title: 23_Young_STHSC

city: Singapore

first: Takayoshi

last: Matsumura

address: 14 Medical Drive #12-01

country: Singapore

institute: National University of Singapore

data_processing:
Reads that passed the quality filter step by trim_galore were mapped to the reference mouse genome sequence (mm10) using HISAT2, and counted using featureCounts.
Assembly: mm10
Supplementary files format and content: A tab-delimited text file. An expression matrix made by featureCounts

source_name: bone marrow

extract_protocol:
RNA-seq was performed as previously described (PMID 33710340). Briefly, sorted cells were used to synthesize the first strand of cDNA with PrimeScript RT reagent kit (TAKARA Bio Inc.) and not so random primers. The first strand was treated with Klenow Fragments (3'-5' exo-; New England Biolabs Inc.) and complement chains of not so random primers to synthesize the second-strand cDNA.
After purifying double-strand cDNA, the library for RNA-seq was prepared and amplified using Nextera XT DNA sample prep kit (Illumina Inc.).

treatment_protocol: LT-HSCs (CD150+CD48-Lin-Sca1+Kit+), ST-HSCs (CD150-CD48-Lin-Sca1+Kit+), and MPPs  (CD150-CD48+Lin-Sca1+Kit+) sorted from CD117+ cells-enriched bone marrow of 4 young (12 weeks old) and 4 aged (107 weeks old) male mice

value: bone marrow

value: ST-HSC

tag: strain

tag: age

value: Young


title: HUVEC 2

status: Public on Jan 08 2025

type: SRA

city: Cambridge

first: Rudolf

last: Jaenisch

state: MA

address: 455 Main St.

country: USA

institute: Whitehead Institute for Biomedical Research

description: Library name: HUVEC 2

library_source: transcriptomic

data_processing:
RNA-seq reads were mapped to the GRCh38 (human) reference and genome using the STAR aligner
Counts were tabulated using ENSEMBL release 101 annotations with featureCounts.
Assembly: GRCh38, ENSEMBL release 101
Supplementary files format and content: Raw feature counts per sample as tab delimited text.

molecule: total RNA

organism: Homo sapiens

source_name: Primary

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Micro Kit
Libraries were prepared using the SMART-Seq  v4 low input RNA kit

tag: cell line

value: Primary

tag: cell type

value: Endothelial cell

tag: treatment

value: No treatment


title: HUVEC 3

description: Library name: HUVEC 3


title: 24_Young_MPP

organism: Mus musculus

tag: tissue

value: MPP


title: 21_Young_MPP


title: 20_Young_STHSC


title: 19_Young_LTHSC

value: LT-HSC


title: 18_Young_MPP


title: brain, wild type, AAV9, JeT,SLc6A1

city: Dallas

first: Weirui

last: Guo

state: Texas

address: 6000 Harry Hines Blvd.

department: Pediatrics

institute: UT Southwestern Medical Center

description: 10x genomic

library_source: transcriptomic single cell

data_processing:
The demultiplexing is performed using cellranger (v5.0.1) mkfastq
The reference transcriptome is generated using cellranger (v5.0.1) mkref
The gene counting is performed using cellranger (v5.0.1) count
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Brain cortex

extract_protocol:
WT C57BL/6J mouse was IT injected with 5 µL AAV9/ JeT-SLC6A1 vector at postnatal 10 days old. At 6 months post-injection, treated mouse was perfused, the brain cortex tissue was collected and processed for Single-nuclei RNA sequencing analysis (10x Genomics)
Library was performed according to the manufacter's instructions(Single Cell 3' v3, 10x genomic)

value: Brain cortex

value: brain cell

tag: genotype

value: WT

value: Intrathecal(IT) injection of AAV9


title: HUVEC 1

description: Library name: HUVEC 1


title: APC_female_apc_5

city: Fayetteville

first: Nicholas

middle: P

last: Greene

state: Arkansas

address: 155 Stadium Dr. HPER Building 321

institute: University of Arkansas

data_processing:
Raw counts were obtained using Salmon 1.10.2 and imported into R 4.4.1 using the tximport package, with GRCm39 annotation from AH116909.
The RNA-seq count data was stored in a DGEList object from the edgeR package, which was then transformed using the voom function from the limma package.
CPM and calcNormFactors were used to normalize the data.
Assembly: mm39
Supplementary files format and content: Matrix table with raw gene counts.

source_name: Tibialis anterior

extract_protocol:
TA were snap frozen in liquid nitrogen. RNA was extracted using trizol and a commercial kit (Thermo Fisher, PureLink RNA Mini Kit, Cat. No. 12183025).
The RNA sequencing was rered to Novogene for a mRNA library preparation (poly A enrichment)

value: Tibialis anterior

tag: Sex

value: female

tag: timepoint

value: APC+/Min


title: BSMC C

description: Library name: BSMC C

value: Smooth muscle cell


title: APC_female_apc_3


title: 17_Young_STHSC


title: APC_female_apc_4


title: BSMC B

description: Library name: BSMC B


title: 22_Young_LTHSC


title: APC_female_apc_2


title: 16_Young_LTHSC


title: 15_Young_MPP


title: 14_Young_STHSC


title: APC_female_apc_1


title: 13_Young_LTHSC


title: 12_Old_MPP

value: Aged


title: BSMC A

description: Library name: BSMC A


title: H1 EC B

description: Library name: H1 EC B


title: 11_Old_STHSC

value: bone marrow


title: 10_Old_LTHSC


title: APC_female_wt_7

value: wild type


title: H1 EC C

description: Library name: H1 EC C


title: H1 EC A

description: Library name: H1 EC A


title: 8_Old_STHSC

value: ST-HSC


title: APC_female_wt_8


title: 9_Old_MPP


title: APC_female_wt_6


title: 5_Old_STHSC


title: 6_Old_MPP


title: H1 SMC B

description: Library name: H1 SMC B

value: hPSC-derived smooth muscle cell


title: 7_Old_LTHSC


title: H1 SMC C

description: Library name: H1 SMC C


title: APC_female_wt_4


title: APC_female_wt_5


title: 3_Old_MPP


title: 2_Old_STHSC


title: APC_female_wt_3


title: H1 SMC A

description: Library name: H1 SMC A


title: 1_Old_LTHSC


title: APC_female_wt_2


title: H1 PC B

description: Library name: H1 PC B

value: hPSC-derived Pericyte


title: CPN_02

city: Stanford

first: Suzanne

last: Tharin

state: California

address: 450 Jane Stanford Way

institute: Stanford

library_source: genomic

data_processing:
ATAC-Seq data were analyzed using nf-core/atacseq v1.2.1 pipeline with Nextflow v22.10.0 and nf-core/tools v2.6.
ATAC-Seq reads were aligned to the UCSC mm10 genome using BWA v0.7.17.
Narrow peaks were called using MACS v2.2.7.1.
Normalized bigWig files scaled to 1 million mapped reads were generated using BEDTools v2.29.2 and bedGraphToBigWig v2.9.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

molecule: genomic DNA

source_name: brain

extract_protocol:
Viable FACS sorted cells, 50,000 per biological replicate, were lysed in non-ionic detergent to isolate the nuclei. The nuclei were suspended in a transposition mix, and incubated at 37oC to generate DNA fragments.
The DNA fragments were amplified using indexing primers. The product was purified once more to give the final library. Library concentrations were in the nano-molar range. The library quality was assessed using a BioAnalyzer. Samples with an RNA integrity number above 9 were used for ATAC-seq library sequencing.

value: brain

value: callosal projection neurons


title: CPN_01


title: APC_female_wt_1


title: C26_male_25days_8

value: male

value: 25 days


title: H1 PC A

description: Library name: H1 PC A

value: No treatment


title: Primary PC C

description: Library name: Primary PC C

value: Primary

value: Pericyte


title: 4_Old_LTHSC

value: LT-HSC


title: C26_male_25days_6

value: Tibialis anterior


title: C26_male_25days_5


title: Primary PC A

description: Library name: Primary PC A


title: EC SMC BA5.1 C L2

description: Library name: EC SMC BA5.1 C L2

data_processing:
RNA-seq reads were mapped to GRCh38 (human) reference and SARS-CoV-2 (MN988713.1) genome using STAR aligner
Counts were tabulated for human protein coding genes, lncRNAs (ENSEMBL release 93 annotations) and viral genes (MN988713.1) using featureCounts.
Assembly: GRCh38, ENSEMBL release 93, GenBank MN988713.1
Supplementary files format and content: Raw feature counts per sample as tab delimited text.

value: hPSC derived Endothelial cell

value: Media from BA5.1(omicron) infected SMCs

tag: treatment time_(hours)


title: H1 PC C

description: Library name: H1 PC C


title: CSMN_01

value: corticospinal motor neuron


title: C26_male_25days_4


title: Gallium 3

city: Calgary

first: Daniel Armando

last: Salazar-Alemán

state: Alberta

address: 2500 University Drive NW

department: Department of Biological Sciences

country: Canada

institute: University of Calgary

data_processing:
Initial FASTQ files were assessed and trimmed with the Bioconductor package rfastp (version 1.10).
Gene expression counts were obtained by aligning to the E. coli K12 BW25113 RefSeq assembly annotation file GCF_000750555.1using the Bioconductor package Rsubread(version 2.14.2), with counts assigned to the CDS meta-feature.
A counts matrix for the 4,378 identified features was imported into the Bioconductor package DESeq2(version 1.40.2) for differentially expressed genes determination. The adjusted p-value (p-adj) for multiple test adjustment (Benjamini-Hochberg correction, FDR < 0.05) was set to 0.05.
DEGs were defined as those with a p-adj value < 0.05 and whose expression had an absolute fold-change (FC) of at least 2 (|log2 FC| > 1) when contrasting the gallium treatment versus the unchallenged control; those with a negative FC were deemed as down-regulated genes in the gallium treatment, while a positive FC indicated up-regulation.
Assembly: E. coli K12 BW25113 from NCBI RefSeq (GCF_000750555.1)
Supplementary files format and content: Tab-delimited text file specifies gene name (or its "BW25113_" gene ID, if the gene name was not found), along with their respective raw counts for each sample.
Supplementary files format and content: Comma-delimited file with DESeq2 outputs including log2-fold change and p-values. Each gene is identified by its gene name, gene_id and uniprot entry.

organism: Escherichia coli

source_name: Bacterial cell

growth_protocol: Escherichia coli K12 BW25113 was cultured in 15mL of M9-glucose minimal media and incubated at 37 ºC 150 rpm for 10 hours in a shaker incubator.

extract_protocol:
2 mL of samples were centrifuged at 14,000 X g for 2 minutes to pellet the cells. Zirconia beads were used for cell lysis for 10 minutes using a bead beater instrument. Total RNA was then extracted with a RiboPure Bacteria RNA Isolation Kit AM1925 (Invitrogen, USA) according to the manufacturer's recommendations, including DNase treatment.
Ribosomal RNA depletion was performed using the NEB rRNA Depletion Bacterial Module (New England Biolabs, USA). The cDNA library preparation for Illumina sequencing was executed using the NEBNext Ultra II Directional RNA Library Prep Kit and NEB Indexing Kit (New England Biolabs, USA). After adaptor ligation and amplification, the average library fragment size was 360 bp.

treatment_protocol: Control treatments were grown for 10 hours in regular culture media. Experimental treatments were grown for 10 hours in culture media that had been spiked with a sublethal concentration of gallium nitrate (1.25 mM) prior to inoculation.

value: Wild type

value: Bacterial cell

tag: time

value: 10 hours

value: 1.25 mM gallium nitrate sublethal concentration


title: EC SMC BA5.1 C L1

description: Library name: EC SMC BA5.1 C L1


title: MSCs _ control_5

type: RNA

city: Warsaw

first: Agnieszka

last: Piekiełko-Witkowska

address: Marymoncka 99/103

department: Department of Biochemistry and Molecular Biology

country: Poland

institute: FCentre of Postgraduate Medical Education

description: Gene expression data from MSC transfected with non-target scrambled control oligonucleotide

hyb_protocol: Samples were hybridized with Affymetrix™ HuGene 2.1 ST Array Strips (Affymetrix, Santa Clara, CA, USA)

scan_protocol: Arrays were scanned in Gene Atlas Imaging Station (Affymetrix)

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) v4.0.3 with default settings

label: biotin

source_name: MSC

label_protocol: Total RNA was treated according to manufacturers protocol for GeneChip™ WT PLUS Reagent Kit (ThermoFisher Scientific, Waltham, MA, USA)

growth_protocol: MSCs were cultured in Dulbecco’s modified Eagle’s medium with low glucose (Biowest, Riverside, MO, USA) supplemented with 10% FBS (Biowest, Riverside, MO, USA), Glutamine-Penicillin–Streptomycin (Biowest, Riverside, MO, USA) and amphotericin B (Biowest, Riverside, MO, USA). The identity of MSCs was confirmed by flow-cytometry analysis and induction of adipogenesis, chondrogenesis and osteogenesis.

extract_protocol: 48h after transfections cells were trypsinized, and RNA was isolated using Universal RNA/miRNA Purification Kit (EURx).

treatment_protocol: 0.75×105 cells were seeded at 12-well plates and cultured for 24h cells with the following transfection with 45 pmol of piR_004153 synthetic mimic or negative control oligonucleotide using Lipofectamine 2000 (Thermo Fisher Scientific). Medium was renewed every 24h.

value: Mesenchymal stromal cells


title: MSCs _ control_4


title: MSCs _ control_1


title: MSCs _ piR_004153_4

description: Gene expression data from MSC transfected with piR_004153


title: MSCs _ piR_004153_5


title: MSCs _ piR_004153_2


title: MSCs _ control_3


title: Gallium 2


title: MSCs _ control_2


title: C26_male_25days_7


title: Primary PC B

description: Library name: Primary PC B


title: MSCs _ piR_004153_3


title: C26_male_25days_2


title: Control 2

value: Control - no metal challenge


title: MSCs _ piR_004153_1


title: C26_male_25days_1


title: Control 1


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, selected sgRNA #11

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: Lewis-Sigler Institute for Integrative Genomics, Princeton University

institute: Princeton University

description: Library name: Sample 31

data_processing:
fastq files from amplicon seq experiements were aligned to the specific locus and edited reads were called by CRISPRESSO2.  fastq files from CRISPR screen was analyzed using MAGeCK.
Assembly: mm10 for mouse, hg19 for human.
Supplementary files format and content: processed data is in XLSX format and contains results for the F1 cross (C57BL/6 and 129S1/SVlmJ) and essentiality (A549) screens.

source_name: cell line

extract_protocol:
phenol chloroform
For random/selected sgRNA sequencing (Samples 1-31), PCR encompassing ~250bp surrounding the edit site was performed using loci-specific primers, and standard P7/P5 adapters were added to the PCR amplicon by Genewiz/Azenta for subsequent NGS.  For CRISPR sequencing (Samples 32-43), a 2 step PCR approach was used to first amplify the region of sgRNA region after genomic DNA extraction, then standard P7/P5 adapters and unique barcodes were added in a second PCR reaction.

value: cell line

value: C57BL/6, 129S1/SvlmJ F1 cross

value: embryonic stem cells


title: EC SMC BA5.1 A L2

description: Library name: EC SMC BA5.1 A L2


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, selected sgRNA #10

description: Library name: Sample 30


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, selected sgRNA #9

description: Library name: Sample 29


title: C26_male_25days_3

value: male

value: 25 days


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, selected sgRNA #7

description: Library name: Sample 27


title: C26_male_20days_7

value: 20 days


title: EC SMC BA5.1 A L1

description: Library name: EC SMC BA5.1 A L1


title: EC SMC BA5.1 B L2

description: Library name: EC SMC BA5.1 B L2


title: Gallium 1


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, selected sgRNA #6

description: Library name: Sample 26


title: C26_male_20days_6


title: C26_male_20days_5


title: EC PC CoV2 C L2

description: Library name: EC PC CoV2 C L2

value: Media from SARS-CoV-2 infected PCs


title: Control 3


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, selected sgRNA #4

description: Library name: Sample 24


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, selected sgRNA #5

description: Library name: Sample 25


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, selected sgRNA #3

description: Library name: Sample 23


title: EC PC CoV2 C L1

description: Library name: EC PC CoV2 C L1


title: EC SMC BA5.1 B L1

description: Library name: EC SMC BA5.1 B L1


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, selected sgRNA #1

description: Library name: Sample 21


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, selected sgRNA #2

description: Library name: Sample 22


title: C26_male_20days_4

value: Tibialis anterior


title: EC PC CoV2 B L2

description: Library name: EC PC CoV2 B L2

value: hPSC derived Endothelial cell


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, random sgRNA #9

description: Library name: Sample 19


title: EC PC CoV2 B L1

description: Library name: EC PC CoV2 B L1


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, random sgRNA #8

description: Library name: Sample 18


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, random sgRNA #7

description: Library name: Sample 17


title: C26_male_20days_1


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, random sgRNA #3

description: Library name: Sample 13


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, random sgRNA #5

description: Library name: Sample 15


title: PC CoV2 C L2

description: Library name: PC CoV2 C L2

value: hPSC-derived Pericyte


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, random sgRNA #4

description: Library name: Sample 14


title: EC PC CoV2 A L1

description: Library name: EC PC CoV2 A L1


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, random sgRNA #6

description: Library name: Sample 16


title: C26_male_10days_8

value: 10 days


title: C26_male_10days_7


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, random sgRNA #1

description: Library name: Sample 11


title: C26_male_10days_6


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, random sgRNA #10

description: Library name: Sample 20


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, 129S1/SvlmJ allele targeting, random sgRNA #2

description: Library name: Sample 12


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, random sgRNA #9

description: Library name: Sample 9


title: C26_male_20days_3


title: C26_male_10days_5


title: PC CoV2 C L1

description: Library name: PC CoV2 C L1


title: C26_male_10days_4


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, random sgRNA #6

description: Library name: Sample 6


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, random sgRNA #7

description: Library name: Sample 7


title: PC CoV2 A L2

description: Library name: PC CoV2 A L2


title: PC CoV2 B L2

description: Library name: PC CoV2 B L2


title: C26_male_20days_2


title: EC PC CoV2 A L2

description: Library name: EC PC CoV2 A L2


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, random sgRNA #10

description: Library name: Sample 10


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, random sgRNA #8

description: Library name: Sample 8


title: PC CoV2 B L1

description: Library name: PC CoV2 B L1


title: C26_male_10days_3


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, random sgRNA #4

description: Library name: Sample 4


title: PC CoV2 A L1

description: Library name: PC CoV2 A L1


title: C26_male_10days_2


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, random sgRNA #2

description: Library name: Sample 2


title: H3K9ac_Hay_am

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

country: China

institute: Yangzhou University

description: Library name: Sample 11

data_processing:
Different sequencing adapters of CUT&Tag-seq were cut using cutadapt software (v4.9). All reads were aligned to then reference genome in sheep (ARS-UI_Ramb_v3.0) using the Bowtie2 (v 2.5.4). Reads arising from PCR amplifications were discarded as duplicate reads using MarkDuplicates function of Picard software (v1.67). The Samtools software (v1.21) was used to sort and convert the SAM files to BAM format and remove mitochondria reads. Uniquely mapped reads were normalized and converted to BIGWIG files using bamCoverage function of deeptools software (v3.5.5) with the parameters --binSize 50 --normalizeUsing RPKM -extendReads to visualize CUT&Tag-seq signals at specific genomic loci by the Integrative Genomics Viewer (IGV) software (v2.6.0). Peak calling of CUT&Tag-seq data was performed using MACS3 software (v3.0.2) taking a q-value of 0.05 as threshold, and the different peaks were compared and identified between am and pm of each treatment was selected using bdgdiff function of MACS3 software. To annotate the locations of peaks in genomic features, BED files were used to perform peak annotation with ChIPseeker software (v1.42.0). The multiBamSummary function of deeptools software was used to perform the PCA analysis and the Pearson’s correlation analysis of CUT&Tag-seq data. To visualize the genomic occupancy of the peaks ± the 3 kb of the transcription start site (TSS), the computeMatrix, plotProfile, and plotHeatmap functions in deeptools software were applied to generated the TSS’s line chart and heatmap with normalized read counts.
Assembly: sheep reference genome ARS-UI_Ramb_v3.0
Supplementary files format and content: Peak density files in bigWig format.
Library strategy: CUT&Tag

organism: Ovis aries

source_name: ovine ruminal epithelial cells

extract_protocol:
DNA was extracted using CUT&Tag-seq DNA Extract Beads Pro with the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro following the manufacturer’s instructions (TD901, Vazyme).
CUT&Tag-seq experiment was using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro following the manufacturer’s instructions (TD901, Vazyme). The libraries were finally performed Illumina sequencing using NovaSeq 6000 (PE150).

value: ovine ruminal epithelial cells

value: Hay-VFAs

tag: chip antibody


title: H3K9ac_Hay_pm

description: Library name: Sample 12


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, random sgRNA #3

description: Library name: Sample 3


title: C26_male_10days_1


title: SMC CoV2 72hr B

description: Library name: SMC CoV2 72hr B

value: hPSC-derived smooth muscle cell


title: H3K9ac_Grain_pm

description: Library name: Sample 10

value: Grain-VFAs


title: C26_male_pbs_7

value: control

value: pbs


title: SMC CoV2 72hr A

description: Library name: SMC CoV2 72hr A


title: SMC mock 72hr B

description: Library name: SMC mock 72hr B

value: Mock infection


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, random sgRNA #1

description: Library name: Sample 1

value: cell line

value: C57BL/6, 129S1/SvlmJ F1 cross


title: Tsix-stop cells, KDM6A wildtype control, Day7,rep2

city: Riverside

first: Wenxiu

last: Ma

address: 900 University Ave

institute: University of California Riverside

description: Library name: Sample 14

data_processing:
Sequencing reads were obtained from MiSeq, paired-end, 75bp for each end.
Demultiplexed fastq files were mapped to NCBI v38/mm10 mouse genome using bowtie2-2.4.5. A pseudo-129 genome was assembled by replacing available SNPs of 129 (Sanger Center) into the BL6 mm10 reference genome. A pseudo-cast genome was assembled by replacing available SNPs of cast (Sanger Center) into the BL6 mm10 reference genome.
CutRun-seq reads were mapped using bowtie/v2.4.5 and tophat/v2.1.1 to the genome and transcriptome of both the pseudo-129 and the pseudo-cast genomes. Only those reads that mapped uniquely and with a high-quality mapping score (MAPQ ≥ 30) to either the pseudo-129 or pseudo-cast genomes were kept for further analyses.  Non-allelic: CutRun-seq reads were mapped mm10 using bowtie. bedtools(v2.30.0) were used to generate bedgraph from alignment file
Assembly: NCBI v38/mm10
Supplementary files format and content: bedgraph
Library strategy: CUT&RUN

source_name: embryonic stem cells

growth_protocol: ES cells were maintained in the presence of 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on a inactivated MEFs, in high glucose DMEM media supplemented with 15% fetal bovine serum (FBS), 1% non-essential amino acids, 10 mg/ml APS, 0.1mM 2mercaptoethanol and 25mM L-glutamine, in a humidified incubator at 37. Differentiation was induced by culturing as embryoid bodies and removal of LIF ºC and 5% CO2.

extract_protocol:
Cells were immoblized on beads, and following permeabilization using digitonin, incubated with antibodies specific for KDM6A or H3K27me3
Genomic DNA libraries were constructed using the Epicypher CUTANA kit (Epicypher)

treatment_protocol: CRISPR/Cas9 and sgRNA constructs targeting Kdm6a were transfected at the stem cell stage (day0) followed by differentiation using lipid based methods.

value: embryonic stem cells

value: Tsix-stop

value: KDM6A (Cell Signaling, D3Q1I)

value: WT

value: nondirected differentiation


title: C57BL/6 and 129S1/SvlmJ F1 cross cells, C57BL/6 allele targeting, random sgRNA #5

description: Library name: Sample 5


title: C26_male_pbs_6

value: Tibialis anterior

value: male


title: H3K9ac_Grain_am

description: Library name: Sample 9


title: Tsix-stop cells, KDM6A wildtype control, Day7,rep1

description: Library name: Sample 13


title: Tsix-stop cells, KDM6A wildtype control, Day4,rep2


title: C26_male_pbs_5


title: SMC mock 72hr A

description: Library name: SMC mock 72hr A


title: H3K4me3_Grain_pm

description: Library name: Sample 6


title: C26_male_pbs_8


title: H3K27ac_Hay_pm

description: Library name: Sample 4


title: Tsix-stop cells, KDM6A wildtype control, Day2,rep1


title: C26_male_pbs_2


title: H3K27ac_Hay_am

description: Library name: Sample 3


title: C26_male_pbs_1


title: PC mock B

description: Library name: PC mock B

value: hPSC-derived Pericyte


title: Tsix-stop cells, knockout, IgG, Day15

value: IgG (Epicypher, 13-0042)


title: H3K4me3_Grain_am

description: Library name: Sample 5

value: ovine ruminal epithelial cells


title: C26_female_25days_6

value: female

value: 25 days


title: H3K27ac_Grain_am

description: Library name: Sample 1

value: Grain-VFAs


title: H3K27ac_Grain_pm

description: Library name: Sample 2


title: ATAC_Hay_pm

description: Library name: Sample 4

data_processing:
Different sequencing adapters of ATAC-seq were cut using cutadapt software (v4.9). All reads were aligned to then reference genome in sheep (ARS-UI_Ramb_v3.0) using the Bowtie2 (v 2.5.4). Reads arising from PCR amplifications were discarded as duplicate reads using MarkDuplicates function of Picard software (v1.67). The Samtools software (v1.21) was used to sort and convert the SAM files to BAM format and remove mitochondria reads. Uniquely mapped reads were normalized and converted to BIGWIG files using bamCoverage function of deeptools software (v3.5.5) with the parameters --binSize 50 --normalizeUsing RPKM -extendReads to visualize ATAC-seq signals at specific genomic loci by the Integrative Genomics Viewer (IGV) software (v2.6.0). Peak calling of ATAC-seq data was performed using MACS3 software (v3.0.2) taking a q-value of 0.05 as threshold, and the different peaks were compared and identified between am and pm of each treatment was selected using bdgdiff function of MACS3 software. To annotate the locations of peaks in genomic features, BED files were used to perform peak annotation with ChIPseeker software (v1.42.0). The multiBamSummary function of deeptools software was used to perform the PCA analysis and the Pearson’s correlation analysis of ATAC-seq data. To visualize the genomic occupancy of the peaks ± the 3 kb of the transcription start site (TSS), the computeMatrix, plotProfile, and plotHeatmap functions in deeptools software were applied to generated the TSS’s line chart and heatmap with normalized read counts.
Assembly: sheep reference genome ARS-UI_Ramb_v3.0
Supplementary files format and content: Peak density files in bigWig format.

extract_protocol:
DNA was extracted using ATAC DNA Extract Beads Pro, washed twice gently using 80% ethanol, and eluted in 26 μL of ddH2O for DNA extraction.
ATAC-seq library construction was using Hyperactive ATAC-Seq Library Prep Kit for Illumina (TD711, Vazyme) following the manufacturer’s instructions (TD901, Vazyme).The libraries were finally performed Illumina sequencing using NovaSeq 6000 (PE150).

value: Hay-VFAs


title: Tsix-stop cells, wildtype control, IgG, Day15


title: C26_female_25days_5


title: C26_female_25days_4


title: Tsix-stop cells, knockout, IgG, Day0


title: CUTTag LEDGF_HCT116_DMSO

city: nanjing

first: shuhan

last: si

state: jiangsu

address: sipailou

institute: Southeast University

data_processing:
Raw CUT&Tag adaptors and low-quality reads were removed as described in ChIP-seq analysis and the paired-reads were aligned to the human h19 genomes using Bowtie v2.4.5 with the options ’--local --very-sensitive --no-mixed --no-discordant -I 10 -X 700’
PCR duplicates were filtered using Picard 2.27.4.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: The HCT 116 cell lines were cultured in DMEM (HyClone) supplemented with 10% FBS (Ex-Cell Bio), 1% Penicillin-Streptomycin (HyClone), and maintained at 37°C incubators with 5% CO2. For passaging, cells were washed with 1 × PBS (Hyclone). 0.25% Trypsin-EDTA (Gibco) was used to detach cells from plates. Trypsin-EDTA was quenched by addition of FBS containing media. For serum stimulation, cells were first starved by washing three times with 1 × PBS and culturing for 40 hours in serum free media, then either left untreated or treated with serum for indicated time before harvesting.

extract_protocol:
CUT&Tag was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme) according to the manufacturer’s protocol. For each CUT&Tag reaction, 5× 105 HCT 116 cells were harvested using StemPro Accutase (Gibco) to prevent overdigestion. After centrifugation, cells were washed twice with Wash Buffer. Concanavalin-A-coated magnetic beads (ConA Beads Pro, Vazyme) were pre-activated and resuspended in an equal volume of Binding Buffer. Subsequently, 10 μl of activated ConA Beads Pro were added to cells, followed by a 10-minute incubation under gentle rotation. The bead-bound cells were magnetized to remove excess liquid, then resuspended in 50 μl of Antibody Buffer. Next, 1 μg of LEDGF (Bethyl) antibody was added, and the mixture was rotated 2 hours at room temperature. After incubation, the bead-bound cells were subjected to successive incubations with goat anti-rabbit IgG (diluted 1:100) in 50 μl of Dig-wash Buffer for 1 hour at room temperature. Subsequently, the cells were washed four times with Dig-wash Buffer to remove unbound antibodies. The pA/G-Tnp Pro was prepared in Dig-300 Buffer to a final concentration of 0.04 μM. The bead-bound cells were resuspended in 100 μl of pA/G-Tnp Pro mix and incubated at room temperature for 1 hour before supernatant removal. Following thorough washing, the tagmentation reaction was initiated in 40 μl of Dig-300 Buffer with 10 μl 5× TTBL at 37 ℃ for 1 hour. To halt the reaction, 2 μl of 10% SDS was added, and appropriate amount of DNA Spike-in was added. After a 10-minute incubation at 55 ℃, DNA purification was performed using DNA Extract Beads Pro (Vazyme). The purified DNA was then subjected to amplification using TruePrep Index Kit V2 for Illumina (Vazyme) with a universal i5 primer and a uniquely barcoded i7 primer. The exact number of PCR cycles was determined by qPCR prior to amplification, with 11 cycles typically sufficient to yield an adequate library for sequencing.
Following library size-selection with VAHTS DNA Clean Beads (Vazyme) to achieve library sizes ranging from 200 to 700 bp, sequencing was performed using an Illumina NovaSeq 6000 platform.

value: Human Colorectal Carcinoma Cells

tag: cut&tag antibody

value: LEDGF


title: CUTTag LEDGF_HCT116_dTAG3h


title: SMC CoV2 72hr C

description: Library name: SMC CoV2 72hr C

value: hPSC-derived smooth muscle cell


title: Tsix-stop cells, wildtype control, IgG, Day0

value: embryonic stem cells


title: ATAC_Hay_am

description: Library name: Sample 3


title: EC infection media A

description: Library name: EC infection media A

value: hPSC-derived Endothelial cell

value: Treatment with infection media only (no virus)


title: CUTTag LEDGF_HCT116_generated_in_house


title: C26_female_25days_3


title: C26_male_pbs_3

value: control

value: pbs


title: Tsix-stop cells, K27, knockout, Day15

description: K15_me_129allele.fragments.bedgraph,K15_me_CASTallele.fragments.bedgraph,K15_me_S6_norm.fragments.bedgraph

value: Tsix-stop

value: H3K27me3 (Millipore, 07-449)

value: Kdm6a knockout

value: nondirected differentiation


title: ATAC_Grain_pm

description: Library name: Sample 2

value: ovine ruminal epithelial cells


title: CUTTag LEDGF_HCT116_Bethyl


title: C26_female_25days_2

value: Tibialis anterior

value: female


title: Tsix-stop cells, K27, knockout, Day0

description: K0_me_129allele.fragments.bedgraph,K0_me_CASTallele.fragments.bedgraph,K0_me_S4_norm.fragments.bedgraph


title: C26_female_25days_1

value: 25 days


title: ATAC_Grain_am

description: Library name: Sample 1

value: Grain-VFAs


title: Primary Human CD14+ cells, aavs1 control, biol rep 3

city: Dublin

first: Kory

last: Melton

state: CA

address: 6253 Dougherty Road

institute: Self

data_processing:
Reads were aligned using kallisto with the pre-built human index (k-mer = 31, boostrapping n=100)
Normalized transcripts were tested for differential expression using DESeq2, aggregated at the gene level. Genes with an average of less than 10 counts per sample were filtered out.
A blind variance stabilizing transformation was applied before principal component analysis with the top 500 weighted genes. Log fold changes were shrunk using the apeglm algorithm before differential expression testing was performed. Genes were classified as differentially expressed if the log2 fold change was less than 0.58 and the adjusted p-value was less than 0.05, only genes with a base mean of 3 are shown.
Assembly: hg38
Supplementary files format and content: excel file with deseq2 results for all gRNAs
Supplementary files format and content: excel file with PCA of deseq2 results

source_name: Primary CD14+ cells

growth_protocol: Cells were magnetically isolated from PBMC and differentiated into macrophages by culturing 7 days in media supplemented with 50 ng/mL M-CSFPrimary human CD14+ cells magnetically isolated from PBMC were thawed and differentiated into macrophages by culturing 7 days in media supplemented with 50 ng/mL M-CSF (Peprotech). Macrophages were plated in 96-well flat bottom, low attachment plates at 1 x 105 cells per well.

extract_protocol:
Total RNA was harvested using XX. 350 nanograms of total RNA was used for the construction of sequencing libraries.
Libraries for RNA-seq were prepared with the Standard RNA-Seq service at Azenta Life Sciences.

treatment_protocol: RNPs with either ADAR-targeting gRNAs or negative control gRNAs (targeting either AAVS1 as a safe harbor locus, an intronic region of HPRT, or BFP as a non-targeting control) were generated and used to treat the macrophage. The RNPs were delivered to M0 macrophages using a peptide-assisted method similar to the previously described approaches (Foss et al., 2023; Zhang et al., 2024). This approach was more tractable than nucleofection of macrophages and also allowed for evaluation of gRNAs delivered by a different method. Cells were co-incubated with 1 µM Cas9 complexed with ADAR-targeting gRNAs, plus 10 µM INF7-Tat-like peptide  (GLFEKIEGFIENGWEGMIDGWYGYGRKKRRQRR, Algayer et al., 2019) for 24 h . Media was removed and replaced with fresh supplemented media and cells were returned to culture for another 48h

value: Primary CD14+ cells

value: M0 Macrophages

value: off-target control

value: aavs1 RNP


title: Primary Human CD14+ cells, aavs1 control, biol rep 2


title: Tsix-stop cells, K27, wildtype control, Day0

description: Wt0_me_129allele.fragments.bedgraph,Wt0_me_CASTallele.fragments.bedgraph,Wt0_me_S5_norm.fragments.bedgraph

value: embryonic stem cells

value: WT


title: C26_female_20days_8

value: 20 days


title: Primary Human CD14+ cells, aavs1 control, biol rep 1


title: C26_female_20days_7


title: Primary Human CD14+ cells, bfp non-target control, biol rep 3

value: vehicle control

value: bfp RNP


title: 18S_H-RF8-T18

description: Library name: Sample 95

data_processing:
For the data processing of rumen microbiomes, raw fastq reads were demultiplexed according to sample-specific barcodes and imported to QIIME2 software (version QIIME2-202402)
The poor-quality bases, adapters and specific primers were trimmed, and the sequences were denoised and binned to amplicon sequence variants (ASVs) using the denoise-paired function of DADA2 plugin for QIIME2.
The feature-classifier plugin was used to construct the specific primer classifiers for the protozoa (316F and 539R of the 18S rRNA gene) based on the SILVA database (version 138). The ASVs were then classified taxonomically based on the specific protozoal classifiers.
The align-to-tree-mafft-fasttree function of the phylogeny plugin was used to construct the phylogenetic trees after the filtering the rare ASVs, and the mitochondria and chloroplast reads. The unweighted unifrac distances for ordination and clustering were calculated using the beta-phylogenetic function of the diversity plugin, and the principal coordinate analysis (PCoA) was performed and visualization by the R software (v4.2) package ggplot2 (v3.4.4).
The alpha diversity parameters (Faith-PD, Chao 1, Shannon, and Simpson) were calculated using the alpha or alpha-phylogenetic function of the diversity plugin. The relative abundance of ruminal protozoa at phylum, family, and genus levels were generated using the relative-frequency function of the feature-table plugin.
Assembly: The V4 region of the eukaryotic 18S rRNA gene was amplified with primers 316F (GCTTTCGWTGGTAGTGTATT) and 539R (CTTGCCCTCYAATCGTWCT).
Supplementary files format and content: 18S_feature_table_with_taxonomy.xlsx, 18S-repset-seqs.fasta

source_name: ruminal fluid

extract_protocol:
Total genomic DNA was isolated from 1 mL of freeze rumen fluid using TIANamp Stool DNA Kit (DP328, Tiangen) according to manufacturer's instruction.
Amplicon sequencing of rumen 18S rRNA sequencing were performed according to Illumina  protocols with all amplicon libraries being sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA) with 250-base-paired end reads.

value: ruminal fluid

value: Hay-diet treatment


title: 18S_H-RF8-T14

description: Library name: Sample 94


title: C26_female_20days_6


title: ASOPDX_1570_R4

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

description:
Library name: ASOPDX_1570_R4
rMATS_PSI_matrix_GEO_ASO_PDX.csv
Gene_count_matrix_GEO_ASO_PDX.csv

data_processing:
Mouse read removal with Xenome (only applicable to PDX samples)
Read QC with fastqc and multiqc
Trimming with trimmomatic
Genome alignment with STAR
Transcriptome assembly with stringtie
Splicing analysis and quantification with rMATS
Assembly: GRCh38/hg38
Supplementary files format and content: Comma seperated matrix of PSI values from rMATS
Supplementary files format and content: Comma seperated matrix of gene counts

source_name: Breast carcinoma PDX mouse model

growth_protocol: MDA-MB231 and U87MG cells were transfected with ASOs at either 50nM or 200nM (CTL or TRA2B-1570 targeting), or siRNAs at 10nM (CTL or TRA2B targeting). RNA was extracted 48h later and subjected to library prep. For mouse PDX samples, breast tumors were implanted in immunocompetent mice, which were treated with either ASO-CTL or ASO-1570 at 50mg/kg for four weeks prior to collection, RNA extraction, and library prep.

extract_protocol:
Libraries were prepared using the RNA-seq stranded mRNA kit from Illumina and sequenced as 151 PE reads on a HiSeq 2000
Stranded, paired-end, RNA-seq

treatment_protocol: 50nM or 200nM ASOs, and 10nM siRNAs, were transfected in cell lines using lipofectamine 3000. Mouse PDX models were treated with intratumoral injections of ASOs at 50mg/kg three times weekly for four weeks.

value: Breast carcinoma PDX mouse model

value: JAX PDX tumor TM00096

value: PDX


title: ASOPDX_1570_R5

description:
Library name: ASOPDX_1570_R5
rMATS_PSI_matrix_GEO_ASO_PDX.csv
Gene_count_matrix_GEO_ASO_PDX.csv


title: 18S_H-RF8-T10

description: Library name: Sample 93


title: C26_female_20days_5

value: Tibialis anterior

value: female


title: Primary Human CD14+ cells, bfp non-target control, biol rep 2


title: ASOPDX_1570_R3

description:
Library name: ASOPDX_1570_R3
rMATS_PSI_matrix_GEO_ASO_PDX.csv
Gene_count_matrix_GEO_ASO_PDX.csv


title: 18S_H-RF8-T22

description: Library name: Sample 96


title: Tsix-stop cells, K27, wildtype control, Day15

description: Wt15_me_129allele.fragments.bedgraph,Wt15_me_CASTallele.fragments.bedgraph,Wt15_me_S5_norm.fragments.bedgraph

value: Tsix-stop

value: H3K27me3 (Millipore, 07-449)

value: nondirected differentiation


title: Primary Human CD14+ cells, bfp non-target control, biol rep 1

value: Primary CD14+ cells

value: M0 Macrophages


title: H3K4me3_Hay_am

description: Library name: Sample 7

value: ovine ruminal epithelial cells

value: Hay-VFAs


title: 18S_H-RF8-T6

description: Library name: Sample 92


title: C26_female_20days_4

value: 20 days


title: Primary Human CD14+ cells, hprt control, biol rep 2

value: off-target control

value: hprt RNP


title: 18S_H-RF7-T22

description: Library name: Sample 90

value: ruminal fluid


title: C26_female_20days_2


title: Primary Human CD14+ cells, hprt control, biol rep 1


title: ASOPDX_1570_R2

description:
Library name: ASOPDX_1570_R2
rMATS_PSI_matrix_GEO_ASO_PDX.csv
Gene_count_matrix_GEO_ASO_PDX.csv


title: 18S_H-RF7-T18

description: Library name: Sample 89

value: Hay-diet treatment


title: C26_female_20days_3


title: 18S_H-RF8-T2

description: Library name: Sample 91


title: ASOPDX_CTL_R5

description:
Library name: ASOPDX_CTL_R5
rMATS_PSI_matrix_GEO_ASO_PDX.csv
Gene_count_matrix_GEO_ASO_PDX.csv

value: Breast carcinoma PDX mouse model

value: ASO-CTL 50mg/kg


title: ASOPDX_1570_R1

description:
Library name: ASOPDX_1570_R1
rMATS_PSI_matrix_GEO_ASO_PDX.csv
Gene_count_matrix_GEO_ASO_PDX.csv

value: JAX PDX tumor TM00096

value: PDX


title: 18S_H-RF7-T10

description: Library name: Sample 87


title: Tsix-stop cells, KDM6A wildtype control, Day2,rep2

value: embryonic stem cells

value: KDM6A (Cell Signaling, D3Q1I)

value: WT


title: Primary Human CD14+ cells, cg242, biol rep 2

value: adar knockdown

value: cg242 RNP


title: C26_female_10days_8

value: Tibialis anterior

value: female

value: 10 days


title: ASOPDX_CTL_R3

description:
Library name: ASOPDX_CTL_R3
rMATS_PSI_matrix_GEO_ASO_PDX.csv
Gene_count_matrix_GEO_ASO_PDX.csv


title: C26_female_10days_7


title: ASOPDX_CTL_R4

description:
Library name: ASOPDX_CTL_R4
rMATS_PSI_matrix_GEO_ASO_PDX.csv
Gene_count_matrix_GEO_ASO_PDX.csv


title: 18S_H-RF7-T14

description: Library name: Sample 88


title: C26_male_pbs_4

value: male

value: control

value: pbs


title: C26_female_20days_1

value: 20 days


title: ASOPDX_CTL_R2

description:
Library name: ASOPDX_CTL_R2
rMATS_PSI_matrix_GEO_ASO_PDX.csv
Gene_count_matrix_GEO_ASO_PDX.csv


title: Primary Human CD14+ cells, cg242, biol rep 3

value: Primary CD14+ cells

value: M0 Macrophages


title: Primary Human CD14+ cells, cg223, biol rep 3

value: cg223 RNP


title: C26_female_10days_6


title: 18S_H-RF7-T6

description: Library name: Sample 86

value: ruminal fluid

value: Hay-diet treatment


title: Primary Human CD14+ cells, hprt control, biol rep 3

value: off-target control

value: hprt RNP


title: 18S_H-RF7-T2

description: Library name: Sample 85


title: C26_female_10days_5


title: ASOPDX_CTL_R1

description:
Library name: ASOPDX_CTL_R1
rMATS_PSI_matrix_GEO_ASO_PDX.csv
Gene_count_matrix_GEO_ASO_PDX.csv

value: Breast carcinoma PDX mouse model

value: JAX PDX tumor TM00096

value: PDX

value: ASO-CTL 50mg/kg


title: U87_siRNA_TRA2B_R3

description:
Library name: U87_siRNA_TRA2B_R3
rMATS_PSI_matrix_GEO_siRNA.csv
Gene_count_matrix_GEO_siRNA.csv

source_name: glioblastoma

value: glioblastoma

value: adherent glioblastoma

value: siRNA-TRA2B 10nM


title: Primary Human CD14+ cells, cg223, biol rep 2

value: adar knockdown


title: U87_siRNA_TRA2B_R2

description:
Library name: U87_siRNA_TRA2B_R2
rMATS_PSI_matrix_GEO_siRNA.csv
Gene_count_matrix_GEO_siRNA.csv


title: C26_female_10days_4

value: Tibialis anterior

value: female

value: 10 days


title: 18S_H-RF6-T22

description: Library name: Sample 84


title: Primary Human CD14+ cells, cg223, biol rep 1

value: Primary CD14+ cells

value: M0 Macrophages


title: Primary Human CD14+ cells, cg214, biol rep 3

value: cg214 RNP


title: 18S_H-RF6-T18

description: Library name: Sample 83

value: ruminal fluid

value: Hay-diet treatment


title: Primary Human CD14+ cells, cg242, biol rep 1

value: cg242 RNP


title: C26_female_10days_2


title: Primary Human CD14+ cells, cg214, biol rep 2


title: C26_female_10days_3


title: U87_siRNA_CTL_R3

description:
Library name: U87_siRNA_CTL_R3
rMATS_PSI_matrix_GEO_siRNA.csv
Gene_count_matrix_GEO_siRNA.csv

value: siRNA-CTL 10nM


title: 18S_H-RF6-T10

description: Library name: Sample 81


title: C26_female_10days_1


title: Primary Human CD14+ cells, cg214, biol rep 1


title: U87_siRNA_CTL_R2

description:
Library name: U87_siRNA_CTL_R2
rMATS_PSI_matrix_GEO_siRNA.csv
Gene_count_matrix_GEO_siRNA.csv


title: 18S_H-RF6-T6

description: Library name: Sample 80


title: U87_siRNA_CTL_R1

description:
Library name: U87_siRNA_CTL_R1
rMATS_PSI_matrix_GEO_siRNA.csv
Gene_count_matrix_GEO_siRNA.csv


title: 18S_H-RF6-T2

description: Library name: Sample 79


title: Primary Human CD14+ cells, cg202, biol rep 3

value: cg202 RNP


title: C26_female_pbs_6

value: control

value: pbs


title: PC mock C

description: Library name: PC mock C

value: hPSC-derived Pericyte

value: Mock infection


title: MB231_siRNA_TRA2B_R3

description:
Library name: MB231_siRNA_TRA2B_R3
rMATS_PSI_matrix_GEO_siRNA.csv
Gene_count_matrix_GEO_siRNA.csv

source_name: breast carcinoma

value: breast carcinoma

value: adherent glioblastoma

value: siRNA-TRA2B 10nM


title: Primary Human CD14+ cells, cg202, biol rep 2

value: adar knockdown


title: C26_female_pbs_7

value: Tibialis anterior

value: female


title: 18S_H-RF5-T22

description: Library name: Sample 78


title: MB231_siRNA_TRA2B_R2

description:
Library name: MB231_siRNA_TRA2B_R2
rMATS_PSI_matrix_GEO_siRNA.csv
Gene_count_matrix_GEO_siRNA.csv


title: C26_female_pbs_5


title: U87_siRNA_TRA2B_R1

description:
Library name: U87_siRNA_TRA2B_R1
rMATS_PSI_matrix_GEO_siRNA.csv
Gene_count_matrix_GEO_siRNA.csv

value: glioblastoma


title: 18S_H-RF6-T14

description: Library name: Sample 82


title: Primary Human CD14+ cells, cg202, biol rep 1

value: Primary CD14+ cells

value: M0 Macrophages


title: 18S_H-RF5-T18

description: Library name: Sample 77

value: ruminal fluid

value: Hay-diet treatment


title: MB231_siRNA_TRA2B_R1

description:
Library name: MB231_siRNA_TRA2B_R1
rMATS_PSI_matrix_GEO_siRNA.csv
Gene_count_matrix_GEO_siRNA.csv


title: Primary Human CD14+ cells, cg174, biol rep 2

value: cg174 RNP


title: 18S_H-RF5-T14

description: Library name: Sample 76


title: MB231_siRNA_CTL_R3

description:
Library name: MB231_siRNA_CTL_R3
rMATS_PSI_matrix_GEO_siRNA.csv
Gene_count_matrix_GEO_siRNA.csv

value: siRNA-CTL 10nM


title: Primary Human CD14+ cells, cg174, biol rep 3


title: C26_female_pbs_4

value: control


title: H3K4me3_Hay_pm

description: Library name: Sample 8

value: ovine ruminal epithelial cells

value: Hay-VFAs


title: C26_female_pbs_2

value: pbs


title: 18S_H-RF5-T6

description: Library name: Sample 74


title: Primary Human CD14+ cells, cg174, biol rep 1


title: Primary Human CD14+ cells, cg156, biol rep 2

value: cg156 RNP


title: Primary Human CD14+ cells, cg156, biol rep 3


title: RNA_seq_BCAS_3

city: Shanghai

first: Lei

last: Zhu

address: No. 12, Wulumuqi Road (M)

department: Department of Vascular Surgery

institute: Huashan Hospital, Fudan University

data_processing:
FastQC was used to do quality control on the raw data to verify whether the sequencing data were adequate for further analysis.
Trim-galore was utilized to eliminate adapter sequences, low-quality reads, and too short reads from raw data in order to produce clean data.
Sequencing reads were aligned to annotated RefSeq genes in the mouse reference genome (UCSC mm10) with HISAT2. Samtools v1.9 was also used to sort and build the alignment file index.
Using featureCounts v1.6.3, a gene count matrix containing raw transcript counts for each annotated gene was generated.
We relied onthe automatic and independent filtering performed by the DESeq2 R package (1.16.1) to identify the most suitable threshold for eliminating genes with low counts. In addition, raw transcript counts were normalized, log2 transformed, and analyzed in DESeq2 using the default protocols to identify genes that were differentially regulated after CCH.
Assembly: mm10
Supplementary files format and content: RNA-seq: raw gene counts text files

growth_protocol: The mice were housed at 25°C and supplied conventional rodent food and water.

extract_protocol:
The TRIzol Reagent (Life Technologies, California, USA) was used to extract RNA. The sequencing libraries were built using 1 ug of total RNA.
Following the manufacturer's guidelines, sequencing libraries were created using the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA), and index codes were added to attribute sequences to each. sample.

treatment_protocol: The control group was exposed to sham operation. The experimental group was exposed to bilateral carotid artery stenosis (BCAS) operation

value: the right  striatum

value: WT

value: 14 weeks


title: 18S_H-RF5-T2

description: Library name: Sample 73


title: 18S_H-RF4-T22

description: Library name: Sample 72


title: RNA_seq_BCAS_2

value: bilateral carotid artery stenosis (BCAS) operation


title: U87_50nM_1570_R3

description:
Library name: U87_50nM_1570_R3
rMATS_PSI_matrix_GEO_50nM_ASO.csv
Gene_count_matrix_GEO_50nM_ASO.csv

value: adherent glioblastoma


title: MB231_siRNA_CTL_R1

description:
Library name: MB231_siRNA_CTL_R1
rMATS_PSI_matrix_GEO_siRNA.csv
Gene_count_matrix_GEO_siRNA.csv

value: breast carcinoma


title: U87_50nM_1570_R2

description:
Library name: U87_50nM_1570_R2
rMATS_PSI_matrix_GEO_50nM_ASO.csv
Gene_count_matrix_GEO_50nM_ASO.csv

value: glioblastoma


title: Primary Human CD14+ cells, cg156, biol rep 1

value: Primary CD14+ cells

value: M0 Macrophages

value: adar knockdown


title: 18S_H-RF4-T18

description: Library name: Sample 71

value: ruminal fluid

value: Hay-diet treatment


title: C26_female_pbs_3

value: Tibialis anterior

value: female

value: control


title: Primary Human CD14+ cells, cg145, biol rep 3

value: cg145 RNP


title: U87_50nM_1570_R1

description:
Library name: U87_50nM_1570_R1
rMATS_PSI_matrix_GEO_50nM_ASO.csv
Gene_count_matrix_GEO_50nM_ASO.csv


title: RNA_seq_BCAS_1


title: 18S_H-RF4-T14

description: Library name: Sample 70


title: RNA_seq_Sham_3

value: Sham operation


title: U87_50nM_CTL_R3

description:
Library name: U87_50nM_CTL_R3
rMATS_PSI_matrix_GEO_50nM_ASO.csv
Gene_count_matrix_GEO_50nM_ASO.csv

value: ASO-CTL 50nM


title: Tsix-stop cells, KDM6A wildtype control, Day4,rep1

value: embryonic stem cells

value: Tsix-stop

value: KDM6A (Cell Signaling, D3Q1I)

value: WT

value: nondirected differentiation


title: C26_female_pbs_1

value: pbs


title: PC mock A

description: Library name: PC mock A

value: hPSC-derived Pericyte

value: Mock infection


title: 18S_H-RF4-T10

description: Library name: Sample 69


title: MB231_siRNA_CTL_R2

description:
Library name: MB231_siRNA_CTL_R2
rMATS_PSI_matrix_GEO_siRNA.csv
Gene_count_matrix_GEO_siRNA.csv

value: breast carcinoma

value: adherent glioblastoma

value: siRNA-CTL 10nM


title: RNA_seq_Sham_2

value: the right  striatum

value: 14 weeks


title: 18S_H-RF4-T6

description: Library name: Sample 68

value: ruminal fluid

value: Hay-diet treatment


title: Primary Human CD14+ cells, cg145, biol rep 1

value: Primary CD14+ cells

value: M0 Macrophages

value: adar knockdown

value: cg145 RNP


title: 18S_H-RF5-T10

description: Library name: Sample 75


title: U87_50nM_CTL_R1

description:
Library name: U87_50nM_CTL_R1
rMATS_PSI_matrix_GEO_50nM_ASO.csv
Gene_count_matrix_GEO_50nM_ASO.csv

value: glioblastoma

value: ASO-CTL 50nM


title: RNA_seq_Sham_1

value: WT

value: Sham operation


title: 18S_H-RF4-T2

description: Library name: Sample 67


title: Primary Human CD14+ cells, cg113, biol rep 3

value: cg113 RNP


title: Primary Human CD14+ cells, cg113, biol rep 2


title: MB231_50nM_1570_R3

description:
Library name: MB231_50nM_1570_R3
rMATS_PSI_matrix_GEO_50nM_ASO.csv
Gene_count_matrix_GEO_50nM_ASO.csv


title: ATAC_seq_BCAS_4

data_processing:
FastQC was used for quality control to ensure sequencing data quality.
Clean paired-end reads were aligned to the mouse reference genome (UCSC mm10) using Bowtie2.
Samtools v1.9 was utilized to sort, convert, and index alignment files post-duplication removal.
MACS2 callpeak function was employed for peak calling, and differential peaks were identified using the R package DiffBind. Peak annotation was conducted with the R packages 'ChIPseeker,' 'clusterProfiler,' and 'TxDb.Mmusculus.UCSC.mm10.knownGene.'
Motif analysis was performed using the HOMER tool 'findMotifsGenome.pl,' with subsequent TF annotation.
Assembly: mm10
Supplementary files format and content: ATAC-seq: punctuate peaks (narrowPeaks)

extract_protocol:
The nuclei were extracted from freshly isolated striatum using a lysis buffer with centrifugation for 10 minutes at 2000 rcf.
ATAC-seq libraries were prepared by transposing approximately 100,000 nuclei using a transposition mix and Tn5 enzyme, followed by DNA purification and PCR amplification. Libraries were sequenced on the Illumina Nova-Seq 6000 platform with 150-bp paired-end reads.

value: bilateral carotid artery stenosis (BCAS) operation


title: 18S_H-RF3-T22

description: Library name: Sample 66


title: Primary Human CD14+ cells, cg145, biol rep 2


title: MB231_50nM_1570_R2

description:
Library name: MB231_50nM_1570_R2
rMATS_PSI_matrix_GEO_50nM_ASO.csv
Gene_count_matrix_GEO_50nM_ASO.csv

value: breast carcinoma


title: Primary Human CD14+ cells, cg113, biol rep 1


title: 18S_H-RF3-T18

description: Library name: Sample 65


title: ATAC_seq_BCAS_3


title: MB231_50nM_1570_R1

description:
Library name: MB231_50nM_1570_R1
rMATS_PSI_matrix_GEO_50nM_ASO.csv
Gene_count_matrix_GEO_50nM_ASO.csv

value: adherent glioblastoma


title: ATAC_seq_BCAS_2


title: 18S_H-RF3-T14

description: Library name: Sample 64


title: Primary Human CD14+ cells, cg096, biol rep 3

value: cg096 RNP


title: U87_50nM_CTL_R2

description:
Library name: U87_50nM_CTL_R2
rMATS_PSI_matrix_GEO_50nM_ASO.csv
Gene_count_matrix_GEO_50nM_ASO.csv


title: ATAC_seq_BCAS_1

value: the right  striatum


title: Primary Human CD14+ cells, cg096, biol rep 2


title: MB231_50nM_CTL_R3

description:
Library name: MB231_50nM_CTL_R3
rMATS_PSI_matrix_GEO_50nM_ASO.csv
Gene_count_matrix_GEO_50nM_ASO.csv


title: 18S_H-RF3-T10

description: Library name: Sample 63


title: Primary Human CD14+ cells, cg096, biol rep 1


title: MB231_50nM_CTL_R2

description:
Library name: MB231_50nM_CTL_R2
rMATS_PSI_matrix_GEO_50nM_ASO.csv
Gene_count_matrix_GEO_50nM_ASO.csv


title: ATAC_seq_Sham_4

value: 14 weeks


title: 18S_H-RF3-T6

description: Library name: Sample 62

value: ruminal fluid


title: ATAC_seq_Sham_3


title: MB231_50nM_CTL_R1

description:
Library name: MB231_50nM_CTL_R1
rMATS_PSI_matrix_GEO_50nM_ASO.csv
Gene_count_matrix_GEO_50nM_ASO.csv


title: Primary Human CD14+ cells, cg094, biol rep 3

value: cg094 RNP


title: 18S_H-RF3-T2

description: Library name: Sample 61

value: Hay-diet treatment


title: ATAC_seq_Sham_2


title: IPZ-3

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Fragments per kilobase per million (FPKM) estimation was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq (a Python framework to work with high-throughput sequencing data), and differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: acute myeloid leukemia cell

growth_protocol: NB-4 were maintained inRPMI1640 with 15% fetal bovine serum (FBS) (Gibico) and 1% penicillin/streptomycin (Hyclone).

extract_protocol:
Total RNA was extracted with miRNeasy Kit (QIAGEN).
The mRNA was reverse-transcribed and amplified according to the method Geo-seq, then the library was constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) according to the manufacturer’s instruction.

treatment_protocol: NB-4 cultured with DMSO, Importazole (IPZ, 5 µM) for 48 h, followed by RNA-seq

value: acute myeloid leukemia cell

value: Wild-type

value: Importazole


title: 18S_H-RF2-T22

description: Library name: Sample 60


title: ATAC_seq_Sham_1


title: IPZ-2


title: Primary Human CD14+ cells, cg094, biol rep 1

value: Primary CD14+ cells

value: M0 Macrophages

value: adar knockdown


title: 18S_H-RF2-T18

description: Library name: Sample 59


title: Primary Human CD14+ cells, cg065, biol rep 3

value: cg065 RNP


title: IPZ-1


title: MEL/ch11, dSub-TAD, H3K27ac, rep1

city: Busan

first: Jin

last: Kang

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Department of Molecular Biology

country: South Korea

institute: Pusan National University

data_processing:
ChIP-seq raw reads were filtered to remove input read ends with poor quality values (quality score 20) and then aligned to the hg19 chomosome 11 reference genome using Bowtie2. Aligned BAM files were filtered by Minimum MAPQ quality score 20 and sorted by chromosomal coordinates. Potential PCR duplicates were removed from BAM files. H3K27me3 BAM file was converted to bigwig files using bamCoverage to visualize ChIP-seq signal. H3K27ac BAM files were visualized using S3V2 normalization method.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: MEL/ch11 cells, MEL cells containing a human chromosome 11, were cultured in DMEM medium containing 10% FBS.

extract_protocol:
Nuclei were digested with 100 units of MNase at 37°C for 15 min. Mono or di-nucleosomes sized chromatin was incubated with antibodies for 3 h at 4°C and recovered with protein A agarose beads.
ChIP DNA (1 ng for H3K27me3 and 10 ng for H3K27ac) was processed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) with manufacturer’s instructions. The ends of ChIP DNA were repaired by NEBNext Ultra II End Prep enzyme mix and ligated with NEBNext adaptors. Adaptor-ligated DNA was selected at 200 bp size using NEBNext sample purification bead and amplified using the adaptor primers (11 cycles for H3K27me3; 7 cycles for H3K27ac). The fragments are purified using NEBNext sample purification beads.

treatment_protocol: MEL/ch11 cells were treated by HMBA to induce human β-globin gene transcription for 72 h.

value: erythroleukemia cells

value: dSub-TAD

value: HMBA for 72 h


title: MEL/ch11, dTAD, H3K27ac, rep1

value: dTAD


title: DMSO-3

value: DMSO


title: 18S_H-RF2-T10

description: Library name: Sample 57


title: Primary Human CD14+ cells, cg065, biol rep 1


title: MEL/ch11, Con, H3K27me3, rep1

value: Con


title: MEL/ch11, Con, H3K27ac, rep1


title: DMSO-2


title: 18S_H-RF2-T6

description: Library name: Sample 56


title: Primary Human CD14+ cells, cg030, biol rep 3

value: cg030 RNP


title: DMSO-1


title: Primary Human CD14+ cells, cg094, biol rep 2


title: 18S_H-RF1-T22

description: Library name: Sample 54

value: ruminal fluid


title: AoV structure pooled replicate 3

city: Milwaukee

first: Joy

last: Lincoln

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: 10X genomics 3' gene expression

data_processing:
The libraries were sequenced on two SP lanes of an Illumina NovaSeq with 28x90nt reads. Read1 is 28nt in length, Read2 is 90nt in length, I1 and I2 are 10nt in length. Fastq.gz files were generated and demultiplexed with 10x Genomics Cell Ranger v7.0.1.
A custom reference was made using 10x Genomics Cell Ranger 7.1.0 mkref to add the EGFP gene to NCBI's GRCm39 genome, Annotation Release 109, then cellranger count was run including the argument --chemistry=ARC-v1
Assembly: GRCm39, NCBI Annotation Release 109
Supplementary files format and content: barcodes.tsv.gz - filtered cell barcodes in tab-separated format. features.tsv.gz - gene IDs and symbols in tab-separated format. matrix.mtx.gz - gene counts per cell in mtx format.

molecule: nuclear RNA

source_name: Aortic valve structure

extract_protocol:
Nuclei were isolated using the Chromium Nuclei Isolation Kit (CG000505, Rev A PN-1000494) following manufacturer’s protocols for frozen tissue for Single Cell Multiome ATAC + Gene Expression (10X Genomics, Pleasanton, CA)
Sequencing libraries were created following manufacturer’s protocols for Single Cell Multiome ATAC + Gene Expression (CG000338, Rev F PN-1000285) (10X Genomics, Pleasanton, CA)

value: Aortic valve structure

value: aortic valve (heterogeneous)

value: B6.Cg-Scx<tm1.1(EGFP)Skom (RBRC11098)

value: postnatal day 1


title: Primary Human CD14+ cells, cg030, biol rep 2


title: GB1

city: Tampere

first: Reetta

last: Nätkin

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology, Prostate Cancer Research Center

country: Finland

institute: Tampere University and Tays Cancer Center

description:
GB1 as in manuscript
Bulk-RNA sequencing of a primary glioblastoma brain tumor (patient sample GB1 in manuscript) extracted from tissue; aiming to capture the transcriptome of the cells composing the brain tumor immune microenvironment without any prior enrichment. This primary sample allows TiME comparison between this sample (GB1) and recurrent ones (reGB1 L1 and L2).

data_processing:
The read alignment and read count quantification were performed with STAR version 2.5.3a, Ensembl reference genome GRC38 and Gencode annotation release 29.
Assembly: hg38
Supplementary files format and content: tab delimited file with STAR --quantMode GeneCounts output

molecule: polyA RNA

source_name: (patient sample) brain tumor

extract_protocol:
RNA was harvested using TRI reagent (TRIzol) with phenol-chloroform centrifugation, collecting the aqueous phase (total RNA), followed by glycogen and isopropanol precipitation.
Total RNA

value: (patient sample) brain tumor

tag: tissue type

value: Primary Glioblastoma [patient GB1]


title: GS

description:
GS as in manuscript
Bulk-RNA sequencing of a primary gliosarcoma [glioblastoma subtype] brain tumor (patient sample GS in manuscript) extracted from tissue; aiming to capture the transcriptome of the cells composing the brain tumor immune microenvironment without any prior enrichment. As a characteristic feature of this sample, in particular presented an exceptional lymphocyte infiltration (based on FCM analysis).

value: Glioblastoma subtype [Glisarcoma]


title: 18S_H-RF2-T2

description: Library name: Sample 55

value: Hay-diet treatment


title: AoV structure pooled replicate 2

description: 10X genomics 3' gene expression


title: 18S_H-RF1-T18

description: Library name: Sample 53


title: AoV structure pooled replicate 1

description: 10X genomics 3' gene expression


title: 18S_H-RF1-T14

description: Library name: Sample 52


title: Primary Human CD14+ cells, cg020, biol rep 3

value: Primary CD14+ cells

value: M0 Macrophages

value: adar knockdown

value: cg020 RNP


title: 18S_H-RF2-T14

description: Library name: Sample 58


title: Primary Human CD14+ cells, cg020, biol rep 2


title: Primary Human CD14+ cells, cg065, biol rep 2

value: cg065 RNP


title: Tumor_36, TGFb_vacc

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Data alinged using STAR (V.2.7.9). Reads in genes (Ensembl gene transcripts GRCm39.104.gtf) were quantified using featureCounts within the Subread package (V.2.0.3).
Assembly: GRCm39
Supplementary files format and content: count matrix text file

source_name: Tumor

growth_protocol: Pan02 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C. Mice were injected subcutaneously (s.c.) on the right flank with 0.5 million  Pan02 cancer cells.

extract_protocol:
Tumor fragments (≤ 20 mg) in RNAlater (Invitrogen) were transferred to RLT buffer (Qiagen) and mechanically homogenized with a Tissue Lyser (Qiagen). RNA was extracted with the RNEasy Plus Mini Kit (Qiagen),
RNA with RIN > 7 was used. mRNA was enriched using using Oligo dT beads (NEBNext). The mRNA was fragmented, random-primed for cDNA synthesis (NEBNext). Hairpin adapotors were ligated to end repaired cDNA and PCR was used to add index (NEBNext). Library was size selected using AMPure beads and quantified using KAPA (Roche).

treatment_protocol: Pan02 tumor-bearing mice were either left untreated or vaccinated with TGFβ vaccine on days 8 and 15 post-inoculation. Anti-IL-6R antibody was administered on day 8 post-inoculation and every 3rd-4th day for a total of six injections.

value: Tumor


title: reGB1_L1

description:
reGB1 L1 as in manuscript
Bulk-RNA sequencing of a recurrent (relapse) glioblastoma brain tumor Locus 1 (patient sample GB1 in manuscript) extracted from tissue; aiming to capture the transcriptome of the cells composing the tumor immune microenvironment (TiME) of a relapse sample, allowing comparison between primary and recurrent TiME.

value: Recurrent [relapse] Glioblastoma Locus 1 brain tumor of patient GB1


title: Tumor_25, TGFb_vacc


title: GB2

description:
GB2 as in manuscript
Bulk-RNA sequencing of a primary glioblastoma brain tumor (patient GB2 sample) extracted from tissue; aiming to capture the transcriptome of the cells composing the brain tumor immune microenvironment without any prior enrichment.

value: Primary Glioblastoma


title: Primary Human CD14+ cells, cg019, biol rep 3

value: cg019 RNP


title: Tumor_22, TGFb_vacc


title: 18S_H-RF1-T2

description: Library name: Sample 49

value: ruminal fluid


title: CCL7_500_3,Bone marrow derived macrophages, 500ng/ml CCL7 24h

city: Guangzhou

first: Jun

address: No. 1023-1063, Satai South Road, Baiyun District

institute: Southern Medical University

description: Library name: SAMPLE11

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low- quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q-p 4 -e100-y-a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Mus marrow

extract_protocol:
The preparation of RNA samples is the first step of transcriptome sequencing. RNA within the cells is extracted and purified through a sequence of steps including lysis with Trizol, phase separation with chloroform, precipitation with isopropanol, and washing with 75% anhydrous ethanol.
Total RNA was extracted from mouse BMDMs and primary chondrocytes using TRIzol reagent (NR0002, Leagene, China). Chloroform and isopropanol were subsequently added, followed by centrifugation to precipitate the RNA at the bottom. After that, the precipitated RNA was washed with 75% anhydrous ethanol, and upon drying, it was resuspended in RNase-free water to complete the RNA extraction process. For mRNA quantification, reverse transcription was carried out using 5x HiScript II qRT SuperMix II (Vazyme Biotech, Nanjing, China). Each PCR amplification reaction consisted of 10μl 2X ChamQ SYBR qPCR Master Mix (Vazyme), 10μM of both forward and reverse primers, and 500 ng of cDNA.

value: Mus marrow

value: Bone marrow derived macrophages

value: leukocyte

value: WT

value: 500ng/ml CCL7 24h


title: CCL7_500_2,Bone marrow derived macrophages, 500ng/ml CCL7 24h

description: Library name: SAMPLE9


title: Tumor_24, TGFb_vacc_IL6R_block


title: Primary Human CD14+ cells, cg030, biol rep 1

value: cg030 RNP


title: Primary Human CD14+ cells, cg020, biol rep 1


title: Primary Human CD14+ cells, cg019, biol rep 2


title: 18S_H-RF1-T6

description: Library name: Sample 50

value: Hay-diet treatment


title: Tumor_18, TGFb_vacc_IL6R_block


title: reGB1_L2

description:
reGB1 L2 as in manuscript
Bulk-RNA sequencing of a recurrent (relapse) glioblastoma brain tumor Locus 2 (patient sample GB1 in manuscript) extracted from tissue; aiming to capture the transcriptome of the cells composing the tumor immune microenvironment (TiME) of a relapse sample, allowing comparison between primary and recurrent TiME. Also, comparison between L1 and L2 within the same tumor.

value: (patient sample) brain tumor

value: Recurrent [relapse] Glioblastoma Locus 2 brain tumor of patient GB1


title: 18S_G-RF8-T18

description: Library name: Sample 47

value: Grain-diet treatment


title: 18S_G-RF8-T22

description: Library name: Sample 48


title: Tumor_17, TGFb_vacc_IL6R_block


title: Ctrl_3,Bone marrow derived macrophages, control 24h

description: Library name: SAMPLE5

value: control 24h


title: Tumor_14, Untreated

value: Untreated


title: Ctrl_2,Bone marrow derived macrophages, control 24h

description: Library name: SAMPLE3


title: 18S_H-RF1-T10

description: Library name: Sample 51


title: Primary Human CD14+ cells, cg007, biol rep 2

value: Primary CD14+ cells

value: M0 Macrophages

value: adar knockdown

value: cg007 RNP


title: 18S_G-RF8-T10

description: Library name: Sample 45

value: ruminal fluid


title: Tumor_12, Untreated

value: Tumor


title: Ctrl_1,Bone marrow derived macrophages, control 24h

description: Library name: SAMPLE1

value: Mus marrow

value: Bone marrow derived macrophages


title: Primary Human CD14+ cells, cg007, biol rep 1


title: 18S_G-RF8-T6

description: Library name: Sample 44


title: Tumor_11, Untreated


title: 18S_G-RF8-T2

description: Library name: Sample 43


title: Aged_aorta_compound 8.5 ip _2

city: hangzhou

first: yanan

last: liu

address: NO.2318, Yuhangtang Rd, Yuhang District, 311121, Hangzhou, Zhejiang, P.R.China

institute: Hangzhou Normal University

data_processing:
Reads were aligned to mouse genome mm10 by HISAT2, and raw read count of each gene were obtained by featureCounts.
Assembly: mm10
Supplementary files format and content: includes gene count for each Sample

source_name: aorta

growth_protocol: Male C57BL/6J mice were obtained from Beijing Vital River Laboratory Animal Technology (Beijing, China). Mice were placed on a 12:12 h light/dark cycle under SPF facility conditions (7:00 am lights on, 7:00 pm lights off) prior to experiments.

extract_protocol:
Total RNA with the TransZol Up Plus RNA Kit (Cat. No. ER501-01; TransGen Biotech; Beijing, China) was isolated. 1 ug of total RNA was used for the sequencing libraries.
RNA libraries for RNA-seq was prepared using SMARTER mRNA-seq library Prep kit follow manufactuer's protocol

treatment_protocol: 24 (aged) months mice were administered PBS or compound 8.5 (0.25mg / kg / d) intraperitoneally for 3 weeks, followed by the aorta of the mice were used to perform RNA-Seq (sequencing).

value: aorta

value: aged mice

value: ip_compound 8.5


title: CCL7_500_1,Bone marrow derived macrophages, 500ng/ml CCL7 24h

description: Library name: SAMPLE7

value: leukocyte

value: WT

value: 500ng/ml CCL7 24h


title: Tumor_33, IL6R_block


title: Primary Human CD14+ cells, cg019, biol rep 1

value: cg019 RNP


title: Aged_aorta_compound 8.5 ip _1


title: 18S_G-RF7-T22

description: Library name: Sample 42

value: Grain-diet treatment


title: Tumor_5, IL6R_block


title: Aged_aorta_3


title: 13B_62cocultureTC

city: Toronto

first: Laurie

last: Ailles

state: ON

address: 101 College St.

department: Princess Margaret Cancer Centre

institute: University Health Network

data_processing:
Reads were aligned to the human genome using STAR (v 2.6.1c).
Aligned reads were filtered to remove poorly aligned reads and multimappers.
Uniquely aligned reads were counted to exons to generate gene-level expression counts using HTSeq-count.
Raw gene expression was converted to counts per million (CPM)
Assembly: Gencode GRCh38
Supplementary files format and content: tab-delimited raw gene-level counts and counts per million (CPM) in .txt format

growth_protocol: Cal33 was cultured in IMDM (Wisent) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. Cal27 was cultured in DMEM (Wisent) supplemented with 10% FBS and 1% penicillin/streptomycin. CAF lines (ID 6113 and ID 61162) were cultured in IMDM with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Qiagen Rneasy Plus Micro Kit
NEB mRNA stranded library kit at Genome Québec (McGill University)

treatment_protocol: Large numbers of mono- and co-culture spheroids were generated using AggreWellÔ Microwell 24-well plates (StemCell Technologies) according to the manufacturer’s guidelines. Briefly, 900,000 total cells were seeded in IMDM (10% FBS, 1% PenStrep) per well; co-cultures were seeded using 600,000 61137 or 61162 CAFs and 300,000 Cal33gfp+ or Cal27gfp+ cells. The plate was spun down at 100 x g for 3-5 minutes and placed in a humidified 37°C (5% CO2) incubator for 48 hours to allow spheroids to fully form within each microwell.

value: Tongue Squamous Cell Carcinoma

value: Co-cultured with 61137


title: 18S_G-RF8-T14

description: Library name: Sample 46


title: Tumor_2, IL6R_block


title: 11B_37cocultureTC


title: 18S_G-RF7-T18

description: Library name: Sample 41


title: 12B_37cocultureF

value: Carcinoma-Associated Fibroblast

value: Co-cultured with Cal27


title: Primary Human CD14+ cells, cg007, biol rep 3

value: Primary CD14+ cells

value: M0 Macrophages

value: adar knockdown

value: cg007 RNP


title: Aged_aorta_2


title: Tumor_1, IL6R_block

value: Tumor


title: 10B_61162CTL

value: Control


title: LPS_500_3.R1,Bone marrow derived macrophages, 200ng/ml LPS 24h

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low- quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q-p 4 -e100-y-a -m 10 --best --strata.
Reads Per Kilobase ofexon per Megabase oflibrary size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research,2009.In short, exons from all isoforms of a gene were merged to create one meta- transcript. The number ofreads falling in the exons of this meta- transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
The preparation of RNA samples is the first step of transcriptome sequencing. For LPS-induced BMDMs, RNA within the cells is extracted and purified through a sequence of steps including lysis with Trizol, phase separation with chloroform, precipitation with isopropanol, and washing with 75% anhydrous ethanol.
Total RNA was extracted from mouse BMDMs and primary chondrocytes using TRIzol reagent (NR0002, Leagene, China). Chloroform and isopropanol were subsequently added, followed by centrifugation to precipitate the RNA at the bottom. After that, the precipitated RNA was washed with 75% anhydrous ethanol, and upon drying, it was resuspended in RNase-free water to complete the RNA extraction process. For mRNA quantification, reverse transcription was carried out using 5x HiScript II qRT SuperMix II (Vazyme Biotech, Nanjing, China). Each PCR amplification reaction consisted of 10μl 2X ChamQ SYBR qPCR Master Mix (Vazyme), 10μM of both forward and reverse primers, and 500 ng of cDNA.

value: Mus marrow

value: Bone marrow derived macrophages

value: 200ng/ml LPS 24h


title: 4MOSC1 cells, oHSV, 35 Days, sep3

city: wuhan

first: Meng-Jie

last: Zhang

state: hubei

address: No. 237, Luoyu Road, Hongshan District

institute: wuhan university

data_processing:
Illumina NovaSeq 6000
The adapter and low-quality reads were filtered out through cutadapt (version 1.11).
Filtered sequence reads were mapped to NCBI/GCF_000001635.27_GRCm39_genomic.gff.gz
featureCounts (v1.6.0) is used to calculate the number of reads mapped to each gene.
Assembly: GRCm39
Supplementary files format and content: xls file includes counts for each sample

source_name: tumor

growth_protocol: 4MOSC1 cells were cultured in keratinocyte serum-free medium (K-SFM, Gibco-BRL) supplemented with  1% penicillin/streptomycin at 37 °C and 5% CO2. 4MOSC1 cells (2 × 10^6/per mouse) were subcutaneously injected into the dorsal sides ofC57/BL6 mice to construct ectopic OSCC transplantation model.

extract_protocol:
RNA extraction using TRIZOL was performed. All the RNA samples were assessed for their integrity using Qsep400 instrument
To construct RNA libraries with the VAHTS mRNA-seq V8 Library Prep Kit for Illumina, 1 μg of total RNA was used

treatment_protocol: 4MOSC1 tumor-bearing mice were treated with oHSV on day 10, 14,  and 18

value: tumor

value: 4MOSC1 cell

value: murine OSCC cell

value: WT

value: oHSV


title: Aged_aorta_1

value: aorta

value: aged mice


title: 18S_G-RF7-T10

description: Library name: Sample 39

value: ruminal fluid

value: Grain-diet treatment


title: 9B_61137CTL

value: Carcinoma-Associated Fibroblast


title: 18S_G-RF7-T6

description: Library name: Sample 38


title: 14B_62cocultureF

value: Co-cultured with Cal27


title: 4MOSC1 cells, oHSV, 35 Days, sep2


title: LPS_500_1.R1,Bone marrow derived macrophages, 200ng/ml LPS 24h

value: leukocyte


title: 4MOSC1 cells, oHSV, 35 Days, sep1


title: 18S_G-RF6-T22

description: Library name: Sample 36


title: 7A_62cocultureF_2

value: Co-cultured with Cal33


title: EC infection media B

city: Cambridge

first: Rudolf

last: Jaenisch

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

description: Library name: EC infection media B

data_processing:
RNA-seq reads were mapped to GRCh38 (human) reference and SARS-CoV-2 (MN988713.1) genome using STAR aligner
Counts were tabulated for human protein coding genes, lncRNAs (ENSEMBL release 93 annotations) and viral genes (MN988713.1) using featureCounts.
Assembly: GRCh38, ENSEMBL release 93, GenBank MN988713.1
Supplementary files format and content: Raw feature counts per sample as tab delimited text.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Micro Kit
Libraries were prepared using the SMART-Seq  v4 low input RNA kit

value: hPSC derived Endothelial cell

value: Treatment with infection media only (no virus)


title: 18S_G-RF7-T14

description: Library name: Sample 40


title: Ctrl_3.R1,Bone marrow derived macrophages, control 24h

value: Mus marrow

value: Bone marrow derived macrophages

value: control 24h


title: 18S_G-RF6-T18

description: Library name: Sample 35


title: 18S_G-RF7-T2

description: Library name: Sample 37


title: 4MOSC1 cells, control, 35 Days, sep2

value: tumor

value: 4MOSC1 cell

value: Control


title: Ctrl_2.R1,Bone marrow derived macrophages, control 24h

value: WT


title: 6A_62cocultureTC_2

value: Tongue Squamous Cell Carcinoma

value: Co-cultured with 61162


title: 18S_G-RF6-T14

description: Library name: Sample 34

value: ruminal fluid


title: 4MOSC1 cells, control, 35 Days, sep3

value: murine OSCC cell


title: 4MOSC1 cells, control, 35 Days, sep1


title: Ctrl_1.R1,Bone marrow derived macrophages, control 24h


title: 1A_Cal33CTL_2


title: oocytes, SN_rep3

city: Nanjing

first: Jiashuo

last: Li

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

data_processing:
The raw reads were trimmed by trim_galore (V0.6.10) with default parameters to remove adaptors and low-quality bases. Trimmed reads were aligned by using Bismark(50) (V0.24.1) against the mouse reference genome GRCm39 with parameters: --non_directional --bowtie2 –bam --single_end. PCR duplicates were filtered by Deduplicate_bismark with default parameters. Only high-quality reads (MAPQ > 10) were retained for further analysis. The DNA methylation level of individual cytosine sites within the reference genome sequence was determined as the percentage of reads supporting the presence of a methylated cytosine (C). Unless specified, the DNA methylation level of CpG sites within a given sample or region reflects the overall DNA methylation level of that particular sample or region. Given the use of low-input cells, analysis of DNA methylation levels was conducted based on 1X read coverage. Additionally, the DNA methylation level were analyzed by using CGmapTools(51) (V0.1.3).  To identify differentially methylated regions (DMRs), metilene(52) (V 0.2-8) was utilized with default parameters, and genome annotation was carried out using ChIPseeker(53) (V 1.38.0) with parameters: tssRegion=c(-2000,0) downstream Distance=0.
Assembly: GRCm39
Supplementary files format and content: Wig including CG sites methylation values for each sample

source_name: oocyte

extract_protocol:
Collect 20 oocytes into 2.5 μL of Buffer RLT Plus (Qiagen, 1053393) for cell lysis.
The construction of BS-seq libraries was adapted from previously outlined method(47), with some adjustments.Incubate the lysate with 65 μL of CT conversion reagent (Zymo, d5455) for 8 minutes at 98°C, followed by 180 minutes at 65°C. The BS-converted DNA, purified with Agencourt AMPure XP beads, received preamp oligo and 50 U of Klenow exo- polymerase addition for preamplification, which was then subjected to exonuclease I treatment and subsequent preamplification purification. Double-tagged products were generated through PCR with adapter oligo. Finally, the libraries were constructed by a 15-cycle of PCR amplification using Illumina universal indexed primers.

value: oocyte

tag: Stage

value: SN


title: URD4

city: Jerusalem

first: Yaniv

last: Makayes

address: Kalman Ya'Akov Man Street

country: Israel

institute: Hadassah Hebrew University Medical Center

description: Unrestricted diet 4

data_processing:
DNA methylation was analyzed by using sequencing reads from RRBS that were trimmed and quality filtered by trim galore software (v0.3.3), fastQC, and cutadapt, using default parameters for RRBS. Read alignment (genome build mm10) and extraction of single-base resolution methylation levels were carried out by BISMARK v0.13.1.  Percent methylation was calculated for 100 bp tiles with a minimum coverage of 10 CpGs. It should be noted that bisulfite sequencing does not distinguish between 5mC and 5-hmC, which was assumed to be minimal.
Differential methylation analysis was performed using the R methylKit package. CpG sites were tiled using a window and step size of 100, and the tiles were filtered based on a minimum coverage depth of 15 for both treated and control samples. A set of tiles was selected to include at least 3 of 4 treated and 3 of 4 control replicate samples (custom R script). Tiles exhibiting a minimum methylation difference of 10 percent (averaged over samples) and a minimum q-value of 0.01 were selected as the set DMRs.
Assembly: mm10
Supplementary files format and content: all processed data are in methkit format

source_name: Embryonic kidney

growth_protocol: All animal experiments were approved by the Institutional Animal Care and Use Committee of the Hadassah Hebrew University. All mice were housed in the Hebrew University Specific Pathogen–Free Animal Facility Unit. The study utilized CD1 outbred mice, including transgenic mice. Specifically, we used the transgenic mice line Tg(Six2-EGFP/cre) Amc (herein Six2 Cre+/tg). Heterozygous Six2 Cre+/tg embryos were generated by mating male Six2 Cre+/tg  mice (8 to 10 weeks old) with wild-type (WT) CD1 females (8 to 10 weeks old). The day of vaginal plug detection was considered embryonic day 0.5 of pregnancy. Pregnant females were randomly assigned to the different experimental groups. 70% of the average daily intake was provided once daily to the calorie restricted diet (CRD) treated pregnant females. Unrestricted diet (URD)–treated mice were not subjected to any food restriction during pregnancy. On E17.5, pregnant females were euthanized using ketamine/xylazine, followed by cervical dislocation. Kidneys were dissected from all embryos, and no gender-specific analysis was performed.

extract_protocol:
The E17.5 embryonic kidneys were carefully dissected and excised in ice-cold HBSS buffer. Using a surgical scalpel, the kidneys were sliced and chopped into approximately 0.5- to 1-mm pieces on ice. The chopped kidney fragments were then transferred into an HBSS solution supplemented with 1 mg/ml collagenase (11213865001; Sigma-Aldrich) and dispase (D4693-1G; Sigma-Aldrich) and incubated at 37°C for 30 minutes. The cell suspension was filtered through a 40-mm nylon cell strainer (Corning) and washed twice with cold HBSS. Six2 Cre+/tg GFP+ NPCs were isolated by cell flow cytometry-based cell sorting at the Hebrew University Faculty of Medicine Core Facility. For the RRBS analysis, DNA was isolated from FACS-sorted nephron progenitor cells using the Qiagen DNeasy Blood & Tissue Kit (Cat. 69504) following the manufacturer's instructions. Bisulfite conversion of genomic DNA was carried out using the Qiagen Epitect Bisulfite Kit (Cat. 59104), according to the manufacturer's protocol.
. RRBS libraries were prepared using 20 ng of DNA and sequenced on a HiSeq 2500 (Illumina) using 100 bp paired-end sequencing. Samples were distributed across multiple lanes during high-throughput sequencing to minimize batch effects.

value: Embryonic kidney

value: nephron progenitor cells

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos

value: Unrestricted diet (dams)


title: 5A_37cocultureF

value: Carcinoma-Associated Fibroblast

value: Co-cultured with Cal33


title: 18S_G-RF6-T6

city: Yangzhou

first: Yongkang

last: Zhen

address: Yangzhou University

institute: Yangzhou University

description: Library name: Sample 32

data_processing:
For the data processing of rumen microbiomes, raw fastq reads were demultiplexed according to sample-specific barcodes and imported to QIIME2 software (version QIIME2-202402)
The poor-quality bases, adapters and specific primers were trimmed, and the sequences were denoised and binned to amplicon sequence variants (ASVs) using the denoise-paired function of DADA2 plugin for QIIME2.
The feature-classifier plugin was used to construct the specific primer classifiers for the protozoa (316F and 539R of the 18S rRNA gene) based on the SILVA database (version 138). The ASVs were then classified taxonomically based on the specific protozoal classifiers.
The align-to-tree-mafft-fasttree function of the phylogeny plugin was used to construct the phylogenetic trees after the filtering the rare ASVs, and the mitochondria and chloroplast reads. The unweighted unifrac distances for ordination and clustering were calculated using the beta-phylogenetic function of the diversity plugin, and the principal coordinate analysis (PCoA) was performed and visualization by the R software (v4.2) package ggplot2 (v3.4.4).
The alpha diversity parameters (Faith-PD, Chao 1, Shannon, and Simpson) were calculated using the alpha or alpha-phylogenetic function of the diversity plugin. The relative abundance of ruminal protozoa at phylum, family, and genus levels were generated using the relative-frequency function of the feature-table plugin.
Assembly: The V4 region of the eukaryotic 18S rRNA gene was amplified with primers 316F (GCTTTCGWTGGTAGTGTATT) and 539R (CTTGCCCTCYAATCGTWCT).
Supplementary files format and content: 18S_feature_table_with_taxonomy.xlsx, 18S-repset-seqs.fasta

extract_protocol:
Total genomic DNA was isolated from 1 mL of freeze rumen fluid using TIANamp Stool DNA Kit (DP328, Tiangen) according to manufacturer's instruction.
Amplicon sequencing of rumen 18S rRNA sequencing were performed according to Illumina  protocols with all amplicon libraries being sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA) with 250-base-paired end reads.

value: Grain-diet treatment


title: LPS_500_2.R1,Bone marrow derived macrophages, 200ng/ml LPS 24h

value: Mus marrow

value: Bone marrow derived macrophages

value: leukocyte

value: 200ng/ml LPS 24h


title: 4A_37cocultureTC

value: Tongue Squamous Cell Carcinoma

value: Co-cultured with 61137


title: URD3

description: Unrestricted diet 3

treatment_protocol: Pregnant females were randomly assigned to the different experimental groups. 70% of the average daily intake was provided once daily to the calorie restricted diet (CRD) treated pregnant females. Unrestricted diet (URD)–treated mice were not subjected to any food restriction during pregnancy. On E17.5, pregnant females were euthanized using ketamine/xylazine, followed by cervical dislocation. Kidneys were dissected from all embryos, and no gender-specific analysis was performed.


title: 18S_G-RF6-T2

description: Library name: Sample 31

value: ruminal fluid


title: oocytes, SN_rep2


title: 8B_Cal27CTL

value: Control


title: oocytes, SN_rep1

value: oocyte


title: 3A_61162CTL


title: URD1

description: Unrestricted diet 1


title: 2A_61137CTL


title: URD2

description: Unrestricted diet 2


title: 18S_G-RF5-T18

description: Library name: Sample 29


title: oocytes, NSN_rep3

value: NSN


title: oocytes, NSN_rep1


title: CRD4

description: Calorie restricted diet 4

value: Embryonic kidney

value: Calorie restricted diet (dams)


title: 18S_G-RF5-T10

description: Library name: Sample 27


city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

description:
EZH2-mutant DLBCL PDX were grown in NSG mice and treated with either tazemetostat or vehicle for 14 days in vivo. Tumor tissues were isolated from mice at the end of the treatment and put into RNAlater (Thermo) for RNA extraction.
SICER2 peaks
Sample_46_PDX_DLBCL-EZB_tazemetostat_H3K27me3CnR_repl4

data_processing:
H3K27me3 CUT&RUN sequencing results were aligned to a concatenated mm10 and dm6 genome using BWA-MEM and normalized to dm6 spike-in reads using CompChIPseq algorithm.  Peaks were called using SICER2 algorithm.
Assembly: mm10
Supplementary files format and content: bed
Library strategy: CUT&RUN

source_name: Patient derived xenograft

extract_protocol:
CUT&RUN was performed according to EpiCypher CUTANA CUT&RUN protocol.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (#E7645L). Pooled libraries were sequenced using Novaseq 6000 with a target of 10 million paired end reads per sample.

value: Patient derived xenograft

value: tri-methyl-histone H3 (Lys27) (C36B11) rabbit mAb (Cell Signaling #9733)

value: t(14;18) translocation; EZH2Y641F

value: 250 mg/kg tazemetostat PO, BID for 14 days


title: 18S_G-RF5-T14

description: Library name: Sample 28

value: Grain-diet treatment


title: 18S_G-RF5-T22

description: Library name: Sample 30


title: 1A_Cal33CTL


title: 18S_G-RF6-T10

description: Library name: Sample 33


title: CRD2

description: Calorie restricted diet 2

value: nephron progenitor cells

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos


description:
EZH2-mutant DLBCL PDX were grown in NSG mice and treated with either tazemetostat or vehicle for 14 days in vivo. Tumor tissues were isolated from mice at the end of the treatment and put into RNAlater (Thermo) for RNA extraction.
SICER2 peaks
Sample_47_PDX_DLBCL-EZB_tazemetostat_H3K27me3CnR_repl5


title: CRD3

description: Calorie restricted diet 3


title: oocytes, NSN_rep2


description:
EZH2-mutant DLBCL PDX were grown in NSG mice and treated with either tazemetostat or vehicle for 14 days in vivo. Tumor tissues were isolated from mice at the end of the treatment and put into RNAlater (Thermo) for RNA extraction.
SICER2 peaks
Sample_45_PDX_DLBCL-EZB_tazemetostat_H3K27me3CnR_repl3


title: SN_rep1

data_processing:
Adaptors and low-quality bases were removed by using trim_galore (v0.6.10) with default parameters from raw reads. Retained reads were mapped to mouse reference genome (GRCm39) by using HISAT2(54) (v2.2.0) with gencode annotation (vM34). Read quantification was carried out with FeatureCounts(55) (v2.0.6) (parameters: -t exon -g gene_id -Q 10 --primary -s 0 -p --countReadPairs) and normalized to fragments per kilobase of transcript per million mapped (FPKM) values using customized script. To determined differential expression genes, DESeq2(56) (V1.40.1) was used with parameters: foldchange ≥ 1.2, padj < 0.05.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
The zona pellucidae of oocytes were removed with 0.5% pronase E (Sigma). 15 oocytes per sample (3 samples for each group) were lysed and subjected to first strand synthesis.
The transcriptome analysis of GV oocytes was conducted via Smart-seq2, following our previously described methodology(49). 15 oocytes were lysed in 0.2% Triton X-100 containing 80 U RNase Inhibitor. First-strand cDNA synthesis involved the Oligo(dT) VN primer, followed by the 5’TS oligo primer. Subsequently, cDNA amplification was carried out using an ISPCR primer in an 18-cycle PCR and the products underwent purification via VAHTS DNA Clean Beads (Vazyme, N411). Quality control for the amplification products involved measuring cDNA concentration with Qubit 4 and assessing cDNA fragment distribution with Qsep 400. Following this, sequencing libraries were prepared with the TruePrep DNA Library Prep Kit for Illumina (Vazyme, TD503).


title: SN_rep2


title: 18S_G-RF5-T6

description: Library name: Sample 26


title: CRD1

description: Calorie restricted diet 1


title: PDX_DLBCL-EZB_tazemetostat_H3K27me3CnR_repl2

description:
EZH2-mutant DLBCL PDX were grown in NSG mice and treated with either tazemetostat or vehicle for 14 days in vivo. Tumor tissues were isolated from mice at the end of the treatment and put into RNAlater (Thermo) for RNA extraction.
SICER2 peaks
Sample_44_PDX_DLBCL-EZB_tazemetostat_H3K27me3CnR_rep2


title: 18S_G-RF5-T2

description: Library name: Sample 25


title: NSN_rep2


title: 8wk_C57-WT_batch-1_sample-p646c

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

data_processing:
read trimming, alignment, read de-duplication, counting, and quantification using nf-core/rnaseq v3.7 with default parameters
differential gene expression testing using DEseq2 v1.38.0 with batch, age, and genotype as factors in the design formula
batch effect regression and heatmap generation using scanpy v.1.8.1
Assembly: GRCm38
Supplementary files format and content: gene_counts_scaled.tsv is a tab separated value file containing scaled counts for each gene in each sample (as quantified in the nf-core/rnaseq pipeline by salmon). It serves as a ‘raw’ counts table suitable for downstream processing with DEseq2 or similar tools.

source_name: lung

extract_protocol:
AT2 cells were isolated by FACS from dissociated primary mouse lung tissue and sorted into trizol for bulk RNA extraction.
poly-A selection was performed on isolated bulk RNA to enrich for mRNA. Subsequently, enriched mRNA was fragmented and Illumina sequencing adapters were ligated before QC and sequencing.

value: lung

tag: batch


description:
EZH2-mutant DLBCL PDX were grown in NSG mice and treated with either tazemetostat or vehicle for 14 days in vivo. Tumor tissues were isolated from mice at the end of the treatment and put into RNAlater (Thermo) for RNA extraction.
SICER2 peaks
Sample_43_PDX_DLBCL-EZB_tazemetostat_H3K27me3CnR_repl1


title: 18S_G-RF4-T22

description: Library name: Sample 24


title: 8wk_C57-WT_batch-1_sample-p646b


title: 18S_G-RF4-T18

description: Library name: Sample 23