title: Liver Tissue for Double-2

city: Suwon

first: younghwa

last: Kim

address: youngtonggu

institute: Ajou university

description:
Library name: double.1
Column name in raw_counts.csv:double.1

data_processing:
MGI DNBSEQ-G400 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to mm10 whole genome using STAR (version 2.5.4) with parameters -outFilterIntronMotifs RemoveCotrolcaCotrolicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Assembly: mm10
Supplementary files format and content: csv file includes raw_counts for each Sample

source_name: Liver

extract_protocol:
Mice were sacrificed 24 hours post-APAP administration under anesthesia. Liver tissues were collected, immediately snap-frozen in liquid nitrogen for molecular analysis, or fixed in 4% paraformaldehyde for histological examination. Blood samples were also collected for biochemical analysis.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Kit

treatment_protocol: Mice were divided into four groups: Control (PBS only), SLIT2 (SLIT2 only, 2 μg/mouse, intraperitoneally for 3 days), APAP (PBS + APAP, 400 mg/kg), and Double (SLIT2 + APAP). Mice were sacrificed 24 hours post-APAP administration.

value: Liver

value: WT

value: Slit2 (2 μg/mouse, intraperitoneally for 3 days), APAP (APAP, 400 mg/kg, 24h)


title: VDAC2KO2

status: Public on Mar 19 2025

type: RNA

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

country: USA

institute: St Jude Children's Research Hospital

hyb_protocol: Labeled cDNA was included in a hybridization mix that was incubated on the Clariom S human array for 16 hours at 45◦c while rotating at 60 rpm.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: VDAC2 KO LOVO tumor cells without IFNg treatment

label_protocol: High-quality RNA was processed using Thermo Fisher (Affymetrix) Whole Transcript (WT) Plus assay kit

growth_protocol: Cells were cultured with EMEM medium ( 10% FBS).

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen

treatment_protocol: WT and VDAC2 KO LOVO tumor cells were left untreated or treated with IFNg treatment (10ng/ml) for 48 hours.

tag: cell type

value: LOVO tumor cells


title: tumor, vehicle, mouse 228, rep4

type: SRA

city: Nashville

first: Matthew

middle: A

last: Cottam

address: 2301 Vanderbilt Place

department: Surgical Sciences

institute: Vanderbilt University Medical Center

description:
Library name: S000005-42059-002
Treated subcutaneously with 100 uL water every other day

library_source: transcriptomic

data_processing:
Reads from RNAseq data were quality controlled and aligned using the nf-core/RNAseq pipeline.
Aligned transcript counts were imported into R v4.2.2 using Tximport v1.32.0. Low capture genes with less than ten total counts summed across all samples were removed.
Assembly: GRCm39
Supplementary files format and content: Normalized_counts_all-samples.csv contains normalized counts of aligned reads using Deseq2.

organism: Mus musculus

source_name: KPCY pancreatic cancer tumor

growth_protocol: The UTHSC Animal Care and Use Committee (IACUC) approved all protocols and methods following protocol #24-0504.0. All animals in the study were kept on a 12 hr light/dark cycle and fed 60 kcal% from high-fat diet (D12492i, Research Diets Inc.). KPCY 2838 mouse pancreatic cancer cell line was acquired from Kerafast® (Shirley, MA). KPCY cells were cultured in DMEM (Cat. No. 11965092, Gibco, Waltham, MA) supplemented with 1% penicillin-streptomycin (Cat. No. SV30010, HyClone™, Cytiva, Marlborough, MA), 1% GlutaMAX (Cat. No. 35050061, Gibco, Waltham, MA), and 10% FBS (Cat. No. 26140-087 Gibco, Waltham, MA) per instructions from Kerafast® for subcutaneous injections in N = 36 male obese C57BL/6J mice (21 weeks old). Two x 10^5 KPCY 2838 cells in sterile PBS were injected subcutaneously in the right flank. Mice were palpated at injection sites every three days for one week after injecting the cells, after which the tumors were measured every other day using a digital caliper.

extract_protocol:
At the beginning of the treatment, mice were randomly segregated into three groups that included vehicle (water, N = 10), RETA (30 nmol/Kg, N = 12), or RETA-withdrawal (switched from 30 nmol/Kg RETA to water after stabilized weight loss, N = 14). Tumor size was calculated using the formula (width^2 × length/2). Body weights were recorded every day. Mice were sacrificed at endpoint and tumors were excised, weighed, and snap-frozen in liquid nitrogen. Tumor RNA seq analysis was performed for a subset of mice from each treatment group.
mRNA-seq libraries for the Illumina platform were generated and sequenced at Azenta using the Illumina HiSeq 2 × 150 bp configuration following the manufacturer’s protocol. ~30 million paired-end reads per sample.

tag: tissue

value: KPCY pancreatic cancer tumor

tag: cell line

value: KPCY

value: KPCY 2838 pancreatic cancer cells

tag: strain

tag: treatment

value: Vehicle

tag: batch


title: WT1

source_name: WT LOVO tumor cells without IFNg treatment


title: CCRF-CEM, WCE

city: Salt Lake City

first: Birgit

last: Knoechel

address: 2000 Circle of Hope

institute: HCI

library_source: genomic

data_processing:
Nextflow ChIP-seq pipeline 1.0.0. was used with default settings to analyze ChIP-sequencing data. Sequencing reads were aligned to the hg19 genome.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (IRF1/TFAP4 ChIP only), broadPeak (H3K27ac ChIP only)

molecule: genomic DNA

source_name: CCRF-CEM

growth_protocol: RPMI1640, 10% fetal bovine serum, 25mM HEPES, 55nM B-mercapthoethanol, 1% pen/strep, 1% glutamine,  1% NEAA, 1% Sodium pyruvate at 37C and 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min at RT with rotation. After quenching and cell lysis, chromatin was sonicated using a Covaris S220 Sonicator
ChIP-seq libraries were prepared using the End-It DNA End-Repair Kit (Lucigen), Klenow enzyme (3’-5’ exo 5U/ul, NEB) for A-tailing and Quick Ligation Kit (NEB) for adapter ligation. Libraries were amplified (PFU Ultra II HS (Agilent)) using 14 cycles on the thermocycler. Post amplification libraries were purified using Agencourt AMPure XP beads (Beckman Coulter) and validated using the Agilent High Sensitivity DNA kit.

value: CCRF-CEM

value: T cell acute lymphoblastic leukemia

tag: chip antibody


title: H37Rv_RAB@80uM+-1h_b3_3

city: Seattle

first: Ethan

last: Bustad

state: WA

address: 1900 Ninth Ave.

department: CGIDR

institute: Seattle Children's Research Institute

description: Library name: CR80_S23

data_processing:
Libraries were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 kit (Illumina Inc., San Diego, CA). The sequencing run generated an average of 75 million base-pair paired-end raw read counts per library.
Read alignment and gene expression estimation was carried out using a custom processing pipeline in R that harnesses the Bowtie 2 utilities, which is publicly accessible at https://github.com/robertdouglasmorrison/DuffyTools, and https://github.com/robertdouglasmorrison/DuffyNGS.
TPM (transcripts per million) reads were calculated and used as the expression value reported in the second processed data file.
Assembly: Accession # AL123456.3 | Mycobacterium tuberculosis H37Rv complete genome
Supplementary files format and content: FrontiersInTb_INDIGO2PPIs_GEO_processed_reads.txt is a matrix of aligned read values representing the expression levels of each gene for each sample. Each row represents a different sample, and each column represents the expression of each gene. The first 6 columns give the metadata information associated with each sample.
Supplementary files format and content: FrontiersInTb_INDIGO2PPIs_GEO_processed_tpm.txt is a matrix of TPM values representing the expression levels of each gene for each sample. Each row represents a different sample, and each column represents the expression of each gene. The first 6 columns give the metadata information associated with each sample.

organism: Mycobacterium tuberculosis

source_name: Bacteria

growth_protocol: Mycobacterium tuberculosis was routinely grown in Middlebrook 7H9 broth supplemented with 10% OADC and 0.05% Tyloxapol or 0.025% Tween80 (v/v) at 37°C on a rotary shaker.

extract_protocol:
Bacterial pellets suspended in TRIzol were transferred to a tube containing Lysing Matrix B (QBiogene) and vigorously shaken in a homogenizer. The mixture was centrifuged, and RNA was extracted from the supernatant with chloroform, followed by RNA precipitation by isopropanol and high-salt solution (0.8 M Na citrate, 1.2 M NaCl). Total RNA was purified using a RNeasy kit following the manufacturer’s recommendations (Qiagen). rRNA was depleted from samples using a custom-designed set of biotinylated oligonucleotides based on the method described in PMID: 32317317.
Illumina sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep kit for Illumina (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions, and using the AMPure XP reagent (Agencourt Bioscience Corporation, Beverly, MA) for size selection and cleanup of adaptor-ligated DNA. We used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) to barcode the libraries to enable sample multiplexing per sequencing run. The prepared libraries were quantified using the Kapa quantitative PCR (qPCR) quantification kit.

value: Bacteria

tag: genotype

value: Wildtype

value: RAB, 80uM

tag: time

value: 16 hours


title: Liver Tissue for Double-1

country: South Korea

description:
Library name: double
Column name in raw_counts.csv:double


title: H37Rv_PAN@80uM+-1h_b3_3

description: Library name: CP80_S25

value: PAN, 80uM


title: Liver Tissue for APAP-4

description:
Library name: apap.1
Column name in raw_counts.csv:apap.1

value: APAP (PBS + APAP, 400 mg/kg)


title: H37Rv_RAB@80uM+-1h_b3_2

description: Library name: BR80_S17


title: CCRF-CEM, TFAP4, ChIP

value: TFAP4 (Sigma Aldrich, HPA001912)


title: CCRF-CEM, IRF1, ChIP

value: IRF1 (Cell Signaling, 8478)


title: tumor, vehicle, mouse 226, rep2

description:
Library name: S000005-42047-002
Treated subcutaneously with 100 uL water every other day

treatment_protocol: At the beginning of the treatment, mice were randomly segregated into three groups that included vehicle (water, N = 10), RETA (30 nmol/Kg, N = 12), or RETA-withdrawal (switched from 30 nmol/Kg RETA to water after stabilized weight loss, N = 14). Tumor size was calculated using the formula (width^2 × length/2). Body weights were recorded every day. Mice were sacrificed at endpoint and tumors were excised, weighed, and snap-frozen in liquid nitrogen. Tumor RNA seq analysis was performed for a subset of mice from each treatment group.


title: Liver Tissue for APAP-3

description:
Library name: apap
Column name in raw_counts.csv:apap

value: Liver

value: WT


title: U87/MSC_MT n3

city: SEVILLA

first: Vivian

last: Capilla-Gonzalez

state: Sevilla

address: Avda. Americo Vespucio 24

country: Spain

institute: CABIMER

data_processing:
Quality control Analyses, FASTQ generation files, adapters trimming and filtering of sequencing were performed using the manufacturer’s software BaseSpace and the FASTQ toolkit v1.0.0.
Differential analysis for all comparisons and raw counts were generated with DRAGEN and DESeq2 from Illumina, respectivelly.
Assembly: Library UCSC hg19
Supplementary files format and content: U87_vs_U87MSCyU87MT.genes.deseq.counts.csv (The file includes raw counts for each sample)

growth_protocol: U87 cells were cultured in growth media composed of Dulbecco's Modified Eagle Medium (DMEM; Life Technologies, Carlsbad, CA), supplemented with 10% fetal bovine sera (FBS) and 1% penicillin-streptomycin

extract_protocol:
Total RNA was extracted using the RNAeasy Mini kit (Qiagen) following the instructions of the manufacturer.
RNA-seq libraries were made with the illumina stranded mRNA prep ligation kit following the corresponding user guide

treatment_protocol: U87 cells were co-culture with MSC or melatonin-pretreated MSC using an indirect transwell assay

value: tumor

value: Wild type

value: melatonin-pretreated MSC


title: H37Rv_RAB@200uM+-1h_b3_2

description: Library name: BR200_S16

value: RAB, 200uM


title: tumor, vehicle, mouse 201, rep1

description:
Library name: S000005-42029-002
Treated subcutaneously with 100 uL water every other day

value: KPCY pancreatic cancer tumor

value: KPCY

value: KPCY 2838 pancreatic cancer cells

value: Vehicle


title: U87/MSC_MT n1


title: U87/MSC_MT n2


title: H37Rv_PAN@80uM+-1h_b3_2

description: Library name: BP80_S19

value: Bacteria

value: Wildtype


title: Liver Tissue for Slit2-1

description:
Library name: slit2
Column name in raw_counts.csv:slit2

value: Slit2 (2 μg/mouse, intraperitoneally for 3 days)


title: Liver Tissue for Slit2-2

description:
Library name: slit2.1
Column name in raw_counts.csv:slit2.1


title: H37Rv_PAN@800uM+-1h_b3_2

description: Library name: BP800_S18

value: PAN, 800uM

value: 16 hours


title: U87/MSC n3

value: MSC


title: H37Rv_Untreated@0+-1h_b3_2

description: Library name: BUNT_S21

value: Untreated


title: Liver Tissue for Control-1

description:
Library name: control
Column name in raw_counts.csv:control

value: Liver


title: H37Rv_Untreated@0+-1h_b3_1

description: Library name: AUNT_S15


title: U87/MSC n2


title: H37Rv_VER@80uM+-1h_b3_1

description: Library name: AV80_S14

value: VER, 80uM


title: Liver Tissue for Control-2

description:
Library name: control.1
Column name in raw_counts.csv:control.1

value: WT


title: U87/MSC n1

value: tumor

value: Wild type


title: H37Rv_RAB@80uM+-1h_b3_1

description: Library name: AR80_S11

value: RAB, 80uM


title: tumor, vehicle, mouse 227, rep3

description:
Library name: S000005-42048-002
Treated subcutaneously with 100 uL water every other day

value: KPCY pancreatic cancer tumor


title: Fr_AINK1

city: Tokyo

first: MIKI

last: MAEMURA

state: Select

address: 1-5-8,Hatanodai,Shinagawa-ku, 1st building, 343

country: Japan

institute: Showa University

data_processing:
Sequence reads were removed for adaptor pollution,N reads and low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).(SOAPnuke:Version v1.5.2,Parameters -l 15 -q 0.2 -n 0.05
Clean reads were mapped to GCF_000001635.27_GRCm39 using HISAT2(Version：v2.0.4,Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF)
We used Bowtie2 to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM to calculate the gene expression level of each sample.(Bowtie2:Version：v2.2.5,Parameters：-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200;RSEM:Version：v1.2.8,Parameters：-p 8 --forward-prob 0 --paired-end)
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: tab-delimited text files include Annotations_Up and Dn_(AINK)devided(WT)_csv for each sample

source_name: callus

extract_protocol:
The soft and hard calluses in the tibia were stored at -80°C until RNA was extracted using TRIzol reagent (Invitrogen). After homogenization with zirconia beads in a TRIzol-containing tube, the mixture was incubated and then centrifuged. The supernatant was removed, RNA was isolated, and the total RNA was dissolved in RNase-free water. RNA was harvested using the Direct-zol™ RNA MicroPrep kit (ZYMO RESEARCH). A total of 0.2 μg of RNA was used for the construction of sequencing libraries
RNA library construction was done by MGIEasy RNA directional kit
Optimal Dual-mode mRNA Library Prep Kit

value: callus

value: AINK


title: Fr_AINK2


title: H37Rv_RAB@200uM+-1h_b3_1

description: Library name: AR200_S10

value: RAB, 200uM


title: U87 n3

value: untreated


title: Steatosis sample:  LM236_020517_G05.CEL

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

hyb_protocol: The standard Affymetrix hybridization protocol was used

scan_protocol: Standard Affy scanning protocol

data_processing: Standard RMA processing using affyPLM bioconductor R package(v.3.6)

label: Biotin

source_name: Liver Biopsy

label_protocol: Samples were labeled using the Affymetrix Labeling Kit as per manufacturer's protocols.

extract_protocol: mRNA was isolated from fresh human liver tissues using Trizol and following manufacturer’s manual instructions (Invitrogen, Carlsbad, CA, USA).

value: Liver Biopsy

tag: steatosis group


title: Fr_WT2


title: Steatosis sample:  LM235_020517_F05.CEL


title: U87 n2


title: Steatosis sample:  LM243_020517_H05.CEL


title: H37Rv_PAN@80uM+-1h_b3_1

description: Library name: AP80_S13

value: Bacteria

value: Wildtype

value: PAN, 80uM


title: Fr_WT1


title: U87 n1


title: H37Rv_PAN@800uM+-1h_b3_1

description: Library name: AP800_S12

value: PAN, 800uM

value: 16 hours


title: bulkATAC-Seq, 10daysChronicRestraint_0min_CRS3_v46

status: Public on Mar 18 2025

city: Zürich

first: Pierre-Luc

last: Germain

address: Winterthurerstrasse 190

department: D-HEST Institute for Neuroscience

country: Switzerland

institute: ETH Zürich

description: Library name: CRS7_8_31

data_processing:
Reads were trimmed with trimmomatic and aligned to the GRCm38 genome using bowtie2 with --dovetail --no-mixed --no-discordant -I 15 -X 2000. Duplicates were marked using Picard.
Peaks were called using Genrich 0.6.1 with ATAC mode with a FDR threshold of 0.05, discarding PCR duplicates and excluding the mitochondria and ENCODE blacklisted regions. Quantification was performed by counting the number of insertions events (i.e. shifted fragment starts/ends) within peaks or promoter regions.
Assembly: GRCm38
Supplementary files format and content: A zipped csv file with peak coordinates in the first column, and the raw read counts of each sample in the following columns.

source_name: ventral hippocampus

extract_protocol:
Nuclei isolation was performed as described in Grandi et al., 2022. All steps were performed on ice. Briefly, one vHC was homogenized in lysis buffer (26 mM Sucrose, 30 mM KCl, 10 mM MgCl2, 20 mM Tricine-KOH (pH 7.8), 1 mM DTT, 0.5 mM Spermidine, 0.15 mM Spermine, 0.3% NP-40, Complete protease inhibitor in nuclease-free water) by 10 strokes with pestle A and 20 strokes with pestle B. The sample was filtered through a 70 μm Flowmi strainer and centrifuged for 5 min at 400 g at 4°C. Supernatant was removed and additional lysis buffer was added to resuspend the pellet. The sample was then mixed with 50% Iodixanol solution (30 mM KCl, 26 mM Sucrose, 10 mM MgCl2, 20mM Tricine-KOH (pH 7.8), 50% Iodixanol solution in nuclease-free water) and underlaid by 30% Iodixanol solution (50% Iodixanol solution in lysis buffer) and 40% Iodixanol (50% Iodixanol solution in lysis buffer) layers. The sample was centrifuged for 20 min at 3000 g at 4°C with brakes off. The nuclei band was collected and mixed with ATAC buffer (10 mM NaCl, 10 mMTris-HCl (pH7.5), 3 mM MgCl2, 0.1% Tween20 in nuclease-free water). The nuclei count was assessed and 50’000 nuclei were transferred to a new tube with ATAC buffer. The samples was centrifuged for 10 min at 500g at 4°C and supernatant was removed.
Nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer, 2.5 μl transposase (Diagenode, C01070012), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl nuclease-free water). Transposition reactions were incubated at 37 °C for 30 min while shaking at 1,000 r.p.m.. Tagmented DNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, 28204). Purified DNA was amplified using the NEBNext high-Fidelity 2X master mix (New England Biolabs, Ipswich, Massachusetts, United States, M0541) and Diagenode primers (Diagenode, Marlborough, Massachusetts, United States, C01011036) at 72 °C for 5 min, 98 °C for 30 s and 5 cycles of 98 °C for 10 s, 63 °C for 30 s, and 72 °C for 1 min. A fraction of the amplification product was used to determine the number of additional cycles using qPCR, resulting in a total of 8-9 amplification cycles for all samples. A double-sided size selection (0.5X and 1.3X) was performed to remove large and very small library fragments. Insert size of the library was validated and quantified on an Agilent 2100 Bioanalyzer.

value: ventral hippocampus

tag: Sex

value: Female

tag: ars timepoint


title: bulkATAC-Seq, Handling_45min_CRS3_v71

description: Library name: CRS7_8_32

value: Male

value: Handling


title: LCMV_d36_Kidney_Trm_2

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description: Library name: LCMV_d36_Kidney_Trm_2

library_source: genomic single cell

data_processing:
Fastqs were demultplexed with CellRanger-ATAC v2
Fragment files were generated via running CellRanger-ATAC v2 with standard default settings and indexed with tabix
Assembly: mm10
Supplementary files format and content: Fragment files of open chromatin from the 10x ATAC workflow

source_name: CD8+ TRM T cell

extract_protocol: 10x Genomics scATAC-seq

tag: infection

value: LCMV Day 36

tag: organ

value: Kidney

tag: replicate

value: CD8+ TRM T cell


title: bulkATAC-Seq, Handling_0min_CRS3_v45

description: Library name: CRS7_8_30


title: LCMV_d35_SG_Trm_1

description: Library name: LCMV_d35_SG_Trm_1

value: LCMV Day 35

value: Salivary glands


title: LCMV_d36_FRT_Trm_1

description: Library name: LCMV_d36_FRT_Trm_1

value: Female reproductive tract


title: LCMV_d36_IEL_Trm_2

description: Library name: LCMV_d36_IEL_Trm_2

value: Skin / intraepithelial lymphocyte


title: LCMV_d35_Kidney_Trm_1

description: Library name: LCMV_d35_Kidney_Trm_1


title: bulkATAC-Seq, 10daysChronicRestraint_0min_CRS3_v24

description: Library name: CRS7_7_28


title: bulkATAC-Seq, 10daysChronicRestraint_45min_CRS3_v23

description: Library name: CRS7_7_27


title: LCMV_d35_IEL_Trm_1

description: Library name: LCMV_d35_IEL_Trm_1


title: bulkATAC-Seq, 10daysChronicRestraint_45min_CRS3_v66

description: Library name: CRS7_6_24


title: bulkATAC-Seq, Handling_45min_CRS3_v59

description: Library name: CRS7_6_22


title: bulkATAC-Seq, 10daysChronicRestraint_45min_CRS3_v56

description: Library name: CRS7_5_20


title: Steatosis sample:  LM119_020517_A05.CEL

value: Liver Biopsy


title: Steatosis sample:  LM203_020517_E05.CEL


title: bulkATAC-Seq, Handling_45min_CRS3_v52

description: Library name: CRS7_5_19


title: bulkATAC-Seq, 10daysChronicRestraint_0min_CRS3_v51

description: Library name: CRS7_5_18


title: Steatosis sample:  LM245_020517_A07.CEL


title: bulkATAC-Seq, Handling_0min_CRS3_v49

description: Library name: CRS7_5_17


title: Steatosis sample:  LM160_020517_B05.CEL


title: bulkATAC-Seq, Handling_0min_CRS3_v40

description: Library name: CRS7_4_16


title: bulkATAC-Seq, 10daysChronicRestraint_45min_CRS3_v36

description: Library name: CRS7_4_14


title: bulkATAC-Seq, Handling_45min_CRS3_v39

description: Library name: CRS7_4_15


title: bulkATAC-Seq, 10daysChronicRestraint_0min_CRS3_v34

description: Library name: CRS7_4_13


title: bulkATAC-Seq, Handling_45min_CRS3_v27

description: Library name: CRS7_3_9


title: bulkATAC-Seq, 10daysChronicRestraint_0min_CRS3_v33

description: Library name: CRS7_3_12


title: bulkATAC-Seq, Handling_0min_CRS3_v14

description: Library name: CRS7_2_7


title: bulkATAC-Seq, Handling_45min_CRS3_v18

description: Library name: CRS7_2_8


title: bulkATAC-Seq, 10daysChronicRestraint_45min_CRS3_v5

description: Library name: CRS7_1_4


title: bulkATAC-Seq, 10daysChronicRestraint_0min_CRS3_v63

description: Library name: CRS7_6_23


title: bulkATAC-Seq, Handling_0min_CRS3_v20

description: Library name: CRS7_7_25


title: bulkATAC-Seq, 10daysChronicRestraint_45min_CRS3_v4

description: Library name: CRS7_1_3


title: bulkATAC-Seq, 10daysChronicRestraint_0min_CRS3_v7

description: Library name: CRS7_2_5


title: bulkATAC-Seq, 10daysChronicRestraint_45min_CRS3_v31

description: Library name: CRS7_3_11


title: bulkATAC-Seq, 10daysChronicRestraint_0min_CRS3_v3

description: Library name: CRS7_1_2


title: bulkATAC-Seq, Handling_0min_CRS3_v29

description: Library name: CRS7_3_10


title: 20daysChronicRestraint_3h_CRS4_v73

description: Library name: CRS4_v73

data_processing:
Transcript-level quantification was performed with Kallisto using the GENCODE M17 annotation.
Counts from protein-coding transcripts were aggregated for gene-level quantification.
Assembly: GRCm38
Supplementary files format and content: bulkRNA_GeneCounts.csv.zip : a matrix of counts per gene symbol.
Supplementary files format and content: bulkRNA.SE.rds.zip : A R SummarizedExperiment containing the gene counts, metadata, and DEA results.

molecule: polyA RNA

source_name: Ventral hippocampus

extract_protocol:
One snap-frozen ventral hippocampus per animal was homogenized in 500 µl Trizol (Invitrogen 15596018) using metal beads (Qiagen 69989) in a tissue lyser bead mill (Qiagen, Germany) at 4°C for 2 min at 20 Hz. RNA was extracted according to the manufacturer’s recommendations.
The CRS1 experiment was prepared using the Illumina TruSeq stranded RNA kit, while the other libraries were prepared at Novogene using the NEBNext® Ultra RNA Library Prep Kit.

value: Ventral hippocampus

value: female


title: Handling_0min_CRS4_v8

description: Library name: CRS4_v8


title: 20daysChronicRestraint_1h30min_CRS4_v9

description: Library name: CRS4_v9

value: male


title: bulkATAC-Seq, Handling_0min_CRS3_v57

description: Library name: CRS7_6_21


title: bulkATAC-Seq, Handling_45min_CRS3_v1

description: Library name: CRS7_1_1


title: 20daysChronicRestraint_0min_CRS4_v7

description: Library name: CRS4_v7


title: Handling_24h_CRS4_v69

description: Library name: CRS4_v69


title: 20daysChronicRestraint_24h_CRS4_v67

description: Library name: CRS4_v67


title: 20daysChronicRestraint_1h30min_CRS4_v68

description: Library name: CRS4_v68


title: 20daysChronicRestraint_45min_CRS4_v66

description: Library name: CRS4_v66


title: 20daysChronicRestraint_24h_CRS4_v65

description: Library name: CRS4_v65


title: 20daysChronicRestraint_0min_CRS4_v63

description: Library name: CRS4_v63


title: Handling_24h_CRS4_v61

description: Library name: CRS4_v61


title: 20daysChronicRestraint_3h_CRS4_v62

description: Library name: CRS4_v62


title: bulkATAC-Seq, Handling_0min_CRS3_v8

description: Library name: CRS7_2_6


title: Handling_45min_CRS4_v59

description: Library name: CRS4_v59


title: 20daysChronicRestraint_5h30min_CRS4_v60

description: Library name: CRS4_v60


title: 20daysChronicRestraint_1h30min_CRS4_v58

description: Library name: CRS4_v58


title: 20daysChronicRestraint_45min_CRS4_v56

description: Library name: CRS4_v56


title: 20daysChronicRestraint_5h30min_CRS4_v71

description: Library name: CRS4_v71


title: Handling_0min_CRS4_v57

description: Library name: CRS4_v57


title: 20daysChronicRestraint_1h30min_CRS4_v55

description: Library name: CRS4_v55


title: 20daysChronicRestraint_0min_CRS4_v51

description: Library name: CRS4_v51


title: 20daysChronicRestraint_5h30min_CRS4_v48

description: Library name: CRS4_v48


title: 20daysChronicRestraint_45min_CRS4_v5

description: Library name: CRS4_v5


title: Handling_0min_CRS4_v49

description: Library name: CRS4_v49


title: 20daysChronicRestraint_1h30min_CRS4_v47

description: Library name: CRS4_v47


title: Handling_0min_CRS4_v45

description: Library name: CRS4_v45


title: 20daysChronicRestraint_24h_CRS4_v54

description: Library name: CRS4_v54


title: Handling_45min_CRS4_v52

description: Library name: CRS4_v52


title: Handling_24h_CRS4_v50

description: Library name: CRS4_v50


title: 20daysChronicRestraint_0min_CRS4_v46

description: Library name: CRS4_v46


title: 20daysChronicRestraint_45min_CRS4_v44

description: Library name: CRS4_v44


title: 20daysChronicRestraint_5h30min_CRS4_v64

description: Library name: CRS4_v64


title: 20daysChronicRestraint_3h_CRS4_v53

description: Library name: CRS4_v53


title: Handling_24h_CRS4_v43

description: Library name: CRS4_v43


title: Handling_0min_CRS4_v40

description: Library name: CRS4_v40


title: 20daysChronicRestraint_45min_CRS4_v4

description: Library name: CRS4_v4


title: Handling_45min_CRS4_v39

description: Library name: CRS4_v39


title: 20daysChronicRestraint_1h30min_CRS4_v38

description: Library name: CRS4_v38


title: 20daysChronicRestraint_24h_CRS4_v37

description: Library name: CRS4_v37


title: Handling_24h_CRS4_v6

description: Library name: CRS4_v6


title: 20daysChronicRestraint_45min_CRS4_v36

description: Library name: CRS4_v36


title: 20daysChronicRestraint_5h30min_CRS4_v42

description: Library name: CRS4_v42


title: 20daysChronicRestraint_0min_CRS4_v34

description: Library name: CRS4_v34


title: 20daysChronicRestraint_45min_CRS4_v31

description: Library name: CRS4_v31


title: Handling_0min_CRS4_v29

description: Library name: CRS4_v29


title: 20daysChronicRestraint_0min_CRS4_v33

description: Library name: CRS4_v33


title: 20daysChronicRestraint_3h_CRS4_v32

description: Library name: CRS4_v32


title: 20daysChronicRestraint_0min_CRS4_v3

description: Library name: CRS4_v3


title: 20daysChronicRestraint_3h_CRS4_v28

description: Library name: CRS4_v28


title: Handling_24h_CRS4_v26

description: Library name: CRS4_v26


title: 20daysChronicRestraint_0min_CRS4_v24

description: Library name: CRS4_v24


title: Handling_45min_CRS4_v27

description: Library name: CRS4_v27


title: 20daysChronicRestraint_3h_CRS4_v21

description: Library name: CRS4_v21


title: Handling_0min_CRS4_v20

description: Library name: CRS4_v20


title: Handling_45min_CRS4_v22

description: Library name: CRS4_v22


title: Handling_24h_CRS4_v41

description: Library name: CRS4_v41


title: 20daysChronicRestraint_45min_CRS4_v23

description: Library name: CRS4_v23


title: 20daysChronicRestraint_24h_CRS4_v19

description: Library name: CRS4_v19


title: Handling_24h_CRS4_v17

description: Library name: CRS4_v17


title: 20daysChronicRestraint_1h30min_CRS4_v16

description: Library name: CRS4_v16


title: 20daysChronicRestraint_5h30min_CRS4_v15

description: Library name: CRS4_v15


title: Handling_45min_CRS4_v18

description: Library name: CRS4_v18


title: 20daysChronicRestraint_24h_CRS4_v13

description: Library name: CRS4_v13


title: 20daysChronicRestraint_3h_CRS4_v12

description: Library name: CRS4_v12


title: Handling_0min_CRS4_v14

description: Library name: CRS4_v14


title: Handling_45min_CRS4_v1

description: Library name: CRS4_v1


title: 20daysChronicRestraint_5h30min_CRS4_v11

description: Library name: CRS4_v11


title: 20daysChronicRestraint_1h30min_CRS4_v25

description: Library name: CRS4_v25


title: 20daysChronicRestraint_24h_CRS4_v30

description: Library name: CRS4_v30


title: 10daysChronicRestraint_3h_CRS3_v72

description: Library name: CRS3_v72


title: 10daysChronicRestraint_5h30min_CRS3_v70

description: Library name: CRS3_v70


title: 20daysChronicRestraint_24h_CRS4_v2

description: Library name: CRS4_v2


title: 10daysChronicRestraint_0min_CRS3_v7

description: Library name: CRS3_v7


title: Handling_0min_CRS3_v8

description: Library name: CRS3_v8


title: 10daysChronicRestraint_1h30min_CRS3_v9

description: Library name: CRS3_v9


title: Handling_24h_CRS3_v69

description: Library name: CRS3_v69


title: 10daysChronicRestraint_1h30min_CRS3_v68

description: Library name: CRS3_v68


title: 10daysChronicRestraint_24h_CRS3_v67

description: Library name: CRS3_v67


title: 10daysChronicRestraint_3h_CRS3_v62

description: Library name: CRS3_v62


title: 10daysChronicRestraint_0min_CRS3_v63

description: Library name: CRS3_v63


title: Handling_24h_CRS3_v61

description: Library name: CRS3_v61


title: 10daysChronicRestraint_24h_CRS3_v65

description: Library name: CRS3_v65


title: 10daysChronicRestraint_5h30min_CRS3_v64

description: Library name: CRS3_v64


title: 10daysChronicRestraint_45min_CRS3_v66

description: Library name: CRS3_v66


title: 10daysChronicRestraint_5h30min_CRS3_v60

description: Library name: CRS3_v60


title: Handling_24h_CRS3_v6

description: Library name: CRS3_v6


title: 10daysChronicRestraint_1h30min_CRS3_v55

description: Library name: CRS3_v55


title: 10daysChronicRestraint_45min_CRS3_v56

description: Library name: CRS3_v56


title: Handling_0min_CRS3_v57

description: Library name: CRS3_v57


title: 10daysChronicRestraint_24h_CRS3_v54

description: Library name: CRS3_v54


title: 10daysChronicRestraint_3h_CRS3_v53

description: Library name: CRS3_v53


title: Handling_45min_CRS3_v59

description: Library name: CRS3_v59


title: Handling_45min_CRS3_v52

description: Library name: CRS3_v52


title: 10daysChronicRestraint_0min_CRS3_v51

description: Library name: CRS3_v51


title: Handling_45min_CRS3_v71

description: Library name: CRS3_v71


title: Handling_24h_CRS3_v50

description: Library name: CRS3_v50


title: Handling_0min_CRS3_v49

description: Library name: CRS3_v49


title: 10daysChronicRestraint_5h30min_CRS3_v48

description: Library name: CRS3_v48


title: 10daysChronicRestraint_1h30min_CRS3_v47

description: Library name: CRS3_v47


title: Handling_0min_CRS3_v45

description: Library name: CRS3_v45


title: 10daysChronicRestraint_0min_CRS3_v46

description: Library name: CRS3_v46


title: Handling_24h_CRS3_v43

description: Library name: CRS3_v43


title: 10daysChronicRestraint_45min_CRS3_v44

description: Library name: CRS3_v44


title: Handling_24h_CRS3_v41

description: Library name: CRS3_v41


title: Handling_45min_CRS3_v39

description: Library name: CRS3_v39


title: Handling_0min_CRS3_v40

description: Library name: CRS3_v40


title: 10daysChronicRestraint_24h_CRS3_v37

description: Library name: CRS3_v37


title: 10daysChronicRestraint_1h30min_CRS3_v38

description: Library name: CRS3_v38


title: 10daysChronicRestraint_45min_CRS3_v4

description: Library name: CRS3_v4


title: 10daysChronicRestraint_1h30min_CRS3_v58

description: Library name: CRS3_v58


title: 10daysChronicRestraint_45min_CRS3_v36

description: Library name: CRS3_v36


title: 10daysChronicRestraint_5h30min_CRS3_v35

description: Library name: CRS3_v35


title: 10daysChronicRestraint_3h_CRS3_v32

description: Library name: CRS3_v32


title: 10daysChronicRestraint_0min_CRS3_v34

description: Library name: CRS3_v34


title: 10daysChronicRestraint_0min_CRS3_v33

description: Library name: CRS3_v33


title: 10daysChronicRestraint_45min_CRS3_v31

description: Library name: CRS3_v31


title: Handling_0min_CRS3_v29

description: Library name: CRS3_v29


title: 10daysChronicRestraint_0min_CRS3_v3

description: Library name: CRS3_v3


title: 10daysChronicRestraint_3h_CRS3_v28

description: Library name: CRS3_v28


title: Handling_45min_CRS3_v27

description: Library name: CRS3_v27


title: Handling_24h_CRS3_v26

description: Library name: CRS3_v26


title: 10daysChronicRestraint_45min_CRS3_v5

description: Library name: CRS3_v5


title: 10daysChronicRestraint_1h30min_CRS3_v25

description: Library name: CRS3_v25


title: Handling_45min_CRS3_v22

description: Library name: CRS3_v22


title: 10daysChronicRestraint_3h_CRS3_v21

description: Library name: CRS3_v21


title: Handling_45min_CRS3_v18

description: Library name: CRS3_v18


title: 10daysChronicRestraint_24h_CRS3_v2

description: Library name: CRS3_v2


title: Handling_0min_CRS3_v20

description: Library name: CRS3_v20


title: 10daysChronicRestraint_24h_CRS3_v19

description: Library name: CRS3_v19


title: 10daysChronicRestraint_45min_CRS3_v23

description: Library name: CRS3_v23


title: 10daysChronicRestraint_1h30min_CRS3_v16

description: Library name: CRS3_v16


title: 10daysChronicRestraint_5h30min_CRS3_v15

description: Library name: CRS3_v15


title: 10daysChronicRestraint_3h_CRS3_v12

description: Library name: CRS3_v12


title: 10daysChronicRestraint_5h30min_CRS3_v11

description: Library name: CRS3_v11


title: 10daysChronicRestraint_0min_CRS3_v24

description: Library name: CRS3_v24


title: Handling_24h_CRS3_v17

description: Library name: CRS3_v17


title: Handling_45min_CRS3_v1

description: Library name: CRS3_v1


title: 10daysChronicRestraint_3h_CRS3_v10

description: Library name: CRS3_v10


title: 10daysChronicRestraint_24h_CRS3_v30

description: Library name: CRS3_v30


title: Handling_0min_CRS3_v14

description: Library name: CRS3_v14


title: Primary NEPs, Dam-empty, day 6, replicate 4

city: Cambridge

first: Jens

middle: Bager

last: Christensen

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description:
Library name: DamID_Dam-empty_day6_replicate4
D6.DamOnly.gatc.bedgraph
D6.scaled.DamOnly.gatc.bedgraph

data_processing:
Reads were mapped to mm10 genome assembly, indexed using Bowtie2 and binned into 5’-GATC-3’ fragments. Each fusion protein (FOXO1/ASCL1) sample was normalised against each replicate of Dam-empty treatment, then averaged using RPM normalisation, in 300 bp bins. Binding intensity values were quantile normalised across all replicates for each stage and backtransformed. Files were converted to bigwig format using bedGraphToBigWig (v4). Macs2 (v2.1.2) was used to call broad peaks for fusion and Dam-only pairs using the bam file output of the damidseq_pipeline. Bed-files and BedGraph-files were construted from the BAM-files using BedTools (v2.26.0).Macs298 (v2.1.2) was used to call broad peaks for fusion and Dam-only pairs using the bam file output of the damidseq_pipeline. A FDR-threshold of <0.05 was used to identify significant binding peaks. For reproPeaks, significant peaks were further filtered to those present only in 3/4 replicates (repropeaks) using bedtools (v2.26.0).
Assembly: mm10
Supplementary files format and content: Bedgraph-files containing non-scaled and scaled average tracks for ASCL1-Dam, FOXO1-Dam and Dam-empty.
Supplementary files format and content: Bed-files containing significant peaks in any replicate (mergePeak) or in 3/4 replicates (reproPeak).
Library strategy: DamID-Seq

source_name: Primary cerebellar neurosphere culture modified with lentivirus expressing respective Dam constructs

growth_protocol: Neurobasal (ThermoFisher, #10888022) with 1X B27 (ThermoFisher, #A3353501), 1X N2 (ThermoFisher, #11520536), 2mM L-glutamine (ThermoFisher, #A2916801), 1X non-essential amino acids (ThermoFisher, 11140035), 100 U/mL penicillin-streptomycin (ThermoFisher, #15140122) and 2% fetal bovine serum (ThermoFisher, #10438026).

extract_protocol:
The cultures were then incubated for 24 hours at 37C. After 24 hours of incubation, cultures were rinsed twice with PBS-/- (ThermoFisher, #14190144). The cells were dissociated by incubating with 75µL/cm2 accutase (ThermoFisher, #A1110501) for 7.5 minutes at 37C. The dissociation was stopped by adding mL of neural stem cell media with 2% fetal bovine serum (ThermoFisher, #10438026). The cell suspension was pelleted in 1.5 mL Eppendorf tubes (Merck, #EP0030125150-1PAK) by centrifugation for 5 minutes at 500g. The supernatant was discarded, and the cell pellets snapfrozen on dry ice. Samples were stored at -80C until library preparation.
Described in Marshall et al., 2016 (PMCID: PMC7032955)

value: Nestin-expressing progenitors (NEPs)


title: Primary NEPs, Dam-empty, day 6, replicate 2

description:
Library name: DamID_Dam-empty_day6_replicate2
D6.DamOnly.gatc.bedgraph
D6.scaled.DamOnly.gatc.bedgraph

value: Primary cerebellar neurosphere culture modified with lentivirus expressing respective Dam constructs


title: Primary NEPs, Dam-empty, day 2, replicate 3

description:
Library name: DamID_Dam-empty_day2_replicate3
D2.DamOnly.gatc.bedgraph
D2.scaled.DamOnly.gatc.bedgraph


title: Primary NEPs, Dam-empty, day 6, replicate 1

description:
Library name: DamID_Dam-empty_day6_replicate1
D6.DamOnly.gatc.bedgraph
D6.scaled.DamOnly.gatc.bedgraph


title: Primary NEPs, Dam-empty, day 2, replicate 4

description:
Library name: DamID_Dam-empty_day2_replicate4
D2.DamOnly.gatc.bedgraph
D2.scaled.DamOnly.gatc.bedgraph


title: Primary NEPs, Dam-empty, day 2, replicate 1

description:
Library name: DamID_Dam-empty_day2_replicate1
D2.DamOnly.gatc.bedgraph
D2.scaled.DamOnly.gatc.bedgraph


title: Primary NEPs, Dam-empty, day 6, replicate 3

description:
Library name: DamID_Dam-empty_day6_replicate3
D6.DamOnly.gatc.bedgraph
D6.scaled.DamOnly.gatc.bedgraph


title: Primary NEPs, Dam-empty, day 2, replicate 2

description:
Library name: DamID_Dam-empty_day2_replicate2
D2.DamOnly.gatc.bedgraph
D2.scaled.DamOnly.gatc.bedgraph


title: Primary NEPs, FOXO1-Dam, day 6, replicate 4

description:
Library name: DamID_FOXO1-Dam_day6_replicate4
D6_FOXO1-vs-DAM.gatc.quant.norm.average.bedgraph
D6_FOXO1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
FOXO1_D6_5.mergePeak.bed
FOXO1_D6_5.reproPeak.bed


title: Primary NEPs, FOXO1-Dam, day 6, replicate 3

description:
Library name: DamID_FOXO1-Dam_day6_replicate3
D6_FOXO1-vs-DAM.gatc.quant.norm.average.bedgraph
D6_FOXO1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
FOXO1_D6_5.mergePeak.bed
FOXO1_D6_5.reproPeak.bed


title: Primary NEPs, FOXO1-Dam, day 6, replicate 2

description:
Library name: DamID_FOXO1-Dam_day6_replicate2
D6_FOXO1-vs-DAM.gatc.quant.norm.average.bedgraph
D6_FOXO1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
FOXO1_D6_5.mergePeak.bed
FOXO1_D6_5.reproPeak.bed


title: Primary NEPs, FOXO1-Dam, day 2, replicate 4

description:
Library name: DamID_FOXO1-Dam_day2_replicate4
D2_FOXO1-vs-DAM.gatc.quant.norm.average.bedgraph
D2_FOXO1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
FOXO1_D2_5.mergePeak.bed
FOXO_D2.5.reproPeak.bed


title: 10daysChronicRestraint_24h_CRS3_v13

description: Library name: CRS3_v13


title: Primary NEPs, FOXO1-Dam, day 6, replicate 1

description:
Library name: DamID_FOXO1-Dam_day6_replicate1
D6_FOXO1-vs-DAM.gatc.quant.norm.average.bedgraph
D6_FOXO1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
FOXO1_D6_5.mergePeak.bed
FOXO1_D6_5.reproPeak.bed


title: E12TelWT

city: paris

first: Frederic

last: Causeret

address: 24 bd de montparnasse

department: Imagine Institute

country: France

institute: Inserm

description:
Library name: E12TelWT
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed to counts matrix with Cell Ranger version 7.1.0 using default parameters and the mm10 mouse genome reference.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: embryonic brain

extract_protocol:
Tissue was dissociated using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec) and a gentleMACS Octo Dissociator following the manufacturer’s instructions. Cell clumps and debris were removed via filtration through 30 µm cell strainers (Miltenyi Biotec) followed by two consecutive rounds of centrifugation for 3 min at 200 g. Pipetting through Gel Saver tips (QSP) and a final filtration using a 10 µm cell strainer (pluriSelect) allowed to obtain a single-cell suspension. Cell viability and concentration were assessed using a MACSQuant flow cytometer (Miltenyi Biotec). Approximatively 20000 cells were used as input on the 10X Genomics Chromium controller.
Chromium Single Cell 3' Library & Gel Bead Kit v3.1

value: embryonic brain

tag: developmental stage

value: wild-type


title: Primary NEPs, FOXO1-Dam, day 2, replicate 1

description:
Library name: DamID_FOXO1-Dam_day2_replicate1
D2_FOXO1-vs-DAM.gatc.quant.norm.average.bedgraph
D2_FOXO1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
FOXO1_D2_5.mergePeak.bed
FOXO_D2.5.reproPeak.bed


title: Primary NEPs, FOXO1-Dam, day 2, replicate 2

description:
Library name: DamID_FOXO1-Dam_day2_replicate2
D2_FOXO1-vs-DAM.gatc.quant.norm.average.bedgraph
D2_FOXO1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
FOXO1_D2_5.mergePeak.bed
FOXO_D2.5.reproPeak.bed


title: Primary NEPs, FOXO1-Dam, day 2, replicate 3

description:
Library name: DamID_FOXO1-Dam_day2_replicate3
D2_FOXO1-vs-DAM.gatc.quant.norm.average.bedgraph
D2_FOXO1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
FOXO1_D2_5.mergePeak.bed
FOXO_D2.5.reproPeak.bed


title: Primary NEPs, ASCL1-Dam, day 6, replicate 4

description:
Library name: DamID_ASCL1-Dam_day6_replicate4
D6_ASCL1-vs-DAM.gatc.quant.norm.average.bedgraph
D6_ASCL1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
ASCL1_D6_5.mergePeak.bed
ASCL1_D6_5.reproPeak.bed


title: Primary NEPs, ASCL1-Dam, day 6, replicate 3

description:
Library name: DamID_ASCL1-Dam_day6_replicate3
D6_ASCL1-vs-DAM.gatc.quant.norm.average.bedgraph
D6_ASCL1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
ASCL1_D6_5.mergePeak.bed
ASCL1_D6_5.reproPeak.bed


title: Primary NEPs, ASCL1-Dam, day 6, replicate 2

description:
Library name: DamID_ASCL1-Dam_day6_replicate2
D6_ASCL1-vs-DAM.gatc.quant.norm.average.bedgraph
D6_ASCL1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
ASCL1_D6_5.mergePeak.bed
ASCL1_D6_5.reproPeak.bed


title: Primary NEPs, ASCL1-Dam, day 2, replicate 3

description:
Library name: DamID_ASCL1-Dam_day2_replicate3
D2_ASCL1-vs-DAM.gatc.quant.norm.average.bedgraph
D2_ASCL1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
ASCL1_D2_5.mergePeak.bed
ASCL1_D2_5.reproPeak.bed


title: Primary NEPs, ASCL1-Dam, day 6, replicate 1

description:
Library name: DamID_ASCL1-Dam_day6_replicate1
D6_ASCL1-vs-DAM.gatc.quant.norm.average.bedgraph
D6_ASCL1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
ASCL1_D6_5.mergePeak.bed
ASCL1_D6_5.reproPeak.bed


title: Primary NEPs, ASCL1-Dam, day 2, replicate 1

description:
Library name: DamID_ASCL1-Dam_day2_replicate1
D2_ASCL1-vs-DAM.gatc.quant.norm.average.bedgraph
D2_ASCL1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
ASCL1_D2_5.mergePeak.bed
ASCL1_D2_5.reproPeak.bed


title: Primary NEPs, ASCL1-Dam, day 2, replicate 2

description:
Library name: DamID_ASCL1-Dam_day2_replicate2
D2_ASCL1-vs-DAM.gatc.quant.norm.average.bedgraph
D2_ASCL1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
ASCL1_D2_5.mergePeak.bed
ASCL1_D2_5.reproPeak.bed


title: NIH/3T3 cells treated with Dox (INPUT)

city: Warsaw

first: Weronika

last: Skarzynska

address: Banacha 2c

country: Poland

institute: Centre of New Technologies

description: Library name: INPUT_Dox

data_processing:
CUT&RUN raw sequencing reads were aligned using Bowtie2, peaks were called using MACS2, and annotated using R package ChIPseeker. Enriched motifs were found using Homer (Heinz et al., Molecular Cell, 2010). Functional enrichement analysis and visualization were performed with the use of ChIPseeker and clusterProfiler R packages.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Gli3R-HA Tet-On control, Gli3R-HA Tet-On Hira KO, and Hira-HA Gli3R TetOn cells were starved for 24 h with 300ug/ml doxycycline to induce Gli3R/Gli3R-HA expression. 200k cells were taken and subjected to cut and run protocol with the use of Cell Signaling CUT&RUN Assay Kit (#86652). Cells were immobilized on concavanilin A magnetic beads then permeabilized and anti-HA primary antibody was added for overnight incubation. Next day enzymatic cleavage with pAGMNase was performed and desired chromatin fragments were isolated with the Mag-Bind Total Pure NGS Kit (Omega BIO-TEK, #M1378-01)
DNA libraries were constructed using Kapa HyperPrep reagent kit (KAPA Biosciences, cat. no. KK8504) and KAPA UDI Adapters Kit 15 μm (KAPA Biosystems, cat. no. 8861919702). The manufacturer’s protocol was followed, with the following modifications: the incubation temperature during end repair (ERAT) was lowered from 65 °C to 50 °C, the concentration of adapters used in the ligation reaction was lowered to 300 nM, increased the reagent-to-sample ratio during polygenic purification to 1.1x, and the annealing and extension times during the PCR reaction were lowered to 15 s. The procedure used 25 ng each of input samples and 15 ul each of CUT&RUN samples. Nine cycles of enrichment by amplification were used. A final selection of fragment lengths in a two-step purification at a sample: reagent volume ratio: (1) stage − 1:0.55, (2) stage 1:1 (expected fragment length range 100–700 bp). Libraries were pooled equimolar and purified from adapter dimers. The resulting libraries and pools were subjected to fragment length control using an Agilent TapeStation 2200 analyzer and a set of High Sensitivity D1000 Screen Tape (Agilent, cat. no. 5067–5584) and High Sensitivity D1000 Reagents (Agilent, cat. no. 5067–5585). Library concentrations were then determined by qPCR using the Kapa Library Quantification kit (Kapa Biosciences, cat. no. KK4824).


title: NIH/3T3 with Hira loss-of-function cells treated with Dox in order to induce HA-Gli3R expression_1

description: Library name: HIRA_KO_Dox_1


title: NIH/3T3 with Hira loss-of-function cells treated with DMSO_2

description: Library name: HIRA_KO_DMSO_2


title: NIH/3T3 with Hira loss-of-function cells treated with DMSO_1

description: Library name: HIRA_KO_DMSO_1


title: NIH/3T3 cells treated with Dox in order to induce HA-Gli3R expression_2

description: Library name: Control_Dox_2


title: NIH/3T3 cells treated with Dox in order to induce HA-Gli3R expression_1

description: Library name: Control_Dox_1


title: NIH/3T3 with Hira loss-of-function cells treated with Dox in order to induce HA-Gli3R expression_2

description: Library name: HIRA_KO_Dox_2


title: NIH/3T3 cells treated with DMSO_1

description: Library name: Control_DMSO_1


title: NIH/3T3 cells treated with DMSO_2

description: Library name: Control_DMSO_2


title: RNA-seq of CRISPR Y-Scr MB49 cells Replicate 3

city: Baltimore

first: XINGYU

last: CHEN

state: MD

address: 3501 St Paul St, Baltimore, MD 21218

department: Department of Urology

institute: Cedars-Sinai Medical Center

description:
Library name: MB_49YSCR_3N
RNA-seq data for FACS-isolated CD45⁻ cells

data_processing:
Quality control: FASTQ files were assessed using FastQC v0.12.1, and MultiQC v1.13 was used for summary statistics.
Adapter trimming: Reads were trimmed using Trimmomatic v0.39 to remove Illumina Truseq adapters, polyA, and polyT sequences.
Alignment: Reads were mapped to the mouse genome (GRCm39/mm39) using STAR aligner v2.5.2b, with ENCODE-recommended parameters.
Quantification: Gene-level expression was quantified using featureCounts v1.5.3, employing Ensembl gene annotations (release 113).
Genome: Mus musculus (GRCm39/mm39)
Assembly: Annotation: Ensembl release 113
Supplementary files format and content: Format: counts.txt (Tab-delimited text file)
Supplementary files format and content: Content: Raw gene counts per sample (rows: gene IDs, columns: samples).

source_name: MB49 Tumor

growth_protocol: MB49 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin, maintained at 37°C with 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) with gDNA Eliminator columns, following the manufacturer’s protocol.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Poly-A RNA was enriched, fragmented, and reverse-transcribed into cDNA, followed by PCR amplification.

treatment_protocol: CRISPR Y-KO and CRISPR Y-Scr MB49 cells were injected subcutaneously into C57Bl/6J mice. Tumors were harvested when they reached 500 mm³ and processed for FACS isolation of CD45⁻ cells.

value: MB49 Tumor

value: CD45-negative cells

value: CRISPR Y-Scr


title: RNA-seq of CRISPR Y-Scr MB49 cells Replicate 1

description:
Library name: MB_49YSCR_1N
RNA-seq data for FACS-isolated CD45⁻ cells


title: RNA-seq of CRISPR Y-Scr MB49 cells Replicate 2

description:
Library name: MB_49YSCR_2N
RNA-seq data for FACS-isolated CD45⁻ cells


title: RNA-seq of CRISPR Y-KO MB49 cells Replicate 3

description:
Library name: MB_49YKO_3N
RNA-seq data for FACS-isolated CD45⁻ cells

value: CRISPR Y-KO


title: RNA-seq of CRISPR Y-KO MB49 cells Replicate 2

description:
Library name: MB_49YKO_2N
RNA-seq data for FACS-isolated CD45⁻ cells


title: RNA-seq of CRISPR Y-KO MB49 cells Replicate 1

description:
Library name: MB_49YKO_1N
RNA-seq data for FACS-isolated CD45⁻ cells


title: Primary NEPs, ASCL1-Dam, day 2, replicate 4

description:
Library name: DamID_ASCL1-Dam_day2_replicate4
D2_ASCL1-vs-DAM.gatc.quant.norm.average.bedgraph
D2_ASCL1-vs-DAM.scaled.gatc.quant.norm.average.bedgraph
ASCL1_D2_5.mergePeak.bed
ASCL1_D2_5.reproPeak.bed


title: CRISPR-YScr Replicate 3

description:
Library name: RC_3
CRISPR-YScr replicate 3

data_processing:
Quality control: FASTQ files were assessed using FastQC v0.12.1, and MultiQC v1.13 was used for summary statistics.
Adapter trimming: Reads were trimmed for Illumina Truseq adapters, polyA, and polyT sequences using Trimmomatic v0.39.
Alignment: Reads were mapped to the mouse genome (GRCm39/mm39) using STAR aligner v2.5.2b with ENCODE-recommended parameters.
Quantification: Gene-level expression was quantified using featureCounts v1.5.3 with Ensembl gene annotations (release 113).
Normalization: Gene counts were normalized using DESeq2 for downstream analysis.
Assembly: Genome: Mus musculus (GRCm39/mm39)
Supplementary files format and content: Format: gene_count.xlsx (Tab-delimited or Excel file)
Supplementary files format and content: Content: Contains raw gene counts per sample. Columns represent different samples, and rows represent gene IDs.

growth_protocol: CRISPR Y-Scr control cells: Generated using a non-targeting gRNA.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) with gDNA Eliminator columns, following the manufacturer’s protocol. RNA integrity was assessed using Agilent Bioanalyzer 2100.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s instructions. mRNA was enriched using poly-A selection, fragmented, and reverse-transcribed into cDNA. Libraries were indexed and amplified by PCR, followed by quality control and quantification.

treatment_protocol: After transduction, cells were sorted based on tRFP expression and expanded as single-cell clones.

value: Bladder Cancer Cells


title: CRISPR Y-KO Replicate 2

description:
Library name: RP_2
CRISPR Y-KO replicate 2


title: CRISPR Y-KO Replicate 1

description:
Library name: RP_1
CRISPR Y-KO replicate 1


title: CRISPR-YScr Replicate 2

description:
Library name: RC_2
CRISPR-YScr replicate 2


title: CRISPR-YScr Replicate 1

description:
Library name: RC_1
CRISPR-YScr replicate 1


title: WES of CRISPR Y-Scr (control) MB49 cells

description:
Library name: WES_CRISPR_Y-Scr
Genomic DNA from CRISPR–Cas9-mediated scrambled (control) MB49 Y+ cells

data_processing:
Raw reads were adapter- and quality-trimmed (e.g., with Trimmomatic).
Clean reads were aligned to the GRCm39/mm39 reference genome using BWA.
Aligned reads were sorted (e.g., with Sambamba) and duplicates were marked using Picard.
Variant calling was performed using GATK (Best Practices workflow).
Resulting VCF files were annotated and filtered for downstream analyses.
Assembly: GRCm39/mm39.
Supplementary files format and content: Coordinate-sorted BAM and VCF files with annotated variants.
Supplementary files format and content: QC metrics, coverage reports, or other derived files may also be included.

source_name: n/a (cell)

growth_protocol: CRISPR Y-KO and CRISPR Y-Scr (control) MB49 Y+ cells were maintained in DMEM supplemented with 5% FBS at 37°C with 5% CO2.

extract_protocol:
Genomic DNA was isolated using the Invitrogen kit (#K1820), following the manufacturer’s instructions.
DNA was randomly fragmented, end-repaired, A-tailed, ligated with Illumina adapters, PCR-amplified, and size-selected. Libraries were validated using a bioanalyzer before sequencing.

treatment_protocol: No additional pharmacological or chemical treatment was applied.

value: n/a (cell)

value: bladder carcinoma


title: NIH/3T3 cells treated with DMSO (INPUT)

description: Library name: INPUT_DMSO


title: scRNA-seq of mouse tumor tissues 1

description:
Library name: D1-1
scRNA-seq data for MB49 tumors in C57Bl/6J mice (n=4)

data_processing:
Read processing: Raw FASTQ files were processed using CellRanger (10X Genomics) with the pre-mRNA GRCm39/mm39 reference genome.
Doublet filtering: Potential doublet cells were identified using Scrublet, analyzing the top 10% most variable genes with Scanpy. A 10% doublet rate was predicted, and doublets were removed.
Quality control: Cells with >10% mitochondrial gene UMIs or in the top/bottom 5% based on unique gene and UMI count were filtered out.
Normalization: Gene expression was normalized using Scanpy (v1.9.5) with log normalization and highly variable gene selection.
Assembly: Genome: Mus musculus (GRCm39/mm39)
Supplementary files format and content: Format: filtered_feature_bc_matrix.h5 (10X Genomics format)

growth_protocol: MB49 clone 5 (C5) cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. Cells were maintained at 37°C with 5% CO₂.

extract_protocol:
Tumors were dissociated in MACS C-tubes with Miltenyi Biotech tumor dissociation enzymes (#130-096-730). The dissociated cells were processed using ACK Lysis buffer (Gibco, #2537772), dead cell removal kit (Stem Cell Technologies #17899), and EasySep™ Mouse CD45 Positive Selection Kit (#18945). CD45+ cells were sorted into CD4+, CD8+, and CD11b+ populations, combined at equal ratios, and mixed 1:1 with live CD45⁻ cells before sequencing.
10X Genomics 3' single-cell RNA-seq (scRNA-seq) libraries were prepared following the manufacturer’s instructions. Libraries were amplified by PCR and underwent quality control before sequencing.

treatment_protocol: 1 × 10⁵ LOY MB49 clone 5 (C5) cells were injected subcutaneously into C57Bl/6J mice (n=4). Tumors were collected when they reached 500 mm³ and processed for scRNA-seq.

value: MB49 Clone 5 (C5)

value: CD45+ and CD45- cells

value: LOY MB49


title: WES of CRISPR Y-KO MB49 cells

description:
Library name: WES_CRISPR_Y-KO
Genomic DNA from CRISPR–Cas9-mediated Y chromosome knockout MB49 cells


title: SB28-TSP1-KO in vivo brain tumor, KO-4

city: San Francisco

first: Hideho

last: Okada

state: CA

department: Neurological Surgery

institute: University of California, San Francisco

description:
Library name: KO-4
Column name in TNHO02_stringtie_mm10_merged_count.tsv: KO-4

data_processing:
Quality checking, trimming, and removal of barcodes from FASTQ sequencing reads were performed using fastp (version 0.20.0) with default parameters.
The FASTQ reads were aligned to the mouse reference genome mm10 (GRCm38.p6) using STAR (v2.7.9a), with transcriptome annotation guidance from gencode.vM25.annotation.gtf. Sorting and indexing were performed using samtools (v1.14).
Gene-level expression counts were estimated using StringTie (v2.0).
A gene-level expression count data table was prepared by merging all eight sample count data and excluding irrelevant genes, such as long noncoding genes, based on the GTF annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: brain tumor

growth_protocol: SB28 tumor cells (10,000 cells/uL/mouse) were inoculated intracerebrally targeting right striatum of 5-7 week-old female C57BL/6J mice.

extract_protocol:
Intracranial tumor-bearing mice were euthanized and then perfused via transcardial injection of 10 mL of cold PBS. Whole brains were harvested, and visible tumor tissues were excised and stored in RNAlater (Invitrogen, AM7024) at 4°C for up to one week before RNA extraction. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74106) and the RNase-Free DNase Set (Qiagen, 79254), following the manufacturer’s protocol.
Because of their low RIN scores, we chose ribosomal depletion for mRNA enrichment. The subsequent library preparation and sequencing were performed by the UCSF Genomics CoLab. Starting material of 500 ng of total RNA was used according to vendor instructions with Universal plus mRNA with Nu Quant (TECAN, 0520), with noted changes to the protocol as follows. First, the Poly(A) Selection step was omitted. Second, we started with RNA fragmentation and used QIAseq FastSelect −rRNA/Globin Kit (Qiagen, 335377) to remove rRNA as follows: 0.1 µL of FastSelect rRNA and 1 µL of 1X Fragmentation Buffer was added to 10 µL of total RNA, with the addition of 10 µL of 2X Fragmentation Buffer. PCR program was used as follows: 94 ℃/3min, 75 ℃/2min, 70 ℃/2min, 65 ℃/2min, 60 ℃/2min, 55 ℃/2min, 37 ℃/5min, 25 ℃/5min, 10 ℃/hold. After the rRNA depletion step, Universal plus mRNA with Nu Quant protocol was followed, starting with the first strand cDNA synthesis step but omitting the steps of AnyDeplete and NuQuant. After final library PCR amplification of 15 cycles and bead clean-up, individual libraries were pooled equally by volume, and quantified on Fragment Analyzer (Agilent, DNF-474). The quantified library pool was diluted to 1 nM and sequenced on MiniSeq (Illumina, FC-420-1001) to check for the quality of reads. Finally, individual libraries were normalized according to MiniSeq output reads, specifically by % protein-coding genes, and were sequenced on one lane of NovaSeq6000 SP PE150 (Illumina, 20028400) at UCSF Center for Advanced Technology (CAT).

value: brain tumor

value: mouse syngeneic glioma cell

tag: age

value: 8-10 weeks old


title: SB28-TSP1-KO in vivo brain tumor, KO-3

description:
Library name: KO-3
Column name in TNHO02_stringtie_mm10_merged_count.tsv: KO-3

tag: cell type


title: SB28-TSP1-KO in vivo brain tumor, KO-2

description:
Library name: KO-2
Column name in TNHO02_stringtie_mm10_merged_count.tsv: KO-2

tag: tissue


title: SB28-TSP1-KO in vivo brain tumor, KO-1

description:
Library name: KO-1
Column name in TNHO02_stringtie_mm10_merged_count.tsv: KO-1

tag: cell line


title: SB28-TSP1-WT in vivo brain tumor, WT-3

description:
Library name: WT-3
Column name in TNHO02_stringtie_mm10_merged_count.tsv: WT-3

value: WT

tag: strain


title: SB28-TSP1-WT in vivo brain tumor, WT-2

description:
Library name: WT-2
Column name in TNHO02_stringtie_mm10_merged_count.tsv: WT-2


title: TT-seq_A18_rep3

city: Shanghai

first: Aixia

last: Song

address: Dong'an Road

country: China

institute: Fudan University

data_processing:
*library strategy: transient transcriptome sequencing (TT-seq)
The TT-seq raw reads were trimmed and then aligned to the mm10 genome using STAR v2.7.5c with parameters “--outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 -- outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate”.
triplicate and low-quality reads were removed, retaining only properly paired reads for downstream analyses.
The spike-in mm10 reads were quantified to generate the normalization factor. Strand-specific normalized bigwigs were generated with deepTools v3.5.0.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: BMDM

growth_protocol: Bone marrow cells were harvested from the femur and tibia, and differentiated in DMEM (containing 10% fetal calf serum, 1% penicillin–streptomycin and 20 ng/ml M-CSF) for 6 days

extract_protocol:
RNA was isolated with TRIzol. 100 μg RNA was fragmentated and  biotinylated. The biotinylated RNA  was immunoprecipitated and purified.
Libraries were prepared according to  ABclonal's instructions accompanying the ABclonal Stranded mRNA-seq Lib Prep Module for Illumina (ABclonal, RK20349). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: For TT-seq, BMDM cells were treated with different S. Tm strains for indicated time. Cells were labeled by 4SU for 15min.

value: BMDM

value: Bone Marrow-Derived Macrophage

tag: treatment

value: treated with aceA△ salmonella for 18 hours


title: TT-seq_A18_rep2


title: CRISPR Y-KO Replicate 3

description:
Library name: RP_3
CRISPR Y-KO replicate 3

value: MB49 Tumor

tag: batch


title: TT-seq_A18_rep1


title: TT-seq_H18_rep2

value: treated with heat-killed salmonella for 18 hours


title: TT-seq_W18_rep3

value: treated with WT salmonella for 18 hours


title: TT-seq_A8_rep3

value: treated with aceA△ salmonella for 8 hours


title: TT-seq_W18_rep1


title: TT-seq_A8_rep1


title: TT-seq_A8_rep2


title: TT-seq_H8_rep3

value: treated with heat-killed salmonella for 8 hours


title: TT-seq_H8_rep1


title: TT-seq_W8_rep3

value: treated with WT salmonella for 8 hours


title: TT-seq_H8_rep2


title: scRNA-seq of mouse tumor tissues 2

description:
Library name: D1-2
scRNA-seq data for MB49 tumors in C57Bl/6J mice (n=4)


title: TT-seq_W8_rep1


title: TT-seq_W8_rep2


title: SB28-TSP1-WT in vivo brain tumor, WT-1

description:
Library name: WT-1
Column name in TNHO02_stringtie_mm10_merged_count.tsv: WT-1


title: TT-seq_NC18_rep1

value: treated with PBS for 18 hours


title: TT-seq_NC18_rep2


title: SB28-TSP1-WT in vivo brain tumor, WT-4

description:
Library name: WT-4
Column name in TNHO02_stringtie_mm10_merged_count.tsv: WT-4


title: siRif1_Morula_071

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description:
binary.siRif1_Morula.txt
RT.siRif1_Morula.bedgraph

data_processing:
library strategy: Single-cell Repli-seq
Sequencing reads were aligned to the GRCm38 genome using bowtie2 (version 2.5.1) 59 with the parameters --local --no-unal --no-mixed --no-discordant. Reads were filtered by mapping quality using samtools with the parameter -q 20. Read duplicates were removed using picard MarkDuplicates (version 3.0.0) with the parameter -REMOVE_DUPLICATES true. Using bedtools intersect (version 2.31.0), read counts were obtained for contiguous 50kb genomic bins.
The window counts were first normalised to RPM (reads per million). Aiming to correct for the mappability biases intrinsic to the genomic regions, for each bin its respective average of all samples within the same condition was calculated. Outlier regions were then masked, specifically the windows of the lower 5th percentile and the upper 1st percentile values. To correct for low mappability, the windows were segmented with the R package copynumber (version 1.38.0, R version 4.2.3) to keep the segments with the highest 95% of values. The data were centred by the mean and scaled by the interquartile range for each cell and smoothed using a median filter with a running window width of 15 windows, followed by a segmentation with the R package copynumber. Finally, using the function normalmixEM from R package mixtools (version 2.0.0), the segmented values were used to fit a mixture model with two components to identify replicated and non-replicated window populations.
To obtain replication timing values and to correct for potential sampling bias of cells, we calculated the fraction of replicated cells in overlapping intervals of the genome-wide replication score with interval size of 35% and increment of 4.33% (e.g. 0-35%, 4.33-39.33% etc.) for each genomic bin. The average of these 16 intervals served as replication timing value that was used for downstream analyses.
Assembly: GRCm38
Supplementary files format and content: tab-separated txt file with binary replication status
Supplementary files format and content: bedgraph file with replication timing values

source_name: morula

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2 until they reached 4-cell, 8-cell and morula stage.

extract_protocol:
Early stage zygotes were collected and cultured until they reached the S-phase at each developmental stage, based on their time after hCG injection. Embryos were collected at different time points to achieve sampling over the entire S-phase. Zona pellucida was removed by exposure to acid Tyrode and each blastomere was dissociated by gentle pipetting after trypsin treatment.
Individual blastomeres were placed into 8-strip PCR tubes containing lysis buffer and extracted DNA was fragmented by heat incubation. Fragmented DNA was tagged by the universal primer (5’-TGTGTTGGGTGTGTTTGGKKKKKKKKKKNN-3’) and amplified with WGA primer sets which have individual barcode. Amplified DNA was purified by the QIAquick 96 PCR Purification Kit (QIAGEN) and concentration was determined by the NanoDrop (Thermo Scientific). Equal amount of DNA from each samples (up to 96 samples) were pooled and 1ug of them was ligated with the illumina adaptors using the NEBNext Ultra II DNA Library Prep Kit (NEB). Illumina sequence (NEBNext Multiplex Oligos for Illumina; NEB) were added to the adaptor- ligated samples by the PCR. Clean up and size selection of the PCR product was done using SPRIselect (Beckman Coulter) and the quality of the library was confirmed by 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent).

treatment_protocol: 20 μM siControl (Dharmacon, D-001210-01) or 20 μM siRif1 (Dharmacon, D-040028-01) were injected into zygotes at 17-18 hours post-hCG injection and embryos were cultured until 4-cell, 8-cell and morula stage, respectively.

value: morula

value: (C57BL/6J xCBA) x DBA/2J


title: siRif1_Morula_070


title: siRif1_Morula_069


title: siRif1_Morula_068


title: siRif1_Morula_067


title: TT-seq_H18_rep1


title: TT-seq_H18_rep3


title: TT-seq_W18_rep2


title: siRif1_Morula_066


title: siRif1_Morula_064


title: siRif1_Morula_065


title: siRif1_Morula_063


title: siRif1_Morula_062


title: siRif1_Morula_058


title: siRif1_Morula_056


title: siRif1_Morula_057


title: siRif1_Morula_060


title: siRif1_Morula_059


title: siRif1_Morula_055


title: siRif1_Morula_054


title: TT-seq_NC18_rep3


title: siRif1_Morula_072


title: siRif1_Morula_053


title: siRif1_Morula_052


title: siRif1_Morula_051


title: siRif1_Morula_049


title: siRif1_Morula_050


title: siRif1_Morula_047


title: siRif1_Morula_046


title: siRif1_Morula_048


title: 20daysChronicRestraint_3h_CRS4_v10

description: Library name: CRS4_v10

value: Ventral hippocampus

value: female


title: siRif1_Morula_043


title: siRif1_Morula_042


title: siRif1_Morula_041


title: siRif1_Morula_044


title: 20daysChronicRestraint_5h30min_CRS4_v35

description: Library name: CRS4_v35

value: male


title: siRif1_Morula_061


title: siRif1_Morula_040


title: siRif1_Morula_038


title: siRif1_Morula_039


title: siRif1_Morula_037


title: siRif1_Morula_036


title: siRif1_Morula_033


title: siRif1_Morula_031


title: siRif1_Morula_035


title: siRif1_Morula_030


title: siRif1_Morula_034


title: siRif1_Morula_032


title: siRif1_Morula_029


title: siRif1_Morula_028


title: siRif1_Morula_026


title: siRif1_Morula_023


title: siRif1_Morula_025


title: siRif1_Morula_027


title: siRif1_Morula_022


title: siRif1_Morula_045


title: siRif1_Morula_021


title: siRif1_Morula_020


title: siRif1_Morula_018


title: siRif1_Morula_017


title: siRif1_Morula_016


title: siRif1_Morula_014


title: siRif1_Morula_013


title: siRif1_Morula_015


title: siRif1_Morula_019


title: siRif1_Morula_012


title: siRif1_Morula_009


title: siRif1_Morula_008


title: siRif1_Morula_007


title: siRif1_Morula_011


title: siRif1_Morula_006


title: siRif1_Morula_005


title: siRif1_Morula_004


title: siRif1_Morula_003


title: siRif1_Morula_024


title: siCont_Morula_071

description:
binary.siCont_Morula.txt
RT.siCont_Morula.bedgraph

value: siControl


title: siCont_Morula_070


title: siCont_Morula_067


title: siCont_Morula_069


title: siCont_Morula_068


title: siCont_Morula_066


title: siCont_Morula_064


title: siCont_Morula_063


title: siCont_Morula_060


title: siCont_Morula_065


title: siCont_Morula_057


title: siCont_Morula_058


title: siCont_Morula_059


title: siRif1_Morula_010


title: siCont_Morula_061


title: siCont_Morula_056


title: siCont_Morula_055


title: siCont_Morula_062


title: siCont_Morula_053


title: HS/AAV6 + SC514 - Sample11

city: Milan

first: Raffaella

last: Di Micco

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description: Library name: Sample57_168_C17_BM

data_processing:
Data analyzed withthe CRISPResso2 pipeline:
Reads were trimmed using the Trimmomatic
Trimmed sequences were mapped to the input amplicon reference (by providing also the sequence for the sgRNA)
Computed alleles were quantified by measuring the number of reads and their relative abundance based on total read counts
Assembly: Custom reference vector AAV sequence and guide
Supplementary files format and content: Tab-separated results of the different allele found with corresponding quantifications

source_name: Bone Marrow

extract_protocol:
Genomic DNA was isolated with QIAamp DNA Micro Kit (QIAGEN)
PCR amplicons for individual samples were generated by nested PCR starting from >50–100 ng of purified gDNA. The first PCR step was performed with GoTaq G2 DNA Polymerase 1007 (Promega) according to the manufacturer’s instructions using the following amplification protocol: 95°C for 5 min, (95 °C for 0.5 min, 60 °C for 0.5 min, 72 °C for 0.25 min) × 20 cycles, 72 °C for 5 min. The second PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to manufacturer’s instructions using 5 μl of the first-step PCR product and the following amplification protocol: 95 °C for 5min; 95°C x 0.5 min, 60°C x 0.5 min, 72°C x 0.3 min, (20cycles); 72°C x 5 min. Second-step PCR primers were endowed with tails containing P5/P7 sequences, i5/i7 Illumina tags to allow multiplexed sequencing and R1/R2 primer binding sites. The PCR amplicon from each sample was separately purified by using a QIAquick PCR Purification kit (Qiagen).

value: Bone Marrow

value: HS/AAV6 + SC514


title: siCont_Morula_054


title: siRif1_Morula_002


title: siRif1_Morula_001


title: siCont_Morula_051


title: siCont_Morula_052


title: HS/AAV6 + SC514 - Sample10

description: Library name: Sample56_168_C16_BM


title: HS/AAV6 + SC514 - Sample9

description: Library name: Sample55_168_C15_BM


title: siCont_Morula_072


title: HS/AAV6 + SC514 - Sample8

description: Library name: Sample54_168_C14_BM


title: siCont_Morula_050


title: siCont_Morula_048


title: HS/AAV6 + SC514 - Sample7

description: Library name: Sample53_168_C13_BM


title: siCont_Morula_047


title: HS/AAV6 + SC514 - Sample6

description: Library name: Sample52_168_B12_BM


title: siCont_Morula_046


title: HS/AAV6 + SC514 - Sample5

description: Library name: Sample51_168_B11_BM


title: siCont_Morula_045


title: HS/AAV6 + SC514 - Sample4

description: Library name: Sample50_168_B10_BM


title: siCont_Morula_044


title: siCont_Morula_043


title: HS/AAV6 + SC514 - Sample3

description: Library name: Sample49_168_B9_BM


title: HS/AAV6 + SC514 - Sample12

description: Library name: Sample58_168_C18_BM


title: HS/AAV6 + SC514 - Sample1

description: Library name: Sample47_168_B7_BM


title: siCont_Morula_041


title: HS/AAV6 + ANAK - Sample12

description: Library name: Sample16_148_E30_BM

value: HS/AAV6 + ANAK


title: HS/AAV6 + ANAK - Sample11

description: Library name: Sample15_148_E29_BM


title: HS/AAV6 + SC514 - Sample2

description: Library name: Sample48_168_B8_BM


title: siCont_Morula_040


title: HS/AAV6 + ANAK - Sample10

description: Library name: Sample14_148_E28_BM


title: siCont_Morula_039


title: siCont_Morula_049


title: HS/AAV6 + ANAK - Sample8

description: Library name: Sample13_148_E16_BM


title: HS/AAV6 + ANAK - Sample7

description: Library name: Sample29_148_E12_BM


title: siCont_Morula_036


title: siCont_Morula_038


title: HS/AAV6 + ANAK - Sample9

description: Library name: Sample28_148_E27_BM


title: siCont_Morula_035


title: HS/AAV6 + ANAK - Sample4

description: Library name: Sample7_148_C6_BM


title: siCont_Morula_033


title: HS/AAV6 + ANAK - Sample6

description: Library name: Sample30_148_C9_BM


title: siCont_Morula_034


title: HS/AAV6 + ANAK - Sample5

description: Library name: Sample8_148_C8_BM


title: siCont_Morula_031


title: siCont_Morula_032


title: HS/AAV6 + ANAK - Sample2

description: Library name: Sample32_148_C23_BM


title: siCont_Morula_030


title: HS/AAV6 + GSE56 - Sample12

description: Library name: Sample20_152_B9_BM

value: HS/AAV6 + GSE56


title: siCont_Morula_042


title: HS/AAV6 + ANAK - Sample1

description: Library name: Sample31_148_C17_BM


title: HS/AAV6 + ANAK - Sample3

description: Library name: Sample9_148_C24_BM


title: siCont_Morula_027


title: siCont_Morula_028


title: HS/AAV6 + GSE56 - Sample11

description: Library name: Sample22_152_B13_BM


title: HS/AAV6 + GSE56 - Sample9

description: Library name: Sample64_168_D24_BM


title: HS/AAV6 + GSE56 - Sample10

description: Library name: Sample21_152_B11_BM


title: siCont_Morula_029


title: siCont_Morula_037


title: HS/AAV6 + GSE56 - Sample8

description: Library name: Sample63_168_D23_BM


title: siCont_Morula_025


title: HS/AAV6 + GSE56 - Sample6

description: Library name: Sample61_168_D21_BM


title: siCont_Morula_024


title: HS/AAV6 + GSE56 - Sample7

description: Library name: Sample62_168_D22_BM


title: siCont_Morula_023


title: siCont_Morula_022


title: HS/AAV6 + GSE56 - Sample5

description: Library name: Sample60_168_D20_BM


title: HS/AAV6 + GSE56 - Sample4

description: Library name: Sample59_168_D19_BM


title: siCont_Morula_021


title: siCont_Morula_020


title: HS/AAV6 + GSE56 - Sample3

description: Library name: Sample5_148_B7_BM


title: HS/AAV6 + GSE56 - Sample2

description: Library name: Sample4_148_B3_BM


title: siCont_Morula_019


title: siCont_Morula_017


title: siCont_Morula_018


title: HS/AAV6 + GSE56 - Sample1

description: Library name: Sample6_148_B18_BM


title: HS/AAV6 - Sample12

description: Library name: Sample18_152_A4_BM


title: HS/AAV6 - Sample13

description: Library name: Sample19_152_A5_BM


title: siCont_Morula_016


title: HS/AAV6 - Sample11

description: Library name: Sample17_152_A3_BM


title: HS/AAV6 - Sample10

description: Library name: Sample46_168_A6_BM


title: HS/AAV6 - Sample9

description: Library name: Sample44_168_A4_BM


title: siCont_Morula_026


title: siCont_Morula_014


title: siCont_Morula_013


title: siCont_Morula_012


title: HS/AAV6 - Sample7

description: Library name: Sample42_168_A2_BM


title: HS/AAV6 - Sample8

description: Library name: Sample43_168_A3_BM


title: siCont_Morula_011


title: siCont_Morula_010


title: HS/AAV6 - Sample6

description: Library name: Sample41_168_A1_BM


title: HS/AAV6 - Sample5

description: Library name: Sample26_148_A4_BM


title: siCont_Morula_008


title: siCont_Morula_009


title: HS/AAV6 - Sample4

description: Library name: Sample1_148_A2_BM


title: siCont_Morula_007


title: HS/AAV6 - Sample2

description: Library name: Sample2_148_A13_BM


title: siCont_Morula_006


title: siCont_Morula_005


title: HS/AAV6 + GSE56 - Sample15

description: Library name: Sample_168_D24_BM

data_processing:
Barcodes computed with BAR-seq2 pipeline: barcode sequences were extracted with the TagDust software (v2.33) and processed to merge similar (erroneous) barcodes
Supplementary files format and content: Tab-separated matrix with barcode counts

extract_protocol:
QIAamp DNA Micro Kit (QIAGEN)
Custom library construction protocol. PCR starting from >50–100 ng of purified gDNA. The first PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to the manufacturer’s instructions using the following amplification protocol: 95 °C for 5 min, (95 °C for 0.5 min, 60 °C for 0.5 min, 72 °C for 0.5 min) × 20 cycles, 72 °C for 5 min. Forward primer was designed to bind the donor template upstream of the BAR sequence, while the reverse primer annealed outside the homology arm, thus amplifying 328 bp of the on-target integrated cassette. For targeted deep sequencing of the plasmid and AAV libraries, the reverse primer was annealed to the homology arm. The second PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to the manufacturer’s instructions using 5 μl of the first-step PCR product and the following amplification protocol: 95 °C for 5 min, (95 °C for 0.5 min,60 °C for 0.5 min, 72 °C for 0.5 min) × 20 cycles, 72 °C for 5 min. Second-step PCR primers were endowed with tails containing P5/P7 sequences, i5/i7 1000 Illumina tags to allow multiplexed sequencing, and R1/R2 primer binding sites.


title: HS/AAV6 - Sample1

description: Library name: Sample27_148_A1_BM


title: siCont_Morula_004


title: siCont_Morula_002


title: siCont_Morula_003


title: siCont_Morula_015


title: HS/AAV6 + GSE56 - Sample13

description: Library name: Sample_168_D22_BM


title: siRif1_4Cell_071

description:
binary.siRif1_4Cell.txt
RT.siRif1_4Cell.bedgraph

source_name: 4-cell embryo

value: 4-cell embryo


title: HS/AAV6 + GSE56 - Sample10

description: Library name: Sample_168_D19_BM


title: HS/AAV6 + GSE56 - Sample12

description: Library name: Sample_168_D21_BM


title: HS/AAV6 + GSE56 - Sample11

description: Library name: Sample_168_D20_BM


title: siRif1_4Cell_072


title: HS/AAV6 + SC514 - Sample12

description: Library name: Sample_168_C18_BM


title: siCont_Morula_001


title: HS/AAV6 - Sample3

description: Library name: Sample3_148_A15_BM


title: HS/AAV6 + SC514 - Sample11

description: Library name: Sample_168_C17_BM


title: HS/AAV6 + SC514 - Sample9

description: Library name: Sample_168_C15_BM


title: siRif1_4Cell_067


title: HS/AAV6 + SC514 - Sample8

description: Library name: Sample_168_C14_BM


title: siRif1_4Cell_070


title: HS/AAV6 + SC514 - Sample10

description: Library name: Sample_168_C16_BM


title: siRif1_4Cell_069


title: HS/AAV6 + SC514 - Sample7

description: Library name: Sample_168_C13_BM


title: siRif1_4Cell_068


title: siRif1_4Cell_066


title: siRif1_4Cell_065


title: HS/AAV6 + GSE56 - Sample14

description: Library name: Sample_168_D23_BM


title: siRif1_4Cell_064


title: siRif1_4Cell_063


title: HS/AAV6 + SC514 - Sample5

description: Library name: Sample_168_B8_BM


title: HS/AAV6 + SC514 - Sample4

description: Library name: Sample_168_B7_BM


title: siRif1_4Cell_062


title: HS/AAV6 + SC514 - Sample2

description: Library name: Sample_168_B11_BM


title: siRif1_4Cell_061


title: HS/AAV6 + SC514 - Sample3

description: Library name: Sample_168_B12_BM


title: siRif1_4Cell_060


title: HS/AAV6 + SC514 - Sample1

description: Library name: Sample_168_B10_BM


title: siRif1_4Cell_059


title: HS/AAV6 - Sample19

description: Library name: Sample_168_A6_BM


title: siRif1_4Cell_058


title: HS/AAV6 - Sample18

description: Library name: Sample_168_A5_BM


title: siRif1_4Cell_057


title: HS/AAV6 - Sample17

description: Library name: Sample_168_A4_BM


title: siCont_4Cell_064

description:
binary.siCont_4Cell.txt
RT.siCont_4Cell.bedgraph


title: siCont_4Cell_063


title: HS/AAV6 - Sample16

description: Library name: Sample_168_A3_BM


title: HS/AAV6 - Sample14

description: Library name: Sample_168_A1_BM


title: siCont_4Cell_062


title: HS/AAV6 + GSE56 - Sample9

description: Library name: Sample_152_B9_BM


title: siCont_4Cell_060


title: HS/AAV6 - Sample15

description: Library name: Sample_168_A2_BM


title: HS/AAV6 + SC514 - Sample6

description: Library name: Sample_168_B9_BM


title: HS/AAV6 + GSE56 - Sample8

description: Library name: Sample_152_B13_BM


title: HS/AAV6 + GSE56 - Sample7

description: Library name: Sample_152_B11_BM


title: siCont_4Cell_058


title: siCont_4Cell_057


title: siCont_4Cell_059


title: HS/AAV6 - Sample13

description: Library name: Sample_152_A5_BM


title: HS/AAV6 - Sample11

description: Library name: Sample_152_A3_BM


title: HS/AAV6 + ANAK - Sample19

description: Library name: Sample_148_E30_BM


title: siRif1_8Cell_062

description:
binary.siRif1_8Cell.txt
RT.siRif1_8Cell.bedgraph

source_name: 8-cell embryo

value: 8-cell embryo


title: HS/AAV6 - Sample12

description: Library name: Sample_152_A4_BM


title: siRif1_8Cell_061


title: siRif1_8Cell_064


title: siRif1_8Cell_063


title: siRif1_8Cell_060


title: HS/AAV6 + ANAK - Sample17

description: Library name: Sample_148_E28_BM


title: siRif1_8Cell_059


title: HS/AAV6 + ANAK - Sample15

description: Library name: Sample_148_E16_BM


title: siCont_4Cell_061


title: HS/AAV6 + ANAK - Sample18

description: Library name: Sample_148_E29_BM


title: HS/AAV6 + ANAK - Sample14

description: Library name: Sample_148_E12_BM


title: siRif1_8Cell_057


title: siRif1_8Cell_058


title: HS/AAV6 + ANAK - Sample13

description: Library name: Sample_148_C9_BM


title: HS/AAV6 + ANAK - Sample12

description: Library name: Sample_148_C8_BM


title: siCont_8Cell_072

description:
binary.siCont_8Cell.txt
RT.siCont_8Cell.bedgraph


title: siCont_8Cell_071


title: HS/AAV6 + ANAK - Sample10

description: Library name: Sample_148_C24_BM


title: HS/AAV6 + ANAK - Sample9

description: Library name: Sample_148_C23_BM


title: HS/AAV6 + ANAK - Sample11

description: Library name: Sample_148_C6_BM


title: siCont_8Cell_069


title: HS/AAV6 + ANAK - Sample8

description: Library name: Sample_148_C17_BM


title: siCont_8Cell_068


title: siCont_8Cell_067


title: HS/AAV6 + GSE56 - Sample6

description: Library name: Sample_148_B7_BM


title: siCont_8Cell_066


title: HS/AAV6 + GSE56 - Sample5

description: Library name: Sample_148_B3_BM


title: siCont_8Cell_065


title: HS/AAV6 + ANAK - Sample16

description: Library name: Sample_148_E27_BM


title: HS/AAV6 - Sample10

description: Library name: Sample_148_A4_BM


title: siCont_8Cell_063


title: HS/AAV6 + GSE56 - Sample4

description: Library name: Sample_148_B18_BM


title: HS/AAV6 - Sample9

description: Library name: Sample_148_A2_BM


title: HS/AAV6 - Sample8

description: Library name: Sample_148_A15_BM


title: HS/AAV6 - Sample7

description: Library name: Sample_148_A13_BM


title: HS/AAV6 - Sample6

description: Library name: Sample_148_A1_BM


title: siCont_8Cell_060


title: siCont_8Cell_058


title: siCont_8Cell_059


title: HS/AAV6 + ANAK - Sample6

description: Library name: Sample_137_C7_BM


title: siCont_8Cell_070


title: HS/AAV6 + ANAK - Sample7

description: Library name: Sample_137_C8_BM


title: siCont_8Cell_056


title: HS/AAV6 + ANAK - Sample4

description: Library name: Sample_137_C5_BM


title: siCont_8Cell_055


title: siCont_8Cell_057


title: HS/AAV6 + ANAK - Sample5

description: Library name: Sample_137_C6_BM


title: HS/AAV6 + ANAK - Sample1

description: Library name: Sample_137_C1_BM


title: HS/AAV6 + ANAK - Sample2

description: Library name: Sample_137_C2_BM


title: siCont_8Cell_052


title: siCont_8Cell_053


title: siCont_8Cell_064


title: HS/AAV6 + GSE56 - Sample2

description: Library name: Sample_137_B5_BM


title: siCont_8Cell_051


title: siCont_8Cell_062


title: siCont_8Cell_049


title: HS/AAV6 + GSE56 - Sample1

description: Library name: Sample_137_B2_BM


title: siCont_8Cell_061


title: HS/AAV6 - Sample5

description: Library name: Sample_137_A8_BM


title: siCont_8Cell_047


title: siCont_8Cell_046


title: HS/AAV6 - Sample4

description: Library name: Sample_137_A7_BM


title: HS/AAV6 - Sample2

description: Library name: Sample_137_A3_BM


title: HS/AAV6 - Sample1

description: Library name: Sample_137_A1_BM


title: siCont_8Cell_045


title: siCont_8Cell_044


title: HS/AAV6 + ANAK - Sample3

description: Library name: Sample_137_C3_BM


title: siCont_8Cell_043


title: siCont_8Cell_054


title: HS/AAV6 + GSE56 - Sample3

description: Library name: Sample_137_B6_BM


title: siCont_8Cell_040


title: siCont_8Cell_042


title: CD138+, AL8_AL9_HD6_HD7, rep1, GEX

city: Boston

first: Nicolas

middle: Alejandro

last: Gort-Freitas

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

description: Library name: BRI-2108

data_processing:
Raw FASTQ files were processed by Cell Ranger 6.1.1 using GRCh38-2020-A and cellranger-vdj- GRCh38-alts-ensembl-5.0.0 as references for the mapping of transcript counts and immune receptor calls respectively. Count matrices for transcripts and V(D)J sequences were generated simultaneously using cellranger multi.
Demultiplexing: Each barcoded cell was genotyped for a panel of human SNPs with minor allele frequency smaller than 5% (Fairley et al., 2019) through Cellsnp-lite. Subsequently, Vireo was used to infer the genotypes of each original group of samples included in each CD138- library. Whenever two libraries included overlapping identities, a distance matrix was computed to verify that the algorithm had independently learned the same genotypes in both. The genotypes associated to the cells from the CD138+ fractions, which had weaker coverage of SNPs were elucidated by treating the genotypes inferred in the CD138- libraries as ground truths and computing maximum likelihood estimates from these. Barcodes that were not given a singlet assignment by Vireo were not discarded from the embedding but excluded from comparisons across individuals or conditions.
Ambient RNA correction: SoupX was used to compute ambient RNA profiles for each library. These profiles were used to compute corrected count matrices, which were in turn converted to integer values through randomized rounding. Corrected counts were employed for differential gene expression and gene set enrichment analyses.
Cells expressing more than 5% mitochondrial transcripts or fewer than 500 total transcripts were excluded as low quality cells. Barcodes not included in the filtered count matrix generated by CellRanger were deemed empty droplets and discarded. Cells expressing more than 10,000 total transcripts were considered potential doublets and also excluded.
Doublet detection: Scrublet (0.2.3) was used, under default parameters, to detect barcodes corresponding to doublets. Barcodes labeled as doublets were excluded from all analyses. Further removal of plasma cell doublets was required as a second step as described below.
Annotation of CD138- cells: After filtering, CD138- libraries were concatenated and its transcriptomes were projected to the reference map constructed by Zeng et al. through its associated software package BoneMarrowMap. Each cell was assigned low-dimensional embedding coordinates, a cell state label, a pseudotime, and a mapping score based on its proximity to cells from the reference.
Identification of CD138+ plasma cells: CD138+ and CD138- fractions were concatenated and jointly embedded. Cells were annotated through CellTypist31 using the model Immune_All_AddPIP as a reference. Leiden clustering (resolution = 1.5) was performed on all cells, and cells from clusters whose modal identity was neither “Plasma cells” nor “Plasmablasts” were excluded. Subsequently, a panel of marker genes corresponding to blood populations was selected as identifiers of contamination. Expression thresholds for these markers were computed through an iterative method. For each gene, cell states among CD138- cells were ranked by average expression. A baseline set of reference states, starting with the four highest-ranked states, was established to differentiate true expression against background. Additional states were then sequentially considered for inclusion, with the requirement that each new state added must enhance the true positive rate (TPR) while maintaining a false positive rate (FPR) of 5% against non-reference states. The process was concluded when the inclusion of further states ceased to improve the TPR, thus defining the optimal reference states and the associated expression thresholds for each gene. These thresholds were used to determine anomalous expression in plasma cell clusters.  Subsequently, cells from clusters that had anomalously high expression of any marker marker genes corresponding to other blood populations (see Fig. S4A) were identified manually and excluded. Clusters where more than 50% of the cells were considered doublets during genetic demultiplexing or had mitochondrial transcript fractions above 5% were also discarded (Fig S4B). Surviving barcodes were re-embedded and re-clustered, and the obtained clusters were subjected to another round of filtering (Fig. S4C & S4D). Lastly, individual cells with expression of any contamination marker above its respective threshold were discarded.
Definition of plasma cell subsets: An scVI model with 30 latent variables was trained on the identified plasma cells to construct a batch-integrated embedding of plasma cell subsets. Leiden clustering was performed on the nearest neighbors graph (k = 15) computed from the learned latent variables (resolution = 0.4). Clusters primarily represented by cells from one or two AL patients were named after the overrepresented individual(s). Clusters with significant representation from individuals across both conditions were assigned the prefix "PC".
Assembly: GRCh38-2020-A and cellranger-vdj-GRCh38-alts-ensembl-5.0.0
Supplementary files format and content: Raw counts (tsv.gz): library identity, barcode, and raw counts for all cells included in each sample after SoupX correction.
Supplementary files format and content: Immune receptor repertoires (.airr): data associated with each filter-passing cell in each sample.
Supplementary files format and content: Library barcodes and metadata (.csv): library identity, barcode, donor/patient identity, annotation, and associated metadata for all cells across CD138- (CD138-_barcodes_and_metadata.csv) and CD138+ (CD138+_barcodes_and_metadata.csv) libraries

source_name: Bone marrow

extract_protocol:
Bone marrow aspirates were obtained from patients with newly diagnosed AL amyloidosis seen at our center between 2019 and 2023. Healthy samples were obtained from discarded surgical material of patients undergoing primary, elective total hip arthroplasty, according to a Brigham and Women’s Hospital IRB approved protocol. Samples were processed within 2 hours from collection. Bone marrow mononuclear cells (BMMC) were separated by Ficoll Paque PLUS (Sigma) according to protocol and plasma cells were enriched by CD138-positive selection with anti-CD138 magnetic activated cell separation microbeads (Miltenyi Biotec). Viable CD138 positive and negative fractions were resuspended in FBS with 10% DMSO or Bambanker (Bulldog Bio) and stored in liquid nitrogen until the day of analysis.
10X Chromium Next GEM Single Cell 5’ reagent kits and BCR/TCR amplification kits were used for joint transcriptional and immune profiling of bone marrow samples. For the CD138+ samples, a combined profiling of BCR and 5’RNA was performed. For CD138- samples, a combined profiling of BCR, TCR, and 5’RNA was performed. The samples were aggregated into a fewer number of fraction-specific pools and loaded at a concentration of 20,000 cells per lane. The resulting libraries were sequenced on Illumina NovaSeq S1.

value: Bone marrow

tag: disease state

value: Healthy & diseased (AL)

tag: enrichment


title: CD138+, AL8_AL9_HD6_HD7, rep2, GEX

description: Library name: BRI-2110


title: CD138+, AL8_AL9_HD6_HD7, rep1, BCR

description: Library name: BRI-2109


title: CD138+, AL7_HD5, rep1, GEX

description: Library name: BRI-2106


title: siCont_8Cell_050

tag: genotype


title: CD138+, AL8_AL9_HD6_HD7, rep2, BCR

description: Library name: BRI-2111


title: CD138+, AL7_HD5, rep1, BCR

description: Library name: BRI-2107


title: CD138+, AL5_AL6_AL7_HD5, rep2, BCR

description: Library name: BRI-2105


title: siCont_8Cell_038


title: siCont_8Cell_048


title: siCont_8Cell_039


title: CD138+, AL5_AL6_AL7_HD5, rep1, BCR

description: Library name: BRI-2103


title: CD138+, AL5_AL6_AL7_HD5, rep2, GEX

description: Library name: BRI-2104


title: HS/AAV6 - Sample3

description: Library name: Sample_137_A5_BM


title: siCont_8Cell_036


title: CD138+, AL5_AL6_AL7_HD5, rep1, GEX

description: Library name: BRI-2102


title: siCont_8Cell_035


title: CD138+, AL3_AL4_HD3_HD4, rep2, BCR

description: Library name: BRI-2099


title: CD138+, AL3_AL4_HD3_HD4, rep2, GEX

description: Library name: BRI-2098


title: CD138+, AL3_AL4_HD3_HD4, rep1, BCR

description: Library name: BRI-2097


title: siCont_8Cell_033


title: siCont_8Cell_034


title: siCont_8Cell_041


title: CD138+, AL3_AL4_HD3_HD4, rep1, GEX

description: Library name: BRI-2096


title: siCont_8Cell_031


title: siCont_8Cell_030


title: CD138+, AL1_AL2_HD1, rep1, BCR

description: Library name: BRI-2093


title: siCont_8Cell_029


title: CD138+, AL1_AL2_HD1, rep1, GEX

description: Library name: BRI-2092


title: siCont_8Cell_028


title: CD138+, AL1_AL2_HD1_HD2, rep1, GEX

description: Library name: BRI-2090


title: siCont_8Cell_027


title: CD138-, AL8_AL9, rep1, BCR

description: Library name: BRI-2083

value: Diseased (AL)


title: siCont_8Cell_037


title: siCont_8Cell_026


title: CD138-, AL8_AL9, rep1, GEX

description: Library name: BRI-2081


title: CD138-, AL8, rep1, BCR

description: Library name: BRI-2080


title: siCont_8Cell_023


title: siCont_8Cell_025


title: siCont_8Cell_022