title: FF sample 46524

description:
Genomic DNA from FF sample 46524
203991390144_R08C01


title: H3K36me3 CUT&Tag, Dox, rep2

status: Public on Mar 30 2026

type: SRA

city: Worcester

first: Chun-Hao

last: Chao

address: 364 Plantation St. LRB560D

department: MCCB

country: USA

institute: UMass Chan Medical School

description: Library name: H3K36me3_Dox_rep2

library_source: genomic

data_processing:
Fastq files were trimmed with Trimmomatic, then aligned by Bowtie2 with GRCm38. SAM files were sorted and deduplicate by Picard. Reads were filtered by MAPQ > 10 and -f 99, -f 147, -f 83 or -f 163 for the unique mapped reads. HOMER and deeptools were applied on bam file for aggregation plot, heatmap, bedgraph, bigwig and peak annotation.
Peakcalling of H2A.Z was perform through getDifferentialPeaksReplicates.pl from HOMER with IgG as background signal and '-style histone -tagThreshold 40'.
Assembly: GRCm38 with Gencode vM25 annotation
Supplementary files format and content: H2AZ_peak.bed is a BED file containing consensus ATAC-seq peaks identified from overlapping peak regions across all replicates.
Supplementary files format and content: Downpeak_annotation.csv is the significant down peaks with annotation in Dox treatment condition
Supplementary files format and content: Uppeak_annotation.csv is the significant up peaks with annotation in Dox treatment condition
Supplementary files format and content: H2A.Z_control_rep1.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_control_rep2.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_control_rep3.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_control_rep4.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_Dox_rep1.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_Dox_rep2.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_Dox_rep3.bw is the bigwig file for the corresponded condition
Supplementary files format and content: H2A.Z_Dox_rep4.bw is the bigwig file for the corresponded condition
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: cell line

growth_protocol: Cells were detached with accutase and plated at a density of 2–2.5 × 105 cells per 6-cm dish at 37°C in a 5% CO₂ atmosphere. Culture medium was 2i/LIF medium (NDiff 227 supplemented with LIF, 2% FBS, 3 µM CHIR-99021, and 1 µM PD0325901).

extract_protocol:
Cells were bound on ConA beads and incubate with the primary antibody or proteins overnight in antibody buffer. For CUT&Tag, cells were incubated with secondary antibody and pA-Tn5 sequentially and then tagmented with tagmentation buffer. Tagmentation was stopped by EDTA buffer and DNA were then recovered and directly subjected to library amplification. For CUT&RUN, cells were incubated with pA-MNase and digested on ice-water in buffer containing CaCl2. Digestion was stopped by 2X STOP buffer and DNA were recovered by high speed spin, Proteinase K/SDS digestion and PCI extraction. For MapR, cell were directly applied for digestion and the rest step as described in CUT&RUN.
For CUT&Tag, tagmented DNA was recovered and directly PCR with Nextera primer for library amplification. For CUT&RUN and MapR, NEBNext Ultra II DNA library prep was used for library construction with 14 cycle of library amplification.

treatment_protocol: Dox condition was treated with doxycycline 500 ng/ml for 48 hours

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: mouse embryonic stem cell

tag: genotype

value: HA-Rnaseh1 knock-in

tag: antibody


title: H3K36me3 CUT&Tag, Dox, rep4

description: Library name: H3K36me3_Dox_rep4


title: H3K36me3 CUT&Tag, control, rep2

description: Library name: H3K36me3_control_rep2


title: FF sample 9667

type: genomic

city: Washington

first: Bernard

last: Kwabi-Addo

state: DC

address: 520 W. Street N.W.

department: Biochemistry and Molecular Biology

institute: Howard University College of Medicine

description:
Genomic DNA from FF sample 9667
203991410098_R08C01

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

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

data_processing:
Illumina GenomeStudio Methylation Module V2011.1
[processed value definition] Average Beta

label: Cy3, Cy5

organism: Homo sapiens

source_name: Prostate

label_protocol: Standard Illumina Protocol

extract_protocol: DNA extracted from fresh frozen samples using Qiagen DNA Mini kit according to standard instructions

tag: disease state

value: Normal

value: Prostate

tag: gleason

tag: psa

tag: recurrence


title: FF sample 23979

description:
Genomic DNA from FF sample 23979
203991410097_R08C01


title: H3K27me3 CUT&Tag, Dox, rep1

description: Library name: H3K27me3_Dox_rep1


title: H3K27me3 CUT&Tag, control, rep3

description: Library name: H3K27me3_control_rep3


title: H3K27me3 CUT&Tag, Dox, rep3

description: Library name: H3K27me3_Dox_rep3


title: FF sample 19285

description:
Genomic DNA from FF sample 19285
203991390136_R08C01


title: FF sample 30380 (203991410089)

description:
Genomic DNA from FF sample 30380
203991410089_R08C01


title: H3K27me3 CUT&Tag, control, rep4

description: Library name: H3K27me3_control_rep4


title: FF sample 39037

description:
Genomic DNA from FF sample 39037
203991390168_R08C01


title: H3K27me3 CUT&Tag, Dox, rep2

description: Library name: H3K27me3_Dox_rep2


title: H3K27me3 CUT&Tag, control, rep2

description: Library name: H3K27me3_control_rep2


title: H3K27ac CUT&Tag, Dox, rep2

description: Library name: H3K27ac_Dox_rep2


title: FF sample 20673

description:
Genomic DNA from FF sample 20673
203991410008_R08C01

value: Cancer

value: no


title: FF sample 42937

description:
Genomic DNA from FF sample 42937
203991400154_R08C01


title: H3K27me3 CUT&Tag, control, rep1

description: Library name: H3K27me3_control_rep1


title: H3K27ac CUT&Tag, Dox, rep1

description: Library name: H3K27ac_Dox_rep1


title: FF sample 47314

description:
Genomic DNA from FF sample 47314
203991410061_R08C01

value: no data

value: unknown


title: FF sample 30380 (203991410099)

description:
Genomic DNA from FF sample 30380
203991410099_R08C01


title: FF sample 37307

description:
Genomic DNA from FF sample 37307
203991410132_R08C01


title: H3K27ac CUT&Tag, control, rep2

description: Library name: H3K27ac_control_rep2


title: FF sample 9660

description:
Genomic DNA from FF sample 9660
203991390144_R07C01


title: FF sample 58355

description:
Genomic DNA from FF sample 58355
203990170155_R08C01


title: H3K27ac CUT&Tag, control, rep1

description: Library name: H3K27ac_control_rep1


title: FF sample 53985

description:
Genomic DNA from FF sample 53985
203991410097_R07C01


title: FF sample 19205

description:
Genomic DNA from FF sample 19205
203991390161_R07C01


title: H3K9me3 CUT&Tag, control, rep1

description: Library name: H3K9me3_control_rep1


title: H3K9me3 CUT&Tag, Dox, rep1

description: Library name: H3K9me3_Dox_rep1


title: H3K9me3 CUT&Tag, Dox, rep2

description: Library name: H3K9me3_Dox_rep2


title: H3K4me3 CUT&Tag, Dox, rep2

description: Library name: H3K4me3_Dox_rep2

value: anti-H3K4me3(Millipore 05-745R)


title: FF sample 58655

description:
Genomic DNA from FF sample 58655
203991390137_R07C01


title: FF sample 40814

description:
Genomic DNA from FF sample 40814
203991410098_R07C01


title: H3K9me3 CUT&Tag, control, rep2

description: Library name: H3K9me3_control_rep2


title: FF sample 46101

description:
Genomic DNA from FF sample 46101
203991390136_R07C01


title: FF sample 40581

description:
Genomic DNA from FF sample 40581
203991410099_R07C01


title: H3K4me3 CUT&Tag, control, rep2

description: Library name: H3K4me3_control_rep2


title: FF sample 36849_R

description:
Genomic DNA from FF sample 36849_R
203991390167_R08C01


title: H3K4me3 CUT&Tag, Dox, rep1

description: Library name: H3K4me3_Dox_rep1


title: FF sample 46155

description:
Genomic DNA from FF sample 46155
203991410089_R07C01


title: FF sample 14670

description:
Genomic DNA from FF sample 14670
203991390168_R07C01


title: H2A.Z CUT&Tag, Dox, rep3

description: Library name: H2A.Z_Dox_rep3

value: anti-H2A.Z(Active Motif 39113)


title: H2A.Z CUT&Tag, Dox, rep4

description: Library name: H2A.Z_Dox_rep4


title: FF sample 31704

description:
Genomic DNA from FF sample 31704
203991400154_R07C01


title: H2A.Z CUT&Tag, Dox, rep1

description: Library name: H2A.Z_Dox_rep1


title: H2A.Z CUT&Tag, control, rep4

description: Library name: H2A.Z_control_rep4


title: FF sample 37308

description:
Genomic DNA from FF sample 37308
203990170155_R07C01


title: H2A.Z CUT&Tag, Dox, rep2

description: Library name: H2A.Z_Dox_rep2


title: H2A.Z CUT&Tag, control, rep1

description: Library name: H2A.Z_control_rep1


title: FF sample 55081

description:
Genomic DNA from FF sample 55081
203991410132_R07C01


title: H2A.Z CUT&Tag, control, rep2

description: Library name: H2A.Z_control_rep2


title: H3K4me3 CUT&Tag, control, rep1

description: Library name: H3K4me3_control_rep1


title: FF sample 32594_R

description:
Genomic DNA from FF sample 32594_R
203991390167_R07C01


title: H2A.Z CUT&Tag, control, rep3

description: Library name: H2A.Z_control_rep3


title: FF sample 30385

description:
Genomic DNA from FF sample 30385
203991410008_R07C01


title: FF sample 42955

description:
Genomic DNA from FF sample 42955
203991390161_R06C01


title: scRNA-Seq gastruloid differentiation day5 (120hrs), Dox, rep4

description: Library name: Day5_Dox_rep4

library_source: transcriptomic single cell

data_processing:
Fastq file were applied to cellrange count v6.1.2 with '--include-introns True' to generate barcode, feature and gene count matrix. And Seurat v5.0.1 were used for doublet remove, cell filter, normalization, cell cycle regression and PCA. Harmony v1.0.3 were used for batch effect correction. pyVIA was used for cluster and trajectory inference. CellMatch v0.0.0.9000 were used for cell annotation with mouse embryo scRNA-seq data (E3.5-E8.5). MAST v1.24.1were used for differentially expressed gene analysis between control and Dox in each cell type. CellChat v2.1.1 were used for cell-cell communication analysis. SCENIC v 0.12.1 and scMTNI were used to reconstitute GRN for each cell type.
Assembly: GRCm38 with Gencode vM23 annotation (mm10-2020)
Supplementary files format and content: Rnaseh1_D0_N_rep1_barcodes.tsv.gz, Rnaseh1_D0_N_rep1_features.tsv.gz, Rnaseh1_D0_N_rep1_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D0_N_rep2_barcodes.tsv.gz, Rnaseh1_D0_N_rep2_features.tsv.gz, Rnaseh1_D0_N_rep2_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D0_Dox_rep1_barcodes.tsv.gz, Rnaseh1_D0_Dox_rep1_features.tsv.gz, Rnaseh1_D0_Dox_rep1_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D0_Dox_rep2_barcodes.tsv.gz, Rnaseh1_D0_Dox_rep2_features.tsv.gz, Rnaseh1_D0_Dox_rep2_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D3_N_rep1_barcodes.tsv.gz, Rnaseh1_D3_N_rep1_features.tsv.gz, Rnaseh1_D3_N_rep1_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D3_N_rep2_barcodes.tsv.gz, Rnaseh1_D3_N_rep2_features.tsv.gz, Rnaseh1_D3_N_rep2_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D3_N_rep3_barcodes.tsv.gz, Rnaseh1_D3_N_rep3_features.tsv.gz, Rnaseh1_D3_N_rep3_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D3_N_rep4_barcodes.tsv.gz, Rnaseh1_D3_N_rep4_features.tsv.gz, Rnaseh1_D3_N_rep4_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D3_Dox_rep1_barcodes.tsv.gz, Rnaseh1_D3_Dox_rep1_features.tsv.gz, Rnaseh1_D3_Dox_rep1_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D3_Dox_rep2_barcodes.tsv.gz, Rnaseh1_D3_Dox_rep2_features.tsv.gz, Rnaseh1_D3_Dox_rep2_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D3_Dox_rep3_barcodes.tsv.gz, Rnaseh1_D3_Dox_rep3_features.tsv.gz, Rnaseh1_D3_Dox_rep3_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D3_Dox_rep4_barcodes.tsv.gz, Rnaseh1_D3_Dox_rep4_features.tsv.gz, Rnaseh1_D3_Dox_rep4_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D5_N_rep1_barcodes.tsv.gz, Rnaseh1_D5_N_rep1_features.tsv.gz, Rnaseh1_D5_N_rep1_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D5_N_rep2_barcodes.tsv.gz, Rnaseh1_D5_N_rep2_features.tsv.gz, Rnaseh1_D5_N_rep2_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D5_N_rep3_barcodes.tsv.gz, Rnaseh1_D5_N_rep3_features.tsv.gz, Rnaseh1_D5_N_rep3_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D5_N_rep4_barcodes.tsv.gz, Rnaseh1_D5_N_rep4_features.tsv.gz, Rnaseh1_D5_N_rep4_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D5_N_rep5_barcodes.tsv.gz, Rnaseh1_D5_N_rep5_features.tsv.gz, Rnaseh1_D5_N_rep5_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D5_Dox_rep1_barcodes.tsv.gz, Rnaseh1_D5_Dox_rep1_features.tsv.gz, Rnaseh1_D5_Dox_rep1_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D5_Dox_rep2_barcodes.tsv.gz, Rnaseh1_D5_Dox_rep2_features.tsv.gz, Rnaseh1_D5_Dox_rep2_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D5_Dox_rep3_barcodes.tsv.gz, Rnaseh1_D5_Dox_rep3_features.tsv.gz, Rnaseh1_D5_Dox_rep3_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: Rnaseh1_D5_Dox_rep4_barcodes.tsv.gz, Rnaseh1_D5_Dox_rep4_features.tsv.gz, Rnaseh1_D5_Dox_rep4_matrix.mtx.gz is the cellranger output for the indicated sample.
Supplementary files format and content: ref_RH_final.rds is a seurat object contained processed results
Supplementary files format and content: sample_information.xlsx is the meta information of all sample in the seurat object.

molecule: polyA RNA

extract_protocol:
On the day of collection, gastruloids were dissociated with accutase at 37°C for 5–10 minutes (ensuring minimal over-digestion). Cells were pelleted, washed twice with PBS, and resuspended in 0.04% BSA/PBS for cell counting. Viability was assessed using trypan blue, and cell numbers were determined on a hemocytometer with appropriate dilutions. Cells were diluted to the recommended density for the 10x Genomics Chromium Next GEM Single Cell 3’ kit, targeting 10,000 cells per sample.
Library prep were following the protocol described in 10x Genomics Chromium Next GEM Single Cell 3’ kit

treatment_protocol: For Dox condition, cells were pre-treated with 500ng/ml doxycycline for 2 days for differentiation and Dox was kept for whole differentiation process.

value: mouse stem embryonic cell

tag: treatment

value: gastruloid differentiation+Dox


title: FF sample 13012

description:
Genomic DNA from FF sample 13012
203991410061_R07C01


title: FF sample 39663

description:
Genomic DNA from FF sample 39663
203991390144_R06C01


title: FF sample 56889

description:
Genomic DNA from FF sample 56889
203991410089_R06C01


title: FF sample 58359

description:
Genomic DNA from FF sample 58359
203991390137_R06C01


title: scRNA-Seq gastruloid differentiation day5 (120hrs), Dox, rep3

description: Library name: Day5_Dox_rep3


title: FF sample 32776

description:
Genomic DNA from FF sample 32776
203991410099_R06C01


title: FF sample 50738

description:
Genomic DNA from FF sample 50738
203991390136_R06C01


title: FF sample 32842

description:
Genomic DNA from FF sample 32842
203991410098_R06C01


title: scRNA-Seq gastruloid differentiation day5 (120hrs), control, rep4

description: Library name: Day5_control_rep4

value: gastruloid differentiation


title: scRNA-Seq gastruloid differentiation day5 (120hrs), Dox, rep2

description: Library name: Day5_Dox_rep2


title: scRNA-Seq gastruloid differentiation day5 (120hrs), control, rep5

description: Library name: Day5_control_rep5


title: scRNA-Seq gastruloid differentiation day5 (120hrs), control, rep3

description: Library name: Day5_control_rep3


title: FF sample 8885

description:
Genomic DNA from FF sample 8885
203991410008_R06C01


title: scRNA-Seq gastruloid differentiation day5 (120hrs), Dox, rep1

description: Library name: Day5_Dox_rep1


title: scRNA-Seq gastruloid differentiation day3 (72hrs), Dox, rep4

description: Library name: Day3_Dox_rep4


title: FF sample 10042

description:
Genomic DNA from FF sample 10042
203991410097_R06C01


title: FF sample 39436

description:
Genomic DNA from FF sample 39436
203991400154_R06C01


title: scRNA-Seq gastruloid differentiation day5 (120hrs), control, rep1

description: Library name: Day5_control_rep1


title: FF sample 24677_R

description:
Genomic DNA from FF sample 24677_R
203991390167_R06C01


title: FF sample 7582

description:
Genomic DNA from FF sample 7582
203991410061_R06C01


title: FF sample 36914

description:
Genomic DNA from FF sample 36914
203991410132_R06C01


title: scRNA-Seq gastruloid differentiation day3 (72hrs), Dox, rep2

description: Library name: Day3_Dox_rep2


title: scRNA-Seq gastruloid differentiation day3 (72hrs), Dox, rep1

description: Library name: Day3_Dox_rep1


title: FF sample 56832

description:
Genomic DNA from FF sample 56832
203991410097_R05C01


title: FF sample 29291

description:
Genomic DNA from FF sample 29291
203990170155_R06C01


title: scRNA-Seq gastruloid differentiation day3 (72hrs), control, rep3

description: Library name: Day3_control_rep3


title: FF sample 24672

description:
Genomic DNA from FF sample 24672
203991390137_R05C01


title: scRNA-Seq gastruloid differentiation day5 (120hrs), control, rep2

description: Library name: Day5_control_rep2


title: FF sample 20671

description:
Genomic DNA from FF sample 20671
203991390168_R06C01


title: scRNA-Seq gastruloid differentiation day3 (72hrs), control, rep1

description: Library name: Day3_control_rep1


title: scRNA-Seq gastruloid differentiation day3 (72hrs), control, rep2

description: Library name: Day3_control_rep2


title: scRNA-Seq gastruloid differentiation day3 (72hrs), control, rep4

description: Library name: Day3_control_rep4


title: scRNA-Seq gastruloid differentiation day3 (72hrs), Dox, rep3

description: Library name: Day3_Dox_rep3


title: scRNA-Seq gastruloid differentiation day0 (0hr), control, rep2

description: Library name: Day0_control_rep2


title: FF sample 40591

description:
Genomic DNA from FF sample 40591
203991410089_R05C01


title: gastruloid differentiation day5 (120hrs), Dox, rep3

description: Library name: Day5_Dox_rep3

library_source: transcriptomic

data_processing:
Fastq file were trimmed with Trimmomatic, then aligned by STAR v2.7.10a. Gene counts were generated by RSEM v1.3.3 and DESeq2 v1.38.2 were applied for differentially expressed gene analysis.
Assembly: GRCm38 with Gencode vM25 annotation
Supplementary files format and content: B_D0_N_rep1.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D0_N_rep2.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D0_N_rep3.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D0_D_rep1.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D0_D_rep2.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D0_D_rep3.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D3_N_rep1.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D3_N_rep2.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D3_N_rep3.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D3_D_rep1.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D3_D_rep2.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D3_D_rep3.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D5_N_rep1.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D5_N_rep2.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D5_N_rep3.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D5_D_rep1.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D5_D_rep2.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample
Supplementary files format and content: B_D5_D_rep3.RSEM.genes.results contains raw gene counts from RSEM for the indicated sample

extract_protocol:
Gastruloid samples were lysed in 350 µl RLT buffer (Qiagen) with 3.5 µl β-mercaptoethanol and stored at –80°C until processing. For RNA extraction, 350 µl of 70% ethanol was added to the lysate, mixed thoroughly, and applied to Direct-zol RNA Microprep kit (Zymo)
For each sample, 1 µg of RNA was used to prepare libraries with the Illumina stranded mRNA prep kit according to the manufacturer’s protocol (10 PCR cycles for library amplification).

treatment_protocol: Dox condition was treated with doxycycline 500 ng/ml for 48 hours and cells were applied for gastruloid differentiation

tag: batch


title: FF sample 19204

description:
Genomic DNA from FF sample 19204
203991390168_R05C01


title: gastruloid differentiation day5 (120hrs), Dox, rep2

description: Library name: Day5_Dox_rep2


title: FF sample 59702

description:
Genomic DNA from FF sample 59702
203991400154_R05C01


title: FF sample 51530

description:
Genomic DNA from FF sample 51530
203991390161_R05C01


title: FF sample 38736

description:
Genomic DNA from FF sample 38736
203991410099_R05C01


title: gastruloid differentiation day5 (120hrs), control, rep3

description: Library name: Day5_control_rep3


title: scRNA-Seq gastruloid differentiation day0 (0hr), control, rep1

description: Library name: Day0_control_rep1


title: FF sample 42792

description:
Genomic DNA from FF sample 42792
203991390144_R05C01


title: scRNA-Seq gastruloid differentiation day0 (0hr), Dox, rep2

description: Library name: Day0_Dox_rep2


title: gastruloid differentiation day5 (120hrs), Dox, rep1

description: Library name: Day5_Dox_rep1


title: scRNA-Seq gastruloid differentiation day0 (0hr), Dox, rep1

description: Library name: Day0_Dox_rep1


title: FF sample 10525

description:
Genomic DNA from FF sample 10525
203991410098_R05C01


title: FF sample 5047

description:
Genomic DNA from FF sample 5047
203990170155_R05C01


title: FF sample 25540

description:
Genomic DNA from FF sample 25540
203991390137_R04C01


title: FF sample 46702

description:
Genomic DNA from FF sample 46702
203991390136_R05C01


title: gastruloid differentiation day5 (120hrs), control, rep1

description: Library name: Day5_control_rep1


title: gastruloid differentiation day5 (120hrs), control, rep2

description: Library name: Day5_control_rep2


title: FF sample 59473_R

description:
Genomic DNA from FF sample 59473_R
203991390167_R05C01


title: FF sample 53988

description:
Genomic DNA from FF sample 53988
203991410061_R05C01


title: FF sample 53132

description:
Genomic DNA from FF sample 53132
203991410132_R05C01


title: gastruloid differentiation day3 (72hrs), Dox, rep2

description: Library name: Day3_Dox_rep2


title: gastruloid differentiation day3 (72hrs), Dox, rep3

description: Library name: Day3_Dox_rep3


title: FF sample 20402

description:
Genomic DNA from FF sample 20402
203991390136_R04C01

value: yes


title: FF sample 51581

description:
Genomic DNA from FF sample 51581
203991390161_R04C01


title: gastruloid differentiation day3 (72hrs), Dox, rep1

description: Library name: Day3_Dox_rep1


title: gastruloid differentiation day3 (72hrs), control, rep3

description: Library name: Day3_control_rep3


title: FF sample 31703

description:
Genomic DNA from FF sample 31703
203991410097_R04C01


title: FF sample 39664

description:
Genomic DNA from FF sample 39664
203991410098_R04C01


title: gastruloid differentiation day3 (72hrs), control, rep2

description: Library name: Day3_control_rep2


title: gastruloid differentiation day0 (0hr), Dox, rep3

description: Library name: Day0_Dox_rep3


title: FF sample 46149

description:
Genomic DNA from FF sample 46149
203991410008_R05C01


title: gastruloid differentiation day3 (72hrs), control, rep1

description: Library name: Day3_control_rep1


title: gastruloid differentiation day0 (0hr), Dox, rep2

description: Library name: Day0_Dox_rep2


title: gastruloid differentiation day0 (0hr), Dox, rep1

description: Library name: Day0_Dox_rep1


title: FF sample 53748

description:
Genomic DNA from FF sample 53748
203991390144_R04C01


title: FF sample 50741

description:
Genomic DNA from FF sample 50741
203991390168_R04C01


title: gastruloid differentiation day0 (0hr), control, rep3

description: Library name: Day0_control_rep3


title: FF sample 58149

description:
Genomic DNA from FF sample 58149
203991410008_R04C01


title: FF sample 59351

description:
Genomic DNA from FF sample 59351
203991410089_R04C01


title: gastruloid differentiation day0 (0hr), control, rep2

description: Library name: Day0_control_rep2


title: MNase-seq, Dox, 50U digestion, rep2

description: Library name: MNase_Dox_50U_rep2

data_processing:
Fastq files were trimmed with Trimmomatic v0.39 with TruSeq adatper sequence, then aligned by Bowtie2 v2.5.0 with GRCm38. SAM files were sorted and deduplicate by Picard v2.10.9. Reads were filtered by MAPQ > 10 and -f 99, -f 147, -f 83 or -f 163 for the unique mapped reads with Samtools v1.16.1. Reads ≤ 120 were filtered by awk as subnucleosome fragment and 150 ≤ Reads ≤ 200 were filtered by awk as mononucleosome fragments. Bam file of different titers were merge through MergeSamFiles from Picard v2.10.9. HOMER v4.11 and Deeptools v3.5.1 were applied on pooled bam file for aggregation plot, heatmap, bedgraph, bigwig and peak annotation.
Assembly: GRCm38 with Gencode vM25 annotation
Supplementary files format and content: MNase_control_mono_pool_rep1.bw is a BigWig file representing mononucleosome fragment coverage derived from the combined BAM file of all titers in control replicate 1.
Supplementary files format and content: MNase_control_sub_pool_rep1.bw is a BigWig file representing subnucleosome fragment coverage derived from the combined BAM file of all titers in control replicate 1.
Supplementary files format and content: MNase_control_mono_pool_rep2.bw is a BigWig file representing mononucleosome fragment coverage derived from the combined BAM file of all titers in control replicate 2.
Supplementary files format and content: MNase_control_sub_pool_rep2.bw is a BigWig file representing subnucleosome fragment coverage derived from the combined BAM file of all titers in control replicate 2.
Supplementary files format and content: MNase_Dox_mono_pool_rep1.bw is a BigWig file representing mononucleosome fragment coverage derived from the combined BAM file of all titers in Dox replicate 1.
Supplementary files format and content: MNase_Dox_sub_pool_rep1.bw is a BigWig file representing subnucleosome fragment coverage derived from the combined BAM file of all titers in Dox replicate 1.
Supplementary files format and content: MNase_Dox_mono_pool_rep2.bw is a BigWig file representing mononucleosome fragment coverage derived from the combined BAM file of all titers in Dox replicate 2.
Supplementary files format and content: MNase_Dox_sub_pool_rep2.bw is a BigWig file representing subnucleosome fragment coverage derived from the combined BAM file of all titers in Dox replicate 2.

extract_protocol:
5 × 10^6 cells in 4 ml medium were fixed with 100 µl 37% formaldehyde for 15 minutes at room temperature. The fixation was quenched by adding 1 ml 2.5 M glycine, and cells were pelleted by centrifugation at 600 g for 5 minutes at 4°C. Nuclei were isolated in NE buffer (20 mM HEPES, pH 7.9; 10 mM KCl; 0.5 mM spermidine; 0.1% Triton X-100; 20% glycerol with 1× protease inhibitors) and divided into five reactions (~ 1 million cells per reaction). Nuclei were resuspended in 150 µl wash buffer (20 mM HEPES-NaOH, pH 7.5; 150 mM NaCl; 0.5 mM spermidine; 1× Halt protease inhibitor), and 3 µl 100 mM CaCl₂ was added. MNase was added in varying amounts (1 µl, 2.5 µl, or 5 µl corresponding to 10 U, 25 U, and 100 U, respectively) and incubated at 37°C for 5 minutes on a thermomixer. The reaction was stopped with 150 µl 2× STOP buffer. The digested DNA were incubate with RNaseA for 3 hours at 4°C and proteinaseK +SDS overnight at 55°C. The DNA were recoveried by PCI extraction and ethanol precipitation.
1µg recovered DNA were subjected to library preparation as described in CUT&RUN protocol. In brief, DNA were end-repair, add-A with Taq+T4 DNA polymerase+T4 PNK cocktails with 12°C 15 min, 37°C 15 min and 72°C 20min. The end-repaired DNA were ligated with barcoded TruSeq adapters with Quick ligase for 15 min at 20°C. Ampure XP bead (38 µl) were used to remove unligated adapters and P5/P7 primer were used for library amplification with KAPA-HS HiFi polymerase. Gel extraction was applied to purify library with 150-650bp size range.


title: FF sample 36849

description:
Genomic DNA from FF sample 36849
203991410099_R04C01


title: MNase-seq, Dox, 100U digestion, rep1

description: Library name: MNase_Dox_100U_rep1


title: FF sample 46561

description:
Genomic DNA from FF sample 46561
203991400154_R04C01


title: gastruloid differentiation day0 (0hr), control, rep1

description: Library name: Day0_control_rep1


title: FF sample 58465

description:
Genomic DNA from FF sample 58465
203991390167_R04C01


title: FF sample 3846

description:
Genomic DNA from FF sample 3846
203991410097_R03C01


title: FF sample 52014

description:
Genomic DNA from FF sample 52014
203991410132_R04C01


title: FF sample 56767

description:
Genomic DNA from FF sample 56767
203991390161_R03C01


title: FF sample 54179

description:
Genomic DNA from FF sample 54179
203990170155_R04C01


title: MNase-seq, Dox, 100U digestion, rep2

description: Library name: MNase_Dox_100U_rep2


title: FF sample 54177

description:
Genomic DNA from FF sample 54177
203991410098_R03C01


title: MNase-seq, Dox, 50U digestion, rep1

description: Library name: MNase_Dox_50U_rep1


title: FF sample 58130

description:
Genomic DNA from FF sample 58130
203991410089_R03C01


title: MNase-seq, Dox, 20U digestion, rep1

description: Library name: MNase_Dox_20U_rep1


title: FF sample 53801

description:
Genomic DNA from FF sample 53801
203991410061_R04C01


title: FF sample 5049

description:
Genomic DNA from FF sample 5049
203991390137_R03C01


title: pA-MNase, rep4

description: Library name: pA_MNase_rep4

data_processing:
Fastq files were trimmed with Trimmomatic v0.39, then aligned by Bowtie2 v2.5.0 with GRCm38. SAM files were sorted and deduplicate by Picard v2.10.0. Reads were filtered by MAPQ > 10 and -f 99, -f 147, -f 83 or -f 163 for the unique mapped reads with Samtools v1.16.1. HOMER v4.11 and Deeptools v3.5.1 were applied on bam file for aggregation plot, heatmap, bedgraph, bigwig and peak annotation.
Peakcalling of MapR was perform through getDifferentialPeaksReplicates.pl from HOMER with pA-MNase as background signal and '-genome mm10 -style factor -tagThreshold 40 -region'.
Assembly: GRCm38 with Gencode vM25 annotation
Supplementary files format and content: control.bw is a BigWig file derived from the combined BAM file of all replicates in MapR.
Supplementary files format and content: control_RNaseA.bw is a BigWig file derived from the combined BAM file of all replicates in MapR+RNaseA.
Supplementary files format and content: control_pA.bw is a BigWig file derived from the combined BAM file of all replicates in pA-MNase
Library strategy: CUT&Run

extract_protocol:
Cells were bound on ConA beads and incubate with the primary antibody or proteins overnight in antibody buffer. For CUT&RUN, cells were incubated with pA-MNase and digested on ice-water in buffer containing CaCl2. Digestion was stopped by 2X STOP buffer and DNA were recovered by high speed spin, Proteinase K/SDS digestion and PCI extraction. For MapR, cell were directly applied for digestion and the rest step as described in CUT&RUN.
For CUT&RUN and MapR, NEBNext Ultra II DNA library prep was used for library construction with TruSeq adapter and 14 cycle for library amplification

value: pA-MNase


title: MNase-seq, Dox, 20U digestion, rep2

description: Library name: MNase_Dox_20U_rep2


title: FF sample 58461

description:
Genomic DNA from FF sample 58461
203991390136_R03C01


title: MNase-seq, control, 100U digestion, rep2

description: Library name: MNase_control_100U_rep2


title: MNase-seq, control, 100U digestion, rep1

description: Library name: MNase_control_100U_rep1


title: pA-MNase, rep3

description: Library name: pA_MNase_rep3


title: MNase-seq, control, 50U digestion, rep2

description: Library name: MNase_control_50U_rep2


title: MNase-seq, control, 50U digestion, rep1

description: Library name: MNase_control_50U_rep1


title: FF sample 40813

description:
Genomic DNA from FF sample 40813
203990170155_R03C01


title: Bone Marrow and Spleen, P2 mice, 2 samples, Tppp3 labeled, Tube 2, FB

city: BARCELONA

first: Elvira

last: Gonzalez-Saiz

state: BARCELONA

address: CARRER BALDIRI REIXAC 10

country: Spain

institute: IRB BARCELONA

description:
Library name: BM_Spl_labeled_P2_tube2_FB
10x Genomics

library_source: other

data_processing:
The gene counting and aggregation were made using the Cell Ranger software 7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
For more detailed information regarding the processing see code availability section of the present manuscript or contact daniel.fernandez@irbbarcelona.org, elvira.gonzalez@irbbarcelona.org.
Assembly: mm10
Supplementary files format and content: tab-separated values and matrices

molecule: protein

source_name: mixed sample (Bone Marrow and Spleen)

growth_protocol: E19 HSCs and P2 HSCs have been grown in the mouse embryo/pups until HSC isolation.

extract_protocol:
Fetal liver and spleen was collected, chopped and filtered through a 100 um strainer. Bone marrow was collected from the femur, tibia, pelvis, sternum and column through mechanical bone crushing. Cells were filtered through a 100um strainer and resuspended in PBS with 2% fetal bovine serum (FBS), followed by lysis of red blood cells using RBC lysis buffer (Biolegend, Catalog no. 420302). Cells were then enriched for c-Kit expression using CD117 MicroBeads (Miltenyi Biotec, Catalog no. 130-091-224). The resulting cKit-enriched fraction was washed and stained with fluorescently labeled antibodies: APC anti-mouse CD117, clone ACK2 (Biolegend, Catalog no. 105812), PE/Cy7 anti-mouse Ly6a (Sca-1) (Biolegend, Catalog no. 108114), Pacific Blue anti-mouse Lineage Cocktail (Biolegend, Catalog no. 133310) and PE anti-mouse CD201 (EPCR) (Biolegend, Catalog no. 141504). Cells were then washed and HSCs were purified through Flow Cytometry Cell Sorting using a CytoFLEX SRT (Beckman Coulter, Catalog no. C71883).
Unperturbed P2 and E19 HSC isolation and sequencing were performed in different days and loaded on different reactions per tissue. Labeled P2 pups were stained and isolated as following: Pup1 BM - Totalseq #1, Pup2 BM - Totalseq #2, Pup1 Spl - Totalseq #3, Pup2 Spl - Totalseq #4. Then TdTomato+ from one pup was pooled with the TdTomato- of the other and viceversa: Tube 1 - 145 tdtomato positive from Pup1 (both BM and spleen mixed) + 5500 tdtomato negative from Pup2 (both BM and spleen mixed) and Tube 2 - 5156 tdtomato negative from Pup1 (both BM and spleen mixed) + 180 tdtomato positive from Pup2 (both BM and spleen mixed). These tubes were loaded into 2 single-cell reactions. Single-cell libraries using Chromium Single Cell 3’ Reagent Kits (v3) following the manufacturer’s guidelines (10X Genomics).

treatment_protocol: 2 P2 Tppp3CreER LSLTdTomato pups (P2 replicates) were treated with tamoxifen at P0.

value: mixed sample (Bone Marrow and Spleen)

tag: sex donor_mice

value: Unknown

value: Tppp3CreER LSLTdTomato mice

tag: age

value: 2 days after birth (P2)

value: Tamoxifen at P0


title: MapR, RNaseA, rep4

description: Library name: MapR_RNaseA_rep4

value: cell line

value: mouse embryonic stem cell

value: HA-Rnaseh1 knock-in

value: RHD-MNase


title: MNase-seq, control, 20U digestion, rep2

description: Library name: MNase_control_20U_rep2


title: Bone Marrow and Spleen, P2 mice, 2 samples, Tppp3 labeled, Tube 2, GEX

description:
Library name: BM_Spl_labeled_P2_tube2_GEX
10x Genomics

molecule: total RNA


title: MNase-seq, control, 20U digestion, rep1

description: Library name: MNase_control_20U_rep1


title: FF sample 52013_R

description:
Genomic DNA from FF sample 52013_R
203991390144_R03C01

value: Normal

value: Prostate


title: FF sample 32594

description:
Genomic DNA from FF sample 32594
203991410099_R03C01

value: Cancer

value: no


title: Bone Marrow and Spleen, P2 mice, 2 samples, Tppp3 labeled, Tube 1, FB

description:
Library name: BM_Spl_labeled_P2_tube1_FB
10x Genomics


title: FF sample 3845

description:
Genomic DNA from FF sample 3845
203991390168_R03C01


title: pA-MNase, rep2

description: Library name: pA_MNase_rep2


title: Bone Marrow and Spleen, P2 mice, 2 samples, Tppp3 labeled, Tube 1, GEX

description:
Library name: BM_Spl_labeled_P2_tube1_GEX
10x Genomics


title: FF sample 37700

description:
Genomic DNA from FF sample 37700
203991410008_R03C01


title: FF sample 32845

description:
Genomic DNA from FF sample 32845
203991410132_R03C01


title: MapR, RNaseA, rep3

description: Library name: MapR_RNaseA_rep3


title: FF sample 56882

description:
Genomic DNA from FF sample 56882
203991410061_R03C01


title: FF sample 51579

description:
Genomic DNA from FF sample 51579
203991400154_R03C01

value: no data


title: FF sample 48692

description:
Genomic DNA from FF sample 48692
203991390167_R03C01


title: MapR, rep4

description: Library name: MapR_rep4


title: KPCH_Parental_3

city: Pamplona

first: Silvestre

last: Vicent

address: Avenida Pío XII 55

department: Oncology

institute: Center for Applied Medical Research (CIMA)

description: Library name: KPCH_3_S34

data_processing:
The quality of the samples was verified using FastQC v0.12.1 software.
FASTQ files were mapped to GRCm39 mouse assembly using STAR 2.7.11b with default parameters.
featureCounts v2.0.6 software and Gencode M38 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: Liver

growth_protocol: hKP117-RR, KPCh972-RR, KPCh993-RR, hKP and KPCh were maintained in in DMEM with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1,5ug of total RNA was used for the construction of sequencing libraries.
All sequencing libraries were constructed from 100 ng of total RNA according to the manufacturer's instruction. Briefly, the protocol selects and purifies poly(A) containing RNA molecules using magnetic beads coated with poly(T) oligos. Poly(A)-RNAs are fragmented and reverse transcribed into first cDNA strand using random primers. The second cDNA strand is synthesized in the presence of dUTP to ensure strand specificity. Resulting cDNA fragments are purified with AMPure XP beads (Beckman Coulter), adenylated at 3′ ends and then ligated with uniquely indexed sequencing adapters. Ligated fragments are purified and PCR amplified to obtain the final libraries. The quality and quantity of the libraries were verified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity D1000 ScreenTape (Agilent Technologies). Libraries were then sequenced using a NextSeq2000 sequencer (Illumina)

value: Liver

value: KPCh

value: Cholangiocytes

value: KRASG12D TP67


title: hKP_Parental_2

description: Library name: hKP_2_S42

value: hKP

value: KRASG12D TP63


title: MapR, RNaseA, rep2

description: Library name: MapR_RNaseA_rep2


title: KPCH_Parental_2

description: Library name: KPCH_2_S33

value: KRASG12D TP66


title: KPCH_Parental_1

description: Library name: KPCH_1_S32

value: KRASG12D TP65


title: MapR, rep3

description: Library name: MapR_rep3

value: cell line


title: FF sample 59138

description:
Genomic DNA from FF sample 59138
203991410097_R02C01

value: unknown


title: MapR, RNaseA, rep1

description: Library name: MapR_RNaseA_rep1

value: mouse embryonic stem cell

value: HA-Rnaseh1 knock-in


title: pA-MNase, rep1

description: Library name: pA_MNase_rep1

value: pA-MNase


title: hKP_Parental_3

description: Library name: hKP_3_S43

value: KRASG12D TP64


title: MapR, rep2

description: Library name: MapR_rep2

value: RHD-MNase


title: FF sample 32592

description:
Genomic DNA from FF sample 32592
203991390137_R02C01

value: Normal

value: Prostate


title: FF sample 56835

description:
Genomic DNA from FF sample 56835
203991390161_R02C01

value: Cancer


title: hKP_Parental_1

description: Library name: hKP_1_S41

value: Liver

value: KRASG12D TP62

value: no


title: KPCH_993_R3

description: Library name: 993_3_S40

value: Cholangiocytes

value: KRASG12D TP61


title: KPCH_972_R1

description: Library name: 972_1_S35

value: KRASG12D TP56


title: hKP_R3

description: Library name: 1171_3_S46

value: KRASG12D TP55


title: FF sample 46562

description:
Genomic DNA from FF sample 46562
203991390136_R02C01

value: no data


title: hKP_R2

description: Library name: 1171_2_S45

value: KRASG12D TP54


title: KPCH_972_R3

description: Library name: 972_3_S37

value: KRASG12D TP58


title: KPCH_972_R2

description: Library name: 972_2_S36

value: KRASG12D TP57


title: KPCH_993_R1

description: Library name: 993_1_S38

value: KRASG12D TP59


title: MapR, rep1

description: Library name: MapR_rep1

value: cell line

value: mouse embryonic stem cell

value: HA-Rnaseh1 knock-in


title: IgG CUT&RUN, Dox, rep2

description: Library name: IgG_Dox_rep2_CR

value: rabbit IgG (ab37415)


title: FF sample 10108

description:
Genomic DNA from FF sample 10108
203991410098_R02C01

value: Normal

value: Prostate


title: KPCH_993_R2

description: Library name: 993_2_New_S39

value: Liver

value: KRASG12D TP60


title: iAKP_T2

description: Library name: DT2_S52

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm39 mouse assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode M34 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

growth_protocol: Cells were maintained in in DMEM with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using NucleoSpin RNA, Mini kit (Macherey-nagel). 2ug of total RNA was used for the construction of sequencing libraries.
All sequencing libraries were constructed from 100 ng of total RNA according to the manufacturer's instruction. Briefly, the protocol selects and purifies poly(A) containing RNA molecules using magnetic beads coated with poly(T) oligos. Poly(A)-RNAs are fragmented and reverse transcribed into first cDNA strand using random primers. The second cDNA strand is synthesized in the presence of dUTP to ensure strand specificity. Resulting cDNA fragments are purified with AMPure XP beads (Beckman Coulter), adenylated at 3′ ends and then ligated with uniquely indexed sequencing adapters. Ligated fragments are purified and PCR amplified to obtain the final libraries. The quality and quantity of the libraries were verified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity D1000 ScreenTape (Agilent Technologies). Libraries were then sequenced using a NextSeq2000 sequencer (Illumina)

value: iAKP

value: Cholangiocytes

value: KRASG12D TP53


title: hKP_R1

description: Library name: 1171_1_S44


title: iAKP_T1

description: Library name: DT1_S51


title: FF sample 22694

description:
Genomic DNA from FF sample 22694
203991390168_R02C01

value: Cancer

value: no


title: IgG CUT&RUN, Dox, rep1

description: Library name: IgG_Dox_rep1_CR


title: iAKP_C3

description: Library name: D3_S50


title: IgG CUT&RUN, control, rep2

description: Library name: IgG_control_rep2_CR


title: IgG CUT&RUN, control, rep1

description: Library name: IgG_control_rep1_CR


title: iAKP_C2

description: Library name: D2_S49


title: FF sample 59395

description:
Genomic DNA from FF sample 59395
203991410089_R02C01


title: iAKP_T3

description: Library name: DT3_S53


title: FF sample 10050

description:
Genomic DNA from FF sample 10050
203991400154_R02C01

value: unknown


title: KPCH_C3

description: Library name: 7_S7

value: KPCh

value: Cholangiocytes EpCAM+


title: FF sample 37689

description:
Genomic DNA from FF sample 37689
203991410008_R02C01


title: FF sample 19335

description:
Genomic DNA from FF sample 19335
203990170155_R02C01

value: yes


title: FF sample 8680

description:
Genomic DNA from FF sample 8680
203991390167_R02C01


title: KPCH_T3

description: Library name: 8_S8


title: tppp3 v3.1 FB

description:
Library name: 1340_2024-FB
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
For more detailed information regarding the processing see code availability section of the present manuscript or contact daniel.fernandez@irbbarcelona.org, elvira.gonzalez@irbbarcelona.org.
Assembly: mm10
Supplementary files format and content: tab-separated values and matrices

source_name: Bone Marrow (BM)

growth_protocol: HSC naively growing during 3 months in the mice, then isolated

extract_protocol:
Bone marrow was collected from the femur, tibia, pelvis, sternum and column through mechanical bone crushing. Cells were filtered through a 100um strainer and resuspended in PBS with 2% fetal bovine serum (FBS), followed by lysis of red blood cells using RBC lysis buffer (Biolegend, Catalog no. 420302). Cells were then enriched for c-Kit expression using CD117 MicroBeads (Miltenyi Biotec, Catalog no. 130-091-224). The resulting cKit-enriched fraction was washed and stained with fluorescently labeled antibodies: APC anti-mouse CD117, clone ACK2 (Biolegend, Catalog no. 105812), PE/Cy7 anti-mouse Ly6a (Sca-1) (Biolegend, Catalog no. 108114), Pacific Blue anti-mouse Lineage Cocktail (Biolegend, Catalog no. 133310). Cells were then washed and HSCs were purified through Flow Cytometry Cell Sorting using a CytoFLEX SRT (Beckman Coulter, Catalog no. C71883).
HSCs were labelled  with a specific Biolegend TotalSeq B antibody (one per mouse per condition) to do Feature Barcoding in order to multiplex the Tppp3 labelled and non-labelled mice. TdTomato positive stained cells were sorted on the same tube and TdTomato negative stained cells were sorted on other tube. These two tubes (with sorted TdTomato positive or negative from the 2 different mice) were loaded in a run for performing single-cell libraries using Chromium Single Cell 3’ Reagent Kits (v3) or GEM-X following the manufacturer’s guidelines (10X Genomics).

treatment_protocol: tamoxifen treatment during the 3 first days of mice life.

value: Bone Marrow (BM)

value: Male

value: Tppp3CreER LSLTdTomato mice

value: Lin-Sca+Kit+

value: 3 months

value: Tamoxifen injection at P0 and P3 (first days postbirth)

value: 2 mice, 4 samples in one library with cell hashing


title: KPCH_C2

description: Library name: 4_S4

value: Liver


title: iAKP_C1

description: Library name: D1_S48

value: iAKP


title: FF sample 24677

description:
Genomic DNA from FF sample 24677
203991410099_R02C01

value: Prostate


title: FF sample 55081_R

description:
Genomic DNA from FF sample 55081_R
203991390144_R02C01

value: no data


title: TPPP3 GEM-X GEX

description:
Library name: 1573_2024
10x Genomics


title: CTCF CUT&RUN, Dox, rep1

description: Library name: CTCF_Dox_rep1

value: cell line

value: mouse embryonic stem cell

value: HA-Rnaseh1 knock-in

value: anti-CTCF (Millipore 07-729)


title: CTCF CUT&RUN, control, rep2

description: Library name: CTCF_control_rep2


title: KPCH_T1

description: Library name: 2_S2

value: KPCh

value: Cholangiocytes EpCAM+

value: KRASG12D TP53


title: tppp3 v3.1 GEX

description:
Library name: 1340_2024-GEX
10x Genomics

value: Bone Marrow (BM)

value: Male


title: CTCF CUT&RUN, Dox, rep2

description: Library name: CTCF_Dox_rep2


title: FF sample 13011

description:
Genomic DNA from FF sample 13011
203991410132_R02C01

value: Cancer

value: unknown


title: 0614_2025-GEX, Sample_Day2, Tam, Tam+Rapa  and Late-rapa treated isolated hematopoietic cells bio reps 2

description:
Library name: 0614_2025-GEX
10x Genomics

growth_protocol: Sequenced naive HSC isolated from 6 6-weeks-old mice.

extract_protocol:
Mice grew for 6 weeks and were processed  for HSC isolated single cell RNA sequencing (6 weeks post labeling). Processed them in two rounds (two days). Isolated bone marrow and stained with Lin, Sca, Kit, CD48, CD150 and EPCR (full HSC panel).
Each treatment condition, tam-treated tam+rapa-treated and late-rapa-treated were labelled  with a specific Biolegend TotalSeq B antibody (one per mouse) to do Feature Barcoding in order to multiplex the mice (independent of the labelling). These cells were loaded in a run for performing single-cell libraries using Chromium Single Cell 3’ Reagent Kits (v3).

treatment_protocol: Each mice were injected at P0 (birth day) and at P3 (3 days after birth) with either Tamoxifen (n=2) or Tamoxifen+Rapamycin (n=2).The control rapamycin were injected at P30 with rapamycin (not labeled) (n=2).

value: Female

value: Tppp3CreER LSLTdTomato mice

value: Lin-Sca+Kit+, Lin-Sca-Kit+, Whole bone marrow

value: 6 weeks old

value: Mouse 4:tamoxifen-treated at P0 and P3, mouse 5:tamoxifen+rapa-treated at P0 and P3, mouse 6:rapa-treated at P30

value: Mice treated differently are multiplexed with Totalseq


title: CTCF CUT&RUN, control, rep1

description: Library name: CTCF_control_rep1

value: cell line


title: KPCH_T2

description: Library name: 5_S5

value: Liver

value: KRASG12D  TP53


title: ATAC, Dox, rep2

description: Library name: ATAC_Dox_rep2

data_processing:
Fastq files were trimmed with Trimmomatic v0.39, then aligned by Bowtie2 v2.5.0 with GRCm38. Mitochondria reads were excluded by egrep throught chromosome name "chrM". SAM files were sorted and deduplicate by Picard v2.10.9. Reads were filtered by MAPQ > 10 and -f 99, -f 147, -f 83 or -f 163 for the unique mapped reads with Samtools v1.16.1. Reads ≤ 120 were filtered by awk. HOMER v4.11 and Deeptools v3.5.1 were applied on bam file for aggregation plot, heatmap, bedgraph, bigwig and peak annotation.
Assembly: GRCm38 with Gencode vM25 annotation
Supplementary files format and content: ATAC_peak.bed is a BED file containing consensus ATAC-seq peaks identified from overlapping peak regions across all replicates.

extract_protocol:
1 × 10^5 cells were lysed in 50 µl lysis buffer (10 mM Tris-HCl, pH 7.5; 10 mM NaCl; 3 mM MgCl₂; 0.1% NP-40; 0.1% Tween-20; 0.01% digitonin) on ice for 15 minutes. Subsequently, 1 ml wash buffer (10 mM Tris-HCl, pH 7.5; 10 mM NaCl; 3 mM MgCl₂; 0.1% Tween-20) was added and the samples were gently mixed before centrifugation at 500 g for 10 minutes at 4°C. The pellet was resuspended in 50 µl tagmentation buffer (1× TD buffer; 0.1% Tween-20; 0.01% digitonin; and 2.5 µl Tn5 in PBS) and incubated at 37°C for 30 minutes on a thermomixer at 1000 rpm. Tagmented DNA was purified using the Qiagen MinElute Reaction Cleanup kit and eluted in 10 µl EB.
Libraries were amplified with Nextera indexed P5/P7 primers and NEBNext High-Fidelity 2× PCR Master Mix (8–10 cycles), purified by gel extraction (selecting fragments of 150–500 bp), recovered using Qiagen QG buffer, quality controlled by Bioanalyzer, quantified by Qubit HS kit

value: mouse stem embryonic cell

value: HA-Rnaseh1 knock-in


title: 0604_2025-GEX_Sample_Day1, Tam, Tam+Rapa  and Late-rapa treated isolated hematopoietic cells bio reps 1

description:
Library name: 0604_2025-GEX
10x Genomics

value: Mouse 1:tamoxifen-treated at P0 and P3, mouse 2:tamoxifen+rapa-treated at P0 and P3, mouse 3:rapa-treated at P30


title: ATAC, Dox, rep4

description: Library name: ATAC_Dox_rep4


title: 2573_2024_larry, Transplanted tomato negative larry-barcoded HSCs, bio reps 1-4

description:
Library name: 2573_2024
10x Genomics

source_name: Hematopoietic Stem and Progenitor Cells (HSPCs)

growth_protocol: Isolated and labeled HSCs from 4 mice (4 months old) were infected with LarryGFP. They were cultured for 3 days on exvivo HSC PVA culture media and sorted for Larry-reporter+ for transplantation into 4 CD45.1 recipient mice. On recipient mice for 8 months.

extract_protocol:
In both isolations (donor and recipient): bone marrow was collected from the femur, tibia, pelvis, sternum and column through mechanical bone crushing. Cells were filtered through a 100vm strainer and resuspended in PBS with 2% fetal bovine serum (FBS), followed by lysis of red blood cells using RBC lysis buffer (Biolegend, Catalog no. 420302). Cells were then enriched for c-Kit expression using CD117 MicroBeads (Miltenyi Biotec, Catalog no. 130-091-224). The resulting cKit-enriched fraction was washed and stained with fluorescently labeled antibodies: APC anti-mouse CD117, clone ACK2 (Biolegend, Catalog no. 105812), PE/Cy7 anti-mouse Ly6a (Sca-1) (Biolegend, Catalog no. 108114), Pacific Blue anti-mouse Lineage Cocktail (Biolegend, Catalog no. 133310), PE anti-mouse CD201 (EPCR) (Biolegend, Catalog no. 141504), PE/Cy5 anti-mouse CD150 (Biolegend, Catalog no. 115912) and APC/Cy7 anti-mouse CD48 (Biolegend, Catalog no. 103432). Cells were then washed and HSCs were purified through Flow Cytometry Cell Sorting using a CytoFLEX SRT (Beckman Coulter, Catalog no. C71883).
From each recipient mice, donor Lin-, LSK and Mk TdTomato+ and TdTomato- were extracted and labelled  with a specific Biolegend TotalSeq B antibody (one per mouse) to do Feature Barcoding in order to multiplex the mice (independently of the labeling). TdTomato positive stained cells were sorted on the same tube and TdTomato negative stained cells were sorted on other tube. These two tubes (with sorted TdTomato positive or negative from the 4 different mice) were loaded each of them in a run for performing single-cell libraries using Chromium Single Cell 3’ Reagent Kits (v3) following the manufacturer’s guidelines (10X) Genomics). Remnants of amplified cDNA were used to perform two sequential PCRs in a nested-PCR design to enrich for the LARRY-barcode transcripts and ensure correct coverage of the full barcode sequence.

treatment_protocol: Tamoxifen treatment at P0 and P3 in the donor organism before HSC isolation.

value: Mix 2Males 2Females

value: Megakaryocytes, Lin- HSPCs, Lin-Sca+Kit+ HSPCs

tag: transplant time

value: 8 months transplant

value: tamoxifen at P0 and P3 donor HSCs

tag: reporter labeling

value: TdTomato negative

value: TdTomato negative cells from mouse 1 to mouse 4 multiplexed with Totalseq


title: ATAC, Dox, rep1

description: Library name: ATAC_Dox_rep1


title: TPPP3 GEM-X FB

description:
Library name: 1574_2024
10x Genomics

value: Bone Marrow (BM)

value: Male

value: Tppp3CreER LSLTdTomato mice

value: Lin-Sca+Kit+

value: 3 months

value: Tamoxifen injection at P0 and P3 (first days postbirth)

value: 2 mice, 4 samples in one library with cell hashing


title: ATAC, Dox, rep3

description: Library name: ATAC_Dox_rep3

value: cell line


title: 2404_2024-FB, Transplanted tomato positive larry-barcoded HSCs, bio reps 1-4

description:
Library name: 2404_2024-FB
10x Genomics

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: TdTomato positive

value: TdTomato positive cells from mouse 1 to mouse 4 multiplexed with Totalseq


title: 0614_2025-FB, Sample_Day2,  Tam, Tam+Rapa  and Late-rapa treated isolated hematopoietic cells bio reps 2

description:
Library name: 0614_2025-FB
10x Genomics

value: Female

value: Lin-Sca+Kit+, Lin-Sca-Kit+, Whole bone marrow

value: 6 weeks old

value: Mouse 4:tamoxifen-treated at P0 and P3, mouse 5:tamoxifen+rapa-treated at P0 and P3, mouse 6:rapa-treated at P30

value: Mice treated differently are multiplexed with Totalseq


title: FF sample 58151

description:
Genomic DNA from FF sample 58151
203991390161_R01C01

value: Normal

value: Prostate


title: 0604_2025-FB, Sample_Day1,  Tam, Tam+Rapa  and Late-rapa treated isolated hematopoietic cells bio reps 1

description:
Library name: 0604_2025-FB
10x Genomics

value: Bone Marrow (BM)

value: Mouse 1:tamoxifen-treated at P0 and P3, mouse 2:tamoxifen+rapa-treated at P0 and P3, mouse 3:rapa-treated at P30


title: 2404_2024-GEX, Transplanted tomato positive larry-barcoded HSCs, bio reps 1-4

description:
Library name: 2404_2024-GEX
10x Genomics

value: Mix 2Males 2Females

value: Tppp3CreER LSLTdTomato mice

value: Megakaryocytes, Lin- HSPCs, Lin-Sca+Kit+ HSPCs

value: 8 months transplant

value: tamoxifen at P0 and P3 donor HSCs


title: FF sample 10184

description:
Genomic DNA from FF sample 10184
203991410061_R02C01

value: Cancer

value: unknown


title: Bone Marrow, E19 mice

description:
Library name: BoneMarrowE19
10x Genomics

source_name: Fetal liver

value: Fetal liver

value: Unknown

value: WT

value: ~19 days after fertilization (E19)


title: KPCH_C1

description: Library name: 1_S1

value: Liver

value: KPCh

value: Cholangiocytes EpCAM+

value: KRASG12D TP53

value: no


title: FF sample 51531

description:
Genomic DNA from FF sample 51531
203991390136_R01C01

value: Prostate


title: FF sample 37655

description:
Genomic DNA from FF sample 37655
203991390137_R01C01


title: RNA-seq_S7WT_TTF_Rep3

city: Piscataway

first: Joshua

middle: K

last: Thackray

state: NEW JERSEY

address: 145 Bevier Road

department: Human Genetics Institute of New Jersey

institute: Rutgers University

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with HISAT2 (version 2.1.0, option --dta) and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
StringTie (version 1.3.3) was used to estimate transcript abundance using the Ensembl GRCm38 reference GTF file (obtained from the Illumina iGenomes).
Differential expression was analyzed with DESeq2 (version 1.32.0)
Assembly: mm10
Supplementary files format and content: csv files contain count matricies estimated by StringTie.
Supplementary files format and content: BigWig files contain Counts Per Million RNA-seq read signal

source_name: TTF cells

extract_protocol:
RNA was extracted with TRIZOL reagent (Thermo Fisher, #15596026) following the manufacturer instructions.
Purified RNA was sent to BGI, which perfomed polyA selection, library construction and sequencing.

tag: Sex

value: Female

value: TTF cells

tag: strain

value: C57BL6/CAST hybrid


title: 2572_2024_larry, Transplanted tomato positive larry-barcoded HSCs, bio reps 1-4

description:
Library name: 2572_2024
10x Genomics

tag: tissue

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: Mix 2Males 2Females

value: Tppp3CreER LSLTdTomato mice

value: Megakaryocytes, Lin- HSPCs, Lin-Sca+Kit+ HSPCs

value: 8 months transplant

value: TdTomato positive

value: TdTomato positive cells from mouse 1 to mouse 4 multiplexed with Totalseq


title: RNA-seq_S7KO_TTF_Rep3


title: ATAC, control, rep1

description: Library name: ATAC_control_rep1

value: cell line

tag: cell line

value: mouse stem embryonic cell

value: HA-Rnaseh1 knock-in


title: ATAC, control, rep4

description: Library name: ATAC_control_rep4

tag: cell type


title: MEF_Male_WT_rep2

description: Library name: MEF_Male_WT_rep2

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with HISAT2 (version 2.1.0, option --dta) and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
StringTie (version 1.3.3) was used to estimate transcript abundance using the Ensembl GRCm38 reference GTF file (obtained from the Illumina iGenomes).
Differential expression was analyzed with DESeq2 (version 1.32.0)
Assembly: mm10
Supplementary files format and content: txt files contain count matricies estimated by StringTie.
Supplementary files format and content: BigWig files contain Counts Per Million RNA-seq read signal

source_name: MEF

extract_protocol:
RNA was extracted with TRIZOL reagent (Thermo Fisher, #15596026) following the manufacturer instructions.
Purified RNA was sent to NovaGene, which perfomed polyA selection, library construction and sequencing.

value: Male

value: MEF

tag: genotype

value: WT


title: INPUT_S7WT

description:
normalized_read_counts_per_1MB_bin.tsv
raw_read_counts_per_1MB_bin.tsv

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with Bowtie2 (version 2.2.9) with options --n 2 --k 10 and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
Assembly: mm10
Supplementary files format and content: tsv files contain [normalized] read counts per 1Mb non-overlapping bins in the genome.

source_name: TTF

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with 0.2 M glycine for 5 min and washed once with cold PBS. 8-10 million cross-linked cells were resuspended in 1 mL of Lysis buffer 1 (5 mM HEPES, 85 mM KCL, 0.5 % NP-40) and incubated for 5 min on ice. Chromatin was sonicated to an average fragment size range of 300-500bp and subsequently centrifugated at 12,000 x g at 4°C for 15 min. Supernatants were diluted with Dilution Buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, and cOmplete protease inhibitors). ChIP-grade protein A/G magnetic beads (Pierce, 26162) were conjugated for at least 3 hours in 1X PBS and 0.05% NP-40 with anti-SIRT7 (Cell Signaling, #5360). Chromatin samples and antibody-conjugated magnetic beads were incubated overnight at 4°C on a rotator. Magnetic beads were then washed 3 times with ice-cold RIPA buffer (1% NP-40, 0.7% Na-deoxycholate, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 M LiCl2, and complete protease inhibitors) and once with Buffer TE (0.1 mM EDTA, 10 mM Tris-HCl pH 8.0). Magnetic beads and input samples (1% of total chromatin) were resuspended in freshly prepared RC buffer (0.1 M NaHCO3 and 1% SDS) in the presence of proteinase K for 5 hours at 60°C on a thermomixer with 900 rpm. DNA was purified using a Binding Buffer NTB and Nucleospin PCR Clean-up Kit from Macherey-Nagel.
library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.

tag: chip antibody

value: TTF


title: 2405_2024-FB, Transplanted tomato negative larry-barcoded HSCs, bio reps 1-4

description:
Library name: 2405_2024-FB
10x Genomics

value: tamoxifen at P0 and P3 donor HSCs

value: TdTomato negative

value: TdTomato negative cells from mouse 1 to mouse 4 multiplexed with Totalseq


title: RNA-seq_S7KO_TTF_Rep1

value: Female

value: TTF cells

value: C57BL6/CAST hybrid


title: FF sample 55907

description:
Genomic DNA from FF sample 55907
203991410097_R01C01

tag: disease state

value: Cancer

value: Prostate

value: unknown


title: ATAC, control, rep3

description: Library name: ATAC_control_rep3


title: INPUT_S7KO


title: MEF_Male_WT_rep1

description: Library name: MEF_Male_WT_rep1


title: FF sample 52013

description:
Genomic DNA from FF sample 52013
203991410008_R01C01

value: Normal

tag: gleason


title: 2405_2024-GEX, Transplanted tomato negative larry-barcoded HSCs, bio reps 1-4

description:
Library name: 2405_2024-GEX
10x Genomics

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: Mix 2Males 2Females

value: Tppp3CreER LSLTdTomato mice

value: Megakaryocytes, Lin- HSPCs, Lin-Sca+Kit+ HSPCs

value: 8 months transplant


title: ATAC, control, rep2

description: Library name: ATAC_control_rep2

value: cell line

value: mouse stem embryonic cell

value: HA-Rnaseh1 knock-in


title: FF sample 21275

description:
Genomic DNA from FF sample 21275
203991410098_R01C01

tag: psa

value: no data

value: no


title: MEF_Male_KO_rep3

description: Library name: MEF_Male_KO_rep3

value: Male

value: MEF


title: FF sample 29290

description:
Genomic DNA from FF sample 29290
203991390168_R01C01

tag: recurrence


title: ChIP_SIRT7_S7WT_Rep2

value: Female

value: TTF

value: C57BL6/CAST hybrid

value: WT


title: RNA-seq_S7WT_TTF_Rep2

value: TTF cells


title: RNA-seq_S7WT_TTF_Rep1


title: ChIP_SIRT7_S7KO


title: FF sample 54739

description:
Genomic DNA from FF sample 54739
203991410089_R01C01

value: Normal

value: Prostate


title: MEF_Male_WT_rep3

description: Library name: MEF_Male_WT_rep3


title: MEF_Male_KO_rep1

description: Library name: MEF_Male_KO_rep1


title: INPUT_H3K36Ac_S7KO_d0_Rep1

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with Bowtie2 (version 2.2.9) with options --n 2 --k 10 and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
BigWig ChIP signal files were generated from BAM data using deepTools (version 2.4.2) using a bin size of 50 bp, scaled with SES, and normalized by INPUT.
Peak calling was performed using MACS (version 2.2.7.1) by providing ChIP as --treatment and matched Input as --control. Peak calling was performed in --broad mode with --broad-cutoff 0.1 --qvalue 0.1 --scale-to small.
Assembly: mm10
Supplementary files format and content: BigWig signal files contain INPUT normalized ChIP-seq read counts using a bin size of 50bp and scaled with SES.
Supplementary files format and content: BroadPeak files contain broad peaks as called by MACS.

source_name: ES cells

extract_protocol:
cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with 0.2 M glycine for 5 min and washed once with cold PBS. Nuclei were resuspended in 300 μl Lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, and cOmplete protease inhibitors) and incubated on ice for 30 min. Chromatin was sonicated to an average fragment size range of 300-500bp and subsequently centrifugated at 12,000 x g at 4°C for 15 min. Supernatants were diluted with Dilution Buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, and cOmplete protease inhibitors). SNAP-ChIP Spike-ins controls for K-AcylStat and K-MetStat (EpiCypher, #19-1001, #19-3001) were added for quantitative normalization and antibody validation purposes by following the manufacturer's instructions.  ChIP-grade protein A/G magnetic beads (Pierce, 26162) were conjugated for at least 3 hours in 1X PBS and 0.05% NP-40 with anti-H3K36ac (EpiCypher, #13-0035, Cell Signaling, #27683). Chromatin samples and antibody-conjugated magnetic beads were incubated overnight at 4°C on a rotator. Magnetic beads were then washed 3 times with ice-cold RIPA buffer (1% NP-40, 0.7% Na-deoxycholate, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 M LiCl2, and complete protease inhibitors) and once with Buffer TE (0.1 mM EDTA, 10 mM Tris-HCl pH 8.0). Magnetic beads and input samples (1% of total chromatin) were resuspended in freshly prepared RC buffer (0.1 M NaHCO3 and 1% SDS) in the presence of proteinase K for 5 hours at 60°C on a thermomixer with 900 rpm. DNA was purified using a Binding Buffer NTB and Nucleospin PCR Clean-up Kit from Macherey-Nagel.
library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.

treatment_protocol: mouse ES cells were treated with LIF through day 0, after which LIF was withdrawn.

value: ES cells

tag: treatment

value: LIF

tag: timepoint

value: day 0


title: RNA-seq_S7KO_TTF_Rep2


title: FF sample 47603

description:
Genomic DNA from FF sample 47603
203991390167_R01C01

value: Cancer

value: unknown


title: ChIP_H3K36Ac_S7WT_d7_Rep1

value: day 7


title: INPUT_H3K36Ac_S7WT_d7_Rep1


title: FF sample 59473

description:
Genomic DNA from FF sample 59473
203991410099_R01C01

value: no data


title: ChIP_H3K36Ac_S7WT_d0_Rep1


title: FF sample 52014_R

description:
Genomic DNA from FF sample 52014_R
203991390144_R01C01

value: no


title: MEF_Female_WT_rep2

description: Library name: MEF_Female_WT_rep2


title: FF sample 7585

description:
Genomic DNA from FF sample 7585
203991410132_R01C01


title: MEF_Female_KO_rep3

description: Library name: MEF_Female_KO_rep3


title: ChIP_H3K36Ac_S7KO_d7_Rep1


title: ChIP_H3K36Ac_S7KO_d0_Rep1


title: KKU213A_T3

description: Library name: KT3_S47

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode v45 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: Human Intrahepatic bile duct epithelium

growth_protocol: Cells were maintained in DMEM low glucose (1 g/L glucose) with 10% FBS, 1% Hepes (1M), 1% penicillin/streptomycin and 0,1% amphotericin B.

value: Human Intrahepatic bile duct epithelium

value: Bile duct epithelial cells -Cholangiocytes

tag: batch


title: KKU213A_T2

description: Library name: KT2_S46


title: FF sample 53803

description:
Genomic DNA from FF sample 53803
203991410061_R01C01


title: KKU213A_T1

description: Library name: KT1_S45


title: INPUT_H3K36Ac_S7KO_d7_Rep1

value: Female


title: KKU213A_C3

description: Library name: K3_S44


title: MEF_Female_WT_rep3

description: Library name: MEF_Female_WT_rep3

value: MEF


title: KKU213A_C1

description: Library name: K1_S42


title: MEF_Female_KO_rep2

description: Library name: MEF_Female_KO_rep2


title: FFPE sample 14162 A2

description:
Genomic DNA from FFPE sample 14162 A2
207166150136_R04C01

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

source_name: Bone

extract_protocol: DNA extracted from FFPE samples using Zymo Quick-DNA FFPE kit according to standard instructions

value: Tumor

value: Bone

tag: diagnosis

value: Metastasis

tag: age

tag: smoking

value: Y

tag: drinking


title: MEF_Female_WT_rep1

description: Library name: MEF_Female_WT_rep1

tag: Sex

tag: strain

value: WT


title: HUCCT1_T3

description: Library name: HT3_S41

source_name: Human liver (bile duct)

tag: tissue

value: Human liver (bile duct)

tag: cell line

value: Epithelial-like, moderate adenocarcinoma cells

value: TP53 KRASG12D


title: MEF_Female_KO_rep1

description: Library name: MEF_Female_KO_rep1

tag: cell type

tag: genotype


title: INPUT_WT_rep2

description: Library name: INPUT_WT_rep2

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with Bowtie2 (version 2.2.9) with options --n 2 --k 10 and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
BigWig ChIP signal files were generated from BAM data using deepTools (version 2.4.2) using a bin size of 50 bp, scaled with SES, and normalized by INPUT.
Peak calling was performed using MACS (version 2.2.7.1) by providing ChIP as --treatment and matched Input as --control. Peak calling was performed in --broad mode with --broad-cutoff 0.1 --qvalue 0.1 --scale-to small.
Assembly: mm10
Supplementary files format and content: BigWig signal files contain INPUT normalized ChIP-seq read counts using a bin size of 50bp and scaled with SES.

extract_protocol:
cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with 0.2 M glycine for 5 min and washed once with cold PBS. Nuclei were resuspended in 300 μl Lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, and cOmplete protease inhibitors) and incubated on ice for 30 min. Chromatin was sonicated to an average fragment size range of 300-500bp and subsequently centrifugated at 12,000 x g at 4°C for 15 min. Supernatants were diluted with Dilution Buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, and cOmplete protease inhibitors). ChIP-grade protein A/G magnetic beads (Pierce, 26162) were conjugated for at least 3 hours in 1X PBS and 0.05% NP-40 with anti-SIRT7 (Cell Signaling, #5360). Chromatin samples and antibody-conjugated magnetic beads were incubated overnight at 4°C on a rotator. Magnetic beads were then washed 3 times with ice-cold RIPA buffer (1% NP-40, 0.7% Na-deoxycholate, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 M LiCl2, and complete protease inhibitors) and once with Buffer TE (0.1 mM EDTA, 10 mM Tris-HCl pH 8.0). Magnetic beads and input samples (1% of total chromatin) were resuspended in freshly prepared RC buffer (0.1 M NaHCO3 and 1% SDS) in the presence of proteinase K for 5 hours at 60°C on a thermomixer with 900 rpm. DNA was purified using a Binding Buffer NTB and Nucleospin PCR Clean-up Kit from Macherey-Nagel.
library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.

tag: chip antibody

value: TTF

value: C57BL6/CAST hybrid


title: FF sample 59394

description:
Genomic DNA from FF sample 59394
203990170155_R01C01

extract_protocol: DNA extracted from fresh frozen samples using Qiagen DNA Mini kit according to standard instructions

tag: disease state

value: Cancer

value: Prostate

tag: gleason

value: unknown


title: KKU213A_C2

description: Library name: K2_S43

value: Human Intrahepatic bile duct epithelium

value: no


title: INPUT_H3K36Ac_S7WT_d0_Rep1

value: Female

value: ES cells

value: LIF

value: day 0


title: FF sample 54329

description:
Genomic DNA from FF sample 54329
203991400154_R01C01

value: Normal

tag: psa

tag: recurrence


title: ChIP_SIRT7_S7WT_Rep1


title: HUCCT1_C3

description: Library name: H3_S38

tag: treatment


title: HUCCT1_T1

description: Library name: HT1_S39

tag: batch


title: FFPE sample 14160 A1

description:
Genomic DNA from FFPE sample 14160 A1
207166150136_R02C01

value: Tumor

value: Bone

tag: diagnosis

value: Metastasis

value: N


title: MEF_Male_KO_rep2

description: Library name: MEF_Male_KO_rep2

value: Male

value: MEF


title: FFPE sample 14161 C1

description:
Genomic DNA from FFPE sample 14161 C1
207166150136_R03C01

tag: age

value: Y


title: FFPE sample 14159 A2

description:
Genomic DNA from FFPE sample 14159 A2
207166150136_R01C01

source_name: Bladder

value: Bladder

tag: smoking


title: HUCCT1_C1

description: Library name: H1_S36

value: Human liver (bile duct)

value: Epithelial-like, moderate adenocarcinoma cells

value: TP53 KRASG12D


title: INPUT_KO_rep2

description: Library name: INPUT_KO_rep2

value: TTF

value: C57BL6/CAST hybrid


title: INPUT_WT_rep1

description: Library name: INPUT_WT_rep1

value: Female

value: WT


title: SC Islets HNF1A-MODY 3

city: Bergen

first: Lucas

last: Unger

address: Haukelansbakken 15

country: Norway

institute: University of bergen

description: Library name: Sample 6

data_processing:
CLC Genomic Workbench version 24.0
Assembly: hg38 (Refseq)
Supplementary files format and content: Geneexpression Track for each sample als xlsx file

source_name: Stem cell islets

extract_protocol:
RNA was extracted using QIAGEN RNeasy mini
Performed by QIAGEN

value: Stem cell islets

value: induced pluripotent stem cells

value: Differentiation to stem cell islets


title: HUCCT1_T2

description: Library name: HT2_S40


title: INPUT_KO_rep1

description: Library name: INPUT_KO_rep1


title: SC Islets HNF1A-MODY 1

description: Library name: Sample 4


title: SC Islets HNF1A-MODY 2

description: Library name: Sample 5


title: SC Islets Non carrier  1

description: Library name: Sample 1

value: non carrier


title: SC Islets Non carrier  3

description: Library name: Sample 3


title: FFPE sample 14157 A1

description:
Genomic DNA from FFPE sample 14157 A1
206702520041_R07C01

data_processing:
Illumina GenomeStudio Methylation Module V2011.1
[processed value definition] Average Beta

value: Tumor

value: Bone

value: Metastasis

tag: drinking


title: FFPE sample 14158 B

description:
Genomic DNA from FFPE sample 14158 B
206702520041_R08C01

value: Liver


title: FFPE sample 14156 A3

description:
Genomic DNA from FFPE sample 14156 A3
206702520041_R06C01

source_name: Lungs

value: Lungs

value: Y


title: ChIP_SIRT7_WT_rep2

description: Library name: ChIP_SIRT7_WT_rep2

tag: Sex


title: HUCCT1_C2

description: Library name: H2_S37

value: Human liver (bile duct)

value: no


title: SC Islets Non carrier  2

description: Library name: Sample 2


title: ChIP_SIRT7_WT_rep1

description: Library name: ChIP_SIRT7_WT_rep1

tag: strain


title: Astbur2_p5, bulkRNA

city: Basel

first: Antoine

last: Fages

address: Vesalgasse 1

country: Switzerland

institute: University of Basel

data_processing:
Trimmomatic, STAR, HTSeq
Assembly: Oreochromis niloticus GCA_001858045.3, RefSeq assembly GCF_001858045.2
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

organism: Haplochromis burtoni

source_name: intestine

extract_protocol:
Each intestine was divided into five equally long parts along the anterior-posterior axis, and each section was processed independently. The sections were first mechanically chopped with a razor blade, then homogenized on a FastPrep 24 instrument (MP BioMedicals), and total RNA was extracted using a Zymo Direct-Zol RNA Miniprep kit (Zymo Research), following the manufacturer’s protocol.
Illumina Truseq library preparation protocol

tag: tissue

value: intestine


title: Astbur, scRNAseq

data_processing:
Cell Ranger v5.0 software (10X Genomics)
Assembly: Oreochromis niloticus GCA_001858045.3, RefSeq assembly GCF_001858045.2
Supplementary files format and content: Tab-separated values and matrix files

extract_protocol:
Intestinal samples were flushed, chopped and dissociated at 25ºC for 20 minutes in pre-warmed DMEM/F-12 medium 1X (Fisher Scientific) supplemented with 1 mg / mL of dispase II (Sigma). Suspensions were centrifuged at 500 rcf for 7 minutes at 4ºC, resuspended in 10% Fetal Bovine Serum (FBS) in DMEM/F-12, filtered with a 20 µm cell strainer (CellTrics), centrifuged again with the same conditions, resuspended in 10% FBS in DMEM/F-12, and centrifuged one last time at low speed (200-250 rcf) for 5 minutes at 4ºC.
Following instructions from 10X Genomics Chromium Next GEM  Gene Expression 3' v3.1


title: FFPE sample 14154 A

description:
Genomic DNA from FFPE sample 14154 A
206702520041_R05C01

value: N


title: FFPE sample 14153 A1

description:
Genomic DNA from FFPE sample 14153 A1
206702520041_R04C01


title: Astbur2_p3, bulkRNA


title: ChIP_SIRT7_KO_rep2

description: Library name: ChIP_SIRT7_KO_rep2

value: TTF

value: C57BL6/CAST hybrid


title: Astbur2_p1, bulkRNA


title: ChIP_SIRT7_KO_rep1

description: Library name: ChIP_SIRT7_KO_rep1

value: Female


title: Astbur2_p2, bulkRNA


title: FFPE sample 14152 A1

description:
Genomic DNA from FFPE sample 14152 A1
206702520027_R06C01


title: INPUT_WT_Male

description: Library name: INPUT_WT_Male

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with Bowtie2 (version 2.2.9) with options --n 2 --k 10 and converted to BAM format with SAMtools (version 0.1.19).
BigWig ChIP signal files were generated from BAM data using deepTools (version 2.4.2) using a bin size of 50 bp, scaled with SES, and normalized by INPUT.
Peak calling was performed using MACS (version 2.2.7.1) by providing ChIP as --treatment and matched Input as --control. Peak calling was performed in --broad mode with --broad-cutoff 0.1 --qvalue 0.1 --scale-to small.
Assembly: mm10
Supplementary files format and content: BigWig signal files contain INPUT normalized ChIP-seq read counts using a bin size of 50bp and scaled with SES.

value: Male

value: MEF

value: WT


title: Astbur1_p5, bulkRNA


title: FFPE sample 14149 A1

description:
Genomic DNA from FFPE sample 14149 A1
206702520041_R02C01


title: FFPE sample 14087 B10

description:
Genomic DNA from FFPE sample 14087 B10
206702520041_R01C01

source_name: Prostate

value: Tumor&Normal

value: Prostate

value: Adenocarcinoma

value: Gleason's pattern 7 (3+4), grade group 2


title: Astbur1_p3, bulkRNA


title: INPUT_WT_Female

description: Library name: INPUT_WT_Female


title: FFPE sample 14065 A25

description:
Genomic DNA from FFPE sample 14065 A25
206702520044_R08C01

value: Former


title: Astbur1_p2, bulkRNA


title: Orenil, scRNAseq

organism: Oreochromis niloticus


title: VEEV TC-83-infected primary mouse neurons, 24hpi, biol rep3

city: Albuquerque

first: Steven

last: Bradfute

state: NM

address: 1 University of New Mexico

institute: University of New Mexico Health Sciences Center

description:
Library name: Sample39
column name in VEEV_infected_vs_control_All_counts.tsv: MNT33TC83T24h

data_processing:
After checking the reads quality using FASTQC, the Fasta reference genome was indexed using Samtools. STAR aligner used to generate genome indecies for alignment and to map the reads to the reference genome. The read counts were generated using HTSEQ. DESeq2 was used to perform differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: Tab seperated value (tsv) file contains the raw counts for all the samples

source_name: Primary mouse cortical neurons

growth_protocol: Mouse C57 brain mixed primary astrocytes were grown in ABM Basal Medium supplemented with AGM SingleQuots and maintained at 37 °C and 5% CO2 for 24 hours. Primary mouse cortical neurons were grown in Neurobasal Medium supplemented with 0.5 mM GlutaMAX-I and 2% (v/v) B-27 and maintained at 37°C and 5% CO2 for 4 days.

extract_protocol:
Total RNA extracted from infected cells at 16 and 24hpi and from uninfected cells using Direct-Zol RNA Microprep Kit following the manufacturer's protocol.
Ribosomal RNA was depleted using the RiboGone Kit according to the manufacturer's instructions. The RNA was prepared for sequencing using the SMARTer Universal Low  Input RNA Kit for Sequencing following the manufacturer's instructions. Samples were  then prepared using the Ion Plus Fragment Library Kit (Ion Torrent) at the UNM ATG core facility, starting at the Ligation and Nick Repair step, with the only modification being the use of 80% ethanol instead of 70% ethanol for bead washes.

treatment_protocol: At 24h post-seeding primary mouse astrocytes were incubated with either VEEV TrD or VEEV TC-83 (MOI 5) for 1h. The medium changed to fresh medium and cells were maintained at 37C and 5% CO2 for 16h and 24h. The infection was done for primary mouse neurons at 4days after seeding following a similar protocol that used for astrocytes.

value: Primary mouse cortical neurons

value: VEEV TC-83 infected - 24hpi


title: FFPE sample 13961 A3

description:
Genomic DNA from FFPE sample 13961 A3
206702520044_R07C01

value: Y


title: INPUT_KO_Female

description: Library name: INPUT_KO_Female


title: INPUT_KO_Male

description: Library name: INPUT_KO_Male


title: VEEV TC-83-infected primary mouse neurons, 24hpi, biol rep2-2

description:
Library name: Sample38
column name in VEEV_infected_vs_control_All_counts.tsv: MN2T24r2


title: FFPE sample 13957 A3

description:
Genomic DNA from FFPE sample 13957 A3
206702520044_R06C01


title: VEEV TC-83-infected primary mouse neurons, 24hpi, biol rep1-1

description:
Library name: Sample35
column name in VEEV_infected_vs_control_All_counts.tsv: MN1T24r1

value: VEEV TC-83 infected -16hpi


title: VEEV TC-83-infected primary mouse neurons, 24hpi, biol rep1-2

description:
Library name: Sample36
column name in VEEV_infected_vs_control_All_counts.tsv: MN1T24r2


title: ChIP_SIRT7_WT_rep2_Male

description: Library name: ChIP_SIRT7_WT_rep2_Male


title: Astbur2_p4, bulkRNA

value: intestine


title: ChIP_SIRT7_WT_rep2_Female

description: Library name: ChIP_SIRT7_WT_rep2_Female


title: VEEV TC-83-infected primary mouse neurons, 24hpi, biol rep2-1

description:
Library name: Sample37
column name in VEEV_infected_vs_control_All_counts.tsv: MN2T24r1


title: FFPE sample 13953 E19

description:
Genomic DNA from FFPE sample 13953 E19
206702520044_R05C01

value: Gleason's pattern 8 (4+4), grade group 2

value: N


title: Astbur1_p4, bulkRNA


title: VEEV TC-83-infected primary mouse neurons, 16hpi, biol rep3

description:
Library name: Sample34
column name in VEEV_infected_vs_control_All_counts.tsv: MNT32TC83T16h


title: VEEV TC-83-infected primary mouse neurons, 16hpi, biol rep2-1

description:
Library name: Sample32
column name in VEEV_infected_vs_control_All_counts.tsv: MN2T16r1


title: Astbur1_p1, bulkRNA


title: FFPE sample 8943 C5

description:
Genomic DNA from FFPE sample 8943 C5
206702520044_R04C01


title: ChIP_SIRT7_WT_rep1_Male

description: Library name: ChIP_SIRT7_WT_rep1_Male


title: FFPE sample 14097 A13

description:
Genomic DNA from FFPE sample 14097 A13
206702520044_R03C01


title: ChIP_SIRT7_KO_rep2_Male

description: Library name: ChIP_SIRT7_KO_rep2_Male


title: Uninfected primary mouse neurons, control-in-TC83-infection, biol rep3-1

description:
Library name: Sample29
column name in VEEV_infected_vs_control_All_counts.tsv: MNT31TC83T0

value: Untreated


title: VEEV TC-83-infected primary mouse neurons, 16hpi, biol rep1-2

description:
Library name: Sample31
column name in VEEV_infected_vs_control_All_counts.tsv: MN1T16r2


title: Uninfected primary mouse neurons, control-in-TC83-infection, biol rep2-2

description:
Library name: Sample28
column name in VEEV_infected_vs_control_All_counts.tsv: MN2T0r2


title: FFPE sample 14096 A15

description:
Genomic DNA from FFPE sample 14096 A15
206702520044_R02C01


title: VEEV TC-83-infected primary mouse neurons, 16hpi, biol rep2-2

description:
Library name: Sample33
column name in VEEV_infected_vs_control_All_counts.tsv: MN2T16r2


title: ChIP_SIRT7_KO_rep2_Female

description: Library name: ChIP_SIRT7_KO_rep2_Female

value: Female


title: ChIP_SIRT7_WT_rep1_Female

description: Library name: ChIP_SIRT7_WT_rep1_Female


title: Uninfected primary mouse neurons, control-in-TC83-infection, biol rep1-2

description:
Library name: Sample26
column name in VEEV_infected_vs_control_All_counts.tsv: MN1T0r2


title: ChIP_SIRT7_KO_rep1_Female

description: Library name: ChIP_SIRT7_KO_rep1_Female


title: VEEV TrD-infected primary mouse neurons, 24hpi, biol rep2

description:
Library name: Sample24
column name in VEEV_infected_vs_control_All_counts.tsv: MNr43

value: VEEV TrD infected - 24hpi


title: FFPE sample 14077 A11

description:
Genomic DNA from FFPE sample 14077 A11
206702520105_R06C01


title: VEEV TC-83-infected primary mouse neurons, 16hpi, biol rep1-1

description:
Library name: Sample30
column name in VEEV_infected_vs_control_All_counts.tsv: MN1T16r1


title: FFPE sample 14078 A17

description:
Genomic DNA from FFPE sample 14078 A17
206702520105_R07C01

value: Normal


title: VEEV TrD-infected primary mouse neurons, 16hpi, biol rep1

description:
Library name: Sample21
column name in VEEV_infected_vs_control_All_counts.tsv: MNr22

value: VEEV TrD infected - 16hpi


title: Uninfected primary mouse neurons, control-in-TC83-infection, biol rep1-1

description:
Library name: Sample25
column name in VEEV_infected_vs_control_All_counts.tsv: MN1T0r1


title: Uninfected primary mouse neurons, control-in-TC83-infection, biol rep2-1

description:
Library name: Sample27
column name in VEEV_infected_vs_control_All_counts.tsv: MN2T0r1


title: INPUT_WT_XRAY_rep1

description: Library name: INPUT_WT_XRAY_rep1

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with Bowtie2 (version 2.2.9) with options --n 2 --k 10 and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
BigWig ChIP signal files were generated from BAM data using deepTools (version 2.4.2) using a bin size of 50 bp, scaled with SES, and normalized by INPUT.
Peak calling was performed using MACS (version 2.2.7.1) by providing ChIP as --treatment and matched Input as --control. Peak calling was performed in --broad mode with --broad-cutoff 0.1 --qvalue 0.1 --scale-to small.
Assembly: mm10
Supplementary files format and content: broadPeak files contain peaks as called by macs

extract_protocol:
cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with 0.2 M glycine for 5 min and washed once with cold PBS. Nuclei were resuspended in 300 μl Lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, and cOmplete protease inhibitors) and incubated on ice for 30 min. Chromatin was sonicated to an average fragment size range of 300-500bp and subsequently centrifugated at 12,000 x g at 4°C for 15 min. Supernatants were diluted with Dilution Buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, and cOmplete protease inhibitors). ChIP-grade protein A/G magnetic beads (Pierce, 26162) were conjugated for at least 3 hours in 1X PBS and 0.05% NP-40 with anti-H2A.X antibody (ab20669, Abcam), or anti-ɣH2AX (Sigma, 05-636-I). Chromatin samples and antibody-conjugated magnetic beads were incubated overnight at 4°C on a rotator. Magnetic beads were then washed 3 times with ice-cold RIPA buffer (1% NP-40, 0.7% Na-deoxycholate, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 M LiCl2, and complete protease inhibitors) and once with Buffer TE (0.1 mM EDTA, 10 mM Tris-HCl pH 8.0). Magnetic beads and input samples (1% of total chromatin) were resuspended in freshly prepared RC buffer (0.1 M NaHCO3 and 1% SDS) in the presence of proteinase K for 5 hours at 60°C on a thermomixer with 900 rpm. DNA was purified using a Binding Buffer NTB and Nucleospin PCR Clean-up Kit from Macherey-Nagel.
library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.

treatment_protocol: Cells were treated with 5Gy of Xrays and allowed to recover for 30 minutes

value: TTF

value: C57BL6/CAST hybrid

value: 5Gy XRAY

value: WT


title: FFPE sample 14076 A11

description:
Genomic DNA from FFPE sample 14076 A11
206702520105_R05C01

value: Prostate

value: Adenocarcinoma


title: VEEV TC-83-infected primary mouse astrocytes, 24hpi, biol rep3

description:
Library name: Sample18
column name in VEEV_infected_vs_control_All_counts.tsv: MAT43

source_name: Brain mixed primary mouse astrocytes

value: Brain mixed primary mouse astrocytes

value: VEEV TC-83 infected - 24hpi


title: VEEV TrD-infected primary mouse neurons, 16hpi, biol rep2

description:
Library name: Sample22
column name in VEEV_infected_vs_control_All_counts.tsv: MNr42

value: Primary mouse cortical neurons


title: Uninfected primary mouse neurons, control-in-TrD-infection, biol rep1

description:
Library name: Sample19
column name in VEEV_infected_vs_control_All_counts.tsv: MNr21


title: Uninfected primary mouse neurons, control-in-TrD-infection, biol rep2

description:
Library name: Sample20
column name in VEEV_infected_vs_control_All_counts.tsv: MNr41


title: VEEV TrD-infected primary mouse neurons, 24hpi, biol rep1

description:
Library name: Sample23
column name in VEEV_infected_vs_control_All_counts.tsv: MNr23


title: VEEV TC-83-infected primary mouse astrocytes, 24hpi, biol rep2

description:
Library name: Sample17
column name in VEEV_infected_vs_control_All_counts.tsv: MAT33


title: FFPE sample 14075 A5

description:
Genomic DNA from FFPE sample 14075 A5
206702520105_R04C01

value: Tumor&Normal

value: Gleason's pattern 7 (3+4), grade group 2

value: Y


title: VEEV TC-83-infected primary mouse astrocytes, 24hpi, biol rep1

description:
Library name: Sample16
column name in VEEV_infected_vs_control_All_counts.tsv: MAT13


title: VEEV TC-83-infected primary mouse astrocytes, 16hpi, biol rep3

description:
Library name: Sample15
column name in VEEV_infected_vs_control_All_counts.tsv: MAT42

value: VEEV TC-83 infected - 16hpi


title: FFPE sample 14080 A13

description:
Genomic DNA from FFPE sample 14080 A13
206702520044_R01C01


title: INPUT_WT_XRAY_rep2

description: Library name: INPUT_WT_XRAY_rep2

value: Female


title: VEEV TC-83-infected primary mouse astrocytes, 16hpi, biol rep2

description:
Library name: Sample14
column name in VEEV_infected_vs_control_All_counts.tsv: MAT32


title: FFPE sample 14074 A24

description:
Genomic DNA from FFPE sample 14074 A24
206702520105_R03C01


title: ChIP_SIRT7_KO_rep1_Male

description: Library name: ChIP_SIRT7_KO_rep1_Male

value: Male

value: MEF


title: FFPE sample 14079 A8

description:
Genomic DNA from FFPE sample 14079 A8
206702520105_R08C01

value: Normal


title: Uninfected primary mouse astrocytes, control-in-TC-83-infection, biol rep3

description:
Library name: Sample12
column name in VEEV_infected_vs_control_All_counts.tsv: MAT41

value: Untreated


title: VEEV TC-83-infected primary mouse astrocytes, 16hpi, biol rep1

description:
Library name: Sample13
column name in VEEV_infected_vs_control_All_counts.tsv: MAT12


title: INPUT_KO_XRAY_rep2

description: Library name: INPUT_KO_XRAY_rep2

value: TTF

value: C57BL6/CAST hybrid


title: Uninfected primary mouse astrocytes, control-in-TC-83-infection, biol rep2

description:
Library name: Sample11
column name in VEEV_infected_vs_control_All_counts.tsv: MAT31


title: ChIP_gH2AX_WT_XRAY_rep1

description: Library name: ChIP_gH2AX_WT_XRAY_rep1

value: 5Gy XRAY

value: WT


title: FFPE sample 13954 A14

description:
Genomic DNA from FFPE sample 13954 A14
206702520105_R02C01

value: Prostate

value: Adenocarcinoma


title: FFPE sample 14073 B24

description:
Genomic DNA from FFPE sample 14073 B24
206702520105_R01C01

value: Gleason's pattern 7 (3+4), grade group 3


title: INPUT_KO_XRAY_rep1

description: Library name: INPUT_KO_XRAY_rep1


title: VEEV TrD-infected primary mouse astrocytes, 24hpi, biol rep2

description:
Library name: Sample8
column name in VEEV_infected_vs_control_All_counts.tsv: MAr33

value: Brain mixed primary mouse astrocytes

value: VEEV TrD infected - 24hpi