title: H2AZ_CC_3

city: New York

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw reads from single-end sequencing with a 75 bp read length were processed by trimming the adapter sequences using Cutadapt
Trimmed reads were mapped to the reference mm10 genome using HISAT
Duplicate fragments were discarded, retaining only unique reads.
Reads were sorted by chromosomal coordinates using samtools
We utilized MACS2 (Model-based Analysis of ChIP-Seq) to identify peaks
Assembly: mm10
Supplementary files format and content: peaks

extract_protocol:
Chromatin was extracted using truChIP Chromatin Shearing Kit with formaldehyde and prepared according to manufacturer’s Low Cell protocol (Covaris PN010179 Rev O, Dec 2020). 11.1% formaldehyde was made fresh from 16% concentrated formaldehyde. Room temperature (RT) 1X Fixing Buffer A was added to samples and the 11.1% formaldehyde was then added to make a final concentration of 1% only. Samples were incubated for 5 min on rocker at RT to allow for efficient cross-linking and terminated immediately by adding quenching Buffer E and incubating for another 5 min. Supernatants were discarded and the tissue samples were washed with cold 1X PBS twice. Lysis Buffer B was added and samples were homogenized using the Dounce Tissue homogenizer (~20 strokes) and left to incubate on rocker for 10 min at 4℃. Samples were then centrifuged at 1700xg for 5 min at 4℃ and the supernatant discarded followed by resuspension in wash buffer C and incubated for 10 min at 4℃. Supernatants were discarded after centrifuging at 2000xg for 5 min at 4℃ and shearing buffer D3 was added without disturbing the nuclei pellet followed by two rounds of centrifugation at 1700xg for 5 min at 4℃ while the supernatants were decanted. The nuclei pellets were resuspended in shearing buffer D3 and transferred to AFA microtubes (8 microTUBE-130 AFA Fiber H Slit Strip V2, PN520239) for low cell chromatin shearing using Covaris ultrasonicator with the following settings: 75.0 peak power; 15.0 Duty % Factor; 1000 Cycles; 11.3 Avg Power for durations of 810.0 sec and 540.0 sec, respectively.
After shearing, samples were transferred into pre-chilled microcentrifuge tubes and diluted 1:1 with Covaris 2X IP Dilution buffer and microcentrifuged at 10000xg for 5 min at 4℃ before proceeding to IP with the supernatant. 30 µL of beads (Invitrogen Dynabeads Protein G) per IP was aliquoted into 1.5 ml Eppendorf tubes and separated on magnet for ~1 min and the supernatant removed by aspiration. The beads were resuspended and mixed in 1 ml Block solution (1X PBS, 0.5% BSA) by inversion. Supernatants were separated on magnet and aspirated and the wash process repeated once more. Finally, the beads were resuspended in 250 ml Block solution and 4 µg/per IP of H2A.Z and H3 antibodies, respectively, and the tubes rotated at 4℃ for 2 h. The beads were collected on magnet and washed in 1 ml Block solution for a total of 3 washes before resuspension in 50 µl/per IP Block solution. Chromatin lysates from each sample were aliquoted respectively for H2A.Z and H3 antibody IP into 1.5 ml lo-bind protein Eppendorf tubes, 50 µl of the beads and 300 µl of block solution added and mixed by inversion. The IP tubes were rotated at 4℃ overnight. The IP/bead mixture were transferred to new pre-chilled tubes and the beads were collected on magnet and the supernatant aspirated. 1 ml of cold RIPA wash buffer (50 mM HEPES-KOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) was added and mixed by inversion. The beads were collected, followed by a total of 5 RIPA washes before resuspension in 1 ml Final ChIP Wash buffer (1X TE, 50 mM NaCl) and subsequent collection on a magnet. The beads were then resuspended in 210 µl Elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) and incubated at 65℃ for 30 min with 400 rpm on a thermomixer. The beads were collected again on magnet and 200 µl of the supernatant transferred to fresh tubes. The tubes were then boiled at 95℃ for 7 min for DNA reverse cross-linking. The DNA were purified using Qiagen MinElute PCR purification kit and eluted with 20 µl Buffer EB (10mM Tris-Cl, pH 8.5) and transferred to 8-strip PCR tubes.

value: Brain

value: Nucleus accumbens

tag: antibody treatment


title: PAT21, HDP-high, d0

status: Public on Oct 09 2024

type: SRA

city: Siena

first: Simone

last: Lucchesi

address: Viale Bracci, 16

country: Italy

institute: University of Siena

library_source: transcriptomic

data_processing:
Trimming and removal of low-quality reads was performed with Trimmomatic v0.39 using the following parameters: SLIDINGWINDOW 4:5, MINLEN:36.
STAR v2.7.3 was used to align reads to reference Grch38 human genome
htseq v.2.0.2was used to count the reads of annotated genes
DESeq2 package v1.36.0 was used to normalize gene expression and to perfor diferential gene expression analysis
Assembly: Grch38 human genome
Supplementary files format and content: CSV file containing raw counts for each sample
Supplementary files format and content: CSV file containing vst normalized counts (log2-like) using vst function

molecule: total RNA

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
RNA  was extracted from PBMC using RNeasy mini kit (Qiagen)
Libraries were prepared using “Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus” kit and sequenced on NovaSeq 6000 System (Illumina)

tag: tissue

value: PBMCs

tag: cell type

tag: group

value: HDP-high

tag: time

value: d0, Pre-priming


title: A1S56naive3

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

country: USA

institute: Purdue University

description:
single-cell mRNA-seq data
batch3_inflamedVsNaive_counts.txt

data_processing:
FastX-Toolkit v. 0.0.13.2 (Gordon, A., FastX-Toolkit. 2009) quality trimmer was used to further trim reads based on quality score and FASTX-Toolkit quality chart was used to make read per-base quality plots. A trimscore and a trim length of 30 were used.
Tophat2 was used to align reads to the reference genome. Tophat2 was run with defaults except that the number of mismatches allowed was 1.
The htseq-count script in HTSeq v.0.6.151 and Biopython v.2.7.3 were used to generate a counts matrix in “intersection-nonempty” mode, with feature set to “exon” and attribute parameter set to “gene_id”.
R version R-3.4.1 and the package Seurat v. 1.4 was used to cluster cells into subpopulations using the first 4 principal components, a resolution of 0.5, and k.param = 4.
The FindAllMarkers() function within Seurat was used to identify cluster markers using the zero-inflated “bimod” model and a false discovery rate (FDR) of 0.01. FindAllMarkers() was likewise used to identify differentially expressed genes between inflamed and naïve cells, controlling the FDR at 5%.
Assembly: Mus musculus GRCm38.p6 reference genome49
Supplementary files format and content: count matrices are provided as tab delimited text files

molecule: polyA RNA

organism: Mus musculus

source_name: prostate

extract_protocol:
tissue procurement: Prosates from naïve or inflamed POET3 mice
Minced mouse prostate tissues were digested in 1 mg/mL collagenase (Sigma-Aldrich) in RPMI-1640 (Gibco) media containing 10% FBS (Corning) with shaking at 37ºC for 2 hours, followed by trypsinization. Dissociated cells were passed through 20G needles and 40 µm cell strainers to eliminate aggregates, followed by removal of red blood cells by ACK buffer. To enrich basal prostate stem cells (bPSC), isolated cells were stained with Zombie Violet Live/Dead Fixable Viability Dye (Biolegend) in PBS, followed by incubation with 1:100 diluted fluorescence-conjugated specific antibodies (Biolegend): CD45-FITC (#103108), CD31-FITC (#102506), Sca-1-APC (#122512) and CD49f-PE (#313612). Once stained, fluorescence activated cell sorting was performed on the BD FACSAria under sterile conditions.
Data was collected using the C1 Fluidigm instrument with SMARTer chemistry (Clontech) to generate cDNA from captured single cells. Libraries were prepared using a Nextera kit (Illumina).
Single-end 1x50 bp reads were sequenced using the HiSeq2500 on rapid run mode.

value: prostate

value: basal prostate stem cells

tag: Sex

value: male

tag: batch

tag: condition

value: naive

tag: wellid


title: PAT21, HDP-high, d7

value: d7, Post-priming


title: A2S127inflamed2

description:
single-cell mRNA-seq data
batch2_inflamedVsNaive_counts.txt

value: inflamed


title: rpoC mutant host infected with phage K- 30 min time point (replicate B)

city: Silver Spring

first: Ramchander Rohit

last: Kongari

state: Maryland

address: 10903 New Hampshire Ave

department: Department of Bacterial, Parasitic and Allergenic products

institute: United States Food and Drug Administration

description:
Novaseq S2 100 bp paired end run
MR206_30_B

data_processing:
Initial quality check was done using FastQC and read mapping distribution was analyzed using MultiQC
Reads were mapped using Bowtie2 and visualized using IGV. For quantitative analysis, read counts were obtained using Kallisto and differntial expression analysis was done using EdgeR package on the Rstudio platform
Assembly: Reads were mapped to the full length genome of phage K (NC_005880.2) and NRS384 (CP027476.1) using Bowtie2 to check for transcriptional activity. No genome building/assembly was performed for our analysis purposes.
Supplementary files format and content: Transcripts per million (TPM) data for all the gene and tRNA features annotated in phage K (as calculated by Kallisto) from all the samples are provided as a separate file

organism: Staphylococcus aureus

growth_protocol: 25 ml TSB cultures were innoculated with 100 ul of overnight cultures and  grown at 30 °C

extract_protocol:
1 mL samples were collected at 2, 5, 10, 20, 30, 40 min after addition of phage, and total RNA was extracted from these samples using the QIAGEN RNEasy Mini Kit.
The samples were further treated with Turbo DNAse to degrade phage/bacterial DNA, and the RNA quality was measured using an Agilent 2100 Bioanalyzer. Ribosomal RNA was depleted using the Illumina Ribozero plus kit, and Illumina RNA-seq libraries were prepared without any enrichment.
A strand-specific RNA seq Novaseq S2 100-bp paired end run was performed on the samples using an Illumina Novaseq 6000 instrument

treatment_protocol: Phage K was added at an MOI of ~5 once the O.D. of the cultures reached 0.3

tag: time point

value: 30 min

tag: cell line

value: bacterial cells

tag: genotype

value: rpoC G17D

tag: treatment

value: infected with phage K


title: PAT19, HDP-low, d28

value: HDP-low

value: d28, Post-boost


title: rpoC mutant host infected with phage K -30 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
MR206_30_A


title: A1S14inflamed3


title: H2AZ_CC_1

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

molecule: genomic DNA

source_name: Brain

value: Brain


title: H2AZ_CC_2

value: Nucleus accumbens


title: A1S120inflamed2


title: PAT19, HDP-low, d0

value: PBMCs


title: PAT19, HDP-low, d21

value: d21, Pre-boost


title: rpoC mutant host infected with phage K- 20 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
MR206_20_C

value: 20 min


title: rpoC mutant host infected with phage K- 20 min time point (replicate D)

description:
Novaseq S2 100 bp paired end run
MR206_20_D


title: A12S87inflamed3

value: prostate


title: A12S7inflamed2

value: basal prostate stem cells


title: H2AZ_CS_3


title: rpoC mutant host infected with phage K -20 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
MR206_20_A


title: rpoC mutant host infected with phage K- 20 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
MR206_20_B


title: PAT14, HDP-high, d28

value: HDP-high


title: rpoC mutant host infected with phage K- 10 min time point (replicate D)

description:
Novaseq S2 100 bp paired end run
MR206_10_D

value: 10 min


title: PAT14, HDP-high, d0

value: d0, Pre-priming


title: H2AZ_CS_2


title: H2AZ_CS_1


title: H2AZ_SS_3


title: BC19127, scRNAseq

city: Seoul

first: SUMIN

last: CHA

address: 88, Olympic-ro 43-gil, Songpa-gu

country: South Korea

institute: Asan Institute for Life Sciences, Asan Medical Center

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger 6.1.2
Assembly: hg38
Supplementary files format and content: tab-separated value files and matrix files

source_name: Breast cancer

extract_protocol:
Breast cancer tissues were placed in RPMI 1640 medium (11875093, Thermo Fisher Scientific, Waltham, MA, USA) and promptly transported to the laboratory within two hours post-resection. After washing with Dulbecco’s Phosphate Buffered Saline (DPBS, L0615, Biowest, Nuaillé, France) containing 1× ZellShield anticontaminant agent (Minerva Biolabs, Berlin, Germany), the tumour tissues were minced into 1-mm-diameter pieces. The minced breast cancer tissue was incubated for 1 h in digestion buffer (DMEM-F12 (11330032, Thermo Fisher Scientific), 2% FBS (Corning, VA, USA), 1% penicillin/streptomycin (15140-122, Thermo Fisher Scientific), 10 μg/mL insulin (51500056, Thermo Fisher Scientific), and 10 ng/mL epidermal growth factor (PHG0311, Thermo Fisher Scientific) supplemented with 1× collagenase/ hyaluronidase (CA094-002, Gendepot, Barker, TX, USA). The digested samples were centrifuged at 80 × g for 30 s, and the resultant supernatant was filtered through a 70-μm nylon mesh strainer (352350, Corning Life Sciences, Tewksbury, MA, USA). The pellets from the digested samples were resuspended in 0.25% trypsin/EDTA (25200072, Thermo Fisher Scientific) and incubated for 3–5 min to release single cells. Once a single cell suspension was obtained, cold Hank’s balanced salt solution (L0612, Biowest) containing 2% FBS was added, and cells were recovered through centrifugation at 300 × g for 5 min. Subsequently, the cells from the supernatants and the single cells from the pellet were combined, counted, and cryopreserved. CD45+ cells were isolated either through magnetic bead sorting or fluorescence-activated cell sorting (FACS). In the magnetic separation method, dead cells were initially removed using a dead cell removal kit (130-090-101, Miltenyi Biotec, Auburn, CA, USA), followed by cell labelling with CD45-microbeads (130-045-801, Miltenyi Biotec) and enriched using a magnetic-activated cell sorting (MACS) column (130-042-901, Miltenyi Biotec) and MACS separator (130-091-051, Miltenyi Biotec). For FACS sorting, single cells were stained with an anti-human CD45 antibody (304016, Biolegend, San Diego, CA, USA) and resuspended in 4',6-diamidino-2-phenylindole solution (D1306, Thermo Fisher Scientific). CD45+ live cells were sorted using FACSAria (BD bioscience, San Jose, CA, USA). The isolated cells were resuspended in CS10 freezing media (100-1061, Stemcell Technologies, Bothell, WA, USA) and stored in an NL2 tank until the next use or were immediately sequenced
scRNA-seq library preparation was conducted using the Chromium Single Cell 3′ Kit v2 and the Chromium Next GEM Single Cell 3′ Kit v3 platform (10x Genomics, Pleasanton, CA, USA)

value: Breast cancer

value: CD45+ cells

tag: subtype

value: TNBC

tag: til value_(%)

tag: til level

value: High


title: A11S190inflamed2

value: male

value: inflamed


title: H2AZ_SC_3


title: A10S79inflamed3


title: BC19115, scRNAseq

value: Low


title: H2AZ_SC_2

value: Brain


title: rpoC mutant host infected with phage K - 10 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
MR206_10_A

value: bacterial cells

value: rpoC G17D

value: infected with phage K


title: H2AZ_SS_2

value: Nucleus accumbens


title: BC19108, scRNAseq


title: A10S39naive2

value: prostate

value: naive


title: PAT14, HDP-high, d21

value: PBMCs

value: HDP-high

value: d21, Pre-boost


title: rpoC mutant host infected with phage K- 05 min time point (replicate D)

description:
Novaseq S2 100 bp paired end run
MR206_05_D

value: 05 min


title: A11S82inflamed3

value: basal prostate stem cells


title: BC19104, scRNAseq

value: Breast cancer

value: CD45+ cells

value: TNBC


title: rpoC mutant host infected with phage K- 05 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
MR206_05_C


title: A11S44naive2

value: male


title: A10S183inflamed2

value: inflamed


title: H2AZ_SS_1

value: Brain


title: rpoC mutant host infected with phage K- 05 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
MR206_05_B

value: bacterial cells


title: BC18050, scRNAseq

value: High


title: H_Prog_7

city: Amsterdam

first: Lisa

last: van Pul

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

data_processing:
The library pools were sequenced on a NextSeq® 500 sequencing instrument according to the manufacturer instructions with 100 bp read length for read 1 and 27 bp for read 2. Raw data was demultiplexed and FASTQ files for each pool was generated using the bcl2fastq Conversion Software (Illumina® Inc.). The "Demultiplex QIAseq UPX 3' reads" tool of the CLC Genomics Workbench 12.0.4 was used to demultiplex the raw sequencing reads according to the sample indices. The "Quantify QIAseq UPX 3' workflow" was used to process the demultiplexed sequencing reads with default settings. In short, the reads are annotated with their UMI and are then trimmed for poly(A) and adapter sequences, minimum reads length (15 nucleotides), read quality, and ambiguous nucleotides (maximum of 2). They are then deduplicated using their UMI. Reads are grouped into UMI groups when they (1) start at the same position based on the end of the read to which the UMI is ligated (i.e., Read2 for paired data), (2) are from the same strand, and (3) have identical UMIs. Groups that contain only one read (singletons) are merged into non-singleton groups if the singleton's UMI can be converted to a UMI of a non-singleton group by introducing an SNP (the biggest group is chosen). The reads were then mapped to the Human genome GRCh38 and annotated using the NCBI RefSeq GRCh38.p11 gene annotation.
Genes with less than 1 read in more than one-third of the samples per group were excluded from further analysis. HIV- and CMV-specific CD8 T cell data were analysed separately.
Differential expression analysis between groups was performed using the EdgeR statistical software package (Bioconductor, http://bioconductor.org/) in RStudio. For normalization, the trimmed mean of M-values (TMM) method was used.
logCPM values were calculated in Rstudio.
Genome_build: GRCh38.p11
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with logCPM values.

source_name: PBMC

extract_protocol: QIAseq UPX 3' transcriptome kit (Qiagen) according to manufacturer's protocol.

value: CD8 T cells

tag: cd8 virus specificity

value: HIV

tag: participant status

value: Progressor


title: BC17172, scRNAseq

tag: tissue

value: HR+


title: rpoC mutant host infected with phage K- 10 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
MR206_10_C

value: 10 min

tag: cell type

value: rpoC G17D

value: infected with phage K


title: H_Prog_6


title: Lung, mono_SEV, rep4

city: St. Louis

first: Michael

middle: J

last: Holtzman

state: MO

address: 4939 Childrens Pl

department: Pulmonary & Critical Care

institute: Washington University in St. Louis School of Medicine

data_processing:
RNAseq was using a NovaSeq 6000 with S4 flow cell.
Gene and transcript levels were quantified using the RSEM (version 1.3.2) pipeline, and the estimated counts were stored as the appropriate raw data to feed into the edgeR (version 3.24.3), limma (version 3.38.3), and voom (version 3.38.3) pipeline.
The list of Ensemble gene ids was annotated by the biomaRt (version 2.38.0), which queried BioMart databases to retrieve additional information including entrezgene identifiers for gene symbol and chromosome.
A DGEList appropriate for our data was declared, and filterByExpr function in edgeR was used to maintain 35% of the genes in the gene list by filtering out lowly expressed genes automatically and in a principled way. The data were then normalized to account for variability in sequencing depth, library size, and other external factors that are not of biological interest.
After TMM normalization, unsupervised heirarchical clustering with the hclust function in base R (version 3.5.3) and principal component analysis with the prcomp function were conducted to identified treatment and control clusters. The correlations between replicate samples were also examined, with the lowest value of 0.94. We invoked voom software to compute precision weights and fitted linear models to the data using the lmFit function. Then, we refitted the model using the contrasts.fit function and computed moderated t- and F-statistics using the eBayes and treat functions, respectively. We chose the outputs from treat function for a more stringent definition of statistical significance to test against a fold change threshold.
Two heatmaps were generated with heatmap.2 function in gplots (version 3.1.0), based on subsets of the top 100 most significant genes sorted separately by the F-statistic and fold change. We also generated scatter plots with ggplot2 (version 3.3.2) with the top genes ranked by fold change labelled of our interest.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: lung

growth_protocol: Male and female wild-type (WT) C57BL/6J mice (000664) mice (5-6 wk of age) were obtained from Jackson Laboratory (Bar Harbor, ME). All mice were maintained and co-housed in a barrier facility using cages fitted with micro-isolator lids.

extract_protocol:
Lung tissue RNA was purified from four mice per sample condition (moDCs or monocytes for 12 d after SeV infection or PBS control challenge) and subjected to RNAseq using a NovaSeq 6000 with S4 flow cell (Illumina, San Diego, CA) in the Genome Technology Access Center in the McDonnell Genome Institute (Washington University, St. Louis).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Virus or an equivalent amount of UV-inactivated virus or PBS alone was delivered intranasally in 30 μl of PBS under ketamine/xylazine anesthesia at 5-6 weeks of age.

value: lung

tag: strain

value: monocyte

value: wild type

value: treated with SeV for 12 days


title: rpoC mutant host infected with phage K - 05 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
MR206_05_A

value: 05 min


title: rpoC mutant host infected with phage K- 10 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
MR206_10_B


title: Lung, mono_SEV, rep3


title: H_Prog_5


title: rpoC mutant host infected with phage K- 02 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
MR206_02_C

value: 02 min


title: BC17157, scRNAseq

value: Breast cancer

value: CD45+ cells

value: TNBC


title: H_Prog_4


title: Lung, mono_SEV, rep1


title: H2AZ_SC_1

value: Brain

value: Nucleus accumbens

tag: antibody treatment


title: A10S104naive3

description:
single-cell mRNA-seq data
batch3_inflamedVsNaive_counts.txt

value: prostate

value: basal prostate stem cells

tag: Sex

value: male

value: naive


title: rpoC mutant host infected with phage K- 02 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
MR206_02_B

value: bacterial cells

value: rpoC G17D


title: BC18051, scRNAseq

value: Low


title: BC17148, scRNAseq

value: HR+

value: High


title: BC17146, scRNAseq


title: Lung, DC_SEV, rep4

value: lung

value: monocyte-derived dendritic cell

value: wild type

value: treated with SeV for 12 days


title: H_Prog_3

value: CD8 T cells

value: HIV

value: Progressor


title: rpoC mutant host infected with phage K - 02 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
MR206_02_A

value: 02 min

value: infected with phage K


title: H_Prog_2


title: H_Prog_1


title: rpoC mutant host infected with phage K- 0 min time point (replicate D)

description:
Novaseq S2 100 bp paired end run
MR206_0_D

value: 0 min


title: BC17140, scRNAseq

value: Breast cancer

value: CD45+ cells


title: Lung, DC_SEV, rep2


title: BC17134, scRNAseq


title: H_MAVS_7

value: MAVS-/-


title: rpoC mutant host infected with phage K- 0 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
MR206_0_C

value: bacterial cells

value: rpoC G17D


title: rpoC mutant host infected with phage K- 0 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
MR206_0_B


title: BC17122, scRNAseq

value: HR+

value: Low


title: H_MAVS_6


title: Lung, DC_SEV, rep1

value: lung


title: Lung, mono_SEV, rep2

value: monocyte


title: rpoC mutant host infected with phage K - 0 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
MR206_0_A


title: Lung, mono_control, rep4

value: wild type

value: PBS control


title: H_MAVS_5

value: CD8 T cells


title: Wild type host infected with phage K- 40 min time point (replicate D)

description:
Novaseq S2 100 bp paired end run
WT_40_D

value: 40 min

value: WT


title: BC17121, scRNAseq


title: H_MAVS_4

value: HIV


title: Lung, mono_control, rep3


title: Lung, DC_SEV, rep3

value: monocyte-derived dendritic cell

value: treated with SeV for 12 days


title: Lung, mono_control, rep2


title: BC17100, scRNAseq

value: Breast cancer

value: High


title: Lung, mono_control, rep1


title: Wild type host infected with phage K- 40 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
WT_40_C

value: infected with phage K


title: Wild type host infected with phage K - 40 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
WT_40_A

value: bacterial cells


title: H_MAVS_3

value: MAVS-/-


title: BC17114, scRNAseq

value: CD45+ cells

value: TNBC


title: Lung, DC_control, rep4

value: lung


title: BC17087, scRNAseq

value: Low


title: Wild type host infected with phage K- 40 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
WT_40_B


title: Wild type host infected with phage K- 30 min time point (replicate D)

description:
Novaseq S2 100 bp paired end run
WT_30_D

value: 30 min


title: Lung, DC_control, rep3

value: wild type

value: PBS control


title: BC17080, scRNAseq

value: HR+


title: BC17083, scRNAseq


title: Lung, DC_control, rep2


title: H_MAVS_1

value: CD8 T cells


title: Wild type host infected with phage K- 30 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
WT_30_C

value: WT


title: H_non-B57_6

value: HIV

value: non-B*57 LTNP


title: BC17079, scRNAseq

value: Breast cancer


title: Lung, DC_control, rep1

value: monocyte-derived dendritic cell


title: Wild type host infected with phage K- 30 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
WT_30_B

value: infected with phage K


title: OC013_TREM2

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

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

country: Spain

institute: Josep Carreras Research Institute (IJC)

description: TREM2 macs

data_processing:
Fastq files were quality controlled with fastqc (v0.11.9) and multiqc (v1.0)
Fastq files were pseudoaligned to GRCh38 and quantified using Kallisto (v0.44)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw counts values for each sample.

source_name: ovarian cancer tumor

growth_protocol: Distinct populations of macrophages (FOLR2, IL4I1, TREM2) were sorted from human ovarian cancer tumors through flow cytometry.

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to manufacturer’s instruction.
Libraries were prepared using the NEBNext Ultra II Directional RNA, according to the manufacturer’s instructions.

value: ovarian cancer tumor

value: TREM2 macs

value: tumor associated macrophage

tag: donor

value: F


title: Il22r-/--3

city: Beijing

first: Yanli

last: Pang

state: Beijing

address: No.49 Huayuan-Bei Road , Haidian District

country: China

institute: Reproductive Medicial Center , Peking University Third Hospital

data_processing:
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: ovary

extract_protocol:
mouse granulosa cells were separated with density gradient centrifugation and culture in DMEM-F12 supplemented with 10% fetal bovine serum (FBS), and 1% penicillin-streptomycin (5,000 U/mL) for 12h, and subsequently collected for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

value: granulosa cell


title: Wild type host infected with phage K -30 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
WT_30_A

value: 30 min

value: bacterial cells


title: H_MAVS_2

value: MAVS-/-


title: H_non-B57_3


title: OC013_IL4I1

description: IL4I1 macs

tag: condition

value: IL4I1 macs


title: Wild type host infected with phage K- 20 min time point (replicate D)

description:
Novaseq S2 100 bp paired end run
WT_20_D

value: 20 min


title: OC013_FOLR2

description: FOLR2 macs

value: FOLR2 macs


title: Il22r-/--1


title: H_non-B57_2

value: CD8 T cells

value: HIV


title: H_non-B57_1

value: non-B*57 LTNP


title: Wild type host infected with phage K- 20 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
WT_20_B

value: WT


title: Wild type host infected with phage K- 20 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
WT_20_C

value: infected with phage K


title: OC005_IL4I1

description: IL4I1 macs

value: ovarian cancer tumor


title: H_B57_6

value: B*57 LTNP


title: Il22r+/+ -1


title: Wild type host infected with phage K -20 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
WT_20_A


title: H_B57_5


title: Wild type host infected with phage K- 10 min time point (replicate D)

description:
Novaseq S2 100 bp paired end run
WT_10_D

value: 10 min


title: H_non-B57_5


title: OC005_FOLR2

description: FOLR2 macs

value: tumor associated macrophage

value: F


title: H_non-B57_4


title: OC001_TREM2

description: TREM2 macs

value: TREM2 macs


title: H_B57_4


title: Il22r-/--2

value: ovary

value: granulosa cell


title: Wild type host infected with phage K- 10 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
WT_10_C

value: bacterial cells


title: H_B57_3


title: OC001_IL4I1

description: IL4I1 macs

value: IL4I1 macs


title: LPSday42_cDNA

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

country: Japan

institute: Tokyo University of Science

description: cDNA reads

data_processing:
Adapter trimming of sequencing data was performed by using Cutadapt 3.4. Filtered reads were chunked to 16 parts for parallel processing by using Seqkit 0.15.0. Filtered cell barcode reads were annotated by Python script provided by BD with minor modification for compatible to Python3.8. Associated cDNA reads were mapped to reference RNA (build GRCm38 release-101) by using bowtie2-2.4.2 by the following parameters: -p 2 –very-sensitive-local -N 1 –norc –seed 656565 –reorder. Then, cell barcode information of each read were added to the bowtie2-mapped BAM files, and read counts of each gene in each cell barcode were counted by using mawk. Resulted count data was converted to genes x cells matrix file and inflection threshold of the knee-plot was detected by using DropletUtils package in R version 4.1.3. (2022-03-10). Demultiplexing of hashed samples were performed according to the expression level of each Sampletags.
Assembly: GRCm38
Supplementary files format and content: txt

extract_protocol:
We sampled mouse lungs of untreated, day3, 7, 14, 28, 42, 63 (BLM model, 1.25 mg/kg), day3, 7, 14 (3 mg/kg), and day7, 14, 42 (LPS model) with 5 biological replicates (except BLM 3mg/kg at day 14 which includes 2 biological replicate).  Lungs were cut into small pieces with a razor blade and digested enzymatically using 0.25 mg/ml Liberase TM (Roche) and 20 kU/mL DNase I (Sigma-Aldrich, St Louis, MO) for 60 min at 37°C in RPMI1640/10%FBS/10mM HEPES pH7.4. Erythrocytes and dead cells were removed by 25%/65% Percoll PLUS (Cytiva, Buckinghamshire, UK) density separation. Resulting cells were stained with BD SampleTag (anti-CD45 and anti-MHC class I) for 30min at 4°C for cell hashing. Resulted cells are pooled and stained with Calcein AM for 5 min at 37°C, immediately chilled on ice, and filtered through 40 μm strainer according to the BD Rhapsody protocol. 25000 cells were loaded onto BD Rhapsody cartrige and captured cell number was asessed by BD Rhapsody scanner. Cell lysis, mRNA trap, cDNA synthesis, and primer digestion were performed according to the manufacture's instruction.
cDNA amplification was performed by TAS-Seq protocol (Shichino et al Commune Biol 2022). Sequencing libraries from amplified cDNAs were produced by using NEB UltraII FS Kit (New England Biolabs) with some modifications. Sequencing was performed by using a Novaseq S4 200 cycle kit and a Novaseq 6000 sequencer (Illumina) according to the manufacture's instructions. 20% PhiX spike-in was used for sequencing.
BD Rhapsody WTA

treatment_protocol: C57BL/6J female mice were administered with a single dose of bleomycin sulfate (1.25 or 3 mg/kg dissolved in 50 μL of sterile saline solution; Nippon Kayaku) or LPS(SIGMA E.coli O55:B5, 1mg/ml, 50ul/head) by oropharyngeal aspiration under deep anesthesia.

value: lung

value: whole cell

value: LPS administered intratracheally


title: OC001_FOLR2

description: FOLR2 macs

value: FOLR2 macs


title: LPSday42_SampleTag

description: sampletag reads, sampletag1-5 LPS

library_source: other

molecule: protein


title: Wild type host infected with phage K- 10 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
WT_10_B


title: LPSday7day14_SampleTag

description: sampletag reads, sampletag1-5 LPS day7, 6-10 LPS day14


title: Wild type host infected with phage K - 10 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
WT_10_A


title: Il22r+/+ -3


title: OC005_TREM2

description: TREM2 macs


title: H_B57_2

value: CD8 T cells

value: HIV


title: H_B57_1


title: shIGF2BP3, rep3

city: guangzhou

first: Yongbo

last: Pan

address: 106 Zhongshan 2 Lu, Guangzhou

department: Guangdong Provincial People's Hospital

institute: Guangdong Academy of Medical Sciences

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
All clean reads were mapped to human genome version hg38 by hisat2
Read counts were calculated using featureCounts
Assembly: Hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Adenocarcinoma of the esophagogastric junction

growth_protocol: OE-19 cells cultured in RPMI1640 medium (Gibco) with 10% fetal bovine serum and 1% penicillin/streptomycin (Invitrogen)

extract_protocol:
Total RNA was isolated from OE-19 cells using RNAiso Plus (Takara)
NEBNext Ultra Directional RNA Library Prep Kit

value: cell line

value: IGF2BP3 knockdown


title: Wild type host infected with phage K- 05 min time point (replicate D)

description:
Novaseq S2 100 bp paired end run
WT_05_D

value: 05 min

value: WT

value: infected with phage K


title: Il22r+/+ -2


title: LPSday7day14_cDNA

description: cDNA reads


title: C_Prog_7

value: CMV

value: Progressor


title: C_Prog_6


title: Wild type host infected with phage K- 05 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
WT_05_C


title: BLMday63_SampleTag

description: sampletag reads, sampletag1-5 BLM 1.25mg/kg

value: bleomycin administered intratracheally


title: BLMday63_cDNA

description: cDNA reads


title: shIGF2BP3, rep1

value: Adenocarcinoma of the esophagogastric junction


title: Wild type host infected with phage K- 05 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
WT_05_B

value: bacterial cells


title: shControl, rep3

value: control knockdown


title: shControl, rep2


title: BLMday42_SampleTag

value: lung


title: Wild type host infected with phage K - 05 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
WT_05_A


title: BLMday42_cDNA

description: cDNA reads

value: whole cell


title: Wild type host infected with phage K- 02 min time point (replicate D)

description:
Novaseq S2 100 bp paired end run
WT_02_D

value: 02 min


title: C_Prog_3


title: shControl, rep1


title: BLMday28_SampleTag


title: shIGF2BP3, rep2


title: C_Prog_2


title: meRIP-Input  rep2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
All clean reads were mapped to human genome version hg38 by hisat2
peaks were called using MACS2
Assembly: Hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Cells were fixed with 264 nm UV for 400mJ, then lysed in protein lysis buffer
NEBNext Ultra Directional RNA Library Prep Kit

tag: rip antibody

value: none (input)


title: BLMday28_cDNA

description: cDNA reads


title: meRIP-Input  rep1


title: Wild type host infected with phage K- 02 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
WT_52_B

tag: time point


title: C_Prog_1

value: CD8 T cells


title: BLMday14_SampleTag

description: sampletag reads, sampletag1-5 BLM 1.25mg/kg sampletag6-7 BLM 3mg/kg


title: meRIP rep2

tag: cell line


title: Wild type host infected with phage K - 02 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
WT_02_A

tag: genotype


title: C_MAVS_7

value: MAVS-/-


title: BLMday14_cDNA

description: cDNA reads

tag: treatment


title: meRIP rep1

value: cell line


title: C_MAVS_6


title: BLMday7_SampleTag

description: sampletag reads, sampletag1-5 BLM 1.25mg/kg sampletag6-10 BLM 3mg/kg


title: C_Prog_5


title: C_Prog_4


title: Wild type host infected with phage K- 0 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
WT_0_C

value: 0 min


title: Wild type host infected with phage K- 02 min time point (replicate C)

description:
Novaseq S2 100 bp paired end run
WT_02_C


title: C_MAVS_5


title: IGF2BP3.RIP-Input  rep2


title: Wild type host infected with phage K- 0 min time point (replicate B)

description:
Novaseq S2 100 bp paired end run
WT_0_B


title: C_MAVS_4


title: BLMday3_SampleTag


title: Wild type host infected with phage K - 0 min time point (replicate A)

description:
Novaseq S2 100 bp paired end run
WT_0_A


title: C_MAVS_3


title: IGF2BP3.RIP rep2


title: IGF2BP3.RIP-Input  rep1


title: BLMday3_cDNA

description: cDNA reads


title: IGF2BP3.RIP rep1


title: T3 biol rep 3

first: Xi

last: Sun

address: Gongchen Street, Fangshan District

institute: Beijing University of Chinese Medicine

data_processing:
Fastp v 0.19.5 (https://github.com/OpenGene/fastp)was used for sequencing data quality control.
Hisat2 v 2.1.0 was used to align the quality-controlled raw data, cleandata ( reads ), with the reference genome to obtain mappeddata ( reads ) for subsequent transcript assembly, expression calculation, etc.
Quantitative analysis of gene and transcript expression levels was performed using software RSEM v 1.3.3(http://deweylab.biostat.wisc.edu/rsem/), respectively.
Assembly: Rattus _ norvegicus, reference genome version Rnor _ 6.0, reference genome source http://asia.ensembl.org/Rattus_norvegicus/Info/Index
Supplementary files format and content: tab-delimited matrix file includes gene TPM values counts for each Sample
Supplementary files format and content: tab-delimited matrix file includes transcript TPM values counts for each Sample

organism: Rattus norvegicus

extract_protocol:
Total RNA was extracted from cells using TRIzol ® Reagent ( Invitrogen ).
RNA libraries were prepared for sequencing using standard lllumina protocols.

tag: group

value: high-dose water extract of Poecilobdella manillensis lyophilized powder

value: glomerular mesangial cells


title: Untreated_SampleTag

description: sampletag reads, sampletag1-5

value: untreated


title: Wild type host infected with phage K- 0 min time point (replicate D)

description:
Novaseq S2 100 bp paired end run
WT_0_D

value: WT

value: infected with phage K


title: T2 biol rep 2


title: C_MAVS_1

value: CMV


title: Untreated_cDNA

description: cDNA reads


title: C_non-B57_6

value: non-B*57 LTNP


title: M3 biol rep 3

value: LPS-induced


title: IGF2BP3_LACE rep1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
All clean reads were mapped to human genome version hg38 by hisat2
peaks were called using MACS2
Assembly: Hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: LACE-seq

molecule: other

value: Adenocarcinoma of the esophagogastric junction


title: IGF2BP3_LACE rep2


title: BLMday7_cDNA

description: cDNA reads

value: lung

value: bleomycin administered intratracheally


title: NSC-34 cells transfected with SOD1 DI 48 hrs

city: Hummelstown

first: Esther

middle: S

last: Choi

state: PA

address: 1214 Research Blvd

department: Pharmacology

institute: Penn State College of Medicine

data_processing:
Novogene quality checked the raw data with error rate distribution, GC-content, and data filtering. Then, the data was mapped to the reference genome and gene expression was quantified.
Assembly: Differential analysis of the RNA-seq data was performed using DESeq259 (v1.26.0) with a p-adjusted value of ≤ 0.05.
Supplementary files format and content: Functional analysis included enrichment analysis, oncogene analysis and protein-protein interaction analysis. The enrichment analysis was performed using ClusterProfiler60 (v.3.8.1) with a p-adjusted value < 0.05.

source_name: cell line

growth_protocol: We cultured differentiated NSC-34 cells (RRID:CVCL_D356) (differentiation media DMEM:F12 10 % FBS, 1 % L-Glutamate, 1 % Penn/Strep, 0.5 % non-essential amino acids, 10 mM Retinoic acid) over 3 days and performed a transfection (jetOPTIMUS) with SOD1 WT and trimer constructs for expression.

extract_protocol:
We collected the cell lysates with RIPA buffer at 24- and 48-hour timepoints post-transfection. RNA was extracted using the RNeasy mini kit (Qiagen) and total RNA concentration was determined using NanoDrop OD readings at 260/280 wavelengths.
Thee samples were then sent for RNA-seq analysis (Novogene, Beijing, China).

value: NSC-34 (RRID:CVCL_D356)

value: Neuroblastoma x Spinal Cord-34 hybrid

value: SOD1 DI mutant


title: T1 biol rep 1


title: adult muscle biopsy age 56 years

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

data_processing:
Demutliplexing and FASTQ extraction was performed using bcl2fastq v2.20.0.422.
Primary processing of FASTQ data including quality control, filtering, trimming,alignment of reads and counting of gene-sprecific genes was done using nf-core RNA-seq pipeline v3.7
Analysis of differentially expressed genes was performed using DESeq2.
Assembly: Assembly: HG38
Supplementary files format and content: Supplementary files format and content: Supplementary files format and content: RNA-seq read counts per gene (csv)

source_name: M. deltoideus

extract_protocol:
Total RNA was isolated with the RNeasy® Mini Kit (Qiagen) following the manufacturer’s instructions
Illumina Stranded mRNA Prep

value: M. deltoideus


title: NSC-34 cells transfected with SOD1 DI 24 hrs

value: cell line


title: adult muscle biopsy age 40 years

source_name: M. quadriceps femoris

value: M. quadriceps femoris


title: M2 biol rep 2


title: C_non-B57_4

value: CD8 T cells


title: NSC-34 cells transfected with SOD1 HG 48 hrs

value: SOD1 HG mutant


title: adult muscle biopsy age 35 years


title: M1 biol rep 1

value: glomerular mesangial cells


title: NSC-34 cells transfected with SOD1 HG 24 hrs


title: C3 biol rep 3

value: control


title: adult muscle biopsy age 44 years

source_name: M. gastrocnemius

value: M. gastrocnemius


title: C_non-B57_3

value: CMV


title: C_MAVS_2

value: MAVS-/-


title: C_non-B57_2

value: non-B*57 LTNP


title: NSC-34 cells transfected with SOD1 FH 48 hrs

value: SOD1 FH mutant


title: adult muscle biopsy age 45 years


title: C_non-B57_1


title: NSC-34 cells transfected with SOD1 FH 24 hrs


title: C1 biol rep 1


title: adult muscle biopsy age 55 years


title: C_B57_5

value: B*57 LTNP


title: NSC-34 cells transfected with SOD1 A4V 48 hrs

value: SOD1 A4V mutant


title: C_non-B57_5


title: Advance PD 2, scRNAseq

city: Chengdu

first: Li

last: Chen

state: Sichuann

address: No.17, South Renmin Road

institute: Sichuan University West China Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

growth_protocol: Peripheral Blood Mononuclear Cells (PBMCs) in the blood samples were obtained from normal individuals and PD patients.

extract_protocol:
PBMCs were purified by Ficoll gradient separation, according to the instructions of the manufacturer (Ficoll–PaqueTM Plus, GE Healthcare, Sweden). In short, 3 mL of Ficoll-Paque gradient was pipetted into two 15-ml centrifuge tubes. The blood was diluted with a ratio 1:1 in phosphate-buffered saline (PBS) and carefully layered over the Ficoll-Paque gradient. The tubes were centrifuged for 30 min at 400 × g. The cell interface layer was harvested carefully (8 ml/tube), and the cells were washed twice in PBS (for 10 min at 100 × g). PBMCs were resuspended in 1 mL complete culture medium (DMEM medium supplemented with 10 % newborn calf serum, 1 % PS).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Late Parkinson's disease (PD)

value: blood

value: peripheral blood mononuclear cell


title: C_B57_4


title: adult muscle biopsy age 30 years


title: Advance PD 1, scRNAseq

description: 10x Genomics


title: NSC-34 cells transfected with SOD1 WT 48 hrs

value: NSC-34 (RRID:CVCL_D356)

value: Neuroblastoma x Spinal Cord-34 hybrid

value: SOD1 dimer


title: infant muscle biopsy age 7 months

value: M. quadriceps femoris


title: Early PD 2, scRNAseq

description: 10x Genomics

value: Early Parkinson's disease (PD)


title: infant muscle biopsy age 28 months


title: C_BD_6

value: CD8 T cells

value: Blood donor


title: C2 biol rep 2

value: control

value: glomerular mesangial cells


title: infant muscle biopsy age 18 months


title: C_BD_5

value: CMV


title: C_BD_4


title: Normal 2, scRNAseq

description: 10x Genomics

value: Normal


title: G5: G31A-NFE2L2 + hMET, JY-122

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic
Reads were aligned to mouse reference genome mm10 by STAR aligner
Gene counts were quantified by STRA
Assembly: mm10
Supplementary files format and content: TAB

source_name: liver

extract_protocol:
Using fresh frozen liver tissue, RNA was isolated using the RNeasy Mini kit (Qiagen) according to standard manufacturer protocols for tissue RNA isolation
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: G5:G31A-NFE2L2 + hMET

value: FVB/NJ

tag: gender

value: Male


title: Early PD 1, scRNAseq

description: 10x Genomics

value: blood


title: G5: G31A-NFE2L2 + hMET, JY-121


title: NSC-34 cells transfected with SOD1 WT 24 hrs

value: cell line


title: Normal 1, scRNAseq

description: 10x Genomics

value: peripheral blood mononuclear cell


title: C_BD_3

tag: cd8 virus specificity


title: C_B57_2

tag: participant status

value: B*57 LTNP


title: C_BD_2


title: NSC-34 cells transfected with SOD1 A4V 24 hrs

tag: tissue

value: NSC-34 (RRID:CVCL_D356)

value: Neuroblastoma x Spinal Cord-34 hybrid

value: SOD1 A4V mutant


title: PBMCs, Healthy control-3

city: Adelaide

first: Nick

last: Warnock

state: South Australia

address: UniSA Bradley Building, North Terrace

department: Centre for Cancer Biology

country: Australia

institute: SA Pathology

data_processing:
Adapters were trimmed using cutadapt version 4.1 and the following parameters: -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT --minimum-length=18 --error-rate 0.2 --overlap=5
Reads were aligned to the hg38 reference genome using STAR version 2.7.7a, producing gene counts for each sample
Assembly: GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz using RefSeq annotations
Supplementary files format and content: <library_name>.hg38.ReadsPerGene.out.tab: tab-separated gene counts file for each sample
Supplementary files format and content: gene_counts.tsv: tab-separated file containing strand-specific gene counts for all samples

extract_protocol:
Total RNA was extracted from the peripheral blood mononuclear cells (PBMCs) of  patients and healthy controls using Blood RNA purification kit (Macherey-Nagel).
RNA libraries were prepared using an Illumina Stranded mRNA Prep kit according to the manufacturer's protocols
polyA+ RNA-Seq

value: PBMCs


title: PBMCs, Healthy control-2


title: G4: S45Y-CTNNB1 + G31A-NFE2L2, JY-118

value: G4:S45Y-CTNNB1 + G31A-NFE2L2


title: G5: G31A-NFE2L2 + hMET, JY-120


title: WT3-R: Col-0  red-light rep3

city: Austin

first: Enamul

last: Huq

state: TX

address: NHB 2.616, Stop A5000 100 East 24th St.

institute: University of Texas at Austin

data_processing:
FastQC
Hisat2
Htseq
EdgeR
Genome_build: Hisat2 with TAIR10
Supplementary_files_format_and_content: txt file with htseq counts

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana seedlings

growth_protocol: Total ttwo genotypes; Col-0 and b''ab''b plants were used for mRNA sequencing analysis.

extract_protocol:
Total RNA was isolated using sigma plant total RNA kit(Sigma, Cat.# STRN250).
3'Tag-Seq method article was used to generate TagSeq library according to the manufacturer’s instruction. (doi: 10.1111/1755-0998.12529)

treatment_protocol: The seeds were surface sterilized and plated on the MS media without sucrose, cold stratified for three days in dark to induce germination. After three days, seeds were further treated  for 3 hours in 22℃ with white light (25 µmole/s2/m2) and then wrap with two layers foil, keep in dark for 4 days in 22 dgree.  After 4 days, seedlings were either treated with 1 hour of continuous red light (8 µmole/s2/m2) or just keep in dark at 22 degree.

value: WT

value: seedling

value: dark grown 4-days seedlings+1 hour 8 μmol/m2s  red-light exposure


title: WT3-D: Col-0 dark rep3

value: dark grown 4-days seedlings


title: C_BD_1

tag: cell type

value: CD8 T cells

value: CMV

value: Blood donor


title: WT2-R: Col-0 red-light rep2


title: G4: S45Y-CTNNB1 + G31A-NFE2L2, JY-117

value: liver

tag: strain

value: FVB/NJ

value: Male


title: infant muscle biopsy age 11 months

value: M. quadriceps femoris


title: PBMCs, Healthy control-1

value: control


title: PBMCs, Patient-3 with G167R mutation in IKKα

value: G167R mutation in IKKalpha


title: Baseline_KO+library

first: Connor

middle: Antonio

last: Richterich

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

library_source: genomic

data_processing:
Sequence reads were aligned to a reference library (suplementary file [ Identifiers.txt]), reads containing mismatches removed, and sgRNA distributions quantified and scored using MAGeCK RRA (version 0.5.6)
Reads were demultiplexed based on sample barcodes (Supplemental file [Legend_Sample_Indices.txt]) and aligned against reference library (Suplementary file [Identifiers.txt])  and reads with missmatches removed (see processed data file. A single file [Raw_Reads.txt] was generated for simplicity)
Processed datafile was used as input file for mageck analysis. Null distribution was generated for calculating p-values based on control sgRNAs within library.
Outputs for mageck sgRNA summaries supplied as supplementary file (C_TrWtvVeWt.sgrna_summary.txt; D_TrKOvVeKO.sgrna_summary.txt)
Assembly: N/A
Supplementary files format and content: Tabular data containing read counts for each sample (demultiplexed based on sample barcode) and sgRNA (aligned against reference library).
Library strategy: CRISPR Screen

growth_protocol: All cells were cultured at 37C and 5% CO2 in RPMI (ThermoFisher #11875093) supplemented with 10% (v/v)  FCS (ThermoFisher #26140079), penicillin-streptomycin (ThermoFisher #15140148) and 0.2ng/mL recombinant murine IL-3 (Immunotools #12340032)

extract_protocol:
DirectPCR Lysis reagent (Viagen Biotech #301-C)
SgRNA sequences were  amplified using NebNext High-Fidelity 2X PCR Master Mix (New England Biolabs #M0541S), following the manufacturer’s instructions, using primers containing sample barcodes

value: ITPK1_KO, library-transduced


title: G4: S45Y-CTNNB1 + G31A-NFE2L2, JY-116


title: G3: S45Y-CTNNB1 + hMET, JY-112-1

value: G3:S45Y-CTNNB1 + hMET


title: Baseline_WT+library

value: ITPK1_WT, library-transduced


title: WT2-D: Col-0 dark rep2


title: PBMCs, Patient-1 with G167R mutation in IKKα

value: PBMCs


title: Huh7_KO_ARID1A_V2084D_shSTUB1_rep3

city: Shanghai

first: Fang

address: 227, south chongqin road

institute: Shanghai Jiao Tong University School of Medicines

data_processing:
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit CPM（Counts Per Million total reads)
Differential gene expression analyses were performed using edgeR.
Assembly: GRCh38
Supplementary files format and content: text file of gene raw count values

extract_protocol:
RNA was harvested using Trizol reagent and the Qiagen miRNeasy Mini kit. 500ng total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using Illumina’s NEBNext Ultra II RNA Library Prep Kit (following standard protocols, E7775S)

treatment_protocol: ARID1A knocked out Huh7 cells with lentiviral stably expressed ARID1A WT/V2084D-Flag and knockdown STUB1

value: Hepatocellular carcinoma cells

value: ARID1A knockout, ARID1A V2084D_Flag overexpression and knockdown STUB1


title: G3: S45Y-CTNNB1 + hMET, JY-111


title: WT1-R: Col-0 red-light rep1

value: WT

value: seedling

value: dark grown 4-days seedlings+1 hour 8 μmol/m2s  red-light exposure


title: M 8_KO+library

description: 6905_16_M_8_16_AACTGTGC_S16_R1_001.fastq


title: Huh7_KO_ARID1A_V2084D_shSTUB1_rep2


title: M 8_WT+library

description: 6905_15_M_8_15_TTCTCATA_S15_R1_001.fastq


title: M3-R: b''ab''b red-light rep3

value: b''ab''b


title: M 7_KO+library

description: 6905_14_M_7_14_CCGAGTAT_S14_R1_001.fastq


title: Huh7_KO_ARID1A_V2084D_rep3

value: ARID1A knockout and ARID1A V2084D_Flag overexpression


title: M3-D: b''ab''b dark rep3

value: dark grown 4-days seedlings


title: G2: S45Y-CTNNB1 + G31A-NFE2L2 + hMET, JY-106

value: liver

value: G2:S45Y-CTNNB1 + G31A-NFE2L2 + hMET

value: FVB/NJ


title: WT1-D: C-ol-0 dark rep1


title: M 7_WT+library

description: 6905_13_M_7_13_AATCCAAT_S13_R1_001.fastq


title: G2: S45Y-CTNNB1 + G31A-NFE2L2 + hMET, JY-108

value: Male


title: Huh7_KO_ARID1A_V2084D_shSTUB1_rep1


title: M2-R: b''ab''b red-light rep2


title: M 6_KO+library

description: 6905_12_M_6_12_TTGATGCG_S12_R1_001.fastq


title: Huh7_KO_ARID1A_V2084D_rep2


title: G2: S45Y-CTNNB1 + G31A-NFE2L2 + hMET, JY-105


title: G3: S45Y-CTNNB1 + hMET, JY-110


title: M2-D: b''ab''b dark rep2


title: Huh7_KO_ARID1A_V2084D_rep1


title: M 6_WT+library

description: 6905_11_M_6_11_CCAGTGAT_S11_R1_001.fastq


title: G1: Wild-type FVB liver, JY-113

value: G1:Wild-type FVB liver


title: Huh7_KO_ARID1A_WT_rep3

value: ARID1A knockout and ARID1A WT_Flag overexpression


title: M1-R: b''ab''b red-light rep1


title: M 5_KO+library

value: ITPK1_KO, library-transduced


title: Huh7_KO_ARID1A_WT_rep2


title: G1: Wild-type FVB liver, JY-103


title: M1-D: b''ab''b dark rep1


title: M 5_WT+library

value: ITPK1_WT, library-transduced


title: G1: Wild-type FVB liver, JY-101


title: ATAC_CM_SRF_KO_day4_rep2

city: Berlin

first: Pavel

last: Tsaytler

address: Ihnestrasse  63-73

institute: MPI Molecular Genetics

description: processed data linked to rep1 sample

data_processing:
The ATAC-seq reads were trimmed to 35 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie [Langmead, 2009] (version 1.1.2) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M, chr Y, or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from independent experiment replicates were combined, and the data were normalized and converted to bw format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 3 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
ATAC-seq was performed as previously described [Buenrostro, 2013]. At day 4 of cardiac mesoderm differentiation, Srf-flex1 cells carrying H2B-mCherry (WT) or H2B-Venus-T2A-Cre (KO) were trypsinized, resuspended in 3% BSA in PBS, and 50,000 cells (per replicate) expressing mCherry or Venus were sorted on a FACS Aria II. The cells were washed with 1 ml cold PBS, pelleted by centrifugation, lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), and immediately centrifuged at 500g, 4°C for 10 minutes.
The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen). The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 5-6 cycles and the libraries were purified using the MinElute kit. The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips. Samples were pooled and paired-end sequencing was performed on the HiSeq 4000 (Illumina) using 2x 75 bp read length.

value: embryonic stem cells

value: SRF KO

value: cardiac mesoderm differentiation


title: Huh7_KO_ARID1A_WT_rep1

value: Hepatocellular carcinoma cells


title: M 4_KO+library


title: HiC_ES_dKO_SRF_Cre_CTCF_dTAG13

data_processing:
The Hi-C reads were mapped using HiC-Pro (3.1.0) with the following bowtie2 arguments: --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder (global); --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder (local). Genome fragment file for the HiC-Pro was generated for the following ligation sites: GATCGATC, GAATGATC, GATTGATC, GACTGATC, GAGTGATC, GATCAATC, GATCATTC, GATCACTC, GATCAGTC, GAATAATC, GAATATTC, GAATACTC, GAATAGTC, GATTAATC, GATTATTC, GATTACTC, GATTAGTC, GACTAATC, GACTATTC, GACTACTC, GACTAGTC, GAGTAATC, GAGTATTC, GAGTACTC, GAGTAGTC and using MIN_INSERT_SIZE = 100, MAX_INSERT_SIZE = 900. Independent replicates were mapped individually and valid pairs (allValidPairs file generated by HiC-Pro) were concatenated to generate contact matrices. Hi-C contact matrices in h5 format at 10 kb resolution were generated using hicBuildMartix tool from HiCExplorer (3.7.2) [Ramirez, 2018] with the following arguments: --minMappingQuality 10 --skipDuplicationCheck -rs ResSites_combined.bed -seq GATC GAATC GATTC GACTC GAGTC --danglingSequence GATC AAT ATT ACT AGT -bs 10000. hicBuildMatrix input sam files containing the mapped reads were generated by converting the allValidPairs into the sam format using custom scripts. The file containing all restriction cut sites (ResSites_combined.bed) was created using hicFindRestSite tool with the argument --searchPattern GATC, followed by the argument --searchPattern GA.TC and concatenation of the output bed files. For independent replicates, the h5 format matrices were merged using hicSumMatrices tool from HiCExplorer. The merged matrices were corrected using hicCorrectMatrix tool with the Knight-Ruiz (KR) matrix balancing algorithm (--correctionMethod KR). Hi-C contact matrices in hic format for Juicebox and Juicer tools analyses were created from a list of all valid pairs (allValidPairs file generated by HiC-Pro; for independent replicates, allValidPairs files were concatenated) using hicpro2juicebox.sh script from the HiC-Pro Utilities with the following argument: -j juicer_tools.2.20.00.jar.
genome build/assembly: mm10
processed data files format and content: Contact matrices in h5 (at 20kb resolution, corrected using Knight and Ruiz (KR) balancing algorithm) and hic formats. For normalization, merging or other processing steps, HiCExplorer (h5) or Juicer tools (hic) can be used.

extract_protocol:
HiC was performed using a total of 5x105 cells per sample. Cells were treated and collected as follows. For non-differentiated ESCs, 2x106 Srf-flox1 cells encoding endogenous CTCF-FKBP were deprived of feeder cells and transfected with 25 μg GFP (Addgene, #11150) or 25 μg GFP-Cre plasmid (Addgene, #13776) using Lipofectamine 2000. 24 hours after the transfection, the medium was refreshed and supplemented with 250 nM dTAG13 or the matching volume of DMSO. After 24 hours of incubation with dTAG13 or DMSO, 5x105 of GFP-positive WT (GFP + DMSO), SRF KO (GFP-Cre + DMSO), CTCF KO (GFP + dTAG13), or SRF/CTCF dKO (GFP-Cre + dTAG13) cells were sorted using FACS Aria II. For dTAG13-induced SRF KO ESCs, 1x106 F1G4 cells encoding endogenous SRF-FKBP were treated with 250 nM dTAG13 for 24 hours, and 5x105 cells were collected using FACS Aria II. For CM cells, Srf-flex1 cells carrying H2B-mCherry (WT) or H2B-Venus-T2A-Cre (KO) were trypsinized at day 4 of cardiac mesoderm differentiation, and 5x105 cells expressing mCherry or Venus were sorted on a FACS Aria II. Sorted cells were crosslinked using Low Input crosslinking protocol provided by the Arima-HiC Kit user guide (A 160134 v01) and frozen in liquid nitrogen.
Proximally-ligated DNA was generated using Arima-HiC Kit (A510008) following the manufacturer’s protocol. HiC library was generated using KAPA Hyper Prep Kit (Roche, 07962312001) and KAPA single-indexed adapters (Roche, 08005702001) according to Arima’s Library preparation user guide. Covaris S220 was used for DNA shearing. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS Bioanalyzer chips. Paired-end sequencing was performed on the HiSeq 4000 with 2x 75 bp read length or on the NovaSeq 6000 with 2x 100 bp read length.

value: SRF/CTCF dKO

value: untreated


title: M 4_WT+library


title: ATAC_CM_SRF_KO_day4_rep1


title: M 3_KO+library


title: 293T_KO_ARID1A_K2025E_rep3

value: Human kidney epithelial cells

value: ARID1A knockout and ARID1A K2025E_Flag overexpression


title: HiC_ES_CTCF_KO_dTAG13

value: CTCF KO


title: 293T_KO_ARID1A_K2025E_rep2


title: HiC_ES_SRF_KO_dTAG13


title: 293T_KO_ARID1A_K2025E_rep1


title: ATAC_CM_WT_day4_rep2

description: processed data linked to rep1 sample

value: WT


title: M 3_WT+library


title: Mice,Jet lag,CNV,S3 (sRNA-seq)

city: Nantong

first: Aimin

last: Sang

address: xisi road

department: Department of Ophthalmology

institute: Affiliated Hospital of Nantong University

data_processing:
not provided
Assembly: mm10

source_name: RPE-choroid-scleral complex

growth_protocol: Maintain a constant temperature, provide sufficient light, good ventilation, and minimize noise as much as possible.

extract_protocol:
Dissect mouse eyeballs and extract RPE choroidal sclera complex.
Use the TRIzol method to extract total RNA from tissue samples and utilized,six,Nanodrop2000 was used to detect the concentration and purity of the extracted RNA, and low temperature agarose gel electrophoresis and biological analyzer were used,(Agilent 2100) Two methods are used to detect the integrity of total RNA.

treatment_protocol: C57BL/6J male mice (aged 6weeks) were randomly divided into two groups (Group A: 9:00-21:00 light period (300Lux); Group B: 8-hour phase advance once every 4 days).

value: RPE-choroid-scleral complex

value: CNV model+Circadian rhythm disorder model


title: ATAC_CM_WT_day4_rep1


title: 293T_KO_ARID1A_G2087R_rep3

value: ARID1A knockout and ARID1A G2087R_Flag overexpression


title: M 2_KO+library


title: HiChIP_ES_WT_SRF

data_processing:
SRF HiChIP reads and the public SMC1A HiChIP reads [Mumbach, 2016] were mapped using HiC-Pro (3.1.0) [Servant, 2015] with the following bowtie2 arguments: --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder (global); --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder (local). Genome fragment file for the HiC-Pro was generated for the following ligation site: GATCGATC and using MIN_INSERT_SIZE = 100, MAX_INSERT_SIZE = 900. HiC-Pro contact matrices were generated with the following arguments: GET_ALL_INTERACTION_CLASSES=1; RM_SINGLETON=1; RM_MULTI=1; RM_DUP=1. ICE normalization was performed with the following arguments: MAX_ITER=100; FILTER_LOW_COUNT_PERC=0.02; FILTER_HIGH_COUNT_PERC=0; EPS=0.1. HiChIP contact matrices in h5 format at 10 kb resolution were generated using hicBuildMartix tool from HiCExplorer (3.5) [Ramirez, 2018] with the following arguments: --binSize 10000 --restrictionSequence GATC. The bam files containing mapped reads and generated using HiC-Pro were used as the input for hicBuildMartix. The HiChIP matrices in h5 format were corrected using hicCorrectMatrix correct. The correction thresholds were identified using hicCorrectMatrix diagnostic_plot. HiChIP contact matrices in hic format for Juicebox and Juicer tools analyses were created from the list of all valid pairs (allValidPairs file generated by HiC-Pro) using hicpro2juicebox.sh script from the HiC-Pro Utilities with the following argument: -j juicer_tools.2.20.00.jar.
genome build/assembly: mm10
processed data files format and content: Contact matrices in h5 (at 10kb resolution, corrected using Knight and Ruiz (KR) balancing algorithm) and hic formats. Hicexplorer (h5) or Juicer tools (hic) can be used for further processing.
Library strategy: HiChIP

extract_protocol:
HiChIP was performed as described previously [Mumbach, 2016] with the following modifications. 5e107 ESCs were trypsinized, pelleted by centrifugation, resuspended in 20 ml 1% formaldehyde and incubated at room temperature for 10 minutes. 2 ml 2.5 M glycine was added followed by 5 minute incubation and centrifugation. The pelleted cells were lysed in 2.1 ml HiC lysis buffer (LB) (10 mM Tris pH8, 10 mM NaCl, 0.2% NP-40, protease inhibitors), split equally in 3x 1.5 ml eppendorf tubes, rotated at 4°C for 30 minutes, and centrifuged at 2,500xg for 5 minutes. Each pellet was once again resuspended in 700 μl HiC LB, centrifuged, resuspended in 100 μl 0.5% SDS and incubated at 62°C for 10 minutes. 285 μl H2O and 50 μl 10% TX-100 were added followed by incubation at 37°C for 15 minutes.
For restriction digestion, 15 μl (375 units) MboI (NEB, R0147M) and 50 μl 10x NEBuffer 2.1 were added, and incubated at 35°C for 9 hours. MboI was then heat inactivated at 62°C for 20 minutes. For biotin incorporation and proximity ligation, 52 μl of the mix containing 37.5 μl 0.4 mM biotin-14-dATP (ThermoFisher, 19524016), 1.5 μl 10 mM dTTP, 1.5 μl 10 mM dCTP, 1.5 μl 10 mM dGTP, 10 μl 5 units/μl DNA Pol. I, Large (Klenow) Fragment (NEB, M0210L) were added and rotated at 37°C for 90 minutes. 948 μl ligation master mix (150 μl 10x T4 DNA Ligase Reaction buffer (NEB, B0202S), 125 μl 10% TX-100, 3 μl 50 mg/ml BSA, 10 μl 400 units/μl T4 DNA ligase (NEB, M0202S), 660 μl H2O) were added and incubated at room temperature for 5 hours. The tubes were the then centrifuged and the pellets resuspended in 1 ml sonication buffer (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine), transferred to 15 ml Falcon tubes and sonicated using a W-450D Digital Sonifier sonicator for 18 cycles of 10 seconds on/50 seconds off with Amplitude set at 18 in a 4°C room with tubes chilled in ice water. After sonication, 110 μl of 10% Triton X-100 were added per tube, transferred to two 1.5 ml Eppendorf tubes and debris was pelleted by centrifugation at 20,000g and 4°C for 10 minutes. For ChIP, 3.3 ml of the combined cleared samples were mixed with 1.5 ml of dilution buffer (16.7 mM Tris pH 7.5, 167 mM NaCl, 1.1% Triton X-100, 1.2 mM EDTA) containing protease inhibitors. In parallel with biotin incorporation, 150 μl protein G-coated Dynabeads were washed 3x with 1 ml of blocking buffer (PBS, 0.5% BSA), resuspended in 500 μl of blocking buffer containing 12 μg SRF ChIP antibody and rotated at 4°C for 10 hours, followed by 3x washing with 1 ml blocking buffer. 4.8 ml cleared sonicated samples were added to 150 μl beads pre-incubated with the SRF antibody and rotated overnight at 4°C. The following day, 5 washing steps with 1 ml RIPA buffer (50 mM Hepes pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and one washing step with 1 ml of TEN (10 mM Tris pH 8, 1 mM EDTA, 50 mM NaCl) were performed. The elution was performed in two subsequent steps using 150 μl of 1x elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) and incubation at 65°C while shaking for 10 minutes each. 300 μl of TE buffer were added to the combined eluates, and RNA was digested using 0.2 μg/ml RNase A at 37°C for 30 minutes. Proteins were digested with the addition of 0.2 μg/ml proteinase K and incubation at 55°C for 45 minutes. Crosslinking was reversed by incubation at 65°C for 4 hours. The post-ChIP DNA was purified using MinElute (Qiagen) and quantified using the Qubit DNA HS assay. For biotin pull-down, 5 μl of MyOne Streptavidin C1 Dynabeads (ThermoFisher, 65001) were washed with 1 ml Tween wash buffer (5 mM Tris pH 7.5, 0.5 mM EDTA, 1M NaCl, 0.05% Tween-20), resuspended in 10 μl 2x Biotin binding buffer (10 mM Tris pH 7.5, 1 mM EDTA, 2M NaCl), combined with 50 ng post-ChIP DNA in 10 μl of H2O, and incubated at room temperature for 15 minutes. The beads were then washed twice with 500 μl Tween wash buffer at 55°C for 2 minutes each and resuspended in 50 μl of the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, and 22.5 μl H2O) followed by a 9 minute incubation at 55°C. The beads were then incubated in 50 mM EDTA at 50°C for 30 minutes, washed twice with 500 μl of 50 mM EDTA at 50°C for 3 minutes, twice with 500 μl of Tween wash buffer at 55°C for 2 minutes, and once with 500 μl of 10 mM Tris pH 7.5. The beads were then resuspended in 50 μl of master mix (25 μl 2x Kapa HiFi Hotstart Ready Mix, 1.25 μl of 10 μM Nextera Ad1.1, 1.25 μl of 10 μM Nextera Ad2.2, 22.5 μl H2O) and amplification was performed for 45 seconds at 98°C, 8 cycles of [15 seconds at 98°C, 30 seconds at 63°C and 45 seconds at 72°C] and a final 1 minute incubation at 72°C. After PCR, 46 μl of the library were transferred to a new tube. 38 μl of AMPure XP beads (Beckman Coulter) were used for a single purification and the DNA was eluted using 10 μl of elution buffer. The library was quantified using the Qubit DNA HS assay and the library size was validated using DNA HS Bioanalyzer chips.


title: HiC_CM_SRF_KO_Cre_rep2

description: processed data linked to rep1 sample


title: M 2_WT+library


title: 293T_KO_ARID1A_G2087R_rep1


title: M 1_KO+library


title: Mice,Control,CNV,N3 (sRNA-seq)

value: CNV model+Circadian rhythm model


title: Mice,Jet lag,CNV,S1 (sRNA-seq)


title: HiC_CM_WT_rep2

description: processed data linked to rep1 sample


title: 293T_KO_ARID1A_G2087E_rep3

value: ARID1A knockout and ARID1A G2087E_Flag overexpression


title: M 1_WT+library


title: Mice,Control,CNV,N2 (sRNA-seq)


title: HiC_CM_WT_rep1


title: PDAC_NFAT5_ChIP

city: Newark

first: Pingping

last: Hou

state: New Jersey

address: 205 South Orange Ave

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University

data_processing:
The raw data for each sample was trimmed using Trimmomatic v0.38 and quality was assessed via FastQC.
Cleaned reads were then aligned to the reference genome hg38 using bowtie2.
Aligned reads were filtered using samtools 1.9 to keep alignments that have a minimum mapping quality of 30, are aligned concordantly, and are the primary-called alignments.
PCR or optical duplicates were marked using Picard 2.18.26 and removed.
Prior to peak calling, reads mapping to mitochondria (mt) were called and filtered and reads mapping to unplaced contigs were removed.
MACS2 2.1.2 was used for peak calling with the significance cut-off q value <0.01
DeepTools to generate bigwig files
Assembly: GRCm38
Supplementary files format and content: bigWig, peaks.bed

source_name: pancreas

growth_protocol: RPMI with 10% Tet-approved FBS, 100U Penicillin-Streptomycin and 1 μg/mL doxycycline

extract_protocol:
Cells were cross-linked with 1% paraformaldehyde and then quenched with 0.125 mol/L glycine. Subsequently, cells were lysed on ice for 30 minutes using lysis buffer.
NEBNext Ultra DNA Library Preparation kit was used following the manufacturer’s recommendations (New England Biolabs, Ipswich, MA, USA). Briefly, the ChIP DNA was end repaired and adapters were ligated after adenylation of the 3’ends. Adapter-ligated DNA was size selected, followed by clean up, and limited cycle PCR enrichment. The ChIP library was validated using Agilent TapeStation and quantified using Qubit 2.0 Fluorometer as well as real time PCR (Applied Biosystems, Carlsbad, CA, USA).

treatment_protocol: murine recombinant TGFβ (0.5 ng/ml) for 3 days, doxycycline withdrawn

value: pancreas

value: iKPC mouse cells

value: cancer cells

value: p48-Cre, tetO_LKrasG12D, ROSA_rtTA, Trp53Lox/+

value: dox withdrawal, TGFβ treatment for 3 days

tag: chip antibody


title: HiC_ES_SRF_KO_Cre_rep2

description: processed data linked to rep1 sample

value: embryonic stem cells

value: SRF KO


title: 293T_KO_ARID1A_G2087E_rep2


title: Mice,Jet lag,CNV,S3 (lncRNA-seq)


title: PDAC_SMAD4_ChIP


title: HiC_ES_SRF_KO_Cre_rep1

value: untreated


title: 293T_KO_ARID1A_V2084D_rep3

value: Human kidney epithelial cells

value: ARID1A knockout and ARID1A V2084D_Flag overexpression


title: Mice,Jet lag,CNV,S2 (lncRNA-seq)


title: PDAC_SMAD3_ChIP


title: Mice,Jet lag,CNV,S2 (sRNA-seq)


title: 293T_KO_ARID1A_G2087R_rep2


title: 293T_KO_ARID1A_V2084D_rep2


title: HiC_CM_SRF_KO_Cre_rep1

value: cardiac mesoderm differentiation


title: PDAC_SMAD2_ChIP


title: HiC_ES_WT_rep1

value: WT


title: Mice,Jet lag,CNV,S1 (lncRNA-seq)

value: RPE-choroid-scleral complex


title: 293T_KO_ARID1A_V2084D_rep1


title: 293T_KO_ARID1A_WT_rep3

value: ARID1A knockout and ARID1A WT_Flag overexpression


title: Mice,Control,CNV,N3 (lncRNA-seq)


title: PDAC_KRN2_rep 3

data_processing:
Image analysis and base calling were conducted by the Control software.
Raw sequence data (.bcl files) generated the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality.
The trimmed reads were mapped to a reference genome created using the three synthetic RNA fasta files provided by CRISPRTX the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA extraction was conducted using the RNA Extraction Kit from Qiagen.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA).

value: mouse iKPC cells

value: dox withdrawal, TGFβ+KRN2 treatment for 3 days


title: Mice,Control,CNV,N1 (sRNA-seq)

value: CNV model+Circadian rhythm model


title: time point 120, aa depletion, rep2

city: Stockholm

first: Sherwin

last: Chan

address: Solnavagen 9

country: Sweden

institute: Karolinska Institutet

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2A120

data_processing:
Basecalls were performed using Generate FASTQ v 2.0.1 for NextSeq output
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic with default setting
Trimmed reads were mapped to the genome using HISAT2 v2.2.1 with default parameters
Read counts on gene feature were extracted from htseq-count v0.9.1
Assembly: PlasmoDB-46_Pfalciparum3D7
Supplementary files format and content: tab-delimited text (tabular) files of raw count for each Sample

organism: Plasmodium falciparum

growth_protocol: infected red blooc cells were grown in RPMI 1640 supplemented with 10% pooled human serum, cultured at 37C at 5% CO2, 5% O2

extract_protocol:
Total RNA extraction was performed using Trizol reagent (sigma)
library was constructed using TruSeq Stranded mRNA library Prep kit, 100ng RNA was used as input

treatment_protocol: At 36hr post invasion, cultures were equally splited into two, half of the culture was growth in complete medium while the other half was growth in amino acid depleted medium. After 3 hours, 20ug/ml actinomycinD was added to the cutlure to block transcription, samples were extracted at 0, 5, 10, 20, 40, 60 and 120mins after actinomycinD addition

value: Infected red blood cell

value: aa depleted medium


title: 293T_KO_ARID1A_G2087E_rep1

value: ARID1A knockout and ARID1A G2087E_Flag overexpression


title: time point 60, aa depletion, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2A60


title: 293T_KO_ARID1A_WT_rep2


title: Mice,Control,CNV,N2 (lncRNA-seq)


title: time point 40, aa depletion, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2A40


title: PDAC_DMSO_rep 3

value: pancreas

value: cancer cells

value: p48-Cre, tetO_LKrasG12D, ROSA_rtTA, Trp53Lox/+

value: dox withdrawal, TGFβ+DMSO treatment for 3 days


title: time point 20, aa depletion, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2A20


title: HiC_ES_WT_rep2

description: processed data linked to rep1 sample

value: embryonic stem cells

value: untreated


title: 293T_KO_rep3

value: Human kidney epithelial cells

value: ARID1A knockout


title: time point 10, aa depletion, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2A10


title: 293T_KO_ARID1A_WT_rep1


title: Brainstem,nuclei,Scn2a cKO

city: Ann Arbor

first: Han-Gyu

last: Bae

state: MI

address: 1301 CATHERINE ST

institute: University of Michigan

data_processing:
Split-pipe (from PARSE) was used for mapping and count data extraction
Assembly: GRCm39
Supplementary files format and content: all_genes.csv: gene ID information
Supplementary files format and content: cell_metadata.csv: Cell and sample identification.
Supplementary files format and content: DGE.mtx: gene count data.

molecule: nuclear RNA

extract_protocol:
Single nulei were isolated by minsed brain stem using Dunce homogenizer. The isolated nuclei were fixed using 1% PFA, and those were barcoded using PARSE Evercode WT mini kit.
The library was generated from barcoded nuclei using PARSE Evercode WT mini kit

value: Brain

value: Brain stem

value: Single nuclei

value: Scn2a cKO


title: MEFs-R-Scm-24h-2

first: Xiang

last: He

address: 280 South Chongqing Road, Shanghai, China

institute: Shanghai Jiaotong University School of Medicine

data_processing:
The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China)
Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) and sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
Paired-end sequence files (fastq) were mapped to the reference genome GRCm38.102 using Hista2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5).
Assembly: GRCm38.102
Supplementary files format and content: tab-delimited text files includes raw_counts for each Sample

source_name: embryonic fibroblasts

growth_protocol: MEFs cultured in Scm or Rcm medium. Scm, the S-FBS complete medium. Rcm, the R-FBS complete medium.

extract_protocol:
extract by RNeasy mini kit (Qiagen, Germany)
Paired-end libraries were synthesized by using the mRNA-seq Lib Prep Kit for Illumina (ABclonal, China) following Sample Preparation Guide

treatment_protocol: MEFs originally cultured in Rcm then changed medium to Scm for 12h or 24h which referred to as R-Scm-12h or R-Scm-24h, respectively. MEFs originally cultured in Scm then changed meidum to Rcm for 12h and 24h which referred to as S-Rcm-12h or S-Rcm-24h, respectively.

value: embryonic fibroblasts

value: MEFs

value: embryonic fibroblasts cells

value: WT

value: changed medium from Rcm to Scm for 24h


title: time point 5, aa depletion, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2A5

value: Infected red blood cell

value: aa depleted medium


title: MEFs-R-Scm-24h-3


title: 293T_KO_rep1


title: PDAC_DMSO_rep 2

value: pancreas

value: mouse iKPC cells

value: cancer cells

value: p48-Cre, tetO_LKrasG12D, ROSA_rtTA, Trp53Lox/+


title: PDAC_DMSO_rep 1

value: dox withdrawal, TGFβ+DMSO treatment for 3 days


title: time point 0, aa depletion, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2A0


title: MEFs-R-Scm-24h-1


title: Huh7_ARID1A_KO_WT_input_rep2

data_processing:
The raw fastq files were subjected to trimmomatic to remove low-quality reads, then aligned to the reference genome hg38 using bowtie2.
The aligned SAM files were converted to BAM files with samtools. Picard tools was used to remove PCR duplicates from the BAM files, and reads with ambiguous chromosome assignments (chrM or chrUn) were removed by samtools.
MACS2 was used for peak calling from BAM files, followed by blacklist removal with bedtools.
The bamCoverage function in Deeptools was used to convert bam files into bigwig files.
Assembly: hg38
Supplementary files format and content: bigwig: nucleotide resolution signal coverage tracks; narrowpeaks: punctuate peaks showing regions of enrichment.

extract_protocol:
Cells were fixed with 1% formaldehyde for 5min and quenched using 125 mM glycine for 5 min at RT. After quenching and cell lysis, chromatin was sonicated using bioruptor (diagenode).
ChIP-seq libraries were prepared using Illumina’s NEBNext Ultra II DNA Library Prep Kit (following standard protocols, E7645S).

value: Hepatocellular carcinoma cells

value: ARID1A knockout and ARID1A WT_Flag overexpression


title: PDAC_KRN2_rep 2

value: dox withdrawal, TGFβ+KRN2 treatment for 3 days


title: PDAC_Scramble_ctrl_rep 3

description: total normalized_counts_KD group.txt

value: dox withdrawal, TGFβ treatment for 3 days, Scramble_ctrl


title: time point 120, complete medium, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2C120

value: complete medium


title: Mice,Control,CNV,N1 (lncRNA-seq)

value: RPE-choroid-scleral complex

value: CNV model+Circadian rhythm model


title: MEFs-R-Scm-12h-3

value: embryonic fibroblasts

value: MEFs

value: embryonic fibroblasts cells

value: changed medium from Rcm to Scm for 12h


title: PDAC_Scramble_ctrl_rep 2

description: total normalized_counts_KD group.txt


title: PDAC_KRN2_rep 1


title: Huh7_ARID1A_KO_WT_input_rep1


title: time point 60, complete medium, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2C60

value: Infected red blood cell


title: MEFs-R-Scm-12h-2

value: WT


title: PDAC_Scramble_ctrl_rep 1

description: total normalized_counts_KD group.txt

value: pancreas

value: mouse iKPC cells


title: 293T_KO_rep2

value: Human kidney epithelial cells

value: ARID1A knockout


title: MEFs-R-Scm-12h-1


title: PDAC_Smad3_kd_rep 3

description: total normalized_counts_KD group.txt

value: cancer cells

value: p48-Cre, tetO_LKrasG12D, ROSA_rtTA, Trp53Lox/+

value: dox withdrawal, TGFβ treatment for 3 days, Smad3_kd


title: Huh7_ARID1A_KO_V2084D_shSTUB_ChIP_rep2

value: Hepatocellular carcinoma cells

value: Flag (sigma,#F1804)

value: ARID1A knockout, ARID1A V2084D_Flag overexpression and  knockdown STUB1


title: Huh7_ARID1A_KO_V2084D_shSTUB_ChIP_rep1


title: time point 20, complete medium, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2C20

value: complete medium


title: PDAC_Smad3_kd_rep 2

description: total normalized_counts_KD group.txt


title: Huh7_ARID1A_KO_V2084D_ChIP_rep2

value: ARID1A knockout and ARID1A V2084D_Flag overexpression


title: MEFs-Rcm-0h-2

value: embryonic fibroblasts

value: MEFs

value: cultured in Rcm


title: time point 40, complete medium, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2C40

value: Infected red blood cell


title: time point 10, complete medium, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2C10


title: Huh7_ARID1A_KO_V2084D_ChIP_rep1


title: MEFs-Rcm-0h-3

value: embryonic fibroblasts cells

value: WT


title: time point 5, complete medium, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2C5


title: MEFs-Rcm-0h-1


title: PDAC_Nfat5_kd_rep 3

description: total normalized_counts_KD group.txt

value: pancreas

value: mouse iKPC cells

value: dox withdrawal, TGFβ treatment for 3 days, Nfat5_kd


title: time point 0, complete medium, rep2

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R2C0


title: Huh7_ARID1A_KO_WT_ChIP_rep2

value: ARID1A knockout and ARID1A WT_Flag overexpression


title: PDAC_Smad3_kd_rep 1

description: total normalized_counts_KD group.txt

value: cancer cells

value: p48-Cre, tetO_LKrasG12D, ROSA_rtTA, Trp53Lox/+


title: PDAC_Nfat5_kd_rep 2

description: total normalized_counts_KD group.txt


title: MEFs-S-Rcm-24h-3

value: changed medium from Scm to Rcm for 24h


title: time point 120, aa depletion, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1A120

value: aa depleted medium


title: Huh7_ARID1A_KO_WT_ChIP_rep1

value: Hepatocellular carcinoma cells

value: Flag (sigma,#F1804)


title: MEFs-S-Rcm-24h-2


title: time point 60, aa depletion, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1A60


title: MEFs-S-Rcm-24h-1


title: Cas9-3

first: Chenxi

last: Zhao

address: 1 Tian Tan Xi Li

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample …

growth_protocol: 4T1 breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) with 5% CO2 at 37 ℃

extract_protocol:
Breast cancer cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Breast cancer

value: Breast cancer cells

value: culture


title: Huh7_ARID1A_KO_V2084D_shSTUB1_ATAC_rep1

extract_protocol:
Frozen relative hepatocellular carcinoma cells nuclears were harvested and genomic DNA were tagged following the ATAC-seq protocol.
ATAC-seq libraries were prepared for sequencing using standard ATAC-seq protocol.

treatment_protocol: ARID1A knocked out Huh7 cells with lentiviral stably expressed ARID1A WT/V2084D and knockdown STUB1

value: ARID1A knockout, ARID1A V2084D_Flag overexpression and  knockdown STUB1


title: MEFs-S-Rcm-12h-3

value: embryonic fibroblasts

value: MEFs

value: changed medium from Scm to Rcm for 12h


title: Huh7_ARID1A_KO_V2084D_ATAC_rep2

value: ARID1A knockout and ARID1A V2084D_Flag overexpression


title: time point 20, aa depletion, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1A20

value: Infected red blood cell


title: Huh7_ARID1A_KO_V2084D_ATAC_rep1


title: MEFs-S-Rcm-12h-2

value: embryonic fibroblasts cells

value: WT


title: time point 10, aa depletion, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1A10


title: MEFs-S-Rcm-12h-1


title: Ctrl-3

value: Ctrl


title: PDAC_Nfat5_kd_rep 1

description: total normalized_counts_KD group.txt

value: pancreas

value: mouse iKPC cells

value: cancer cells

value: p48-Cre, tetO_LKrasG12D, ROSA_rtTA, Trp53Lox/+

value: dox withdrawal, TGFβ treatment for 3 days, Nfat5_kd


title: time point 0, aa depletion, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1A0

value: aa depleted medium


title: Huh7_ARID1A_KO_WT_ATAC_rep1

value: Hepatocellular carcinoma cells

value: ARID1A knockout and ARID1A WT_Flag overexpression


title: Ctrl-2

value: Breast cancer

value: Breast cancer cells

value: culture


title: Huh7_ARID1A_KO_V2084D_shSTUB1_ATAC_rep2

value: ARID1A knockout, ARID1A V2084D_Flag overexpression and  knockdown STUB1


title: MEFs-Scm-0h-3

value: embryonic fibroblasts

value: MEFs

value: cultured in Scm


title: Ctrl-1


title: GSH-3

value: GSH


title: MEFs-Scm-0h-2

value: embryonic fibroblasts cells

value: WT


title: MEFs-Scm-0h-1


title: time point 120, complete medium, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1C120

value: Infected red blood cell

value: complete medium


title: RSM3_3

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

data_processing:
RNA-seq reads were filtered by fastp software with default parameters.
RNA-seq reads were aligned to the Ensembl hg38 genome using STAR v2.7.1a with default settings.
The featurecounts software was utilized to quantify gene expression.
The DESeq2 package was utilized to identify differentially expressed genes.
Assembly: hg38
Supplementary files format and content: txt, gene count

growth_protocol: RPMI-1640, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells with Total RNA  KitI (Omega,USA) according to the manufacturer's protocol.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Human prostate cancer

tag: agent


title: time point 40, aa depletion, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1A40


title: time point 60, complete medium, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1C60


title: RSM3_2


title: Female_Saline rep5

city: Guangzhou

first: Wenjun

last: Yu

address: Nanfang Hospital, Southern Medical University

institute: Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology

data_processing:
Quality control was performed by FastQC (v0.11.8) with passing all criteria.
Sequence reads were aligned to mouse genome MM10 (UCSC) using STAR (v2.7.1a) under the default parameters.
Aligned reads were quantified using HTSeq-counts (v0.11.2)
Low and un-expressed genes with < 3 reads in at least 5 samples in a group were omitted from the analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for all Samples

source_name: Whole brain

extract_protocol:
Total RNA was isolated using the RNeasy Plus Universal Mini Kit (Qiagen) according to the instruction.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: The female mice (16th day of pregnancy) received an intraperitoneal injection with LPS (150ug/kg) or saline (150ug/kg). For each treatment group, 5 whole brain RNA samples of the female offspring (postnatal 56 days) were prepared.

value: Whole brain

value: Maternal Saline injection

tag: time

value: 8 weeks


title: Cas9-2

city: Beijing

source_name: Breast cancer


title: RSM3_1


title: Cas9-1


title: GSH-2


title: GSH-1


title: time point 40, complete medium, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1C40


title: Control_3

value: Control


title: Female_Saline rep4


title: time point 20, complete medium, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1C20


title: Huh7_ARID1A_KO_WT_ATAC_rep2

value: Hepatocellular carcinoma cells

value: ARID1A knockout and ARID1A WT_Flag overexpression


title: time point 5, aa depletion, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1A5

value: aa depleted medium


title: Female_Saline rep3


title: WT-3

value: Breast cancer

value: Breast cancer cells

value: culture


title: Control_2


title: WT-2


title: time point 10, complete medium, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1C10


title: Control_1


title: time point 5, complete medium, rep1

description:
fastq files from four lanes of the same flow cells were concatenated into one fastq file
R1C5


title: Female_Saline rep1


title: WT-1