title: PDX27_S

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

description: Library name: PDX27_S

data_processing:
We processed the data using the BETSY system, which aligned the reads to the hg19 genome with STAR estimated the transcript abundance as transcripts per million (TPM) with RSEM.
Assembly: hg19
Supplementary files format and content: expression.counts.txt.  Read counts for each gene and sample.  Tab-delimited text file.
Supplementary files format and content: expression.tpm.txt.  Transcripts per million for each gene and sample.  Tab-delimited text file.

source_name: breast cancer tumor

growth_protocol: The fourth mammary fat pads of 4-to-8-week-old female NOD/SCID mice were implanted with 500,000 PDX tumor cells suspended in 30 µL of a 50:50 mixture of DMEM/F12 media and Matrigel. Cells in Matrigel were maintained on ice until engraftment.

extract_protocol:
The RNA was extracted using PicoPure RNA isolation kit and RNA concentration was quantified by Nanodrop.
Whole transcriptome RNA-seq libraries were prepared using RNA HyperPrep kit with RiboErase following the manufacturer's instructions. Paired-end sequencing was performed on Illumina instruments, which varied across batches.

treatment_protocol: Patients were treated with single agent talazoparib.  Tumors were extracted before (pre) and after (post) treatment (if material available) and engrafted into mice as xenograft models.

value: breast cancer tumor

value: talazoparib

tag: time point

value: post


title: R (biol rep 1)

status: Public on Mar 24 2026

type: SRA

city: Bergen

first: Salwa

last: Suliman

address: Årstadveien 19

department: Department of Clinical Dentistry

country: Norway

institute: Faculty of Medicine, University of Bergen

description: Library name: Sample 9

library_source: transcriptomic

data_processing:
Broad picard pipeline
HiSat2 version 2.0.5
Quantification FeatureCounts (v 1.5.2) (Counts_genocode_vM13_UiB-S10-2022.txt)
Normalization and Differential Expression : DESeq2 version 1.42.0
Assembly: Reference gencode M13 Mus musculus
Fastq files (FASTQ files were extracted from BAMs aligned using STAR and deduplicated using Picard MarkDuplicates)
Bam files(STAR aligned, Picard deduplicated with mm13 reference)
Supplementary files format and content: Counts_genocode_vM13_UiB-S10-2022.txt

molecule: total RNA

organism: Mus musculus

source_name: subcutaneous implant

extract_protocol:
RNA was isolated using Rneasy Mini Kit (Qiagen) following manufacturer's protocol
Illumina TruSeq Stranded mRNA sample preparation

tag: tissue

value: subcutaneous implant


title: Line XIII scramble H3.3 CutRun rep2

city: Sacramento

first: Paul

last: Knoepfler

state: CA

address: 2425 Stockton Blvd, Room 633

department: Cell Biology and Human Anatomy

country: USA

institute: University of California Davis

description: Library name: XIII_scramble_H3.3_rep2

library_source: genomic

data_processing:
Reads were trimmed of adapters using bbduk
Reads were aligned to the hg19 genome with bowtie2
Aligned reads were only retained if they aligned to the same chromosome and within 1000bp of eachother.
Bedtools was used to generate bedgraph files of the aligned reads
Peaks were called with SEACR using the stringent setting with a cutoff of the top 1% of peaks.
Assembly: hg19
Supplementary files format and content: bigwig or bed (peak file)
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

source_name: DIPG Line XIII

growth_protocol: Cells were grown in Tumor Stem Medium, which contains DMEM/F12 1:1 (Invitrogen), Neurobasal-A (Invitrogen), 10mM HEPES (Invitrogen), 1X MEM sodium pyruvate (Invitrogen), 1X MEM nonessential amino acids (Invitrogen), 1% GlutaMax (Invitrogen), human-bFGF (20 ng/ml) (Shenandoah), human-EGF (20 ng/ml) (Shenandoah), human PDGF-A and PDGF-B (20ng/ml) (Shenandoah), heparin (10 ng/ml) (StemCell Technologies) and B27 without Vitamin A (Invitrogen) (27).

extract_protocol:
Cut&Run was performed for CTCF (rabbit anti-CTCF, Millipore #07-729), H3.3 (Millipore #09-838) and H3K27me3 (Cell Signaling C36B11)  using the ActiveMotif Cut&Run kit (ActiveMotif #53180) according to the protocol. Input was used as the control.
Libaries were prepared using the NEB Next Ultra II DNA Library Prep Kit.

treatment_protocol: For CTCF knockdown and scramble control samples, cells were transfected with 90 nM of either scramble control or CTCF siRNA using the RNAi Max reagent (Invitrogen 13778075) and OptiMEM medium (Gibco 31985070). Samples were collected 72 hours after transfection.

tag: cell line

value: DIPG Line XIII

tag: cell type

value: pediatric glioma tumor cells

tag: genotype


title: PC3_20_Hx_rep2_H3

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: PC3_20_Hx_rep2_H3

data_processing:
ChIP-seq reads were sequentially aligned to the Drosophila melanogaster BDGP6 genome and to the Human GRCh37 genome using BWA (0.7.5a-r405). The output SAM files were converted to BAM using SAMtools view (0.1.19) and the number of mapped reads were counted with SAMtools flagstat for later normalisation.
Reads mapping to both genomes and human reads mapping to the Duke Encode blacklist regions were excluded using Bedtools (2.17.0)34. Less than 0.001% of all reads mapped to both species.
The final normalised read counts for each ChIP-seq sample were calculated by dividing the total number of Human mapped reads by the total number of Drosophila mapped reads to provide a scaling factor for normalisation of each sample.
Assembly: Human GRCh37 and Drosophila melanogaster BDGP6 genomes.
Supplementary files format and content: BAM files were firstly indexed with SAMtools (0.1.19). Next, Bedtools genomecov (2.17.0) was used to assess genome-wide sequencing coverage. The bedGraph output files were then normalised using the scaling factors above and converted to BigWig using the bedGraphtoBigWig tool.

source_name: prostate cancer

growth_protocol: PC3 cells were grown in DMEM/Hams F12 medium and HCT116 cells were grown in McCoy's 5a medium. Cells were grown at 37oC in a humidified incubator with 5% CO2 with 100 U/mL penicillin, 100 mg/mL streptomycin, 2mM L-glutamine and 10% fetal bovine serum (Sigma-Aldrich) and regularly tested for mycoplasma infection.

extract_protocol:
Chromatin immunoprecipitation (ChIP) experiments were performed using anti-H3K4me3 (Cell Signaling, 9751S), anti-H3K9me3 (Cell Signaling, 13969S), anti-H3K27me3 (Cell Signaling, 9733S), anti-H3K36me3 (Cell Signaling, 4909S), anti-H3 (Abcam, ab1791) antibodies. In addition, 10ng of Drosophila melanogaster chromatin (Active Motif, 53083) and 1µg of Drosophila-specific histone variant H2Av antibody (Active Motif, 61686) were added to each reaction as a spike-in control for downstream normalisation.
All libraries were prepared and sequenced by the US NCI CCR Genomics Core.

treatment_protocol: Hypoxia incubations were performed at 0.5% O2 for 16 hours in a hypoxia chamber (In Vivo2 400 Hypoxia Work Station, Ruskinn Technology)

value: prostate cancer

value: prostate cancer cell line

tag: treatment

value: hypoxia


title: PC3_18_Hx_rep1_H3

description: Library name: PC3_18_Hx_rep1_H3


title: PDX27_B

description: Library name: PDX27_B

molecule: polyA RNA

value: pre


title: Line XIII scramble H3.3 CutRun rep1

description: Library name: XIII_scramble_H3.3_rep1


title: PC3_17_Nx_rep1_H3

description: Library name: PC3_17_Nx_rep1_H3

value: normoxia


title: PDX18_S

description: Library name: PDX18_S


title: BCP (biol rep 3)

description: Library name: Sample 3


title: Line XIII siCTCF H3.3 CutRun rep2

description: Library name: XIII_siCTCF_H3.3_rep2


title: PDX18_B

description: Library name: PDX18_B


title: BCP (biol rep 4)

description: Library name: Sample 4


title: PC3_16_Hx_rep2_K36me3

description: Library name: PC3_16_Hx_rep2_K36me3


title: BCP (biol rep 1)

description: Library name: Sample 1


title: PDX34_B

description: Library name: PDX34_B


title: BCP (biol rep 2)

description: Library name: Sample 2


title: MSC (biol rep 2)

description: Library name: Sample 6


title: Line XIIIH3.3WT CTCF CutRun rep1

description: Library name: XIII_H3.3WT_CTCF_rep1

source_name: DIPG Line XIIIH3.3WT

value: DIPG Line XIIIH3.3WT


title: PDX17_B

description: Library name: PDX17_B


title: Line XIII CTCF CutRun rep2

description: Library name: XIII_CTCF_rep2


title: Single Cell ATAC-seq of Mus musculus embryonic tissue

city: Plön

first: Stella

last: Kyomen

address: August-Thienemann-Strasse 2

country: Germany

institute: Max Planck Institute for Evolutionary Biology

description: Library name: kyomen_ME11_scATAC

library_source: genomic single cell

data_processing:
Raw sequencing reads were processed using the Cell Ranger ATAC pipeline (v2.1.0). Base calls were demultiplexed with the “cellranger-atac mkfastq” function.  For the mouse dataset, the pre-computed mm10 reference from 10x Genomics was used. Sequencing reads were aligned to their respective references with the “cellranger-atac count” function.
Assembly: mm10
Supplementary files format and content: Tab-separated file containing fragments of mouse scATAC-seq data

source_name: Facial prominences

extract_protocol:
Frontonasal prominences were carefully dissected from freshly collected mouse E11.5 embryos using sharp forceps. For both single-cell technologies, facial prominences from at least 30 embryos were pooled. The following procedure was applied to both species independently. Dissected facial tissues were placed into 1.5ml Eppendorf tubes containing ice-cold PBS. The samples were centrifuged at 500g for 5 minutes at +4°C. After carefully removing the PBS, 1 ml of pre-warmed Trypsin solution (0.05% Trypsin/0.02% EDTA, Pan Biotech, P10-0235SP) was added to each tube and incubated in a thermomixer at 37°C for 15 minutes with gentle agitation. To ensure thorough mixing, the samples were gently vortexed for 30 seconds every 5 minutes during the incubation period. Following incubation, tissue dissociation was carried out by carefully pipetting the samples up and down for 15 seconds. Once the cell suspension appeared homogeneous, 200µl of pre-warmed FBS was added to the samples to quench the enzymatic reaction. After another round of centrifugation at 500g for 5 minutes at +4°C, the supernatant was carefully removed without disrupting the pellet. The cells were then resuspended in 1ml of cold PBS and 2.5µl of RNAse inhibitor (Thermo Fisher Scientific, N8080119) and spun down at 500g for 5 minutes at +4°C. The washing step was repeated three more times to remove any excess trypsin and cell debris. The resulting suspension was subsequently filtered through a 35µm cell strainer (Falcon™, 352235). Assessment of cell viability and concentration was performed by adding 1:1 proportion of 0.4% Trypan blue dye (Gibco™, 15250061) to an aliquot of the cell suspension. Cells were loaded in C-Chip haemocytometer slides (NanoEnTek, DHC-N01) and assessed using a stereomicroscope. When the cell viability was at least 95%, the cell suspension was diluted in nuclease-free water to contain 1.2k cells/µl, ensuring optimal conditions for downstream processes and aligned with the experimental requirements outlined by 10x Genomics protocol, targeting 10,000 cells. For scATAC-seq, the nuclei isolation protocol was executed following the guidelines of 10x Genomics. After dissociation, cells were centrifuged for 5 min 500g at 4+C. The supernatant was removed and the cell pellet was incubated in 100µl of cold Lysis Buffer (Tris-HCL 10mM, NaCl 10mM, MgCl2 3mM, Tween-20 0.1%, Nonidet P40 Substitute 0.1%, BSA 1%) for 5 minutes on ice. After incubation, 500µl of Wash Buffer (Tris-HCL 10mM, NaCl 10mM, MgCl2 3mM, Tween-20 0.1%, BSA 1%) was added. The samples were then centrifuged at 500g for 5 minutes at +4°C, and the resulting nuclei pellet was resuspended in Diluted Nuclei Buffer (10x Genomics Nuclei Buffer; 2000153). Nuclei concentration and viability were assessed using the same procedures as for the scRNA-seq. The nuclei concentration was appropriately adjusted to achieve the desired input for tagmentation.
The scATAC-seq libraries were generated in accordance with the recommended protocol provided by 10x Genomics (Chromium Single Cell ATAC). In summary, 5µl of resuspended nuclei dilution was combined with 10µl of Transposition Mix to yield a final volume of 15µl. These samples were then subjected to an incubation step in a thermal cycler at 37°C for 30 minutes. GEM generation was performed using the Chromium Next GEM Chip H, following the protocol of the manufacturer. After the incubation, 40µl of eluted DNA was retrieved using the magnetic separator. An additional cleanup step was conducted using reagent SPRIselect (Beckman Coulter SPRIselect Reagent Kit B23318). For library preparation, each sample was supplemented with 57.5µl of Sample Index PCR Mix along with 2.5µl of individual Single Index N Set A (3000427). These samples were then incubated following the 10x Genomics protocol for a specified number of cycles that match the targeted nuclei recovery. Subsequent to amplification, fragment size selection was carried out until a recovered sample volume of 20µl was obtained. DNA was quantified using Invitrogen™ Qubit™ dsDNA assay-kit and a Qubit™ fluorometer (Thermo Fisher Scientific, 10616763). The resulting libraries were stored at -20°C until sequencing. Libraries were sequenced with paired-end 50 bp reads, targeting 50k reads per nucleus on the Illumina NovaSeq 6000 S1.

value: Facial prominences

value: WT

tag: time

value: E11.5 embryonic stage


title: PC3_14_Hx_rep1_K36me3

description: Library name: PC3_14_Hx_rep1_K36me3


title: PC3_13_Nx_rep1_K36me3

description: Library name: PC3_13_Nx_rep1_K36me3


title: Line XIII H3K4me3 ChIP-seq rep 2

description: Library name: DIPG_XIII_H3K4me3_rep2

data_processing:
Reads were trimmed of adapters using bbduk and aligned to the hg19 genome with bowtie2.
MACS2 was used to call peaks, with an input sample used as the background control and an FDR of .05.
Assembly: hg19
Supplementary files format and content: bedgraph

extract_protocol:
Briefly, cells were crosslinked with 1% formaldehyde, lysed, and sonicated using a Bioruptor Pico (Diagenode) to generate chromatin fragments <500bp. For each ChIP, 20-30ug of sonicated chromatin was used and immunoprecipitated on magnetic Dynabeads (Pierce #88802). The following antibodies were used: IgG (Santa Cruz, #sc-2027), mouse anti-H3 (Upstate/EMD-Millipore, #05-499), rabbit anti-H3K4me3 (Millipore 04-745).
Libaries were prepared using the NEB Next Ultra II DNA Library Prep Kit


title: Single Cell RNA-seq of Mus musculus embryonic tissue

description: Library name: kyomen_ME11_scRNA

library_source: transcriptomic single cell

data_processing:
The mouse single-cell RNA-seq dataset analyzed in this study was derived from an scRNA-seq experiment conducted on E11.5 facial tissue, encompassing the lateral nasal, medial nasal, and maxillary prominences. The dataset is part of a manuscript under consideration. Facial prominences were dissected and dissociated following the protocol outlined earlier. The experiment utilized the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3, adhering to the manufacturer’s standard protocol. Sequencing data were aligned using Cell Ranger (v7.1.0) with the prebuilt Mus musculus reference genome (mm10) provided by 10x Genomics. Quality control and initial analyses were performed in Scanpy (v1.9.3), with doublet detection executed using Scrublet67. Doublet thresholds were determined based on the multiplet rate table from 10x Genomics, and identified doublets were excluded. Quality control metrics—including total counts, unique gene counts, mitochondrial gene content, and ribosomal gene content—were calculated using Scanpy's “pp.calculate_qc_metrics” function. Cells not meeting the following thresholds were excluded: total counts (12,000–50,000), unique gene counts (3,200–8,000), mitochondrial content (1.9–5.2%), and ribosomal content (15–33%). For cell type annotation, the expression matrix was normalized using “pp.normalize_total” and log-transformed via “pp.log1p”. Highly variable genes were identified with “pp.highly_variable_genes”, followed by PCA for initial dimensionality reduction. Cells were visualized in a two-dimensional space using the UMAP algorithm, clustered using “tl.leiden”, and annotated based on established marker genes. Mesenchymal and ectodermal cells were subsetted, and the same analysis pipeline was applied to refine their annotation. Further analysis was conducted in Seurat after exporting the dataset to R.
Assembly: mm10
Supplementary files format and content: Tab-separated files containing barcodes, features and matrix of mouse scRNA-seq

extract_protocol:
Frontonasal prominences were carefully dissected from freshly collected mouse E11.5 embryos using sharp forceps. For both single-cell technologies, facial prominences from at least 30 embryos were pooled. The following procedure was applied to both species independently. Dissected facial tissues were placed into 1.5ml Eppendorf tubes containing ice-cold PBS. The samples were centrifuged at 500g for 5 minutes at +4°C. After carefully removing the PBS, 1 ml of pre-warmed Trypsin solution (0.05% Trypsin/0.02% EDTA, Pan Biotech, P10-0235SP) was added to each tube and incubated in a thermomixer at 37°C for 15 minutes with gentle agitation. To ensure thorough mixing, the samples were gently vortexed for 30 seconds every 5 minutes during the incubation period. Following incubation, tissue dissociation was carried out by carefully pipetting the samples up and down for 15 seconds. Once the cell suspension appeared homogeneous, 200µl of pre-warmed FBS was added to the samples to quench the enzymatic reaction. After another round of centrifugation at 500g for 5 minutes at +4°C, the supernatant was carefully removed without disrupting the pellet. The cells were then resuspended in 1ml of cold PBS and 2.5µl of RNAse inhibitor (Thermo Fisher Scientific, N8080119) and spun down at 500g for 5 minutes at +4°C. The washing step was repeated three more times to remove any excess trypsin and cell debris. The resulting suspension was subsequently filtered through a 35µm cell strainer (Falcon™, 352235). Assessment of cell viability and concentration was performed by adding 1:1 proportion of 0.4% Trypan blue dye (Gibco™, 15250061) to an aliquot of the cell suspension. Cells were loaded in C-Chip haemocytometer slides (NanoEnTek, DHC-N01) and assessed using a stereomicroscope. When the cell viability was at least 95%, the cell suspension was diluted in nuclease-free water to contain 1.2k cells/µl, ensuring optimal conditions for downstream processes and aligned with the experimental requirements outlined by 10x Genomics protocol, targeting 10,000 cells.
The scRNA-seq library was generated following the 10x Genomics protocol designed for the Chromium Next GEM Single Cell 3 Reagent Kits v3. Briefly, the Chromium Next GEM Chip G was loaded with a mixture of the final cell suspension and Master Mix (RT Reagent B 2000165, Template Switch Oligo 3000228, Reducing Agent B 2000087, and RT Enzyme C 2000085/2000102). The remaining rows were allocated for Single Cell 3 v3.1 Gel Beads (2000164) and partitioning oil, with one row left unfilled. Any unused wells were filled with a 50% glycerol solution, in line with the 10x Genomics protocol. The droplet formation was visually assessed according to the manufacturer's protocol. Upon the conclusion of the run, the GEMs were recovered from the chip and placed into a PCR tube on ice. The GEMs were subsequently incubated in a thermal cycler lasting 55 minutes (53C for 45 seconds, followed by 85C for 5 seconds). The GEMs cleanup procedure was performed according to the manufacturer's instructions similarly to what was previously described for scATAC-seq. Post-cleanup, and a recovered sample volume of 35l was combined with the cDNA Amplification Reaction Mix. An additional round of incubation was conducted, as following the settings described in the cDNA Amplification process outlined in the manufacturer s 10x Genomics protocol, for a total of 13 cycles. Finally, the sample underwent cleanup using SPRIselect (Beckman Coulter SPRIselect Reagent Kit, B23318), after which the quantification of cDNA was assessed using Invitrogen Qubit dsDNA assay-kits and a Qubit fluorometer (Thermo Fisher Scientific, 10616763).


title: Line XIII H3K4me3 ChIP-seq rep 1

description: Library name: DIPG_XIII_H3K4me3_rep1


title: PC3_15_Nx_rep2_K36me3

description: Library name: PC3_15_Nx_rep2_K36me3


title: Ba-7

city: wuxi

first: Zhixuan

last: Zhang

state: Jiangsu

address: North Hospital, No. 200 Huihe Road, Binhu District

country: China

institute: Jiangnan University

description: Library name: sample10

data_processing:
Illumina / BGI
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw gene counts for each Sample
Supplementary files format and content: tab-delimited file include FPKM values for each Sample

source_name: cardiac

extract_protocol:
RNA was harvested using using TRIzol®Reagent according the manufacturer’s instructions (Magen).1.0μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following manufacture's protocols.

value: cardiac

value: Ba+LPS


title: Library4: Lung, RAS, control, other

city: Hannover

first: Jonas

last: Schupp

address: Carl-Neuberg-Str. 1

department: Respiratory Medicine

institute: Hannover Medical School

description:
Library name: Flex_CLAD4_PH_200623
10x Genomics

data_processing:
Basecalls were converted to reads using the software Cell Ranger (v7.1.0) and its bcl2fastq implementation “mkfastq”.
Subsequent read processing was conducted using the the software Cell Ranger (v7.1.0).
Reads of probes were aligned to the human reference genome GRCh38  (GENCODE v32/Ensembl 98, “GRCh38-2020-A”) using the Chromium Human Transcriptome Probe Set _v1.0.1 for GRCh38-2020-A
Nuclei-UMI count matrices were analyzed using the R package Seurat (version 4.3.0). UMI counts were normalized with a scale factor of 10,000 UMIs per nuclei and then natural log transformed using a pseudocount of 1. To filter structural lung cells from immune cells, a recursive process of integration, graph embedding, and cluster analysis was employed
Assembly: GRCh38-2020
Supplementary files format and content: RAS.raw.counts.mtx: sparce matrix of UMI counts in MatrixMarket format; RAS.genes.tsv: tab-separated text file of gene names; RAS.barcodes.tsv: tab-separated text file of cell identifiers; RAS.Seurat.obj.final.rds: final Seurat object

source_name: tissue

extract_protocol:
Nuclei isolation from formalin fixed lung tissue, Fluorescence Activated Nuclei Sorting of DAPI+ single nuclei
Library construction according to the 10x Genomivs Chromium Fixed RNA Profiling  for Multiplexed Samples protocol (CG000527, Rev B)

value: tissue


title: Line XIII siCTCF H3.3 CutRun rep1

description: Library name: XIII_siCTCF_H3.3_rep1


title: Ba-5

description: Library name: sample9


title: PC3_12_Hx_rep2_K27me3

description: Library name: PC3_12_Hx_rep2_K27me3


title: Line XIIIH3.3WT CTCF CutRun rep2

description: Library name: XIII_H3.3WT_CTCF_rep2


title: Line XIII CTCF CutRun rep1

description: Library name: XIII_CTCF_rep1


title: Ba-3

description: Library name: sample8


title: PC3_11_Nx_rep2_K27me3

description: Library name: PC3_11_Nx_rep2_K27me3


title: PC3_10_Hx_rep1_K27me3

description: Library name: PC3_10_Hx_rep1_K27me3


title: B6.Sst1S BMDMs Biological reolicate 3 Mtb

city: Baltimore

first: Somnath

last: Shee

state: MD

address: 1550 Orleans St, CRB2 Building, Room-176

department: Medicine, Infectious diseases

institute: Johns Hopkins University

description: Library name: SSR 4-6

data_processing:
Image analysis and base calling were conducted by HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Raw sequencing reads were trimmed to remove adapter sequences and low-quality bases using Trimmomatic v0.36, and the filtered reads were aligned to the Mus musculus GRCm38 reference genome (ENSEMBL) using the splice-aware STAR aligner v2.5.2b, generating BAM files.
Gene hit counts were quantified using featureCounts from the Subread package v1.5.2, counting only uniquely mapped reads overlapping annotated exon regions, with strand specificity applied where appropriate.
Differential expression analysis was performed using the  DESeq2 package86. Genes with an adjusted p-value <0.05 and a log₂ fold change > 1 or <-1 were deemed differentially expressed between groups.
Assembly: GRCm38
Supplementary files format and content: xlsx file includes raw counts for each sample
Supplementary files format and content: xlsx file includes TPM counts (transcript per million) for each sample

source_name: bone marrow derived macrophages

growth_protocol: BMDMs were isolated from the tibias and femurs of mice and were differentiated into macrophages in RPMI-Glutamax (Thermo Fisher Scientific; 61870127) containing 10% heat-inactivated FBS (Millipore Sigma, Catalog no.- F4135), 1X antibiotic antimycotic Solution (Sigma Aldrich; A5955) and 10% (v/v) L929 fibroblast-conditioned medium (as a source of M-CSF) for 5 days. L929 fibroblast cell lines were cultured in DMEM-Glutamax (Thermo Fisher Scientific; 10566016) containing 10% heat-inactivated FBS, 10 mM HEPES, and 1X antibiotic antimycotic Solution. L929 cells were mycoplasma-negative (Venorgem Mycoplasma detection kit; Millipore Sigma- MP0025). BMDMs were washed, scrapped out, counted, and replated overnight prior to the experiments. All experiments were done with confluency of BMDMs 60-75%.

extract_protocol:
BMDMs were lysed in TRIzol (Thermo Fisher Scientific; 15596026), and RNA was extracted using Qiagen RNeasy Mini Kit (74104) and RNase-free DNase Set (Qiagen; 79254), following the manufacturer’s protocol. RNA purity and concentration was quantified using Nanodrop One (Thermo Fisher Scientific) and stored at -80 ºC.
Total RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. The next steps included performing rRNA depletion using QIAseq® FastSelect™−rRNA HMR kit (Qiagen, Germantown, MD, USA), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were generated with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94°C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end-repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered on one lane of a flow cell. After clustering, the flow cell was loaded on the Illumina HiSeq 4000 instrument according to the manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration.

treatment_protocol: BMDMs were  treated with 10 ng/ml of murine-TNFα (Peprotech; 315-01A) in  RPMI-Glutamax containing 10% heat-inactivated FBS and 10% (v/v) L929 fibroblast-conditioned medium, for 48 hours at 37°C in 5% CO2. For the second condition, BMDMs were infected with Mtb H37Rv for 4 hours at MOI=10. After 4 hours, extracellular Mtb were removed by extensive washing with warm RPMI media and RPMI+ TNFα was added to the cells. RNA was isolated after 24 hours.

value: bone marrow derived macrophages

value: Mtb H37Rv (MOI=10; 24 hours) infection only.


title: Ba-2

description: Library name: sample7


title: B6.Sst1S BMDMs Biological reolicate 2 Mtb

description: Library name: SSR 4-5


title: Library2: Lung, RAS, control, other

description:
Library name: Flex_CLAD2_070223
10x Genomics


title: PDX16_B

description: Library name: PDX16_B

value: breast cancer tumor


title: PC3_9_Nx_rep1_K27me3

description: Library name: PC3_9_Nx_rep1_K27me3


title: B6.Sst1S BMDMs Biological reolicate 1 Mtb

description: Library name: SSR 4-4


title: LPS5

description: Library name: sample5

value: LPS


title: Library1: Lung, RAS, control, other

description:
Library name: Flex_CLAD_010223
10x Genomics


title: PC3_8_Hx_rep2_K9me3

description: Library name: PC3_8_Hx_rep2_K9me3


title: B6 BMDMs Biological replicate 3 Mtb

description: Library name: SSR 3-8

value: WT C57BL/6J


title: PC3_7_Nx_rep2_K9me3

description: Library name: PC3_7_Nx_rep2_K9me3

value: prostate cancer


title: Ba-1

description: Library name: sample6


title: B6 BMDMs Biological replicate 2 Mtb

description: Library name: SSR 3-7


title: HSJD-DIP007_FB232_RNAseq_Rep3

city: Sydney

first: Samuel

middle: Ernest

last: Ross

state: NSW

address: The University of Sydney

country: Australia

institute: The University of Sydney

data_processing:
RNA-seq reads were trimmed using Trimmomatic  and aligned to the GRCh38 genome using STAR. Quantification of transcript and gene abundance was then performed using RSEM.
Direct RNA-seq libraries were mapped to the GRCh38 Ensembl annotations release version 91  using minimap2 (-ax map-ont -uf  --secondary=no). m6A site probabilities were calculated using nanopolish and m6anet (--num_iterations 1000)
Assembly: hg38
Supplementary files format and content: tab-delimited text files provide TPM counts for RNAseq experiments
Supplementary files format and content: csv files provide m6A site scores from m6Anet for direct-RNAseq experiments

extract_protocol:
total RNA was extracted using the ISOLATE II RNA Mini Kit from Bioline
cDNA libraries were prepared at the Ramaciotti Centre for Genomics using the Illumina Stranded mRNA prep kit. Direct RNA-seq libraries were prepared by the Garvan Sequencing Platform using the SQK-RNA002 kit and sequences on PromethION using FLO-PRO002 flow cells
RNA-seq and directRNA-seq

value: H3K27 altered DMG


title: PC3_6_Hx_rep1_K9me3

description: Library name: PC3_6_Hx_rep1_K9me3

value: prostate cancer cell line

value: hypoxia


title: LPS3

description: Library name: sample3


title: B6 BMDMs Biological replicate 1 Mtb

description: Library name: SSR 3-6


title: HSJD-DIP007_FB232_RNAseq_Rep2


title: LPS4

description: Library name: sample4


title: HSJD-DIP007_DMSO_RNAseq_Rep3

value: DMSO


title: B6.Sst1S BMDMs Biological reolicate 2 TNF

description: Library name: SSR 2-3

value: 10 ng/ml TNFα treatment (48 hours) only


title: Library3: Lung, RAS, control, other

description:
Library name: Flex_CLAD3_300223
10x Genomics


title: PC3_4_Hx_rep2_K4me3

description: Library name: PC3_4_Hx_rep2_K4me3


title: B6.Sst1S BMDMs Biological reolicate 3 TNF

description: Library name: SSR 2-4


title: HSJD-DIP007_DMSO_RNAseq_Rep2


title: HSJD-DIP007_FB232_RNAseq_Rep1


title: PAO-Mock-M5

city: Singapore

first: Damien

last: Chua

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University, Singapore

description: Library name: smple20

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT2 . FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: lungs

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

value: lungs


title: PC3_3_Nx_rep2_K4me3

description: Library name: PC3_3_Nx_rep2_K4me3

value: normoxia


title: LPS1

description: Library name: sample1


title: HSJD-DIP007_DMSO_RNAseq_Rep1


title: LPS2

description: Library name: sample2


title: B6.Sst1S BMDMs Biological reolicate 1 TNF

description: Library name: SSR 2-2


title: B6 BMDMs Biological replicate 2 TNF

description: Library name: SSR 1-5


title: PC3_2_Hx_rep1_K4me3

description: Library name: PC3_2_Hx_rep1_K4me3


title: B6 BMDMs Biological replicate 1 TNF

description: Library name: SSR 1-4


title: PAO-Mock-M2

description: Library name: smple17

value: WT


title: T cells_Keap1_KO_D

type: RNA

city: Aachen

first: Christopher

middle: Thomas

last: Neullens

address: Pauwelsstraße 30, 52074

institute: RWTH Aachen University Medical Faculty

description:
gene expression data from CD4+CD25- slenic T cells from Keap KO mice
KO6 CD4_(MoGene-2_0-st).BD_CD4_2014.rma-gene-full-Signal

hyb_protocol: Samples were hybrized using Affymetrix hybridization kit material according to the manufyctures instructions: hybridization 45°C for 16 hours at 60 rpm; Fluidics Station Program FS_450_0001

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

data_processing:
Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with SST robust multiarray average algorithm (Affymetrix): SST-RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.
log2 sst rma signal intensity; only subset of normalized date is provided due to file loss.

label: biotin

source_name: Keap1_KO_T cell

label_protocol: Fragmented, biotinylated cDNA were prepared from 40 ng total RNA using the NuGen Ovation Pico WTA System 2 Kit according to the manufactures instructions.

growth_protocol: Experiments were performed with sex- and age- matched 6-10 week old VAVcreKeapfl/fl and respective WT mice. VAVcreKeapfl/fl mice were generated by crossing Keap1-flox mice (Okawa et al. With VAVcre mice.

extract_protocol: Total RNA was isolated from CD4+CD25- cells by using Quiagen Rneasy Micro Kits

treatment_protocol: CD4+CD25- cells were isolated by magnetic cell separation from spleens, mice were untreated.

tag: strain background

value: KO

tag: age

value: 6-10 weeks

value: spleen

value: CD4+ CD25- T cell


title: PC3_1_Nx_rep1_K4me3

description: Library name: PC3_1_Nx_rep1_K4me3


title: PAO-Mock-M3

description: Library name: smple18


title: PC3_5_Nx_rep1_K9me3

description: Library name: PC3_5_Nx_rep1_K9me3


title: PAO-Mock-M4

description: Library name: smple19


title: PAO-ASO-M5

description: Library name: smple15


title: SU-DIPGXIII_FB232_RNAseq_Rep1

source_name: SU-DIPGXIII

value: SU-DIPGXIII


title: SU-DIPGXIII_FB232_RNAseq_Rep2


title: p53null STIFF mammary tumors Sample 42

city: San Francisco

first: Hugo

middle: A

last: Gonzalez

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California San Francisco

description:
Library name: Sample_42
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

data_processing:
Raw reads were mapped to the mouse reference genome (GRCm38) and counts and transcripts per million (TPMs) were estimated using Kallisto quant (version 0.46.1). Genes with fewer than combined 10 raw counts were excluded from further analyses. Differential expression analysis between soft (n = 22) and stiff (n = 21) mammary tumors was performed using the edgeR package (version 4.6.2) (63), within the statistical computing language R (version 4.3.1).
Assembly: mouse reference genome (GRCm38)
Supplementary files format and content: kallisto output .tsv files exported from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

source_name: mammary tumor/end-point

extract_protocol:
Tumor tissues were mechanically digested in DNA lysis buffer (4 M guanidine thiocynate, 100 mM Tris/HCl pH 7.4, 30 mM EDTA pH 8.0, 1% Triton X-100, 100 mM b-mercaptoethanol). Lysates were incubated with acid-washed diatomaceous earth to enhance nucleic acid binding, followed by silica column-based purification (Promega). Column-bound DNA was purified through sequential washes with guanidine- and ethanol-based DNA wash buffers. RNA was isolated from the DNA flowthrough by sodium acetate-phenol:chloroform extraction. The aqueous phase was incubated with acid-washed diatomaceous earth and ethanol to promote RNA binding to the column, followed by purification through guanidine- and ethanol-based RNA wash buffers. DNA was used in WES, and RNA was used in RNA-Seq and RT-qPCR analyses.
RNA-Seq libraries were prepared as previously described (60), with the following modifications. Briefly, 1 mg total RNA was enriched for poly(A) transcripts using oligo(dT)-conjugated magnetic beads (KAPA mRNA HyperPrep Kit, Roche, Cat # 08098123702), followed by fragmentation, template-switch reverse transcription, and dual-index barcode PCR amplification (Roche, Cat #KK8725). To minimize ribosomal RNA contamination, two consecutive rounds of bead binding using 25 mL were performed, and intact poly(A) RNA was eluted in 5 mL nuclease-free water at 65 °C for 2 mins. Custom-magnetic immobilizers—3 mm × 1 mm neodymium disc magnets (K&J Magnetics) embedded at a 45 o angle in polydimethylsiloxane (PDMS) at the base of 0.2 mL PCR tubes—were used to localize magnetic beads during washes and minimize carryover. Enriched RNA was chemically fragmented and reverse-transcribed using a modified SMART-Seq3 protocol (61). Briefly, RNA was fragmented by heating a 1:1 mixture of RNA and 2X fragmentation buffer (50 mM Tris-HCl pH 8.3, 60 mM NaCl, 6 mM MgCl₂, 13.3% PEG-8000, 0.27% Triton X-100, and 2.7 µM oligo(dT)₃₀) at 94 °C for 2 min, to generate a target library size of 300–400 bp (corresponding to ~120–220 bp inserts). Samples were cooled on ice and combined with 3 µL of 4X reverse transcription master mix (25 mM Tris-HCl pH 8.3, 30 mM NaCl, 3 mM MgCl₂, 4 mM neutralized GTP, 32 mM DTT, 2 mM each dNTP, 4 µM template-switching oligo), 1 U/µL Ribolock RNase inhibitor (Thermo, Cat #EO0381), and 2 U/µL Maxima H Minus Reverse Transcriptase (Thermo, Cat #EP0751). First-strand synthesis was performed at 42 °C for 90 mins, followed by 10 cycles of 2 mins each at 50 °C and 42 °C, with enzyme inactivation at 85 °C for 5 mins. cDNA fragments were size-selected on a 2% agarose gel (200-650 bp), excised, dissolved in solubilization buffer, incubated with acid-washed diatomaceous earth, followed by column-based purification (Promega) and eluted with pre-heated elution buffer. Libraries were amplified using KAPA HiFi master mix and dual-index barcodes, for 16–18 cycles of 98 °C 15 sec, 60 °C 30 sec, 72 °C 1 min, with amplification monitored from cycle 14 by gel electrophoresis. Final libraries were ethanol-precipitated with linear acrylamide and sodium acetate and stored at –80 °C. Single-end, 150-bp sequencing was performed on a HiSeq 4000 (The University of California, San Francisco, Center for Advanced Technology).

treatment_protocol: Orthotopic animal models. High concentration rat tail Col1 (Corning, Cat #354249) was incubated with 0.1% acetic acid (non-crosslinked; soft) or 0.1% acetic acid with 500 mM L-ribose (Chem Impex, Cat #28127) (crosslinked; stiff) for 10-14 days. The Col1 mixtures were then combined with BM extract (R&D Systems, Cat #3532-005-02) at a final concentration of 20%. Col1/BM hydrogels were injected into a cleared fourth mammary pat pad of 3- to 4-week-old mice prior to implantation of a mammary fragment isolated from an 8- to 10-week-old syngeneic p53null mouse. Mice were euthanized at a tumor end-point of a maximum tumor diameter of 2 cm for tissue analysis.

value: mammary tumor/end-point

value: Mammary Breast Tumor

value: Balb/c mammary p53null

value: non-metabolizable L-ribose crosslinked) collagen 1/ basement membrane (Col1/BM) hydrogels (STIFF Group)


title: PAO-ASO-M4

description: Library name: smple14


title: Lung, Sarcoidosis, Granuloma, 9

description: Library name: SARH21

data_processing:
Basecalls were converted to reads using the software Cell Ranger and its bcl2fastq implementation “mkfastq”.
Subsequent read processing was conducted using the the software spaceranger
Reads of probes were aligned to the human reference genome GRCh38  (GENCODE v32/Ensembl 98, “GRCh38-2020-A”) using the Chromium Human Transcriptome Probe Set _v1.0.1 for GRCh38-2020-A
Assembly: GRCh38-2020
Supplementary files format and content: matrix.mtx.gz: gene expression count data in MatrixMarket Exchange format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hires image of tissue
Supplementary files format and content: tissue_lowres_image.png: lowres image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: lung

extract_protocol:
FFPE tissue blocks were cut on a routine microtome into of 5 µm thick sections
Library construction according to the 10x Genomics Visium CytAssist Gene Expression protocol (CG000495 Rev A)

value: lung


title: B6 BMDMs Biological replicate 3 TNF

description: Library name: SSR 1-6

value: bone marrow derived macrophages

value: WT C57BL/6J


title: Lung, Sarcoidosis, Granuloma, 8

description: Library name: SARH14


title: PAO-Mock-M1

description: Library name: smple16


title: SU-DIPGXIII_FB232_RNAseq_Rep3

value: H3K27 altered DMG


title: T cells_Keap1_KO_B

description:
gene expression data from CD4+CD25- slenic T cells from Keap KO mice
KO4 CD4_(MoGene-2_0-st).BD_CD4_2014.rma-gene-full-Signal


title: SU-DIPGXIII_DMSO_RNAseq_Rep3

value: DMSO


title: T cells_Keap1_KO_C

description:
gene expression data from CD4+CD25- slenic T cells from Keap KO mice
KO5 CD4_(MoGene-2_0-st).BD_CD4_2014.rma-gene-full-Signal


title: p53null STIFF mammary tumors Sample 44

description:
Library name: Sample_44
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: SW480, Fedratinib, 2 hour, biological replicate 2

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were trimmed using BBDuk (BB Tools v38.46). The bundled adapter sequences and following parameters were used: ktrim=r, mink=11, hdist=1, k=31.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3).
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27.
Coverages were determined using bedtools 2 v2.28.0 as (1 / read length) for each base in the genome. These base coverages were used to obtain pseudo-read counts in strand-specific regions of interest using bedtools intersect. Reads Per Kilobase per Million mapped reads (RPKM) were calculated for meta-transcripts ("genes") defined by merging exons and intervening intronic spaces from all isoforms of a gene in the GENCODE v27 "basic" annotation. Genes were quantified by summing pseudo-counts falling within the features (exons and intronic spaces) and normalized by the effective gene length (sum of feature lengths) and by the size of the library (uniquely mapped read count).
Assembly: hg38
Supplementary files format and content: The provided sample quantifications bed files have the following columns: (1) chromosome; (2) start; (3) end; (4) name; (5) placeholder score; (6) strand; (7) type of feature; (8) effective gene length; (9) read counts; (10) RPKM
Library strategy: BrU-seq

growth_protocol: SW480 colorectal adenocarcinoma cells were grown in Dulbecco's Modified Eagle Medium (DMEM), supplemented with 10% fetal bovine serum and 5% antibiotics (Penicillin and Streptomycin) in a humidified incubator maintained at 37'C and 5% CO2 concentration.

extract_protocol:
Cells were lysed directly in TRIzol followed by isolation of total RNA.The isolated total RNA was further treated with DNAse (TURBO DNA-free Kit; Invitrogen) and a spike-in cocktail of Bru-labeled and unlabeled RNA was mixed in with total RNA. Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences).
Strand-specific libraries were prepared from a modified protocol as described previously (McShane et al., bioRxiv, 2024). Ribosomal RNA was reduced via QiaSeq FastSelect (Qiagen) prior to first-strand synthesis. A universal ligation adapter and dual-index, barcoded primers for were used for PCR in the preparation of these libraries. Size selection for all libraries was performed via agarose gel excision.

treatment_protocol: Cells were treated with 1uM Fedratinib or equal volume of DMSO vehicle control for 30 min or 2 hour.

value: Colorectal cancer cells

value: Fedratinib 1uM

value: 2 hour


title: p53null STIFF mammary tumors Sample 40

description:
Library name: Sample_40
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: p53null STIFF mammary tumors Sample 41

description:
Library name: Sample_41
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: p53null STIFF mammary tumors Sample 43

description:
Library name: Sample_43
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: SU-DIPGXIII_DMSO_RNAseq_Rep1


title: PAO-ASO-M3

description: Library name: smple13

value: lungs

value: WT


title: SU-DIPGXIII_DMSO_RNAseq_Rep2


title: p53null STIFF mammary tumors Sample 39

description:
Library name: Sample_39
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: PAO-ASO-M1

description: Library name: smple11


title: T cells_Keap1_WT_C

description:
gene expression data from CD4+CD25- slenic T cells from Keap WT mice
WT3 CD4_(MoGene-2_0-st).BD_CD4_2014.rma-gene-full-Signal

source_name: Keap1_WT_T cell

value: 6-10 weeks

value: spleen


title: SW480, Fedratinib, 2 hour, biological replicate 1


title: Mock-Mock-M4

description: Library name: smple9

value: mock


title: SW480, DMSO, 2 hour, biological replicate 1


title: T cells_Keap1_WT_B

description:
gene expression data from CD4+CD25- slenic T cells from Keap WT mice
WT2 CD4_(MoGene-2_0-st).BD_CD4_2014.rma-gene-full-Signal

value: CD4+ CD25- T cell


title: PAO-ASO-M2

description: Library name: smple12


title: p53null STIFF mammary tumors Sample 38

description:
Library name: Sample_38
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

value: mammary tumor/end-point

value: Mammary Breast Tumor


title: SW480, Fedratinib, 30 min, biological replicate 1

value: 30 min


title: T cells_Keap1_WT_D

description:
gene expression data from CD4+CD25- slenic T cells from Keap WT mice
WT4 CD4_(MoGene-2_0-st).BD_CD4_2014.rma-gene-full-Signal


title: Mock-Mock-M5

description: Library name: smple10


title: T cells_Keap1_KO_A

description:
gene expression data from CD4+CD25- slenic T cells from Keap KO mice
KO1 CD4_(MoGene-2_0-st).BD_CD4_2014.rma-gene-full-Signal

value: KO


title: Mock-Mock-M3

description: Library name: smple8


title: SW480, DMSO, 30 min, biological replicate 2


title: p53null STIFF mammary tumors Sample 36

description:
Library name: Sample_36
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

value: Balb/c mammary p53null

value: non-metabolizable L-ribose crosslinked) collagen 1/ basement membrane (Col1/BM) hydrogels (STIFF Group)


title: p53null STIFF mammary tumors Sample 35

description:
Library name: Sample_35
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: p53null STIFF mammary tumors Sample 34

description:
Library name: Sample_34
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: Mock-Mock-M2

description: Library name: smple7


title: p53null STIFF mammary tumors Sample 37

description:
Library name: Sample_37
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: Human iPSC-derived INFRA cells from New muscle culture protocol engrafted in mice Tibialis Anterior

city: Boston

first: Yannis

last: Djeffal

state: Massachusetts

address: 60 Fenwood road

department: Pathology/Genetics

institute: Brigham and Women’s Hospital/Harvard Medical School

description:
yannis_pool_july17_N70i_TGTAGTCATT
GRCh38_and_mm10-2020-A

data_processing:
cell ranger 7.1.0
Assembly: GRCh38-2020-A and GRCh38_and_mm10-2020-A
Supplementary files format and content: tsv and mtx - barcodes, features and matrix

organism:
Homo sapiens
Mus musculus

source_name: Differenciated hiPSCs and Mouse cells

extract_protocol:
Cultures were dissociated with Accutase or Trypsin or directly following FACS-sorting, or directly following INFRA cell dissociation protocol.
The Chromium Next GEM Single Cell 3ʹ Kit v3.1 was used to encapsulate single cells. Library preparation was performed according to 10x Genomics protocols.

value: Differenciated hiPSCs and Mouse cells

tag: culture protocol

value: New


title: Replicate 3, LMNA KO cells grown for 3-4 d followed by compression and a 2 h recovery

city: Tampere

first: Elina

last: Mantyla

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University Foundation

description: Library name: ERAS240012603-1r

data_processing:
Quantified libraries were pooled and sequenced on the Illumina platform using paired-end 150 bp reads (Illumina Sequencing PE150 Illumina), generating approximately 6 Gb of raw data per sample. Base calling was done using Illumina software (CASAVA base calling), generating raw FASTQ files.
Sequencing reads were mapped to CanFam_3.1 (domestic dog, canis lupus familiaris). Gene-level counts were generated using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome.
For bioinformatics analysis, raw data were processed through Novogene’s in-house Perl scripts, and the data were quality checked with FastQC. Relative expression levels were normalized based on gene length and sequencing depth (fragments per kilobase of transcript per million mapped reads, FPKM).
Assembly: GCF_000002285.3 (CanFam3.1)
Supplementary files format and content: csv file "gene_count_Comp_Mantyla.csv" includes raw counts for each sample
Supplementary files format and content: csv file "gene_fpkm_Comp_Mantyla.csv" includes FPKM values for each sample

organism: Canis lupus familiaris

source_name: cell line

growth_protocol: Madine Darby canine kidney type II epithelial cells and their derivative LMNA KO cells were maintained in MEM supplemented with 10 % fetal bovine serum (FBS) and 5 % penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy midi kit (Qiagen).
The mRNA quantity and integrity were assessed using the 5200 Fragment Analyzer. The libraries  were produced and sequencing with bioinformatics analysis was done by Novogene. RNA libraries for RNA-seq were prepared from mRNA enriched using oligo(dT) beads. The mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies). Insert size was checked on an Agilent 2100 and quantified using quantitative PCR. Oligonucleotide sequences of adapters from TruSeqTM RNA Sample Prep Kit.

treatment_protocol: Cells were grown until confluent monolayer (3-4 d); or grown for 3-4 d followed by lateral compression and 2 h recovery

value: cell line

value: MDCKII

value: epithelial

value: Grown for 3-4 d, compressed, 2 h recovery


title: Mock-Mock-M1

description: Library name: smple6

value: lungs

value: WT


title: SW480, Fedratinib, 30 min, biological replicate 2

value: Colorectal cancer cells

value: Fedratinib 1uM


title: Mock-ASO-M5

description: Library name: smple5

value: ASO


title: SW480, DMSO, 30 min, biological replicate 1

value: DMSO


title: T cells_Keap1_WT_A

description:
gene expression data from CD4+CD25- slenic T cells from Keap WT mice
WT1 CD4_(MoGene-2_0-st).BD_CD4_2014.rma-gene-full-Signal

value: 6-10 weeks

value: spleen

value: CD4+ CD25- T cell


title: miRNA_AC16 exosomes, exo-S-Ang3

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

data_processing:
Raw data were processed with Cutadapt.
The clean reads were aligned to the reference Database of miRBase22.1, piRNABank and RfamV14.1
The UMI Counts of miRNA ,piRNA and SmallRNA were calculated by perl.
The expression of miRNA ,piRNA and SmallRNA was normalized to CPM
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text file includes row counts for each Sample

source_name: AC16 exosome

extract_protocol:
Total RNA was extracted using miRNeasy Micro Kit (Cat #217084, Qiagen), and RNA quality was checked using Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US) according to standard procedures. The exosomes were isolated and total RNA was extracted using exoRNeasy Maxi Kit (#77164, Qiagen). RNA quality was checked using Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US) according to standard procedures.
Sequencing libraries were constructed by QIAseq miRNA Library Kit for Illumina (Cat #331505, Qiagen) according to manufacturer's instructions.

tag: cell compartment

value: exosome


title: Replicate 2, LMNA KO cells grown for 3-4 d followed by compression and a 2 h recovery

description: Library name: ERAS240012602-1r


title: miRNA_AC16 exosomes, exo-S-Ang2


title: p53null STIFF mammary tumors Sample 31

description:
Library name: Sample_31
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

value: mammary tumor/end-point

value: Mammary Breast Tumor

value: Balb/c mammary p53null

value: non-metabolizable L-ribose crosslinked) collagen 1/ basement membrane (Col1/BM) hydrogels (STIFF Group)


title: Mock-ASO-M4

description: Library name: smple4


title: Replicate 2, non-compressed LMNA KO cells grown for 3-4 d

description: Library name: ERAS240012599-1r

value: cell line

value: MDCKII

value: Grown for 3-4 d, noncompressed ctrl


title: miRNA_AC16 exosomes, exo-S-Ang1


title: Mock-ASO-M3

description: Library name: smple3

value: lungs


title: Replicate 1, non-compressed LMNA KO cells grown for 3-4 d

description: Library name: ERAS240012598-1r

value: epithelial


title: miRNA_AC16 exosomes, exo-S-Con3


title: Mock-ASO-M2

description: Library name: smple2

value: WT


title: p53null STIFF mammary tumors Sample 33

description:
Library name: Sample_33
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: p53null STIFF mammary tumors Sample 29

description:
Library name: Sample_29
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: Replicate 3, WT cells grown for 3-4 d followed by compression and a 2 h recovery

description: Library name: ERAS240012597-1r

value: Grown for 3-4 d, compressed, 2 h recovery


title: Mock-ASO-M1

description: Library name: smple1

value: ASO


title: p53null STIFF mammary tumors Sample 28

description:
Library name: Sample_28
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: miRNA_AC16 exosomes, exo-S-Con2


title: Replicate 2, WT cells grown for 3-4 d followed by compression and a 2 h recovery

description: Library name: ERAS240012596-1r


title: Replicate 1, LMNA KO cells grown for 3-4 d followed by compression and a 2 h recovery

description: Library name: ERAS240012601-1r


title: p53null STIFF mammary tumors Sample 30

description:
Library name: Sample_30
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: miRNA_AC16 cells, cell-S-Ang3

value: whole cells


title: Nrg_3

city: Winnipeg

first: Soheila

last: Karimi

state: Manitoba

address: 745 Bannatyne Avenue

department: Physiology and Pathophysiology

country: Canada

institute: University of Manitoba

description:
Library name: Sample6
Column name in Processed data file - All Samples.csv: Nrg_3

data_processing:
Data were processed using the Galaxy workflow.
Following QC, data were trimmed using Trimmomatic package.
After trimming, transcripts were mapped to to the mouse genome.
Read counts were extracted and normalized using Bowtie2 package in Galaxy workflow
Assembly: Assembly: mm 10
Supplementary files format and content: Supplementary files format and content: txt file containing gene counts for all of the samples

source_name: MACS sorted for anti-GFP from Hippocampus

extract_protocol:
Cell lysates of GFP+  hip-NPCs  were preserved in TRIzol. RNA was extracted using the ThermoFisher PureLink RNA Mini Kit. RNA libraries were then prepared using the NEB RNA library preparation kit at Genome Québec.
RNA-Seq

treatment_protocol: To study the properties of hippocampal NPC (hip-NPC) progenies (GFP+) under prolonged demyelination conditions, RNA sequencing was performed on cells isolated via MACS sorting from Nrg-1β1 and vehicle-treated mice following long-term demyelination.

value: Neural progenitor cells

value: Nestin-CreERT2;Rosa26-mGFP mice

value: 10-week cuprizone diet + 4-week recovery and 60 g/kg/day Neuregulin 1 beta 1 peptide (Shenandoah Biotechnology, USA, 100-46)


title: miRNA_AC16 exosomes, exo-S-Con1

value: exosome


title: Nrg_2

description:
Library name: Sample5
Column name in Processed data file - All Samples.csv: Nrg_2

value: MACS sorted for anti-GFP from Hippocampus


title: Replicate 3, WT cells non-compressed control cells grown for 3-4 d

description: Library name: ERAS240012594-1r


title: Replicate 1, WT cells grown for 3-4 d followed by compression and a 2 h recovery

description: Library name: ERAS240012595-1r


title: miRNA_AC16 cells, cell-S-Ang2


title: p53null STIFF mammary tumors Sample 25

description:
Library name: Sample_25
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

value: mammary tumor/end-point

value: Mammary Breast Tumor


title: p53null STIFF mammary tumors Sample 26

description:
Library name: Sample_26
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

value: Balb/c mammary p53null

value: non-metabolizable L-ribose crosslinked) collagen 1/ basement membrane (Col1/BM) hydrogels (STIFF Group)


title: Replicate 2, WT cells non-compressed control cells grown for 3-4 d

description: Library name: ERAS240012593-1r

value: cell line

value: MDCKII


title: Nrg_1

description:
Library name: Sample4
Column name in Processed data file - All Samples.csv: Nrg_1


title: p53null STIFF mammary tumors Sample 24

description:
Library name: Sample_24
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: miRNA_AC16 cells, cell-S-Ang1


title: Replicate 1, WT cells non-compressed control cells grown for 3-4 d

description: Library name: ERAS240012592-1r

value: Grown for 3-4 d, noncompressed ctrl


title: Vehicle_3

description:
Library name: Sample3
Column name in Processed data file - All Samples.csv: Vehicle_3

value: 10-week cuprizone diet + 4-week recovery and 0.1% bovine serum albumin (BSA) in saline


title: miRNA_AC16cells, cell-S-Con3


title: p53null STIFF mammary tumors Sample 23

description:
Library name: Sample_23
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: Vehicle_1

description:
Library name: Sample1
Column name in Processed data file - All Samples.csv: Vehicle_1


title: Vehicle_2

description:
Library name: Sample2
Column name in Processed data file - All Samples.csv: Vehicle_2


title: BIT#5(TCRseq)

city: Frederick

first: Yongmei

last: Zhao

address: Post Office Box B

department: Advanced Biomedical Computational Science

institute: Frederick National Labroatory for Cancer Research

description: Library name: BIT5_S20

data_processing:
Reads were aligned to mouse TRA and TRB reference from imgt.202214-2.sv8 using miXCR v4.7.0 with default settings. Clone assembly and extraction were also done using miXCR v4.7.0 with default settings
Assembly: Mouse mm10
Supplementary files format and content: Text delimited text files containing the TRA and TRB clones
Library strategy: TCR-Seq

source_name: lymph nodes

extract_protocol:
10⁶ CD8⁺ T cells were sorted from lymph nodes and spleens of WT, β5i-KO, β5t-KO and BIT mice (9–12 weeks old, male, n = 4–5 individual mice per group, >98% purity.Total RNA was prepared from sorted cells with the RNeasy Kit (Qiagen). The quality of RNA was assessed by Bioanalyzer (Agilent).
The library was made by using the SMARTer® Mouse TCR a/b Profiling Kit (Takara)

value: lymph nodes

value: TCRbeta highCD4-CD8+ T cells


title: miRNA_AC16 cells, cell-S-Con2


title: BIT#4(TCRseq)

description: Library name: BIT4_S16


title: miRNA_AC16 cells, cell-S-Con1


title: p53null SOFT mammary tumors Sample 22

description:
Library name: Sample_22
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

value: collagen 1/ basement membrane (Col1/BM) hydrogels (SOFT group)


title: BIT#3(TCRseq)

description: Library name: BIT3_S12


title: AC16 exosomes,exo-L-Ang3

data_processing:
Raw data were processed through Seqtk.
The clean reads were aligned to the reference genome (GRCh38.104) using HISAT2.
The Read Counts of transcripts and ncRNAs were calculated by Stringtie（version:2.1.4）
In cells, the expression of mRNA and lncRNA was normalized to FPKM. CIRI2 was utilized for circRNA identification identification and quantification. In exosomes, the expression of mRNA and lncRNA was normalized to TPM (transcripts per kilobase million). CIRI2 was utilized for circRNA identification and quantification.
The identified circRNA was annotated using circBase. The expression of circRNA was normalized to SPRBM.
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text file includes row counts for each Sample

extract_protocol:
Total RNA was extracted using miRNeasy Micro Kit (Cat #217084, Qiagen), and RNA quality was checked using Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US) according to standard procedures.The exosomes were isolated and total RNA was extracted using exoRNeasy Maxi Kit (#77164, Qiagen), and RNA quality was checked using Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US) according to standard procedures
Sequencing libraries were constructed by VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Cat #NR604, Vazyme) according to manufacturer's instructions. In exosomes, sequencing libraries were constructed by SMARTer Stranded Total RNA-Seq Kit for Illumina (Cat#634414, Takara) according to manufacturer's instructions.


title: p53null SOFT mammary tumors Sample 21

description:
Library name: Sample_21
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: p53null SOFT mammary tumors Sample 20

description:
Library name: Sample_20
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: fetal liver, E14.5, BulkRNA-seq, RORgtmid_gtpos_Runx3pos_2

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

description:
SMART-Seq HT PLUS
mid_2

data_processing:
Raw RNA-seq reads were trimmed and filtered for quality control using fastp. The clean reads were mapped to the GRCm39 reference genome using HISAT2 and then read counts for each sample were obtained using featureCounts.
Assembly: GRCm39
Supplementary files format and content: normalized_counts txt files

source_name: fetal liver

growth_protocol: RPMI supplemented with 10%FBS, IL-7(20ng/ml), SCF(20ng/ml), MEN-NEAA and sodium pyruvate with 5%CO2 at 37℃.

extract_protocol:
Runx3-negative CLPs fractions and RORγt-mid fractions were each cultured on TSt4/DLL4 for 10-12 days. After collection by pipetting, the RORγt-positive cells with or without Runx3 expression were re-sorted respectively.
Bulk RNA-seq was performed on 50-200 sorted cells using the SMART-Seq HT PLUS Kit following the manufacturer's instructions (Takara Bio).

value: fetal liver

value: CD45+ CD3- CD19- RORgt+ Runx3+

tag: strain

value: Runx3-tdTomato; RORgt-EGFP

value: embryonic day 14.5


title: fetal liver, E14.5, BulkRNA-seq, CD127negRunx3posRORgtneg_gtposRunx3pos_1

description:
SMART-Seq HT PLUS
mid_5


title: p53null STIFF mammary tumors Sample 27

description:
Library name: Sample_27
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: AC16 exosomes,exo-L-Ang1

value: exosome


title: fetal fetus, E14.5, BulkRNA-seq, RORgt_LTi_5

description:
SMART-Seq HT PLUS
WT.LTi_8

source_name: fetal fetus

extract_protocol:
E14.5 fetal livers were separated under a microscope, and single-cell suspension was generated by pipetting with a 1000-micropipette. The cell suspension  was then filtered through a 100 μm strainer and resuspended in FACS buffer (2% FBS/0.05% NaN3/1% PBS).
Bulk RNA-seq was performed on 50-200 sorted cells using the SMART-Seq HT PLUS Kit following the manufacturer's instructions (Takara Bio).

value: fetal fetus

value: Lin-c-kit+GFPhigh

value: RORgt-EGFP


title: p53null SOFT mammary tumors Sample 19

description:
Library name: Sample_19
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

value: mammary tumor/end-point

value: Mammary Breast Tumor

value: Balb/c mammary p53null


title: BIT#2(TCRseq)

description: Library name: BIT2_S8


title: AC16 exosomes,exo-L-Ang2


title: BIT#1(TCRseq)

description: Library name: BIT1_S4


title: β5t-KO#5(TCRseq)

description: Library name: b5tKO5_S19


title: p53null SOFT mammary tumors Sample 18

description:
Library name: Sample_18
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: AC16 exosomes,exo-L-Con3


title: fetal liver, E14.5, BulkRNA-seq, RORgt_high_CD127neg_MHC2pos_2

description:
SMART-Seq HT PLUS
ChiLP.6_3


title: p53null SOFT mammary tumors Sample 16

description:
Library name: Sample_16
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: p53null SOFT mammary tumors Sample 17

description:
Library name: Sample_17
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: AC16 exosomes,exo-L-Con2


title: β5t-KO#4(TCRseq)

description: Library name: b5tKO4_S15


title: fetal liver, E14.5, BulkRNA-seq, RORgt_high_CD127pos_MHC2pos_2

description:
SMART-Seq HT PLUS
ChiLP.5_3


title: fetal liver, E14.5, BulkRNA-seq, RORgt_high_CD127neg_MHC2pos_1

description:
SMART-Seq HT PLUS
ChiLP.6_2


title: fetal fetus, E14.5, BulkRNA-seq, RORgt_LTi_4

description:
SMART-Seq HT PLUS
WT.LTi_7


title: AC16 cells, cell-L-Ang3

value: whole cells


title: β5t-KO#2(TCRseq)

description: Library name: b5tKO2_S7


title: p53null SOFT mammary tumors Sample 14

description:
Library name: Sample_14
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: AC16 exosomes,exo-L-Con1


title: β5t-KO#3(TCRseq)

description: Library name: b5tKO3_S11


title: AC16 cells, cell-L-Ang2


title: fetal liver, E14.5, BulkRNA-seq, RORgt_high_CD127pos_MHC2pos_1

description:
SMART-Seq HT PLUS
ChiLP.5_1


title: β5t-KO#1(TCRseq)

description: Library name: b5tKO1_S3


title: fetal liver, E14.5, BulkRNA-seq, RORgt_high_CD127pos_MHC2neg_2

description:
SMART-Seq HT PLUS
ChiLP.4_3


title: β5i-KO#5(TCRseq)

description: Library name: b5iKO5_S18


title: p53null SOFT mammary tumors Sample 15

description:
Library name: Sample_15
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: AC16 cells, cell-L-Ang1


title: p53null SOFT mammary tumors Sample 11

description:
Library name: Sample_11
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: AC16 cells, cell-L-Con2


title: β5i-KO#4(TCRseq)

description: Library name: b5iKO4_S14


title: p53null SOFT mammary tumors Sample 10

description:
Library name: Sample_10
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: 2 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150hi Sca1lo, CITE-seq, rep2

city: Chengdu

first: Yujun

last: Deng

address: No. 17, Section 3, Renmin South Road, Chengdu

institute: Sichuan University

description:
10x Genomics
Ab2-SL

library_source: other

data_processing:
Sequencing data from 10x Genomics were mapped against the mm10 genome and quantified using the CellRanger software with default settings to generate raw gene expression matrix.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: protein

source_name: Bone marrow

extract_protocol:
C57BL/6J mice were sacrificed by cervical dislocation, and bone marrow cells were isolated from the tibia, femur and pelvis. Then, RBC lysis buffer (Biosharp) was used to remove erythrocytes. For progenitor analysis, Lin− bone marrow progenitors were enriched by magnetic beads using biotinylated rat anti-mouse antibodies against CD3, CD11b, Gr-1, CD45R/B220, and Ter119, followed by negative selection with anti-rat microbeads (Miltenyi Biotec). Enriched Lin− cells were then stained with antibodies against CD34, CD135, CD127, Sca1, CD117, CD48, and CD150 to label hematopoietic progenitors and streptavidin-PE-Cy7 to label Lin+ cells.
For 10x scRNA-seq, CD150hi SCA1hi, CD150hi SCA1lo, and CD150lo LT-HSC from mice of different ages were sorted by using FACS AriaTM III sorter. After centrifugation, cells were resuspended in DPBS + 0.04% BSA for library preparation using the Chromium™ Single Cell 3’ reagents. And scRNA-seq datasets were produced following the manufacturer’s instructions. Suspended cells were loaded on a Chromium Controller (10X Genomics) to generate Gel beads in EMulsion (GEMs). Immediately following GEMs generation, the Gel Bead is dissolved, primers are released, and any co-partitioned cell is lysed. Mixed the cell lysate with a Master Mix containing reverse transcription reagents and incubated the GEMs to produce barcoded full-length cDNA from polyadenylated mRNA. Then cDNA was amplified to generate sufficient mass for library construction, and sequencing was performed on an Illumina Hi-Seq X Ten with pair end 150bp (PE150).
For CITE-seq, the cells consistent with the above were stained with the surface proteins TotalSeq-B antibodies CD201, CD9, and CD63 (Biolegend), to enable protein detection in addition to Single Cell 3’ v3 and Single Cell V(D)J Feature Barcoding technology from 10x Genomics. Single-cell RNA-seq libraries were prepared following the manufacture’s introduction as described briefly above, and sequencing was performed on an Illumina with pair end 150bp (PE150).

value: Bone marrow

value: LT-HSC

tag: sorted cells

value: 2 months-old

tag: library type

value: ADT


title: β5i-KO#2(TCRseq)

description: Library name: b5iKO2_S6

value: lymph nodes

value: TCRbeta highCD4-CD8+ T cells


title: p53null SOFT mammary tumors Sample 12

description:
Library name: Sample_12
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

value: collagen 1/ basement membrane (Col1/BM) hydrogels (SOFT group)


title: fetal liver, E14.5, scRNA-seq, RORgt_LTi

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
E14.5 fetal livers were separated under a microscope, and single-cell suspension was generated by pipetting with a 1000-micropipette. The cell suspension was then filtered through a 100 μm strainer and resuspended in FACS buffer (2% FBS/0.05% NaN3/1% PBS).
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics) with slight modification.  Cells up to 10,000 were directly sorted into the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).

value: fetal liver


title: AC16 cells, cell-L-Con1


title: p53null SOFT mammary tumors Sample 9

description:
Library name: Sample_9
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: p53null SOFT mammary tumors Sample 8

description:
Library name: Sample_8
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: 2 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150hi Sca1hi, CITE-seq, rep2

description:
10x Genomics
Ab2-SH


title: 2 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150hi Sca1lo, CITE-seq, rep1

description:
10x Genomics
Ab-SL


title: Human iPSC-derived FACS-sorted PAX7 cells from Chal et al. muscle culture protocol

description:
6-13-22_pool_D8_SI-TT-C3
GRCh38-2020-A

source_name: Differenciated hiPSCs

value: Differenciated hiPSCs

value: Chal et al.


title: p53null SOFT mammary tumors Sample 6

description:
Library name: Sample_6
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: Human iPSC-derived INFRA cells from New muscle culture protocol

description:
yannis_may25_pool_INFRA_V_1_5_GTAACATGCG
GRCh38-2020-A

value: New


title: WT#4(TCRseq)

description: Library name: WT4_S13


title: 2 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150hi Sca1hi, CITE-seq, rep1

description:
10x Genomics
Ab-SH


title: β5i-KO#3(TCRseq)

description: Library name: b5iKO3_S10


title: WT#3(TCRseq)

description: Library name: WT3_S9


title: Human iPSC-derived cells from Chal et al. muscle culture protocol at day 30

description:
6-13-22_pool_P30_SI-TT-C1
GRCh38-2020-A


title: p53null SOFT mammary tumors Sample 13

description:
Library name: Sample_13
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: p53null SOFT mammary tumors Sample 5

description:
Library name: Sample_5
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: WT#2(TCRseq)

description: Library name: WT2_S5


title: p53null SOFT mammary tumors Sample 4

description:
Library name: Sample_4
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: WT#1 (TCRseq)

description: Library name: WT1_S1


title: 28 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150lo, scRNAseq

description:
10x Genomics
CL28

value: 28 months-old

value: GEX


title: Human iPSC-derived cells from New muscle culture protocol at day 30

description:
yannis_june26_pool_PV15_TTATTCGAGG
GRCh38-2020-A


title: fetal liver, E14.5, BulkRNA-seq, RORgt_high_CD127pos_MHC2neg_1

description:
SMART-Seq HT PLUS
ChiLP.4_2

value: RORgt-EGFP

value: embryonic day 14.5


title: AC16 cells, cell-L-Con3


title: p53null SOFT mammary tumors Sample 1

description:
Library name: Sample_1
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

value: mammary tumor/end-point

value: Mammary Breast Tumor

value: Balb/c mammary p53null


title: MecomWT:R751W, bio rep 1

city: Tokyo

first: Mayuko

last: Nakanishi

address: 4-6-1 Shirokanedai, Minato-ku

institute: The University of Tokyo

description:
Library name: Sample 4
hKI1

data_processing:
The fastq file was imported into R (https://www.r-project.org) for analysis and mapped to the mouse reference genome (mm10). Reads were then counted using Feature Count, and the resulting data were normalized by the TPM method. Differentially expressed genes were identified using DESeq2 in R.
Assembly: mm10
Supplementary files format and content: csv file include TPM for each Sample

source_name: mouse bone marrow

extract_protocol:
the SLAM-LSK (CD150+, CD48-, lineage-, Sca1+, cKit+) population was sorted directly into TRIZOL-LS using FACS Aria III (BD Biosciences, San Jose, CA, USA).
500 ng total RNA is used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420)Poly-A purification: Poly-T column kit (NEB, E7490), followed by NEB kit (E7420)Low-input: For RNA less than 50ng, rRNA-depletion and library synthesis by Takara SMARTer kit (usually input RNA amount is not defined due to low RNA concentration)

value: mouse bone marrow


title: p53null SOFT mammary tumors Sample 3

description:
Library name: Sample_3
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).


title: MSC1-wogonin [C-1]

city: guangzhou

first: Wu

middle: Meng

last: ye

state: Guangdong

address: Guangzhou Yuexiu

department: The Biotherapy Center,

institute: the Third Affiliated Hospital, Sun Yat-Sen University

data_processing:
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9)
We aligned reads of all samples to the < research species > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: umbilical cord

growth_protocol: mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and  and 2 ng/mL basic fibroblast growth factor in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT)(Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmentedninto short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module(NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H(NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: mesenchymal cells were treated with wogonin for 24h

value: umbilical cord

value: mesenchymal stem cells

value: 25uM wogonin 24h


title: 8 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150hi Sca1hi, scRNAseq

description:
10x Genomics
SH8

value: Bone marrow

value: LT-HSC

value: 8 months-old


title: MecomWT:R751W, bio rep 3

description:
Library name: Sample 6
hKI3


title: WT, bio rep 3

description:
Library name: Sample 3
WT3

value: WT


title: 28 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150hi Sca1hi, scRNAseq

description:
10x Genomics
SH28


title: B6.Sst1S BMDMs Biological reolicate 2

description: Library name: SSR4-8

data_processing:
Image analysis and base calling were conducted by HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Raw sequencing reads were trimmed to remove adapter sequences and low-quality bases using Trimmomatic v0.36, and the filtered reads were aligned to the Mus musculus GRCm38 reference genome (ENSEMBL) using the splice-aware STAR aligner v2.5.2b, generating BAM files.
Gene hit counts were quantified using featureCounts from the Subread package v1.5.2, counting only uniquely mapped reads overlapping annotated exon regions, with strand specificity applied where appropriate.
Differential expression analysis was performed using the  DESeq2 package86. Genes with an adjusted p-value <0.05 and a log₂ fold change > 1 or <-1 were deemed differentially expressed between groups.
Assembly: GRCm38
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes TPM counts (transcript per million) for each sample

source_name: bone marrow derived macrophages

extract_protocol:
BMDMs were lysed in TRIzol (Thermo Fisher Scientific; 15596026), and RNA was extracted using Qiagen RNeasy Mini Kit (74104) and RNase-free DNase Set (Qiagen; 79254), following the manufacturer’s protocol. RNA purity and concentration was quantified using Nanodrop One (Thermo Fisher Scientific) and stored at -80 ºC.
Total RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. The next steps included performing rRNA depletion using QIAseq® FastSelect™−rRNA HMR kit (Qiagen, Germantown, MD, USA), which was conducted following the manufacturer’s protocol. RNA sequencing libraries were generated with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 minutes at 94°C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end-repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered on one lane of a flow cell. After clustering, the flow cell was loaded on the Illumina HiSeq 4000 instrument according to the manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration.

treatment_protocol: BMDMs were either left untreated or treated with 10 ng/ml of murine-TNFα (Peprotech; 315-01A) in  RPMI-Glutamax containing 10% heat-inactivated FBS and 10% (v/v) L929 fibroblast-conditioned medium, for 18 hours (overnight) at 37°C in 5% CO2. This followed by infection with Mtb H37Rv for 4 hours at MOI=10. After 4 hours, extracellular Mtb were removed by extensive washing with warm RPMI media and RPMI+ TNFα was added to the cells. RNA was isolated after 24 hours.

value: bone marrow derived macrophages

value: 10 ng/ml TNFα pretreatment (18 hours), followed by Mtb H37Rv (MOI=10; 24 hours) infection in the continued presence of TNFα


title: β5i-KO#1(TCRseq)

description: Library name: b5iKO1_S2

value: lymph nodes

value: TCRbeta highCD4-CD8+ T cells


title: p53null SOFT mammary tumors Sample 7

description:
Library name: Sample_7
Fastq.gz raw file and .tsv file from kallisto quant, including counts (est-counts) and transcripts per million (tpm).

value: collagen 1/ basement membrane (Col1/BM) hydrogels (SOFT group)


title: 2 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150lo, CITE-seq, rep2

description:
10x Genomics
Ab2-CL

value: 2 months-old

value: ADT


title: B6.Sst1S BMDMs Biological reolicate 1

description: Library name: SSR4-7


title: 2 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150hi Sca1lo, scRNAseq

description:
10x Genomics
SL2

value: GEX


title: biol rep 1, A7d, MDCKII cells, 7 d old cells

description: Library name: EKRN190001850-1A

data_processing:
Quantified libraries were pooled and sequenced on the Illumina platform using paired-end 150 bp reads (Illumina Sequencing PE150 Illumina), generating approximately 6 Gb of raw data per sample. Base calling was done using Illumina software (CASAVA base calling), generating raw FASTQ files.
Sequencing reads were mapped to CanFam_3.1 (domestic dog, canis lupus familiaris). Gene-level counts were generated using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome.
For bioinformatics analysis, raw data were processed through Novogene’s in-house Perl scripts, and the data were quality checked with FastQC. Relative expression levels were normalized based on gene length and sequencing depth (fragments per kilobase of transcript per million mapped reads, FPKM).
Assembly: GCF_000002285.3 (CanFam3.1)
Supplementary files format and content: csv file "genes_readcount_Mantyla.csv" includes raw counts for each sample
Supplementary files format and content: csv file "genes_FPKM_Mantyla.csv" includes FPKM values for each sample

growth_protocol: Madine Darby canine kidney type II epithelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 5 % penicillin-streptomycin  in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: Cells were grown until full maturity (7 d), or grown for 7 d, detached and reseeded for 2 h

value: cell line

value: MDCKII

value: epithelial

value: Grown for 7 d


title: S2, 7minEdU 15minBrdU, HU treated, rep1

city: Nashville

first: Jared

last: Nordman

state: TN

address: 465 21st Ave S

department: Biological Sciences

institute: Vanderbilt University

description:
Library name: MinION_2_HU
ONT MinION sequencing performed on S2 cells treated with EdU and BrdU pulses with HU inhibition

data_processing:
Raw Oxford Nanopore sequencing data in POD5 format were processed using a custom DNAscent analysis pipeline. First, POD5 files were converted to FAST5 using the Oxford Nanopore pod5 utility. Basecalling was performed with Guppy v6.4.2 (dna_r10.4.1_e8.2_400bps_5khz_hac DNAscent indexing was used to generate searchable indices from the FAST5 files and sequencing summary data. Replication detection was performed with DNAscent (GPU-accelerated) using a minimum read length threshold of 15 kb. ForkSense analysis was conducted with all detection modes enabled, including forks, origins, terminations, analogues, and stress signatures, using EdU and BrdU as replication markers. Bedgraph files were generated using DNAscent utility scripts to visualize replication features across the genome.configuration, GPU-enabled). Reads were aligned to the Drosophila melanogaster dm6 reference genome using Minimap2 v2.24 with the map-ont preset, followed by conversion and indexing using Samtools v1.10.
Assembly: Drosophila dm6
Supplementary files format and content: BED files of EdU and BrdU labeled tracks identified as left forks, right forks, origins, or terminations

organism: Drosophila melanogaster

growth_protocol: S2 cell stocks were maintained in T225 Flasks with room temperature Schneider S2 Media supplemented with 10% fetal bovine serum (FBS), 100 U/mL Penicillin, and 100 µg/mL Streptomycin. Cells were passaged 1:5 dilution (1-part old media: 5-part final volume) when flasks reached 90-100% confluency (fully confluent). New stocks were thawed and maintained after 30 passages.

extract_protocol:
uHMW gDNA extraction and library preparation was conducted as a variation on New England Biolab’s adaption for their T3050L Kit for Oxford Nanopore Sequencing. EB+ was prepared by supplementing 1mL of Monarch Elution Buffer 2 with 2µL of 10% Triton X-100. 100 million previously labeled and frozen cells were resuspended to a concentration of 50 million cells per 100uL 1x PBS and divided into two 1.5mL Eppendorf for parallel extraction. The cells were lysed using 100µL Nuclei Prep Buffer and 50µL of 10mg/mL RNase A and mixed at room temperature for two minutes. Nuclei Lysis Solution was prepared using 200µL Nuclei Lysis Buffer and 80µL 1mg/mL Proteinase K. The nuclei were then lysed using 150µL Nuclei Lysis Solution. The sample was inverted to mix, incubated at 56oC and 300rpm for 10 minutes, then incubated at room temperature for 20 minutes. The sample was precipitated using 150µL of Precipitation Enhancer, two DNA Capture Beads, and 700µL of isopropanol and incubated on a vertical rotating mixer at six rpm for eight minutes. The samples were then washed twice with 500µL each of Wash Buffer before incubating in 200µL 1mg/mL Proteinase K for 16 hours at room temperature. The following morning, the precipitation step was repeated with 75µL Precipitation Enhancer and 350µL isopropanol and incubated on a vertical rotating mixer at six rpm for eight minutes. The samples were washed twice more with 500µL each Wash Buffer, the beads with naked DNA were transferred to a spin column and quickly tapped on an absorbent pad to remove excess buffer, then transferred to 385µL of EB+ buffer. The DNA was allowed to solubilize at room temperature for 16 hours. The sample was poured into a bead retainer seated in a 1.5mL LoBind Eppendorf tube and spun at 16,000xg for one minute. The sample was examined and if DNA strands were visible between the flow through and the beads, the sample was spun again. The sample was mixed gently with a wide-bore pipette until maximally solubilized, pipetted roughly 10-20 times, then stored in the fridge.
Sample libraries were prepared using Oxford Nanopore’s Ultra-Long Sequencing Kit (Cat# SQK-ULK114, Batch #ULK114.20.0003). Dilute fragmentation mix was prepared using 6µL Fragmentation Mix (FRA) and 244µL Fragmentation dilution buffer (FDB) before the dilute fragmentation mix was mixed with the sample via gently pipetting with a wide-bore pipette for two minutes at room temperature. The sample was then incubated for eight more minutes at room temperature followed by 10 minutes at 75oC, five minutes on ice, and finally five minutes at room temperature. 5µL of Rapid Adaptor (RA) was added and mixed thoroughly via wide-bore pipetting and the sample was incubated at room temperature for 30 minutes. Precipitation and sample clean-up was carried out by adding a precipitation star sample followed by 500µL Precipitation Buffer (PTB). The sample was precipitated on a vertical rotating mixer for 20 minutes at 6 rpm. The sample was then spun briefly, and the supernatant was removed. The sample was eluted in 300µL Elution Buffer (EB) overnight at room temperature before being stored at 4oC.

treatment_protocol: 24-hours prior to labeling, a fully confluent flask was passaged 1:2 or 1:3 to achieve 60-80% confluency at the time of labeling to ensure cells were actively replicating. The two flasks of cells resulting from this split were labeled at the same time and combined during a later step. The day of labeling, old media was removed and immediately replaced with 25 mL of new media supplemented with 10µM EdU. Cells were returned to the 25oC incubator for 3 or 7 minutes for labeling. After the appropriate time had passed, media was removed, and the cells were gently washed three times with 10mL of 1x Phosphate Buffer Saline (1x PBS). Cells were then incubated with 25mL of new media supplemented with 10µM BrdU. For HU treatment, 1mM was added to the BrdU media. Cells were returned to the 25 oC incubator for 6 or 15 minutes for labeling. After the appropriate time had passed, media was removed, and the cells were gently wash three times with 10mL of 1x Phosphate Buffer Saline (1x PBS). The cells were then incubated with 25mL of new media supplemented with 50µM thymidine. Cells were returned to the 25 oC incubator for 20 minutes before harvesting. Cells from pairs of flasks labeled at the same time were combined into a single 50mL conical and 200µL of cells were set aside on ice for later counting and labeling validation. The remaining cells were pelleted at 600xg for 5 minutes and the old media was removed. The cells were then washed via resuspending in 10mL 1x PBS and subsequent pelleting at 600xg for 5 minutes. This wash step was repeated once. After washing, the cells were resuspended into 1mL 1x PBS, transferred to a 1.5mL Eppendorf tube, and pelleted at 600xg for 5 minutes.

value: Embryonic Cells

value: 7 minutes EdU followed by 15 minutes BrdU and HU

tag: batch


title: 2 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150hi Sca1hi, scRNAseq

description:
10x Genomics
SH2

value: Bone marrow

value: LT-HSC


title: B6 BMDMs Biological replicate 3

description: Library name: SSR4-3

value: WT C57BL/6J


title: MSC2-wogonin [C-2]

value: umbilical cord

value: mesenchymal stem cells

value: 25uM wogonin 24h


title: 28 months-old, Bone marrow, Lin- CD127-CD135-Sca1+CD117+CD150+CD48-CD34-CD150hi Sca1lo, scRNAseq

description:
10x Genomics
SL28

value: 28 months-old