title: Custom Panel1 HCMS, PHH Donor3, CRMA-1001 0.5 µg/mL, 4

description: Library name: NGSHC3324


title: Custom Panel1 HCMS, PHH Donor3, CRMA-1001 0.5 µg/mL, 2

status: Public on Jun 28 2026

type: SRA

city: Boston

first: Jennifer

last: Marlowe

state: Massachusetts

address: 201 Brookline Avenue

country: USA

institute: nChroma Bio

description: Library name: NGSHC3310

library_source: genomic

data_processing:
The nf-core Methyl-Seq pipeline (v1.6.1) was used to map sequencing reads to the human reference genome (GRCh38) using the Bismark methylation extraction workflow, with default parameters except for the following: clip_r1 = 10, clip_r2 = 10, three_prime_clip_r1 = 10, three_prime_clip_r2 = 10, cytosine_report = true.
Assembly: GRCh38
Supplementary files format and content: Bismark methylation bedgraph file
Supplementary files format and content: Bismark methylation coverage file
Library strategy: EM-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Liver

growth_protocol: Primary human hepatocytes (PHH) isolated from mice with a chimeric humanized liver (PXB cells®) were obtained from Phoenix Bio. Pre-plated cells were kept in hepatocyte growth medium (dHCGM media [PhoenixBio], 10% FBS). Primary human splenic endothelial cells (HSECs) (Innoprot and Accegen) were cultured in media (endothelial cell medium (ScienCell) with 5% FBS, 1% Pen-Strep, and 1% endothelial cell growth supplement [ScienCell]) and incubated at 37˚C and in 5% CO2. Primary human adrenal cortical cells (HAdCCs) (Accegen) were cultured in media (Mesenchymal Stem Cell Medium (Innoprot) with 5% FBS, 1% Pen-Strep and 1% Mesenchymal Stem Cell Growth Serum (Innoprot) and incubated at 37˚C and in 5% CO2.

extract_protocol:
From each PHH donor, 4 x 105 µL aliquots of lysate were processed for DNA extraction. From each HAdCC and HSEC donor, 4 x 63 µL aliquots of lysate were mixed with 42 µL of additional LBE buffer per aliquot and processed for DNA extraction. For all samples, lysate aliquots were transferred to separate technical replicate wells of a 0.5 mL deep well plate and mixed with Beckman Coulter patented SPRI paramagnetic beads to bind total DNA from the cell lysate. DNA-bound beads were then pelleted with a plate magnet, and the supernatants were removed and discarded before DNA-bound beads were treated with RNase in Beckman Coulter WBA buffer, pelleted with a plate magnet, and the supernatants removed. The retained DNA-bound beads were then washed twice with 70% ethanol. gDNA was eluted from the paramagnetic beads in 10 mM Tris pH 8.0, all twelve technical replicate wells combined and transferred to a clean storage plate.
The first step of the Hybrid Capture Methylation Sequencing (HCMS) workflow was the preparation of EM-seq libraries using Twist NGS Methylation Detection System. Samples were normalized in 10 mM Tris pH 8.0 to generate aliquots containing 200 ng of gDNA in 50 µL. Samples were then mechanically sheared on a Covaris R230 Focused Ultrasonicator to a size range of 350 – 450 bp and at least 5% of the samples were evaluated on a D1000 HS ScreenTape to ensure target size range was reached. The second step of the HCMS workflow was enrichment of DNA fragments for sequencing. Target-enrichment for subsequent methylation sequencing was accomplished through a hybridization reaction in which biotinylated DNA probes were used to capture regions of interest from the whole genome EM-seq library. The biotinylated DNA probe panel and capture reagents were supplied by Twist Biosciences and the workflow was performed following the manufacturer’s recommendations. Briefly, the hybridization reaction was carried out by first drying down 8-plex library pools in a mix of the custom biotinylated DNA probe panel, reaction buffer, and universal blocking oligos, which prevent library fragments from annealing to each other at their adapter sequences. The dried reactions were then resuspended in prewarmed hybridization buffer (65˚C) and incubated on a thermocycler for a hybridization time of 16 hours. Following hybridization, biotinylated DNA probes bound to target gDNA sequences were enriched using streptavidin beads. Streptavidin beads bound to the probe-library complex were pelleted on a magnet and unbound (i.e., off panel) fragments removed through a series of heated washes. The final bead slurry was resuspended in water before performing a PCR amplification to enrich the captured library fragments. Following amplification, libraries were purified with Twist Total Purification beads. Final library concentrations were determined by using the Quant-iT High Sensitivity DNA kit on the VICTOR Nivo plate reader. Library fragment size was assessed on a High Sensitivity DNA 1000 ScreenTape on the Agilent 4200 Tapestation instrument. Libraries were pooled in an equimolar manner and, to ensure proper quantitation of sequenceable library molecules, qPCR was also performed using the NEBNext Library Quant Kit for Illumina.  Enriched EM-seq libraries were shipped to SeqCenter for sequencing on a NovaSeq X. Sequencing used a 2 x 151 bp configuration and a targeted sequencing depth of >200 M read-pairs per library.

treatment_protocol: For PHH, on the day of treatment cells were treated with 500 µL culture media supplemented with 1 µg/mL of rhApoE3 and 0.5 or 1 µg/mL CRMA-1001 or control articles, or rhApoE3 only (mock treatment control). For HSEC, one day before test or control article treatment, 10,000 cells per well were seeded into a 96-well tissue culture plate pre-coated with 150 µg/mL of human fibronectin and containing 200 µL culture media. On the day of treatment (Day 0), culture media was replaced with 100 µL of fresh media containing 1 µg/mL of rhApoE3 and CRMA-1001 or control articles, or rhApoE3 only (mock treatment control). For HAdCCs, one day before test or control article treatment, 10,000 cells per well were seeded into a 96-well tissue culture plate pre-coated with 150 µg/mL of Poly-L-Lysine (Sigma-Aldrich) and containing 200 µL culture media. On the day of treatment (Day 0), culture media was replaced with 100 µL of media containing 1 µg/mL of rhApoE3 and CRMA-1001 or control articles, or rhApoE3 only (mock treatment control). Plates were maintained, cells sub-cultured (cell trypsinization every 3-4 days, followed by transfer of ~10,000 cells to a new 96-well culture plate with fresh media). All cells were collected for extraction 14 days after treatment.

tag: tissue

value: Liver

tag: cell line

value: PXB cells

tag: cell type

value: Primary Human Hepatocyte


title: Custom Panel1 HCMS, PHH Donor3, CRMA-1001 0.5 µg/mL, 1

description: Library name: NGSHC3303


title: Custom Panel1 HCMS, PHH Donor3, CRMA-1001 0.5 µg/mL, 3

description: Library name: NGSHC3317


title: Custom Panel1 HCMS, PHH Donor2, Untreated, 3

description: Library name: NGSHC3282


title: Custom Panel1 HCMS, PHH Donor2, Untreated, 4

description: Library name: NGSHC3290


title: Custom Panel1 HCMS, PHH Donor2, Untreated, 2

description: Library name: NGSHC3274


title: Custom Panel1 HCMS, PHH Donor2, Untreated, 1

description: Library name: NGSHC3266


title: Custom Panel1 HCMS, PHH Donor2, PCSK9-EE7000, 4

description: Library name: NGSHC3293


title: Custom Panel1 HCMS, PHH Donor2, PCSK9-EE7000, 3

description: Library name: NGSHC3285


title: Custom Panel1 HCMS, PHH Donor3, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3320


title: Custom Panel1 HCMS, PHH Donor2, PCSK9-EE7000, 2

description: Library name: NGSHC3277


title: Custom Panel1 HCMS, PHH Donor2, PCSK9-EE7000, 1

description: Library name: NGSHC3269


title: Custom Panel1 HCMS, PHH Donor2, Mock-treatment, 3

description: Library name: NGSHC3283


title: Custom Panel1 HCMS, PHH Donor2, Mock-treatment, 4

description: Library name: NGSHC3291


title: Custom Panel1 HCMS, PHH Donor2, Mock-treatment, 2

description: Library name: NGSHC3275


title: Custom Panel1 HCMS, PHH Donor2, Mock-treatment, 1

description: Library name: NGSHC3267


title: Custom Panel1 HCMS, PHH Donor2, HBV-CRISPRi, 3

description: Library name: NGSHC3287


title: Custom Panel1 HCMS, PHH Donor2, HBV-CRISPRi, 4

description: Library name: NGSHC3295


title: Custom Panel1 HCMS, PHH Donor2, HBV-CRISPRi, 1

description: Library name: NGSHC3271


title: Custom Panel1 HCMS, PHH Donor2, HBV-CRISPRi, 2

description: Library name: NGSHC3279


title: Custom Panel1 HCMS, PHH Donor2, EE7000 mRNAOnly, 4

description: Library name: NGSHC3294


title: Custom Panel1 HCMS, PHH Donor2, EE7000 mRNAOnly, 3

description: Library name: NGSHC3286


title: Custom Panel1 HCMS, PHH Donor2, EE7000 mRNAOnly, 2

description: Library name: NGSHC3278


title: Custom Panel1 HCMS, PHH Donor2, EE7000 mRNAOnly, 1

description: Library name: NGSHC3270


title: Custom Panel1 HCMS, PHH Donor2, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3292


title: Custom Panel1 HCMS, PHH Donor2, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3284


title: Custom Panel1 HCMS, PHH Donor2, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3276


title: Custom Panel1 HCMS, PHH Donor2, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3268


title: Custom Panel1 HCMS, PHH Donor2, CRMA-1001 0.5 µg/mL, 4

description: Library name: NGSHC3296


title: Custom Panel1 HCMS, PHH Donor2, CRMA-1001 0.5 µg/mL, 3

description: Library name: NGSHC3288


title: C57BL/6, ALW-II-49-7 treatment, rep3

city: Beijing

first: Jianfa

last: Qiu

address: No. 16, Tianrong Street, Daxing District

department: Institute of Pathogen Biology

country: China

institute: Chinese Academy of Medical Sciences

description:
Library name: B3
Column name in raw_counts_all.csv : B3. The insturment model: Illumina HiSeq PE150.

library_source: transcriptomic

data_processing:
Data was quality controled using FastQC, and sequence reads were trimmed the adaptors using Trim Galore.
HISAT2 was used for reads alignment. FeatureCounts was used to quantify read counts.
Assembly: GRCm38
Supplementary files format and content: comma-delimited .csv file includes raw counts for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: lung

extract_protocol:
RNA was extracted using TRIzol™. 100ng of total RNA was used for the construction of the sequencing library.
poly(A)-RNA was firstly enriched and reverse transcripted into cDNA, and then the cDNA was fragmented prior to index ligation. Libraries for RNA-Seq were then amplified by PCR.

value: lung

tag: genotype

value: WT

tag: treatment

tag: batch


title: Custom Panel1 HCMS, PHH Donor2, CRMA-1001 0.5 µg/mL, 2

description: Library name: NGSHC3280


title: C57BL/6, ALW-II-49-7 treatment, rep2

description:
Library name: B2
Column name in raw_counts_all.csv : B2. The insturment model: Illumina HiSeq PE150.


title: Custom Panel1 HCMS, PHH Donor2, CRMA-1001 0.5 µg/mL, 1

description: Library name: NGSHC3272


title: C57BL/6, ALW-II-49-7 treatment, rep1

description:
Library name: B1
Column name in raw_counts_all.csv : B1. The insturment model: Illumina HiSeq PE150.


title: Custom Panel1 HCMS, PHH Donor1, Untreated, 4

description: Library name: NGSHC3349


title: Custom Panel1 HCMS, PHH Donor1, Untreated, 3

description: Library name: NGSHC3341


title: C57BL/6, lithocholic acid treatment, rep2

description:
Library name: A2
Column name in raw_counts_all.csv : A2. The insturment model: Illumina HiSeq PE150.

value: lithocholic acid


title: C57BL/6, lithocholic acid treatment, rep3

description:
Library name: A3
Column name in raw_counts_all.csv : A3. The insturment model: Illumina HiSeq PE150.


title: Custom Panel1 HCMS, PHH Donor1, Untreated, 2

description: Library name: NGSHC3333


title: C57BL/6, lithocholic acid treatment, rep1

description:
Library name: A1
Column name in raw_counts_all.csv : A1. The insturment model: Illumina HiSeq PE150.


title: Custom Panel1 HCMS, PHH Donor1, Untreated, 1

description: Library name: NGSHC3325


title: C57BL/6, solvent control, rep3

description:
Library name: F3
Column name in raw_counts_all.csv : F3. The insturment model: Illumina HiSeq PE150.

value: solvent


title: Custom Panel1 HCMS, PHH Donor1, PCSK9-EE7000, 4

description: Library name: NGSHC3352


title: C57BL/6, solvent control, rep2

description:
Library name: F2
Column name in raw_counts_all.csv : F2. The insturment model: Illumina HiSeq PE150.


title: Custom Panel1 HCMS, PHH Donor1, PCSK9-EE7000, 3

description: Library name: NGSHC3344


title: C57BL/6, solvent control, rep1

description:
Library name: F1
Column name in raw_counts_all.csv : F1. The insturment model: Illumina HiSeq PE150.


title: Custom Panel1 HCMS, PHH Donor1, PCSK9-EE7000, 2

description: Library name: NGSHC3336


title: peritoneal immune cells, HFD, BCR

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

description:
Library name: HFD_BCR
10x Genomics

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.3.0) was used for generation of Seurat object.
The count matrix was normalized with NormalizeData function.
tSNE and UMAP were performed by R package Seurat (version 4.3.0).
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: BCR-Seq

molecule: total RNA

source_name: peritoneal immune cells

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

treatment_protocol: CD and HFD mice were placed on a high-fat diet beginning at 4 weeks of age and maintained for three months. To obtain peritoneal immune cells, mice were intraperitoneally injected with serum-free RPMI 1640 medium, and the lavage fluid was collected. CD45⁺ immune cells were then isolated by flow cytometry and subjected to single-cell RNA sequencing to profile the peritoneal immune microenvironment.

value: peritoneal immune cells

value: HFD


title: Custom Panel1 HCMS, PHH Donor1, PCSK9-EE7000, 1

description: Library name: NGSHC3328


title: peritoneal immune cells, HFD

description:
Library name: HFD
10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.3.0) was used for generation of Seurat object.
The count matrix was normalized with NormalizeData function.
tSNE and UMAP were performed by R package Seurat (version 4.3.0).
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files


title: Custom Panel1 HCMS, PHH Donor1, Mock-treatment, 4

description: Library name: NGSHC3350


title: peritoneal immune cells, CD, BCR

description:
Library name: CD_BCR
10x Genomics

value: CD


title: Custom Panel1 HCMS, PHH Donor1, Mock-treatment, 3

description: Library name: NGSHC3342


title: peritoneal immune cells, CD

description:
Library name: CD
10x Genomics


title: Custom Panel1 HCMS, PHH Donor1, Mock-treatment, 2

description: Library name: NGSHC3334


title: upper incisor tissues from neural crest-specific Alx1 conditional knockout mice at E13.5_3

city: Fuzhou

first: Xi

last: Zheng

address: No.18 Middle Wulongjiang Avenue, Shangjie, Minhou, Fuzhou, Fujian

institute: Fujian Medical University

description:
Library name: E13_5_WA_inc_3
Colume name in gene_count.txt: E13_5_WA_inc_3

data_processing:
Raw sequencing reads were subjected to quality control using FastQC, and low-quality reads and adaptor sequences were removed.
Clean reads were then aligned to the mouse reference genome (mm10) using HISAT2.
Gene expression levels were quantified as fragments per kilobase of transcript per million mapped reads (FPKM) using FeatureCounts.
Differentially expressed genes (DEGs) between control and mutant samples were identified using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: upper incisor

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (74106, QIAGEN, Germany) according to the manufacturer’s instructions.
RNA sequencing libraries were prepared using a poly(A) mRNA enrichment strategy following the manufacturer's protocol.

value: upper incisor

value: Alx1 conditional knockou


title: Custom Panel1 HCMS, PHH Donor1, Mock-treatment, 1

description: Library name: NGSHC3326


title: upper incisor tissues from neural crest-specific Alx1 conditional knockout mice at E13.5_2

description:
Library name: E13_5_WA_inc_2
Colume name in gene_count.txt: E13_5_WA_inc_2


title: Custom Panel1 HCMS, PHH Donor1, HBV-CRISPRi, 4

description: Library name: NGSHC3354


title: Custom Panel1 HCMS, PHH Donor1, HBV-CRISPRi, 3

description: Library name: NGSHC3346


title: upper incisor tissues from neural crest-specific Alx1 conditional knockout mice at E13.5_1

description:
Library name: E13_5_WA_inc_1
Colume name in gene_count.txt: E13_5_WA_inc_1


title: upper incisor tissues from wildtype mice at E13.5_3

description:
Library name: E13_5_WT_inc_3
Colume name in gene_count.txt: E13_5_WT_inc_3


title: upper incisor tissues from wildtype mice at E13.5_2

description:
Library name: E13_5_WT_inc_2
Colume name in gene_count.txt: E13_5_WT_inc_2


title: Custom Panel1 HCMS, PHH Donor1, HBV-CRISPRi, 2

description: Library name: NGSHC3338


title: Custom Panel1 HCMS, PHH Donor1, HBV-CRISPRi, 1

description: Library name: NGSHC3330


title: Custom Panel1 HCMS, PHH Donor1, EE7000 mRNAOnly, 4

description: Library name: NGSHC3353


title: upper incisor tissues from wildtype mice at E13.5_1

description:
Library name: E13_5_WT_inc_1
Colume name in gene_count.txt: E13_5_WT_inc_1


title: Lung_30M_220

city: Tokyo

first: Keiko

last: Akasaka-Manya

address: 35-2 Sakae-cho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

description: Library name: Lung_30M_220

data_processing:
The quality of raw paired-end sequence reads was evaluated using FastQC (version 0.11.7). Low-quality bases and adapter sequences were removed using Trimmomatic software (version 0.38). The trimmed reads were aligned to the reference genome using the RNA-seq aligner, HISAT2 (version 2.1.0). The frequency of the uniquely mapped reads was estimated using feature counts (version 1.6.3).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed data files include a raw gene count matrix generated by featureCounts.

source_name: Lung

extract_protocol:
Total RNA was extracted from mice using ISOGEN II (Nippon Gene, Tokyo, Japan), following the manufacturer’s instructions.
mRNA was purified from the total RNA sample using the poly-A selection method and sequenced on an Illumina platform to generate paired-end reads.

value: Lung


title: Custom Panel1 HCMS, PHH Donor1, EE7000 mRNAOnly, 3

description: Library name: NGSHC3345


title: Lung_30M_218

description: Library name: Lung_30M_218


title: Custom Panel1 HCMS, PHH Donor1, EE7000 mRNAOnly, 2

description: Library name: NGSHC3337


title: Lung_30M_216

description: Library name: Lung_30M_216


title: Custom Panel1 HCMS, PHH Donor1, EE7000 mRNAOnly, 1

description: Library name: NGSHC3329


title: Custom Panel1 HCMS, PHH Donor1, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSHC3351


title: Lung_20M_213

description: Library name: Lung_20M_213


title: Custom Panel1 HCMS, PHH Donor1, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSHC3343


title: Lung_20M_221

description: Library name: Lung_20M_221


title: Custom Panel1 HCMS, PHH Donor1, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSHC3335


title: Lung_20M_222

description: Library name: Lung_20M_222


title: Custom Panel1 HCMS, PHH Donor1, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSHC3327


title: Lung_12M_208

description: Library name: Lung_12M_208


title: Lung_12M_207

description: Library name: Lung_12M_207


title: Custom Panel1 HCMS, PHH Donor1, CRMA-1001 0.5 µg/mL, 4

description: Library name: NGSHC3355


title: Lung_12M_206

description: Library name: Lung_12M_206


title: Custom Panel1 HCMS, PHH Donor1, CRMA-1001 0.5 µg/mL, 3

description: Library name: NGSHC3347


title: Lung_6M_203

description: Library name: Lung_6M_203


title: Custom Panel1 HCMS, PHH Donor1, CRMA-1001 0.5 µg/mL, 2

description: Library name: NGSHC3339


title: Lung_6M_202

description: Library name: Lung_6M_202


title: Lung_6M_201

description: Library name: Lung_6M_201


title: RNAseq, HSEC Donor2-repeat, Untreated, 4

description: Library name: NGSRS3413

data_processing:
Sequencing reads were aligned to the human reference genome (GRCh38) and gene and transcript counts and normalized counts (TPM) were calculated using the nf-core RNA-seq pipeline using the STAR aligner and RSEM workflow for transcript quantification.
Assembly: GRCh38
Supplementary files format and content: genes.results file generated by RSEM containing the following columns: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

source_name: Spleen

growth_protocol: Primary human hepatocytes (PHH) from three different human donors isolated from mice with a chimeric humanized liver (PXB cells®) were obtained from Phoenix Bio. Pre-plated cells were kept in hepatocyte growth medium (dHCGM media [PhoenixBio], 10% FBS). Primary human splenic endothelial cells (HSECs) (Innoprot and Accegen) from three different human donors were cultured in media (endothelial cell medium (ScienCell) with 5% FBS, 1% Pen-Strep, and 1% endothelial cell growth supplement [ScienCell]) and incubated at 37˚C and in 5% CO2. Primary human adrenal cortical cells (HAdCCs) (Accegen) from three different human donors were cultured in media (Mesenchymal Stem Cell Medium (Innoprot) with 5% FBS, 1% Pen-Strep and 1% Mesenchymal Stem Cell Growth Serum (Innoprot) and incubated at 37˚C and in 5% CO2.

extract_protocol:
For RNA extraction of all donors and sample types, Beckman Coulter RNAdvance v2 Kit was used. For RNA extraction from each PHH donor, two 24-well replicate plates per donor containing 336 µL cell lysate were combined and 4 x 63 µL aliquots of lysate were processed . For RNA extraction from each HAdCC donor, all replicate wells of each condition from two replicate plates each containing 3 wells of 63 µL cell lysate were combined and 3 x 63 µL aliquots of lysate were processed. For RNA extraction from HSEC, all replicate wells of each condition from two replicate plates each containing 3 wells of 63 µL cell lysate were combined and 3 x 63 µL aliquots of lysate were processed. The remaining lysate from each cell type was used for DNA extraction. For all samples, lysate aliquots were transferred to separate technical replicate wells of a 0.5 mL deep well plate and mixed with Beckman Coulter-patented SPRI paramagnetic beads to bind total RNA from the cell lysate. Bound RNA was then pelleted with a plate magnet, removing the supernatant allowing DNA and other contaminants to be removed through DNase treatment and a series of buffer (Wash WBD) and 70% ethanol washes, respectively. Total RNA was then eluted from the magnetic beads in nuclease-free water (HAdCC and HSEC samples (96-well plate format) were eluted in 22 uL per sample combining the replicates for a total of 44 uL eluate. PHH samples (24-well format) were eluted in 26 uL.).
Total RNA sequencing libraries were generated using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus. Samples were normalized with nuclease-free water to 100 ng in 11 µL total volume. Concentrations of final libraries were determined by using either the Quant-iT High Sensitivity DNA kit on the VICTOR Nivo plate reader or the Qubit DNA High Sensitivity kit on the Qubit Flex Fluorometer. Library fragment size was also checked on a DNA D1000 or HSD1000 ScreenTape on the Agilent 4200 Tapestation instrument. To ensure proper quantification of sequenceable library molecules, a qPCR reaction was also performed using the NEBNext Library Quant Kit for Illumina.  Total RNA-seq libraries were shipped to SeqCenter for sequencing on a NovaSeq X. Sequencing used a 2 x 151 bp configuration and targeted sequencing depth was >100 M read-pairs per library. Note that PHH Donor 3 sequencing data had a high percentage of duplicates. Therefore, the library prep and sequencing were repeated, with RNA-seq libraries sequenced in the Sponsor’s laboratory on a NextSeq2000 with a 2 x 151 bp configuration and targeted sequencing depth >100 M read-pairs per library.

value: Spleen

value: HSEC cells

value: Human Splenic Endothelial Cells


title: Custom Panel1 HCMS, PHH Donor1, CRMA-1001 0.5 µg/mL, 1

description: Library name: NGSHC3331


title: HBV HCMS, cccDNA, Mock-treatment, 3

description: Library name: NGSHC3202

library_source: other

data_processing:
The nf-core Methyl-Seq pipeline (v1.6.1) was used to map sequencing reads to a genotype specific HBV reference genome (dependant on sample) using the Bismark methylation extraction workflow, with default parameters except for the following: clip_r1 = 10, clip_r2 = 10, three_prime_clip_r1 = 10, three_prime_clip_r2 = 10, cytosine_report = true.
Assembly: Genotype D (GenBank Accession: U95551.1) or Genotype A (GenBank Accession: AF305422.1)
Supplementary files format and content: Bismark methylation bedgraph file
Supplementary files format and content: Bismark cytosine report file
Library strategy: EM-seq

molecule: other

organism: Hepatitis B virus

source_name: HBV covalently closed circular DNA from infected HepG2-NTCP cells

growth_protocol: HepG2.2.15 cells were cultured in DMEM (Gibco, 11965092) with 10% fetal bovine serum (FBS) (Gibco, A5670501) and 1% Pen-Strep (Gibco, 15140122). One day prior to treatment, 20,000 cells/well were seeded in collagen type I-coated 96-well plates. Plates were maintained and subcultured (cell trypsinization every 3-4 days).  HepG2-NTCP cells were plated at 20,000 cells/well in collagen coated 96-well plates and infected 24 hours later with HBV Genotype D at 2,000 multiplicity of genome equivalents (MGE) using DMEM media supplemented with 4% PEG8000 and 2.5% DMSO. At 16 hours post-infection, media was removed, cells were washed with PBS and were maintained in DMEM media supplemented with 2.5% DMSO.  C57BL/6-HBV transgenic mice (Tg-HBV), 5-6 weeks old, carrying two copies per diploid host genome of the 1.28× Genotype A HBV genome were obtained from Beijing Vitalstar Biotechnology Co., Ltd.

extract_protocol:
HepG2.2.15, cell samples were collected at a timepoint 14 days after treatment. Nucleic acids were extracted using simultaneous RNA and DNA extraction protocols (Beckman Coulter) for methylation assessments.  cccDNA was extracted from HepG2-NTCP using a modified Hirt protocol, using the MasterPure Complete DNA and RNA Purification Kit (LucigenEpicentre) without the proteinase K digestion. Total DNA was digested using 10 U of T5 exonuclease per 1 ug of DNA for 30 mins at 37°C, followed by heat inactivation at 80°C for 20 minutes. One third of the extracted total DNA was not digested and used as a control. After digestion, all samples were concentrated using a standard sodium acetate DNA precipitation protocol.  Tg-HBV mice were euthanized, and liver samples were collected for methylation assessment.
Genomic or cccDNA was sheared to a target size of 350bp using a Covaris 96 AFA-Tube TPX plate. Sequencing libraries were then constructed from the sheared genomic DNA using the NEBNext Enzymatic Methyl-seq (EM-seq) kit plus NEBNext Multiplex Oligos for Enzymatic Methyl-seq. After methylation conversion, a custom panel targeting the appropriate HBV genome (genotype A for Tg-HBV mouse and genotype D for HepG2.2.15 cells and cccDNA) was used to enrich for regions of interest, following the recommended Twist protocol for 8-plex pools. Libraries were then amplified and sequenced using an Illumina NextSeq2000 running NextSeq1000/2000 Control software version 1.7.0.45751 with 2 x 150 bp reads to a sequencing depth of > 5 million read pairs per sample.

treatment_protocol: HepG2.2.15 cells were treated with 100 µL of fresh media supplemented with LNP-formulated epigenetic silencers at a dose of 0.5 µg/mL (or 1.0 µg/mL for CRMA-1001) and/or 1 µg/mL of rhApoE3. Untreated controls were also included for one study.  Infected HepG2-NTCP cells were treated with 1 µg/mL of CRMA-1001 or vehicle. Cells were washed with PBS and snap frozen on Day 7.  All Tg-HBV mice were acclimated for 10 days before receiving a single IV bolus administration of vehicle, or HBV-EE4000 (0.2, 0.5, 1 and 3 mg/kg).

value: HBV Genotype D


title: HBV HCMS, cccDNA, Mock-treatment, 2

description: Library name: NGSHC3201

value: HBV covalently closed circular DNA from infected HepG2-NTCP cells


title: RNAseq, HSEC Donor2-repeat, Untreated, 2

description: Library name: NGSRS3411


title: RNAseq, HSEC Donor2-repeat, Untreated, 3

description: Library name: NGSRS3412


title: HBV HCMS, cccDNA, Mock-treatment, 1

description: Library name: NGSHC3200


title: RNAseq, HSEC Donor2-repeat, Untreated, 1

description: Library name: NGSRS3410


title: HBV HCMS, cccDNA, CRMA-1001 1.0  µg/mL, 3

description: Library name: NGSHC3196


title: RNAseq, HSEC Donor2-repeat, PCSK9-EE7000, 4

description: Library name: NGSRS3401


title: RNAseq, HSEC Donor2-repeat, PCSK9-EE7000, 3

description: Library name: NGSRS3400


title: HBV HCMS, cccDNA, CRMA-1001 1.0  µg/mL, 1

description: Library name: NGSHC3194


title: RNAseq, HSEC Donor2-repeat, PCSK9-EE7000, 2

description: Library name: NGSRS3399


title: HBV HCMS, cccDNA, CRMA-1001 1.0  µg/mL, 2

description: Library name: NGSHC3195


title: RNAseq, HSEC Donor2-repeat, PCSK9-EE7000, 1

description: Library name: NGSRS3398


title: R1242, after selection, replicate2

city: Shenzhen

first: Zhe

last: Zhang

state: Guangdong

address: Gaoke Innovation Center

department: Institute of Physical and Systems Biology

institute: Shenzhen Bay Laboratory

description:
Library name: R1242-A-r2
R1242-r2.ra.txt

data_processing:
Paired-end fastq files from next-generation sequencing were merged by using PEAR. Both 5’ constant regions and 3’ constant regions of the assembled reads were trimmed by cutadapt. We used FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and vsearch to filter sequencing reads with low quality, and count the read number of identical sequences. The read numbers before and after selection were then summed up for each unique sequence. RNA-specific CODA Analysis was used for downstream analysis.
Supplementary files format and content: The ra.txt files contain tab-separated values in each line. The values from left to right are: number of mutations, mutated position, mutation type, read counts before selection, read counts after selection, relative enrichment ratio (fitness).

organism: Escherichia coli

extract_protocol:
The assembled products were mixed with electrocompetent cells and transformed into electrocompetent cells in a 2-mm Gene Pulser cuvette (Bio-Rad, 165-2086) using an electroporation instrument (Bio-Rad, MicroPulser). The transformants were cultured on 20 mL LB for 1 h at 37 °C on a rotator with 220 rpm. After 1 h, the size of the constructed library was detected by the number of colonies after a gradient dilution on LB-agar plate (containing 100 μg/mL ampicillin). Then 100 μg/mL ampicillin was added to 20 mL LB and allowed to grow at 37 °C for 10 h and collected using centrifugation. The pellet was resuspended in LB medium containing 15% glycerol and stored at -80 °C for long term use. 10^7 clones from the mutated library were cultured and amplified. The corresponding plasmids were extracted. The BspQ I linearized vectors were transcribed to RNAs.
The purified RNA was reverse transcribed using ProtoScript® II Reverse Transcriptase (NEB, M0368L). The 20 μL reaction volume containing 4 µL 5 × ProtoScript II buffer, 2 μL 0.1 M DTT, 1 μL 10 mM dNTP, 0.2 μL RNase inhibitor (40 U/μL), 1 μL ProtoScript II RT (200 U/µL), 2 μL M13-RP and the RNA template. The reaction system was incubated at 42 °C for 1 h and then inactivated at 65 °C for 20 min. The cDNA product was stored at -20 °C for further use. A 10 μL cDNA product was utilized as the template for amplification (10 cycles) of the fragments with primers M13-FP/M13-RP. Then, the DNA sequence library was constructed using recycled fragments as the template with adaptor primers in PCR amplification reactions. The PCR products were purified by agarose gel electrophoresis with a Gel Extraction Kit (Omega, D2500-02).

treatment_protocol: The fragments of the mutated DNA library (from EP-PCR or Oligo pool) were amplified with primers M13-Plus-FP/M13-Plus-RP and the linearized pUC57-T7Q vector was amplified with primers AS-FP/AS-RP using PrimerSTAR HS DNA polymerase (Takara, R040A). The DNA fragments were loaded on the agarose-gel and the target bands were excised and recycled using a Gel Extraction Kit (Omega, D2500-02). DNA fragments and pUC57-T7Q vector were mixed with Exnase II in the reaction buffer on ice and the reaction system was incubated at 37 ℃ for 30 min (CloneExpress II One Step Cloning Kit, Vazyme, C112-02). The assembled products were purified with the RNA Clean & ConcentratorTM-5 (Zymo Research, R1016) and eluted with nuclease-free water.

tag: time point

value: after selection


title: R1242, after selection, replicate1

description:
Library name: R1242-A-r1
R1242-r1.ra.txt


title: RNAseq, HSEC Donor2-repeat, Mock-treatment, 4

description: Library name: NGSRS3409


title: R1242, before selection

description:
Library name: R1242-B
R1242-r1.ra.txt
R1242-r2.ra.txt

value: before selection


title: RNAseq, HSEC Donor2-repeat, Mock-treatment, 3

description: Library name: NGSRS3408


title: R1203, after selection, replicate2

description:
Library name: R1203-A-r2
R1203-r2.ra.txt


title: RNAseq, HSEC Donor2-repeat, Mock-treatment, 2

description: Library name: NGSRS3407


title: R1203, after selection, replicate1

description:
Library name: R1203-A-r1
R1203-r1.ra.txt


title: RNAseq, HSEC Donor2-repeat, Mock-treatment, 1

description: Library name: NGSRS3406


title: PZ62, after selection

description:
Library name: PZ62-A
PZ62.ra.txt


title: RNAseq, HSEC Donor2-repeat, EE7000 mRNAOnly, 4

description: Library name: NGSRS3397


title: RNAseq, HSEC Donor2-repeat, EE7000 mRNAOnly, 2

description: Library name: NGSRS3395


title: PZ62, before selection

description:
Library name: PZ62-B
PZ62.ra.txt


title: R1203, before selection

description:
Library name: R1203-B
R1203-r1.ra.txt
R1203-r2.ra.txt


title: RNAseq, HSEC Donor2-repeat, EE7000 mRNAOnly, 3

description: Library name: NGSRS3396


title: RNAseq, HSEC Donor2-repeat, EE7000 mRNAOnly, 1

description: Library name: NGSRS3394


title: PZ51, after selection

description:
Library name: PZ51-A
PZ51.ra.txt


title: RNAseq, HSEC Donor2-repeat, CRMA-1001 1.0 µg/mL, 4

description: Library name: NGSRS3405


title: Amplicon Bisulfiteseq, NHP Liver, Vehicle Day 54, 1

description: Library name: NGSTB2989

data_processing:
The nf-core Methyl-Seq pipeline (v1.6.1) was used to map sequencing reads to the cynologous monkey reference genome using the Bismark methylation extraction workflow, with default parameters except for the following: clip_r1 = 0, clip_r2 = 20, three_prime_clip_r1 = 20, three_prime_clip_r2 = 0, non-directional = true, cytosine_report = true and skip_deduplication = true.
Assembly: Macaca_fascicularis_6.0
Supplementary files format and content: Bismark methylation bedgraph file

organism: Macaca fascicularis

growth_protocol: The cynomolgus monkey studies were conducted at Altasciences (Everett, USA) in accordance with IACUC guidelines.

extract_protocol:
gDNA was extracted from NHP liver biopsies using a DNAdvance Kit (Beckman Coulter).
gDNA was denatured and treated with sodium bisulfite and heated to deaminate unmethylated cytosines to uracil using the EZ-96 Methylation-Gold MagPrep bisulfite conversion kit (Zymo Research). Primers were designed to amplify the region around the NHP PCSK9 TSS, as seven short, partially overlapping, amplicons. Amplicons were generated using Platinum Taq polymerase (Invitrogen) and pooled for each condition so that each sample contained all associated amplicons and was used as input for NEBNext Ultra II DNA library prep, amplified with unique dual indexes to allow for multiplexing. Libraries were sequenced using an Illumina NextSeq 2000 or MiSeq instrument (2 × 150-bp paired-end reads) to a read depth of at least 9 million read pairs per sample.

value: Liver


title: RNAseq, HSEC Donor2-repeat, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSRS3404


title: Amplicon Bisulfiteseq, NHP Liver, Vehicle Day 54, 2

description: Library name: NGSTB2990


title: PZ51, before selection

description:
Library name: PZ51-B
PZ51.ra.txt


title: Amplicon Bisulfiteseq, NHP Liver, Vehicle Day -35, 1

description: Library name: NGSTB2953


title: PZ50, after selection

description:
Library name: PZ50-A
PZ50.ra.txt


title: RNAseq, HSEC Donor2-repeat, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSRS3402


title: RNAseq, HSEC Donor2-repeat, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSRS3403


title: RNAseq, PHH Donor3, Untreated, 2

description: Library name: NGSRS3310

value: PXB cells

value: Primary Human Hepatocyte


title: Amplicon Bisulfiteseq, NHP Liver, PCSK9-EE700 Day 54, 3

description: Library name: NGSTB3001


title: RNAseq, PHH Donor3, Untreated, 1

description: Library name: NGSRS3306


title: PZ50, before selection

description:
Library name: PZ50-B
PZ50.ra.txt


title: RNAseq, PHH Donor3, PCSK9-EE7000, 3

description: Library name: NGSRS3321


title: Amplicon Bisulfiteseq, NHP Liver, PCSK9-EE700 Day 54, 2

description: Library name: NGSTB3000


title: RNAseq, PHH Donor3, PCSK9-EE7000, 2

description: Library name: NGSRS3313


title: Whole brain, WT-5_S3

city: Nathan

first: Oak

last: Hatzimanolis

state: QLD

address: 46 Don Young Rd

department: IBG

country: Australia

institute: Griffith University

description:
Library name: WT-5_S3
column name in raw_counts.csv: WT-5_S3

data_processing:
Quality control of Fastq reads performed using FastQC (v0.11.9), multiQC (v1.9). Removal of low-quality sequences and adaptor was done with Trimmomatic (v0.39).
Trimmed sequences were aligned to GRCz11 (release 113) using STAR (v2.7.11b) using --twopassMode Basic --quantMode GeneCounts
Assembly: GRCz11 (release 113)
Supplementary files format and content: csv file containing raw counts from STAR alignment

organism: Danio rerio

source_name: Whole brain

extract_protocol:
Total RNA was extracted from adult brain tissues using the Direct-zol™ RNA Miniprep Kit (Zymo Research, California, USA). Tissue samples were homogenised in TRIzol, and total RNA was isolated according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepered using Illumina TruSeq Stranded mRNA Library Prep Kit.

value: Whole brain

value: Wildtype

tag: developmental stage

value: Adult


title: RNAseq, PHH Donor3, PCSK9-EE7000, 1

description: Library name: NGSRS3309


title: Whole brain, WT-3_S2

description:
Library name: WT-3_S2
column name in raw_counts.csv: WT-3_S2


title: Amplicon Bisulfiteseq, NHP Liver, PCSK9-EE700 Day -35, 3

description: Library name: NGSTB2964


title: RNAseq, PHH Donor3, HBV-CRISPRi, 4

description: Library name: NGSRS3332


title: Amplicon Bisulfiteseq, NHP Liver, PCSK9-EE700 Day 54, 1

description: Library name: NGSTB2999


title: RNAseq, PHH Donor3, Mock-treatment, 1

description: Library name: NGSRS3307


title: RNAseq, PHH Donor3, Mock-treatment, 2

description: Library name: NGSRS3311


title: Whole brain, WT-1_S1

description:
Library name: WT-1_S1
column name in raw_counts.csv: WT-1_S1


title: RNAseq, PHH Donor3, HBV-CRISPRi, 3

description: Library name: NGSRS3329


title: Amplicon Bisulfiteseq, NHP Liver, PCSK9-EE700 Day -35, 2

description: Library name: NGSTB2963


title: Whole brain, 3a3bT-5_S24

description:
Library name: 3a3bT-5_S24
column name in raw_counts.csv: 3a3bT-5_S24

value: Double mutant(nrxn3a_tmr:nrxn3b_tmr)

value: CRISPR/Cas9-mediated double gene transmemebrane region deletion


title: RNAseq, PHH Donor3, HBV-CRISPRi, 2

description: Library name: NGSRS3326


title: RNAseq, PHH Donor3, HBV-CRISPRi, 1

description: Library name: NGSRS3323


title: RNAseq, PHH Donor3, EE7000 mRNAOnly, 4

description: Library name: NGSRS3331


title: Whole brain, 3a3bT-4_S23

description:
Library name: 3a3bT-4_S23
column name in raw_counts.csv: 3a3bT-4_S23


title: Amplicon Bisulfiteseq, NHP Liver, PCSK9-EE700 Day -35, 1

description: Library name: NGSTB2962


title: Whole brain, 3a3bT-3_S22

description:
Library name: 3a3bT-3_S22
column name in raw_counts.csv: 3a3bT-3_S22


title: OE3

city: Shijiazhuang

first: Zhang

last: Zhilei

address: No.12, Jiankang Road, Chang'an District, Shijiazhuang City

institute: The Fourth Hospital of Hebei Medical University

description: Library name: Sample6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: Homo_sapiens.GRCh37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was extracted from tissues or cells using standard extraction methods, followed by rigorous quality control of the RNA samples. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: PDAC

value: overexpressing DUSP5


title: RNAseq, PHH Donor3, EE7000 mRNAOnly, 3

description: Library name: NGSRS3328


title: RNAseq, PHH Donor3, EE7000 mRNAOnly, 2

description: Library name: NGSRS3325


title: RNAseq, PHH Donor3, EE7000 mRNAOnly, 1

description: Library name: NGSRS3322


title: OE2

description: Library name: Sample5


title: RNAseq, PHH Donor3, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSRS3320


title: RNAseq, PHH Donor3, CRMA-1001 1.0 µg/mL, 2

description: Library name: NGSRS3312


title: Whole brain, 3a3bF-4_S21

description:
Library name: 3a3bF-4_S21
column name in raw_counts.csv: 3a3bF-4_S21

value: Double mutant(nrxn3a_full:nrxn3b_full)

value: CRISPR/Cas9-mediated double full gene deletion


title: OE1

description: Library name: Sample4


title: RNAseq, PHH Donor3, CRMA-1001 1.0 µg/mL, 1

description: Library name: NGSRS3308


title: Whole brain, 3a3bF-3_S20

description:
Library name: 3a3bF-3_S20
column name in raw_counts.csv: 3a3bF-3_S20


title: RNAseq, PHH Donor3, CRMA-1001 0.5 µg/mL, 4

description: Library name: NGSRS3333


title: Ctrl3

description: Library name: Sample3

value: control cells


title: RNAseq, PHH Donor3, CRMA-1001 0.5 µg/mL, 3

description: Library name: NGSRS3330


title: Whole brain, 3a3bF-2_S19

description:
Library name: 3a3bF-2_S19
column name in raw_counts.csv: 3a3bF-2_S19


title: RNAseq, PHH Donor3, CRMA-1001 0.5 µg/mL, 2

description: Library name: NGSRS3327


title: Ctrl2

description: Library name: Sample2


title: RNAseq, PHH Donor3, CRMA-1001 0.5 µg/mL, 1

description: Library name: NGSRS3324


title: Whole brain, 2a2bT-3_S18

description:
Library name: 2a2bT-3_S18
column name in raw_counts.csv: 2a2bT-3_S18

value: Double mutant(nrxn2a_tmr:nrxn2b_tmr)


title: HBV HCMS, HepG2.2.15, Mock-treatment, 3

description: Library name: NGSHC3265

source_name: HepG2.2.15 cells

value: HepG2.2.15 cells

value: HBV Genotype D


title: Ctrl1

description: Library name: Sample1


title: HBV HCMS, HepG2.2.15, Mock-treatment, 2

description: Library name: NGSHC3261


title: Whole brain, 2a2bT-2_S17

description:
Library name: 2a2bT-2_S17
column name in raw_counts.csv: 2a2bT-2_S17


title: HBV HCMS, HepG2.2.15, Mock-treatment, 1

description: Library name: NGSHC3257


title: KO4

city: Lausanne

first: Giovanna

last: Ambrosini

address: Station 19

country: Switzerland

institute: EPFL

description: Library name: Sample8

data_processing:
Libraries were quantified by a fluorometric method (QubIT, Life Technologies) and their quality assessed on a Fragment Analyzer (Agilent Technologies). Sequencing was performed on an Element Biosciences Aviti with a 2x75 cycles sequencing kit Cloudbreak FS High Output (run as single read 150).  Base calling and demultiplexing was done with bases2fastq version: 2.0 with filter mask R1:N15Y15N*.
Raw FASTQ reads were processed using cutadapt to remove TruSeq adapter sequences and poly(A) tails.
Raw reads were aligned to the human (hg38) genome using STAR (2.7.11a)
Gene counts were generated using FeatureCounts (v2.0.4). Data preprocessing was done using the DESeq2 package (1.46.0) from Bioconductor (v3.30).
Assembly: hg38
Supplementary files format and content: raw_counts.txt
Supplementary files format and content: norm_counts.txt

growth_protocol: MDA-MB-231 CDK4WT and CDK4KO cells were cultured in RPMI media supplemented with HEPES and Sodium Pyruvate and FBS

extract_protocol:
RNA extracted from tumors by Trizol
RNA-seq libraries were prepared from 500 ng of total RNA with the Watchmaker mRNA Library Prep Kit (Watchmaker Genomics) using a unique dual indexing strategy, and following the official protocol

value: Triple Negative Breast Cancer cell


title: HBV HCMS, HepG2.2.15, CRMA-1001 1.0  µg/mL, 3

description: Library name: NGSHC3262


title: HBV HCMS, HepG2.2.15, CRMA-1001 1.0  µg/mL, 2

description: Library name: NGSHC3258


title: Whole brain, 2a2bT-1_S16

description:
Library name: 2a2bT-1_S16
column name in raw_counts.csv: 2a2bT-1_S16


title: KO3

description: Library name: Sample7


title: Whole brain, 2a2bF-3_S15

description:
Library name: 2a2bF-3_S15
column name in raw_counts.csv: 2a2bF-3_S15

value: Double mutant(nrxn2a_full:nrxn2b_full)


title: HBV HCMS, HepG2.2.15, CRMA-1001 1.0  µg/mL, 1

description: Library name: NGSHC3254


title: MCF7 RB KO abemaciclib H3K4me3 positive control

city: Melbourne

first: Shom

last: Goel

state: Victoria

address: 305 Grattan St

institute: Peter MacCallum Cancer Centre

description: Library name: Sample 4

data_processing:
Adapters and low quality reads were removed using BBMap v38.90 bbduk.sh with the following parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20
Reads were aligned using Bowtie2 v2.3.4.1 to the GCA hg38 genome with the following parameters: --dovetail --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Reads that aligned to ChIP blacklisted regions were removed, as well as reads aligned to mitrochondria DNA. Duplicates were kept.
bigwigs for treated samples were created using deeptools/3.5.0 bamCoverage function using paramters --binSize 20, --smoothLength 60, --scaleFactor scalefactor, --extendReads, where the scalefactor generated by a background normalisation from DiffBind was used as a normalisation factor. Bigwig for the input sample was normalised with BPM.
peaks were called using MACS2 v2.2.7.1 callpeak using the negative input in the --control parameter, --format BAMPE -gsize hs. Peaks for the negative input (IgG) and positive control (H3K4me3) were called without a control parameter.
Assembly: GCA hg38
Supplementary files format and content: bigwigs, narrowPeaks
Library strategy: CUT&Run

growth_protocol: RPMI-1640 supplemented with 10% FBS, 1% GlutaMax, and 1% HEPES, incubated at 37C at 5% CO2.

extract_protocol:
CUT&RUN was performed using the Cell Signaling Technologies (CST) CUT&RUN Assay Kit (#86652) as per manufacturer's protocol.
CUT&RUN libraries were prepared using the NEBNext® Ultra II DNA Library Prep Kit for Illumina, following the CST DNA Library Prep Kit protocol for CUT&RUN.

treatment_protocol: Abemaciclib 500 nM or equal volume of DMSO (control) for 2 days.

value: Abemaciclib

tag: antibody


title: MCF7 Parent DMSO Rabbit IgG negative control

description: Library name: Sample 3

value: Parent

value: DMSO


title: KO2

description: Library name: Sample6


title: Whole brain, 2a2bF-2_S14

description:
Library name: 2a2bF-2_S14
column name in raw_counts.csv: 2a2bF-2_S14

value: Whole brain


title: MCF7 Parent DMSO ER C&R

description: Library name: Sample 1


title: Whole brain, 2a2bF-1_S13

description:
Library name: 2a2bF-1_S13
column name in raw_counts.csv: 2a2bF-1_S13

value: Adult


title: OVCAR3 Parent INX315 RNAseq replicate 3

description: Library name: Sample 6

data_processing:
Adapters and low quality reads were removed using BBMap v38.90 bbduk.sh with the following parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20
trimmed reads were aligned using STAR (v2.7.5b) to the human reference genome (hg38)
Aligned reads were counted using featurecounts (v2.0.1)  using annotations from GENCODE (gencode.v35.annotation.gtf )
Assembly: hg38
Supplementary files format and content: csv file include raw count (non-normalised) values for each sample

growth_protocol: OVCAR-3 cells were cultured in RPMI-1640, supplemented with 10% FBS and 1x Glutamax. All cells were maintained at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
RNA was extracted using NucleoSpin RNA Plus kit (Macherey-Nagel).
Libraries were prepared using the QuantaSeq Lexogen 3’mRNA RW kit.

treatment_protocol: Cells were treated with INX-315 300 nM or the equivalent volume of DMSO (control) for 2 days.

tag: replicate


title: OVCAR3 Parent INX315 RNAseq replicate 2

description: Library name: Sample 5


title: Whole brain, 1a1bT-5_S9

description:
Library name: 1a1bT-5_S9
column name in raw_counts.csv: 1a1bT-5_S9

value: Double mutant(nrxn1a_tmr:nrxn1b_tmr)


title: WT4

description: Library name: Sample4


title: OVCAR3 Parent INX315 RNAseq replicate 1

description: Library name: Sample 4


title: Custom Panel2 HCMS, PHH Donor1, CRMA-1001 0.5 µg/mL, 4

description: Library name: NGSHC3673

value: Liver

value: PXB cells

value: Primary Human Hepatocyte


title: Custom Panel2 HCMS, PHH Donor1, CRMA-1001 0.5 µg/mL, 2

description: Library name: NGSHC3667


title: WT3

description: Library name: Sample3


title: OVCAR3 Parent DMSO RNAseq replicate 3

description: Library name: Sample 3


title: Whole brain, 1a1bT-4_S8

description:
Library name: 1a1bT-4_S8
column name in raw_counts.csv: 1a1bT-4_S8

value: CRISPR/Cas9-mediated double gene transmemebrane region deletion


title: KO1

description: Library name: Sample5


title: OVCAR3 Parent DMSO RNAseq replicate 2

description: Library name: Sample 2


title: WT2

description: Library name: Sample2


title: MCF7 Parent abemaciclib ER C&R

description: Library name: Sample 2


title: OVCAR3 Parent DMSO RNAseq replicate 1

description: Library name: Sample 1


title: WT1

description: Library name: Sample1


title: Whole brain, 1a1bT-3_S7

description:
Library name: 1a1bT-3_S7
column name in raw_counts.csv: 1a1bT-3_S7


title: MCF7 siKDM5A-2 Abema Rep3

description: Library name: Sample 18

extract_protocol:
RNA was extracted from cell pellets using NucleoSpin® RNA plus kit (MachereyNagel, 40955) per manufacturers protocol.
Libraries were prepared using QuantSeq 3’ mRNA-Library Prep Kit FWD (Lexogen). RNA quantity and quality were assessed on TapeStation 4150 (Agilent). Reads were sequenced on NextSeq500 (Illumina) using 75-cycle High Output Reagent kits

treatment_protocol: Cells were transfected with non-targeting control siRNA or one of two KDM5A-targeting siRNA using Dharmafect. The next day, media was changed, and cells were treated with abemaciclib 500 nM or equal volume of DMSO (control) for 2 days.

tag: sirna


title: MCF7 siKDM5A-2 Abema Rep2

description: Library name: Sample 17


title: MCF7 siKDM5A-2 Abema Rep1

description: Library name: Sample 16


title: Whole brain, 1a1bP-3_S12

description:
Library name: 1a1bP-3_S12
column name in raw_counts.csv: 1a1bP-3_S12

value: Double mutant(nrxn1a_part:nrxn1b_part)

value: CRISPR/Cas9-mediated double gene partial deletion


title: MCF7 siKDM5A-2 DMSO Rep3

description: Library name: Sample 15


title: Apical, w normal breathing, 48h after infection, 3

first: Yuncheng

last: Man

state: MA

address: 201 Brookline Ave

institute: Wyss Institute, Harvard University

description:
Library name: Sample 14
AlveolusChipwMac-Apical-48hpi-wStretch-3

data_processing:
Genewiz Azenta and Pluto software
Assembly: GRCh37
Supplementary files format and content: Excel file with raw counts

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen)
Genewiz Azenta

value: Lung

value: Human alveolar epithelium and macrophages


title: Whole brain, 1a1bP-2_S11

description:
Library name: 1a1bP-2_S11
column name in raw_counts.csv: 1a1bP-2_S11


title: MCF7 siKDM5A-2 DMSO Rep2

description: Library name: Sample 14


title: Apical, w normal breathing, 48h after infection, 2

description:
Library name: Sample 13
AlveolusChipwMac-Apical-48hpi-wStretch-2


title: MCF7 siKDM5A-2 DMSO Rep1

description: Library name: Sample 13


title: MCF7 siKDM5A-1 Abema Rep3

description: Library name: Sample 12


title: Whole brain, 1a1bP-1_S10

description:
Library name: 1a1bP-1_S10
column name in raw_counts.csv: 1a1bP-1_S10


title: Apical, w normal breathing, 48h after infection, 1

description:
Library name: Sample 12
AlveolusChipwMac-Apical-48hpi-wStretch-1


title: MCF7 siKDM5A-1 Abema Rep2

description: Library name: Sample 11


title: Apical, w hyperventilation, 48h after infection, 3

description:
Library name: Sample 11
AlveolusChipwMac-Apical-48hpi-wOverStretch-3


title: MCF7 siKDM5A-1 Abema Rep1

description: Library name: Sample 10


title: Whole brain, 1a1bF-5_S6

description:
Library name: 1a1bF-5_S6
column name in raw_counts.csv: 1a1bF-5_S6

value: Double mutant(nrxn1a_full:nrxn1b_full)

value: CRISPR/Cas9-mediated double full gene deletion


title: Whole brain, 1a1bF-3_S5

description:
Library name: 1a1bF-3_S5
column name in raw_counts.csv: 1a1bF-3_S5


title: Apical, w hyperventilation, 48h after infection, 2

description:
Library name: Sample 10
AlveolusChipwMac-Apical-48hpi-wOverStretch-2


title: MCF7 siKDM5A-1 DMSO Rep3

description: Library name: Sample 9


title: MCF7 siKDM5A-1 DMSO Rep1

description: Library name: Sample 7


title: MCF7 siKDM5A-1 DMSO Rep2

description: Library name: Sample 8


title: Whole brain, 1a1bF-2_S4

description:
Library name: 1a1bF-2_S4
column name in raw_counts.csv: 1a1bF-2_S4


title: MCF7 siControl Abema Rep3

description: Library name: Sample 6


title: RNAseq, HAdCC Donor3, CRMA-1001 1.0 µg/mL, 3

description: Library name: NGSRS3250

source_name: Adrenal

value: Adrenal

value: HAdCC cells

value: Human Adrenal Cortical Cells


title: RNAseq, HAdCC Donor1, Mock-treatment, 1

description: Library name: NGSRS3212


title: RNAseq, HAdCC Donor1, PCSK9-EE7000, 3

description: Library name: NGSRS3206


title: Apical, w hyperventilation, 48h after infection, 1

description:
Library name: Sample 9
AlveolusChipwMac-Apical-48hpi-wOverStretch-1


city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description:
Library name: p24155-s012_NA73-Day294-ARTposVenetoclaxposantiposCD8
Column name in raw_count_p24155_Tomas_Processing.csv

data_processing:
Alignment was performed using STAR version 2.7.9a and transcripts were annotated using a composite genomic assembly and annotation of the Mmul10 Indian rhesus macaque and SIVsm804ECL757 (Accession MF370842). Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count.
Assembly: Mmul10
Assembly: MF370842
Supplementary files format and content: csv files containing raw counts for each sample (in columns) and transcript (in rows)

organism: Macaca mulatta

source_name: Blood

extract_protocol:
CD4+ T-cells were lyse in 350 L of Buffer RLT and then extracted using the RNeasy Mini / kit (Qiagen) with on-column DNase digestion. RNA quality was assessed using a TapeStation 4200 (Agilent)
Ten nanograms of total RNA was used as input for cDNA synthesis using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000, yielding ~21 million reads per sample on average.

value: Blood

value: CD4+ T-cells

tag: timepoint

tag: venetoclax treatment

value: Venetoclax

tag: anti-cd8a treatment


title: MCF7 siControl Abema Rep2

description: Library name: Sample 5

value: Abemaciclib


title: MCF7 siControl Abema Rep1

description: Library name: Sample 4


title: MCF7 siControl DMSO Rep3

description: Library name: Sample 3

value: DMSO


description:
Library name: p24155-s011_NA11-Day294-ARTposVenetoclaxposantiposCD8
Column name in raw_count_p24155_Tomas_Processing.csv


title: Apical, wo Stretch, before infection, 4

description:
Library name: Sample 8
AlveolusChipwMac-Apical-woStretch-beforeinfection-4


title: MCF7 siControl DMSO Rep2

description: Library name: Sample 2


title: Apical, wo Stretch, before infection, 3

description:
Library name: Sample 7
AlveolusChipwMac-Apical-woStretch-beforeinfection-3


title: MCF7 siControl DMSO Rep1

description: Library name: Sample 1


title: MN86-Day294-ARTposVenetoclax

description:
Library name: p24155-s010_MN86-Day294-ARTposVenetoclax
Column name in raw_count_p24155_Tomas_Processing.csv


title: Apical, wo Stretch, before infection, 2

description:
Library name: Sample 6
AlveolusChipwMac-Apical-woStretch-beforeinfection-2


title: Combination R

description: Library name: Sample 7

data_processing:
Adapters and low quality reads were removed using BBMap v38.90 bbduk.sh with the following parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=5 minlen=20
trimmed reads were aligned using STAR (v2.7.5b) independently to the human reference genome (hg38) and the mouse genome (mm10). Then, XenofilteR was used filter out the mouse reads to create BAM files that were human specific reads.
Aligned reads were counted using featurecounts (v2.0.1)  using annotations from GENCODE (gencode.v35.annotation.gtf )
Assembly: hg38, mm10
Supplementary files format and content: csv file include raw count (non-normalised) values for each sample

source_name: Patient-derived xenograft; ER+ breast cancer

growth_protocol: Patient derived xenograft KCC-P-3837 tumour pieces were implanted into theleft and right 4th inguinal mammary glands of 6–8-week-old female NSG mice, under oestradiol supplementation

extract_protocol:
RNA was extracted from flash frozen tumour pieces using NucleoSpin RNA Plus kit (Macherey-Nagel).
Libraries were prepared using the QuantaSeq Lexogen 3’mRNA RW kit.

treatment_protocol: Mice were treated with palbociclib (100 mg/kg in water 5 days per week by oral gavage), fulvestrant (5 mg/mouse in 100 μL peanut oil once weekly by subcutaneous injections), the combination of palbociclib and fulvestrant, or vehicles only for 19 days.

tag: tumour stage

value: grade 3, ER+, PR+, HER2− primary invasive ductal carcinoma

value: Palbociclib + fulvestrant


title: MN79-Day294-ARTposVenetoclax

description:
Library name: p24155-s009_MN79-Day294-ARTposVenetoclax
Column name in raw_count_p24155_Tomas_Processing.csv


title: Combination L

description: Library name: Sample 8

value: Patient-derived xenograft; ER+ breast cancer


title: Fulvestrant L

description: Library name: Sample 6

value: Fulvestrant


title: Apical, wo Stretch, before infection, 1

description:
Library name: Sample 5
AlveolusChipwMac-Apical-woStretch-beforeinfection-1


title: Fulvestrant R

description: Library name: Sample 5


title: Palbociclib L

description: Library name: Sample 4

value: Palbociclib


title: Apical, w Stretch, before infection, 4

description:
Library name: Sample 4
AlveolusChipwMac-Apical-wStretch-beforeinfection-4

value: Lung


title: MN10-Day294-ART

description:
Library name: p24155-s008_MN10-Day294-ART
Column name in raw_count_p24155_Tomas_Processing.csv


title: Palbociclib R

description: Library name: Sample 3


title: Vehicle L

description: Library name: Sample 2

value: Vehicle


title: Apical, w Stretch, before infection, 3

description:
Library name: Sample 3
AlveolusChipwMac-Apical-wStretch-beforeinfection-3

value: Human alveolar epithelium and macrophages


title: ME53-Day294-ART

description:
Library name: p24155-s007_ME53-Day294-ART
Column name in raw_count_p24155_Tomas_Processing.csv


description:
Library name: p24155-s006_NA01-Day294-ARTposVenetoclaxposantiposCD8
Column name in raw_count_p24155_Tomas_Processing.csv


title: Vehicle R

description: Library name: Sample 1


title: MCF7 RB1 KO abemaciclib RNAseq replicate 3

description: Library name: Sample 12

treatment_protocol: Abemaciclib 500 nM or equal volume of DMSO (control) for 5 days.

value: RB1 knockout


title: Apical, w Stretch, before infection, 2

description:
Library name: Sample 2
AlveolusChipwMac-Apical-wStretch-beforeinfection-2


description:
Library name: p24155-s005_MR11-Day294-ARTposVenetoclaxposantiposCD8
Column name in raw_count_p24155_Tomas_Processing.csv


title: Apical, w Stretch, before infection, 1

description:
Library name: Sample 1
AlveolusChipwMac-Apical-wStretch-beforeinfection-1


title: MCF7 RB1 KO abemaciclib RNAseq replicate 1

description: Library name: Sample 10


title: MCF7 RB1 KO DMSO RNAseq replicate 3

description: Library name: Sample 9


title: MM88-Day294-ARTposVenetoclax

description:
Library name: p24155-s004_MM88-Day294-ARTposVenetoclax
Column name in raw_count_p24155_Tomas_Processing.csv


title: Amplicon Bisulfiteseq, NHP Liver, Vehicle Day 373, 2

description: Library name: NGSTB3113

value: Liver


title: MM12-Day294-ARTposVenetoclax

description:
Library name: p24155-s003_MM12-Day294-ARTposVenetoclax
Column name in raw_count_p24155_Tomas_Processing.csv


title: MCF7 RB1 KO DMSO RNAseq replicate 2

description: Library name: Sample 8


title: Amplicon Bisulfiteseq, NHP Liver, Vehicle Day 176, 2

description: Library name: NGSTB3084


title: HBV HCMS, HepG2.2.15, Untreated, 2

description: Library name: NGSHC878

value: HepG2.2.15 cells

value: HBV Genotype D


title: Amplicon Bisulfiteseq, NHP Liver, Vehicle Day 373, 1

description: Library name: NGSTB3112


title: HBV HCMS, HepG2.2.15, Untreated, 1

description: Library name: NGSHC874


title: MCF7 RB1 KO DMSO RNAseq replicate 1

description: Library name: Sample 7


title: MK02-Day294-ART

description:
Library name: p24155-s001_MK02-Day294-ART
Column name in raw_count_p24155_Tomas_Processing.csv

value: Blood


title: Amplicon Bisulfiteseq, NHP Liver, Vehicle Day 176, 1

description: Library name: NGSTB3083


title: MCF7 Parent abemaciclib RNAseq replicate 3

description: Library name: Sample 6

value: Parent


title: Amplicon Bisulfiteseq, NHP Liver, PCSK9-EE700 Day 373, 3

description: Library name: NGSTB3116


title: MCF7 Parent abemaciclib RNAseq replicate 2

description: Library name: Sample 5


title: HBV HCMS, HepG2.2.15, HBV-gRNA4-EE4000, 3

description: Library name: NGSHC869


description:
Library name: p24027-s011_NA73-Day25-ARTposVenetoclaxposantiposCD8
Column name in raw_count_p24027_Tomas_Analysis.csv

value: CD4+ T-cells

value: Venetoclax


title: Amplicon Bisulfiteseq, NHP Liver, PCSK9-EE700 Day 373, 2

description: Library name: NGSTB3115


title: MN86-Day25-ARTposVenetoclax

description:
Library name: p24027-s010_MN86-Day25-ARTposVenetoclax
Column name in raw_count_p24027_Tomas_Analysis.csv


title: MCF7 Parent abemaciclib RNAseq replicate 1

description: Library name: Sample 4

value: Abemaciclib


title: Amplicon Bisulfiteseq, NHP Liver, PCSK9-EE700 Day 373, 1

description: Library name: NGSTB3114


title: MCF7 RB1 KO abemaciclib RNAseq replicate 2

description: Library name: Sample 11


title: HBV HCMS, HepG2.2.15, HBV-gRNA4-EE4000, 1

description: Library name: NGSHC855


title: MN79-Day25-ARTposVenetoclax

description:
Library name: p24027-s009_MN79-Day25-ARTposVenetoclax
Column name in raw_count_p24027_Tomas_Analysis.csv


title: HBV HCMS, HepG2.2.15, HBV-gRNA3-EE4000, 3

description: Library name: NGSHC868


title: MCF7 Parent DMSO RNAseq replicate 3

description: Library name: Sample 3

value: DMSO


title: Amplicon Bisulfiteseq, NHP Liver, PCSK9-EE700 Day 176, 3

description: Library name: NGSTB3093


title: MN10-Day25-ART

description:
Library name: p24027-s008_MN10-Day25-ART
Column name in raw_count_p24027_Tomas_Analysis.csv


title: HBV HCMS, HepG2.2.15, HBV-gRNA3-EE4000, 2

description: Library name: NGSHC861


title: Amplicon Bisulfiteseq, NHP Liver, PCSK9-EE700 Day 176, 2

description: Library name: NGSTB3092


title: ME53-Day25-ART

description:
Library name: p24027-s007_ME53-Day25-ART
Column name in raw_count_p24027_Tomas_Analysis.csv


title: MCF7 Parent DMSO RNAseq replicate 1

description: Library name: Sample 1


title: Amplicon Bisulfiteseq, NHP Liver, PCSK9-EE700 Day 176, 1

description: Library name: NGSTB3091


title: HBV HCMS, HepG2.2.15, HBV-gRNA3-EE4000, 1

description: Library name: NGSHC854


description:
Library name: p24027-s006_NA01-Day25-ARTposVenetoclaxposantiposCD8
Column name in raw_count_p24027_Tomas_Analysis.csv


title: ZR-75-1 Parent abemaciclib RNAseq replicate 3

description: Library name: Sample 6

treatment_protocol: Abemaciclib 500 nM or equal volume of DMSO (control) for 4 days.


title: HBV HCMS, HepG2.2.15, HBV-gRNA2-EE4000, 3

description: Library name: NGSHC866


title: theta, rep3

city: London

first: Sofia

last: Peressotti

address: Exhibition Rd, South Kensington, London

country: United Kingdom

institute: Imperial College London

description: Library name: Stim3

data_processing:
The hisat2 software (2.0.5) was used with default parameters to map the data to the reference genome: mRatBN7.2 from Ensembl. Stringtie (1.3.3b) was used for the assembly (transcripts of class code type 'u'). featureCounts (1.5.0-p3) was used for the qunatification with default parameters. The data quality control was performed using a base calling error rate distribution of Q30 (99.9%), a GC content distribution control (with cut-off at 50%), and non-clean reads were removed from the analysis (defined as containing adapter contamination, a percentage of uncertain nucleotides >10%, and a percentage of low-quality nucleotides >50%).
Assembly: Ensembl mRatBN7.2
Supplementary files format and content: All .bam files contain the raw data. The gene_count.xlsx file contains the gene count for each sample and the gene_fpkm.xls contains the corresponding FPKM values for each sample.

organism: Rattus norvegicus

source_name: ventral mesencephalon embryonic day 14

growth_protocol: Primary neurogprogenitor cells were plated in 24-well plates at a density of 60,000 cells/cm2 with 0.75 ml of proliferation medium (DMEM)/F12 supplemented with 33 mM D-glucose, 1% L-glutamine, 1% penicillin/streptomycin (P/S), 2% B27, 1% fetal bovine serum (FBS), 20 ng/ml EGF, 20 ng/ml FGF). The cultures were then gradually transitioned from proliferation medium to differentiation medium: Dulbecco’s modified Eagle’s medium (DMEM)/F12 supplemented with 33 mM D-glucose, 1% L-glutamine, 1% penicillin/streptomycin (P/S), 50 mg/ml BSA, 1% N2. 75% of the medium was replaced every 2 days, increasing the ratio of differentiation medium by a third at every first medium change, until the transition was complete. Cells were grown for 10 days in total.

extract_protocol:
The mRNA was extracted using a commercial RNeasy Micro Kit (Cat. 74004, Quiagen) following the manufacturer protocol. Only samples with a purity ratio above 1.9 were included in the dataset.
Poly(A) enrichment was utilised for library preparation followed by 150 bp paired-end (40 million reads) sequencing using an Illumina Sequencing PE150 system.

treatment_protocol: Cells were stimulated in vitro with a temporal interference protocol (10 Hz amplitude modulation, 1 kHz frequency, 2 s on-2 s off, 2 mA peak-to peak, 300-500 mV/mm) for 3 days (day in vitro 7,8,9), 6 h per day. RNA extraction was performed at day in vitro 10.

value: ventral mesencephalon embryonic day 14

value: embryonic neuroprogenitor cells

value: WT

value: theta TI stimulation


title: ZR-75-1 Parent abemaciclib RNAseq replicate 2

description: Library name: Sample 5


description:
Library name: p24027-s005_MR11-Day25-ARTposVenetoclaxposantiposCD8
Column name in raw_count_p24027_Tomas_Analysis.csv


title: HBV HCMS, HepG2.2.15, HBV-gRNA2-EE4000, 2

description: Library name: NGSHC859


title: ZR-75-1 Parent abemaciclib RNAseq replicate 1

description: Library name: Sample 4


title: MM88-Day25-ARTposVenetoclax

description:
Library name: p24027-s004_MM88-Day25-ARTposVenetoclax
Column name in raw_count_p24027_Tomas_Analysis.csv


title: ZR-75-1 Parent DMSO RNAseq replicate 3

description: Library name: Sample 3


title: MM12-Day25-ARTposVenetoclax

description:
Library name: p24027-s003_MM12-Day25-ARTposVenetoclax
Column name in raw_count_p24027_Tomas_Analysis.csv


title: HBV HCMS, HepG2.2.15, HBV-gRNA1-EE4000, 3

description: Library name: NGSHC864


title: MK92-Day25-ART

description:
Library name: p24027-s002_MK92-Day25-ART
Column name in raw_count_p24027_Tomas_Analysis.csv


title: ZR-75-1 Parent DMSO RNAseq replicate 2

description: Library name: Sample 2


title: sham, rep3

description: Library name: Ctrl3

value: control (no treatment)


title: HBV HCMS, HepG2.2.15, HBV-gRNA1-EE4000, 2

description: Library name: NGSHC857


title: sham, rep2

description: Library name: Ctrl2


title: MK02-Day25-ART

description:
Library name: p24027-s001_MK02-Day25-ART
Column name in raw_count_p24027_Tomas_Analysis.csv


title: HBV HCMS, HepG2.2.15, HBV-gRNA1-EE4000, 1

description: Library name: NGSHC850


title: sham, rep1

description: Library name: Ctrl1


title: 3-Month High-Fat Diet Fast

status: Public on Jun 27 2026

city: Bronx

first: Jeffrey

middle: E

last: Pessin

state: NY

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

description: Library name: 3MHFD Fast

data_processing:
Raw sequencing data were processed using Space Ranger (v2.0.0 for normal chow and high-fat diet studies, v3.1.0 for humanized liver studies, 10x Genomics) to align reads to the reference genome and generate spatial gene expression matrices.
Assembly: For normal chow and high-fat diet studies: mm10-2020-A. For humanized liver studies: GRCh38-2020-A.
Supplementary files format and content: barcode.tsv.gz: list of spatial barcodes
Supplementary files format and content: feature.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: spatial_enrichment.csv: table of Moran's I values for each gene
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: cytassist_image.tiff: CytAssist image
Supplementary files format and content: aligned_tissue_image.jpg: aligned tissue image
Library strategy: Spatial Transcriptomics

extract_protocol:
For high-fat diet studies, fresh frozen mouse livers were embedded in Neg-50 and stored at -80 °C until sectioning. After sectioned at 10 μm thickness, sections were adhered to capture areas by brief warming onto Visium v1 slides (10x Genomics). For humanized liver studies, livers were fixed in 4% paraformaldehyde (PFA) for 3 hours, cryoprotected in PFA + 30 % sucrose for overnight, embedded in OCT, and tissue blocks were kept at -80 °C until sectioning. After sectioned at 10 μm thickness, Visium v2 (prepared with CytAssist) was performed using the CytAssist instrument.
For both studies, the sample preparation was performed according to the manufacturer’s guidelines. Briefly, tissue sections were stained with hematoxylin and eosin (H&E), imaged using a brightfield microscope for histological reference and spatial registration. RNA capture, reverse transcription, second-strand synthesis, cDNA amplification, and library construction were performed. Libraries were indexed, quality-controlled, and sequenced on an Illumina platform using paired-end sequencing.

treatment_protocol: NCD mice were fed laboratory mouse chow diet (LabDiet, 5053) whereas 3MHFD mice were fed a 60% fat diet (Research Diets, D12492) beginning at 6 weeks of age for 3 months. uPA SCID-based humanized liver chimeric mice were generated as previously described and maintained with vitamin C containing chow diet (modified LabDiet 5053 containing 130 ppm vitamin C).

value: 3-Month High-Fat Diet Fast


title: Normal Chow Diet Fast

description: Library name: NCD Fast

value: Normal Chow Diet Fast


title: TetKO_D0_WGBS

city: Paris

first: Marlet

last: Morales Franco

state: Île-de-France

address: 15 rue Hélène Brion

country: France

institute: Institut Jacques Monod, CNRS, Université Paris Cité

description: Library name: TetKO_D0_WGBS

data_processing:
Sequencing adaptors and low-quality nucleotides were removed using Trimmomatic (v0.39) with parameters ‘ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36’.
Processed reads were aligned to the mm10 genome using Bismark (v0.23.1) and default parameters. Aligned reads were deduplicated with ‘deduplicate_bismark’.
Methylation information of individual cytosines was extracted with ‘bismark_methylation_extractor’.
BigWig files for 5mC levels were generated from Bismark's CpG report by extracting the coordinates and methylation percentage of Cs covered by at least five reads. The resulting file was transformed with bedGraphToBigWig (v4).
Assembly: mm10
Supplementary files format and content: Bigwig format. Percentage of methylated Cs at CpG dinucleotides covered by at least 5 reads.

growth_protocol: The ESCs were grown on 0.1% gelatin-coated flask in serum culture conditions using Glasgow medium (Gibco) supplemented with 15% Fetal bovine Serum (FBS), MEM non-essential amino acid, sodium pyruvate, l-glutamine, penicillin, streptomycin, 0.1 mM β-mercaptoethanol and leukemia inhibitory factor (LIF), and passed with trypsin. Before EpiLC differentiation, cells were transitioned from serum to 2i + Vitamin C (vitC) cell culture conditions for at least 7 days. For the 2i + vitC culture conditions, N2B27 medium (50% neurobasal medium, 50% DMEM) supplemented with N2, B27, l-glutamine, β-mercaptoethanol, penicillin, streptomycin, LIF and 2i (Gsk3, and MEK inhibitors) and ascorbic acid. To induce EpiLC differentiation, cells were replated on Fibronectin (10 μg/ml, Sigma)-coated plates in N2B27 medium supplemented with FGF2 and Activin A.

extract_protocol:
Genomic DNA was extracted using NucleoSpin tissue kit (Macherey-Nagel ref. 740952) as per the manufacturer instructions, RNAse-treated, and re-purified using phenol-chloroform and ethanol precipitation.
WGBS libraries were generated using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences).

value: embryonic stem cells

value: Tet1/2 DKO

value: 2i + vitamin C

tag: time

value: Day 0


title: TetKO_D2_WGBS

description: Library name: TetKO_D2_WGBS

value: epiblast like-cells

value: EpiLC differentiation

value: Day 2


title: WT_D2_WGBS

description: Library name: WT_D2_WGBS


title: TetKO_D7_RNA_rep1

description: Library name: TetKO_D7_RNA_rep1

data_processing:
PCR duplicate reads were removed pre-alignment using BBmap Clumpify (v38.18) with parameters ‘dedupe=t k=19 passes=6 subs=(0.01 x readlength)’.
Sequencing adaptors and low-quality nucleotides were removed using Trimmomatic (v0.39) with parameters ‘ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24’.
Processed reads were aligned to the mm10 genome using STAR (v2.7.9a) and default parameters.
BigWig files were generated using deepTools (v3.5.1) bamCoverage and parameters ‘--binSize 1 --smoothLength 0 --minMappingQuality 255 --normalizeUsing CPM --blackListFileName ENCFF547MET.bed --ignoreForNormalization chrX chrM chrY’. Blacklisted regions are those defined by Amemiya et al., 2019.
Assembly: mm10
Supplementary files format and content: Bigwig format. CPM-normalized counts of RNA signal.

extract_protocol:
Total RNA was extracted from cell pellets using the NucleoSpin RNA kit (Macherey-Nagel).
Total RNA was sent to Novogene for poly(A) RNA library constructions.

value: Day 7


title: TetKO_D4_WGBS

description: Library name: TetKO_D4_WGBS

value: Day 4


title: TetKO_D4_RNA_rep2

description: Library name: TetKO_D4_RNA_rep2


title: RNAseq, HSEC Donor2, Mock-treatment, 1

description: Library name: NGSRS3172

extract_protocol:
For RNA extraction of all donors and sample types, Beckman Coulter RNAdvance v2 Kit was used. For RNA extraction from each PHH donor, two 24-well replicate plates per donor containing 336 µL cell lysate were combined and 4 x 63 µL aliquots of lysate were processed . For RNA extraction from each HAdCC donor, all replicate wells of each condition from two replicate plates each containing 3 wells of 63 µL cell lysate were combined and 3 x 63 µL aliquots of lysate were processed. For RNA extraction from HSEC, all replicate wells of each condition from two replicate plates each containing 3 wells of 63 µL cell lysate were combined and 3 x 63 µL aliquots of lysate were processed. The remaining lysate from each cell type was used for DNA extraction. For all samples, lysate aliquots were transferred to separate technical replicate wells of a 0.5 mL deep well plate and mixed with Beckman Coulter-patented SPRI paramagnetic beads to bind total RNA from the cell lysate. Bound RNA was then pelleted with a plate magnet, removing the supernatant allowing DNA and other contaminants to be removed through DNase treatment and a series of buffer (Wash WBD) and 70% ethanol washes, respectively. Total RNA was then eluted from the magnetic beads in nuclease-free water (HAdCC and HSEC samples (96-well plate format) were eluted in 22 uL per sample combining the replicates for a total of 44 uL eluate. PHH samples (24-well format) were eluted in 26 uL.).
Total RNA sequencing libraries were generated using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus. Samples were normalized with nuclease-free water to 100 ng in 11 µL total volume. Concentrations of final libraries were determined by using either the Quant-iT High Sensitivity DNA kit on the VICTOR Nivo plate reader or the Qubit DNA High Sensitivity kit on the Qubit Flex Fluorometer. Library fragment size was also checked on a DNA D1000 or HSD1000 ScreenTape on the Agilent 4200 Tapestation instrument. To ensure proper quantification of sequenceable library molecules, a qPCR reaction was also performed using the NEBNext Library Quant Kit for Illumina.  Total RNA-seq libraries were shipped to SeqCenter for sequencing on a NovaSeq X. Sequencing used a 2 x 151 bp configuration and targeted sequencing depth was >100 M read-pairs per library. Note that PHH Donor 3 sequencing data had a high percentage of duplicates. Therefore, the library prep and sequencing were repeated, with RNA-seq libraries sequenced in the Sponsor’s laboratory on a NextSeq2000 with a 2 x 151 bp configuration and targeted sequencing depth >100 M read-pairs per library.

value: Spleen

value: HSEC cells

value: Human Splenic Endothelial Cells


title: TetKO_D4_RNA_rep1

description: Library name: TetKO_D4_RNA_rep1


title: TetKO_D2_RNA_rep2

description: Library name: TetKO_D2_RNA_rep2


title: TetKO_D2_RNA_rep1

description: Library name: TetKO_D2_RNA_rep1


title: E10/E13/E16/P0 embryo

status: Public on Jun 29 2026

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

description:
Library name: 285849
10X Geomics FLEX

data_processing:
Fastq files were analysed using the Cell Ranger pipeline (10xGenomics, version 8.0.0) with Gfp and tdTom sequence added to Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv to generate count matrices
Assembly: mm10
Supplementary files format and content: feature-barcode matrices HDF5

source_name: telencephalic vesicles/cerebral cortex

growth_protocol: Organoids: mESCs were plated at high density so that colonies covered approximately half of the well area after 2 days of incubation. Medium was changed 1-2 hours prior to dissociation with StemPro Accutase (Thermo Fisher Scientific) or CTS TrypLE (Thermo Fisher Scientific) for 5 min at 37°C. Cells were counted with an automated cell counter, and were only used if >90% of cells were alive based on Trypan blue staining (Thermo Fisher Scientific). mESCs were centrifuged for 5 min at 200 x g, resuspended in Solution 1, and plated at a density of 3500 cells/microwell in a 24w-Aggrewell plate (Stem Cell Technologies). Solution 1 contained G-MEM (Thermo Fisher Scientific), 10% knockout serum replacement (Thermo Fisher Scientific), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin and WNT inhibitor (3 µM, IWR1, Sigma). No SMAD inhibitors were used as they were not required to direct cortical differentiation in mouse. Embryoid bodies were generated by day (D) 1, which were then transferred to 10 cm dishes with fresh Solution 1 and 2% growth factor-reduced Matrigel (Corning). On D5, organoids were gently pipetted to remove Matrigel and Solution 2 was added, containing DMEM/F12 (Thermo Fisher Scientific), 1% N2 supplement (Thermo Fisher Scientific), 0.1 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin, 1% chemically defined lipid concentrate (Thermo Fisher Scientific), and heparin (1 mg/ml; Sigma). On D7, organoids were transferred to 6-well plates and placed on an orbital shaker at low speed (50 r.p.m.) to prevent organoid fusion. From D9, organoids were grown in medium containing a 50:50 mix of DMEM/F12 and Neurobasal (Thermo Fisher Scientific), 0.5% N2, 1% B27 (Thermo Fisher Scientific), 0.5 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml pen/strep, 1% chemically defined lipid concentrate, and 50 mM 2-mercaptoethanol. Throughout the protocol medium was replaced as necessary every 2-3 days, and orbital shaker speed was increased after D9 (80 r.p.m.). Fused organoids and/or organoids that failed to grow were discarded throughout the procedure. Standard cell culture conditions (37°C with 5% CO2) were applied throughout all procedures. Mice: All animal procedures were approved by the Austrian Federal Ministry of Women, Science and Research in accordance with the Austrian and European Union animal law. Experimental mice were bred and maintained according to regulations approved by institutional animal care and use committee, institutional ethics committee and the guidelines of the preclinical facility (PCF) at ISTA. Mice were bred and maintained in experimental rodent facilities (room temperature 21 ± 1°C [mean ± SEM]; relative humidity 40%–55%; photoperiod 12L:12D). Food (V1126, Ssniff Spezialitaten GmbH, Soest, Germany) and tap water were available ad libitum. Emx1-Cre (PMID: 12151506) and mTmG reporter (PMID: 17868096) mouse lines have been reported previously. All mouse lines were kept in a mixed C57/Bl6 and CD1 genetic background. Mice were used at an age range from 2 – 8 months for general breeding. All efforts were made to minimize the number of animals by following the 3R principles.

extract_protocol:
In order to collect 1-2 million fixed cells per replicate, appropriate numbers of organoids/embryos were pooled for dissociation per replicate. Embryos: A total 40, 30, 10, and 4 brains were pooled from 8, 4, 2, and 2 litters for E10, E13, E16 and P1 timepoints, respectively. Organoids D8: organoids generated from 4-5 Aggrewells, ~800 organoids; D13: ~300 organoids; D20: 80 organoids; D25: 60 organoids). Organoids/Embryos were dissociated following a previously published protocol with some modifications (PMID: 33377108). Organoids/Embryos were first incubated in Earle’s Balanced Salt Solution (EBSS, Thermo Fischer Scientific) containing Papain (Worthington) and DNaseI (Worthington) for a total of 20 (D8, D13) or 25 min at 37°C with gentle shaking at 150 rpm. Organoids/Embryos were gently pipetted 3x with a P1000 tip. After adding Ovomucoid I-Albumin (Worthington), tissue suspension was briefly dissociated mechanically with a pipette. After centrifugation at 1000 rpm for 10 mins at room temperature, the cell pellet was re-suspended and further mechanically dissociated until a homogeneous cell suspension was obtained (up to 20X with a P1000 tip). The cell suspension was passed through a 70 µm filter, and centrifuged again at 1500 rpm for 10 mins at room temperature. Samples were next processed to remove debris prior to fixation. Cell pellets were re-suspended and mixed with cold Debris Removal Solution (Miltenyi Biotec). The mixture was carefully overlaid with cold PBS before centrifugation at 3000 x g for 10 mins at 4°C. The top two layers containing PBS and debris were then aspirated and removed. The remaining cleaned cell suspension was collected by a last centrifugation step at 1000 x g for 10 mins at 4°C. Following manual cell counting with Trypan blue, 1-2 million cells were collected and pelleted. Cells were then fixed with the kit and protocol for Chromium Fixed RNA Profiling (10X Genomics, protocol CG000478, RevD). Pellets were re-suspended in a solution containing 4% formaldehyde and 1X Fix and Perm Buffer, and were stored at 4°C for 22h. Cells were then pelleted and re-suspended in a solution containing 1X Quenching Buffer. Cells were counted again, followed by addition of Enhancer solution and glycerol, after which samples were stored at -80°C until processed.
Library construction performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF-NGS), member of the Vienna BioCenter (VBC), Austria. Single cell libraries were prepared based on the 10X Genomics Flex workflow according to manufacturer’s instructions (CG000527). Four samples were barcoded (BC001 – BC004) and processed together. In order to detect Gfp and tdTom mRNA expression, custom probes were designed according to 10X Genomics Technical Note CG000621 and ordered from Integrated DNA Technologies (IDT) as 4 different oPools, one for each FLEX barcode sequence (BC001 - BC004, custom probe sequence are provided as supplementary file in tab separated text format). Custom probes were added to the mouse probes (PN-100496, 10X Genomics) following manufacturer instructions (CG000621).

value: telencephalic vesicles/cerebral cortex

tag: barcode

tag: age


title: TetKO_D0_RNA_rep2

description: Library name: TetKO_D0_RNA_rep2

tag: cell line


title: WT_D4_5hmCseq_rep2

description: Library name: WT_D4_5hmCseq_rep2

data_processing:
Sequencing adaptors and low-quality nucleotides were removed using Trimmomatic (v0.39) with parameters ‘ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:36’.
Processed reads were aligned to the mm10 genome using Bismark (v0.23.1) and default parameters. Aligned reads were deduplicated with ‘deduplicate_bismark’.
Hydroxymethylation information of individual cytosines was extracted with ‘bismark_methylation_extractor’.
BigWig files for 5hmC levels were generated from Bismark's CpG report by extracting the coordinates and hydroxymethylation percentage of Cs covered by at least five reads. The resulting file was transformed with bedGraphToBigWig (v4).
Assembly: mm10
Supplementary files format and content: Bigwig format. Percentage of hydroxymethylated Cs at CpG dinucleotides covered by at least 5 reads.
Library strategy: EM-seq

extract_protocol:
Genomic DNA was extracted using NucleoSpin tissue kit (Macherey-Nagel ref. 740952) as per the manufacturer instructions and sonicated using covaris instrument.
Sonicated DNA was processed through the NEB Enzymatic 5hmC-seq complete kit as per the manufacturer instructions.

tag: cell type

value: WT


title: DNA from ATRT tumor patient INI288

type: genomic

first: Franck

last: Bourdeaut

address: 26 rue d'ulm

institute: Institut Curie

hyb_protocol: please refer to GEO:GSE175892

scan_protocol: please refer to GEO:GSE175892

data_processing: RnBeads Bioconductor R package version 2.12.2 was used to process the data from IDAT files. All samples and all probes were kept after quality control. Probe intensities were normalized using the rnb.execute.normalization() function with the “swan” method. Probes outside CpG context, targeting single nucleotide polymorphisms or targeting X and Y chromosomes were all filtered out before subsequent analysis.

label: Cy3 and Cy5

source_name: DNA from ATRT tumor patient

label_protocol: please refer to GEO:GSE175892

growth_protocol: I2A cells were maintained in RPMI containing 10% fetal bovine serum (FBS) and supplemented with 50 ng/mL doxycycline, 50 μg/mL hygromycin B and 300 μg/mL geneticin. In order to induce SMARCB1 expression, medium was changed every 3-4 days to renew drugs and cells were washed three times in Phosphate Buffer Saline (PBS) to completely remove doxycycline.

extract_protocol: please refer to GEO:GSE175892

treatment_protocol: I2A cells were treated with DMSO as a control for 21 days.

tag: tissue

value: tumor

value: Rhabdoid tumor

tag: genotype


title: TetKO_D0_RNA_rep1

description: Library name: TetKO_D0_RNA_rep1

tag: treatment


title: WT_D2_5hmCseq_rep2

description: Library name: WT_D2_5hmCseq_rep2


title: WT_D2_5hmCseq_rep1

description: Library name: WT_D2_5hmCseq_rep1


title: WT_D0_5hmCseq_rep2

description: Library name: WT_D0_5hmCseq_rep2


title: day1survived_24

first: Riho

last: Saito

address: 7-3-1 Hongo Bunkyo-ku

department: Graduate School of Pharmaceutical Sciences

institute: University of Tokyo

description: Library name: Sample24

data_processing:
Sequences were mapped to the mouse reference genome (mm10) with the use of STAR (v 2.7.10a). Raw read counts of each gene was calculated using featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: csv file includes raw read counts for each sample

extract_protocol:
Approximately 150 µl of blood was collected from the tail artery into a tube containing 100 µl of 50 mM EDTA-2K in PBS. The red blood cells were lysed with ACK lysing buffer (Thermo, A1049201). Cells were incubated at 4°C for 15 min firstly with anti-CXCR2 antibody (1:50, clone SA044G4, BioLegend, 149304) and subsequently with anti-PE microbeads (1:100, Miltenyi Biotec, 130-048-801). Subsequently, cells were subjected to Magnetic Activated Cell Sorting (MACS) (Miltenyi Biotec) and magnetically retained cells were eluted from the MS column and collected by centrifugation for 5 min at 400 x g/4°C. Total RNA was isolated from isolated with the use of RNAiso Plus reagent (Takara).
RNA libraries were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer’s protocols.
Sequencing was carried out on an Illumina NextSeq 2000 platform with paired-end 36 bp reads or on a DNBSEQ-G400RS platform with 100 bp single-end reads. For DNBSEQ-G400RS sequencing, adaptor sequences were converted into the DNBSEQ format using the MGIEasy Universal Library Conversion Kit (App-A) (MGI).

treatment_protocol: 8 weeks old C57B6J WT male mice received intranasal vesicular stomatitis virus infection with 1.0 x 10^7 PFU in 50μl PBS under 5% isoflurane anesthesia. Their survival and body weight were monitored for 14 days. Mice lost more than 30% of body weight at the time of the infection or survived over 14 days after the infection was euthanized for humane endpoint.

value: Blood

value: CXCR2+ cells

value: C57B6J WT

value: VSV (New Jersey) intranasal infection

tag: batch

tag: group

value: Survival group


title: TetKO_D4_hMATAC

description: Library name: TetKO_D4_hMATAC

data_processing:
PCR duplicate reads were removed pre-alignment using BBmap Clumpify (v38.18) with parameters ‘dedupe=t k=19 passes=6 subs=(0.01 x readlength)’.
Sequencing adaptors and low-quality nucleotides were removed using Trimmomatic (v0.39) with parameters ‘HEADCROP:18 ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24’.
Processed reads were aligned to the mm10 genome using Bismark (v0.23.1) and default parameters. Reads that lost their mate pair during read trimming and/or that could not be aligned in paired-end mode were kept and re-aligned as single-end reads. Aligned reads were deduplicated with ‘deduplicate_bismark’.
Hydroxymethylation information of individual cytosines was extracted with ‘bismark_methylation_extractor’.
BigWig files were generated using deepTools (v3.5.1) bamCoverage and parameters ‘--binSize 1 --smoothLength 0 --minMappingQuality 10 --normalizeUsing CPM --blackListFileName ENCFF547MET.bed --ignoreForNormalization chrX chrM chrY’. Blacklisted regions are those defined by Amemiya et al., 2019.
BigWig files for 5hmC levels were generated from Bismark's CpG report by extracting the coordinates and hydroxymethylation percentage of Cs covered by at least five reads. The resulting file was transformed with bedGraphToBigWig (v4).
Assembly: mm10
Supplementary files format and content: Bigwig format. CPM-normalized counts of ATAC signal.
Supplementary files format and content: Bigwig format. Percentage of hydroxymethylated Cs at CpG dinucleotides covered by at least 5 reads.

extract_protocol:
Nuclei were prepared from 50,000 cells for each transposition reaction.
A transposome was assembled with hydroxymethylated adaptors for transposition reaction. Tagmented purified DNA was submitted to 5hmC conversion module kit (NEB) as per the manufacturer instructions.

value: epiblast like-cells

value: Tet1/2 DKO


title: WT_D4_hMATAC_rep1

description: Library name: WT_D4_hMATAC_rep1

value: EpiLC differentiation


title: WT_D2_hMATAC_rep2

description: Library name: WT_D2_hMATAC_rep2

value: Day 2


title: WT_D0_hMATAC_rep1

description: Library name: WT_D0_hMATAC_rep1

value: embryonic stem cells

value: 2i + vitamin C

value: Day 0