title: MDA-MB-231 siNC biological replicate 1

description:
Library name: MDA_MB_231_siNC_1
MDA-MB-231 cells transfected with negative-control siRNA; biological replicate 1.


title: Atherosclerosis3

status: Public on Jul 27 2026

type: SRA

city: Stockholm

first: Cenk

last: Gurdap

address: SciLifeLab, Tomtebodavägen 23

country: Sweden

institute: Karolinska Institute

description:
Library name: Sample 7
10x genomics

library_source: transcriptomic single cell

data_processing:
cellranger-9.0.1
Assembly: GRCh38
Supplementary files format and content: H5

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
PBMC samples (four atherosclerosis and four sex- and age-matched healthy controls: A. Healthy) were processed for scRNA-seq using the 10x Genomics Chromium Single Cell 3' v4 platform, following the manufacturer’s protocol. Briefly, after thawing and washing, cells were resuspended in PBS containing 0.04% BSA, counted, and assessed for viability.
Cell suspensions were loaded into the Chromium Controller to generate Gel Bead-In-Emulsions, followed by reverse transcription, cDNA amplification, and library construction using the Single Cell 3' v4 Reagent Kit. Final libraries were quality-checked using an Agilent Bioanalyzer and quantified by qPCR. Sequencing was performed on an Illumina NovaSeq X Plus system (NovaSeq X Series Control Software v1.2.2.48004) using a 151 nt (Read 1) – 10 nt (Index 1) – 10 nt (Index 2) – 151 nt (Read 2) configuration on a ‘25B’ mode flow cell.

tag: cell type

value: PBMCs

tag: genotype

value: Atherosclerosis


title: Atherosclerosis4

description:
Library name: Sample 8
10x genomics


title: MDS_AZA_072

city: Miami

first: Qin

last: Yang

state: FL

address: 1501 NW 10th Avenue

department: Sylvester Comprehensive Cancer Center

country: USA

institute: University of Miami Miller School of Medicine

library_source: transcriptomic

data_processing:
The quality of the resulting reads was assessed using FastQC (v0.11.8) and multiQC (1.11). Then all reads were processed using Trim Galore (version 0.6.2) to trim to paired end 50 basepairs and remove adapters.
The resulting reads were aligned to the hg19 Gencode v19 reference genome using the STAR aligner (version 2.7.6a) with specific parameters: outFilterType=BySJout, outFilterMultimapNmax=20, alignSJoverhangMin=8, alignSJDBoverhangMin=1, outFilterMismatchNmax=999, alignIntronMin=20, alignIntronMax=1000000, alignMatesGapMax=1000000, and alignEndsType=EndToEnd.
Gene expression was quantified using featureCounts (v2.0.1), which was run in paired-end mode with the hg19 gencode annotation file (excluding entries for ribosomal RNA).
Differential expression analysis was performed using DESeq2 (v1.32.0) with a multifactor design that accounted for both the donor's condition and any batch effects. Genes with an absolute fold change of at least 1.5 and a p-value adjusted for multiple comparisons of less than or equal to 0.05 were considered significant.
Assembly: hg19
Supplementary files format and content: featureCounts  files

molecule: total RNA

source_name: Bone marrow

extract_protocol:
RNA extracted from the CD34+ fraction was employed for RNA-seq. To guarantee RNA quality, Tapestation was utilized prior to library preparation. The RNA was treated with Illumina Ribo-Zero
For library preparation, we used the Nugen Ovation Solo RNA-seq ultra-low input kit, following the manufacturer's instructions. Subsequently, the prepared libraries were sequenced on an Illumina NextSeq platform. These libraries were paired-end and they were strand-specific.

tag: tissue

value: Bone marrow

tag: cell line

tag: individual

value: MDS patient

tag: age

tag: Sex

value: Male

tag: responder

value: Responder


title: Atherosclerosis2

description:
Library name: Sample 6
10x genomics


title: 67, ALL, CD154

city: Doha

first: Asmma

last: Doudin

address: Al Gharrafa Street, Ar Rayyan

department: Research

country: Qatar

institute: Sidra Medicine

description: Library name: 200901521

data_processing:
Raw sequencing data were demultiplexed using bcl2fastq v2.20 to generate FASTQ files for each sample. Downstream processing of RNA-seq data was carried out using the bcbio-nextgen v1.2.0 pipeline.Reads were aligned to the reference genome using STAR v2.6.1d, and gene-level quantification was performed using featureCounts v2.0.0.
Assembly: GRCh38
Supplementary files format and content: CPM_ComBat_seq_geo.csv
Supplementary files format and content: a gene expression matrix that contains normalized CPM (Counts Per Million) values — after batch correction using ComBat-seq.

growth_protocol: Cells revived in RPMI 1640 GlutaMAX medium  and 10% human serum

extract_protocol:
Cells were sorted based on the surface staining of CD154+CD137- for TconCM+ cells and CD137+CD154- for TregCM+ cells and RNA was extracted using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing based on manufacturer's instructions.
Isolated RNA was used to create double-stranded cDNA fragments using SMARTer® Pico PCR cDNA Synthesis Kit (Takara) according to the manufacturer’s protocol. SeqAmp DNA Polymerase (Takara) was used to amplify purified first-strand cDNA into RNA-seq libraries based on the manufacturer’s instructions. Nextera XT Index Kit v2 (Illumina, USA) was used for library indexing.

treatment_protocol: Cells stimulated in RPMI 1640 GlutaMAX medium and 10% human serum, for 6 hours (5% CO2, 37oC) with 100μg CM,  1 μg/ml CD40 and 1μg/ml CD28 functional grade antibodies.

tag: sample group

value: ALL

tag: batch


title: MDS_AZA_071

value: NonResp


title: 66, ALL, CD137

description: Library name: 200901511


title: Healthy4

description:
Library name: Sample 4
10x genomics

value: Healthy


title: MDS_AZA_070


title: 65, ALL, CD154

description: Library name: 200901501


title: Healthy1

description:
Library name: Sample 1
10x genomics


title: MDS_AZA_069

value: Female


title: snRNAseq_PAT

city: orlando

first: Adeline

last: Divoux

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

description: Library name: Sample1

data_processing:
Initial analyses of the single cell libraries were performed using CellRanger Analysis Pipeline (10× Genomics, V6.1.1) with GRCh38 as the reference genome.
Assembly: GRCh38
Supplementary files format and content: compressed files including raw read count values of all the single nuclei profiles for that sample

molecule: nuclear RNA

source_name: peripancreatic adipose tissue

extract_protocol:
Peripancreatic Adipose tissue biopsy was collected from peripancreatic adipose tissue from 1 healthy organ donor.  Snap frozen tissue was pulverized under liquid nitrogen and homogenized in 2mL of homogenization buffer (5mM MgCl2, 25mM Tris Buffer pH 8.0, 25mM KCL, 250mM sucrose, 1μm DDT, 1 x protease inhibitor, 0.2 U/μL SUPERase · In RNase Inhibitor (Thermofisher Scientific) in nuclease-free water) with a glasscol homogenizer. The homogenate was incubated for 30 minutes on ice with the addition of Triton-X100 (0.1% v/v) with regular vortexing. Samples were filtered through a 100μm and 40μm strainer (BD Falcon), centrifuged at 2,700g for 10 min at 4°C, resuspended in homogenization buffer and recentrifuged again at 2,700g for 10 min at 4°C. The pellet was then re-suspended in 1mL nuclei isolation medium (5mM MgCl2, 25mM Tris Buffer pH 8.0, 25mM KCL, 1 mM EDTA, 0.2 U/μL Ribolock RNAase inhibitor, 1% BSA in nuclease-free water) and centrifuged at 2,700g for 10 min at 4°C. Following re-suspension in 500μL nuclei isolation medium, sample was filtered 10 x with a 25g syringe. Nuclei was stained with Hoechst 33342 (ReadyProbes Cell Viability Imaging Kit, Thermofisher Scientific) prior to counting with a countess II automated cell counter (Thermofisher Scientific).
A targeted nuclei recovery of 10,000 nuclei was loaded to a Chromium Chip G (10X Genomics) for generation of Gel beads‐in‐Emulsion (GEMs). Library preparation was performed using the 10X Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 according to the manufacturer’s instruction. The libraries were sequenced on the NovaSeq X Plus platform using run cycle 151 + 10 + 10 + 151 and targeting 50G raw data per sample.

value: peripancreatic adipose tissue


title: 64, ALL, CD137

description: Library name: 200901491


title: MDS_AZA_068


title: HEC-1A, UNTREATED, ATAC-seq, Biol rep 3

city: L'Hospitalet de Llobregat

first: David

last: Llobet

state: Barcelona

address: Gran Via de L'Hospitalet 199-203

department: Gynecologic cancer

country: Spain

institute: Bellvitge Biomedical Research Institute (IDIBELL)

description: Library name: T4

library_source: genomic

data_processing:
RNA-seq TPM generated with Salmon and Tximport; ATAC-seq Raw FASTQ files were trimmed with Trim Galore, quality assessed with FastQC. Reads aligned to GRCh38 using Bowtie2. Mitochondrial reads removed, properly paired reads retained with samtools. Library complexity estimated with ATACseqQC, datasets normalized by subsampling. PCR duplicates removed with Picard MarkDuplicates. Reads converted to BEDPE format, fragment coordinates adjusted for Tn5 bias (+4/-5 bp). Broad peaks called with MACS3 (FDR < 0.05, no control input).; Cut&run reads were processed with nf-core/cutandrun pipeline (v3.2.2) using Nextflow (v24.10.5). Aligned to GRCh38 human reference genome. GRCh38 unified blacklist regions excluded. Peaks called using MACS2 (v2.2.7.1) against IgG controls. narrowPeak files generated for each biological replicate.
Assembly: GRCh38
Supplementary files format and content: RNA-seq: Tab-delimited text file includes TPM values for each sample. ATAC-seq: broadPeak per sample. Cut&run narrowPeak except for NEG sample

molecule: genomic DNA

source_name: endometrial adenocarcinoma

extract_protocol:
RNA-seq: Total RNA was purified using the RNeasy Mini Kit (QIAgen, 74104) following manufacturer's instructions. ATAC-seq: 50x10^3 HEC-1A cells per condition were pelleted (500xg, 4°C, 5min), washed with PBS, and lysed in buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630) for 20min at 4°C. Nuclei were isolated by centrifugation and resuspended in 2x transposition reaction mix (Diagenode, C01070012) for 1h at 37°C. DNA was purified with cleanup buffer containing 5% SDS and Proteinase K, followed by 2x SPRI bead cleanup and elution in 10mM Tris-HCl pH 8. Cut&run: 10x10^4 HEC-1A cells per condition were isolated with concanavalin A magnetic beads, permeabilized with digitonin, and incubated with anti-H3K4me3 antibody or IgG control. Cut&Run was performed using pAG-MNase digestion following manufacturer's protocol (Cell Signaling Technology, 86652).
RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA library prep kit according to manufacturer's protocol; ATAC-seq Genomic libraries were prepared using Buenrostro et al. 2013 primers with PCR program: 72°C 5min, 98°C 30sec, 9 cycles of (98°C 10sec, 63°C 30sec, 72°C 1min). Libraries purified with SPRI beads, eluted in 21μL 10mM Tris-HCl pH 8.0. DNA quantified using Qubit dsDNA BR assay kit (ThermoFisher Scientific, Q32850).;  Cut&run DNA libraries were purified and prepared with standard end repair/adapter ligation, and sequenced on NextSeq550 (150bp paired-end)

value: endometrial adenocarcinoma

value: endometrial adenocarcinoma epithelial cells

value: WT

tag: treatment

value: Untreated


title: HEC-1A, UNTREATED, ATAC-seq, Biol rep 2

description: Library name: T3


title: 63, ENP, CD154

description: Library name: 200901481

value: ENP


title: HEC-1A, UNTREATED, ATAC-seq, Biol rep 1

description: Library name: T2


title: MDS_AZA_067


title: 62, ENP, CD137

description: Library name: 200901471


title: HEC-1A, THC 20uM, 72h, ATAC-seq, Biol rep 2

description: Library name: 72_2


title: MDS_AZA_066


title: HEC-1A, THC 20uM, 72h, ATAC-seq, Biol rep 1

description: Library name: 72_1


title: 61, AD, CD154

description: Library name: 200901461

value: AD


title: HEC-1A, THC 20uM, 24h, ATAC-seq, Biol rep 3

description: Library name: 24_3


title: MDS_AZA_065


title: 60, AD, CD137

description: Library name: 200901451


title: HEC-1A, THC 20uM, 24h, ATAC-seq, Biol rep 2

description: Library name: 24_2


title: MDS_AZA_082


title: 430LNA treated 6 hours post fertilization rep3

city: Farmington

first: Jean-Denis

last: Beaudoin

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health Center

description:
Library name: 430LNA_6hpf_Rep3
Merged with 430LNA_6hpf_Rep2 for analysis. The raw data are available in the European Nucleotide Archive database.
SDataset6_aAMLNA_perread_processed_pa_filtered.csv
SDataset10_per_read_aAMLNA_allsamples.csv

data_processing:
Master of Pores pipeline version 2 (MOP2):The mop_preprocess module was used to basecall the raw signal with Guppy v6.0.6 (Oxford Nanopore Technologies) using the m6A-aware basecalling model rna_r9.4.1_70bps_m6A_hac.cfg (m6Abasecaller).
The DeePlexiCon algorithm was used to demultiplex multiplexed reads.
ModPhred used to encode the modification probabilities and map reads to the GRCz11 genome with minimap2 2.17-r941 using the parameters “-ax map-ont -k13”.
Per-read gene and isoform annotation using the samtools flag “-F 3488”, with Isoquant v3.3.0 using parameters “--complete_genedb --data_type nanopore” and the zebrafish Ensembl annotation version 110. Poly(A) tail length estimation was performed using the mop_tail module of MoP2 with tailfindr v1.3.
m6AB_PerRead pipeline generated replicable m6A sites and per_read tables. For isoform-level and read-level analysis, reads were required to map uniquely to a single isoform that had at least 25 reads per replicate. Reads lacking a tailfindr poly(A) tail estimate (NaN values) were removed (pa_filtered files).
Assembly: GRCz11
Supplementary files format and content: SDataset5,6,7... .csv file of per_read tables produced by the m6AB_PerRead pipeline (m6Abasecaller_per_read_analysis) that has been filtered for isoform-level and read-level analysis. This includes isoform/gene assignment, m6A modification number and location, read length, poly(A) tail length, and relevant timepoint/treatment for each read.
Supplementary files format and content: SDataset8.. .tsv file of replicable m6A sites with information on their chromosome position, coverage, and modification frequency.
Supplementary files format and content: SDataset9,10,11... .csv file of pre_read tables produced by the m6AB_PerRead pipeline that includes m6A modification number and location, chromosomal alignment information, poly(A) tail length, isoform/gene assignment information, and sample for each read.

organism: Danio rerio

source_name: embryos

growth_protocol: Embryos were maintained at 28 °C

extract_protocol:
RNA from frozen embryos was extracted using TRIzol (Invitrogen).  Poly(A)+ mRNAs were isolated with oligo d(T)25 magnetic beads (New England BioLabs) according to the manufacturer’s protocol and eluted in 30 µL of water.
RNA libraries were prepared using the direct RNA sequencing kit (SQK-RNA002), following ONT protocol version DRS_9080_v2_revI_14Aug2019 with half reactions of 250 ng of poly(A)+ RNA for each library up to the RNA Adapter (RMX) ligation step, with the following adaptations. Samples were ligated to pre-annealed custom RT adaptors (IDT) containing barcodes. For non-barcoded runs, the commercial RT adapter included in the SQK-RNA002 kit was used instead. Reverse transcription was then performed. Ligated products were purified using 1.8X Agencourt RNAClean XP beads (Fisher Scientific, NC0068576).For the final ligation, 50 ng of reverse-transcribed RNA from each reaction was pooled, and ligated with the RMX adapter. For non-barcoded runs, 200 ng of reverse-transcribed RNA was used for ligation with the RMX adapter. The ligated RNA:DNA hybrid was purified using 1X Agencourt RNAClean XP beads. Samples were run on a R9.4.1 flowcell on a MinION or PromethION device.

treatment_protocol: All injections into zebrafish embryos were performed on dechorionated one-cell stage embryos with 1 nL volumes. To inhibit RNA Polymerase II, embryos were injected with 0.2 ng of α-amanitin (Sigma-Aldrich, A2263) resuspended in nuclease-free water. To inhibit miR-430 activity, embryos were injected with 10 µM of tiny locked nucleic acid (tinyLNA), complementary to the seed region of miR-430 (5′-TAGCACTT-3′ (Exiqon)).

value: embryos

value: locked nucleic acid


title: 59, ENP, CD154

description: Library name: 200901441


title: 430LNA treated 6 hours post fertilization rep2

description:
Library name: 430LNA_6hpf_Rep2
Merged with 430LNA_6hpf_Rep3 for analysis. The raw data are available in the European Nucleotide Archive database.
SDataset6_aAMLNA_perread_processed_pa_filtered.csv
SDataset10_per_read_aAMLNA_allsamples.csv


title: 430LNA treated 6 hours post fertilization rep1

description:
Library name: 430LNA_6hpf_Rep1
The raw data are available in the European Nucleotide Archive database.
SDataset6_aAMLNA_perread_processed_pa_filtered.csv
SDataset10_per_read_aAMLNA_allsamples.csv


title: alpha-amanitin treated 6 hours post fertilization rep2

description:
Library name: aAM_6hpf_Rep2
The raw data are available in the European Nucleotide Archive database.
SDataset6_aAMLNA_perread_processed_pa_filtered.csv
SDataset10_per_read_aAMLNA_allsamples.csv

value: alpha-amanitin


title: MDS_AZA_062

value: Bone marrow

value: MDS patient


title: MDS_AZA_063

value: Male


title: 58, ENP, CD137

description: Library name: 200901431


title: alpha-amanitin treated 6 hours post fertilization rep1

description:
Library name: aAM_6hpf_Rep1
The raw data are available in the European Nucleotide Archive database.
SDataset6_aAMLNA_perread_processed_pa_filtered.csv
SDataset10_per_read_aAMLNA_allsamples.csv


title: wildtype timecourse 6 hours post fertilization rep3

description:
Library name: WT_6hpf_Rep3
The raw data are available in the European Nucleotide Archive database.
SDataset5_WT_perread_processed_pa_filtered.csv
SDataset8_MZT_ZF_MZT_Decay_Cov25_RawData_ReplicableSites.tsv
SDataset9_per_read_WT_allsamples.csv


title: MDS_AZA_061

value: Responder


title: wildtype timecourse 6 hours post fertilization rep2

description:
Library name: WT_6hpf_Rep2
Merged with WT_6hpf_Rep1 for analysis. for analysis. The raw data are available in the European Nucleotide Archive database.
SDataset5_WT_perread_processed_pa_filtered.csv
SDataset8_MZT_ZF_MZT_Decay_Cov25_RawData_ReplicableSites.tsv
SDataset9_per_read_WT_allsamples.csv


title: wildtype timecourse 6 hours post fertilization rep1

description:
Library name: WT_6hpf_Rep1
Merged with WT_6hpf_Rep2 for analysis. The raw data are available in the European Nucleotide Archive database.
SDataset5_WT_perread_processed_pa_filtered.csv
SDataset8_MZT_ZF_MZT_Decay_Cov25_RawData_ReplicableSites.tsv
SDataset9_per_read_WT_allsamples.csv


title: 56, AD, CD137

description: Library name: 200901411


title: MDS_AZA_037

value: NonResp


title: 55, ALL, CD154

description: Library name: 200901401

value: ALL


title: wildtype timecourse 4 hours post fertilization rep1

description:
Library name: WT_4hpf_Rep1
The raw data are available in the European Nucleotide Archive database.
SDataset5_WT_perread_processed_pa_filtered.csv
SDataset8_MZT_ZF_MZT_Decay_Cov25_RawData_ReplicableSites.tsv
SDataset9_per_read_WT_allsamples.csv


title: MDS_AZA_036


title: wildtype timecourse 2 hours post fertilization rep2

description:
Library name: WT_2hpf_Rep2
The raw data are available in the European Nucleotide Archive database.
SDataset5_WT_perread_processed_pa_filtered.csv
SDataset8_MZT_ZF_MZT_Decay_Cov25_RawData_ReplicableSites.tsv
SDataset9_per_read_WT_allsamples.csv


title: wildtype timecourse 2 hours post fertilization rep1

description:
Library name: WT_2hpf_Rep1
The raw data are available in the European Nucleotide Archive database.
SDataset5_WT_perread_processed_pa_filtered.csv
SDataset8_MZT_ZF_MZT_Decay_Cov25_RawData_ReplicableSites.tsv
SDataset9_per_read_WT_allsamples.csv


title: 54, ALL, CD137

description: Library name: 200901391


title: MDS_AZA_035


title: DASMC7 siCOX4I2

city: Kingston

first: Rachel

middle: Emily Teresa

last: Bentley

state: Ontario

address: 18 Stuart St, 342 Botterell Hall

department: Medicine

country: Canada

institute: Queen's University

description: Library name: DASMC7siCOX4i2_S30_R1_001

data_processing:
Sequence files were demultiplexed, and processed using fastqc and multiqc (v1.12) prior to trimming with BBDuk (BBMap_39.06), aligned to the human GRCh genome with Star (v2.4.0), and counts files created with HT-Seq Count (v2.0.5). Differential analysis was performed using a pair-wise approach and implemented in DESeq2 package (v1.44) in R (v4.4.0)and they were included in the GO:BP (Gene Ontology Biological Process) analysis using gprofiler2(v.0.2.3)
Assembly: GRCh38.113
Supplementary files format and content: tab limited text. Files with raw counts for each sample

source_name: Ductus Arteriosus

growth_protocol: All cell culture reagents were acquired from Thermo Fisher Scientific (Mississauga, ON, CA). Primary cell lines were previously established from surgically harvested DAs of infants undergoing congenital heart surgery. Cell lines were purified using fluorescence activated cell sorting and phenotypically confirmed using flow cytometry. Human DASMC were grown in Human Vascular Smooth Muscle Cell Basal Medium, supplemented with 5% Smooth Muscle Growth Supplement, 10% Fetal Bovine Serum, 1% L-Glutamine, 1% penicillin/streptomycin, and 10µg/mL ciprofloxacin HCl. Cells were used within the first five passages and were carefully maintained in hypoxia (2.5% oxygen, 5% CO2, balance nitrogen) to mimic fetal oxygen conditions.

extract_protocol:
Cells were collected 48-hours after treatment and lysed in TRI Reagent (Cat# T9424-100ML, Lot# MKCK9023, Sigma-Aldrich, Oakville, ON, CA). RNA was extracted using the Direct-zol RNA Miniprep kit (Cat# R2050, Zymo Research, California, USA) following the manufacturer's protocol.
Samples were prepared for sequencing using the QuantSeq 3' FWD mRNA-Seq Library Prep Kit for Illumina (Lexogen, Austria), according to the manufacturers' protocol, and validated using Qubit 4 (Thermofisher Scientific) with 130ng RNA as the input. Successful libraries were pooled and diluted to an equimolar concentration resulting in a total pool of 4nM. Dilution and denaturation were performed according to Illumina protocols to result in a 2.2pM input (optimized for the Lexogen 3' kit). Single-end sequencing of 75 cycles was performed on an Illumina Nextseq550 using a High Output v2 reagent cartridge with each sample having a minimum depth of 5 million reads.

treatment_protocol: Silencing RNAs targeted at NDUFS1, NDUFS7, UQCRFS1, COX4I2, and Negative Control (Cat# 51-01-14-04) were obtained from Integrated DNA Technologies (IDT, Coralville, Iowa, USA) and silencing RNA targeted at NDUFS2 was obtained from Qiagen (Hilden, Germany). Cells were seeded one day prior to siRNA treatment into 6-well plates. siRNAs were transfected with LipofectamineTM RNAiMAX Transfection Reagent (Cat#13778150, ThermoFisher Scientific, Mississauga, ON, CA) following the manufacturer's protocol.

value: Ductus Arteriosus

value: DASMC


title: 53, AD, CD154

description: Library name: 200901381


title: MDS_AZA_034


title: DASMC7 siNDUFS7

description: Library name: DASMC7siNDUFS7_S28_R1_001


title: DASMC7 siNDUFS1

description: Library name: DASMC7siNDUFS1_S27_R1_001


title: MDS_AZA_032

value: Female


title: 51, CON, CD137

description: Library name: 200901351

value: CON


title: DASMC7 Control siRNA

description: Library name: DASMC7siNC_S25_R1_001


title: DASMC6 siCOX4I2

description: Library name: DASMC6siCOX4i2_S24_R1_001


title: 50, AD, CD154

description: Library name: 200901321


title: DASMC6 siUQCRFS1

description: Library name: DASMC6siUQCRFS1_S23_R1_001


title: MDS_AZA_031


title: DASMC6 siNDUFS1

description: Library name: DASMC6siNDUFS1_S21_R1_001


title: DASMC6 siNDUFS7

description: Library name: DASMC6siNDUFS7_S22_R1_001


title: 49, AD, CD137

description: Library name: 200901311


title: MDS_AZA_030


title: DASMC6 siNDUFS2

description: Library name: DASMC6siNDUFS2_S20_R1_001


title: 48, ALL, CD154

description: Library name: 200901301


title: DASMC6 Control siRNA

description: Library name: DASMC6siNC_S19_R1_001


title: DASMC5 siCOX4I2

description: Library name: DASMC5siCOX4i2_S18_R1_001


title: 52, AD, CD137

description: Library name: 200901371


title: 47, ALL, CD137

description: Library name: 200901291


title: DASMC5 siUQCRFS1

description: Library name: DASMC5siUQCRFS1_S17_R1_001


title: MDS_AZA_028


title: DASMC5 siNDUFS7

description: Library name: DASMC5siNDUFS7_S16_R1_001


title: 46, AD, CD154

description: Library name: 200901281


title: DASMC5 siNDUFS1

description: Library name: DASMC5siNDUFS1_S15_R1_001


title: 45, ENP, CD154

description: Library name: 200901241


title: DASMC5 Control siRNA

description: Library name: DASMC5siNC_S13_R1_001


title: MDS_AZA_025


title: DASMC4 siCOX4I2

description: Library name: DASMC4siCOX4i2_S12_R1_001


title: 44, ENP, CD137

description: Library name: 200901231


title: MDS_AZA_026


title: DASMC4 siUQCRFS1

description: Library name: DASMC4siUQCRFS1_S11_R1_001


title: DASMC7 siUQCRFS1

description: Library name: DASMC7siUQCRFS1_S29_R1_001


title: MDS_AZA_024


title: DASMC4 siNDUFS7

description: Library name: DASMC4siNDUFS7_S10_R1_001


title: 43, CON, CD154

description: Library name: 200901221


title: DASMC7 siNDUFS2

description: Library name: DASMC7siNDUFS2_S26_R1_001


title: MDS_AZA_023


title: NRCM cells，H/R-AS8351-3

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

country: China

institute: Sun Yat-sen University

description: Library name: Sample9

data_processing:
Raw reads were trimmed with Trimmomatic (v0.39) and aligned to the rat genome (rn6) using STAR (v2.7.3a). Gene counts were quantified by featureCounts (v2.0.1). Differential expression analysis was performed with DESeq2 (v1.32.0; P.adj< 0.05, |log₂FC| > 1). PCA and heatmaps were generated using ggplot2 package (v3.5.1) and pheatmap package (v1.0.12) in R.
Assembly: rn6
Supplementary files format and content: txt

organism: Rattus norvegicus

source_name: heart

growth_protocol: Cells were maintained in DMEM/F12 (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco) at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted from NRCMs under normoxia, H/R, or H/R + AS8351 (0.5 μM) using TRIzol (Monad Biotech)
Libraries were prepared with the NEBNext Ultra II Kit (NEB)

treatment_protocol: NRCMs were placed in a hypoxic chamber (0.1% O₂, 5% CO₂, 94.9% N₂, 37°C) for 6 h in glucose- and sodium pyruvate-free DMEM (Gibco), followed by 12 h of reoxygenation under normoxic conditions (21% O₂, 5% CO₂) in standard culture medium. The Kdm5b inhibitor AS8351 was dissolved in DMSO and applied during the reoxygenation phase at final concentrations of 0.25 μM or 0.5 μM. Vehicle-treated cells received an equal volume of DMSO (final concentration <0.1%).

value: heart

value: cardiomyocytes

value: hypoxic


title: 42, CON, CD137

description: Library name: 200901211


title: MDS_AZA_027


title: DASMC4 siNDUFS1

description: Library name: DASMC4siNDUFS1_S9_R1_001


title: NRCM cells，H/R-AS8351-2

description: Library name: Sample8


title: MDS_AZA_022


title: DASMC4 siNDUFS2

description: Library name: DASMC4siNDUFS2_S8_R1_001


title: 41, ALL, CD154

description: Library name: 200901201


title: NRCM cells，H/R-AS8351-1

description: Library name: Sample7


title: DASMC4 Control siRNA

description: Library name: DASMC4siNC_S7_R1_001


title: MDS_AZA_021


title: 40, ALL, CD137

description: Library name: 200901191


title: MDS_AZA_020


title: NRCM cells，H/R-DMSO-3

description: Library name: Sample6

value: DMSO


title: DASMC11 siCOX4I2

description: Library name: DASMC11siCOX4i2_S6_R1_001


title: 39, ENP, CD154

description: Library name: 200901181

value: ENP


title: MDS_AZA_018


title: NRCM cells，H/R-DMSO-2

description: Library name: Sample5


title: DASMC11 siUQCRFS1

description: Library name: DASMC11siUQCRFS1_S5_R1_001


title: 38, ENP, CD137

description: Library name: 200901171


title: NRCM cells，H/R-DMSO-1

description: Library name: Sample4


title: DASMC11 siNDUFS7

description: Library name: DASMC11siNDUFS7_S4_R1_001


title: MDS_AZA_029


title: exp09_memory_NupHox_LCMV_OVA_D3_D5_Hashtag_Data

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

description: Library name: exp09-W2-CSP

library_source: other

data_processing:
Sequencing was performed on NovaSeq 6000 platform.
Base calling and FASTQ generation were performed using the Illumina BaseSpace GenerateFASTQ workflow v1.37.0.
The murine reference genome used for read alignment was obtained from Ensembl release 102 and prepared using the mkref tool from 10x Cell Ranger v5.0.1 (Zheng et al., 2017). Count matrices were generated using the count tool from either 10x Cell Ranger v5.0.1 using paired-end sequencing mode.
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.3.0 package (Hao et al., 2024).
Assembly: GRCm38 v102 (Ensembl)
Supplementary files format and content: File containing specification of each hashtag and sample, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell. Due to low counts in Day 3 samples, only Day 5 samples were analyzed.
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results
Supplementary files format and content: RDS file containing Seurat object of processed samples from Day 5 only.
Library strategy: CITE-seq

molecule: protein

organism: Mus musculus

source_name: spleen

growth_protocol: Immortalized bone marrow hematopoietic stem cells from Vβ5 Rag2-/- mice were transduced with MSCV retroviral vectors encoding Clone 2 or Clone 12 TCRs and GFP or LNGFR selection markers as previously described {Ruedl et al., 2008; Drobek et al., 2018; Paprckova et al., 2022).

extract_protocol:
The progeny was FACS-isolated frrom the spleen.
Cells from all experiments were loaded onto a Chromium Controller (10x Genomics).cDNA libraries  were prepared using the Chromium Single Cell V(D)J Reagent Kits with Feature Barcode technology for Cell Surface Protein protocol (#CG000186 Rev D) and the Chromium Single Cell 5′ Library & Gel Bead Kit and Chromium Single Cell 5′ Feature Barcode Library Kit (10x Genomics; #PN-1000014, #PN-1000020, #PN-1000080, #PN-1000009, #PN-1000084).

treatment_protocol: FACS-sorted GFP+/LNGFR+ CD45.2+ cells were transplanted into irradiated (6 Gy) congenic CD45.1 recipient mice. At least 8 weeks after the transplantation, the GFP+ or LNGFR+ retrogenic T cells were FACS-sorted from the spleens and lymph nodes, FACS-sorted, and transferred into another congenic hosts followed by LCMV-OVA infection day after.

value: spleen

value: CD8+ T cells

value: Progeny of Tn/Tm

value: LCMV-OVA infection

tag: time

value: Day 3/ Day5


title: 37, ENP, CD154

description: Library name: 200901161


title: NRCM cells，normoxia-3

description: Library name: Sample3

value: normoxia


title: exp09_memory_NupHox_LCMV_OVA_D3_D5_GEX_Data

description: Library name: exp09-W2-GEX

data_processing:
Sequencing was performed on NovaSeq 6000 platform.
Base calling and FASTQ generation were performed using the Illumina BaseSpace GenerateFASTQ workflow v1.37.0.
The murine reference genome used for read alignment was obtained from Ensembl release 102 and prepared using the mkref tool from 10x Cell Ranger v5.0.1 (Zheng et al., 2017). Count matrices were generated using the count tool from either 10x Cell Ranger v5.0.1 using paired-end sequencing mode.
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.3.0 package (Hao et al., 2024).
Assembly: GRCm38 v102 (Ensembl)
Supplementary files format and content: File containing specification of each hashtag and sample, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell. Due to low counts in Day 3 samples, only Day 5 samples were analyzed.
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results
Supplementary files format and content: RDS file containing Seurat object of processed samples from Day 5 only.


title: NRCM cells，normoxia-2

description: Library name: Sample2


title: 36, ENP, CD137

description: Library name: 200901151


title: DASMC11 siNDUFS1

description: Library name: DASMC11siNDUFS1_S3_R1_001


title: WT, Pg+Sg, biol rep 2

city: Buffalo

first: Jason

last: Kay

state: NY

address: 3435 Main Street

institute: University at Buffalo

description: Library name: Sample 18

data_processing:
HISAT2 (version 2.21) using default parameters
No adapter timming was performed on sequence reads
Sequence reads were mapped to GRCm38
Counting of mapped reads for genomic features was performed using Subread featureCounts (version 2.0.4) (parameters: -p 02 2 -g gene_name -t exon -Q 60 -B -C)
Assembly: mm10
Supplementary files format and content: Text file of raw counts of each sample labeled by raw file title
Supplementary files format and content: csv file of identifiers for each raw file (genotype, treatment, and group)

source_name: Oral gingival

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit and eluted in 50 ul of nuclease-treated water. The extracted RNA was treated with Dnase1 using the New England Biolabs Monarch Spin RNA Cleanup Kit (T2020L). 100 ng of the total RNA was used as input.
Library construction was done using the Illumina Stranded Total RNA prep, ligation with Ribo-Zero Plus following manufacturer's protocols.

treatment_protocol: WT and NLRP6-KO mice were divided into 5 groups (8-10 mice per group (4-5 female and 4-5 male)) as i) sham, ii) ligature alone, iii) ligature + P. gingivalis, iv) ligature + S. gordonii, and v) ligature + P. gingivalis & S. gordonii. After treatment with antibiotics to reduce the existing oral microflora (Kanamycin Sulphate 1 mg/ml for 5 days followed by a 3-day antibiotic free period), mice were intraperitoneally anesthetized with a 200 μl mixture of ketamine (10 mg/ml) and xylazine. A black braided silk ligature (6.0) was placed on the left side second maxillary molars inoculated with 100 μl (1 × 10^9 CFU/ml) of S. gordonii or P. gingivalis, or both, while the sham group received 2% CMC alone (Day-0). Booster doses with 100 μl of P. gingivalis, S. gordonii or both (1x10^9 CFU/ml) were administered on the following Day-1 and 2 to the respective groups. After 14 days of ligature placement, mice were sacrificed and the gingival tissue was harvested.

value: Oral gingival

value: WT

value: Pg+Sg


title: DASMC11 siNDUFS2

description: Library name: DASMC11siNDUFS2_S2_R1_001

value: Ductus Arteriosus

value: DASMC


title: 35, AD, CD154

description: Library name: 200901141

value: AD


title: NLRP6-KO, Sg, biol rep 3

description: Library name: Sample 17

value: Sg


title: NRCM cells，normoxia-1

description: Library name: Sample1

value: heart

value: cardiomyocytes


title: DASMC11 Control siRNA

description: Library name: DASMC11siNC_S1_R1_001

value: Female


title: 34, AD, CD137

description: Library name: 200901131


title: NRCM cells，IgG

description: Library name: IgG

data_processing:
Reads were trimmed and mapped to the rat genome (rn6) using Bowtie2 (v2.4.2). Peaks were called with MACS2 (v2.2.7.1) using default settings, and differential peaks were analyzed with DiffBind (v3.2). Tracks were visualized with IGV (v2.8.0).
Assembly: rn6
Supplementary files format and content: BigWig
Library strategy: CUT&Tag

extract_protocol:
1×10⁵ NRCMs per sample were harvested and subjected to CUT&Tag analysis using the CUT&Tag Assay Kit (pAG-Tn5) for Illumina (ABclonal, RK20265) according to the manufacturer's instructions. Primary antibodies against H3K4me3 (1:50, ABclonal, A2357) or Kdm5b (1:50, ABclonal, A7772) were added and incubated overnight at 4°C. After incubation with anti-Rabbit IgG secondary antibody, samples were treated with pAG-Tn5 transposase, followed by tagmentation and DNA purification.
Libraries were amplified with indexed primers.

value: hypoxic

value: DMSO


title: NLRP6-KO, Pg+Sg, biol rep 2

description: Library name: Sample 16


title: DASMC5 siNDUFS2

description: Library name: DASMC5siNDUFS2_S14_R1_001

value: Male


title: 86, ENP, CD137

description: Library name: 200901711

value: ENP


title: 33, AD, CD154

description: Library name: 200901121


title: NLRP6-KO, Pg+Sg, biol rep 1

description: Library name: Sample 15


title: NRCM cells，H/R-AS8351, H3K4me3-2 (CUT&Tag)

description: Library name: H/R-AS8351, H3K4me3-2


title: HEK293T cells, empty vector, IP, Rep3

city: Regensburg

first: Davor

last: Lessel

address: Franz-Josef-Strauss-Allee 11

department: Institut für Humangenetik

country: Germany

institute: Universität Regensburg

description: Library name: Rep3-IP-empty

data_processing:
sRNAtoolbox suite
Processing with sRNAbench (default parameters, except mean quality score with Phred threshold of 20)
annotation with MirGeneDB 2.1 reference database for Homo sapiens
Assembly: GRCh38
Supplementary files format and content: tab separated text file containing expression data of mature sense miRNAs with adjusted read counts normalized as total RPM and filtered to retain miRNAs with a minimum expression of 1

extract_protocol:
miRNeasy micro kit (Qiagen)
TruSeq Small RNA Library Prep Kit (Illumina)


title: HEK293T cells, empty vector, IP, Rep2

description: Library name: Rep2-IP-empty


title: 32, AD, CD137

description: Library name: 200901111


title: NLRP6-KO, Pg, biol rep 2

description: Library name: Sample 14

value: Pg


title: NRCM cells，H/R-AS8351, H3K4me3-1 (CUT&Tag)

description: Library name: H/R-AS8351, H3K4me3-1


title: 31, ENP, CD154

description: Library name: 200901101


title: HEK293T cells, empty vector, IP, Rep1

description: Library name: Rep1-IP-empty


title: NRCM cells，KDM5B (CUT&Tag)

description: Library name: KDM5B


title: NLRP6-KO, Pg, biol rep 1

description: Library name: Sample 13


title: HEK293T cells, empty vector, Input, Rep3

description: Library name: Rep3-IN-empty


title: 30, ENP, CD137

description: Library name: 200901091


title: NLRP6-KO, Negative, biol rep 1

description: Library name: Sample 12

value: Negative


title: snrk_45d_5

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: Library name: snrk_45d_5

data_processing:
In our sequencing strategy, the R1 reads of pooled libraries contain two parts of UMI split by the barcode. We rearrange UMI sequences to position them next to each other and remove additional low-quality nucleotides, including  the oligo(dT) fragment and those that follow it. For this, we utilise the awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 of pooled libraries were demultiplexed into separate fastq files for each replicate using BRBseqTools (v 1.6) Demultiplex and R1 with parameters -p UB -UMI 14 -n 1. The resulting reads were trimmed to eliminate potential contamination with the poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then, they were mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes.
Assembly: TAIR10
Supplementary files format and content: count text files

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Plants were grown in a growth chamber under long-day conditions (16 hours of light at 22ºC / 8 hours of darkness at 21ºC; light intensity approximately 110 µmol photons m-2s-1).

extract_protocol:
RNA was extracted using Trizol (Molecular Research Center) following the manufacturer’s instructions and treated with DNase I (Thermo Scientific).
500 ng of RNA was utilised in reverse transcription with 50 mM of various barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled. cDNA pools were purified with Ampure beads (1.5x beads to sample volumes) and then eluted in 17 µl of water. 15 µl of the recovered cDNA pools were mixed by pipetting with 15 µl of the second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 µM dNTPs) and incubated overnight at 16°C. The reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 µl of water. 3 µl of the recovered dsDNA samples were used for tagmentation with 3 µl of 5x diluted B-loaded Tn5 enzyme (homemade) and 6 µl of freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). The reactions were mixed by pipetting and incubated for 7 minutes at 55°C, followed by 5 minutes at 80°C. Water was added to a total volume of 36 µl; samples were purified with Ampure beads (1.2x beads to sample volumes) and eluted with 21 µl of water. Illumina indexing PCRs were performed using 20 µl of the tagmented DNA in a 50 µl reaction with Q5 2× PCR Master Mix (NEB) and a final concentration of 0.5 µM of primers. Libraries were sequenced on the Illumina Nova-seq to obtain two reads: R1 (containing barcode and UMI) and R2 (containing mRNA sequence).
3'RNA-seq

treatment_protocol: Rosette leaves were collected at 25 and 45 DAS, immediately frozen, and stored at -80ºC until the extraction of RNA.

value: leaves

tag: ecotype

value: 45 DAS


title: HEK293T cells, empty vector, Input, Rep2

description: Library name: Rep2-IN-empty


title: 29, ENP, CD154

description: Library name: 200901081


title: snrk_45d_4

description: Library name: snrk_45d_4


title: HEK293T cells, empty vector, Input, Rep1

description: Library name: Rep1-IN-empty


title: 28, ENP, CD137

description: Library name: 200901071


title: NLRP6-KO, Sg, biol rep 2

description: Library name: Sample 11

value: Oral gingival


title: snrk_45d_3

description: Library name: snrk_45d_3


title: NLRP6-KO, Sg, biol rep 1

description: Library name: Sample 10


title: HEK293T cells, AGO2-D619N, IP, Rep3

description: Library name: Rep3-IP-D619N


title: 27, ALL, CD154

description: Library name: 200901061

value: ALL


title: snrk_45d_2

description: Library name: snrk_45d_2


title: WT, Negative, biol rep 2

description: Library name: Sample 19

value: WT


title: HEK293T cells, AGO2-D619N, IP, Rep2

description: Library name: Rep2-IP-D619N


title: 26, ALL, CD137

description: Library name: 200901051


title: MDS_AZA_077

value: Bone marrow

value: MDS patient

value: NonResp


title: snrk_45d_1

description: Library name: snrk_45d_1


title: WT, Pg, biol rep 2

description: Library name: Sample 8


title: HEK293T cells, AGO2-D619N, IP, Rep1

description: Library name: Rep1-IP-D619N


title: 25, AD, CD154

description: Library name: 200901041

value: AD


title: snrk_25d_5

description: Library name: snrk_25d_5

value: 25 DAS


title: WT, Sham, biol rep 2

description: Library name: Sample 7

value: Sham


title: HEK293T cells, AGO2-D619N, Input, Rep3

description: Library name: Rep3-IN-D619N


title: 24, AD, CD137

description: Library name: 200901031


title: snrk_25d_4

description: Library name: snrk_25d_4


title: WT, Negative, biol rep 1

description: Library name: Sample 6


title: HEK293T cells, AGO2-D619N, Input, Rep2

description: Library name: Rep2-IN-D619N


title: 23, CON, CD154

description: Library name: 200901021

value: CON


title: snrk_25d_3

description: Library name: snrk_25d_3


title: WT, Pg, biol rep 1

description: Library name: Sample 5


title: HEK293T cells, AGO2-D619N, Input, Rep1

description: Library name: Rep1-IN-D619N


title: 22, CON, CD137

description: Library name: 200901011


title: snrk_25d_2

description: Library name: snrk_25d_2


title: WT, Sham, biol rep 1

description: Library name: Sample 4


title: HEK293T cells, AGO2-G604R, IP, Rep3

description: Library name: Rep3-IP-G604R


title: 21, ENP, CD154

description: Library name: 200901001


title: snrk_25d_1

description: Library name: snrk_25d_1


title: WT, Pg+Sg, biol rep 1

description: Library name: Sample 3

value: Pg+Sg


title: HEK293T cells, AGO2-G604R, IP, Rep2

description: Library name: Rep2-IP-G604R


title: WT_45d_5

description: Library name: WT_45d_5

value: wildtype


title: 20, ENP, CD137

description: Library name: 200900991

value: ENP


title: WT, Sg, biol rep 2

description: Library name: Sample 2

value: Sg


title: HEK293T cells, AGO2-G604R, IP, Rep1

description: Library name: Rep1-IP-G604R


title: 19, AD, CD154

description: Library name: 200900981


title: WT_45d_4

description: Library name: WT_45d_4


title: WT, Sg, biol rep 1

description: Library name: Sample 1


title: HEK293T cells, AGO2-G604R, Input, Rep3

description: Library name: Rep3-IN-G604R


title: 18, AD, CD137

description: Library name: 200900971


title: WT_45d_3

description: Library name: WT_45d_3


title: Uninfected Ezh2-deficient Hoxb8-derived macrophages, biological replicate 3

city: Ithaca

first: bom nae rin

last: lee

address: 930 Campus Road

department: Microbiology&Immunology

institute: Cornell university

description:
Library name: 7028D-BL6-EZH3
Column name in mouse count matrix: EZH_3

data_processing:
Reads were mapped separately to the mouse GRCm39 and M. tuberculosis ASM19595v2 genome assemblies using STAR.
Gene-level raw counts were generated using STAR --quantMode GeneCounts.
DESeq2 was used to generate normalized count matrices separately for mouse and M. tuberculosis.
Assembly: GRCm39, ASM19595v2
Supplementary files format and content: ZIP archives containing raw gene-count tables and gzip-compressed tab-separated files containing DESeq2-normalized counts for mouse and M. tuberculosis.
Supplementary files format and content: The mouse raw and normalized count matrices contain all 12 libraries; the M. tuberculosis raw and normalized count matrices contain the six infected libraries.

source_name: Cas9-expressing Hoxb8 myeloid progenitor cells

growth_protocol: Cas9-expressing, estrogen-responsive Hoxb8 myeloid progenitor cells were maintained in RPMI supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 1 mM sodium pyruvate, 20 ng/ml murine GM-CSF, 0.5 uM beta-estradiol, 10 mM HEPES and 1% penicillin-streptomycin. To induce macrophage differentiation, progenitor cells were washed to remove beta-estradiol and cultured in macrophage differentiation medium for 7 days at 37 degrees C with 5% CO2.

extract_protocol:
RNA was extracted using TRIzol. Total RNA from the aqueous phase was purified using the Zymo RNA Clean & Concentrator kit.
Barcoded RNA-seq libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit after ribosomal RNA depletion using the QIAseq FastSelect pan-bacterial and H/M/R kits. Libraries were sequenced on an Illumina NovaSeq 6000 S4 flow cell.

treatment_protocol: EZH2-deficient cells were generated by transducing Cas9-expressing Hoxb8 progenitors with a pLentiGuide-Puro vector containing an sgRNA targeting mouse Ezh2, followed by puromycin selection. Parental Cas9-expressing Hoxb8 progenitors without an Ezh2-targeting sgRNA were used as wild-type controls. Differentiated macrophages were infected with Mycobacterium tuberculosis Erdman smyc'::mCherry at a multiplicity of infection of 2. At 3 days post-infection, mCherry-positive macrophages were isolated by flow sorting. Uninfected samples were collected in parallel.

value: Hoxb8-derived macrophages

value: Uninfected


title: 17, ALL, CD154

description: Library name: 200900961


title: WT_45d_2

description: Library name: WT_45d_2

value: leaves

value: 45 DAS


title: Uninfected Ezh2-deficient Hoxb8-derived macrophages, biological replicate 2

description:
Library name: 7028D-BL5-EZH2
Column name in mouse count matrix: EZH_2

value: Cas9-expressing Hoxb8 myeloid progenitor cells


title: HEK293T cells, AGO2-G604R, Input, Rep2

description: Library name: Rep2-IN-G604R


title: HEK293T cells, AGO2-G604R, Input, Rep1

description: Library name: Rep1-IN-G604R


title: 16, ALL, CD137

description: Library name: 200900951

value: ALL


title: WT_45d_1

description: Library name: WT_45d_1


title: Uninfected Ezh2-deficient Hoxb8-derived macrophages, biological replicate 1

description:
Library name: 7028D-BL4-EZH1
Column name in mouse count matrix: EZH_1


title: HEK293T cells, AGO2-N359H, IP, Rep3

description: Library name: Rep3-IP-N359H


title: 15, AD, CD154

description: Library name: 200900941


title: WT_25d_5

description: Library name: WT_25d_5


title: Uninfected parental Hoxb8-derived macrophages, biological replicate 3

description:
Library name: 7028D-BL3-HOX3
Column name in mouse count matrix: HOX_3

value: Parental (WT)


title: HEK293T cells, AGO2-N359H, IP, Rep2

description: Library name: Rep2-IP-N359H


title: 14, AD, CD137

description: Library name: 200900931


title: WT_25d_4

description: Library name: WT_25d_4


title: Uninfected parental Hoxb8-derived macrophages, biological replicate 2

description:
Library name: 7028D-BL2-HOX2
Column name in mouse count matrix: HOX_2


title: HEK293T cells, AGO2-N359H, IP, Rep1

description: Library name: Rep1-IP-N359H


title: 13, CON, CD154

description: Library name: 200900921


title: WT_25d_3

description: Library name: WT_25d_3


title: Uninfected parental Hoxb8-derived macrophages, biological replicate 1

description:
Library name: 7028D-BL1-HOX1
Column name in mouse count matrix: HOX_1


title: HEK293T cells, AGO2-N359H, Input, Rep3

description: Library name: Rep3-IN-N359H


title: 12, CON, CD137

description: Library name: 200900911


title: WT_25d_2

description: Library name: WT_25d_2


title: WT_TBI_D3_Cortex_6

city: Baltimore

first: Marta

middle: M

last: Lipinski

state: MD

address: 685 W Baltimore St

department: STAR

institute: University of Maryland, Baltimore

description: Library name: WT_6TBI_D3I_L_C

data_processing:
The read counts for each transcript are generated by HTseq, the reads are either normalized as CPM (count per million reads), or RPKM (Reads Per Kilobase Million). The alignments were generated by HISAT2 for eukaryotes
Assembly: Paired-end Illumina libraries were mapped to the Mouse reference, Ensembl release GRCm39.108, using HiSat2 v2.0.4, using default mismatch parameters.
Supplementary files format and content: txt files include rpkm values for each file

source_name: Ipsilateral cortex

growth_protocol: Male mice on C57BL/6 genetic background were utilized for the expeiment and Rubicon mutant mice were obtained from the Jackson Laboratory (stock #032581). Mice were housed in cages with sterilized bedding at the University of Maryland, Baltimore (UMB) animal facility and maintained on a 12-hour light/dark cycle.

extract_protocol:
Total RNA was extracted from the frozen ipsilateral cortical tissues using QIAzol Lysis reagent (Qiagen; 79306) and purified with the RNeasy mini kit (Qiagen; 74104) according to the manufacturer’s protocol.
Samples were enriched for mRNA containing Poly A tails using bead-based enrichment kit (NEBNext Poly(A) mRNA Magnetic Isolation Module, New England Biolabs). Enriched Poly A RNA was used to create Strand-specific, dual unique indexed libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Manufacturer protocol was modified by diluting adapter 1:30 and using 3 ul of this dilution. Size selection of the library was performed using SPRI-select beads (Beckman Coulter Genomics). Glycosylase digestion of adapter and 2nd strand was done in the same reaction at the final amplification. Revvity GX touch was used to assess libraries for size and quantity. The libraries were pooled, assessed by qPCR using the KAPA Library Quantification Kit (Complete, Universal, Kapa Biosystems) and sequenced on an Illumina NovaSeq 6000 using 100 bp PE reads.

treatment_protocol: Mice were subjected to moderate TBI using a controlled cortical impact device customized with a microprocessor-regulated pneumatic impactor equipped with a 2.3-mm diameter tip. Briefly, mice were anesthetized with 3% isoflurane and underwent a 4-mm craniotomy over the left parietal bone following a 10-mm midline scalp incision. Moderate CCI was induced on the exposed portion of the brain using the pneumatic impactor at an impact velocity of 4 m/s, a deformation depth of 1.5 mm, and a dwell time of 100 ms. The incision sites were then closed with sterile sutures. Sham mice were subjected to the same procedures, excluding the craniotomy and impact. Ipsilateral cortical samples were collected at 3 days post injury and flash-frozen for RNA extraction.

value: Ipsilateral cortex

tag: strain

value: Male

value: Wild-type

value: CCI Day 3


title: HEK293T cells, AGO2-N359H, Input, Rep2

description: Library name: Rep2-IN-N359H


title: 11, ALL, CD154

description: Library name: 200900901


title: WT_25d_1

description: Library name: WT_25d_1

value: 25 DAS


title: WT_Sham_Cortex_6

description: Library name: WT_6ShamI_L_C

value: Sham


title: 10, ALL, CD137

description: Library name: 200900891


title: HEK293T cells, AGO2-N359H, Input, Rep1

description: Library name: Rep1-IN-N359H


title: RKP

type: RNA

city: Houston

first: Kyung Pil

last: Ko

state: Tx

address: 1515 Holcombe Blvd

institute: The University of Texas M.D. Anderson Cancer Center

description: Section of RKP tumor

hyb_protocol: Followed Xenium In Situ Gene Expression protocol from the manufacturer (CG000582)

scan_protocol: Followed Xenium Analyzer User Guide (CCG000584)

data_processing: Data were processed with the Xenium Analyzer (10x Genomics) and imported into R for further processing using Seurat (v4.4.0), including quality control, normalization, and object construction.

source_name: subcutaneous tumor

label_protocol: Followed Xenium In Situ for FFPE - Tissue Preparation Guide from the manufacturer (CG000578)

growth_protocol: Five-week-old C57BL/6 mice were housed in the Division of Laboratory Animal Resources at MD Anderson. For subcutaneous allograft experiments, 2D-cultured EKP and RKP cells (3 × 10⁶) were mixed 1:1 with Matrigel and injected into both flanks of each mouse. Tumor volume was measured every 3–4 days using calipers and calculated as (length × width²)/2.

extract_protocol: Mice were euthanized when tumors reached similar final volumes across groups. Collected tumors were photographed and paraffin-embedded for histological analysis.

value: Diffuse gastric cancer


title: WT_TBI_D3_Cortex_5

description: Library name: WT_5TBI_D3I_L_C


title: 9, ALL, CD154

description: Library name: 200900881


title: HEK293T cells, AGO2-F182del, IP, Rep3

description: Library name: Rep3-IP-F182del


title: EKP

description: Section of EKP tumor


title: WT_Sham_Cortex_5

description: Library name: WT_5ShamI_L_C


title: HEK293T cells, AGO2-F182del, IP, Rep2

description: Library name: Rep2-IP-F182del


title: RAD51D tile 6 replicate #3 passage 2

city: Ann Arbor

first: Jacob

last: Kitzman

state: MI

address: 4811 Med Sci II, 1241 E Catherine St

department: Department of Human Genetics

institute: University of Michigan

description: Library name: t06_rep3_p2

data_processing:
Paired end reads were overlapped and an error-corrected consensus was taken by PEAR, and  aligned to MUTYH reference with bwa mem. Variant counts were tabulated by a custom pipeline (https://github.com/kitzmanlab/tileseq/). Amino acid level counts were processed by Rosace.
Supplementary files format and content: Tab delimited table with read counts for each single-residue mutation, for input to rosace or other modeling software.

organism: synthetic construct

growth_protocol: Human osteosarcoma  RAD51D CRISPR knockout (clone #4, purchased from DSMZ, no. ACC835) were cultured in Corning DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin antibiotic (50 U/mL). Cells were incubated at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Genomic DNA from P0 and P2 cell populations was isolated using CleanNA Blood and Tissue magnetic bead kit (Bulldog Bio)
To amplify integrated RAD51D mutant libraries, “outer PCR” was performed on a 500 ng gDNA template with primers flanking the RAD51D cDNA using the PrimeSTAR GXL kit (Takara), with 16 replicate PCR reactions for each gDNA sample to maintain library complexity. To quantify mutation frequency in sorted cells, mutant libraries were subjected to deep amplicon tile sequencing as described (Hemker et al, 2025). Briefly, 1 µL of outer PCR library product was amplified in a limited (≤10) cycle PCR, using primers directed at constant bases flanking the targeted tile within the RAD51D cDNA. Primer 5’ tails contained constant sequencing adaptor stub sequences. Each resulting product was then diluted and further amplified to add sequencing adaptors and sample-specific unique dual 10 bp index sequences.

treatment_protocol: Mutant library-expressing cells were cultured in experimental triplicates in T175 flasks in DMEM media (supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin) with 1 mg/mL doxycycline added to induce RAD51D expression. From each baseline passage (‘‘P0’’) culture, one million cells were collected for gDNA extraction and three million cells were seeded for olaparib selection, with media containing 50 µg/ml hygromycin, 1 mg/mL doxycycline, 1 µg/mL blasticidin (to enforce RAD51D expression), and 250 nM olaparib. Cells were grown to 90% confluence for two rounds, at each round seeding with three million cells to avoid population bottlenecks.


title: 8, ALL, CD137

description: Library name: 200900871


title: WT_TBI_D3_Cortex_4

description: Library name: WT_4TBI_D3I_L_C


title: HEK293T cells, AGO2-F182del, IP, Rep1

description: Library name: Rep1-IP-F182del


title: RAD51D tile 6 replicate #3 passage 0

description: Library name: t06_rep3_p0


title: 7, CON, CD154

description: Library name: 200900861

value: CON


title: WT_Sham_Cortex_4

description: Library name: WT_4ShamI_L_C


title: HEK293T cells, AGO2-F182del, Input, Rep3

description: Library name: Rep3-IN-F182del


title: 6, CON, CD137

description: Library name: 200900851


title: RAD51D tile 6 replicate #2 passage 2

description: Library name: t06_rep2_p2


title: 5, ENP, CD154

description: Library name: 200900821

value: ENP


title: HEK293T cells, AGO2-F182del, Input, Rep2

description: Library name: Rep2-IN-F182del


title: HEK293T cells, AGO2-F182del, Input, Rep1

description: Library name: Rep1-IN-F182del


title: 4, ENP, CD137

description: Library name: 200900811


title: RAD51D tile 6 replicate #1 passage 2

description: Library name: t06_rep1_p2


title: RAD51D tile 6 replicate #1 passage 0

description: Library name: t06_rep1_p0


title: WT_TBI_D3_Cortex_1

description: Library name: WT_1TBI_D3I_L_C


title: WT_TBI_D3_Cortex_3

description: Library name: WT_3TBI_D3I_L_C


title: RAD51D tile 6 replicate #2 passage 0

description: Library name: t06_rep2_p0


title: WT_Sham_Cortex_3

description: Library name: WT_3ShamI_L_C


title: 3, CON, CD137

description: Library name: 200900791


title: WT_TBI_D3_Cortex_2

description: Library name: WT_2TBI_D3I_L_C


title: HEK293T cells, AGO2-WT, IP, Rep3

description: Library name: Rep3-IP-WT

value: WT


title: 2, AD, CD137

description: Library name: 200900771

value: AD


title: HEK293T cells, AGO2-WT, IP, Rep2

description: Library name: Rep2-IP-WT


title: RAD51D tile 5 replicate #3 passage 2

description: Library name: t05_rep3_p2


title: 1, ALL, CD137

description: Library name: 200900751


title: HEK293T cells, AGO2-WT, IP, Rep1

description: Library name: Rep1-IP-WT


title: WT_Sham_Cortex_1

description: Library name: WT_1ShamI_L_C


title: Rubcn_Mutant_TBI_D3_Cortex_6

description: Library name: RubcnKO_6TBI_D3I_L_C

value: Rubicon Mutant


title: HEK293T cells, AGO2-WT, Input, Rep3

description: Library name: Rep3-IN-WT


title: RAD51D tile 5 replicate #3 passage 0

description: Library name: t05_rep3_p0


title: RAD51D tile 5 replicate #2 passage 2

description: Library name: t05_rep2_p2


title: ATAC-seq-H9_DOT1L_KO_D9

city: guangzhou

first: chen

last: huan

address: guangzhou

institute: guangzhou laboratory

data_processing:
All of the sequencing data were aligned to the human genome assembly (hg38) using bowtie2
Alignment BAM files were transformed into read coverage files (bigWig format) using deepTools using the RPKM normalization method
MACS2 was used to call narrow peaks with default options
Assembly: Hg38
Supplementary files format and content: BigWig for each sample

growth_protocol: hESCs (H9) and the HNF1B and DOT1L knockout (KO) cell lines were cultured in mTeSR1 (STEMCELL Technologies) on Matrigel (Corning)-coated plates in a 5% CO2 cell incubator

extract_protocol:
ATAC-seq was performed using TruePrepTM DNA Library Prep Kit V2 for Illumina® (Vazyme), a total of 50,000-80,000 cell pellets were resuspended in 50 μL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) IGEPAL CA-630).
The suspension was subjected to a transposition reaction and purification with a MinElute Kit (QIAGEN). After PCR amplification of transposed DNA fragments, the amplified libraries were purified using a QIAquick PCR (QIAGEN) column. Then, purified libraries were assessed by gel electrophoresis and Qsep100 (Bioptic)

treatment_protocol:
By adjusting the WNT, TGFβ, and FGF signaling pathway and other compounds in stages, human embryonic stem cells (hESCs, H9) differentiated through the primitive streak (day3), nephrogenic intermediate mesoderm (D6), nephron progenitor cells (D9), and kidney organoid(D16)
H9 cells were treated with 8 µM CHIR99021 (Targetmol) in basic medium Advanced RPMI 1640 medium (GIBCO) supplemented with 1X L-GlutaMAX (GIBCO) for 3-4 days, followed by 10 ng/mL Activin (PeproTech) for 2-3 days. To induce nephron progenitor cells (NPCs), the medium was changed to 10 ng/mL FGF9 (Peprotech) for 7 days. During this stage, the cells were treated with 3 µM CHIR after 1-2 days of 10 ng/mL FGF9 treatment for 1-2 days. Next, the medium was changed to basal medium with no additional factors until harvest on day 19

value: DOT1L knockout


title: Rubcn_Mutant_TBI_D3_Cortex_5

description: Library name: RubcnKO_5TBI_D3I_L_C


title: HEK293T cells, AGO2-WT, Input, Rep1

description: Library name: Rep1-IN-WT


title: RAD51D tile 5 replicate #1 passage 2

description: Library name: t05_rep1_p2


title: Rubcn_Mutant_TBI_D3_Cortex_3

description: Library name: RubcnKO_3TBI_D3I_L_C


title: ATAC-seq-H9_DOT1L_KO_D8


title: HEC-1A, IgG negative control (CUT&RUN)

description: Library name: NEG

data_processing:
RNA-seq TPM generated with Salmon and Tximport; ATAC-seq Raw FASTQ files were trimmed with Trim Galore, quality assessed with FastQC. Reads aligned to GRCh38 using Bowtie2. Mitochondrial reads removed, properly paired reads retained with samtools. Library complexity estimated with ATACseqQC, datasets normalized by subsampling. PCR duplicates removed with Picard MarkDuplicates. Reads converted to BEDPE format, fragment coordinates adjusted for Tn5 bias (+4/-5 bp). Broad peaks called with MACS3 (FDR < 0.05, no control input).; Cut&run reads were processed with nf-core/cutandrun pipeline (v3.2.2) using Nextflow (v24.10.5). Aligned to GRCh38 human reference genome. GRCh38 unified blacklist regions excluded. Peaks called using MACS2 (v2.2.7.1) against IgG controls. narrowPeak files generated for each biological replicate.
Assembly: GRCh38
Supplementary files format and content: RNA-seq: Tab-delimited text file includes TPM values for each sample. ATAC-seq: broadPeak per sample. Cut&run narrowPeak except for NEG sample
Library strategy: Cut&Run

value: endometrial adenocarcinoma

value: endometrial adenocarcinoma epithelial cells

value: Untreated


title: HEK293T cells, AGO2-WT, Input, Rep2

description: Library name: Rep2-IN-WT


title: ATAC-seq-H9_DOT1L_KO_D6


title: Rubcn_Mutant_TBI_D3_Cortex_4

description: Library name: RubcnKO_4TBI_D3I_L_C


title: ATAC-seq-H9_DOT1L_KO_D19


title: RAD51D tile 5 replicate #1 passage 0

description: Library name: t05_rep1_p0


title: Rubcn_Mutant_TBI_D3_Cortex_2

description: Library name: RubcnKO_2TBI_D3I_L_C


title: ATAC-seq-H9_DOT1L_KO_D16


title: RAD51D tile 4 replicate #3 passage 2

description: Library name: t04_rep3_p2


title: Rubcn_Mutant_TBI_D3_Cortex_1

description: Library name: RubcnKO_1TBI_D3I_L_C


title: HEC-1A, THC 20uM, H3K4me3 (CUT&RUN), Biol rep 2

description: Library name: THC_K4_2

value: THC


title: RAD51D tile 5 replicate #2 passage 0

description: Library name: t05_rep2_p0


title: RAD51D tile 4 replicate #3 passage 0

description: Library name: t04_rep3_p0


title: ATAC-seq-H9_DOT1L_KO_D12


title: Rubcn_Mutant_Sham_Cortex_4

description: Library name: Rubcn_N_N_4_Sham_I_L_C

value: Ipsilateral cortex


title: HEC-1A, THC 20uM, H3K4me3 (CUT&RUN), Biol rep 1

description: Library name: THC_K4_1


title: RAD51D tile 4 replicate #2 passage 2

description: Library name: t04_rep2_p2


title: Rubcn_Mutant_Sham_Cortex_3

description: Library name: Rubcn_N_N_3_Sham_I_L_C

value: Male


title: ATAC-seq-H9_D9


title: HEC-1A, UNTREATED, H3K4me3 (CUT&RUN), Biol rep 3

description: Library name: NA_K4_3


title: HEC-1A, THC 20uM, H3K4me3 (CUT&RUN), Biol rep 3

description: Library name: THC_K4_3


title: ATAC-seq-H9_D8


title: RAD51D tile 4 replicate #2 passage 0

description: Library name: t04_rep2_p0


title: Rubcn_Mutant_Sham_Cortex_2

description: Library name: Rubcn_N_N_2_Sham_I_L_C


title: HEC-1A, UNTREATED, H3K4me3 (CUT&RUN), Biol rep 2

description: Library name: NA_K4_2


title: ATAC-seq-H9_D6


title: RAD51D tile 4 replicate #1 passage 2

description: Library name: t04_rep1_p2


title: Rubcn_Mutant_Sham_Cortex_1

description: Library name: Rubcn_N_N_1_Sham_I_L_C


title: HEC-1A, UNTREATED, H3K4me3 (CUT&RUN), Biol rep 1

description: Library name: NA_K4_1


title: ATAC-seq-H9_D3


title: RAD51D tile 4 replicate #1 passage 0

description: Library name: t04_rep1_p0


title: HEC-1A THC 20uM 72h Biol rep 3

description: Library name: S18


title: NF1 Selumetinib treated 3

first: Rajasekaran

last: Mahalingam

state: TX

address: 6565 MD Anderson Blvd

department: Symptom Research

institute: University of Texas MD Anderson Cancer Center

description: Library name: Sample12

data_processing:
Raw seqeuning qualit assessed with FastQC, trimmed with Trimmomatic
Aligned to the mouse reference genome (mm10) using the STAR aligner
Gene-level quantification was performed with HTSeq-count
Differential gene expression analysis was performed using the DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimted text file raw counts for each sample

source_name: Optic nerve

extract_protocol:
RNA was extrated using Rneasy mini plus kit and poly-T oligo-attached magnetic beads were used to isolate mRNA from the total RNA
The library construction included end repair, A-tailing, adapter ligation, size selection, and PCR amplification, concluding with purification

value: Optic nerve

value: Nerve cells

value: Selumetinib


title: RAD51D tile 3 replicate #3 passage 2

description: Library name: t03_rep3_p2


title: ATAC-seq-H9_D16


title: NF1 Selumetinib treated 2

description: Library name: Sample11


title: HEC-1A THC 20uM 72h Biol rep 2

description: Library name: S17

data_processing:
RNA-seq TPM generated with Salmon and Tximport; ATAC-seq Raw FASTQ files were trimmed with Trim Galore, quality assessed with FastQC. Reads aligned to GRCh38 using Bowtie2. Mitochondrial reads removed, properly paired reads retained with samtools. Library complexity estimated with ATACseqQC, datasets normalized by subsampling. PCR duplicates removed with Picard MarkDuplicates. Reads converted to BEDPE format, fragment coordinates adjusted for Tn5 bias (+4/-5 bp). Broad peaks called with MACS3 (FDR < 0.05, no control input).; Cut&run reads were processed with nf-core/cutandrun pipeline (v3.2.2) using Nextflow (v24.10.5). Aligned to GRCh38 human reference genome. GRCh38 unified blacklist regions excluded. Peaks called using MACS2 (v2.2.7.1) against IgG controls. narrowPeak files generated for each biological replicate.
Assembly: GRCh38
Supplementary files format and content: RNA-seq: Tab-delimited text file includes TPM values for each sample. ATAC-seq: broadPeak per sample. Cut&run narrowPeak except for NEG sample


title: ATAC-seq-H9_D14


title: RAD51D tile 3 replicate #2 passage 2

description: Library name: t03_rep2_p2


title: NF1 Selumetinib treated 1

description: Library name: Sample10


title: HEC-1A THC 20uM 72h Biol rep 1

description: Library name: S16


title: ATAC-seq-H9

value: control


title: RAD51D tile 3 replicate #1 passage 2

description: Library name: t03_rep1_p2


title: HEC-1A THC 20uM 24h Biol rep 3

description: Library name: S15


title: RNA-seq-H9_DOT1L_KO-D9

data_processing:
Sequenced reads were aligned to a transcriptome index generated from the GENCODE annotations transcriptome (Hg38) using RSEM, bowtie2
The transcripts per kilobase million (TPM) values were used for downstream analysis
Assembly: Hg38
Supplementary files format and content: files includes raw counts, RPKM, and TPM for each Sample
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
After the total RNA extracts were prepared, RNA libraries were established using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s protocol
1000 ng of total high-quality RNA (RIN value >7) was used to ensure sufficient mRNA for library construction. mRNA was enriched by the Poly(A) method with VAHTS mRNA Capture Beads (Vazyme #N401)


title: RAD51D tile 3 replicate #3 passage 0

description: Library name: t03_rep3_p0


title: NF1 control 5

description: Library name: Sample8

value: PBS


title: RNA-seq-H9_DOT1L_KO-D8


title: NF1 control 6

description: Library name: Sample9


title: RAD51D tile 3 replicate #2 passage 0

description: Library name: t03_rep2_p0


title: HEC-1A THC 20uM 24h Biol rep 2

description: Library name: S14


title: NF1 control 4

description: Library name: Sample7


title: HEC-1A THC 20uM 24h Biol rep 1

description: Library name: S13


title: RNA-seq-H9_DOT1L_KO-D6


title: RAD51D tile 3 replicate #1 passage 0

description: Library name: t03_rep1_p0


title: NF1 Carboplatin treated 3

description: Library name: Sample6

value: Carboplatin


title: HEC-1A UNTREATED Biol rep 3

description: Library name: S12


title: RNA-seq-H9_DOT1L_KO-D19


title: RAD51D tile 2 replicate #3 passage 2

description: Library name: t02_rep3_p2


title: NF1 Carboplatin treated 2

description: Library name: Sample5


title: HEC-1A UNTREATED Biol rep 2

description: Library name: S11


title: RNA-seq-H9_DOT1L_KO-D16


title: RAD51D tile 2 replicate #2 passage 2

description: Library name: t02_rep2_p2


title: NF1 Carboplatin treated 1

description: Library name: Sample4


title: HEC-1A UNTREATED Biol rep 1

description: Library name: S10


title: RAD51D tile 2 replicate #1 passage 2

description: Library name: t02_rep1_p2


title: RNA-seq-H9_D9


title: NF1 control 3

description: Library name: Sample3


title: SAHA_303_C5_E_R3

city: Ottawa

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

description:
Library name: Sample 144
raw cell lysate and Illumina NextSeq 2143

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with qCount in the QuasR R package v1.38.0
Normalization was performed with DESeq2 v1.38.0
Assembly: Biospyder Human Whole Transcriptome Gene Set
Supplementary files format and content: 260722_count_table_GEO.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.

source_name: liver tumor associated with chronic hepatitis C

growth_protocol: Cryopreserved differentiated HepaRG cells (Biopredic International, Saint-Grégoire, France) were cultivated according to the manufacturer’s protocol. Differentiated HepaRG cells were thawed and seeded into collagen-coated wells at a density of approximately 0.072 x 10e6 viable cells per well (i.e. 100 μL of the cell suspension per well) in 96-well plates, using HepaRG Thawing/Plating/General Purpose Medium 670 (ADD670C, Biopredic International, Saint-Grégoire, France). After 24h, the media were changed to HepaRG Maintenance Medium 620 (ADD620C, Biopredic International, Saint-Grégoire, France) for cell maintenance. Cells were incubated for 7 days at 37C, 5% CO2 and saturating humidity.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building.
TempO-Seq® gene expression analysis was conducted on exposed and control HepaRG cell lysates. Libraries were prepared in a 96-well plate format using the TempO-Seq® Human Whole Transcriptome Panel reagent kit (BioSpyder Technologies, Carlsbad, CA, USA), following the manufacturer’s protocol. Human Brain Total RNA and qPCR Human Reference Total RNA (Takara Bio, CA, USA) were included as positive assay controls and a no-lysate control (1X TempO-Seq® R Lysis Buffer only) was included as a negative assay control (two replicates per control). In brief, 2 µl cell lysates were hybridized with the targeted detector oligo (DO) probe mix in 1X TempO-Seq® R Lysis Buffer for 10 min at 70C followed by a temperature gradient with a ramp rate of 0.5C/min to 45C over a 50 min period, followed by a nuclease digestion at 37C for 90 min to remove excess, unbound, or incorrectly bound DOs enzymatically. Ligation of the DO pairs bound to adjacent target sequences was then completed with a 60 min incubation at 37C, immediately followed with a 15 min enzyme denaturation at 80C to generate a pool of amplification templates. All amplification templates (i.e., 10 µl of ligated DOs) were transferred to its corresponding well of the 96-well PCR Pre-Mix and Primers plate. Amplification proceeded with a CFX96 Real-Time PCR Detection System (Bio-Rad, Mississauga, ON, Canada) to attach a unique sequence tag and the sequencing adaptors to each sample using the following PCR program settings: 37C for 10 min, 95C for 2 min; 6 cycles of 95C for 30 sec, 54C for 30 sec, 72C for 120 sec; 16 cycles of 95C for 30 sec; 72C for 2 min; 72C for 1 min. The TempO-Seq® libraries were pooled (5 µl of all 96 samples) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Clean-Up kit (Clontech Laboratories Inc., Bethlehem, PA, USA), according to the manufacturer’s instructions for PCR cleanup with three modifications outlined in the TempO-Seq® Assay User Guide. The pooled, purified TempO-Seq® libraries were sequenced using a NextSeq® 2000 High Output flow cell (v2 kit, 75 cycles) on an Illumina NextSeq® 2000 Sequencing platform (Illumina, San Diego, CA, USA).

treatment_protocol: At day 7, cells were exposed in triplicate to 5 concentrations of test chemical and refreshed with test chemical in HepaRG Induction Medium 640 (ADD640C, Biopredic International, Saint-Grégoire, France) daily for 72 hours (i.e., 3-day repeat exposures; 0 h, 24 h, 48 h). Cells were exposed to trichostatin A ( 0.018811, 0.056433, 0.1693, 0.5079, 1.5237 µM), panobinostat (0.001468, 0.004403, 0.01321, 0.03963, 0.084 µM), valproic acid (0.100478, 0.301433, 0.9043, 2.7129, 3.038 µM), mocetinostat (0.177222, 0.531667, 1.595, 2.5, 3.9 µM), apicidin (0.041722, 0.125167, 0.3755, 0.5, 0.86 µM), tacedinaline (1.143333, 3.43, 10.29, 30.87, 44 µM), scriptaid  (4.94, 14.82, 44.46, 60, 94.5 µM), vorinostat (0.404778, 1.214333, 3.643, 10.929, 23.5 µM). After 72 h exposure, cells were used to generate cell lysates for gene expression analysis (n = 3 per treatment group per assay for TempO-Seq®).

value: HepaRG

value: liver progenitor cells

tag: chemical shortname

value: SAHA

tag: chemical longname

value: vorinostat

tag: dose

tag: well

tag: dose group

tag: plate

value: E

tag: index

value: GGGTTGTTA

value: AGCCTACTT

tag: group

tag: replicate

tag: chemical type

value: test

tag: cas-nr

tag: batch nr_heparg


title: RNA-seq-H9_D8

tag: cell line

tag: genotype

value: WT


title: NF1 control 2

description: Library name: Sample2

tag: tissue

tag: cell type

tag: treatment


title: RAD51D tile 2 replicate #3 passage 0

description: Library name: t02_rep3_p0


title: SAHA_330_C5_E_R2

description:
Library name: Sample 143
raw cell lysate and Illumina NextSeq 2142

value: liver tumor associated with chronic hepatitis C

tag: chemical shortname

value: GACCTTGCT


title: RNA-seq-H9_D6

tag: time


title: NF1 control 1

description: Library name: Sample1

value: Optic nerve


title: SAHA_326_C5_E_R1

description:
Library name: Sample 142
raw cell lysate and Illumina NextSeq 2141

tag: chemical longname

tag: dose

value: GTTTATACT

value: GATGGTTGT


title: RNA-seq-H9_D3


title: RAD51D tile 2 replicate #2 passage 0

description: Library name: t02_rep2_p0


title: RAD51D tile 2 replicate #1 passage 0

description: Library name: t02_rep1_p0


title: SAHA_303_C4_E_R3

description:
Library name: Sample 141
raw cell lysate and Illumina NextSeq 2140

tag: well

tag: dose group

value: AAGACTCTT


title: 4 days post injury, Pax7 Progeny cells2 (2mo)

city: Paris

first: Takuto

last: HAYASHI

address: 160 Rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades

description: Library name: Sample9-2/2

data_processing:
feature-barcode matrices were generated by aligning the reads to the mouse genome (mm10 Ensemble: version 92) with CellRanger v8.0.1.
Assembly: mm10
Supplementary files format and content: The Cell Ranger output includes three files: features.tsv, barcodes.tsv, and matrix.mtx, which together represent the gene expression count matrix. The matrix contains UMI counts for each gene (features) in each cell (barcodes)., For 10X genomics: data processing pipeline Cell Ranger version 8.0.1 Data analysis for 10X genomics using Seurat version 5.2.2

source_name: Skeletal muscle

extract_protocol:
Approximately 10,000 cells were processed using the Chromium Next GEN Single Cell 3’Reagent Kits v3.1
RNA libraries were prepared using a chromium controller from10X Genomics, according to the manufacturer’s instructions.

value: Skeletal muscle

value: Pax7 progeny

value: Pax7CreERT2; Rosa26HTB::GFP

value: After five administrations of tamoxifen, muscle injury was induced, and the tissue was harvested on day 4.


title: RNA-seq-H9_D16


title: RAD51D tile 1 replicate #3 passage 2

description: Library name: t01_rep3_p2


title: SAHA_330_C4_E_R2

description:
Library name: Sample 140
raw cell lysate and Illumina NextSeq 2139

value: HepaRG

value: liver progenitor cells

value: SAHA

tag: plate

tag: index


title: 4 days post injury, Pax7 Progeny cells1 (2mo)

description:
Library name: Sample9-1/2
Each sample was sequenced across 2lanes of the flow cell.


title: RNA-seq-H9_D14


title: Postnatal Day7, Pax7-NICD-Cells2

description: Library name: Sample7-2/2

value: Pax7CreERT2; NICD

value: Tamoxifen was administered at P1–P3 (postnatal days 1 to 3)


title: RAD51D tile 1 replicate #2 passage 2

description: Library name: t01_rep2_p2


title: SAHA_326_C4_E_R1

description:
Library name: Sample 139
raw cell lysate and Illumina NextSeq 2138

value: vorinostat

value: E

value: GAACTGTAT

tag: group

tag: replicate

value: test


title: RNA-seq-H9

value: WT

value: control


title: RAD51D tile 1 replicate #1 passage 2

description: Library name: t01_rep1_p2


title: RAD51D tile 1 replicate #3 passage 0

description: Library name: t01_rep3_p0


title: SAHA_303_C3_E_R3

description:
Library name: Sample 138
raw cell lysate and Illumina NextSeq 2137

value: liver tumor associated with chronic hepatitis C

value: TCCTCAGCC

value: AGCCTACTT

tag: chemical type

tag: cas-nr


title: HiC mutant crispr

city: Mexico City

first: Mayra

last: Furlan-Magaril

state: Mexico City

address: Circuito exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

data_processing:
Hi-C experiments were processed following the HiC-Pro (v2.11.1) with default parameters. The alignment of the reads was performed with Bowtie2 v2.3.4.1 against the hg19 human genome. The normalized ICE matrices were generated with same number of valid pairs and computed at 20kb resolution.
Assembly: hg19
Supplementary files format and content: Tabular separated data with chromatin interactions counts

extract_protocol:
HiC in nuclei were performed with 2x106 cells. The cells were fixed with formaldehyde 2%. Chromatin was digested with DpnII enzyme and incubating overnight. The 5′ overhangs were filled with dCTP, dGTP, dTTP and Biotin-14-dATP and re-ligated in nuclei. DNA fragments were purified and sonicated in COVARIS S220. The DNA were selected using Ampure SPRI Beads to get 300-600bp fragments. The pull-down was performed with Dynabeads MyOne Streptavidine C1.
The libraries were marked with Illumina TrueSeq DNA Adapters and amplified using Taq Phusion NEB. The paired-end sequencing was performed in Illumina NovaSeq 6000.

tag: cell line

value: mutant


title: Postnatal Day7, Pax7-NICD-Cells1

description:
Library name: Sample7-1/2
Each sample was sequenced across 2lanes of the flow cell.

value: Skeletal muscle

value: Pax7 progeny

tag: genotype


title: Postnatal Day7, Pax7-tdTomato-Cells2

description: Library name: Sample6-2/2

tag: tissue

value: Pax7CreERT2; tdTomato


title: SAHA_330_C3_E_R2

description:
Library name: Sample 137
raw cell lysate and Illumina NextSeq 2136

value: HepaRG

tag: cell type

value: liver progenitor cells

value: GACCTTGCT

tag: batch nr_heparg


title: HiC control crispr


title: RAD51D tile 1 replicate #2 passage 0

description: Library name: t01_rep2_p0


title: Postnatal Day7, Pax7-tdTomato-Cells1

description:
Library name: Sample6-1/2
Each sample was sequenced across 2lanes of the flow cell.

tag: treatment

value: Tamoxifen was administered at P1–P3 (postnatal days 1 to 3)


title: SAHA_326_C3_E_R1

description:
Library name: Sample 136
raw cell lysate and Illumina NextSeq 2135

tag: chemical shortname

value: SAHA

value: vorinostat

value: GGGTTGTTA

value: GATGGTTGT


title: RAD51D tile 1 replicate #1 passage 0

description: Library name: t01_rep1_p0


title: Single cell sequencing of pooled 6dpf brains of Río Choy surface fish, replicate 4

city: Columbia

first: Wesley

middle: C

last: Warren

state: MO

address: 1201 Rollins St.

department: Bond Life Sciences Center

institute: University of Missouri

description: Library name: Surface_2

data_processing:
Align all reads to Amex3 and make gene counts matrix using CellRanger
Assembly: Amex3
Supplementary files format and content: Raw count matrices

organism: Astyanax mexicanus

source_name: whole brain

extract_protocol:
Pooled brains of ~100 6dpf fish
3’ single cell gene expression libraries (Next GEM v4) using the 10x Genomics Chromium system. The libraries were sequenced with ~400 million PE150 reads per sample on Illumina NovaSeq

value: whole brain

tag: age

tag: ecotype

value: Rio Choy


title: SAHA_303_C2_E_R3

description:
Library name: Sample 135
raw cell lysate and Illumina NextSeq 2134

value: liver tumor associated with chronic hepatitis C

tag: chemical longname

tag: dose

tag: well

value: E

value: TAGCTCTTC

value: GACGCGTTA

value: test


title: Single cell sequencing of pooled 6dpf brains of Río Choy surface fish, replicate 3

description: Library name: Surface_1


title: Rpl41 KO mouse kidney disome-seq replicate 3

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

country: Japan

institute: Nagoya University

description: Library name: Sample 74

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt. Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit. Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR. Multiple mappings were allowed. Metagene analysis was performed with custom Python script and with the use of Numpy (v1.17.3) and Pysam (v0.15.3). Reads of Ribo-seq and RNA-seq mapped to human coding transcripts were counted with the use of featureCounts (Subread package).
Assembly: hg38 / mm10
Supplementary files format and content: Excel file includes raw counts for each sample
Library strategy: Ribo-Seq

source_name: Kidney

growth_protocol: HEK293T cells were obtained from American Type Culture Collection and were checked for mycoplasma contamination with the use of MycoAlert (Lonza). The cells were cultured under an atmosphere of 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Life Technologies) and antibiotics.

extract_protocol:
Extract protocol for RNA-seq Total RNA was extracted from cell lysates with the use of a PureLink RNA Mini Kit (Thermo Fisher Scientific), and the quality of the purified RNA was assessed with a 2100 Bioanalyzer (Agilent). Extract protocol for Ribo-seq, Disome-seq, and harringtonine run-off assay For the harringtonine run-off assay, cells were treated with 2 μg/ml harringtonine (MedChemExpress) at 37 °C for 60, 120, or 180 s, followed by treatment with 100 μg/ml cycloheximide for 1 minute to halt translation. Cells were then immediately harvested. Cell and tissue lysate supernatants were assayed for RNA concentration with a Qubit RNA BR Assay Kit (Thermo Fisher Scientific), incubated with RNase I (20 U per 10 μg of RNA, Epicentre) for 45 min at 25°C, and placed on ice before the addition of SUPERase•In RNase inhibitor (Invitrogen) to a concentration of 20 U/ml. The samples were then loaded on a 1 M sucrose cushion (containing 20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, SUPERase•In (10 U/ml), 1 mM dithiothreitol, and cycloheximide (100 μg/ml)), and the gradients were centrifuged at 100,000 rpm (417,200 × g) for 1 h at 4°C in a Beckman TLA110 rotor. Ribosome footprints were purified using ISOGEN (Fujifilm). The recovered RNA was size-selected by electrophoresis on a 15% polyacrylamide TBE–urea gel (SuperSep RNA, Fujifilm), isolating fragments of 17–34 nucleotides for Ribo-seq and 50–80 nucleotides for Disome-seq. Extract protocol for SLAM-seq To label newly synthesized RNA, cells were incubated for 24 h in culture medium containing 50 μM 4-thiouridine (4sU, Merck). The medium was then replaced with fresh medium containing 50 μM uridine, and cells were harvested at 0, 3, 6, 12, and 24 h after the switch. Total RNA was extracted using ISOGEN (NIPPON GENE) according to the manufacturer’s instructions.
Library construction protocol for RNA-seq For RNA-seq, after mRNA selection via the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs), and the libraries were sequenced with a NovaSeq (Illumina). Library construction protocol for Ribo-seq, Disome-seq, and harringtonine run-off assay The footprint fragments were treated with T4 polynucleotide kinase (New England Biolabs) to repair the 2'-3' cyclic phosphates, a DNA linker including barcode sequences (NI-810 to NI-817) was ligated with the use of T4 RNA ligase 2, truncated K227Q (New England Biolabs), and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. Ribosomal RNAs were further depleted with the use of RiboZero Gold (Illumina). Reverse transcription (RT) was performed with the NI-802 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The purified cDNAs were circularized with circLigase II (Lucigen), and index sequences were then added by amplification with the polymerase chain reaction (PCR) as performed with the common primer (NI-798) and primers including index sequences (NI-799 and NI-822 to NI-826). Products of the desired size were purified on a 15% polyacrylamide nondenaturing gel (SuperSep DNA, Fujifilm), and the libraries were sequenced with a NovaSeq 6000 system (Illumina). Library construction protocol for SLAM-seq The purified RNA was alkylated by adding iodoacetamide (IAA) to a final concentration of 10 mM, followed by incubation at 50 °C for 15 min. The reaction was quenched by adding DTT to a final concentration of 20 mM. RNA was then purified, and libraries were prepared using the QuantSeq 3' mRNA-Seq V2 Library Prep Kit (Forward) with Unique Dual Indices (12 nt) (Lexogen). Sequencing was performed on a NovaSeq platform (Illumina).

value: Kidney


title: Perturb-seq in SB28 cells treated with vehicle/selumetinib/RMC-4550, 10x lane 4

city: San Francsico

first: Sixuan

last: Pan

state: California

institute: UCSF

description:
Library name: sample-4
10x Genomics

data_processing:
Perturb dataset: Cell Ranger (v6.1.2) was used to align reads to mm10, count UMIs, and assign sgRNAs, while deMULTIplex2 was used to demultiplex MULTI-seq sample hashes. Seurat SCTransform v2 normalization and QC filtering retained only cells with correct dual-sgRNA capture and adequate knockdown. Differential expression was performed with DElegate (DESeq2 pseudoreplicates), followed by fgsea-based pathway analysis. Perturbation signatures were visualized using LDA and UMAP, and interaction modeling between gene perturbations and drug treatment was performed using Theil-Sen regression and random forest-based feature importance.  Xeno dataset: FASTQs were processed with PIPseeker for alignment to a combined human–mouse reference, droplet calling, and UMI matrix generation. Human tumor cells were identified by >85% human read mapping. Subsequent analyses were performed in Seurat using QC filtering, SCTransform v2 normalization, and Scanorama integration. Cell states were assigned with Neftel et al. signatures, and differential gene expression and GSEA were performed to characterize drug-specific transcriptional programs.
Assembly: Perturb dataset: mm10  Xeno dataset: GRCh38
Supplementary files format and content: Feature Barcode Market Exchange Matrices

extract_protocol:
Perturb datasest: SB28 glioma cells expressing dCas9-KRAB were transduced with a dual-sgRNA CRISPRi library, FACS-sorted, treated with MEK inhibitor, SHP2 inhibitor, or vehicle for five days, then collected by trypsinization. Single-cell suspensions were labeled using MULTI-seq lipid barcodes through sequential incubation with anchor, barcode, and co-anchor oligos, washed in BSA-PBS, pooled, and loaded onto the 10x Chromium Controller for droplet partitioning.  Xeno dataset: Tumors from GBM43 intracranial xenografts were surgically harvested after in vivo drug treatment, mechanically minced, and enzymatically dissociated using the Papain Dissociation System to generate a single-cell suspension. The dissociated cells were filtered through a 70-µm strainer, centrifuged, washed in PBS, and prepared on ice for downstream PIPseq single-cell RNA-sequencing.
Perturb dataset: Dual-sgRNA constructs were cloned with direct-capture tags and used to generate the CRISPRi perturbation pool. Single-cell 3′ transcriptome and sgRNA-capture libraries were constructed using the 10x Genomics Chromium Next GEM Single Cell 3′ v3.1 kit with Feature Barcoding. MULTI-seq barcode libraries were amplified separately from cDNA supernatant after the SPRI cleanup step. All libraries were sequenced on an Illumina NovaSeq X.  Xeno dataset: Single-cell suspensions were processed using the Fluent BioSciences PIPseq T20 3′ Single Cell RNA Kit (v3.0), following the manufacturer’s workflow for barcoding, reverse transcription, amplification, and library preparation. Completed libraries were sequenced on an Illumina NovaSeq X to generate paired-end FASTQ files for downstream processing.

treatment_protocol: Vehicle (DMSO), selumetinib (MEK inhibitor), or RMC-4550 (SHP2 inhibitor)

value: glioblastoma


title: Rpl41 KO mouse kidney disome-seq replicate 2

description: Library name: Sample 73


title: SAHA_330_C2_E_R2

description:
Library name: Sample 134
raw cell lysate and Illumina NextSeq 2133

value: HepaRG

tag: dose group

tag: plate

tag: index

value: AATTCGGAA


title: Single cell sequencing of pooled 6dpf brains of Pachón cavefish, replicate 4

description: Library name: Cave_2

value: Pachon cave


title: Rpl41 KO mouse kidney disome-seq replicate 1

description: Library name: Sample 72


title: SAHA_326_C2_E_R1

description:
Library name: Sample 133
raw cell lysate and Illumina NextSeq 2132

value: liver progenitor cells

value: CTAATGCAC

tag: group

tag: replicate

tag: chemical type


title: Perturb-seq in SB28 cells treated with vehicle/selumetinib/RMC-4550, 10x lane 3

description:
Library name: sample-3
10x Genomics

tag: cell line


title: Single cell sequencing of pooled 6dpf brains of Pachón cavefish, replicate 3

description: Library name: Cave_1

tag: tissue


title: Perturb-seq in SB28 cells treated with vehicle/selumetinib/RMC-4550, 10x lane 2

description:
Library name: sample-2
10x Genomics

tag: cell type


title: Single cell sequencing of pooled 6dpf brains of Río Choy surface fish, replicate 2

description: Library name: SF2


title: SAHA_303_C1_E_R3

description:
Library name: Sample 132
raw cell lysate and Illumina NextSeq 2131

value: SAHA

value: vorinostat

value: GACTTCATT

tag: cas-nr

tag: batch nr_heparg


title: WT mouse kidney disome-seq replicate 3

description: Library name: Sample 71


title: Perturb-seq in SB28 cells treated with vehicle/selumetinib/RMC-4550, 10x lane 1

description:
Library name: sample-1
10x Genomics


title: WT mouse kidney disome-seq replicate 2

description: Library name: Sample 70


title: SAHA_330_C1_E_R2

description:
Library name: Sample 131
raw cell lysate and Illumina NextSeq 2130

tag: chemical shortname


title: Single cell sequencing of pooled 6dpf brains of Río Choy surface fish, replicate 1

description: Library name: SF1

value: whole brain

tag: age


title: FE-5594-5-START

city: New York

first: Ezequiel

middle: Carlos

last: Dantas

state: Y

address: 550E First Street

institute: NYU Langone

data_processing:
Read alignments were done using Galaxy (https://usegalaxy.org/), where paired-end FASTQ files were processed with Cutadapt for adapter removal.
Reads were mapped using STAR (2-pass mapping) with the GENCODE v43 basic annotation was performed on genome assembly GRCh38 (hg38).
Counts were obtained with featureCounts, and quality control was performed with FastQC and MultiQC
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Fixated Whole Blood

extract_protocol:
Total RNA was extracted from fixed whole blood using Qiagen PAXgene Blood RNA Kit following the manufacturer’s instructions (Qiagen, Hilden, Germany). RNA quality control was performed using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit for Illumina.Enriched RNAs were fragmented for 15 minutes at 94 °C. First-strand and second-strand cDNA were subsequently synthesized and fragments were end-repaired and adenylated at 3’ends.  Universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR.

value: Fixated Whole Blood

tag: timepoint

value: START

tag: randomization

value: Before randomization

tag: diet group

value: Starch


title: WT mouse kidney disome-seq replicate 1

description: Library name: Sample 69


title: SAHA_326_C1_E_R1

description:
Library name: Sample 130
raw cell lysate and Illumina NextSeq 2129

value: liver tumor associated with chronic hepatitis C

tag: chemical longname

tag: dose

tag: well

value: E


title: Single cell sequencing of pooled 6dpf brains of Pachón cavefish, replicate 2

description: Library name: CF2

tag: ecotype


title: FE-5594-5-POS

value: POS

value: Post randomization


title: Rpl41 KO mouse kidney RNA-seq replicate 3

description: Library name: Sample 68

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt. Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit. Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR. Multiple mappings were allowed. Metagene analysis was performed with custom Python script and with the use of Numpy (v1.17.3) and Pysam (v0.15.3). Reads of Ribo-seq and RNA-seq mapped to human coding transcripts were counted with the use of featureCounts (Subread package).
Assembly: hg38 / mm10
Supplementary files format and content: Excel file includes raw counts for each sample

value: Kidney


title: VPA_303_C5_H_R3

description:
Library name: Sample 129
raw cell lysate and Illumina NextSeq 2128

value: HepaRG

value: VPA

tag: dose group

tag: plate

value: H

tag: index

value: ATTCGAATC

value: TAAGTTACG

tag: group

value: test


title: FE-4900-4-START

tag: tissue


title: Rpl41 KO mouse kidney RNA-seq replicate 2

description: Library name: Sample 67

tag: cell line


title: Single cell sequencing of pooled 6dpf brains of Pachón cavefish, replicate 1

description: Library name: CF1

value: Pachon cave


title: VPA_330_C5_H_R2

description:
Library name: Sample 128
raw cell lysate and Illumina NextSeq 2127

tag: cell type

value: liver progenitor cells

value: ACCTGAGGC

value: AATAGGTGC

tag: replicate

tag: chemical type

tag: cas-nr


title: FE-4900-4-POS

value: Fixated Whole Blood

tag: timepoint