title: VM108_Primary ccRCC

description: Library name: VM44

source_name: Primary ccRCC

value: Primary ccRCC


title: sWAT_3_Control

status: Public on May 06 2025

type: SRA

city: Iowa city

first: Bhagirath

last: Chaurasia

state: Iowa

address: 431 Newton Road

country: USA

institute: University of Iowa

description: Library name: sWAT_Sample 3

library_source: transcriptomic

data_processing:
Salmon was used for mapping and quantifying the expression of transcripts from RNA-seq data.
FastQC and MultiQC were used to check the quality of RNA sequencing data
Differential gene expression analysis was performed on the raw counts after removing the samples with zero counts using the DESeq2 (version 1.38.3)
Assembly: mm32
Supplementary files format and content: Comma Separated Values (CSV) file for FPKM of each sample

molecule: total RNA

organism: Mus musculus

source_name: Subcutaneous white adipose tissue

extract_protocol:
RNA was extracted from the adipose tissue (epididymal white, subcutaneous and brown adipose) using Qiagen RNAeasy mini kit.
1 ug of RNA was used for constructing sequencing libraries. Sequencing was performed by Illumina HiSeq2000 with 50 cycle single/paired end sequencing

tag: tissue

value: Subcutaneous white adipose tissue

tag: genotype

value: WT


title: sWAT_1_Fgf13_Ko

description: Library name: sWAT_Sample 4

value: Fgf13 KO


title: Combo1-NR-2

type: RNA

city: Kyoto

first: Kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

country: Japan

institute: Graduate School of Medicine, Kyoto University

description: post-treatment

hyb_protocol: cRNA was hybridized to Clariom D Assay human array (Thermofisher), washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with median polish summarization and quantile normalization by Thermo Fisher Expression Console 1.4.1 software, and obtained normalized intensity values.

label: biotin

organism: Homo sapiens

source_name: Peripheral blood, CD8+ sorted

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit (ThermoFisher) according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.

value: Blood

tag: cell type

value: PBMC CD8+T cells

tag: phenotype

value: NR

tag: treatment

value: nivolumab and bezafibrate

tag: time

value: post-treatment


title: Combo2-NR-1

description: pre-treatment

value: untreated

value: pre-treatment


title: Cas9 A2-CAR Treg, donor 1151

city: Vancouver

first: Megan

middle: K

last: Levings

state: BC

address: 938 W 28th Ave

country: Canada

institute: BC Children's Hospital Research Institute

description: Library name: 51-Cas9

data_processing:
Sequencing data was demultiplexed using llumina's BCL Convert.
The de-multiplexed read sequences were then aligned to the Homo sapiens (hg38 no Alts, with decoys) reference sequence and a custom exogenous IL10 sequence using the DRAGEN RNA pipeline.
Immunoglobulin gene segments, pseudo genes, sex-linked genes (Y-chromosome & Xist), and genes aligned to virally-inserted sequences (CAR, tNGFR, and tCD19) were filtered out as well as genes with < 10 counts across samples.
Differential expression analysis was performed using DESeq2 in R.
Gene annotation was obtained by AnnotationDbi package and visualization with ggplot2, RColorBrewer, pheatmap and EnhancedVolcano.
Assembly: Homo sapiens (hg38 no Alts, with decoys) reference sequence and a custom exogenous IL10 sequence.
Supplementary files format and content: Excel spreadsheet for all 15 samples (mlevings_PD1koIL10ki_total counts.xlsx), raw counts were generated using the counts produced by DRAGEN RNA and were corrected using the tximport function in R.

molecule: polyA RNA

source_name: Treg

growth_protocol:
A2-CAR Tregs: (Day 0) Naive Tregs were flow-sorted (CD4+CD25hiCD127loCD45RA+CD45RO-) and stimulated with artificial antigen presenting cells (L cells), anti-CD3, and 1000 IU/mL IL-2. (Day 1) They were transduced with an HLA-A2-specific CAR, and (Day 5) were CRISPR-edited using AAV6-mediated homology directed repair, to generate Cas9 alone controls, PD1KO cells, and PD1KOIL10KI cells (referred to as IL10KI). Cells were restimulated with A2+ L cells, then (Day 12) PD1KO and IL10KI CAR-Tregs were bead-purified by positive selection of a truncated CD19 reporter (tCD19). All CAR-Tregs were rested overnight in low (100 IU/mL) IL-2. (Day 13) CAR-Tregs were stimulated with A2+ beads for 16 hours.
A2-CAR Tconvs: (Day 0) Naive Tconvs were flow-sorted (CD4+CD25loCD127hiCD45RA+CD45RO-) and stimulated with L cells, anti-CD3, and 100 IU/mL IL-2. (Day 1) They were transduced with an HLA-A2-specific CAR, and (Day 5) were restimulated with A2+ L cells. (Day 12) CAR-Tconvs were rested overnight in low (10 IU/mL) IL-2, then (Day 13) were stimulated with A2+ beads for 16 hours.
A2-CAR Tr1s: (Day 0) CD4+ T cells were stimulated with CD3/CD28 beads overnight, then Tr1s were flow-sorted using an IL-10 capture approach and were stimulated with L cells, anti-CD3, and 100 IU/mL IL-2. (Day 1) They were transduced with an HLA-A2-specific CAR, and (Day 5) were restimulated with A2+ L cells. (Day 12) CAR-Tr1s were rested overnight in low (10 IU/mL) IL-2, then (Day 13) were stimulated with A2+ beads for 16 hours.
All cells were cultured in in Immunocult-XF T cell media and 1% penicillin-streptomycin.

extract_protocol:
Cells were lysed 16-hrs post-stimulation using TRIzol® and total RNA was extracted with the PureLink RNA MicroKit (as per manufacturer's guidelines).
RNA integrity was confirmed to be >8.0, then RNA was prepared using the Illumina® Stranded mRNA Prep kit.

value: Treg

tag: sample group

value: Cas9 A2-CAR

tag: donor

tag: Sex

value: male


title: o_sgCtrl_r3

city: Boston

first: Ninghe

last: Sun

state: Massachusetts

address: 200 Longwood Avenue

institute: Harvard Medical School / Boston Children's Hospital

data_processing:
RNA FASTQ files were processed with the RNAseq pipeline
Assembly: GRCm38_mm10
Supplementary files format and content: FPKM

source_name: Hematopoietic stem and progenitor cells

extract_protocol:
cDNA was generated according to manufacturer’s protocol of SMART-Seq v4 Ultra Low Input RNA Kit
RNA library was generated according to manufacturer’s protocol of Nextera XT DNA Sample Preparation Kit

value: Hematopoietic stem and progenitor cells


title: VM106_Primary ccRCC

city: Dallas

first: Javier

last: Garcia Bermudez

state: TX

address: 6000 Harry Hines Blvd

department: CRI

institute: UT Southwestern Medical Center

description: Library name: VM40

data_processing:
Ends of sequences were trimmed with remaining adapter or quality scores <25.
Sequencing reads were aligned to the human reference genome (hg19) by STAR 2.7.3.a with default parameters in the 2-pass mod.
Counts for each gene were generated using htseq-count v0.6.1. DEGs were identified by DESeq2 v1.14.1.
Ends of sequences were trimmed with remaining adapter or quality scores <25. Sequence less than 35bp after trimming were removed.
The trimmed Fastq files were aligned to the GRCh38 using HiSAT272 and duplicates were marked with SAMBAMBA. Features (genes, transcripts and exons) were counted using featureCounts73. Differential expression analysis was performed using EdgeR74 and DESeq75. Genes with 0 values for all samples were trimmed from the processed data.
Assembly: hg19
Supplementary files format and content: Excel file includes log2CPM counts for each Sample

extract_protocol:
RNA was isolated using Trizol (Thermo Fisher Scientific, Cat. No. 15596018) and an Rneasy Mini Kit (Qiagen, Cat. No. 74106). Total RNA was quantified using a Qubit fluorometer and the Invitrogen Qubit RNA High Sensitivity kit (Invitrogen, Cat. No. Q32852). Samples were diluted in ultrapure water prior to sequencing.
RNA-seq libraries were prepared using the NEBNext Ultra II directional RNA library prep kit with the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs, Cat. No. E7490L, E7760L) according to manufacturer’s instructions. Libraries were stranded using standard N.E.B indices according to manufacturer’s instructions (New England Biolabs, Cat. No. E7730L, E7335L, E7500L).


title: K-562 and HEK293T VASA-seq plate 2

city: Grand Rapids

first: Benjamin

last: Johnson

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

description:
Library name: Sample5
VASA-seq of K-562 and HEK293T

library_source: transcriptomic single cell

data_processing:
Unmapped Smart-seq3xpress (SS3x) HEK293T and K-562 BAM files were demultiplexed to individual cell FASTQ files by extracting reads assigned to expected cell barcodes in the CB BAM tag (concatenation of i5 and i7 indices, yielding a 20 bp barcode) and appending conserved sequences to delineate internal and 5’ UMI containing reads. Briefly, to reconstruct the expected 4 FASTQs per cell file structure, cell barcodes (CB BAM tag) were added to index 1 and index 2 FASTQ files, and respective read 1 and read 2 reads to separate FASTQ files. If the UB BAM tag (UMI) was populated, the conserved ‘ATTGCGCAATG’ sequence motif was added, then the UMI (UB tag), followed by the ‘GGG’ motif. Internal and 5’ UMI containing reads from SS3x were separated as previously described, using the conserved ‘ATTGCGCAATG’ sequence motif at the start of read 1 to delineate 5’ UMI reads. VASA-seq data were demultiplexed to single cell FASTQ files using provided scripts from https://github.com/hemberg-lab/VASAseq_2022. Scripts for STORM-seq de-multiplexing from GEO/SRA/ENA FASTQs can be found at https://github.com/biobenkj/stormseq_protocols/tree/main/analysis/stormseq_manuscript/demux_storm.
VASA-seq data were pre-processed and trimmed using cutadapt (v4.4) through provided scripts at https://github.com/hemberg-lab/VASAseq_2022. After trimming, the UMI and cell barcode were appended to the 5’ end of the read. Importantly, in the provided concatenator.py, a conversion error occurs when extracting and appending the UMI and cell barcode where a base quality score of 14 (ASCII character ‘/’) is unintentionally converted to a base quality score of 46 (ASCII character ‘O’). As a result, during the addition of the UMI and cell barcode to the 5’ end of the read, these base qualities were reverted to their original value.
All subsampling was performed using seqtk (v1.4-r122) sample on pre-processed/trimmed reads across technologies, setting the random seed to 100, unless specified otherwise.
STORM-seq HEK293T, K-562, and RMG-2 reads were mapped and quantified at the gene and transcript isoform level using kallisto|bustools (kallisto: v0.50.1, bustools: v0.43.2) and kb_python (v0.28.2) with the -x STORM-seq preset. For transcript isoform quantification, kb_python was called with the --tcc option enabled to output transcript compatibility counts (TCC). TCCs were quantified using kallisto quant-tcc to produce transcript isoform level counts. Further, fragment length bias was accounted for in quant-tcc as well as including at least 50 bootstraps for gene/transcript isoform quantification. Per-cell mapping rates were extracted from the log files.
Passage matched (for direct comparison to STORM-seq) K-562 and HEK293T VASA-seq data generated by Single Cell Discoveries were mapped and quantified against Ensembl 101 using kallisto|bustools (kallisto: v0.50.1, bustools: v0.43.2) following the kb_python analysis toolchain, with modifications to support this data type. Briefly, kallisto bus was used with default parameters and 1) -x 0,6,8:0,0,6:0,14,0, 2) --fr-stranded. Next, bus files were sorted (bustools sort), inspected (bustools inspect), and counted (bustools count). For bustools count, default parameters were used with the following modifications, 1) --multimapping, 2) --umi-gene. Next, kallisto quant-tcc was used to quantify transcript abundance with default parameters and 1) -t 8, 2) -l 550, 3) -s 300, 4) -b 50, and 5) --matrix-to-files. The average fragment length and standard deviation parameters were specified based on VASA-seq bioanalyzer traces provided (Supp. Fig. 19). Per-cell mapping rates were extracted from the log files.
HEK293T and K-562 pre-processed SS3x FASTQs were mapped and quantified using a similar strategy as VASA-seq, using kallisto|bustools. Briefly, per-cell 5’ UMI reads and internal reads were extracted as described above, prior to subsampling and mapping/quantification. Next, for gene/transcript quantification, kallisto bus was used with 5’ UMI reads with default parameters and the following modifications, 1) -x 0,0,0,1,0,0:2,0,21:2,24,0,3,0,0, 2) --tag ATTGCGCAATG, 3) --paired, 4) --fr-stranded, and 5) -t 8. Transcript abundance quantification was performed using kallisto quant-tcc with default parameters and the following modifications 1) -b 50 and 2) --matrix-to-files.
Assembly: GRCh38 (Ensembl 101)
Supplementary files format and content: Text file STORM-seq metadata for demultiplexing
Supplementary files format and content: Text files of raw UMI counts with multimappers from kallisto|bustools using Ensembl 101 annotations

source_name: K-562 and HEK293T

growth_protocol: The K-562 cell line was purchased from ATCC (CCL-243). Cells were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% Penicillin/Streptomycin (Gibco). HEK293T cells were purchased from the American Type Culture Collection (ATCC; CRL-3216) and cultured in DMEM medium supplemented with 10% FBS, 2 mM L-glutamine, and 1% Penicillin/Streptomycin (Gibco). RMG-2 cells were purchased from the JCRB Cell Bank and Seikiusi XenoTech, LLC. RMG-2 cells were maintained in DMEM/F12, supplemented with 10% FBS and sub-cultured at 1:3-1:5 every 7-9 days. Fresh media was added every 2-3 days between sub-culturing.

extract_protocol:
Single cells were deposited in a 384-well plate using a BD FACSymphony S6 equipped with a 130 um nozzle at 14 psi. Single cells were lysed in their respective lysis buffer (e.g., STORM-seq, VASA-seq, or Smart-seq3xpress). Passage matched K-562 and HEK293T cells were deposited same day for both STORM-seq and VASA-seq.
Libraries were constructed as previously described for Smart-seq3xpress (https://doi.org/10.1038/s41587-022-01311-4) or by Single Cell Discoveries following the VASA-seq protocol (https://www.scdiscoveries.com/services/vasa-seq/; https://doi.org/10.1038/s41587-022-01361-8). For STORM-seq, libraries were constructed following https://doi.org/10.5281/zenodo.15178455.

tag: cell line

value: K-562 and HEK293T


title: Young HSC-5

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

description: Library name: Young_5

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the mouse genome mm10 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
total RNA
The libraries were prepared with SMART-Seq® Ultra Low Input RNA Kit for Sequencing – v4 (TaKaRa, Cat. 634888) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit. Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51cycle.

value: hematopoietic stem cells

value: wt


title: Combo6-R-1

description: pre-treatment

value: R


title: o_sgClu_r1


title: VM107_Primary ccRCC

description: Library name: VM42

value: Primary ccRCC


title: o_sgCtrl_r2


title: sWAT_2_Control

description: Library name: sWAT_Sample 2

value: Subcutaneous white adipose tissue

value: WT


title: sWAT_1_Control

description: Library name: sWAT_Sample 1


title: VM107_Adjacent Kidney

description: Library name: VM41

source_name: Adjacent Kidney

value: Adjacent Kidney


title: Old HSC-1

description: Library name: Old_1


title: VM106_Adjacent Kidney

description: Library name: VM39


title: VM105_Primary ccRCC

description: Library name: VM38


title: isWAT_1_Fgf13_Ko

description: Library name: isWAT_Sample 4

value: Fgf13 KO


title: Young HSC-4

description: Library name: Young_4


title: y_Tx_r3


title: o_sgCtrl_r1


title: VM105_Adjacent Kidney

description: Library name: VM37


title: E3

city: shanghai

first: Yao

last: Zhang

address: No. 500, Dongchuan Road

country: China

institute: East China Normal University

description:
Library name: Sample 6
Column name in counts_anno.xls: E3

data_processing:
Libraries were sequenced on the Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads.   Approximately 4.7 × 10⁷ raw reads were obtained per sample.   Raw FASTQ files were processed using fastp to remove low-quality reads, resulting in ~4.6 × 10⁷ clean reads per sample for downstream analysis.   Clean reads were aligned to the reference genome using HISAT2.   Gene expression levels were quantified as FPKM, and read counts were obtained using HTSeq-count.
Assembly: GRCm38
Supplementary files format and content: raw read counts for each sample
Supplementary files format and content: FPKM values for each sample

source_name: Tumor

growth_protocol: The murine colorectal cancer cell line CT26 was cultured in DMEM supplemented with 10% fetal bovine serum (FBS; Gibco, Waltham, MA, USA) and 1% penicillin-streptomycin (Gibco) at 37°C in a humidified incubator with 5% CO2. A total of 5 × 10⁵ CT26 cells suspended in 100 μL PBS were subcutaneously injected into the flanks of mice. When tumor volumes reached 100–200 mm³ (calculated as V = 0.52 × longest diameter × [shortest diameter]²), mice were randomized into 2 treatment groups.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to themanufacturer’s protocol.  RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).  RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: CT26 tumor-bearing mouse were treated with vehicle or TP-18  (50 mg/kg, QD, orally) for 3 weeks.  Then subcutaneous tumors were harvested and processed into single-cell suspensions. CD11b+ cells were isolated using magnetic bead–based selection. Total RNA was extracted using TRIzol reagent (Invitrogen, USA) and stored in liquid nitrogen for subsequent sequencing.

value: Tumor

value: murine colorectal cancer cell line


title: isWAT_3_Control

description: Library name: isWAT_Sample 3


title: Old HSC-3

description: Library name: Old_3


title: E2

description:
Library name: Sample 5
Column name in counts_anno.xls: E2


title: VM104_Primary ccRCC

description: Library name: VM36


title: Combo1-NR-1

description: pre-treatment

value: Blood

value: PBMC CD8+T cells

value: NR

value: untreated


title: y_Tx_r2


title: isWAT_2_Control

description: Library name: isWAT_Sample 2


title: Old HSC-2

description: Library name: Old_2


title: y_Tx_r1


title: E1

description:
Library name: Sample 4
Column name in counts_anno.xls: E1


title: VM104_Adjacent Kidney

description: Library name: VM35


title: isWAT_2_Fgf13_Ko

description: Library name: isWAT_Sample 5


title: isWAT_1_Control

description: Library name: isWAT_Sample 1


title: C3

description:
Library name: Sample 3
Column name in counts_anno.xls: C3

value: vehicle


title: VM103_Primary ccRCC

description: Library name: VM34


title: o_sgClu_r2

value: Hematopoietic stem and progenitor cells


title: o_Tx_r3


title: VM103_Adjacent Kidney

description: Library name: VM33


title: ieWAT_1_Fgf13_Ko

description: Library name: ieWAT_Sample 4

source_name: Epididymal white adipose tissue

value: Epididymal white adipose tissue


title: C1

description:
Library name: Sample 1
Column name in counts_anno.xls: C1


title: o_Tx_r1


title: VM102_Primary ccRCC

description: Library name: VM32


title: tp18_3

description:
Library name: Sample 6
Column name in counts_anno.xls: tp18_3

data_processing:
Libraries were sequenced on the Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads.   Approximately 4.6 × 10⁷ raw reads were obtained per sample.   Raw FASTQ files were processed using fastp to remove low-quality reads, resulting in ~4.0 × 10⁷ clean reads per sample for downstream analysis.   Clean reads were aligned to the reference genome using HISAT2.   Gene expression levels were quantified as FPKM, and read counts were obtained using HTSeq-count.
Assembly: GRCm38
Supplementary files format and content: raw read counts for each sample
Supplementary files format and content: FPKM values for each sample

treatment_protocol: CT26 tumor-bearing mouse were treated with vehicle or TP-18  (50 mg/kg, QD, orally) for 3 weeks. Then subcutaneous tumors were excised and stored in liquid nitrogen for subsequent sequencing.


title: ieWAT_3_Fgf13_Ko

description: Library name: ieWAT_Sample 6


title: C2

description:
Library name: Sample 2
Column name in counts_anno.xls: C2


title: o_Tx_r2


title: ieWAT_2_Fgf13_Ko

description: Library name: ieWAT_Sample 5


title: ieWAT_3_Control

description: Library name: ieWAT_Sample 3


title: tp18_2

description:
Library name: Sample 5
Column name in counts_anno.xls: tp18_2


title: VM101_Primary ccRCC

description: Library name: VM30


title: tp18_1

description:
Library name: Sample 4
Column name in counts_anno.xls: tp18_1


title: A375, Tunicamycin, replicate 3

city: Philadelphia

first: Constantinos

last: Koumenis

state: PA

address: 13400 Civic Center Blvd

department: Radiation Oncology

institute: University of Pennsylvania

description:
Genome-Wide CRISPR/Cas9 screen
38014

library_source: other

data_processing:
*library strategy: CRISPR/Cas9-based screen
Demultiplexing and adapter removal was performed with combined use of cutadapt, FASTX_toolkit and seqtk.
FASTQC was utilized for quality control of raw and trimmed FASTQ files.
Alignment against the GeCKO v2 sgRNA library was performed with Bowtie2, retaining reads uniquely mapped on sgRNA sequences with MAPQ >10.
sgRNA and gene ranking analysis was conducted by contrasting UT-DMSO against their respective TG/TN samples with MAGeCK test call (RRA analysis).
Assembly: Reference GeCKO v2 library sgRNA sequences
Supplementary files format and content: per-sample: tab-delimited file containing sgRNA sequence, associated gene and respective counts
Supplementary files format and content: supplementary files: (tab-delimited) default, unfiltered, MAGeCK RRA analysis results for the conducted contrasts

molecule: other

growth_protocol: GeCKO_V2 1 vector system lentiviral library was purchased from Addgene (1000000048) and propagated as described previously (Joung et al., 2017)

extract_protocol:
After a 72h recovery and expansion, the genomic DNA was extracted from cells (40x coverage over the GeCKO library) using the blood and cell culture midi kit (Qiagen, 13343).
Amplification first step PCR was performed to sgRNA sequences using the Herculase II Fusion DNA polymerase (Agilent Technologies, 600675). A second PCR was performed to attach Illumina adaptors and barcode samples. Amplicons from the second PCR were extracted (Qiagen), analyzed using a Bioanalyzer High Sensitivity DNA Analysis Kit (Agilent), and quantified using a NEBNext Library Quant Kit for Illumina.

treatment_protocol: After selection with puromycin, the cells were left to repopulate the plates and were treated for 24h with 0.5uM of Thapsigargin or Tunicamycin.  After 50% of the cells died due to ER stress, cells were left to grow and treatment with Thapsigargin or Tunicamycin was repeated one more time to increase the resistance to ER stress population. Cells were collected for lysing and DNA isolation.

value: melanoma cells

value: Tunicamycin (TN)


title: VM102_Adjacent Kidney

description: Library name: VM31


title: A375, Tunicamycin, replicate 4

description:
Genome-Wide CRISPR/Cas9 screen
38015


title: VM101_Adjacent Kidney

description: Library name: VM29


title: o_Tx_r4


title: ieWAT_1_Control

description: Library name: ieWAT_Sample 1


title: A375, Tunicamycin, replicate 2

description:
Genome-Wide CRISPR/Cas9 screen
38011


title: con3

description:
Library name: Sample 3
Column name in counts_anno.xls: Con3


title: VM100_Primary ccRCC

description: Library name: VM28


title: PNMG7_6_3

city: hangzhou

first: xiao

middle: chen

last: wen

address: desheng_road NO.298

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: ABySS_70bp_45k_152cov_v1（https://www.ncbi.nlm.nih.gov/genome/?term=txid523103[orgn]）
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Trichophyton mentagrophytes

source_name: mycelium

growth_protocol: SDA plates were prepared respectively. The fungi were inoculated on the medium and cultured for 10 days.

extract_protocol:
For extraction of total RNA, TRIzol Reagent (Invitrogen) was used per manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: mycelium


title: con2

description:
Library name: Sample 2
Column name in counts_anno.xls: Con2


title: VM100_Adjacent Kidney

description: Library name: VM27


title: PNMG7_6_2

treatment_protocol: SDA plates were prepared respectively. The fungi were inoculated on the medium and cultured for 10 days.


title: VM99_Primary ccRCC

description: Library name: VM26

value: Primary ccRCC


title: A375, DMSO, TN control, replicate 4

description:
Genome-Wide CRISPR/Cas9 screen
38013

value: DMSO, TN control


title: con1

description:
Library name: Sample 1
Column name in counts_anno.xls: Con1


title: A375, DMSO, TN control, replicate 3

description:
Genome-Wide CRISPR/Cas9 screen
38012


title: A375, DMSO, TN control, replicate 2

description:
Genome-Wide CRISPR/Cas9 screen
38009


title: VM98_Primary ccRCC

description: Library name: VM24


title: ieWAT_2_Control

description: Library name: ieWAT_Sample 2

value: WT


title: PNMG7_6_1


title: HETStra8 mouse 3

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

description: Library name: 22034R-01-06V1_S77

data_processing:
FastQC (version v0.11.8) was applied to check the quality of raw reads. Trimmomatic (version v0.38) was applied to cut adaptors and trim low-quality bases with default setting. STAR Aligner version 2.7.1a was used to align the reads. Picard tools (version 2.20.4) was applied to mark duplicates of mapping. The StringTie version 2.0.4 was used to assemble the RNA-Seq alignments into potential transcripts. The featureCounts (version 1.6.0)/HTSeq was used to count mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. The De-Seq2 (version 1.14.1) was used to do the differential analysis. The Chipseeker package was used to annotate the peaks. The Gene Ontology Analysis was done using ClusterProfiler package in R.
Assembly: Mouse Mus musculus ; mm10 (GRCm38)
Supplementary files format and content: Normalized expression (FPKM);Htseq count output

source_name: testis

growth_protocol: 7-week-old Heterozygous testis-  HETStra8

extract_protocol:
Total RNA was extracted from the testis using RNA-Stat 60 (IsoTex Diagnostics), chloroform, followed by purification using a total RNA extraction kit (Omega Bio-Tek-R6834-02) with DNaseI digestion (Roche). RNA quality and concentration were examined using the Agilent tapeStation and AccuBlue Broad Range RNA Quantitation assay, respectively.
Library constructions were done according to the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc., Massachusetts, USA). Final libraries were assessed for quantity and quality with an average size of 430bp. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina Novaseq platform with 150PE reads (Illumina, California, USA).

treatment_protocol: 7-week-old SEL1L Knockout testis- KOStra8

value: testis

tag: batch

value: total RNA


title: PNMR6_5_2


title: VM97_Primary ccRCC

description: Library name: VM22


title: A375, untreated, TN control

description:
Genome-Wide CRISPR/Cas9 screen
38007

value: untreated, TN control (UT)


title: A375, DMSO, TN control, replicate 1

description:
Genome-Wide CRISPR/Cas9 screen
38008


title: PNMR6_5_1


title: HETStra8 mouse 2

description: Library name: 22034R-01-03V1_S74


title: A375, Thapsigargin, replicate 3

description:
Genome-Wide CRISPR/Cas9 screen
34669

value: Thapsigargin (TG)


title: A375, Tunicamycin, replicate 1

description:
Genome-Wide CRISPR/Cas9 screen
38010


title: T9_21_3


title: KOStra8 mouse 2

description: Library name: 22034R-01-04V1_S75


title: A375, Thapsigargin, replicate 2

description:
Genome-Wide CRISPR/Cas9 screen
34668


title: T9_21_2


title: HETStra8 mouse 1

description: Library name: 22034R-01-02V1_S73


title: VM96_Primary ccRCC

description: Library name: VM20


title: VM99_Adjacent Kidney

description: Library name: VM25

value: Adjacent Kidney


title: KOStra8 mouse 1

description: Library name: 22034R-01-01V1_S72


title: T9_21_1


title: PNMR6_5_3


title: A375, Thapsigargin, replicate 1

description:
Genome-Wide CRISPR/Cas9 screen
34667


title: KO_Naph_d14

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA51072

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Lung

extract_protocol:
RNA samples were extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer's instruction.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: Lung

value: digested lung tissue

value: Aldh1a1 -/-

value: naphthalene (4 mg / 100µL corn oil, i.p.)

value: 14 days after Intraperitoneal administration


title: KOStra8 mouse 3

description: Library name: 22034R-01-05V1_S76


title: T4_12_3


title: A375, DMSO, TG control

description:
Genome-Wide CRISPR/Cas9 screen
34664

value: DMSO, TG control


title: WT_Naph_d14

description: Library name: GA51071

value: Wildtype


title: VM98_Adjacent Kidney

description: Library name: VM23


title: T4_12_2


title: VM95_Primary ccRCC

description: Library name: VM18


title: A375, untreated, TG control

description:
Genome-Wide CRISPR/Cas9 screen
34663

value: melanoma cells

value: untreated, TG control (UT)


title: KO_Naph_d7

description: Library name: GA51070

value: 7 days after Intraperitoneal administration


title: VM95_Adjacent Kidney

description: Library name: VM17


title: VM94_Primary ccRCC

description: Library name: VM16

value: Primary ccRCC


title: SQ20B, Thapsigargin, replicate 3

description:
Genome-Wide CRISPR/Cas9 screen
34005

value: laryngeal squamous cell carcinoma cells


title: Tm_3

value: mycelium


title: WT_Naph_d7

description: Library name: GA51069


title: T4_12_1


title: SQ20B, Thapsigargin, replicate 2

description:
Genome-Wide CRISPR/Cas9 screen
34004


title: VM94_Adjacent Kidney

description: Library name: VM15


title: YB328

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

state: Chiba

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center

institute: National Cancer Center

description:
Library name: YB328
Column name in BMDC_gene_expression.xlsx : YB328_TPM, YB328_count

data_processing:
DRAGEN Bio-IT Platform 3.6.3
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone marrow derived dendritic cell

extract_protocol:
Total RNA was extracted from BMDCs with an RNeasy Micro Kit (QIAGEN)
RNA libraries were processed with a SMART-Seq v4 Ultra Low Input RNA Kit (TaKaRa Bio, Shiga, Japan). Complementary DNA (cDNA) library preparation was conducted with a Nextera XT DNA Library Preparation Kit (Illumina).

value: Bone marrow derived dendritic cell

value: WT


title: P_vulgatus

description:
Library name: P_vulgatus
Column name in BMDC_gene_expression.xlsx : P_vulgatus_TPM, P_vulgatus_count

value: P. vulgatus


title: Tm_2


title: Tm_1


title: VM96_Adjacent Kidney

description: Library name: VM19

value: Adjacent Kidney


title: Control

description:
Library name: Control
Column name in BMDC_gene_expression.xlsx : Control_TPM, Control_count

value: untreated


title: SQ20B, DMSO, TG control, replicate 2

description:
Genome-Wide CRISPR/Cas9 screen
34001


title: fetal cat epidermis, enriched with anti-cKIT from an Arhgap36del/Y late-gestation embryo [C96F2]

city: Huntsville

first: Christopher

middle: Bryan

last: Kaelin

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
Library name: C96F2
C96agg_filtered_feature_bc_matrix.h5
S19C96agg.csv

data_processing:
The library was sequenced on a single Illumina HiSeq4000 lane to generate ~450 million reads, which were aligned to the domestic cat fca126 genome assembly (GCF_018350175.1 with NCBI Felis catus Annotation Release 105) using the 10x Genomics CellRanger software (v7.1.0). The ‘cellranger count’ pipeline was used to output feature-barcode matrices. The ‘cellranger aggr’ pipeline was used to aggregate data from C96F1 and C96F2 into a combined matrix (linked to the C96F1 sample records).
Assembly: Domestic cat Fca126 genome assembly (GCF_018350175.1 with NCBI Felis catus Annotation Release 105)
Supplementary files format and content: Filtered feature barcode matrix in HDF5 format

organism: Felis catus

source_name: epidermis

extract_protocol:
Single cell preparations from the late gestation embryo followed a workflow designed to enrich for melanoblasts. Dorsal skin was excised with micro scissors and treated overnight in Dispase (Stem Cell Technologies). Epidermal sheets, comprised of keratinocytes and migrating melanoblasts, were isolated by gentle scraping with a No.15-blade scalpel and dissociated with trypsin. Red blood cells were removed with a red blood cell lysis solution (Miltenyi Biotec) and then size-filtered to recover dissociated cell suspensions. To enrich for melanoblasts, ten million dissociated cells were incubated with a phycoerythrin-conjugated, CD117 (c-Kit) Monoclonal Antibody (clone 2B8, eBioscience, ThermoFisher Scientific). The antibody bound fraction was then captured using a column-magnetic bead separation procedure (Miltenyi Biotech). In each case, the bound cell fraction was ~200,000 cells, or ~2% of the unenriched population.
3’ end, single-cell barcoded libraries were prepared from cell suspensions using 10x Genomics single-cell RNA sequencing platform for targeted capture of 6000 cells, using  v3.0 chemistry. Library construction precisely followed 10x Genomics protocol for v.3.0 chemistry.

treatment_protocol: Dissociated cells were enriched for melanoblasts using a magnetic bead approached with a phycoerythrin-conjugated, CD117 (c-Kit) Monoclonal Antibody (clone 2B8, eBioscience, ThermoFisher Scientific).

value: epidermis

value: enrichment with anti-cKIT antibody

tag: age

value: fetal stage 20 (44-48 days p.c.)

value: male


title: VM93_Adjacent Kidney

description: Library name: VM13


title: SQ20B, DMSO, TG control, replicate 1

description:
Genome-Wide CRISPR/Cas9 screen
34000

value: DMSO, TG control


title: fetal cat epidermis, enriched with anti-cKIT from an Arhgap36+/Arhgap36del late-gestation embryo [C56F3]

description: Library name: C56F3

value: female


title: SQ20B, untreated, TG control

description:
Genome-Wide CRISPR/Cas9 screen
33999


title: VM92_Adjacent Kidney

description: Library name: VM11


title: VM91_Primary ccRCC

description: Library name: VM10


title: VM93_Primary ccRCC

description: Library name: VM14


title: human_ONB5_bulkSeq

first: Matthew

middle: Joseph

last: Zunitch

state: MA

address: 150 Harrison Ave

institute: Tufts University

data_processing:
Single cell gene expression quantification was performed using 10X Cell Ranger v2.1.1
Alignment of bulk RNAseq reads was performed using STAR v2.5.2 and --quantMode=GeneCounts
Genome_build: hg19 (bulk RNAseq) or mm10 (scRNAseq)
Supplementary_files_format_and_content: Bulk RNAseq: tab-delimited text file containing raw counts per sample. Single cell RNAseq: counts matrix plus barcode and feature information required for constructing a Seurat object.

source_name: olfactory neuroblastoma

extract_protocol:
Biopsy specimens were rinsed briefly in normal saline then snap-frozen in a dry centrifuge tube placed on dry ice. Samples were stored at -80˚C until library construction.
RNA was extracted using the Zymo Research Direct-zol RNA Microprep Kit. Libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit. All bulk tissue samples were processed at the same time following kit manufacturer’s instructions.

value: olfactory neuroblastoma


title: MCF-7_PIT_rep3

city: Santiago de Compostela

first: Leandro

middle: Avila

last: Concepcion

state: Coruña

address: Ave Barcelona

department: Department of Physiology, Center for Molecular Medicine and Chronic Diseases

country: Spain

institute: University  Santiago de Compostela

description: Library name: Sample 6

data_processing:
Quality control was performed using FastQC (v0.11.5) and trimming with TrimGalore (v0.6.7). Strand specificity was verified using how-are-we-stranded-here (v1.0.1) and Kallisto (v0.46.2).
Reads were aligned to GRCh38 using STAR (v2.7.9a) with Ensembl annotations using default parameters
Read counting was performed using HTSeq (v0.13.5) with -r=pos, -i=gene_id, and -s=reverse
Differential expression analysis was conducted using DESeq2 with the Benjamini-Hochberg method. Log2 fold-change values were shrunk using apeglm to reduce extreme value impacts.
Assembly: Grch38 Release 108
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Breast

growth_protocol: MCF-7 cells  were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using DNA, RNA, and protein purification kit (Macherey-Nagel, Düren, Germany)
TruSeq Stranded Total RNA Library Prep (Human/Mouse/Rat)/(Plant)+ NEBNext® Ultra™ Directional RNA Library Prep Kit

treatment_protocol: POU1F1 overexpression was carried out using lentiviral vector stalble expression with ORF-POU1F1 under promoter EF1

value: Breast

value: ephitelial cells

value: WT_POU1F1 overexpression

value: lentiviral Infection


title: SQ20B, Thapsigargin, replicate 1

description:
Genome-Wide CRISPR/Cas9 screen
34003

value: laryngeal squamous cell carcinoma cells

value: Thapsigargin (TG)


title: SQ20B, DMSO, TG control, replicate 3

description:
Genome-Wide CRISPR/Cas9 screen
34002


title: VM97_Adjacent Kidney

description: Library name: VM21


title: cat whole skin, enriched with anti-CD49f from an Arhgap36del/Y mid-gestation embryo

description: Library name: C4F1

data_processing:
The library was sequenced on a single Illumina HiSeq4000 lane to generate ~450 million reads, which were aligned to the domestic cat fca126 genome assembly (GCF_018350175.1 with NCBI Felis catus Annotation Release 105) using the 10x Genomics CellRanger software (v7.1.0). The ‘cellranger count’ pipeline was used to output feature-barcode matrices.
Assembly: Domestic cat fca126 genome assembly (GCF_018350175.1 with NCBI Felis catus Annotation Release 105)
Supplementary files format and content: Filtered feature barcode matrix in HDF5 format

source_name: whole skin

extract_protocol:
A single embryo (4 cm crown-rump length) was treated with Dispase (Stem Cell Technologies) for 40 minutes, after which skin was removed by scraping with a No.15-blade scalpel. Isolated skin was dissociated with trypsin (Gibco) for 5 minutes and red blood cells were removed with a red blood cell lysis solution (Miltenyi Biotec).
3’ end, single-cell barcoded libraries were prepared from cell suspensions using 10x Genomics single-cell RNA sequencing platform for targeted capture of 6000 cells, using  v2.0 chemistry. Library construction precisely followed 10x Genomics protocol for v.3.0 chemistry.

treatment_protocol: anti-CD49f antibody conjugated with phycoerythrin (ThermoFisher Scientific, clone NKI-GoH3 12-0495-82) and the antibody-bound fraction was captured after incubation with anti-phycoerythrin beads and enriched using a column-magnetic bead separation procedure (Miltenyi Biotec).

value: whole skin

value: mixed skin cell types

value: enrichment with anti-CD49f antibody

value: fetal stage 17 (28-32 days p.c.)


title: VM92_Primary ccRCC

description: Library name: VM12

source_name: Primary ccRCC

value: Primary ccRCC


title: VM91_Adjacent Kidney

description: Library name: VM09

value: Adjacent Kidney


title: seedling, b23_raf_man3

city: Shenzheng

first: Xinyong

last: Wang

address: 1088 Xueyuan Avenue, Shenzhen 518055, P.R. China

institute: South University of Science and Technology of China

description: Library name: b23_raf_man3

data_processing:
The paired-end reads were cleaned by Trimmomatic. After trimming the adapter sequence, removing low-quality bases, and filtering short reads, clear read pairs were retained for further analysis.
Differentially expressed transcript was analyzed between the control and treatment using the likelihood ratio test in the DESeq2 or the quasi-likelihood method in the EdgeR
Genes with at least four-fold changes in expression and with an FDR < 0.05 were considered differentially expressed genes
Assembly: Oryza sativa japonica genomics (IRGSP1.0)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

organism: Oryza sativa Japonica Group

source_name: seedling

growth_protocol: Rice seedling was grown in a growth room (14 h light at 30 °C/10 h dark at 25 °C) with a relative humidity of around 70%.

extract_protocol:
Total RNA was isolated from 5-day-old seedlings of WT/NIP and raf-b2/3 mutant, with and without mannitol treatment, using a Kit (Promega Eastep Super, LS1040)
Library preparation with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7765) following the manufacturer’s instructions

treatment_protocol: 5-day-old seedlings of WT/NIP and raf-b2/3 mutant with or without 6 hours of 800 mM mannitol treatments.

value: seedling

value: B2/3 RAF knockdown

value: mannitol


title: human_ONB1_bulkSeq


title: seedling, b23_raf_man2

description: Library name: b23_raf_man2


title: human_OM3_bulkSeq

source_name: human olfactory mucosa

value: olfactory mucosa


title: human_ONB2_bulkSeq

value: olfactory neuroblastoma


title: Intestinal epithelial cells, villus, rep 4

city: San Francisco

first: Nathan

middle: Daniel

last: Rossen

address: 600 16th Street Genentech Hall Room N-272E Genentech Hall Room N-272E

department: Physiology

institute: University of California, San Francisco

description:
Library name: Villi-Epi-8
Column name in Rossen_FKPM.csv: 4_4_villi_epi8

data_processing:
Image analysis and base calling were conducted by the NovaSeq Control Software (NCS).
Raw sequence data (.bcl files) generated from Illumina instrument was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification. About 50 million reads were obtained per sample.
Sequences were aligned to mouse transcriptome (mm10) using Kallisto in gene mode.
Differential gene expression was evaluated by Sleuth.
Assembly: mm10
Supplementary files format and content: Rossen_FKPM.csv contains processed gene expression data (FKPM) for each sample.

source_name: small intestine, villus

growth_protocol: Samples were collected from untreated 8-16 w/o mice.

extract_protocol:
Total RNA was extracted from cells using Qiagen RNeasy Plus Universal mini kit following the manufacturer’s instructions (Qiagen, Hilden, Germany).
Ultra-low input RNA sequencing library was prepared by using SMART-Seq HT kit for full-length cDNA synthesis and amplification (Takara, San Jose, CA, USA), and Illumina Nextera XT (Illumina, San Diego, CA, USA) library was used for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Thermo Fisher Scientific) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell.

value: small intestine, villus

value: intestinal epithelial cell


title: seedling, b23_raf_man1

description: Library name: b23_raf_man1


title: MCF-7 rep3

description: Library name: Sample 3

value: Breast

value: ephitelial cells

value: WT_Plasmid control


title: human_OM2_bulkSeq


title: seedling, b23_raf_con3

description: Library name: b23_raf_con3

value: control


title: Intestinal epithelial cells, villus, rep 3

description:
Library name: Villi-Epi-7
Column name in Rossen_FKPM.csv: 4_3_villi_epi7


title: MCF-7 rep2

description: Library name: Sample 2

value: lentiviral Infection


title: MCF-7_PIT_rep2

description: Library name: Sample 5

value: WT_POU1F1 overexpression


title: seedling, b23_raf_con2

description: Library name: b23_raf_con2


title: human_OM1_bulkSeq


title: MCF-7 rep1

description: Library name: Sample 1


title: PBSL3

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

description: IL-1β-induced and PBSL-treated cells, rep3

data_processing:
Adaptor or low-quality sequence bases were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/).
The reads were aligned to the human reference genome (hg38) using a STAR aligner
The read count was calculated as gene expression abundance using the HTSeq-count
Assembly: hg38
Supplementary files format and content: Read count was calculated as gene expression abundance using the HTSeq-count
Supplementary files format and content: tab-delimited txt files include log2 count values for each sample

growth_protocol: The cells (SW1353) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic‒antimycotic (Gibco) at 37℃ in a 5% CO2 incubator.

extract_protocol:
Total RNA was isolated from tissues using an easy-spin™ Total RNA Extraction Kit.
Total RNA (1 mg) was processed to prepare an mRNA-sequencing library using the MGIEasy RNA Directional Library Prep Kit (MGI) according to the manufacturer’s instructions.

treatment_protocol: SW1353 cells (2 × 105 cells/mL in a 6-well plate) were cultured for 24 h at 37℃. The cells were pretreated with PBSL (0, 50, 100 and 200 µg/mL) for 2 h and then induced with IL-1β (20 ng/mL) (Pepro Tech, East Windsor, NJ, USA) for 20 h.

value: chondrosarcoma cells

value: IL-1{beta}-induced and PBSL-treated cells


title: Intestinal epithelial cells, villus, rep 1

description:
Library name: Villi-Epi-1
Column name in Rossen_FKPM.csv: 4_1_villi_epi1


title: MCF-7_PIT rep1

description: Library name: Sample 4


title: HMEC POU1F1 overexpression rep3

first: Sandra

last: Rodríguez González

address: Campus Vida Avenida Barcelona, s/n, 15782, A Coruña

institute: CiMUS

description: Library name: HMECPIT1_3

data_processing:
The RAW were uploaded to the Galaxy web platform, and we used the public server at usegalaxy.org to analyze the data
Quality control was performed using FastQC  and trimming with Trimmomatic.
Reads were aligned to GRCh38 using HISAT2
Read counting was performed using featureCounts
Differential expression analysis was conducted using DESeq2 with the Benjamini-Hochberg method
Assembly: GRCh38/hg38 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: HMEC cells  were maintained in  DMEM F12 (Gibco) suplemented with 5% horse serum, 0.5% penicillin/streptomycin, 1% fetal bovine pituitary extract,  10µg/ml insuline, 0.5µg/ml Hydrocortisone, 20ng/ml hEGF, 100ng/ml colhera toxin,  0.1mM glutamax and 12.5ng/ml ascorbic acid at 37C in a 5% CO2.

value: HMEC


title: PBSL2

description: IL-1β-induced and PBSL-treated cells, rep2


title: Intestinal epithelial cells, villus, rep 2

description:
Library name: Villi-Epi-2
Column name in Rossen_FKPM.csv: 4_2_villi_epi2


title: HMEC POU1F1 overexpression rep2

description: Library name: HMECPIT1_2


title: Enterochromaffin cells, villus, rep 3

description:
Library name: Villi-EC-6
Column name in Rossen_FKPM.csv: 3_3_villi_EC6

value: enterochromaffin cell


title: seedling, WT_man3

description: Library name: WT_man3

value: seedling

value: WT


title: Enterochromaffin cells, villus, rep 2

description:
Library name: Villi-EC-5
Column name in Rossen_FKPM.csv: 3_2_villi_EC5


title: Enterochromaffin cells, villus, rep 4

description:
Library name: Villi-EC-7
Column name in Rossen_FKPM.csv: 3_4_villi_EC7


title: seedling, WT_man2

description: Library name: WT_man2

value: mannitol


title: HMEC control rep3

description: Library name: HMEC_3


title: seedling, WT_con3

description: Library name: WT_con3


title: Intestinal epithelial cells, crypt, rep 4

description:
Library name: Crypts-Epi-5
Column name in Rossen_FKPM.csv: 2_4_crypt_epi5

source_name: small intestine, crypt

value: small intestine, crypt


title: HMEC POU1F1 overexpression rep1

description: Library name: HMECPIT1_1


title: Ib3

description: IL‒1β‒induced SW1353 cells, rep 3

value: IL-1{beta}-induced SW1353 cells


title: NC3

description: Untreated cells, rep3

value: untreated cells


title: DNA from MCF-7 POU1F1 3

type: genomic

description: DNA from MCF-7 POU1F1 3

hyb_protocol: Bisulphite converted DNA (protocol EZ-DNA Methylation (D5001/Zymo Research) was amplified fragmentet and hybridized to human Infinitum MethylationEPIC V.2 BeadChip (Illumina)

scan_protocol: Arrays were imaged using BeadArray Reader (iScan) and standard recommended Illumina scanner setting

data_processing: Genome Studio Illumina Software (v210.3)

label: Cy3 and Cy5

molecule: genomic DNA

source_name: cell culture

label_protocol: Standard Illumina Protocol

extract_protocol: MasterPure DNA Extraction Kit (Epicentre Biotechnologies, Madison, WI, EE. UU),

value: cell culture

value: breast cancer luminal A

value: overexpression of POU1F1


title: Intestinal epithelial cells, crypt, rep 3

description:
Library name: Crypts-Epi-4
Column name in Rossen_FKPM.csv: 2_3_crypt_epi4

value: intestinal epithelial cell


title: Ib2

description: IL‒1β‒induced SW1353 cells, rep 2


title: seedling, WT_con1

description: Library name: WT_con1

value: control


title: seedling, WT_con2

description: Library name: WT_con2


title: NC2

description: Untreated cells, rep2


title: 10: iPSCs (LN521+mTeSR)

type: other

city: Kyoto

first: Yoshiki

last: Nakashima

address: Kyoto Research Park KISTIC Building Room 501, 5th floor, KISTIC building,  134 Chudoji Minami-cho, Shimogyo-ku

department: Research and Development Center

institute: Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation)

description: total DNA and RNA

hyb_protocol: Arrays were washed and stained using a GeneChip Fluidics Station 450 (Thermo Fisher Scientific) and scanned using a GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

scan_protocol: Scanned data files were generated using the GeneChip Command Console software program and analyzed using the Chromosome Analysis Suite v4.3 (ChAS), considering 1-2 MB for gains/losses and 5 MB for LOH(heterozygosity)/AOH(absence of heterozygosity).

data_processing:
We used the KaryoStat™ assay service provided by Life Technologies Corporation (Carlsbad, CA, USA) [Regen Med 14, 505-524 (2019)]. We used the PluriTest™ analysis service from Life Technologies Corporation (Carlsbad, CA, USA)[Regen Med 14, 505-524 (2019)]. This assay assesses 36,000 transcripts and variants against a reference set of >450 samples for gene expression analysis.   The transcriptomes of all samples were analyzed and processed in the PluriTest™ algorithm to generate pluripotency and novelty scores. The pluripotency score is based on many samples (pluripotent, somatic, and tissue) in the stem cell model matrix, which consists of an extensive reference set of >450 cell/tissue types, including 223 hESC lines (Stem Cell Matrix-2’ (SCM2) database)[Nat Methods 8, 315-317 (2011)] lines, 41 iPSC lines, somatic cells, and tissues.
The final quantitative data file can be viewed on proprietary software provided by Life Technologies Corporation (Carlsbad, CA, USA).[https://assets.thermofisher.com/TFS-Assets/BID/Flyers/Stem-Characterization-Services-Flyer.pdf]

source_name: iPSCs (CFiS-S01)

label_protocol: gDNA was processed according to the manufacturer's protocol. Briefly, 250 ng of gDNA was digested with the restriction enzyme NspI. The digested DNA was then ligated to the NspI adapter and amplified by PCR. The PCR products were purified and fragmented with DNase I. The fragmented products were end-labeled with biotin and hybridized overnight to KaryoStat arrays (Thermo Fisher Scientific) in a GeneChip Hybridization Oven 645 (Thermo Fisher Scientific).

growth_protocol: Two different methods, StemFit AK03 (Ajinomoto) + iMatrix-511 (Matrixome)[iMatrix511+StemFit] and mTeSR™ Plus-cGMP (STEMCELL Technologies) + Biolaminin 521 LN (BioLamina)[LN521+mTeSR], were used to culture the iPSCs.

extract_protocol: RNA purification with this system involves cell preparation using a PureLink™ RNA Mini Kit (Catalog #12183025;(Thermo Fisher Scientific, Waltham, MA, USA) and quantification using the NanoDrop™2 (Thermo Fisher Scientific, Waltham, MA, USA). The GeneChip® for the PluriTest™ is prepared using 100 ng of total RNA. Genomic DNA (gDNA) was prepared using the Genomic DNA Purification Kit (Catalog K 0512;(Qiagen, Hilden, Germany) and quantified using the Qubit™ dsDNA BR Assay Kit (Catalog Q 32850GeneChip® Preparation;(Thermo Fisher Scientific, Waltham, MA, USA). A total of 250 ng of gDNA was used to prepare the GeneChip® for KaryoStat™ according to the instructions, which is an array that looks for copy number variants and single nucleotide polymorphisms across the genome.

treatment_protocol: Cell pellets were prepared by detaching cells using TrypLE™ Select Enzyme (Fisher Scientific).

value: iPSCs


title: HMEC control rep2

description: Library name: HMEC_2

value: Breast

value: ephitelial cells

value: WT_Plasmid control

value: lentiviral Infection


title: 9: iPSCs (LN521+mTeSR)

description: total DNA and RNA


title: DNA from MCF-7 control 3

description: DNA from MCF-7 control 3


title: Intestinal epithelial cells, crypt, rep 2

description:
Library name: Crypts-Epi-2
Column name in Rossen_FKPM.csv: 2_2_crypt_epi2


title: 3'-end mRNA-seq of OSC[DoraHA] and OSC[DoraHA-KO], rep1+rep2

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

description: The quantification of genes with SOLO

data_processing:
#Trimming of adapters: fastp -j 20 -i R1.fastq.gz -I R2.fastq.gz -l 18 --trim_poly_g --trim_poly_x -3 --adapter_fasta=../adapter.fasta \ -o trimmed.R1.fastq.gz  -O trimmed.R2.fastq.gz  unpigz -c trimmed.R1.fastq.gz | seqkit grep -j 20 -s -r -p ^[ATGCN]{10}[AGC]T{10} | \ Seqkit grep -j 20 -s -v -r -p ^T{11} | pigz > trimmed.filtered.R1.fastq.gz  python fastqCombinePairedEnd.py trimmed.filtered.R1.fastq.gz trimmed.R2.fastq.gz  cat ../adapter.fasta >Illumina TruSeq Adapter Read 1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA >Illumina TruSeq Adapter Read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT >polyA AAAAAAAAAAAAAAAAAAAA >polyG GGGGGGGGGGGGGGGGGGGG
#STAR solo mapping: STAR --genomeDir indexes/STAR_index_dmel_clenaed/ \ --runThreadN 16 \ --readFilesIn trimmed.R2.fastq.gz_pairs_R2.fastq.gz trimmed.filtered.R1.fastq.gz_pairs_R1.fastq.gz \ --readFilesCommand 'unpigz -c' \ --soloType CB_UMI_Simple \ --soloCBwhitelist bc_full_mRNA.txt \ --soloCBstart 8 --soloCBlen 4 --soloUMIstart 1 --soloUMIlen 7 \ --soloBarcodeReadLength 0 \ --outSAMtype BAM SortedByCoordinate \ --outSAMattributes NH HI nM AS CR UR CB UB GX GN sS sQ sM \ --clip3pAdapterSeq polyA \   --outFilterType BySJout \   --outFilterMultimapNmax 20 \   --outFilterMismatchNmax 999 \   --outFilterMismatchNoverLmax 0.1 \   --alignSJoverhangMin 8 \   --alignSJDBoverhangMin 1 \   --alignIntronMin 20 \   --alignIntronMax 100000 \   --alignMatesGapMax 100000 \   --soloCellFilter None \   --soloUMIdedup Exact \ --soloUMIfiltering - \ --limitBAMsortRAM 8295462913 \ --soloStrand  Forward \ --outWigType wiggle read1_5p \ --soloFeatures Gene Velocyto
# deduplication file= '' # resilt of SOLO name=$(basename ${file} .bam)  samtools index ${file}    # deduplex of BAM (remove PCR duplicates based on UMI) umi_tools dedup --umi-separator=: --umi-tag=UR --cell-tag=CR --extract-umi-method=tag --per-gene \ –gene-tag=GX -I ${file} --output-stats=${name}.test.umi_dedup -S ${name}.test.umi_dedup.bam -L ${name}.test.log samtools index ${name}.test.umi_dedup.bam      # extract individual samples (based on CR tag in bam) bamtools filter -in ${name}.test.umi_dedup.bam -script bam_filter.json -out ${name}.test.umi_dedup.filtered.bam bamtools split -tag CR -in ${name}.test.umi_dedup.filtered.bam  cat bam_filter.json { "filters" : [ { "id" : "A", "tag" : "CR:ATGC" }, {"id" : "C", "tag" : "CR:CGTA"}, {"id" : "G", "tag" : "CR:GTCA"}, {"id" : "T", "tag" : "CR:TACG"} ], "rule" : "A | C | G | T " }
Assembly: dm6

organism: Drosophila melanogaster

source_name: OSC

growth_protocol: The culture of Drosophila ovarian somatic cells OSC (Niki et al. 2006) (kindly provided by Dr. M. Siomi, University of Tokyo) was grown at 25°C in Shields and Sang M3 insect medium (Sigma-Aldrich, #S3652) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Gibco, #10270106), 10% fly extract, 10 µg/ml insulin (Sigma-Aldrich, #I9278), 0.6 mg/ml L-glutathione (Sigma-Aldrich, #G6013), 50 units/ml penicillin and 50 g/ml streptomycin. To prepare the fly extract, 1 g of 3-7 day-old flies were homogenized in 6.8 ml of M3 medium and centrifuged for 15 min at 1,500 g. The supernatant was heated for 10 min at 60°C and cleaned with centrifugation at 1,500 g for 1.5 h at 4°С. The obtained extract was filter-sterilized through 0.22 µm filters before usage.The medium for OSC[DoraHA] was supplemented with blasticidin; the medium for OSC[DoraHA-KO] was supplemented with hygromycin.

extract_protocol:
Total RNA
150 ng of total RNA was mixed with 40 ng of SID-X oligonucleotide (where X = 1, 2, 3 or 4), denatured at 85oC for 3 min followed by cooling to 35oC and kept at this temperature for 2 min. The SID-X oligonucleotide anneals at the poly-A tail of mRNA and contains 8 nt UMI part and 4 nt sample barcode part (Table S1). For RNA from different samples, SID-X (X = 1, 2, 3, or 4) oligonucleotides with sample-specific barcodes were used. After preheating the reverse transcription premix at 35oC, SuperScript II (Invitrogen) was added and the reaction continued at 42oC for 15 min. The short reaction time is required for reverse transcription of only the 3’-end of mRNAs instead of the entire transcript. To prevent SID-X primer hybridization at non-poly-A sites, cooling of the reverse transcription reaction mix lower than room temperature should be avoided. Reverse transcription was terminated with 3 µl of 0.5 M EDTA and then four samples tagged with different SID-X were pooled. The RNA:cDNA duplexes were purified with DCC-5 and eluted with water with subsequent alkaline hydrolysis of RNA with 250 mM NaOH at 65oC for 15 min. Single-stranded cDNAs were purified with OCC-5 and synthesis of the second strand of cDNA was performed. For this, cDNA was mixed with 1 µg of Random_hex_2 oligonucleotide (Table S1), denatured at 98oC and cooled to 25oC; the annealing at this temperature was carried out for 30 min. Synthesis was performed with a Large Fragment of Pol l (NEB) at 30oC for 1 h. To remove excess primers, the reaction mixture was treated with ExoSAP-IT (Promega) at 37oC for 30 min and purified with the DCC-5. Double-stranded cDNA was amplified by PCR with universal P5 and index P7 primers (Table S1) and products of 300-550 bp in length were cut from the agarose gel and purified with the GeneJET gel extraction kit (Thermo Scientific). The traces of adapter dimers were depleted using AMPure XP beads (Beckman) with a 0.8:1 ratio to gain the final library. The structure of SID-X primers and used sample-specific barcodes see the accompanied paper.

value: OSC

value: Pooled Cas9+;DoraHA+ and Cas9+;DoraHA+;DoraHA-KO


title: Ib1

description: IL‒1β‒induced SW1353 cells, rep 1

value: chondrosarcoma cells


title: PBSL1

description: IL-1β-induced and PBSL-treated cells, rep1

value: IL-1{beta}-induced and PBSL-treated cells


title: Intestinal epithelial cells, crypt, rep 1

description:
Library name: Crypts-Epi-1
Column name in Rossen_FKPM.csv: 2_1_crypt_epi1

value: small intestine, crypt


title: HMEC control rep1

description: Library name: HMEC_1

value: HMEC


title: small RNA-seq of OSC[DoraHA-KO], rep2

description: The result of miRNA quantification; gff

data_processing:
Trimming: skewer -x AGATCGGAAGAGCACACGTCT -t 20 -n -m tail -l 18 -1
# miRNA quantification with mirtop bcbio_nextgen.py -w template ../srna-template.yaml ../mirna_samples.csv *.fq.gz bcbio_nextgen.py /state/partition1/raid10/software/biosoft/bcbio_share/galaxy/bcbio_system.yaml mirna_samples/config/mirna_samples.yaml -n 8  mirtop gff -d --format seqbuster --sps dme --hairpin mirbase/hairpin_dme_mirbase22.fa \ --gtf mirbase/dm6_mirbase22.gff3 --database mirbase -o 5_miRNAs_bcbio/ $(find 5_miRNAs_bcbio/ \ -name "**.mirna") cp 5_miRNAs_bcbio/mirtop.gff 5_miRNAs/mirtop_bcbio_same_strand.gff mirtop export --sps dme --hairpin mirbase/hairpin_dme_mirbase22.fa --gtf mirbase/dm6_mirbase22.gff3 \ --format isomir -o 5_miRNAs $(find 5_miRNAs/ -name "mirtop_bcbio_same_strand.gff")
Assembly: dm6

extract_protocol:
Gel-fractioned 20-25 nt small RNAs
10 µg of small RNA fraction extracted with RNAzol RT (MRC) was separated in 15% denaturing PAGE and a gel piece containing 20-25 nt in length RNA was excised. RNA was eluted from the gel overnight in 400 µl of 0.4 M NaCl with rotation at RT and precipitated with 96% ethanol in the presence of linear acrylamide (NEB). Approximately 100 ng of purified RNA was used for library preparation according to the protocol with randomized splint ligation (Maguire et al. 2020). The sequences of the used oligonucleotides are in Table S1. After PCR amplification by universal P5 and index P7 primers, the libraries were treated with ExoSAP-IT (Promega) and purified with the DNA Clean and Concentrator kit (DCC-5, Zymo Research) to rid of any traces of primers and free adapters.


title: seedling, b23_raf_con1

description: Library name: b23_raf_con1

value: seedling

value: B2/3 RAF knockdown


title: seedling, WT_man1

description: Library name: WT_man1

value: WT

value: mannitol


title: WT_control_3

description: Library name: GA93941

data_processing:
Sequencing was performed on the Illumina NovaSeq X platform in 151-base single-end mode.
Generated reads were mapped to the mouse (mm10) reference genome using HISAT2 ver. 2.1.0. and SAMtools ver. 1.20.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: lung

extract_protocol:
RNA samples were extracted using RNeasy Mini Kit (QIAGEN) accroding to manufacturer's instruction.
The cDNA libraries were constructed according to the manufacturer's instructions using the TruSeq Stranded mRNA Library Prep (Illumina, Inc., San Diego, CA).

value: lung

value: Wildtype


title: KO_control_3

description: Library name: GA93942

value: Aldh1a1 KO


title: 7: iPSCs (iMatrix511+StemFit)

description: total DNA and RNA

value: iPSCs


title: Enterochromaffin cells, crypt, rep 3

description:
Library name: Crypts-EC-4
Column name in Rossen_FKPM.csv: 1_3_crypt_EC4

value: enterochromaffin cell


title: 6: iPSCs (iMatrix511+StemFit)

description: total DNA and RNA


title: 8: iPSCs (LN521+mTeSR)

description: total DNA and RNA


title: DNA from MCF-7 POU1F1 2

description: DNA from MCF-7 POU1F1 2

value: cell culture

value: breast cancer luminal A

value: overexpression of POU1F1


title: DNA from MCF-7 control 2

description: DNA from MCF-7 control 2

value: control


title: small RNA-seq of OSC[DoraHA], rep2

description: The result of miRNA quantification; gff

value: OSC


title: Enterochromaffin cells, crypt, rep 2

description:
Library name: Crypts-EC-3
Column name in Rossen_FKPM.csv: 1_2_crypt_EC3


title: Enterochromaffin cells, crypt, rep 4

description:
Library name: Crypts-EC-5
Column name in Rossen_FKPM.csv: 1_4_crypt_EC5


title: NC1

description: Untreated cells, rep1

value: chondrosarcoma cells

value: untreated cells


title: small RNA-seq of OSC[DoraHA-KO], rep1

description: The result of miRNA quantification; gff


title: small RNA-seq of OSC[DoraHA], rep1

description: The result of miRNA quantification; gff


title: KO_control_2

description: Library name: GA93940


title: 5: iPSCs (iMatrix511+StemFit)

description: total DNA and RNA


title: Enterochromaffin cells, villus, rep 1

description:
Library name: Villi-EC-3
Column name in Rossen_FKPM.csv: 3_1_villi_EC3

value: small intestine, villus


title: Enterochromaffin cells, crypt, rep 1

description:
Library name: Crypts-EC-1
Column name in Rossen_FKPM.csv: 1_1_crypt_EC1

value: small intestine, crypt


title: S.purpuratus female gonad heavy MNase digest replicate 2

status: Public on May 05 2025

city: Tallahassee

first: Jonathan

middle: H

last: Dennis

state: FL

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University

description:
Library name: Spur_heavy_rep2
replicate 2 heavy digest

library_source: genomic

data_processing:
The reads from heavy and light files were merged together to create total distribution files and processed in parallel with separate heavy and light digest files. All replicate files were processed in parallel. The quality of the raw fastq sequences was assessed with fastqc (v0.11.9) and trimmed with Trimmomatic v0.39 under moderate stringency conditions (Bolger et al., 2014). The post-trimming file quality was assessed with fastqc (v0.11.9) to ensure removal of poor-quality regions. The trimmed files were aligned with bowtie2 (v2.3.5.1) to the Spur 5.0 genome assembly (Langmead & Salzberg, 2012). SAM files were converted to BAM format and low-quality reads were removed with samtools view 1.10 (Li et al., 2009). Sorted BAM files were indexed with samtools index and mitochondrial reads were removed with samtools idxstats and samtools view. Resulting BAM files were deduplicated with picardtools markduplicates (v2.27.3 Picard Toolkit, 2019). Samples were read depth normalized with picardtools DownSampleSam within each replicate for each heavy and light files and across replicates for total distribution files. The genome coverage was calculated with Deeptools (v3.5.5) plotcoverage and GC bias was assessed with Deeptools computeGCBias (Ramírez et al., 2014). Nucleosome positioning was called with the dpos tool from DANPOS3 (v2.2.2) for heavy, light, and merged samples with the -m (mate paired) option (Chen et al., 2013). Resulting wig files were converted to bigwig format with the wigtoBigWig tool from the UCSC genome browser (Kent et al., 2010). MNase sensitivity was determined with Deeptools bigWigCompare by calculating the log2ratio of light to heavy digests.
The light digest bam files were converted into a bed format with bedtools v2.27.1 (Quinlan & Hall, 2010) bamTobed using the paired end flag. A custom awk script was used to isolate reads less than 70 bp and calculate the 20 bp centers of each read. Small fragment peaks were called using the centered data with MACS3 v3.0.0b1 (Zhang et al., 2008) using the effective S.pur genome size (calculated with the faCount tool from the UCSC genome browser binary utilities (Kent et al., 2010)) and the following flags:  --nomodel --nolambda --nomodel –bdg. The Xstreme tool from the meme suite v5.5.2 (Bailey et al., 2015) was used to identify enriched TF motifs from the JASPAR2022 (Castro-Mondragon et al., 2022; Sandelin et al., 2004) non-redundant database under the called peaks.
Assembly: Spur_5.0
Supplementary files format and content: All processed files are in bigwig format. *merged*bw files contain quantile normalized nucleosome distribution signal from combined light and heavy digests. *log2ratio*bw files contain MNase sensitivity signal (log2 ratio of light/heavy digests). Negative values reflect resistance to MNase and positive values reflect sensitivity to MNase digestion. *small*bw files contain coverage signal for reads less than 70bp.

organism: Strongylocentrotus purpuratus

source_name: gonad

growth_protocol: Wild Strongylocentrotus purpuratus individuals were collected from Ucluelet, British Columbia, Canada (48.935716, -125.558527) in September 2021. Urchin gonads were dissected out of the animal using a sterile scalpel and crosslinked in 1% v/v formaldehyde solution in 34 parts per thousand salinity seawater for 10 minutes at room temperature. Gonad samples were flash frozen in liquid nitrogen (-200°C) and stored at -80°C. The animal used for MNase digestion was determined to be female based on SNP analysis of Nodal (LOC579010) and SOXE (LOC581729) promoters (as described by Pieplow et al., 2023).

extract_protocol:
Samples were thawed and formaldehyde was quenched with 125mM Glycine while tissue was disrupted with a Dounce homogenizer. The homogenized tissue was divided into aliquots and pelleted by centrifugation for 10 minutes at 1000g at room temperature. The glycine supernatant was removed, and the sample was resuspended in nuclei isolation buffer (NIB: 10 mM HEPES at pH 7.8, 2 mM MgOAc2, 0.3 M sucrose, 1 mM CaCl2 and 1% Triton-X). The resuspended gonad nuclei were centrifuged for 10 minutes at 1000g at room temperature and pellets were rinsed twice in NIB. Rinsed and homogenized gonad samples diluted in NIB were pre-heated to 37°C prior to MNase digestion. A titration of MNase was added to each sample and pipetted gently to mix. Light and heavy digests were incubated at 37ºC for between 5-20 minutes.  Reactions were halted with the addition of 0.5M EDTA and crosslinks were reversed by overnight incubation at 65°C in the presence of SDS and Proteinase K.
Mononucleosomal and subnucleosomal DNA fragments from triplicate heavy and light digests were isolated using the Select-a-Size DNA Clean & Concentrator Kit (Zymo Research, cat D4080) by depletion of large fragments over 400bp. Between 200-300 ng of DNA was used to prepare libraries with the NEBNext Ultra II Library Prep Kit for Illumina with unique dual indices and 12 cycles of PCR amplification. Paired end 50 bp sequences were generated on the Florida State University College of Medicine’s NovaSeq 6000 Illumina sequencer.

value: gonad

value: female

tag: digest level

value: heavy


title: S.purpuratus female gonad light MNase digest replicate 2

description:
Library name: Spur_light_rep2
replicate 2 light digest

value: light


title: S.purpuratus female gonad heavy MNase digest replicate 1

description:
Library name: Spur_heavy_rep1
replicate 1 heavy digest


title: S.purpuratus female gonad light MNase digest replicate 1

description:
Library name: Spur_light_rep1
replicate 1 light digest


title: S.purpuratus female gonad heavy MNase digest replicate 0

description:
Library name: Spur_heavy_rep0
replicate 0 heavy digest


title: DNA from MCF-7 control 1

description: DNA from MCF-7 control 1


title: WT_control_2

description: Library name: GA93939

value: lung

value: Wildtype


title: S.purpuratus female gonad light MNase digest replicate 0

description:
Library name: Spur_light_rep0
replicate 0 light digest


title: S.purpuratus female gonad merged MNase digest replicate 2

description:
Library name: Spur_merged_rep2
replicate 2 merged digest

value: heavy + light


title: biofilm, B2

city: Xiamen

first: qiu

last: li

address: No. 185, Yinjiang Road, Jimei District, Xiamen City, Fujian Province

institute: Jimei University

description: Library name: B2

data_processing:
Reads were processed using the VITAseer v1.2 pipeline with default and recommended parameters.First, primer sequences and capture adpator sequences were trimmed in raw sequencing data. Then for each Read1, we extracted UMI (8 nts) and cell-specific barcode (20 nts) and merged sequenced barcodes that can be uniquely assigned to the same accepted barcode with a Hamming distance of 1 nts or less. Read2 was used to generate the gene expression matrix by the STARsolo module in STAR(2.7.10a) . The valid bacteria were identified by STARsolo.
Assembly: ASM2316962v1 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_023169625.1/)
Supplementary files format and content: gene matrix:barcodes.tsv.gz,features.tsv.gz,matrix.mtx.gz

organism: Vibrio alginolyticus

source_name: Vibrio algalinolyticus biofilm

extract_protocol:
The prepared bacteria suspension was permaeablized and blocked for single-stranded DNA-blocking. Random primers were then added for the reverse transcription of total RNA inside the cell. Subsequently, the generated cDNA fragments were ligated to adaptors inside the bacteria. The reverse-transcribed single-bacteria suspension and reagents, along with barcode beads containing cell barcodes and UMIs, were mixed. The mixture underwent encapsulation, capturing and barcoding using the VITAcruizer DP400 instrument. The resulting product underwent extension, resulting in barcoded cDNA strands.
PCR amplification was conducted using the cDNA as the template. The purified products after cDNA amplification were then used to constructed a standard next-generation sequencing library. The constructed single-cell library contained P5 and P7 adapters and was sequenced on a Xplus sequencer (Illumina) with 150 bp paired-end reads.

value: Vibrio algalinolyticus biofilm


title: S.purpuratus female gonad merged MNase digest replicate 0

description:
Library name: Spur_merged_rep0
replicate 0 merged digest


title: CRISPRgate library pool

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

country: Germany

institute: University Stuttgart

data_processing:
Data Filtering: Discard PhiX genome and remove low quality reads (<20)
Trimm forward read 5' end: 21 bp and 3' end: 39bp
Reverse complement reverse read and trimm 5' end: 22 bp and 3' end 6 bp
Join forward and reverse reads to one megaread
Split reads based on barcodes and trimm 3' end: 27 bp
Mageck count and normalized to reads per million
Library strategy: CRISPR screen

organism: synthetic construct

growth_protocol: TF-1 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS), 4 mM L-Glutamine, 10 mM HEPES, 1 mM Sodium pyruvate solution, 100 U/mL Penicillin and 100 µg/mL Streptomycin, 2 ng/mL recombinant GM-CSF in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
After 14 days post induction of ZIM3-Cas9 expression cells were harvested in a 1000x library representation and genomic DNA for the three single cell clones was isolated with phenol-extraction using PhaseLock tubes, followed by ethanol precipitation.
Multiple parallel 50 µL PCR reactions, each containing 1 µL gDNA template adding up to 7 µg gDNA, were performed to maintain sgRNA representation. sgRNAs were PCR amplified using the AmpliTaq Gold Polymerase (Life technologies). In a first round of PCRs, random barcodes and sample barcodes were added to the sgRNA sequences. PCR products for each single cell clone were combined and purified using the NucleoSpin Gel and PCR clean-up kit (macherey-Nagel). Afterwards using a second round PCR, using similar cycling conditions with the exception of 10 ng input as template and 7 total cycles the standard Illumina P7 and P5 adaptors were added. The final libraries were cleaned up from a 2% agarose gel, pooled and analyzed on an P2 flow cell (400 mio reads).

treatment_protocol: TF-1 cells expressing dox inducbile ZIM3-Cas9 were spinfected (900g) with 4µg/mL polybrene with lentivirus for the CRISPRgate library. sgRNA positive cells were measured after 2 days of transduction and selected for one week using 500 µg/mL G418 solution. ZIM3-Cas9 expression was induced using DOX and cells were cultivated for two weeks


title: E. coli, sgRNA pool, rep3

source_name: produced in E. coli

value: produced in E. coli

value: MegaX DH10B T1


title: E. coli, sgRNA pool, rep2


title: E. coli, sgRNA pool, rep1


title: MORC2 WT HEK293T cell line with transfected MORC2 - Replicate 2

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Library name: WT2

data_processing:
Processing of ATAC-seq reads followed closely the ENCODE data processing pipeline (https://www.encodeproject.org/data-standards/chip-seq). Briefly, sequence reads were trimmed prior to alignment to the human reference genome. Post-alignment filtering was performed to remove unmapped reads and read mates, not primary alignments, reads failing platform, orphan reads, read pairs mapping to different chromosomes, and low-quality reads (MAPQ < 30), while keeping only properly paired reads. Duplicated reads were marked and removed with Picard-tools.
ATAC-seq reads were aligned with bowtie2.
Assembly: T2T-CHM13v2.0
Supplementary files format and content: BigWig files were created with the deepTools BamCoverage program with reads per genomic content (RPGC) normalization in 10 bp windows. Duplicated reads and reads from sex and mitochondrial chromosomes from the T2T-CHM13v2.0 genome were discarded for normalization purposes.
Supplementary files format and content: narrowPeak files (in BED format) are peak regions called by MACS2 for each experiment in wild-type cell lines. Biological replicates were combined by the MACS2 program during the peak calling step.

extract_protocol:
50,000 cells were pelleted at 500 x g for 5 minutes at 4C then lysed on ice for 3 minutes in 50 μL ATAC-RSB Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2) also containing 0.1% (v/v) IGEPAL CA-630, 0.1% (v/v) Tween-20, 0.01% (w/v) Digitonin. After lysis, 1mL of ATAC-RSB containing only 0.1% (v/v) Tween-20 but no IGEPAL CA-630 or Digitonin was added, and nuclei were pelleted at 500 x g for 10 minutes at 4C. All supernatant was aspirated and discarded, and each pellet of nuclei was resuspended in 50 μL of transposition mix (25 μL 2x TD Buffer, 2.5 μL Tn5 transposase (100 nM final), 16.5 μL PBS, 0.1 μL 5% digitonin, 0.5 μL 10% Tween-20, 5 μL H2O) and incubated at 37 °C for 30 minutes exactly in a thermomixer with 1000 RPM mixing.
DNA was then purified using Zymo DNA Clean & Concentrator-5 Kit to generate 20 μL of product which was pre-amplified for 5 cycles using NEBNext 2x Master Mix (#E7649A) and indexed primers as described previously57. A 5 μL of pre-amplified DNA was then used in a 15 μL qPCR reaction using Promega GoTaq qPCR Master Mix to determine the required number of additional cycles to yield minimally amplified DNA for optimal library diversity for next-generation sequencing (determined to be 3-4 additional cycles for these libraries). Amplified DNA was then purified using NucleoMag NGS Clean-up and Size Select beads (Macherey-Nagel) using a 0.5x ratio of beads to DNA to initially clear large DNA fragments from the library and then a 1.5x ratio of beads to supernatant to adsorb DNA fragments of appropriate size for sequencing. DNA-bound beads were then washed twice with 80% EtOH and size-selected DNA was eluted in nuclease-free water. Libraries were sequenced on an Illumina NextSeq 2000 to produce 65bp paired-end reads.

tag: morc2 expression

value: Overexpression


title: MORC2 WT HEK293T cell line with transfected MORC2- Replicate 1

description: Library name: WT1


title: biofilm, B1

description: Library name: B1


title: MORC2 KO HEK293T cell line with MORC2 phosphomimetic-GFP overexpression - Replicate 1

description: Library name: RC-G1S6D

data_processing:
Processing of ATAC-seq reads followed closely the ENCODE data processing pipeline (https://www.encodeproject.org/data-standards/chip-seq). Briefly, sequence reads were trimmed prior to alignment to the human reference genome. Post-alignment filtering was performed to remove unmapped reads and read mates, not primary alignments, reads failing platform, orphan reads, read pairs mapping to different chromosomes, and low-quality reads (MAPQ < 30), while keeping only properly paired reads. Duplicated reads were marked and removed with Picard-tools.
ATAC-seq reads were aligned with bowtie2.
Assembly: T2T-CHM13v2.0
Supplementary files format and content: BigWig files were created with the deepTools BamCoverage program with reads per genomic content (RPGC) normalization in 10 bp windows. Duplicated reads and reads from sex and mitochondrial chromosomes from the T2T-CHM13v2.0 genome were discarded for normalization purposes.
Supplementary files format and content: narrowPeak files (in BED format) are peak regions called by MACS2 for each experiment in wild-type cell lines. Biological replicates were combined by the MACS2 program during the peak calling step.
Supplementary files format and content: ATAC-seq reads were summarized to promoter regions (TSS +/- 2kb ) using a strict RefSeq gene annotation with the Subread program (v2.0.6) and its featureCounts function. Read counts for Entrez IDs for all the samples were assembled as a count matrix in a tab-delimited text file.

value: MORC2 knock-out (sgRNA 1)

tag: plasmid


title: MORC2 KO HEK293T cell line with MORC2 phosphodead-GFP overexpression - Replicate 2

description: Library name: RC-G2S6A

value: MORC2 knock-out (sgRNA 2)


title: MORC2 KO HEK293T cell line with MORC2-GFP overexpression - Replicate 2

description: Library name: RC-G2WT

value: WT


title: MORC2 KO HEK293T cell line with MORC2 phosphomimetic-GFP overexpression - Replicate 2

description: Library name: RC-G2S6D


title: MORC2 KO HEK293T cell line with MORC2-GFP overexpression - Replicate 1

description: Library name: RC-G1WT


title: ChIP-seq MORC2 library from MORC2 WT HEK293T cell line - Replicate 2

data_processing:
Processing of ChIP-seq reads followed closely the ENCODE data processing pipeline. Briefly, sequence reads were trimmed prior to alignment to the human reference genome. Post-alignment filtering was performed to remove unmapped reads and read mates, not primary alignments, reads failing platform, orphan reads, read pairs mapping to different chromosomes, and low-quality reads (MAPQ < 30), while keeping only properly paired reads. Duplicated reads were marked and removed with Picard-tools.
ChIP-seq reads were aligned with the bowtie2 program following the data processing guidelines from ENCODE project [https://www.encodeproject.org/data-standards/chip-seq/].
Assembly: T2T-CHM13v2.0
Supplementary files format and content: BigWig files were created with the deepTools BamCoverage program with reads per genomic content (RPGC) normalization in 10 bp windows. Duplicated reads and reads from sex and mitochondrial chromosomes from the T2T-CHM13v2.0 genome were discarded for normalization purposes.
Supplementary files format and content: narrowPeak and broadPeak files (in BED format) are peak regions called by MACS2 for each experiment in wild-type cell lines. Biological replicates were combined by the MACS2 program during the peak calling step and IgG libraries were used as negative controls during ChIP-seq peak calling.

extract_protocol:
5-10 x 106 cells per IP were cross-linked by adding 1/10 volume of fresh 11% formaldehyde solution (50mM HEPES-KOH pH 7.4, mM NaCl, 1 mM EDTA, 1 mM EGTA, 11% formaldehyde) to a 1 x 106 cell suspension for 20 minutes at room temperature with mixing. 1/12.5 volumes of 2.5 M glycine was added to quench formaldehyde and cells were washed twice in ice-cold PBS. Cross-linked cells were lysed in Lysis Buffer 1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% (v/v) glycerol, 0.5% (v/v) IGEPAL CA-630, 0.25% (v/v) Triton X-100, 1x Roche cOmpleteTM, EDTA-free Protease Inhibitor Cocktail) for 10 minutes at 4 °C with rocking, pelleted at 1350 x g for 5 minutes at 4°C, then Lysis Buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x Roche cOmpleteTM, EDTA-free Protease Inhibitor Cocktail) for 10 minutes at room temperature with rocking, pelleted again at 1350 x g for 5 minutes at 4 °C, then resuspended in Lysis Buffer 3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) Na-Deoxycholate, 0.5% (v/v) N-lauroylsarcosine, 1x Roche cOmpleteTM, EDTA-free Protease Inhibitor Cocktail) and transferred to Covaris miniTUBEs. Cell lysates were sonicated using a Covaris E220 focused-ultrasonicator with the following settings to shear DNA to a size of 300-500 bp suitable for high-throughput sequencing: Fill Level 10, Duty Cycle 10, PIP 175, Cycles/Burst 200 for 80 seconds. 1/10 volume of 10% (v/v) Triton X-100 was then added to the sonicated lysate and cellular debris was pelleted at 20,000 x g for 10 minutes at 4 °C. Immunoprecipitation was then performed overnight at 4 °C with rotation using ProteinG Dynabeads (50 μL per IP) pre-coupled with antibody (5 μL per IP) in 0.5% BSA/PBS for >5 h. Antibodies used were anti-MORC2 Rabbit pAb (Invitrogen #PA5-51172), H3K9me3 Rabbit pAb (Abcam #8898), Rabbit IgG pAb (Abcam #ab46540). Following immunoprecipitation, beads were collected using a magnet and washed 5 times with Wash Buffer (50 mM HEPES-KOH pKa 7.55, 500 mM LiCl, 1 mM EDTA, 1% (v/v) IGEPAL CA-630, 0.7% (w/v) Na-Deoxycholate, then 1 time with Tris-EDTA-NaCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 50 mM NaCl). DNA was then eluted from beads by incubation in Elution Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% (w/v) SDS) at 65 °C for 30 minutes with shaking. Bead-free supernatant was reverse crosslinked by incubation at 65 °C for 6-15 h, diluted with equal volume of TE Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA), then digested sequentially with RNaseA (0.2 mg/mL) at 37 °C for 2h and Proteinase K (0.2 μg/mL) at 55 °C for 2 h.
Final immunoprecipitated DNA was then purified using Zymo ChIP DNA Clean & Concentrator kit and prepared for sequencing using Illumina Truseq 1⁄2 reaction library preparation kit. Libraries were sequenced on an Illumina NextSeq 2000 to produce 65bp paired-end reads.

value: Wild-type

tag: chip antibody

value: Anti-MORC2 Rabbit pAb (Invitrogen #PA5-51172)

tag: knock-out sgrna


title: S.purpuratus female gonad merged MNase digest replicate 1

description:
Library name: Spur_merged_rep1
replicate 1 merged digest

tag: tissue


title: ChIP-seq MORC2 library from MORC2 KO HEK293T cell line - Replicate 2

tag: genotype

value: MORC2 knock-out


title: ChIP-seq IgG library from MORC2 WT HEK293T cell line - Replicate 2

value: Rabbit IgG pAb (Abcam ab46540)


title: ChIP-seq IgG library from MORC2 KO HEK293T cell line - Replicate 2


title: ChIP-seq IgG library from MORC2 KO HEK293T cell line - Replicate 1


title: ChIP-seq IgG library from MORC2 WT HEK293T cell line - Replicate 1


title: ChIP-seq MORC2 library from MORC2 KO HEK293T cell line - Replicate 1


title: ChIP-seq H3K9me3 library from MORC2 WT HEK293T cell line - Replicate 2

value: H3K9me3 Rabbit pAb (Abcam #8898)


title: MORC2 WT HEK293T cell line with lipofectamine - Replicate 1

description: Library name: LIPO1

value: Control


title: ChIP-seq H3K9me3 library from MORC2 WT HEK293T cell line - Replicate 1


title: Raw_ID 101, Male, WT, Hu_ASO, Rep 4

city: Seattle

first: Robert

last: Bragg

state: Washington

address: 300 9th Ave

institute: University of Washington

description:
Library name: 101
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta

data_processing:
Sequence reads were trimmed to remove adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. Reads were aligned to the Mus musculus GRCm38 ERCC reference genome assembly (ENSEMBL) using STAR aligner v.2.5.2b. Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2.
Assembly: GRCm38
Supplementary files format and content: Text count files from featureCounts

source_name: Cerebellum

extract_protocol:
RNA was extracted and prepared using rRNA depletion
PE 2x150bp cDNA libraries were constructed at Azenta using the Illumina TruSeq RNA Sample Prep Kit with ERCC spike-in

value: Cerebellum


title: MORC2 WT HEK293T cell line with lipofectamine - Replicate 2

description: Library name: LIPO2


title: Raw_ID 35, Male, WT, Hu_ASO, Rep 3

description:
Library name: 35
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: Raw_ID 28, Female, WT, Hu_ASO, Rep 1

description:
Library name: 28
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: ChIP-seq H3K9me3 library from MORC2 KO HEK293T cell line - Replicate 1


title: MORC2 WT HEK293T cell line, Replicate 1

description:
ATAC_WT1_S17.trimmed.filt.nodup.bam
ATAC_WT_peaks.narrowPeak

data_processing:
Processing of ATAC-seq reads followed closely the ENCODE data processing pipeline. Briefly, sequence reads were trimmed prior to alignment to the human reference genome. Post-alignment filtering was performed to remove unmapped reads and read mates, not primary alignments, reads failing platform, orphan reads, read pairs mapping to different chromosomes, and low-quality reads (MAPQ < 30), while keeping only properly paired reads. Duplicated reads were marked and removed with Picard-tools.
ATAC-seq reads were aligned with the bowtie2 program following the data processing guidelines from ENCODE project [https://www.encodeproject.org/data-standards/chip-seq/].
Assembly: T2T-CHM13v2.0
Supplementary files format and content: BigWig files were created with the deepTools BamCoverage program with reads per genomic content (RPGC) normalization in 10 bp windows. Duplicated reads and reads from sex and mitochondrial chromosomes from the T2T-CHM13v2.0 genome were discarded for normalization purposes.
Supplementary files format and content: narrowPeak files (in BED format) are peak regions called by MACS2 for each experiment in wild-type cell lines. Biological replicates were combined by the MACS2 program during the peak calling step
Supplementary files format and content: ATAC-seq reads were first summarized to narrow windows of 250bp for differential analyses with the R/Bioconductor package csaw (v1.38.0). ATAC-seq reads were then summarized to promoter regions (TSS +/- 2kb ) for visualization purposes using a strict RefSeq gene annotation with the Subread program (v2.0.6) and its featureCounts function.


title: Raw_ID 118, Male, WT, Mo_ASO, Rep 5

description:
Library name: 118
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: fetal cat epidermis, enriched with anti-cKIT from an Arhgap36+/Y late-gestation embryo [C96F1]

description: Library name: C96F1

data_processing:
The library was sequenced on a single Illumina HiSeq4000 lane to generate ~450 million reads, which were aligned to the domestic cat fca126 genome assembly (GCF_018350175.1 with NCBI Felis catus Annotation Release 105) using the 10x Genomics CellRanger software (v7.1.0). The ‘cellranger count’ pipeline was used to output feature-barcode matrices. The ‘cellranger aggr’ pipeline was used to aggregate data from C96F1 and C96F2 into a combined matrix (linked to the C96F1 sample records).
Assembly: Domestic cat Fca126 genome assembly (GCF_018350175.1 with NCBI Felis catus Annotation Release 105)
Supplementary files format and content: Filtered feature barcode matrix in HDF5 format

source_name: epidermis

extract_protocol:
Single cell preparations from the late gestation embryo followed a workflow designed to enrich for melanoblasts. Dorsal skin was excised with micro scissors and treated overnight in Dispase (Stem Cell Technologies). Epidermal sheets, comprised of keratinocytes and migrating melanoblasts, were isolated by gentle scraping with a No.15-blade scalpel and dissociated with trypsin. Red blood cells were removed with a red blood cell lysis solution (Miltenyi Biotec) and then size-filtered to recover dissociated cell suspensions. To enrich for melanoblasts, ten million dissociated cells were incubated with a phycoerythrin-conjugated, CD117 (c-Kit) Monoclonal Antibody (clone 2B8, eBioscience, ThermoFisher Scientific). The antibody bound fraction was then captured using a column-magnetic bead separation procedure (Miltenyi Biotech). In each case, the bound cell fraction was ~200,000 cells, or ~2% of the unenriched population.
3’ end, single-cell barcoded libraries were prepared from cell suspensions using 10x Genomics single-cell RNA sequencing platform for targeted capture of 6000 cells, using  v3.0 chemistry. Library construction precisely followed 10x Genomics protocol for v.3.0 chemistry.

value: epidermis

tag: cell type

value: enrichment with anti-cKIT antibody

value: fetal stage 20 (44-48 days p.c.)

value: male


title: MORC2 KO HEK293T cell line, Replicate 1


title: MORC2 KO HEK293T cell line with MORC2 phosphodead-GFP overexpression - Replicate 1

description: Library name: RC-G1S6A


title: Raw_ID 89, Male, WT, Mo_ASO, Rep 4

description:
Library name: 89
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta


title: Raw_ID 88, Male, WT, Mo_ASO, Rep 3

description:
Library name: 88
2x150, extraction, sequencing, alignment, and counts compmleted by Azenta