title: PB00146-02 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: SMALL_MYCPOS_2

status: Public on Sep 12 2025

type: SRA

city: London

first: Mariia

last: Yuneva

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Library name: SET2504A47

library_source: transcriptomic

data_processing:
RNA-sequencing reads were processed using the nf-core RNA-seq pipeline (version 3.3) with the STAR/RSEM option. Reads were aligned to the mouse genome assembly GRCm38 using Ensembl release 95 transcript annotations. Gene-level abundance estimates were obtained from RSEM and imported into R using the DeSeqDataSetFromMatrix function in DESeq2. Normalization factors were computed per gene, correcting for library size and feature length. Variance stabilizing transformation (VST) was applied to abundance estimates to standardize gene expression across samples.
Assembly: GRCm38 using Ensembl release 95
Supplementary files format and content: VST normalised expression values. Rows are transcripts. Columns are samples.
Supplementary files format and content: Raw counts matrix. Output of RSEM-STAR alignments and counting.. Rows are transcipts. Columns are samples.

molecule: total RNA

organism: Mus musculus

source_name: Mammary gland tumour

extract_protocol:
RNA was extracted from a scoop of frozen tissue and then ground by homogenizing in TRIzol™ following the manufacturer’s protocol.   200ng of extracted RNA was submeeted for RNA sequencing.
KAPA mRNA polyA HyperPrep

tag: tissue

value: Mammary gland tumour

tag: genotype

value: MMTV-MYC

tag: treatment

value: Tumour

tag: batch

value: FVB/N


title: PB00017-01 Flu Year 1 Day 7

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

country: USA

institute: Allen Institute

library_source: transcriptomic single cell

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software (version 3.1.0; Released July 24, 2019), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each Well.
To identify cells originating from each sample, we utilized software tools for HTO quantification and sample demultiplexing to generate separate HDF5-formatted files for each originating sample (as described in Swanson, et al. (2021); DOI: 10.1186/s12859-022-04620-2). This process also removes Cell Barcodes that contain HTOs from multiple samples (doublets or multiplets) or with no detectable sample label (no hash).
After demultiplexing, data from individual samples assembled across all hashed wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For analysis, high quality cells were selected based on the following cutoffs: <10% mitochondria reads, number of genes detected between 200 and 5000, RNA UMIs/cells between 1500 and 750000. After QC filtering, all remaining cells were clustered using a Scanpy (v1.9.6) workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; log transformation using scanpy.pp.log1p; highly variable gene detection using scanpy.pp.highly_variable_genes; scaling of highly variable gene data using sc.pp.scale; Dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

organism: Homo sapiens

source_name: Blood

extract_protocol:
PBMCs were removed from liquid nitrogen and immediately thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca. After adding 30 mL cold AIM V media, cells were re-pelleted and resuspended to the appropriate concentrations for scRNAseq.
scRNAseq libraries were generated using a modified 10x genomics chromium 3′ single cell gene expression assay with Cell Hashing. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq platform. Hashed 10x Genomics scRNA-seq data processing was carried out using BarWare (71) to generate sample-specific output files.

value: Blood

tag: cell type

value: PBMC

tag: subject id

tag: birth year

tag: Sex

value: Male

tag: race

value: Caucasian

tag: cmv status

value: Negative

tag: days since_first_visit

tag: visit

value: Flu Year 1 Day 7

tag: batch id

tag: sample bridging_control

value: FALSE


title: PB00010-02 Flu Year 1 Day 0

value: Flu Year 1 Day 0


title: SMALL_MYCPOS_1

description: Library name: SET2504A46


title: 12WK_MYCPOS_4

description: Library name: SET2504A44

source_name: Mammary gland

value: Mammary gland

value: Hyperplesia


title: 12WK_MYCPOS_5

description: Library name: SET2504A45


title: PB02581-001 Flu Year 3 Stand-Alone

value: Female

value: Flu Year 3 Stand-Alone


title: 12WK_MYCPOS_3

description: Library name: SET2504A43


title: PB02266-01 Immune Variation Day 7

value: Immune Variation Day 7


title: PB02257-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB02480-001 Immune Variation Day 90

value: Immune Variation Day 90


title: 12WK_MYCPOS_1

description: Library name: SET2504A41

value: MMTV-MYC


title: 12WK_MYCPOS_2

description: Library name: SET2504A42

value: FVB/N


title: 6WK_MYCPOS_5

description: Library name: SET2504A40


title: PB01457-01 Flu Year 2 Day 90

value: Blood

value: Flu Year 2 Day 90


title: PB00587-01 Flu Year 2 Day 7

value: PBMC

value: Flu Year 2 Day 7


title: 6WK_MYCPOS_3

description: Library name: SET2504A38


title: PB00040-01 Flu Year 1 Day 90

value: Caucasian

value: Negative

value: Flu Year 1 Day 90


title: PB00576-01 Flu Year 2 Day 0

value: Flu Year 2 Day 0

value: FALSE


title: SMALL_MYCPOS_3

description: Library name: SET2504A48

value: Mammary gland tumour

value: Tumour


title: PB00551-01 Flu Year 2 Day 0

value: Male


title: PB00006-01 Flu Year 1 Day 0

value: Female

value: Flu Year 1 Day 0


title: 6WK_NEG_5

description: Library name: SET2504A35

value: Mammary gland

value: WT

value: Control


title: 6WK_MYCPOS_2

description: Library name: SET2504A37

value: MMTV-MYC

value: Hyperplesia

value: FVB/N


title: 6WK_MYCPOS_1

description: Library name: SET2504A36


title: PB00013-01 Flu Year 1 Day 7

value: Blood

value: PBMC

value: Flu Year 1 Day 7


title: PB02245-02 Immune Variation Day 90

value: Caucasian

value: Negative

value: Immune Variation Day 90


title: 6WK_NEG_2

description: Library name: SET2504A32


title: 6WK_NEG_3

description: Library name: SET2504A33


title: 6WK_NEG_1

description: Library name: SET2504A31


title: PB01538-01 Immune Variation Day 7

value: Immune Variation Day 7

value: FALSE


title: PB01526-01 Immune Variation Day 0

value: Male

value: Immune Variation Day 0


title: 6WK_NEG_4

description: Library name: SET2504A34


title: dRBSdATG, xylA, UTR 300bp, BCM-treated, replicate 2

city: Seoul

first: Sang Woo

last: Seo

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
Library name: Sample52
For the ChIP experiment, anti-E. coli RNA Polymerase β antibody (Biolegend, #663006) was used.

library_source: genomic

data_processing:
The quality of the sequence reads obtained from ChIP-exo was checked by FastQC (version 0.11.8).
The sequence reads were aligned to the reference genome using bowtie (version 1.2.2) with the following options to generate SAM output files: -X 5000 -n 2 -p 3 -3 9 -S. For the raw data generated from NovaSeq 6000, the bowtie options were as follows: -X 5000 -n 2 -p 3 -3 69 -S.
For Bowtie alignment, we updated the reference genome by applying innate mutations in our lab strain. Strains for the lacZ-related experiment are lack of lacY and lacA gene, which, however, does not affect lacZ expression. prepared multiple variants of the reference genome in advance by updating some of the sequences on the genome, such as dRBSdATG and modified UTR, to properly map the sequence reads generated from different genotype samples.
In the xylA samples, the aligned reads were manually normalized by dividing 10^9 × (reads on the xylAB operon and its upstream region) into total reads aligned to genome. The reads from the other gene samples, galE, galP, lacZ, and rhaB, were also normalized respectively in accordance with their operon sequences.
Assembly: NC_000913.3
Supplementary files format and content: gff, normalized counts of sequencing reads around the target region

molecule: genomic DNA

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli K-12 MG1655

extract_protocol:
E. coli cells induced for 4 hours with proper inducer were cross-linked by 1% formaldehyde at room temperature for 30 min. The cross-linked cells were harvested and lysed, followed by sonication for DNA fragmentation. If necessary, cells were treated with 50 μg/mL bicyclomycin (BCM) for 30 minutes or 150 μg/mL rifampicin for 15 minutes prior to harvest.
The sheared DNA was immunoprecipitated by proper antibodies (anti-RNAP β or c-Myc). After binding to chromatin beads, immunoprecipitated DNA was end-repaired, dA-tailed, and ligated with the first adapter using the KAPA HyperPrep Kit (KAPA Biosystems). Adapter-ligated DNA samples were then nick-repaired and exonuclease-treated. The DNA samples were eluted from the beads by reversing protein-DNA crosslinking at 65 °C. Primer extension and second adapter ligation were performed in sequence. Finally, the DNA samples were enriched by PCR, using KAPA HotStart ReadMix in HyperPrep Kit (KAPA Biosystems). DNAs after each reaction were purified and size-selected using either AMPure XP beads (Beckman Coulter, Brea, CA, USA) or Zymo DNA Clean & Concentrator (Zymo, Irvine, CA, USA).

value: Escherichia coli K-12 MG1655

value: Deletion of RBS & start codon of xylA with UTR 300 bp

value: 0.4% D-xylose induction for 4 hours; 50 μg/mL BCM treatment for 30 min


title: PB00343-01 Flu Year 2 Day 7

value: Flu Year 2 Day 7


title: PB00265-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: dRBSdATG, xylA, UTR 300bp, BCM-treated, replicate 1

description:
Library name: Sample51
For the ChIP experiment, anti-E. coli RNA Polymerase β antibody (Biolegend, #663006) was used.


title: PB00335-05 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: xylA, UTR 300bp, BCM-treated, replicate 2

description:
Library name: Sample50
For the ChIP experiment, anti-E. coli RNA Polymerase β antibody (Biolegend, #663006) was used.

value: xylA with UTR 300 bp


title: xylA, UTR 300bp, BCM-treated, replicate 1

description:
Library name: Sample49
For the ChIP experiment, anti-E. coli RNA Polymerase β antibody (Biolegend, #663006) was used.


title: 6WK_MYCPOS_4

description: Library name: SET2504A39

value: Mammary gland

value: MMTV-MYC

value: Hyperplesia

value: FVB/N


title: PB00011-01 Flu Year 1 Day 7

value: Blood

value: PBMC

value: Caucasian

value: Negative

value: Flu Year 1 Day 7


title: pigMLO_D45_B

city: Cheongju

first: Sang-Hwan

last: Hyun

state: Please select your state

address: 1 Chungdae-ro, Seowon-gu

department: Veterinary Medical Center and College of Veterinary Medicine

institute: Chungbuk national university

description:
Library name: Samlpe 6
Day 45 of organoid culture

data_processing:
BCL files were converted to FASTQ using cellranger mkfastq, and processed with cellranger count using the Sscrofa11.1 genome.
Count matrices were aggregated with cellranger aggr, and downstream analysis including filtering, normalization, PCA, clustering, UMAP, and DEG analysis was performed using Seurat v4.3.0.
Assembly: Sscrofa11.1 (GCA_000003025.6)
Supplementary files format and content: Filtered expression matrices (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz) are provided per sample. Additional files include cluster annotations and DEG tables.

organism: Sus scrofa

source_name: Midbrain-like organoid

extract_protocol:
Single-cell suspensions were processed using the Chromium X system and GEM-X Single Cell 3’ v4 Kit (10x Genomics, CG000731). Libraries were constructed via reverse transcription, cDNA amplification, adapter ligation, and PCR enrichment. Quality was assessed with qPCR and Agilent TapeStation.
Single-cell RNA sequencing (scRNA-seq) libraries were prepared using the Chromium X platform following the 10x Genomics GEM-X Single Cell 3’ Reagent Kit v4 protocol (CG000731).

value: Midbrain-like organoid

tag: cell line

value: IVF_1_ pESC_FIW

value: midbrain dopaminergic neurons


title: PB00004-01 Flu Year 1 Day 0

value: Male

value: Flu Year 1 Day 0

value: FALSE


title: PB02242-02 Immune Variation Day 90

value: Female

value: Immune Variation Day 90


title: PB01574-01 Immune Variation Day 7

value: Immune Variation Day 7


title: pigMLO_D28_A

description:
Library name: Sample 3
Day 28 of organoid culture


title: PB01559-01 Immune Variation Day 0

value: Immune Variation Day 0


title: PB00643-01 Flu Year 2 Day 90

value: Flu Year 2 Day 90


title: pigMLO_D28_B

description:
Library name: Sample 4
Day 28 of organoid culture


title: pigMLO_D45_A

description:
Library name: Sample 5
Day 45 of organoid culture


title: PB02330-001 Flu Year 3 Stand-Alone

value: Flu Year 3 Stand-Alone


title: pigMLO_D11_A

description:
Library name: Sample 1
Day 11 of organoid culture


title: PB00372-01 Flu Year 2 Day 7

value: Blood

value: Flu Year 2 Day 7


title: PB00355-01 Flu Year 2 Day 0

value: PBMC

value: Caucasian

value: Flu Year 2 Day 0


title: pigMLO_D11_B

description:
Library name: Sample 2
Day 11 of organoid culture

value: Midbrain-like organoid


title: PB00609-02 Flu Year 2 Day 90

value: Negative


title: PB00035-01 Flu Year 1 Day 90

value: Flu Year 1 Day 90


title: Siberian Hamster, PVN, 24wk SD, Rep 6

city: Glasgow

first: Calum

last: Stewart

address: Jarrett Building, University of Glasgow

institute: University of Glasgow

description:
PVN188
PVNExpressedGenesTranscripts.CSV

data_processing:
Raw reads were demultiplexed and basealled using guppy basecaller
Porechop was used to trim adapters
Filtlong used to select long reads (>25 reads)
Minimap2 used to align reads to Mus musculus genome (GCRm39)
Transcript expression levels generated  using Salmon
Assembly: GRCmm39
Supplementary files format and content: Transcript expression levels generated  using Salmon

molecule: polyA RNA

organism: Phodopus sungorus

source_name: Paraventricular Nucleus Microdissection

extract_protocol:
RNA was extracted using the Qiagen RNEasy plus mini-kit
RNA Libraries were constructed using the PCR_cDNA sequencing barcoding kit (SQK-PCB109, Oxford Nanopore) as per manufacturers instructions

value: Paraventricular Nucleus Microdissection


title: Siberian Hamster, PVN, 28wk SD, Rep 6

description:
PVN172
PVNExpressedGenesTranscripts.CSV


title: PB00007-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7


title: BmN,BG4,rep2

city: Guangzhou

first: Lijun

last: Xiang

state: Guangdong

address: No.55, West of Zhongshan Avenue

department: Guangzhou Key Laboratory of Insect Development Regulation and Application Research

country: China

institute: South China Normal University

description: Library name: BmN_BG4_rep2

data_processing:
The CUT&Tag reads were aligned to the genome GCA_014905235.2 with Bowtie2
CUT&Tag reads were trimmed using TrimGalore, reads were trimmed from 3' end until the final base had a quality score > 20, discarding reads left with < 20 bp
The aligned reads were removed with Picard MarkDuplicates and the BAM files were normalized (bins per million mapped reads, BPM) to generate a bigwig file with the bamCoverage command in deepTools 3.3.0
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=1E-5
Assembly: GCA_014905235.2
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

organism: Bombyx mori

source_name: BmN

growth_protocol: The B. mori strain P50 was obtained from the Research and Development Center of the Sericultural Research Institute, Academy of Agricultural Sciences of Guangdong Province, China. Larvae were reared on fresh mulberry leaves under 14:10 h light/dark cycles at 26 ℃. The B. mori cell line BmN, originally developed from ovarian tissues, was maintained at 28°C in Grace medium (Gibco, New York, USA) supplemented with 10% foetal bovine serum (FBS, Thermo Scientific, MA, USA).

extract_protocol:
1 mL of nuclear lysis buffer (10 mM Tris-HCl, pH=7.4; 10 mM NaCl; 3 mM MgCl₂; 0.1% NP40; 0.1% Tween 20; 0.01% Digoxigenin) was added to resuspend the tissues. The samples were then homogenized using a Dounce homogenizer with 10 strokes each using pestle A and pestle B. The nuclear suspension was filtered through a 40 µm Flowmi Cell strainer, followed by centrifugation at 800 × g for 5 min at 4 °C. The resulting pellet was resuspended in wash buffer. Nuclear integrity was assessed by methylene blue staining, and nuclei concentration was determined using a hemocytometer (BS-QT-1103, Biosharp, Anhui, China) under a Nikon Eclipse Ni DIC microscope (model YTV55).
CUT&Tag according the Hyperactive Universal CUT&Tag Assay Kit protocol (Vazyme, Nanjing, China).Cell counting was performed by using a Cellometer Mini (Nexcelom Bioscience, Boston, MA, USA). pA-Tn5 transposase was used to cut the genome and add a special adaptor sequence to build a library.

value: BmN

value: ovarian cell line

value: WT


title: PB02013-01 Immune Variation Day 90

value: Male

value: Immune Variation Day 90

value: FALSE


title: BmN,BG4,rep1

description: Library name: BmN_BG4_rep1


title: P0,Brian,wildtype,P50 strain,BG4

description: Library name: P0_Bm_Brian_BG4

source_name: Brain

value: Brain

tag: strain


title: PB01560-01 Immune Variation Day 7

value: Blood

value: Immune Variation Day 7


title: PB01544-01 Immune Variation Day 0

value: PBMC

value: Immune Variation Day 0


title: Siberian Hamster, PVN, 12wk SD, Rep 6

description:
PVN280
PVNExpressedGenesTranscripts.CSV


title: PB00644-01 Flu Year 2 Day 90

value: Caucasian

value: Flu Year 2 Day 90


title: Siberian Hamster, PVN, 32wk SD, Rep 6

description:
PVN113
PVNExpressedGenesTranscripts.CSV


title: PB00400-01 Flu Year 2 Day 7

value: Negative

value: Flu Year 2 Day 7


title: PB00378-01 Flu Year 2 Day 0

value: Flu Year 2 Day 0


title: Siberian Hamster, PVN, 8wk SD, Rep 6

description:
PVN397
PVNExpressedGenesTranscripts.CSV

value: Paraventricular Nucleus Microdissection


title: L5D3,Fat body,wildtype,P50 strain,BG4,rep1

description: Library name: L5D3_Bm_Fat_body_BG4_rep1

source_name: Fat body

value: Fat body


title: Siberian Hamster, PVN, 4wk SD, Rep 6

description:
PVN314
PVNExpressedGenesTranscripts.CSV


title: PB00274-03 Flu Year 2 Stand-Alone

value: Flu Year 2 Stand-Alone


title: PB00276-03 Flu Year 2 Stand-Alone

value: Female


title: PB00034-01 Flu Year 1 Day 90

value: Male

value: Flu Year 1 Day 90


title: PB00009-01 Flu Year 1 Day 7

value: Flu Year 1 Day 7

value: FALSE


title: Siberian Hamster, PVN, LD, Rep 6

description:
PVN141
PVNExpressedGenesTranscripts.CSV


title: L5D3,Brian,wildtype,P50 strain,BG4,rep2

description: Library name: L5D3_Bm_Brian_BG4_rep2

value: Brain

value: WT


title: PB00002-01 Flu Year 1 Day 0

value: Blood

value: PBMC

value: Flu Year 1 Day 0


title: PB00037-01 Flu Year 1 Day 90

value: Caucasian


title: L5D3,Brian,wildtype,P50 strain,BG4,rep1

description: Library name: L5D3_Bm_Brian_BG4_rep1


title: Siberian Hamster, PVN, 32wk SD, Rep 5

description:
PVN152
PVNExpressedGenesTranscripts.CSV


title: Siberian Hamster, PVN, 20wk SD, Rep 6

description:
PVN217
PVNExpressedGenesTranscripts.CSV


title: L5D3, IgG

description: Library name: L5D3_Bm_IgG

source_name: Brain&Fat body

value: Brain&Fat body


title: Siberian Hamster, PVN, 16wk SD, Rep 6

description:
PVN265
PVNExpressedGenesTranscripts.CSV


title: PB00003-01 Flu Year 1 Day 0

value: Negative


title: PB00001-01 Flu Year 1 Day 0


title: Siberian Hamster, PVN, 28wk SD, Rep 5

description:
PVN163
PVNExpressedGenesTranscripts.CSV


title: L5D3,Fat body,wildtype,P50 strain,ATAC-seq,rep2

description: Library name: L5D3_Bm_Fat_body_ATAC_rep2

data_processing:
The reads were aligned to the genome GCA_014905235.2 with Bowtie2
Reads were trimmed using TrimGalore, reads were trimmed from 3' end until the final base had a quality score > 20, discarding reads left with < 20 bp
The aligned reads were removed with Picard MarkDuplicates and the BAM files were normalized (bins per million mapped reads, BPM) to generate a bigwig file with the bamCoverage command in deepTools 3.3.0
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=1E-5
Assembly: GCA_014905235.2
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: The B. mori strain P50 was obtained from the Research and Development Center of the Sericultural Research Institute, Academy of Agricultural Sciences of Guangdong Province, China. Larvae were reared on fresh mulberry leaves under 14:10 h light/dark cycles at 26 ℃.

extract_protocol:
1 mL of nuclear lysis buffer (10 mM Tris-HCl, pH=7.4; 10 mM NaCl; 3 mM MgCl₂; 0.1% NP40; 0.1% Tween 20; 0.01% Digoxigenin) was added to resuspend the tissues. The samples were then homogenized using a Dounce homogenizer with 10 strokes each using pestle A and pestle B. The nuclear suspension was filtered through a 40 µm Flowmi Cell strainer, followed by centrifugation at 800 × g for 5 min at 4 °C. The resulting pellet was resuspended in wash buffer. Nuclear integrity was assessed by methylene blue staining, and nuclei concentration was determined using a hemocytometer (BS-QT-1103, Biosharp, Anhui, China) under a Nikon Eclipse Ni DIC microscope (model YTV55).
50,000 nuclei were resuspended in 1 mL of cold wash buffer and centrifuged at 500 × g for 5 min at 4 ℃. The pellet was resuspended in 40 μL of tagmentation buffer (0.3× PBS, 0.1% Tween-20, 0.01% digitonin, 1× TD buffer, 1× pA-Tn5 transposome mix) and incubated at 37 °C for 30 min. The reaction was stopped by adding 10 μL of stop buffer, followed by incubation at 55 °C for 5 min. DNA was then purified using 100 μL of Tagment DNA extract beads and eluted in 37 μL of elution buffer. The purified DNA was amplified with 5× AmpliMix using the N5 and N7 index primers. The purified DNA libraries were size selected using NovoNGS® DNA Clean Beads (N240, Novoprotein, Shanghai, China) and sequenced on the NovaSeq X platform.


title: Siberian Hamster, PVN, 24wk SD, Rep 5

description:
PVN180
PVNExpressedGenesTranscripts.CSV


title: L5D3,Fat body,wildtype,P50 strain,BG4,rep2

description: Library name: L5D3_Bm_Fat_body_BG4_rep2


title: VI PT#25 Mix mTAA_hTCR

city: Houston

first: Shamika

last: Ketkar

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of edicine

description:
Library name: VI PT_25 Mix_hTCR
5v2_VI_mix_1_hTCR_library_S17
VImix_barcodes.tsv.gz
VImix_features.tsv.gz
VImix_matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)”. The Seurat R package (v4.4.0) was used to run principal components analysis (PCA), t-stochastic neighbor embedding (t-SNE), and k-means clustering algorithms to visualize clustered cells in a two-dimensional space.
Assembly: GRCh38/ hg38
Supplementary files format and content: Tab separated value files and matrix files
Library strategy: TCR-Seq

source_name: Peripheral blood

extract_protocol:
mTAA-T cells were thawed, rested in T cell medium and resuspended at 2 × 10^6 cells/ml, and 200 μl was added per well of a 96-well plate. mTAA-T cells were incubated overnight with either 200ng of stimulating pepmix (PRAME, SSX2, MAGEA4, NY-ESO-1, and Survivin) or DMSO alone (unstimulated control). The following day, cells were harvested and passed through a 30-μm cell strainer, and dead cells were magnetically removed (Dead Cell Removal kit, Miltenyi Biotec).
The resulting single-cell suspensions (1 × 10^5 cells/100 μl in RPMI + 10% fetal bovine serum) were loaded onto a Chromium chip, and captured with barcoded gel beads at a target rate of ~5000 cells per patient sample (10x Genomics, Pleasanton, CA). Barcoded and amplified cDNAs were divided into two fractions for TCR V(D)J enrichment and 5′ gene expression analysis. V(D)J and 5′ expression libraries were pooled and sequenced by Illumina NovaSeq sequencer [read 1, 26 base pairs (bp); index, 8 bp; read 2, 98 bp].

value: Peripheral blood

value: Primary cell culture

value: T cell (autologous, expanded)

value: mTAA


title: L5D3,Fat body,wildtype,P50 strain,ATAC-seq,rep1

description: Library name: L5D3_Bm_Fat_body_ATAC_rep1

value: Fat body


title: SA PT#12 Mix mTAA_hTCR

description:
Library name: SA PT_12 Mix_hTCR
5v2_Samix_3_hTCR_library_S13
SAmix_barcodes.tsv.gz
SAmix_features.tsv.gz
SAmix_matrix.mtx.gz


title: Siberian Hamster, PVN, 20wk SD, Rep 5

description:
PVN216
PVNExpressedGenesTranscripts.CSV

value: Paraventricular Nucleus Microdissection


title: MT PT#9 Mix mTAA_hTCR

description:
Library name: MT PT_9 Mix_hTCR
5v2_MTmix1_Htcr_library_S11
MTmix_barcodes.tsv.gz
MTmix_features.tsv.gz
MTmix_matrix.mtx.gz


title: Siberian Hamster, PVN, 16wk SD, Rep 5

description:
PVN283
PVNExpressedGenesTranscripts.CSV


title: L5D3,Brian,wildtype,P50 strain,ATAC-seq,rep2

description: Library name: L5D3_Bm_Brain_ATAC_rep2


title: L5D3,Brian,wildtype,P50 strain,ATAC-seq,rep1

description: Library name: L5D3_Bm_Brain_ATAC_rep1


title: JL PT#5 Mix mTAA_hTCR

description:
Library name: JL PT_5 Mix_hTCR
5v2_JL_mix_3_hTCR_library_S19
JLmix_barcodes.tsv.gz
JLmix_features.tsv.gz
JLmix_matrix.mtx.gz


title: VI PT#25 Neg_hTCR

description:
Library name: VI PT_25 Neg_hTCR
5v2_VI_neg_2_hTCR_library_S18
VIneg_barcodes.tsv.gz
VIneg_features.tsv.gz
VIneg_matrix.mtx.gz

value: Negitive


title: SA PT#12 Neg_hTCR

description:
Library name: SA PT_12 Neg_hTCR
5v2_SAneg4_hTCR_library_S14
SAneg_barcodes.tsv.gz
SAneg_features.tsv.gz
SAneg_matrix.mtx.gz


title: Siberian Hamster, PVN, 12wk SD, Rep 5

description:
PVN278
PVNExpressedGenesTranscripts.CSV


title: Siberian Hamster, PVN, 8wk SD, Rep 5

description:
PVN306
PVNExpressedGenesTranscripts.CSV


title: MT PT#9 Neg_hTCR

description:
Library name: MT PT_9 Neg_hTCR
5v2_Mtneg_2_Htcr_library_S12
MTneg_barcodes.tsv.gz
MTneg_features.tsv.gz
MTneg_matrix.mtx.gz


title: JL PT#5 Neg_hTCR

description:
Library name: JL PT_5 Neg_hTCR
5v2_JL_neg_4_hTCR_library_S20
JLneg_barcodes.tsv.gz
JLneg_features.tsv.gz
JLneg_matrix.mtx.gz


title: Siberian Hamster, PVN, 4wk SD, Rep 5

description:
PVN352
PVNExpressedGenesTranscripts.CSV


title: VI PT#25 Mix mTAA_GEX

description:
Library name: VI PT_25 Mix_GEX
5v2_VI_mix_1_GEX_S7

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)”. The Seurat R package (v4.4.0) was used to run principal components analysis (PCA), t-stochastic neighbor embedding (t-SNE), and k-means clustering algorithms to visualize clustered cells in a two-dimensional space.
Assembly: GRCh38/ hg38
Supplementary files format and content: Tab separated value files and matrix files


title: L5D3,Brian,wildtype,P50 strain,RNA-seq,rep3

description: Library name: L5D3_Bm_brain_rep3

data_processing:
The reads were aligned to the genome GCA_014905235.2 with Hisat2.
RNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using TrimGalore, discarding reads left with < 20 bp.
RAW counts table file indicating the number of reads per gene in each sample was generated using FeatureCounts
The transcripts per million (TPM) of each gene was calculated based on the gene expression unit that was normalized for sequencing depth
Assembly: GCA_014905235.2
Supplementary files format and content: tab-delimited text files include rawcounts for each Sample
Supplementary files format and content: xls files include TPM values for each Sample

extract_protocol:
Total RNA wasextracted using Trizol reagent kit (Invitrogen,Carlsbad,CA,USA). After 1 μg total RNA for the library construction
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).

tag: time point

value: at the 3rd day of the 5th larval instar


title: PB00008-01 Flu Year 1 Day 7

tag: tissue

value: Female

value: Flu Year 1 Day 7

value: FALSE


title: L5D3,Brian,wildtype,P50 strain,RNA-seq,rep2

description: Library name: L5D3_Bm_brain_rep2

value: Brain

tag: genotype

value: WT


title: Expanded bispecific-secreting T cells, PBMC starting material, donor 3

city: Baltimore

first: Natalie

last: Holl

state: MD

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University School of Medicine

data_processing:
Reads were aligned to a reference genome using Hisat2 v2.0.5.
Fragments mapped to each gene were quantified using featureCounts v1.5.0-p3.
Differential expression was assessed using DESeq2Rpackage v1.20.0.
Assembly: hg38
Supplementary files format and content: Excel file containing gene counts

source_name: T cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from fresh donor blood by layering over Lymphoprep (STEMCELL) and centrifuging. Buffy coat was collected and washed. PBMCs were frozen in complete RPMI with 10% DMSO and stored long-term in liquid nitrogen.  CD4+ and CD8+ cells were isolated from thawed PBMCs using a 1:1 mixture of CD4 and CD8 MACS microbeads (Miltenyi) following the manufacturer's instructions. After purity was confirmed with flow cytometry, selected cells and unselected cells were plated on anti-CD3- and anti-CD28-coated 24-well plates in RPMI complete with 10% FBS and 2mM of GlutaMAX (Gibco).  The day after activation, cells were fed with fresh complete medium supplemented with 10 ng/mL recombinant human IL-7 (rhIL-7) and 5 ng/mL recombinant human IL-15 (rhIL-15, Biological Resources Branch Preclinical Biorepository, NCI).).  Two days after activation, cells were transduced with CD123xCD3 bispecific engager construct by plating on virus immobilized to 24-well plates coated with RetroNectin (Takara Bio). Cells were removed from RetroNectin on day 4 after activation and expanded in 24-well tissue culture-treated plates. T cells were refreshed with complete RPMI supplemented with rhIL-7 and rhIL-15 every 2-3 days. On day 7 after activation, 1e6 engineered T cells were pelleted, frozen, and stored at -80°C until processing.

extract_protocol:
Total RNA was isolated from lysed cells using a RNeasy mini kit (QIAGEN) following the manufacturer’s protocol.
Bulk RNA sequencing was performed by Novogene using a non-directional library and a sequencing depth of 20M reads. Briefly, a non-directional library was prepared by purifying mRNA using poly-T oligo-attached magnetic beads, fragmenting, converting to cDNA, and PCR amplification after end repair, A-tailing, and adapter ligation. Libraries were sequenced using an Illumina platform and clean reads were processed.

value: T cells


title: RT PT#42 Mix mTAA_GEX

description:
Library name: RT PT_42 Mix_GEX
EN_72858_S3

tag: treatment


title: BMJ PT#53 Mix mTAA_hTCR

description:
Library name: BMJ PT_53 Mix_hTCR
5v2_BMJmix5_hTCR_library_S15
BMJmix_barcodes.tsv.gz
BMJmix_features.tsv.gz
BMJmix_matrix.mtx.gz


title: BMJ PT#53 Mix mTAA_GEX

description:
Library name: BMJ PT_53 Mix_GEX
5v2_BMJmix5_GEX_S5


title: L5D3,Brian,wildtype,P50 strain,RNA-seq,rep1

description: Library name: L5D3_Bm_brain_rep1


title: SA PT#12 Mix mTAA_GEX

description:
Library name: SA PT_12 Mix_GEX
5v2_Samix_3_GEX_S3


title: Siberian Hamster, PVN, 32wk SD, Rep 4

description:
PVN153
PVNExpressedGenesTranscripts.CSV


title: BMJ PT#53 Neg_hTCR

description:
Library name: BMJ PT_53 Neg_hTCR
5v2_BMJneg_6_hTCR_library_S16
BMJneg_barcodes.tsv.gz
BMJneg_features.tsv.gz
BMJneg_matrix.mtx.gz


title: JL PT#5 Mix mTAA_GEX

description:
Library name: JL PT_5 Mix_GEX
5v2_JL_mix_3_GEX_S9


title: Siberian Hamster, PVN, 28wk SD, Rep 4

description:
PVN162
PVNExpressedGenesTranscripts.CSV


title: MS PT#3 Mix mTAA_GEX

description:
Library name: MS PT_3 Mix_GEX
EN_72856_S1


title: Expanded bispecific-secreting T cells, PBMC starting material, donor 2


title: VI PT#25 Neg_GEX

description:
Library name: VI PT_25 Neg_GEX
5v2_VI_neg_2_GEX_S8


title: Siberian Hamster, PVN, 24wk SD, Rep 4

description:
PVN196
PVNExpressedGenesTranscripts.CSV


title: Expanded bispecific-secreting T cells, CD4+ and CD8+ starting material, donor 3


title: Expanded bispecific-secreting T cells, PBMC starting material, donor 1


title: SA PT#12 Neg_GEX

description:
Library name: SA PT_12 Neg_GEX
5v2_SAneg4_GEX_S4


title: MT PT#9 Neg_GEX

description:
Library name: MT PT_9 Neg_GEX
5v2_Mtneg_2_GEX_S2


title: JL PT#5 Neg_GEX

description:
Library name: JL PT_5 Neg_GEX
5v2_JL_neg_4_GEX_S10


title: Siberian Hamster, PVN, 16wk SD, Rep 4

description:
PVN255
PVNExpressedGenesTranscripts.CSV


title: Expanded bispecific-secreting T cells, CD4+ and CD8+ starting material, donor 1


title: MS PT#3 Neg_GEX

description:
Library name: MS PT_3 Neg_GEX
EN_72857_S2


title: Siberian Hamster, PVN, LD, Rep 5

description:
PVN238
PVNExpressedGenesTranscripts.CSV


title: Siberian Hamster, PVN, 12wk SD, Rep 4

description:
PVN289
PVNExpressedGenesTranscripts.CSV


title: Siberian Hamster, PVN, 8wk SD, Rep 4

description:
PVN398
PVNExpressedGenesTranscripts.CSV


title: Activated-Mock_ATAC9_1

city: Pamplona

first: Laura

last: Pilar Aguado Alvaro

address: Av. de Pío XII, 55

country: Spain

institute: Center for Applied Medical Research (CIMA)- University of Navarra

description: Primary Cas9 cardiac fibroblasts were treated with DMSO vehicle condition

data_processing:
We followed the ATAC-seq nf-core pipeline
ATAC-seq reads were trimmed with default parameters using Trim Galore v0.6.6 with Cutadapt v3.4
ATAC-seq reads were aligned to the GRCm38/mm10 reference genome assembly using Bowtie version 2.3.4.2 with parameters -X 1000 --no-discordant --no-mixed --very-sensitive
we removed duplicated regions with Picard v2.25.4 and filtered out ENCODE blacklist regions v2.0 and non-interesting chromosomes
We removed Tn5 adaptors with alignmentSieve v3.5.1
We pooled replicates and converted the paired BAM files to single-read bed format using function bamToBed from BEDTools v2.27.1
Peaks were called uing MACS v2.2.7.1 with parameters –broad -f BED --keep-dup all --nomodel --shift -75 --extsize 150
Assembly: GRCm38/mm10 or GRCh38
Supplementary files format and content: broadPeak

source_name: Heart

growth_protocol: Cardiac fibroblasts were isolated from Cas9-mice and seeded on serum-free media (DMEM KO + 20% knockout serum replacement (KSR) (Gibco) + 1% non-essential amino acids (NEAA) (Gibco) + 100 μM beta-mercaptoethanol (Gibco) + 1% P/S + 1% L-Glutamine)

extract_protocol:
Cells expressing sgRNAs (BFP+) were FACS sorted in 1X PBS + 0.05% BSA, pelleted and permeabilized in 1X TD buffer containing 2 ul Tn5 enzyme (Illumina) and 0.01% Digtonin in Molecular Biology Grade water
Omni-ATAC protocol: Tagmentation was performed at 37 ºC for 30 minutes with agitation at 1000 rpm, then stopped by adding EDTA 5 mM final concentration. Next, 2 uL of Proteinase K were added and the samples were incubated for 30 minutes at 40 ºC. Genomic DNA was purified with a 2X SPRI cleanup and tagmented sites were PCR-amplified with 25 uL Kappa HIFI 2X and 2.5 uL of 10 uM P5-i5-read1 and P7-i7-Read2 primers. The PCR cycling conditions are: 5 min at 72 ºC, 10 x [2 min at 98 ºC, 20 s at 98 ºC, 30s at 60 ºC, 1 minute at 72 ºC] 3 min at 72 ºC. Amplified ATAC-seq libraries were purified with a 1.6X SPRI Cleanup, quantified using the Qubit dsDNA high sensitivity assay kit, and then analysed on a Tape Station 4000. ATAC-seq libraries were sequenced at 50 million reads on a NextSeq 2000.

treatment_protocol: Primary Cas9 cardiac fibroblasts were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors or treated with NU-9056 chemical inhibitor of Kat5 Chromatin factor

value: Heart

value: Fibroblast

value: TGFb


title: Activated-Mock_ATAC9_2


title: B173-PC flex scRNA-seq

description:
SRR30239537, SRR30239518, SRR30239519, SRR30239520, SRR30239502, SRR30239501, SRR30239517, SRR30239516, SRR30239515, SRR30239514, SRR30239512, SRR30239511, SRR30239510, SRR30239509, SRR30239508, SRR30239507, SRR30239506, SRR30239485, SRR30239483, SRR30239482, SRR30239480, SRR30239500, SRR30239499, SRR30239498
10x Flex ligation probe-based sequencing

library_source: other

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software using the  Fixed RNA Profiling capability (version 7.0.0, released May 17, 2022), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each sample
Data from individual samples assembled across all wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
For all initial analyses, we used a Python single-cell data analysis package – Scanpy (v1.9.6). High quality cells were selected based on the following cutoffs: <4.5% mitochondria reads, number of genes detected between 500 and 5000, RNA UMIs/cells less than 12000 and number of reads less than 30000. Doublets were detected and filtered out with the Scrublet package accessed through scanpy.external.pp.scrublet call and the doublet filtration threshold was set at less than 0.2
After QC filtering, all remaining cells were clustered using a workflow that consisted of normalization using scanpy.pp.normalize_total with the parameter target_sum = 1e4; natural log transformation using scanpy.pp.log1p; dimensionality reduction using scanpy.tl.pca with the parameter svd_solver = 'arpack'; nearest neighbor distance matrix and neighborhood graph computed using scanpy.pp.neighbors with the parameters n_neighbors=50, use_rep='X_pca', n_pcs=30;
Assembly: GRCh38/hg38
Supplementary files format and content: h5 files

molecule: other

extract_protocol:
PBMCs were removed from liquid nitrogen and immediately thawed in a 37°C water bath. Cells were diluted dropwise into 40 mL AIM V media (Thermo Fisher Scientific) pre-warmed to 37°C. Cells were pelleted at 400 x g for 5–10 min at 4–10°C, resuspended in 5 mL cold AIM V media, and counted using a Cellometer Spectrum or Cellaca. After adding 30 mL cold AIM V media, cells were re-pelleted and resuspended to the appropriate concentrations for scRNAseq.
scRNAseq libraries were generated using a modified 10x genomics flex single cell gene expression assay. Sample libraries were constructed across different batches, with the addition of a common healthy donor leukopak sample in each library as batch control. Libraries were sequenced on the Illumina Novaseq 6000 or X platform.

value: Blood

value: PBMC

value: pooled male and female

tag: pooled sample_id

tag: probe barcode_id


title: Siberian Hamster, PVN, 4wk SD, Rep 4

description:
PVN351
PVNExpressedGenesTranscripts.CSV

tag: cell type


title: MT PT#9 Mix mTAA_GEX

description:
Library name: MT PT_9 Mix_GEX
5v2_MTmix1_GEX_S1

value: Peripheral blood

value: Primary cell culture

value: T cell (autologous, expanded)

value: mTAA


title: Siberian Hamster, PVN, LD, Rep 4

description:
PVN247
PVNExpressedGenesTranscripts.CSV

value: Paraventricular Nucleus Microdissection


title: Siberian Hamster, PVN, 20wk SD, Rep 4

description:
PVN231
PVNExpressedGenesTranscripts.CSV


title: Activated-Kat5_ATAC9_2

description: Primary Cas9 cardiac fibroblasts were treated with NU-9056 chemical inhibitor of Kat5 Chromatin factor


title: RT PT#42 Neg_GEX

description:
Library name: RT PT_42 Neg_GEX
EN_72859_S4

value: Negitive


title: B173-PA flex scRNA-seq

description:
SRR30239410, SRR30239409, SRR30239408, SRR30239407, SRR30239406, SRR30239405, SRR30239404, SRR30239403, SRR30239420, SRR30239401, SRR30239400, SRR30239471, SRR30239451, SRR30239450, SRR30239449, SRR30239448, SRR30239464, SRR30239463, SRR30239461, SRR30239460, SRR30239459, SRR30239458, SRR30239457, SRR30239456
10x Flex ligation probe-based sequencing

tag: subject id


title: B172-PC flex scRNA-seq

description:
SRR30239415, SRR30239414, SRR30239432, SRR30239431, SRR30239430, SRR30239429, SRR30239428, SRR30239427, SRR30239426, SRR30239425, SRR30239424, SRR30239423, SRR30239421, SRR30239419, SRR30239418, SRR30239417, SRR30239470, SRR30239469, SRR30239468, SRR30239467, SRR30239466, SRR30239465, SRR30239412, SRR30239411
10x Flex ligation probe-based sequencing

tag: Sex


title: exVivo_OP2_TGFb_2

description: Primary Cas9 cardiac fibroblasts were transduced with Lentiviral-CRISPR library containing sgRNAs targeting specific Chromatin factors

data_processing:
Raw reads were processed and aligned to the GRCm38/mm10 reference genome assembly (refdata-gex-mm10-2020-A) using the software cellranger count (version 6.1.1).
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: standard cell ranger output files: a cell-gene count matrix in HDF5 format and a "protospacer_calls_per_cell" table mapping cells to a CRISPR guides. For details see: https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-crispr-overview and https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-gex-overview

extract_protocol:
Cells expressing sgRNAs (BFP+)cardiac fibroblasts were FACS-sorted and processed in a 10X single-cell RNA-seq partition aimed at a final coverage of 200 single-cells per sgRNA
Single-cell libraries were generated using the Chromium Next GEM Single-Cell 3' Reagent Kits v3.1 (Dual Index) using the 10x Genomics manufacturer recommended protocol


title: B173-PB flex scRNA-seq

description:
SRR30239455, SRR30239454, SRR30239453, SRR30239452, SRR30239540, SRR30239538, SRR30239539, SRR30239521, SRR30239522, SRR30239523, SRR30239524, SRR30239503, SRR30239504, SRR30239505, SRR30239526, SRR30239527, SRR30239528, SRR30239529, SRR30239530, SRR30239531, SRR30239532, SRR30239533, SRR30239534, SRR30239535
10x Flex ligation probe-based sequencing

tag: race


title: Activated-Kat5_ATAC9_1


title: Siberian Hamster, PVN, 32wk SD, Rep 3

description:
PVN160
PVNExpressedGenesTranscripts.CSV


title: exVivo_OP2_TGFb_1

treatment_protocol: Primary Cas9 cardiac fibroblasts were transduced with Lentiviral-CRISPR library containing sgRNAs targeting specific Chromatin factors


title: B172-PA flex scRNA-seq

description:
SRR30239543, SRR30239542, SRR30239492, SRR30239434, SRR30239445, SRR30239433, SRR30239422, SRR30239413, SRR30239402, SRR30239462, SRR30239541, SRR30239525, SRR30239536, SRR30239513, SRR30239481, SRR30239497, SRR30239496, SRR30239495, SRR30239494, SRR30239493, SRR30239491, SRR30239490, SRR30239489, SRR30239488
10x Flex ligation probe-based sequencing

tag: cmv status


title: B163-PC flex scRNA-seq

description:
SRR30204383, SRR30204382, SRR30204381, SRR30204380, SRR30204379, SRR30204378, SRR30204376, SRR30204375
10x Flex ligation probe-based sequencing


title: Siberian Hamster, PVN, 24wk SD, Rep 3

description:
PVN187
PVNExpressedGenesTranscripts.CSV


title: B172-PB flex scRNA-seq

description:
SRR30239487, SRR30239486, SRR30239484, SRR30239438, SRR30239437, SRR30239435, SRR30239479, SRR30239478, SRR30239477, SRR30239476, SRR30239475, SRR30239474, SRR30239473, SRR30239472, SRR30239447, SRR30239446, SRR30239444, SRR30239443, SRR30239442, SRR30239441, SRR30239440, SRR30239439, SRR30239436, SRR30239416
10x Flex ligation probe-based sequencing


title: B171-PC flex scRNA-seq

description:
SRR30204393, SRR30204392, SRR30204391, SRR30204390, SRR30204389, SRR30204388, SRR30204363, SRR30204362, SRR30204361, SRR30204360, SRR30204358, SRR30204357, SRR30204356, SRR30204355, SRR30204354, SRR30204353, SRR30204352, SRR30204351, SRR30204350, SRR30204349, SRR30204347, SRR30204346, SRR30204345, SRR30204344
10x Flex ligation probe-based sequencing


title: B171-PA flex scRNA-seq

description:
SRR30204374, SRR30204373, SRR30204372, SRR30204371, SRR30204370, SRR30204369, SRR30204368, SRR30204367, SRR30204365, SRR30204364, SRR30204291, SRR30204290, SRR30204289, SRR30204288, SRR30204287, SRR30204286, SRR30204285, SRR30204284, SRR30204282, SRR30204281, SRR30204280, SRR30204279, SRR30204278, SRR30204277
10x Flex ligation probe-based sequencing


title: B171-PB flex scRNA-seq

description:
SRR30204276, SRR30204275, SRR30204274, SRR30204273, SRR30204271, SRR30204270, SRR30204269, SRR30204268, SRR30204411, SRR30204410, SRR30204409, SRR30204408, SRR30204407, SRR30204406, SRR30204404, SRR30204403, SRR30204402, SRR30204401, SRR30204400, SRR30204399, SRR30204398, SRR30204397, SRR30204396, SRR30204395
10x Flex ligation probe-based sequencing


title: exVivo_OP2_resting_2

value: Unstimulated


title: Siberian Hamster, PVN, 28wk SD, Rep 3

description:
PVN165
PVNExpressedGenesTranscripts.CSV


title: Siberian Hamster, PVN, 20wk SD, Rep 3

description:
PVN226
PVNExpressedGenesTranscripts.CSV


title: Expanded bispecific-secreting T cells, CD4+ and CD8+ starting material, donor 2


title: exVivo_OP2_resting_1


title: B155-PC flex scRNA-seq

description:
SRR30204317, SRR30204316, SRR30204315, SRR30204314, SRR30204313, SRR30204312, SRR30204310, SRR30204309, SRR30204308, SRR30204307, SRR30204306, SRR30204305, SRR30204304, SRR30204303, SRR30204302, SRR30204301, SRR30204299, SRR30204298, SRR30204297, SRR30204296, SRR30204295, SRR30204294, SRR30204293, SRR30204292
10x Flex ligation probe-based sequencing

value: FALSE


title: B151-PB flex scRNA-seq

description:
SRR30204300, SRR30204265, SRR30204412, SRR30204377, SRR30204366, SRR30204283, SRR30204272, SRR30204405
10x Flex ligation probe-based sequencing


title: Siberian Hamster, PVN, 16wk SD, Rep 3

description:
PVN251
PVNExpressedGenesTranscripts.CSV


title: BMJ PT#53 Neg_GEX

description:
Library name: BMJ PT_53 Neg_GEX
5v2_BMJneg_6_GEX_S6


title: B163-PA flex scRNA-seq

description:
SRR30204267, SRR30204266, SRR30204264, SRR30204263, SRR30204262, SRR30204261, SRR30204260, SRR30204259
10x Flex ligation probe-based sequencing


title: Quiescent_OP1L_NM_NA_Rep1


title: Siberian Hamster, PVN, 12wk SD, Rep 3

description:
PVN276
PVNExpressedGenesTranscripts.CSV


title: exVivo_OP2_IL1b_2


title: B163-PB flex scRNA-seq

description:
SRR30204258, SRR30204257, SRR30204256, SRR30204254, SRR30204387, SRR30204386, SRR30204385, SRR30204384
10x Flex ligation probe-based sequencing


title: Siberian Hamster, PVN, 4wk SD, Rep 3

description:
PVN332
PVNExpressedGenesTranscripts.CSV


title: Quiescent_OP1L_NM_NA_Rep2


title: exVivo_OP2_IL1b_1


title: Siberian Hamster, PVN, LD, Rep 3

description:
PVN248
PVNExpressedGenesTranscripts.CSV


title: Siberian Hamster, PVN, 32wk SD, Rep 2

description:
PVN149
PVNExpressedGenesTranscripts.CSV


title: PB03209-003 flex scRNA-seq

tag: age at_enrollment

value: Male

value: Asian

value: Positive


title: PB03304-003 flex scRNA-seq

description:
SRR30239537, SRR30239518, SRR30239519, SRR30239520, SRR30239502, SRR30239501, SRR30239517, SRR30239516, SRR30239515, SRR30239514, SRR30239512, SRR30239511, SRR30239510, SRR30239509, SRR30239508, SRR30239507, SRR30239506, SRR30239485, SRR30239483, SRR30239482, SRR30239480, SRR30239500, SRR30239499, SRR30239498
10x Flex ligation probe-based sequencing

value: Caucasian


title: PB03320-003 flex scRNA-seq

value: Female

value: Hispanic or Latino origin


title: Activated_OP1L_NM_NA_Rep1

value: Heart

value: Fibroblast

value: TGFb


title: PB03207-003 flex scRNA-seq

value: Blood

value: PBMC


title: PB03210-003 flex scRNA-seq


title: Activated_OP1L_NM_NA_Rep2


title: PB03333-003 flex scRNA-seq

value: Negative


title: PB03345-001 flex scRNA-seq


title: PB03315-003 flex scRNA-seq


title: B155-PB flex scRNA-seq

description:
SRR30204234, SRR30204233, SRR30204232, SRR30204231, SRR30204339, SRR30204338, SRR30204337, SRR30204336, SRR30204335, SRR30204334, SRR30204332, SRR30204331, SRR30204330, SRR30204329, SRR30204328, SRR30204327, SRR30204326, SRR30204325, SRR30204324, SRR30204323, SRR30204321, SRR30204320, SRR30204319, SRR30204318
10x Flex ligation probe-based sequencing

value: pooled male and female


title: Siberian Hamster, PVN, 8wk SD, Rep 3

description:
PVN399
PVNExpressedGenesTranscripts.CSV

value: Paraventricular Nucleus Microdissection


title: B155-PA flex scRNA-seq

description:
SRR30204394, SRR30204359, SRR30204348, SRR30204343, SRR30204341, SRR30204340, SRR30204255, SRR30204253, SRR30204252, SRR30204251, SRR30204250, SRR30204249, SRR30204248, SRR30204247, SRR30204245, SRR30204244, SRR30204243, SRR30204242, SRR30204241, SRR30204240, SRR30204239, SRR30204238, SRR30204237, SRR30204236
10x Flex ligation probe-based sequencing


title: B151-PA flex scRNA-seq

description:
SRR30204414, SRR30204413, SRR30204342, SRR30204246, SRR30204235, SRR30204333, SRR30204322, SRR30204311
10x Flex ligation probe-based sequencing


title: PB03359-001 flex scRNA-seq

description:
SRR30239410, SRR30239409, SRR30239408, SRR30239407, SRR30239406, SRR30239405, SRR30239404, SRR30239403, SRR30239420, SRR30239401, SRR30239400, SRR30239471, SRR30239451, SRR30239450, SRR30239449, SRR30239448, SRR30239464, SRR30239463, SRR30239461, SRR30239460, SRR30239459, SRR30239458, SRR30239457, SRR30239456
10x Flex ligation probe-based sequencing


title: PB03321-003 flex scRNA-seq


title: PB03358-001 flex scRNA-seq


title: TGFb_H2Az-Ac_Rep1

description: Primary Cas9 cardiac fibroblasts were grown on serum-free media and stimulated with TGFb for 24 hours

data_processing:
Quality control was performed using FastQC v0.11.9 to evaluate sequencing data quality.
Adapters and low-quality bases (below Q20) were trimmed using Cutadapt v3.4, ensuring high-quality reads for alignment.
Reads were aligned to the reference genome using Bowtie2 v2.4.2, with sorted and indexed alignment outputs generated by Samtools v1.10.
Duplicate reads were removed and sequences corresponding to mitochondrial DNA (chrM), Epstein-Barr virus (chrEBV), 'chrUn', 'random', and ENCODE blacklist regions v2.0 were filtered out.
Peak calling was conducted with MACS2 v2.2.7.1 using the '--broad' flag and a broad-cutoff of 0.1, suitable for identifying broad regions of histone modifications.
Overlapping peaks across biological replicates were merged using HOMER's mergePeaks function, and consensus peak regions were annotated using annotatePeaks.pl from HOMER.
Read counts within consensus peaks were aggregated using featureCounts (Subread package v2.0.1), followed by differential binding analysis with DESeq2 v1.30.0. Significant peaks were identified based on an absolute log2(fold change) > 0.75 and an adjusted P-value (Padj) < 0.01.
Custom R scripts were employed for visualization and exploratory analyses, including principal component analysis (PCA), scatter plots, and hierarchical clustering, facilitating the interpretation of biologically meaningful differences.
Assembly: mm10
Supplementary files format and content: Bigwig
Supplementary files format and content: Differential binding analysis csv

extract_protocol:
Cells were lysed in lysis buffer (10 mM NaCl, 0,2% NP-40 + Prot Inhibitors) and Chromatin was extracted by Sonication (Bioruptor Nano) in 0.5% SDS, 5mM EDTA + Prot Inhibitors. Then, chromatin fragments were extracted using 4 volumes of 25 mM HEPES, 185 mM NaCl, 1.25% Tx-100 + Protease Inhibitors. Next, samples were incubated for 10-12 hours with the H2Az-Ac antibody, then captured using 25 uL Magna ChIP Prot A+G and incubating for 3h at 4 ºC. Next, ChIPed DNA was released and reversed crosslinking by 30 min incubation with 2 uL of Proteinase K in ChIP Elution buffer followed by 1-hour incubation at 68 ºC. Finally, the ChIPed DNA was purified with a 2.2X SPRI Cleanup and quantified by Qbit.
ChIP-seq libraries were prepared from 5 ng of DNA with NEB Next Ultra II kit, QCed for concentration (Qbit) and size (Tape-Station) and sequenced to 50 million reads per sample.

treatment_protocol: Cells were dual-crosslinked with 3 mM DSG,DMA,EGS for 20 minutes at room temperature followed by 1% Formaldehyde for 5 more minutes. The reaction was quenched by adding Glycine to 125 mM final concentration, then cells were pelleted, washed twice with cold 0.5% BSA/PBS containing 1X Protease Inhibitors and frozen at -80C.

tag: chip antibody

value: C15410202, Diagenode


title: Siberian Hamster, PVN, 28wk SD, Rep 2

description:
PVN174
PVNExpressedGenesTranscripts.CSV


title: Siberian Hamster, PVN, 20wk SD, Rep 2

description:
PVN214
PVNExpressedGenesTranscripts.CSV


title: Unstimulated_H2Az-Ac_Rep1

description: Primary Cas9 cardiac fibroblasts were grown on serum-free media under unstimulated conditions

value: Unstimulated


title: PB03293-003 flex scRNA-seq

tag: batch id

value: FALSE


title: Siberian Hamster, PVN, 24wk SD, Rep 2

description:
PVN181
PVNExpressedGenesTranscripts.CSV


title: Siberian Hamster, PVN, 12wk SD, Rep 2

description:
PVN292
PVNExpressedGenesTranscripts.CSV


title: Siberian Hamster, PVN, 16wk SD, Rep 2

description:
PVN252
PVNExpressedGenesTranscripts.CSV


title: Unstimulated_H2Az-Ac_Rep2


title: TGFb_H2Az-Ac_Rep2


title: PB03385-003 flex scRNA-seq

value: Equivocal

tag: sample bridging_control


title: PB03367-001 flex scRNA-seq

value: Male

value: Asian


title: PB03396-003 flex scRNA-seq

value: Caucasian

value: Positive


title: PB03858-003 flex scRNA-seq


title: Quiescent-Srcap_ATAC_2

description: Primary Cas9 cardiac fibroblasts were transduced with Lentiviral vectors expressing sgRNAs targeting specific Chromatin factors

data_processing:
We followed the ATAC-seq nf-core pipeline
ATAC-seq reads were trimmed with default parameters using Trim Galore  v0.6.6 with Cutadapt v3.4
ATAC-seq reads were aligned to the GRCm38/mm10 reference genome assembly using Bowtie version 2.3.4.2 with parameters -X 1000 --no-discordant --no-mixed --very-sensitive
we removed duplicated regions with Picard v2.25.4 and filtered out ENCODE blacklist regions v2.0 and non-interesting chromosomes
We removed Tn5 adaptors with alignmentSieve v3.5.1
We pooled replicates and converted the paired BAM files to single-read bed format using function bamToBed from BEDTools v2.27.1
Peaks were called uing MACS v2.2.7.1 with parameters –broad -f BED --keep-dup all --nomodel --shift -75 --extsize 150
Assembly: GRCm38/mm10
Supplementary files format and content: broadPeak


title: PB03364-001 flex scRNA-seq

description:
SRR30239415, SRR30239414, SRR30239432, SRR30239431, SRR30239430, SRR30239429, SRR30239428, SRR30239427, SRR30239426, SRR30239425, SRR30239424, SRR30239423, SRR30239421, SRR30239419, SRR30239418, SRR30239417, SRR30239470, SRR30239469, SRR30239468, SRR30239467, SRR30239466, SRR30239465, SRR30239412, SRR30239411
10x Flex ligation probe-based sequencing


title: PB03366-001 flex scRNA-seq

value: Female


title: Quiescent-Wdr82_ATAC5_1

value: Heart


title: Siberian Hamster, PVN, 4wk SD, Rep 2

description:
PVN333
PVNExpressedGenesTranscripts.CSV


title: Quiescent-Srcap_ATAC_1

value: Fibroblast


title: Siberian Hamster, PVN, 8wk SD, Rep 2

description:
PVN310
PVNExpressedGenesTranscripts.CSV


title: PB03363-001 flex scRNA-seq

description:
SRR30239543, SRR30239542, SRR30239492, SRR30239434, SRR30239445, SRR30239433, SRR30239422, SRR30239413, SRR30239402, SRR30239462, SRR30239541, SRR30239525, SRR30239536, SRR30239513, SRR30239481, SRR30239497, SRR30239496, SRR30239495, SRR30239494, SRR30239493, SRR30239491, SRR30239490, SRR30239489, SRR30239488
10x Flex ligation probe-based sequencing

value: Hispanic or Latino origin


title: Siberian Hamster, PVN, LD, Rep 2

description:
PVN205
PVNExpressedGenesTranscripts.CSV


title: PB03372-003 flex scRNA-seq

value: Blood


title: PB03369-001 flex scRNA-seq

value: PBMC


title: PB03856-003 flex scRNA-seq


title: PB03850-003 flex scRNA-seq


title: PB03849-003 flex scRNA-seq

value: Negative


title: PB03848-003 flex scRNA-seq


title: Quiescent-NtC5_ATAC5_2


title: Quiescent-NtC5_ATAC_2


title: PB03378-003 flex scRNA-seq


title: Siberian Hamster, PVN, 32wk SD, Rep 1

description:
PVN161
PVNExpressedGenesTranscripts.CSV


title: Siberian Hamster, PVN, 28wk SD, Rep 1

description:
PVN175
PVNExpressedGenesTranscripts.CSV


title: Quiescent-NtC5_ATAC_1


title: Siberian Hamster, PVN, 16wk SD, Rep 1

description:
PVN244
PVNExpressedGenesTranscripts.CSV


title: PB03838-003 flex scRNA-seq


title: Siberian Hamster, PVN, 24wk SD, Rep 1

description:
PVN178
PVNExpressedGenesTranscripts.CSV


title: Quiescent-NtC5_ATAC3_2


title: PB03842-003 flex scRNA-seq

value: African American


title: Siberian Hamster, PVN, 20wk SD, Rep 1

description:
PVN213
PVNExpressedGenesTranscripts.CSV

value: Paraventricular Nucleus Microdissection


title: PB03824-003 flex scRNA-seq


title: PB03840-003 flex scRNA-seq

description:
SRR30239487, SRR30239486, SRR30239484, SRR30239438, SRR30239437, SRR30239435, SRR30239479, SRR30239478, SRR30239477, SRR30239476, SRR30239475, SRR30239474, SRR30239473, SRR30239472, SRR30239447, SRR30239446, SRR30239444, SRR30239443, SRR30239442, SRR30239441, SRR30239440, SRR30239439, SRR30239436, SRR30239416
10x Flex ligation probe-based sequencing


title: Quiescent-NtC5_ATAC5_1


title: Quiescent-NtC5_ATAC4_1


title: Siberian Hamster, PVN, 8wk SD, Rep 1

description:
PVN305
PVNExpressedGenesTranscripts.CSV


title: Siberian Hamster, PVN, 12wk SD, Rep 1

description:
PVN277
PVNExpressedGenesTranscripts.CSV


title: PB03839-003 flex scRNA-seq


title: PB03826-003 flex scRNA-seq


title: PB03830-003 flex scRNA-seq


title: PB03813-001 flex scRNA-seq


title: PB03846-003 flex scRNA-seq

description:
SRR30204374, SRR30204373, SRR30204372, SRR30204371, SRR30204370, SRR30204369, SRR30204368, SRR30204367, SRR30204365, SRR30204364, SRR30204291, SRR30204290, SRR30204289, SRR30204288, SRR30204287, SRR30204286, SRR30204285, SRR30204284, SRR30204282, SRR30204281, SRR30204280, SRR30204279, SRR30204278, SRR30204277
10x Flex ligation probe-based sequencing


title: PB03811-001 flex scRNA-seq

description:
SRR30204317, SRR30204316, SRR30204315, SRR30204314, SRR30204313, SRR30204312, SRR30204310, SRR30204309, SRR30204308, SRR30204307, SRR30204306, SRR30204305, SRR30204304, SRR30204303, SRR30204302, SRR30204301, SRR30204299, SRR30204298, SRR30204297, SRR30204296, SRR30204295, SRR30204294, SRR30204293, SRR30204292
10x Flex ligation probe-based sequencing


title: Siberian Hamster, PVN, 4wk SD, Rep 1

description:
PVN356
PVNExpressedGenesTranscripts.CSV


title: PB03807-001 flex scRNA-seq

description:
SRR30204393, SRR30204392, SRR30204391, SRR30204390, SRR30204389, SRR30204388, SRR30204363, SRR30204362, SRR30204361, SRR30204360, SRR30204358, SRR30204357, SRR30204356, SRR30204355, SRR30204354, SRR30204353, SRR30204352, SRR30204351, SRR30204350, SRR30204349, SRR30204347, SRR30204346, SRR30204345, SRR30204344
10x Flex ligation probe-based sequencing


title: Quiescent-NtC5_ATAC4_2


title: PB03804-001 flex scRNA-seq

description:
SRR30239455, SRR30239454, SRR30239453, SRR30239452, SRR30239540, SRR30239538, SRR30239539, SRR30239521, SRR30239522, SRR30239523, SRR30239524, SRR30239503, SRR30239504, SRR30239505, SRR30239526, SRR30239527, SRR30239528, SRR30239529, SRR30239530, SRR30239531, SRR30239532, SRR30239533, SRR30239534, SRR30239535
10x Flex ligation probe-based sequencing


title: Quiescent-Kat8_ATAC3_2


title: PB03835-003 flex scRNA-seq


title: PB03795-003 flex scRNA-seq


title: Siberian Hamster, PVN, LD, Rep 1

description:
PVN417
PVNExpressedGenesTranscripts.CSV


title: PB03790-003 flex scRNA-seq


title: PB03789-001 flex scRNA-seq


title: Quiescent-Kat5_ATAC4_1


title: Siberian Hamster, DMH, 28wk SD, Rep 6

description:
DMH172
DMHExpressedGenesTranscripts.CSV


title: Quiescent-Kat5_ATAC4_2


title: Activated-Wdr82_ATAC5_2

value: TGFb


title: PB03787-003 flex scRNA-seq


title: PB03805-001 flex scRNA-seq


title: PB03778-003 flex scRNA-seq


title: Siberian Hamster, DMH, 20wk SD, Rep 6

description:
DMH217
DMHExpressedGenesTranscripts.CSV


title: PB03786-003 flex scRNA-seq

description:
SRR30204276, SRR30204275, SRR30204274, SRR30204273, SRR30204271, SRR30204270, SRR30204269, SRR30204268, SRR30204411, SRR30204410, SRR30204409, SRR30204408, SRR30204407, SRR30204406, SRR30204404, SRR30204403, SRR30204402, SRR30204401, SRR30204400, SRR30204399, SRR30204398, SRR30204397, SRR30204396, SRR30204395
10x Flex ligation probe-based sequencing


title: Quiescent-NtC5_ATAC3_1

value: Unstimulated


title: Siberian Hamster, DMH, 24wk SD, Rep 6

description:
DMH188
DMHExpressedGenesTranscripts.CSV


title: PB03765-002 flex scRNA-seq

value: FALSE


title: Siberian Hamster, DMH, 16wk SD, Rep 6

description:
DMH265
DMHExpressedGenesTranscripts.CSV


title: Activated-Wdr82_ATAC5_1


title: Activated-Srcap_ATAC_2


title: PB03763-003 flex scRNA-seq


title: Quiescent-Kat8_ATAC3_1


title: PB03764-003 flex scRNA-seq


title: PB03758-003 flex scRNA-seq


title: PB03756-003 flex scRNA-seq


title: Activated-Srcap_ATAC_1


title: Siberian Hamster, DMH, 12wk SD, Rep 6

description:
DMH280
DMHExpressedGenesTranscripts.CSV


title: PB03752-003 flex scRNA-seq


title: PB03745-003 flex scRNA-seq


title: PB03743-003 flex scRNA-seq


title: Activated-NtC5_ATAC_2


title: Siberian Hamster, DMH, 8wk SD, Rep 6

description:
DMH397
DMHExpressedGenesTranscripts.CSV


title: Siberian Hamster, DMH, 32wk SD, Rep 6

description:
DMH113
DMHExpressedGenesTranscripts.CSV


title: PB03766-001 flex scRNA-seq


title: PB03747-003 flex scRNA-seq


title: Siberian Hamster, DMH, 4wk SD, Rep 6

description:
DMH314
DMHExpressedGenesTranscripts.CSV


title: PB03741-004 flex scRNA-seq


title: Activated-NtC5_ATAC_1


title: Siberian Hamster, DMH, LD, Rep 6

description:
DMH141
DMHExpressedGenesTranscripts.CSV


title: PB03740-003 flex scRNA-seq


title: Activated-NtC5_ATAC5_2


title: PB03739-003 flex scRNA-seq


title: Siberian Hamster, DMH, 32wk SD, Rep 5

description:
DMH152
DMHExpressedGenesTranscripts.CSV


title: Siberian Hamster, DMH, 28wk SD, Rep 5

description:
DMH163
DMHExpressedGenesTranscripts.CSV


title: Activated-NtC5_ATAC4_2


title: PB03727-003 flex scRNA-seq


title: PB03721-003 flex scRNA-seq


title: PB03720-003 flex scRNA-seq


title: PB03723-003 flex scRNA-seq


title: Siberian Hamster, DMH, 24wk SD, Rep 5

description:
DMH180
DMHExpressedGenesTranscripts.CSV


title: Activated-NtC5_ATAC4_1


title: Siberian Hamster, DMH, 20wk SD, Rep 5

description:
DMH216
DMHExpressedGenesTranscripts.CSV


title: Activated-NtC5_ATAC3_2


title: PB03717-003 flex scRNA-seq

value: American Indian


title: PB03710-003 flex scRNA-seq


title: PB03707-003 flex scRNA-seq


title: Siberian Hamster, DMH, 16wk SD, Rep 5

description:
DMH283
DMHExpressedGenesTranscripts.CSV


title: PB03713-003 flex scRNA-seq


title: Activated-NtC5_ATAC3_1


title: Activated-Mock_ATAC7_2

description: Primary Cas9 cardiac fibroblasts were treated with DMSO vehicle condition


title: PB03706-003 flex scRNA-seq

value: Male


title: Activated-NtC5_ATAC5_1


title: PB03693-001 flex scRNA-seq

value: Asian


title: PB03700-002 flex scRNA-seq


title: Siberian Hamster, DMH, 8wk SD, Rep 5

description:
DMH306
DMHExpressedGenesTranscripts.CSV


title: PB03692-003 flex scRNA-seq

value: Caucasian


title: PB03701-003 flex scRNA-seq

value: Positive


title: Activated-Mock_ATAC7_1


title: Siberian Hamster, DMH, 4wk SD, Rep 5

description:
DMH352
DMHExpressedGenesTranscripts.CSV


title: PB03680-001 flex scRNA-seq

value: Female


title: PB03667-001 flex scRNA-seq


title: Activated-Kat8_ATAC3_2

value: Heart


title: PB03675-001 flex scRNA-seq


title: Siberian Hamster, DMH, LD, Rep 5

description:
DMH238
DMHExpressedGenesTranscripts.CSV


title: PB03666-001 flex scRNA-seq


title: PB03663-001 flex scRNA-seq


title: Activated-Kat8_ATAC3_1

value: Fibroblast


title: Activated-Kat5_ATAC7_2

description: Primary Cas9 cardiac fibroblasts were treated with NU-9056 chemical inhibitor of Kat5 Chromatin factor


title: PB03660-003 flex scRNA-seq


title: Siberian Hamster, DMH, 12wk SD, Rep 5

description:
DMH278
DMHExpressedGenesTranscripts.CSV


title: Siberian Hamster, DMH, 32wk SD, Rep 4

description:
DMH153
DMHExpressedGenesTranscripts.CSV


title: PB03657-001 flex scRNA-seq


title: PB03653-001 flex scRNA-seq

description:
SRR30239537, SRR30239518, SRR30239519, SRR30239520, SRR30239502, SRR30239501, SRR30239517, SRR30239516, SRR30239515, SRR30239514, SRR30239512, SRR30239511, SRR30239510, SRR30239509, SRR30239508, SRR30239507, SRR30239506, SRR30239485, SRR30239483, SRR30239482, SRR30239480, SRR30239500, SRR30239499, SRR30239498
10x Flex ligation probe-based sequencing


title: Siberian Hamster, DMH, 28wk SD, Rep 4

description:
DMH162
DMHExpressedGenesTranscripts.CSV


title: Activated-Kat5_ATAC7_1


title: Siberian Hamster, DMH, 24wk SD, Rep 4

description:
DMH196
DMHExpressedGenesTranscripts.CSV


title: PB03623-001 flex scRNA-seq


title: Activated-Kat5_ATAC4_2


title: PB03643-001 flex scRNA-seq


title: Siberian Hamster, DMH, 20wk SD, Rep 4

description:
DMH231
DMHExpressedGenesTranscripts.CSV


title: Activated-Kat5_ATAC4_1


title: PB03638-001 flex scRNA-seq


title: Siberian Hamster, DMH, 16wk SD, Rep 4

description:
DMH255
DMHExpressedGenesTranscripts.CSV


title: PB03621-001 flex scRNA-seq


title: PB03620-001 flex scRNA-seq


title: Siberian Hamster, DMH, 12wk SD, Rep 4

description:
DMH289
DMHExpressedGenesTranscripts.CSV


title: PB03617-001 flex scRNA-seq

description:
SRR30204234, SRR30204233, SRR30204232, SRR30204231, SRR30204339, SRR30204338, SRR30204337, SRR30204336, SRR30204335, SRR30204334, SRR30204332, SRR30204331, SRR30204330, SRR30204329, SRR30204328, SRR30204327, SRR30204326, SRR30204325, SRR30204324, SRR30204323, SRR30204321, SRR30204320, SRR30204319, SRR30204318
10x Flex ligation probe-based sequencing

value: Hispanic or Latino origin


title: Pooled library of SP-EPN-A 3 (BC-001), SP-EPN-A 4 (BC-002), SP-EPN-B 1 (BC-003), and SP-EPN-B 2 (BC-004)

city: Hamburg

first: Karoline

last: Hack

address: Martinistraße 52

department: Children's Cancer Center Hamburg

country: Germany

description:
Library name: ffpe_scRNAseq_20231106_Pool2
10x Genomics Flex Gene Expression (1000475, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 4 BC)

data_processing:
Demultiplexed fastq format data (cellranger mkfastq) were received from the sequencing facilities. Cellranger v7.2.0 was used to generate feature-barcode matrices using the command cellranger multi with default parameters. GRCh38 was used as the reference genome (version refdata-gex-GRCh38-2020-A) together with the probe set file Chromium_Human_Transcriptome_Probe_Set_v1.0.1_GRCh38-2020-A.csv. One sequencing library of this project contained samples of different, unpublished project. Therefore, fastq data of this library is not provided here. Instead, bam files of the cellranger v7.2.0 multi function are provided for these samples.
One sequencing library of this project contained samples of a different, unpublished project. Therefore, fastq data of this library is not provided here. Instead, bam files of the cellranger v7.2.0 multi function output are provided for the respective samples (SPEPN_B_3, SPEPN_B_4, MPE_A_4, MPE_A_5, MPE_A_6, MPE_A_7, MPE_A_12, MPE_A_13, MPE_A_14, and MPE_A_15).
Assembly: refdata-gex-GRCh38-2020-A together with the probe set file Chromium_Human_Transcriptome_Probe_Set_v1.0.1_GRCh38-2020-A.csv (files downloaded from 10x genomics website)
Supplementary files format and content: Processed 10x Genomics snRNAseq data is provided as filtered feature-barcode matrices reveived from the output of the cellranger multi function (barcodes.tsv, features.tsv, and matrix.mtx).

molecule: nuclear RNA

source_name: FFPE-tumor tissue

extract_protocol:
The tumor material was first subjected to 4% formaldehyde fixation for approximately 24h and subsequently dehydrated and embedded in paraffin (FFPE) for long-term storage. For the generation of single nucleus RNA sequencing data, we performed the 10x Genomics Chromium Single Cell Flex Gene Expression (specific workflow is currently termed Next GEM). The preparation of single nucleus solutions from archival FFPE-tissue was performed according to the instructions of the 10x Genomics protocol CG000632 (RevB). The sample input varied between 3 to 22 slices of 25 µm thickness. For different subsets of samples, the pestle-based dissociation or the gentleMACS™ OctoDissociator (Miltenyi Biotec) protocol arm was performed. Deviating from the original protocol, we stained all single nucleus solutions after the FFPE-tissue dissociation with 4',6-diamidino-2-phenylindole (DAPI, 1:5000). Immediately afterwards, fluorescence activated cell sorting (FACS) on a BD FACSAria-Fusion™ Flow Cytometer was conducted at the technology platform FACS of the Leibniz Institute of Virology (Hamburg, Germany). The experiment was performed at 4°C and the gating strategy first excluded obvious debris and subsequently sorted for DAPI-positive nuclei at the wavelength of 450 nm. This sorting step was performed to remove debris and non-DAPI-stained erythrocytes that otherwise skewed cell counting results of the following protocol steps.
The generation of single nucleus RNA sequencing libraries was performed at the single cell core facility of the University Medical Center Hamburg-Eppendorf (Germany) according to the 10x Genomics protocol CG000527 (Rev. D). The Chromium Fixed RNA (Human Transcriptome) kits PN-1000475 (4 rxns x 4 BC) or PN-1000476 (4 rxns x 16 BC) were used on different samples. The hybridization was conducted at a maximum of 7 days after the DAPI-sorting in appropriate storage buffer according to 10x Genomics protocol CG000632. No fluorescence-based cell counter was available for the experiments. Instead, a TC20 Automated Cell Counter (Bio-Rad Laboratories) was used for every cell counting step. Libraries were sequenced at different facilities (Leibniz Institute of Virology in Hamburg, Germany or CeGaT GmbH in Tübingen, Germany).

value: FFPE-tumor tissue

tag: batch


title: PB03613-001 flex scRNA-seq

value: Blood

value: PBMC


title: PB03615-001 flex scRNA-seq

description:
SRR30239410, SRR30239409, SRR30239408, SRR30239407, SRR30239406, SRR30239405, SRR30239404, SRR30239403, SRR30239420, SRR30239401, SRR30239400, SRR30239471, SRR30239451, SRR30239450, SRR30239449, SRR30239448, SRR30239464, SRR30239463, SRR30239461, SRR30239460, SRR30239459, SRR30239458, SRR30239457, SRR30239456
10x Flex ligation probe-based sequencing


title: Siberian Hamster, DMH, 8wk SD, Rep 4

description:
DMH398
DMHExpressedGenesTranscripts.CSV


title: Pooled library of MPE-A 3 (BC-001), MPE-B 3 (BC-002), SP-EPN-A 1 (BC-003), and SP-EPN-A 2 (BC-004)

institute: University Medical Center Hamburg-Eppendorf

description:
Library name: ffpe_scRNAseq_20231106_Pool1
10x Genomics Flex Gene Expression (1000475, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 4 BC)


title: PB03610-001 flex scRNA-seq

value: Negative


title: Siberian Hamster, DMH, 4wk SD, Rep 4

description:
DMH351
DMHExpressedGenesTranscripts.CSV


title: PB03604-001 flex scRNA-seq


title: Pooled library of MPE-A 1 (BC-001), MPE-A 2 (BC-002), MPE-B 1 (BC-003) and MPE-B 2 (BC-004)

description:
Library name: ffpe_scRNAseq_run_20230912
10x Genomics Flex Gene Expression (1000475, Chromium Fixed RNA Kit, Human Transcriptome, 4rxns x 4 BC)


title: PB03598-001 flex scRNA-seq


title: PB03600-001 flex scRNA-seq


title: hCF1-Mock_ATAC10_2

description: Primary human cardiac fibroblasts were treated with DMSO vehicle condition


title: Siberian Hamster, DMH, LD, Rep 4

description:
DMH247
DMHExpressedGenesTranscripts.CSV


title: PB03595-001 flex scRNA-seq


title: hCF1-Mock_ATAC10_1


title: Tj-Upd L Fraction 4 Replicate 2-SE

first: Daniel

last: Ringwalt

address: 3400N Charles St

department: Biology

institute: Johns Hopkins University

description: Library name: Sample 14

data_processing:
Reads were aligned to dm6 using Bowtie 2 (version 2.4.5). For PE (paired-end) indicated samples only, reads were filtered for proper pairs (SAM flag 2).
The template (the long single-end read or the alignment of the mates) was categorized using the midpoint base pair into bins of size 1 kb and step 1 kb.
Each pileup series is divided by a normalization factor: The total count of fragments itself divided by one million, and then the entry is further divided by the bin's width in kb. This yields FPKM quantification.
The timing enrichment is estimated on each bin also including one adjacent bin in each direction of the reference (if present). Thus, FPKM is effectively taken over 3 kb windows.
Assembly: dm6
Supplementary files format and content: CSV: Chromosome (dm6), start and end sliding window coordinates using BED file format semantics, and each series pileup of fragments divided by a normalization factor.

organism: Drosophila melanogaster

source_name: testis tumor

growth_protocol: Fly crosses were maintained on standard molasses media at 25C.

extract_protocol:
Whole tumor testes of the appropriate genotype were dissected in Schneider's media to obtain 100-200 pairs. The dissected testes were incubated for 15 minutes in media containing 100mM BrdU. After removing the media, nuclei were isolated by resuspending testes in 1mL homogenization buffer. Testis tissues were dounce homogenized with 20 strokes with loose pestle (A), followed by 40 strokes with tight pestle (B), before pipetting gently ~20 times with a wide bore tip. Nuclei were filtered through at 40uM cell strainer, then 10uM cell strainer into a fresh tube. The homozenization buffer was removed after pelleting nuclei. The pelleted nuclei were resuspended in resuspension buffer containing propidium iodide and incubated on ice for 30 minutes before proceeded to the cell sorter.  Nuclei were sorted on a MoFlo XDP cell sorter by gating for GSP+ nuclei and dividing S-phase nuclei into 4 equal fractions corresponding to early, early-mid, late-mid, or late replicating nuclei. Following the sort, DNA was purified from the nuclei. The purified DNA was next sonicated into ~200bp fragments, before initiating library preparion.
The NEB DNA Ultra II library prep kit for Illumina was incorporated into the Repli-seq protocol.  The first two steps of the NEBNext Ultra II DNA Library Prep Kit (End Prep and Adapter Ligation) were performed according to the manufacturer's instructions. The adapter-ligated DNA fragments were cleaned using the Zymo Research DNA Clean & Concentrator-5 kit. Next,  BrdU-containing DNA was immunoprecipitated, which enriches for DNA that was actively replicating at a specific stage in S-phase. The immunoprecipitated DNA was purified using a DNA Clean & Concentrator-5 kit from Zymo Research. Efficiency of the BrdU-immunoprecipitation was calculated using qPCR of the sample DNA compared against a serial dilution of known DNA concentrations. This method determined the number of PCR cycles required for library amplification. PCR amplification of the DNA fragments was performed following the NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: Whole dissected tumor testes were incubated with BrdU for 15 minutes at room temperature.

value: testis tumor

value: w[1118]; traffic Jam - GAL4 / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO

value: CySC-like


title: PB03594-001 flex scRNA-seq

value: FALSE


title: Siberian Hamster, DMH, 32wk SD, Rep 3

description:
DMH160
DMHExpressedGenesTranscripts.CSV


title: Tj-Upd ML Fraction 3 Replicate 2-SE

description: Library name: Sample 13


title: PB03592-001 flex scRNA-seq

value: African American


title: hCF1-Kat5_ATAC10_2

description: Primary human cardiac fibroblasts were treated with NU-9056 chemical inhibitor of Kat5 Chromatin factor

value: TGFb


title: PB03591-001 flex scRNA-seq


title: Siberian Hamster, DMH, 28wk SD, Rep 3

description:
DMH165
DMHExpressedGenesTranscripts.CSV


title: PB03584-001 flex scRNA-seq


title: hCF1-Kat5_ATAC10_1


title: PB03582-001 flex scRNA-seq

value: Male


title: hCF3-Mock_ATAC9_2


title: Siberian Hamster, DMH, 24wk SD, Rep 3

description:
DMH187
DMHExpressedGenesTranscripts.CSV


title: Tj-Upd EM Fraction 2 Replicate 2-SE

description: Library name: Sample 12


title: hCF3-Mock_ATAC9_1


title: Tj-Upd L Fraction 4 Replicate 1-SE

description: Library name: Sample 10


title: PB03605-001 flex scRNA-seq

value: Caucasian


title: Siberian Hamster, DMH, 16wk SD, Rep 3

description:
DMH251
DMHExpressedGenesTranscripts.CSV


title: hCF3-Kat5_ATAC9_2


title: PB03574-001 flex scRNA-seq


title: Siberian Hamster, DMH, 12wk SD, Rep 3

description:
DMH276
DMHExpressedGenesTranscripts.CSV


title: hCF3-Kat5_ATAC9_1


title: Nanos-Upd ML Fraction 3 Replicate 1-SE

description: Library name: Sample 3

value: y[1] w[1118] P{hs70FLP} ; P{w[+mC]=GAL4::VP16-nanos.UTR} / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO

value: GSC-like


title: Siberian Hamster, DMH, 8wk SD, Rep 3

description:
DMH399
DMHExpressedGenesTranscripts.CSV


title: Nanos-Upd L Fraction 4 Replicate 1-SE

description: Library name: Sample 4


title: Siberian Hamster, DMH, 4wk SD, Rep 3

description:
DMH332
DMHExpressedGenesTranscripts.CSV


title: PB03569-001 flex scRNA-seq

description:
SRR30239543, SRR30239542, SRR30239492, SRR30239434, SRR30239445, SRR30239433, SRR30239422, SRR30239413, SRR30239402, SRR30239462, SRR30239541, SRR30239525, SRR30239536, SRR30239513, SRR30239481, SRR30239497, SRR30239496, SRR30239495, SRR30239494, SRR30239493, SRR30239491, SRR30239490, SRR30239489, SRR30239488
10x Flex ligation probe-based sequencing

value: Female

value: Positive


title: Nanos-Upd EM Fraction 2 Replicate 1-SE

description: Library name: Sample 2


title: Nuclear run-on RNA, late S/G2/M population of BJ-Fucci cells, Rep2

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: Library name: KI752

data_processing:
GRO-seq read pairs with maximum fragment length of 2000 bp were aligned to the GRCh38 human reference genome using Bowtie2 with the parameter set of -X 2000 --no-mixed --no-discordant. Reads with MAPQ score greater than 20 were used in downstream analyses.
For each transcript in the Gencode v38 basic gene annotation (111,832 transcripts), we counted the number of the overlapping paired-end fragments at their 5’-end (1 base). Out of the 111,832 transcripts, we selected a single transcript with the longest transcript size (sum of exons) to represent one of the 60,649 genes. The per-gene GRO-seq fragment counts were processed in Combat-seq in R to correct for the sorting batch. The corrected fragment counts were used to compute counts per million (CPM), such that CPM =106 x CPK/sum(CPK), where CPK is [1+corrected fragment count]/[gene length in kb], and sum(CPK) is sum of CPKs for all genes.
To generate the genomic density profile for visualization, the fragment counting was performed at every base in the genome after extending +/–10 bp from the 5’ end.
Assembly: GRCh38
Supplementary files format and content: List of CPM for each gene for each biological replicate in plain text
Supplementary files format and content: Per-base extended fragment count for each strand in bigwig format
Library strategy: GRO-Seq

source_name: cell line

growth_protocol: BJ-Fucci cells are the hTERT-immortalized human dermal fibroblast cell line BJ-5ta (source: foreskin of male neonate; ATCC catalog # CRL-4001) transduced with Fucci4 reporters. To introduce Fucci4 fluorescent markers, BJ-5ta cells were co-transduced with the two lentivirus Clover-Gemininaa1-110-IRES-mKO2-Cdt1aa30-120 (Addgene ID83841) and mTurquoise2- SLBPaa18-126-IRES-H1-mMaroon1 (Addgene ID83842). The transduced cells were selected for their simultaneous expression of Clover and mMaroon1 and then for their simultaneous expression of mKO2 and mMaroon1 using FACS. The resultant double-selected cells are “BJ-Fucci” cells (cell ID cc1357-2ss) used in this study. BJ-Fucci cells were cultured in high-glucose DMEM (Gibco, 11965-092) containing 9% fetal bovine serum (FBS), 90 U/mL penicillin, 90 µg/mL streptomycin streptomycin at 37ºC under 5% CO2.

extract_protocol:
Nuclei were isolated by incubating cells in hypotonic NP40 lysis buffer (10 mM NaCl, 3 mM MgCl2, 0.5% MP-40, 10 mM Tris, pH 7.5) supplemented with RNase Inhibitor on ice and resuspended in Nuclear Storage buffer (50 mM Tris pH 8.0, 0.1 mM EDTA, 5 mM MgCl2, 40% glycerol, RNase inhibitor). The nuclear suspension was mixed with an equal volume of 2x NRO buffer (10 mM Tris pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 0.5 mM ATP, 0.5 mM GTP, 0.5 mM BrUTP, 2 µM CTP). The sample was incubated without sarkosyl for 4 min at 30ºC and then with 0.5% sarkosyl for 4 min at 30ºC (total 8 min). RNAs were purified from the reaction by Trizol LS (Invitrogen 10296028) followed by isopropanol precipitation. RNAs were treated with TurboDNase (Ambion AM18907) and fragmented by Fragmentation Buffer (Ambion AM8740). BrU-incorporated RNA fragments were immunoprecipitated with mouse monoclonal anti-BrdU antibody 3D4 (BD Biosciences 555627 Lot 7033666).
BrU-incorporated RNA fragments were used to construct DNA sequencing libraries using NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs E7760).

treatment_protocol: Approximately 20 hours before FACS sorting, BJ-Fucci cells that reached confluency were passaged to 8–20 15-cm culture dishes at a density of 2.5 million cells per dish. Cells were dissociated from the dishes with TrypLE (Thermo Fisher), filtered through a 40-µm cell strainer, resuspended in the complete culture medium, and sorted into the culture medium using BD FACSAriaII (sorting experiment ID: KI2834 and KI2847) or BD FACSAriaIIu (KI2858) sorters. The following populations were sorted: mKO2–Clover–mTurquoise2– (early G1), mKO2+Clover– (G1), mKO2+Clover+mTurquois+ (early S), and mKO2–Clover+ (late-S/G2/M). The following excitation (ex) lasers and emission (em) filter settings were used: mTurquioise2, ex 405 nm, em 450/50 nm; Clover, ex 488 nm, em 530/30 nm; mKO2, ex 561 nm, em 582/15 nm; mMaroon1, ex 561 nm, em 670/30 nm (FACSAriaII) or em 670/14 (FACSAriaIIu). After sorting, cells were directly proceeded to nuclear isolation described in the GRO-seq section.

value: cell line

tag: cell line

value: BJ-Fucci

value: fibroblast

value: Late S/G2/M

value: FACS KI2858


title: Tj-Upd E Fraction 1 Replicate 2-SE

description: Library name: Sample 11

value: testis tumor


title: Nuclear run-on RNA, early G1 population of BJ-Fucci cells, Rep2

description: Library name: KI753

value: Early G1


title: PB03559-001 flex scRNA-seq

description:
SRR30239415, SRR30239414, SRR30239432, SRR30239431, SRR30239430, SRR30239429, SRR30239428, SRR30239427, SRR30239426, SRR30239425, SRR30239424, SRR30239423, SRR30239421, SRR30239419, SRR30239418, SRR30239417, SRR30239470, SRR30239469, SRR30239468, SRR30239467, SRR30239466, SRR30239465, SRR30239412, SRR30239411
10x Flex ligation probe-based sequencing

value: Blood

value: PBMC

value: Negative


title: Siberian Hamster, DMH, LD, Rep 3

description:
DMH248
DMHExpressedGenesTranscripts.CSV


title: Nanos-Upd E Fraction 1 Replicate 1-SE

description: Library name: Sample 1


title: Nuclear run-on RNA, G1 population of BJ-Fucci cells, Rep2

description: Library name: KI751


title: Siberian Hamster, DMH, 20wk SD, Rep 3

description:
DMH226
DMHExpressedGenesTranscripts.CSV


title: PB03579-001 flex scRNA-seq

description:
SRR30239487, SRR30239486, SRR30239484, SRR30239438, SRR30239437, SRR30239435, SRR30239479, SRR30239478, SRR30239477, SRR30239476, SRR30239475, SRR30239474, SRR30239473, SRR30239472, SRR30239447, SRR30239446, SRR30239444, SRR30239443, SRR30239442, SRR30239441, SRR30239440, SRR30239439, SRR30239436, SRR30239416
10x Flex ligation probe-based sequencing

value: FALSE


title: PB03551-001 flex scRNA-seq

value: Male


title: Tj-Upd E Fraction 1 Replicate 1-SE

description: Library name: Sample 9

value: w[1118]; traffic Jam - GAL4 / UAS - Upd ; + / UAS-FRT-H3-GFP-FRT-H3-mKO

value: CySC-like


title: Spinal cord_Replicate 6

city: New Haven

first: Sviatoslav

middle: N

last: Bagriantsev

state: Connecticut

address: 333 Cedar St

department: Cellular and Molecular Physiology

institute: Yale University

description:
Library name: SpinalCord_6
Column names: RawCounts_SpinalCord_6 and TPM_SpinalCord_6

data_processing:
Signal intensities are converted to individual base calls during a run using the system's Real Time Analysis (RTA) software. Primary analysis is performed using Illumina's CASAVA 1.8.2 software suite.
Raw sequencing reads were trimmed and filtered using Trimmomatic v0.39 with default parameters.
Filtered reads were aligned to the reference genome of a closely related species, Paramormyrops kingsleyae (PKINGS_0.1; NCBI, accessed June 2021), using STAR v2.7.7a with default parameters
Aligned reads were quantified using featureCounts (Subread v2.0.1) with strandedness set to 0.
Raw read counts were then normalized to Transcripts Per Million (TPM) in R.
Assembly: The reference genome is GCF_002872115.1 (PKINGS_0.1), from a closely related species, Paramormyrops kingsleyae (NCBI, accessed June 2021).
Supplementary files format and content: The processed data file in CSV format contains raw read counts and TPM values for six replicates each of trigeminal ganglion, brain, and spinal cord, covering all protein-coding genes annotated in the reference genome.

organism: Gnathonemus petersii

source_name: Spinal cord

extract_protocol:
Total RNA was extracted separately from trigeminal ganglia, brains (cerebella), and spinal cords from 6 individual fish using TRIzol reagent (Invitrogen, cat. no. 15596026), following the manufacturer’s instructions. RNA concentration and integrity number (RIN) were assessed by Agilent 2100 Bioanalyzer (Agilent, cat. no. G2946CA). RNA concentrations for all samples were in the range of 5.2–146.1 ng/µl and RIN values were in the range of 7.9–9.5.
Libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs, cat. no. E6420L).

value: Spinal cord


title: PB03549-001 flex scRNA-seq

description:
SRR30204374, SRR30204373, SRR30204372, SRR30204371, SRR30204370, SRR30204369, SRR30204368, SRR30204367, SRR30204365, SRR30204364, SRR30204291, SRR30204290, SRR30204289, SRR30204288, SRR30204287, SRR30204286, SRR30204285, SRR30204284, SRR30204282, SRR30204281, SRR30204280, SRR30204279, SRR30204278, SRR30204277
10x Flex ligation probe-based sequencing

value: Female

value: Caucasian


title: Siberian Hamster, DMH, 28wk SD, Rep 2

description:
DMH174
DMHExpressedGenesTranscripts.CSV


title: PB03572-001 flex scRNA-seq

value: Positive


title: Nuclear run-on RNA, late S/G2/M population of BJ-Fucci cells, Rep1

description: Library name: KI749

value: cell line

value: BJ-Fucci

value: FACS KI2847


title: Siberian Hamster, DMH, 24wk SD, Rep 2

description:
DMH181
DMHExpressedGenesTranscripts.CSV


title: PB03544-001 flex scRNA-seq

description:
SRR30239455, SRR30239454, SRR30239453, SRR30239452, SRR30239540, SRR30239538, SRR30239539, SRR30239521, SRR30239522, SRR30239523, SRR30239524, SRR30239503, SRR30239504, SRR30239505, SRR30239526, SRR30239527, SRR30239528, SRR30239529, SRR30239530, SRR30239531, SRR30239532, SRR30239533, SRR30239534, SRR30239535
10x Flex ligation probe-based sequencing


title: Spinal cord_Replicate 4

description:
Library name: SpinalCord_4
Column names: RawCounts_SpinalCord_4 and TPM_SpinalCord_4


title: Siberian Hamster, DMH, 20wk SD, Rep 2

description:
DMH214
DMHExpressedGenesTranscripts.CSV


title: Next 25% brightest cells

first: Vishal

last: Nigam

state: WA

address: 1900 9th Ave

department: Pediatrics

institute: Seattle Childrens Research Institute

description: LH3 (subsequent 25% sorted)

data_processing:
MAGeCKFlute was used to analyze the sequencing data for gRNAs that were enriched. Data from the 10% brightest cell population were compared to the data from the next 25% brightest and unsheared cell populations.
Assembly: Human GRCh38.p14 Primary Assembly
Supplementary files format and content: Read counts for each target sgRNA are provided in an Excel spreadsheet, along with metadata about target genes and genomic coordinates.

extract_protocol:
Sorted and fixed cells were spun at 300g for 3 mins. Proteinase K (Zymo) was added at 5uL and incubated at 55C for 2 hours. Samples were then de-crosslinked by incubation at 94C for 20 mins and subsequently lysed and extracted for genomic DNA (gDNA) using the Quick-DNA/RNA Miniprep Kit (Zymo D7005T). gDNA samples of both samples were sent to Cellecta Inc. for next-generation sequencing, using Illumina NextSeq.
Libraries were prepared using the NGS Prep Kit for sgRNA Libraries in LentiCRISPRv2 (GeCKO, Brunello Kinome) from Cellecta, Inc.
OTHER: sgRNA-Seq

treatment_protocol: Wild-type and IL8-GFP THP-1 cells were transduced with a lentiviral preparation of the Brunello gRNA pooled library in lentiCRISPRv2 (a gift from David Root and John Doench, Addgene #73179-LV) at multiplicity of infection (MOI) of 1. Cells were puromycin selected after 4 days post transduction and recovered for another 2 days. Then, sheared in an in vitro CPB system at 2 million cells/mL at a rate of 10mL/min for 2 hours. After shear, cells were prepared for flow cytometry and fluorescence-activated cell sorting (FACS). Sheared Brunello library transduced THP-1 cells were sorted using FACS analysis (BD FACSAria) for GFP intensity. Cells were sorted into two groups, the top 10% intensity and the next or subsequent 25% intensity. Transduced but non-sheared cells were fixed and stained using the same protocol to serve as the baseline.

value: monocytic

value: THP-1 IL8-GFP cells transduced with CRISPR library and sheared


title: PB03535-001 flex scRNA-seq

value: Asian


title: PB03555-001 flex scRNA-seq

description:
SRR30204394, SRR30204359, SRR30204348, SRR30204343, SRR30204341, SRR30204340, SRR30204255, SRR30204253, SRR30204252, SRR30204251, SRR30204250, SRR30204249, SRR30204248, SRR30204247, SRR30204245, SRR30204244, SRR30204243, SRR30204242, SRR30204241, SRR30204240, SRR30204239, SRR30204238, SRR30204237, SRR30204236
10x Flex ligation probe-based sequencing

value: Blood


title: Nuclear run-on RNA, G1 population of BJ-Fucci cells, Rep1

description: Library name: KI748

value: fibroblast


title: Spinal cord_Replicate 2

description:
Library name: SpinalCord_2
Column names: RawCounts_SpinalCord_2 and TPM_SpinalCord_2


title: Siberian Hamster, DMH, 16wk SD, Rep 2

description:
DMH252
DMHExpressedGenesTranscripts.CSV

data_processing:
Raw reads were demultiplexed and basealled using guppy basecaller
Porechop was used to trim adapters
Filtlong used to select long reads (>25 reads)
Minimap2 used to align reads to Mus musculus genome (GCRm39)
Transcript expression levels generated  using Salmon
Assembly: GRCmm39
Supplementary files format and content: Transcript expression levels generated  using Salmon


title: Sheared 10% brightest cells

description: LH2 (top 10% sorted)


title: Siberian Hamster, DMH, 32wk SD, Rep 2

description:
DMH149
DMHExpressedGenesTranscripts.CSV


title: Static control

description: LH1 (static)

value: THP-1 IL8-GFP cells transduced with CRISPR library static controls


title: Spinal cord_Replicate 1

description:
Library name: SpinalCord_1
Column names: RawCounts_SpinalCord_1 and TPM_SpinalCord_1


title: Nuclear run-on RNA, early G1 population of BJ-Fucci cells, Rep1

description: Library name: KI750

value: Early G1


title: PB03534-001 flex scRNA-seq

value: PBMC

value: Negative

value: FALSE


title: PB03531-001 flex scRNA-seq

value: Hispanic or Latino origin


title: Siberian Hamster, DMH, 8wk SD, Rep 2

description:
DMH310
DMHExpressedGenesTranscripts.CSV


title: Siberian Hamster, DMH, 4wk SD, Rep 2

description:
DMH333
DMHExpressedGenesTranscripts.CSV


title: Brain_Replicate 6

description:
Library name: Brain_6
Column names: RawCounts_Brain_6 and TPM_Brain_6

source_name: Cerebellum

value: Cerebellum


title: Medial olivocochlear neuron MOC13

city: Bethesda

first: Robert

last: Morell

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

description:
Library name: MOC13
Column name in RawCountFile.txt= MOC13

data_processing:
RNA-seq libraries were prepared using Nextera DNA Library Preparation kits (Illumina) and sequenced on an Illumina MiSeq in 75 bp paired end configuration. FASTQ files were extracted using bcl2fastq and the reads were mapped to the mouse genome (GRCm38.vM11) using the STAR v2.5.2 aligner.
Read counts are generated during mapping with the quantMode utility of the STAR aligner, producing a‘RAWCOUNTFILE’. We also generated normalized counts per gene (CPM, or counts per million reads).  DGE analyses were performed using the R packages DESeq2, EdgeR and Limma-Voom.
Assembly: mm10 (GRCm38.vM11)
Supplementary files format and content: Tab-delimited file with raw counts per sample
Supplementary files format and content: Tab-delimited file with normalized (CPM) counts per sample.

source_name: medial olivocochlear neuron

growth_protocol: Transgenic mice, acute brainstem slices

extract_protocol:
cytoplasm aspiration, cDNA library generation with SmartSEQ2
Nextera DNA Library Preparation kits (Illumina)

value: medial olivocochlear neuron

value: wild-type

value: RNA-seq after patch clamp


title: PB03530-001 flex scRNA-seq

source_name: Blood

value: Female

value: Positive


title: Brain_Replicate 5

description:
Library name: Brain_5
Column names: RawCounts_Brain_5 and TPM_Brain_5


title: Spinal cord_Replicate 5

description:
Library name: SpinalCord_5
Column names: RawCounts_SpinalCord_5 and TPM_SpinalCord_5

value: Spinal cord


title: Spinal cord_Replicate 3

description:
Library name: SpinalCord_3
Column names: RawCounts_SpinalCord_3 and TPM_SpinalCord_3


title: Medial olivocochlear neuron MOC12

description:
Library name: MOC12
Column name in RawCountFile.txt= MOC12


title: Siberian Hamster, DMH, LD, Rep 2

description:
DMH205
DMHExpressedGenesTranscripts.CSV


title: Brain_Replicate 4

description:
Library name: Brain_4
Column names: RawCounts_Brain_4 and TPM_Brain_4


title: PB03525-001 flex scRNA-seq

description:
SRR30239410, SRR30239409, SRR30239408, SRR30239407, SRR30239406, SRR30239405, SRR30239404, SRR30239403, SRR30239420, SRR30239401, SRR30239400, SRR30239471, SRR30239451, SRR30239450, SRR30239449, SRR30239448, SRR30239464, SRR30239463, SRR30239461, SRR30239460, SRR30239459, SRR30239458, SRR30239457, SRR30239456
10x Flex ligation probe-based sequencing

value: Male

value: Caucasian


title: PB03527-001 flex scRNA-seq

description:
SRR30204317, SRR30204316, SRR30204315, SRR30204314, SRR30204313, SRR30204312, SRR30204310, SRR30204309, SRR30204308, SRR30204307, SRR30204306, SRR30204305, SRR30204304, SRR30204303, SRR30204302, SRR30204301, SRR30204299, SRR30204298, SRR30204297, SRR30204296, SRR30204295, SRR30204294, SRR30204293, SRR30204292
10x Flex ligation probe-based sequencing

value: Blood


title: Medial olivocochlear neuron MOC11

description:
Library name: MOC11
Column name in RawCountFile.txt= MOC11


title: Siberian Hamster, DMH, 12wk SD, Rep 2

description:
DMH292
DMHExpressedGenesTranscripts.CSV


title: Brain_Replicate 3

description:
Library name: Brain_3
Column names: RawCounts_Brain_3 and TPM_Brain_3


title: Siberian Hamster, DMH, 32wk SD, Rep 1

description:
DMH161
DMHExpressedGenesTranscripts.CSV


title: Medial olivocochlear neuron MOC10

description:
Library name: MOC10
Column name in RawCountFile.txt= MOC10


title: Brain_Replicate 2

description:
Library name: Brain_2
Column names: RawCounts_Brain_2 and TPM_Brain_2


title: Medial olivocochlear neuron MOC09

description:
Library name: MOC09
Column name in RawCountFile.txt= MOC09


title: Siberian Hamster, DMH, 28wk SD, Rep 1

description:
DMH175
DMHExpressedGenesTranscripts.CSV


title: PB03524-001 flex scRNA-seq

description:
SRR30239415, SRR30239414, SRR30239432, SRR30239431, SRR30239430, SRR30239429, SRR30239428, SRR30239427, SRR30239426, SRR30239425, SRR30239424, SRR30239423, SRR30239421, SRR30239419, SRR30239418, SRR30239417, SRR30239470, SRR30239469, SRR30239468, SRR30239467, SRR30239466, SRR30239465, SRR30239412, SRR30239411
10x Flex ligation probe-based sequencing


title: Medial olivocochlear neuron MOC08

description:
Library name: MOC08
Column name in RawCountFile.txt= MOC08


title: Brain_Replicate 1

description:
Library name: Brain_1
Column names: RawCounts_Brain_1 and TPM_Brain_1


title: PB03518-001 flex scRNA-seq

description:
SRR30239537, SRR30239518, SRR30239519, SRR30239520, SRR30239502, SRR30239501, SRR30239517, SRR30239516, SRR30239515, SRR30239514, SRR30239512, SRR30239511, SRR30239510, SRR30239509, SRR30239508, SRR30239507, SRR30239506, SRR30239485, SRR30239483, SRR30239482, SRR30239480, SRR30239500, SRR30239499, SRR30239498
10x Flex ligation probe-based sequencing


title: Siberian Hamster, DMH, 20wk SD, Rep 1

description:
DMH213
DMHExpressedGenesTranscripts.CSV


title: Trigeminal ganglion_Replicate 6

description:
Library name: TG_6
Column names: RawCounts_TG_6 and TPM_TG_6

source_name: Trigeminal ganglion

value: Trigeminal ganglion


title: PB03528-001 flex scRNA-seq

description:
SRR30239543, SRR30239542, SRR30239492, SRR30239434, SRR30239445, SRR30239433, SRR30239422, SRR30239413, SRR30239402, SRR30239462, SRR30239541, SRR30239525, SRR30239536, SRR30239513, SRR30239481, SRR30239497, SRR30239496, SRR30239495, SRR30239494, SRR30239493, SRR30239491, SRR30239490, SRR30239489, SRR30239488
10x Flex ligation probe-based sequencing


title: Medial olivocochlear neuron MOC07

description:
Library name: MOC07
Column name in RawCountFile.txt= MOC07