title: RNASEQ_C

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

institute: CNRS

description: RNA-seq

data_processing:
TRIM ADAPTER SEQUENCES + READS FILTERING AND QUALITY CONTROL  Trim Galore version: 0.4.0 cutadapt 1.8.3 FastQC_v0.11.7 python-2.7.2 trim_galore -q 20 -stringency 5 --fastqc_args "--nogroup --outdir ./fastqc/trimmed_fqc" -o ./fastq/trimmed_fq ./fastq/C_1_1_qseq.fastq.gz
READS ALIGNMENT  STAR-2.5.2b   STAR --readFilesCommand zcat --genomeDir ./r6.13 --runThreadN 20 --readFilesIn ./fastq/trimmed_fq/C_1_1_qseq_trimmed.fq.gz --outFileNamePrefix ./SAM/C_1_1_qseq_trimmed --outSJfilterReads Unique
ALIGNED READS FILTERING  samtools-1.3.1   samtools view -bS -F 1540 -q 30 ./SAM/C_1_1_qseq_trimmedAligned.out.sam -o ./BAM/C_1_1_filt.bam
ALIGNED READS SORTING  samtools-1.3.1   samtools sort ./BAM/C_1_1_filt.bam -o ./BAM_Sorted/C_1_1_filt_sort.bam
CONVERT TO BIGWIG FORMAT  python-3.4.3 / deepTools-2.5.3   bamCoverage --bam ./BAM_Sorted/C_1_1_filt_sort.bam --binSize 10 --normalizeTo1x 125464728 -o ./BIGWIG/C_1_1_filt_sort_RPGC.bw
QUANTIFICATION MATRIX OVER GENES  python-3.4.3 / deepTools-2.5.3   computeMatrix scale-regions -S ./BIGWIG/C_1_1_filt_sort.bw -R ./r6.13/TxDb.Dmelanogaster.Ensembl.dm6.bed -bs 10 -m 4000 -a 2000 -b 4000 -out ./PROFIL_MATRIX/GB/C_1_1_filt_sort.out --outFileNameMatrix ./PROFIL_MATRIX/GB/C_1_1_filt_sort.outmatrix
Genome_build: dm6 r6.13
gene reference
http://bioconductor.org/packages/release/data/annotation/html/TxDb.Dmelanogaster.UCSC.dm6.ensGene.html
Supplementary_files_format_and_content: RNA-seq reads coverage

organism: Drosophila melanogaster

source_name: Late embryonic derived S2 cells

growth_protocol: S2 cells were grown in Schneider’s Drosophila medium supplemented with 10% Fetal Bovine Serum (FBS, Sigma) and 1% penicillin/ (GIBCO, Invitrogen).

extract_protocol:
RNA were purified into Trizol.
Tru-seq PolyA RNA-seq

treatment_protocol: S2 cells were treated for RNAi-mediated depletion, T7-driven synthesis of double-stranded RNAs (dsRNA) specific for Mes-4/NSD, Hypb/dSET2 or Luciferase were used. 400 µg of dsRNA were added to 36 millions cells in 10 mL media without FBS following for 2h at 25°C before adding FBS. Depletion was optimized for incubation of 4 days and cells were then harvested.

value: S2 (Schneider 2) cell line

tag: passages


title: Eightweek-old male C57Bl/6J mouse [1.4A-1]

status: Public on Jul 01 2023

type: SRA

city: nanjing

first: Kaiqiang

last: Ye

state: jiangsu

address: NO.2 SiPaiLou, Xuanwu district, Nanjing, Jiangsu Province, China

country: China

institute: Southeast University

library_source: transcriptomic

data_processing:
Clean data were processed by FastQC software (v0.11.4) for quality control (QC) and mapped to the mouse reference genome mm10 using Hisat2 software with default parameters
Reads uniquely mapped to reference were conducted by HTSeq, while counts ˃ 0 or ＞1 were used to calculate the number of genes detected.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Eightweek-old male C57Bl/6J mouse

extract_protocol:
We use LIFT-based isolation method to collect small tissues from section.
Based on Smart-seq2 protocols and standard illumina protocols

tag: tissue

value: brain

tag: strain

tag: Sex

value: male

tag: age

value: 8 weeks

tag: group

value: isolated by a laser device with a current intensity of 1.4A


title: RNASEQ_MES4

country: France

description: RNA-seq

molecule: total RNA

tag: cell line

tag: genotype

value: Mes-4 KD


title: RNASEQ_Hypb

description: RNA-seq

value: HypB KD


title: WT（biol rep 2）

city: Beijing

first: Gu

last: Qianchong

address: No. 3, yard 1, Beichen West Road

institute: Institute of Microbiology, Chinese Academy of Sicences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl script
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1)
Assembly: mm10
Supplementary files format and content: tab-delimited Excel files include RPKM values for each Sample

source_name: Tregs

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparation.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

tag: cell type

value: Tregs

value: WT


title: Eightweek-old male C57Bl/6J mouse [1.2A-4]

value: isolated by a laser device with a current intensity of 1.2A


title: WT, Mock, Rep1

city: Seattle

first: Daphne

last: Avgousti

state: WA

address: 1100 Fairview Avenue North C1-201

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis software v3.4.4, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v2.20.
Sequencing reads were mapped using 2-pass mapping in STAR v2.7.1 to a combined reference of human genome assembly hg38 and HSV1 genome JN555585.1 in conjunction with GENCODE human gene annotation V31 and GCA_000859985.2_ViralProj15217. HSV1 annotated genes were collapsed into non-overlapping transcription units for alignment and expression quantification.
QC was performed using FastQC v0.11.8 and RSeQC v4.0.0 to examine read quality, insert fragment size, read duplication rates, gene body coverage and read distribution in different genomic regions.
Gene-level expression was quantified by counting unstranded paired-end reads using FeatureCounts in Subread v1.6.5.
Differential gene expression were analyzed between genotype groups using Bioconductor package edgeR v3.26.8. Protein-coding and lncRNA genes with low expression were excluded by requiring at least one count per million in at least N samples (N is equal to the number of samples in the smallest group). The filtered expression matrix was normalized by TMM method and subject to significance testing using quasi-likelihood pipeline. Genes were deemed differentially expressed if BH-corrected p-values are less than 0.05.
Assembly: hg38, HSV1 genome JN555585.1
Supplementary files format and content: Both files are in text format containing raw read counts of annotated human or HSV1 genes across samples.

organism: Homo sapiens

source_name: Skin

extract_protocol:
Three biological replicates per time point were obtained by independent infections. Cells were harvested at the indicated times post-infection by trypsinization, washed with PBS and centrifuged at 5000 xg for 2 minutes. The resulting pellets were lysed with TRIzol (Thermo Fisher 15-596-026) and total RNA was harvested according to manufacturer’s instructions. RNAs were then treated with DNase (Qiagen 79254) on RNeasy columns (Qiagen 74104) per manufacturer’s instructions. To improve RNA quality, RNAs were precipitated with 3 volumes ice-cold 96% ethanol (Fisher BP8202500), 1 volume 3 M sodium acetate pH 5.5 (Fisher BP333-500) and 1 µL glycogen (Thermo Fischer R055) overnight at -80 °C. Precipitated RNAs were pelleted at 15,000 xg and 4 °C for 30 min, washed with ice-cold 75% ethanol and spun as above for 10 min. Ethanol was removed and RNAs were resuspended in nuclease-free water in Lo-Bind microcentrifuge tubes (Eppendorf 022-43-102-1).
RNA concentrations were quantified by Nanodrop and their integrity confirmed using the 4200 Tapestation Bioanalyzer system (Agilent). 500 ng of total RNA with an RNA Integrity Number (RIN) greater than 9.5 were used to prepare sequencing libraries with the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina). Library concentrations were measured with Invitrogen Qubit dsDNA HS Assay Kit then analyzed with Agilent High Sensitivity D5000 ScreenTape System and pooled. Libraries were sequenced with 100-bp paired-end reads on an Illumina NovaSeq 6000 SP sequencer at the Fred Hutch Genomics Core Facility.

value: Skin

value: HFF-T

value: Tert-immortalized human foreskin fibroblast

value: wild-type

tag: infection

value: mock

tag: time

value: Mock (no infection)


title: skin, 1h depilation

city: Guangzhou

first: Yang

last: Sun

address: Nanfang Hospital

institute: Nanfang Hospital, Southern Medical University

description: Dorsal skin 1h after depilation

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 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library 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 of reads 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 FPKM values for each Sample.Matrix table with raw gene counts for every gene and every sample.

source_name: skin

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols

value: skin

value: NOD/SCID

tag: treatment

value: Depilation


title: Eightweek-old male C57Bl/6J mouse [1.2A-3]

value: brain

value: male


title: WT（biol rep 1）


title: KO8

city: Tampa

first: Feng

last: Cheng

state: FL

address: 12901 Bruce B Downs Blvd MDC 30

department: Department of Pharmaceutical Science

institute: University of South Florida

description: KO8 mouse Gastrocnemius muscle was excised from the euthanized mice and immediately processed in RNA later and later stored at -80 degree Celsius without RNA later for further processing

data_processing:
RNA-seq data was analyzed by using two open source software programs: TopHat and Cufflinks
Raw reads was mapped to mice GRCm38 genome by using Tophat
Cufflinks quantified genes across WT and KO groups to find differentially expressed genes (q-value <0.05)
Assembly: GRCm38
Supplementary files format and content: FPKMs_allsamples.csv
Supplementary files format and content: Ensembl_gene_id, Gene_Symbol, and FPKM

source_name: Gastrocnemius

extract_protocol:
Total RNA was extracted using RNeasy Mini Plus kit (Qiagen). 1.0-1.5µl of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared by TruSeq Stranded mRNA library prep Kit (Cat#20020595)

value: Gastrocnemius

value: muscle

value: tissue

value: KO

value: No treatment


title: JK2-169-24 RNA-Seq for CRC organoids

city: Madison

first: Dustin

last: Deming

state: WI

address: 1111 Highland Ave., WIMR II, Rm. 6507

department: Hematology-Oncology

institute: University of Wisconsin

description:
Patient-derived colorectal adenocarcinoma
Raw_gene_counts_matrix2.txt

data_processing:
Adapter-trimmed (Skewer v0.1.123; Jiang et al., 2014)
Aligned using Spliced Transcripts Alignment to a Reference (STAR v2.5.3a) software (Dobin, et al., 2013) using ensembl annotation
Expression estimation using RSEM v1.2.31 (RNASeq by Expectation Maximization; Li and Dewey, 2011)
Assembly: Mus musculus GRCm38.p5
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: PCO suspensions were immediately mixed at a 1:1 ratio with Matrigel matrix (Corning). Droplet suspensions were plated and set for three to five minutes at 37°C then least 30 minutes to solidify the matrix andavoid direct interface of PCOs with plastic interface. Plated cultures were overlaid with 450uL of feeding medium of 1:1 advanced DMEM/F12 with 1x Glutamax, 10mM HEPES and 100 U/ml pen/strep combined with WNT3a conditioned media and supplemented with EGF 50ng/ml. Plates were incubated at 37°C in 5% CO2 and medium was replaced every 48-72 hours.

extract_protocol:
Organoids were collected from ~4-6 wells, and washed in 1x sterile PBS, and stored at -80°C as a cell pellet until both DNA and RNA isolation. All RNA samples were collected from triplicate biological replicates at baseline and resistance to EGFRi with persistent growth at 100% physiologic Cmax.
An RNA library was constructed using TruSeq Stranded total RNA with rRNA reduction (Illumina). Quality control was performed by Eukaryote Total RNA electrophoresis using NanoDropOne. The library included 2x150bp paired end reads with sequencing was performed by NovaSeq 6000 using MiSeq NanoCell at UW Biotechnology Center.

treatment_protocol: Following maturation, PCOs were treated with stepwise dose escalation. Cultures were started at 20% physiologic Cmax panitumumab (46ug/ml) and assessed for growth (normalized change in diameter at 96hours). If cultures surpassed ≥20% growth, stepwise dose escalation was repeated with interval increase of 20% Cmax. Time to resistant (TTR) was defined by duration of time from the initiation of dose escalation to persistent growth at 100% Cmax panitumumab (230ug/ml).

value: CRC organoid

value: Panitumumab 230ug/mL

tag: sample type

value: Panitumumab Resistant

value: RASwt/RAFwt


title: PBMC, Input, SOD1

city: Ulm

first: Karin

middle: M

last: Danzer

state: Baden-Wurttemberg

address: University of Ulm Campus, Building N24, R3306 Albert-Einstein-Allee 11

department: Department of Neurology

country: Germany

institute: University of Ulm / DZNE, Ulm

library_source: genomic

data_processing:
The adaptor contamination and overrepresented sequences identified after a round of pre-alignment quality control (FASTQC v0.11.9) were removed using Trim Galore! v0.6.7. All sequencing libraries were confirmed for cross-species contamination that was likely missed at the QC step using FastQ Screen v0.15.2. These refined single-end reads of length 101 bp were then aligned to the human genome (NCBI; GRCh38) using Bowtie v1.3.1 one library at a time with the parameter "-m 1" to retain uniquely mapped reads only.
As post-alignment QC steps, QualiMap v2.2.2 and PreSeq v3.2.0 were used to examine sequencing alignment for biases in the mapping and to estimate the complexity of the libraries, respectively. The R packages ChIPQC v1.20.0 and PhantomPeakQualTools v1.2.2 were used to confirm the quality of the aligned bam files based on the ChIP-seq guidelines by ENCODE consortium. QC-confirmed bam files were subject to "callpeak" sub-command of MACS2 v 2.2.7.1 with the following parameters: -t sample.sam -c input.sam -f SAM -g hs -B --nomodel --extsize 146 --broad --qvalue 0.01 --broad-cutoff 0.01. Considering the ENCODE guidelines, pairwise reproducibility (consistency between two biological replicates) for all samples in a sample group was calculated using IDR v2.0.4.2 while the fraction of all mapped reads that overlap significant peaks was computed using the "featureCounts" command by SubRead v2.0.3.
ChIP-R v1.2.0 was used to combine through a rank-product test multiple experimental replicates from the same condition, and thereby, to generate a set of reproducible peaks per sample group for downstream analysis. To extract shared or unique peak regions by condition (i.e., C9orf72-specific, SOD1-specific, wild type control), the "intersect" command by bedtools v2.30.0 was used. Post peak-calling steps, such as peak annotation and visualization, were performed using the R packages ChIPseeker v1.20.0 and clusterProfiler v3.12.0, respectively.
Tests for over-representation within the scope of functional enrichment were performed using the R package ReactomePA v1.28.0 or EnrichR v29.04.2022. An enrichment analysis was performed to identify target genes and colocalizing factors in the input data set based on the public ChIP-seq peak calls in the ChIP-Atlas dB. STRING v11.5 network analysis was used at a minimal interaction score of 0.400 (and at FET p-value = 1e-03). The TF binding motif analysis and motif enrichments within peak regions were done using RSAT v2018 and HOMER v4.11 ("findMotifs.pl" command) with default parameters against the vertebrate and human backgrounds, respectively. Finally, cytoHubba v1.0.0 was used to predict important nodes and to explore sub-networks in a given network by several topological algorithms.
Assembly: hg38
Supplementary files format and content: broadPeak files were generated using the "callpeak" sub-command of MACS2 v 2.2.7.1 in broad peak mode, considering the H3K27me3 peak topology. Basically, these files are 9-column BED files with the following order of columns: chrom, chromStart, chromEnd, name, score, strand, fold change and significance values.

molecule: genomic DNA

source_name: Blood

growth_protocol: Chromatin isolation from PBMCs was performed using the Chroma Flash Chromatin Isolation and Shearing Kit (Epigentek) according to manufacturer’s introduction. Briefly, PBMCs were cross-linked with 4 % paraformaldehyde for 10 min at RT followed by quenching with 1.25 M Glycine. After washing, cells were lysed for 10 min on ice (buffer provided).

extract_protocol:
The samples were centrifuged at 13,800 x g for 10 min at 4 °C and the supernatant was mixed with chromatin buffer (provided) in a 1:1 ratio. Sheared chromatin was pre-cleared with 1 % BSA blocked protein A and G mag Sepharose Xtra magnetic beads (GE Healthcare) and subsequently incubated overnight at 4 °C on a rotator with antibody-labelled beads (10 µg antibody, H3K27m3 Merck or Chrom Pure Rabbit IgG from Jackson Immuno Research). Beads were washed with buffers of increasing stringency (low salt (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8], 150 mM NaCl) to high salt (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 500 mM NaCl)) and bound chromatin complexes were eluted (100 mM NaHCO3, 1% SDS).
The DNA-antibody bead complex was reverse-crosslinked at 65 °C for 5 h (1300 rpm) and digested with proteinase K for further 2 h at 65 °C (1300 rpm) to remove proteins. Finally, DNA was purified using the ChIP DNA clean and concentrator kit (Zymo research). Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (Illumina) and subjected to single-end sequencing (101 bp) on a HiSeq2500 platform (Illumina).

treatment_protocol: The suspension was mixed and centrifugated at 3,000 x g for 5 min. The pellet was resuspended in extraction buffer (provided), incubated on ice for 10 min and occasionally mixed. The lysate was sonicated in special sonication tubes (Diagenode) on high power settings for 3 runs of 30 min (30 sec on/30 sec off) using a Bioruptor Pico (Diagenode) to cut the DNA into 200 to 500 bp fragments.

value: Blood

value: PBMC

value: Peripheral Blood Mononuclear Cells

value: SOD1 mutation-positive

tag: chip antibody

value: IgG, Chrom Pure by Jackson Immuno Research


title: Bergapten-treated IMQ-challenged mouse back skin 3

city: Shanghai

first: Shengjie

last: Zhu

state: Shanghai Municipality

address: 110 Ganhe Road Hongkou District

institute: Shanghai University of TCM

data_processing:
Trimmomatic was used to filter low-quality data and adapter sequence.(Parameter: Q-score < 20, sequence lenth < 50bp or single-end)
Resulting data were mapped to Genome Reference GRCm39 (http://asia.ensembl.org) using HISAT2 software
Read count extraction and normalization were performed using htseq-count (v0.6.0)
Assembly: GRCm39
Supplementary files format and content: QC_stats.xls  Data passed Quality control
Supplementary files format and content: Readcount.xls Read counts and FPKMs

source_name: Back skin

growth_protocol: SPF Balb/c mice of 6-8 weeks purchased from SHANGHAI SLAC LABORATORY ANIMAL

extract_protocol:
RNA was extracted using RNAiso Plus (TaKaRa 9109) . 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using AMPure XP Reagent and Agilent fragmentation buffer.

treatment_protocol: Shaving

value: Back skin

value: SPF Balb/c

value: 6-8 weeks

value: WT

value: 7-day IMQ Challenging and 2-day Bergapten gel


title: JK2-169-23 RNA-Seq for CRC organoids


title: Eightweek-old male C57Bl/6J mouse [1.2A-2]

value: brain

value: male

value: 8 weeks

value: isolated by a laser device with a current intensity of 1.2A


title: JK2-169-22 RNA-Seq for CRC organoids

value: CRC organoid

value: Panitumumab 230ug/mL


title: PBMC, Input, C9ORF72

value: C9orf72 mutation-positive


title: Eightweek-old male C57Bl/6J mouse [1.2A-1]


title: PBMC, Healthy Control, Rep3

value: Blood

value: wild type

value: H3K27m3, Merck


title: Bergapten-treated IMQ-challenged mouse back skin 2


title: Exon2KO （biol rep 1）

value: Tregs


title: JK2-169-21 RNA-Seq for CRC organoids

value: Base culture

value: RASwt/RAFwt


title: MHV1_D30_AJ_BM_Recovered_aIL6

city: New York

first: Jin-Gyu

last: Cheong

address: 1300 York Avenue

institute: Weill Cornell Medicine

description:
nuclei RNA and genomic DNA fragment
Chromium Single Cell Multiome ATAC + Gene Expression
MHV_BM_progenitor_RNA_norm_count.mtx
MHV_BM_progenitor_metadata.csv

library_source: other

data_processing:
All preprocessing steps were performed by 10X Genomics Cell Ranger ARC software
Assembly: hg38 for human, mm10 for mouse
Supplementary files format and content: h5 file for feature-barcode matrix
Library strategy: MultiomeRNA

molecule: other

source_name: Bone Marrow

extract_protocol:
10X Genomics CG000365
10X Genomics CG000338

value: Bone Marrow

value: mononuclear cell


title: MHV1_D30_AJ_BM_Recovered


title: PBMC, Healthy Control, Rep2

value: PBMC

value: Peripheral Blood Mononuclear Cells


title: IMQ-challenged mouse back skin 3

value: Back skin

value: SPF Balb/c

value: 6-8 weeks

value: WT

value: 7-day IMQ challenging after shaving


title: Bergapten-treated IMQ-challenged mouse back skin 1

value: 7-day IMQ Challenging and 2-day Bergapten gel


title: PBMC, Input, Healthy Control

value: IgG, Chrom Pure by Jackson Immuno Research


title: PBMC, Healthy Control, Rep1

value: Blood


title: JK2-169-19 RNA-Seq for CRC organoids

value: CRC organoid


title: JK2-169-20 RNA-Seq for CRC organoids


title: IMQ-challenged mouse back skin 1


title: MHV1_D30_AJ_BALF_Recovered

description:
nuclei RNA and genomic DNA fragment
Chromium Single Cell Multiome ATAC + Gene Expression
MHV_BALF_RNA_norm_count.mtx
MHV_BALF_metadata.csv

source_name: BAL Fluid

value: BAL Fluid


title: PBMC, ALS, SOD1, Rep1

value: SOD1 mutation-positive

value: H3K27m3, Merck


title: JK2-169-18 RNA-Seq for CRC organoids

value: Panitumumab 230ug/mL

value: Panitumumab Resistant

value: RASwt/RAFwt


title: Vasline-treated mouse back skin 3

value: 7-day vaseline treatment after shaving


title: PBMC, ALS, C9ORF72, Rep3

value: PBMC

value: Peripheral Blood Mononuclear Cells

value: C9orf72 mutation-positive


title: JK2-169-17 RNA-Seq for CRC organoids


title: MHV1_D30_AJ_BALF_Naive

value: mononuclear cell


title: Vasline-treated mouse back skin 2

value: Back skin

value: SPF Balb/c

value: 6-8 weeks

value: WT


title: PBMC, ALS, C9ORF72, Rep2

value: Blood


title: JK2-169-16 RNA-Seq for CRC organoids

value: CRC organoid


title: PBMC, ALS, C9ORF72, Rep1


title: MHV1_D30_AJ_BM_Recovered [MultiomeATAC-seq]

description:
nuclei RNA and genomic DNA fragment
Chromium Single Cell Multiome ATAC + Gene Expression
MHV_BM_progenitor_peaks_norm_count.mtx
MHV_BM_progenitor_metadata.csv

library_source: genomic single cell

data_processing:
All preprocessing steps were performed by 10X Genomics Cell Ranger ARC software
Assembly: hg38 and mm10
Supplementary files format and content: mtx file for peak-barcode count matrix
Supplementary files format and content: bam file for post-sort cells

extract_protocol: 10X Genomics CG000338

value: Bone Marrow


title: Vasline-treated mouse back skin 1


title: JK2-169-15 RNA-Seq for CRC organoids

value: Base culture


title: MHV1_D30_AJ_BM_Recovered_aIL6 [MultiomeATAC-seq]


title: IMQ-challenged mouse back skin 2

value: 7-day IMQ challenging after shaving


title: CSPG4 Crispant Sample 2

city: Doha

first: Sahar

middle: I.

last: Daas

state: Other

address: Sidra Medicine

country: Qatar

institute: Sidra Medicine

data_processing:
Reads were mapped to the Danio rerio GRCz11 (Genome Reference Consortium Zebrafish Build 11), INSDC Assembly GCA_000002035.4, May 2017using STAR_2.6.1d aligner
HTSeq-count (v0.9.1) was used to generate the raw counts.
We used Limma-voom to normalize the raw counts.
Differentially expressed genes (DEGs) between zebrafish CSPG4 model and WT controls were identified as described previously (Unlu, Qi et al. 2020). Data in fastq format were mapped to the zebrafish (Danio rerio) genome assembly GRCz11 (danRer11) [https://www.ncbi.nlm.nih.gov/grc/zebrafish] using STAR_aligner (v2.6.1d) [https://github.com/alexdobin/STAR]. Reads were summarized using Counts (v2.0.0) [http://subread.sourceforge.net/]. Differential expression analysis was performed using the limma package [https://bioconductor.org/packages/release/bioc/html/limma.html], and gene set enrichment analysis (GSEA) was performed using Cluster-Profiler package [https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html].
Assembly: GRCz11
Supplementary files format and content: Gene list Supplemental_Table_2.xls, SPG4_ZF_CRISPANTS_LEX8_Rawcounts.tsv

organism: Danio rerio

source_name: pooled heads

extract_protocol:
mRNA libraries were prepared using Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit according to manufacturer's protocols.
3' mRNA Seq

value: pooled heads

value: CSPG4 sgRNA- Cas9


title: sample 8_PLC/PRF/5 CCDC137-knockdown cells

city: Guang zhou

first: Shuang

last: Tao

address: 2693 Kaichuang Avenue

institute: Sun Yat-sen University

data_processing:
The raw data were processed using an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexities, common RNA families (rRNA, tRNA, snRNA, snoRNA) (http://rfam.sanger.ac.uk/), repeats (http://www.girinst.org/repbase), and sequences <18 nt or >26 nt in length.
The unique sequences that aligned to the known miRNAs sequences in miRBase 22.0 were identified as known miRNA.
miRNA differential expression based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2x2 test
Assembly: ftp://mirbase.org/pub/mirbase/CURRENT/
Supplementary files format and content: xlsx files include the fold changes of miRNA expression in each group

extract_protocol:
RNA was harvested using Trizol reagent (thermofisher, 15596018). Approximately 1 ug of total RNA was used for the construction of sequencing libraries.
TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA)

value: Human Hepatocellular Carcinoma Cells

value: CCDC137 knockdown


title: PBMC, ALS, SOD1, Rep2

value: PBMC

value: SOD1 mutation-positive

value: H3K27m3, Merck


title: CSPG4 Crispant Sample 1


title: JK2-169-14 RNA-Seq for CRC organoids

value: RASwt/RAFwt


title: CSPG4 Control 2

value: wildtype


title: MHV1_D30_AJ_BM_Naive

value: mononuclear cell


title: sample 6_Huh-7 CCDC137-overexpressing cells

value: CCDC137 overexpressing


title: MHV1_D30_AJ_BALF_Recovered [MultiomeATAC-seq]

description:
nuclei RNA and genomic DNA fragment
Chromium Single Cell Multiome ATAC + Gene Expression
MHV_BALF_peaks_norm_count.mtx
MHV_BALF_metadata.csv

value: BAL Fluid


title: MHV1_D30_AJ_BALF_Recovered_aIL6_2


title: sample 7_PLC/PRF/5 control cells

value: control vector


title: MHV1_D30_AJ_BM_Naive [MultiomeATAC-seq]


title: MHV1_D30_AJ_BALF_Recovered_aIL6_2 [MultiomeATAC-seq]


title: sample 5_Huh-7 empty cells

value: empty vector


title: JK2-169-12 RNA-Seq for CRC organoids

value: CRC organoid

value: Panitumumab 230ug/mL

value: Panitumumab Resistant


title: JK2-169-11 RNA-Seq for CRC organoids


title: MHV1_D30_AJ_BALF_Naive [MultiomeATAC-seq]


title: White adipocyte,repite 2, ATAC

city: Nanjing

first: Kai

last: Li

address: #818, East Tianyuan Road

institute: Nanjing Medical University

data_processing:
Alignment by BWA
Filtering by Samtools
Narrow peaks by Macs2
BigWig files by Deeptools bamCoverage
Deseq2 for differential analysis
Assembly: mm10
Supplementary files format and content: BigWig files
Supplementary files format and content: fastq files

source_name: subcutaneous adipose

extract_protocol:
SVF cells were obtained from adipose tissue in the inguinal position of male C57BL/6J mice at 3-4 weeks old. Type I collagenase (2mg/ml, Sigma, SCR103) was preconfigured using DMEM basic medium (Gibco, C11995500BT) containing 2% volume of FBS (Gibco), 100 U/ml penicillin, 100 μg/ml streptomycin, and stored in the dark after removal of bacteria by filtration using a 0.22 μM filter. The volume ratio of collagenase to adipose tissue was maintained at 2:1. Then the adipose pad was cut into pieces to 1mm³ and digested in 37℃ water bath for 1h, during which the tube was reversed and mixed every five minutes. The digested adipocytes were filtered (70 μm), then centrifuged at 1000 rpm for 10 min. After re-suspension with PBS, centrifuge at the same speed and time. DMEM/F-12 (Meilunbio, MA0214) containing 10% FBS (Gibco) and 1% penicillin-streptomycin was used to culture the primary SVF, and then the cells were implanted into the pore plate of appropriate size. The medium was changed 24 h later, and then every 48 h until the cells grew to contact inhibition state.   The plate-fully-covered cells then subjected to differentiation. As for beige adipogenesis, culture medium was added insulin (5μg/ml, sigma, I3536), Dexamethasone (5μM, sigma, D4902), 3,3',5-Triiodo-L-thyronine (T3, 1nM, sigma, T2977), Rosiglitazone (1μM, sigma, R2408), Isobutyl methylxanthine (0.5mM, sigma, I5879). The above differentiation medium were changed 48 h later with medium only containing insulin, T3 and rosiglitazone, and renewed every 48 h. Lipid droplet formation was observed at day 7-8, indicating successful induction of beige adipogenesis.  As for white adipogenesis, insulin (5μg/ml), Dexamethasone (1μM), Isobutyl methylxanthine (0.5mM) were added into the same induction medium. The medium was changed 48 h later, only containing insulin to maintain the differentiation of adipocytes.  Cells were incubated at 37℃ in a suitable atmosphere containing 5% CO2.
Native nuclei were purified from adipocytes，and washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). For ATAC seq,  the Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer's manual. 50,000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen). ATAC Libraries were pooled to a final concentration of 10nM and sequenced paired-end using the Illumina NovaSeq 6000.

value: subcutaneous adipose

value: primary adipocyte

value: adipocyte

value: wild type C57

value: SVF cells isolated from subcutaneous adipose tissue were cultured in vitro and induced to differentiate into white fat and beige fat, respectively. After 7 days, the cells were collected for cell library construction and sequencing


title: NPC-4% DMS-Rep3

city: SINGAPORE

first: Yue

last: Wan

address: 60 Biopolis Street, Genome, #07,

country: Singapore

institute: GIS, A*STAR

description: DMS-MAP sequencing

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequencing reads from DMS-Map library were first processed to remove the first 5 bases using seqtk (version v1.3), collapsed to remove PCR duplicates using BBMap (version 38.60), and trimmed to remove adaptoers using cutadaptor (version 1.12)
The processed reads were then mapped to an in-house reference transcriptome using bowtie (version: 0.12.8)
Only the nucleotides whose reference allele is A or C and the mutation rate is ≤ 20% were considered
Mutation calling was performed using RNA framework (version 2.6.8)
Assembly: GRCh38 based transcriptome
Library strategy: DMS-MAP sequencing

source_name: NPCs derived from H9 cells

growth_protocol: Human ESCs, neural stem cell induction and neuronal differentiation were performed as previously described. Briefly, human embryonic stem cells (H9) were cultured in mTeSRTM1 (#05851, stem cell technologies) medium, in the presence of 1X Supplement (#05852, stem cell technologies). hESC H9 cells were used as Day 0 sample in this manuscript.

extract_protocol:
RNA was extracted by Trizol method
After DMSO or DMS treated RNA were reverse transcribed, the derived DNA was used for library prep by illumina nextra library prep kit

treatment_protocol: Human ESCs and neural precursor cells were treated with DMSO or DMS to probe RNA structure

value: NPCs derived from H9 cells

value: neural precusor cells

value: 4% DMS


title: GW7647 1 uM, rep2

city: Pittsburgh

first: Donghun

last: Shin

address: 3501 5th Ave

institute: University of Pittsburgh

data_processing:
CLC Genomics Workbench v 11.0.3
Trimmed sequence reads were mapped to Denio rerio using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Danio rerio
Supplementary files format and content: TPM
Supplementary files format and content: RPKM

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA (PolyA+) 1-47 following manufacturer's protocols.

value: Liver

tag: developmental stage

value: 15 dpf


title: NPC-4% DMS-Rep2

description: DMS-MAP sequencing


title: GW7647 1 uM, rep1


title: JK2-169-13 RNA-Seq for CRC organoids

value: Base culture

value: RASwt/RAFwt


title: NPC-4% DMS-Rep1

description: DMS-MAP sequencing


title: JK2-169-7 RNA-Seq for CRC organoids


title: DMSO, rep3

value: DMSO


title: CSPG4 Control 1

value: pooled heads

value: wildtype


title: White adipocyte,repite 1, ATAC


title: DMSO, rep2


title: Beige adipocyte,repite 2, ATAC


title: JK2-169-6 RNA-Seq for CRC organoids

value: CRC organoid

value: Panitumumab 230ug/mL


title: JK2-169-5 RNA-Seq for CRC organoids

value: Panitumumab Resistant


title: Beige adipocyte,repite 1, ATAC

value: subcutaneous adipose

value: primary adipocyte


title: JK2-169-8 RNA-Seq for CRC organoids


title: DMSO, rep1


title: NPC-CTRL-Rep2

description: DMS-MAP sequencing


title: JK2-169-4 RNA-Seq for CRC organoids


title: GW7647 1 uM, rep3


title: hECS-CTRL-Rep2

description: DMS-MAP sequencing

source_name: H9 cells

value: H9 cells

value: human embryonic stem cells


title: CL35: ID8 cells

first: Anda

middle: M.

last: Vlad

state: PA

address: 204 Craft Avenue, B403

institute: Magee-Womens Research Institute

data_processing:
Quality control was performed by Fastqc
Perform trimming by trimmomatic, allign the sequence using Hisat2 with Ensembl reference and read count with Hiseq
Genes are filtered by filterByExpr function in the edgeR package with default values of parameters; Genes Krt5, Krt7, Hnf1b, Kash5 and Aldh genes are purposely preserved.
Assembly: grcm38
Supplementary files format and content: comma-separated file of the original count for filtered genes and all samples
Supplementary files format and content: comma-separated files of raw counts for all genes and samples

source_name: ovary

extract_protocol: Qiagen DNA/RNA extraction kit

value: ovary

value: carcinosarcoma


title: JK2-169-10 RNA-Seq for CRC organoids


title: JK2-169-9 RNA-Seq for CRC organoids


title: CL33: KPOSE-AdCre cells

value: KPOSE-AdCre

value: KrasG12D/+  Pten-/-

value: AdCre infection


title: JK2-169-3 RNA-Seq for CRC organoids

value: Base culture


title: PLC/PRF/5 AdGFP rep3

city: chongqing

first: tang

last: ni

address: yixueyuan Road NO.1

institute: Chongqing Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
MapSplice mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: PLC/PRF/5 cells

growth_protocol: PLC/PRF/5 cells were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum, 100 IU penicillin, and 100 mg/ml streptomycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
cDNA Library Construction:  The cDNA libraries were constructed for each pooled RNA sample using the VAHTSTM Total RNA-seq (H/M/R) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: depletion of rRNA and fragmented into 150-200 bp using divalent cations at 94 ℃ for 8 min. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, second-strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads .The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina Xten with 51 plus 7 cycles by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: Adenoviral recombinant AdSLC27A5 was generated using the AdEasy system, and green fluorescent protein-expressing analogous adenovirus (AdGFP) was used as a control.

value: hepatoma cells

value: liver

tag: adenovirus

value: adenovirus with GFP control


title: PLC/PRF/5 AdGFP rep2


title: PLC/PRF/5 AdGFP rep1


title: NPC-CTRL-Rep1

description: DMS-MAP sequencing

value: NPCs derived from H9 cells

value: neural precusor cells

value: DMSO


title: JK2-169-2 RNA-Seq for CRC organoids

value: CRC organoid

value: RASwt/RAFwt


title: hECS-4% DMS-Rep2

description: DMS-MAP sequencing

value: 4% DMS


title: CL32: KPOSE-AdCre cells


title: hECS-CTRL-Rep1

description: DMS-MAP sequencing

value: H9 cells


title: hECS-4% DMS-Rep1

description: DMS-MAP sequencing

value: human embryonic stem cells


title: CL34: ID8 cells

value: ovary


title: CL30: KPOSE cells

value: KPOSE

value: epithelial

value: LSL-KrasG12D (silent) PtenloxP/loxP (silent)


title: PLC/PRF/5 AdSCL27A5 rep3

value: adenovirus overexpression SLC27A5


title: CL31: KPOSE cells


title: JK2-169-1 RNA-Seq for CRC organoids

value: Base culture


title: T265 cell, shNCOR2, rep3

city: Shang hai

first: Yuehua

state: State...

address: Manufacturing Bureau Road, Huangpu District, Shanghai

institute: The Ninth People's Hospital of Medical College of Shanghai Jiaotong University

data_processing:
the Cutadapt tool
Raw paired-end fastq reads were filtered by TrimGaloreto discard the adapters and low quality bases via calling the Cutadapt tool
The clean reads obtained were then aligned to the hg19 human genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie
Differentially expressed geneswere identified by DEseq2 with a cut-off value of log2|fold-change|>1 and p-adjust <0.05.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts and tpm for each gene.

growth_protocol: T265 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extractibn kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample.
High-quality RNA with a 260/280 absorbance ratio of 1.8-2.2 was used for library construction and sequencing. Illumina HiSeq library construction was performed according to the manufacturer's instructions (Illumina,USA).

treatment_protocol: cells were infected with lentivirus vector packaging plasmids containing short hairpin RNA targeting NCOR2 or a random nonsense targeted sequence.

value: schwann cell

value: NCOR2 knockdown


title: sorted_mCh_dark rep 3

city: Berkeley

first: Nicole

middle: Anne

last: Repina

state: CA

address: Stanley Hall

department: Bioengineering

institute: UC Berkeley

data_processing:
Quality of reads was evaluated using the FASTQC tool
Adapter trimming was performed using Fastq-mcf and Cutadapt
Contamination removal using Bowtie2
Paired-end reads were aligned to the reference human genome (GRCh38, Ensemble database) using STAR alignment software
Raw read counts were estimated using HTSeq
Normalization and differential expression analysis were performed with DESeq
Assembly: GRCh38
Supplementary files format and content: csv file includes normalized counts for each sample (DESeq output)

growth_protocol: hESC H9 cells grown in E8 media

extract_protocol:
Cells were lifted with Accutase at 37 ˚C for 5min, centrifuged, and resuspended in TRI reagent (Zymo Research). To achieve higher RNA yields, two to three wells were pooled, constituting a single biological replicate. RNA was purified using an RNA extraction kit (R2051, Zymo Research) as per manufacturer recommendations with an on-column DNase digestion to remove residual genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Cells were kept in dark or illuminated with 0.8 uW/mm2 light for 48 hrs

value: stem cell

value: optoWnt

value: co-culture dark


title: sorted_GFP_dark rep 3

value: WT


title: PLC/PRF/5 AdSCL27A5 rep1

value: hepatoma cells

value: liver


title: PLC/PRF/5 AdSCL27A5 rep2


title: sorted_GFP_dark rep 2


title: T265 cell, shNCOR2, rep1


title: CL28: KOSE-AdCre cells

value: KOSE-AdCre

value: adenocarcinoma

value: AdCre infection


title: Duroc2

first: Siqian

last: Chen

address: 2rd, Yuanmingyuan West Road

department: College of Animal Science and Technology

institute: China Agricultural University

data_processing:
FastQC v 0.11.2 and Trim Galore v 0.4.0 was used to assess the quality of the sequence data and filter low-quality reads (q < 30), respectively. The cleaned data were then mapped to the sscrofa11.1 genomes using bowtie2 under the Bismark software (0.14.5) with default parameters
Duplicated reads were removed using deduplicate_bismark
bismark_methylation_extractor was employed to obtain methyl CpG site information using bismark software
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: CpG report files

organism: Sus scrofa

source_name: Sperm

extract_protocol:
Sperm DNA was extracted using a salt fractionation protocol.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Sperm

tag: breed

value: Duroc


title: CL27: KOSE cells

value: ovary

value: KOSE

value: epithelial

value: LSL-KrasG12D (silent)


title: T265 cell, shNCOR2, rep2

value: schwann cell


title: sorted_GFP_dark rep 1


title: Landrace2

value: Landrace


title: T265 cell, shControl, rep2


title: CL26: KOSE cells


title: CL23: 2F8cis cells

value: carcinosarcoma

value: MUC1+/- KrasG12D/+  Pten-/-

value: Cisplatin resistant


title: Large_White1


title: sorted_mCh_dark rep 1

value: stem cell

value: optoWnt

value: co-culture dark


title: sorted_GFP_light rep 3

value: WT

value: co-culture light


title: CL22: 2F8cis cells


title: Duroc1


title: CL29: KOSE-AdCre cells

value: KOSE-AdCre

value: adenocarcinoma

value: AdCre infection


title: sorted_mCh_light rep 3


title: HDf [snATAC-seq]

description: Chromium Single Cell ATAC

data_processing:
Single Cell ATAC FASTQ files were processed using cellranger-atac
Single Cell ATAC count matrices were processed using Signac.
Signac and Amulet were used to filter out low quality cells and doublets for Single Cell ATAC samples..
The Single Cell ATAC samples were annotated using a predefined PBMC object provided by Seurat.
Genome_build: hg38
Supplementary_files_format_and_content: Peak/Cell Matrix containing raw counts for each sample post QC and Metadata containing annotations for each Single Cell ATAC sample.

source_name: PBMC

extract_protocol:
Nuclei were isolated using 10X Genomics-provided protocol "CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevB".
Library was generated following 10X Genomics-provided protocols; "CG000209_Chromium_NextGEM_SingleCell_ATAC_ReagentKits v1.1_UserGuide_RevF" for snATAC-seq.

value: PBMC

tag: age (in years)

value: Female

tag: clinical status

value: Healthy


title: Landrace1

tag: tissue

value: Sperm


title: sorted_GFP_light rep 2


title: CL18: 2F8 cells

value: ovary


title: sorted_mCh_dark rep 2


title: CL19: 2F8 cells


title: jcov31 [snATAC-seq]

description: Chromium Single Cell ATAC

tag: Sex

value: Male


title: lgtd8m [RNA-seq]

data_processing:
Multiome FASTQ files were processed using cellranger-arc.
Multiome RNA count matrices generated using cellranger were processed using Seurat.
Low Quality Cells were filtered using Seurat and Doublets were filtered using Scrublet for each Multiome RNA sample.
Multiome RNA Samples were merged together using Seurat. Further cells were removed post reduction and clustering for the merged object.
Cells removed during Multiome ATAC processing were also removed from the Multiome RNA object to maintain uniformity.
The Multiome RNA object was annotated using Marker genes and differential analysis was carried out using Seurat.
Genome_build: hg38
Supplementary_files_format_and_content: Gene/Cell Raw count matrix for merged samples post QC for Multiome RNA merged object. Metadata tables for Multiome RNA object.

extract_protocol:
Nuclei were isolated using 10X Genomics-provided protocol "CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevB".
Library was generated following 10X Genomics-provided protocols; "CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User Guide_RevE" for Multiome


title: T265 cell, shControl, rep3

value: schwann cell


title: CL16: MKPOSE2-C2-Trp53-/--IP  cells

value: MUC1+/- , Trp53-/- , LSL-KrasG12D (silent), PtenloxP/loxP (silent)


title: lgtd4m [RNA-seq]


title: CL17: MKPOSE2-C2-Trp53-/--IP  cells


title: sorted_mCh_light rep 2


title: Cox10-/- regenerating liver, H3K27Ac ChIP-seq, replicate 3

city: Dallas

first: Prashant

last: Mishra

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Reads were aligned against the mm10 reference genome with BWA (version 0.7.5).
Peak calling was performed using MACS14 using option -nomodel and p-value cutoff of 1e-5.
Bigwig files were generated from mapped reads using bamCoverage from deeptools (version 3.5.0) using a 10bp binsize and a smooth length of 50bp.
Assembly: mm10
Supplementary files format and content: bw

growth_protocol: Animals were maintained on standard chow diet, ad libitum, under a standard 12 hr light-dark cycle.

extract_protocol:
Minced livers were crosslinked in 1% formaldehyde in PBS, and then quenched with 125mM glycine for 10minutes at room temperature. The tissue was then dounced in cold PBS, filtered through a 40uM cell strainer and washed with cold PBS. Chromatin was sonicated to approximatley 500bp, mixed with spike-in chromatin (Active Motif 61686), and incubated with primary antibody (Abcam ab4729) and spike-in anitbody (Active Motifi 61686) overnight at 4C. The mixture was incubated with protein A/G Dynabeads for 3hr at 4C. After washing, chromatin was eluted in 1% SDS buffer, followed by reverse crosslinking at 65C overnight. Pulldown DNA was incubated with RNaseA and proteinase K for 2 hr, and then purified with QIAquick spin column (Qiagen, 28004).
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina Kit (NEB, #E7645S) following the manufacturer's instructions.

treatment_protocol: AAV8-GFP or AAV8-Cre (5x10^10 GC, once) was adminstered by retroorbital injection to mice containing the Cox10-floxed conditional allele. Four weeks later, mice were subjected to a 70% partial hepatectomy protocol. Two days after partial hepatectomy, regenerating livers were dissected for further analysis.

value: Liver

value: Day 2 post partial hepatectomy

tag: antibody


title: Cox10-/- regenerating liver, H3K27Ac ChIP-seq, replicate 2


title: sorted_GFP_light rep 1

value: stem cell


title: Large_White2

city: Beijing


title: lgtd19 [RNA-seq]


title: CL15: MKPOSE2-C2-Trp53-/- cells

value: epithelial


title: sorted_mCh_light rep 1

value: optoWnt


title: Cox10-/- regenerating liver, input, replicate 3

value: Input


title: M121224, Talazoparib and Encorafenib, replicate 3

city: Geneva

first: Phil

middle: Fang

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

data_processing:
Raw reads were trimmed with skewer v0.2
Filtered reads were then aligned to GRCh38 using STAR v2.7.5
Gene quantification was performed with GeneCounts from STAR
Assembly: GRCh38
Supplementary files format and content: tab delimited text file with raw counts for each sample by column and genes by row

source_name: Skin metastasis

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit
TruSeq RNA library Prep Kit v2

value: Skin metastasis

value: melanoma cell culture

value: BRAF V600E

value: Encorafenib and Talazoparib


title: lgtd18 [RNA-seq]

value: PBMC


title: lgtd17 [RNA-seq]

value: Healthy


title: CL14: MKPOSE2-C2-Trp53-/- cells


title: T265 cell, shControl, rep1

value: WT


title: M121224, Talazoparib and Encorafenib, replicate 2


title: Cox10-/- regenerating liver, input, replicate 2


title: Cox10-/- regenerating liver, input, replicate 1


title: M121224, Talazoparib and Encorafenib, replicate 1


title: CL13: MKPOSE2-C2 cells

value: ovary

value: MUC1+/-LSL-KrasG12D (silent) PtenloxP/loxP (silent)


title: jcov93 [RNA-seq]

value: Male


title: wild-type regenerating liver, H3K27Ac ChIP-seq, replicate 3

value: wild-type


title: M121224, Talazoparib  replicate 3

value: Talazoparib


title: CL12: MKPOSE2-C2 cells


title: wild-type regenerating liver, H3K27Ac ChIP-seq, replicate 2

value: Liver

value: Day 2 post partial hepatectomy


title: M121224, Talazoparib  replicate 2


title: jcov72_5 [RNA-seq]

value: Female


title: wild-type regenerating liver, H3K27Ac ChIP-seq, replicate 1


title: jcov92 [RNA-seq]


title: Cox10-/- regenerating liver, H3K27Ac ChIP-seq, replicate 1


title: jcov69_8 [RNA-seq]


title: CL11: MOSE-Trp53-/--IP  cells

value: adenocarcinoma


title: jcov60_6 [RNA-seq]


title: CL9: MOSE-Trp53-/-  cells

value: epithelial


title: wild-type regenerating liver, input, replicate 3

value: Input


title: CL8: MOSE-Trp53-/-  cells


title: M121224, Talazoparib  replicate 1

value: Skin metastasis

value: melanoma cell culture


title: M121224, Encorafenib, replicate 3

value: BRAF V600E

value: Encorafenib


title: wild-type regenerating liver, input, replicate 2


title: CL10: MOSE-Trp53-/--IP  cells


title: M121224, Encorafenib, replicate 2


title: jcov56_9 [RNA-seq]

value: PBMC


title: wild-type regenerating liver, input, replicate 1


title: M121224, Encorafenib, replicate 1


title: CL6: MOSE cells

value: MOSE


title: jcov49_2 [RNA-seq]


title: C/B TSC Airn truncation clone 10 rep2 EZH2 calibrated ChIP

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Rd

department: Pharmacology

institute: UNC Chapel Hill

description: WIG files contain spike-in-normalized counts; mm9-aligned MAPQ>=30 reads were multiplied by 1/h, where h = hg19-aligned reads.

data_processing:
ChIP-Seq reads were aligned using bowtie2 with default parameters (Langmead and Salzberg 2012).
For all ChIP-Seq analyses in this study, reads that had a mapping quality greater than or equal to 30 were extracted with Samtools, and allele-specific read retention (i.e., reads that overlap at least one B6 or CAST SNP) was performed as in (Calabrese et al. 2012; Calabrese et al. 2015; Schertzer et al. 2019a) using a custom perl script (intersect_reads_snps16.pl: see github).
Assembly: All mouse reference NCBI build 37/mm9 genome annotations were obtained from the UCSC genome browser (Lee et al. 2022). Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/; (Keane et al. 2011). The CAST/EiJ (CAST) pseudogenome creation was performed as in (Calabrese et al. 2012; Calabrese et al. 2015; Schertzer et al. 2019a).
Supplementary files format and content: Wiggle density files were created using a custom perl script (bigbowtie_to_wig3_mm9.pl; see github). Where indicated, the WIG file includes reads pooled from the two or more biological replicates.

source_name: F1-hybrid C/B trophoblast stem cells

growth_protocol: TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco, cat #: 11875093], 20% qualified FBS [Gibco, cat #: 26140079], 0.1mM penicillin-streptomycin [Gibco, cat #: 15140122], 1mM sodium pyruvate [Gibco, cat #: 11360070], 2mM L-glutamine [Gibco, cat #: 25030081], 100uM beta-mercaptoethanol [Sigma-Aldrich, cat #: 63689]) supplemented with 25ng/mL FGF4 (Gibco, cat #: PHG0154) and 1ug/mL Heparin (Sigma-Aldrich, cat #: H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco, cat #: 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate, and then cultured for three days in 70% irMEF-conditioned TSC media supplemented with growth factors as above. Mouse E14 ESCs were cultured on gelatin-coated plates in ESC media (DMEM high glucose and sodium pyruvate [Gibco, cat #: 11995073], 15% qualified FBS, 0.1mM MEM non-essential AA [Gibco, cat #: 11140050], 0.1mM penicillin-streptomycin, 2mM L-glutamine, 100M beta-mercaptoethanol, 1:500 LIF [ESC media conditioned with Lif-1Cα/COS cells]) at 37°C in a humidified incubator with 5% CO2. At passage, ESCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution for ~5 minutes at room temperature and dislodged from the plate at single-cell suspension.  ESCs were passaged every other day and provided fresh media daily.

extract_protocol:
For all ChIP DNA elution steps, washed beads were resuspended in Elution buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) and placed on a 65°C heat block for 17 minutes with frequent vortexing. RAD21 ChIP DNA was eluted for 1 hour under the same conditions. ChIP DNA was then reverse crosslinked in 0.5% SDS and 100mM NaCl overnight at 65°C, followed by a 1-hour RNaseA (3uL; Thermo Scientific, cat #: EN0531) treatment at 37°C and a 2.5-hour Proteinase K (10uL; Invitrogen, cat #: 25530015) treatment at 56°C. DNA was then extracted with 1 volume of phenol:chloroform:isoamyl alcohol (Sigma-Aldrich, cat #: P3803) and precipitated with 2 volumes 100% ethanol, 1/10 volume 3M sodium-acetate pH 5.4, and 1/1000 volume linear acrylamide (Invitrogen, cat #: AM9520) overnight at -20°C. Precipitated DNA was then extracted with a 30-minute max speed spin at 4°C, washed once with 80% ethanol, and resuspended in TE.
ChIP-Seq libraries were prepared with NEBNext End Repair Module (NEB, cat #: E6050S), A-tailing by Klenow Fragment (3’--5’ exo-; NEB, cat #: M0212S), and TruSeq 6-bp index adaptor ligation by Quick ligase (NEB, cat #: M2200S), and NEBNext High-Fidelity 2X PCR Master Mix (NEB, cat #: M0541S). All DNA clean-up steps were performed with AMPure XP beads (Beckman Coulter, cat #: A63880). Single-end, 75-bp sequencing was performed using an Illumina NextSeq 500/550 High Output v2.5 kit (Illumina, cat #: 20024906) on a NextSeq 500 System.

treatment_protocol: Prior to crosslinking for ChIP, ESCs were induced with 1ug/mL doxycycline for 4 days and TSCs were passaged once off of irMEFs. For all ChIP experiments, except those for PRC components, adhered cells were crosslinked with 0.6% formaldehyde (Fisher Scientific, cat #: BP531-500) in RPMI media with 10% FBS for 10 minutes at room temperature, then quenched with 125mM glycine for 5 minutes at room temperature. Crosslinked cells were then washed twice with ice-cold PBS and scraped with ice-cold PBS with 0.05% Tween (Fisher Scientific, cat #: EW-88065-31) and PIC (Sigma Aldrich, cat #: P8340). The cells were then spun at 1,200 x g at 4°C to remove PBS, followed by resuspension in ice-cold PBS with PIC and divided into 10-million cell aliquots. For PRC component ChIPs, adhered C/B TSCs were crosslinked in PBS with 2mM DSG (disuccinimidyl glutarate; Thermo Scientific, cat #: 20593) for 45 minutes at room temperature and then in PBS with 1% formaldehyde (Thermo Scientific, cat #: 28906) for 15 minutes at room temperature. Crosslinking was quenched with 200mM glycine for 5 minutes at room temperature. Cells were then washed, scraped, and aliquoted as above.

value: F1-hybrid C/B trophoblast stem cells

tag: parent of_origin

value: CAST/EiJ mother X C57BL/6J father

tag: passage number

value: Airn Truncation

value: Ezh2 (D2C9) XP ® (Cell Signaling, cat #:5246)


title: jcov42 [RNA-seq]

value: Male


title: C/B TSC Airn truncation clone 10 rep1 EZH2 calibrated ChIP

tag: cell line

tag: genotype


title: C/B TSC Dox-treated Airn-gRNA TRE-dCas9-VP160 rep 2 EZH2 calibrated ChIP

value: Airn Highly-Expressing


title: CL4: M3230-IP cells

value: ovary

tag: cell type

value: MUC1+/- PtenloxP/loxP (silent)


title: M121224, DMSO, replicate 2

value: DMSO


title: CL7: MOSE cells

value: epithelial


title: jcov42_20 [RNA-seq]


title: jcov21 [RNA-seq]


title: C/B TSC Dox-treated Airn-gRNA TRE-dCas9-VP160 rep 1 EZH2 calibrated ChIP


title: M121224, DMSO, replicate 1


title: M111031, Talazoparib and Encorafenib, replicate 3

source_name: Lymph node metastasis

value: Lymph node metastasis

value: Encorafenib and Talazoparib


title: CL2: MPOSE-AdCre cells

value: MPOSE-AdCre

value: MUC1+/-  Pten-/-

value: AdCre infection


title: CL3: MPOSE-AdCre cells


title: CL5: M3230-IP cells

value: adenocarcinoma


title: M121224, DMSO, replicate 3

value: Skin metastasis

value: melanoma cell culture

value: BRAF V600E


title: M111031, Talazoparib and Encorafenib, replicate 2


title: M111031, Talazoparib and Encorafenib, replicate 1


title: jcov124 [RNA-seq]

value: PBMC

value: Female

value: nonCoV


title: C/B TSC EZH2 calibrated ChIP

value: F1-hybrid C/B trophoblast stem cells

value: CAST/EiJ mother X C57BL/6J father

value: Wildtype

value: Ezh2 (D2C9) XP ® (Cell Signaling, cat #:5246)


title: jcov127 [RNA-seq]


title: C/B TSC Airn truncation clone 10 H3K27me3 calibrated ChIP

value: Airn Truncation

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) (H3K27me3) (Cell Signaling, cat #:9733)


title: M_JC-A-A

city: Saint Louis

first: Pan

last: Ma

state: United States

address: CSRB, Room 9918, 425 S Euclid, Saint Louis, MO, 63110

institute: Washington University in Saint Louis

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Alignment: Cell Ranger V3, aligned to mm10 transcriptome, or custom pre-mrna reference.
QC and Filtering: Seurat V3/V4
Unsupervised Clustering: Seurat V3/V4
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
Heart tissue from wide type mice were minced with a razor blade and transferred into a 15 ml conical tube containing DMEM with Collagenase I (450 U/ml), DNAse I (60 U/ml), and Hyaluronidase (60 U/ml) and incubated at 37°C for 1 hour with agitation. Digestion was then stopped by addition of HBB buffer (2% FBS, 0.2% BSA in HBSS) and filtered through a 40 μm filter into 50 mL conical, transferred to a clean 15ml conical and centrifuged at 350 x G for 5 minutes at 4°C. Supernatant was then removed and pellet resuspended in 1 mL ACK lysing buffer (Gibco, A10492) and incubated at room temperature for 5 minutes followed by the addition of 9 mL DMEM. Suspension was then centrifuged at above conditions, followed by removal of supernatant, and resuspension in 5 mL FACS buffer (2% FBS, 2mM EDTA in calcium/magnesium free PBS). Centrifugation was repeated at above conditions, supernatant removed, and pellet resuspended in 300uL cell resuspension buffer (0.04% BSA in 1X PBS) and 1uL each of CD45 (Thermo Scientific, 46162251) and DAPI (BD Biosciences, 564907) and allowed to incubate 5 minutes before sorting CD45+/DAPI- cells were collected in cell resuspension buffer. Collected cells were then recentrifuged according to above parameters and resuspended in cell resuspension buffer to a target concentration of 1000 cells/μL. Cells were counted on a hemocytometer and concentration adjusted as necessary.
10X Genomics Chromium Single Cell 5’ Reagent V1.1

value: heart

value: CD45+DAPI- alive cells

tag: technology

value: Single Cell


title: jcov52 [RNA-seq]


title: C/B TSC Dox-treated Airn-gRNA TRE-dCas9-VP160 H3K27me3 calibrated ChIP

value: Airn Highly-Expressing


title: M111031, Talazoparib  replicate 3

last: Cheng

value: Lymph node metastasis

tag: treatment

value: Talazoparib


title: C/B TSC H3K27me3 calibrated ChIP


title: jcov122 [RNA-seq]

value: Male


title: M_JC-L5-L5

description:
Single Cell
10x Genomics

data_processing:
Alignment: Cell Ranger V3, aligned to GRCh38 transcriptome, or custom pre-mrna reference.
QC and Filtering: Seurat V3/V4
Unsupervised Clustering: Seurat V3/V4
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Heart tissue from Ctla4+/-Pdcd1-/- and Ctla4+/+Pdcd1-/- mice were minced with a razor blade and transferred into a 15 ml conical tube containing DMEM with Collagenase I (450 U/ml), DNAse I (60 U/ml), and Hyaluronidase (60 U/ml) and incubated at 37°C for 1 hour with agitation. Digestion was then stopped by addition of HBB buffer (2% FBS, 0.2% BSA in HBSS) and filtered through a 40 μm filter into 50 mL conical, transferred to a clean 15ml conical and centrifuged at 350 x G for 5 minutes at 4°C. Supernatant was then removed and pellet resuspended in 1 mL ACK lysing buffer (Gibco, A10492) and incubated at room temperature for 5 minutes followed by the addition of 9 mL DMEM. Suspension was then centrifuged at above conditions, followed by removal of supernatant, and resuspension in 5 mL FACS buffer (2% FBS, 2mM EDTA in calcium/magnesium free PBS). Centrifugation was repeated at above conditions, supernatant removed, and pellet resuspended in 300uL cell resuspension buffer (0.04% BSA in 1X PBS) and 1uL each of DRAQ5 (Thermo Scientific, 46162251) and DAPI (BD Biosciences, 564907) and allowed to incubate 5 minutes before sorting DRAQ5+/DAPI- cells were collected in cell resuspension buffer. Collected cells were then recentrifuged according to above parameters and resuspended in cell resuspension buffer to a target concentration of 1000 cells/μL. Cells were counted on a hemocytometer and concentration adjusted as necessary.
10X Genomics Chromium Single Cell 5’ Reagent V1.1

value: DRAQ9+DAPI- alive cells


title: M111031, Talazoparib  replicate 2

value: melanoma cell culture

value: BRAF V600E


title: jcov119 [RNA-seq]

value: PBMC

value: Female

value: nonCoV


title: jcov117 [RNA-seq]


title: M_JC-L4-L4

description:
Single Cell
10x Genomics

value: DRAQ8+DAPI- alive cells


title: C/B TSC JARID2 biol rep 3

description: Replicates were averaged to generate the wiggle files and downstream analysis .

value: F1-hybrid C/B trophoblast stem cells

value: CAST/EiJ mother X C57BL/6J father

value: Wildtype

value: JARID2 (D6M9X) (Cell Signaling, cat #:13594)


title: jcov115 [RNA-seq]


title: M111031, Encorafenib, replicate 3

value: Encorafenib


title: M_JC-L3-L3

description:
Single Cell
10x Genomics

value: heart

value: DRAQ7+DAPI- alive cells


title: C/B TSC JARID2 biol rep 2


title: CL1: MPOSE cells

value: ovary

value: MPOSE

value: epithelial

value: MUC1+/- PtenloxP/loxP (silent)


title: M111031, Encorafenib, replicate 2

value: Lymph node metastasis

value: melanoma cell culture


title: C/B TSC JARID2 biol rep 1


title: jcov114 [RNA-seq]

value: PBMC

value: Male


title: M111031, Encorafenib, replicate 1

value: BRAF V600E


title: C/B TSC MTF2 biol rep 2

value: MTF2 (Proteintech, cat #:16208-1-AP)


title: M_JC-L1-L1

description:
Single Cell
10x Genomics

value: DRAQ5+DAPI- alive cells


title: C/B TSC MTF2 biol rep 1

value: F1-hybrid C/B trophoblast stem cells

value: CAST/EiJ mother X C57BL/6J father


title: M111031, DMSO, replicate 3

value: DMSO


title: YS005

city: NEW YORK

first: Robert

middle: F

last: Schwabe

state: NY

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

institute: Columbia University

description: PROJECT ID- 191108_ROBERT_YOSHINOB_10_MOUSE_RNA_STRDPOLYA_20M_PE100_NOVASEQ

data_processing:
For Bulk RNA-seq, 20M paired-end 100bp sequencing was performed using the Illumina NovaSeq 6000
HTVI of EF1a TAZS89A + CCl4 treated liver samples were normalized with  control normal livers (n=3), and then performed DEseq2 analysis between TAZS89A + CCl4 and contorl group
Assembly: mm10
Supplementary files format and content: text files includeTPM values for each Sample

source_name: HTVI of EF1a-TAZS89A +CCl4 x 30 times (three times a week for 10 weeks) in C57BL/6J

extract_protocol:
After euthanising the mice according to animal protocol, we collected the liver and make it into pieaces for analysis. RNA was isolated using Roche High pure RNA extraction kit or QIAGEN RNeasy mini kit accoring to the manual protocol.
We use poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry.
Libraries are then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.

value: liver

value: Wild type


title: YS004

value: CCl4 x 30 times  (three times a week for 10 weeks)


title: M111031, DMSO, replicate 2


title: YS003


title: C/B TSC EZH2 biol rep 2

value: Wildtype

value: Ezh2 (D2C9) XP ® (Cell Signaling, cat #:5246)


title: C/B TSC EZH2 biol rep 1


title: jcov101 [RNA-seq]


title: jcov110 [RNA-seq]


title: YS002


title: jcov101_2 [RNA-seq]


title: C/B TSC KDM2B biol rep 2

value: Anti-JHDM1B (Sigma-Aldrich, cat #:09-864)


title: HDv [RNA-seq]

value: Female

value: Healthy


title: M_JC-L2-L2

description:
Single Cell
10x Genomics

value: heart

value: DRAQ6+DAPI- alive cells


title: M111031, Talazoparib  replicate 1

value: Lymph node metastasis

value: melanoma cell culture

value: Talazoparib


title: HDu [RNA-seq]

value: PBMC

value: Male


title: HDj [RNA-seq]


title: C/B TSC KDM2B biol rep 1

value: F1-hybrid C/B trophoblast stem cells

value: CAST/EiJ mother X C57BL/6J father


title: C/B TSC RYBP biol rep 3

value: Anti-DEDAF (Sigma-Aldrich, cat #:AB3637)


title: ICC CTRL2

description:
PROJECT ID- 190905_ROBERT_SILVIA_11_MOUSE_RNA_STRDPOLYA_20M_PE100_NOVASEQ
GSM4794833

source_name: C57BL/6J control

value: liver

value: Wild type

value: no treatment


title: YS001

value: CCl4 x 30 times  (three times a week for 10 weeks)


title: ICC CTRL3

description:
PROJECT ID- 190905_ROBERT_SILVIA_11_MOUSE_RNA_STRDPOLYA_20M_PE100_NOVASEQ
GSM4794834


title: ICC CTRL1

description:
PROJECT ID- 190905_ROBERT_SILVIA_11_MOUSE_RNA_STRDPOLYA_20M_PE100_NOVASEQ
GSM4794832


title: HD_AD [RNA-seq]


title: jcov111 [RNA-seq]


title: C/B TSC RYBP biol rep 1

value: Wildtype


title: lgtd8m [MultiomeATAC-seq]

data_processing:
Multiome FASTQ files were processed using cellranger-arc.
Multiome ATAC count matrices were processed using Signac.
Signac and Amulet were used to filter out low quality cells and doublets for Multiome ATAC samples.
Multiome ATAC samples were merged using Signac. Further cells were removed post reduction and clustering for the merged object.
Cells removed during Multiome RNA processing were also removed from the Multiome ATAC object to maintain uniformity.
The Multiome ATAC object was annotated using the Multiome RNA annotated object and differential analysis was carried out using Signac.
Genome_build: hg38
Supplementary_files_format_and_content: Peak/Cell Raw count matrix for merged samples post QC for Multiome ATAC object. Metadata tables for Multiome ATAC object.

extract_protocol:
Nuclei were isolated using 10X Genomics-provided protocol "CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevB".
Library was generated following 10X Genomics-provided protocols; "CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User Guide_RevE" for Multiome.


title: HDa [RNA-seq]

value: Female


title: lgtd4m [MultiomeATAC-seq]


title: M111031, DMSO, replicate 1

value: BRAF V600E

value: DMSO


title: C/B TSC CBX7 biol rep 3

value: Anti-cbx7 (Abcam, cat #:ab21873)


title: PLX3AP_2

first: Xiaoyang

state: Jiangsu

address: No.163, Xianlin Avenue, Qixia District

department: School of life sciecne

institute: Nanjing University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters.
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software
The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach.
The expression level of each gene was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: mm10
Supplementary files format and content: comma-delimited csv files include raw count for each Sample
Supplementary files format and content: comma-delimited csv files include TPM for each Sample

source_name: 3-AP treated mice after PLX3397 microglia depletion

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). RNA degradation and contamination was monitored on 1% agarose gels. Then RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥8.0, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA).

value: Cerebellum

value: 3-AP after PLX3397


title: PLX3AP_3


title: PLX3AP_1


title: C/B TSC CBX7 biol rep 2


title: lgtd19 [MultiomeATAC-seq]

first: Jin-Gyu

address: 1300 York Avenue

institute: Weill Cornell Medicine

value: Healthy


title: C/B TSC CBX7 biol rep 1


title: 3AP_3

source_name: 3-AP treated mice


title: lgtd18 [MultiomeATAC-seq]

value: PBMC


title: 3AP_2


title: C/B TSC RING1B biol rep 3

value: RING1B (D22F2) XP® (Cell Signaling, cat #:5694)


title: lgtd17 [MultiomeATAC-seq]

value: Male


title: C/B TSC RING1B biol rep 2

value: F1-hybrid C/B trophoblast stem cells

value: CAST/EiJ mother X C57BL/6J father


title: jcov93 [MultiomeATAC-seq]


title: C/B TSC RYBP biol rep 2

value: Anti-DEDAF (Sigma-Aldrich, cat #:AB3637)


title: C/B TSC RING1B biol rep 1


title: control_3

source_name: Control

value: Saline


title: jcov92 [MultiomeATAC-seq]


title: control_2


title: C/B TSC T-gRNA-Cas9 clone 6 H2AK119ub

value: T CGI CRISPR-deletion

value: Ubiquityl-Histone H2A (Lys119) (D27C4) XP® (H2AK119ub1) (Cell Signaling, cat #:8240)


title: jcov72_5 [MultiomeATAC-seq]


title: C/B TSC Cluster-gRNA-Cas9 clone 7 H2AK119ub

value: SMC1A/CT F Cluster CRISPR-deletion


title: C/B TSC Cluster-gRNA-Cas9 clone 4 H2AK119ub


title: C/B TSC Pde10a-gRNA-Cas9 clone 28 HiC library

description:
delta-pde_merged_mm9-B6.hic.gz
delta-pde_merged_mm9-CAST.hic.gz

data_processing:
Hi-C reads were aligned using BWA as a part of the Juicer pipeline (Durand et al. 2016a).
For all Hi-C analyses in this study, read pairs that had a mapping quality greater than or equal to 10 were used. For allele-specific retention of Hi-C contacts, read pairs in which at least one read end overlaps a B6/CAST SNP were extracted from the Juicer output merged_nodups.txt file using a modified Juicer diploid script.
Assembly: All mouse reference NCBI build 37/mm9 genome annotations were obtained from the UCSC genome browser (Lee et al. 2022). Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/; (Keane et al. 2011). The CAST/EiJ (CAST) pseudogenome creation was performed as in (Calabrese et al. 2012; Calabrese et al. 2015; Schertzer et al. 2019a).
Supplementary files format and content: HIC files of allele-specific Hi-C contacts; files are generated from merged biological replicate/clone data.

growth_protocol: TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco, cat #: 11875093], 20% qualified FBS [Gibco, cat #: 26140079], 0.1mM penicillin-streptomycin [Gibco, cat #: 15140122], 1mM sodium pyruvate [Gibco, cat #: 11360070], 2mM L-glutamine [Gibco, cat #: 25030081], 100uM beta-mercaptoethanol [Sigma-Aldrich, cat #: 63689]) supplemented with 25ng/mL FGF4 (Gibco, cat #: PHG0154) and 1ug/mL Heparin (Sigma-Aldrich, cat #: H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco, cat #: 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate, and then cultured for three days in 70% irMEF-conditioned TSC media supplemented with growth factors as above.

extract_protocol: Arima-HiC+, performed according to manufacturer instruction.

treatment_protocol: Prior to crosslinking for Hi-C, TSCs were passaged once off of irMEFs as described above. TSCs were then trypsinized and washed once with PBS. 5-10 million cells were crosslinked in resuspension with 10mL of 1% formaldehyde (Thermo Scientific, cat #: 28906) in PBS solution for 10 minutes at room temperature, quenched with 200mM glycine for 5 minutes at room temperature, and then washed twice with ice-cold PBS. Cells were then divided into 5 aliquots (1-2 million cells/aliquot), where one aliquot was used for each Hi-C experiment. Importantly, for the removal of all PBS washes and crosslinking solution, cells were spun at 160 x g for 5 minutes.

value: Pde10a CGI CRISPR-Cas9 deletion


title: C/B TSC Slc22a3-gRNA-Cas9 clone 13 HiC library

description:
delta-slc_merged_mm9-B6.hic.gz
delta-slc_merged_mm9-CAST.hic.gz

value: Slc22a3 CGI CRISPR-Cas9 deletion


title: control_1


title: jcov60_6 [MultiomeATAC-seq]


title: C/B TSC T-gRNA-Cas9 clone 1 H2AK119ub


title: C/B TSC Pde10a-gRNA-Cas9 clone 28 H2AK119ub

value: Pde10a CGI CRISPR-deletion


title: jcov52 [MultiomeATAC-seq]

value: Female


title: C/B TSC Slc22a3-gRNA-Cas9 clone 13 H2AK119ub

value: Slc22a3 CGI CRISPR-deletion


title: jcov56_9 [MultiomeATAC-seq]


title: C/B TSC Pde10a-gRNA-Cas9 clone 5 HiC library


title: jcov49_2 [MultiomeATAC-seq]


title: jcov42 [MultiomeATAC-seq]


title: C/B TSC Pde10a-gRNA-Cas9 clone 5 H2AK119ub


title: C/B TSC Slc22a3-gRNA-Cas9 clone 12 H2AK119ub


title: C/B TSC NTG-gRNA-Cas9 clone 12 H2AK119ub

value: NTG CRISPR-deletion


title: C/B TSC NTG-gRNA-Cas9 clone 1 HiC library

description:
ntg_merged_mm9-B6.hic.gz
ntg_merged_mm9-CAST.hic.gz

value: NTG CRISPR-Cas9 deletion


title: C/B TSC NTG-gRNA-Cas9 clone 12 HiC library


title: jcov42_20 [MultiomeATAC-seq]

value: PBMC


title: SE_psmDhldecpA_3KO_3

city: La Jolla

first: Michael

middle: R

last: Williams

address: 9500 Gilman Drive

department: Dermatology

institute: UC San Diego

data_processing:
Fastqc-->STAR-->featurecounts-->Rstudio (EdgeR)
Assembly: Gencode GrCh38.p13
Supplementary files format and content: excel workbork files

source_name: nHEK

growth_protocol: nHEK cells were maintained in Epilife medium (60uM CaCl2) supplemented with human keratnocyte growth supplement (HKGS)  and antibiotic/antimycotic in humidified atmosphere with 5% CO2 at 37C. Used between passages 3-5.

extract_protocol:
mRNA was harvested using Purelinke RNA Mini kit.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep Kit following manufacturer's protocols.

treatment_protocol:
10uM of synthetic S. epidermidis or S. aureus PSMS were applied to 70% confluent (48h 2mM CaCl2 differentiated) nHEKs for 6h.
PSM peptide dissolved in DMSO and treated at final concentraiton of 0.1% on nHEK cells.

value: nHEK

value: 1e7 CFU/cm2 S. epidermidis 1457  psmDhldecpA_3KO

tag: time


title: SE_psmDhldecpA_3KO_2


title: jcov127 [MultiomeATAC-seq]


title: C/B TSC T-gRNA-Cas9 clone 47 H3K27me3

value: F1-hybrid C/B trophoblast stem cells

tag: chip antibody

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) (H3K27me3) (Cell Signaling, cat #:9733)


title: C/B TSC NTG-gRNA-Cas9 clone 1 H2AK119ub

value: CAST/EiJ mother X C57BL/6J father


title: jcov21 [MultiomeATAC-seq]

value: Male


title: C/B TSC T-gRNA-Cas9 clone 42 H3K27me3

value: T CGI CRISPR-deletion


title: jcov122 [MultiomeATAC-seq]

value: nonCoV


title: C/B TSC T-gRNA-Cas9 clone 6 H3K27me3


title: C/B TSC Slc22a3-gRNA-Cas9 clone 12 HiC library


title: SE_ecpA_KO_3

value: 1e7 CFU/cm2 S. epidermidis 1457 ecpA_KO


title: SE_ecpA_KO_1


title: C/B TSC T-gRNA-Cas9 clone 1 H3K27me3


title: jcov69_8 [MultiomeATAC-seq]


title: jcov115 [MultiomeATAC-seq]


title: C/B TSC Cluster-gRNA-Cas9 clone 7 H3K27me3

value: SMC1A/CT F Cluster CRISPR-deletion


title: C/B TSC Cluster-gRNA-Cas9 clone 4 H3K27me3


title: SE_psmDhld_2KO_3

value: 1e7 CFU/cm2 S. epidermidis 1457 psmDhld_2KO


title: SE_psmDhld_2KO_2


title: jcov114 [MultiomeATAC-seq]


title: C/B TSC Pde10a-gRNA-Cas9 clone 28 H3K27me3

value: Pde10a CGI CRISPR-deletion


title: jcov117 [MultiomeATAC-seq]

value: Female


title: SE_psmDhld_2KO_1


title: C/B TSC Slc22a3-gRNA-Cas9 clone 13 H3K27me3

value: Slc22a3 CGI CRISPR-deletion


title: C/B TSC Pde10a-gRNA-Cas9 clone 5 H3K27me3


title: jcov110 [MultiomeATAC-seq]


title: jcov124 [MultiomeATAC-seq]


title: C/B TSC Slc22a3-gRNA-Cas9 clone 12 H3K27me3


title: SE_psmDhldecpA_3KO_1


title: jcov111 [MultiomeATAC-seq]


title: SE_WT_2

value: 1e7 CFU/cm2 S. epidermidis 1457 WT


title: SE_WT_1


title: jcov119 [MultiomeATAC-seq]


title: C/B TSC NTG-gRNA-Cas9 clone 12 H3K27me3

value: NTG CRISPR-deletion


title: SE_ecpA_KO_2


title: jcov101_2 [MultiomeATAC-seq]

value: PBMC


title: Ctl_3

value: nHEK

value: Control Tryptic Soy Broth Medium Only


title: C/B TSC NTG-gRNA-Cas9 clone 8 H3K27me3

value: F1-hybrid C/B trophoblast stem cells


title: HDv [MultiomeATAC-seq]

value: Healthy


title: C/B TSC NTG-gRNA-Cas9 clone 4 H3K27me3

value: CAST/EiJ mother X C57BL/6J father

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) (H3K27me3) (Cell Signaling, cat #:9733)


title: HDj [MultiomeATAC-seq]

value: Male


title: C/B TSC NTG-gRNA-Cas9 clone 1 H3K27me3


title: Ctl_2


title: WT207_2

city: hangzhou

first: Hu

last: Wang

state: zhejiang

address: yuhangtang road

institute: Hangzhou normal university

data_processing:
get raw data
Use fatstp (version 0.22.0) for quality control and data filtering
Sequence alignment (reference genome mm10)
Counting with featureCounts v2.0.1
Assembly: mm10
Supplementary files format and content: count_data.txt

source_name: bone marrow

extract_protocol:
Mouse HSCs were directly lysed and used for cDNA synthesis using the SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech, 634936).
After amplification, the cDNA samples were fragmented using a Covaris M220 sonicator (Covaris). Sequencing libraries were made with the fragmented cDNA using NEBNext Ultra DNA Library Prep Kit for Illumina according to manufacturer’s instructions (New England Biolabs, E7370).

treatment_protocol: HSC sorted from ythdc1 ko mice and wild type mice.

value: bone marrow

tag: strain

value: HSC

value: wild type cells


title: E14 ESC Dox Airn-gRNA TRE-dCas9-VP160 H3K27me3

source_name: E14 embryonic stem cells

value: E14 embryonic stem cells

value: Airn Highly-Expressing ESCs


title: WT207_1


title: HDa [MultiomeATAC-seq]

city: New York

last: Cheong

value: Female


title: jcov101 [MultiomeATAC-seq]


title: E14 ESC Untreated Airn-gRNA TRE-dCas9-VP160 H3K27me3

value: ESCs


title: WT180_2


title: WT180_1


title: E14 ESC Untreated Airn-gRNA TRE-dCas9-VP160 Airn CHART

data_processing:
CHART-Seq reads were aligned using bowtie2 with default parameters (Langmead and Salzberg 2012).
For all CHART-Seq analyses in this study, reads that had a mapping quality greater than or equal to 30 were extracted with Samtools, and allele-specific read retention (i.e., reads that overlap at least one B6 or CAST SNP) was performed as in (Calabrese et al. 2012; Calabrese et al. 2015; Schertzer et al. 2019a) using a custom perl script (intersect_reads_snps16.pl: see github).
Assembly: All mouse reference NCBI build 37/mm9 genome annotations were obtained from the UCSC genome browser (Lee et al. 2022). Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/; (Keane et al. 2011). The CAST/EiJ (CAST) pseudogenome creation was performed as in (Calabrese et al. 2012; Calabrese et al. 2015; Schertzer et al. 2019a).
Supplementary files format and content: Wiggle density files were created using a custom perl script (bigbowtie_to_wig3_mm9.pl; see github). Where indicated, the WIG file includes reads pooled from the two or more biological replicates.
Library strategy: CHART-Seq

growth_protocol: TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco, cat #: 11875093], 20% qualified FBS [Gibco, cat #: 26140079], 0.1mM penicillin-streptomycin [Gibco, cat #: 15140122], 1mM sodium pyruvate [Gibco, cat #: 11360070], 2mM L-glutamine [Gibco, cat #: 25030081], 100M -mercaptoethanol [Sigma-Aldrich, cat #: 63689]) supplemented with 25ng/mL FGF4 (Gibco, cat #: PHG0154) and 1g/mL Heparin (Sigma-Aldrich, cat #: H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco, cat #: 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate, and then cultured for three days in 70% irMEF-conditioned TSC media supplemented with growth factors as above.

extract_protocol:
CHART-Seq libraries were prepared with NEBNext End Repair Module (NEB, cat #: E6050S), A-tailing by Klenow Fragment (3’--5’ exo-; NEB, cat #: M0212S), and TruSeq 6-bp index adaptor ligation by Quick ligase (NEB, cat #: M2200S), and NEBNext High-Fidelity 2X PCR Master Mix (NEB, cat #: M0541S). All DNA clean-up steps were performed with AMPure XP beads (Beckman Coulter, cat #: A63880). Single-end, 75-bp sequencing was performed using an Illumina NextSeq 500/550 High Output v2.5 kit (Illumina, cat #: 20024906) on a NextSeq 500 System.
Capture Hybridization Analysis of RNA Target DNA sequencing (CHART-Seq)

treatment_protocol: CHART was performed as in the detailed protocol from (Davis and West 2015). TSCs were passaged once off of irMEFs as above. Airn Highly-Expressing TSCs from (Schertzer et al. 2019a) and ESCs were induced with 1g/mL doxycycline 4 days prior to crosslinking. Adhered TSCs and ESCs were crosslinked with 1% formaldehyde (Fisher Scientific, cat #: BP531-500) in PBS solution for 10 minutes at room temperature. On ice, cells were washed twice with ice-cold PBS and twice with ice-cold PBS + 0.05% Tween before being scraped, spun at 1,000 x g for 5 minutes at 4°C, and divided into 25-million cell aliquots.

value: ESC


title: PLC_EV_4

first: Yan

last: Liang

address: 9500 Gilman Drive, BRFII Room 1220 Bay B

data_processing:
Sequenced reads were processed using STAR, htseq-count, and DESeq2.
genome build: hg19
Supplementary_files_format_and_content: h5 files with raw counts for every gene and every cell; raw counts

source_name: PLC cells (liver cancer cell line)

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit.
Ribo-depleted total RNA library prep

treatment_protocol: Cells were treated with MEK inhibitor

tag: cell line/type

value: PLC (liver cancer cell line)

tag: cell/sample type

value: extracellular vesicle


title: 3AP_1

value: Cerebellum


title: KO209_2

value: Ythdc1 KO cells


title: PLC_EV_1


title: PLC_EV_3


title: WT178_1


title: C/B Airn Truncation TSC Airn CHART biol rep 2

value: F1-hybrid C/B trophoblast stem cells

value: C/B Airn Truncation TSC


title: C/B Airn Truncation TSC Airn CHART biol rep 1

value: CAST/EiJ mother X C57BL/6J father


title: PLC_EV_2


title: C/B TSC Dox Airn-gRNA TRE-dCas9-VP160 Airn CHART biol rep1

value: C/B Airn Highly-Expressing TSC


title: WT178_2


title: KO209_1


title: PLC_whole_cell_4

value: whole cells


title: KO177_2

value: bone marrow


title: PLC_CD133_2

value: CD133+ vesicle


title: Ctl_1

value: nHEK

value: Control Tryptic Soy Broth Medium Only


title: C/B TSC Airn CHART biol rep 2

value: C/B Wildtype TSC


title: KO176_1

value: HSC


title: PLC_whole_cell_2


title: PLC_whole_cell_3


title: KO176_2


title: C/B TSC Airn CHART biol rep 1


title: PLC_whole_cell_1


title: PLC_CD133_1


title: SE_WT_3

value: 1e7 CFU/cm2 S. epidermidis 1457 WT


title: E14 ESC Dox Airn-gRNA TRE-dCas9-VP160 Airn CHART

value: Airn Highly-Expressing ESC


title: HDu [MultiomeATAC-seq]

value: PBMC

tag: age (in years)

value: Male

value: Healthy


title: C/B TSC Cluster-gRNA-Cas9 clone 7 RNA

description:
Ribo-depleted RNA
delta-cluster_avg_rna_negative.wig.gz
delta-cluster_avg_rna_positive.wig.gz

data_processing:
RNA-Seq reads were aligned using STAR with default parameters (Dobin et al. 2013).
For all RNA-Seq analyses in this study, reads that had a mapping quality greater than or equal to 30 were extracted with Samtools, and allele-specific read retention (i.e., reads that overlap at least one B6 or CAST SNP) was performed as in (Calabrese et al. 2012; Calabrese et al. 2015; Schertzer et al. 2019a) using a custom perl script (intersect_reads_snps16.pl: see github).
Strand-specific reads were separated using samtools: samtools view -Sq 30 (negative) -F 0x10 or (positive) -f 0x10
Assembly: All mouse reference NCBI build 37/mm9 genome annotations were obtained from the UCSC genome browser (Lee et al. 2022). Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/; (Keane et al. 2011). The CAST/EiJ (CAST) pseudogenome creation was performed as in (Calabrese et al. 2012; Calabrese et al. 2015; Schertzer et al. 2019a).
Supplementary files format and content: Wiggle density files were created using a custom perl script (bigbowtie_to_wig3_mm9.pl; see github). The WIG file includes reads pooled from the two or more biological clones.

growth_protocol: TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco, cat #: 11875093], 20% qualified FBS [Gibco, cat #: 26140079], 0.1mM penicillin-streptomycin [Gibco, cat #: 15140122], 1mM sodium pyruvate [Gibco, cat #: 11360070], 2mM L-glutamine [Gibco, cat #: 25030081], 100uM beta-mercaptoethanol [Sigma-Aldrich, cat #: 63689]) supplemented with 25ng/mL FGF4 (Gibco, cat #: PHG0154) and 1ug/mL Heparin (Sigma-Aldrich, cat #: H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco, cat #: 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate, and then cultured for three days in 70% irMEF-conditioned TSC media supplemented with growth factors as above. For RNA isolation, TSCs were passaged once off of irMEFs as above onto a single well of a 6-well plate.

extract_protocol:
ESCs were grown to >75% confluency prior to RNA harvest using 1mL TRIzol, followed by the addition of 200uL chloforom, which were vortexed and subsequently spun at max speed for 5 minutes at 4°C for phase separation. The aqueous layer was collected and combined with 1 volume of 100% isopropanol and 5uL linear acrylamide. Precipitation was achieved at -80°C  for 1 hour, followed by a max speed spin for 30 minuttes at 4°C and one wash of the RNA pellet with ice-cold 80% ethanol. The pellet was then resuspended in 100uL pico H2O and quantified via Qubit (Invitrogen, cat #: Q32855).
RNA-Seq libraries were prepared from 1ug of total RNA using KAPA RNA HyperPrep Kit with Ribose Erase (Kapa Biosystems, cat #: KR1351) according to the manufacturer instructions. Single-end, 75-bp sequencing was performed using an Illumina NextSeq 500/550 High Output v2.5 kit on a NextSeq 500 System.

value: SMC1A/CT F Cluster CRISPR-deletion


title: KO177_1

value: Ythdc1 KO cells


title: C/B TSC Dox Airn-gRNA TRE-dCas9-VP160 Airn CHART biol rep2

value: F1-hybrid C/B trophoblast stem cells


title: HFD_6

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: csv of RPKM normalized read counts for each detected gene

source_name: Ear

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: Ear

value: T regulatory cells

value: Pparg-Tdt Foxp3-thy1.1

value: HFD for 16 weeks


title: C/B TSC Cluster-gRNA-Cas9 clone 4 RNA

value: CAST/EiJ mother X C57BL/6J father


title: HD_AD [MultiomeATAC-seq]

tag: clinical status


title: HFD_3

tag: tissue


title: C/B TSC Pde10a-gRNA-Cas9 clone 5 RNA

description:
Ribo-depleted RNA
delta-pde_avg_rna_negative.wig.gz
delta-pde_avg_rna_positive.wig.gz

value: Pde10a CGI CRISPR-deletion


title: C/B TSC Slc22a3-gRNA-Cas9 clone 13 RNA

description:
Ribo-depleted RNA
delta-slc_avg_rna_negative.wig.gz
delta-slc_avg_rna_positive.wig.gz

value: Slc22a3 CGI CRISPR-deletion


title: JK2-78-32 RNA-Seq for CRC organoids

city: Madison

first: Dustin

last: Deming

address: 1111 Highland Ave., WIMR II, Rm. 6507

institute: University of Wisconsin

data_processing:
Adapter-trimmed (Skewer v0.1.123; Jiang et al., 2014)
Aligned using Spliced Transcripts Alignment to a Reference (STAR v2.5.3a) software (Dobin, et al., 2013) using ensembl annotation
Expression estimation using RSEM v1.2.31 (RNASeq by Expectation Maximization; Li and Dewey, 2011)
Genome_build: Mus musculusGRCm38.p5 (assembly accession GCA_00001635.7)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Colorectal Cancer Organotypic culture

growth_protocol: PCO suspensions were immediately mixed at a 1:1 ratio with Matrigel matrix (Corning).Droplet suspensions were plated and set for three to five minutes at37°C then least 30 minutes to solidify the matrix andavoid direct interface of PCOs with plastic interface. Plated cultures were overlaid with 450uL of feeding medium of 1:1 advanced DMEM/F12 with 1x Glutamax, 10mM HEPES and 100 U/ml pen/strep combined with WNT3a conditioned media and supplemented with EGF 50ng/ml. Plates were incubated at 37°C in 5% CO2 and medium was replaced every 48-72 hours.

extract_protocol:
Organoids were collected from ~4-6 wells, and washed in 1x sterile PBS, and stored at -80°C as a cell pellet until both DNA and RNA isolation. All RNA samples were collected fromin triplicate biological replicates at baseline and resistance to EGFRi with persistent growth at 100% physiologic Cmax.
An RNA library was constructed using TruSeq Stranded total RNA with rRNA reduction (Illumina). Quality control was performed by Eukaryote Total RNA electrophoresis using NanoDropOne. The library included 2x150bp paired end reads with sequencing was performed by NovaSeq 6000 using MiSeq NanoCell at UW Biotechnology Center.

treatment_protocol: Following maturation, PCOs were treated with stepwise dose escalation.  Cultures were started at 20% physiologic Cmax panitumumab (46ug/ml) and assessed for growth (normalized change in diameter at 96hours). If cultures surpassed ≥20% growth, stepwise dose escalation was repeated with interval increase of 20% Cmax. Time to resistant (TTR) was defined by duration of time from the initiation of dose escalation to persistent growth at 100% Cmax panitumumab (230ug/ml).

value: Panitumumab 230ug/mL

tag: sample type

value: Panitumumab Resistant


title: C/B TSC Slc22a3-gRNA-Cas9 clone 12 RNA


title: JK2-78-33 RNA-Seq for CRC organoids


title: NCD_6

value: NCD for 16 weeks


title: NCD_5


title: JK2-78-30 RNA-Seq for CRC organoids


title: C/B TSC NTG-gRNA-Cas9 clone 12 RNA

description:
Ribo-depleted RNA
ntg_avg_rna_negative.wig.gz
ntg_avg_rna_positive.wig.gz

value: NTG CRISPR-deletion


title: NCD_3


title: C/B TSC NTG-gRNA-Cas9 clone 8 RNA


title: Skin.Tregs.PA.3

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: tab delimited text file of RPKM normalized read counts for each detected gene

source_name: Skin

growth_protocol: cells were cultured in the presence of 2000 U/ml recombinant human IL-2 and 20 ng/ml IL-33 in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: cells were cultured with 300uM BSA-conjugated palmitic acid or BSA alone for 3 days and live Tregs were sorted for library preperation

value: Skin

value: 300 uM BSA-conjugated Palmitic acid


title: JK2-78-29 RNA-Seq for CRC organoids


title: JK2-78-28 RNA-Seq for CRC organoids


title: C/B TSC NTG-gRNA-Cas9 clone 4 RNA


title: JK2-78-27 RNA-Seq for CRC organoids


title: Skin.Tregs.PA.2


title: C/B TSC NTG-gRNA-Cas9 clone 1 RNA


title: JK2-78-26 RNA-Seq for CRC organoids


title: C/B TSC Pde10a-gRNA-Cas9 clone 28 RNA


title: Skin.Tregs.BSA.3

value: 300 uM BSA


title: HFD_5


title: Skin.Tregs.PA.1


title: siMCs-FRESH

city: Zurich

first: Tomas

last: Valenta

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

institute: University of Zurich

data_processing:
The nf-core/rnaseq bioinformatics pipeline version 3.5 [doi: https://doi.org/10.1101/610741] was used for subsequent read processing. Individual steps included removal of sequencing adapters and low-quality reads with Trim Galore! (www.bioinformatics.babraham.ac.uk/projects/trim_galore) and quantification of gene expression with Salmon [doi: https://doi.org/10.1038/nmeth.4197] using GRCm39 reference [doi: https://doi.org/10.1093/nar/gkaa1077]. Estimated expression per gene served as input for differential expression analysis using the DESeq2 R Bioconductor package [doi: https://doi.org/10.1186/s13059-014-0550-8]. Genes exhibiting a minimum absolute log2 fold change of 1 (|log2| FC ≥ 1) and statistical significance (adjusted p-value < 0.05) between the compared sample groups were considered differentially expressed.
Assembly: GRCm39 reference
Supplementary files format and content: BMPs_normcounts.csv: ;-delimited file containing normalized gene expression for each sample
Supplementary files format and content: TGFb_normcounts.csv: ;-delimited file containing normalized gene expression for each sample
Supplementary files format and content: MCs_normcounts.csv: ;-delimited file containing normalized gene expression for each sample

source_name: Small intestinal mesenchyme

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen 74004), DNAseI treatment was included
Sequencing libraries were prepared from total RNA using the KAPA mRNA Hyperprep Kit, , followed by size distribution analysis in the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent)

value: Small intestinal mesenchyme

value: Pdgfra positive mesenchymal cells

value: Mesenchymal cells

value: Untreated (control)


title: JK2-78-31 RNA-Seq for CRC organoids


title: Skin.Tregs.BSA.1

value: T regulatory cells


title: Skin.Tregs.BSA.2

value: Pparg-Tdt Foxp3-thy1.1


title: JK2-78-23 RNA-Seq for CRC organoids


title: TGFbeta-II

source_name: Small intestinal epithlelium

value: Small intestinal epithlelium

value: Small intestinal organoids

value: Epithelilal cells

value: recombinant Tgfb, 500 ng/ml, 24 h


title: TGFbeta-III