title: gill, wild-source, time 2, s. salar, 3

description: Library name: g2_W3


title: Patient 0716b PBMCs, GEX

status: Public on Apr 18 2025

type: SRA

city: Chicago

first: Huiping

last: Liu

state: IL

address: 303 E Superior St, Room 5-250B

country: USA

institute: Northwestern University

description:
Library name: WBC_0716B_GEX
WBC_071621B_barcodes.tsv.gz
WBC_071621B_features.tsv.gz
WBC_071621B_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using CellRanger v4.0.0
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
White blood cells from breast cancer patients or healthy controls were isolated from peripheral blood samples and sorted using FACS
Patient cells were labelled with hashtag barcode oligo and libraries were prepared per manufacturer's instructions. Briefly, cells were loaded onto a 10X Chromium controller, and library was constructed using 10X Chromium Next GEM Single Cell 5' Library and Geal Bead kits (v1.1)

tag: tissue

value: PBMCs

tag: disease state

value: Cancer

tag: Sex

value: Female

tag: age

tag: race

value: White

tag: breast cancer_subtype

value: TNBC

tag: tumor stage

tag: ctc status

tag: alive


title: gill, farm-source, time 2, s. salar, 5

city: St. Andrews

first: Marc

last: Trudel

state: NB

address: 125 Marine Science Dr

country: Canada

institute: Department of Fisheries and Oceans Canada

description: Library name: g2_F6

library_source: transcriptomic

data_processing:
FastQC was completed on all raw sequence files for quality control.
Sequences were trimmed using the TruSeq3-PE-2 adapter sequence in Trimmomatic (version 0.39).
Splice-aware mapping was completed using STAR (Spliced Transcripts Alignment to the Reference). Two alignments were made on the sample set. Once for the L. salmonis genome and another for the S. salar genome.
FeatureCount was used to generate raw read counts.
EdgeR and DEseq2 were used to normalize and generate differential expression data.
The RNAseq short variant discovery pipeline from Genome Analysis Toolkit 4 (GATK4) was used to identify SNPs and In/Dels. Filtered using: QD< 2.0, QUAL< 30.0, SOR> 3.0, FS> 60.0, MQ< 40.0, MQRankSum< -12.5 and ReadPosRankSum< -8.0.
Pilot GWAS was completed using PLINK (version 1.9): missingness per individual (0.1), missingness per marker/SNP (0.1), minor allele frequency (0.05) and Hardy-Weinberg equilibrium (1x10-6).
Assembly: LSalAlt2s
Assembly: Ssal_v3.1: GCA_905237065.2
Supplementary files format and content: tab-delimited text file, includes raw counts for all samples. L. salmonis alignment.
Supplementary files format and content: tab-delimited text file, includes raw counts for all samples. S. salar alignment.

organism: Salmo salar

source_name: gill

growth_protocol: Laboratory cultured L. salmonis: 6 generations. S. salar in flow-through tanks.

extract_protocol:
RNA was extracted using a modified phenol-chloroform method described in (Chomczynski, 1993). Extracted RNA was then treated using TURBO DNase and followed by the RNeasy MinElute Cleanup Kit™ (Qiagen) as per manufacturers instructions prior to submission for RNA sequencing.
Library construction and subsequent sequencing was completed by Genome Quebec.

treatment_protocol: Reduced tank flow and exposed S. salar to L. salmonis for 1 hr at 50 copepodid/fish.

value: gill

tag: treatment

value: farm

tag: time


title: skin, wild-source, time 2, s. salar, 4

description: Library name: Sk2_W4

source_name: skin

value: skin

value: wild


title: gill, wild-source, time 2, s. salar, 1

description: Library name: g2_W1


title: gill, farm-source, time 2, s. salar, 4

description: Library name: g2_F5


title: gill, farm-source, time 2, s. salar, 3

description: Library name: g2_F4


title: gill, wild-source, time 2, s. salar, 4

description: Library name: g2_W4


title: gill, wild-source, time 1, s. salar, 3

description: Library name: g1_W3


title: gill, farm-source, time 1, s. salar, 3

description: Library name: g1_F3


title: gill, wild-source, time 1, s. salar, 2

description: Library name: g1_W2


title: gill, wild-source, time 1, s. salar, 1

description: Library name: g1_W1


title: gill, farm-source, time 1, s. salar, 2

description: Library name: g1_F2


title: gill, farm-source, time 1, s. salar, 1

description: Library name: g1_F1


title: MDA-MB-231, RB-BC, 1

status: Public on Apr 15 2025

city: Lianyungang

first: Song

middle: meng

last: wei

address: China

country: China

institute: Jiangsu Ocean University

description: Library name: RB-BC_1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files includes the raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, and the cells were treated with or without Rib_CA for 24 hr, respectively, and incubated in 5% CO2 at 37oC.

tag: cell line

tag: cell type

value: Human Breast Cancer Cell

value: RB-BC


title: MDA-MB-231, DMSO, 1

description: Library name: DMSO_1

value: DMSO


title: Neoribocic_2

status: Public on Apr 11 2025

description: Library name: Neoribocic_2

source_name: Human Breast Cancer Cell

value: Neoribocic


title: MDA-MB-231, DMSO, 2

description: Library name: DMSO_2


title: MDA-MB-231, RB-BC, 2

description: Library name: RB-BC_2


title: YW-LF_2

description: Library name: YW-LF_2

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, and the cells were treated with or without YW-LF for 24 hr, respectively, and incubated in 5% CO2 at 37oC.

value: YW-LF


title: MDA-MB-231, RB-1_1

status: Public on Apr 12 2025

first: Sen

last: Wang

address: No. 59 Cangwu Road, Haizhou District, Lianyungang City, Jiangsu Province

description: Library name: RB-1_1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: csv file includes the raw counts for each sample

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, and the cells were treated with or without RB-1 for 24 hr, respectively, and incubated in 5% CO2 at 37oC.


title: DMSO_1

description: Library name: DMSO_1


title: Neoribocic_1

description: Library name: Neoribocic_1


title: MDA-MB-231, RB-1_2

description: Library name: RB-1_2

treatment_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, and the cells were treated with or without RB-1 for 24 hr, respectively, and incubated in 5% CO2 at 37oC.


title: MDA-MB-231, DMSO_2

description: Library name: DMSO_2


title: DPSCs, R1, 3days

status: Public on Apr 10 2025

city: Changchun

first: Siyu

last: Chen

address: Qinghua Road

institute: Jilin University

description:
Library name: Sample7
Cells co-cultured with PRF treated with ROT/AA in Transwell system

data_processing:
FastQC for quality control STAR aligner to hg38 DESeq2 for differential expression
Assembly: GRCh38/hg38
Supplementary files format and content: RNA-seq

source_name: Dental pulp

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: Dental pulp

value: Primary human dental pulp stem cells (DPSCs)

value: Mesenchymal stem cell

value: PRF treated with ROT/AA (3 days)


title: DMSO_2

description: Library name: DMSO_2


title: DPSCs, R2, 3days

description:
Library name: Sample8
Cells co-cultured with PRF treated with ROT/AA in Transwell system


title: DPSCs, R3, 3days

description:
Library name: Sample9
Cells co-cultured with PRF treated with ROT/AA in Transwell system


title: YW-LF_1

description: Library name: YW-LF_1


title: DPSCs, P3, 3days

description:
Library name: Sample6
Cells co-cultured with pure PRF in Transwell system

value: Pure PRF (3 days)


title: MDA-MB-231, DMSO_1

description: Library name: DMSO_1


title: gill, farm-source, time 2, s. salar, 1

description: Library name: g2_F2


title: gill, farm-source, time 2, s. salar, 2

description: Library name: g2_F3


title: DMSO_2

description: Library name: DMSO_2


title: DPSCs, P2, 3days

description:
Library name: Sample5
Cells co-cultured with pure PRF in Transwell system


title: DPSCs, P1, 3days

description:
Library name: Sample4
Cells co-cultured with pure PRF in Transwell system


title: DPSCs, Controll3, 3days

description:
Library name: Sample3
control

value: control (3 days)


title: DPSCs, Controll2, 3days

description:
Library name: Sample2
control


title: Alzheimer’s Disease, IgG (control antibody)

status: Public on Apr 09 2025

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: Library name: Sample_AD_IgG.bw

library_source: genomic

data_processing:
Raw reads were trimmed using Trimmomatic (0.39). Further barcode trimming was performed using the Kseq trimmer. Trimmed reads were aligned to the human genome (hg19) using the BWA aligner
Assembly: hg19
Supplementary files format and content: Aligned deduplicated and normalized bigwig files
Library strategy: CUT&Run

molecule: genomic DNA

source_name: human brain

extract_protocol:
Frozen human brain tissue was thawed on ice and minced sharply into <1mm pieces. Next, 500 μl of chilled Nuclei EZ Lysis Buffer (Millipore Sigma, NUC-101, no. N3408) was added, and tissue was homogenized 10–20 times in a Dounce homogenizer. The homogenate was transferred to a 1.5-ml Eppendorf tube, and 1 ml of chilled Nuclei EZ Lysis Buffer was added. The homogenate was mixed gently with a wide-bore pipette and incubated for 5 min on ice. The homogenate was then filtered through a 70-μm mesh strainer and centrifuged at 500g for 5 min at 4 °C. Supernatant was removed, and nuclei were resuspended in 1.5 ml of Nuclei EZ Lysis Buffer and incubated for 5 min on ice. Nuclei were centrifuged at 500g for 5 min at 4 °C. After carefully removing the supernatant (pellet might be loose), nuclei were washed in wash buffer (1× PBS, 1.0% BSA and 0.2 U μl−1 of RNase Inhibitor). Nuclei were then centrifuged and resuspended in 1.4 ml of wash buffer for two additional washes. Nuclei were then filtered through a 40-μm mesh strainer. Intact nuclei were counted after counterstaining with Trypan blue in a standard cell counter.
The CUT&RUN Library Prep was performed using the Illumina NovaSeq 6000 Sequencing System at the University of Kansas Medical Center – Genomics Core (Kansas City, KS). Fragmented input and immunoprecipitated chromatin (5ng) was used to initiate the TruSeq ChIP Sample Prep Kit library preparation protocol with modifications for CUT&RUN sample input (Illumina Cat# IP-202-1012).

value: human brain

tag: chip antibody

value: IgG

value: Alzheimers Disease


title: Alzheimer’s Disease, antibody PARP, biol rep 3

description: Library name: Sample_ADC13_PARP.bw

value: PARP


title: healthy human brain, IgG (control antibody)

description: Library name: Sample_Ctrl_IgG.bw

value: healthy


title: Alzheimer’s Disease, antibody PARP, biol rep 1

description: Library name: Sample_ADC7_PARP.bw


title: healthy human brain, antibody PARP, biol rep 3

description: Library name: Sample_ADC14_PARP.bw


title: Alzheimer’s Disease, antibody PARP, biol rep 2

description: Library name: Sample_ADC11_PARP.bw


title: AsPC-1/MR/tet-MUC1shRNA_DOX+ Rep3

status: Public on Apr 08 2025

city: Brookline

first: Hiroki

last: Ozawa

address: 450 Brookline

institute: Dana-Farber Cancer Institute

description: Library name: 20241230_AsPC_1_MR_DOX_pos_3

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using the EdgeR-based TCC package.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: hg38
Supplementary files format and content: comma separated value file include raw counts for each sample
Supplementary files format and content: comma separated value file include TPM for each sample

source_name: pancreas

growth_protocol: AsPC-1/MR cells were maintained in Gibco RPMI 1640 Media containing 20% heat inactivated FBS.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

value: pancreas

value: panceatic cancer

tag: genotype

value: DOX

tag: batch


title: healthy human brain, antibody PARP, biol rep 1

description: Library name: Sample_ADC3_PARP.bw


title: AsPC-1/MR/tet-MUC1shRNA_DOX+ Rep1

description: Library name: 20241230_AsPC_1_MR_DOX_pos_1


title: AsPC-1/MR/tet-MUC1shRNA_DOX- Rep3

description: Library name: 20241230_AsPC_1_MR_DOX_neg_3

value: DMSO


title: AsPC-1/MR/tet-MUC1shRNA_DOX+ Rep2

description: Library name: 20241230_AsPC_1_MR_DOX_pos_2


title: AsPC-1/MR/tet-MUC1shRNA_DOX- Rep1

description: Library name: 20241230_AsPC_1_MR_DOX_neg_1


title: DMSO_1

description: Library name: DMSO_1

value: Human Breast Cancer Cell


title: GFP::ergo-1, IP, rep3

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

description:
Library name: Lib623
16-30 nt purified RNAs from Argonaute-RNA-co-IP

data_processing:
End-to-end data processing was done using the default configuration in the tinyRNA pipeline v1.5.0 (https://github.com/MontgomeryLab/tinyRNA).
Assembly: WS279
Supplementary files format and content: GFP-RDE-1_coIP_nrfl-1_oma-1-RNAi_norm_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in each of the conditions indicated.
Supplementary files format and content: rde-4_54h_norm_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in each of the conditions indicated.
Supplementary files format and content: rde-4_rde-1_72h_norm_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in each of the conditions indicated.
Supplementary files format and content: HA-ALG-1_coIP_nrfl-1-RNAi_norm_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in each of the conditions indicated.
Supplementary files format and content: GFP-RDE-1_coIP_nrfl-1-RNAi_norm_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in each of the conditions indicated.
Supplementary files format and content: GFP-ALG-3_coIP_norm_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in each of the conditions indicated.
Supplementary files format and content: GFP-ERGO-1_coIP_norm_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in each of the conditions indicated.

organism: Caenorhabditis elegans

source_name: gravid hermaphroditic adult whole animals

growth_protocol: Worms were grown for 50 or 54 hours (L4) or 68 or 72 hours (adults) from synchronized L1 larvae at 20˚C on media containing E. coli (OP50 or HT115).

extract_protocol:
Worms were washed from plates and rinsed with M9 3 times and flash frozed in liquid nitrogen. Total RNA from cell lysates or Argonaute co-immunoprecipitates was isolated using trizol/chloroform and isopropanol precipitation.
Small RNAs (~16-30-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and in some instances treated with NEB RNA 5' Pyrophosphohydrolase (RppH) to facilitate capture of 22G-RNAs. Libraries were then prepared according to the NEBNext Multiplex Small RNA kit protocol. PCR products (~134-148 bp) were size selected using 10% polyacrylamide gels.


title: GFP::ergo-1, rde-4(syb6665), IP, rep2

description:
Library name: Lib625
16-30 nt purified RNAs from Argonaute-RNA-co-IP

value: gravid hermaphroditic adult whole animals


title: GFP::ergo-1, rde-4(syb6665), IP, rep3

description:
Library name: Lib626
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::ergo-1, rde-4(syb6665), input, rep2

description:
Library name: Lib619
16-30 nt purified RNAs from cell lysate


title: GFP::ergo-1, IP, rep1

description:
Library name: Lib621
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::ergo-1, IP, rep2

description:
Library name: Lib622
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::ergo-1, rde-4(syb6665), input, rep1

description:
Library name: Lib618
16-30 nt purified RNAs from cell lysate


title: GFP::ergo-1, input, rep3

description:
Library name: Lib617
16-30 nt purified RNAs from cell lysate


title: GFP:, ergo-1, rde-4(syb6665), IP, rep1

description:
Library name: Lib624
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::ergo-1, input, rep2

description:
Library name: Lib616
16-30 nt purified RNAs from cell lysate


title: GFP::ergo-1, rde-4(syb6665), input, rep3

description:
Library name: Lib620
16-30 nt purified RNAs from cell lysate


title: GFP::ergo-1, input, rep1

description:
Library name: Lib615
16-30 nt purified RNAs from cell lysate


title: DPSCs, Controll1, 3days

description:
Library name: Sample1
control

value: Dental pulp

value: Wild-type


title: GFP::alg-3, rde-4(syb6665), IP, rep2

description:
Library name: Lib614
16-30 nt purified RNAs from Argonaute-RNA-co-IP

source_name: L4 stage larvae

value: L4 stage larvae


title: GFP::alg-3, rde-4(syb6665), IP, rep1

description:
Library name: Lib613
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::alg-3, IP, rep2

description:
Library name: Lib612
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: healthy human brain, antibody PARP, biol rep 2

description: Library name: Sample_ADC5_PARP.bw


title: GFP::alg-3, rde-4(syb6665), input, rep1

description:
Library name: Lib609
16-30 nt purified RNAs from cell lysate


title: GFP::alg-3, rde-4(syb6665), input, rep2

description:
Library name: Lib610
16-30 nt purified RNAs from cell lysate


title: GFP::alg-3, input, rep2

description:
Library name: Lib608
16-30 nt purified RNAs from cell lysate


title: GFP::alg-3, input, rep1

description:
Library name: Lib607
16-30 nt purified RNAs from cell lysate


title: AsPC-1/MR/tet-MUC1shRNA_DOX- Rep2

description: Library name: 20241230_AsPC_1_MR_DOX_neg_2


title: GFP::rde-1, rde-4(syb6665), nrfl-1, RNAi, IP, rep3

description:
Library name: Lib606
16-30 nt purified RNAs from Argonaute-RNA-co-IP

value: nrfl-1 RNAi


title: GFP::rde-1, rde-4(syb6665), nrfl-1, RNAi, IP, rep2

description:
Library name: Lib605
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::rde-1, nrfl-1, RNAi, IP, rep3

description:
Library name: Lib603
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::rde-1, rde-4(syb6665), nrfl-1, RNAi, IP, rep1

description:
Library name: Lib604
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::rde-1, nrfl-1, RNAi, IP, rep1

description:
Library name: Lib601
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::rde-1, rde-4(syb6665), nrfl-1, RNAi, input, rep3

description:
Library name: Lib600
16-30 nt purified RNAs from cell lysate


title: GFP::rde-1, rde-4(syb6665), nrfl-1, RNAi, input, rep2

description:
Library name: Lib599
16-30 nt purified RNAs from cell lysate


title: GFP::rde-1, nrfl-1, RNAi, IP, rep2

description:
Library name: Lib602
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: rde-4(syb6665), nrfl-1, oma-1, RNAi, 72h, adults, rep3

description:
Library name: Lib576
RppH-treated, 16-30 nt purified RNAs from cell lysate

value: nrfl-1 and oma-1 RNAi


title: rde-4(syb6665), nrfl-1, oma-1, RNAi, 72h, adults, rep2

description:
Library name: Lib575
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: rde-4(syb6665), nrfl-1, oma-1, RNAi, 72h, adults, rep1

description:
Library name: Lib574
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: GFP::rde-1, nrfl-1, RNAi, input, rep2

description:
Library name: Lib596
16-30 nt purified RNAs from cell lysate


title: rde-1(ne300), nrfl-1, oma-1, RNAi, 72h, adults, rep3

description:
Library name: Lib573
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: rde-1(ne300), nrfl-1, oma-1, RNAi, 72h, adults, rep1

description:
Library name: Lib571
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: HA::alg-1, rde-4(syb6665), nrfl-1, IP, rep3

description:
Library name: Lib594
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: rde-1(ne300), nrfl-1, oma-1, RNAi, 72h, adults, rep2

description:
Library name: Lib572
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: HA::alg-1, rde-4(syb6665), nrfl-1, IP, rep2

description:
Library name: Lib593
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::rde-1, nrfl-1, RNAi, input, rep1

description:
Library name: Lib595
16-30 nt purified RNAs from cell lysate


title: GFP::rde-1, nrfl-1, RNAi, input, rep3

description:
Library name: Lib597
16-30 nt purified RNAs from cell lysate


title: HA::alg-1, rde-4(syb6665), nrfl-1, IP, rep1

description:
Library name: Lib592
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::alg-3, IP, rep1

description:
Library name: Lib611
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: N2, nrfl-1, oma-1, RNAi, 72h, adults, rep2

description:
Library name: Lib569
RppH-treated, 16-30 nt purified RNAs from cell lysate

value: wild-type (N2)


title: HA::alg-1, nrfl-1, RNAi, IP, rep2

description:
Library name: Lib590
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: N2, nrfl-1, oma-1, RNAi, 72h, adults, rep1

description:
Library name: Lib568
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: N2, nrfl-1, oma-1, RNAi, 72h, adults, rep3

description:
Library name: Lib570
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: HA::alg-1, nrfl-1, RNAi, IP, rep3

description:
Library name: Lib591
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: HA::alg-1, nrfl-1, RNAi, IP, rep1

description:
Library name: Lib589
16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: rde-4(syb6665), 54h, L4s, rep2

description:
Library name: Lib566
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: HA::alg-1, rde-4(syb6665), nrfl-1, RNAi, input, rep3

description:
Library name: Lib588
16-30 nt purified RNAs from cell lysate


title: GFP::rde-1, rde-4(syb6665), nrfl-1, RNAi, input, rep1

description:
Library name: Lib598
16-30 nt purified RNAs from cell lysate


title: HA::alg-1, rde-4(syb6665), nrfl-1, RNAi, input, rep2

description:
Library name: Lib587
16-30 nt purified RNAs from cell lysate


title: rde-4(syb6665), 54h, L4s, rep1

description:
Library name: Lib565
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: HA::alg-1, rde-4(syb6665), nrfl-1, RNAi, input, rep1

description:
Library name: Lib586
16-30 nt purified RNAs from cell lysate


title: N2, 54h, L4s, rep3

description:
Library name: Lib564
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: HA::alg-1, nrfl-1, RNAi, input, rep2

description:
Library name: Lib584
16-30 nt purified RNAs from cell lysate


title: N2, 54h, L4s, rep2

description:
Library name: Lib563
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: HA::alg-1, nrfl-1, RNAi, input, rep1

description:
Library name: Lib583
16-30 nt purified RNAs from cell lysate


title: GFP::rde-1, rde-4(syb6665), nrfl-1, oma-1, RNAi, IP, rep1

description:
Library name: Lib554
RppH-treated, 16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::rde-1, rde-4(syb6665), nrfl-1, oma-1, RNAi, IP, rep2

description:
Library name: Lib555
RppH-treated, 16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::rde-1, nrfl-1, oma-1, RNAi, IP, rep2

description:
Library name: Lib553
RppH-treated, 16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::rde-1, rde-4(syb6665), nrfl-1, oma-1, RNAi, input, rep2

description:
Library name: Lib551
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: GFP::rde-1, nrfl-1, oma-1, RNAi, IP, rep1

description:
Library name: Lib552
RppH-treated, 16-30 nt purified RNAs from Argonaute-RNA-co-IP


title: GFP::rde-1, nrfl-1, oma-1, RNAi, input, rep1

description:
Library name: Lib548
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: GFP::rde-1, rde-4(syb6665), nrfl-1, oma-1, RNAi, input, rep1

description:
Library name: Lib550
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: GFP::rde-1, nrfl-1, oma-1, RNAi, input, rep2

description:
Library name: Lib549
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: iMOP-derived neurons_Control (Secondary antibody only)_CUT&Tag

status: Public on Apr 07 2025

city: Piscataway

first: Kelvin

middle: Y.

last: Kwan

state: NJ

address: 604 Allison Rd.

department: Cell Biology & Neuroscience

institute: Rutgers University

description: Library name: N_Control

data_processing:
Paired-end CUT&Tag reads were mapped to the mm10 reference genome using bowtie2.
deepTools bamCoverage was utilized to filter out duplicate reads and generate normalized bigiwig (per kilobase per million, RPKM) files.
Replicate bigiwig files were merged to generate the averaged bigwig files using deepTools bigwigCompare.
Peaks were identified using SAECR under norm and relaxed conditions, with the no primary antibody control serving as the threshold.
Assembly: mm10
Supplementary files format and content: bigwig, averaged bigwig signals from two replicates.
Supplementary files format and content: SEACR called CHD7, CTCF, H3K4me3, and EP300 peaks, consensus SEACR peaks from two replicates
Library strategy: CUT&Tag

organism: Mus musculus

source_name: iMOPs

growth_protocol: Proliferating iMOPs: DMEM/F12, 1XN21, 25 µg/ml carbenicillin and 20 ng/ml bFGF. iMOP-derived neurons: Neurobasal media, 1XN21, 2 mM L-glutamine, and 1 µM K03861.

extract_protocol:
For each CUT&Tag library preparation, 500,000 cells were used. Cells were incubated with primary antibodies targeting CHD7, CTCF, H3K4me3, and EP300, whereas the control sample was not treated with a primary antibody. DNA libraries were amplified via PCR and purified using SPRI beads. Sequencing was performed on the Illumina HiSeq 3000 platform with a 2×150 bp read configuration.
CUT&Tag-IT Assay kit from Active Motif (cat# 53160).

value: iMOPs

value: iMOP-derived neurons

value: wild-type


title: iMOP-derived neurons_EP300_CUT&Tag

description: Library name: N_EP300


title: iMOP-derived neurons_H3K4me3_CUT&Tag

description: Library name: N_H3K4me3


title: iMOP-derived neurons_CHD7_CUT&Tag

description: Library name: N_CHD7


title: rde-4(syb6665), 54h, L4s, rep3

description:
Library name: Lib567
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: iMOP-derived neurons_CTCF_CUT&Tag

description: Library name: N_CTCF


title: Proliferating iMOPs_EP300_CUT&Tag

description: Library name: P_EP300

value: Poliferating iMOPs


title: Proliferating iMOPs_Control (Secondary antibody only)_CUT&Tag

description: Library name: P_Control


title: Proliferating iMOPs_H3K4me3_CUT&Tag

description: Library name: P_H3K4me3


title: Proliferating iMOPs_CHD7_CUT&Tag

description: Library name: P_CHD7


title: Proliferating iMOPs_CTCF_CUT&Tag

description: Library name: P_CTCF


title: P7F1_RNAseq_mDOX_Rep3

status: Public on Apr 03 2025

city: Badalona

first: Gerard

last: Martinez-Cebrian

state: Barcelona

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

country: Spain

institute: Institut Josep carreras

data_processing:
For RNA-seq, raw sequencing reads were aligned to the human reference genome (hg38 assembly) with bowtie2 v2.3.5.1. Quantification of gene expression was performed with featureCounts from Subread v1.6.3 using uniquely mapping reads.
Assembly: hg38
Supplementary files format and content: Counts files

source_name: induced pluripotent stem cell muscle progenitor

growth_protocol: Human iPS cells expressing PAX7 (muscle progenitors)(Wu et al., 2016) were grown on 0.1% gelatin-coated culture plates in GlutaMAX supplemented IMDM (Gibco) with 15% stem cell qualified fetal bovine serum (Gemini), 1% penicillin/streptomycin (Corning), 50 μg/ml L-ascorbic acid (Sigma), 4.5mM 1-thioglycerol (Sigma), and 10 ng/ml recombinant human basic-FGF (Peprotech). These muscle progenitors were infected using lentiviral doxycycline-inducible or constitutive (EF1α promoter) constructs driving expression of a cDNA encoding the exact PAX7-FOXO1 or PAX3-FOXO1 fusion protein found in ARMS tumors. PAX7 transgene expression was induced by adding Dox (Sigma-Aldrich, final concentration 1 μg/ml), and then maintained throughout the protocol by replacing the medium (including dox) with 10 ng/ml human basic-FGF (Preprotech) every 2 days.

extract_protocol:
For RNAseq, total RNA was extracted from iPS control and iPS-MPPAX7-FOXO1 cells (in three technical replicates) using RNA Zymo-Spin columns (Zymo R1015). Before library preparation, rRNA was depleted with NEBNext rRNA Depletion Kit (NEB E6310).
RNA-seq libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760) and sequenced (2x50bp paired end) using an Illumina NextSeq 2000 machine.

treatment_protocol: For cultures without Dox, cells were harvested at day 3 following Dox removal for analysis.

value: -Dox


title: HA::alg-1, nrfl-1, RNAi, input, rep3

description:
Library name: Lib585
16-30 nt purified RNAs from cell lysate


title: N2, 54h, L4s, rep1

description:
Library name: Lib562
RppH-treated, 16-30 nt purified RNAs from cell lysate


title: P7F1_RNAseq_mDOX_Rep1

value: induced pluripotent stem cell muscle progenitor


title: P7F1_RNAseq_mDOX_Rep2


title: Control_RNAseq_mDOX_Rep3

value: WT


title: P3F1_RNAseq_mDOX_Rep1


title: P3F1_RNAseq_mDOX_Rep3


title: P3F1_RNAseq_mDOX_Rep2


title: invitro DMS0 DMminus rep1

status: Public on Mar 29 2025

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

data_processing:
Raw sequences reads were demultiplexed using Je to detect encoded barcode reads. Following this, reads were aligned to curated Sacchromyces tRNA reference genome.
The aligned reads were then used to determine RNA sequence abundance using custom python script. RNA modifications were detected based on aligned reads using samtools sort (http://www.htslib.org/,Li et al., 2009) feature sort the reads in a bam file format. Then IGVtools count (https://software.broadinstitute.org/software/igv/igvtools) count feature was utilized to output a wig files using the following parameters: -z 5 -w 1 -e 250 —bases. The resulting wig files were processed using a custom python script to identify nucleotide mutations as well as coverage of aligned reads.
Assembly: hg38
Supplementary files format and content: tsv files with gene name and abundance per sample
Supplementary files format and content: .sam.tsv files with mutation, deletion, coverage for each gene position per sample

source_name: human embryonic kidney cell

growth_protocol: HEK 293T cells (ATCC, CRL-11268) were cultured with complete DMEM medium under standard conditions according to ATCC

extract_protocol:
Total RNA was extracted from cells using Tri-zol extraction.
MSR-seq (PMID 35513407)

treatment_protocol: For in vivo cells, DMS was treated to live HEK293T cells. For in vitro cells, total RNA was extracted and then treated with DMS. DMS treatment concentrations were at 5% and 2%. Following MSR-seq, DM treatment was conducted on libaries using AlkB, as described in Li et al.

value: human embryonic kidney cell

value: invitro DMS0 DMminus


title: invitro DMS0 DMplus rep3

value: invitro DMS0 DMplus


title: AsO2 DMS0.05 DMplus rep3

value: AsO2 DMS0.05 DMplus


title: Control_RNAseq_mDOX_Rep2


title: invivo DMS0.05 DMplus rep3

value: invivo DMS0.05 DMplus


title: invivo DMS0 DMplus rep3

value: invivo DMS0 DMplus


title: AsO2 DMS0.02 DMminus rep3

value: AsO2 DMS0.02 DMminus


title: AsO2 DMS0 DMminus rep3

value: AsO2 DMS0 DMminus


title: Blood cells, mannitol buffer

status: Public on Apr 02 2025

city: Boston

first: Tal

middle: Deborah

last: Scully

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

description:
Library name: Cr_blood_mannitol
10x Genomics, Chromium Next GEM Single Cell 3′ v3.1

data_processing:
Single cell analysis (alignment, cell identification, gene counts) done by 10X Genomics Cell Ranger 6.1.2. No additional cell filtering or preprocessing was done on the processed data files.
Assembly: Ciona robusta genome HT 2019 assembly with KY21 gene models (Ghost Database http://ghost.zool.kyoto-u.ac.jp/download_ht.html ), plus mitochondrial genes from Ensembl KH (GCA_000224145.1) Ciona intestinalis genome. Fasta and gtf files for the combined genome are available on https://github.com/AllonKleinLab/paper-data/tree/master/Scully_mannitol_2025/C_robusta_genome_HT2019_KY21_with_Ensembl_mito
Supplementary files format and content: H5 Hierarchical Data Format

molecule: polyA RNA

organism: Ciona robusta

source_name: blood

growth_protocol: Animals were collected from the wild (Carlsbad, California, USA) and kept in a saltwater aquarium system the lab for 1-2 days prior to sample collection.

extract_protocol:
Animals were relaxed by incubating for 3 hours at 4 °C in about 400 mL artificial seawater with approximately 5 g of 99% L-menthol crystals (3 adults per 400 mL volume). Relaxed adults were dissected to expose the endostyle and large blood vessel on the ventral side of the animal. Blood was drawn from this vessel using a zero dead space tuberculin syringe with a 25G needle, then transferred to a microcentrifuge tube on ice which had previously been coated with bovine serum albumin (BSA) by washing with 0.5 mL of 10% (v./v.) BSA in Dulbecco’s phosphate-buffered saline (DPBS). Pooled blood was split into two tubes coated with 10% (v./v.) BSA in DPBS. Cells were pelleted by spinning at 800 g for 10 min at 4 °C in a swinging bucket centrifuge. The supernatant was gently removed, and cells were resuspended to a concentration of 1000-2000 cells/uL in the appropriate buffer: Ca2+- and Mg2+-free artificial seawater (CMF-ASW; 0.5 M NaCl, 9 mM KCl, 5 mM HEPES, pH 7.4) for Cr_blood_asw, or 0.7 M D-mannitol in PBS for Cr_blood_mannitol.
Library preparation was performed following the manufacturer's instructions for Chromium Next GEM Single Cell 3′ v3.1 Kits (10X Genomics 1000123, 1000127, and 1000190), with the following exception: When preparing the RT mix prior to cell encapsulation, the manufacturer protocol instructs to add nuclease-free water, then to add the cell suspension. The Cr_blood_asw sample was diluted with nuclease-free water as directed. The Cr_blood_mannitol sample was instead diluted with 0.7 M D-mannitol in PBS.

value: blood

value: wild-caught animals from Carlsbad, CA, USA

value: prepared in a low-salt, high osmolarity buffer (0.7 M D-mannitol in PBS)


title: AsO2 DMS0.05 DMminus rep3

value: AsO2 DMS0.05 DMminus


title: invivo DMS0.02 DMplus rep3

value: invivo DMS0.02 DMplus


title: invitro DMS0 DMminus rep3


title: AsO2 DMS0.05 DMplus rep2


title: invitro DMS0 DMplus rep1


title: invivo DMS0.05 DMminus rep3

value: invivo DMS0.05 DMminus


title: invivo DMS0.02 DMminus rep3

value: invivo DMS0.02 DMminus


title: AsO2 DMS0 DMplus rep3

value: AsO2 DMS0 DMplus


title: AsO2 DMS0.02 DMplus rep3

value: AsO2 DMS0.02 DMplus


title: AsO2 DMS0.05 DMminus rep2

value: human embryonic kidney cell


title: invitro DMS0 DMplus rep2


title: invitro DMS0 DMminus rep2

value: invitro DMS0 DMminus


title: invivo DMS0.02 DMplus rep2


title: AsO2 DMS0 DMminus rep2


title: AsO2 DMS0.02 DMminus rep2


title: AsO2 DMS0 DMplus rep2


title: invivo DMS0 DMminus rep3

value: invivo DMS0 DMminus


title: Control_RNAseq_mDOX_Rep1

value: induced pluripotent stem cell muscle progenitor

value: WT

value: -Dox


title: invivo DMS0.05 DMplus rep2

value: invivo DMS0.05 DMplus


title: AsO2 DMS0.02 DMplus rep2


title: invivo DMS0 DMplus rep2

value: invivo DMS0 DMplus


title: AsO2 DMS0.02 DMplus rep1


title: AsO2 DMS0 DMplus rep1


title: invivo DMS0 DMminus rep2


title: AsO2 DMS0.05 DMplus rep1

value: AsO2 DMS0.05 DMplus


title: invivo DMS0.02 DMminus rep2


title: invivo DMS0 DMplus rep1


title: AsO2 DMS0.05 DMminus rep1


title: AsO2 DMS0.02 DMminus rep1

value: AsO2 DMS0.02 DMminus


title: invivo DMS0.02 DMminus rep1


title: invitro DMS0.05 DMplus rep3

value: invitro DMS0.05 DMplus


title: invivo DMS0.05 DMplus rep1


title: invivo DMS0.05 DMminus rep1


title: invitro DMS0.05 DMplus rep2


title: invitro DMS0.05 DMplus rep1


title: invivo DMS0 DMminus rep1


title: invitro DMS0.05 DMminus rep3

value: invitro DMS0.05 DMminus


title: invitro DMS0.05 DMminus rep1


title: invitro DMS0.05 DMminus rep2


title: E40E

status: Public on Mar 27 2025

city: Montreal

first: Lorenzo

last: Ferri

state: Quebec

address: 1650 Cedar Avenue

department: Surgery & Oncology

institute: McGill University

description: Library name: E40E_R2130400190016_10156

data_processing:
fastqs generated with bcl2fastq (2.20.0.422) for illumina or by fgbio (1.3.0) for MGI G400
Assembly: GRCh38/ENSEMBL release 96
Supplementary files format and content: hdf5 file with anndata objects

source_name: esophageal adenocarcinoma

extract_protocol:
single cell capture using 10x genomics 3' mRNA library contruction from cells (v3)
After the dissociation protocol, using the single cell 3’ v3 protocol (10x Genomics), the cells were captured with the maximum target of 6000 cells.  During the capture the transcripts are first converted to cDNA and amplified.  The cell barcode and unique molecular identifier are added during the first strand synthesis of the double stranded cDNA.  The full length cDNA is then further processed to fragment the library to size for short read sequencing and amplified further to add the sequencing adapters and capture library index.

treatment_protocol: Tissue specimens were dissected and dissociated into single cell suspensions

value: esophageal adenocarcinoma

value: Normal esophagus


title: E40A

description: Library name: E40A_R2130400190016_10157

value: Normal stomach


title: E40D

description: Library name: E40D_R2130400190016_10157

value: Dysplasia


title: invivo DMS0.05 DMminus rep2

value: invivo DMS0.05 DMminus


title: E39E

description: Library name: E39E_R2130400190016_10144


title: E39C

description: Library name: E39C_R2130400190016_10144


title: E39A

description: Library name: E39A_R2130400190016_10144

value: Normal stomach+Metaplasia


title: E39D

description: Library name: E39D_R2130400190016_10144


title: E36E

description: Library name: E36E_R2130400190016_10140


title: E36D

description: Library name: E36D_R2130400190016_10137

value: Tumor


title: invivo DMS0.02 DMplus rep1

value: human embryonic kidney cell

value: invivo DMS0.02 DMplus


title: E36B

description: Library name: E36B_R2130400190016_10137

value: Metaplasia


title: E36C

description: Library name: E36C_R2130400190016_10137

value: Metaplasia+Dysplasia


title: E36A

description: Library name: E36A_R2130400190016_10137


title: AsO2 DMS0 DMminus rep1

value: AsO2 DMS0 DMminus


title: E35B

description: Library name: E35B_R2130400190016_10136


title: E35A

description: Library name: E35A_R2130400190016_10136


title: E35C

description: Library name: E35C_R2130400190016_10136


title: E34A

description: Library name: E34A_R2130400190016_10127


title: E33E

description: Library name: E33E_R2130400190016_10127


title: E34D

description: Library name: E34D_R2130400190016_10126


title: E33D

description: Library name: E33D_R2130400190016_10126


title: E34C

description: Library name: E34C_R2130400190016_10127


title: E34B

description: Library name: E34B_R2130400190016_10127


title: E33C

description: Library name: E33C_R2130400190016_10126


title: E40B

description: Library name: E40B_R2130400190016_10157


title: E31C

description: Library name: E31C_R2130400190016_10126


title: E33B

description: Library name: E33B_R2130400190016_10126


title: E33A

description: Library name: E33A_R2130400190016_10126


title: E31A

description: Library name: E31A_R2130400190016_10126


title: E31B

description: Library name: E31B_R2130400190016_10126


title: E30E

description: Library name: E30E_R2130400190018_10097


title: E30C

description: Library name: E30C_R2130400190018_10097


title: E30A

description: Library name: E30A_R2130400190018_10097


title: E28D

description: Library name: E28D_R2130400190016_10088


title: E28C

description: Library name: E28C_R2130400190016_10088


title: E28A

description: Library name: E28A_R2130400190016_10088


title: E27E

description: Library name: E27E_R2130400190016_10088


title: E27C

description: Library name: E27C_R2130400190016_10087

value: Metaplasia+Tumor


title: E27A

description: Library name: E27A_R2130400190016_10087


title: E26C

description: Library name: E26C_V300085343_1


title: E26E

description: Library name: E26E_V300085393_1


title: E27B

description: Library name: E27B_R2130400190016_10087

value: Dysplasia+Tumor


title: E26A

description: Library name: E26A_V300085343_1


title: E24C

description: Library name: E24C_V300085343_1


title: E26D

description: Library name: E26D_V300085343_1


title: E23D

description: Library name: E23D_V300074410_1


title: E23B

description: Library name: E23B_V300074410_1


title: E23E

description: Library name: E23E_V300074410_1


title: E30D

description: Library name: E30D_R2130400190018_10097


title: E23C

description: Library name: E23C_V300074410_1


title: E23A

description: Library name: E23A_V300074410_1


title: E24D

description: Library name: E24D_V300085343_1


title: E30B

description: Library name: E30B_R2130400190018_10097


title: E19D

description: Library name: E19D_V300063024_1


title: E19E

description: Library name: E19E_V300063024_1


title: E19C

description: Library name: E19C_V300063024_1


title: E19F

description: Library name: E19F_V300063024_1


title: E17D

description: Library name: E17D_V300057170_1


title: E17E

description: Library name: E17E_V300057170_1


title: E19B

description: Library name: E19B_V300063024_1


title: E19A

description: Library name: E19A_V300063024_1


title: E17C

description: Library name: E17C_V300057170_1

value: Metaplasia+Dysplasia+Tumor


title: E15D

description: Library name: E15D_V300039753_1


title: E17A

description: Library name: E17A_V300057170_1


title: E26B

description: Library name: E26B_V300085343_1


title: E15C

description: Library name: E15C_V300039753_1


title: E15A

description: Library name: E15A_V300039753_1


title: E24B

description: Library name: E24B_V300085343_1


title: E24A

description: Library name: E24A_V300085343_1


title: E15B

description: Library name: E15B_V300039753_1


title: E14D

description: Library name: E14D_V300035355_1


title: E14A

description: Library name: E14A_V300035355_1


title: E12A

description: Library name: E12A_V300035355_1


title: E21F

description: Library name: E21F_A00266_0457


title: E21E

description: Library name: E21E_A00266_0457


title: E21D

description: Library name: E21D_A00266_0457


title: E21A

description: Library name: E21A_A00266_0457


title: E21B

description: Library name: E21B_A00266_0457


title: E20C

description: Library name: E20C_A00266_0457


title: E20B

description: Library name: E20B_A00266_0457


title: E20D

description: Library name: E20D_A00266_0457


title: E20A

description: Library name: E20A_A00266_0457


title: E12D

description: Library name: E12D_A00266_0321


title: E13D

description: Library name: E13D_A00266_0317


title: E17B

description: Library name: E17B_V300057170_1


title: E13C

description: Library name: E13C_A00266_0317


title: E13B

description: Library name: E13B_A00266_0317


title: E12C

description: Library name: E12C_A00266_0321


title: E12B

description: Library name: E12B_A00266_0321


title: E11E

description: Library name: E11E_A00266_0321


title: E11D

description: Library name: E11D_A00266_0321


title: E11C

description: Library name: E11C_A00266_0321


title: E14C

description: Library name: E14C_V300035355_1


title: E14B

description: Library name: E14B_V300035355_1


title: E08D

description: Library name: E08D_A00266_0317


title: E11B

description: Library name: E11B_A00266_0321


title: E08C

description: Library name: E08C_A00266_0317


title: E08A

description: Library name: E08A_A00266_0317


title: E08B

description: Library name: E08B_A00266_0317


title: E21C

description: Library name: E21C_A00266_0457


title: E07D2

description: Library name: E07D2_A00266_0317


title: E07C

description: Library name: E07C_A00266_0317


title: E04T

description: Library name: E04T_A00266_0216


title: E07A

description: Library name: E07A_A00266_0317


title: E07D1

description: Library name: E07D1_A00266_0317


title: E07B

description: Library name: E07B_A00266_0317


title: E02M

description: Library name: E02M_A00266_0216


title: E02T

description: Library name: E02T_A00266_0216


title: NCI109B_USP22sg1_CE3

status: Public on Mar 11 2025

city: Seattle

first: David

last: MacPherson

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

data_processing:
STAR with 2-pass mapping was used to align single-end reads to human genome assembly hg38 and GENCODE gene annotation and mouse genome assembly mm10 and GENCODE gene annotation vM23. STAR2.7.7a and GENCODE v38 were used for NextSeq data. STAR v2.7.1a and GENCODE annotation v31 were used for HiSeq data. R package XenofilteR was used to remove reads of mouse origin with parameters recommended by authors. FastQC 0.11.9, RNA-SeQC 2.3.4, RSeQC 4.0.0 were used to check various QC metrics including insert fragment size, read quality, read duplication rates, rRNA rates, gene body coverage and read distribution in different genomic regions. FeatureCounts in Subread 2.0.0 was used to quantify gene-level expression by counting reads in an unstranded fashion.
Assembly: hg38
Supplementary files format and content: FHSC14_rawCounts.txt contains a gene-by-sample read count matrix. The total exonic length for each gene is included.
Supplementary files format and content: NCI109B_rawCounts.txt contains a gene-by-sample read count matrix. The total exonic length for each gene is included.

source_name: SCLC PDX tumor

growth_protocol: SCLC PDX models were grown subcutaneously in the flanks of immunocompromised NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen). mRNA was was poly(A) enriched using the NEBNext Poly (A) mRNA Magnetic Isolation Module (New England Biolabs) kit. 50 ng RNA was used for library construction.
RNA libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer’s protocol.

treatment_protocol: SCLC PDX models were treated for 48-hours with cisplatin (5 mg/kg)+etoposide (10 mg/kg) or saline vehicle. Treatments were administered intraparotineally.

value: SCLC PDX tumor

value: cisplatin+etoposide


title: NCI109B_USP22sg1_CE5


title: NCI109B_USP22sg1_CE4


title: Vascular smooth muscle cells, Healthy, DM

status: Public on Mar 25 2025

city: Scarborough

first: Lucy

last: Liaw

state: ME

address: 81 Research Drive

department: Center for Molecular Medicine

institute: MaineHealth Institute for Research

description:
Library name: 916-DM
10x Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger v7.0.1 (10x Genomics). The cellranger multi pipeline was used to generate gene expression count matrices from single-cell RNA sequencing data.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart, Aorta

growth_protocol: Cells were grown in SmGM2 media until passage 6, at which point they were seeded at a concentration of 1x10^5 cells/dish, and grown for two days before treatment.

extract_protocol:
Cell cultures for the 10x Genomics Flex assay were trypsinized, washed in PBS and resuspended in fixation buffer according to the 10x Genomics protocol for cell/nuclei fixation (CG000478). Fixed samples were stored at -80C and shipped to the Genomics Shared Resource at Dartmouth Cancer Center.
Cell suspensions were counted on a Cellometer K2 automated cell counter (Revity) using AO/PI fluorescent live/dead staining. Up to 1x106 cells were used as input into the hybridization reaction using the Human Transcriptome Probe Kit which contains sample specific barcodes. Four barcoded samples were pooled together in equal amounts and loaded onto a Chromium X instrument targeting 10,000 cells per sample. Libraries were prepared according to the manufacturer’s protocol (CG000527) and sequenced on a NextSeq2000 instrument (Illumina) targeting 25,000 reads/cell.

treatment_protocol: Cells were treated with either VSMC differentiation medium (DM, SmBM2 containing 2% FBS and 1mg/ml heparin), or lipogenesis treatment (Lipo-T Supplemental Table 3), and then replaced with maintenance medium (SmGM2 containing 5uM T091317, 33uM Biotin, and 1.25uM insulin) until harvested.

value: Heart, Aorta

value: ATCC:PCS-100-012 (HASMC)

value: Vascular smooth muscle cells

value: DM

value: Healthy


title: Vascular smooth muscle cells, Healthy, AdipoB

description:
Library name: 916-AdiopB
10x Genomics

value: Lipo-T


title: Vascular smooth muscle cells, AAA, DM

description:
Library name: 49-DM
10x Genomics

source_name: Abdominal, Aorta

value: Abdominal, Aorta

value: Abdominal aortic aneurysm

value: male


title: NCI109B_USP22sg1_CE1


title: NCI109B_USP22sg1_SAL2

value: saline


title: NCI109B_USP22sg1_SAL3


title: NCI109B_USP22sg1_SAL4


title: NCI109B_Ctrlsg1_CE3


title: NCI109B_USP22sg1_SAL1


title: NCI109B_Ctrlsg1_CE5


title: NCI109B_Ctrlsg1_CE2


title: NCI109B_Ctrlsg1_CE4


title: NCI109B_Ctrlsg1_SAL3


title: NCI109B_Ctrlsg1_SAL5


title: NCI109B_Ctrlsg1_SAL4


title: NCI109B_Ctrlsg1_SAL2


title: NCI109B_Ctrlsg1_SAL1


title: E04M

description: Library name: E04M_A00266_0216

value: esophageal adenocarcinoma

value: Metaplasia


title: FHSC14_USP22sg2_CE5


title: FHSC14_USP22sg2_CE4


title: NCI109B_Ctrlsg1_CE1


title: Vascular smooth muscle cells, AAA, AdipoB

description:
Library name: 49-AdipoB
10x Genomics


title: FHSC14_USP22sg1_CE2


title: FHSC14_USP22sg1_CE3


title: NCI109B_USP22sg1_CE2


title: FHSC14_USP22sg2_SAL5


title: FHSC14_USP22sg1_CE1


title: FHSC14_USP22sg2_SAL4


title: NCI109B_USP22sg1_SAL5


title: FHSC14_USP22sg2_SAL6


title: FHSC14_USP22sg1_SAL1


title: FHSC14_USP22sg1_SAL2


title: FHSC14_Ctrlsg2_CE6


title: FHSC14_Ctrlsg2_CE5


title: FHSC14_Ctrlsg1_CE3


title: FHSC14_Ctrlsg2_CE4


title: FHSC14_Ctrlsg1_CE1


title: FHSC14_Ctrlsg1_CE2


title: FHSC14_Ctrlsg2_SAL5


title: FHSC14_Ctrlsg2_SAL6


title: FHSC14_Ctrlsg1_SAL2


title: FHSC14_Ctrlsg1_SAL3


title: FHSC14_Ctrlsg2_SAL4


title: FHSC14_Ctrlsg1_SAL1


title: FHSC14_USP22sg2_CE6


title: H14_KEAP1g1_SAL6


title: H14_KEAP1g1_CE5


title: H14_KEAP1g1_CE4


title: H14_KEAP1g1_CE6


title: H14_Ctrlsg1_SAL4


title: H14_Ctrlsg1_SAL6


title: H14_Ctrlsg1_CE4


title: H14_Ctrlsg1_CE6


title: FHSC14_USP22sg1_SAL3


title: H14_Ctrlsg1_CE5


title: H14_KEAP1g1_CE3


title: H14_Ctrlsg1_SAL5


title: H14_Ctrlsg1_SAL3


title: H14_Ctrlsg1_SAL2


title: H14_KEAP1g1_SAL3


title: H14_Ctrlsg1_CE2


title: H14_Ctrlsg1_CE1


title: H14_Ctrlsg1_CE3


title: H14_Ctrlsg1_SAL1


title: H14_KEAP1g1_CE2


title: H14_KEAP1g1_SAL2


title: Mor_D2_SS_5

status: Public on Mar 04 2025

city: New York

first: Molly

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

data_processing:
Raw sequencing reads were mapped to the mm10 genome using the NGS-Data-Charmer pipeline.  In brief, reads were trimmed to remove adaptor and low-quality sequences, then the reads were aligned to the reference genome. Duplicate alignments were removed prior to gene counting and downstream analysis. Counts of mapped reads were obtained using featureCounts against the GENCODE m25 annotation.
Assembly: mm10
Supplementary files format and content: Morphine_raw_counts.txt: Tab-delimited text file containing the raw read counts for annotated genes, with individual samples present as columns. Morphine_FPKM.txt: Tab-delimited text file containing the normalized read counts (in fragments per kilobase per million) for annotated genes, with individual samples present as columns. DEGs.xlsx: DESeq2 differential expression analysis among D1 or D2 cells pertaining to morphine-treated mice.

source_name: Nucleus Accumbens

extract_protocol:
Direct-zol RNA microprep kit (Zymo Research)
SMARTer Stranded Total RNA-seq kit v3-Pico Input Mammalian (Takara Bio, CA)

treatment_protocol: Mice were euthanized by cervical dislocation, and bilateral NAc tissue was rapidly dissected on ice from 1-mm thick coronal sections using a 14G punch and flash frozen on dry ice. Nuclei were purified using fluorescence activated nuclei sorting (FANS)

value: Nucleus Accumbens

tag: drug

value: Mor

value: SS


title: Mor_D2_SS_3

tag: tissue


title: Mor_D2_SM_5

value: SM


title: H14_KEAP1sg1_CE1

value: SCLC PDX tumor

value: cisplatin+etoposide


title: H14_KEAP1sg1_SAL1


title: IP

status: Public on Mar 10 2025

city: Chengdu

first: Hongyu

last: Gao

state: Sichuan

address: hengdu City, Sichuan Province, Wuhou District people's South Road, three 14

institute: Sichuan University

description: Library name: IP

data_processing:
Trimmomatic (version 0.36) was used to filter out low-quality reads. Clean reads were mapped to the hg38 genome by BWA (version 0.7.15). Samtools (version 1.3.1) was used to remove potential PCR duplicates. MACS2 software (version 2.1.1.20160309) was used to call peaks by default parameters (bandwidth, 300 bp; model fold, 5, 50; p value, 0.00001). If the midpoint of a peak located closest to the TSS of one gene, the peak will be assigned to that gene. HOMER (version3) was used to predict motif occurrence within peaks with default settings for a maximum motif length of 12 base pairs. ClusterProfiler in R package was employed to perform Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. The GO and KEGG enrichment analysis were calculated using hypergeometric distribution with a q value cutoff of 0.05.
Assembly: hg38
Supplementary files format and content: This table contains genomic DNA peak information identified for each sample.
Library strategy: CUT&Run

source_name: human adipose-derived mesenchymal stem cell

growth_protocol: Human adipose-derived mesenchymal stem cells were cultured in basal medium at 5% CO2 and 37°C. When the cell density reached 70-80%, the cells were induced to osteogenic differentiation for 10 days.

extract_protocol:
Hyperactive pG-MNase CUT&RUN Assay Kit (Vazyme, China) was used to perform the experiment according to the manufacturer's instructions. Living hASCs were collected and bound using Concanavalin A-coated magnetic beads pro. Cell membranes were permeabilized using Digitonin. Through the mediation of PHC2/IgG antibody and Protein G, the MNase nuclease fused to Protein G targeted and cleaved the DNA sequence near the target protein. Finally, DNA fragmentation was terminated and released, and DNA extraction and purification were conducted.
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the I NEXTFLEX® ChIP-Seq Library Prep Kit for Illumina® Sequencing（NOVA-5143-02, Bioo Scientific） and sequenced on Illumina Novaseq 6000 with PE 150 method.


title: IgG

description: Library name: IgG

value: human adipose-derived mesenchymal stem cell


title: MC38 tum reaction 1, GEX

status: Public on Mar 07 2025

city: San Francisco

first: Mark

last: Bridge

state: CA

address: 513 Parnassus Ave

institute: UCSF

description:
Library name: A57-1_GEX
Gene expression

data_processing:
Cell Ranger v3.1.0 and v.7.0.0 were used to align the raw sequencing data and to generate count matrices.
Did not run separate HTO libraries ... (fastq files), but cells with each hashtag were extracted from the multiplexed sample computationally.
Assembly: GRCm38 - mm10
Supplementary files format and content: Tab-separated values files and matrix files from CellRanger output

source_name: Subcutaneous Tumor

extract_protocol:
Inguinal tumor-draining lymph nodes (TDLNs) and tumors were surgically removed with sterilized equipment. Lymph nodes were mechanically dissociated between two super-frosted microscope slides and washed into wells of 6-well plates containing cold PBS. Tumors were minced with scalpel blades and digested to single cell suspensions by incubation for 1h at 37C in tumor digestion media containing DMEM, 10%FBS, 2 mg/ml Collagenase IV (C5138, Sigma-Aldrich) and DNAse I (D5025, Sigma-Aldrich). Then, tumor lysates were filtered through a 100 μm filter into 50 ml conical tubes and filled with cold PBS. Tissue single cell lysates were centrifuged at 450 g for 5 minutes at 4C. Supernatants were discarded and pellets were resuspended in 5 ml ACK Lysing Buffer (118-156-101, Quality Biological), mixed well and kept on ice for 5 minutes. Lysis was stopped by filling the tubes with cold PBS. Samples were centrifuged again and finally resuspended in 1 ml cold PBS. Viable cells for downstream use were counted in a Vi-CELL cell counter (Beckman Coulter) at a 1:60 dilution.
Library was performed according to the manufacter’s instructions (single cell 10x 5’ version 2 protocol, 10x Genomics). Briefly, cell suspensions were combined with master mix and loaded into the chip with gel beads to generate the gel bead-in-emulsion (GEM), which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. Reverse transcription was performed on the poly-A RNA within each GEM. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads and amplified by PCR. To prepare libraries from cDNA, SPRIselect beads were used to isolate the correct size fragments. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added during library construction.

value: Subcutaneous Tumor


title: TDLN reaction 1

description:
Library name: A52-1
Gene expression

source_name: Lymph node

value: Lymph node


title: MC38 tum reaction 2, GEX

description:
Library name: A57-2_GEX
Gene expression


title: H14_KEAP1g1_SAL4


title: Mor_D2_MS_7

value: MS


title: TDLN reaction 2

description:
Library name: A52-2
Gene expression


title: Mor_D2_SS_7


title: Mor_D2_SS_6


title: Mor_D2_MS_4


title: Mor_D2_MS_1


title: Mor_D2_SS_2


title: Mor_D2_SM_7


title: Mor_D2_MM_7

value: MM


title: Mor_D2_SS_1


title: Mor_D2_SS_4


title: Mor_D2_SM_4


title: Mor_D2_SM_3


title: Mor_D2_SM_1


title: Mor_D2_SM_6


title: Mor_D2_MM_6


title: TDLN reaction 3

description:
Library name: A52-3
Gene expression


title: Mor_D1_SS_8


title: Mor_D2_MM_1


title: Mor_D1_SS_7


title: Mor_D2_MS_6


title: Mor_D2_MS_8


title: Mor_D2_MS_5


title: Mor_D2_MS_2


title: Mor_D2_MM_4


title: Mor_D2_MS_3


title: Mor_D2_SM_2


title: Mor_D2_MM_5


title: Mor_D1_SS_1


title: Mor_D1_SM_8


title: Mor_D2_MM_3


title: Mor_D1_SS_2


title: Mor_D1_SS_6


title: Mor_D2_MM_2


title: Mor_D1_SM_7


title: Mor_D1_SM_5


title: Mor_D1_SS_5


title: Mor_D1_MS_9


title: Mor_D1_SS_4


title: Mor_D1_SS_3


title: Mor_D1_MS_8


title: Mor_D1_SM_3


title: Mor_D1_MS_7


title: Mor_D1_MS_5


title: Mor_D1_SM_2


title: Mor_D1_SM_1


title: Mor_D1_MS_3


title: Mor_D1_MS_2


title: Mor_D1_MS_4


title: Mor_D1_MM_7


title: Mor_D1_MS_6


title: Mor_D1_MM_6


title: Mor_D1_MM_4


title: Mor_D1_MM_5


title: Mor_D1_MM_3


title: DarG silenced (Input) replicate 3

status: Public on Feb 26 2025

city: Southampton

first: Alex

last: COUTO ALVES

address: 216 Tremona Street

department: School of Human Development and Health

country: United Kingdom

institute: University of Southampton

description: Library name: 9-R2in

data_processing:
The raw sequencing reads were pre-processed with fastp (version 0.23.4) to remove sequencing adapters and low-quality bases.
The reads were then aligned to the reference genome of Mycobacterium bovis subsp. bovis strain AF2122/9739 using bwa-mem2 (version 2.2.1) with default settings.
Misaligned and multimapping reads were filtered out by excluding reads with MAPQ scores below 30 and retaining only primary alignments (–F 256) and properly paired reads (–f 2) using samtools (v1.18)41.
A custom R script was used to count paired-reads that mapped to both ends of each DNA fragment generated by the Alu1 restriction enzyme across the genome.
Assembly: Mycobacterium bovis subsp. bovis strain AF2122/97
Supplementary files format and content: csv file containing the raw counts for all samples and the genomic coordinates of the features (fragments).

organism: Mycobacterium tuberculosis variant bovis

source_name: Bacille Calmette-Guérin (BCG)

extract_protocol:
Cultures were centrifuged and resuspended in TE pH8.0.  An equal volume of methanol:chloroform (2:1) was added, and cultures were rocked for 5 minutes by hand.  The bacilli were centrifuged and the pellet dried, then resuspended in TE pH8.0 and distributed into Lysing Matrix B tubes (MP Biomedicals).  An equal volume of phenol:chloroform:isoamyl alcohol (25:24:1) was added, and the bacilli were disrupted using a FastPrep homogeniser.   The mixture was centrifuged to pellet the debris and to separate the phases.  The upper aqueous phase was subjected to a further extraction with phenol:chloroform:isoamyl alcohol, and two extractions with chloroform.  gDNA was precipitated with 0.1 volumes of 3M sodium acetate pH5.2, and 1 volume of propan-2-ol, pelleted by centrifugation, washed with 70% ethanol, resuspended in TE pH8.0 and frozen at -20°C. 10µg aliquots of gDNA were digested in a total volume of 250 µL with 20U of Alu1 enzyme (NEB) and 1µg RNAse (DNase free; Roche) in 1x CutSmart buffer, overnight at 37°C.Fragmented DNA was purified using the Genomic DNA Clean and Concentrator Kit – 10 (Zymed), following the manufacturer’s protocol.
Libraries were prepared using the TruSeq DNA Library Preparation kit following to manufacture’s instructions

value: Bacille Calmette-Guerin (BCG)

value: plasmids pRH2502 (dCas9Spy) and pRH5982 (darG-sgRNA)

value: anhydrotetracyline (ATC)

tag: chip-antibody


title: DarG silenced (Input) replicate 2

description: Library name: 8-R2in


title: DarG silenced (ChIP/ADPrSeq) affinity purified for ADP-ribose, replicate 3

description: Library name: 12-R2out

value: rabbit anti-poly/mono-ADP ribose antibody (E6F6A, Cell Signaling Technology)


title: Mor_D1_MM_2


title: Mor_D1_SM_4


title: Mor_D1_SM_6


title: DarG silenced (Input) replicate 1

description: Library name: 7-R2in


title: DarG non-silenced (ChIP/ADPrSeq)  affinity purified for ADP-ribose, replicate 3

description: Library name: 6-R1out


title: DarG non-silenced (Input) replicate 2

description: Library name: 2-R1in


title: DarG non-silenced (ChIP/ADPrSeq)  affinity purified for ADP-ribose, replicate 2

description: Library name: 5-R1out


title: DarG non-silenced (ChIP/ADPrSeq)  affinity purified for ADP-ribose, replicate 1

description: Library name: 4-R1out


title: DarG non-silenced (Input) replicate 1

description: Library name: 1-R1in


title: DarG silenced (ChIP/ADPrSeq) affinity purified for ADP-ribose, replicate 1

description: Library name: 10-R2out


title: TfhZG_S, rep1, bulk seq

status: Public on Feb 24 2025

city: Columbus

first: Hsin-Jung

middle: Joyce

last: Wu

state: Ohio

address: 1322 Neil Ave, Columbus OH 43201

department: Internal medicine

institute: Ohio State University

description:
exp1_raw count.txt
exp1_normalized count.txt

data_processing:
Partek Flow (https://www.partek.com/partek-flow/)
Unaligned reads were aligned with STAR and mapped to mm39 using Partek Flow.
Read counts were normalized by DESeq2 by using Partek Flow.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each samples.
Supplementary files format and content: tab-delimited text file includes normalized counts for each samples.

source_name: spleen

extract_protocol:
Total RNA was extracted using Trizol reagent (Thermo Fisher) according to the manufacturer protocol.
Poly A enrichment or non-directional library preparation for ultra low input mRNA

value: spleen

value: follicular helper T cells

tag: sorted cell_type

value: ZG


title: TfhZG_PP, rep2, bulk seq

description:
exp2_raw count.txt
exp2_normalized count.txt

source_name: Peyer's patch

value: Peyer's patch


title: DarG non-silenced (Input) replicate 3

description: Library name: 3-R1in


title: Tfh_PP, rep2, bulk seq

value: control


title: TfhZG_PP, rep1, bulk seq


title: TfhZG_S, rep2, bulk seq


title: Mor_D1_MS_1

value: Nucleus Accumbens

value: Mor


title: Tfh_PP, rep1, bulk seq


title: MDA-PCa-2b, SMARCA2/4 degrader, AR, rep2

status: Public on Feb 01 2025

city: South San Francisco

first: Tomasz

last: Włodarczyk

state: California

address: 1 DNA Way

institute: Genentech

description: DNA-seq

data_processing:
ChIP-seq sequence data was processed using an ENCODE-DC/chip-seq-pipeline2 -based workflow (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Briefly, fastq files were aligned on the hg38 human genome reference using Bowtie2 (v2.2.6) followed by alignment sorting (samtools v1.7) of resulting bam files with filtering out of unmapped reads and keeping reads with mapping quality higher than 30. Duplicates were removed with Picard’s MarkDuplicates (v1.126) function, followed by indexation of resulting bam files with samtools. For each bam file, genome coverage was computed with bedtools (v2.26.0), followed by the generation of bigwig (wigToBigWig v377) files. Peaks were called with SPP for each treatment sample using a pooled input alignment (.bam file) as control.
Assembly: GRCh38-2020-A
Supplementary files format and content: bigwig and bed files returned by the encode chip-seq pipeline. They contain information about peak positions.

growth_protocol: MDA-PCa-2b and DU145 cells were obtained from ATCC. MDA-PCa-2b cells were cultured with HCP1 medium (Enzo, catalog number AES-0403), 20% FBS, 1x Glutamine and pen/strep. DU145 was cultured with RPMI-1640 media with 10% FBS and 2mM L-Glutamine. The cells were split every 4-5 days to maintain the appropriate density.

extract_protocol:
Cells (10 x 10^6) were crosslinked by 10-minutes of 1% formaldehyde. Formaldehyde was quenched by the addition of glycine. Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0). Nuclei were sheared with Covaris sonicator (E220) using the following setup: Fill level – 10, Duty Cycle – 15, PIP – 350, Cycles/Burst – 200, Time – 8-minutes). Sheared chromatin was immunoprecipitated overnight with the following antibodies: SMARCA4 (ab110641), FOSL1 (PA5-66880 – Invitrogen) and TEAD1 (BD #610923). Antibody chromatin complexes were pulled down with Protein A or Protein A/G magnetic beads and washed twice in IP wash buffer I. (1% Triton, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer II (1% Triton, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer III. (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC) and once in TE buffer (10 mM EDTA and 200 mM Tris, pH 8.0). DNA was eluted from the beads by vigorous shaking for 20-minutes in elution buffer (100mM NaHCO3, 1% SDS). DNA was de-crosslinked overnight at 65C and purified with MinElute PCR purification kit (Qiagen).
Sequencing ready libraries were generated using NEBNext ® Ultra™ II DNA Library Prep Kit for Illumina ® (New England Biolabs E7645). Libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and profiled using the D5000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on an Illumina sequencer to generate 25 million paired end 50-base pair reads per library.

treatment_protocol: DU145 and MDA-PCa-2b were treated with 100 nM SMARCA2_4.1 (SMARCA2/4 degrader) or DMSO for 24 hours before cells were harvested for ChIP-seq

value: prostate adenocarcinoma

value: Abcam ab110641


title: Tfh_S, rep1, bulk seq


title: Tfh_S, rep2, bulk seq


title: MDA-PCa-2b, SMARCA2/4 degrader, AR, rep1

description: DNA-seq


title: MDA-PCa-2b, DMSO, AR, rep2

description: DNA-seq


title: MDA-PCa-2b, DMSO, AR, rep1

description: DNA-seq


title: Mor_D1_MM_1


title: 90

status: Public on Jan 31 2025

first: Matthew

last: Smith-Raska

address: 1300 York Ave.

department: Pediatrics

institute: Weill Cornell Medicine

description: Library name: Sample 8

data_processing:
Adapter and quality trimming of sequencing reads were performed using cutadapt
HISAT2 was used for aligning sequncing reads against the mouse genome GRCm38
Gene quantification was done using feature-counts
DESeq2 was used for normalization and differential gene expression analysis
Assembly: GRCm38
Supplementary files format and content: excel file of log2 normalized counts

source_name: Liver

extract_protocol:
RNA was isolated using the Qiagen RNeasy Lipid Tissue RNA Kit
NEB Ultra II Directional RNA Library Prep

value: Liver

value: Hepatocyte

value: Wild type descended from Khdc3-null maternal grandmother (F2 outcross)


title: 88

description: Library name: Sample 7


title: 86

description: Library name: Sample 6


title: 120

description: Library name: Sample 4

value: Wild type (WT)


title: 85

description: Library name: Sample 5


title: 118

description: Library name: Sample 3


title: 116

description: Library name: Sample 1


title: 117

description: Library name: Sample 2


title: S24, Viral Hepatitis

status: Public on Jan 20 2025

city: Solna

first: Hong

last: Yang

state: Stockholm

address: Tomtebodavägen 23A

country: Sweden

institute: KTH Royal Institute of Technology/Science For Life Laboratory

description: Library name: S24

data_processing:
The output of Kallisto, including estimated counts and TPM (transcript per kilobase million)-based transcript-level expressions,were then converted to gene-level expressions by the Bioconductor package tximport (v1.22.0)with the tx2gene option set to link transcripts to the respective genes. Protein-coding genes were considered for the mentioned step and subsequent analyses. Differential expression analysis was carried out using the DESeq2 Bioconductor package (v1.34.0), following a standard protocol across all the pairwise comparisons.
Assembly: Bulk RNA-seq data from tissues were aligned and quantified using Kallisto (v0.46.2) following a standard procedure against the Human genome (GRCh38, version 102) downloaded from Ensembl official website (https://www.ensembl.org/index.html).
Supplementary files format and content: Tab-delimited Raw counts for every gene and samples

source_name: Explant Liver

extract_protocol:
For total RNA extraction, snap-frozen human liver tissues were subjected to homogenization using stain-free steel beads in PowerLyzer 24 (Hilden, Germany) followed by Zymo Research Quick RNA Miniprep kit (Irvine, CA, USA) manufacturer’s protocol. The quality and quantity of the extracted RNA were assessed spectrophotometrically using NanoDrop (Thermofisher, Waltham, MA, USA), and the RNA integrity number (RIN) values were measured by TapeStation (Agilent Tech, Santa Clara, CA, USA). The amount of total RNA was measured more accurately by fluorometric determination with an RNA Broad Range kit (Thermofisher, Waltham, MA, USA) by using Qubit (Thermofisher, Waltham, MA, USA, USA).
Preparation of total RNA-Seq libraries was performed with Illumina Stranded Total RNA Prep and Ligation with Ribo-Zero Plus kit following the manufacturer’s standard protocol. The libraries were then pair-end (2X100bp) sequenced on the NovaSeq 6000 platform, generating, on average, 25 million fragment reads per sample. Raw sequence data (.bcl) was converted to FASTQ with the Dragen Bio-IT platform (v3.9.5). The quality of RNA-seq data was assessed by FastQC(v0.11.9).

value: Explant Liver


title: S25, Viral Hepatitis

description: Library name: S25


title: 22057P3BM; dBM; NGS-2709

status: Public on Jan 21 2025

city: Heraklion

first: Matthieu

middle: David

last: Lavigne

address: Nikolaou Plastira 100

country: Greece

institute: IMBB-FORTH

description:
Library name: 2709
22057P3BM

data_processing:
The quality of the FASTQ files was assessed with the FastQC software. Reads were aligned to the human (hg38) genomewith the Hisat2 aligner (hisat2 -p32 -x $REFERENCE_GENOME -q fastq/$FILE_ID.fastq -S $FILE_ID.sam --score-min L,0,-0.5 -k 2). Htseq-counts was utilized to summarize reads at the gene level (htseq-count -f bam -s yes -i gene_id bam/$FILE_ID.bam data/refs/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf> $COUNTS_DIR/NGS$FILE_ID).
For downstream analysis presented in the paper, differential expression analysis (DEA) was conducted by running EdgeR via SARTools 1.5.0. For each comparison (dPB (peripheral M-MDSCs from DLBCL patients) vs hPB (peripheral M-MDSCs from healthy individuals)  and  M-MDSCs from blood dPB) vs M-MDSCs from BM (dBM)  of DLBCL patients, DEGs in either group of the comparison) were defined by applying the following threshold p-value <0.05, which was considered statistically significant. Heatmaps and GO Bubbleplots were created in R with an in-house   developed script which is based on the complex heatmap R package. GO analysis was run on the webtool Metascape using default parameters.
Assembly: hg38
Supplementary files format and content: The processed data consists of a count table of the number of raw reads per gene for all samples.

source_name: Bone marrow

growth_protocol: The DLBCL cohort consisted of 33 newly diagnosed patients recruited through the Haematology Clinic at the University General Hospital of Heraklion, Greece and an age-matched group of 12 healthy individuals. Diagnosis was based on the 5th WHO criteria. Eligible healthy donors had no history of autoimmune disease or immunosuppression due to a known disease or medication. Bone marrow was obtained from healthy volunteers during total hip arthroplasty at the Orthopedic Clinic of the University General Hospital of Heraklion, Greece.

extract_protocol:
Flow cytometry analysis in whole blood and bone marrow samples: Peripheral blood (PB) and BM samples were collected into tubes containing EDTA, and mononuclear cells (PBMCs and BMMCs) were isolated over a density gradient using Ficoll-Paque Plus (GE Healthcare) within 24 hours of sample collection. Following density gradient centrifugation, at least one million single cells per sample were stained with fluorochrome-coupled antibodies. The monoclonal antibodies used for labelling of samples were: ECD-labelled anti-HLA-DR (Immu-357), PC7-labeled anti-CD33 (D3HL60.251), APC-labeled anti-CD14 (RM052), FITC-labeled anti-CD11b (94), PE-labeled anti-CD15 (80H5), all antibodies from Beckman Coulter-Immunotech. Total MDSCs, monocytic MDSCs (M-MDSCs) and granulocytic myeloid derived suppressor cells (PMN-MDSCs) were measured by flow cytometry using the NAVIOS cytometry system (Beckmann Coulter) and analysed using KALUZA software (Beckmann Coulter).  Gating strategy is shown in Figure 1. Briefly, total MDSCs were assessed as CD11b+CD33+ HLADRlow/−, while M-MDSCs were gated as CD11b+CD33+ HLADRlow/−CD14+ CD15− and PMN-MDSCs as CD11b+ CD33+ HLA-DRlow/−CD14− CD15+. Cell sorting of MDSCs was performed under aseptic conditions using 70-micron nozzle with a BD FACS Aria III (BD Biosciences). RNA Isolation and 3′ RNA sequencing. RNA from FACS-sorted M-MDSCs was isolated using Nucleospin RNA XS kit (Macherey-Nagel), according to the manufacturer’s instructions. The quality and quantity of isolated RNA were measured using 2100 Bioanalyser  (Agilent)  and RNA 6000 Pico Kit reagents (Agilent).
RNA samples with RNA integrity number (RIN)>7 were used for library construction using the 3′ mRNA-Seq Library Prep Kit FWD for Illumina (QuantSeq-LEXOGEN) as per the manufacturer’s instructions. Amplification was controlled to obtain optimal unbiased libraries across samples by assessing the number of cycles (ranging from 20-24) required by qPCR. DNA High Sensitivity Kit for bioanalyzer was used to assess the quantity and quality of libraries, according to the manufacturer’s instructions (Agilent). Libraries were multiplexed and sequenced on an Illumina Nextseq 500 at the genomics facility of IMBB FORTH according to the manufacturer’s instructions.

treatment_protocol: All DLBCL patients were treated homogeneously with the RCHOP immunochemotherapy combination. Exclusion criteria were infections, autoimmune diseases, or prior steroid treatment. Demographics, disease characteristics, and outcomes were collected from the patients’ medical files after signing informed consent.

value: Bone marrow

value: Myeloid derived suppressor cells (MDSCs)

value: RCHOP immunochemotherapy


title: S23, Viral Hepatitis

description: Library name: S23


title: S21, Viral Hepatitis

description: Library name: S21


title: S16, Viral Hepatitis

description: Library name: S16


title: S20, Viral Hepatitis

description: Library name: S20


title: S17, Viral Hepatitis

description: Library name: S17


title: S14, Alcohol-related liver disease

description: Library name: S14


title: S15, Alcohol-related liver disease

description: Library name: S15


title: S19, Viral Hepatitis

description: Library name: S19


title: S11, Alcohol-related liver disease

description: Library name: S11


title: S18, Viral Hepatitis

description: Library name: S18


title: DarG silenced (ChIP/ADPrSeq) affinity purified for ADP-ribose, replicate 2

description: Library name: 11-R2out

value: Bacille Calmette-Guerin (BCG)

value: plasmids pRH2502 (dCas9Spy) and pRH5982 (darG-sgRNA)

value: anhydrotetracyline (ATC)

value: rabbit anti-poly/mono-ADP ribose antibody (E6F6A, Cell Signaling Technology)


title: S13, Alcohol-related liver disease

description: Library name: S13


title: S12, Alcohol-related liver disease

description: Library name: S12


title: S10, Alcohol-related liver disease

description: Library name: S10


title: S09, Alcohol-related liver disease

description: Library name: S09


title: S08, Viral Hepatitis and peri-tumor

description: Library name: S08


title: S06, Viral Hepatitis and peri-tumor

description: Library name: S06


title: S05, Viral Hepatitis and peri-tumor

description: Library name: S05


title: S07, Viral Hepatitis and peri-tumor

description: Library name: S07


title: S04, Viral Hepatitis and peri-tumor

description: Library name: S04


title: S03, Viral Hepatitis and peri-tumor

description: Library name: S03


title: S01, Viral Hepatitis and peri-tumor

description: Library name: S01


title: S02, Viral Hepatitis and peri-tumor

description: Library name: S02


title: Tanalith dilution 37,000X C

status: Public on Jan 17 2025

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

description:
Library name: NAT37C
This sample is from mycelium grown with Tanalith diluted 37,000X. It is the third of three biological replicates used in this experiment.

data_processing:
Illumina sofware was used by IGA to generate fastq raw data files
raw reads were paired, trimmed (quality limit=0.05, automatic read through adapter trimming, discard short reads) and mapped against Phanerochaete chrysosporium RP78 v4.0 transcripts (https://mycocosm.jgi.doe.gov/Phchr4_2/Phchr4_2.home.html) using CLC Genomics Workbench v23.0.5 (Qiagen, Courtaboeuf, France).
For mapping, the minimum length fraction was 0.9, the minimum similarity fraction 0.9, and the maximum number of hits for a read was set to 10.
Differentially expressed genes (DEGs) were calculated using DESeq2 (v1.32) and unique mapped gene reads as entry .
Condition-specific differentially expressed genes (DEGs) were identified for each pairwise condition, using a false discovery rate (FDR) < 0.05 and a log2 fold-change (Log2FC) ≥ |1| as cut-off.
Assembly: Phanerochaete chrysosporium RP78 v4.0 transcripts  (https://mycocosm.jgi.doe.gov/Phchr4_2/Phchr4_2.home.html)
Supplementary files format and content: tab-delimited text files include Protein ID, raw counts, RPKM, TPM and CPM values for each sample

organism: Phanerodontia chrysosporium

source_name: Mycelium

growth_protocol: Phanerochaete chrysosporium RP78 was cultivated on solid 1% malt 3% agar plates at 37°C with or without Tanalith E3474 and Korasit KS2.

extract_protocol:
The fungal mycelium was harvested post 3 days fungal growth on both formulation at two different concentrations using a scalpel, and was immediately snap-frozen in liquid nitrogen. From harvested sample, total RNA from P. chrysosporium was extracted using the RNeasy Plant Mini Kit (Qiagen), following the standard protocol of the provider, with additional Dnase treatment and LiCl precipitation.
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology Services (Udine, Italy)

treatment_protocol: Stock solutions of Tanalith E3474 and Korasit KS2 were prepared by diluting them by 145 fold in pure water. These stock solutions were then filtered using a 0.22 µM filter and used to reach final dilutions of 37,000X and 18,000X in the culture medium.  For Tanalith E3474, a dilution of 37,000X corresponds to 3 mg/L of copper and to 59 ng/mL of each azole (i.e 0.19 µM of tebuconazole and 0.17 µM of propiconazole). This dilution was chosen because the concentration of copper is in line with the amount of copper we measured in the 24h water-leachate of Tanalith E3474 treated wood (personal data) and with the one measured in the 24h water-leachate of wood vacuum-pressure impregnated using a commercial copper ethanolamine solution. For Korasit KS2, a dilution of 37 000X corresponds to 2.75 mg/L of copper and 4.9 mg/L of quaternary ammonium compounds (QAC).

value: Mycelium

value: Tanalith dilution 37,000X


title: Tanalith dilution 37,000X B

description:
Library name: NAT37B
This sample is from mycelium grown with Tanalith diluted 37000X. It is the second of three biological replicates used in this experiment.


title: Tanalith dilution 37,000X A

description:
Library name: NAT37A
This sample is from mycelium grown with Tanalith diluted 37000X. It is the first of three biological replicates used in this experiment.


title: S22, Viral Hepatitis

description: Library name: S22


title: Korasit dilution 37,000X C

description:
Library name: NAK37C
This sample is from mycelium grown with Korasit diluted 37,000X. It is the third of three biological replicates used in this experiment.

value: Korasit dilution 37,000X


title: Korasit dilution 37,000X B

description:
Library name: NAK37B
This sample is from mycelium grown with Korasit diluted 37,000X. It is the second of three biological replicates used in this experiment.


title: Tanalith dilution 18,000X A

description:
Library name: NAT18A
This sample is from mycelium grown with Tanalith diluted 18000X. It is the first of three biological replicates used in this experiment.

value: Tanalith dilution 18,000X


title: Tanalith dilution 18,000X C

description:
Library name: NAT18C
This sample is from mycelium grown with Tanalith diluted 18000X. It is the third of three biological replicates used in this experiment.


title: Tanalith dilution 18,000X B

description:
Library name: NAT18B
This sample is from mycelium grown with Tanalith diluted 18000X. It is the second of three biological replicates used in this experiment.


title: Korasit dilution 18,000X B

description:
Library name: NAK18B
This sample is from mycelium grown with Korasit diluted 18000X. It is the second of three biological replicates used in this experiment.

value: Korasit dilution 18,000X


title: Korasit dilution 18,000X A

description:
Library name: NAK18A
This sample is from mycelium grown with Korasit diluted 18000X. It is the first of three biological replicates used in this experiment.


title: PBMC (cartridge 1)

status: Public on Jan 06 2025

city: Newcastle upon tyne

first: Tegan

last: McTaggart

address: Framlington Place

institute: Newcastle University

description: BD Rhapsody

data_processing:
For human scRNAseq, fastq files were transferred to seven brdiges platform and files were checked for quality control and DBEC files (.csv, .mtx, .tsv) were obtained through the BD Rhapsody Targeted Analysis Pipeline run. The DBEC files were imported to R using ReadMtx() function.
Assembly: hs1 (human data)
Supplementary files format and content: C1_Sample_Tag_Metrics.csv, C2_Sample_Tag_Metrics.csv, C3_Sample_Tag_Metrics.csv: assigned sample tag for each putative cell
Supplementary files format and content: C1_Sample_Tag_ReadsPerCell.csv, C2_Sample_Tag_ReadsPerCell.csv, C3_Sample_Tag_ReadsPerCell.csv: Reads per bioproduct per cell
Supplementary files format and content: C1 barcodes.tsv, C2 barcodes.tsv, C3 barcodes.tsv: cell barcode
Supplementary files format and content: C1 matrix.mtx, C2 matrix.mtx, C3 matrix.mtx: cell matrix
Supplementary files format and content: C1 features.tsv, C2 features.tsv, C3 features.tsv: gene expression
Supplementary files format and content: C1 sample tag.csv, C2 sample tag.csv, C3 sample tag.csv: sample tag

source_name: PBMC

extract_protocol:
PBMCs isolated from healthy control and patient blood, remaining as per manufacturers instruction
As per manufacturer's instruction

value: PBMC

value: Immune cells


title: Korasit dilution 37,000X A

description:
Library name: NAK37A
This sample is from mycelium grown with Korasit diluted 37000X. It is the first of three biological replicates used in this experiment.


title: SCG8

status: Public on Dec 20 2024

first: Bushra

last: Samad

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counts were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: .tsv metadata file
Supplementary files format and content: Seurat .RData file

source_name: myometrium/endometrium

extract_protocol:
Dissected uterine tissues were thoroughly minced and stored in 90% fetal bovine serum (FBS) (R&D Systems, cat. #S11150) and 10% DMSO (Sigma-Aldrich, cat. #D8418) in liquid nitrogen until the day of processing. scRNA-Seq data was collected over 3 separate experimental batches and 10 pools. For non-pregnant and GD5.5 IIS samples, each replicate consisted of uteri from 2 mice pooled together. At the time of processing, tissues were thawed, washed twice in PBS, and enzymatically disaggregated with Liberase TM (Roche, cat. #5401127001; 0.28 WU/ml), DNase I (Roche, cat. #1010415901; 30 μg/ml) and trypsin (ThermoFisher, cat. #15090046; 0.05%) in Ca++/Mg++-containing HBSS for 60 minutes at 37°C with trituration every 10 minutes. 5 mM EDTA (Life Technologies, cat. #15575020) was added for the final 15 minutes of the incubation. The cell suspensions were filtered through 100 μm filters and checked for viability. All sequencing experiments were performed on samples with a minimum of 70% viable cells, as determined by a Nexcelom Cellaca MX cell counter. Cells were washed in PBS with 0.04% BSA and then incubated with lipid-conjugated oligonucleotides for cell hashing (10X Genomics) for 5 minutes at room temperature. Cells were then washed twice with PBS with 1% BSA. 125,000 cells per sample were multiplexed and, from these pools, 340,000 cells were loaded onto the Chromium Controller (10X Genomics). Samples were processed for single-cell encapsulation and cDNA library generation using the Chromium Single Cell 3’ v3.1 Reagent Kits (10X Genomics). Libraries were subsequently sequenced on an Illumina NovaSeq 6000 (Illumina). All samples were sequenced at a sequencing depth of 30,000 reads per cell.
Libraries were generated using the Chromium Single Cell 3’ v3.1 Reagent Kits (10X Genomics)

value: myometrium/endometrium


title: PBMC (cartridge 2)

description: BD Rhapsody


title: SCG9

description: 10X Genomics


title: Control C

description:
Library name: NA-CtrC
This sample is from Control mycelium. It is the third of three biological replicates used in this experiment.

value: Control


title: SCG7

description: 10X Genomics


title: SCG5

description: 10X Genomics


title: PBMC (cartridge 3)

description: BD Rhapsody


title: SCG4

description: 10X Genomics


title: Control B

description:
Library name: NA-CtrB
This sample is from Control mycelium. It is the second of three biological replicates used in this experiment.


title: SCG10

description: 10X Genomics


title: SCG6

description: 10X Genomics


title: Adult_HPT_Het_Male_09 [RNA-Seq]

status: Public on Dec 18 2024

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

institute: Washington University in St. Louis

data_processing:
Adapator trimming using Trimmomatic
Reads alignment using Bowtie2 and STAR
Peak calling using MASC2
Reads counts using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Peak, Reads counts

source_name: Hypothalamus

extract_protocol:
Zymo RNA extraction kit
SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech)
ATAC-seq: Corces et al., 2017, Nature Methods

value: Het

tag: Sex

value: m

tag: mouse age


title: Adult_HPT_WT_Female_06 [RNA-Seq]

value: WT

value: f


title: Adult_HPT_Het_Male_08 [RNA-Seq]


title: Korasit dilution 18,000X C

description:
Library name: NAK18C
This sample is from mycelium grown with Korasit diluted 18000X. It is the third of three biological replicates used in this experiment.


title: Adult_HPT_Het_Female_07 [RNA-Seq]


title: Adult_HPT_WT_Male_07 [RNA-Seq]


title: Control A

description:
Library name: NA-CtrA
This sample is from Control mycelium. It is the first of three biological replicates used in this experiment.


title: Adult_HPT_Het_Female_04 [RNA-Seq]


title: Adult_HPT_Het_Female_02 [RNA-Seq]


title: Adult_HPT_Het_Male_05 [RNA-Seq]


title: Adult_HPT_WT_Male_03 [RNA-Seq]


title: Adult_HPT_WT_Male_56 [ATAC-Seq]


title: Adult_HPT_WT_Male_11 [RNA-Seq]


title: Adult_HPT_Het_Male_42 [ATAC-Seq]


title: Adult_HPT_WT_Female_04 [RNA-Seq]


title: Adult_HPT_Het_Female_48 [ATAC-Seq]


title: Adult_HPT_WT_Female_33 [ATAC-Seq]


title: atac_smarca5_ko2

status: Public on Dec 05 2024

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

institute: Yale University

description: 150bp PE ATAC-seq from Smarca5 cKO testes

data_processing:
Adapter trimming was performed using Cutadapt (Martin, 2011). Trimmed reads were aligned to the mouse genome (mm10) using Bowtie2 in very sensitive mode (Langmead and Salzberg, 2012). Mitochondrial reads were removed by excluding any reads aligning to chrMT. Peak calling was performed using MACS2 with default parameters.
Assembly: mm10
Supplementary files format and content: scRNA-seq: index (.tsv), feature (.tsv), and matrix (.mtx) files
Supplementary files format and content: ATAC-seq: .bed files of peaks

source_name: sorted testicular cells

extract_protocol:
A polypropylene collection tube was coated with 3 ml Collection Buffer (20% FBS in 1X PBS) for 2 hours at RT with end-over-end mixing. Seminiferous tubules were mechanically isolated from the tunica and transferred to a 15ml conical tube containing 5ml Digestion Solution I [0.75 mg/ml collagenase type IV (Gibco, 17104-019) in Dulbecco’s modified Eagle’s media (DMEM, Gibco, 11965092) supplemented with 1:1000 with 1 mg/ml DNase I (StemCell Technologies, 07900)] warmed to 37 °C, followed by incubation at 37 °C for 10 mins with end-over-end rotation. 5ml of cold DMEM was added and tubules allowed to settle on ice. The supernatant was discarded and the tubules were washed again with 5ml cold DMEM to deplete Leydig cells. 5ml of DMEM was added followed by centrifugation at 500xg for 5 mins at 4°C. The supernatant was removed and 5ml of Digestion Solution II [Accutase (Gibco, A1110501) supplemented with 1 mg/ml DNase I at 1:1000 at room temperature)] was added to the tubules followed by incubation with end-over-end rotation for 10 mins at RT with gentle pipetting after 5 mins to disperse the tubules. 5ml of cold Complete Media (10% FBS in DMEM) was added and the sample was centrifuged at 500 xg for 5 mins at 4 °C. The cell pellet was then resuspended in 5 ml of cold Complete Medium, filtered through a 100 μm strainer, and the cell suspension was transferred to a fresh 15 ml conical tube and centrifuged at 500 xg for 5 mins at 4 °C.Cells were stained with Hoechst dye and isolated by flow cytometry based on 4C DNA content.  50,000 sorted pachytene or pachytene-like cells were processed for each ATAC-seq library using the Active Motif kit (53150) as per the manufacturer’s protocol.
50,000 sorted cKIT+ cells were processed for each ATAC-seq library using the Active Motif kit (53150) as per the manufacturer’s protocol.

value: sorted testicular cells

value: Smarca5 fl/delta; Ddx4-Cre+ (Smarca5 cKO)


title: atac_wt2

description: 150bp PE ATAC-seq from control testes

value: wild type C57BL6


title: smarca5_scRNAseq

description: 150bp PE scRNA-seq from Smarca5 cKO testes

data_processing:
Raw count matrices were generated using CellRanger (10X Genomics) and imported to Seurat 4.1.0 (Hao et al., 2021) and combined into one Seurat object. Reads were filtered to exclude doublets (nCount_RNA < mean + one standard deviation), dead or dying cells (nFeature_RNA > mean – one standard deviation) or high mitochondrial content (present.mt < mean + standard deviation). This filtered subset was log normalized and scaled. A linear dimensional reduction was performed using principal component analysis (PCA). Clusters were identified at a resolution of 0.5, and the “RunUMAP()” function was used to further investigate the dataset.
Assembly: mm10
Supplementary files format and content: scRNA-seq: index (.tsv), feature (.tsv), and matrix (.mtx) files
Supplementary files format and content: ATAC-seq: .bed files of peaks

source_name: whole testis

extract_protocol:
A polypropylene collection tube was coated with 3 ml Collection Buffer (20% FBS in 1X PBS) for 2 hours at RT with end-over-end mixing. Seminiferous tubules were mechanically isolated from the tunica and transferred to a 15ml conical tube containing 5ml Digestion Solution I [0.75 mg/ml collagenase type IV (Gibco, 17104-019) in Dulbecco’s modified Eagle’s media (DMEM, Gibco, 11965092) supplemented with 1:1000 with 1 mg/ml DNase I (StemCell Technologies, 07900)] warmed to 37 °C, followed by incubation at 37 °C for 10 mins with end-over-end rotation. 5ml of cold DMEM was added and tubules allowed to settle on ice. The supernatant was discarded and the tubules were washed again with 5ml cold DMEM to deplete Leydig cells. 5ml of DMEM was added followed by centrifugation at 500xg for 5 mins at 4°C. The supernatant was removed and 5ml of Digestion Solution II [Accutase (Gibco, A1110501) supplemented with 1 mg/ml DNase I at 1:1000 at room temperature)] was added to the tubules followed by incubation with end-over-end rotation for 10 mins at RT with gentle pipetting after 5 mins to disperse the tubules. 5ml of cold Complete Media (10% FBS in DMEM) was added and the sample was centrifuged at 500 xg for 5 mins at 4 °C. The cell pellet was then resuspended in 5 ml of cold Complete Medium, filtered through a 100 μm strainer, and the cell suspension was transferred to a fresh 15 ml conical tube and centrifuged at 500 xg for 5 mins at 4 °C.15,000 dissociated testis cells were processed using a Chromium Next GEM Single Cell 3’ v3.1 kit (10X Genomics) and sequenced using an Illumina NovaSeq machine with 150 base pair paired-end reads at a depth of 250 million reads.
Whole testis single cell suspension was diluted to 10,000 cells/mL and single cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ GEM Library Kit. Libraries were sequenced on an Illumina NovaSeq.

value: whole testis