title: 6402_V2+1 (tempus)

description: Library name: 6402_V2+1


title: 6451_V1+1 (tempus)

status: Public on Aug 29 2025

type: SRA

city: Oxford

first: Lucy

last: Garner

address: Experimental Medicine, Level 5, John Radcliffe Hospital

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: 6451_V1+1

library_source: transcriptomic

data_processing:
BCL files were converted to FASTQ files using Illumina bcl2fastq. FASTQ files were processed to a gene count matrix using a custom CGAT-Core (v0.6.15) pipeline. Briefly, sequencing quality was assessed using FASTQC (Babraham Bioinformatics; v0.12.1), then FASTQ files trimmed to remove low quality bases and adapter sequences using Trimmomatic (v0.39). Reads were aligned to the GRCh38 human genome using STAR (v2.7.10b) and reads mapping to each gene quantified using featureCounts (v2.0.6).
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt (tab-delimited file containing raw counts for each sample)

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Whole blood RNA was extracted from Tempus tubes in batches of 12-24 samples, with a mixture of vaccination groups and timepoints, using the Tempus Spin RNA Isolation Kit (Thermo Fisher Scientific). Samples were thawed, diluted in a 50 ml conical with 1× PBS, vortexed for 30 s, then centrifuged (3000 × g, 30 min, 4°C) to pellet RNA. Supernatants were removed and RNA pellets resuspended in RNA Purification Resuspension Solution, then transferred to purification filters for microcentrifuge RNA elution. RNA quantity and integrity was assessed using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and Agilent TapeStation and submitted to the Oxford Genomics Centre (Centre for Human Genetics, University of Oxford) for library generation and sequencing (Illumina NovaSeq 6000, 150 base pair paired-end reads).
NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, #E7760) with Globin & rRNA Depletion (New England Biolabs, #E7750).

tag: tissue

value: Blood

tag: donor

tag: timepoint

tag: vaccine

tag: prior infection

value: FALSE

tag: regimen

value: Short

tag: library preparation_batch


title: 18-078

city: Tokyo

first: Harutaka

last: Katano

address: 1-23-1 Toyama, Shinjuku

department: Department of Pathology

country: Japan

institute: National Institute of Infectious Diseases

description: Case MTB2_18-078

data_processing:
Libraries were subjected to pair-end sequencing (300 cycles) on a Nextseq 1000 platform (Illumina, San Diego, CA).
Quality filtering, adapter trimming, and RNAseq analyzing was performed using CLC genomics workbench (version 23, Qiagen, Hilden, Germany).
Homo sapience refseq GRCh38.p13 was used as a reference genome of RNA sequences.
Assembly: Minimap2, CLC genomics workbench
Supplementary files format and content: ExpressonRNAseq.csv file including raw counts for each sample

source_name: Lung

extract_protocol:
Quick-DNA/RNA FFPE Miniprep Kit (Zymo Research).
Barcoded RNA-seq library was established with NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA) according to the manufacturer’s instructions.

value: Lung

tag: cell type

value: FFPE


title: 6402_V1+1 (tempus)

description: Library name: 6402_V1+1


title: 6451_V2 (tempus)

description: Library name: 6451_V2


title: 18-077

description: Case NTM4_18-077


title: 6451_V2+1 (tempus)

description: Library name: 6451_V2+1


title: 6402_V2 (tempus)

description: Library name: 6402_V2


title: 18-080

description: Case NTM2_18-080


title: 18-079

description: Case MTB3_18-079


title: 6402_V1 (tempus)

description: Library name: 6402_V1


title: 6527_V1+2 (tempus)

description: Library name: 6527_V1+2


title: 18-076

description: Case NTM1_18-076


title: 6400_V2+1 (tempus)

description: Library name: 6400_V2+1

value: Long


title: 18-075

description: Case NTM9_18-075


title: 18-074-16

description: Case NTM8_18-074-16


title: 6400_V2 (tempus)

description: Library name: 6400_V2


title: 6506_V1+1 (tempus)

description: Library name: 6506_V1+1


title: 18-074-4

description: Case NTM7_18-074-4


title: 6400_V1+1 (tempus)

description: Library name: 6400_V1+1


title: 6400_V1 (tempus)

description: Library name: 6400_V1


title: 18-073-7

description: Case NTM5_18-073-7


title: 18-073-14

description: Case NTM6_18-073-14


title: 6398_V2+1 (tempus)

description: Library name: 6398_V2+1


title: 18-072-9

description: Case MTB1_18-072-9


title: 6398_V2 (tempus)

description: Library name: 6398_V2


title: 6398_V1+1 (tempus)

description: Library name: 6398_V1+1


title: 18-071-15

description: Case MTB5_18-071-15


title: 6398_V1 (tempus)

description: Library name: 6398_V1


title: 18-070

description: Case MTB4_18-070


title: 6397_V2+1 (tempus)

description: Library name: 6397_V2+1


title: 6397_V2 (tempus)

description: Library name: 6397_V2


title: 6396_V2 (tempus)

description: Library name: 6396_V2


title: 6396_V2+1 (tempus)

description: Library name: 6396_V2+1


title: 6395_V2 (tempus)

description: Library name: 6395_V2

value: TRUE


title: IL10R treated B16, mRNA

city: New York

first: Yacine

last: Marouf

state: NY

address: 413 E 69th St

department: MCC

country: USA

institute: Weill Cornell Medecine

description: Library name: Sample_IL10R

library_source: transcriptomic single cell

data_processing:
Cellranger v3.1.0
Assembly: GRCm38-2020-A
Supplementary files format and content: csv and mtx files

molecule: polyA RNA

organism: Mus musculus

source_name: Tumor

growth_protocol: Intradermal tumor implantation

extract_protocol:
mice were treated as indicated and twelve hours after treatment mice were euthanized and tumors were harvested. Samples were then passed through a 100 μm filter and resuspended in 3 ml of 40% Percoll (Fisher Scientific). Samples were then centrifuged at 1500 rpm for 5 minutes. To remove red blood cells, Samples were resuspended in ACK Lysing Buffer (Thermo Fisher) on ice. Cells were then resuspended in FACS Buffer at 1-2 x 106 cells per 100 μL. All wells were treated with DAPI viability dye, washed and then incubated with Fc block. Cells were subsequently pooled according to treatment group. Samples were then sequenced and analyzed.
The single-cell RNA-Seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X Genomics) following the user guide manual for 3′ v3. FACS-sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA. The viability of cells was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by polymerase chain reaction (PCR) amplification per manual instruction. Between 5,000 to 20,000 cells were targeted for each sample. Samples were multiplexed together on one lane of 10X Chromium. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

treatment_protocol: Intratumoral injection of isotype control, anti-IL-10R alone, anti-CD40/Monophosphoryl Lipid A (CM), or a combination of anti-CD40/MPL/anti-IL-10R (CMI)

value: Tumor

tag: cell line

tag: treatment


title: ISO treated B16, mRNA

description: Library name: Sample_ISO

value: ISO


title: 12-week SN Grin2b WT Sample 5

city: Cambridge

first: Morgan

last: Sheng

state: MA

address: 75 Ames St

institute: Broad Institute of MIT and Harvard

description: Library name: grin2b_12w_SN_WT_5

data_processing:
Reads were aligned to mm10 and gene and isoform level expression leves were estimated using Salmon (version 1.7.0, with arguments -l A --posBias --seqBias --gcBias --validateMapping)
Assembly: mm10
Supplementary files format and content: CSV file contains Salmon's counts estimation for all genes and all samples

source_name: Substantia Nigra

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Grin2a and Dagla mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.

value: Substantia Nigra

tag: genotype

value: WT

tag: age


title: CMI treated B16, mRNA

description: Library name: Sample_CMI

value: CMI


title: 6396_V1 (tempus)

description: Library name: 6396_V1


title: 6395_V2+1 (tempus)

description: Library name: 6395_V2+1


title: SCI

city: Xi'an

first: Beibei

last: Yu

state: Shannxi

address: No. 157, Xiwu Road, Xincheng District, Xi'an City, Shaanxi Province

country: China

institute: Xijing hospital

description: Library name: SCI

data_processing:
CeleScope
Assembly: mm10
Supplementary files format and content: Rdata

source_name: Spinal cord

extract_protocol:
Single-cell suspensions were prepared from spinal cord injury sites at 7 dpi. Briefly, mice were anesthetized and perfused with ice-cold PBS. Spinal cord segments encompassing approximately 1 mm  of tissue centered on the injury epicenter were carefully dissected under a stereomicroscope. The tissue  samples were immediately transferred to ice-cold Hibernate-E medium (Thermo Fisher Scientific) supplemented with B27 and GlutaMAX to maintain cell viability during processing. For single-cell dissociation, the collected spinal cord segments were enzymatically digested using the Neural Tissue Dissociation Kit (Miltenyi Biotec) according to the manufacturer's protocol.
The Matrix NEO™ Automated Single-Cell Library Construction System, which streamlines the process of single-cell RNA sequencing (scRNA-seq). This system utilizes NEO-CHIP microfluidic chips based on the Poisson distribution principle, allowing cells to naturally settle into micro-wells, ensuring that each well contains a single cell and thereby reducing doublet rates. The Matrix NEO™ system automates critical steps in the scRNA-seq workflow, including chip priming, single-cell partitioning, cell lysis, and mRNA capture, all initiated with a single click. This automation enhances experimental efficiency and reproducibility by minimizing manual intervention. By integrating the Matrix NEO™ system into your scRNA-seq workflow, you can achieve efficient and reproducible single-cell library construction, suitable for various applications including whole transcriptome profiling, immune repertoire profiling, and targeted gene expression analysis.

value: Spinal cord

value: Global cells

value: Injury


title: 6396_V1+1 (tempus)

description: Library name: 6396_V1+1


title: Eupatilin

description: Library name: Eupatilin

value: Eupatilin treatment for injury mice


title: 12-week SN Grin2b WT Sample 4

description: Library name: grin2b_12w_SN_WT_4


title: 12-week SN Grin2b WT Sample 3

description: Library name: grin2b_12w_SN_WT_3


title: 18-072-11

description: Case MTB6_18-072-11


title: 6394_V2 (tempus)

description: Library name: 6394_V2


title: 6394_V2+1 (tempus)

description: Library name: 6394_V2+1


title: 6394_V1+1 (tempus)

description: Library name: 6394_V1+1


title: 12-week SN Grin2b WT Sample 2

description: Library name: grin2b_12w_SN_WT_2


title: 12-week SN Grin2b WT Sample 1

description: Library name: grin2b_12w_SN_WT_1


title: 6394_V1 (tempus)

description: Library name: 6394_V1


title: 12-week SN Grin2b +/- Sample 5

description: Library name: grin2b_12w_SN_HT_5

value: Grin2b +/-


title: 6393_V2+1 (tempus)

description: Library name: 6393_V2+1

value: Blood


title: 6393_V2 (tempus)

description: Library name: 6393_V2

value: FALSE


title: 12-week SN Grin2b +/- Sample 4

description: Library name: grin2b_12w_SN_HT_4


title: CM treated B16, mRNA

description: Library name: Sample_CM

value: CM


title: 12-week SN Grin2b +/- Sample 3

description: Library name: grin2b_12w_SN_HT_3


title: 6393_V1 (tempus)

description: Library name: 6393_V1


title: 12-week SN Grin2b +/- Sample 2

description: Library name: grin2b_12w_SN_HT_2


title: 12-week SN Grin2b +/- Sample 1

description: Library name: grin2b_12w_SN_HT_1


title: 6392_V2 (tempus)

description: Library name: 6392_V2


title: 6392_V1+1 (tempus)

description: Library name: 6392_V1+1


title: 4-week SN Grin2b +/- Sample 4

description: Library name: grin2b_4w_SN_HT_4


title: 4-week SN Grin2b WT Sample 2

description: Library name: grin2b_4w_SN_WT_2


title: 4-week SN Grin2b WT Sample 4

description: Library name: grin2b_4w_SN_WT_4


title: 4-week SN Grin2b WT Sample 5

description: Library name: grin2b_4w_SN_WT_5


title: 4-week SN Grin2b WT Sample 1

description: Library name: grin2b_4w_SN_WT_1


title: HSC – young confined 5um 2

city: Hospitalet de Llobregat

first: Maria Carolina

last: Florian

state: Barcelona

address: Gran Via de l’Hospitalet, 199

department: Regenerative Medicine

country: Spain

institute: Bellvitge Biomedical Research Institute (IDIBELL)

library_source: genomic

data_processing:
The ENCODE ATAC-seq pipeline v2.1.3 was used to process the FASTQ files, including adapter trimming, alignment to the reference genome, filtering and peak calling, and using the parameters "atac.pipeline_type" : "atac", "atac.align_only" : false, "atac.true_rep_only" : false, "atac.paired_end" : true, "atac.auto_detect_adapter" : true, "atac.multimapping" : 20, "atac.mapq_thresh" : 20.
Samtools v1.14 was used to index BAM files.
ATACseqQC v1.20.2, BSgenome v1.64.0, Bsgenome.Mmusculus.UCSC.mm10 v1.4.3 and TxDb.Mmusculus.UCSC.mm10.knownGene v3.10.0 in R v4.2.0 and Bioconductor v3.15.2 were used for quality control and Tn5 shifting.
A consensus set of peaks was defined by taking those peaks detected in at least 6 samples. This threshold was determined using Monte Carlo simulation. Briefly, a binary matrix was generated including all detected peaks as rows and all samples as columns, with 1 for presence of the peaks and 0 for absence. The binary matrix was randomized 1,000 times and the number of peaks detected in all possible minimum number of samples was calculated for each randomized matrix. The chosen minimum number of samples was the one where the mean number of consensus peaks in the simulated data was ≈6% of the number of consensus peaks in the empirical data (false positive rate, FPR). The final 42,632 consensus peaks were resized to have a width of 700 bp.
In R v4.2.0 and Bioconductor v3.15.2, the featureCounts function from Rsubread v2.10.5 was used to count the number of reads in consensus peaks with parameters largestOverlap = TRUE, countMultiMappingReads = TRUE, fraction = TRUE, isPairedEnd = TRUE, countReadPairs = TRUE, requireBothEndsMapped = TRUE, checkFragLength = TRUE, minFragLength = 0, maxFragLength = 2000.
Assembly: mm10
Supplementary files format and content: Read count matrix (consensus peaks as rows, samples as columns)
Supplementary files format and content: BED file for the coordinates of the consensus peaks

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: LT-HSC were incubated for 13-16h in HBSS 10%FBS 1%P/S at 37ºC 3%O2 and 5%CO2.

extract_protocol:
Lysis buffer contains 0.15% NP40, TD buffer and Transposase (from llumina Tagment DNA Enzyme and Buffer Small Kit, ref 20034197).
Nextera XT kit (Illumina) was used to generate the libraries following manufacturer instructions.

treatment_protocol: For young control LT-HSCs, ATAC protocol was done after 16h of incubation in culturing conditions. For young confined LT-HSCs, after 13h incubation at culturing conditions, cells were  seeded on fibronectin functionalized glass coverslips and incubated in HBSS 10%FBS 1%P/S at 37ºC 3%O2 and 5%CO2 for half an hour to let them attach. Then, confinement coverslip with pillars of 5µm was assembled on top of the cells and incubated at culturing conditions for 2h. After that, we recovered the cells from the glass using Gentle Dissociation Reagent (StemCell #100-0485). Then, both young control LT-HSCs and young confined LT-HSCs were subjected to the ATAC-seq protocol.

value: Bone marrow

tag: strain

value: Hemtopoietic stem cells

value: 10-16 weeks old

value: confined 5um

tag: experimental batch


title: 6391_V1 (tempus)

description: Library name: 6391_V1

value: Long


title: 4-week SN Grin2b +/- Sample 3

description: Library name: grin2b_4w_SN_HT_3


title: 6390_V2+1 (tempus)

description: Library name: 6390_V2+1

value: Short


title: 6391_V2+1 (tempus)

description: Library name: 6391_V2+1


title: 6389_V2+1 (tempus)

description: Library name: 6389_V2+1


title: 6391_V1+2 (tempus)

description: Library name: 6391_V1+2


title: 4-week SN Grin2b +/- Sample 2

description: Library name: grin2b_4w_SN_HT_2

value: Substantia Nigra


title: 6393_V1+1 (tempus)

description: Library name: 6393_V1+1


title: 6392_V1 (tempus)

description: Library name: 6392_V1


title: HSC – young control unconfined 2

value: control


title: 6389_V2 (tempus)

description: Library name: 6389_V2


title: 6390_V2 (tempus)

description: Library name: 6390_V2


title: 6392_V2+1 (tempus)

description: Library name: 6392_V2+1


title: 4-week SN Grin2b +/- Sample 1

description: Library name: grin2b_4w_SN_HT_1


title: HSC – young control unconfined 3


title: HSC – young confined 5um 1


title: 12-week SN Grin2a WT Sample 5

description: Library name: grin2a_12w_SN_WT_5

value: WT


title: HSC – young confined 5um 3


title: 4-week SN Grin2b WT Sample 3

description: Library name: grin2b_4w_SN_WT_3


title: HSC – young control unconfined 1


title: 4-week SN Grin2b +/- Sample 5

description: Library name: grin2b_4w_SN_HT_5


title: 6389_V1+1 (tempus)

description: Library name: 6389_V1+1


title: ATAC-Seq - HSC - aged + RhoA-inhibitor (Ri) 4

data_processing:
The ENCODE ATAC-seq pipeline v2.1.3 was used to process the FASTQ files, including adapter trimming, alignment to the reference genome, filtering and peak calling, and using the parameters "atac.pipeline_type" : "atac", "atac.align_only" : false, "atac.true_rep_only" : false, "atac.paired_end" : true, "atac.auto_detect_adapter" : true, "atac.multimapping" : 20, "atac.mapq_thresh" : 20.
Samtools v1.14 was used to index BAM files.
ATACseqQC v1.20.2, BSgenome v1.64.0, Bsgenome.Mmusculus.UCSC.mm10 v1.4.3 and TxDb.Mmusculus.UCSC.mm10.knownGene v3.10.0 in R v4.2.0 and Bioconductor v3.15.2 were used for quality control and Tn5 shifting.
A consensus set of peaks was defined by taking those peaks detected in at least 6 samples. This threshold was determined using Monte Carlo simulation. Briefly, a binary matrix was generated including all detected peaks as rows and all samples as columns, with 1 for presence of the peaks and 0 for absence. The binary matrix was randomized 1,000 times and the number of peaks detected in all possible minimum number of samples was calculated for each randomized matrix. The chosen minimum number of samples was the one where the mean number of consensus peaks in the simulated data was ≈10% of the number of consensus peaks in the empirical data (false positive rate, FPR). The final 57,289 consensus peaks were resized to have a width of 700 bp.
In R v4.2.0 and Bioconductor v3.15.2, the featureCounts function from Rsubread v2.10.5 was used to count the number of reads in consensus peaks with parameters largestOverlap = TRUE, countMultiMappingReads = TRUE, fraction = TRUE, isPairedEnd = TRUE, countReadPairs = TRUE, requireBothEndsMapped = TRUE, checkFragLength = TRUE, minFragLength = 0, maxFragLength = 2000.
Assembly: mm10
Supplementary files format and content: Read count matrix (consensus peaks as rows, samples as columns)
Supplementary files format and content: BED file for the coordinates of the consensus peaks

growth_protocol: LT-HSC were incubated for 16h in HBSS 10%FBS 1%P/S at 37ºC 3%O2 and 5%CO2.

extract_protocol:
Lysis buffer contains 0.15% NP40,TD buffer and Transposase (fromllumina Tagment DNA Enzyme and Buffer Small Kit, ref20034197).
Nextera XT kit (Illumina) was used to generate the libraries following manufacturer instructions.

treatment_protocol: Ri (RhoA inhibitor, Rhosin) was added to one of the aged cell samples to a concentration of 100µM for the 16h incubation commented above.

value: Hematopoietic stem cells

value: >80 weeks old

value: RhoA-inhibitor (Ri) treatment

tag: sequencing batch


title: 12-week SN Grin2a WT Sample 4

description: Library name: grin2a_12w_SN_WT_4


title: 6388_V2+1 (tempus)

description: Library name: 6388_V2+1

value: TRUE


title: ATAC-Seq - HSC - aged + RhoA-inhibitor (Ri) 3


title: ATAC-Seq - HSC - aged + RhoA-inhibitor (Ri) 2


title: ATAC-Seq - HSC - aged + RhoA-inhibitor (Ri) 1


title: 12-week SN Grin2a WT Sample 3

description: Library name: grin2a_12w_SN_WT_3


title: 6388_V1+1 (tempus)

description: Library name: 6388_V1+1


title: ATAC-Seq - HSC - aged control 3


title: 6387_V2+1 (tempus)

description: Library name: 6387_V2+1


title: 12-week SN Grin2a WT Sample 1

description: Library name: grin2a_12w_SN_WT_1


title: 6388_V1 (tempus)

description: Library name: 6388_V1


title: ATAC-Seq - HSC - aged control 4


title: 12-week SN Grin2a WT Sample 2

description: Library name: grin2a_12w_SN_WT_2


title: ATAC-Seq - HSC - aged control 2


title: ATAC-Seq - HSC - aged control 1


title: 12-week SN Grin2a -/- Sample 6

description: Library name: grin2a_12w_SN_KO_6

value: Grin2a -/-


title: ATAC-Seq - HSC - young control 1


title: 6387_V2 (tempus)

description: Library name: 6387_V2

value: Blood


title: ATAC-Seq - HSC - young control 2


title: RNA-Seq - HSC - aged + RhoA-inhibitor (Ri) 3

data_processing:
Adapters were removed from the FASTQ files using Cutadapt v1.18 with parameters -m 20 -O 6 -q 20.
Reads were mapped to the reference genome using STAR v2.7.0.
BAM files were sorted and indexed using Samtools v1.14.
In R v4.2.0 and Bioconductor v3.15.2, the featureCounts function from Rsubread v2.10.5 was used to count the number of reads in genes for each sample, using Ensembl GTF annotation for GRCm38 102 version, filtered for protein coding genes and with parameters GTF.featureType = "exon", GTF.attrType = "gene_name", useMetaFeatures = TRUE, isPairedEnd = TRUE, countReadPairs = TRUE, requireBothEndsMapped = TRUE, countMultiMappingReads = TRUE, fraction = TRUE.
Assembly: mm10 (Mus Musculus GRCm38, Ensembl 102 Nov 2020)
Supplementary files format and content: Read count matrix (genes as rows, samples as columns)

growth_protocol: LT-HSC young, aged and aged+Ri were incubated for 16h in HBSS 10%FBS 1%P/S at 37ºC 3%O2 and 5%CO2.

extract_protocol:
Manufacturer instructions fromSMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech, ref 634893).
Nextera XT kit (Illumina) was used to generate the libraries following manufacturer instructions starting with 150pmoles of cDNA.


title: ATAC-Seq - HSC - young control 3


title: 12-week SN Grin2a -/- Sample 4

description: Library name: grin2a_12w_SN_KO_4


title: RNA-Seq - HSC - aged + RhoA-inhibitor (Ri) 2


title: 12-week SN Grin2a -/- Sample 3

description: Library name: grin2a_12w_SN_KO_3


title: 6386_V2+2 (tempus)

description: Library name: 6386_V2+2

value: FALSE


title: RNA-Seq - HSC - aged + RhoA-inhibitor (Ri) 1


title: RNA-Seq - HSC - aged control 3


title: 12-week SN Grin2a -/- Sample 2

description: Library name: grin2a_12w_SN_KO_2


title: 6386_V2 (tempus)

description: Library name: 6386_V2


title: 12-week SN Grin2a -/- Sample 1

description: Library name: grin2a_12w_SN_KO_1


title: RNA-Seq - HSC - aged control 2


title: RNA-Seq - HSC - aged control 1


title: RNA-Seq - HSC - young control 2


title: GvHD patient 3

city: New Haven

first: Ian

last: Odell

state: CT

address: 330 Cedar St. LMP-5040

department: Dermatology

institute: Yale University

description: Library name: GvHD4

data_processing:
The 10x genomics Cell Ranger pipeline was used to align reads, perform clustering and gene expression analysis, and aggregate the samples with normalized read counts
Assembly: GRCh38/3.0.0
Supplementary files format and content: h5

source_name: skin

extract_protocol:
6 mm punch biopsy specimen was first incubated in RPMI 1640 medium (Gibco) containing 5% fetal bovine serum (5% FBS/RPMI) and 10 mg/ml Dispase II (Sigma D4693-1G) for 45 minutes at 37° C shaking at 200-250 rpm. The sample was then removed from the media and minced with sterile iris scissors, followed by digestion with Liberase TM (Sigma) 0.5 mg/ml and DNase I 30 Units/ml in 5% FBS/RPMI for 45 minutes at 37° C shaking at 200-250 rpm. The resulting single cell suspension was then filtered through a 70 mm nylon membrane and washed. Live cells were sorted on a FACSAria and their final concentration and viability quantified with Trypan blue on a hemacytomer. The cells were pelleted and suspended in phosphate buffered saline containing 0.04% bovine serum albumin between 500-1000 cells/ml. 3000-6000 cells with greater than 80% viability were submitted to the Yale DNA Sequencing facility for generation of single-cell cDNA libraries using the Chromium Single Cell Controller (10x Genomics).
per 10x Genomics protocol using Single Cell 3' v2. Each cDNA library was sequenced paired-end on 1 lane with 75 base-pair read length using the Illumina HiSeq 2500 System generating at least 75,000 reads per cell.

value: skin


title: GvHD patient 2

description: Library name: GvHD3


title: 6383_V2 (tempus)

description: Library name: 6383_V2


title: RNA-Seq - HSC - young control 3

value: Bone marrow


title: 6057_V1 (tempus)

description: Library name: 6057_V1


title: 12-week SN Grin2a +/- Sample 6

description: Library name: grin2a_12w_SN_HT_6

value: Grin2a +/-


title: RNA-Seq - HSC - young control 1

value: Hemtopoietic stem cells

value: 10-16 weeks old


title: 6383_V1+1 (tempus)

description: Library name: 6383_V1+1


title: HBV-HDV 63

city: Bethesda

first: Amanda

last: Henning

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

data_processing:
Illumina BaseSpace Sequencing Hub applications were used for data processing. Specifically, alignment and transcript quantification was performed using the RNA-Seq Alignment application (v2.0.2). This application utilizes the STAR aligner and Salmon for transcript quantification. These analyses were conducted using the default parameters.
Assembly: hg19
Supplementary files format and content: *.quant.sf is the transcript quantification output file from Salmon. There are plain-text, tab-separated files with a single header line.

extract_protocol:
B cells were isolated from frozen PBMC using the EasySep Human B cell Isolation kit (StemCell Tech), and RNA was isolated from B cells using the RNeasy Plus Micro kit (Qiagen).
Libraries were prepared using the TruSeq RNA Exome kit (Illumina) following manufacturer's protocol.

value: B cells

tag: diagnosis

value: HBV+HDV+


title: TGFb-LCC-TRL 1

first: Zhenghan

last: Wang

address: 417 East 68th St

department: CBG

institute: Memorial Sloan Kettering Cancer Centerr

description: Library name: Sample 1

data_processing:
An in-house method called SHARP (github.com/hisplan/sharp, version 0.2.1) subsequently assigned a cell as labeled by a particular Hashtag oligo, identifying the source of the cell as the TGF-β treatment condition barcoded with that oligo, or as a doublet or low-quality droplet for removal. Following SHARP, we used the Scanpy software  (version 1.6.0) in Python (version 3.8.5) to evaluate multiple complementary quality control (QC) metrics and further select high-quality single-cell droplets. 1)  To eliminate residual empty droplets, we filtered out cells with a library size (i.e., total number of UMIs) below the saddle point of the size distribution histogram, corresponding to approximately the 5th percentile value (i.e., 2638 counts). 2) To exclude apoptotic cells, we filtered out droplets with a high fraction of mitochondrial gene transcripts (mtRNA% ≥ 0.2), indicative of cellular stress. 3) To clean out any remaining lower-quality droplets, we used Scanpy’s pp.normalize_total function to normalize the count matrices by library size, performed principal component analysis (PCA), and ran PhenoGraph  (version 1.5.6, k = 30) to cluster the droplets. We examined the gene-gene expression covariance of each PhenoGraph cluster computed on its top 500 highly expressed genes and removed cells constituting the PhenoGraph clusters that did not exhibit apparent covariance structures. 4) After the above filtering steps, we ran DoubletDetection (version 2.5.2, github.com/dpeerlab/DoubletDetection) to infer and remove any potential droplets that may still contain more than one cell.
Assembly: hg38 reference human genome
Supplementary files format and content: A log-transformed, normalized count matrix in CSV format, including an additional column indicating the TGF-β treatment condition from which each individual cell (row) was collected

source_name: lung adenocarcinoma

growth_protocol: H2087-LCC cells were plate in 10cm dishes for each treatment condition and incubated overnight for attachment.

extract_protocol:
Single-cell suspensions from each treatment condition were harvested and incubated with anti-human Hashtag antibodies conjugated to unique DNA barcodes and 1:100 human TruStain FcX (Fc Receptor Blocking Solution) to prevent nonspecific binding. After three PBS washes, cells from different treatment conditions were pooled for single-cell droplet encapsulation and sequencing. In both samples, Hashtag TotalSeq-A0251 and A0252 were used together to label cells following TGF-β treatment at 0 h (control), while A0253, A0254, A0255, A0256, and A0257 were used for the 3 h, 1 d, 3 d, 5 d, and 7 d time points, respectively. The original treatment conditions of individual cells were then identified based on sequencing reads of the distinct Hashtag sequences.
FASTQ files of sequenced samples were processed using the SEQC pipeline  (version 0.2.1) with default parameters for the 10x single-cell 3' library and mapped to the hg38 reference human genome. The SEQC pipeline performed read alignment, multi-mapping read resolution, and cell barcode and UMI correction to generate a raw UMI-based (cell × gene) count matrix.

treatment_protocol: The medium was replaced with fresh MLM medium supplemented with 10pg/mL TGF-β for 0 h (control), 3 h, 1 d, 3 d, 5 d, and 7 d, with the medium changed every 2 days, before being harvested for scRNA-seq analysis.

value: lung adenocarcinoma


title: 6053_V2+1 (tempus)

description: Library name: 6053_V2+1


title: 12-week SN Grin2a +/- Sample 3

description: Library name: grin2a_12w_SN_HT_3

value: Substantia Nigra


title: 6383_V1 (tempus)

description: Library name: 6383_V1

value: Short


title: 6057_V1+1 (tempus)

description: Library name: 6057_V1+1

value: Long


title: 12-week SN Grin2a +/- Sample 4

description: Library name: grin2a_12w_SN_HT_4


title: 12-week SN Grin2a +/- Sample 2

description: Library name: grin2a_12w_SN_HT_2


title: TGFb-LCC-TRL 2

description: Library name: Sample 2


title: HBV-HDV 71


title: GvHD patient 1

description: Library name: GvHD1


title: 4-week SN Grin2a WT Sample 5

description: Library name: grin2a_4w_SN_WT_5

value: WT


title: 6383_V2+1 (tempus)

description: Library name: 6383_V2+1


title: 12-week SN Grin2a +/- Sample 1

description: Library name: grin2a_12w_SN_HT_1


title: HBV-HDV 61


title: HBV-HDV 66


title: 6053_V2 (tempus)

description: Library name: 6053_V2


title: hCD2.SII d9 YFP+CD45+ rep3

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description: Library name: S167

data_processing:
To pre-process FASTQ files, we used the nf-core RNA-seq pipeline version 3.14.0 with default parameters, except for UMI extraction: --with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*".
In brief, we mapped the paired-end reads to the human genome (Ensembl, release 109) using STAR 2.7.9a and performed downstream quantification with Salmon 1.10.1.
Assembly: mm10
Supplementary files format and content: count tables (.txt) and metadata tables (.txt)

growth_protocol: After transduction with lentivirus, MEFs were cultured in gelatin-coated plates in DMEM+10%FBS.

extract_protocol:
Total RNA from 5000 cells was extracted using the Qiagen RNeasy Kit following the manufacturer’s protocol. cDNA was transcribed with a RNA, SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara Bio), amplified by 13 to 14 cycles of PCR, and purified with AMPure XP beads (Beckman). cDNA was quantified using a High Sensitivity DNA kit on TapeStation 4200 (Agilent).
Library preparation was performed using a Nextera XT DNA library preparation kit (Illumina) according to the manufacturer’s protocol. Libraries were normalized with beads, pooled, and sequenced on an NovaSeq X Series 10B Reagent Kit (300 Cycle) (read length 150-8-8-150).

treatment_protocol: Cells were sorted by FACS.

value: mouse embryonic fibroblast

value: heterozygous hCD2(Cre/WT) Rosa26 (YFP/WT) mice with a C57BL/6 background

tag: transduction

value: Cells were transduced with Spib, Irf8, Ikzf2 (SII)

tag: time

value: Cells were collected 9 days after viral transduction

tag: sorted cells

value: live(DAPI-) and YFP+CD45+


title: HBV-HDV 58

tag: tissue

value: Blood


title: 4-week SN Grin2a WT Sample 4

description: Library name: grin2a_4w_SN_WT_4


title: 6053_V1+1 (tempus)

description: Library name: 6053_V1+1

tag: donor

tag: timepoint

tag: vaccine

value: FALSE


title: 6053_V1 (tempus)

description: Library name: 6053_V1

tag: prior infection

tag: library preparation_batch


title: HBV-HDV 56

tag: cell type


title: hCD2.SII d9 YFP+ rep4

description: Library name: S164

tag: cell line

value: live(DAPI-) and YFP+


title: hCD2.SII d9 YFP+CD45+ rep1

description: Library name: S165

tag: genotype


title: 6031_V2+1 (tempus)

description: Library name: 6031_V2+1

tag: regimen


title: HBV-HDV 53


title: 4-week SN Grin2a WT Sample 1

description: Library name: grin2a_4w_SN_WT_1

tag: age


title: HBV 60

value: HBV+


title: 6031_V1+1 (tempus)

description: Library name: 6031_V1+1


title: 6031_V1 (tempus)

description: Library name: 6031_V1


title: hCD2.SII d9 YFP+ rep1

description: Library name: S161


title: 6031_V2 (tempus)

description: Library name: 6031_V2


title: 4-week SN Grin2a -/- Sample 3

description: Library name: grin2a_4w_SN_KO_3

value: Grin2a -/-


title: HBV 75

value: B cells


title: hCD2.SII d9 YFP+ rep2

description: Library name: S162


title: 4-week SN Grin2a -/- Sample 4

description: Library name: grin2a_4w_SN_KO_4


title: 4-week SN Grin2a -/- Sample 5

description: Library name: grin2a_4w_SN_KO_5


title: hCD2.SII d9 CD45+ rep3

description: Library name: S160

value: live(DAPI-) and CD45+


title: 6029_V2+1 (tempus)

description: Library name: 6029_V2+1


title: HBV 59


title: hCD2.SII d9 YFP+CD45+ rep2

description: Library name: S166


title: 4-week SN Grin2a -/- Sample 2

description: Library name: grin2a_4w_SN_KO_2


title: BNHL-HBV-HDV 31

value: HBV/HDV-associated BNHL


title: 4-week SN Grin2a WT Sample 2

description: Library name: grin2a_4w_SN_WT_2

value: Substantia Nigra


title: 4-week SN Grin2a WT Sample 3

description: Library name: grin2a_4w_SN_WT_3


title: hCD2.SII d9 CD45+ rep2

description: Library name: S159


title: hCD2.SII d9 YFP+ rep3

description: Library name: S163


title: 6029_V2 (tempus)

description: Library name: 6029_V2


title: HBV 85


title: 4-week SN Grin2a -/- Sample 1

description: Library name: grin2a_4w_SN_KO_1


title: BNHL-HBV-HDV 8


title: 4-week SN Grin2a +/- Sample 5

description: Library name: grin2a_4w_SN_HT_5

value: Grin2a +/-


title: hCD2.SII d9 CD45+ rep1

description: Library name: S158


title: 6029_V1+1 (tempus)

description: Library name: 6029_V1+1


title: 4-week SN Grin2a +/- Sample 4

description: Library name: grin2a_4w_SN_HT_4


title: HD 72

value: Healthy Donor


title: hCD2.SII d6 YFP+CD45+ rep3

description: Library name: S157

value: Cells were collected 6 days after viral transduction


title: hCD2.SII d6 YFP+CD45+ rep1

description: Library name: S155

value: mouse embryonic fibroblast


title: hCD2.SII d6 YFP+ rep4

description: Library name: S154

value: heterozygous hCD2(Cre/WT) Rosa26 (YFP/WT) mice with a C57BL/6 background


title: 6017_V1+1 (tempus)

description: Library name: 6017_V1+1

value: Long


title: HD 67


title: 6017_V2+1 (tempus)

description: Library name: 6017_V2+1


title: HD 48


title: 4-week SN Grin2a +/- Sample 3

description: Library name: grin2a_4w_SN_HT_3


title: hCD2.SII d6 YFP+CD45+ rep2

description: Library name: S156

value: Cells were transduced with Spib, Irf8, Ikzf2 (SII)


title: 6017_V2 (tempus)

description: Library name: 6017_V2


title: HD 44


title: hCD2.SII d6 YFP+ rep3

description: Library name: S153


title: 4-week SN Grin2a +/- Sample 1

description: Library name: grin2a_4w_SN_HT_1


title: 4-week SN Grin2a +/- Sample 2

description: Library name: grin2a_4w_SN_HT_2


title: HD 19


title: BNHL-HBV-HDV 23


title: 6017_V1 (tempus)

description: Library name: 6017_V1


title: hCD2.SII d6 YFP+ rep2

description: Library name: S152


title: 6029_V1 (tempus)

description: Library name: 6029_V1


title: HD 2


title: 12-week TH Dagla WT Sample 5

description: Library name: dagla_12w_TH_WT_5

source_name: Thalamus

value: Thalamus

value: WT


title: 6007_V1+1 (tempus)

description: Library name: 6007_V1+1

value: Blood

value: TRUE


title: 12-week TH Dagla WT Sample 4

description: Library name: dagla_12w_TH_WT_4


title: hCD2.SII d6 YFP+ rep1

description: Library name: S151

value: live(DAPI-) and YFP+


title: BNHL 37

value: BNHL


title: 6007_V1 (tempus)

description: Library name: 6007_V1


title: hCD2.SII d6 CD45+ rep4

description: Library name: S150


title: 5995_V2 (tempus)

description: Library name: 5995_V2

value: FALSE


title: BNHL 32

value: B cells


title: 12-week TH Dagla WT Sample 3

description: Library name: dagla_12w_TH_WT_3


title: BNHL 20


title: BNHL 27


title: hCD2.SII d6 CD45+ rep1

description: Library name: S147

value: live(DAPI-) and CD45+


title: hCD2.SII d6 CD45+ rep3

description: Library name: S149


title: 5995_V2+1 (tempus)

description: Library name: 5995_V2+1


title: 5995_V1 (tempus)

description: Library name: 5995_V1


title: 12-week TH Dagla WT Sample 1

description: Library name: dagla_12w_TH_WT_1


title: 12-week TH Dagla -/- Sample 4

description: Library name: dagla_12w_TH_KO_4

value: Dagla -/-


title: 12-week TH Dagla -/- Sample 5

description: Library name: dagla_12w_TH_KO_5


title: hCD2.SII d3 YFP+CD45+ rep4

description: Library name: S146

value: Cells were collected 3 days after viral transduction

value: live(DAPI-) and YFP+CD45+


title: BNHL 10


title: 5952_V2+1 (tempus)

description: Library name: 5952_V2+1


title: BNHL 7


title: hCD2.SII d3 YFP+CD45+ rep3

description: Library name: S145


title: 12-week TH Dagla -/- Sample 3

description: Library name: dagla_12w_TH_KO_3


title: 5952_V2 (tempus)

description: Library name: 5952_V2


title: 12-week TH Dagla -/- Sample 2

description: Library name: dagla_12w_TH_KO_2


title: K562_SSRP1_dTAG_Micro-C_S4Rep3

city: Göttingen

first: Clemens

last: Mauksch

address: Am Faßberg 11

country: Germany

institute: Max-Planck-Institut für Multidisziplinäre Naturwissenschaften

description: Library name: Sample 12

data_processing:
Micro-C data were analyzed with the nfcore/hic pipeline (Nicolas Servant et al. 2023)
Assembly: hg38
Supplementary files format and content: pairs file, valid genomic interactions

growth_protocol: K562 SSRP1-dTAG cells27 were cultured in RPMI medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific) and 1×GlutaMax (Thermo Fisher Scientific). Cultures were maintained at 37°C with 5% CO₂, with cell densities between 1×10⁵ and 7×10⁵ cells/mL. Quarterly mycoplasma testing using the PlasmoTest kit (InvivoGen) confirmed that the cells were free of mycoplasma contamination.

extract_protocol:
30 M cells per replicate were divided into 6 reactions each and crosslinked in phosphate buffered saline (PBS, Thermo Fisher Scientific) supplemented with 3 nM disuccinimidyl glutarate (DSG, Thermo Fisher Scientific) and 1% formaldehyde (Thermo Fisher Scientific). The reactions were quenched with 0.375 M Tris-HCl pH 7.5 (Thermo Fisher Scientific). For the following steps, all reactions were consecutively performed in the same tube. To prepare the samples for digestion, they were lysed in buffer cMB#1 (50 mM NaCl, 10 mM Tris, 5 mM MgCl2, 1 mM CaCl2, 0.2% NP-40, 1×Protease Inhibitor Cocktail (PIC)) at 4°C. Subsequent digestion with 34 Kunitz U of Micrococcal nuclease (MNase, NEB, M0247) per 1 M cells was performed for 20 min at 37°C. 4 mM ethylene glycol-bis(2-aminoethylether)-N,N,N′,N′-tetraacetic acid (EGTA, Sigma-Aldrich, E3889) was added to quench the reaction. A 5% aliquot was assessed for digestion efficiency by de-crosslinking and extracting DNA using DNeasy blood and tissue kit (Qiagen). Samples with 80-90% mono-nucleosomal fragments were selected for further processing. For end-chewing, nuclei were subjected to 1×NEBuffer 2.1 (NEB), 2 mM adenosine 5'-triphosphate (ATP, Jena Bioscience), 5mM 1,4-dithiothreitol (DTT, Roche), and 0.1 U/μL T4 Polynucleotide Kinase (T4 PNK, NEB, M0201L) for 15 min at 37°C with mixing. 0.05 U/μL Klenow fragment (NEB, M0210L) was added and incubated for 15 min at 37°C with mixing. Fragment ends were labelled with biotin by adding 66 μM Biotin-14-dATP (Jena Bioscience), 66 μM Biotin-11-dCTP (Jena Bioscience), 66 μM ddGTP (Jena Bioscience), 66 μM ddTTP (Jena Bioscience), 1×T4 DNA ligase buffer (NEB), and 100 μg/mL bovine serum albumin (BSA, Sigma-Aldrich). The reaction was incubated for 45 min at 25°C with interval mixing and quenched with 30 mM ethylenediaminetetraacetic acid (EDTA, Sigma-Aldrich). For proximity ligation, biotinylated samples were incubated with 1×T4 DNA ligase buffer (NEB), 100 μg/mL BSA (Sigma-Aldrich), and 20 U/μL T4 DNA ligase (NEB, M0202L) for 2.5 h at 25°C. Subsequently, biotin-dNTPs from unligated ends were removed with 1×NEBuffer#1 (NEB) and 5 U/μL Exonuclease III (NEB, M0206L). The ligated product was de-crosslinked and purified using DNeasy blood and tissue kit (Qiagen, 69504). Di-nucleosomal fragments (~360 bp) were selected by a two-sided size selection using Mag-Bind TotalPure NGS beads (Omega Bio-tek).
After pulldown of biotinylated fragments with Dynabeads MyOne Streptavidin T1 beads (NEB), the samples were indexed "on-bead" using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645).

treatment_protocol: SSRP1 depletion was performed by adding 500 nM dTAG7 ligand in DMSO to the medium. Cells treated with DMSO only served as controls. Both treatments were performed at a 1:20,000 DMSO dilution for 4 h.

value: Leukemia cell line

value: K562 subclone SSRP1-dTAG (dTAG7 inducible degron)

tag: treatment

value: 4h dTAG7, Rep4


title: 5952_V1+1 (tempus)

description: Library name: 5952_V1+1


title: hCD2.SII d3 YFP+CD45+ rep2

description: Library name: S144

value: mouse embryonic fibroblast

value: heterozygous hCD2(Cre/WT) Rosa26 (YFP/WT) mice with a C57BL/6 background


title: 12-week TH Dagla WT Sample 2

description: Library name: dagla_12w_TH_WT_2

value: Thalamus


title: 12-week TH Dagla -/- Sample 1

description: Library name: dagla_12w_TH_KO_1


title: hCD2.SII d6 CD45+ rep2

description: Library name: S148

value: Cells were transduced with Spib, Irf8, Ikzf2 (SII)

value: Cells were collected 6 days after viral transduction


title: 5995_V1+1 (tempus)

description: Library name: 5995_V1+1

value: Blood


title: 5952_V1 (tempus)

description: Library name: 5952_V1


title: K562_SSRP1_dTAG_Micro-C_S4Rep1

description: Library name: Sample 10


title: hCD2.SII d3 YFP+ rep5

description: Library name: S142

value: live(DAPI-) and YFP+


title: 5939_V2 (tempus)

description: Library name: 5939_V2


title: K562_SSRP1_dTAG_Micro-C_S3Rep3

description: Library name: Sample 9

value: 4h dTAG7, Rep3


title: hCD2.SII d3 YFP+ rep4

description: Library name: S141


title: 12-week TH Dagla +/- Sample 4

description: Library name: dagla_12w_TH_HT_4

value: Dagla +/-


title: 5939_V1+1 (tempus)

description: Library name: 5939_V1+1

value: FALSE


title: hCD2.SII d3 YFP+ rep3

description: Library name: S140


title: K562_SSRP1_dTAG_Micro-C_S3Rep1

description: Library name: Sample 7


title: K562_SSRP1_dTAG_Micro-C_S3Rep2

description: Library name: Sample 8


title: 12-week TH Dagla +/- Sample 3

description: Library name: dagla_12w_TH_HT_3


title: 5939_V1 (tempus)

description: Library name: 5939_V1


title: 12-week TH Dagla +/- Sample 2

description: Library name: dagla_12w_TH_HT_2


title: K562_SSRP1_dTAG_Micro-C_S4Rep2

description: Library name: Sample 11


title: 5918_V2+1 (tempus)

description: Library name: 5918_V2+1


title: hCD2.SII d3 YFP+ rep1

description: Library name: S138


title: 12-week TH Dagla +/- Sample 1

description: Library name: dagla_12w_TH_HT_1


title: K562_DMSO_Micro-C_S2Rep3

description: Library name: Sample 6

value: 4h DMSO, Rep2


title: 5918_V2 (tempus)

description: Library name: 5918_V2


title: hCD2.SII d3 YFP+ rep2

description: Library name: S139


title: hCD2.SII d3 YFP+CD45+ rep1

description: Library name: S143


title: hCD2.SII d3 CD45+ rep5

description: Library name: S137

value: live(DAPI-) and CD45+


title: 12-week ST Dagla WT Sample 5

description: Library name: dagla_12w_ST_WT_5

source_name: Striatum

value: Striatum

value: WT


title: 5918_V1+1 (tempus)

description: Library name: 5918_V1+1


title: K562_DMSO_Micro-C_S2Rep2

description: Library name: Sample 5

value: Leukemia cell line


title: K562_DMSO_Micro-C_S2Rep1

description: Library name: Sample 4

value: K562 subclone SSRP1-dTAG (dTAG7 inducible degron)


title: 12-week ST Dagla WT Sample 4

description: Library name: dagla_12w_ST_WT_4


title: 12-week TH Dagla +/- Sample 5

description: Library name: dagla_12w_TH_HT_5


title: hCD2.SII d3 CD45+ rep4

description: Library name: S136

value: Cells were collected 3 days after viral transduction


title: K562_DMSO_Micro-C_S1Rep3

description: Library name: Sample 3

value: 4h DMSO, Rep1


title: 5917_V2+1 (tempus)

description: Library name: 5917_V2+1


title: K562_DMSO_Micro-C_S1Rep2

description: Library name: Sample 2


title: hCD2.SII d3 CD45+ rep2

description: Library name: S134

value: mouse embryonic fibroblast

value: heterozygous hCD2(Cre/WT) Rosa26 (YFP/WT) mice with a C57BL/6 background


title: 12-week ST Dagla WT Sample 1

description: Library name: dagla_12w_ST_WT_1


title: 5917_V2 (tempus)

description: Library name: 5917_V2


title: 5917_V1+1 (tempus)

description: Library name: 5917_V1+1


title: K562_DMSO_Micro-C_S1Rep1

description: Library name: Sample 1


title: C9a.SII d9 tdT+CD45+ rep4

description: Library name: S132

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: Cells were transduced with Spib, Irf8, Ikzf2 (SII)

value: Cells were collected 9 days after viral transduction

value: live(DAPI-) and tdT+CD45+


title: 12-week ST Dagla -/- Sample 5

description: Library name: dagla_12w_ST_KO_5

value: Dagla -/-


title: C9a.SII d9 tdT+CD45+ rep3

description: Library name: S131


title: 12-week ST Dagla -/- Sample 4

description: Library name: dagla_12w_ST_KO_4


title: SMC1A_dTAG_rep1

description: Library name: Sample 17

data_processing:
ChIPmentation data were first trimmed to remove adaptor sequences using Trim Galore (v.0.6.10) and then mapped to human genome hg38 and D. melanogaster genome dm6 with Bowtie2 (v.2.3.4.1). Duplicates were marked with Picard tools (v.2.20.2). After removal of duplicated reads and reads mapped to blacklisted regions of the human genome65, bigWig coverage tracks were generated with deepTools66 (v.3.5.5) bamCoverage function, using a binning size of 10 bp. All coverage tracks were normalized using spike-in read counts, defined by the total number of properly paired, deduplicated reads mapped to the D. melanogaster genome. Coverage tracks of replicates were merged using deepTools bigwigAverage function.
Assembly: hg38
Supplementary files format and content: bigWig files, read coverage

extract_protocol:
1.5 M cells were crosslinked with 1% formaldehyde (Thermo Scientific) for 10 min at room temperature, followed by quenching with 125 mM ice-cold glycine (Sigma-Aldrich) for 5 min and 2 washes with ice-cold PBS. Nuclei isolation was performed with Farnham lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% NP-40) and followed by nuclear lysis with 0.5% SDS buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5% SDS). For CTCF ChIPmentation, chromatin fragmentation was performed by sonication for 7 min with the following settings on the S220 Covaris sonicator: duty factor: 5%, peak incident power: 140 W, cycles per burst: 200). For SSRP1-HA and SMC1A ChIPmentation, chromatin was first digested by a titrated amount of MNase (2.5 kunitz; NEB, M0247S) at 37°C for 10 min and followed by gentle sonication (duty factor: 2%, peak incident power: 105W, cycles per burst: 200) for 1 or 12 min, respectively. The supernatant of the sheared chromatin was mixed with IP buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 150 mM NaCl, 1% Triton-X-100, 1×PIC). Protein A and Protein G dynabeads (Invitrogen) were mixed in a 1:1 ratio and after 3 washes with 0.5% BSA blocking solution (Sigma-Aldrich), the mixture was incubated with 2 μg of primary antibody (HA: Cell Signaling, 3724S; CTCF: Diagenode, C15410210-50; SMC1A: Abcam, ab9262) and 1 μg of spike-in antibody (Active Motif, 61686) for 6 h at 4°C. Sheared chromatin was then added with 200 ng of Drosophila spike-in chromatin to the bead-bound antibodies for 16 h at 4°C. Post-immunoprecipitation washes were performed using buffers with varying salt concentrations at 4°C.
Sequencing adapters were added using "on-bead" tagmentation using the Illumina Tagment DNA Enzyme (Illumina, 20034197), after which overnight de-crosslinking was performed at 65°C with proteinase K at a final concentration of 0.2 mg/mL. DNA extraction was performed with 1.8 volumes of Mag-Bind TotalPure NGS beads (Omega Bio-Tek). Library preparation was performed using the NEBNext High-Fidelity 2×PCR Master Mix (NEB, M0541) and two rounds of size selection with 1.2 volumes of Mag-Bind TotalPure NGS beads were performed.

value: 4h dTAG7, Rep1


title: 5464_V2+1 (tempus)

description: Library name: 5464_V2+1

value: Blood

value: FALSE

value: Short


title: 5917_V1 (tempus)

description: Library name: 5917_V1


title: 5918_V1 (tempus)

description: Library name: 5918_V1


title: 12-week ST Dagla -/- Sample 3

description: Library name: dagla_12w_ST_KO_3

value: Striatum


title: C9a.SII d9 tdT+CD45+ rep2

description: Library name: S130


title: 5464_V2 (tempus)

description: Library name: 5464_V2


title: 5457_V1+1 (tempus)

description: Library name: 5457_V1+1

value: TRUE

value: Long


title: hCD2.SII d3 CD45+ rep3

description: Library name: S135

value: live(DAPI-) and CD45+


title: SMC1A_DMSO_rep2

description: Library name: Sample 15

value: Leukemia cell line

value: K562 subclone SSRP1-dTAG (dTAG7 inducible degron)

value: 4h DMSO, Rep2


title: 12-week ST Dagla -/- Sample 2

description: Library name: dagla_12w_ST_KO_2


title: C9a.SII d9 tdT+CD45+ rep1

description: Library name: S129

value: mouse embryonic fibroblast


title: 12-week ST Dagla WT Sample 3

description: Library name: dagla_12w_ST_WT_3

value: WT


title: 12-week ST Dagla -/- Sample 1

description: Library name: dagla_12w_ST_KO_1


title: 12-week ST Dagla WT Sample 2

description: Library name: dagla_12w_ST_WT_2


title: C9a.SII d9 tdT+ rep4

description: Library name: S128

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: Cells were transduced with Spib, Irf8, Ikzf2 (SII)

value: live(DAPI-) and tdT+


title: hCD2.SII d3 CD45+ rep1

description: Library name: S133

value: heterozygous hCD2(Cre/WT) Rosa26 (YFP/WT) mice with a C57BL/6 background

value: Cells were collected 3 days after viral transduction


title: SMC1A_dTAG_rep3

description: Library name: Sample 19

value: 4h dTAG7, Rep3


title: SMC1A_DMSO_rep1

description: Library name: Sample 14

value: 4h DMSO, Rep1


title: C9a.SII d9 tdT+ rep3

description: Library name: S127

value: Cells were collected 9 days after viral transduction


title: 12-week ST Dagla +/- Sample 5

description: Library name: dagla_12w_ST_HT_5

value: Striatum

value: Dagla +/-


title: 12-week ST Dagla +/- Sample 4

description: Library name: dagla_12w_ST_HT_4


title: C9a.SII d9 tdT+ rep2

description: Library name: S126


title: 5449_V2+1 (tempus)

description: Library name: 5449_V2+1

value: Blood

value: FALSE

value: Short


title: FACT_DMSO_rep2

description: Library name: Sample 12

value: Leukemia cell line

value: K562 subclone SSRP1-dTAG (dTAG7 inducible degron)


title: SMC1A_DMSO_rep3

description: Library name: Sample 16

value: 4h DMSO, Rep3


title: FACT_dTAG_rep1

description: Library name: Sample 13

value: 4h dTAG, Rep1


title: C9a.SII d9 tdT+ rep1

description: Library name: S125

value: mouse embryonic fibroblast

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)


title: 12-week ST Dagla +/- Sample 3

description: Library name: dagla_12w_ST_HT_3


title: FACT_DMSO_rep1

description: Library name: Sample 11


title: 12-week ST Dagla +/- Sample 2

description: Library name: dagla_12w_ST_HT_2


title: 5449_V1+1 (tempus)

description: Library name: 5449_V1+1


title: C9a.SII d9 CD45+ rep4

description: Library name: S124

value: Cells were transduced with Spib, Irf8, Ikzf2 (SII)

value: live(DAPI-) and CD45+


title: 5278_V1+1 (tempus)

description: Library name: 5278_V1+1

value: TRUE


title: 5278_V1 (tempus)

description: Library name: 5278_V1


title: CTCF_dTAG_rep5

description: Library name: Sample 10

value: 4h dTAG7, Rep5


title: 5457_V1 (tempus)

description: Library name: 5457_V1

value: Long


title: 12-week ST Dagla +/- Sample 1

description: Library name: dagla_12w_ST_HT_1


title: C9a.SII d9 CD45+ rep2

description: Library name: S122

value: Cells were collected 9 days after viral transduction


title: C9a.SII d9 CD45+ rep3

description: Library name: S123


title: CTCF_dTAG_rep4

description: Library name: Sample 9

value: 4h dTAG7, Rep4


title: CTCF_dTAG_rep3

description: Library name: Sample 8

value: 4h dTAG7, Rep3


title: 5264_V1+1 (tempus)

description: Library name: 5264_V1+1

value: Blood


title: 12-week SSC Dagla WT Sample 5

description: Library name: dagla_12w_SSC_WT_5

source_name: Somatosensory Cortex

value: Somatosensory Cortex

value: WT


title: 5449_V2 (tempus)

description: Library name: 5449_V2

value: FALSE

value: Short


title: 12-week SSC Dagla WT Sample 4

description: Library name: dagla_12w_SSC_WT_4


title: C9a.SII d9 CD45+ rep1

description: Library name: S121


title: SMC1A_dTAG_rep2

description: Library name: Sample 18

value: Leukemia cell line

value: K562 subclone SSRP1-dTAG (dTAG7 inducible degron)

value: 4h dTAG7, Rep2


title: 12-week SSC Dagla WT Sample 3

description: Library name: dagla_12w_SSC_WT_3


title: CTCF_dTAG_rep2

description: Library name: Sample 7


title: C9a.SII d6 tdT+CD45+ rep4

description: Library name: S120

value: mouse embryonic fibroblast

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: Cells were collected 6 days after viral transduction

value: live(DAPI-) and tdT+CD45+


title: CTCF_dTAG_rep1

description: Library name: Sample 6

value: 4h dTAG7, Rep1


title: 5264_V1 (tempus)

description: Library name: 5264_V1

value: TRUE


title: 5226_V1+2 (tempus)

description: Library name: 5226_V1+2

value: Long


title: CTCF_DMSO_rep5

description: Library name: Sample 5

value: 4h DMSO, Rep5


title: 5226_V1 (tempus)

description: Library name: 5226_V1


title: 5195_V1+1 (tempus)

description: Library name: 5195_V1+1


title: CTCF_DMSO_rep4

description: Library name: Sample 4

value: 4h DMSO, Rep4


title: C9a.SII d6 tdT+CD45+ rep2

description: Library name: S118

value: Cells were transduced with Spib, Irf8, Ikzf2 (SII)


title: 12-week SSC Dagla -/- Sample 5

description: Library name: dagla_12w_SSC_KO_5

value: Somatosensory Cortex

value: Dagla -/-


title: 12-week SSC Dagla WT Sample 1

description: Library name: dagla_12w_SSC_WT_1

value: WT


title: C9a.SII d6 tdT+CD45+ rep1

description: Library name: S117


title: C9a.SII d6 tdT+ rep5

description: Library name: S116

value: live(DAPI-) and tdT+


title: C9a.SII d6 tdT+CD45+ rep3

description: Library name: S119


title: 5195_V1 (tempus)

description: Library name: 5195_V1

value: Blood


title: C9a.SII d6 tdT+ rep4

description: Library name: S115


title: 5167_V2 (tempus)

description: Library name: 5167_V2


title: CTCF_DMSO_rep2

description: Library name: Sample 2

value: Leukemia cell line

value: K562 subclone SSRP1-dTAG (dTAG7 inducible degron)

value: 4h DMSO, Rep2


title: CTCF_DMSO_rep3

description: Library name: Sample 3

value: 4h DMSO, Rep3


title: C9a.SII d6 tdT+ rep3

description: Library name: S114

value: mouse embryonic fibroblast

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: Cells were collected 6 days after viral transduction


title: 12-week SSC Dagla -/- Sample 2

description: Library name: dagla_12w_SSC_KO_2


title: C9a.SII d6 tdT+ rep2

description: Library name: S113


title: 12-week SSC Dagla WT Sample 2

description: Library name: dagla_12w_SSC_WT_2


title: CTCF_DMSO_rep1

description: Library name: Sample 1

value: 4h DMSO, Rep1


title: 12-week SSC Dagla -/- Sample 3

description: Library name: dagla_12w_SSC_KO_3


title: 5167_V2+1 (tempus)

description: Library name: 5167_V2+1

value: TRUE


title: 5167_V1+1 (tempus)

description: Library name: 5167_V1+1


title: 12-week SSC Dagla -/- Sample 1

description: Library name: dagla_12w_SSC_KO_1


title: ko-Taf4a_2

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

description: Library name: Sample 5

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.11b (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a7 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq).
Remaining peaks were unified to represent a common set of regions for all samples.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized for sequencing depth.
Peaks were annotated with the promoter (TSS +- 10000 nt) of the nearest gene based on Ensembl release 101.
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: Muscle stem cells

extract_protocol:
50.000 cells were used for ATAC library preparation using Tn5 Transposase from Nextera DNA Sample Preparation Kit (Illumina).
Cells were pelleted and resuspended in 50µl Lysis/Transposition reaction (12.5µl THS-TD-Buffer, 2.5µl Tn5, 5µl 0.1% Digitonin and 30µl water) and was incubated at 37°C for 30min with occasional snap mixing. Following purification of the DNA fragments was done by MinElute PCR Purification Kit (Qiagen). Amplification of Library together with Indexing was performed as described elsewhere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced on NextSeq500 platform (Illumina) using P3 flowcell with ZZZbp ZZZ setup.

tag: mouse strain

value: Muscle stem cells

tag: cell state

value: freshly isolated MuSCs


title: ko-Taf4a_3

description: Library name: Sample 6


title: 5167_V1 (tempus)

description: Library name: 5167_V1


title: 12-week SSC Dagla -/- Sample 4

description: Library name: dagla_12w_SSC_KO_4


title: C9a.SII d6 tdT+ rep1

description: Library name: S112

tag: transduction

value: Cells were transduced with Spib, Irf8, Ikzf2 (SII)


title: ko-Taf4a_1

description: Library name: Sample 4


title: 5097_V2+1 (tempus)

description: Library name: 5097_V2+1

value: Short


title: 12-week SSC Dagla +/- Sample 4

description: Library name: dagla_12w_SSC_HT_4

value: Somatosensory Cortex

value: Dagla +/-


title: 5097_V1 (tempus)

description: Library name: 5097_V1


title: C9a.SII d6 CD45+ rep5

description: Library name: S111

tag: time

value: live(DAPI-) and CD45+


title: 12-week SSC Dagla +/- Sample 3

description: Library name: dagla_12w_SSC_HT_3


title: WT_3

description: Library name: Sample 3

value: Control


title: C9a.SII d6 CD45+ rep4

description: Library name: S110

tag: sorted cells


title: WT_1

description: Library name: Sample 1


title: C9a.SII d6 CD45+ rep3

description: Library name: S109


title: 5083_V2 (tempus)

description: Library name: 5083_V2

tag: tissue

value: Blood

value: FALSE


title: 5083_V2+1 (tempus)

description: Library name: 5083_V2+1

tag: donor


title: C9a.SII d6 CD45+ rep1

description: Library name: S107


title: 12-week SSC Dagla +/- Sample 1

description: Library name: dagla_12w_SSC_HT_1


title: WT_2

description: Library name: Sample 2


title: C9a.SII d6 CD45+ rep2

description: Library name: S108


title: 5083_V1+1 (tempus)

description: Library name: 5083_V1+1

tag: timepoint


title: 12-week SN Dagla WT Sample 4

description: Library name: dagla_12w_SN_WT_4

value: Substantia Nigra

value: WT


title: 12-week SN Dagla WT Sample 5

description: Library name: dagla_12w_SN_WT_5


title: MuSC_Taf4a-KO_Nfya_2_igg

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a7 with FDR < 0.1 and additional parameters "--extsize 100 --nomodel --to-large" (Zhang et al., Model-based Analysis of ChIP-Seq).
Remaining peaks were unified to represent a common set of regions for all samples.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 10000 nt) of the nearest gene based on Ensembl release 101.
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.
Library strategy: CUT&Run

extract_protocol:
4x10^5 control and Taf4asKO in vitro cultured muscle stem cells (MuSCs) were immobilized on Concanavalin A-coated magnetic beads (Bangs Laboratories), permeated with 0.05% Digitonin (EMD Millipore) and incubated with NF-YA (Sc-17753, Santa Cruz) or mouse IgG ( 12-371B, Millipore) with 1:100 dilution at 4 °C overnight on a rotator. After washing, the beads were incubated with home-made pA-MNase (0.3 ng/µl final concentration) at room temperature for 1 h and DNA was cleaved by incubation with buffer containing 10 mM CaCl2 and 3.5 mM HEPES pH 7.5 at 0 °C for 20 min. Under this high-calcium/low-salt condition, cleaved DNA fragments were released and then extracted using phenol-chloroform.
For Cut’n’Run library preparation, precipitated DNA samples was purified and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). All precipitated DNA (max. 10 ng) were used as input for SMARTer® ThruPLEX® DNA-Seq Kit following manufacture’s protocol (Takara Bio). Sequencing was performed on NextSeq2000 platform (Illumina) using P3 flowcell with 2x 36bp paired-end setup.

tag: cut&run antybody

value: Mouse IgG, 12-371B, Millipore

value: activated/proliferating


title: 12-week SSC Dagla +/- Sample 5

description: Library name: dagla_12w_SSC_HT_5


title: C9a.SII d3 tdT+CD45+ rep4

description: Library name: S106

value: mouse embryonic fibroblast

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: Cells were collected 3 days after viral transduction

value: live(DAPI-) and tdT+CD45+


title: MuSC_Taf4a-KO_Nfya_1_igg

value: Muscle stem cells


title: C9a.SII d3 tdT+CD45+ rep3

description: Library name: S105

value: Cells were transduced with Spib, Irf8, Ikzf2 (SII)


title: 5083_V1 (tempus)

description: Library name: 5083_V1

tag: vaccine

tag: prior infection

value: Short


title: 12-week SN Dagla WT Sample 3

description: Library name: dagla_12w_SN_WT_3


title: 5067_V2 (tempus)

description: Library name: 5067_V2

value: TRUE

tag: library preparation_batch


title: 12-week SN Dagla WT Sample 2

description: Library name: dagla_12w_SN_WT_2


title: C9a.SII d3 tdT+CD45+ rep2

description: Library name: S104

tag: cell line

tag: cell type


title: 5067_V1+2 (tempus)

description: Library name: 5067_V1+2

tag: regimen


title: C9a.SII d3 tdT+CD45+ rep1

description: Library name: S103

tag: genotype


title: 12-week SN Dagla WT Sample 1

description: Library name: dagla_12w_SN_WT_1

tag: age


title: MuSC_WT_Nfya_2_igg

tag: mouse strain


title: 5067_V1 (tempus)

description: Library name: 5067_V1


title: C9a.SII d3 tdT+ rep3

description: Library name: S102

value: live(DAPI-) and tdT+


title: 5067_V2+1 (tempus)

description: Library name: 5067_V2+1


title: MuSC_WT_Nfya_1_igg

tag: cell state


title: MuSC_WT_Nfya_2

value: NF-YA, Sc-17753, Santa Cruz


title: 12-week SSC Dagla +/- Sample 2

description: Library name: dagla_12w_SSC_HT_2

value: Somatosensory Cortex

value: Dagla +/-


title: 12-week SN Dagla -/- Sample 5

description: Library name: dagla_12w_SN_KO_5

value: Dagla -/-


title: C9a.SII d3 tdT+ rep2

description: Library name: S101

tag: transduction


title: MuSC_WT_Nfya_1

value: Control


title: 12-week SN Dagla -/- Sample 3

description: Library name: dagla_12w_SN_KO_3

value: Substantia Nigra


title: 4213_V2 (tempus)

description: Library name: 4213_V2

value: Blood

value: FALSE


title: C9a.SII d3 tdT+ rep1

description: Library name: S100

value: mouse embryonic fibroblast

tag: time


title: 4213_V1+1 (tempus)

description: Library name: 4213_V1+1


title: 12-week SN Dagla -/- Sample 4

description: Library name: dagla_12w_SN_KO_4


title: 12-week SN Dagla -/- Sample 2

description: Library name: dagla_12w_SN_KO_2


title: MuSC_WT_NF-YA_3_igg

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.9a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 2.25.5 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 2.1.1 with FDR < 0.05 and additional parameters "--extsize 100 --nomodel --to-large" (Zhang et al., Model-based Analysis of ChIP-Seq).
Remaining peaks were unified to represent a common set of regions for all samples.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 10000 nt) of the nearest gene based on Ensembl data.
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.
Library strategy: CUT&Run

extract_protocol:
1x106 wild type in vitro cultured muscle stem cells (MuSCs) were immobilized on Concanavalin A-coated magnetic beads (Bangs Laboratories), permeated with 0.05% Digitonin (EMD Millipore) and incubated with NF-YA (Sc-17753, Santa Cruz) or mouse IgG ( 12-371B, Millipore) with 1:100 dilution at 4 °C overnight on a rotator. After washing, the beads were incubated with home-made pA-MNase (0.3 ng/µl final concentration) at room temperature for 1 h and DNA was cleaved by incubation with buffer containing 10 mM CaCl2 and 3.5 mM HEPES pH 7.5 at 0 °C for 20 min. Under this high-calcium/low-salt condition, cleaved DNA fragments were released and then extracted using phenol-chloroform.
For Cut’n’Run library preparation, precipitated DNA samples was purified and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). 20ng of DNA was used as input for SMARTer® ThruPLEX® DNA-Seq Kit following manufacture’s protocol (Takara Bio).

value: wild type

value: Mouse IgG, 12-371B, Millipore

value: activated/proliferating


title: MuSC_Taf4a-KO_Nfya_1

value: Muscle stem cells


title: MuSC_WT_NF-YA_3


title: C9a.SII d3 CD45+ rep5

description: Library name: S99

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: Cells were transduced with Spib, Irf8, Ikzf2 (SII)

value: Cells were collected 3 days after viral transduction

tag: sorted cells

value: live(DAPI-) and CD45+


title: C9a.SII d3 CD45+ rep4

description: Library name: S98


title: 12-week SN Dagla -/- Sample 1

description: Library name: dagla_12w_SN_KO_1

tag: tissue


title: 4213_V2+1 (tempus)

description: Library name: 4213_V2+1

data_processing:
BCL files were converted to FASTQ files using Illumina bcl2fastq. FASTQ files were processed to a gene count matrix using a custom CGAT-Core (v0.6.15) pipeline. Briefly, sequencing quality was assessed using FASTQC (Babraham Bioinformatics; v0.12.1), then FASTQ files trimmed to remove low quality bases and adapter sequences using Trimmomatic (v0.39). Reads were aligned to the GRCh38 human genome using STAR (v2.7.10b) and reads mapping to each gene quantified using featureCounts (v2.0.6).
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt (tab-delimited file containing raw counts for each sample)

extract_protocol:
Whole blood RNA was extracted from Tempus tubes in batches of 12-24 samples, with a mixture of vaccination groups and timepoints, using the Tempus Spin RNA Isolation Kit (Thermo Fisher Scientific). Samples were thawed, diluted in a 50 ml conical with 1× PBS, vortexed for 30 s, then centrifuged (3000 × g, 30 min, 4°C) to pellet RNA. Supernatants were removed and RNA pellets resuspended in RNA Purification Resuspension Solution, then transferred to purification filters for microcentrifuge RNA elution. RNA quantity and integrity was assessed using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and Agilent TapeStation and submitted to the Oxford Genomics Centre (Centre for Human Genetics, University of Oxford) for library generation and sequencing (Illumina NovaSeq 6000, 150 base pair paired-end reads).
NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, #E7760) with Globin & rRNA Depletion (New England Biolabs, #E7750).

tag: donor


title: MuSC_Taf4a-KO_Nfya_2

value: NF-YA, Sc-17753, Santa Cruz


title: 3871_V2 (tempus)

description: Library name: 3871_V2

tag: timepoint

value: Long


title: MuSC_WT_NF-YA_2_igg

tag: cut&run antybody


title: 12-week SN Dagla +/- Sample 5

description: Library name: dagla_12w_SN_HT_5

value: Dagla +/-


title: C9a.SII d3 CD45+ rep3

description: Library name: S97


title: 3871_V2+1 (tempus)

description: Library name: 3871_V2+1

tag: vaccine


title: 3871_V1+1 (tempus)

description: Library name: 3871_V1+1

tag: prior infection


title: MuSC_WT_NF-YA_2


title: 12-week SN Dagla +/- Sample 4

description: Library name: dagla_12w_SN_HT_4


title: C9a.SII d3 CD45+ rep2

description: Library name: S96


title: 12-week SN Dagla +/- Sample 3

description: Library name: dagla_12w_SN_HT_3


title: C9a.SII d3 CD45+ rep1

description: Library name: S95


title: MuSC_WT_Kansl2_4_igg

extract_protocol:
1x10^6 wild type in vitro cultured muscle stem cells (MuSCs) wild type were immobilized on Concanavalin A-coated magnetic beads (Bangs Laboratories), permeated with 0.05% Digitonin (EMD Millipore) and incubated with Kansl2 (Proteintech #27261-1-AP) or rabbit IgG (Diagenode #C15410206) with 1:100 dilution at 4 °C overnight on a rotator. After washing, the beads were incubated with home-made pA-MNase (0.3 ng/µl final concentration) at room temperature for 1 h and DNA was cleaved by incubation with buffer containing 10 mM CaCl2 and 3.5 mM HEPES pH 7.5 at 0 °C for 20 min. Under this high-calcium/low-salt condition, cleaved DNA fragments were released and then extracted using phenol-chloroform.
For Cut’n’Run library preparation, precipitated DNA samples were purified and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). 20ng of DNA was used as input for SMARTer® ThruPLEX® DNA-Seq Kit following manufacture’s protocol (Takara Bio).

value: Rabbit IgG, Diagenode, C15410206


title: MuSC_WT_Kansl2_4

value: Kansl2,27261-1-AP Proteintech


title: 12-week SN Dagla +/- Sample 2

description: Library name: dagla_12w_SN_HT_2

value: Substantia Nigra


title: PIP d9 tdT+CD45+ rep4

description: Library name: S94

value: Cells were transduced with Pu.1, Irf4, Prdm1 (PIP)

value: Cells were collected 9 days after viral transduction

value: live(DAPI-) and tdT+CD45+


title: 3871_V1 (tempus)

description: Library name: 3871_V1

value: Blood

value: FALSE

tag: library preparation_batch


title: 12-week SN Dagla +/- Sample 1

description: Library name: dagla_12w_SN_HT_1


title: 2794_V1 (tempus)

description: Library name: 2794_V1


title: PIP d9 tdT+CD45+ rep3

description: Library name: S93

tag: cell line

value: mouse embryonic fibroblast


title: MuSC_WT_Kansl2_3

tag: cell type

value: Muscle stem cells

value: wild type

value: activated/proliferating


title: MuSC_WT_Kansl2_3_igg


title: 12-week PFC Dagla WT Sample 5

description: Library name: dagla_12w_PFC_WT_5

source_name: Prefrontal Cortex

value: Prefrontal Cortex

value: WT


title: PIP d9 tdT+CD45+ rep2

description: Library name: S92

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)


title: 2699_V2 (tempus)

description: Library name: 2699_V2

tag: regimen

value: Short


title: MuSC_WT_Kansl2_2_igg

tag: genotype


title: 2689_V2+1 (tempus)

description: Library name: 2689_V2+1


title: PIP d9 tdT+CD45+ rep1

description: Library name: S91


title: 12-week PFC Dagla WT Sample 4

description: Library name: dagla_12w_PFC_WT_4

tag: age


title: 12-week PFC Dagla WT Sample 3

description: Library name: dagla_12w_PFC_WT_3


title: MuSC_WT_Kansl2_2

tag: mouse strain


title: PIP d9 tdT+ rep4

description: Library name: S90

value: live(DAPI-) and tdT+


title: MuSC_WT_Kansl2_1_igg

value: Rabbit IgG, Diagenode, C15410206

tag: cell state


title: 12-week PFC Dagla WT Sample 2

description: Library name: dagla_12w_PFC_WT_2


title: 2532_V2+1 (tempus)

description: Library name: 2532_V2+1


title: MuSC_WT_Kansl2_1

value: Kansl2,27261-1-AP Proteintech


title: PIP d9 tdT+ rep3

description: Library name: S89

tag: transduction


title: 2794_V2+1 (tempus)

description: Library name: 2794_V2+1

value: Long


title: MuSC_WT_Taf4a_3_igg

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.9a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 2.21.7 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 2.1.1 with FDR < 0.05 and additional parameters "--extsize 100 --nomodel --to-large" (Zhang et al., Model-based Analysis of ChIP-Seq).
Remaining peaks were unified to represent a common set of regions for all samples.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
Mapping and counting was repeated similarly versus spike-in organism Escherichia coli str. K-12 substr. MG1655 genome version ASM584v2 (Ensembl release 49).
The raw count matrix was normalized with factors based on E. coli mapped read count.
Peaks were annotated with the promoter (TSS +- 10000 nt) of the nearest gene based on Ensembl data.
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows spike-in normalized counts.
Library strategy: CUT&Run

extract_protocol:
1x10^6 wild type in vitro cultured muscle stem cells (MuSCs) were immobilized on Concanavalin A-coated magnetic beads (Bangs Laboratories), permeated with 0.05% Digitonin (EMD Millipore) and incubated with TAF4A (Santa Cruz #sc-136093) or mouse IgG (Santa Cruz, #Sc-136093) with 1:100 dilution at 4 °C overnight on a rotator. After washing, the beads were incubated with home-made pA-MNase (0.3 ng/µl final concentration) at room temperature for 1 h and DNA was cleaved by incubation with buffer containing 10 mM CaCl2 and 3.5 mM HEPES pH 7.5 at 0 °C for 20 min. Under this high-calcium/low-salt condition, cleaved DNA fragments were released and then extracted using phenol-chloroform.Ecoli spike-in comes from Mnase enzyme purified from E.coli, it is not added additionally.
For Cut’n’Run library preparation, precipitated DNA samples were purified and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). For MuSC samples 5ng precipitated DNA was used as input for SMARTer® ThruPLEX® DNA-Seq Kit following manufacture’s protocol (Takara Bio).

value: Mouse IgG, 12-371B, Millipore


title: 2699_V2+1 (tempus)

description: Library name: 2699_V2+1


title: 12-week PFC Dagla WT Sample 1

description: Library name: dagla_12w_PFC_WT_1

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Grin2a and Dagla mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.


title: 2532_V2 (tempus)

description: Library name: 2532_V2


title: PIP d9 tdT+ rep1

description: Library name: S87

value: Cells were transduced with Pu.1, Irf4, Prdm1 (PIP)

tag: time

value: Cells were collected 9 days after viral transduction


title: PIP d9 tdT+ rep2

description: Library name: S88

tag: sorted cells


title: 2689_V2 (tempus)

description: Library name: 2689_V2

tag: tissue

value: Blood


title: 12-week PFC Dagla -/- Sample 5

description: Library name: dagla_12w_PFC_KO_5

value: Dagla -/-


title: 12-week PFC Dagla -/- Sample 4

description: Library name: dagla_12w_PFC_KO_4


title: 12-week PFC Dagla -/- Sample 3

description: Library name: dagla_12w_PFC_KO_3


title: 2436_V2+1 (tempus)

description: Library name: 2436_V2+1

tag: donor

value: FALSE


title: PIP d9 CD45+ rep4

description: Library name: S86

value: mouse embryonic fibroblast

value: live(DAPI-) and CD45+


title: dcg-axni-abd-2

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

institute: Tulane University

data_processing:
STAR for alignment
FeatureCount for count table summarization
DESeq2 for differential expression analyses
Assembly: dm6
Supplementary files format and content: tab delimited table; FeatureCount output count tables

organism: Drosophila melanogaster

source_name: 3rd instar fat body abdomen region

extract_protocol:
total RNA was extracted in Trizol with standard protocol
The ribosome depletion stranded RNA library was generated by using TruSeq Stranded Total RNA Library Prep kit (Illumina, 20020596) according to the manufacturer’s manual

value: 3rd instar fat body abdomen region


title: 2532_V1 (tempus)

description: Library name: 2532_V1

tag: timepoint


title: 2532_V1+1 (tempus)

description: Library name: 2532_V1+1


title: 2436_V2 (tempus)

description: Library name: 2436_V2


title: 12-week PFC Dagla -/- Sample 2

description: Library name: dagla_12w_PFC_KO_2

data_processing:
Reads were aligned to mm10 and gene and isoform level expression leves were estimated using Salmon (version 1.7.0, with arguments -l A --posBias --seqBias --gcBias --validateMapping)
Assembly: mm10
Supplementary files format and content: CSV file contains Salmon's counts estimation for all genes and all samples

value: Prefrontal Cortex


title: dcg-axni-abd-3


title: PIP d9 CD45+ rep3

description: Library name: S85


title: PIP d9 CD45+ rep1

description: Library name: S83


title: dcg-axni-head-3

source_name: 3rd instar fat body head region

value: 3rd instar fat body head region


title: 2436_V1+1 (tempus)

description: Library name: 2436_V1+1


title: 12-week PFC Dagla +/- Sample 5

description: Library name: dagla_12w_PFC_HT_5

value: Dagla +/-


title: PIP d9 CD45+ rep2

description: Library name: S84

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)


title: PIP d6 tdT+CD45+ rep4

description: Library name: S82

value: Cells were collected 6 days after viral transduction

value: live(DAPI-) and tdT+CD45+


title: 2436_V1 (tempus)

description: Library name: 2436_V1


title: MuSC_WT_Taf4a_3

value: Muscle stem cells

value: wild type

tag: cut&run antybody

value: Taf4a Sc-136093 Santa Cruz

value: activated/proliferating


title: dcg-axni-head-2


title: PIP d6 tdT+CD45+ rep3

description: Library name: S81

value: Cells were transduced with Pu.1, Irf4, Prdm1 (PIP)


title: 12-week PFC Dagla +/- Sample 4

description: Library name: dagla_12w_PFC_HT_4


title: dcg-axni-head-1


title: 12-week PFC Dagla +/- Sample 3

description: Library name: dagla_12w_PFC_HT_3


title: 2269_V2+1 (tempus)

description: Library name: 2269_V2+1

value: Blood

tag: vaccine

value: Long


title: PIP d6 tdT+CD45+ rep2

description: Library name: S80


title: 12-week PFC Dagla +/- Sample 2

description: Library name: dagla_12w_PFC_HT_2


title: PIP d6 tdT+CD45+ rep1

description: Library name: S79


title: 2269_V1+1 (tempus)

description: Library name: 2269_V1+1

tag: prior infection

value: FALSE


title: dcg+abd-2


title: dcg-axni-abd-1


title: 2269_V1 (tempus)

description: Library name: 2269_V1

tag: library preparation_batch


title: 12-week PFC Dagla +/- Sample 1

description: Library name: dagla_12w_PFC_HT_1


title: PIP d6 tdT+ rep4

description: Library name: S78

tag: cell line

value: mouse embryonic fibroblast

value: live(DAPI-) and tdT+


title: 12-week PFC Dagla -/- Sample 1

description: Library name: dagla_12w_PFC_KO_1

value: Dagla -/-


title: 2255_V2+1 (tempus)

description: Library name: 2255_V2+1


title: 12-week HP Dagla WT Sample 5

description: Library name: dagla_12w_HP_WT_5

source_name: Hippocampus

value: Hippocampus

value: WT


title: PIP d6 tdT+ rep3

description: Library name: S77

tag: cell type


title: 12-week HP Dagla WT Sample 4

description: Library name: dagla_12w_HP_WT_4


title: PIP d6 tdT+ rep2

description: Library name: S76


title: dcg+head-3

value: 3rd instar fat body head region


title: dcg+head-2


title: 2255_V2 (tempus)

description: Library name: 2255_V2

tag: regimen


title: 2269_V2 (tempus)

description: Library name: 2269_V2


title: 2255_V1+1 (tempus)

description: Library name: 2255_V1+1


title: dcg+abd-3

value: 3rd instar fat body abdomen region


title: dcg+head-1


title: 12-week HP Dagla WT Sample 3

description: Library name: dagla_12w_HP_WT_3

tag: genotype


title: 12-week HP Dagla WT Sample 2

description: Library name: dagla_12w_HP_WT_2

tag: age


title: PIP d6 CD45+ rep5

description: Library name: S74

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

value: Cells were collected 6 days after viral transduction

value: live(DAPI-) and CD45+


title: 2255_V1 (tempus)

description: Library name: 2255_V1


title: 12-week HP Dagla WT Sample 1

description: Library name: dagla_12w_HP_WT_1


title: PIP d6 CD45+ rep4

description: Library name: S73


title: dcg-AiBi-4

source_name: 3rd instar fat body

value: 3rd instar fat body


title: PIP d6 CD45+ rep3

description: Library name: S72


title: dcg-AiBi-3


title: dcg+abd-1


title: 12-week HP Dagla -/- Sample 5

description: Library name: dagla_12w_HP_KO_5


title: 2231_V2 (tempus)

description: Library name: 2231_V2

source_name: Blood


title: 2231_V2+1 (tempus)

description: Library name: 2231_V2+1


title: PIP d6 CD45+ rep2

description: Library name: S71


title: dcg-AiBi-2


title: dcg-AiBi-1


title: 12-week HP Dagla -/- Sample 4

description: Library name: dagla_12w_HP_KO_4


title: 2231_V1+1 (tempus)

description: Library name: 2231_V1+1


title: 12-week HP Dagla -/- Sample 3

description: Library name: dagla_12w_HP_KO_3


title: PIP d6 CD45+ rep1

description: Library name: S70


title: 2231_V1 (tempus)

description: Library name: 2231_V1


title: 12-week HP Dagla -/- Sample 2

description: Library name: dagla_12w_HP_KO_2


title: PIP d6 tdT+ rep1

description: Library name: S75


title: dcg+4


title: PIP d3 tdT+CD45+ rep3

description: Library name: S69

value: Cells were collected 3 days after viral transduction

value: live(DAPI-) and tdT+CD45+


title: dcg+3


title: 12-week HP Dagla -/- Sample 1

description: Library name: dagla_12w_HP_KO_1


title: 12-week HP Dagla +/- Sample 5

description: Library name: dagla_12w_HP_HT_5

value: Dagla +/-


title: PIP d3 tdT+CD45+ rep1

description: Library name: S67

value: Cells were transduced with Pu.1, Irf4, Prdm1 (PIP)


title: dcg+2


title: PIP d3 tdT+CD45+ rep2

description: Library name: S68


title: 12-week HP Dagla +/- Sample 4

description: Library name: dagla_12w_HP_HT_4


title: drug_1

city: zhengzhou

first: Deqian

last: Kong

state: henan

address: No.1 Longhu Zhonghuan Road, Jinshui District

institute: The First Affiliated Hospital of Zhengzhou University

description: Library name: sample 4

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:GRCm38.p4）using TopHat（version:2.0.9).
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include lnc_RNA count for each sample.
Supplementary files format and content: tab-delimited text files include gene count for each sample.

source_name: drug group, replicate biosample 1

extract_protocol:
Total RNA was extracted from six samples, and ribosomal RNA was removed. The mRNA was fragmented, and a specific library was constructed using the NEBNext® UltraTM RNA Library Prep Kit for Illumina
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human lens epithelial cells (HLECs)

tag: treatment

value: drug


title: drug_2

description: Library name: sample 5

source_name: drug group, replicate biosample 2


title: PIP d3 tdT+ rep5

description: Library name: S66

value: mouse embryonic fibroblast


title: ctrl_2

description: Library name: sample 2

source_name: control group, replicate biosample 2

value: no


title: 12-week HP Dagla +/- Sample 3

description: Library name: dagla_12w_HP_HT_3


title: PIP d3 tdT+ rep4

description: Library name: S65

value: live(DAPI-) and tdT+


title: 12-week HP Dagla +/- Sample 2

description: Library name: dagla_12w_HP_HT_2

value: Hippocampus


title: ctrl_3

description: Library name: sample 3

source_name: control group, replicate biosample 3


title: PIP d3 tdT+ rep3

description: Library name: S64


title: 12-week HP Dagla +/- Sample 1

description: Library name: dagla_12w_HP_HT_1


title: PIP d3 tdT+ rep2

description: Library name: S63


title: Postmortem, Ventrolateral prefrontal cortex, female, 94 yrs, 6 hr, snRNA-Seq

city: Budapest

first: Karolina

last: Pircs

address: Tűzoltó street 37-47

department: Institute of Translational Medicine

country: Hungary

institute: Semmelweis University

description: Library name: AA106_KP_168_VLPFCX_female_ctrl

data_processing:
Raw base calls were demultiplexed to obtain sample-specific FastQ files and reads were aligned to the GRCh38 genome assembly using the Cell Ranger pipeline (10x Genomics Cell Ranger 7.0.0; RRID:SCR_017344)43 with default parameters and include-introns set to true. The resulting matrix files were used for further analysis. All downstream analysis was done using R (v4.3.1; RRID:SCR_001905) and the standard workflow of Seurat (v4.4.0; RRID:SCR_016341)52. Nuclei with read counts between 1,200 and 100,000, gene counts between 800 and 12,000, and less than 5% mitochondrial transcripts were alone included for the analysis. The data was integrated using Harmony (v1.1.0; RRID:SCR_022206)53, where both sequencing batches and individual samples were regressed out, and the first 39 principal components were chosen. Clusters resolved at a resolution of 0.2 were annotated based on canonical cell type markers of the human prefrontal cortex. Further, any doublets or multiplets detected using scDblFinder (v1.14.0; RRID:SCR_022700)54 were removed.
Assembly: GRCh38
Supplementary files format and content: Compressed .gz files containing tab-separated values and matrix files obtained from Cell Ranger output.

molecule: nuclear RNA

source_name: Postmortem Prefrontal Cortex

extract_protocol:
Post mortem tissue collection: Human post mortem brain tissue samples were obtained from the Human Brain Tissue Bank (Semmelweis University, Budapest, Hungary). Tissue samples were collected from 31 individuals who had not been diagnosed with any psychiatric disorder and neurodegenerative disorders. The brains were removed with a PMI of 2 – 12 hours, drop frozen using dry ice, and stored at −80 °C until further dissection. Samples were punched out from the lateral surface of the prefrontal cortices of the diseased subjects using specialized microdissection needles with 8- and 15-mm internal diameters. While most of the samples were dissected from the ventrolateral prefrontal cortex, some originated from the dorsolateral prefrontal cortex and from the middle frontal gyrus (the dorsal part of which belongs to the dorsolateral prefrontal cortex and its ventral part to the ventrolateral prefrontal cortex). The dissected cortical tissue pellets included both gray and white matter portions within the gyrus. Samples were collected in 1.5 mL Eppendorf tubes and stored at −80 °C until further use. Throughout the microdissection procedure, the tissue samples were kept frozen.  Single-nuclei Isolation: The nuclei isolation from the frozen post mortem brain tissue was performed as described previously in Soderstan et. al. 2018 and Jonsson et al 2021. Briefly, the tissue was thawed and dissociated in ice-cold lysis buffer [0.32 M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM EDTA, 10 mM tris-HCl (pH 8.0), and 1 mM dithiothreitol] using a 1 ml tissue douncer (Wheaton). The homogenate was carefully layered on top of a sucrose cushion [1.8 M sucrose, 3 mM MgAc, 10 mM tris-HCl (pH 8.0), and 1 mM dithiothreitol] before centrifugation at 30,000 g for 2 hours and 15 minutes. After supernatant removal, the pelleted nuclei were softened for 10 minutes in 50 μl of nuclear storage buffer [15% sucrose, 10 mM tris-HCl (pH 7.2), 70 mM KCl, and 2 mM MgCl2] before being resuspended in 300 μl of dilution buffer [10 mM tris-HCl (pH 7.2), 70 mM KCl, and 2 mM MgCl2] and filtered through a cell strainer (70 μm). Nuclei were stained with Draq7 and run through FACS (FACS Aria, BD Biosciences) at 4°C at a low flow rate using a 100 μm nozzle (reanalysis showed >99% purity). 8,500 nuclei were sorted and used for downstream applications (snRNA Sequencing). Detailed protocol can be found at doi: dx.doi.org/10.17504/protocols.io.5jyl8j678g2w/v1.
Nuclei intended for single-nucleus RNA-sequencing (8,500 nuclei per sample) were directly loaded onto the Chromium Next GEM Chip G or Chromium Next GEM Chip K Single Cell Kit along with the reverse transcription master mix following the manufacturer’s protocol for the Chromium Next GEM single cell 3′ kit (PN-1000268, 10x Genomics), to generate single-cell gel beads in emulsion. cDNA amplification was done as per the guidelines from 10x Genomics using 13 cycles of amplification. Sequencing libraries were generated with unique dual indices (TT set A) and pooled for sequencing on a Novaseq6000 using a 100-cycle kit and 28-10-10-90 reads.

value: Postmortem Prefrontal Cortex

tag: brain region

value: Ventrolateral prefrontal cortex

tag: Sex

value: female

tag: age group

value: Old

tag: age (years)

tag: post mortem_interval_(hours)

tag: cause of_death

value: cardiac failure

tag: pre-manifest alzheimer's_disease

value: Negative

tag: sequencing batch


title: drug_3

description: Library name: sample 6

source_name: drug group, replicate biosample 3


title: 4-week TH Dagla WT Sample 6

description: Library name: dagla_4w_TH_WT_6

tag: tissue

value: Thalamus

value: WT


title: PIP d3 tdT+ rep1

description: Library name: S62

value: double homozygous Clec9a(Cre/Cre) Rosa26(tdTomato/tdTomato)

tag: transduction

tag: time

value: Cells were collected 3 days after viral transduction

tag: sorted cells


title: Postmortem, Ventrolateral prefrontal cortex, male, 86 yrs, 3 hr, snRNA-Seq

description: Library name: AA100_KP_164_VLPFCX_male_ctrl

value: male

value: acute cardiac insufficiency

value: Positive


title: dcg+1

value: 3rd instar fat body


title: PIP d3 CD45+ rep5

description: Library name: S61

tag: cell line

tag: cell type

value: mouse embryonic fibroblast

value: Cells were transduced with Pu.1, Irf4, Prdm1 (PIP)

value: live(DAPI-) and CD45+


title: Postmortem, Ventrolateral prefrontal cortex, female, 85 yrs, 8 hr, snRNA-Seq

description: Library name: AA114_KP_283_VLPFCX_female_ctrl

value: Postmortem Prefrontal Cortex

value: stroke;hypertension


title: T3(Sup)

type: RNA

city: Changsha

first: Jianyun

last: Lu

state: Hunan

address: Tongzipo Road, Yuelu District

institute: Third Xiangya Hospital, Central South University

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
T3.txt

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.  A

source_name: SKIN

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

extract_protocol: On average, 50 7 um-thick cryostat sections were prepared for the extraction of total RNA from lesion areas, which were identified by a surgical pathologist using every 10th section stained by May-Giemsa.

value: SKIN

tag: disease

value: normal skin


title: PIP d3 CD45+ rep4

description: Library name: S60

tag: genotype


title: 4-week TH Dagla WT Sample 5

description: Library name: dagla_4w_TH_WT_5

source_name: Thalamus

tag: age


title: PIP d3 CD45+ rep3

description: Library name: S59


title: T2(Sup)

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
T2.txt

value: Female


title: 4-week TH Dagla WT Sample 3

description: Library name: dagla_4w_TH_WT_3


title: 4-week TH Dagla WT Sample 4

description: Library name: dagla_4w_TH_WT_4


title: Postmortem, Ventrolateral prefrontal cortex, male, 81 yrs, 5 hr, snRNA-Seq

description: Library name: AA102_KP_192_VLPFCX_male_ctrl

tag: brain region

value: Ventrolateral prefrontal cortex

value: Old

value: acute ischaemic heart failure;cardiogen shock

value: Negative


title: 4-week TH Dagla WT Sample 2

description: Library name: dagla_4w_TH_WT_2

value: Thalamus

value: WT


title: ctrl_1

description: Library name: sample 1

source_name: control group, replicate biosample 1

value: Human lens epithelial cells (HLECs)

tag: treatment

value: no