title: WIBR3 hPSCs maintained in primed conditions

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

data_processing:
Sequencing output were demultiplexed using Cell-Ranger-arc V2.0 (10X Genomics) mkfastq command, and counts were estimated with Cell-Ranger count software.
Cells with low number of features (bottom 10%), high number of UMIs (top 10%) or high mitochondrial percentage (top 10%) were filtered out. Doublet cells were also assessed by RNA data using scDblFinder V1.6. Cells that passed both RNA and ATAC filtering parameters were further examined together.
Seurat integrated analysis and anchoring of RNA data was performed and then normalized by log-normalization using a scale-factor of 10,000. The top 5,000 variable genes were identified by the variance stabilizing transformation method, and subsequently scaled and centered.
UMAP was performed on the first 30 PCs.
Construction of the weighted nearest neighbor was perform using FindMultiModalNeighbors by Seurat based on RNA PC1:30 and ATAC harmony 2:50.
Assembly: hg38
Supplementary files format and content: csv with raw RNA counts

growth_protocol: HENSM and Primed scRNA-seq was processed alongside scATAC-seq measured from the same cells (multimodal strategy), in a protocol described below:  LIS49 and WIBR3 hESCs were cultured for 3 passages in HENSM and primed conditions on Matrigel coated plates.

extract_protocol:
Cell nuclei were isolated using the multiomics protocol provided by 10X genomics (cat CG000365), aiming for ~6000 nuclei.
10X Genomic library preparation was performed via the protocol provided by 10X genomics (cat CG000338) and sequenced by 2 units of NovaSeq SP sequencing system (100 cycles).
Single cell RNA-seq + ATAC-seq (Multiomics)

value: Human embryonic stem cells

value: Primed (TeSR)


title: LIS49 hPSCs maintained in primed conditions

status: Public on Aug 16 2023

type: SRA

city: Rehovot

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: donor7_IL13_3w

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

country: USA

institute: Universty of Iowa

library_source: transcriptomic

data_processing:
Raw fastq files were pseudoaligned to human genome assembly GRCh38.p13 using kallito software version 0.45.0
Assembly: GRCh38.p13
Supplementary files format and content: HDF5 format file containing counts and abundance for each gene (row) and sample (column)

source_name: lung

growth_protocol: DMEM/F12 media with Ultroser G was replaced every two days.

extract_protocol:
RNA was extracted using Qiagen RNeasy Lipid Tissue Mini Kit # 74804.
mRNA libraries were prepared using Illumina TruSeq Stranded Total RNA Gold

treatment_protocol: Air-liquid interface cultures of primary airway epithelia from 1 de-identified human donor with no known disease were exposed to apical and basolateral IL13 or vehicle at a concentration of 20ng/mL for up to 21 days.

tag: time point

tag: tissue

value: lung


title: SS2-ATAC

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

library_source: genomic single cell

data_processing:
Raw sequencing reads generated from 10X ATAC assay were processed by cellranger-atac workflow in Cell Ranger (v6.1, 10X Genomics) with default settings to generate mapping and chromatin accessibility. The mapping and chromatin accessibility data were imported to R package Signac v1.3.0 (31) for downstream analysis.
Low-quality cells with < 3,000 or > 20,000 fragments in peaks, < 15% fraction of fragments in peaks, > 4 ratio of mononucleosomal to nucleosome-free fragments, or < 2 transcriptional start site (TSS) enrichment score were filtered out. A latent semantic indexing (LSI) dimension reduction was performed on the filtered cells.
Assembly: GRCH38
Supplementary files format and content: csv files include peaks( local enrichment of transposase cut-sites) identified from ATAC data

molecule: genomic DNA

source_name: Peripheral Blood of CTCL

extract_protocol:
Peripheral Blood was collected from CTCL patients via green top herapin tubes or apheresis (ECP) and isolated for malignant CD4+CD26- Tcells via STEM CELL kits
The scATAC-Seq libraries were prepared following the protocol provided by the 10X genomics. Target nuclei number for encapsulation was 6,000 to 10,000 cells for single cell ATAC sequencing.  Libraries were prepared with Chromium Single Cell ATAC Reagent kit (v1.1 Chemistry) (10X Genomics, Inc., Pleasanton, CA) and run on NextSeq 500 150 cycles (50bp x 50bp). Read depth was approximately 25,000 reads per sample.

tag: cancer type

value: Sezary syndrome

value: CD4+CD26- T cells


title: SS1-ATAC


title: donor7_IL13_2d


title: LIS49 hPSCs maintained in naïve conditions

value: Human Enhanced Naive Stem Cell Medium (HENSM)


title: WIBR3 hPSCs maintained in naïve conditions


title: donor7_DMSO

value: DMSO


title: MF3-ATAC

value: mycosis fungoides


title: SNU1750 Homo clone #3, Input

city: Singapore

first: Shamaine

last: Ho

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

library_source: genomic

data_processing:
For Nano ChIP-seq, sequenced reads were first trimmed to remove the first and last ten bases. No trimming was required for TF ChIP-seq. Sequenced reads were mapped to the human genome assembly (hg19) using Burrows-Wheeler Aligner (BWA-MEM, version 0.7.10). Only reads with MAPQ value of at least 10 were retained, and PCR duplicates were removed using SAMtools (version 0.1.19). Significant ChIP enrichment peaks relative to input were identified using MACS2 callpeak function. Wiggle track visualizations were generated using MEDIPS (version 1.20.1).
For RNA-seq, sequenced reads were aligned to hg19 using STAR mapper and gene expression abundance was estimated with RSEM as fragments per kilobase per million (FPKM) using default parameters (pipeline available at https://github.com/gis-rpd/pipelines/tree/master/rnaseq/star-rsem).
Assembly: hg19 for ChIP-seq and RNA-seq
Supplementary files format and content: wig/bigwig files for ChIP-seq, RSEM gene count files for RNA-seq

source_name: Gastric Cancer Line

extract_protocol:
For ChIP-seq, sheared chromatin were subjected to immunoprecipitation with 2 μg antibody against H3K27ac (ab4729, Abcam), H3K4me1 (ab8895, Abcam) or 5 μg antibody against TEAD1 (610923, BD Biosciences). For RNA-seq, total RNA was extracted following manufacturer’s protocols (Qiagen)
For Nano histone ChIP-seq, ChIP and input DNA were subjected to whole-genome amplification using the WGA4 kit (Sigma-Aldrich) and a universal primer linked to BpmI restriction site (Qiagen). 30ng of BpmI-digested DNA was used for ChIP-seq library preparation according to manufacturer’s protocols (New England Biolabs). For TF ChIP-seq, 30ng of ChIP and input DNA was used for library preparation. For RNA-seq, libraries were prepared accordingly using Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit (Illumina), with an input of 1 μg total RNA.

tag: chip antibody

value: Input

tag: genotype

value: TEAD1 KO


title: SNU1750 Homo clone #4, Input


title: SNU1750 WT clone #2, Input

value: TEAD1 WT


title: donor6_IL13_3w


title: SNU1750 Homo clone #2, Input


title: SNU1750 Homo clone #1, Input


title: donor6_IL13_2d


title: Model (biol rep 2)

city: Nanning

first: Louyi

last: Shen

address: No. 6 Shuangyong Road

country: China

institute: The First Affiliated Hospital of Guangxi Medical University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Samples were analyzed by the Illumina HiSeq 2500 High-throughput sequencing platform of Genesky Biotechnologies Inc. (Shanghai, China) according to the manufacturer’s instruction
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Mapping to Rattus norvegicus genomes using miRDeep2's mapper.pl
The differentially expressed miRNA was regarded when∣log2 (fold change)∣＞1 and p value＜0.05 by DEseq2.
Assembly: Genome_build: mm10
Supplementary files format and content: known_mirna_expressed.txt,raw counts
Supplementary files format and content: novel_mirna_expressed.txt,raw counts

organism: Mus musculus

source_name: heart

extract_protocol:
Total RNA in exosomes was extracted by TRIzol.
Samples were analyzed by the Illumina HiSeq 2500 High-throughput sequencing platform of Genesky Biotechnologies Inc. (Shanghai, China) according to the manufacturer’s instruction

value: heart

tag: age

value: 4-6 weeks old

value: C-kit+ cardiac progenitor cells

value: WT

value: hypoxia

tag: time

value: 12 hours


title: Model (biol rep 3)


title: HuBrain_Tumour_no493_S10

city: Lund

first: Mattias

last: Belting

state: Skåne

address: Barngatan

department: Clinical Sciences Lund

country: Sweden

institute: Lund University

data_processing:
Single nuclei: Raw base calls were demultiplexed to obtained sample specific FastQ files using mkfastq in default parameters (10x Genomics), and reads were aligned to GRCh38 genome assembly using the Cell Ranger pipeline (10x Genomics, Cellranger count v3.1.0) with default parameters (--include-introns was used for nuclei mapping)
Assembly: GRCh38
Supplementary files format and content: Single cell/nuclei: Cellranger count output matrices

molecule: polyA RNA

source_name: GBM biopsy

extract_protocol:
Single nuclei RNAseq: Protocol based on published nuclei isolation protocol (Södersten et al., 2018). Around 20 μg of -80 C-conserved tissue were thawed and dissociated in ice-cold lysis buffer (0.32M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl pH 8.0, 1 mM DTT) using a 1 ml glass douncer (Wheaton). The homogenate was slowly and carefully layered in the centrifuge tubes on top of a sucrose layer (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl pH 8.0, 1 mM DTT) to create a gradient, and then centrifuged at 15500 rpm for 2 h 15 min. Following centrifugation, the supernatant was removed and the pellet softened for 10 minutes in 100 μl of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl pH 7.2, 70 mM KCl, 2 mM MgCl2) prior resuspension in 300 μl of dilution buffer (10 mM Tris-HCl pH 7.2, 70 mM KCl, 2 mM MgCl2, Draq7 1:1000). The suspension was then filtered (70 μm cell strainer) and sorted via FACS (FACS Aria III, BD Biosciences) at 4° C with low flowrate, using a 100 μm nozzle (Pipette tips and Eppendorf tubes for transferring nuclei were pre-coated with 1% BSA).
Single nuclei RNAseq: 8500 nuclei were sorted for single-nuclei RNA-sequencing and then loaded onto the Chromium Next GEM Single Cell 3’ Kit (10x Genomics). Sequencing libraries samples were multiplexed and sequenced on a Novaseq machine using a 150-cycle kit using the recommended read length from 10x Genomics.

value: GBM biopsy


title: SNU1750 WT clone #4, H3K27ac


title: HuBrain_Tumour_no504_S11


title: Model (biol rep 1)


title: donor6_DMSO


title: Control (biol rep 3)

value: 0 hours


title: SNU1750 WT clone #5, H3K27ac


title: HuBrain_Tumour_no473_S6


title: donor5_IL13_3w

value: lung


title: SNU1750 WT clone #3, H3K27ac


title: SNU1750 WT clone #2, H3K27ac


title: HuBrain_Tumour_no461_S5


title: Control (biol rep 2)


title: donor5_IL13_2d


title: HuBrain_Tumour_no459_S4


title: donor5_DMSO


title: Control (biol rep 1)


title: Control

city: Guangzhou

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

institute: Forevergen

description: RNA-seq

data_processing:
Quality control of the raw reads by Illumina HiSeq™2500 sequencing was assessed by Fast-QC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The remaining clean reads were mapped to the reference human genome (GRCh38) using HISAT2 software (version 2.1.0, https://daehwankimlab.github.io/hisat2/). To predict circRNAs, circRNAs were identified and quantified from mapped splice junction reads using ACFS2 (https://github.com/arthuryxt/acfs).
Differentially expressed circRNAs between HD-SB group and control were analyzed using the DE-Seq algorithm, with significant differences defined as absolute |log2 fold-change| > 1 and p value < 0.05.
The differentially expressed circRNAs and their functional enrichment were further analyzed by Gene Ontology (GO) and KEGG database in DAVID software (6.8). hsa_circ_0039933-miRNAs-wnt11 networks were predicted by miRanda 3.3 and drawn by cytoscape 3.2.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

growth_protocol: Human colorectal cancer cell lines (HT-29, HCT-116, and SW620) were purchased from Cellcook (Guangzhou, China). HT-29 cells were cultured in L-15 high-glucose medium (CM2001, CellCook, China) with 10% fetal bovine serum (FBS, CellCook), 1% penicillin and streptomycin (P/S, 15140-122, Gibco), while HCT-116 and SW620 cells were cultured in RPMI-1640 medium (11875, Gibco) with 10% FBS, 1% P/S, then cultured in 37°C, 5% CO2 incubator. SW620 cells were treated with HD-SB at 1 mg/mL, then collected after 24 h for subsequent experiments.

extract_protocol:
Total RNA was extracted by use of TRIzol reagent (TR118-500, MRC, USA)
RiboMinus™ Eukaryote System v2 kit was used to remove rRNA from total RNA, and RNase R was used to digest linear RNA to enrich circRNAs. RNA was fragmented for circRNAs library construction using the TrueLib mRNA Library Prep Kit for Illumina. The RNA was reverse transcribed to synthesize a two-stranded product, repaired at its end with a plus dA tail, and ligated to Adapter. The enriched product was amplified by pcr reaction. After that, the fragments were screened and purified to obtain the desired libraries.

value: colorectal cancer cell lines

value: Control


title: HuBrain_Tumour_no437_S3


title: donor4_IL13_3w


title: HuBrain_Tumour_no487_S9


title: donor4_IL13_2d


title: NUGC4, Input

value: Untreated


title: SNU1750 Homo clone #5, H3K27ac


title: SNU1750 Homo clone #4, H3K27ac


title: YCC11, H3K4me1


title: donor4_DMSO

value: DMSO


title: SNU484, H3K4me1


title: HuBrain_Tumour_no440_S7


title: HuBrain_Tumour_no435_S6


title: SNU1750 Homo clone #2, H3K27ac


title: SNU1750 Homo clone #1, H3K27ac


title: HuBrain_Tumour_no432_S5


title: SNU719, H3K4me1


title: NUGC4, H3K4me1


title: donor3_IL13_3w


title: donor3_IL13_2d


title: TTseq in dTAG13-treated MM1.S cells with PAF1 endogenously tagged with FKBP12(F36V)

city: London

first: Nick

last: Crump

address: Du Cane Road

department: Dept of Immunology and Inflammation

country: United Kingdom

institute: Imperial College London

description: MM1.S PAF1-FKBP dTAG13 TTseq

data_processing:
RNA-seq reads were aligned to the hg19 genome using STAR
Duplicate reads were removed using samtools rmdup
Read counts were determined using featureCounts (Subread package)
Assembly: hg19
Supplementary files format and content: featurecounts table (unnormalized readcounts)

molecule: nuclear RNA

source_name: Multiple myeloma cell line (MM1.S)

growth_protocol: Cells were continuously grown in RPMI with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
5e7 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. RNA was mildly fragmented by sonication. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
DNA libraries were prepared using the NEB Next Ultra II Directional RNA library preparation kit for Illumina (E7760).

value: Multiple myeloma cell line (MM1.S)

value: Plasma cell line derived from multiple myeloma with t(14;16) translocation

value: dTAG-13 at 0.5 uM for 24h


title: TTseq in DMSO-treated MM1.S cells with PAF1 endogenously tagged with FKBP12(F36V)

description: MM1.S PAF1-FKBP DMSO TTseq

value: DMSO for 24h


title: donor2_IL13_3w


title: SNU1750 WT clone #1, H3K27ac

value: TEAD1 WT


title: P009 RNA-seq

data_processing:
For Nano ChIP-seq, sequenced reads were first trimmed to remove the first and last ten bases. No trimming was required for TF ChIP-seq. Sequenced reads were mapped to the human genome assembly (hg19) using Burrows-Wheeler Aligner (BWA-MEM, version 0.7.10). Only reads with MAPQ value of at least 10 were retained, and PCR duplicates were removed using SAMtools (version 0.1.19). Significant ChIP enrichment peaks relative to input were identified using MACS2 callpeak function. Wiggle track visualizations were generated using MEDIPS (version 1.20.1).
For RNA-seq, sequenced reads were aligned to hg19 using STAR mapper and gene expression abundance was estimated with RSEM as fragments per kilobase per million (FPKM) using default parameters (pipeline available at https://github.com/gis-rpd/pipelines/tree/master/rnaseq/star-rsem).
Genome_build: hg19 for ChIP-seq and RNA-seq
Supplementary_files_format_and_content: wig/bigwig files for ChIP-seq, RSEM gene count files for RNA-seq

source_name: Gastric Cancer Primary Tissue

value: Gastric Cancer Primary Tissue


title: P008 RNA-seq


title: HuBrain_Tumour_no476_S8


title: NCC19, H3K4me1


title: LMSU, H3K4me1

value: LMSU


title: H3K27ac ChIP-seq in dTAG13-treated MM1.S cells with PAF1 endogenously tagged with FKBP12(F36V)

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Bigwig generation using DeepTools
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (PAF1). Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext Ultra DNA II library preparation kit for Illumina (Cat no. E7645).

value: Diagenode C15410196

value: dTAG-13 at 0.5 µM for 24h


title: SNU1750 Homo clone #3, H3K27ac

value: TEAD1 KO


title: donor2_IL13_2d


title: ChIP-seq Input for H3K27ac in dTAG13-treated MM1.S cells with PAF1 endogenously tagged with FKBP12(F36V)


title: donor2_DMSO


title: P007 RNA-seq


title: P006 RNA-seq


title: H3K27ac ChIP-seq in DMSO-treated MM1.S cells with PAF1 endogenously tagged with FKBP12(F36V)


title: AGS, H3K4me1

value: AGS


title: donor1_IL13_3w


title: P005 RNA-seq


title: ChIP-seq Input for H3K27ac in DMSO-treated MM1.S cells with PAF1 endogenously tagged with FKBP12(F36V)


title: donor1_IL13_2d


title: P003 RNA-seq


title: P004 RNA-seq


title: donor3_DMSO


title: MDA-MB-231 cells, FBXL12-KO #2, replicate 3

city: Solna

first: Andrä

last: Brunner

address: Solnavägen 9

department: Department of Cell and Molecular Biology

institute: Karolinska Institutet

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TRIM galore.
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2.
Read count extraction and normalization were performed using Galaxy tools.
Assembly: hg38
Supplementary files format and content: *.tab: Tab-delimited text files include aligned read counts for each sample.

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen) according to the manufacturer's instructions. Sample quality was assessed using Agilent Technologies Bioanalyzer with Agilent RNA 6000 Nano Kit. RIN was 10 for each sample.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq library construction kit following manufacturer's protocols.

value: Basal-like breast cancer


title: donor1_DMSO

value: lung


title: YCC21 H3K4me1


title: YCC3 H3K4me1


title: P002 RNA-seq


title: YCC10 H3K4me1


title: MDA-MB-231 cells, FBXL12-KO #2, replicate 2


title: SNU1967 H3K4me1


title: SON_M125_4

city: Grand Forks

first: John

middle: Andrew

last: Watt

state: North Dakota

address: 504 Nth Hameline St

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Sequence reads were trimmed for adaptor sequences and low-quality using trimmomatic v0.39.
Reads were aligned to the rat assembly (rn7) using Hisat2 v2.2.1, and sorted/indexed by Samtools v1.13.
Annotation/Counts was performed by featureCounts (Subread v2.0.1).
Normalization and differential gene expression analysis was performed by DESeq2 v1.34.0
Assembly: rn7
Supplementary files format and content: Comma-separated values (csv) file, containing normalized counts for each sample

organism: Rattus norvegicus

source_name: Supraoptic Nucleus

extract_protocol:
Rats were anesthetized with isoflurane and euthanized via transcardial perfusion with PBS. Brains were serial sectioned via vibratome and a tissue puncher was used to collected the supraoptic nucleus, which were immediately flash frozen by liquid nitrogen.
Frozen tissue was ground under liquid nitrogen. RNA was collected via phenol-chloroform extraction and Rneasy Mini Kit (Qiagen). Approximately 1.5 ug  of total RNA was used for QC and library construction.
RNA libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and NEBNext Ultra II RNA-seq library kit for Illumina (NEB).

treatment_protocol: Rats were grown to the ages of 35 days old or 125 days old prior to tissue collection.

value: Supraoptic Nucleus

tag: Sex

value: Male

tag: strain

value: Sprague Dawley

value: Age - 125 days old


title: MDA-MB-231 cells, FBXL12-KO #2, replicate 1


title: HGC27, H3K4me1

value: Untreated


title: P001 RNA-seq


title: SON_M125_3


title: MDA-MB-231 cells, FBXL12-KO #1, replicate 3


title: SON_M125_2


title: SNU1750 H3K4me1


title: P009 Input


title: IM95 H3K4me1


title: MDA-MB-231 cells, FBXL12-KO #1, replicate 2


title: Hs746T H3K4me1


title: SON_M125_1


title: P007 Input


title: SON_M35_3

value: Age - 35 days old (Control)


title: MDA-MB-231 cells, FBXL12-WT control, replicate 3


title: SNU16 H3K4me1


title: RERFGC1B H3K4me1


title: MDA-MB-231 cells, FBXL12-WT control, replicate 2


title: SON_M35_2


title: P005 Input


title: OCUM1 H3K4me1


title: MDA-MB-231 cells, FBXL12-WT control, replicate 1


title: RPMI_IgG_setD

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

institute: National University of Singapore

data_processing:
CUT&RUN-seq data were preprocessed and analyzed using cutRunTools pipeline.
This pipeline automated the preprocessing and alignment of CUT&RUN-seq data to hg19 genome. CutRunTools utilized MACS2 and SEACR software to call peaks using the default optimized cutoff for each CUT&RUN-seq data.
The paired control data was further utilized by the cutRunTools step2 script to normalize the MACS2 output peaks.
Each bedGraph output has been further normalized by subtracting the treatment file to the corresponding control file using MACS2 bdgcmp and floored the signal to 0.1 before convert to bigWig using UCSC bedGraphToBigWig tool.
Assembly: hg19
Supplementary files format and content: Peak bed files
Supplementary files format and content: bigWig files
Library strategy: Cut&Run

growth_protocol: RPMI-8402 cells were cultured in RPMI medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Library construction from the Cut&Run-seq samples and sequencing of paired-end-150-bp-long reads by the Illumina NovaSeq were performed at GENEWIZ Azenta Life Sciences Co. Ltd.
Paired-end Cut&Run-Seq sequencing

treatment_protocol: RPMI-8402 cells were incubated with antibodies specific to MYC(CST, #5605), MYCN(CST, #84406), H3K4me3 (Epicypher, 13-0041), H3K27ac (Abcam, ab4729), H3K4me1 (Abcam, ab176877) or control IgG (CST, #2729) overnight and subsequently with CUTANA pA/G-Mnase to release cleaved chromatin fragments. Chromtain fragments were then purified utilizing with DNA purification kit. Libraries were generated using a NEBNext Ultra II DNA library prep kit and sequencing was performed on Illumina NovaSeq at GENEWIZ Azenta Life Sciences Co. Ltd.

value: T-ALL

tag: antibody


title: SON_M35_1


title: P004 Input


title: KATOIII H3K4me1

value: KATOIII


title: RPMI_MYC_CST_setD

tag: control


title: P008 Input


title: P003 Input


title: P002 Input


title: SON_M35_4


title: Aquifex WT1.1

first: Tobias

last: Warnecke

institute: Imperial College

data_processing:
Untrimmed reads were mapped using Bowtie2 for A. aeolicus (single end reads) and using BWA for B. bacteriovorus (paired-end). Read counts of all genes were estimated using the python package HTSeq
Assembly: B.bacteriovorus : GCA_000196175.1; A.aeolicus : GCF_000008625.1
Supplementary files format and content: Aquifex-aeolicus_readcounts; Readcounts and gene Length
Supplementary files format and content: HIID13_WT_Count_and_RPKM: Read counts and gene length

organism: Aquifex aeolicus

source_name: WT

growth_protocol: RNA extraction from B. bacteriovorus HID13, cells were diluted in 10 mL of fresh YP medium at an OD of 0.1 and grown until reaching a density of 0.6 (20 hours at 30°C with shaking). For each replicate, 2 mL of culture were spun at maximum speed, snap frozen and kept at -80°C until RNA extraction. ; Aquifex aeolicus pellets were purchased from the Archaeenzentrum Regensburg, Germany

extract_protocol:
RNEasy kit (Qiagen), including DNase I treatment. RNA quality was assessed using an Agilent 2100 Bioanalyser.
For the B. bacteriovorus samples (all RIN scores > 9.5), ribosomal RNA was depleted using the NEBNext®rRNA Depletion Kit (Bacteria), and NGS libraries made using the NEBNext® Ultra™ II Directional RNALibrary Prep Kit for Illumina® according to manufacturer’s instructions. Paired-end 55bp reads were generated on a NextSeq 2000 with dual 8bp indexing. For the A. aeolicus samples (all RIN scores > 5), rRNA was depleted using Illumina Ribozero Kit (Bacteria), and NGS libraries made using the TruSeq Stranded Total RNA LT Kit according to manufacturer’s instructions. Single End 50bp reads were generated on a MiSeq with single 6bp indexing.

value: WT

value: No treatment


title: RPMI_IgG_setC


title: S4_5xFAD;B2m-/- GEX2

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

data_processing:
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the  raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample for scRNAseq and filtered contig annotations for scTCR-seq

source_name: Sort purified CD45+ immune cells from the brain parenchyma of 5xFAD/B2m-/- mice

extract_protocol: Libraries were prepared using the Chromium Single Cell 3' Gene Expression Library and Gel Bead Kit (10x Genomics)


title: MDA-MB-231 cells, FBXL12-KO #1, replicate 1


title: YCC3 Input

value: Input


title: P001 Input

value: Gastric Cancer Primary Tissue


title: FU97 H3K4me1


title: P009 H3K27ac


title: RPMI_H3K4me1_setC


title: YCC22 Input


title: RPMI_H3K27ac_setC

value: ab4729 (Abcam)


title: S2_5xFAD GEX2

source_name: Sort purified CD45+ immune cells from the brain parenchyma of 5xFAD mice


title: S3_5xFAD;B2m-/- GEX1

value: Sort purified CD45+ immune cells from the brain parenchyma of 5xFAD/B2m-/- mice


title: P006 Input


title: NCC59 H3K4me1


title: RPMI_cMYC_CST_setC


title: Aquifex WT1.2


title: S1_5xFAD GEX1

value: Sort purified CD45+ immune cells from the brain parenchyma of 5xFAD mice


title: YCC21 Input


title: YCC20 Input


title: RPMI_H3K4me3_setB

value: 13-0041 (Epicypher)


title: P008 H3K27ac


title: P007 H3K27ac


title: Mu5

city: Birmingham

first: Chad

last: Hunter

state: AL

address: 1825 University Boulevard

institute: Division of Endocrinology, Diabetes, and Metabolism

data_processing:
FastQ files underwent quality control with FastQC v0.11.9
FastQ files were trimmed for low-quality reads, short reads, and adaptor sequences with Trim Galore v0.6.7 , followed by an additional QC with FastQC.
With STAR v2.7.3a , the trimmed reads were aligned to the GRCm39 genome for exons and were converted to Bam files.
Read counts were generated with FeatureCounts through Rsubread v2.12.3, using the Ensembl GTF annotations (GRCm39.109.gtf)
Assembly: mm39
Supplementary files format and content: csv

source_name: pancreas

extract_protocol:
14-week islet RNA was isolated from SSBP3 knockout and littermate control animals using an RNeasy Micro Kit (Qiagen, #74004)
By Heflin Genomics Core at UAB

value: pancreas

value: Whole Islet

value: SSBP3F/F; MIP-CreER


title: P006 H3K27ac


title: YCC11 Input


title: Mu3


title: YCC10 Input


title: P005 H3K27ac


title: RPMI_IgG_setB


title: Mu2


title: TMK1 Input


title: P004 H3K27ac


title: RPMI_MYCN_CST_setA


title: RPMI_IgG_setA


title: CT6


title: SNU719 Input


title: CT4


title: P002 H3K27ac


title: P003 H3K27ac


title: P001 H3K27ac


title: SNU484 Input


title: CT2


title: Jurkat_ATAC

data_processing:
ATAC-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ATAC-seq reads were remove duplicate with Picard MarkDuplicates package. Multiple mapping reads were removed using samtools view -q 10
ATAC-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is p-value < 1e-5, keep-dup=all, --SPMR were used to normalized the bedGraph output.The signal has been floored to 0.1 after bdgcmp subtract function.
Assembly: hg19
Supplementary files format and content: narrowPeak files of ATAC-seq
Supplementary files format and content: bigWig files of ATAC-seq

source_name: T-ALL cells

growth_protocol: Jurkat and RPMI-8402 T-ALL cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Library construction from the ATAC-seq samples and sequencing of paired-end 150-bp-long reads by the Illumina NovaSeq were performed at GENEWIZ Azenta Life Sciences Co. Ltd.
Paired-end ATAC-Seq sequencing

treatment_protocol: The cells were first incubated with Tn5 transposase. Tagmented DNA fragments are purified with Zymo DNA purification kit. ATAC libraries are purified and sequenced on Illumina NovaSeq at GENEWIZ Azenta Life Sciences Co. Ltd.

value: Jurkat

tag: atac antibody

value: ATAC


title: SNU1967 Input

value: Untreated


title: RPMI_ATAC


title: SNU1750 shTEAD1 #3 RNA-seq


title: SNU1750 Input


title: Human Synthetic Embryoid Models (SEMs), Day8 of the protocol

description: Human Synthetic Embryoid Models (SEMs), generated from cell aggregation, Day8 of the protocol.

data_processing:
Demultiplexing was done with bcl2fastq2
Alignment and quantification of single cell features was done with cellranger/7.1.0 counts
Aggregation of multiple GEM wells was done using  cellranger aggr
Cells with under 1000 expressing genes, over 8000 expressing genes or over 15% mitochondrial gene expression were filtered out for the rest of the analysis.
Seurat integrated analysis and anchoring of 3 individual samples was performed and then normalized by log-normalization using a scale-factor of 10,000. The top 2,000 variable genes were identified by the variance stabilizing transformation method, and subsequently scaled and centered.
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz includes CellRanger output files that were used for the analysis. In addition, there are 3 different matrices created using Seurat 4.3.0: raw_counts - contains raw counts of all genes across all cells, norm_data- contains normalized counts of all genes across filtered cells, norm_meta_annotations.csv contains meta-data of all genes after filtering, normalization and clustering by Seurat.
The order of the samples in filtered_feature_bc_matrix.tgz is: 1 - W3_SEM_Day4, 2 - W3_SEM_Day6, 3 - W3_SEM_Day8.

source_name: Human Synthetic Embryoid Model (SEMs)

growth_protocol: All human SEMs analyzed by scRNA-seq were generated by co-aggregating WT WIBR3 naïve ESC lines grown in HENSM with RCL-induced or BAPJ-induced WT cells.

extract_protocol:
RNA extracted according to 10x Genomics Chromium v3.1 Dual Index system kit instructions
10x Genomics Chromium v3.1 Dual Index system (5000 cell target cell recovery)

treatment_protocol: At day 4, ~80 human SEMs were pooled into one lane of the 10X chromium chip, while at day 6 and 8, a pool of ~50 SEMs were sequenced per lane. All SEMs samples were processed including extraembryonic compartments without any dissection. SEMs were dissociated with Trypsin-EDTA solution C (0.05%) for 10 minutes (Biological Industries; 030501B). Trypsin was neutralized using media with 10% FBS, and cells were washed and resuspended in 1x PBS with 400 µg/ml BSA. Cell suspension was filtered with a 100 µm cell strainer to remove cell clumps. Cell viability of at least 90% was determined by trypan blue staining for all samples. Cells were diluted at a final concentration of 1000 cells/µL in 1x PBS with 400 µg/ml BSA.

value: Human Synthetic Embryoid Model (SEMs)

tag: embryo growth conditions

value: in-vitro

tag: protocol day


title: SNU1750 shTEAD1 #2 RNA-seq

tag: cell line


title: SNU16 Input


title: Human Synthetic Embryoid Models (SEMs), Day6 of the protocol

description: Human Synthetic Embryoid Models (SEMs), generated from cell aggregation, Day6 of the protocol.


title: SNU1750 shTEAD1 #1 RNA-seq


title: 5xFAD;Tcra-/- GEX1 [S3_5xFADTcraKO]

data_processing:
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the  raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample for scRNAseq

source_name: Sort purified CD45+ immune cells plus CD45neg non-immune cells from the brain parenchyma of 5xFAD/Tcra-/- mice

tag: cell type


title: 5xFAD GEX1 [S1_5xFAD]

source_name: Sort purified CD45+ immune cells plus CD45neg non-immune cells from the brain parenchyma of 5xFAD mice


title: Human Synthetic Embryoid Models (SEMs), Day4 of the protocol

description: Human Synthetic Embryoid Models (SEMs), generated from cell aggregation, Day4 of the protocol.


title: TB6545, RSL3

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description: Microwell-based scRNA-seq, 8-base index read, 26-base read 1, 151-base read 2

data_processing:
Raw data obtained from the Illumina NovaSeq 6000 was first corrected for index swapping to avoid cross-talk between sample index sequences using the algorithm described by Griffiths et al, Nature Communications, 2018 before assigning read addresses for each sample.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0 with parameters "-- sjdbOverhang 100 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
Genome build:  GRCh38
supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression level of each individual cell.

source_name: acute slice culture of glioma resection

growth_protocol: Patient specimens were collected immediately after surgical removal  and kept in ice-cold artificial cerebrospinal fluid (ACSF) solution containing 210 mM sucrose, 10 mM glucose, 2.5 mM KCl, 1.25 mM NaH2PO4, 0.5 mM CaCl2, 7 mM MgCl2 and 26 mM NaHCO3 for transportation. collected tumor specimens were placed in a drop of ice-cold ACSF and sliced using a tissue chopper (McIlwain) at a thickness of 500 µm under sterile conditions. The slices were immediately transferred to the ice-cold ACSF solution in 6-well plates using a sterile plastic Pasteur pipette half filled with ice-cold ACSF solution followed by a 15 minutes recovery in ACSF to reach room temperature. Intact and well-shaped slices (approximately 5-10 mm diameter) were then placed on top of a porous membrane insert (0.4 µm, Millipore). Then the membrane inserts were placed into 6-well plates containing 1.5 mL maintenance medium consisting of F12/DMEM (Gibco) supplemented with N-2 Supplement (Gibco) and 1% penicillin/streptomycin (Sigma). To ensure proper diffusion into the slice, culture medium was placed under the membrane insert without bubbles. A drop of 10 µl of culture medium was added directly on top of each slice to prevent the slice surface from drying. The slices were first rested for 6 hrs with the maintenance medium in a humidified incubator at 37℃ and 5% CO2 before drug treatment.

extract_protocol:
Tissue slices were collected for dissociation using Papain Dissociation System (Worthington) as previously described(Mizrak et al., 2020; Mizrak et al., 2019) with following modifications. Briefly, minced tissue was digested with papain (Worthington, 10 units per sample) in PIPES solution (120 mM NaCl, 5 mM KCl, 20 mM PIPES (Sigma), 0.45% glucose, DNase I (Worthington, 100 units per sample), 1xAntibiotic/Antimycotic (GIBCO), pH adjusted to 7.6) for 30 min at 37°C on gentleMACS™ Octo Dissociator with Heaters (Miltenyi Biotec, program 37C_ABDK). After digestion, the cell suspension was applied to a MACS SmartStrainer (70 μm, Miltenyi Biotec) and centrifuged at 300xg for 10 minutes at 4°C. The cell pellets were then subjected to red blood cell removal (Red Blood Cell Lysis Solution (10x), Miltenyi Biotec) and debris removal (Debris Removal Solution, Miltenyi Biotec) according to the manufacturer’s instructions.
mRNA molecues were captured using bead-bound oligo dT(30). Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

treatment_protocol: We performed an 18-hour drug perturbation with 50 nM RSL3 or drug vehicle (DMSO) on spatially adjacent slices. Slices were cultured  in a humidified incubator at 37℃ and 5% CO2. For three patient tumor resections (TB6181, TB6328 and TB6458), we also co-treated slice cultures with 50 nM RSL3 and 10 µM Ferrostatin-1.

value: acute slice culture of glioma resection

tag: disease diagnosis

value: Glioblastoma, WHO Grade IV

value: M

tag: location

value: Right frontal

tag: treatment

value: 50 nM RSL3, 18-hour


title: RERFGC1B Input

value: Input


title: 5xFAD GEX2 [S2_5xFAD]

value: Sort purified CD45+ immune cells plus CD45neg non-immune cells from the brain parenchyma of 5xFAD mice


title: TB6534, RSL3

tag: tissue

value: F

value: Right temporal


title: OCUM1 Input

tag: chip antibody


title: SNU1750 shLuc #2 RNA-seq

value: shLuc


title: NCC59 Input


title: Satellite cells, Islr-Knockout-3, Day4

city: 北京市

first: Fan

last: Liu

state: 北京市

address: 北京市海淀区中国农业大学西校区

institute: 中国农业大学

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
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 and trimming low qulity base with Trimmomatic. 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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Htseq-count 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned adifferentially expressed.  (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Supplementary files format and content: The preprocessed data were aligned to the reference genome using HISAT2.http://asia.ensembl.org
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Skeletal Muscle

growth_protocol: Satellite cells were cultured in growth medium with 20% FBS (Gibco) and basic FGF (Invitrogen) and 1% penicillin-streptomycin at 37 °C in a 5% CO2 atmosphere.

extract_protocol:
3 ug of total RNA was used for the construction of sequencing libraries.
The RNA samples were submitted to Beijing Tangtangtianxia Biotechnology Co (Beijing, China). Library construction, sequencing and bioinformatics analysis were performed, strictly obeying corporate standard operation protocols.

value: Skeletal Muscle

value: Satellite cell

value: stem cell

tag: genotype

value: ko

value: growth culture


title: TB6545, DMSO Control

tag: age

value: drug vehicle (DMSO), 18-hour


title: Satellite cells, Islr-Knockout-2, Day4

address: 北京市海淀区中国农业大学西校区


title: SNU1750 shLuc #1 RNA-seq


title: NCC19 Input

value: Untreated


title: TB6534, DMSO Control

value: acute slice culture of glioma resection


title: 5xFAD;Tcra-/- GEX2 [S4_5xFADTcraKO]

value: Sort purified CD45+ immune cells plus CD45neg non-immune cells from the brain parenchyma of 5xFAD/Tcra-/- mice


title: SNU1750 shTEAD1 #3 Input


title: Satellite cells, Islr-Knockout-1, Day4

address: 北京市海淀区中国农业大学西校区


title: TB6528, RSL3

value: Glioblastoma, WHO Grade IV

value: Left temporal


title: Satellite cells, Control-3, Day4

address: 北京市海淀区中国农业大学西校区

value: control


title: MKN1 Input

value: Input


title: TB6528, DMSO Control


title: Satellite cells, Control-2, Day4

address: 北京市海淀区中国农业大学西校区


title: SNU1750 shTEAD1 #1 Input


title: SNU1750 shLuc #3 RNA-seq


title: T47D, METTL3-Δ238, input

city: Wuhan

first: gao

last: chuan

state: Hubei province

address: bayi road

department: College of life science

institute: Wuhan university

data_processing:
Raw sequencing files were filtered using cutadapt (v1.18), and then aligned against the human reference genome (GRCh38/hg38) using tophat (v2.1.1).
The m6A-enriched regions in each m6A-immunoprecipitation sample were identified by MACS2 (v2.2.6) with the option of “--nomodel” with corresponding input library as control.
Peaks identified with p < 1e-10 were used for downstream analysis. Tracks of signal were computed using MACS2 bdgcmp module with parameter ‘-m FE’, and then visualized using the Integrative Genomics Viewer (IGV) visualization tool.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: T47D cell were cultured in RPMI-1640 (Sigma-Aldrich) containing 10% fetal bovine serum with 1% penicillin–streptomycin.  Cell was maintained in an incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Following purification with poly-T oligo attached magnetic beads (Invitrogen), the poly(A) mRNA fractions is fragmented
mRNA was subjected to incubated for 2 h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany). Eluted m6A-containing fragments (IP) and untreated input control fragments are converted to final cDNA library in accordance with a strand-specific library preparation by dUTP method. Then we performed the paired-end 2×150 bp sequencing on an Illumina Novaseq™ 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) following the vendor's recommended protocol.

value: Human breast cancer

tag: retrovirus


title: T47D, METTL3-Δ198, input


title: SNU1750 shLuc #3 Input

extract_protocol:
For ChIP-seq, sheared chromatin were subjected to immunoprecipitation with 2 μg antibody against H3K27ac (ab4729, Abcam), H3K4me1 (ab8895, Abcam) or 5 μg antibody against TEAD1 (610923, BD Biosciences). For RNA-seq, total RNA was extracted following manufacturer’s protocols (Qiagen)
For Nano histone ChIP-seq, ChIP and input DNA were subjected to whole-genome amplification using the WGA4 kit (Sigma-Aldrich) and a universal primer linked to BpmI restriction site (Qiagen). 30ng of BpmI-digested DNA was used for ChIP-seq library preparation according to manufacturer’s protocols (New England Biolabs). For TF ChIP-seq, 30ng of ChIP and input DNA was used for library preparation. For RNA-seq, libraries were prepared accordingly using Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit (Illumina), with an input of 1 μg total RNA.


title: 5xFADTg TCR brain meninges

source_name: Sort purified CD45+ immune cells from the brain meninges of 5xFADTg mice

extract_protocol: Libraries were prepared using the Chromium Single Cell Immune Profiling v2 Library and Gel Bead Kit (10x Genomics)


title: KATOIII Input

source_name: Gastric Cancer Line

value: KATOIII


title: SNU1750 shLuc #2 Input


title: T47D, METTL3-WT, input


title: IM95 Input


title: Hs746T Input


title: SNU1750 shTEAD1 #3 H3K27ac


title: 5xFADTg TCR2 brain parenchyma

source_name: Sort purified CD45+ immune cells from the brain parenchyma of 5xFADTg mice


title: NonTg TCR brain meninges

source_name: Sort purified CD45+ immune cells from the brain meninges of NonTg mice


title: T47D, sgMETTL3, input


title: MKN7 Input


title: SNU1750 shTEAD1 #2 Input


title: T47D, sgControl, input

description: sgControl.peak.bed

value: sgControl


title: FU97 Input


title: NonTg TCR2 brain parenchyma

source_name: Sort purified CD45+ immune cells from the brain parenchyma of NonTg mice


title: SNU1750 shTEAD1 #2 H3K27ac


title: 5xFADTg TCR1 brain parenchyma

value: Sort purified CD45+ immune cells from the brain parenchyma of 5xFADTg mice


title: SNU1750 shTEAD1 #1 H3K27ac


title: LMSU Input

value: LMSU


title: Satellite cells, Control-1, Day4

address: 北京市海淀区中国农业大学西校区

value: Skeletal Muscle

value: Satellite cell


title: CLS145 Input


title: T47D, METTL3-Δ198, m6A

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)


title: SNU1750 shLuc #3 H3K27ac

value: shLuc


title: AGS Input

value: AGS


title: SNU1750 shLuc #2 H3K27ac


title: 5xFADTg GEX brain meninges

value: Sort purified CD45+ immune cells from the brain meninges of 5xFADTg mice


title: T47D, METTL3-WT, m6A


title: SNU1750 shLuc #1 Input


title: YCC3 H3K27ac

value: Untreated


title: T47D, sgMETTL3, m6A


title: NonTg GEX brain meninges

value: Sort purified CD45+ immune cells from the brain meninges of NonTg mice


title: SNU1750 shLuc #1 H3K27ac


title: HGC27 Input


title: T47D, sgControl, m6A

description: sgControl.peak.bed


title: 5xFADTg GEX2 brain parenchyma


title: T47D, METTL3-Δ238, m6A


title: YCC22 H3K27ac


title: LMSU shTEAD1 #2 RNA-seq


title: YCC20 H3K27ac


title: Human primary lung fibroblasts MRC5 Bax/Bak CRISPR Senescent: IR_BAK_BAX_rep3

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

data_processing:
Real Time Analysis 3.4.4 software used for basecalling.
Sequenced reads were aligned using STAR with a 2-pass pipeline.
Raw counts were generated using htseq.
FPKM values were computed by Cufflinks
Genome_build: hg38
Supplementary_files_format_and_content: FPKM matrix contains FPKM values for each sample and each gene
Supplementary_files_format_and_content: Raw count matrix contains raw counts for each sample and each gene

source_name: human lung

growth_protocol: MRC5 fibroblasts and IMR90 fibroblasts were grown in Dulbecco's Modified Eagle's Medium supplemented with 10% FBD, 100 units/ml penicillin, 100 ug/ml streptomycin and 2mM L-glutamine and maintained at 37 C with 5% CO2. MRC5 fibroblasts were cultured in atmospheric oxygen conditions and IMR90 fibroblasts were cultured under low oxygen (3%) conditions.

extract_protocol:
Cells were scrapped on ice, pellets were collected and RNA was harvested using RNeasy Mini Kit (Qiagen, 74106) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Senescence was induced by exposing cells to 20 Gy X-ray irradiation.

value: Human primary lung fibroblasts MRC5

value: Infected with LentiCRISPR v2 hBAK and LentiCRISPR v2 hBAX

value: Cells were induced to senesce by X-ray irradiation with 20 Gy


title: YCC21 H3K27ac


title: 5xFADTg GEX1 brain parenchyma


title: NonTg TCR1 brain parenchyma

value: Sort purified CD45+ immune cells from the brain parenchyma of NonTg mice


title: Human primary lung fibroblasts MRC5 Bax/Bak CRISPR Senescent: IR_BAK_BAX_rep2


title: LMSU shTEAD1 #1 RNA-seq


title: Human primary lung fibroblasts MRC5 Bax/Bak CRISPR Senescent: IR_BAK_BAX_rep1


title: LMSU shLuc #3 RNA-seq


title: NonTg GEX2 brain parenchyma


title: NonTg GEX1 brain parenchyma


title: 5xFAD;Cxcr6-/- VDJ2

source_name: Sort purified CD45+ immune cells from the brain parenchyma of 5xFAD/Cxcr6-/- mice


title: Human primary lung fibroblasts MRC5 Bax/Bak CRISPR Proliferating: Prolif_BAK_BAX_rep3

value: Not irradiated


title: YCC10 H3K27ac


title: LMSU shLuc #2 RNA-seq


title: TMK1 H3K27ac


title: 5xFAD;Cxcr6-/- VDJ1

value: Sort purified CD45+ immune cells from the brain parenchyma of 5xFAD/Cxcr6-/- mice


title: Human primary lung fibroblasts MRC5 Bax/Bak CRISPR Proliferating: Prolif_BAK_BAX_rep2


title: LMSU shTEAD1 #3 RNA-seq


title: LMSU shTEAD1 #3 Input

value: Input


title: 5xFAD VDJ1

value: Sort purified CD45+ immune cells from the brain parenchyma of 5xFAD mice


title: Human primary lung fibroblasts MRC5 Bax/Bak CRISPR Proliferating: Prolif_BAK_BAX_rep1


title: LMSU shTEAD1 #2 Input

value: LMSU


title: Human primary lung fibroblasts MRC5 Empty CRISPR Senescent: IR_pLenti_rep2

value: Infected with LentiCRISPR v2-puro


title: SNU719 H3K27ac


title: LMSU shTEAD1 #1 Input


title: YCC11 H3K27ac


title: Human primary lung fibroblasts MRC5 Empty CRISPR Senescent: IR_pLenti_rep1


title: 5xFAD VDJ2


title: 5xFAD;Cxcr6-/- GEX2


title: SNU1750 H3K27ac


title: SNU1967 H3K27ac


title: 5xFAD;Cxcr6-/- GEX1


title: SNU16 H3K27ac


title: LMSU shLuc #2 Input


title: 5xFAD GEX2


title: Human primary lung fibroblasts MRC5 Empty CRISPR Proliferating: Prolif_pLenti_rep3


title: LMSU shLuc #3 Input


title: RERFGC1B H3K27ac


title: 5xFAD GEX1


title: LMSU shLuc #1 RNA-seq


title: Human primary lung fibroblasts MRC5 Empty CRISPR Proliferating: Prolif_pLenti_rep2


title: LMSU shLuc #1 Input


title: OCUM1 H3K27ac


title: Human primary lung fibroblasts MRC5 Empty CRISPR Proliferating: Prolif_pLenti_rep1


title: LMSU shTEAD1 #3 H3K27ac


title: Human primary lung fibroblasts MRC5 Empty CRISPR Senescent: IR_pLenti_rep3


title: SNU484 H3K27ac


title: M9 SA1008/9 3

city: Chicago

first: Nathan

last: Waldeck

state: IL

address: 303 E Superior St, Lurie 7-220

institute: Northwestern University

data_processing:
Reads were aligned to the GCF_003546975.1 assembly of the Escherichia coli Nissle 1917 reference genome with  STAR (v2.7.5) using the GeneCounts option.
Gene counts were obtained from EcN annotations (Refseq) using rsem-calculate-expression (v.1.3.0).
Analysis of differential expression between treatments and media conditions using DESeq2 (v1.32.0) after removal of genes with <10 assigned counts.
FDR-adjusted p-value cutoff for significance was set to 0.05. Plots were made in R (v4.0.3) using ggplot2 (v3.3.0), pheatmap (v1.0.12).
Annotations were converted to gene IDs using EcoCyc (www.ecocyc.org). Pathway and biological function assignments of differentially expressed genes were completed using DAVID bioinformatics tools (https://david.ncifcrf.gov).
Assembly: GCF_003546975.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Escherichia coli Nissle 1917

source_name: Nissle 1917

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.
RNA libraries for RNA-seq were prepared using Illumina RNA-seq library prep using ribominus protocol

treatment_protocol: E. Coli Nissle were grown in LB or M9 media until OD 0.5 in 37C then treated with 200 ug/g of calprotectin for 30 mins prior to sequencing

value: Nissle 1917

tag: growth medium

value: M9 (minimal)

value: Calprotectin

tag: time

value: Day 0


title: NCC59 H3K27ac


title: Human primary lung fibroblasts IMR90- Senescence Parkin +CCCP+mtDNA: Parkin_Sen_CCCP_mtDNA_rep3

value: Human primary lung fibroblasts IMR90

value: Infected with LZRS-YFP_Parkin

value: Cells were transfected with 5ug of mtDNA

value: Cells were treated with 12uM of CCCP


title: Human primary lung fibroblasts IMR90- Senescence Parkin +CCCP+mtDNA: Parkin_Sen_CCCP_mtDNA_rep2


title: NCC19 H3K27ac

value: Untreated


title: LMSU shTEAD1 #1 H3K27ac


title: MKN7 H3K27ac


title: MKN1 H3K27ac


title: Human primary lung fibroblasts IMR90- Senescence Parkin +CCCP: Parkin_Sen_CCCP_rep3

value: Cells were induced to senesce by X-ray irradiation with 20 Gy


title: M9 WT 2

growth_protocol: E. Coli Nissle were grown in LB or M9 media until OD 0.5 in 37C

tag: strain


title: M9 WT 3


title: LMSU H3K27ac


title: LMSU shLuc #3 H3K27ac

value: shLuc


title: Human primary lung fibroblasts IMR90- Senescence Parkin +CCCP: Parkin_Sen_CCCP_rep2


title: M9 SA1008/9 2


title: M9 SA1008/9 1


title: LMSU shLuc #2 H3K27ac


title: Human primary lung fibroblasts IMR90- Senescence Parkin +CCCP: Parkin_Sen_CCCP_rep1


title: LB SA1008/9 3

value: LB (rich)


title: LMSU shLuc #1 H3K27ac


title: YCC11 Input (for TEAD1 ChIP)


title: M9 WT 1


title: KATOIII H3K27ac

value: KATOIII


title: Human primary lung fibroblasts IMR90- Senescence Parkin: Parkin_Sen_rep3


title: LB SA1008/9 2


title: Hs746T H3K27ac


title: IM95 H3K27ac


title: LB SA1008/9 1


title: YCC11 TEAD1 ChIP


title: LMSU shTEAD1 #2 H3K27ac


title: Human primary lung fibroblasts IMR90- Senescence Parkin: Parkin_Sen_rep2


title: Human primary lung fibroblasts IMR90- Senescence Parkin +CCCP+mtDNA: Parkin_Sen_CCCP_mtDNA_rep1


title: SNU1750 Input (for TEAD1 ChIP)

value: Input


title: Human primary lung fibroblasts IMR90- Proliferating Parkin: Parkin_Prol_rep2

value: No irradiated


title: LB WT 2


title: SNU1750 TEAD1 ChIP


title: Human primary lung fibroblasts IMR90- Proliferating Parkin: Parkin_Prol_rep1


title: CLS145 H3K27ac


title: HGC27 H3K27ac


title: LMSU TEAD1 ChIP

value: LMSU


title: LMSU Input (for TEAD1 ChIP)


title: LB WT 3


title: Human primary lung fibroblasts IMR90- Proliferating Parkin: Parkin_Prol_rep3


title: FU97 H3K27ac


title: LB WT 1


title: Human primary lung fibroblasts IMR90- Senescence Parkin: Parkin_Sen_rep1


title: FTW_cyESCs, replicate 2, scRNAseq

city: Kunming

first: Mq

last: Peng

state: Yunnan

address: No. 727, Jingming South Road, Chenggong District

institute: Kunming University of Science and Technology

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Subsequently, unique molecular identifiers (UMI) matrices from each sample were merged in R and imported to Seurat(v4.1.1).
hisat2 compiler was run on raw fastq files. FeatureCounts was run on the aligned fastqs. Stringtie was run on the aligned fastqs. Concatenated file was processed in Deseq2 (including normalization, estimation of dispersion effects, and differential gene expression).
Assembly: Mmul_10/rheMac10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca fascicularis

source_name: blastocyst

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (Chromium Single Cell 3’ Reagent Kit v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip G to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. On average, approximately 13,200 single cells were loaded on each channel and approximately 8,000 cells were recovered. Libraries were sequenced on the Illumina NovaSeq 6000 platform

value: Embryo

value: in vitro

tag: sample type

value: Separately cultured cells


title: Ant No. 47 , Size: 5076.51 µM, RNA-seq

status: Public on Aug 15 2023

city: Montreal

first: Moshe

last: Szyf

state: QC Quebec

address: 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology & Therapeutics

country: Canada

institute: McGill University

data_processing:
Base calling was performed with RTA v3.4.4 . Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.
Raw mRNASeq fastq reads (n=48 larvae) were quality/adapter-trimmed using TrimGalore v0.6.7 (https://github.com/FelixKrueger/TrimGalore) under default parameters except for the addition of the option “--paired". Transcripts were quantified using salmon in mapping-based mode using the C. floridanus reference genome (v.7.5) with the options --gcBias, -l A, and --validateMappings enabled.
Salmon quantifications were passed to DeSeq2 for transcript-level normalizations with the DESeq function.
Assembly: cflo_v7.5
Supplementary files format and content: Normalized_count_transcript_level.csv contains DeSeq2-normalized counts for all samples and all transcripts.
Supplementary files format and content: quant.sf files are the output from salmon quantification.

organism: Camponotus floridanus

source_name: whole body

extract_protocol:
DNA and RNA (including miRNA) were extracted with the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN) according to the manufacturer’s instructions.
Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed on a 2100 Bioanalyzer (Agilent Technologies). Libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were normalized and pooled and then denatured in 0.05N NaOH and neutralized using HT1 buffer. The pool was loaded at 225pM. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level.

value: whole body

tag: developmental stage

value: terminal larva

tag: Sex

value: female

tag: size (µm)

tag: colony


title: Ant No. 41 , Size: 7122.86 µM, RNA-seq


title: Ant No. 54 , Size: 5376.84 µM, RNA-seq


title: Ant No. 35 , Size: 5440.79 µM, RNA-seq


title: Ant No. 33 , Size: 6613.4 µM, RNA-seq


title: Ant No. 23 , Size: 4997.25 µM, RNA-seq


title: Ant No. 6 , Size: 6542.04 µM, RNA-seq


title: Ant No. 16 , Size: 5093.47 µM, RNA-seq


title: Ant No. 21 , Size: 5787.72 µM, RNA-seq


title: Ant No. 20 , Size: 5224.96 µM, RNA-seq


title: Ant No. 24 , Size: 5132.63 µM, RNA-seq


title: AGS H3K27ac

first: Shamaine

last: Ho

institute: Genome Institute of Singapore

data_processing:
For Nano ChIP-seq, sequenced reads were first trimmed to remove the first and last ten bases. No trimming was required for TF ChIP-seq. Sequenced reads were mapped to the human genome assembly (hg19) using Burrows-Wheeler Aligner (BWA-MEM, version 0.7.10). Only reads with MAPQ value of at least 10 were retained, and PCR duplicates were removed using SAMtools (version 0.1.19). Significant ChIP enrichment peaks relative to input were identified using MACS2 callpeak function. Wiggle track visualizations were generated using MEDIPS (version 1.20.1).
For RNA-seq, sequenced reads were aligned to hg19 using STAR mapper and gene expression abundance was estimated with RSEM as fragments per kilobase per million (FPKM) using default parameters (pipeline available at https://github.com/gis-rpd/pipelines/tree/master/rnaseq/star-rsem).
Genome_build: hg19 for ChIP-seq and RNA-seq
Supplementary_files_format_and_content: wig/bigwig files for ChIP-seq, RSEM gene count files for RNA-seq

tag: cell line

value: AGS


title: Ant No. 53 , Size: 6754.55 µM, RNA-seq


title: Ant No. 5 , Size: 6943.37 µM, RNA-seq


title: Ant No. 18 , Size: 5018.89 µM, RNA-seq


title: Ant No. 29 , Size: 6827.21 µM, RNA-seq


title: Ant No. 12 , Size: 5248.58 µM, RNA-seq


title: Ant No. 4 , Size: 6120.74 µM, RNA-seq


title: Ant No. 58 , Size: 5161.01 µM, EM-seq

data_processing:
Base calling was performed with RTA v3.4.4 . Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.
Paired-end reads (FASTQ) were trimmed for quality and adapter content using Trim Galore v0.6.7 with default parameters.
A modified cflo_v7.5 sample-specific reference genome (reflecting all SNPs identified with whole-genome sequencing in each sample) was used for alignment. Alignments were performed with bismark v0.23.1 with the options -D 20 -R 3 -N 0 -L 20 --un. All unmapped forward and reverse reads were aligned again separately in the same manner and these single-read alignments were then merged with bamtools, resulting in two BAM files per sample: paired and single-end. Both BAM files (as well as two parallel BAM files from WGBS data) were deduplicated with the bismark deduplicate_bismark script and processed separately with the bismark_methylation_extractor script (options --comprehensive and --paired or --single invoked). The bismark2bedGraph script was then run on all outputs of the bismark_methylation_extractor script to combine paired and single-end calls from EM-seq and WGBS data. The bismark coverage2cytosine script was used to merge CpGs from opposite strands if their methylation values were within 20% (--merge_CpG --discordance 20).
Assembly: cflo_v7.5
Supplementary files format and content: Bismark coverage files containing all covered sites with methylation values and methylated and unmethylated read counts. See Bismark manual.
Library strategy: EM-seq

extract_protocol:
DNA and RNA (including miRNA) were extracted with the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN) according to the manufacturer’s instructions.
gDNA was quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies). Libraries were generated from 200ng of gDNA using the NEBNext® Enzymatic Methyl-seq Kit (New England BioLabs).Adapters were included in the library kit. The libraries were normalized and pooled and then denatured in 0.05N NaOH and neutralized using HT1 buffer. The pool was loaded at 225pM on an Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x150 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 5% level.  Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a LabChip GXII (PerkinElmer) instrument.


title: Ant No. 76 , Size: 7422.84 µM, EM-seq


title: Ant No. 77 , Size: 5571.91 µM, EM-seq


title: Ant No. 72 , Size: 5653.55 µM, EM-seq


title: Ant No. 55 , Size: 5284.36 µM, EM-seq


title: Ant No. 53 , Size: 6754.55 µM, EM-seq


title: Ant No. 68 , Size: 7462.34 µM, EM-seq


title: Ant No. 62 , Size: 5395.82 µM, EM-seq


title: Ant No. 64 , Size: 5502.35 µM, EM-seq


title: Ant No. 79 , Size: 7508.29 µM, EM-seq


title: Ant No. 54 , Size: 5376.84 µM, EM-seq


title: Ant No. 51 , Size: 5054.15 µM, EM-seq


title: Ant No. 49 , Size: 6797.79 µM, EM-seq


title: Ant No. 48 , Size: 6979.4 µM, EM-seq


title: Ant No. 46 , Size: 6689.42 µM, EM-seq


title: Ant No. 40 , Size: 7255.63 µM, EM-seq


title: Ant No. 44 , Size: 7114.6 µM, EM-seq


title: Ant No. 41 , Size: 7122.86 µM, EM-seq


title: Ant No. 38 , Size: 6348.66 µM, EM-seq


title: Ant No. 43 , Size: 7598.06 µM, EM-seq


title: Ant No. 36 , Size: 6171.21 µM, EM-seq


title: Ant No. 35 , Size: 5440.79 µM, EM-seq


title: Ant No. 61 , Size: 5351.99 µM, EM-seq


title: Ant No. 33 , Size: 6613.4 µM, EM-seq


title: Ant No. 32 , Size: 6559.34 µM, EM-seq


title: Ant No. 31 , Size: 6320.12 µM, EM-seq


title: Ant No. 29 , Size: 6827.21 µM, EM-seq


title: Ant No. 27 , Size: 5690.32 µM, EM-seq


title: Ant No. 47 , Size: 5076.51 µM, EM-seq


title: Ant No. 24 , Size: 5132.63 µM, EM-seq


title: Ant No. 42 , Size: 7371.47 µM, EM-seq


title: Ant No. 19 , Size: 5991.09 µM, EM-seq


title: Ant No. 18 , Size: 5018.89 µM, EM-seq


title: Ant No. 21 , Size: 5787.72 µM, EM-seq


title: Ant No. 26 , Size: 7503.35 µM, EM-seq


title: Ant No. 17 , Size: 5850.88 µM, EM-seq


title: Ant No. 20 , Size: 5224.96 µM, EM-seq


title: Ant No. 16 , Size: 5093.47 µM, EM-seq


title: Ant No. 23 , Size: 4997.25 µM, EM-seq


title: Ant No. 9 , Size: 4942.55 µM, EM-seq


title: Ant No. 12 , Size: 5248.58 µM, EM-seq


title: Ant No. 76 , Size: 7422.84 µM, RNA-seq


title: Ant No. 5 , Size: 6943.37 µM, EM-seq


title: Ant No. 6 , Size: 6542.04 µM, EM-seq


title: Ant No. 4 , Size: 6120.74 µM, EM-seq


title: Ant No. 3 , Size: 6892.55 µM, EM-seq


title: Ant No. 2 , Size: 5110.42 µM, EM-seq


title: Ant No. 77 , Size: 5571.91 µM, RNA-seq


title: Ant No. 79 , Size: 7508.29 µM, RNA-seq


title: Ant No. 68 , Size: 7462.34 µM, RNA-seq


title: Ant No. 61 , Size: 5351.99 µM, RNA-seq


title: Ant No. 58 , Size: 5161.01 µM, RNA-seq


title: Ant No. 15 , Size: 4648.07 µM, EM-seq


title: Ant No. 9 (PILOT - colony 6) , Size: 7462.87 µM, WGBS

data_processing:
The Illumina control software was HCS HD 3.4.0.38, the real-time analysis program was RTA v. 2.7.7. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.
Paired-end reads (FASTQ) were trimmed for quality and adapter content using Trim Galore v0.6.7 with default parameters.
A modified cflo_v7.5 sample-specific reference genome (reflecting all SNPs identified with whole-genome sequencing in each sample) was used for alignment. Alignments were performed with bismark v0.23.1 with the options -D 20 -R 3 -N 0 -L 20 --un. All unmapped forward and reverse reads were aligned again separately in the same manner and these single-read alignments were then merged with bamtools, resulting in two BAM files per sample: paired and single-end. Both BAM files (as well as two parallel BAM files from WGBS data) were deduplicated with the bismark deduplicate_bismark script and processed separately with the bismark_methylation_extractor script (options --comprehensive and --paired or --single invoked). The bismark2bedGraph script was then run on all outputs of the bismark_methylation_extractor script to combine paired and single-end calls from EM-seq and WGBS data. The bismark coverage2cytosine script was used to merge CpGs from opposite strands if their methylation values were within 20% (--merge_CpG --discordance 20).
Assembly: cflo_v7.5
Supplementary files format and content: Bismark coverage files containing all covered sites with methylation values and methylated and unmethylated read counts. See Bismark manual.
Supplementary files format and content: For colony 6, bedGraph files output from Bismark. See Bismark user manual.

extract_protocol:
DNA and RNA (including miRNA) were extracted with the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN) according to the manufacturer’s instructions.
gDNA was quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies). Libraries were generated from 250ng of gDNA using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs).  Adapters were purchased from NEB. Size selection of libraries containing the desired insert size was performed using sparQ PureMag Beads (Quantabio). Bisulfite conversion had been carried out with the EZ DNA Methylation-Lightning Kit (Zymo). Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were normalized and pooled and then denatured in 0.05N NaOH and neutralized using HT1 buffer. ExAMP was added to the mix following the manufacturer’s instructions. The pool was loaded at 250pM on an Illumina cBot and the flowcell was run on a HiSeq X for 2x151 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level.


title: Ant No. 13 (PILOT - colony 6) , Size: 6007.21 µM, WGBS


title: Ant No. 22 , Size: 4783.45 µM, EM-seq


title: Ant No. 2 (PILOT - colony 6) , Size: 5581.36 µM, WGBS


title: Ant No. 12 (PILOT - colony 6) , Size: 6249.9 µM, WGBS


title: Ant No. 1 (PILOT - colony 6) , Size: 5047.16 µM, WGBS


title: Ant No. 15 (PILOT - colony 6) , Size: 7123.6 µM, WGBS


title: Ant No. 77 , Size: 5571.91 µM, WGBS


title: Ant No. 79 , Size: 7508.29 µM, WGBS


title: Ant No. 62 , Size: 5395.82 µM, WGBS


title: Ant No. 68 , Size: 7462.34 µM, WGBS


title: Ant No. 76 , Size: 7422.84 µM, WGBS


title: Ant No. 72 , Size: 5653.55 µM, RNA-seq


title: Ant No. 64 , Size: 5502.35 µM, WGBS


title: Ant No. 72 , Size: 5653.55 µM, WGBS


title: Ant No. 53 , Size: 6754.55 µM, WGBS


title: Ant No. 58 , Size: 5161.01 µM, WGBS


title: Ant No. 47 , Size: 5076.51 µM, WGBS


title: Ant No. 61 , Size: 5351.99 µM, WGBS


title: Ant No. 54 , Size: 5376.84 µM, WGBS


title: Ant No. 51 , Size: 5054.15 µM, WGBS


title: Ant No. 49 , Size: 6797.79 µM, WGBS


title: Ant No. 46 , Size: 6689.42 µM, WGBS


title: Ant No. 44 , Size: 7114.6 µM, WGBS


title: Ant No. 43 , Size: 7598.06 µM, WGBS


title: Ant No. 41 , Size: 7122.86 µM, WGBS


title: Ant No. 42 , Size: 7371.47 µM, WGBS


title: Ant No. 40 , Size: 7255.63 µM, WGBS


title: Ant No. 35 , Size: 5440.79 µM, WGBS


title: Ant No. 36 , Size: 6171.21 µM, WGBS


title: Ant No. 38 , Size: 6348.66 µM, WGBS


title: Ant No. 55 , Size: 5284.36 µM, WGBS


title: Ant No. 48 , Size: 6979.4 µM, WGBS


title: Ant No. 32 , Size: 6559.34 µM, WGBS


title: Ant No. 27 , Size: 5690.32 µM, WGBS


title: Ant No. 29 , Size: 6827.21 µM, WGBS


title: Ant No. 33 , Size: 6613.4 µM, WGBS


title: Ant No. 15 , Size: 4648.07 µM, WGBS


title: Ant No. 16 , Size: 5093.47 µM, WGBS


title: Ant No. 20 , Size: 5224.96 µM, WGBS


title: Ant No. 24 , Size: 5132.63 µM, WGBS


title: Ant No. 23 , Size: 4997.25 µM, WGBS


title: Ant No. 9 , Size: 4942.55 µM, WGBS


title: Ant No. 12 , Size: 5248.58 µM, WGBS


title: Ant No. 18 , Size: 5018.89 µM, WGBS


title: Ant No. 4 , Size: 6120.74 µM, WGBS


title: Ant No. 3 , Size: 6892.55 µM, WGBS


title: Ant No. 2 , Size: 5110.42 µM, WGBS


title: Ant No. 17 , Size: 5850.88 µM, WGBS


title: Ant No. 5 , Size: 6943.37 µM, WGBS


title: Ant No. 21 , Size: 5787.72 µM, WGBS


title: Ant No. 31 , Size: 6320.12 µM, WGBS


title: Ant No. 6 , Size: 6542.04 µM, WGBS


title: Ant. No. 49 , Size: 6797.79 µM, miRNA-seq

description: size-selected small RNA

data_processing:
The Illumina control software was HCS HD 3.4.0.38, the real-time analysis program was RTA v. 2.7.7. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.
Small RNA-sequencing reads (FASTQ) were trimmed for quality and adapter content using Trim Galore v0.6.7 with default parameters.
Reads from all 24 samples were merged into a single combined FASTA file to be used for microRNA prediction miRDeep2 with default settings, the colony-specific reference genome, and mature Apis mellifera miRNAs from miRBase.
The resulting predictions were then used for a two-step mapping and quantification for the miRNAs from each sample using mapper.pl and quantification.pl scripts from miRDeep2.
Assembly: cflo_v7.5
Supplementary files format and content: CSV file containing raw and normalized expression for each microRNA.

extract_protocol:
DNA and RNA (including miRNA) were extracted with the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN) according to the manufacturer’s instructions.
Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies). Libraries were generated from 1000 ng of total RNA using the TruSeq® Small RNA Sample Prep Kit (Illumina), as per the manufacturer’s recommendations. cDNA construct purification has been performed on a Pippin Prep instrument (SAGE Science). Final libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were normalized and pooled at 3nM and then denatured in 0.05N NaOH and neutralized using HT1 buffer. ExAMP was added to the mix following the manufacturer’s instructions. The pool now at 200pM was loaded on a Illumina cBot and the flowcell was ran on a HiSeq 4000 for 1x50 cycles. A phiX library was used as a control and mixed with libraries at 1% level.


title: Ant. No. 64 , Size: 5502.35 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 51 , Size: 5054.15 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 48 , Size: 6979.4 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 62 , Size: 5395.82 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 55 , Size: 5284.36 µM, miRNA-seq

description: size-selected small RNA


title: Ant No. 26 , Size: 7503.35 µM, WGBS


title: Ant No. 22 , Size: 4783.45 µM, WGBS


title: Ant. No. 46 , Size: 6689.42 µM, miRNA-seq

description: size-selected small RNA


title: Ant No. 19 , Size: 5991.09 µM, WGBS


title: Ant. No. 43 , Size: 7598.06 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 42 , Size: 7371.47 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 40 , Size: 7255.63 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 44 , Size: 7114.6 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 36 , Size: 6171.21 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 38 , Size: 6348.66 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 31 , Size: 6320.12 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 26 , Size: 7503.35 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 9 , Size: 4942.55 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 19 , Size: 5991.09 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 32 , Size: 6559.34 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 27 , Size: 5690.32 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 17 , Size: 5850.88 µM, miRNA-seq

description: size-selected small RNA


title: Ant. No. 15 , Size: 4648.07 µM, miRNA-seq

description: size-selected small RNA


title: Ant No. 64 , Size: 5502.35 µM, RNA-seq


title: Ant. No. 22 , Size: 4783.45 µM, miRNA-seq

description: size-selected small RNA


title: Ant No. 55 , Size: 5284.36 µM, RNA-seq


title: Ant No. 49 , Size: 6797.79 µM, RNA-seq


title: Ant No. 62 , Size: 5395.82 µM, RNA-seq


title: Ant. No. 3 , Size: 6892.55 µM, miRNA-seq

description: size-selected small RNA


title: Ant No. 46 , Size: 6689.42 µM, RNA-seq


title: Ant No. 44 , Size: 7114.6 µM, RNA-seq


title: Ant No. 51 , Size: 5054.15 µM, RNA-seq


title: Ant. No. 2 , Size: 5110.42 µM, miRNA-seq

description: size-selected small RNA


title: Ant No. 42 , Size: 7371.47 µM, RNA-seq


title: Ant No. 40 , Size: 7255.63 µM, RNA-seq


title: Ant No. 48 , Size: 6979.4 µM, RNA-seq


title: Ant No. 38 , Size: 6348.66 µM, RNA-seq


title: Ant No. 43 , Size: 7598.06 µM, RNA-seq


title: Ant No. 36 , Size: 6171.21 µM, RNA-seq


title: Ant No. 32 , Size: 6559.34 µM, RNA-seq


title: Ant No. 27 , Size: 5690.32 µM, RNA-seq


title: Ant No. 31 , Size: 6320.12 µM, RNA-seq


title: Ant No. 26 , Size: 7503.35 µM, RNA-seq


title: Ant No. 17 , Size: 5850.88 µM, RNA-seq


title: Ant No. 22 , Size: 4783.45 µM, RNA-seq


title: Ant No. 19 , Size: 5991.09 µM, RNA-seq


title: Ant No. 2 , Size: 5110.42 µM, RNA-seq


title: Ant No. 3 , Size: 6892.55 µM, RNA-seq


title: Ant No. 9 , Size: 4942.55 µM, RNA-seq


title: Bcl6-HA

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
All sequencing reads were mapped to the mouse genome mm10 by bowtie2
PCR duplicates were removed using picard MarkDuplicates
The uniquely mapped reads were used to call peak with MACS2 using a q value cutoff 0.05
ChIPseeker was used for peak annotation
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file

source_name: in vitro CD8+ T cells

growth_protocol: Naïve CD8+ T cells were activated cultured with anti-CD3 and anti-28 for 48 hours before retrovirus infection. Two days after infection, the GFP+ infected cells were sorted

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

value: pRV_Bcl6_HA_ires_GFP transfected

tag: antibody

value: HA ChIP antibody (CST,3724)


title: KAT6A_MGD1135_input

city: Los Angeles

first: Valerie

last: Arboleda

address: 615 Charles E. Young Drive South

department: Department of Pathology and Laboratory Medicine

institute: UCLA

data_processing:
Raw read quality, adaptor content, and duplication rates were assessed with FastQC
Raw reads were then aligned to GENCODE Human genome version hg38 (GR38) version 31 using BWA-MEM (Li 2013)
BAM files were then sorted, indexed, and filtered against chrX, chrY, and MT reads using SAMtools. Picard tools were then used to generate insert size histograms and remove duplicates from BAM files
Narrow peaks from each sample were called using MACS2 callpeak (Gaspar 2018); any peak that overlapped by at least one base was then merged using BEDtools (Quinlan and Hall 2010) merge. Reads overlapping merged peaks were counted using featureCounts (Liao et al. 2014).
DESeq2(Love et al. 2014) was used to identify differentially occupied peaks between disease and control samples
Assembly: hg38
Supplementary files format and content: csv file of normalized read counts with columns for differential coverage between case and control groups

source_name: fibroblast cells,KAT6A

growth_protocol: Fibroblast cell lines were cells were grown in DMEM (Gibco™), 10% FBS, 1% Non-essential Amino Acid (100X, Gibco™, 11140-050) and 1% PenStrep at 37℃ in 5% CO2 incubators. Cell lines were tested for mycoplasma on a monthly basis.

extract_protocol:
The dermal fibroblast cells were grown to 80-90% confluency and then fixed using fresh media containing 1% formaldehyde. Cells were incubated in formaldehyde media for 10 minutes, and then the reaction was neutralized with 1.25M glycine. After this, the media was removed and cells were washed twice with ice cold PBS containing protease inhibitor. Post PBS wash, the cells were scraped and collected in a 1.5 ml tube. The cell pellets were resuspended in ChipLysis buffer and sonication was performed using Diagenode bioruptor at high for 45 cycles (30 sec on, 30 sec off). 5 ul of sonicated product was de-crosslinked and purified to check optimal lysis (200-600 bp). The sonicated chromatin was pre-cleared with Antigen G dynabeads for 2 hours on a nutator at 4 0 C. The pre-cleared chromatin was then incubated with 5 ul of H3K9ac (Cell signaling#9649), 2 ul of H3K23ac (AbCam #ab177275), and 4ul of IGg (cell signaling #2729) at 4 0C overnight. The next day, the antibody-chromatin complex was incubated with antigen G dynabeads for an additional 2 hours on a nutator, and then the beads were washed by a series of buffers and then de-crosslinked at 65 0C overnight.
Post de-crosslinking, the DNA was purified and processed for library preparation using illumina Chip library prep (illumina#15034288) was used for library construction. Chip libraries were sequenced on illumina Hiseq3000 using single read 75 bp read-length.

tag: cell type

value: fibroblast

value: F

tag: disease state


title: KAT6A_MGD1149_input

value: M


title: Control_5_input

source_name: fibroblast cells,Control

value: Control


title: Control_6_input


title: Input


title: Control_5_h3k23ac

description:
KAT6A_fibro_ChIP_23ac_feature_counts.txt
ZKW-17-1511_23_ac


title: KAT6A_MGD1149_h3k9ac

description:
KAT6A_fibro_ChIP_9ac_feature_counts.txt
MGD1149_9ac

value: H3K9ac (Cell signaling #9649)


title: KAT6A_MGD1105_h3k9ac

description:
KAT6A_fibro_ChIP_9ac_feature_counts.txt
MGD1105_9ac


title: Control_6_h3k9ac

description:
KAT6A_fibro_ChIP_9ac_feature_counts.txt
MGD1551_9ac


title: KAT6A_MGD1135_h3k9ac

description:
KAT6A_fibro_ChIP_9ac_feature_counts.txt
MGD1135_9ac


title: Control_6_h3k23ac

description:
KAT6A_fibro_ChIP_23ac_feature_counts.txt
MGD1551_23_ac


title: Ant No. 15 , Size: 4648.07 µM, RNA-seq

tag: tissue


title: Control_13 [MGD1549 ATAC-seq]

data_processing:
Raw read quality, adaptor content, and duplication rates were assessed with FastQC
Raw reads were then aligned to GENCODE Human genome version hg38 (GR38) version 31 using BWA-MEM (Li 2013)
BAM files were then sorted, indexed, and filtered against chrX, chrY, and MT reads using SAMtools. Picard tools were then used to generate insert size histograms and remove duplicates from BAM files
Narrow peaks from each sample were called using MACS2 callpeak (Gaspar 2018); any peak that overlapped by at least one base was then merged using BEDtools (Quinlan and Hall 2010) merge. Reads overlapping merged peaks were counted using featureCounts (Liao et al. 2014).
DESeq2(Love et al. 2014) was used to identify differentially open peaks between disease and control samples
Assembly: hg38
Supplementary files format and content: csv file of normalized read counts with columns for differential accessibility between case and control groups

extract_protocol:
ATAC-seq was performed with 50,000 cells in both control and patient derived dermal fibroblast cell lines. ATAC-seq library generation was performed as described in (Corces et al. 2017)
ATAC-seq library generation was performed as described in (Corces et al. 2017).Samples were run on the Agilent DNA TapeStation to confirm tagmentation pattern, and the genomically barcoded libraries were multiplexed and run on the Hiseq3000 with paired end, 150bp libraries for a minimum of 30 million reads per sample


title: Control_9 [GM01651 ATAC-seq]


title: Control_4 [ZKW-17-1510 ATAC-seq]


title: Control_6 [MGD_1551 ATAC-seq]


title: KAT6A_MGD1149_h3k23ac

description:
KAT6A_fibro_ChIP_23ac_feature_counts.txt
MGD1149_23_ac

tag: chip antibody


title: Control_11 [GM00323 ATAC-seq]


title: Control_5 [ZKW-17-1511 ATAC-seq]


title: Control_3 [ZKW-17-2345 ATAC-seq]


title: KAT6A_MGD1105_input


title: Control_5_h3k9ac

description:
KAT6A_fibro_ChIP_9ac_feature_counts.txt
ZKW-17-1511_9ac


title: Control_2 [ZKW-17-2343 ATAC-seq]


title: KAT6A_MGD1135_h3k23ac

description:
KAT6A_fibro_ChIP_23ac_feature_counts.txt
MGD1135_23_ac


title: KAT6A_MGD1618 [MGD_1618 ATAC-seq]


title: KAT6A_MGD1149 [MGD_1149 ATAC-seq]


title: KAT6A_MGD1135 [MGD1135 ATAC-seq]


title: KAT6A_MGD1105 [MGD1105 ATAC-seq]


title: KAT6A_MGD1094 [MGD_1094 ATAC-seq]


title: HRPC-AGEs, rep 3, RNA-seq

city: nanjing

first: XU

last: Ying

state: jiangsu

address: xuanwu district

institute: Nanjing university

data_processing:
scRNA-seq samples: the demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
RNA-seq samples: 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  hg38 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: mm10, hg38
Supplementary files format and content: Tab-separated values files and matrix files for scRNA-seq samples.
Supplementary files format and content: Tab-delimited text files include RPKM values for RNA-seq samples.

source_name: retina

growth_protocol: HMC and HRPC were  maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
21 weeks old wide type (wt) and leptin receptor-deficient (db/db) in C57BLKs/J background mice were sacrificed. Kidneys were perfused with PBS, followed by dynabead perfusion. Minced kidneys were digested with 1 mg/ml collagenase II , 1 mg/ml Protease E  plus 50 units/ml DNase I  at 37 °C for 5 min. Separated glomeruli were washed three times, then placed in 2 ml digestion buffer and incubated for an additional 30 minutes at 37℃ with rotating. Globes were removed and dissected in PBS on ice. Retina tissues were dissociated with dissociation system containing 2 mg/ml collagenase  II  and 200 units/ml DNase I at 37℃ for 30 minutes on a rotator. The retinal cells were then sorted by magnetic bead separation using PE anti-mouse CD140b antibody and PE-anti PECAM1 antibody.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HMC and HRPC was induced by treatment of 100 µg/ml AGEs for 6 hours while 100 µg/ml BSA as control.

value: retina

value: retinal pericyte

tag: treatment

value: 100 ug/ml advanced glycation end products


title: HRPC-control, rep 2, RNA-seq

value: 100 ug/ml bovine serum albumin


title: HRPC-control, rep 1, RNA-seq


title: HRPC-AGEs, rep 2, RNA-seq


title: HMC-AGEs, rep 2, RNA-seq

source_name: kidney

value: kidney

value: mesangial cell


title: HMC-AGEs, rep 3, RNA-seq


title: HRPC-control, rep 3, RNA-seq


title: Liver,180day,rep2,RNA

city: Chengdu

first: Jing

last: Li

state: China

address: No. 211 Huimin Road, Wenjiang District

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

description: RNA-seq

data_processing:
The raw reads were trimmed to remove adapters and low-quality base pairs for all samples.
The high-quality RNA-seq reads were aligned to the pig reference genome using STAR (v 2.6.0c).
Gene-level expression was estimated as transcripts per million (TPM) using the Kallisto(v 0.43.0).
Assembly: Sscrofa 11.1
Supplementary files format and content: All TPM text file include the gene-level expression in each sample were estimated as transcripts per million (TPM) using the Kallisto (v 0.43.0).

organism: Sus scrofa

source_name: Liver

extract_protocol:
All liver tissue samples using a rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq RNA-seq library protocol.
All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced with 100-bp paired-end reads on the BGISEQ-500 platform

value: Liver

tag: age

value: Postnatal day 180

value: Female

value: Domestic pig

tag: breed

value: Crossbred pig


title: KAT6A_MGD1360 [MGD1360 ATAC-seq]


title: Liver,28day,rep1,RNA

description: RNA-seq

value: Postnatal day 28


title: HMC-control, rep 3, RNA-seq


title: Liver,180day,rep1,RNA

description: RNA-seq


title: Control_1 [ZKW-17-1743 ATAC-seq]

value: fibroblast


title: MCF7 cells, shHot_+E2_Input_ChIP-seq

city: Irvine

first: Jiejun

last: Shi

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
The raw reads (single-end, 100 bp) were aligned to human reference genome hg19 using bowtie (v1.1.0) allowing up to one mismatch.
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs.  Peak calling was performed using MACS (v1.4.2) with the default cutoff of P ≤ 1 × 10-8. Clonal reads were automatically removed by MACS.

growth_protocol: MCF7 cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and 1% antibiotics.

extract_protocol:
Chromatin immunoprecipitation (ChIP) assays were performed with following modifications to previously described high-throughput ChIP protocol (Blecher-Gonen et al, 2013). Briefly, cells were crosslinked in 1% formaldehyde for 10 min, followed by incubation with glycine to stop crosslinking. Cells were collected and washed with ice cold PBS, incubated with cell lysis buffer (5mM PIPES pH 8.0, 85 mM KCl and 0.5% NP40) with protease inhibitor cocktail (Roche) to isolate nuclei. The nuclei were lysed for 30 min on ice using nuclei lysis buffer (12 mM Tris-HCl pH 8.0, 6 mM EDTA pH 8.0, 0.5% SDS) supplemented with protease inhibitor cocktail. Lysate were fragmented with a Bioruptor (Diagenode) to obtain DNA fragments ranging 200-600 bp. The supernatant was incubated with respective antibodies conjugated with Dynabeads Protein G (Invitrogen) in dilution buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 0.1% Na-DOC, 1% Triton X-100) overnight at 4°C. The immunocomplexes were collected using Dynamag, washed twice with low-salt buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-DOC) and high-salt buffer (10 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-DOC) and then once with LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP40, 0.5% Na-Deoxycholate), and reverse crosslinked overnight followed by DNA extraction.
ChIP–seq libraries were prepared using NEBNext Ultra II DNA library prep kit.

treatment_protocol: For hormone (estrogen) depletion, cells were changed to charcoal-stripped hormone-free medium (Gibco, Grand Island, NY) supplemented with 10% charcoal dextran-treated fetal bovine serum (Thermal Scientific Hyclone, Logan, UT) for 72 hours. Estrogen induction was performed using 10 nM of 17β-estradiol (Sigma, St. Louis, MO) for the indicated times. Ethanol was used as a vehicle control.

value: Breast Adenocarcinoma cell line MCF7

value: shHOTAIRM1, + estrogen


title: HMC-control, rep 1, RNA-seq


title: KAT6A_MGD1191 [MGD1191 ATAC-seq]

value: M


title: Liver,28day,rep2,RNA

description: RNA-seq


title: MCF7 cells, shHot_-E2_Input_ChIP-seq

value: shHOTAIRM1, - estrogen


title: HMC-control, rep 2, RNA-seq


title: Jlat5A8 vRNA DMSO Rep2

city: Seattle

first: Terry

last: Hafer

email: tjhafe@gmail.com, thafer@fredhutch.org

state: Washington

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Center

library_source: other

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v3.9.25 software followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v2.20.
FASTX barcode splitter was used to separate reads by barcode matching.
Alignment to reference and guide-level quantification was performed using Liu lab's MAGeCK software.
Liu lab's CRISPR analysis tool, Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK), was used to perform differential guide analysis between various groups of interest. PMID: 25476604.
Assembly: HIVDEP library developed by Emerman lab. It contains 527 genes of interest and 210 non-targeting controls.
Supplementary files format and content: Tab delimited file with read counts for each guide sequence across all samples
Library strategy: CRISPR screen

molecule: other

source_name: Jurkat (J-Lat 5A8)

growth_protocol: J-Lat cells were cultured in RPMI 1640 media (ThermoFisher, 11875093) supplemented with Pen/Strep, 10% Fetal Bovine Serum (FBS), and 10 mM HEPES (ThermoFisher, 15630080). Cells were maintained at 37ºC with 5% CO2. 24 hours after viral transduction, cells were subjected to puromycin treatment (Sigma, P8833) at a final concentration of 0.4 ug/mL to select for cells that received the vector. Latency reversal agent drug treatments were performed 11 days after viral transduction, and cell and viral pellets were isolated 12 days after viral transduction.

extract_protocol:
To isolate Genomic DNA  for the screen, cells were spun down for each treatment for 5 minutes at 1,000 xg at room temperature, washed in 1x PBS, spun down again, and cell pellets frozen at -80ºC until ready for extraction. Genomic DNA (gDNA) was isolated from each treatment using the QIAamp DNA Blood Midi Kit (Qiagen #51183). Viral RNA (vRNA) was extrated from supernatant of pelleted cells by concentrating over a 20% sucrose solution (70,000 xg for 1 hour at 4C), and then isolating vRNA from pellets using the QIAamp Viral RNA Mini Kit (Qiagen, #52904).
Genomic DNA (gDNA) or reverse-transcribed viral RNA (vRNA) were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All vRNA was amplified for each sample where appropriate. For gDNA samples, a total of 500-fold coverage of the sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For vRNA, all PCR1 was amplified in the second round. For gDNA, 10 uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided bead cleanup (AMPureXP, Beckman Coulter), quantified with a Qubit dsDNA HS assay and pooled for sequencing.

treatment_protocol: 11 days after transduction, cells were treated with either DMSO, AZD5582 (25 nM, MedChemExpress, HY-12600), I-BET151 (10 uM, SelleckChem, S2780), or combination AZD5582 (1 nM) and I-BET151 (2.5 uM) for 24 hours.

value: Jurkat (J-Lat 5A8)

value: T Lymphocyte

value: DMSO


title: Jlat5A8 vRNA AZD Rep2


title: Jlat5A8 vRNA COMBO Rep2

value: AZD5582 and I-BET151