title: W82 Chitin-24h rep1

status: Public on Feb 28 2023

type: SRA

city: Ames

first: Madan

middle: K

last: Bhattacharyya

state: IA

address: G303 Agronomy 716 Farm House Ln

department: Department of Agronomy

country: USA

institute: Iowa State University

description: N

library_source: transcriptomic

data_processing:
Trapnell et. al, Nature Protocols 7, 562–578 (2012) pipeline was used for analyses.
Reads alignmnet using tophat
Diffrerential expression analysis using cuffdiff
Downstream output processing
reporting significant candidates from output
Assembly: Wm82.a4.v1/Gmax_508_v4.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Glycine max

source_name: Leaves (first trifoliate stage)

growth_protocol: W82, DR1-136, and DR1-107 soybean plants were grown on standard soil in a growth chamber maintained at the constant temperature of 23◦C and a photoperiod of 16 h of light/ 8h of dark.

extract_protocol:
Total RNA was extracted from soybean leaves using the SV total RNA Isolation System (Promega, Inc., Madison, WI, USA).
RNA libraries for RNA-seq were prepared using Illumina RNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Two-week-old seedlings were treated with chitin (Sigma-Aldrich) using the stem-cut method. Half of the plants for each genotype received 0.5 mL of 100 µmol/L chitin dissolved in sodium phosphate (15 mmol/L, pH 6.5), and the second half was treated with 0.5 mL of sodium phosphate buffer (15 mmol/L, pH 6.5). All treatments were followed by distilled water uptake, and plants maintained in the growth chamber under white light (85 µmol · m– 2 · s–1). Leaf samples were harvested at 12- and 24-hour post-treatments. Collected leaves were immediately placed in liquid nitrogen and stored in -80 ˚C freezer for RNA isolation.

tag: genotype

value: Williams 82

tag: tissue

value: Leaves (first trifoliate stage)

tag: time

tag: treatment

value: Chitin


title: DR1-107 Chitin-24h rep2

description: P


title: DR1-107 Buffer-24h rep1

description: M

value: Sodium phosphate buffer


title: DR1-136 Chitin-24h rep3

description: O


title: DR1-136 Chitin-24h rep1

description: O


title: DR1-136 Buffer-24h rep2

description: L


title: W82 Chitin-24h rep3

description: N


title: DR1-107 Buffer-24h rep3

description: M


title: DR1-107 Chitin-24h rep3

description: P


title: DR1-107 Buffer-24h rep2

description: M


title: DR1-136 Chitin-24h rep2

description: O


title: DR1-107 Chitin-24h rep1

description: P


title: DR1-136 Buffer-24h rep1

description: L


title: W82 Buffer-24h rep3

description: I


title: W82 Chitin-24h rep2

description: N


title: W82 Buffer-24h rep2

description: I


title: DR1-136 Buffer-24h rep3

description: L


title: DR1-107 Chitin-12h rep3

description: H


title: W82 Buffer-24h rep1

description: I


title: DR1-107 Chitin-12h rep2

description: H


title: DR1-136 Chitin-12h rep3

description: G


title: DR1-136 Chitin-12h rep2

description: G


title: W82 Chitin-12h rep3

description: E


title: DR1-107 Chitin-12h rep1

description: H


title: DR1-136 Chitin-12h rep1

description: G


title: W82 Chitin-12h rep2

description: E


title: DR1-107 Buffer-12h rep3

description: D


title: W82 Chitin-12h rep1

description: E


title: DR1-136 Buffer-12h rep1

description: C


title: W82 Buffer-12h rep1

description: A


title: DR1-107 Buffer-12h rep2

description: D


title: DR1-136 Buffer-12h rep3

description: C


title: DR1-107 Buffer-12h rep1

description: D


title: W82 Buffer-12h rep3

description: A


title: Donor 2 (S2), CD4+

city: Roma

first: Giuseppe

middle: Rubens

last: Pascucci

state: RM

address: Sant'Onofrio square, 4

department: University Hospital Pediatric Department (DPUO)

country: Italy

institute: Bambino Gesù Children's Hospital

description: S2 T0

data_processing:
Nanopore FAST5 files were basecalled with the stand-alone Guppy basecaller v6.2.11. In not-multiplexed samples (S1 PREc samples), adapters were trimmed during basecalling. For the other samples, adapters and barcodes were trimmed during demultiplexing that was performed using Guppy barcoder v6.2.11. The quality of the reads was checked with the fastqc tool v0.11.9 and the reads with more than 40% of the base with a Phred score of less than 10 were filtered out with fastp v0.12.4.
High-quality reads were aligned against of hg38 Gencode human transcriptome reference v38 using minimap2 v2.21 with map-ont preset parameters. Reads unmapped on hg38 transcriptome, were aligned against the Human immunodeficiency virus type 1 (HXB2) genome sequence (GenBank: K03455.1) using minimap2 with the splice preset parameters. SAM-to-BAM conversion, BAM sorting, indexing, and extraction of alignment statistics were performed with samtools v1.10.
Salmon v0.13.1 with “--gcBias -l U” parameters were used to summarize the mapped reads. Transcript level estimates were aggregated to gene level raw counts using the tximport R package v1.22.0.
Raw count values were then transformed using the edgeR v3.36.0 R package into normalised counts per million (CPM) values. Genes with a mean of CPMs under 5 were excluded.
Assembly: hg38 Gencode human transcriptome reference v38
Supplementary files format and content: Normalized_CPM_allsamples.txt is a tab-delimited text files include normalized CPM values of all samples
Supplementary files format and content: RawCounts_allsamples.txt is a tab-delimited text files include raw counts of all samples

organism: Homo sapiens

source_name: Blood

growth_protocol: CD4+ T cells of ART-treated young adults with perinatal HIV-infection were cultured in round-bottom 96-well plates (≤ 1x10^6 cells/well) for 18 hours (at 37°C, 5% CO2) in autologous plasma (PLSM condition) or 1640 RPMI (RPMI condition) (EuroClone, Cat. #ECM9106L) supplemented with 10% Fetal Bovine Serum (FBS, Gibco, Ref. #10270-106) 1% L-Glutamine (EuroClone, Cat. #ECB3000D) and 1% Penicillin/Streptomycin solution (EuroClone, Cat. #ECB3001D)

extract_protocol:
CD4+ T cells were first lysed in a solution of RNeasy Lysis Buffer (RLT Buffer, QIAGEN) and beta-mercaptoethanol (BME, Gibco REF #21985-023, using 10 ul BME for each ml of RLT) and then stored at -20° overnight for RNA yields maximization. The day after, according to cell number availability, RNA isolation was made via the RNeasy™ Mini and Micro Kit™ (QIAGEN, Cat. #80204 and #80284 respectively) following manufacturers' instructions. Pure, concentrated RNA was eluted in 14 ul (Micro kit) or 30 ul (Mini kit) RNase-free water and 1ul of RNAse Inhibitor (Cat. #AM2694, InvitrogenTM) was added to avoid sample degradation.
The PCR-cDNA Sequencing Kit SQK-PCS109 was used for S1 PREc samples. Meanwhile, the PCR-cDNA Barcoding kit SQK-PCB109 was used to multiplex the samples of each donor in a single library. The sequencing libraries were prepared following the manufacturer’s protocol. In brief, starting from 50 ng of full-length RNA, complementary strand DNA (cDNA) synthesis and strand switching were performed using kit-supplied oligonucleotides. dscDNA was generated by PCR amplification of cDNA (10ul cDNA/sample) using primers with 5’ tags which facilitate the ligase-free attachment of Rapid Sequencing Adapters. The prepared libraries were either immediately used for loading onto the R9.4.1 flow cell (FLO-MIN106) and sequenced or stored at -80°C until use. Libraries were run on MinION flow cells with MinKNOW acquisition software version v.21.02.01.

treatment_protocol: Cells were stimulated with 81 nM Phorbol 12-myristate 13-acetate (PMA, Sigma-Aldrich Cat. #P1585), 1,34 uM IONOMYCIN (IONO, Sigma-Aldrich Cat. #I0634), 20 U/ul recombinant human IL-2 (Peprotech Cat. #200-02) and the HIV-1 reverse transcriptase inhibitor Zidovudine (formerly Azidothymidine, AZT, from NIH HRP, Cat. #3485) used at 400 nM to avoid in vitro HIV re-infections (ST condition), or left unstimulated (US condition).

value: Blood

tag: disease

value: HIV

tag: cell type

value: CD4+ T lymphocytes


title: Donor 3 (S3), CD4+ isolated post colture (POSTc), RPMI, stimulated (ST)

description: S3 POSTc RPMI ST

value: stimutated with PMA, IONO and AZT for 18h


title: Donor 3 (S3), CD4+ isolated post colture (POSTc), plasma (PLSM), stimulated (ST)

description: S3 POSTc PLSM ST


title: Donor 2 (S2), CD4+ isolated pre-colture (PREc), RPMI, unstimulated (US)

description: S2 PREc RPMI US

value: cultured in vitro for 18h


title: Donor 2 (S2), CD4+ isolated pre-colture (PREc), plasma (PLSM), unstimulated (US)

description: S2 PREc PLSM US


title: Donor 3 (S3), CD4+ isolated pre-colture (PREc), RPMI, stimulated (ST)

description: S3 PREc RPMI ST


title: DR1-136 Buffer-12h rep2

description: C


title: Donor 2 (S2), CD4+ isolated pre-colture (PREc), RPMI, stimulated (ST)

description: S2 PREc RPMI ST


title: Donor 3 (S3), CD4+ isolated pre-colture (PREc), plasma (PLSM), unstimulated (US)

description: S3 PREc PLSM US


title: Donor 3 (S3), CD4+ isolated pre-colture (PREc), plasma (PLSM), stimulated (ST)

description: S3 PREc PLSM ST


title: Donor 3 (S3), CD4+ isolated post colture (POSTc), RPMI, unstimulated (US)

description: S3 POSTc RPMI US


title: Donor 2 (S2), CD4+ isolated pre-colture (PREc), plasma (PLSM), stimulated (ST)

description: S2 PREc PLSM ST


title: Donor 3 (S3), CD4+ isolated pre-colture (PREc), RPMI, unstimulated (US)

description: S3 PREc RPMI US


title: W82 Buffer-12h rep2

description: A


title: Donor 3 (S3), CD4+

description: S3 T0


title: Donor 2 (S2), CD4+ isolated post colture (POSTc), RPMI, unstimulated (US)

description: S2 POSTc RPMI US


title: Rice pistil nuclei bulk, replicate1

city: Singapore

first: Hao

last: Yu

address: 16 Science Drive 4

country: Singapore

institute: National University of Singapore

data_processing:
The Bulk RNA-Seq samples were aligned with STAR  to the IRGSP-1.0 reference genome.
The reads count of genes were generated with featureCounts .
The pseudo-bulk scRNA-seq gene expression was generated by summing up the expression of the gene in all cells.
The correlation between the pseudo-bulk gene expression and bulk gene expression was measured with Spearman's rank correlation coefficient.
DEseq2  was adopted to identify differentially expressed genes (DEGs) comparing the upper part and the lower part of the pistil. The DEGs were selected as genes with adjust p-value < 0.05 and  |log2(fold change)| > 1.
Assembly: IRGSP1.0
Supplementary files format and content: tab-delimited text files include reads count values for each Sample

molecule: polyA RNA

organism: Oryza sativa Japonica Group

source_name: pistil

growth_protocol: Rice (Oryza sativa ssp. Japonica cultivar Nipponbare) plants were grown in the potting soil mixed with sand in climate chambers with a relative humidity of 70%, under the following circadian rhythm: 10 h light at 30℃ and 14 h dark at 25℃.

extract_protocol:
Dissected pistils were frozen in liquid nitrogen and ground to powder. RNeasy Micro Kit (Qiagen) was used for RNA extraction. For bulk nuclei RNA sequencing, the powder was suspended by nucleus isolation buffer. Then, the crude nuclei were enriched from the slurry by applying cell strainer, and were subsequently purified by PI-labeled FANS. The purified nuclei were subjected to RNA extraction using RNeasy Micro Kit (Qiagen).
For RNA-seq, the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) was used to construct the library. For bulk nuclei RNA sequencing, RNA libraries for RNA-seq were prepared using SMART-Seq Library Prep Kit following manufacturer's protocols.

value: pistil

value: WT

value: No treatment

tag: developmental stage

value: heading stage


title: Rice pistil nuclei bulk, replicate2


title: Donor 2 (S2), CD4+ isolated post colture (POSTc), RPMI, stimulated (ST)

description: S2 POSTc RPMI ST


title: Rice pistil lower part, replicate 2


title: Donor 2 (S2), CD4+ isolated post colture (POSTc), plasma (PLSM), unstimulated (US)

description: S2 POSTc PLSM US


title: Donor 2 (S2), CD4+ isolated post colture (POSTc), plasma (PLSM), stimulated (ST)

description: S2 POSTc PLSM ST


title: Donor 1 (S1), CD4+

description: S1 T0


title: Rice pistil lower part, replicate 1


title: Rice pistil upper part, replicate 3


title: Donor 1 (S1), CD4+ isolated pre-colture (PREc), plasma (PLSM), unstimulated (US)

description: S1 PREc PLSM US


title: Donor 1 (S1), CD4+ isolated pre-colture (PREc), RPMI, unstimulated (US)

description: S1 PREc RPMI US


title: Donor 1 (S1), CD4+ isolated pre-colture (PREc), RPMI, stimulated (ST)

description: S1 PREc RPMI ST


title: Rice pistil upper part, replicate 1


title: Rice pistil upper part, replicate 2


title: Donor 1 (S1), CD4+ isolated post colture (POSTc), RPMI, unstimulated (US)

description: S1 POSTc RPMI US


title: Donor 1 (S1), CD4+ isolated post colture (POSTc), plasma (PLSM), stimulated (ST)

description: S1 POSTc PLSM ST


title: Donor 1 (S1), CD4+ isolated post colture (POSTc), RPMI, stimulated (ST)

description: S1 POSTc RPMI ST


title: Donor 1 (S1), CD4+ isolated post colture (POSTc), plasma (PLSM), unstimulated (US)

description: S1 POSTc PLSM US


title: Donor 1 (S1), CD4+ isolated pre-colture (PREc), plasma (PLSM), stimulated (ST)

description: S1 PREc PLSM ST


title: Rice pistil lower part, replicate 3


title: leaves, sprayed with 200 mM IAA, 12 h, rep2 (miRNA-seq)

city: Beijing

first: Yi-Qing

last: Wang

address: Beijing University of Agriculture Street

country: China

institute: Beijing University of Agriculture

data_processing:
The rawdata data measured by small RNA will be evaluated firstly, mainly for spurious filtering and preliminary judgment of the data.
Sequence reads were 1)Removelow quality tags  2)Removetagswith5'primer contaminants  3)Removetagswithout3'primer  4)Removetagswithoutinsertion  5)RemovetagswithpolyA  6)Removetagsshorterthan18nt  7)Summarizethelengthdistributionofthecleantags
We used the alignment software AASRA to align clean reads to the reference base and other small RNA databases, except  except for Rfam which was matched using cmsearch.
Assembly: without  reference genome
Supplementary files format and content: Readcount_TPM.txt (tab-delimited text file includes readcount and TPM values for each Sample)

organism: Rosa hybrid cultivar

source_name: leaves

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The Small RNA Sample Pre Kit was used to construct the library, using the special structure of the 3' and 5' ends of Small RNA (complete phosphate group at the 5' end and hydroxyl group at the 3' end), and using total RNA as the starting sample. After PCR amplification, the target DNA fragments were separated by PAGE gel electrophoresis, and the cDNA library was obtained by cutting and recycling.

value: leaves

value: spraying with 200 mM IAA


title: leaves, sprayed with 200 mM IAA, 18 h, rep1 (miRNA-seq)


title: leaves, sprayed with 200 mM IAA, 18 h, rep2 (miRNA-seq)


title: leaves, without spraying with 200 mM IAA, 0 h, rep2 (miRNA-seq)

value: without spraying (control)

value: 0 h


title: leaves, sprayed with 200 mM IAA, 12 h, rep1 (miRNA-seq)


title: leaves, without spraying with 200 mM IAA, 0 h, rep1 (miRNA-seq)


title: leaves, sprayed with 200 mM IAA, 24 h, rep1 (miRNA-seq)


title: leaves, sprayed with 200 mM IAA, 24 h, rep2 (miRNA-seq)


title: leaves, sprayed with 200 mM IAA, 6 h, rep1 (miRNA-seq)

value: 6 h


title: leaves, sprayed with 200 mM IAA, 6 h, rep2 (miRNA-seq)


title: Mw_Cs1

city: Kolkata

first: Suparno

last: Chakrabarti

state: West Bengal

address: PGH Shah Road

department: Cellular Therapy and Immunology

country: India

institute: Manashi Chakrabarti Foundation

description: complementary DNA

data_processing:
FAST5 files were base-called with CPU based Guppy basecaller to generate fastq files.
Demultiplexing of the pooled samples and adapter removal was carried out using inbuilt algorithm of MinKNOW software.
A comprehensive report of the sequencing metrics was generated by NanoComp tool
Sample reads were subjected to a minimum phred quality score of 9 and reads with lower quality were filtered out using NanoFilt tool.
Differential Gene Expression (DGE) analysis was done using “pipeline-transcriptome-de” pipeline from Oxford nanopore technology
Assembly: GRCh38.p13
Supplementary files format and content: Differentially Expressed Genes with log2 Fold Change and associated p-value.

source_name: Peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated from whole blood samples by density gradient centrifugations using HiSep™ LSM 1077 media (Himedia, Mumbai, India). 5 x 106 PBMCs were used for RNA isolation using the Trizol method and followed by DNase treatment for RNA purification. Purified RNA was quantified using a Qubit 4.0 fluorometer. Take 5μg of total RNA used for the polyA RNA selection using NEB NEXT oligo d(T)25 beads (NEB, MA, USA). PolyA RNA was quantified and integrity assessed using Qubit 4.0 fluorometer (Invitrogen, Waltham, Massachusetts, United States) according to manufacturer instructions.
Libraries were prepared according to Oxford nanopore technologies protocol accompanying the Direct cDNA Native Barcoding Sequencing kit (SQK-DCS109 with EXP-NBD104, Oxford, UK). 100ng of polyA RNA was used for the library preparation. Using H minus Reverse Transcriptase (Invitrogen, Waltham, Massachusetts, United States), complementary DNA (cDNA) was synthesised, followed by RNA degradation and second-strand synthesis of cDNA. Double-stranded cDNA was used for the end preparation, followed by native barcoding and adaptor ligation (all steps were followed, according to the manufacturer’s instructions). Ligated cDNA was loaded on the flow cell (R9.4.1) in MinION and were sequenced specifying 72 hours protocol. MinKNOW (v21.06.10, Microsoft Windows OS based) was used to generate FAST5 files.

treatment_protocol: 0.1 ml Mycobacterium-w (Mw, Sepsivac, Cadila Pharmaceuticals, India)  and atleast one dose of ChAdOx1 nCoV-19 vaccine administration intradermally in each arm (Mw + ChAdOx1 group) and two doses of 0.5 ml ChAdOx1 nCoV-19 vaccine.

value: Peripheral blood

value: mononuclear cells

value: Mw and Covishield treated


title: Mw_Cs2

description: complementary DNA


title: Mw_Cs4

description: complementary DNA


title: Mw_Cs3

description: complementary DNA


title: Cs4

description: complementary DNA

value: Covishield treated


title: Donor 3 (S3), CD4+ isolated post colture (POSTc), plasma (PLSM), unstimulated (US)

description: S3 POSTc PLSM US

value: Blood

value: HIV


title: Cs2

description: complementary DNA


title: Cs1

description: complementary DNA


title: Cs3

description: complementary DNA


title: aged.pADA

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

library_source: transcriptomic single cell

data_processing:
Preprocessing of scRNA-seq data was done using CellRanger Suite (v3.1.0, https://support.10xgenomics.com) with refdata-cellranger-mm10-3.0.0 transcriptome as a reference
Assembly: mm10
Supplementary files format and content: standard cellranger output

organism: Mus musculus

source_name: aged mouse, pADA treated

extract_protocol:
Single cell droplets were generated using the Chromium next gem single cell 3' kit v3.1 (10x Genomics)
cDNA synthesis and amplification, library preparation and indexing were done using the 10x Genomics Library Preparation kit (10x Genomics)
10x genomics single cell RNA-seq

value: lymph node

tag: age

value: aged

value: pADA


title: aged.pS

source_name: aged mouse, pS treated

value: pS


title: N3-H-iG-H2A

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 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

molecule: genomic DNA

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

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. 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 HiSeq 4000, 150 cycles total per lane, 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.

tag: cell line

value: Hepatocarcinoma

tag: antibody


title: N3-H-LK-H3


title: N3-H-LK-H4


title: N3-H-DJ-PolII

value: Pol-II


title: N3-H-LK-H2A


title: N3-H-LK-PolII


title: N3-H-DJ-H4


title: N3-H-iG-H3


title: N2-H-LK-PolII


title: N3-H-DJ-H3


title: N3-H-iG-H4


title: N3-H-iG-PolII


title: young.naive

source_name: young mouse, untreated

value: young

value: naive


title: young.pS

source_name: young mouse, pS treated


title: N2-H-iG-H4


title: N2-H-iG-PolII


title: N3-H-DJ-H3K27me3T


title: N2-H-iG-H3


title: young.pADA

source_name: young mouse, pADA treated


title: N2-H-LK-H2A


title: N2-H-LK-H4


title: N3-H-DJ-H2A


title: aged.naive

source_name: aged mouse, untreated


title: s9, scRNAseq

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

country: United Kingdom

institute: University of Birmingham

description: 10x Genomics

data_processing:
Raw reads were processed using CellRanger (10X Genomics, v5.0.1) functions mkfastq and count. Raw bcl files were converted to fastq and aligned to the human reference genome GRCh38
Assembly: GRCh38
Supplementary files format and content: Counts matrix with raw feature counts for each cell

source_name: Adjacent normal Esophagus

growth_protocol: Tumor tissue was collected in MACS® Tissue Storage Solution (Miltenyi Biotec) and cut into small fragments (<0.5mm3) prior to placement in a gentleMACS™ C Tube (Miltenyi Biotec) containing 5ml pre-warmed DMEM media supplemented with 10% FCS, 1% Penicillin/Streptomycin (all Life Technologies), 100µg/ml Primocin (InvivoGen), 1X Gentle Collagenase/Hyaluronidase (STEMCELL™ Technologies), 125µg/ml Liberase TL (Roche) and 50U/ml Benzonase® (Sigma-Aldrich). Dissociation of tissue fragments was achieved using a gentleMACS™ dissociator (Human Tumor Programme 1, 2 and 3) with incubation at 37oC for 30 minutes between each agitation. The single cell suspension was filtered through a 70µm filter and red blood cells were subsequently lysed. Cells were washed and resuspended in MACS buffer (PBS, 0.5% BSA, 2 mM EDTA) prior to immunostaining and FACS sorting.  Single cell suspensions of digested tumor tissue were surface stained with anti-CD45 BV785 (2D1, Biolegend), anti-EpCAM APC (9C4, Biolegend) and anti-Podoplanin AF488 (NC-08, Biolegend) to confirm the presence of immune cells, epithelial cells and fibroblasts, respectively. PI was added prior to sorting to exclude non-viable cells. Sorted cell populations were adjusted to 1x 103/ml.

extract_protocol:
PI was added prior to sorting to exclude non-viable cells. Live CD45+ and CD45- populations were sorted and adjusted to 1 x 103/ml.
Samples with >85% cell viability were processed at the Genomics Birmingham Sequencing Facility (University of Birmingham, UK) for gene expression profiling using the 10X Genomics platform. Around 1.7 x 104 cells per sample were processed using the Chromium Controller (10X Genomics) for a recovery of 1 x 104 cells per sample, and library preparation was performed using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 according to manufacturer’s instructions. Library quantification and quality control was performed using TapeStation (Agilent). Samples were sequenced on an Illumina NextSeq 500 (150 bps, paired-end) at a sequencing depth of >50,000 raw reads/cell.
Illumina NextSeq 500 (150 bps, paired-end) at a sequencing depth of >50,000 raw reads/cell.

value: Adjacent normal Esophagus

value: Mixed

value: Adjacent Normal


title: N2-H-LK-H3


title: s10, scRNAseq

description: 10x Genomics

source_name: EAC tissue post NACT

value: EAC tissue post NACT

value: post NACT


title: N2-H-DJ-PolII


title: N2-H-iG-H2A


title: s8, scRNAseq

description: 10x Genomics

source_name: EAC tissue pre NACT

value: EAC tissue pre NACT

value: pre NACT


title: s7, scRNAseq

description: 10x Genomics


title: s6, scRNAseq

description: 10x Genomics


title: s5, scRNAseq

description: 10x Genomics


title: N2-H-DJ-H3


title: N2-H-DJ-H4


title: N2-H-DJ-H3K27me3T


title: s1, scRNAseq

description: 10x Genomics


title: s3, scRNAseq

description: 10x Genomics


title: N2-H-DJ-H2A


title: s4, scRNAseq

description: 10x Genomics


title: N1-H-LK-PolII


title: NoAb on MED8A SMARCD3 KO-1 rep 3

city: Pittsburgh

first: Baoli

last: Hu

address: 4401 Penn Ave

department: Neurological Surgery

institute: University of Pittsburgh School of Medicine

data_processing:
Library strategy: Cut & Run
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 bowtie2 (v.1.2.0).
qPCR duplicates were removed with sambamba (v.0.6.8).
Replicates were combined with wiggletools (v.1.2.3).
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files for each replicates and combined replicates.

source_name: MED8A cell line

extract_protocol:
DNA was isolated using Qiagen MinElute Reaction Cleanup Kit.
Samples were then PCR amplified using NEBNext High-Fidelity 2X PCR Master Mix and 25µM of Nextera 70* and 25µM Nextera 50* primers.

value: No antibody

value: SMARCD3 KO-1


title: NoAb on MED8A SMARCD3 KO-1 rep 1


title: s2, scRNAseq

description: 10x Genomics


title: NoAb on MED8A SMARCD3 KO-1 rep 2


title: NoAb on MED8A SMARCD3 WT rep 3

value: SMARCD3 WT


title: N1-H-LK-H4


title: N1-H-iG-H4


title: N1-H-LK-H3


title: N1-H-iG-H2A


title: N1-H-DJ-PolII


title: N1-H-iG-PolII


title: N1-H-LK-H2A


title: N1-H-iG-H3


title: N1-H-DJ-H4


title: NoAb on MED8A SMARCD3 WT rep 2


title: N1-H-DJ-H3


title: NoAb on MED8A SMARCD3 WT rep 1


title: N1-H-DJ-H3K27me3T


title: H3K9me3 on MED8A SMARCD3 KO-1 rep 2

value: H3K9me3 (Catlog#Ab8898; Abcam)


title: H3K9me3 on MED8A SMARCD3 WT rep 1


title: H3K9me3 on MED8A SMARCD3 KO-1 rep 1


title: H3K9me3 on MED8A SMARCD3 WT rep 2


title: H3K27me3 on MED8A SMARCD3 WT rep 1

value: H3K27me3 (Catlog#07-449; Millipore)


title: H3K27me3 on MED8A SMARCD3 KO-1 rep 2


title: H3K27me3 on MED8A SMARCD3 WT rep 2


title: N3-H-LK-H3K27me3T


title: N3-H-iG-H3K9me3


title: N3-H-LK-H3K9me3


title: N3-H-LK-H3K27ac


title: N3-H-LK-H3K4me3


title: N3-H-iG-H3K27me3T


title: N3-H-iG-H3K4me3


title: H3K27me3 on MED8A SMARCD3 KO-1 rep 1


title: N3-H-iG-H3K27ac


title: N2-H-LK-H3K9me3


title: N2-H-LK-H3K4me3


title: N2-H-LK-H3K27me3T


title: H3K4me3 on MED8A SMARCD3 KO-1 rep 2

value: H3K4me3 (Catlog#05-745R; Millipore)


title: H3K27ac on MED8A SMARCD3 WT rep 2

value: H3K27ac (Catlog#Ab4729; Abcam)


title: H3K27ac on MED8A SMARCD3 KO-1 rep 1


title: H3K4me3 on MED8A SMARCD3 KO-1 rep 3


title: H3K27ac on MED8A SMARCD3 WT rep 1


title: H3K4me3 on MED8A SMARCD3 KO-1 rep 1


title: N1-H-DJ-H2A

value: Hepatocarcinoma


title: N2-H-iG-H3K4me3


title: N2-H-iG-H3K9me3


title: H3K4me3 on MED8A SMARCD3 WT rep 3


title: H3K27ac on MED8A SMARCD3 KO-1 rep 2


title: N2-H-iG-H3K27me3T


title: N2-H-iG-H3K27ac


title: N2-H-LK-H3K27ac


title: H3K4me3 on MED8A SMARCD3 WT rep 1


title: MED8A SMARCD3 KO-1 rep 1 [ATAC-Seq]

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 bowtie2 (v.1.2.0).
qPCR duplicates were removed with sambamba (v.0.6.8).
Replicates were combined with wiggletools (v.1.2.3).
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files for each replicates and combined replicates.

tag: tag


title: H3K4me1 on MED8A SMARCD3 KO-1 rep 1

value: H3K4me1 (Catlog#710795; Thermo Fisher Scientific)


title: MED8A SMARCD3 KO-1 rep 3 [ATAC-Seq]


title: H3K4me1 on MED8A SMARCD3 WT rep 1


title: N1-H-LK-H3K4me3


title: N1-H-LK-H3K9me3


title: MED8A SMARCD3 WT rep 3 [ATAC-Seq]


title: MED8A SMARCD3 WT rep 1 [ATAC-Seq]


title: N1-H-LK-H3K27me3T


title: MED8A SMARCD3 WT rep 2 [ATAC-Seq]


title: N1-H-LK-H3K27ac


title: N1-H-iG-H3K27ac


title: N3-H-LK-K9me3


title: N3-H-LK-K27ac


title: DpC_3

city: Darlinghurst

first: Heloisa

middle: Helena

last: Milioli

state: NSW

address: 384, Victoria St

department: Cancer

country: Australia

institute: Garvan Institute of Medical Research

description: Human (hg19)

data_processing:
The next generation sequencing data was processed on the Illumina System.
Genome-guided alignment to a human reference (GRCh38) was performed using Rsubread.
Feature counts were computed in R using the package Rsubread.
The differential gene expression analysis was conducted with edgeR and limma packages in the R environment.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: Cell line

extract_protocol:
Isolation of mRNA was then performed using TRIzol® (Invitrogen) according to the manufacturers’ procedures.
RNA sequencing was performed by next generation sequencing (NGS) using the Illumina NextSeq technology at the Ramaciotti Centre for Genomics. Sequences were trimmed using Trim Galore (version 0.4.4) and genome-guided alignment to a human reference (HG38) was performed using the STAR software (version 2.5). Volume: 20 ul, Concentration:  100 ng/ul

treatment_protocol: cell lines protocol: MCF-7 cells were treated with either control media or media containing DpC (5 μM) for 24 h.

value: breast cancer

tag: condition

value: DpC


title: N1-H-iG-H3K27me3T


title: N3-H-DJ-K9me3


title: DpC_1

description: Human (hg19)


title: H3K4me3 on MED8A SMARCD3 WT rep 2


title: N1-H-iG-H3K9me3


title: Control_2

description: Human (hg19)

value: Control


title: MED8A SMARCD3 KO-1 rep 2 [ATAC-Seq]


title: N1-H-iG-H3K4me3


title: Control_1

description: Human (hg19)


title: N3-H-DJ-K4me3


title: N3-H-LK-K4me3


title: N2-H-LK-K27ac


title: N2-H-DJ-K9me3


title: N2-H-LK-K9me3


title: DpC_2

description: Human (hg19)


title: Control_3

description: Human (hg19)


title: N2-H-DJ-K4me3


title: ICN13-VCR 2 nM RNA 7/30/18 rep 1

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

data_processing:
RNA-seq results were aligned to GRCh38.
alignment to the UCSC Genome assembly GRCh38.p13 (GCA_000001405.28) genome annotation files (around 19,862 mainly protein-encoding genes but not including IGHM).
Reads were quality-checked and processed using the nf-core/rnaseq analysis workflow v1.3 pipeline consisting of Nextflow v19.04.1, FastQC v0.11.8 Cutadapt v2.4, Trim Galore! v0.5.0, STAR vSTAR_2.6.1d, HISAT2 v2.1.0, Picard MarkDuplicates v2.18.27, Samtools v1.9, featureCounts v1.6.4, StringTie v1.3.5, Preseq v2.0.3, deepTools, v3.2.0, RSeQC v3.0.0, MultiQCv1.7 software.
Raw count results were analyzed using edgeR (RNA-seq differential expression analysis, two groups) against hg38 to determine significantly regulated genes (criteria: fold change ≥2; p<0.05; low expression filter rpkm <1.0).
QIAGEN Ingenuity Pathway Analysis (IPA) version 62089861 was used to analyse results of RNA-seq for the d30/4 nM vincristine data set for pathways with differential regulation using p-values and FDR at <0.05 and logFc at -1.0 – 1.0
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Gene_rawcounts_vincristine.txt

source_name: ICN13 PDX/patient-derived pre-B ALL cells

growth_protocol: ICN13 cells are stromal-dependent and were grown in co-culture with mitotically inactivated OP9 bone marrow stromal cells (ATCC CRL-2749). OP9 cells allowed to adhere overnight were treated with 10 µg/ml mitomycin C for 3 hrs in complete medium, washed, and used for co-culture with human ALL cells. Cells were co-cultured in α-MEM media supplemented with 20% FBS, 1% L-glutamine and 1% penicillin/streptomycin (Life Technologies, Grand Island, NY).

extract_protocol:
RNA was extracted from frozen cell pellets using Trizol (ThermO-Fisher 315596026) and further purified using an RNEasy Mini kit (Qiagen #74104). Quality control analysis was done using Bioanalyzer RNA Nano and D1000Chips. Nucleic acid concentrations were determined by Qubit.
The mRNA library was prepared using an Illumina Truseq Stranded mRNA High Throughput Prep kit and samples were sequenced using an Illumina NextSeq 500 Mid-Output Sequencing Reagent kit (v2, 150 cycles), 132 M reads on an Illumina NextSeq 500 instrument.

treatment_protocol: Vincristine sulphate diluted in PBS at different concentrations was added freshly every 3 days. Cells cultured with 2 nM vincristine or 4 nM were collected from triplicate wells at day 18 and d30, respectively, along with controls cultured for the same period of time but without drug. Each biological replicate consisting of  1x10^6 cells was used for RNA sequencing. Samples were stored at -80°C until analysis.

value: tissue cultured cells

value: Precursor B leukemia cells

tag: individual

value: 15 year-old female

tag: time in co-culture

value: 18 days

tag: translocation

value: MLL-AF4 t(4;11)(q21;q23) translocation

value: 2 nM vincristine


title: ICN13-VCR 2 nM RNA 7/30/18 rep 3


title: N1-H-LK-K4me3


title: ICN13-PBS RNA 8/1/18 rep 1

value: 30 days

value: no drug (PBS control)


title: ICN13-PBS RNA 7/30/18 rep 3


title: N1-H-DJ-K9me3


title: N3-H-DJ-K27ac


title: ICN13-PBS RNA 7/30/18 rep 2


title: N1-H-DJ-K4me3


title: ICN13-VCR 4 nM RNA 8/1/18 rep 3

value: 4 nM vincristine


title: N1-H-DJ-K27ac


title: ICN13-VCR 4 nM RNA 8/1/18 rep 2


title: ICN13-PBS RNA 7/30/18 rep 1


title: N2-H-LK-K4me3


title: ICN13-VCR 4 nM RNA 8/1/18 rep 1


title: ICN13-PBS RNA 8/1/18 rep 3


title: N2-H-DJ-K27ac


title: ICN13-PBS RNA 8/1/18 rep 2


title: LX-2 cells, Treat-2

city: Kunming

first: hai

last: liu

address: yuhua road

institute: Kunming Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count and  FPKM values for each sample

growth_protocol: LX-2 cells, grown in DMEM (Gibco, USA) with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The cells were activated via treatment with 10 ng/ml of TGF-β1 for 24 h in serum-free media.

value: Human hepatic stellate cells


title: N1-H-LK-K9me3


title: LX-2 cells, Control-3


title: N1-H-LK-K27ac


title: IH69 THC/SIV

type: RNA

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:
QuantStudio run files representing all treatment groups and timepoints were analyzed using ExpressionSuite Software (Life Tech). The results from the ExpressionSuite software analysis containing five columns (well, sample, detector, task and CT values) were saved as a tab-delimited text file which was later imported and analyzed using the Omics Office StatMiner qPCR analysis software, TIBCO Spotfire, (Perkin Elmer, Waltham, MA). Omics Office StatMiner Software utilizes the comparative Cτ (ΔΔCτ) method to rapidly and accurately quantify relative gene expression across many genes and samples.
miRNA expression data was normalized using the global normalization method.
In all experiments, the CT upper limit was set to 28 meaning that all miRNA detectors with a CT value greater than or equal to 28 were excluded.
Due to the small sample size and exploratory nature of the study multiple comparisons correction was not applied. However, differentially expressed miRNAs were confirmed using RT-qPCR.
Omics Office StatMiner qPCR analysis software automatically calculates all deltadeltaCT based fold-change calculations and provides p values from the uploaded QuantStudio data files.
Matrix normalized worksheet reports normalized signal (Normalization using global normalization method).
Fold Change worksheet reports test-1/control (i.e., VEH/SIV vs Uninfected control) and test-1 vs test-2 (THC/SIV vs VEH/SIV) ratios.

organism: Macaca mulatta

source_name: Gingiva

label_protocol: microRNA profiling was performed using the TaqMan® OpenArray® Human microRNA panels (Life Tech) following the manufacturer’s instructions. Reverse transcription was first performed from 100 ng of total RNA using the microRNA reverse transcription kit. 2.5 µL of cDNA was preamplified using the TaqMan® PreAmp Master Mix kit. Preamplified products were first diluted and then loaded onto to OpenArray plates. OpenArray plates were run on the QuanStudio™ 12K Flex Real-Time PCR system (ThermoFisher Scientific) following the manufacturer’s recommended thermal cycling conditions.

extract_protocol: Total RNA (small and large) was extracted using the miRNeasy Mini kit (Qiagen). On-column DNase digestion was also performed to eliminate contaminating genomic DNA.

treatment_protocol: 10 animals were infected intravenously with 100 TCID50 SIVmac251 and 4 remained uninfected. Six SIV-infected rhesus macaques were administered delta-9-tetrahydrocannabinol at 0.18 mg/kg one month before SIV Infection and increased to 0.32 mg/kg on the day of SIV infection until 6 months post SIV infection. Four SIV-infected rhesus macaques were administered the same volume of vehicle one month before SIV Infectionuntil 6 months post SIV infection.

tag: (treatment)

value: SIV infected and THC treated


title: IA04 THC/SIV


title: JB82 THC/SIV


title: HI09 THC/SIV


title: LX-2 cells, Treat-3


title: GV60 THC/SIV


title: LX-2 cells, Control-1


title: LX-2 cells, Control-2


title: ICN13-VCR 2 nM RNA 7/30/18 rep 2


title: JC81 VEH/SIV

value: SIV Infected and Vehicle treated


title: IN24 VEH/SIV


title: HV48 VEH/SIV


title: IH96 VEH/SIV


title: JE51 Uninfected Controls

description: Control

value: Untreated/uninfected


title: LX-2 cells, Treat-1


title: HH75 Uninfected Controls

description: Control


title: HH69 Uninfected Controls

description: Control


title: HF34 Uninfected Controls

description: Control


title: IA83 THC/SIV


title: RNA_LUSC6

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC

data_processing:
In-line UMI sequences were trimmed from the sequencing reads with Marianas (https://github.com/mskcc/Marianas) and aligned to human GRCh37 genome using STAR 2.7.0 (https://github.com/alexdobin/STAR) [25] with Ensembl v75 gene annotation.
Hybrid selection-specific metrics and alignment metrics were calculated for the BAM files using CalculateHsMetrics and CollectRnaSeqMetrics, respectively, from Picard Toolkit (https://github.com/broadinstitute/picard) to determine the quality of the capture.
We quantified RNA-seq reads with Kallisto v.0.45.053 to obtain transcript counts and abundances.
Transcript per million (TPM) normalization by size factors was done from Kallisto output files using Sleuth v0.30.0 run in gene mode.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file with TPM values over all genes for each sample.

source_name: Lung

extract_protocol:
FFPE sections were deparaffinized in mineral oil. Briefly, 800µL mineral oil (Fisher Scientific, #AC415080010) and 180µL Buffer PKD were mixed with the sections, Proteinase K was added for tissue digestion, and the sample was incubated at 56 °C for 15 min. Phase separation was encouraged with centrifugation, and the aqueous phase was chilled 3 min to precipitate RNA. After centrifugation for 15 min at 20,000 g, RNA-containing supernatant was removed for extraction, while DNA remained in the pellet. Nucleic acids were subsequently extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN, #80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water and DNA in 0.5X Buffer ATE.
Approximately 500 ng of FFPE RNA or 100 ng of fresh frozen RNA per sample was used for RNA library construction using the KAPA RNA Hyper library prep kit (Roche, Switzerland) per the manufacturer’s instructions with minor modifications. Customized adapters with unique molecular indexes (UMI) (Integrated DNA Technologies, US) and Sample-specific dual-indexes primers (Integrated DNA Technologies, US) were added to each library. The quantity of libraries was measured with Qubit (Thermo Fisher Scientific, US) and quality measured by TapStation Genomic DNA Assay (Agilent Technologies, US). Equal amounts of each RNA library (around 500 ng) were pooled for hybridization capture with IDT Whole Exome Panel V1 (Integrated DNA Technologies, US) using a customized capture protocol modified from NimbleGen SeqCap Target Enrichment system (Roche, Switzerland). The captured DNA libraries were then sequenced on an Illumina HiSeq4000 with paired end reads (2 Å ~ 100 bp), at 50millions reads/sample.

value: Lung

tag: disease state

value: Lung squamous carcinoma


title: RNA_LUSC7

tag: genotype


title: RNA_LUSC3

tag: tissue


title: RNA_LUSC5


title: RNA_LUSC8


title: RNA_LUSC2


title: RNA_LUAD11

value: Lung adenocarcinoma


title: RNA_LUSC10

value: Control


title: RNA_LUSC11


title: RNA_LUSC1


title: RNA_LUSC4


title: RNA_LUAD8


title: RNA_LUAD10


title: RNA_LUSC9


title: PAN-CB-P10A

city: Memphis

first: John

last: Easton

state: TN

address: 1383 Island Town Dr

department: Computational Biology

institute: St.Jude Children's Research Hospital

description: Single cell were isolated from the cerebellum using Papain dissociation method,resuspended in PBS with 0.4% BSA (https://doi.org/10.1016/j.cub.2018.07.062)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 1.1.0  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/1.0/using/demultiplex)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cerebellum

extract_protocol:
The cerebellum was dissociate following papin enzyme protocol. More details of method refer Carter et.al. Current Biology 28, 2910–2920
The single cells were captured in the droplet in the Chromium droplet generator.The cDNA and Library was generated following Single cell gene expression Kit  V1  from 10X Genomics.
Single cell Gene expression Kit from V1 from 10X Genomics.

value: Cerebellum

tag: biological replicates


title: PAN-CB-E15A


title: PAN-CB-E11B


title: PAN-CB-E16A


title: PAN-CB-E15B


title: PAN-CB-E16B


title: PAN-CB-P10B


title: RNA_LUAD7


title: PAN-CB-E14B


title: RNA_LUAD6


title: PAN-CB-E14A


title: RNA_LUAD5


title: PAN-CB-E12B


title: RNA_LUAD15


title: RNA_LUAD4


title: PAN-CB-E12A


title: RNA_LUAD2


title: RNA_TLUAD19

value: Transforming


title: PAN-CB-P0A


title: PAN-CB-P7A


title: RNA_LUAD1


title: PAN-CB-P0B


title: RNA_LUAD3


title: PAN-CB-E11A


title: PAN-CB-P7B


title: RNA_TLUSC17


title: RNA_TLUSC16


title: PAN-CB-E17B


title: RNA_TLUSC10


title: RNA_TLUSC11


title: RNA_TLUAD11


title: RNA_TLUAD10


title: PAN-CB-P4B


title: PAN-CB-E17A


title: RNA_TLUSC9


title: PAN-CB-E13B


title: PAN-CB-E13A


title: TCKO_3

city: ShangHai

first: Lijun

state: China

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

description:
mRNA
TCKOvsWT_all.xls

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13.
Clean Reads mapped to GRCm38 genome using Hisat2.
Count counting.
Genome_build: GRCm38
Supplementary_files_format_and_content: TCKOvsWT_all.xls: Excel file contains counts for each sample.

source_name: Tet KO osteoblasts

growth_protocol: Cells were cultured in a-MEM containing 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Cells were collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Primary osteoblasts were isolated from 3-day-old WT and TCKO mice. After 3-day culture, cells were harvested and divided into two parts for RNA and DNA extraction.

tag: strain

tag: genotype/variation

value: Tet KO

value: osteoblasts

value: 3 days


title: RNA_TLUSC7


title: WT_3

description:
mRNA
TCKOvsWT_all.xls

source_name: WT osteoblasts

value: WT

tag: cell type


title: RNA_TLUSC14


title: RNA_TLUAD7


title: RNA_TLUSC5


title: TCKO_2

description:
mRNA
TCKOvsWT_all.xls


title: PAN-CB-P4A


title: RNA_TLUAD4


title: hMSCs si rep3

city: Hangzhou

first: Soup

last: Chen

address: Qiutao North road

institute: Zhejiang University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index ofthe reference genome was builtusing Hisat2 v2.0.5 andpaired-end clean reads were aligned to the reference genome using Hisat2v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Homo_sapiens_Ensemble_94.fa
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: human mesenchymal stem cells

growth_protocol: high-glucose DMEM

extract_protocol:
human bone marrow were extracted, cultured in high-glucose DMEM and RNA was harvested using Trizol reagent.
Libraries were prepared according to Illumina's instructions of RNA sample. Paired-end method was adopted for further processes.

value: bone marrow

tag: treatment

value: treated with AFF4 siRNA

value: human mesenchymal stem cells


title: RNA_TLUSC4


title: RNA_TLUSC2


title: RNA_TLUSC3


title: WT_1

description:
mRNA
TCKOvsWT_all.xls

tag: age


title: TCKO_1

description:
mRNA
TCKOvsWT_all.xls


title: hMSCs si rep1


title: hMSCs si rep2


title: RNA_TLUAD9


title: WT_2

description:
mRNA
TCKOvsWT_all.xls


title: hMSCs WT rep2

value: treated with control siRNA


title: hMSCs WT rep1


title: RNA_TLUAD1


title: animal Z5 at DPI 0

city: MONTPELLIER

first: Sophie

last: Thévenon

address: TA A-17/G Campus International de Baillarguet

department: BIOS

country: France

institute: CIRAD

data_processing:
Alignment using STAR 2.4.0j. The STAR index was generated from a unique FASTA file obtained by concatenation of the bovine and trypanosome sequences files. A maximum of three mismatches were allowed and multi-mapping to up to 20 different positions was permitted according to the following parameters: --alignIntronMin 50 --alignIntronMax 500000 --outFilterMultimapNmax 20 --outFilterMismatchNmax 4 --outSAMunmapped Within
Bovine genes count performed using FeatureCounts (Subread package 1.4.6-p4). Bovine gene annotation was downloaded from Ensembl 79 (sequence UMD 3.1). Reads were assigned at the exon level and counts were summarized at the gene level, using default parameters (-t exon -g gene_id), corresponding to unambiguously assign uniquely aligned single-end reads and reversely stranded reads (-s 2).
Genome_build: Bos taurus UMD 3.1, Trypanosoma congolense IL3000 TriTryp DB release 9
Supplementary_files_format_and_content: Matrix table with raw gene counts for each gene and each sample

organism: Bos taurus

source_name: whole blood

extract_protocol:
RNAs were extracted from blood samples using the Tempus™ Spin RNA Isolation Kit (Applied Biosystems™, USA) according to manufacturer instructions. RNA was finally eluted using 80 µl RNase-free buffer. Total RNA was checked and quantified on a Bioanalyzer  using RNA 6000 nano kit (Agilent). Six sample per breed with RNA integrity number >=8.70 were chosen.
RNA-seq libraries were constructed at the MGX platform in Montpellier (France) using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s instruction.

treatment_protocol: Cattle blood samples were collected at the jugular vein using Tempus™ Blood RNA Tubes (Applied Biosystems™, USA), which allowed blocking immediately mRNA transcription and degradation

value: whole blood

tag: breed

value: Zebu Fulani

tag: trypanotolerance

value: trypanosusceptible

tag: animal

tag: identifier

tag: date of sampling

value: 0 days

tag: multiplex

tag: infection

value: not infected


title: ASO-42-1

city: Toronto

first: Yanan

last: Shan

state: ON

address: 4 Goldfinch Court, PH05

country: Canada

institute: Hebei Medical University

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: counts

source_name: human

extract_protocol: none provided by the submitter

value: knocking down of SNORA42

value: esophagus cancer


title: hMSCs WT rep3


title: NC-1

value: transfected with non-targeting control


title: RNA_TLUAD3

value: Lung

value: Lung adenocarcinoma

value: Transforming


title: RNA_TLUAD2


title: animal BA1 at DPI 0

value: Baoule

value: trypanotolerant


title: animal N5 at DPI 30

value: N'Dama

value: 30 days

value: T. congolense


title: animal Z5 at DPI 40

value: 40 days


title: animal BA3 at DPI 40

value: whole blood


title: animal N1 at DPI 0


title: animal Z4 at DPI 30

value: Zebu Fulani


title: RNA_TLUAD5


title: animal LA1 at DPI 40

value: Lagune


title: animal BO1 at DPI 30

value: Borgou

value: African taurine x zebu admixed breed


title: animal N3 at DPI 20

value: 20 days


title: animal N4 at DPI 30


title: animal LA4 at DPI 30


title: animal LA1 at DPI 0

value: 0 days

value: not infected


title: animal BO6 at DPI 0


title: animal BA7 at DPI 20


title: animal BA2 at DPI 40


title: animal LA3 at DPI 20


title: animal Z8 at DPI 0

value: trypanosusceptible


title: animal N8 at DPI 40


title: animal LA1 at DPI 30


title: animal BO2 at DPI 40


title: animal N4 at DPI 20


title: animal BO6 at DPI 30


title: animal BO1 at DPI 20


title: animal BA2 at DPI 30


title: animal N6 at DPI 0


title: animal Z3 at DPI 30


title: animal BA3 at DPI 0


title: animal Z4 at DPI 20


title: animal LA5 at DPI 40


title: animal LA2 at DPI 20


title: animal Z6 at DPI 40


title: animal LA5 at DPI 0


title: animal N6 at DPI 30


title: animal BO5 at DPI 30


title: animal N4 at DPI 40


title: animal LA3 at DPI 30


title: animal LA6 at DPI 20


title: animal BO4 at DPI 20


title: animal Z6 at DPI 0


title: animal BA3 at DPI 20


title: animal Z3 at DPI 40


title: animal BO7 at DPI 0


title: animal BA4 at DPI 30


title: animal BO6 at DPI 20


title: animal BO6 at DPI 40


title: animal N5 at DPI 0


title: animal LA1 at DPI 20


title: animal BA7 at DPI 0


title: animal BA2 at DPI 20


title: animal BO1 at DPI 0


title: animal BA7 at DPI 40


title: animal N3 at DPI 30


title: animal Z2 at DPI 30


title: animal LA3 at DPI 40


title: animal Z2 at DPI 20


title: animal N6 at DPI 40


title: animal N6 at DPI 20


title: animal LA6 at DPI 0


title: animal BO4 at DPI 40


title: animal LA2 at DPI 30


title: animal BO2 at DPI 20


title: animal BO4 at DPI 30


title: animal Z8 at DPI 20


title: animal BA8 at DPI 20


title: animal Z2 at DPI 0


title: animal N8 at DPI 0


title: animal Z4 at DPI 0


title: animal Z8 at DPI 40


title: animal BA7 at DPI 30


title: animal BA4 at DPI 40


title: animal Z5 at DPI 30


title: animal LA6 at DPI 40


title: animal N8 at DPI 30


title: animal BA4 at DPI 0


title: animal BO2 at DPI 30


title: animal Z3 at DPI 0


title: animal LA3 at DPI 0


title: animal BO2 at DPI 0


title: animal N5 at DPI 20


title: animal LA5 at DPI 20


title: animal BO5 at DPI 0


title: animal BA1 at DPI 20


title: CB_P47T/P47T_F10

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

data_processing:
The short-sequenced reads were mapped to the mouse reference genome (mm10) by the splice junction aligner TopHat V2.0.10.
We employed several R/Bioconductor packages to calculate gene expression abundance at the whole-genome level using the aligned records (BAM files) and to identify differentially expressed genes between WwoxWT/WT and WwoxP47T/P47T mice.
Normalization and differentially expression analysis were performed using EdgeR Bioconductor package
Assembly: mm10
Supplementary files format and content: Annotated tab-delimited text files include count values for each sample

source_name: Brain

extract_protocol:
RNA was isolated from HPC, PFC, (parietal) CTX, and CB from WwoxWT/WT and WwoxP47T/P47T mice, 150-280 days of age, n=5 mice/group (2 males, 3 females). Mice were euthanized, brains were extracted, and different tissue regions were collected on a cold plate and flash frozen in liquid N2. Total RNA was extracted using TRIzol reagent (Invitrogen) following standard manufacturer’s protocol. RNA concentration and integrity were measured on an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA samples with RNA integrity number (RIN) over 8.0 were considered for RNA sequencing.
The samples were processed for mRNA-seq library construction using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre) according to the manufacturer's protocol.
We performed 76 nt paired-end sequencing using an Illumina HiSeq3000 platform and obtained ~40 million tags per sample.

value: Brain

tag: region

value: Cerebellum

value: Wwox P47T/P47T


title: animal N5 at DPI 40

value: trypanotolerant


title: CB_P47T/P47T_F8


title: CB_P47T/P47T_M6


title: N3-M-LK-PolII

source_name: Hepa 1-6

tag: cell line

value: Hepa 1-6

tag: disease

value: Hepatoma

tag: antibody

value: Pol-II


title: CB_WT/WT_F4

tag: tissue

tag: genotype

value: Wwox WT/WT


title: N3-M-LK-H4


title: CB_WT/WT_F5


title: N3-M-LK-H3


title: CB_WT/WT_M2


title: animal BA8 at DPI 40

value: whole blood

value: Baoule

value: 40 days

value: T. congolense


title: animal BO1 at DPI 40

value: Borgou

value: African taurine x zebu admixed breed


title: N3-M-LK-H2A


title: CB_WT/WT_M3


title: animal Z6 at DPI 30

value: Zebu Fulani

value: 30 days


title: N3-M-iG-PolII


title: animal LA5 at DPI 30

value: Lagune


title: CTX_P47T/P47T_F10

value: Brain

value: Parietal cortex


title: CTX_P47T/P47T_M6

value: Wwox P47T/P47T


title: N3-M-iG-H4


title: CTX_P47T/P47T_F9


title: CTX_P47T/P47T_F8


title: CTX_P47T/P47T_M7


title: animal BA8 at DPI 0

value: trypanotolerant

value: 0 days

value: not infected


title: CTX_WT/WT_F5


title: animal BA8 at DPI 30


title: CTX_WT/WT_M1


title: CTX_WT/WT_M2


title: CTX_WT/WT_M3


title: N3-M-iG-H3

value: Hepa 1-6

value: Hepatoma


title: N3-M-DJ-PolII

value: Pol-II


title: animal Z5 at DPI 20

value: whole blood

value: trypanosusceptible

value: 20 days


title: CTX_WT/WT_F4

value: Wwox WT/WT


title: N3-M-iG-H2A


title: animal N1 at DPI 20

value: N'Dama

value: T. congolense


title: HPC_P47T/P47T_F8

value: Hippocampus


title: HPC_P47T/P47T_F10


title: N3-M-DJ-H4


title: HPC_P47T/P47T_M6


title: HPC_P47T/P47T_F9


title: animal BO5 at DPI 20

value: Borgou

value: African taurine x zebu admixed breed


title: N3-M-DJ-H3


title: HPC_P47T/P47T_M7

value: Brain


title: animal N4 at DPI 0


title: HPC_WT/WT_F4


title: HPC_WT/WT_F5


title: N3-M-DJ-H3K27me3T


title: HPC_WT/WT_M1


title: animal LA4 at DPI 0

value: Lagune


title: animal BA2 at DPI 0

value: Baoule

value: trypanotolerant


title: N3-M-DJ-H2A


title: HPC_WT/WT_M3


title: HPC_WT/WT_M2


title: N2-M-LK-H4


title: animal Z2 at DPI 40

value: Zebu Fulani

value: 40 days


title: animal Z4 at DPI 40


title: PFC_P47T/P47T_M6

value: Prefrontal cortex

value: Wwox P47T/P47T


title: PFC_P47T/P47T_F10


title: PFC_P47T/P47T_F8


title: N2-M-LK-H3

value: Hepa 1-6

value: Hepatoma


title: PFC_P47T/P47T_M7


title: animal N3 at DPI 40

value: whole blood


title: PFC_WT/WT_F4

value: Wwox WT/WT


title: N2-M-LK-H2A


title: PFC_WT/WT_F5


title: animal BO5 at DPI 40


title: PFC_WT/WT_M1


title: N2-M-iG-PolII

value: Pol-II


title: PFC_WT/WT_M2


title: PFC_WT/WT_M3


title: N2-M-iG-H4


title: PFC_P47T/P47T_F9


title: animal Z8 at DPI 30

value: trypanosusceptible

value: 30 days

value: T. congolense


title: animal N1 at DPI 30

value: N'Dama


title: animal BA1 at DPI 40


title: N2-M-LK-PolII


title: animal BA3 at DPI 30


title: N2-M-iG-H2A


title: N2-M-iG-H3


title: N2-M-DJ-PolII


title: animal Z6 at DPI 20

value: 20 days


title: N2-M-DJ-H3


title: animal N8 at DPI 20


title: animal LA4 at DPI 20

value: Lagune


title: N2-M-DJ-H3K27me3T


title: N2-M-DJ-H2A


title: animal LA2 at DPI 0

value: 0 days

value: not infected


title: animal BO4 at DPI 0

value: Borgou

value: African taurine x zebu admixed breed


title: N1-M-LK-PolII


title: animal LA4 at DPI 40

value: trypanotolerant

value: 40 days


title: animal N1 at DPI 40


title: animal BO7 at DPI 40


title: N1-M-iG-H4

value: Hepa 1-6


title: animal LA6 at DPI 30


title: N1-M-LK-H4

value: Hepatoma


title: animal BO7 at DPI 30

value: whole blood


title: N1-M-iG-H3


title: N2-M-DJ-H4


title: N1-M-DJ-H4


title: N1-M-DJ-PolII


title: animal BA1 at DPI 30

value: Baoule


title: animal Z3 at DPI 20

value: Zebu Fulani


title: animal LA2 at DPI 40


title: N1-M-LK-H3


title: N1-M-LK-H2A


title: animal N3 at DPI 0


title: N1-M-iG-PolII

value: Pol-II


title: animal BA4 at DPI 20


title: N1-M-DJ-H3


title: N1-M-iG-H2A


title: N1-M-DJ-H2A


title: N3-M-LK-H3K4me3


title: animal BO7 at DPI 20


title: N3-M-LK-H3K27me3T


title: R1-LiD-H-LK

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.

value: Hepatocarcinoma


title: R3-LiD-H-iG


title: R2-LiD-H-LK


title: R2-LiD-H-DJ


title: R1-LiD-H-DJ


title: R3-LiD-H-DJ


title: R3-LiD-H-LK


title: 2020A190_CTRL_2

city: Marseille

first: Stéphane

last: Zaffran

address: 27 Bd Jean Moulin

department: U1251 INSERM

institute: Aix Marseille Univ

data_processing:
Image analysis and base calling were performed using STAR v2.5.3a
Assembly: GRCm38
Reads were mapped onto the GRCh38 assembly of the Mus musculus genome using STAR v2.5.3a. Aligned reads in BAM format were annotated against the protein-coding mRNA regions. Stringtie v.1.3.1c platform was utilized to visualize the annotated/mapped read, quantify data (using corrected log2 transformed Reads Per Million Values of nonstrand specific, unmerged isoform), and perform percentile normalization. An intensity difference analysis method was used to identify differentially expressed genes (DEGs) on the normalized quantification data (DESeq2 (v1.18.1).).

source_name: Roche-Kapa mRNA HyperPrep kit

extract_protocol:
Anterior region of the embryo was microdissected, flash frozen on dry ice, and RNA was harvested using the NucleoSpin® RNA XS kit
cDNA was prepared from 500ng of total RNA using the Kapa mRNA HyperPrep Kit (Roche, #KR1352-v5.17) following manufacturer's instructions.

value: anterior region of the embryo

tag: Stage

tag: strain background

value: CTRL


title: 2020A193_Mut_2


title: 2020A192_Mut_1


title: R2-LiD-H-iG

tag: cell type


title: N3-M-iG-H3K9me3


title: N3-M-iG-H3K4me3


title: 2020A189_CTRL_1


title: N3-M-LK-H3K27ac


title: N2-M-LK-H3K9me3


title: N3-M-iG-H3K27me3T


title: 2020A194_Mut_3


title: N1-M-DJ-H3K27me3T


title: N3-M-iG-H3K27ac


title: N2-M-LK-H3K27me3T


title: N2-M-LK-H3K27ac


title: R1-LiD-H-iG


title: 2020A191_CTRL_3


title: N3-M-LK-H3K9me3


title: N2-M-iG-H3K9me3


title: N2-M-iG-H3K27me3T


title: Medial prefrontal cortex (mPFC) Non-avoiders s31

city: Göttingen

first: Thomas

last: Lingner

address: Rudolf-Wissell-Str. 28a

country: Germany

institute: Genevention GmbH

data_processing:
Base-calling was performed using the RTA software (2.0) integrated in the NextSeq platform
Read quality control was assessed with FastQC version 0.11.8
Reads were mapped to the mouse genome (mm10/GRCm38.p6) using the Star alignment software (version 2.5.3a)
Transcript quantification was performed using the FeatureCounts software of the Subread package (version 1.5.3) and GENCODE mouse annotation (version M17)
Genome_build: mm10/GRCm38.p6
Supplementary_files_format_and_content: unnormalized gene counts in FeatureCounts TSV format

source_name: brain

extract_protocol:
Animals were sacrificed by isoflurane inhalation followed by decapitation, brains were extracted instantaneously followed by freezing in methylbutane and storage at -80°C. Frozen brains were sectioned in a cryostat microtome (Microm HM 560 M, ThermoScientific) at 100µm. Sectioning temperature of the knife was -10°C and of the specimen -11°C. The mPFC, blA, and vHC regions were punched with a brain punch tissue needle (Leica Biosystems) and stored at -80°C until processing. Total RNA was extracted according to the manufacturer’s protocol using RNeasy Micro Kit (Qiagen) in combination with TRIzol (Thermo Fisher Scientific). RNA was stored at −80 °C and freshly diluted for application.
Clontech’s SMART-Seq v4 Ultra Low Input RNA Kit (112219) was used for cDNA generation from 0,5ng of total RNA, according to the manufacturer’s protocol. cDNA was amplified by 16 cycles of LD-PCR. NGS library preparation was performed from 1ng of cDNA with Illumina`s Nextera XT DNA library prep Kit Reference Guide (May 2019, Document: 15031942v05), and  amplified in 12 PCR cycles. Libraries were profiled in a High Sensitivity DNA Chip on a 2100 Bioanalyzer (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life Technologies). Samples were pooled in equimolar ratio and sequenced on 8 NextSeq 500 High output Flowcells, SR for 1x75 cycles plus 2x8 cycles for the dual index read.

value: Medial prefrontal cortex (mPFC)

tag: strain

value: brain

tag: behavioural phenotype

value: Non-avoiders


title: Medial prefrontal cortex (mPFC) Non-avoiders s73


title: Medial prefrontal cortex (mPFC) Non-avoiders s25


title: N2-M-LK-H3K4me3

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

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. 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 HiSeq 4000, 150 cycles total per lane, 2x75 paired-end reads, depth of >15M reads per sample.


title: Medial prefrontal cortex (mPFC) Non-avoiders s82


title: N1-M-LK-H3K27me3T


title: N1-M-LK-H3K4me3


title: Ventral hippocampus (vHC) Non-avoiders s81

value: Ventral hippocampus (vHC)


title: N1-M-LK-H3K27ac


title: N1-M-iG-H3K27me3T


title: Ventral hippocampus (vHC) Non-avoiders s33


title: Ventral hippocampus (vHC) Non-avoiders s75


title: Ventral hippocampus (vHC) Non-avoiders s78


title: N1-M-iG-H3K9me3


title: Ventral hippocampus (vHC) Non-avoiders s30


title: N2-M-iG-H3K27ac


title: N1-M-iG-H3K27ac


title: N2-M-iG-H3K4me3


title: Basolateral amygdala (blA) Non-avoiders s83

value: Basolateral amygdala (blA)


title: Medial prefrontal cortex (mPFC) Non-avoiders s28


title: Basolateral amygdala (blA) Non-avoiders s77


title: N1-M-LK-H3K9me3


title: Ventral hippocampus (vHC) Non-avoiders s27


title: N3-M-LK-K27ac


title: N3-M-LK-K9me3


title: N3-M-LK-K4me3


title: Ventral hippocampus (vHC) Non-avoiders s84


title: Basolateral amygdala (blA) Non-avoiders s32


title: Basolateral amygdala (blA) Discriminating-avoiders s26

value: Discriminating-avoiders


title: N2-M-LK-K9me3


title: N1-M-iG-H3K4me3


title: N3-M-DJ-K27ac


title: Medial prefrontal cortex (mPFC) Discriminating-avoiders s67


title: N2-M-LK-K4me3


title: Medial prefrontal cortex (mPFC) Discriminating-avoiders s64


title: Medial prefrontal cortex (mPFC) Discriminating-avoiders s22


title: N2-M-DJ-K9me3


title: N2-M-LK-K27ac


title: N2-M-DJ-K4me3


title: DNA1149_T_Methylation

type: genomic

city: Washington

first: Miriam

last: Bornhorst

state: DC

address: 111 Michigan Ave

institute: Children's National Hospital

hyb_protocol: After whole-genome amplification and enzymatic fragmentation, samples were hybridized to BeadChip arrays using the Infinium Methylation EPIC BeadChip kit according to the manufacturer’s protocol

scan_protocol: The methylation array experiment was performed using equipment available at the Georgetown University Genomics and Epigenomics Shared Resource in Washington, DC.

data_processing: Briefly, the raw methylation signal (iDAT) files were read using minfi   (3.16) and preprocessed using    preprocessIllumina   . Beta values were extracted using    getBeta    from the Methylset object.

label_protocol: Bisilfite-seq

extract_protocol: An input of 300 ng of DNA was bisulfite-converted using the DNA Methylation-Lightning kit

tag: disease state

value: pediatric brain tumor


title: Ventral hippocampus (vHC) Discriminating-avoiders s72


title: Basolateral amygdala (blA) Non-avoiders s74


title: N3-M-DJ-K9me3

city: STANFORD

first: Katja

institute: Stanford School of Medicine


title: Ventral hippocampus (vHC) Discriminating-avoiders s66


title: N2-M-DJ-K27ac


title: N1-M-LK-K9me3


title: N1-M-LK-K4me3


title: Ventral hippocampus (vHC) Discriminating-avoiders s24


title: Basolateral amygdala (blA) Discriminating-avoiders s71


title: Ventral hippocampus (vHC) Discriminating-avoiders s18


title: N3-M-DJ-K4me3


title: Ventral hippocampus (vHC) Discriminating-avoiders s15


title: N1-M-LK-K27ac


title: Medial prefrontal cortex (mPFC) Discriminating-avoiders s70


title: N1-M-DJ-K4me3


title: Basolateral amygdala (blA) Discriminating-avoiders s68


title: Basolateral amygdala (blA) Discriminating-avoiders s23


title: N1-M-DJ-K27ac


title: Basolateral amygdala (blA) Discriminating-avoiders s20


title: Medial prefrontal cortex (mPFC) Indiscriminate-avoiders s94

value: Indiscriminate-avoiders


title: Basolateral amygdala (blA) Discriminating-avoiders s17


title: Basolateral amygdala (blA) Discriminating-avoiders s14


title: Medial prefrontal cortex (mPFC) Indiscriminate-avoiders s91


title: Rep2_etoh_RNaseH_INPUT

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).
Assembly: hg19
Library strategy: DRIP-seq

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

tag: treatment

value: ethanol treated_control

tag: method

value: DRIP-seq, S9.6 IP


title: Rep2_etoh_RNaseH DRIP


title: Medial prefrontal cortex (mPFC) Indiscriminate-avoiders s88


title: Rep2_etoh DRIP


title: R3-D3-LK-H4

last: Pekrun

address: 269 Campus Drive

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

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

value: BALB/c


title: Medial prefrontal cortex (mPFC) Indiscriminate-avoiders s85


title: Rep2_IAA DRIP

value: auxin (IAA) treated_depletion


title: N1-M-DJ-K9me3

value: Hepa 1-6

value: Hepatoma


title: R3-D3-LK-H3K4me3


title: R3-D3-LK-H3K27me3


title: R3-D3-LK-PolII

value: Pol-II


title: R3-D3-LK-H3K9me3


title: R3-D3-LK-H3K27ac


title: Medial prefrontal cortex (mPFC) Indiscriminate-avoiders s34

value: Medial prefrontal cortex (mPFC)


title: Rep1_etoh_RNaseH DRIP


title: Rep2_etoh_INPUT


title: Rep2_IAA_INPUT


title: R3-D3-iG-PolII


title: R3-D3-LK-H2A


title: Medial prefrontal cortex (mPFC) Indiscriminate-avoiders s40

value: brain


title: Ventral hippocampus (vHC) Indiscriminate-avoiders s96


title: Rep1_etoh_RNaseH_INPUT


title: R3-D3-LK-H3


title: Rep1_IAA DRIP


title: Ventral hippocampus (vHC) Indiscriminate-avoiders s93


title: Ventral hippocampus (vHC) Indiscriminate-avoiders s90


title: Rep1_etoh DRIP


title: R3-D3-iG-H3


title: Ventral hippocampus (vHC) Indiscriminate-avoiders s42


title: Ventral hippocampus (vHC) Indiscriminate-avoiders s87


title: Rep1_IAA_INPUT


title: R3-D3-iG-H3K4me3


title: R3-D3-iG-H3K27ac


title: Basolateral amygdala (blA) Indiscriminate-avoiders s92


title: R3-D3-iG-H3K27me3


title: Basolateral amygdala (blA) Indiscriminate-avoiders s41


title: Basolateral amygdala (blA) Indiscriminate-avoiders s35


title: Basolateral amygdala (blA) Indiscriminate-avoiders s89


title: R3-D3-DJ-H3K9me3


title: Ventral hippocampus (vHC) Indiscriminate-avoiders s39


title: R3-D3-iG-H2A


title: Rep1_etoh_INPUT


title: R3-D3-DJ-H4


title: R3-D3-DJ-PolII


title: Ventral hippocampus (vHC) Indiscriminate-avoiders s36


title: Basolateral amygdala (blA) Indiscriminate-avoiders s38


title: R3-D3-DJ-H3K27me3


title: IMR90_TAGMe_DNA_rep3

city: Chicagp

first: Yaping

last: Liu

state: IL

address: 303 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

description: NOMe-HiC DNA library on IMR-90 cell line, rep3

data_processing:
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.
Assembly: hg19
Supplementary files format and content: hic (3D genome)
Supplementary files format and content: bed (WCG, HCG or GCH methylation level)
Supplementary files format and content: gene.sf (quantification of gene expression)
Library strategy: NOMe-HiC

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

value: lung fibroblast cell line

tag: restriction enzyme

value: DpnII

tag: bisulfite conversion

value: Yes


title: Basolateral amygdala (blA) Indiscriminate-avoiders s86

value: Basolateral amygdala (blA)


title: IMR90_TAGMe_RNA_rep3

description: NOMe-HiC RNA library on IMR-90 cell line, rep3

value: No


title: R3-D3-DJ-H3K4me3


title: R3-D3-iG-H3K9me3


title: R3-D3-DJ-H3


title: R3-D3-iG-H4


title: Medial prefrontal cortex (mPFC) Control s97

value: Control


title: PLC-8024, Input control

city: Guangzhou

first: Binkui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: SYXIP1VSSYXinput1_RIP-target.txt

extract_protocol:
total RNA in PLC-8024 cells was extracted by using TRIzol™ Reagent (Invitrogen™, Cat# 15596018) and detected by Bioptic Qseq100 Bio-Fragment Analyzer (Bioptic lnc.).
Fragmented total RNA (Input) and immunoprecipitated RNA (IP) were subjected to library construction by using EpiTM mini longRNA-seq kit (Epibiotek, Cat# E1802) according to the manufacturer’s protocols.

value: hepatocellular carcinoma cell line

tag: rip antibody


title: R3-D3-DJ-H3K27ac


title: Medial prefrontal cortex (mPFC) Control s103


title: PLC-8024, IGF2BP1, Proteintech

value: IGF2BP1 antibody (Proteintech,  Cat#22803-1-Ap)


title: Medial prefrontal cortex (mPFC) Control s52


title: PLC-8024, Input

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: 8024-M6a1_peak_ann_SingleSite.txt.gz


title: R3-D3-DJ-H2A


title: Ventral hippocampus (vHC) Control s105

value: Ventral hippocampus (vHC)


title: R3-D15-LK-H4

value: Liver


title: Medial prefrontal cortex (mPFC) Control s49


title: R3-D15-LK-H3

value: BALB/c


title: R3-D15-LK-H3K9me3


title: R3-D15-LK-H3K4me3


title: R3-D15-LK-PolII


title: Ventral hippocampus (vHC) Control s51


title: Ventral hippocampus (vHC) Control s102


title: PLC-8024, m6A, Sigma-Aldrich

value: anti-m6A antibody (Sigma-Aldrich,  Cat#ABE572)


title: R3-D15-LK-H3K27me


title: Ventral hippocampus (vHC) Control s48


title: Ventral hippocampus (vHC) Control s54


title: R3-D15-LK-H3K27ac


title: Basolateral amygdala (blA) Control s98


title: Basolateral amygdala (blA) Control s101


title: R3-D15-LK-H2A


title: R3-D15-iG-H4


title: Ventral hippocampus (vHC) Control s45


title: R3-D15-iG-PolII


title: Basolateral amygdala (blA) Control s53


title: R3-D15-iG-H3


title: Basolateral amygdala (blA) Control s47


title: Basolateral amygdala (blA) Control s50


title: liver cancer, non-response4654

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver cancer

extract_protocol:
Total RNA of cell was extracted by using Trizol. 1.0 ug of total RNA was used for the construction of sequencing libraries.
Library preparation were performed by Epibiotek (Guangzhou, China). Briefly, total RNA were treated to remove ribosomal RNA by using GeneRead™ rRNA Depletion Kit（Qiagen, Hilden, Germany, Cat No. 180211）. Ribosome depleted RNA was fragmented and then used for constructing strand-specific RNA libraries by using VAHTS Stranded RNA-seq Library Prep Kit for Illumina (Vazyme, Nanjing, China, Cat. No NR602) accoding to manufacturer instructions.

tag: individual

value: patient 4654

value: liver cancer

value: WT

value: oxaliplatin

tag: phenotype

value: oxaliplatin-resistant


title: R3-D15-iG-H3K9me3


title: liver cancer, non-response5453

value: patient 5453


title: R3-D15-iG-H3K4me3


title: 0048

city: Auburn

first: Paul

middle: W

last: Dyce

state: Alabama

address: 559 Devall Dr,

department: Animal Science

institute: Auburn University

data_processing:
Raw sequencing data were subjected to a quality check using FastQC v0.11.9 and MultiQC v1.12. The quality of the reads was evaluated based on parameters such as average read length, adapter content, per sequence GC content and sequence quality scores. The reads were mapped using STAR aligner v2.7.5 to Ensemble’s ARS UCD1.2 Bos taurus genome reference. The read quantification was done to obtain the raw counts per gene. Read counts were transformed to counts per million (CPM) using edgeR v3.28.1. Post mapping quality control was performed using MultiQC v1.12.
Assembly: ARS UCD1.2 Bos taurus
Supplementary files format and content: Matrix table with raw gene count for all genes and samples in mRNA_AllCounts.txt
Supplementary files format and content: Normalized counts for all genes in Normalized_counts.csv

source_name: Blood

extract_protocol:
Total RNA was isolated from 15 heifers using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following standard procedures. RNA purification and DNase digestion were done using an RNA clean and concentrator kit (Zymo Research, Irvine, CA, USA). The quality and RNA integrity of total RNA was assessed using Agilent Bioanalyzer, following the Agilent RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA) instructions.
Library preparation and sequencing were performed on the Nova-Seq platform at the Discovery life sciences (Hudson Alpha Institute of Biotechnology, Huntsville, AL, USA). Paired end 100 bp reads were generated for each sample.

value: Blood

tag: pregnancy outcome

value: Not pregnant to AI

value: Peripheral white blood cells


title: liver cancer, non-response4349

value: patient 4349


title: 0047

value: Pregnant to AI


title: R3-D15-iG-H3K27me

tag: antibody


title: liver cancer, response5640

value: patient 5640

tag: tissue

value: oxaliplatin-non-resistant


title: liver cancer, response4752

value: patient 4752

tag: genotype


title: liver cancer, response3824

value: patient 3824


title: HepG2, oxaliplatin treatment

data_processing:
The sgRNA read count and hits calling were analyzed by MAGeCK v0.5.7 algorithm
the read counts of each sgRNA from different samples were normalized to adjust for the effect of library sizes and read count distributions
Assembly: hg38
Supplementary files format and content: Base Calling, Read count

extract_protocol:
Genomic DNA was isolated using a DNA extraction kit (Omega, D3396)
The sgRNA sequences were amplified using NEBNext® High-Fidelity 2X PCR Master Mix and subjected to massive parallel amplicon sequencing carried out by Novogene Technology (Beijing, China)

tag: cell line

value: hepatocellular carcinoma

value: Cas9 protein overexpressing


title: 0044


title: 0045


title: R3-D15-iG-H2A

value: Liver

value: BALB/c


title: 0043


title: 0041


title: R3-D15-DJ-H3


title: HepG2, vehicle

value: vehicle


title: HepG2, no-treatment

value: no treatment


title: R3-D15-DJ-H4


title: MED8A SMARCD3 KO-2 rep 3

city: Pittsburgh

first: Baoli

last: Hu

address: 4401 Penn Ave

institute: University of Pittsburgh School of Medicine

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.

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.


title: 0040


title: R3-D15-DJ-H3K9me3


title: R3-D15-DJ-H3K4me3


title: MED8A SMARCD3 KO-2 rep 2


title: 0039


title: R3-D15-DJ-H3K27me


title: R3-D15-DJ-H3K27ac


title: 0037


title: MED8A SMARCD3 KO-2 rep 1


title: R3-D15-iG-H3K27ac


title: R3-D15-DJ-PolII

value: Pol-II


title: 0034


title: 0042


title: R3-D15-DJ-H2A


title: 0033


title: MED8A SMARCD3 KO-1 rep 3


title: MED8A SMARCD3 KO-1 rep 2


title: 0006


title: R2-D3-LK-PolII


title: R2-D3-LK-H4


title: MED8A SMARCD3 KO-1 rep 1


title: 0004


title: 0003


title: R2-D3-LK-H3K9me3


title: R2-D3-LK-H3


title: MED8A SMARCD3 WT rep 3

value: WT


title: MED8A SMARCD3 WT rep 2


title: R2-D3-LK-H3K4me3


title: TALL_05

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

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

value: T-ALL

tag: tissue source

value: Primary Tissue

tag: healthy/tumor

value: Cancer


title: EN_FFPE

description: Endometrium Primary Tissue Healthy

source_name: healthy endometrium primary tissue (formalin-fixed paraffin embeded)

value: Endometrium

value: Healthy