title: TAGMe_RNA_GM12878_rep3

description: TAGMe-seq RNA library on GM12878 cell line, rep3

data_processing:
library strategy: TAGMe-seq
DNA part:Raw reads were first trimmed by using Trim Galore! (v0.6.6, with Cutadapt v2.10) with parameters “--paired_end --clip_R1 5 --clip_R2 5 --three_prime_clip_R1 5 --three_prime_clip_R2 5” to remove the adapters and low-quality reads. The clipped length was determined based on the composition of base pairs along the sequencing cycle by FastQC (v0.11.9). The reference genome (b37, human_g1k_v37.fa) was in silico converted to make C/T reference (all Cs were converted to Ts) and G/A reference (all Gs were converted to As). Paired-end reads were mapped by our previously developed bhmem (v0.37) to each converted reference. Only uniquely mapped and mapping quality passed reads (mapQ>30) on both ends were joined. Reads marked as PCR duplicated reads were filtered. The reads with incompletely converted cytosine (WCH, W=A or T, H=A, C, or T) were filtered out. Joint read pairs with more than 20kb insertion size were considered as long-range interactions and subjected to the following interaction analysis. Bam files were further converted to .hic files for the following 3D genome analysis similar to Hi-C data. HCG methylation and GCH accessibility level were calculated by bissnp_easy_usage.pl with Bis-SNP (v0.90) in NOMe-seq mode. Only bases with a quality score of more than 5 were included in the downstream methylation analysis.
RNA part: Raw reads were first trimmed as paired-end reads using Trim Galore! (v0.6.6, with Cutadapt v2.10) with parameters “--paired_end --clip_R1 15 --clip_R2 15 --three_prime_clip_R1 5 --three_prime_clip_R2 5” to remove the adapters and low-quality reads. The clipped length was determined based on the composition of base pairs along the sequencing cycle by FastQC (v0.11.9). Both alignment-based (STAR, v2.7.6a20 ,and  RNA-SeQC, v2.3.521) or alignment-free (Salmon, v1.5.122) approaches were tried. Salmon was finally used for the bias correction, visualization, and data analysis due to the slightly better concordance with the RNA-seq in ENCODE. The reference transcriptome was obtained from Gencode (v33lift37) and indexed by Salmon with k=31. The parameter used for Salmon quantification was: “quant --seqBias --gcBias --posBias -l A --validateMappings”. The differential expression analysis was performed on gene-level by the edgeR (3.32.1) package in R (4.0.5). Only genes with FDR<0.05 and log2 fold change > 1 were considered as the differential expressed genes between IMR-90 and GM12878.
Genome_build: hg19
Supplementary_files_format_and_content: vcf.gz (snp genotype); hic (3D genome); bed (HCG or GCH methylation level); gene.sf (quantification of gene expression)

tag: cell type

value: B-lymphoblastoid cell line


title: MED8A SMARCD3 WT rep 1

status: Public on Feb 28 2023

type: SRA

city: Pittsburgh

first: Baoli

last: Hu

state: PA

address: 4401 Penn Ave

department: Neurological Surgery

country: USA

institute: University of Pittsburgh School of Medicine

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trim Glare (v.0.6.4_dev) and Cutadapt (v.2.6).
Trimmed reads were mapped to hg38 whole genome using Hisat2 (v.2.1.0).
Count matrix was calculated using FeatureCounts (v.1.6.4).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for each sample and gene.

molecule: total RNA

organism: Homo sapiens

source_name: MED8A cell line

extract_protocol:
RNeasy Plus Mini Kit (Catlog#74134; Qiagen) was used for RNA extraction.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

tag: genotype

value: WT


title: TALL_03

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

description: T-ALL Primary Tissue Cancer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC version 2.0 using standard Illumina protocol

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

data_processing: GenomeStudio

label: Cy5 and Cy3

molecule: genomic DNA

source_name: T-cell acute lymphoblastic leukaemia

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from the different samples using Qiagen DNeasy Kit according to standard instructions

tag: tissue

value: T-ALL

tag: tissue source

value: Primary Tissue

tag: healthy/tumor

value: Cancer


title: R2-D3-LK-H3K27me3

city: STANFORD

first: Katja

last: Pekrun

state: CA

address: 269 Campus Drive

department: Pediatrics & Genetics

institute: Stanford School of Medicine

library_source: genomic

data_processing:
Reads were trimmed with Trimmomatic-0.39 program for classical Illumina adapters. Aligned using Bowtie2 version 2.2.5 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.5/) with options: --local --very-sensitive-local --nounal --no-mixed --no-discordant --phred33 -I 10 -X 700; mapping was performed using the mm10 build of the mouse genome, merged with viral genome sequence (gAAV).
PCR duplicates were eliminated with “MarkDuplicates” command of Picard version 2.23 (https://broadinstitute.github.io/picard/index.html).
Tracks were made as bedgraph files of normalized counts, using deeptools 3.3 (https://deeptools.readthedocs.io/en/develop/content/list_of_tools.html) bamCoverage with options: --binSize 1, --normalizeUsing CPM; track plots were made with R package Gviz 4.1. Coverage was calculated as SUM[(normalized count*(end-start position+1))/gAAV size] for each dataset. Importantly, ITR regions were removed from the calculation, as their coverage is overrepresented in all samples, perhaps due to recognition of ITRs from ssDNA.
Assembly: mm10
Supplementary files format and content: Bedgraph
Library strategy: Cut & Tag

organism: Mus musculus

source_name: Liver

extract_protocol:
Mice were sacrificed 3 or 15 days after rAAV injection and liver tissue was flash-frozen in aliquots. Liver tissue (~100 mg) was homogenized in RINO 1.5-ml Screw-Cap tubes filled with stainless steel beads and 1mL of NE buffer using a bead homogenizer (Next Advance Bullet Blender Storm - BBY24M) at speed 8 for 4 minutes. The homogenate was transferred into to a 50mL tube with 12mL of NE buffer and incubated on ice for 10 min. Nuclei were pelleted by a 5 min centrifugation at 600g, the supernatant was decanted, and the pellet was resuspended in 1mL of NE buffer. Nuclei were quantitated after Trypan Blue staining using an automated cell counter (Countess, Thermo Fisher) and diluted accordingly. 1e5 nuclei per target protein were used for Cut&Tag.
Nuclei were mixed with activated Concanavalin A beads. After successive incubations with primary antibody (overnight) and secondary antibody (for 30 min) in antibody and Digitonin150 buffer respectively, the beads were washed with Digitonin150 buffer and resuspended in Digitonin300 buffer with 2.5uL of pA(G)-Tn5 for 1 hr and washed with the same buffer. Incubations were performed at room temperature in low-retention PCR strip tubes (Epicypher). Tagmentation was performed for 1 hr at 37C in Tagmentation buffer that provides MgCl2. Beads were washed with TAPS buffer and DNA material was released by adding SDS Release Buffer and incubating at 58C for 1hr. Quenching of SDS was performed by adding SDS Quench buffer and PCR was performed directly on this material. Universal P5 and indexed P7 primer solutions were used (see Supplemental Table 3 for sequences), and 21 cycles of PCR were performed. Clean-up was performed with AMPure beads, eluted in 15uL 0.1x TE buffer. Qubit and Bioanalyzer were used to verify library qualities before pooling samples for sequencing. The barcoded libraries were mixed to achieve equimolar representation aiming for a 10nM final concentration.
Cut & Tag. Sequencing was performed with Illumina NovaSeq SP100, 150cycles total per lane (4lanes total), 2x75 paired-end reads, depth of >15M reads per sample.

treatment_protocol: Mice were intravenously injected with rAAV packaged using different capsids. The rAAV vector expressed the firefly luciferase under control of a CAG promoter.

value: Liver

tag: strain

value: BALB/c

tag: antibody


title: EN_FF

description: Endometrium Primary Tissue Healthy

source_name: healthy endometrium primary tissue (formalin-fixed)

value: Endometrium

value: Healthy


title: R2-D3-LK-H3K27ac


title: B73, single-end, rep03

city: Johnston

first: Shawn

last: Thatcher

state: Iowa

address: South Drive

institute: Corteva Agriscience

data_processing:
Low-quality reads and adapter sequences were trimmed using custom scripts
Proccessed reads were quantified using Salmon (version 1.1.0) against the transcriptome of each NAM founder line
Assembly: Respective NAM transcriptomes
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Zea mays

source_name: Leaf

growth_protocol: During the seedling stage, all plants were grown in a greenhouse under 16h/8h light/dark conditions with a total of 25 umol/m2/day of total photosynthetic light, a vapor pressure deficit of 12 mmbar and day/night temperatures of 25/22 ⁰C (week 1), 22/19 ⁰C (week 2), 19/17 ⁰C (week 3) and 17/14 ⁰C (week 4). Because of the photoperiod sensitivity of some NAM founder lines, from week 5 until maturity, plants were grown under 12h/12h day/night conditions, at 26/20 ⁰C day/night temperatures to reduce delayed flowering and maturity.

extract_protocol:
Total RNA was isolated from ground frozen tissue with RNeasy (Qiagen Inc., Valencia, CA), according to manufacturer’s protocol.
Sequencing libraries were prepared according to Illumina Inc. (San Diego, CA) TruSeq mRNA-Seq protocols.

value: Leaf

tag: growth stage


title: TALL_04

description: T-ALL Primary Tissue Cancer


title: CML52, single-end, rep03


title: B73, single-end, rep02


title: B73, single-end, rep01


title: TAGMe_RNA_GM12878_rep2

city: Chicagp

first: Yaping

last: Liu

state: IL

address: 303 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

description: TAGMe-seq RNA library on GM12878 cell line, rep2

growth_protocol: The human lung fibroblast cell line IMR-90 was purchased from ATCC and cultured in EMEM(ATCC) with 10% FBS(Gibco) and 1% penicillin/streptomycin. The human B-lymphoblastoid cell line GM12878 was obtained from CORIELL INSTITUTE and cultured with RPMI-1640 supplemented with 15% FBS and 1% penicillin/streptomycin.

extract_protocol:
After reaching 70~80 confluence, IMR-90 cells were detached with 0.5% Trypsin and harvested by centrifuge at 300g for 5min. GM12878 cells were harvested at a density around 0.7M to 0.8M/mL by centrifuge at 300g for 5min.
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature, then quenched by adding 0.2M Glycine. After washing with ice-cold PBS, cells were suspended in the nuclei isolation buffer with RNase inhibitors and incubated on ice for 1hr. Subsequent to nuclei membrane permineralization, chromatin was digested using 100U DpnII (NEB, R0543L) overnight at 37 ℃ with RNase inhibitors. The next day, DpnII was inactivated, and nuclei suspension was cooled to room temperature and subjected to biotin fill-in. Proximal segments were in situ ligated using T4 DNA ligase (NEB, M0202) supplemented with RNase inhibitors. Then GpC methyltransferase footprint was performed by incubating the nuclei with M.CviPI (NEB, M0227L), and PBS was added to stop the reaction. After that, one-third of the nuclei were separated for RNA isolation using MagMAX™ FFPE DNA/RNA Ultra Kit (Thermo A31881). The total RNA library was prepared using SMARTer® Stranded Total RNA-Seq Kit v2 (TAKARA 634413). The rest of the nuclei were reverse crosslinked, DNA was precipitated and sonicated to average 400bp followed by 1xAMPure beads cleanup. Biotin pulldown was performed using streptavidin beads, DNA on beads was end-repaired, d-A tailed, and ligated with truncated cytosine-methylated X-gene Universal Stubby Adapter (IDT). 0.1%~0.5% unmethylated lambda DNA was spiked-in. Bisulfite conversion was conducted using the EZ DNA Methylation-Gold Kit (D5006). Bisulfite converted DNA library was amplified using truncated TruSeq™–Compatible Indexing Primer and KAPA HiFi Uracil+ ReadyMix (Roche, KK2801), supplemented with MgCl2. Library quality was determined by qPCR and BioAnalyzer 2000 (Agilent Technologies). Pooling of multiplexed sequencing samples, clustering, and sequencing was carried out as recommended by the manufacturer on Illumina HiSeq XTen or NovaSeq S6000 with the 150 paired-end. RNA-seq libraries or Phi-X (20%) were spiked in to overcome the imbalance of  GC ratio of the bisulfite-converted DNA libraries

tag: cell line


title: R2-D3-LK-H2A


title: TALL_02

description: T-ALL Primary Tissue Cancer


title: CML52, single-end, rep02


title: TALL_01

description: T-ALL Primary Tissue Cancer


title: R2-D3-iG-PolII

value: Pol-II


title: TALL_CCL_03

description: T-ALL Cell Line Cancer

source_name: T-cell acute lymphoblastic leukaemia cancer cell line

value: Cell Line


title: R2-D3-iG-H4


title: TAGMe_DNA_GM12878_rep3

description: TAGMe-seq DNA library on GM12878 cell line, rep3

tag: restriction enzyme

value: DpnII

tag: bisulfite conversion

value: Yes


title: Mo18W, single-end, rep03


title: R2-D3-iG-H3


title: TAGMe_RNA_IMR90_rep2

description: TAGMe-seq RNA library on IMR-90 cell line, rep2

value: lung fibroblast cell line


title: TALL_CCL_01

description: T-ALL Cell Line Cancer


title: BALL_05

description: B-ALL Primary Tissue Cancer

source_name: B-cell acute lymphoblastic leukaemia

value: B-ALL


title: TAGMe_DNA_GM12878_rep2

description: TAGMe-seq DNA library on GM12878 cell line, rep2


title: BALL_04

description: B-ALL Primary Tissue Cancer


title: TAGMe_RNA_GM12878_rep1

description: TAGMe-seq RNA library on GM12878 cell line, rep1


title: BALL_03

description: B-ALL Primary Tissue Cancer


title: CML277, single-end, rep03


title: R2-D3-iG-H3K4me3


title: TAGMe_DNA_GM12878_rep1

description: TAGMe-seq DNA library on GM12878 cell line, rep1


title: CML277, single-end, rep02


title: R2-D3-iG-H3K9me3


title: CML52, single-end, rep01


title: TAGMe_DNA_IMR90_rep2

description: TAGMe-seq DNA library on IMR-90 cell line, rep2


title: RNA-seq_COLO205_48

city: ShangHai

first: Tong

last: Han

address: 1239 Siping Road

country: China

institute: Tongji University

data_processing:
fastq files were aligned to  hg38 human genome using STAR (v2.5.3a).
RSEM(v1.2.28) was used to map aligned reads and to generate a gene count matrix.
Gene expression for each sample was quantified to TPM using RSEM(v1.2.28).
Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include raw count and Transcripts Per Kilobase Million (TPM) values for each Sample.

source_name: Colon

growth_protocol: Cancer cells were seeded on 10 cm tissue culture plates in RPMI-1640 medium or DMEM, including 10% fetal bovine serum (FBS), glutamine, and 1% penicillin/ streptomycin. Cells were cultured in an incubator at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen Life Technologies, Gaithersburg, MD, USA) according to the manufacturer.
Purified mRNA was fragmented into short fragments with fragment buffer and cDNAs were synthesized using the RNA fragments as templates for random primer, followed by end reparation and ligation to adapters.

treatment_protocol: After allowing 2-3 passages during exponential growth phase at 80% confluence cells were exposed to IFN-γ at concentration 10 ng/ml for 48 hours (Recombinant Human IFN-gamma Protein(rhIFN-γ) (catalog No. 285-IF-100). Culture media without interferon-gamma was added simultaneously to the controls.

value: Colon cancer cell line

tag: treatment

value: after IFN-gamma treatment(48 hours)

tag: medium

value: RPMI

tag: ifn-gamma sensitivity

value: Resistant


title: RNA-seq_SW620_48

value: DMEM


title: Mo18W, single-end, rep01

value: WT


title: R2-D3-iG-H3K27me3

value: Liver


title: BALL_02

description: B-ALL Primary Tissue Cancer

value: Primary Tissue

value: Cancer


title: R2-D3-iG-H3K27ac

value: BALB/c


title: CML277, single-end, rep01

value: Leaf


title: RNA-seq_HGC27_48

source_name: Stomach

value: Gastric cancer cell line


title: R2-D3-iG-H2A


title: BALL_01

description: B-ALL Primary Tissue Cancer


title: RNA-seq_HUH6_48

value: Hepatoblastoma cell line


title: CML247, single-end, rep03


title: R2-D3-DJ-PolII

value: Pol-II


title: BALL_CCL_03

description: B-ALL Cell Line Cancer

source_name: B-cell acute lymphoblastic leukaemia cancer cell line

value: Cell Line


title: Mo18W, single-end, rep02


title: CML247, single-end, rep02


title: RNA-seq_HCT116_48

source_name: Colorectal


title: R2-D3-DJ-H4


title: BALL_CCL_02

description: B-ALL Cell Line Cancer


title: CML247, single-end, rep01


title: BALL_CCL_01

description: B-ALL Cell Line Cancer


title: Tzi8, single-end, rep02


title: RNA-seq_MCF7_48

source_name: Breast

value: Breast cancer cell line


title: R2-D3-DJ-H3K9me3


title: RNA-seq_HCC827_48

source_name: Lung

value: Lung adenocarcinoma cell line

value: Sensitive


title: RNA-seq_A375_48

source_name: Skin

value: Melanoma cell line

value: after IFN-gamma treatment(48 hours)


title: R2-D3-DJ-H3


title: Oh7B, single-end, rep03


title: Tzi8, single-end, rep01


title: R2-D3-DJ-H3K27me3


title: B_H_04

description: Blood Primary Tissue Healthy

source_name: blood primary tissue

value: Blood

value: Healthy


title: R2-D3-DJ-H3K4me3


title: Oh7B, single-end, rep02

value: WT


title: RNA-seq_NCIH1437_48

value: RPMI


title: B_H_03_bis

description: Blood Primary Tissue Healthy

value: Primary Tissue


title: Oh7B, single-end, rep01


title: B_H_03

description: Blood Primary Tissue Healthy


title: RNA-seq_SW620_0

value: Colon cancer cell line

value: before IFN-gamma treatment

value: DMEM

value: Resistant


title: R2-D15-LK-PolII

value: Liver

value: BALB/c


title: Tx303, single-end, rep03

value: Leaf


title: B_H_02

description: Blood Primary Tissue Healthy


title: Tx303, single-end, rep02


title: B_H_01

description: Blood Primary Tissue Healthy


title: TC_H_02

description: T-cell Primary Tissue Healthy

source_name: T-cells primary tissue

value: T-cell


title: RNA-seq_COLO205_0


title: Tx303, single-end, rep01


title: RNA-seq_MDAMB231_48

value: Breast cancer cell lines


title: CML69, single-end, rep03


title: R2-D15-LK-H3


title: TC_H_01

description: T-cell Primary Tissue Healthy


title: R2-D15-LK-H3K9me3


title: BC_T_04

description: Breast Primary Tissue Cancer

source_name: breast cancer primary tissue

value: Breast

value: Cancer


title: R2-D15-LK-H3K4me3


title: R2-D3-DJ-H3K27ac


title: R2-D15-LK-H3K27me


title: R2-D3-DJ-H2A


title: RNA-seq_A549_48

value: Lung adenocarcinoma cell line

value: after IFN-gamma treatment(48 hours)

value: Sensitive


title: BC_T_02

description: Breast Primary Tissue Cancer


title: RNA-seq_HCC827_0


title: R2-D15-LK-H3K27ac


title: CML228, single-end, rep03

value: WT


title: CML228, single-end, rep02


title: BC_T_05

description: Breast Primary Tissue Cancer


title: RNA-seq_A375_0

value: Melanoma cell line


title: RNA-seq_HGC27_0

value: Gastric cancer cell line


title: R2-D15-LK-H4


title: R2-D15-LK-H2A


title: CML69, single-end, rep02


title: RNA-seq_HUH6_0

value: Hepatoblastoma cell line

value: RPMI


title: BC_CCL_02

description: Breast Cell Line Cancer

source_name: breast cancer cell line

value: Cell Line


title: RNA-seq_MDAMB231_0

value: Breast cancer cell line

value: before IFN-gamma treatment

value: DMEM


title: BC_T_03

description: Breast Primary Tissue Cancer

value: Primary Tissue


title: 162W, single-end, rep03

value: Leaf


title: R2-D15-iG-PolII

value: Liver

value: BALB/c

value: Pol-II


title: CML228, single-end, rep01


title: RNA-seq_NCIH1437_0

value: Lung adenocarcinoma cell line


title: BC_T_02_bis

description: Breast Primary Tissue Cancer

value: Breast

value: Cancer


title: R2-D15-iG-H4


title: CML69, single-end, rep01

value: WT


title: RNA-seq_HCT116_0

value: Colon cancer cell line

value: Resistant


title: RNA-seq_MCF7_0


title: 162W, single-end, rep02


title: RNA-seq_A549_0

value: Sensitive


title: Lu_T_06

description: Lung Primary Tissue Cancer

source_name: lung cancer primary tissue

value: Lung


title: R2-D15-iG-H3

source_name: Liver


title: 162W, single-end, rep01


title: Lu_T_04

description: Lung Primary Tissue Cancer


title: U2OS_RFX7-KO2_Nutlin_3

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

data_processing:
Sequence information was extracted in FastQ format using Illumina's bcl2FastQ v2.20.0.422
We utilized Trimmomatic v0.39 (5nt sliding window approach, mean  quality cutoff 22, minimum length 20) for read quality trimming according to  inspections made from FastQC  (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.8 reports.  Illumina universal adapter content was clipped using Cutadapt v2.3 (mimum  overlap 5, minimum length 18). Potential sequencing errors were detected and  corrected using Rcorrector v1.0.3.1. Ribosomal RNA (rRNA) transcripts were  artificially depleted by read alignment against rRNA databases through SortMeRNA  v2.1.
The preprocessed data was aligned to the reference genome hg38, retrieved  along with its gene annotation from Ensembl v.102, using the mapping software  segemehl v0.3.4 with adjusted accuracy (95%) and split-read option enabled.  Mappings were filtered by Samtools v1.10 for uniqueness.
Read quantification  was performed on exon level using featureCounts v1.6.4, parametrized according  to the strand specificity inferred through RSeQC v3.0.0. Differential gene  expression and its statistical significance was identified using DESeq2 v1.20.0.
Genome_build: hg38
Supplementary_files_format_and_content: TSV files. TPM value table and DESeq2 results tables.

molecule: polyA RNA

source_name: U2OS osteosarcoma cells

growth_protocol: U2OS cells were grown in high glucose Dulbecco's modified Eagle's media (DMEM) with pyruvate. Culture media were supplemented with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
Total cellular RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer protocol.
Libraries were constructed from from 500 ng total RNA using NEBNext Ultra II RNA - polyA+ (mRNA) Library Preparation Kit (New England Biolabs) following the manufacturer's description.

treatment_protocol: Cells were treated with DMSO (0.15 %) or Nutlin-3a (10 µM) for 24h

value: osteosarcoma


title: R2-D15-iG-H3K9me3


title: U2OS_RFX7-KO2_Nutlin_1


title: Lu_T_03

description: Lung Primary Tissue Cancer


title: BC_T_01

description: Breast Primary Tissue Cancer


title: KI3, single-end, rep01

source_name: Leaf


title: BC_CCL_01

description: Breast Cell Line Cancer

value: Cell Line


title: Lu_T_05

description: Lung Primary Tissue Cancer


title: Lu_T_02

description: Lung Primary Tissue Cancer


title: R2-D15-iG-H3K27me


title: U2OS_RFX7-KO2_DMSO_3

value: DMSO


title: Lu_T_01

description: Lung Primary Tissue Cancer


title: R2-D15-iG-H3K27ac


title: Lu_CCL_02

description: Lung Cell Line Cancer

source_name: lung cancer cell line


title: CML322, single-end, rep02


title: U2OS_RFX7-KO2_DMSO_1


title: CML322, single-end, rep01


title: R2-D15-DJ-PolII


title: R2-D15-DJ-H4


title: Lu_CCL_01

description: Lung Cell Line Cancer


title: KI3, single-end, rep03


title: U2OS_RFX7-KO2_Nutlin_2


title: R2-D15-iG-H3K4me3


title: KI3, single-end, rep02


title: U2OS_RFX7-KO1_Nutlin_2


title: Lu_H_07

description: Lung Primary Tissue Healthy

source_name: healthy lung primary tissue

value: Healthy


title: R2-D15-iG-H2A


title: U2OS_RFX7-KO2_DMSO_2


title: CML322, single-end, rep03


title: U2OS_RFX7-KO1_Nutlin_1


title: Ki11, single-end, rep01


title: Ki11, single-end, rep02


title: Ky21, single-end, rep03


title: Ky21, single-end, rep02


title: R2-D15-DJ-H3K27me


title: R2-D15-DJ-H3K4me3


title: R2-D15-DJ-H3K9me3


title: R2-D15-DJ-H3


title: U2OS_RFX7-KO1_DMSO_3


title: Lu_H_06

description: Lung Primary Tissue Healthy

value: Primary Tissue


title: U2OS_RFX7-KO1_Nutlin_3


title: Lu_H_04

description: Lung Primary Tissue Healthy


title: U2OS_RFX7-KO1_DMSO_1


title: Lu_H_03

description: Lung Primary Tissue Healthy


title: R2-D15-DJ-H3K27ac


title: Lu_H_05

description: Lung Primary Tissue Healthy


title: U2OS_parental_Nutlin_3

value: wild-type


title: Ky21, single-end, rep01

value: Leaf


title: Ki11, single-end, rep03


title: Lu_H_02

description: Lung Primary Tissue Healthy


title: R2-D15-DJ-H2A

value: Liver

value: BALB/c


title: CML333, single-end, rep03


title: U2OS_parental_Nutlin_2


title: U2OS_RFX7-KO1_DMSO_2


title: Lu_H_01

description: Lung Primary Tissue Healthy


title: U2OS_parental_Nutlin_1


title: R1-D3-LK-PolII

value: Pol-II


title: CML333, single-end, rep01


title: R1-D3-LK-H4


title: NC350, single-end, rep03


title: R1-D3-LK-H3


title: R1-D3-LK-H3K9me3


title: U2OS_parental_DMSO_2


title: U2OS_parental_DMSO_3


title: wtaav2_virus_biol_rep_2

city: Boston

first: Nina

last: Jain

state: Massachusetts

address: CLSB 5FL 528/6c, Center for Life Sciences, 3 Blackfan Circle

department: Wyss Institute

institute: Harvard University

description: sequencing of barcoded AAV2 rep variants to determine representation in the viral library

data_processing:
library strategy: amplicon sequencing
Python was used to extract the barcodes from the fastq files and count the occurrence of each barcode in each sample.
Assembly: AAV2
Supplementary files format and content: CSV files containing barcode counts for each sample

organism: Adeno-associated virus

extract_protocol:
NaCl was added to HEK293T cells. Cells were incubated at 37C for 3 hours to lyse. The resulting material was incubated O/N at 4C. The following morning precipitates were removed and discarded. The supernatant was filtered through a 0.2 um PES filter. PEG was added to precipitate viral particles. The following day, viral genome-containing particles were purified by iodixanol gradient ultracentrifugation. Viral genomes were release by incubation of purified viral particles at 98C for 10 minutes prior to barcode amplification for sequencing.
Illumina adapters were added via PCR


title: R1-D3-LK-H3K4me3


title: NC350, single-end, rep01


title: U2OS_parental_DMSO_1


title: wtaav2_plasmid

description: sequencing of barcoded AAV2 rep variants to determine representation in the plasmid library

source_name: E. coli Agilent SURE

value: E. coli Agilent SURE


title: NC350, single-end, rep02


title: M37W, single-end, rep03


title: R1-D3-LK-H3K27me3


title: rep7868_virus_aav9_capsid_biol_rep_2


title: R1-D3-LK-H3K27ac


title: rep7868_virus_aav9_capsid_biol_rep_1


title: M37W, single-end, rep02


title: R1-D3-LK-H2A


title: rep7868_virus_aav5_capsid_biol_rep_2


title: CML333, single-end, rep02


title: wtaav2_virus_biol_rep_1


title: rep7868_plasmid


title: R1-D3-iG-PolII


title: rep7868_virus_aav5_capsid_biol_rep_1


title: CML103, single-end, rep03


title: R1-D3-iG-H4


title: CML103, single-end, rep02


title: rep7868_virus_aav2_capsid_biol_rep_2


title: CML103, single-end, rep01


title: R1-D3-iG-H3K9me3


title: rep7868_virus_aav2_capsid_biol_rep_1


title: THC/SIV JB82

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

data_processing:
Raw reads were first processed through perl scripts to remove reads containing adapter or -N or with base quality score lower than 20. At the same time, the Q20, Q30 and GC contents of the clean data were calculated. The clean reads were aligned to the genome assembly of Macaca mulatta 10 (https://www.ncbi.nlm.nih.gov/genome/215?genome_assembly_id=468623) using TopHat2, and read numbers mapped to each gene were calculated using the HTSeq program. The fragments per kilobase of transcript sequence per million base pairs of each gene were determined by the length of the gene and read counts mapped to this gene. Differential expression analyses of VEH or THC-treated SIV-infected RMs and control groups were performed using the DESeq of R package. Genes with a P-value <0.05 and |log2 fold change| > 0.585 were defined as differentially expressed.
Assembly: Macaca_mulatta.Ensembl_release_76
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Macaca mulatta

source_name: Basal ganglia

extract_protocol:
Total RNA was extracted from basal ganglia tissues at necropsy using the miRNeasy kit (Qiagen Inc).
Transcriptome profiling by RNA-seq and data analysis were performed by Novogene (Sacremento, CA). cDNA library construction and sequencing were performed by Novogene Co. Ltd, Beijing, CA (http://www.novogene.cn/). For library construction, ~3 μg of total RNA from each sample was used to enrich mRNA with the poly-T oligo-attached magnetic beads. The purified mRNA was then randomly cleaved into small fragments using NEBNEXT RNA fragmentation buffer following the manufacturer’s instructions. First-strand cDNA was synthesized using random hexamers and M-MuLV Reverse Transcriptase (RNase H-). Second-strand cDNA synthesis by nick translation was subsequently performed using E coli DNA polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. The final cDNA library was prepared after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. The cDNA fragments of preferentially 250−300 bp in length were selected using with AMPure XP system (Beckman Coulter, Beverly, U.S.A.) and PCR amplified using Phusion High-Fidelity DNA polymerase (NEB, Beijing, China), Universal PCR primers and Index (X) Primer. PCR products were then purified using AMPure XP system (Beckman Coulter, U.S.A.), and library quality was assessed on the Agilent Bioanalyzer 2100 system (Agilent Technologies, U.S.A.). The clustering of the index-coded samples was performed on a cBot Cluster Generation System, using TruSeq SR Cluster Kit v3-cBot-HS (Illumina), according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired end reads were generated.

treatment_protocol: SIV-infected rhesus macaques were treated with Vehicle or delta-9-tetrahydrocannabinol at 0.32 mg/kg for 6 months post SIV infection.

value: SIV Infected with THC


title: NC358, single-end, rep03

value: WT


title: R1-D3-iG-H3K4me3


title: THC/SIV HI09


title: NC358, single-end, rep02


title: TP19_Rep4

type: RNA

city: York

first: Katherine

last: Denby

address: Department of Biology

country: United Kingdom

institute: University of York

description: Randomised loop design providing dye-swaps between treatments, time points and bioreps

hyb_protocol: The order in which the 152 slides were hybridized and scanned was randomised to minimise the impact on differences between samples of any potential variation in the processing conditions. According to this randomised experimental design combinations of labelled samples were hybridized to slides overnight at 42 oC.

scan_protocol: Following hybridization, slides were washed and scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5).

data_processing:
Cy3 and Cy5 scans for each slide were combined and processed in ImaGene version 8.0 (BioDiscovery) to extract raw intensity and background corrected data values for each spot on the array
Quantified microarray data were Lowess normalied within printip groups and within arrays, then variation due to arrays and dyes was removed by a random effects model, and averaged, in log space, using a modified version of R/MAANOVA (MicroArray ANalysis Of VAriance) (Wu et al. 2003).

label: Cy3, Cy5

organism: Arabidopsis thaliana

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).

growth_protocol: Arabidopsis thaliana plants (Col-0) were obtained from the European Arabidopsis Stock Centre, and were grown under a 8:16-h light:dark cycle at 23°C, 60% relative humidity, and light intensity of 150 µmol m-2 s-1. Arabidopsis seed was stratified for 3 d in 0.1% agarose at 4°C before sowing individual seeds onto a soil mix (Scotts Levingtons F2+S compost : fine grade vermiculite in a ratio of 6:1:) in pots (7cm x 7cm x 9 cm) . Leaf 7 was harvested every 2 days from 25 to 61 days after sowing, from 4 individual plants at each time point.

extract_protocol: Total RNA was isolated from four individual leaves from each sampled time point (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.

treatment_protocol: No treatment - leaf 7 was harvested every 2 days from 25 to 61 days after sowing

tag: days after sowing

value: leaves

tag: cultivar


title: R1-D3-iG-H3K27me3


title: M37W, single-end, rep01


title: NC358, single-end, rep01


title: TP15_Rep4


title: TP17_Rep4


title: TP18_Rep4


title: Ms71, single-end, rep03


title: R1-D3-iG-H3


title: THC/SIV IH69


title: TP16_Rep4


title: TP14_Rep4


title: THC/SIV IA04


title: TP12_Rep4


title: R1-D3-iG-H2A


title: TP11_Rep4


title: Ms71, single-end, rep02


title: R1-D3-iG-H3K27ac


title: R1-D3-DJ-PolII


title: TP10_Rep4


title: THC/SIV IA83


title: VEH/SIV JD66

value: SIV Infected Vehicle


title: Ms71, single-end, rep01


title: B97, single-end, rep03


title: THC/SIV GV60


title: R1-D3-DJ-H4


title: R1-D3-DJ-H3


title: TP13_Rep4


title: B97, single-end, rep02


title: VEH/SIV JH47


title: R1-D3-DJ-H3K9me3


title: B97, single-end, rep01


title: VEH/SIV JC81


title: Oh43, single-end, rep02


title: R1-D3-DJ-H3K27me3


title: R1-D3-DJ-H3K4me3


title: R1-D3-DJ-H3K27ac


title: VEH/SIV IN24


title: Oh43, single-end, rep03


title: VEH/SIV IH96


title: Oh43, single-end, rep01


title: VEH/SIV HV48


title: Uninfected Controls GV92

value: Untreated


title: R1-D15-LK-PolII


title: HP301, single-end, rep02


title: R1-D3-DJ-H2A


title: TP6_Rep4


title: Uninfected Controls IT18


title: TP9_Rep4


title: TP7_Rep4


title: TP5_Rep4


title: HP301, single-end, rep03


title: R1-D15-LK-H4


title: Uninfected Controls IR97


title: TP8_Rep4


title: TP4_Rep4


title: Il14H, single-end, rep03


title: TP2_Rep4


title: HP301, single-end, rep01


title: Uninfected Controls HF34


title: R1-D15-LK-H3K4me3


title: Il14H, single-end, rep02


title: Uninfected Controls HH69


title: R1-D15-LK-H3


title: R1-D15-LK-H3K9me3


title: TP3_Rep4


title: TP19_Rep3


title: Il14H, single-end, rep01


title: TP18_Rep3


title: TP1_Rep4


title: leaves of GS2S360D/gs2 plants, rep3

city: Hangzhou

first: Shuting

last: Ding

state: Zhejiang

address: 866 Yuhangtang Road

department: Department of Horticulture

institute: Zhejiang University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the Solanum lycopersicum（https://solgenomics.net/ftp/genomes/Solanum_lycopersicum/assembly/build_3.00/S_lycopersicum_chromosomes.3.00.fa） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: build_3.00
Supplementary files format and content: tab-delimited text files include FPKM values and counts  for each Sample

organism: Solanum lycopersicum

source_name: leaf

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: leaf

value: GS2S360D in gs2 mutant

value: no treatment


title: leaves of GS2S360D/gs2 plants, rep2


title: leaves of GS2S360D/gs2 plants, rep1


title: R1-D15-LK-H3K27ac


title: R1-D15-LK-H3K27me


title: TP16_Rep3


title: P39, single-end, rep01


title: TP17_Rep3


title: R1-D15-LK-H2A


title: P39, single-end, rep02


title: TP15_Rep3


title: leaves of  GS2/gs2 plants, rep3

value: wild type GS2 in gs2 mutant


title: CML52, paired-end


title: R1-D15-iG-PolII


title: Mo18W, paired-end


title: leaves of  GS2/gs2 plants, rep2


title: TP13_Rep3


title: leaves of  GS2/gs2 plants, rep1


title: TP14_Rep3


title: TP12_Rep3


title: TP11_Rep3


title: CML277, paired-end


title: leaves of GS2S334A/gs2 plants, Pst,rep3

value: GS2S334A in gs2 mutant

value: 24 hours after Pst DC3000 innoculation


title: R1-D15-iG-H3


title: R1-D15-iG-H3K9me3


title: leaves of GS2S334A/gs2 plants, Pst,rep2


title: Tzi8, paired-end


title: R1-D15-iG-H4


title: R1-D15-iG-H3K4me3


title: Oh7B, paired-end


title: leaves of GS2S334A/gs2 plants, Pst,rep1


title: leaves of GS2/gs2 plants, Pst, rep3


title: Tx303, paired-end


title: R1-D15-iG-H3K27me


title: TP10_Rep3


title: leaves of GS2/gs2 plants, Pst, rep2


title: TP8_Rep3


title: CML69, paired-end


title: R1-D15-iG-H3K27ac


title: R1-D15-iG-H2A


title: TP7_Rep3


title: TP9_Rep3


title: leaves of GS2/gs2 plants, Pst, rep1


title: R1-D15-DJ-PolII


title: M162W, paired-end


title: CML228, paired-end


title: R1-D15-DJ-H4


title: leaves of GS2S334A/gs2 lines, mock,rep3

value: 24 hours after mock innoculation


title: CML247, paired-end

value: Leaf


title: KI3, paired-end


title: R1-D15-DJ-H3

value: Liver


title: R1-D15-DJ-H3K9me3

value: BALB/c


title: leaves of GS2S334A/gs2 lines, mock,rep1


title: CML322, paired-end


title: leaves of GS2/gs2 lines, mock, rep2


title: Ki11, paired-end


title: CML333, paired-end


title: leaves of GS2/gs2 lines, mock, rep1


title: R1-D15-DJ-H3K4me3


title: R1-D15-DJ-H3K27me


title: NC350, paired-end


title: TP6_Rep3


title: TP5_Rep3


title: TP4_Rep3


title: TP19_Rep2


title: TP3_Rep3


title: TP2_Rep3


title: TP1_Rep3


title: TP18_Rep2


title: TP17_Rep2


title: NC358, paired-end


title: Ms71, paired-end


title: R1-D15-DJ-H3K27ac


title: B97, paired-end


title: leaves of GS2S334A/gs2 lines, mock,rep2


title: CML103, paired-end


title: R1-D15-DJ-H2A


title: Oh43, paired-end


title: leaves of GS2/gs2 lines, mock, rep3


title: HP301, paired-end


title: M37W, paired-end


title: Il14H, paired-end


title: P39, paired-end


title: R182 cells, Non-treated, rep 2

city: Detroit

first: Gil

middle: G.

last: Mor

state: Michigan

address: 275 E. Hancock

department: C.S. Mott Center for Human Growth and Development

institute: Wayne State University School of Medicine

data_processing:
Base calling was conducted using HiSeq Control Software, converted to fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36
Trimmed sequence reads were mapped to GRCh38 using STAR aligner v.2.5.2b
Read count extraction was performed using Subread package v.1.5.2
Read count normalization was performed using DESeq2 package
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw count values for each sample

source_name: Ovary

extract_protocol:
Total RNA was harvested using Trizol reagent according to manufacturer's instructions. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep Kit (KAPA Biosystem, Wilmington, MA) for Illumina following manufacturer's protocols.

value: Ovary

value: Non-treated

tag: disease state

value: Ovarian cancer


title: R182 cells, Non-treated, rep 1


title: R182 cells, HGF-treated, rep 3

value: HGF-treated


title: R182 cells, Non-treated, rep 3


title: R182 cells, HGF-treated, rep 2


title: TP11_Rep2

value: leaves


title: TP16_Rep2


title: TP14_Rep2


title: R182 cells, HGF-treated, rep 1


title: TP15_Rep2


title: TAGMe_DNA_IMR90_rep1

description: TAGMe-seq DNA library on IMR-90 cell line, rep1

tag: cell type

value: lung fibroblast cell line

value: DpnII

value: Yes


title: TP12_Rep2


title: CRISPR_screen_HUH_IFNg

data_processing:
Library strategy: CRISPR Screen
The occurrence of sgRNAs indexes were summarized from previous paper.
Enriched genes were identified via MAGeCK and MAGeCK-VISPR, a Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout method for prioritizing single-guide RNAs, genes, and pathways in genome-scale CRISPR/Cas9 knockout screens
Genome_build: 6K-cancer library taegeting 6000 cancer related genes.
Supplementary_files_format_and_content: tab-delimited csv files  include  sgRNA sequence in 6K Library and the genes' beta scores of each cell types under different conditons.

growth_protocol: Cancer cells were seeded on 15 cm tissue culture plates in RPMI-1640 medium or DMEM, including 10% fetal bovine serum (FBS), glutamine, and 1% penicillin/ streptomycin. Cells were cultured in an incubator at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Genomic DNA was harvested from the live cells using QIAGEN (Germany) DNeasy Blood & Tissue Kit. sgRNAs were amplified.
sgRNAs were amplified for sequencing on HiSeq X.

treatment_protocol: For the pooled CRISPR screen, a total of 1.2×10^8 cells were infected with the pooled lentiviral library at a multiplicity of infection (MOI) of 0.3. After puromycin selection, the cells were divided into three groups (Day 0, vehicle control, and IFN-γ treatment). The cell pellet of Day 0 group was stored at -80°C. For the other two groups, the cells were cultured for 14 days, with/without 10ng/ml IFN-γ individually. The cells were cultured for 14 days split every 2–3 days until the appearance of visibly viable colonies. Genomic DNA was harvested from the live cells using QIAGEN (Germany) DNeasy Blood & Tissue Kit. sgRNAs were amplified for sequencing on HiSeq X.

value: Hepatoblastoma cell line

tag: condition

value: Day14 IFN-gamma treatment conditon

value: RPMI

value: Resistant


title: sRNA-Seq_Panicle_nrpd1-kd_Rep2

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using UEA sRNA workbench. The sRNAs of appropriate size class was chosen further.
The processed reads were aligned to the rice genome using Bowtie with one allowed mismatch.
Genome_build: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary_files_format_and_content: Text delimited files showing the sequence and raw abundance of the sRNAs.

organism: Oryza sativa

source_name: pre-emerged panicle

growth_protocol: The plants were grown in green house with natural day-night cycles with temperature maintained around 28 degrees celsius.

extract_protocol:
Total RNA from three different tissues, anther before dehiscence, endosperm and pre-emerged panicle were extracted using Trizol (Invitrogen) reagent.
Size fractionation

treatment_protocol: WT and pol IV knockdown lines were handled in the same manner.

tag: tissue

value: pre-emerged panicle

tag: subspecies

value: Indica

value: Pusa Basmati 1 (PB1)

tag: genotype

tag: developmental stage

value: Pre-emerged young panicle


title: TP8_Rep2


title: TP10_Rep2


title: TP9_Rep2


title: TP13_Rep2


title: CRISPR_screen_HUH6_veh

value: Day14 vehicle condition


title: sRNA-Seq_Panicle_nrpd1-kd_Rep1


title: sRNA-Seq_Panicle_WT_Rep2

value: WT


title: TP3_Rep2


title: TP7_Rep2


title: TP5_Rep2


title: TP2_Rep2


title: TP1_Rep2


title: TP4_Rep2


title: TP6_Rep2


title: TP18_Rep1


title: TAGMe_RNA_IMR90_rep1

description: TAGMe-seq RNA library on IMR-90 cell line, rep1


title: CRISPR_screen_HCT116_IFNg

source_name: Colorectal

value: Colon cancer cell line

value: DMEM


title: sRNA-Seq_Panicle_WT_Rep1


title: sRNA-Seq_Endosperm_nrpd1-kd_Rep2

source_name: Endosperm

value: Endosperm

value: semi-solid endosperm (16-20 days after anthesis)


title: CRISPR_screen_HCT116_Day0

value: Day 0 control


title: TP19_Rep1

value: leaves


title: sRNA-Seq_Endosperm_WT_Rep2


title: TP15_Rep1


title: TP16_Rep1


title: CRISPR_screen_HUH6_Day0


title: CRISPR_screen_7860_veh

source_name: kidney

value: renal cancer cell line


title: TP14_Rep1


title: sRNA-Seq_Anther_nrpd1-kd_Rep1

source_name: Anther

value: Anther

value: anther before dehiscence


title: sRNA-Seq_Anther_WT_Rep2


title: CRISPR_screen_HCT116_veh


title: R557

city: chongqing

first: gan

last: yi

address: No. 136, Zhongshan 2nd Road, Yuzhong District, Chongqing

institute: Chongqing Children's Hospital

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: heart

growth_protocol: Mice were fed in the SPF animal room at the children's hospital of chongqing medical university

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: strain

value: heart

tag: age

value: 3 month-old

value: cTnI R193H mutation


title: TP17_Rep1


title: CRISPR_screen_MCF7_veh

source_name: Breast

tag: cell line

value: Breast cancer cell line

value: Resistant


title: R555


title: sRNA-Seq_Endosperm_nrpd1-kd_Rep1

value: Indica

value: Pusa Basmati 1 (PB1)


title: sRNA-Seq_Anther_WT_Rep1

value: WT


title: RNA-Seq_nrpd1_kd_Panicle_Rep2

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using Trimmomatic and rRNA sequences were removed using Sortmerna.
The processed reads were aligned to the rice genome using HISAT2.
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Genome_build: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary_files_format_and_content: Text delimited file including FPKM for each sample.

extract_protocol:
Total RNA was isolated from the anther and pre-emerged panicle. Anthers before dehiscence were chosen and RNA was extracted using TRIzol method.
Libraries were prepared for sequencing using standard Illumina protocols. The kit used is NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalog no-E7765L) and the adapter sequences are Read 1- AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and for read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

value: pre-emerged panicle


title: R549


title: TP11_Rep1


title: CRISPR_screen_Calu1_IFNg

source_name: Lung

value: Lung adenocarcinoma cell line

value: Day14 IFN-gamma treatment conditon

value: RPMI

value: Sensitive


title: sRNA-Seq_Endosperm_WT_Rep1

value: Endosperm

value: semi-solid endosperm (16-20 days after anthesis)


title: CRISPR_screen_786O_Day0

value: renal cancer cell line

value: Day 0 control


title: TP12_Rep1

value: leaves


title: RNA-Seq_nrpd1_kd_Panicle_Rep1


title: sRNA-Seq_Anther_nrpd1-kd_Rep2

value: Anther

value: anther before dehiscence


title: CRISPR_screen_MCF_IFNg

value: Breast cancer cell line

value: DMEM


title: TP8_Rep1


title: TP10_Rep1


title: TP13_Rep1


title: TP9_Rep1


title: CRISPR_screen_Calu1_veh

value: Day14 vehicle condition


title: TP7_Rep1


title: TP6_Rep1


title: W544

value: heart

value: 3 month-old

value: wild type


title: RNA-Seq_WT_Panicle_Rep2

value: pre-emerged panicle

value: Indica

value: Pusa Basmati 1 (PB1)

value: WT


title: CRISPR_screen_Calu1_Day0

value: Lung adenocarcinoma cell line

value: RPMI

value: Sensitive


title: RNA-Seq_WT_Panicle_Rep1


title: CRISPR_screen_MCF7_Day0

value: Day 0 control

value: Resistant


title: TP5_Rep1

value: leaves


title: CRISPR_screen_PC9_IFNg

value: Day14 IFN-gamma treatment conditon


title: W572


title: RNA-Seq_nrpd1_kd_Anther_Rep2

source_name: anther

value: anther


title: rep2_No_WT_yeast_NoUV_UVDE-seq_UGI_A4_1bp

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description: Replicate 2

data_processing:
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the yeast genome (SacCer3) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
FASTA file of lesion-containing dinucleotide sequence extracted using BEDTOOLS2 fastaFromBed
Damage-containing dinucleotide sequences counted using custom perl script
Library strategy: UVDE-seq

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cultures (BY4741) were grown in YPD (yeast extract, peptone, dextrose) to OD600=~0.8 in a yeast shaker.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A (ThermoFisher Scientific) at 37˚C for ~1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and dissolved in sterile deionized H2O.
UVDE-seq procedure is adopted from the published emRiboSeq method (Nature Protocols 2015 10, 1433–1444) and our own CPD-seq method. Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by  terminal transferase and dideoxy-ATP or dideoxy-GTP.  CPD lesions were repaired using purified E. coli CPD photolyase. All other UV-induced lesions were cleaved with purified T. thermophilus UVDE. DNA was then ligated to adaptor  A. Up to 6 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT; A4: ATCGCGAT; A5: TACTGGAT; and A6: GAACTGAT) were used to generate libraries for different experiments. DNA was purified with Streptavidin beads and amplified for up to 8 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.    Control libraries to test for contamination of CPDs followed the protocol described above, with the following modifications: WT cells were cultured and carried through to CPD photolyase treatment. Following this, samples were split in half, with half the samples treated with UVDE to cleave 6-4PP and TA-PP and the other half treated with T4 endo V to cleave any remaining CPD lesions. Following enzyme treatment, DNa was purified using phenol:chloroform:isoamyl alcohol and ethanol precipitation. Library preparation resumed with second (A) adapter ligation.

treatment_protocol: Cells were collected and resuspended in sterile deionized H2O. 20mL of BY4741 and MP072 collected for unirradiated samples. 20mL BY4741 and MP072 irradiated with 600 J/m2 UVC. After UV irradiation, cells were spun down and kept at -80˚C until genomic DNA isolation.

value: Wild-type

tag: repair time


title: TP4_Rep1


title: TP3_Rep1


title: W551


title: CRISPR_screen_PC9_Day0

value: DMEM


title: RNA-Seq_WT_Anther_Rep2


title: rep2_0hr_WT_yeast_600JUVC_UVDE-seq_UGI_A5_1bp

description: Replicate 2

value: UV irradiated 600 J/m2

value: 0 hr


title: WT_yeast_naked_500JUVC_UVDE-seq_UGI_rep1_reseq_A3_1bp

description: Replicate 1 resequenced

source_name: Yeast genomic DNA

value: UV irradiated 500 J/m2


title: WT_yeast_NoUV_UVDE-seq_UGI_rep1_reseq_A1_1bp

description: Replicate 1 resequenced


title: RNA-seq - WT P12-1

city: Baton Rouge

first: Xing

last: Fu

state: LA

address: 229G Animal and Food Sciences laboratory building

department: School of Animal Sciences

institute: Louisiana State University

data_processing:
RNA-seq: sequencing reads were filtered to remove low-quality reads and trimmed to remove adaptors by TrimGalore-0.6. The quality of reads after filtering was assessed by fastQC, followed by aligning reads to the mouse genome (MM10) by STAR (2.5.3a) with parameters used in Encode project (Consortium, 2012).
RNA-seq: the expression quantification (transcripts per million, TPM) of individual genes was obtained by RSEM with gene annotations downloaded from Ensembl.
ATAC-seq: sequencing reads of all samples underwent adapter removal and low-quality reads filtering using TrimGalore-0.6, followed by quality assessment using FastQC. Reads were then aligned to the mouse reference genome MM10 using Bowtie 2.3 with the following options: – very-sensitive -X 2000 – no-mixed – no-discordant.
ATAC-seq: peaks were called separately for each sample by MACS2 (Zhang et al., 2008) with the following options: – keep-dup all – nolambda – nomodel.
Genome_build: MM10
Supplementary_files_format_and_content: narroowPeak
Supplementary_files_format_and_content: TPM

source_name: Adipose tissue

growth_protocol: In vivo

extract_protocol:
RNA-seq: total RNA was extracted from 5,000 FACS-sorted Tcf21 LPs using the miRNeasy Micro Kit (217084) from Qiagen.
RNA-seq: cDNA libraries were constructed using the NEBNext single cell/low input RNA library prep kit for Illumina (E6420) from New England BioLabs.

treatment_protocol: To induce the activity of the MerCreMer, mice were treated with TM (MilliporeSigma, T5648) dissolved in corn oil through gavage at a dosage of 75 mg/kg BW/d for adult mice (including pregnant female mice to induce MerCreMer activity in fetuses) or through intragastric injection at a dosage of 100 µg/d for neonatal mice.

value: Tcf21 lineage cell

value: Tcf21 KO

value: postnatal day 12

tag: diet

value: regular diet (LabDiet #5001)


title: RNA-seq - WT P12-2


title: RNA-Seq_nrpd1_kd_Anther_Rep1

value: Indica

value: Pusa Basmati 1 (PB1)


title: TP1_Rep1


title: MethylC-Seq_nrpd-kd_2

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using cutadapt.
The reads were aligned to IRGSP genome using Bismark and methylation extraction was done using Bismark protocol.
The methylation was calculated using the Bismark tool and cytosine coverage report was used to create the bedgraph files for methylation density genomewide.
Genome_build: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary_files_format_and_content: bigwig files showing the methylation status across the genome.

extract_protocol:
Total DNA was extracted from the tissues using CTAB method.
Libraries were prepared exactly as per the NEBNext® Enzymatic Methyl-seq Kit (Catalog no-E7120) manufaturer protocol. Adapters used: Read 1-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and Read2- AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Other, Methyl C Seq

value: pre-emerged panicle

value: nrpd-kd


title: TP2_Rep1


title: CRISPR_screen_MDAMB231_Day0

value: Breast cancer cell line

value: Day 0 control

value: Sensitive


title: MethylC-Seq_nrpd-kd_1


title: WT_yeast_600JUVC_UVDE-seq_UGI_rep1_reseq_A2_1bp

description: Replicate 1 resequenced

tag: treatment


title: WT_naked_500JUVC_UVDEseq_UGI_A3_1bp

description: Replicate 1


title: CRISPR_screen_MDAMB231_veh

value: Day14 vehicle condition

tag: medium


title: CRISPR_screen_PC9_veh

value: Lung adenocarcinoma cell line

tag: ifn-gamma sensitivity


title: RNA-seq - WT 6M-1

value: WT

value: 6 months of age


title: RNA-seq - WT 3W-7 (pair 5)

value: 3 weeks of age


title: RNA-seq - WT 6M-2


title: RNA-Seq_WT_Anther_Rep1

value: anther


title: RNA-seq - WT 3W-6 (pair 4)

value: Tcf21 lineage cell


title: WT_NoUV_UVDEseq_UGI_A1_1bp

description: Replicate 1

value: Wild-type


title: Degradome_nrpd1-kd_Panicle

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using UEA sRNA workbench.
small RNAs matching rRNA and tRNA are filtered out
18-21nt small RNA reads were size selected
Genome_build: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary_files_format_and_content: Files containing the sequence and raw abundance of the reads obtained.

extract_protocol:
Total RNA was isolated using TRIZol reagent and degradome library was performed using etablished methods.
Degradome cDNA libraries were constructed according to J. Zhai et al., 2014, Methods, 67 (84–90) protocol with slight modifications.
Other, Degradome profiling by high throughput sequencing


title: CRISPR_screen_MDAMB231_IFNg

value: Day14 IFN-gamma treatment conditon

value: DMEM


title: CRISPR_screen_NCIH1437_Day0

value: RPMI


title: WT_0hr_600JUVC_UVDEseq_UGI_A2_1bp

description: Replicate 1

value: UV irradiated 600 J/m2

value: 0 hr


title: RNA-seq - WT 3W-5 (pair 3)

value: regular diet (LabDiet #5001)


title: CRISPR_screen_NCIH1437_IFNg


title: RNA-seq - WT 3W-4


title: Degradome_WT_Panicle

value: pre-emerged panicle

value: Indica

value: Pusa Basmati 1 (PB1)


title: ChIP_PolII_INPUT

data_processing:
The reads obtained were trimmed using cutadapt and aligned to IRGSP rice genome with parameters -q -v 1 -m 100 -y -a --best –strata
The alignment files are converted to coverage files using bam coverage tool of Deeptools with the 100bp bin size.
Genome_build: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary_files_format_and_content: The coverage files of the ChIP seq alignments were provided in bigwig format.

extract_protocol:
Sheared chromatin from the equally developed pre emerged panicle of WT and kd plants were incubated with appropriate antibodies bound to Protein G Dynabeads (Thermo Fisher, catalog number 10003D).  Washes, elution, de-crosslinking and DNA purification was done as described. The purified DNA was taken for library preparation.
The ChIP library was constructed using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (Catalog no-E7103L) as per manufacturer's instructions. The adapter sequence used is AGATCGGAAGAGCACACGTCTGAACTCCAGTCA. The sequencing was done in single end mode in a Illumina HiSeq2500 platform.

tag: chip antibody


title: CRISPR_screen_A549_IFNg

value: Sensitive


title: CRISPR_screen_A549_veh

value: Lung adenocarcinoma cell line

value: Day14 vehicle condition


title: ChIP_PolII_nrpd1-kd

tag: cultivar

value: PolII


title: WT_T4endo_NoUV_A1_1bp

description: Replicate 1

data_processing:
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the yeast genome (SacCer3) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
FASTA file of lesion-containing dinucleotide sequence extracted using BEDTOOLS2 fastaFromBed
Damage-containing dinucleotide sequences counted using custom perl script
Genome_build: SacCer3

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 ?l of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 ?l of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 ?l of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 ?l of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 ?l of TE and incubated with 2 ?l of RNase A (ThermoFisher Scientific) at 37?C for ~1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and dissolved in sterile deionized H2O.
UVDE-seq procedure is adopted from the published emRiboSeq method (Nature Protocols 2015 10, 1433–1444) and our own CPD-seq method. Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by  terminal transferase and dideoxy-ATP or dideoxy-GTP.  CPD lesions were repaired using purified E. coli CPD photolyase. All other UV-induced lesions were cleaved with purified T. thermophilus UVDE. DNA was then ligated to adaptor  A. Up to 6 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT; A4: ATCGCGAT; A5: TACTGGAT; and A6: GAACTGAT) were used to generate libraries for different experiments. DNA was purified with Streptavidin beads and amplified for up to 8 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.    Control libraries to test for contamination of CPDs followed the protocol described above, with the following modifications: WT cells were cultured and carried through to CPD photolyase treatment. Following this, samples were split in half, with half the samples treated with UVDE to cleave 6-4PP and TA-PP and the other half treated with T4 endo V to cleave any remaining CPD lesions. Following enzyme treatment, DNa was purified using phenol:chloroform:isoamyl alcohol and ethanol precipitation. Library preparation resumed with second (A) adapter ligation.
Others (UVDE-seq)

treatment_protocol: Cells were collected and resuspended in sterile deionized H2O. 20mL of BY4741 and MP072 collected for unirradiated samples. 20mL BY4741 and MP072 irradiated with 600 J/m2 UVC. After UV irradiation, cells were spun down and kept at -80?C until genomic DNA isolation.


title: CRISPR_screen_A549_Day0

value: Day 0 control


title: ChIP_PolII_WT

value: WT


title: WT_600juvde_UV0hr_A4_1bp

description: Replicate 1


title: RNA-seq - WT 3W-1 (pair 1)

value: Tcf21 lineage cell

value: Tcf21 KO

value: 3 weeks of age


title: MethylC-Seq_WT


title: ChIP_H3_nrpd1-kd_Rep2


title: WT_uvde_nakeDNA_500J_A3_1bp

description: Replicate 1

value: Wild-type

value: UV irradiated 500 J/m2


title: CRISPR_screen_NCIH1437_veh

value: RPMI


title: pared non-tumorous tissue 3 [miRNA-seq]

city: Shanghai

first: Bin

last: Sun

address: No.225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

description: All.Counts.miRNA.txt

data_processing:
RNA-seq: Reads filtering under criteria removing reads with 20% of the base quality lower than 13
RNA-seq: HISAT2.1.0 mapping to reference genome
RNA-seq: count counting
miRNA-seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 33bp c) adaptor sequence.
miRNA-seq: Utilizing the BWA software, we mapped the clean data to mature miRNAs with annotation from miRBase(v.22).
miRNA-seq: count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

growth_protocol: Fresh tissue samples were placed in serum-free medium

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA of samples  was obtained by TRIzol reagent

tag: tissue type

value: paird non-tumor tissue


title: RNA-seq - WT 3W-2 (pair 2)

tag: cell type

value: regular diet (LabDiet #5001)


title: RNA-seq - WT 1W HFD-4

value: 1 week HFD starting at 6 weeks of age

value: high-fat diet (Teklad #TD.06414)


title: HCC tissue 3 [miRNA-seq]

description: All.Counts.miRNA.txt

value: tumor tissue


title: ChIP_H3_nrpd1-kd_Rep1

value: pre-emerged panicle

value: Indica

value: Pusa Basmati 1 (PB1)


title: WT_uvde_nakeDNA_NoUV_A1_1bp

description: Replicate 1


title: pared non-tumorous tissue 2 [miRNA-seq]

description: All.Counts.miRNA.txt


title: WT_T4endo_UV0hr_A2_1bp

description: Replicate 1

value: UV irradiated 600 J/m2

value: 0 hr


title: RNA-seq - WT 1W HFD-3


title: WT_uvde_nakeDNA_400J_A2_1bp

description: Replicate 1

value: UV irradiated 400 J/m2


title: RNA-seq - WT 3W-3 (pair 3)

value: Tcf21 lineage cell

value: WT


title: ChIP_H3_WT_Rep2


title: HCC tissue 2 [miRNA-seq]

description: All.Counts.miRNA.txt


title: rad16_uvde_UV0hr_rep2_A4_1bp

description: Replicate 2


title: RNA-seq - WT 1W HFD-2

value: Tcf21 KO


title: ChIP_H3_WT_Rep1


title: rad16_uvde_NoUV_rep2_A3_1bp

description: Replicate 2


title: ChIP_H3K27me3_nrpd1-kd_Rep2


title: RNA-seq - WT 1W HFD-1


title: RNA-seq - WT 12W HFD-5

value: 12 weeks HFD starting at 6 weeks of age


title: WT_uvde_NoUV_rep2_A1_1bp

description: Replicate 2

value: Wild-type


title: WT_uvde_UV0hr_rep2_A2_1bp

description: Replicate 2


title: ChIP_H3K27me3_nrpd1-kd_Rep1


title: RNA-seq - WT 12W HFD-4


title: ChIP_H3K27me3_WT_Rep2


title: HCC tissue 3 [RNA-seq]

description: All.counts.RNA.txt


title: MOV10 Input Rep2

city: Urbana

first: Stephanie

last: Ceman

address: 601 S. Goodwin Ave

department: Cell and Developmental Biology

institute: University of Illinois-Urbana Champaign

data_processing:
Librabries were quantified using Tapestation
Initial Reads were mapped to repetitive elements. Then the reads were mapped to find the ones that mapped the genome uniquely.
After removing PCR duplicates the IP reads were normalized to Input reads and peaks were analyzed using Eclipse Bio IDR (Irreproducible Discovery Rate) analysis
A peak is defined as a cluster with log2 fold enrichment ≥ 3 and p-value ≤ 0.001
Assembly: Genome build: UCSC version GRCm38/mm10; Transcriptome: GENCODE Release M24 (GRCm38.p6
Supplementary files format and content: Q0108A_MOV10_IP_vs_Input.IDR.peaks.bed contains peaks found to be reproducible and significant in both replicates by Eclipse Bio IDR (Irreproducible Discovery Rate) analysis. The format is Chromosome, Start position, Stop position, -log10(P-value), Log2 fold enrichment in eCLIP vs. input, Strand (+ or -)
Library strategy: eCLIP-Seq

growth_protocol: N2A cells were maintained in DMEM supplemented with 10% FBS

extract_protocol:
No modifications were made to the published eCLIP methodology for this experiment.
Sequencing was performed as PE150 on the NovaSeq platform to construct libraries.
4 libraries were generated using 1 antibody (2 IP and 2 inputs).

treatment_protocol: Cell pellets from N2A cells were flash-frozen and sent to Eclipse BioInnovations.  eCLIP was performed per Van Nostrad et al. (2016; https://www.nature.com/articles/nmeth.3810) using MOV10 antibody from (Bethyl Labs)

value: Neurocarcinoma cell line

tag: ip antibody

value: anti-MOV10 antibody (A301-571A; Bethyl Laboratories)


title: RNA-seq - WT 12W HFD-3


title: ChIP_H3K27me3_WT_Rep1

tag: tissue


title: MOV10 Input Rep1


title: RNA-seq - WT 12W HFD-2


title: pared non-tumorous tissue 2 [RNA-seq]

description: All.counts.RNA.txt

value: paird non-tumor tissue


title: ChIP_H3K9me2_nrpd1-kd_Rep2

tag: subspecies


title: HCC tissue 2 [RNA-seq]

description: All.counts.RNA.txt


title: RNA-seq - WT 12W HFD-1

tag: genotype


title: ChIP_H3K9me2_nrpd1-kd_Rep1


title: MOV10 eCLIP Rep1


title: pared non-tumorous tissue 1 [RNA-seq]

description: All.counts.RNA.txt


title: pared non-tumorous tissue 1 [miRNA-seq]

description: All.Counts.miRNA.txt


title: RNA-seq - KO 3W-5 (pair 5)

value: 3 weeks of age

value: regular diet (LabDiet #5001)


title: HCC tissue 1 [miRNA-seq]

description: All.Counts.miRNA.txt

value: tumor tissue


title: ChIP_H3K9me2_WT_Rep2

value: pre-emerged panicle


title: HCC tissue 1 [RNA-seq]

description: All.counts.RNA.txt


title: RNA-seq - KO 3W-4 (pair 4)


title: N2A MOV10 KO cells, MOV10 WT transfected replicate 3

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina). Adaptors have been trimmed from the 3'-end of the reads.
Salmon version 1.1.0 was used to quantify the abundance of each transcript using the Selective Alignment method with a decoy-aware transcriptome using the entire GRCm38 genome as the decoy with additional arguments --seqBias and --gcBias to correct sequence-specific and GC content biases, --numBootstraps=30 to compute bootstrap transcript abundance estimates and --validateMappings and --recoverOrphans  to help improve the accuracy of mappings.
Gene-level counts were then estimated based on transcript-level counts using the “bias corrected counts without an offset” method from the tximport package (v.14.2) in R (v3.6.3).
Assembly: GRCm38 (Gencode M24)
Supplementary files format and content: TMM-normalized, log2-tranformed (scaled.prior = 2) count per million expression values in Ceman_logCPMvalues_2020-03-10.xlsx

growth_protocol: MOV10 knockout N2A cells were maintained in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was extracted using Trizol (Ambion)
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a NovaSeq 6000 using a NovaSeq SP reagent kit. Read 1 aligns to the ANTISENSE strand.

treatment_protocol: Confluent cells were transfected with DNA (2ug) for 24 hours and RNA was harvested.

value: MOV10 knockout

tag: dna transfection

value: MOV10 WT transfected


title: pared non-tumorous tissue 3 [RNA-seq]

description: All.counts.RNA.txt


title: ChIP_H3K9me2_WT_Rep1

value: Indica

value: Pusa Basmati 1 (PB1)


title: ChIP_H3K4me3_nrpd1-kd_Rep2


title: N2A MOV10 KO cells, MOV10 S970A transfected replicate 3

value: MOV10 S970A transfected


title: RNA-seq - KO 3W-3 (pair 3)

value: Tcf21 lineage cell


title: N2A MOV10 KO cells, MOV10 S970D transfected replicate 3

value: MOV10 S970D transfected


title: RNA-seq - KO 3W-2 (pair 2)

value: WT


title: MOV10 eCLIP Rep2


title: N2A MOV10 KO cells, MOV10 WT transfected replicate 2


title: RNA-seq - KO 3W-1 (pair 1)


title: ChIP_H3K4me3_WT_Rep2


title: RNA-seq - KO 1W HFD-2

value: 1 week HFD starting at 6 weeks of age

value: high-fat diet (Teklad #TD.06414)


title: N2A MOV10 KO cells, MOV10 S970D transfected replicate 2

value: Neurocarcinoma cell line


title: ChIP_H3K4me3_WT_Rep1


title: N2A MOV10 KO cells, MOV10 S970A transfected replicate 2


title: RNA-seq - KO 1W HFD-1


title: RNA-seq - KO 12W HFD-2

value: 12 weeks HFD starting at 6 weeks of age


title: N2A MOV10 KO cells, MOV10 WT transfected replicate 1


title: CRISPR_screen_786O_IFNg

value: renal cancer cell line

tag: condition

value: Day14 IFN-gamma treatment conditon

value: RPMI

value: Resistant


title: ChIP_H3K4me3_nrpd1-kd_Rep1

value: pre-emerged panicle


title: N2A MOV10 KO cells, MOV10 S970D transfected replicate 1

value: MOV10 knockout


title: N2A MOV10 KO cells, MOV10 S970A transfected replicate 1


title: RNA-seq - KO 12W HFD-1

tag: age


title: ATAC-seq - WT 3W-3 (pair 2)

extract_protocol:
ATAC-seq: 5,000 FACS-sorted Tcf21 LPs were lysed to isolate the nuclei. Isolated nuclei were then incubated with the Tn5 transposase (TDE1, Illumina) and tagmentation buffer at 37°C for 30 minutes with shaking on a thermomixer at 500 g. Tagmentated DNA was purified using MinElute Reaction Cleanup Kit (Qiagen).
ATAC-seq: PCR was performed to amplify the ATACseq libraries using Illumina TrueSeq primers and multiplex by indexes primers. After the PCR reaction, libraries were purified with the 1.1X AMPure beads (Beckman).

value: 3 weeks of age

value: regular diet (LabDiet #5001)


title: ATAC-seq - WT 3W-2


title: hNeuronal cells, JEV treated (I3), 48h

city: Hyderabad

first: Shraddha

last: Tripathi

state: Telangana

address: Shamerpet, Kapra mandal

department: Biological sciences

institute: BITS Pilani Hyderabad

data_processing:
The following data analysis flow was followed: Data QC, Read mapping, expression estimation, differential expression, gene ontology and pathway enrichment; The QC passed reads were mapped onto the indexed Human reference genome (GRCh38.p7) using the HISAT2 aligner.
Raw sequence reads were processed to remove adapter sequences and low quality bases using fastp
Assembly: Human reference genome (GRCh38.p7)
Supplementary files format and content: Excel sheet of expression count file with following description is provided: Ensemble ID, expression counts (control and infected), gene ID, transcript name, gene description, ENTREZ ID, gene biotype, transcript biotype

source_name: Brain

extract_protocol:
Total RNA was isolated using an MN Nucleo Spin RNA Plus isolation kit (Cat. No. 740984.5)
RNA-seq libraries were made with NEBNext® UltraTM II Directional RNA Library prep kit for Illumina according to the manufacturer's instructions.

value: Brain

tag: cell line

value: Neuronal

value: JEV infected (5 MOI)


title: hNeuronal cells, JEV treated (I2), 48h


title: hNeuronal cells, JEV treated (I1), 48h


title: hNeuronal cells, Control (C3), 48h

value: Mock infected


title: R3-D3-M-iG

city: STANFORD

first: Katja

last: Pekrun

address: 269 Campus Drive

institute: Stanford School of Medicine

data_processing:
Reads were trimmed with Trimmomatic-0.39 program for classical Illumina adapters. Aligned using Bowtie2 version 2.2.5 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.5/) with options: --local --very-sensitive-local --nounal --no-mixed --no-discordant --phred33 -I 10 -X 700; mapping was performed using the hg38 or mm10 build of the human and mouse genome respectively, merged with viral genome sequence (gAAV).
PCR duplicates were eliminated with “MarkDuplicates” command of Picard version 2.23 (https://broadinstitute.github.io/picard/index.html).
Tracks were made as bedgraph files of normalized counts, using deeptools 3.3 (https://deeptools.readthedocs.io/en/develop/content/list_of_tools.html) bamCoverage with options: --binSize 1, --normalizeUsing CPM; track plots were made with R package Gviz 4.1. Coverage was calculated as SUM[(normalized count*(end-start position+1))/gAAV size] for each dataset. Importantly, ITR regions were removed from the calculation, as their coverage is overrepresented in all samples, perhaps due to recognition of ITRs from ssDNA.
Assembly: hg38 for human cells, mm10 for mouse cells
Supplementary files format and content: Bedgraph
Library strategy: Cut&Tag

source_name: liver

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x anti-anti. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Mice were sacrificed 3 or 15 days after rAAV injection and liver tissue was flash-frozen in aliquots. Liver tissue (~100 mg) was homogenized in RINO 1.5-ml Screw-Cap tubes filled with stainless steel beads and 1mL of NE buffer using a bead homogenizer (Next Advance Bullet Blender Storm - BBY24M) at speed 8 for 4 minutes. The homogenate was transferred into to a 50mL tube with 12mL of NE buffer and incubated on ice for 10 min. Nuclei were pelleted by a 5 min centrifugation at 600g, the supernatant was decanted, and the pellet was resuspended in 1mL of NE buffer. Nuclei were quantitated after Trypan Blue staining using an automated cell counter (Countess, Thermo Fisher) and diluted accordingly. 5e5 nuclei per sample was used for Tn5 library preparation
Total gDNA was extracted using a QIAamp DNA Mini kit (Qiagen) including RNAse treatment. The protocol for Illumina DNA prep was followed as per manufacturer’s instructions with 100ng of DNA as input, 30min tagmentation and 8 cycles of PCR. The same indexed primers as for Cut&Tag were used for PCR amplification.
Illumina DNA prep kit. Sequencing was performed with Illumina NovaSeq 6000, 150 cycles total per lane (2 lanes total), 2x75 paired-end reads, depth of >15M reads per sample.

value: liver

value: BALB/c


title: R3-D3-M-LK


title: hNeuronal cells, Control (C2), 48h

value: WT


title: ATAC-seq - WT 3W-1 (pair 1)

value: Tcf21 lineage cell


title: R3-D3-M-DJ


title: CYD_TB47_3_L5

city: Dunedin

first: Kiel

last: Hards

address: 720 Cumberland Street

department: Department of Microbiology and Immunology

country: New Zealand

institute: University of Otago

description: Mycobacterium smegmatis cytochrome bd mutant, TB47 treated, Lane 5, Replicate 3

data_processing:
Reads were demultiplexed  and quality control performed using FastQC v0.11.5
Adapter reads were removed using Trimmomatic version 0.39 and trimmed to a quality score > 0.28
Reads were mapped to the reference genome using the Rsubread (version 2.2.6) subjunc aligner with a maximum fragment length of 600
Feature counts were genereated using the Rsubread (version 2.2.6) featureCounts function with a maximum fragment length of 600 and allowing multiple overlap
Differential expresison was calculated using DESeq 2 1.28.1, using a two-factor experimental design (i.e. strain*treatment)
Genome_build: NC_008596
Supplementary_files_format_and_content: Tab delimited Matrix table with raw gene counts for every gene and every sample and lane

organism: Mycolicibacterium smegmatis

source_name: Bacterial cells

growth_protocol: Three 1 L flasks with 200 ml HdeB were inoculated with three biological replicates of M. smegmatis overnight cultures to an OD of 0.005 and grown at 37°C with 200 rpm until an OD of 0.5 was reached. Each biological replicate was then split, and 2x 50 ml of culture was transferred into two sterile 250 ml flasks.

extract_protocol:
Total RNA was extracted using TRIZOL® reagent (Invitrogen) according to the manufacturer's instructions. Cell lysis was achieved by three cycles of bead-beating in a Mini-Beadbeater (Biospec) at 5,000 rpm for 30 sec. DNA was removed from the RNA preparation by treatment with 2 U RNase-free DNase using the TURBO DNA-free kit (Ambion), according to the manufacturer's instructions. RNA concentrations were determined using a NanoDrop® ND-1000 spectrophotometer and the quality of RNA checked on a 1.2% agarose gel.
Library preparation and sequencing of the M. smegmatis transcriptome was carried out by the Otago Genomics and Bioinformatics Facility (OGBF) in conjunction with New Zealand Genomics Limited (NZGL). Prepared RNA was checked for quality on a Bioanalyzer (Agilent), followed by ribosomal RNA depletion with the Bacterial Ribo-zero RNA Removal Kit (Illumina). Quantification of nucleic acids was performed using a Qubit fluorometer® (Thermo Fisher Scientific). Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina), before being sequenced across two lanes on an Illumina HiSeq with paired-end read lengths of 125 base pairs and using the v4 chemistry.

treatment_protocol: One flask was treated with 50 nM final concentration TB47, and the other was treated with the same amount of DMSO as a control.

tag: strain

value: {delta}cydAB

value: TB47 treated

tag: replicate

value: Bacterial cells


title: hNeuronal cells, Control (C1), 48h

tag: treatment


title: CYD_TB47_2_L5

description: Mycobacterium smegmatis cytochrome bd mutant, TB47 treated, Lane 5, Replicate 2


title: ATAC-seq - WT 1W HFD-2

value: 1 week HFD starting at 6 weeks of age

tag: diet

value: high-fat diet (Teklad #TD.06414)


title: R3-D15-M-iG


title: P4 Tumor

city: Guangzhou

first: Zhengzhou

last: Lu

state: Guangdong province

address: 74 Zhongshan Second Road

institute: Sun Yat-Sen University

data_processing:
The raw data were first quality checked and filtered by fastp to obtain the clean reads data with “--cut_front” and “--cut_tail” parameters.
The clean reads data were aligned to human genome GRCh38 with -hisat2, and annotated with GENCODE gene annotation (Release 33)
Gene expression profiling was exported in TPM and read counts by stringtie.
Assembly: GRCh38
Supplementary files format and content: The Excel table contains TPM values for each Sample

source_name: Kaposi’s sarcoma tissue

extract_protocol:
Two KS tissue samples and the corresponding two normal tissue samples were cut and lysed with TRIzol reagent and total RNA was extracted following the manufacturer manual. RNA purity was checked using Qubit 3.0 Fluorometer (Life Technologies).
For each sample, 2 mg RNA was used to generate sequencing libraries with NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530L, NEB), referring to the manufacturer's recommendations. Index codes were added to attribute sequences to each sample. The libraries were sequenced on an Illumina Hiseq 2500 platform and 150-bp paired-end reads were generated.

value: Kaposi's sarcoma tissue


title: ATAC-seq - WT 1W HFD-1


title: rep2_naked_WT_yeast_naked_500JUVC_UVDE-seq_UGI_A6_1bp

description: Replicate 2

value: Wild-type

value: UV irradiated 500 J/m2

tag: repair time


title: CYD_TB47_1_L5

description: Mycobacterium smegmatis cytochrome bd mutant, TB47 treated, Lane 5, Replicate 1


title: ATAC-seq - WT 12W HFD-2

value: 12 weeks HFD starting at 6 weeks of age


title: P4 Normal

source_name: normal tissue

value: normal tissue


title: R3-D15-M-DJ


title: CYD_unt_3_L5

description: Mycobacterium smegmatis cytochrome bd mutant, Untreated, Lane 5, Replicate 3

value: Untreated


title: ATAC-seq - WT 12W HFD-1


title: P2 Tumor


title: lncRNA expression of keratinocytes [patient 5]

first: Yilun

last: Wang

address: No.12 Wulumuqi Zhong Road

institute: Fudan University

description:
patient
patient 5

data_processing:
see manufacturer's web site at http://www.agilent.com/
Use the 75th percentile signal value to normalize Agilent one-color microarray signals for inter-array comparisons.

source_name: keratinocytes

growth_protocol: Skin biopsies were taken from lesional skin areas of patients with psoriasis vulgaris. Skin biopsies obtained from healthy individuals undergoing plastic surgery were used as control samples.

extract_protocol: Total RNA was reversely transcribed using a PrimeScript RT reagent Kit with gDNA Eraser (Perfect Real Time) (TaKaRa, Dalian, China) in accordance with the manufacturer’s instructions.

treatment_protocol: The subcutaneous tissue was removed and skin biopsies were incubated overnight at 4°C in Dispase solution (Grade II; Roche Applied Science).

tag: tissure

value: skin

tag: disease

value: psoriasis vulgaris


title: lncRNA expression of keratinocytes [nc 1]

description:
normal
nc 1

hyb_protocol: see manufacturer's web site at http://www.agilent.com/

value: control


title: lncRNA expression of keratinocytes [nc 5]

description:
normal
nc 5

scan_protocol: see manufacturer's web site at http://www.agilent.com/


title: lncRNA expression of keratinocytes [patient 4]

description:
patient
patient 4

label_protocol: see manufacturer's web site at http://www.agilent.com/


title: R2-D3-M-LK

value: liver

value: BALB/c


title: CYD_unt_2_L5

description: Mycobacterium smegmatis cytochrome bd mutant, Untreated, Lane 5, Replicate 2


title: lncRNA expression of keratinocytes [nc 3]

description:
normal
nc 3


title: P2 Normal


title: R3-D15-M-LK


title: R2-D3-M-iG


title: CYD_unt_1_L5

description: Mycobacterium smegmatis cytochrome bd mutant, Untreated, Lane 5, Replicate 1


title: lncRNA expression of keratinocytes [patient 3]

description:
patient
patient 3


title: RNA-seq - WT P18

data_processing:
The cDNA libraries were sequenced on the Illumina Hi-seq platform using 150 bp paired-end sequencing at a depth of more than 20,000 read pairs/cell. Raw sequencing data were processed using Cell Ranger 6.0.0 (10X Genomics) and MM10 mouse genome.
Genome_build: MM10
Supplementary_files_format_and_content: tsv, mtx

source_name: Epididymal adipose tissue

growth_protocol: Breeding and lactating mice were fed with a breeder diet (LabDiet #5015). After weaning, mice were fed with a regular diet containing 13.384% calories from fat (LabDiet #5001). For HFD challenges, mice were fed with a diet containing 60.3% calories from fat (Teklad #TD.06414) starting at 6 weeks of age for 1 or 12 weeks.

extract_protocol:
scRNAseq were performed using FACS-sorted Tcf21 LPs from epididymal adipose tissue.
Libraries were constructed using Chromium Single Cell 3' Reagent Kits v3 (10x Genomics).

value: Tcf21 lineage progenitor cells

value: WT

value: Postnatal day 12

value: regular diet (LabDiet #5001)


title: lncRNA expression of keratinocytes [nc 4]

description:
normal
nc 4


title: lncRNA expression of keratinocytes [patient 2]

description:
patient
patient 2


title: lncRNA expression of keratinocytes [patient 1]

description:
patient
patient 1


title: Rep2_IAA_Rad21

city: London

first: Suzana

last: Hadjur

address: 72 Huntley street

department: Cancer biology

institute: Ucl

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie allowing 3 mismatches. DRIP-seq reads were trimmed with 14bp from the beginning and 16bp from the end.  Trimmed DRIP-seq reads were aligned to the hg19 genome assembly using Bowtie allowing 3 mismatches and a maximum insert size of 1000.
Data were filtered for PCR duplicates using SAMTOOLS
peaks were called using MISHA (v 3.5.6) with a ChIP percentile threshold (0.995).
Genome_build: hg19

growth_protocol: Human RAD21-mAC cells were cultured in standard conditions of10% FCS and P/S.

extract_protocol:
Chromatin was extracted from cells, sonicated, pre-cleared and this lysate was used for ChIP libarry prep.  For DRIP-seq, chromatin was extracted from cells and treated with RNaseI and proteinase K. Nucleic acids were isolated, sonicated, pre-cleared and RNA:DNA hybrids were IP'd with s9.6 antibody. Purified eluate was converted to dsDNA and this lysate was used for DRIP library prep ahead of sequencing.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit with 6-8 cycles of PCR. DRIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: RAD21-mAC cells were treated with ethanol or IAA for 4hrs before chromatin was collected (see methods for confluence and concentrations).

value: HCT116 cells

value: auxin (IAA) treated_depletion


title: lncRNA expression of keratinocytes [nc 2]

description:
normal
nc 2


title: R2-D3-M-DJ

treatment_protocol: Mice were intravenously injected with rAAV packaged using different capsids. The rAAV vector expressed the firefly luciferase under control of a CAG promoter.


title: R2-D15-M-LK


title: ATAC-seq - KO 3W-1 (pair 1)

value: Tcf21 lineage cell

value: 3 weeks of age


title: ATAC-seq - KO 3W-2 (pair 2)


title: RNA-seq - WT 5W

value: 5 weeks of age


title: WT_TB47_2_L5

description: Mycobacterium smegmatis wild-type, TB47 treated, Lane 5, Replicate 2

value: TB47 treated

value: Bacterial cells


title: WT_TB47_3_L5

description: Mycobacterium smegmatis wild-type, TB47 treated, Lane 5, Replicate 3


title: WT_TB47_1_L5

description: Mycobacterium smegmatis wild-type, TB47 treated, Lane 5, Replicate 1


title: R2-D15-M-iG


title: Rep2_IAA_SA2


title: RNA-seq - WT 12W HFD

value: 12 weeks HFD starting at 6 weeks of age

value: high-fat diet (Teklad #TD.06414)


title: Rep2_IAA_SA1


title: R2-D15-M-DJ


title: WT_unt_3_L5

description: Mycobacterium smegmatis wild-type, Untreated, Lane 5, Replicate 3

value: Untreated


title: Rep2_IAA_CTCF


title: RNA-seq - KO P18 HFD

value: Tcf21 KO


title: RNA-seq - KO 5W HFD


title: WT_unt_2_L5

description: Mycobacterium smegmatis wild-type, Untreated, Lane 5, Replicate 2


title: Rep2_IAA_INPUT


title: R1-D3-M-iG

value: liver


title: WT_unt_1_L5

description: Mycobacterium smegmatis wild-type, Untreated, Lane 5, Replicate 1


title: Rep2_etoh_Smc3

value: ethanol treated_control


title: R1-D3-M-LK

value: BALB/c


title: CYD_TB47_3_L8

description: Mycobacterium smegmatis cytochrome bd mutant, TB47 treated, Lane 8, Replicate 3

value: {delta}cydAB


title: R1-D3-M-DJ


title: Rep2_etoh_Rad21


title: R1-D15-M-iG


title: CYD_TB47_2_L8

description: Mycobacterium smegmatis cytochrome bd mutant, TB47 treated, Lane 8, Replicate 2


title: Rep2_etoh_SA1


title: CYD_TB47_1_L8

description: Mycobacterium smegmatis cytochrome bd mutant, TB47 treated, Lane 8, Replicate 1


title: CYD_unt_3_L8

description: Mycobacterium smegmatis cytochrome bd mutant, Untreated, Lane 8, Replicate 3


title: Rep2_etoh_SA2


title: R1-D15-M-DJ


title: R3-LiD-M-LK

data_processing:
Reads were trimmed with Trimmomatic-0.39 program for classical Illumina adapters. Aligned using Bowtie2 version 2.2.5 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.5/) with options: --local --very-sensitive-local --nounal --no-mixed --no-discordant --phred33 -I 10 -X 700; mapping was performed using the hg38 or mm10 build of the human and mouse genome respectively, merged with viral genome sequence (gAAV).
PCR duplicates were eliminated with “MarkDuplicates” command of Picard version 2.23 (https://broadinstitute.github.io/picard/index.html).
Tracks were made as bedgraph files of normalized counts, using deeptools 3.3 (https://deeptools.readthedocs.io/en/develop/content/list_of_tools.html) bamCoverage with options: --binSize 1, --normalizeUsing CPM; track plots were made with R package Gviz 4.1. Coverage was calculated as SUM[(normalized count*(end-start position+1))/gAAV size] for each dataset. Importantly, ITR regions were removed from the calculation, as their coverage is overrepresented in all samples, perhaps due to recognition of ITRs from ssDNA.
Assembly: hg38 for human cells, mm10 for mouse cells
Supplementary files format and content: Bedgraph
Library strategy: Cut & Tag

source_name: Hepa 1-6

extract_protocol:
Briefly, cells were collected 48 hours after rAAV transduction by trypsinization and washed with PBS. Nuclei were extracted with NE buffer. Nuclei were quantitated after Trypan Blue staining using an automated cell counter (Countess, Thermo Fisher) and diluted accordingly. 5e5 nuclei per sample were used for the Tn5 library preparation.
Total gDNA was extracted using a QIAamp DNA Mini kit (Qiagen) including RNAse treatment. The protocol for Illumina DNA prep was followed as per manufacturer’s instructions with 100ng of DNA as input, 30min tagmentation and 8 cycles of PCR. The same indexed primers as for Cut&Tag were used for PCR amplification.
Illumina DNA prep kit. Sequencing was performed with Illumina NovaSeq 6000, 150 cycles total per lane (2 lanes total), 2x75 paired-end reads, depth of >15M reads per sample.

treatment_protocol: Cells were transduced with rAAV packaged using different capsids. The rAAV vector expressed the firefly luciferase under control of a CAG promoter.

value: Hepa 1-6

value: Hepatoma


title: CYD_unt_2_L8

description: Mycobacterium smegmatis cytochrome bd mutant, Untreated, Lane 8, Replicate 2


title: R3-LiD-M-iG


title: GT1-7 3

city: Milan

first: Anna

last: Cariboni

address: Via Balzaretti 9

department: Disfeb

country: Italy

institute: Università degli Studi di Milano

description: Gene expression data from GT1-7 cells

hyb_protocol: Hybridisation was performed for 17 hr at 45°C on Rat Gene 1.0 ST Array. Chips were washed and stained following Affymetrix protocol.

scan_protocol: Scanning and image acquisition were performed according to Affymetriz standard protocols.

data_processing: Data were processed using the third part AMDA software (Pelizzola, M. et al. AMDA: an R package for the automated microarray data analysis. BMC Bioinformatics 7, 335 (2006). doi: 10.1186/1471-2105-7-335)

label: biotin

source_name: Immortalized mature GnRH neurons

label_protocol: The RNA was converted using the WT Expression kit (Ambion), fragmented and labelled using the WT Terminal Labelling kit (Affymetrix)

extract_protocol: Total RNA was extracted following the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen RNeasy Micro kit clean-up procedure. Bioanalyzer has been run to verify RNA integrity (RNA 6000 Nano kit). RNA with RIN>7 were used

tag: generation


title: R3-LiD-M-DJ

tag: cell type


title: CYD_unt_1_L8

description: Mycobacterium smegmatis cytochrome bd mutant, Untreated, Lane 8, Replicate 1


title: WT_TB47_3_L8

description: Mycobacterium smegmatis wild-type, TB47 treated, Lane 8, Replicate 3


title: GN11 3

description: Gene expression data from GN11 cells

source_name: Immortalized immature GnRH neurons


title: R1-D15-M-LK


title: Rep1_IAA_Rad21

value: HCT116 cells


title: GT1-7 2

description: Gene expression data from GT1-7 cells


title: Rep1_IAA_Smc3

value: auxin (IAA) treated_depletion


title: GN11 2

description: Gene expression data from GN11 cells


title: R2-LiD-M-LK


title: WT_TB47_2_L8

description: Mycobacterium smegmatis wild-type, TB47 treated, Lane 8, Replicate 2


title: WT_TB47_1_L8

description: Mycobacterium smegmatis wild-type, TB47 treated, Lane 8, Replicate 1


title: Rep1_IAA_SA2


title: Rep1_IAA_SA1


title: R2-LiD-M-iG


title: R2-LiD-M-DJ


title: GN11 1

description: Gene expression data from GN11 cells


title: Rep1_IAA_CTCF


title: WT_unt_2_L8

description: Mycobacterium smegmatis wild-type, Untreated, Lane 8, Replicate 2


title: Rep1_IAA_INPUT


title: R1-LiD-M-iG


title: WT_unt_1_L8

description: Mycobacterium smegmatis wild-type, Untreated, Lane 8, Replicate 1


title: Rep1_etoh_Smc3


title: Rep2_etoh_INPUT


title: Rep2_etoh_CTCF


title: Rep1_etoh_Rad21


title: Rep1_etoh_SA2


title: Rep1_etoh_IgG


title: Rep1_etoh_CTCF


title: Rep1_etoh_SA1


title: Rep1_etoh_INPUT