
In order to correct for between RNA-Seq cohort (MAYO, PITT-RCSI) batch driven effect, filtered protein coding gene expression counts were used as input to svaseq R package for batch effect assessment. A multiple linear regression model was fit for each surrogate variable (SV), with the following independent predictors: sequencing batch ID [1,5], disease status (primary breast (P) / brain metastases (M)), estrogen receptor (ER) IHC status (ER+/ER-) and primary tumor histological subtype (DCIS, IDC, ILC, Mixed ILC/IDC). A linear model fitted using SV1 was found to be significantly associated with sequencing batch (P < 0.05; R2 ~0.70).   As such, in order to correct for between RNA-Seq cohort (MAYO, PITT-RCSI) batch driven effect, removeBatchEffect() function in LIMMA package in R, was used with SV1, to adjust gene expression values to account for mean shifts in expression driven by the batch driven effect.
Genome_build: GRCh38.p10 (GENCODE v.27)
Supplementary_files_format_and_content: .xlsx excel spread sheet containing batch corrected log2 TMM normalized CPM proteing coding gene expression values for all 90 samples

source_name: brain metastatic tumor

extract_protocol: 100 ng of total RNA and a TruSeq Stranded Total RNA (Degraded RNA) v2 RNA Exome Library and TS RNA Access capture protocol (Illumina)

tag: cohort

value: MAYO

tag: patient id

tag: disease state

value: breast cancer

value: brain metastatic tumor


title: MAYO_BP_7

source_name: primary breast tumor

value: primary breast tumor


title: MAYO_BM_8


title: MAYO_BP_9


title: MAYO_BP_8


title: MAYO_BM_9


title: MAYO_BP_6


title: MAYO_BM_6


title: MAYO_BP_2


title: MAYO_BM_4


title: MAYO_BP_3


title: MAYO_BM_2


title: MAYO_BM_16


title: MAYO_BP_5


title: MAYO_BP_16


title: MAYO_BP_4


title: MAYO_BM_5


title: MAYO_BP_18


title: MAYO_BP_14


title: MAYO_BM_15


title: MAYO_BM_18


title: MAYO_BP_17


title: MAYO_BM_3


title: MAYO_BM_17


title: MAYO_BP_15


title: MAYO_BP_13


title: MAYO_BM_13


title: MAYO_BM_14


title: MAYO_BP_12


title: MAYO_BP_11


title: MAYO_BM_12


title: MAYO_BM_1


title: MAYO_BP_1


title: MAYO_BM_10


title: TUH69_S27,AraC=Low,VenAraC=Low

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

data_processing:
For each patient samples, all fastq files were mapped to GRCh38.99 whole genome using STAR-2.7.3a with --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --readFilesCommand gunzip -c
Gene count was generated from BAM files using summarizeOverlaps function of R/Bioconductor package GenomicAlignments. In short, for each patient BAM file was loaded into R using function readGAlignmentPairs (GenomicAlignments). Then read position of genome were overlaped with Ensembl GRCh38.99.gft using summarizeOverlap with ignore.strand=T and mode="IntersectionNotEmpty".
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt

source_name: Bone marrow

growth_protocol: Patients’ AML cells were isolated by Ficoll density gradient centrifugation at de novo leukemia stage and cultured in Iscoves modified Dulbecco medium (IMDM) supplemented with 20% FBS. The RNA sequencing was done on the blast cell solution.

extract_protocol:
Total RNA were extracted with RNeasy technology (Qiagen) according to the manufacturer protocol
100 ng of total RNAs were reverse transcribed into cDNA, then transcribed into cRNAs and labeled into biotinylated cRNA using the TruSeq Stranded mRN according to the manufacturer’s standard protocols
Libraries were sequenced in paired end 100 using the instrument model Hiseq 4000

treatment_protocol: Primary AML cells do not receive any treatments before RNA extraction

tag: response to arac (0=low/1=high)

tag: response to ven+arac (0=low/1=high;-1=na)

tag: patient

value: Bone marrow

tag: treatment

value: AraC=Low, VenAraC=Low


title: Template switch library from STARR-seq GP5d binary RNA, replicate 1

description:
sequences start with 6 bp long UMI (unique molecular identifier)
STARR-seq_TSS_flank60_motif_counts.tsv

data_processing:
Library strategy: STARR-seq
Sequences derived from spliced transcripts were identified using the constant sequence spanning the splice site after intron removal (cutadapt program); other sequences were not processed further.
UMI sequence was removed from the 5’ end of each sequence and the last 20 bp of its random part was used to recognize the corresponding promoter from the input DNA (file avaiiable in STARR-seq random promoter-enhancer experiments part of the same study)
To accurately recognize the first base of the transcript and thus the position of the TSS, it was assumed that the template switch process had added at least 3 and at most 4 guanines to the 5’ end of the transcript. On this basis, only the RNA sequences starting with at least three Gs were used in the analysis. Each such sequence was aligned to the corresponding input DNA promoter sequence using an exact 20 bp match starting from the base to allow for the extra Gs. Finally, the Gs added by the template switch were trimmed an discordant sequences removed according to the alignment. The frequency of the four Gs instead of three was estimated from the sequences that do not have G at the fourth position in the alignment to the input. For those that did have a G also in the input sequence, removing three or four Gs was decided randomly but so that the frequency of the fourth G matched the estimate.
The two GP5d template switch libraries were processed separately and then merged so that only one transcript was kept for each input DNA promoter sequence to prevent duplicate promoter sequences.
The exact positions of the TSS at the promoters were recorded and the flanking sequences were used for further analysis.
Motifs were matched to TSS flanking promoter sequences using program MOODS and for each motif only the highest affinity match per sequence was considered. The number of matches for each motif was then counted separately at each position and strand.
Supplementary_files_format_and_content: tab-delimited text file, the columns are: name (name of the TF),   pfm (name of the motif used in the motif matching),  pos (position of the information content center of the motif in relation to TSS at +1),  strand (strand of the motif matches) ,  num (number of motif matches at this position and strand,  pfm.type (either HT-SELEX = in vitro motif from HT-SELEX experiment, promoterCore = promoter motif collected from literature or database,  deNovo = motif mined from the STARR-seq data itself, New = recently published promoter motif)

growth_protocol: GP5d cells were cultured in DMEM media supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency. For each random promoter-enhancer binary STARR-seq experiment, a total of 250 million GP5d cells per replicate were transfected.

extract_protocol:
Total RNA was isolated Qiagen RNeasy maxi kit after 24 hours of transfection.
Input library for random promoter-enhancer binary STARR-seq was constructed as described in Arnold et al. Science 2013. For generating a sequencing library using a template switch strategy, a 40-ug aliquot of isolated total RNA from the random promoter-random enhancer STARR-seq experiment in GP5d cell line was used. Briefly, TurboDNase-treated RNA was incubated at 72 C for 3 min with a custom biotinylated STARR-seq specific RT-primer and dNTPs in two reactions having 25 ng of RNA per reaction, followed by immediate chill on ice. The first strand synthesis was performed using 100 units of Superscript IV RT (Invitrogen) in 1x SS-IV RT buffer containing 10 units of RNase OUT (Invitrogen), 5 mM DTT, 6 mM MgCl2 (Sigma), 1M Betaine (Sigma) and 1 uM custom template switch oligo compatible with the custom CpG-free Illumina sequencing by incubating the reactions at 50 C for 15 min followed by 80 C for 10 min. cDNA was purified using AMPure XP beads and one cDNA reaction product was split into two for PCR amplification using KAPA HiFi master mix (Roche) together with USER enzyme (NEB) and for enrichment of STARR-seq reporter-specific template. The PCR product was purified using AMPure XP beads followed by a second PCR for a total of 5 cycles for Illumina library preparation using custom CpG-free oligos.
Illumina sequencing strategy adapted for  pCpG-free STARR-seq construct for random promoter-enhancer and template switch library using custom adapters, sequencing and index primers.

treatment_protocol: The cells were transfected with random enhancer STARR-seq library using transfex (ATCC) in GP5d cells  using one ug of library per one million cells.

tag: cell line

value: GP5d  colon carcinoma cells


title: MAYO_BP_10

tag: tissue


title: TUH90_S30,AraC=High,VenAraC=NA

value: AraC=High, VenAraC=NA


title: TUH59_S26,AraC=Low,VenAraC=High

value: AraC=Low, VenAraC=High


title: TUH31_S18,AraC=High,VenAraC=NA


title: OIR scrambled RNA 3

first: vikrant

last: singh

state: Ireland

address: 31 York Street

institute: Royal college of Surgeons in Ireland

data_processing:
The quality of the raw reads were were assessed by the FASTQC (Andrews 2010) and assured that all read have phred score > 28.
The transcriptome reads were mapped to the Rattus norvegicus (rn6) refenerce genome retrieved from the iGenomes (obtained on 19th June 2017, https://support.illumina.com/sequencing/sequencing_software/igenome.html).
Differential gene and transcript expression analysis were done by using TopHat and Cufflinks (Trapnell et al. 2012).
Expression level and function analysis were done by using Cuffdiff (Zhang et al. 2014) statistical method and CummeRbund R statistical package (Trapnell et al. 2012).
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Retina

extract_protocol:
The enucleated rat eyes were harvested and stored in the RNAlater (Qiagen), and retinas were dissected immediately under the dissection microscope. Total RNA and miRNA were isolated from the dissected retina by using a miRNeasy mini kit (Qiagen, Hilden, Germany). One microgram of miRNA samples in triplicate was prepared as per the manufacturersâ instructions (Illumina Inc. San Diego, CA, USA). The libraries of cDNA from the biological samples in triplicate were sequenced by using an Illumina Hiseq-2500 RNA-seq platform as 50 bp single-end chemistry.
miRNA libraries were prepared for sequencing using a standard Illumina protocols

value: Sprague Dawley

value: Retina

value: Wild type


title: OIR miR-143 mimic 1


title: TUH28_S16,AraC=Low,VenAraC=High


title: TUH23_S15,AraC=High,VenAraC=NA


title: TUH19_S11,AraC=Low,VenAraC=NA

value: AraC=Low, VenAraC=NA


title: Tumor_miRNA

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

description: miRNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
Trim reads removing first 16bps and last 23bps using fastx_trimmer from fastx (v0.0.14)
Map and quantify reads using mirDeep2 pipeline (v2.0.1.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: Kidney

extract_protocol:
Beckman Coulter FormaPure Total DNA and RNA extraction
Norgen Biotek Small RNA Library Prep Kit

tag: condition

value: Tumor

value: kidney


title: Normal.kidney_miRNA

description: miRNA

value: Normal


title: TUH07_S4,AraC=Low,VenAraC=High


title: TUH10_S6,AraC=Low,VenAraC=Low


title: TUH30_S17,AraC=High,VenAraC=Low

value: AraC=High, VenAraC=Low


title: TUH06_S3,AraC=High,VenAraC=NA


title: MAYO_BM_11

value: MAYO


title: TUH35_S21,AraC=High,VenAraC=High

value: AraC=High, VenAraC=High


title: Methylation_HC2_sp4_Normal_betahydroxybutyrate_ox21_p9

type: genomic

city: New York

first: Gabriel

last: Sturm

address: 40 Haven Avenue

department: Psychiatry

institute: Columbia University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC array using standard Illumina protocol (performed at UNGC)

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting (performed at UNGC)

data_processing:
RStudio (v1.3.1056) using R (v4.0.2). Preprocessing was performed using the 'minfi' (v1.36.0) library and batch corrections using the 'sva' (v3.12.0) library. Quality control excluded 22 samples for a final total of 479 samples.
processed data file contains: ormalized Beta (Functional normalization)

label: Cy5 and Cy3

source_name: Primary Human Fibroblast (breast)

label_protocol: Standard Illumina Protocol

growth_protocol: Primary human dermal fibroblasts were obtained from distributor or in local clinic from 6 healthy and 3 Methylation_SURF1-patient donors (IRB #AAAB0483). Fibroblasts were isolated from biopsy tissue using standard centrifugation procedure. After isolation, fibroblasts were stored in 10% DMSO (Sigma-Aldrich #D4540), 90% fetal bovine serum (FBS, Life Technologies #10437036) in cryogenic tube under liquid nitrogen. To avoid freeze-shock necrosis cells were frozen gradually in an isopropanol container (Thermofisher #5100-0001) at -80°C overnight before storage in liquid nitrogen. Cells were thawed by placement in 37°C (<4min) and immediately transferred to 20ml of preheated DMEM (Invitrogen #10567022). Cells were cultured in T175 flasks (Eppendorf #0030712129) at standard 5% CO2 and atmospheric O2 at 37°C in DMEM (5.5 mM glucose) supplemented 10% FBS, 50 μg/ml uridine (Sigma-Aldrich #U6381), 1% MEM non-essential amino acids (Life Technologies #11140050), 10 μM palmitate (Sigma-Aldrich #P9767) conjugated to 1.7 μM  BSA (Sigma-Aldrich #A8806), and 0.001% DMSO (treatment-matched, Sigma-Aldrich #D4540). Cells were passaged approximately every 6 days (+/- 1 day). Brightfield microscopy images (10x, 20x magnification) were taken before each passaged using inverted phase-contrast microscope (Fisher Scientific #11350119). Cell counts, volume and death were determined at each passage using the Countess II Automated Cell Counter (ThermoFisher Scientific #A27977). Growth rates were used to determine replating density, by pre-calculating number cells needed to reach ~90% confluency (~2.5 million cells) at time of next passage. Cells were never plated below 200,000 cells or above 2.5 million cells to avoid plating artifacts of isolation or contact inhibtion, respectively. Study measurements and treatment began after 15-days of culturing post-thaw to allow for adjustment to in vitro environment. Individual cell lines were terminated after exhibiting less than one population doubling over a 30-day period. Mycoplasma testing was performed on media across the full sampleset with no detectable infection.

extract_protocol: DNA was extracted using the DNeasy kit (Qiagen cat#69506) according to the manufacturer’s protocol and quantified using QUBIT broad range kit (Thermo Fisher Scientific cat#Q32852).

treatment_protocol: Treatment conditions for healthy controls include chronic addition (dosed at every passage) of 100nM dexamethasone (DEX, Sigma-Aldrich #D4902), mitoNUITs; a combination of a) 2μM UK5099 (Sigma-Aldrich #PZ0160) b) 4μM Etomoxir (Sigma-Aldrich #E1905) c) 3μM BPTES t (Sigma-Aldrich #SML0601), 1nM oligomycin (Oligo, Sigma-Aldrich #75351), 5.5mM galactose (Sigma-Aldrich #G5388), 1mM 2-deoxy-d-glucose (2DG, Sigma-Aldrich #D3179), 10mM beta-hydroxybutyrate (Sigma-Aldrich #54965), 10nM MitoQ (PubChem CID:11388332), 2mM N-Acetyl-L-cysteine (NAC, Sigma-Aldrich #A7250), 1mM ⍺-ketoglutarate (⍺-KG, Sigma-Aldrich #75890), contact inhibition (allowing cells to fill up the dish and enter a quiescent state), hypoxia (3% oxygen), acute treatment (10days) of 1μg/mL 5-azacytidine (Sigma-Aldrich #A2385), and pulsated treatment (30min before each passage) of 100nM dexamethasone (DEX, Sigma-Aldrich #D4902).

value: Primary Human Fibroblast (breast)

tag: Sex

value: female

tag: treatments

value: betahydroxybutyrate

tag: passage

tag: slide

tag: array

tag: well


title: Methylation_HC2_sp4_Normal_betahydroxybutyrate_ox21_p8


title: STARR-seq GP5d TF motifs library, pGL4.10-Sasaki-SS vector

description:
STARR-se RNA, Sasaki promoter
STARR-seq_motif_library_GP5d_counts.lfc.tsv

data_processing:
Library strategy: STARR-seq
For each TF motif consensus pattern (see the publication for details of the synthetic sequence design), the reads containing the pattern were counted for the two sequence contexts and promoters
The fold change between RNA and input DNA was estimated using the function PsiLFC in R package lfc for each combination of motif pattern, sequence context, and promoter
Supplementary_files_format_and_content: tab-delimited file with the following columns (see the publication for details of the synthetic sequence design): pfm  (motif embedded in the sequence),  tf (TF of the motif),   configuration (C=consensus, R=reverse complement of consensus),  gap (gap between the instances of the motif), context (UMI length and the context sequence name), input.count (count of the motif pattern in input DNA), rna.count (count of the motif pattern in the STARR-seq RNA),  effect (log2fold change compared to input estimated using R lfc package),  promoter (name of the promoter, E1a=E1alpha)

growth_protocol: GP5d cells were cultured in DMEM with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency. For each motif STARR-seq experiment, a total of 50 and 35 million GP5d cells were transfected for the libraries in pGL4.10-Sasaki-SS (a) and pCpG-free-EF1α-SS (b) vectors, respectively.

extract_protocol:
Total RNA was isolated Qiagen RNeasy maxi kit after 24 hours of transfection followed by polyA(+) purification using direct mRNA purfication beads (ThermoFisher).
First strand cDNA synthesis was done with 2.5-5 ug of polyA(+) RNA and with Superscript III (Invitrogen, #18080-044) using a reporter-RNA specific primer. This was followed by RNase A treatment for 1 h at 37˚C and purification. cDNA amplification was performed with reporter-specific nested cDNA primers corresponding to the respective STARR-seq reporter construct using KAPA HiFi PCR Master mix (Roche) in the same number of reactions as done for the reverse transcription. The final PCR reactions to produce Illumina-compatible sequencing libraries were prepared from the entire amplified cDNA using KAPA HiFi PCR Master mix (Roche) as descriubed in Arnold et al. Science 2013. All purifications were done using AMPure XP beads as per manufacturer’s instruction unless otherwise mentioned.
Illumina sequencing strategy adapted for STARR-seq and for custom CpG-free vector using custom adapters, sequencing and index primers.

treatment_protocol: The cells were transfected with moitf STARR-seq library using transfex (ATCC) in GP5d cells and one ug of library was used per one million cells.

tag: library

value: TF motifs library


title: STARR-seq GP5d TF motifs library, pCpG-free- EF1alpha-SS vector

description:
STARR-se RNA, CpG-free E1alpha promoter
STARR-seq_motif_library_GP5d_counts.lfc.tsv

value: GP5d  colon carcinoma cells


title: Rabbit IgG control used for H3K27me3 in GP5d

data_processing:
The Illumina raw files were demultiplexed using bcl2fastq conversion, followed by alignment to the human genome  using bowtie and peak calling (narrow peaks for TF ChIP-seq and broad peaks for histone modifications) was performed using MACS2 using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 narrowPeak and broadPeak files

source_name: GP5d cell line

growth_protocol: GP5d cells were cultured in DMEM and HepG2 cells in MEM media with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (Sahu et al. EMBO J 2011). For analyzing genomic occupancy of TP53, cells were treated with 350 uM 5-fluorouracil (Sigma) 24 h before harvesting the cells. Briefly, fresh formaldehyde-crosslinked chromatin from GP5d cells was used to immunoprecipitate DNA using Dynal-bead coupled antibodies for TFs or histone modifications and for normal rabbit, mouse and goat IgG, followed by standard ChIP-seq library preparation for Illumina sequencing. The libraries were single-read sequenced on HiSeq4000.
The immunoprecipiated DNA was end-repaired, dA tailed and adapter ligated followed by PCR enrichment of adapter-ligated ChIP DNA as described in Sahu et al. EMBO J. 2011
Illumina TruSeq library strategy

treatment_protocol: Treatment when required for the cells were with DMSO as control, STARR-seq library transfection using Transfex (ATCC) in GP5d cells and Transfectin (Biorad) in HepG2 cells and 350 uM 5-fluorouracil (5-FU) for 24 hours.

value: colon cancer cell line

value: Untreated

tag: antibody

value: Santa-Cruz, sc-2027

value: GP5d cell line


title: Methylation_HC2_sp4_Normal_betahydroxybutyrate_ox21_p11


title: Rabbit IgG control used for FOXA1, HNF4A and MYC in GP5d


title: ChIP-seq GP5d H3K27me3

value: Diagenode, #C15410195


title: Mouse IgG control used for TCF7L2 in GP5d

value: Santa-Cruz, sc-2025


title: Methylation_HC1_sp4_Normal_betahydroxybutyrate_ox21_p11

value: male


title: Methylation_HC2_sp4_Normal_betahydroxybutyrate_ox21_p7


title: Methylation_HC2_sp4_Normal_betahydroxybutyrate_ox21_p6


title: Methylation_HC1_sp4_Normal_betahydroxybutyrate_ox21_p7


title: Methylation_HC1_sp4_Normal_betahydroxybutyrate_ox21_p6


title: Methylation_HC1_sp4_Normal_betahydroxybutyrate_ox21_p10


title: Methylation_HC1_sp4_Normal_betahydroxybutyrate_ox21_p5

tag: notes

value: Treatment Start


title: Methylation_HC1_sp4_Normal_betahydroxybutyrate_ox21_p8

value: Normal


title: ChIP-seq GP5d TCF7L2

value: Xalpha biologicals, X1070M


title: Methylation_HC2_sp4_Normal_betahydroxybutyrate_ox21_p10


title: ChIP-seq GP5d MYC

value: Millipore #06-340


title: LPS_3 (LncRNA)

tag: strain

value: BALB/c

value: lung

value: LPS-induced acute lung injury


title: Rabbit IgG control used for SMC1, H3K9me3 in GP5d


title: ChIP-seq GP5d HNF4A

value: Santa-Cruz, sc-8987x


title: ChIP-seq GP5d H3K9me3

value: Diagenode, #C15410193


title: Methylation_HC2_sp4_Normal_2-Deoxyglucose_ox21_p10

value: Primary Human Fibroblast (breast)

value: female


title: Methylation_HC2_sp4_Normal_2-Deoxyglucose_ox21_p9


title: ChIP-seq GP5d SMC1

value: colon cancer cell line

value: Untreated

value: Bethyl lab, A300-055A


title: Methylation_HC2_sp4_Normal_2-Deoxyglucose_ox21_p11


title: Methylation_HC2_sp4_Normal_2-Deoxyglucose_ox21_p8


title: Methylation_HC2_sp4_Normal_2-Deoxyglucose_ox21_p5


title: Methylation_HC1_sp4_Normal_2-Deoxyglucose_ox21_p11


title: ChIP-seq GP5d H3K27ac

value: Diagenode, #C15410196

value: GP5d cell line


title: Mouse IgG control for ChIP-seq in GP5d-5-FU

value: 350 uM 5-fluorouracil (5-FU) treatment for 24 hours

value: Santa-Cruz, sc-2025


title: Goat IgG control used for CTCF in GP5d

value: Santa-Cruz, sc-2028


title: ChIP-seq GP5d CTCF

value: Santa-Cruz, sc-15914x


title: Methylation_HC2_sp4_Normal_Galactose_ox21_p10

value: Normal

value: Galactose


title: ATAC-seq GP5d

data_processing:
The samples were demultiplexed and paired-end fastq files were processed using an in-house pipeline comprising of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), BWA aligner, Picard (http://broadinstitute.github.io/picard/) and broad-peak calling by MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 broad peak format

extract_protocol:
The cells were extracted and processed as per ATAC-seq protocol (Buenrostro et al. Nature Methods 2013)
The ATAC-seq library was prepared as per the ATAC-seq protocol (Buenrostro et al. Nature Methods 2013)

treatment_protocol: Treatment for the cells were with DMSO as control, STARR-seq library transfection using Transfex (ATCC) in GP5d cells and Transfectin (Biorad) in HepG2 cells and 350 uM 5-fluorouracil (5-FU) for 24 hours.

tag: cell type


title: Methylation_HC1_sp4_Normal_2-Deoxyglucose_ox21_p5

value: male

value: Treatment Start


title: Rabbit IgG control used for H3K27ac in GP5d

value: Santa-Cruz, sc-2027


title: Methylation_HC1_sp4_Normal_2-Deoxyglucose_ox21_p10


title: Methylation_HC2_sp4_Normal_Galactose_ox21_p8


title: Methylation_HC2_sp4_Normal_Galactose_ox21_p11

value: appeared low confluence but quite high count!


title: ChIP-seq GP5d-5-FU TP53

value: Santa-Cruz, sc-126x


title: Methylation_HC1_sp4_Normal_2-Deoxyglucose_ox21_p7

value: Primary Human Fibroblast (breast)


title: Technical_replicate_sp2_Normal__ox21_p_360

data_processing:
360 samples were sent for sequencing; 9 samples did not passed intial QC (low RIN score, high DNA contamination), and 6 samples did not pass post-sequencing QC, for a final of 345 samples.
kallisto alignment v0.44.0 (Bray et al., 2016) using the hg19 genome. Sequence and annotation files were downloaded from the NCBI ftp portal for genome version GRCh37.p13
txi import using lengthScaledTPM (‘tximport’, v1.18.0)
vst normalization (‘DEseq2’, v1.30.1).
log2 transformation
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with log2 transformed vst normalized expression values for every gene and every sample
processed_cell_lifespan_RNAseq_data.csv: log2 vst normalized expression values
raw_counts_cell_lifespan_RNAseq_data.csv: raw counts as outputted by kallisto alignment
txi_transcript_abundance.csv: transcript abundances (‘tximport’, v1.18.0)
txi_transcript_count_lengthScaledTPM.csv: transcript counts length-scaled TPM (‘tximport’, v1.18.0)
txi_transcript_length.csv: transcript lengths (‘tximport’, v1.18.0)
txi_gene_abundance.csv: gene abundances (‘tximport’, v1.18.0)
txi_gene_count_lengthScaledTPM.csv: gene counts length-scaled TPM (‘tximport’, v1.18.0)
txi_gene_length.csv: gene lengths (‘tximport’, v1.18.0)

growth_protocol: Primary human dermal fibroblasts were obtained from distributor or in local clinic from 4 healthy and 3 SURF1-patient donors (IRB #AAAB0483). Fibroblasts were isolated from biopsy tissue using standard centrifugation procedure. After isolation, fibroblasts were stored in 10% DMSO (Sigma-Aldrich #D4540), 90% fetal bovine serum (FBS, Life Technologies #10437036) in cryogenic tube under liquid nitrogen. To avoid freeze-shock necrosis cells were frozen gradually in an isopropanol container (Thermofisher #5100-0001) at -80°C overnight before storage in liquid nitrogen. Cells were thawed by placement in 37°C (<4min) and immediately transferred to 20ml of preheated DMEM (Invitrogen #10567022). Cells were cultured in T175 flasks (Eppendorf #0030712129) at standard 5% CO2 and atmospheric O2 at 37°C in DMEM (5.5 mM glucose) supplemented 10% FBS, 50 μg/ml uridine (Sigma-Aldrich #U6381), 1% MEM non-essential amino acids (Life Technologies #11140050), 10 μM palmitate (Sigma-Aldrich #P9767) conjugated to 1.7 μM  BSA (Sigma-Aldrich #A8806), and 0.001% DMSO (treatment-matched, Sigma-Aldrich #D4540). Cells were passaged approximately every 5 days (+/- 1 day). Brightfield microscopy images (10x, 20x magnification) were taken before each passaged using inverted phase-contrast microscope (Fisher Scientific #11350119). Cell counts, volume and death were determined at each passage using the Countess II Automated Cell Counter (ThermoFisher Scientific #A27977). Growth rates were used to determine replating density, by pre-calculating number cells needed to reach ~90% confluency (~2.5 million cells) at time of next passage. Cells were never plated below 200,000 cells or above 2.5 million cells to avoid plating artifacts of isolation or contact inhibtion, respectively. Study measurements and treatment began after 15-days of culturing post-thaw to allow for adjustment to in vitro environment. Individual cell lines were terminated after exhibiting less than one population doubling over a 30-day period. Mycoplasma testing was performed on media across the full sampleset with no detectable infection.

extract_protocol:
Total genomic RNA was isolated every ~11days across cellular lifespan and stored in 1ml trysol (Invitrogen cat#15596026). RNA was extracted on-column using a RNeasy kit (Qiagen cat# 74104), DNase treated according to the manufacturer’s instructions, and quantified using the QUBIT high sensitivity kit (Thermo Fisher Scientific cat#Q32852). RNA samples underwent QC on bioanalyzer and Nanodrop 2000, all samples had a RIN score >8.0 and no detectable levels of DNA. For cDNA library preparation,1,500ng of RNA at 50ng/μl was processed using Ribo-Zero Gold purification (QIAseq FastSelect -rRNA HMR Kit #334387) and NEBNext® Ultra™ II RNA Library Prep Kit (Illumina #E7770L))  (1,500ng/sample, 50ng/μl). cDNA was sequenced using paired-end 150bp chemistry on a HiSeq 4000 instrument (Illumina, single index, 10 samples/lane, Genewiz Inc), yielding  ~40 million reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment conditions include chronic addition (dosed at every passage) of 100nM dexamethasone (DEX, Sigma-Aldrich #D4902), mitoNUITs; a combination of a) 2μM UK5099 (Sigma-Aldrich #PZ0160) b) 4μM Etomoxir (Sigma-Aldrich #E1905) c) 3μM BPTES t (Sigma-Aldrich #SML0601), 5.5mM galactose (Sigma-Aldrich #G5388), 1nM oligomycin (Oligo, Sigma-Aldrich #75351), 1mM 2-deoxy-d-glucose (2DG, Sigma-Aldrich #D3179), 10mM beta-hydroxybutyrate (Sigma-Aldrich #54965), contact inhibition (allowing cells to fill up the dish and enter a quiescent state), hypoxia (3% oxygen), and acute treatment (10days) of 1μg/mL 5-azacytidine (Sigma-Aldrich #A2385).

value: Control


title: Methylation_HC2_sp4_Normal_Galactose_ox21_p7

value: female


title: Methylation_HC2_sp4_Normal_2-Deoxyglucose_ox21_p7


title: Methylation_HC2_sp4_Normal_Galactose_ox21_p6

value: Failed to aspirate PBS before trypsinization. Trypsin didn't fully separate cells from flask, so used 10 ml pipette to wash plate with the PBS/Trypsin mixture, neutralized with 16 mL media, then re-trypsinized with 3 mL trypsin @ 4 min in 37C incubator, neutralized with 12 mL media.


title: Technical_replicate_sp2_Normal__ox21_p_359


title: HC2_sp4_Normal_betahydroxybutyrate_ox21_p18

value: betahydroxybutyrate


title: ChIP-seq GP5d-Control TP53

value: colon cancer cell line

value: Mock control

value: GP5d cell line


title: Methylation_HC2_sp4_Normal_Galactose_ox21_p5


title: Methylation_HC1_sp4_Normal_Galactose_ox21_p11

value: Measurements had large variability w/r/t count, so values presented are an average of 3 measures. Actual measures were .651, 1.26, and .856 Mcells/mL


title: HC2_sp4_Normal_betahydroxybutyrate_ox21_p13


title: HC2_sp4_Normal_betahydroxybutyrate_ox21_p15


title: HC2_sp4_Normal_betahydroxybutyrate_ox21_p11


title: Methylation_HC1_sp4_Normal_Galactose_ox21_p10


title: Methylation_HC1_sp4_Normal_Galactose_ox21_p9


title: HC2_sp4_Normal_betahydroxybutyrate_ox21_p9


title: HC2_sp4_Normal_betahydroxybutyrate_ox21_p17


title: HC2_sp4_Normal_betahydroxybutyrate_ox21_p5


title: Methylation_HC1_sp4_Normal_Galactose_ox21_p8


title: HC2_sp4_Normal_2-Deoxyglucose_ox21_p25


title: Methylation_HC2_sp4_Normal_Control_ox21_p11


title: Methylation_HC2_sp4_Normal_Control_ox21_p10


title: HC2_sp4_Normal_2-Deoxyglucose_ox21_p24


title: Methylation_HC1_sp4_Normal_Galactose_ox21_p5


title: HC2_sp4_Normal_2-Deoxyglucose_ox21_p20


title: Methylation_HC2_sp4_Normal_Control_ox21_p9


title: HC2_sp4_Normal_2-Deoxyglucose_ox21_p22


title: HC2_sp4_Normal_2-Deoxyglucose_ox21_p19


title: Methylation_HC2_sp4_Normal_Control_ox21_p8


title: HC2_sp4_Normal_betahydroxybutyrate_ox21_p7


title: Methylation_HC1_sp4_Normal_Galactose_ox21_p6


title: Methylation_HC1_sp4_Normal_Galactose_ox21_p7


title: HC2_sp4_Normal_2-Deoxyglucose_ox21_p17


title: Methylation_HC2_sp4_Normal_betahydroxybutyrate_ox21_p5


title: HC2_sp4_Normal_2-Deoxyglucose_ox21_p13


title: HC2_sp4_Normal_2-Deoxyglucose_ox21_p11


title: Methylation_HC2_sp4_Normal_Control_ox21_p3

value: Intial Thawing


title: Methylation_HC2_sp4_Normal_Control_ox21_p7

value: Normal


title: Methylation_HC1_sp4_Normal_Control_ox21_p11

value: three measurements of trypan blue due to large variance between first and second measurement, so the values presented in the column here are the average - each measure was 1.73, .897, and 1.18 Mcells/mL.


title: HC2_sp4_Normal_2-Deoxyglucose_ox21_p15


title: Methylation_HC2_sp4_Normal_Control_ox21_p6


title: Methylation_HC2_sp4_Normal_Control_ox21_p5


title: Methylation_HC1_sp4_Normal_Control_ox21_p5

value: male


title: Methylation_HC2_sp4_Normal_Control_ox21_p4

value: Plating into T175s for growth pre treatment


title: Methylation_HC1_sp4_Normal_Control_ox21_p9


title: Methylation_HC1_sp4_Normal_Control_ox21_p6

value: Insufficient trypsinization may have caused artificially low count


title: Methylation_HC1_sp4_Normal_Control_ox21_p4


title: Methylation_HC1_sp4_Normal_Control_ox21_p7


title: Methylation_HC1_sp4_Normal_Control_ox21_p3


title: Methylation_HC1_sp4_Normal_Control_ox21_p10


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox3_p6_pdt80


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox3_p6_pdt60


title: HC2_sp4_Normal_Galactose_ox21_p11

value: Galactose

value: appeared low confluence but quite high count!


title: HC2_sp4_Normal_Galactose_ox21_p15

value: Primary Human Fibroblast (breast)


title: HC2_sp4_Normal_Galactose_ox21_p13


title: HC2_sp4_Normal_Galactose_ox21_p9


title: HC2_sp4_Normal_Galactose_ox21_p25


title: Methylation_HC1_sp4_Normal_Control_ox21_p8

value: Control


title: HC2_sp4_Normal_2-Deoxyglucose_ox21_p5

value: female

value: Treatment Start


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox3_p6_pdt120


title: HC2_sp4_Normal_2-Deoxyglucose_ox21_p7


title: HC2_sp4_Normal_2-Deoxyglucose_ox21_p9


title: HC2_sp4_Normal_Galactose_ox21_p5


title: HC2_sp4_Normal_Galactose_ox21_p19


title: HC2_sp4_Normal_Control_ox21_p25


title: HC2_sp4_Normal_Galactose_ox21_p17


title: HC2_sp4_Normal_Galactose_ox21_p20


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox3_p6_pdt100


title: HC2_sp4_Normal_Galactose_ox21_p7


title: HC2_sp4_Normal_Control_ox21_p23


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt100


title: HC2_sp4_Normal_Control_ox21_p19


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox3_p6_pdt0


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt120


title: HC2_sp4_Normal_Control_ox21_p20


title: HC2_sp4_Normal_Control_ox21_p18


title: HC2_sp4_Normal_Control_ox21_p17


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox3_p6_pdt20


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt80


title: HC2_sp4_Normal_Control_ox21_p16


title: HC2_sp4_Normal_Control_ox21_p12


title: HC2_sp4_Normal_Control_ox21_p11


title: HC2_sp4_Normal_Control_ox21_p15


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt120

source_name: Primary Human Fibroblast (upper arm)

value: Primary Human Fibroblast (upper arm)


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt20


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt80


title: HC2_sp4_Normal_Control_ox21_p14


title: HC2_sp4_Normal_Control_ox21_p8


title: HC2_sp4_Normal_Control_ox21_p13


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt0


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt60


title: Normal.kidney_methyl

hyb_protocol: Whole genome amplified DNA samples are then fragmented, precipitated, resuspended and hybridized to EPIC BeadChip. On EPIC array 8 samples can be loaded on each chip. The chips are incubated overnight for allele specific hybridization and washed next day to remove unhybridized and nonspecifically hybridized DNA. Following wash chips undergo single base extension and staining. Two bead types correspond to each CpG locus, one bead type corresponds to methylated (C) another bead type to unmethylated (T) site.

scan_protocol: Chips are scanned using Illumina iScan system. BeadChips are scanned using the Illumina BeadArray Reader with High-Density (HD) Technology and BeadScan software.

data_processing: BeadStudio software v3.2. Raw image data is processed using Illumina’s GenomeStudio V2011.1.

label_protocol: The DNA samples will be treated with sodium bisulfite using an Illumina specific bisulfite convertion kit (Zymo EZ DNA methylation kit).

extract_protocol: DNA samples will be quantitated using fluorometric method like picogreen of Qubit and 500ng DNA will be plated in 96 well pates as per layout suitable for 8 sample EPIC chip format.

treatment_protocol: Standard Illumina Protocol

value: kidney


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt40


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt60


title: HC2_sp4_Normal_Control_ox21_p6


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt40


title: HC2_sp4_Normal_Control_ox21_p7


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt20


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt100


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt0


title: HC2_sp4_Normal_Control_ox21_p9


title: ChIP-seq GP5d FOXA1

value: colon cancer cell line

value: Untreated

value: Abcam, ab23738


title: HC2_sp4_Normal_Control_ox21_p5


title: HC2_sp4_Normal_Control_ox21_p4


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt100


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt120


title: HC2_sp4_Normal_Control_ox21_p10


title: HC1_sp4_Normal_betahydroxybutyrate_ox21_p25

value: betahydroxybutyrate


title: HC1_sp4_Normal_betahydroxybutyrate_ox21_p24

value: Normal


title: HC1_sp4_Normal_betahydroxybutyrate_ox21_p22


title: HC1_sp4_Normal_betahydroxybutyrate_ox21_p20


title: HC1_sp4_Normal_betahydroxybutyrate_ox21_p18


title: Tumor_methyl

value: Tumor


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt40


title: HC1_sp4_Normal_betahydroxybutyrate_ox21_p16

value: male


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt80


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt60


title: HC1_sp4_Normal_betahydroxybutyrate_ox21_p13


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt0


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt120


title: Methylation_HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt20


title: HC1_sp4_Normal_betahydroxybutyrate_ox21_p9


title: HC1_sp4_Normal_betahydroxybutyrate_ox21_p7


title: HC1_sp4_Normal_betahydroxybutyrate_ox21_p11


title: HC1_sp4_Normal_betahydroxybutyrate_ox21_p5


title: HC1_sp4_Normal_2-Deoxyglucose_ox21_p25


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt60


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt40


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt80


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt100


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt20


title: Methylation_HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt0


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt100


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt120


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt80


title: HC1_sp4_Normal_2-Deoxyglucose_ox21_p20


title: HC1_sp4_Normal_2-Deoxyglucose_ox21_p22


title: HC1_sp4_Normal_2-Deoxyglucose_ox21_p24


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt60


title: HC1_sp4_Normal_2-Deoxyglucose_ox21_p16


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt40


title: HC1_sp4_Normal_2-Deoxyglucose_ox21_p18


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt0


title: HC1_sp4_Normal_2-Deoxyglucose_ox21_p15


title: Methylation_HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt20


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_Regrowth_ox21_p22

source_name: Primary Human Fibroblast (forearm)

value: Primary Human Fibroblast (forearm)


title: HC1_sp4_Normal_2-Deoxyglucose_ox21_p9


title: HC1_sp4_Normal_2-Deoxyglucose_ox21_p11


title: HC1_sp4_Normal_2-Deoxyglucose_ox21_p13


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_Regrowth_ox21_p20


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_Regrowth_ox21_p17


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_Regrowth_ox21_p15


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_Regrowth_ox21_p13


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_Regrowth_ox21_p9


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_Regrowth_ox21_p7


title: HC1_sp4_Normal_2-Deoxyglucose_ox21_p5


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_Regrowth_ox21_p11


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_Regrowth_ox21_p6


title: HC1_sp4_Normal_Galactose_ox21_p25


title: HC1_sp4_Normal_Galactose_ox21_p22


title: HC1_sp4_Normal_Galactose_ox21_p20


title: HC1_sp4_Normal_Galactose_ox21_p24


title: HC1_sp4_Normal_Galactose_ox21_p18


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_ox21_p5_pdt80


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_ox21_p5_pdt120


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_ox21_p5_pdt100


title: HC1_sp4_Normal_Galactose_ox21_p15


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_ox21_p5_pdt60


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_ox21_p5_pdt20


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_ox21_p5_pdt40


title: HC1_sp4_Normal_Galactose_ox21_p11

value: Measurements had large variability w/r/t count, so values presented are an average of 3 measures. Actual measures were .651, 1.26, and .856 Mcells/mL


title: HC1_sp4_Normal_Control_ox21_p5


title: HC1_sp4_Normal_2-Deoxyglucose_ox21_p7


title: HC1_sp4_Normal_Control_ox21_p6

value: Insufficient trypsinization may have caused artificially low count


title: Methylation_HC2_sp3_Normal_DEX_ox3_p13

value: DEX


title: HC1_sp4_Normal_Control_ox21_p4

value: Primary Human Fibroblast (breast)

value: Plating into T175s for growth pre treatment


title: HC1_sp4_Normal_Galactose_ox21_p13

value: Galactose


title: Methylation_HC2_sp3_Normal_DEX_ox3_p11

value: female


title: HC2_sp3_Normal_Contact_Inhibition_ox3_p6_pdt100


title: Methylation_HC2_sp3_Normal_DEX_ox3_p10


title: Methylation_HC2_sp3_Normal_DEX_ox3_p12


title: HC2_sp3_Normal_Contact_Inhibition_ox3_p6_pdt120


title: Methylation_HC2_sp3_Normal_DEX_ox3_p6

value: Treatment Start


title: Methylation_HC2_sp3_Normal_DEX_ox3_p9


title: HC2_sp3_Normal_Contact_Inhibition_ox3_p6_pdt60


title: Methylation_HC2_sp3_Normal_DEX_ox3_p7


title: HC2_sp3_Normal_Contact_Inhibition_ox3_p6_pdt80


title: HC1_sp4_Normal_Control_ox21_p25

value: Control


title: HC2_sp3_Normal_Contact_Inhibition_ox3_p6_pdt20


title: HC1_sp4_Normal_Control_ox21_p22


title: HC1_sp4_Normal_Control_ox21_p20


title: HC1_sp4_Normal_Control_ox21_p7


title: Methylation_HC1_sp3_Normal_DEX_ox3_p13


title: Methylation_HC1_sp3_Normal_DEX_ox3_p12


title: HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt120


title: HC2_sp3_Normal_Contact_Inhibition_ox3_p6_pdt0


title: Methylation_HC5_sp2_Normal_Contact_Inhibition_ox21_p5_pdt0


title: Methylation_HC1_sp3_Normal_DEX_ox3_p11


title: Methylation_HC1_sp3_Normal_DEX_ox3_p10


title: Methylation_HC1_sp3_Normal_DEX_ox3_p9


title: HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt80


title: HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt40


title: HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt60


title: Methylation_HC1_sp3_Normal_DEX_ox3_p7


title: HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt20


title: HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt0


title: HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt120

value: Primary Human Fibroblast (upper arm)


title: Methylation_HC1_sp3_Normal_DEX_ox3_p8


title: Methylation_HC4_sp3_Normal_DEX_ox3_p15


title: Methylation_HC1_sp3_Normal_DEX_ox3_p6


title: HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt60


title: HC1_sp3_Normal_Contact_Inhibition_ox3_p6_pdt100


title: HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt80


title: Methylation_HC4_sp3_Normal_DEX_ox3_p13


title: Methylation_HC4_sp3_Normal_DEX_ox3_p12


title: Methylation_HC4_sp3_Normal_DEX_ox3_p16


title: Methylation_HC4_sp3_Normal_DEX_ox3_p11


title: HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt20


title: Methylation_HC4_sp3_Normal_DEX_ox3_p14


title: HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt0


title: HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt100


title: HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt120


title: Methylation_HC2_sp3_Normal_Control_ox3_p13


title: Methylation_HC4_sp3_Normal_DEX_ox3_p10


title: Methylation_HC4_sp3_Normal_DEX_ox3_p9


title: Methylation_HC2_sp3_Normal_Control_ox3_p12


title: HC4_sp3_Normal_Contact_Inhibition_ox3_p9_pdt40


title: HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt80


title: HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt100


title: Methylation_HC2_sp3_Normal_Control_ox3_p10


title: HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt60


title: Methylation_HC2_sp3_Normal_Control_ox3_p9


title: HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt40


title: Methylation_HC2_sp3_Normal_Control_ox3_p8


title: Methylation_HC2_sp3_Normal_Control_ox3_p7


title: HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt20


title: HC2_sp3_Normal_Contact_Inhibition_ox21_p6_pdt0


title: Methylation_HC2_sp3_Normal_Control_ox3_p5


title: HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt100


title: Methylation_HC1_sp3_Normal_Control_ox3_p13


title: HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt60


title: Methylation_HC1_sp3_Normal_Control_ox3_p12


title: HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt80


title: Methylation_HC1_sp3_Normal_Control_ox3_p10


title: Methylation_HC1_sp3_Normal_Control_ox3_p9


title: HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt40


title: Methylation_HC1_sp3_Normal_Control_ox3_p6


title: Methylation_HC2_sp3_Normal_Control_ox3_p11


title: Methylation_HC1_sp3_Normal_Control_ox3_p5


title: Methylation_HC1_sp3_Normal_Control_ox3_p8


title: Methylation_HC1_sp3_Normal_Control_ox3_p7


title: 2256_stem cultivar

city: Chuncheon

first: Prakash

last: Basnet

state: Gangwon-do

address: Department of Agriculture and Life Industry, Kangwon National University, Bldg. Asangwan Rm.424, 1 K

department: Agriculture and Life Industries

country: South Korea

institute: Kangwon National University

data_processing:
Trimmomatic v0.36
Trimmomatic sliding window (4:20)
HITSAT2 v2.1.0
String Tie v1.3.4d
DESeq V1.36.0 (for DEGs analysis)
Genome_build: Glycine max Wm82.a2. v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Glycine max

source_name: Stem tissue

growth_protocol: The soybean plants were grown in field, greenhouse and growth room

extract_protocol:
The leaves, stems, and nodes from 12-week-old plants were sampled and harvested immediately in frozen liquid nitrogen (N) for RNA isolation using Genall Ribospin. Illumina Nova SeqHigh-trhroughput platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Stem tissue

tag: developmental stage

value: 45 days plant

tag: genotype

value: Wild type

tag: cultivar


title: HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt100

value: Normal


title: 2256_leaf cultivar

source_name: Leaf tissue

value: Leaf tissue


title: HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt20

value: male


title: HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt120


title: HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt0


title: 2256_Node cultivar

source_name: Node tissue

value: Node tissue


title: Methylation_HC2_sp3_Normal_Control_ox3_p6


title: HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt80


title: HC1_sp3_Normal_Contact_Inhibition_ox21_p6_pdt120


title: HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt60


title: Methylation_HC4_sp3_Normal_Control_ox3_p13


title: Methylation_HC4_sp3_Normal_Control_ox3_p15


title: Methylation_HC4_sp3_Normal_Control_ox3_p14


title: Methylation_HC4_sp3_Normal_Control_ox3_p12


title: 2255_stem weedy

value: 2255 weedy


title: Methylation_HC4_sp3_Normal_Control_ox3_p11


title: HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt40


title: Methylation_HC4_sp3_Normal_Control_ox3_p10


title: Methylation_HC4_sp3_Normal_Control_ox3_p9


title: 2255_leaf weedy


title: Methylation_HC4_sp3_Normal_Control_ox3_p8


title: HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt20


title: Bicellular_Pollen_PARE

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

description: 5-P RNA

data_processing:
Library strategy: PARE-seq
sRNAs were trimmed using Trim Galore
sRNAs were mapped to the Arabidopsis thaliana chromosome sequences from the TAIR10 genome version. For sRNAs two mismatches were allowed while PARE reads were aligned with 0 mismatches. For miRNA accumulation annalysis, sRNAs were aligned to miRbase version 21 allowing two mismatches. In all cases Bowtie-1.1.2 was used for performing the alignments.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed files were generated using Galaxy.

organism: Arabidopsis thaliana

source_name: Bicellular pollen grain

growth_protocol: Plants were grown under standard long day conditions at 22 °C.

extract_protocol:
RNA was extracted using Trizol (Invitrogen)
sRNA libraries were prepared according to NEBNext Small RNA Library Prep Set for Illumina. PARE libraries were constructed according to Zhai et al (2014) (DOI:10.1016/j.ymeth.2013.06.025). AGO immunoprecipitations were prepared according to McCue et al (2012) (doi: 10.1371/journal.pgen.1002474).

tag: ecotype

value: Columbia 0 wild type

value: Bicellular pollen grain


title: 2255_Node weedy

tag: tissue


title: Unicellular_Pollen_AGO5_IP

description: small RNAs (18-28 nts)

data_processing:
sRNAs were trimmed using Trim Galore
sRNAs were mapped to the Arabidopsis thaliana chromosome sequences from the TAIR10 genome version. For sRNAs two mismatches were allowed while PARE reads were aligned with 0 mismatches. For miRNA accumulation annalysis, sRNAs were aligned to miRbase version 21 allowing two mismatches. In all cases Bowtie-1.1.2 was used for performing the alignments.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed files were generated using Galaxy.

source_name: Unicellular pollen grain

value: Unicellular pollen grain


title: HC4_sp3_Normal_Contact_Inhibition_ox21_p9_pdt0


title: Methylation_HC4_sp3_Normal_Control_ox3_p16


title: Methylation_HC2_sp3_Normal_DEX_ox21_p11

value: Primary Human Fibroblast (breast)

value: DEX


title: Unicellular_Pollen_AGO1_IP

description: small RNAs (18-28 nts)


title: HC2_sp3_Normal_Control_ox3_p13

value: female


title: Methylation_HC2_sp3_Normal_DEX_ox21_p13


title: Methylation_HC2_sp3_Normal_DEX_ox21_p10


title: Methylation_HC2_sp3_Normal_DEX_ox21_p8


title: Methylation_HC2_sp3_Normal_DEX_ox21_p6

value: Treatment Start


title: Methylation_HC1_sp3_Normal_DEX_ox21_p13


title: HC2_sp3_Normal_Control_ox3_p9

value: Control


title: HC2_sp3_Normal_Control_ox3_p11


title: Methylation_HC1_sp3_Normal_DEX_ox21_p12


title: Mature_pollen_PARE, bioreplicate2

source_name: Mature pollen grain

value: Mature pollen grain

tag: molecule

value: PARE RNAs (18-28 nts)


title: HC2_sp3_Normal_Control_ox3_p7

tag: Sex


title: Methylation_HC2_sp3_Normal_DEX_ox21_p12

tag: treatments


title: Mature_pollen_PARE, bioreplicate3


title: Methylation_HC1_sp3_Normal_DEX_ox21_p9

tag: passage


title: Methylation_HC1_sp3_Normal_DEX_ox21_p7

tag: slide


title: Unicellular_Pollen_AGO_Input

description: small RNAs (18-28 nts)


title: Methylation_HC1_sp3_Normal_DEX_ox21_p10

tag: array


title: HC2_sp3_Normal_Control_ox3_p5


title: Methylation_HC1_sp3_Normal_DEX_ox21_p8

tag: well


title: Mature_pollen_PARE, bioreplicate1


title: HC1_sp3_Normal_Control_ox3_p13


title: Methylation_HC1_sp3_Normal_DEX_ox21_p6


title: Unicellular_pollen_PARE, bioreplicate2


title: Methylation_HC4_sp3_Normal_DEX_ox21_p16

value: Primary Human Fibroblast (upper arm)


title: Methylation_HC4_sp3_Normal_DEX_ox21_p14


title: Unicellular_pollen_PARE, bioreplicate1


title: HC1_sp3_Normal_Control_ox3_p11


title: HC1_sp3_Normal_Control_ox3_p9


title: Methylation_HC4_sp3_Normal_DEX_ox21_p12


title: Methylation_HC4_sp3_Normal_DEX_ox21_p13


title: Methylation_HC4_sp3_Normal_DEX_ox21_p9


title: HC1_sp3_Normal_Control_ox3_p7


title: Methylation_HC4_sp3_Normal_DEX_ox21_p10


title: Mature_pollen_sRNAs

value: small RNAs (18-28 nts)


title: Methylation_HC2_sp3_Normal_Control_ox21_p13

value: Normal


title: Tricellular_pollen_sRNAs

source_name: Tricellular pollen grain


title: HC1_sp3_Normal_Control_ox3_p5


title: Methylation_HC2_sp3_Normal_Control_ox21_p12


title: Methylation_HC2_sp3_Normal_Control_ox21_p10


title: Bicellular_pollen_sRNAs


title: HC4_sp3_Normal_Control_ox3_p16


title: Methylation_HC4_sp3_Normal_DEX_ox21_p15


title: Unicellular_pollen_sRNAs


title: HC4_sp3_Normal_Control_ox3_p14


title: Methylation_HC2_sp3_Normal_Control_ox21_p8


title: Mature_Leaf_PARE

source_name: Rosette leaves

value: 5-P RNA


title: Methylation_HC2_sp3_Normal_Control_ox21_p9


title: Mature_Pollen_AGO1_Input


title: Methylation_HC2_sp3_Normal_Control_ox21_p7


title: HC4_sp3_Normal_Control_ox3_p10

value: male


title: HC4_sp3_Normal_Control_ox3_p12


title: Mature_Pollen_AGO1_IP


title: Methylation_HC2_sp3_Normal_Control_ox21_p6


title: Methylation_HC1_sp3_Normal_Control_ox21_p12


title: Methylation_HC1_sp3_Normal_Control_ox21_p11


title: Methylation_HC1_sp3_Normal_Control_ox21_p10


title: Mature_Pollen_AGO5_Input


title: HC4_sp3_Normal_DEX_ox21_p16


title: Mature_Pollen_AGO5_IP


title: HC4_sp3_Normal_DEX_ox21_p15


title: Methylation_HC1_sp3_Normal_Control_ox21_p7


title: Methylation_HC2_sp3_Normal_Control_ox21_p11


title: HC4_sp3_Normal_DEX_ox21_p14


title: Methylation_HC4_sp3_Normal_Control_ox21_p15

value: Infected


title: Methylation_HC4_sp3_Normal_Control_ox21_p13


title: HC4_sp3_Normal_DEX_ox21_p13


title: Methylation_HC4_sp3_Normal_Control_ox21_p14


title: KO Tregs Rep 2

city: Buffalo

first: Jie

last: Yu

address: 955 Main Street

department: Department of Obstetrics and Gynecology

institute: SUNY Buffalo

description: 3 mice pooled

data_processing:
Basecalling bcl2fastq v2.20.0.422 (default parameters)
Alignment hisat2 v2.1.0 (default parameters)
Quantification featureCounts v1.6.2 ("-s" "0" "-g" "gene_id" "-t" "exon")
Genome_build: Illumina igenomes UCSC/mm10
Supplementary_files_format_and_content: Processed data is tab separated output file as produced by featureCounts which is part of the subread package.

extract_protocol: none provided by the submitter

value: Spleen

tag: day of infection


title: KO Tregs Rep 3

description: 3 mice pooled


title: HC4_sp3_Normal_Control_ox3_p8


title: Methylation_HC1_sp3_Normal_Control_ox21_p9


title: HC4_sp3_Normal_DEX_ox21_p12


title: KO Tregs Rep 1

description: 3 mice pooled


title: WT Tregs Rep 3

description: 3 mice pooled


title: Methylation_HC2_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p29


title: Methylation_HC4_sp3_Normal_Control_ox21_p12


title: Methylation_HC2_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p25


title: Methylation_HC2_sp2_Normal_5-azacytidine+mitoNUITs_ox21_p23


title: Methylation_HC1_sp3_Normal_Control_ox21_p6


title: HC4_sp3_Normal_DEX_ox21_p11