title: iMK2-KO+MK2 + IL-1α

city: Hannover

first: Sarah

middle: Maria

last: Herr

address: Carl-Neuberg-Str. 1

institute: Medizinische Hochschule Hannover

description: Library name: N4668

data_processing:
Raw data processing and quality control: Raw data processing was conducted by use of nfcore/rnaseq (version 3.9) which is a bioinformatics best-practice analysis pipeline used for RNA sequencing data at the National Genomics Infrastructure at SciLifeLab Stockholm, Sweden. The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. The genome reference and annotation data were taken from GENCODE.org (Mus musculus; GRCm38). Normalization and differential expression analysis: Normalization and differential expression analysis was performed on the internal Galaxy (version 20.05) instance of the RCU Genomics, Hannover Medical School, Germany with DESeq2 (Galaxy Tool Version 2.11.40.6) with default settings except for “Output normalized counts table”, which was set to “Yes” and all additional filters were disabled (“Turn off outliers replacement”, “Turn off outliers filtering”, and “Turn off independent filtering” set “Yes”).
Assembly: The genome reference and annotation data were taken from GENCODE.org (Mus musculus; GRCm38).
Supplementary files format and content: tab-delimited text file includes DESeq2 normalized counts for each sample

source_name: macrophages

growth_protocol: Immortalized MK2-KO (iMK2-KO) macrophages were maintained in DMEM supplemented with 10% fetal bovine serum and penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen)
Library generation, quality control, and quantification: 500ng (N4665-N4668) and 400ng  (N4669-N4680) of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs). All steps were performed as recommended in user manualE7760 (Version 1.0_02-2017; NEB) except that all reactions were downscaled to 2/3 of initial volumes. cDNA libraries were barcoded by dual indexing approach, using ‘NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs’ (6440S; New England Biolabs). All generated cDNA libraries were amplified with 7 cycles of final pcr. One additional purification step was introduced at the end of the standard procedure, using 1.2x ‘Agencourt® AMPure® XP Beads’ (#A63881; Beckman Coulter, Inc.). Fragment length distribution of individual libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).  Library denaturation and Sequencing run: Equal molar amounts of individually barcoded libraries were pooled for a common sequencing run in which each analyzed library constituted around 6.3% of overall flowcell / run capacity. The library pool was denatured with NaOH and was finally diluted to 1.8pM according to the Denature and Dilute Libraries Guide (Document # 15048776 v02; Illumina). 1.3ml of the denatured pool was loaded on an Illumina NextSeq 550 sequencer using a High Output Flowcell (400M cluster) for single reads (20024906; Illumina). Sequencing was performed with the following settings: Sequence reads 1 and 2 with 38 bases each; Index reads 1 and 2 with 8 bases each.  BCL to FASTQ conversion: BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).

treatment_protocol: cells were left untreated or treated with recombinant murine IL-1α (5ng/ml, 1h, Peprotech)

value: macrophages

value: wt

value: IL-1α (5 ng/ml, 1h)


title: sci-RNA-seq3_Arabidopsis_Day0_to_Day4_Biological_Replicate_1_Technical_Replicate_2

status: Public on Apr 02 2026

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description:
Library name: Arabidopsis_Day0_to_Day4_Biological_Replicate_1_Technical_Replicate_2
sci-RNA-seq3

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed as described in https://github.com/JunyueC/sci-RNA-seq3_pipeline
Assembly: Arabidopsis TAIR10
Supplementary files format and content: Seurat object

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown on vermiculite under well-watered conditions for 29 days, before being subject to drought stress

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter.
Library construction was performed following the sci-RNA-seq3 workflow

tag: tissue

value: leaf

tag: age

value: mature rosttes


title: iMK2-KO+MK2 untreated

country: Germany

description: Library name: N4667

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: genotype

tag: treatment

value: untreated


title: lymphocytes_gp_rep1

city: Freiburg

first: Thomas

last: Boehm

address: Stuebeweg 51

department: Developmental Immunology

description: Library name: 4L

data_processing:
Adapters were trimmed using cutadapt v4.9
Trimmed reads were aligned to the primary GRCm39 assembly from Ensembl using STAR 2.7.11b
Gene annotations were fetched from Ensembl (version 112)
Annotations of repeat elements were generated using RepeatMasker v4.1.5
RepeatMasker output was further processed and concatenated with the Ensembl GTF
Mapped reads were counted using featureCounts (subread 2.0.6, -p --countReadPairs -B -O -M –fraction)
Assembly: GRCm39 (primary assembly)
Supplementary files format and content: Tab-delimited text file containing raw counts for all samples

molecule: polyA RNA

source_name: spleen

extract_protocol:
Total RNA was extracted from splenic lymphocytes (CD4+, CD8+, CD19+) of MHCI.GP+ and MHCI.GP- mice with TRI reagent (Sigma-Aldrich).
Libraries were prepared using the Illumina Stranded mRNA Prep Kit (Ligation). Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.

value: spleen

value: CD4+CD8+CD19+ lymphocytes


title: iMK2-KO+GFP + IL-1α

description: Library name: N4666

value: MK2 knockout


title: WT_ECT_5

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.7.8a was used to align the reads to the GRCh38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in GRCh38 version 108
Assembly: GRCh38 version 108
Supplementary files format and content: Tab-delimited gene counts

organism: Homo sapiens

source_name: Engineered conncetive tissue

extract_protocol:
Total RNA isolation using the NucleoSpin RNA kit (Macheray-Nagel)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Engineered conncetive tissue

tag: cell line

value: iPSC-cardiac fibroblasts

value: WT


title: iMK2-KO+GFP untreated

description: Library name: N4665


title: WT_ECT_6


title: lymphocytes_wt_rep3

institute: Max Planck Institute for Immunobiology and Epigenetics

description: Library name: 7L


title: WT_ECT_4


title: lymphocytes_wt_rep2

description: Library name: 2L


title: LZTR1-KO_ECT_3


title: High IRES,Cap GMP Replicate 1

city: Boston

first: Lai Ping

last: Wong

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

description:
Mouse 1443
RNASeq_count.txt

data_processing:
RNASeq sequencing reads were mapped to reference genome mm10 with ENSEMBL annotation using STAR version 2.5.4a
RNASeq read counts for individual genes were produced using the unstranded count feature in HTSeq 0.9.1
Raw sequencing  data of CRISPRi are pre-processed by using MAGeCK to obtain the read counts for each sgRNA
Assembly: mm10
Supplementary files format and content: genes based raw counts of RNA-sequencing reads
Supplementary files format and content: CRISPRi raw sequencing  data are pre-processed by using MAGeCK to obtain the read counts for each sgRNA

source_name: Bone marrow

extract_protocol:
For RNA-Seq, full-length cDNA was prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing  (Takara Bio USA, Inc.)
For CRISPRi, genomic DNA was isolated using NucleoSpin Blood Maxi kit (Macherey-Nagel, 740950).
RNA-Seq libraries prepared using the Nextera XT DNA library preparation kit (Illumina)
CRISPRi sgRNA target regions were PCR amplified  with Illumina adaptors and indexes using Ultra II Q5 (NEB Biolabs, M0544X) and products were purified  with DNA Clean & Concentrator-100 (Zymo Research, D4030). sgRNA target regions (260-280bp) were further enriched by gel extraction (Qiagen, 28704) after running agarose gel
Smart-seq v4

value: Bone marrow

value: GMP

value: Translator


title: Mid IRES,Cap GMP Replicate 3

description:
Mouse 1447
RNASeq_count.txt


title: LZTR1-KO_ECT_2


title: High IRES,Cap Replicate 3

description:
G
CRISPRi_count.txt

library_source: other

data_processing:
RNASeq sequencing reads were mapped to reference genome mm10 with ENSEMBL annotation using STAR version 2.5.4a
RNASeq read counts for individual genes were produced using the unstranded count feature in HTSeq 0.9.1
Raw sequencing  data of CRISPRi are pre-processed by using MAGeCK to obtain the read counts for each sgRNA
Assembly: mm10
Supplementary files format and content: genes based raw counts of RNA-sequencing reads
Supplementary files format and content: CRISPRi raw sequencing  data are pre-processed by using MAGeCK to obtain the read counts for each sgRNA
Library strategy: CRISPR screen

molecule: other

organism: synthetic construct

value: myelogenous leukemia


title: lymphocytes_wt_rep1

description: Library name: 1L


title: Mid IRES,Cap GMP Replicate 2

description:
Mouse 1446
RNASeq_count.txt


title: High IRES,Cap Replicate 2

description:
G
CRISPRi_count.txt


title: tumor, PE150, 12.0_weeks, Sample_ID 29915

city: Stanford

first: Haiqing

last: Xu

address: 327 Campus Drive

department: Biology

institute: Stanford University

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29915

library_source: genomic

data_processing:
Paired-end reads were processed with regular expressions to identify the gRNA and clonal barcodes. When identifying guide sequences, we strictly required a perfect match with the designed sequences.
For the same gRNA, when we encountered low-frequency clonal barcodes within a 1-hamming distance of high-frequency clonal barcodes, we attributed them to sequencing or PCR errors. These low-frequency barcodes were merged with barcodes of higher frequencies
After extracting barcode and gRNA information, we converted the read counts associated with clonal tumors into absolute neoplastic cell numbers. This conversion was accomplished by normalizing the reads of the clonal tumor to the number of reads of the "spike-in" benchmark cell lines added to each sample prior to lung lysis and DNA extraction
Assembly: GRCm39
Supplementary files format and content: Immunoediting_tumor.txt: This file contains processed Tuba-seq data for tumor sample. It includes information on mouse genotype, sex, ID, vector type.sample weight, tumor growth duration, tumor gRNA, tumor clonal barcodes, and tumor size.
Supplementary files format and content: Plasmid_summary.txt: This file contains processed plasmid library information for all three vector type. It includes read count read each gRNA.

molecule: genomic DNA

source_name: Lung

extract_protocol:
Lung lobes were harvested from mice and weighed. Then, each lung was placed into 10mL of digestion buffer containing 100 mM NaCl, 20 mM Tris, 10 mM EDTA, 0.5% SDS, and 100uL of 20mg/mL Proteinase K as previously described. 5x10^5 cells from each of the three benchmark cell lines was added to each sample. Tissue was cut into small pieces and incubated at 55ºC overnight. Once tissue was digested the next day, DNA was extracted from 5mL of each digested sample by phenol-chloroform extraction.
Q5 Hot Start High-Fidelity 2x Master Mix (New England Biolabs, M0494X) was used to amply the barcode-gRNA region. 32ug of gDNA was used as template, split over 8 reactions with a final volume of 100uL each

value: Lung

value: KTC


title: LZTR1-KO_ECT_1


title: Mid IRES,Cap GMP Replicate 1

description:
Mouse 1443
RNASeq_count.txt


title: WT_ECT_3


title: tumor, PE150, 12.0_weeks, Sample_ID 29898

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29898


title: Low IRES,Cap GMP Replicate 2

description:
Mouse 1446
RNASeq_count.txt


title: WT_ECT_2


title: Mid IRES,Cap Replicate 1

description:
M
CRISPRi_count.txt


title: Mid IRES,Cap Replicate 2

description:
M
CRISPRi_count.txt


title: Low IRES,Cap GMP Replicate 1

description:
Mouse 1443
RNASeq_count.txt


title: Mid IRES,Cap Replicate 3

description:
M
CRISPRi_count.txt


title: Low IRES,Cap Replicate 3

description:
R
CRISPRi_count.txt


title: IL-21_treated_reCTLs_2

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: WT1-specific regenerated CD8+ T cells derived from induced pluripotent stem cells (iPSCs) were stimulated with WT1 peptide-pulsed lymphoblastoid cell line (LCL) in the presence of human IL-21 for 7 days.

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Regenerated CD8+ T cells derived from induced pluripotent stem cells (iPSCs)

extract_protocol:
Total RNA was extracted from cells with TRIzol reagent.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: human IL-21


title: tumor, PE150, 12.0_weeks, Sample_ID 29912

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29912


title: Low IRES,Cap GMP Replicate 3

description:
Mouse 1447
RNASeq_count.txt


title: High IRES,Cap SLAM-LKS Replicate 2

description:
Mouse 1446
RNASeq_count.txt

value: SLAM-LKS


title: tumor, PE150, 12.0_weeks, Sample_ID 29837

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29837


title: IL-21_treated_reCTLs_3

value: Regenerated CD8+ T cells derived from induced pluripotent stem cells (iPSCs)


title: IL-21_treated_reCTLs_1


title: High IRES,Cap Replicate 1

description:
G
CRISPRi_count.txt


title: tumor, PE150, 12.0_weeks, Sample_ID 29839

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29839


title: tumor, PE150, 12.0_weeks, Sample_ID 29836

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29836


title: Low IRES,Cap Replicate 2

description:
R
CRISPRi_count.txt


title: Low IRES,Cap Replicate 1

description:
R
CRISPRi_count.txt


title: IL-15_treated_reCTLs_3

description: WT1-specific regenerated CD8+ T cells derived from induced pluripotent stem cells (iPSCs) were stimulated with WT1 peptide-pulsed lymphoblastoid cell line (LCL) in the presence of human IL-15 for 7 days.

value: human IL-15


title: tumor, PE150, 12.0_weeks, Sample_ID 29795

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29795


title: tumor, PE150, 12.0_weeks, Sample_ID 29833

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29833


title: High IRES,Cap SLAM-LKS Replicate 3

description:
Mouse 1447
RNASeq_count.txt


title: Human, adipose-derived precursor cells, input

city: Philadelphia

first: Ryan

middle: Patrick

last: Calhoun

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

description: Library name: human_input

data_processing:
Trim_galore was first applied to the raw fastq files with default parameters.
Data was mapped to the hg38 or mm39 genome using bowtie2 allowing for a maximum of 1 mismatch in alignment.
Using samtools, unmapped reads were dropped and converted to a bam file. This was sorted, duplicate reads removed, reads that were not uniquely mapped removed, and the file was indexed
Bigwig file was generated using bamCoverage from deeptools with default settings.
Assembly: hg38, mm39
Supplementary files format and content: bigWig

source_name: adipose

growth_protocol: DMEM:F12 medium supplemented 10% FBS

extract_protocol:
Sonicated input sample (10% of total chromatin) was saved and subjected to crosslink reversing and column purification. Sonicated chromatin samples were incubated overnight at 4°C with CUX1 antibody in 1 ml ChIP buffer (50 mM HEPES pH 7.8, 140 mM NaCl, 1% Triton X-100, 0.1% Na-Deoxycholate and Complete protease inhibitor). IP was washed and then eluted by incubation at 65°C overnight in 50 μl ChIP elution buffer (50 mM Tris pH 7.5, 10 mM EDTA, 1% SDS) with 10 mM DTT. Beads were pelleted and the supernatant was transferred to a new tube. DNA was subsequently isolated by columns (NucleoSpin, Takara).
For ChIP-seq, ∼10 ng of ChIP DNA was prepared for sequencing according to the amplification protocol from Illumina.  ChIP-Seq libraries were prepared from formaldehyde-crosslinked hMSCs, using approximately 2–8 million cells per condition, depending on the abundance of the factor of interest.

treatment_protocol: Cells were treated with adipogenic differentiation cocktail

value: adipose

value: adipose-derived precursor cells

value: Pooled Wild Type and CUX1 Knockout

value: differentiaion cocktail


title: IL-15_treated_reCTLs_1


title: Mid IRES,Cap SLAM-LKS Replicate 2

description:
Mouse 1446
RNASeq_count.txt


title: Human, adipose-derived precursor cells, CUX1 Knockout

description: Library name: human_CUX1_KO

value: CUX1 Knockout


title: tumor, PE150, 12.0_weeks, Sample_ID 29791

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29791


title: Mid IRES,Cap SLAM-LKS Replicate 3

description:
Mouse 1447
RNASeq_count.txt


title: Human, adipose-derived precursor cells, CUX1 Control

description: Library name: human_CUX1_Ctrl

value: Wild Type


title: Low IRES,Cap SLAM-LKS Replicate 3

description:
Mouse 1447
RNASeq_count.txt


title: HNF4A (PGKP2HNF14)

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Adapter sequences and low quality reads were trimmed using Trim Galore (version 0.4.2) with "-q 20 --length 20".
Reads were then aligned to hg38 genome using bowtie2 (version 2.3.3.1) with "--end-to-end --sensitive".
Low-quality alignments were removed using samtools.
Gene expression was counted using htseq-count with "-s no -m union -t exon".
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include gene expression count values for each sample

source_name: lung

growth_protocol: According to ATCC

extract_protocol:
Trizol and Rneasy MinElute Cleanup Kit
Libraries were made with the Illumina Stranded mRNA protocol.

treatment_protocol: H2122 cells were infected with either control (PGK) lentivirus or human HNF4A8 lentivirus to create HNF4A8 overexpressing H2122 cells.

value: lung

value: H2122 cells

value: cancer cell line

value: lentiviral infection


title: tumor, PE150, 12.0_weeks, Sample_ID 29790

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29790


title: IL-2_treated_reCTLs_2

description: WT1-specific regenerated CD8+ T cells derived from induced pluripotent stem cells (iPSCs) were stimulated with WT1 peptide-pulsed lymphoblastoid cell line (LCL) in the presence of human IL-2 for 7 days.

value: human IL-2


title: tumor, PE150, 12.0_weeks, Sample_ID 29785

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29785

value: Lung


title: Mid IRES,Cap SLAM-LKS Replicate 1

description:
Mouse 1443
RNASeq_count.txt

value: Bone marrow

value: Translator


title: HNF4A (PGKP2HNF12)


title: tumor, PE150, 12.0_weeks, Sample_ID 29558

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29558

value: KTC


title: Low IRES,Cap SLAM-LKS Replicate 2

description:
Mouse 1446
RNASeq_count.txt

value: SLAM-LKS


title: IL-2_treated_reCTLs_1

value: Regenerated CD8+ T cells derived from induced pluripotent stem cells (iPSCs)


title: Small cell lung cancer, patient12

city: Guangzhou

first: Xiaodong

last: Ma

state: Guangdong

address: No.55, West of ZhongShan Avenue, Tianhe District

country: China

institute: Department of Brain Science and Rehabilitation Medicine

description: 10X Visium

data_processing:
Sequencing output and the histology images were processed using space ranger software (10X Genomics). The space ranger mkfastq function was used for sample demultiplexing and to converting spatial barcodes and reads into FASTQ format.
The space ranger count function was used to align reads from FATSQ files to human genome (hg38) and then align microscopic slide image and transcriptome to generate barcode/UMI counts, feature spot matrices, cluster data, and perform gene expression analysis.
Assembly: Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes;features.tsv.gz: list of gene IDs;matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format;scalefactors_json.json: scalefactors in json format;tissue_lowres_image.png: low-res image of tissue;tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

extract_protocol:
Tissues were frozen in liquid nitrogen-chilled isopentane within5 minutes of devascularization.10-µm cryosections were mounted onto the ST arrays (10X Visium) where reverse transcription of cellular transcripts took place in situ after tissue permeabilization.
10X Visium

tag: disease

value: small cell lung cancer

value: No treatment


title: IL-2_treated_reCTLs_3


title: tumor, PE150, 12.0_weeks, Sample_ID 29538

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29538

value: KT


title: HNF4A (PGKP2HNF11)


title: Control (PGK3)

value: Control


title: tumor, PE150, 12.0_weeks, Sample_ID 29535

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29535


title: Low IRES,Cap SLAM-LKS Replicate 1

description:
Mouse 1443
RNASeq_count.txt


title: NGP cells, H2AK119ub1 (CUT&RUN)

city: Kita-adachi-gun

first: Shunpei

last: Satoh

state: Saitama

address: Komuro 818, Ina

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

description: Library name: NGP_H2AK119ub1

data_processing:
Short reads were trimmed by fastp 0.23.4.
We generated BAM files, following the data processing described in this tutorial (https://yezhengstat.github.io/CUTTag_tutorial/), and quantified the coverage of short reads mapped to the proximal regions (± 2 kb) of the transcription start sites (TSS) using BAMscale 1.0.
Bigwig files were created using deepTools 3.5.4, subtracting the input sample from the CUT&RUN samples. We visualized the bigwig and bed files in hg19 using pyGenomeTracks 3.8.
Library-normalized histone modification counts were log-scaled and adjusted based on the input sample.
Bigwig files were created using deepTools 3.5.4, subtracting the input sample from the CUT&RUN samples.
We visualized the bigwig and bed files in hg19 using pyGenomeTracks 3.8.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: NGP

growth_protocol: NGP cells were cultured in RPMI-1640 (Fujifilm Wako, Japan) under humidified 5% CO2 conditions. The medium was supplemented with 10% inactivated fetal bovine serum (Thermo Fisher Scientific, Massachusetts, USA) and 100 units/mL of penicillin/streptomycin (Fujifilm Wako).

extract_protocol:
We followed manufacturer's protocol for CUT&RUN assay and column purification kits (Cell Signaling Technology, #86652 and #14209, Massachusetts, USA).
5 ng of the purified DNA fragments were tagged and amplified using the NEBNext Ultra DNA Library Prep Kit from Illumina (New England Biolabs).

value: NGP

value: Human Neuroblastoma

tag: antibody

value: H2AK119ub1 (CUT&RUN)


title: Control (PGK1)

value: lung

value: H2122 cells


title: Small cell lung cancer, patient4

description: 10X Visium


title: NGP cells, H3K4me3 (CUT&RUN)

description: Library name: NGP_H3K4me3

value: H3K4me3 (CUT&RUN)


title: tumor, PE150, 12.0_weeks, Sample_ID 29537

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29537


title: NGP cells, H3K27me3 (CUT&RUN)

description: Library name: NGP_H3K27me3

value: H3K27me3 (CUT&RUN)


title: Control (PGK2)

value: cancer cell line

value: lentiviral infection


title: NGP cells, Input (CUT&RUN)

description: Library name: NGP_Input

value: Input (CUT&RUN)


title: mESC_L2HGDH_Myxothiazol_IP_replicate 4

city: Chicago

first: Navdeep

middle: S.

last: Chandel

state: IL

address: 303 E. Superior Street

department: Department of Medicine & Biochemistry and Molecular Genetics

institute: Northwestern University

description: Library name: mESC_L2HGDH_Myxothiazol_IP_8

data_processing:
Read alignment was performed using STAR mapping to the GRCm38 mouse genome. m6A peaks consistent across three biological replicates were identified using the exomePeak package. Differential m6A RNA methylation analysis was also performed using the exomePeak package, and differential expression analysis of the RNA-seq data was performed using DESeq2.
Assembly: GRCm38
Supplementary files format and content: Processed data files are tab-delimited text (.txt) and spreadsheet (.xls) files containing condition-level m6A peak calls, differential m6A peak analysis tables, and DESeq2 all-genes differential expression results for untreated and Myxothiazol-treated mESC-EV and mESC-L2HGDH samples.
Library strategy: MeRIP-Seq

source_name: Mouse Embryonic Stem Cells

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in 2i media consisting of 0.5X Neurobasal media (Gibco, catalog no. 21103049), 0.5X DMEM/F12 (Gibco, catalog no. 11320033), 0.5X N-2 Supplement (Gibco, catalog no. 17502048), 0.5X B-27 Supplement (Gibco, catalog no. 17504-044), 0.05% Bovine Albumin Fraction V (Gibco, catalog no. 15260037), 1X Antibiotic-Antimycotic solution (Gibco, catalog no. 15240062),  2.5 µg mL-1 Plasmocin Prophylactic (InvivoGen, catalog no. ant-mpp), 1 μM PD0325901 (Reprocell, catalog no. 04-0006-02), 3 μM CHIR99021 (Reprocell, catalog no. 04-0004-02), 2 mM Glutamine (Gibco, catalog no. 25030081), 150 μM 1-Thioglycerol (Sigma-Aldrich, catalog no. M6145), 1000 U/mL Leukemia Inhibitory Factor (LIF) (Sigma-Aldrich, catalog no. ESG1106), 1 mM methyl pyruvate (Sigma-Aldrich, catalog no. 371173), and 400 µM uridine (Sigma-Aldrich, catalog no. U3003). Cells were incubated at 37 °C, 5% CO2, and 95% humidity.

extract_protocol:
RNA was extracted using Trizol and submitted to library building. m6A-IP samples were subjected to immunoprecipitation using an anti-m6A antibody prior to library building.
Libraries were built using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Mouse embryonic stem cells (mESCs) were treated with vehicle or 500 nM myxothiazol for 16 hours.

value: Mouse Embryonic Stem Cells

value: Wild-Type

value: Myxothiazol

tag: transfection


title: Small cell lung cancer, patient9

description: 10X Visium

value: Lung

value: small cell lung cancer


title: tumor, PE150, 12.0_weeks, Sample_ID 29484

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29484

value: KTC


title: tumor, PE150, 12.0_weeks, Sample_ID 29478

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29478


title: Small cell lung cancer, patient8

description: 10X Visium

value: No treatment


title: mESC_L2HGDH_Myxothiazol_IP_replicate 2

description: Library name: mESC_L2HGDH_Myxothiazol_IP_6


title: ATACseq_RPM_tumor_aPD1_ent_2

city: Baltimore

first: Linying

last: Zhu

state: Maryland

address: 20 Penn St

department: School of Medicine

institute: University of Maryland, Baltimore

description:
Library name: S11_296689
processed bigwig file

data_processing:
For RNA-seq, the raw FASTQ files were trimmed using timGalore (version 0.4.5,  https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and Trimmomatic (version 0.36). Surviving reads were aligned to the mm9 genome with the STAR aligner version 2.5.4a). using the UCSC mm9 gene annotation using the two-pass mode and “best recall at base and read level” settings as shown in Table S37 from. Gene expression raw read counts were quantified using TPMcalculator (version 0.0.3). “ExonReads” column. Differential expression analysis was performed using DESeq2 (version 1.22.2) in R (version 3.5.1).
Assembly: mm9
Supplementary files format and content: tsv. Three replications for each group.

growth_protocol: All animal studies were approved by the National Institutes of Health Institutional Animal Care and Use Committee. Breeder pairs of the Rb1 fl/fl;p53 fl/fl;Myc lsl/lsl T58A SCLC GEM were obtained from The Jackson Laboratory (Bar Harbor, ME). For initial evaluation, SCLC was induced in a cohort of 20 mice at 8 weeks of age by intratracheal instillation of 2.5 x 107 PFU of Ad5CGRP-Cre.

extract_protocol:
Flash-frozen tumor tissue was manually dissected with a scalpel blade and then fully homogenized using a TissueLyzer. After centrifugation, supernatant from the tissue lysates was transferred to an AllPrep DNA spin column (Qiagen) for DNA extraction. Flow-through from the column was transferred to a RNeasy spin column (Qiagen) for RNA purification.
Using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775) and  NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490)

treatment_protocol: Tumor bearing mice (confirmed by MRI) were randomized by volume into four experimental groups: vehicle (control), entinostat monotherapy (15 mg/kg daily for 28 days by oral gavage (PO)), anti–PD-1 antibody monotherapy (10 mg/kg of anti-PD-1 delivered by intraperitoneal injection (IP) twice weekly for four weeks), and combined entinostat and anti–PD-1 antibody treatment. 0.5% methylcellulose (entinostat vehicle) and isotype control (Rat IgG2a) antibody treatment groups served as controls.

value: RPM lung tumor

tag: batch


title: ATACseq_RPM_tumor_aPD1_ent_3

description:
Library name: S12_298090
processed bigwig file


title: mESC_L2HGDH_Myxothiazol_IP_replicate 3

description: Library name: mESC_L2HGDH_Myxothiazol_IP_7


title: tumor, PE150, 12.0_weeks, Sample_ID 29476

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29476


title: tumor, PE150, 12.0_weeks, Sample_ID 29479

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29479


title: Small cell lung cancer, patient3

description: 10X Visium


title: mESC_L2HGDH_Myxothiazol_IP_replicate 1

description: Library name: mESC_L2HGDH_Myxothiazol_IP_5


title: tumor, PE150, 12.0_weeks, Sample_ID 29480

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29480


title: SS, 4.0%Nacl diet, rat 4

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

description: Library name: WS4

data_processing:
Illumina adapters were trimmed with Trim_Galore!  and quality checked with MultiQC. The files were mapped to the rat genome (mRatBN7.2.112) with the program STAR(2.7.11b). The BAM files generated were then used to determine raw counts with featureCounts(v2.0.6) in the package subread. Finally, these count matrixes were used in the R package DESeq2 (v1.44) and the entire dataset was used to generate gene normalized counts.
Assembly: mRatBN7.2.112
Supplementary files format and content: excel file, Deseq2 normalize counts

organism: Rattus norvegicus

source_name: kidney

extract_protocol:
Kidney microvascular RNA was extracted from dissected kidney microvessels with TRIzol (Invitrogen). Samples were treated with DNAase I to remove genomic DNA.
Libraries were prepared for sequencing using standard Illumina protocols, and poly A selection

value: kidney

value: microvasculature

value: 4.0% NaCl


title: SS, 4.0%Nacl diet, rat 5

description: Library name: WS5


title: ATACseq_RPM_tumor_aPD1_ent_1

description:
Library name: S10_295933
processed bigwig file

value: lung


title: IL-15_treated_reCTLs_2

description: WT1-specific regenerated CD8+ T cells derived from induced pluripotent stem cells (iPSCs) were stimulated with WT1 peptide-pulsed lymphoblastoid cell line (LCL) in the presence of human IL-15 for 7 days.

value: Regenerated CD8+ T cells derived from induced pluripotent stem cells (iPSCs)

value: human IL-15


title: SS, 4.0%Nacl diet, rat 3

description: Library name: WS3


title: tumor, PE150, 12.0_weeks, Sample_ID 29475

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29475


title: ATACseq_RPM_tumor_ent_3

description:
Library name: S9_295951
processed bigwig file


title: mESC_L2HGDH_Myxothiazol_Input_replicate 4

description: Library name: mESC_L2HGDH_Myxothiazol_Input_8


title: SS, 4.0%Nacl diet, rat 1

description: Library name: WS1


title: tumor, PE150, 12.0_weeks, Sample_ID 29470

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29470


title: ATACseq_RPM_tumor_ent_1

description:
Library name: S7_295936
processed bigwig file


title: mESC_L2HGDH_Myxothiazol_Input_replicate 1

description: Library name: mESC_L2HGDH_Myxothiazol_Input_5


title: mESC_L2HGDH_Myxothiazol_Input_replicate 3

description: Library name: mESC_L2HGDH_Myxothiazol_Input_7


title: ATACseq_RPM_tumor_aPD1_3

description:
Library name: S6_299534
processed bigwig file


title: ATACseq_RPM_tumor_aPD1_2

description:
Library name: S5_295948
processed bigwig file


title: mESC_L2HGDH_Myxothiazol_Input_replicate 2

description: Library name: mESC_L2HGDH_Myxothiazol_Input_6


title: SS, 0.3%Nacl diet, rat 4

description: Library name: W4

value: 0.3% NaCl


title: tumor, PE150, 12.0_weeks, Sample_ID 29467

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29467


title: SS, 4.0%Nacl diet, rat 2

description: Library name: WS2


title: mESC_EV_Myxothiazol_IP_replicate 2

description: Library name: mESC_EV_Myxothiazol_IP_6

value: EV


title: tumor, PE150, 12.0_weeks, Sample_ID 29463

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29463


title: tumor, PE150, 12.0_weeks, Sample_ID 29469

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29469


title: mESC_EV_Myxothiazol_IP_replicate 4

description: Library name: mESC_EV_Myxothiazol_IP_8


title: ATACseq_RPM_tumor_Ctrl_3

description:
Library name: S3_300334
processed bigwig file


title: tumor, PE150, 12.0_weeks, Sample_ID 29466

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29466


title: SS, 0.3%Nacl diet, rat 3

description: Library name: W3


title: SS, 0.3%Nacl diet, rat 5

description: Library name: W5


title: SS, 0.3%Nacl diet, rat 2

description: Library name: W2


title: mESC_EV_Myxothiazol_IP_replicate 3

description: Library name: mESC_EV_Myxothiazol_IP_7


title: tumor, PE150, 12.0_weeks, Sample_ID 29474

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29474


title: ATACseq_RPM_tumor_ent_2

description:
Library name: S8_295932
processed bigwig file


title: SS, 0.3%Nacl diet, rat 1

description: Library name: W1


title: mESC_EV_Myxothiazol_IP_replicate 1

description: Library name: mESC_EV_Myxothiazol_IP_5


title: tumor, PE150, 12.0_weeks, Sample_ID 29462

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29462


title: ATACseq_RPM_tumor_Ctrl_1

description:
Library name: S1_296701
processed bigwig file


title: SS Ccl2-/-, 4.0%Nacl diet, rat 5

description: Library name: CS5


title: ATACseq_RPM_tumor_aPD1_1

description:
Library name: S4_295947
processed bigwig file


title: mESC_EV_Myxothiazol_Input_replicate 4

description: Library name: mESC_EV_Myxothiazol_Input_8


title: SS Ccl2-/-, 4.0%Nacl diet, rat 4

description: Library name: CS4


title: tumor, PE150, 12.0_weeks, Sample_ID 29458

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_29458


title: ATACseq_RPM_tumor_Ctrl_2

description:
Library name: S2_299538
processed bigwig file


title: RNAseq_RPM_tumor_aPD1_ent_3

description:
Library name: S12_298090
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 12_298090_S12

tag: tissue type


title: mESC_EV_Myxothiazol_Input_replicate 3

description: Library name: mESC_EV_Myxothiazol_Input_7


title: tumor, PE150, 12.0_weeks, Sample_ID 28878

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_28878

value: KT


title: SS Ccl2-/-, 4.0%Nacl diet, rat 1

description: Library name: CS1


title: tumor, PE150, 12.0_weeks, Sample_ID 28858

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_28858


title: SS Ccl2-/-, 4.0%Nacl diet, rat 3

description: Library name: CS3


title: RNAseq_RPM_tumor_aPD1_ent_2

description:
Library name: S11_296689
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 11_296689_S11


title: Sample N3

city: Shanghai

first: Peng

last: Zhou

address: 389 Nanjing Xi Rd

institute: Parkway Gleneagles Medical and Surgical Center

description: Library name: Sample N3

data_processing:
The Cell Ranger software pipeline (version 8.0.1) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: GRCm39-2024-A
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: ocular cup (eyeball without cornea and lens)

extract_protocol:
The femur or cranium tissues of Ctsk-Cre; Nfatc1-Dre; LGRT neonatal mice were dissected and cut into pieces. Then, fibrous callus was digested in 1 ml pre-warmed digestion solution (3 mg/ml collagenase I (Sigma, USA) in αMEM) for 45 min in a water bath at 37 ℃ with gentle agitation every 10 min. Then, the mixture of digested minced bones and target cells were treated with red blood cell lysate on ice for 3 min. The cells were then isolated using Fluorescence Activated Cell Sorting (FACS) , sorting the femur and cranium into ZsGreen+ tdTomato-, ZsGreen- tdTomato+, and ZsGreen+ tdTomato+ cells, which were ultimately analyzed using scRNA-seq.
cDNA was purified using DynaBeads® MyOne™ Silane Beads (Life Technologies, 37002D). The concentration of cDNA samples was quantified using the Qubit dsDNA Assay Kit (Life Technologies, Q328520), and high-sensitivity DNA analysis was performed using the Agilent High Sensitivity DNA Kit (Agilent, 5067-4626). DNA fragments were selected and purified using the SPRIselect Reagent Kit (Life Technologies, B23318), ultimately obtaining high-quality single-cell gene expression data.

value: contracted ciliary muscle

value: saline drops


title: tumor, PE150, 12.0_weeks, Sample_ID 28875

description: Library name: _tumor_PE150_12.0_weeks_Sample_ID_28875


title: RNAseq_RPM_tumor_ent_2

description:
Library name: S8_295932
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 8_295932_S8

value: ent


title: mESC_EV_Myxothiazol_Input_replicate 2

description: Library name: mESC_EV_Myxothiazol_Input_6

value: Mouse Embryonic Stem Cells

value: Wild-Type

value: Myxothiazol


title: RNAseq_RPM_tumor_ent_3

description:
Library name: S9_295951
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 9_295951_S9


title: SS Ccl2-/-, 0.3%Nacl diet, rat 5

description: Library name: C5


title: SS Ccl2-/-, 4.0%Nacl diet, rat 2

description: Library name: CS2


title: mESC_EV_Myxothiazol_Input_replicate 1

description: Library name: mESC_EV_Myxothiazol_Input_5


title: RNAseq_RPM_tumor_aPD1_ent_1

description:
Library name: S10_295933
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 10_295933_S10


title: mESC_L2HGDH_IP_replicate 4

description: Library name: mESC_L2HGDH_IP_8

value: Untreated


title: SS Ccl2-/-, 0.3%Nacl diet, rat 3

description: Library name: C3


title: mESC_L2HGDH_IP_replicate 3

description: Library name: mESC_L2HGDH_IP_7


title: mESC_L2HGDH_IP_replicate 2

description: Library name: mESC_L2HGDH_IP_6


title: Sample N2

description: Library name: Sample N2

value: ocular cup (eyeball without cornea and lens)


title: RNAseq_RPM_tumor_aPD1_3

description:
Library name: S6_299534
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 6_299534_S6

value: RPM lung tumor


title: SS Ccl2-/-, 0.3%Nacl diet, rat 4

description: Library name: C4

value: kidney

value: microvasculature


title: mESC_L2HGDH_IP_replicate 1

description: Library name: mESC_L2HGDH_IP_5


title: Sample M3

description: Library name: Sample M3

value: relaxed ciliary muscle

value: tropicamide eye drops


title: Sample N1

description: Library name: Sample N1


title: SS Ccl2-/-, 0.3%Nacl diet, rat 2

description: Library name: C2


title: RNAseq_RPM_tumor_aPD1_2

description:
Library name: S5_295948
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 5_295948_S1

value: lung


title: RNAseq_RPM_tumor_ent_1

description:
Library name: S7_295936
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 7_295936_S7


title: SS Ccl2-/-, 0.3%Nacl diet, rat 1

description: Library name: C1

value: 0.3% NaCl


title: RNAseq_RPM_tumor_aPD1_1

description:
Library name: S4_295947
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 4_295947_S5


title: mESC_L2HGDH_Input_replicate 3

description: Library name: mESC_L2HGDH_Input_7


title: Sample M1

description: Library name: Sample M1


title: SK-Mel-103,NC siRNA, CX-4945, replicate 2

city: Suzhou

first: Gongjie

last: Wu

address: Renai Road

institute: Xi'an Jiaotong-Liverpool University

description: Library name: M9-NC-CX-2

data_processing:
Sequencing reads were trimmed and aligned to the human reference genome (GRCh38/hg38); low-quality, duplicate and mitochondrial reads were removed, and peaks of accessible chromatin were called using standard ATAC-seq pipelines.
Assembly: GRCh38/hg38
Supplementary files format and content: Bigwig

source_name: Skin

growth_protocol: HeLa S3 and other melanoma cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, High glucose, Biosharp) supplemented with 10% fetal bovine serum (VivaCell), Penicillin-Streptomycin 100 X solution (Hyclone) in a standard incubator with 5% CO2 at 37°C. Cells were passaged every two to three days by Trypsin-EDTA solution (Sigma-Aldrich) after washing with 1 x PBS.

extract_protocol:
ATAC-seq was performed by Active Motif (Shanghai, China) on HeLa S3 wild-type and 1E7 cells, as well as SK-Mel-103 cells with or without CX 4945 treatment.  Cells were trypsinized, resuspended in freezing medium (FBS:growth medium:DMSO = 5:4:1), frozen at a controlled cooling rate and shipped on dry ice.
Library preparation and sequencing were carried out by Active Motif using their standard Tn5-based ATAC-seq protocol and Illumina sequencing.

treatment_protocol: Cells were transfected with DEK-targeting or non-targeting control siRNAs using Lipofectamine 3000 (Thermo Fisher Scientific) according to the manufacturer’s instructions. When cells reached approximately 80% confluency, 40 µM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

value: Skin

value: Melanoma

value: WT

value: NC siRNA knockdown, CX-4945


title: RNAseq_RPM_tumor_Ctrl_3

description:
Library name: S3_300334
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 3_300334_S4

value: Ctrl


title: mESC_L2HGDH_Input_replicate 4

description: Library name: mESC_L2HGDH_Input_8

value: Mouse Embryonic Stem Cells


title: mESC_L2HGDH_Input_replicate 2

description: Library name: mESC_L2HGDH_Input_6

value: Wild-Type


title: Sample M2

description: Library name: Sample M2


title: Batf3_3

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 151-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Spleen

value: Spleen

value: OT-I  T cells

value: Transduction with Batf3-encoding retrovirus


title: High IRES,Cap SLAM-LKS Replicate 1

description:
Mouse 1443
RNASeq_count.txt

value: Bone marrow

value: SLAM-LKS

value: Translator


title: RNAseq_RPM_tumor_Ctrl_2

description:
Library name: S2_299538
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 2_299538_S3

value: RPM lung tumor


title: Batf3_2


title: mESC_L2HGDH_Input_replicate 1

description: Library name: mESC_L2HGDH_Input_5

value: Untreated


title: Batf2_3

value: Transduction with Batf2-encoding retrovirus


title: SK-Mel-103,NC siRNA, DMSO, replicate 1

description: Library name: M9-NC-DM-1

value: NC siRNA knockdown, DMSO


title: mESC_EV_IP_replicate 3

description: Library name: mESC_EV_IP_7

value: EV


title: SK-Mel-103,NC siRNA, CX-4945, replicate 1

description: Library name: M9-NC-CX-1

value: Skin

value: Melanoma


title: RNAseq_RPM_S6_tumor

description:
Library name: 6_mouseID_275075_S6
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 6_mouseID_275075_S6

growth_protocol: All animal studies were approved by the National Institutes of Health Institutional Animal Care and Use Committee. Breeder pairs of the Rb1 fl/fl;p53 fl/fl;Myc lsl/lsl T58A SCLC GEM were obtained from The Jackson Laboratory (Bar Harbor, ME). For initial evaluation, SCLC was induced in a cohort of 20 mice at 8 weeks of age by intratracheal instillation of 2.5 x 10^7 PFU of Ad5CGRP-Cre.

value: lung


title: Batf3_1


title: SK-Mel-103,DEK siRNA, DMSO, replicate 2

description: Library name: M9-DEK-DM-2

value: WT

value: DEK siRNA knockdown, DMSO


title: RNAseq_RPM_S5_tumor

description:
Library name: 5_mouseID_275074_S5
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 5_mouseID_275074_S5


title: SK-Mel-103,NC siRNA, DMSO, replicate 2

description: Library name: M9-NC-DM-2


title: mESC_EV_IP_replicate 2

description: Library name: mESC_EV_IP_6

value: Mouse Embryonic Stem Cells

value: Wild-Type


title: Batf2_2

value: Spleen

value: OT-I  T cells


title: mESC_EV_IP_replicate 1

description: Library name: mESC_EV_IP_5


title: RNAseq_RPM_tumor_Ctrl_1

description:
Library name: S1_296701
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 1_296701_S2

value: Ctrl


title: RNAseq_RPM_S2_control

description:
Library name: 2_mouseID_273899_S2
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 2_mouseID_273899_S2

value: normal lung tissue


title: mESC_EV_Input_replicate 2

description: Library name: mESC_EV_Input_6


title: Batf2_1


title: 1E7, ATAC-seq, replicate 2

description: Library name: 1E7-ATAC-2

source_name: Cervix

value: Cervix

value: HeLa S3

value: Cervical carcinoma cell line

value: DEK knockout


title: SK-Mel-103,DEK siRNA, DMSO, replicate 1

description: Library name: M9-DEK-DM-1


title: SK-Mel-103,DEK siRNA, CX-4945, replicate 2

description: Library name: M9-DEK-CX-2

value: DEK siRNA knockdown, CX-4945


title: mESC_EV_Input_replicate 3

description: Library name: mESC_EV_Input_7

value: Untreated

value: EV


title: Batf_2

value: Transduction with Batf-encoding retrovirus


title: RNAseq_RPM_S1_control

description:
Library name: 1_mouseID_273898_S1
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 1_mouseID_273898_S1

value: lung


title: RNAseq_RPM_S4_tumor

description:
Library name: 4_mouseID_275073_S4
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 4_mouseID_275073_S4

value: RPM lung tumor


title: RNAseq_RPM_S3_tumor

description:
Library name: 3_mouseID_275069_S3
Column name in Mouse_Azam.TPMcalculator.raw_counts.tsv: 3_mouseID_275069_S3


title: mESC_EV_Input_replicate 1

description: Library name: mESC_EV_Input_5


title: SK-Mel-103,DEK siRNA, CX-4945, replicate 1

description: Library name: M9-DEK-CX-1

value: Skin

value: Melanoma

value: WT


title: mESC_L2HGDH_Myxothiazol_rep2_ATAC

description: Library name: mESC_L2HGDH_Myxothiazol_rep2_ATAC

data_processing:
Paired-end ATAC-seq reads were aligned to the mouse reference genome using Bowtie2 with the --very-sensitive-local option. Mapped bam files were converted to bed files using BEDTools. For the four ATACseq samples, 12 million reads from mESC-EV+Myxothiazol (rep 1), 13 million from mESC-EV+Myxothiazol (rep 2), 12 million from mESC-L2HGDH+Myxothiazol (rep 1), 11 million from mESC-L2HGDH+Myxothiazol (rep 2) were used as input for seqMINER. The reads normalization assumes that the samples have similar aggregated intensity around all gene TSS.
Assembly: GRCm38/mm10
Supplementary files format and content: Processed data are provided as bigWig files containing genome-wide normalized Tn5 fold-change signal tracks for each sample after removal of mitochondrial reads.
Supplementary files format and content: Processed data are also provided as bigWig files containing genome-wide normalized Tn5 p-value signal tracks for each sample after removal of mitochondrial reads.

extract_protocol:
Approximately 50,000 cells were pelleted by centrifugation, washed with PBS, and nuclei were isolated using a cold lysis buffer.
We performed the transposition reaction using the Illumina Tagment DNA Enzyme and Buffer Large Kit (Illumina, catalog no. 20034198) and purification steps with the MinElute PCR Purification Kit (Qiagen, catalog no. 28004). We then performed the PCR amplification step using the KAPA HiFi HotStart Ready Mix master mix (KAPA, catalog no. KR0370). To remove small fragments, we performed size selection using KAPA pure beads: 40 µL of KAPA beads were added to 50 µL of the PCR solution. We ran 2 µL of the library on TapeStation to verify the nucleosome footprints and confirm a successful assay.

treatment_protocol: Mouse embryonic stem cells (mESCs) were treated with 500 nM myxothiazol for 16 hours.

value: Mouse Embryonic Stem Cells

value: Wild-Type

value: Myxothiazol


title: Batf_3

value: Spleen

value: OT-I  T cells


title: 1E7, ATAC-seq, replicate 1

description: Library name: 1E7-ATAC-1

value: Cervix

value: HeLa S3


title: mESC_L2HGDH_Myxothiazol_rep1_ATAC

description: Library name: mESC_L2HGDH_Myxothiazol_rep1_ATAC


title: Batf_1


title: Mouse, adipose-derived precursor cells, Cux1 Knockout

description: Library name: mouse_Cux1_KO

value: adipose

value: adipose-derived precursor cells

value: CUX1 Knockout

value: differentiaion cocktail


title: Mouse, adipose-derived precursor cells, input

description: Library name: mouse_input

value: Pooled Wild Type and CUX1 Knockout


title: mESC_EV_Myxothiazol_rep2_ATAC

description: Library name: mESC_EV_Myxothiazol_rep2_ATAC

value: EV


title: Mock_3

value: Transduction with empty retrovirus


title: Mock_2


title: Mouse, adipose-derived precursor cells, Cux1 Control

description: Library name: mouse_Cux1_Ctr1

value: Wild Type


title: Mock_1


title: mESC_EV_Myxothiazol_rep1_ATAC

description: Library name: mESC_EV_Myxothiazol_rep1_ATAC


title: HelaS3, ATAC-seq, replicate 2

description: Library name: HelaS3-ATAC-2

value: Cervical carcinoma cell line


title: HelaS3, ATAC-seq, replicate 1

description: Library name: HelaS3-ATAC-1

value: WT


title: D56MaleD

status: Public on Apr 01 2026

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Reads were trimmed using cutadapt v4.1
Reads were quantified using Salmon v1.9.0
Differential expression analysis was performed within R using DEseq2 v1.40.2 using log2 fold change shrinkage and p value optimisation using ashr.
Assembly: Dmel 6.48
Supplementary files format and content: Transcript-level expression estimates

organism: Drosophila melanogaster

source_name: Excretory tract (Malpighian tubules, hindgut and rectal ampulla)

extract_protocol:
The excretory tract (Malpighian tubules, hindgut and rectal ampulla) was dissected from ice-cold-anaesthetised flies by pulling their intestine from the rectal pad on an RNA stabilisation solution (RNAlater, xxx). The intestine was cut above the insertion of the Malpighian tubules, and the dissected tissue was transferred into 1.5 mL tubes on dry ice (15 samples per tube).
RNA quality and concentration was assessed using the Agilent 2100 Bioanalyser RNA 6000 Nano assay. Starting with 200ng Total RNA, polyA enrichment was performed using NEBNext Poly(A) mRNA Magnetic Isolation module, and NGS RNAseq libraries generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to manufacturer’s instructions. Library quality was assessed using the Agilent 2100 Bioanalyser High-Sensitivity DNA assay
For each sample, a minimum of 20 million Paired End 60bp reads (dual 8bp indexing) were generated on an Illumina NextSeq 2000

tag: dissection date


title: D56MaleE

value: Excretory tract (Malpighian tubules, hindgut and rectal ampulla)


title: D56MaleF


title: D56MaleB


title: D56MaleC


title: D56MaleA


title: D28MaleF


title: D28MaleD


title: Rat kidney ethylene glycol 2 day

type: RNA

city: Tokyo

first: Toshihiko

last: Aki

address: 1-5-45 Yushima, Bunkyo-ku

institute: Institute of Science Tokyo

description: RNA expression value

hyb_protocol: Hybridization was performed according to the manufacturer's instruction.

data_processing:
TAC(Transcriptome analysis console)  software was used without filtering.
#%result_name=Analysis_EG
#%array_type=Clariom_S_Rat
#%annotation=Clariom_S_Rat.r1.na36.rn6.a1.transcript.csv

label: biotin

label_protocol: Labeling was performed according to the manufacturer's instruction.

extract_protocol: RNA was isolated from rat kidney with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: 8 g/kg ethlene glycol was injected orally to rat. Samples were extarcted 2 or 5 days after the treatment.

tag: Sex

value: male


title: Rat kidney control

description: RNA expression value

scan_protocol: Hybridization was performed according to the manufacturer's instruction.


title: D28MaleA


title: D28MaleC


title: D28MaleB


title: Rat kidney ethylene glycol 5 day

description: RNA expression value


title: D28MaleE


title: D7MaleA


title: D7MaleC


title: D7MaleB


title: D7MaleE


title: BV-2 Cells after OGD/R

city: harbin

first: Qian

last: Su

address: youzheng

institute: The First Affiliated Hospital of Harbin Medical University

hyb_protocol: •Cy3 and Cy5 labelled RNAs were  combined together and hybridized to Arraystar Mouse Small RNA Arrays in Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
IP (Cy5-labelled) and Sup (Cy3-labelled) intensities were normalized by the RNA spike-in calibration controls.Multiple probes from the same small RNA (miRNA/pre-miRNA/tsRNA) were combined into RNA level for further data analysis.Normalized IP intensities represent the "m6A abundance" of small RNA comparable across samples.The “m6A quantity” was calculated for the m6A modification amount of each transcript based on the IP (Cy5-labelled) normalized intensities.    m6A quantity=  〖IP〗_(Cy5 normalized intensity)    The m6A quantity is based on the normalized intensities of IP signals (raw signals of Cy5-labelled IP RNA are normalized with the average log2-scaled Spike-in RNA intensities.)    〖IP〗_(Cy5 normalized intensity)=log2(〖IP〗_(Cy5 raw) )-Average[log2(〖IP〗_(spike-in_Cy5 raw) )]    Meanwhile, the percentage of m6A modification (%Modified) for a transcript was calculated based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities.  %Modified=  (modified RNA)/(Total RNA)  =  IP/(IP+Sup)  =  〖IP〗_(Cy5 normalized intensity)/(〖IP〗_(Cy5 normalized intensity)+〖Sup〗_(Cy3 normalized intensity) )    〖IP〗_(Cy5 normalized intensity)=log2(〖IP〗_(Cy5 raw) )-Average[log2(〖IP〗_(spike-in_Cy5 raw) )]  〖Sup〗_(Cy3 normalized intensity)=log2(〖Sup〗_(Cy3 raw) )-Average[log2(〖Sup〗_(spike-in_Cy3 raw) )]
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. Differentially m6A-modified RNAs between two comparison groups were identified by fold change (FC) and statistical significance (p-value) thresholds.

source_name: IP

label_protocol: standard protocol

growth_protocol: BV-2 cells were maintained in alpha-minimum essential medium supplemented with Eagle’s salt, ribonucleosides, deoxyribonucleosides and L-glutamine (MEM; Corning, NY, USA), 10% foetal bovine serum (FBS; HyClone, LA, USA), 1% sodium pyruvate (SP; 100 mmol; Gibco, CA, USA) and 1% penicillin/streptomycin (PS; 100 IU/ml penicillin and 100 µg/ml streptomycin).

extract_protocol: •The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. "IP" and "Sup" RNAs were enzymatically labelled with Cy5 and Cy3 respectively.

treatment_protocol: The cells were cultured in an incubator with 5% CO2 at 37 °C. OGD was induced as described previously. Briefly, the original culture medium was removed and replaced with glucose/serum-free DMEM. Then, the plates were incubated without oxygen in an anaerobic chamber in an atmosphere containing 5% CO2 and 95% N2 for 2 h at 37 °C. OGD was then terminated and reperfusion initiated by returning the cells to normoxic conditions with regular medium.

value: microglia

source_name: Sup


title: BV-2 Cells


title: CTC_PBS-3

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

description: Library name: CTC_PBS-3

data_processing:
Trimmomatic for quality and adapter trimming, aligned to reference genome with STAR 2.7.11a
Assembly: hg38
Supplementary files format and content: raw counts in text format

source_name: Placenta

growth_protocol: CTCs were cultured in a specialized DMEM/Ham's F12 medium containing penicillin, streptomycin, bovine serum albumin, heat-inactivated fetal bovine serum (HI-FBS), and ITS-X, along with CHIR99021, A83-01, SB431542, L-ascorbic acid, valproic acid (VPA), Y27632, and epidermal growth factor to support their proliferation and maintenance. Primary DECs were cultured in Dulbecco's Modified Eagle Medium (DMEM) and Ham's F12 nutrient medium (1:1), supplemented with antibiotics (amphotericin B, penicillin, and streptomycin), 10% HI-FBS. These cells were used up to the 20th passage to ensure experimental consistency. All cultures were maintained in a standard incubator at 37°C with 5% CO₂ and 95% humidity, using the method of isolation mentioned in the previous publications

extract_protocol:
RNA was isolated using the Qiagen's RNeasy kit according to the manufacturer’s instructions
NEBNext Ultra Express RNA preparation kit

treatment_protocol: Decidual cells (DEC) and chorion trophoblast cells (CTC) were cultured under identical conditions and treated with ultrapure LPS (100ng/mL) to induce inflammation, while matched cultures receiving PBS served as vehicle controls.

value: Placenta

value: Chorion trophoblast cells

value: Vehicle


title: DEC_PBS-1

description: Library name: DEC_PBS-1

value: Decidual cells


title: CTC_LPS-3

description: Library name: CTC_LPS-3

value: LPS


title: CTC_LPS-1

description: Library name: CTC_LPS-1


title: DEC_PBS-3

description: Library name: DEC_PBS-3


title: D7MaleF


title: CTC_PBS-2

description: Library name: CTC_PBS-2


title: CTC_PBS-1

description: Library name: CTC_PBS-1


title: DEC_PBS-2

description: Library name: DEC_PBS-2


title: DEC_LPS-2

description: Library name: DEC_LPS-2


title: D7MaleD


title: CTC_LPS-2

description: Library name: CTC_LPS-2


title: DEC_LPS-1

description: Library name: DEC_LPS-1


title: DEC_LPS-3

description: Library name: DEC_LPS-3


title: △gacA 2

first: Chenjie

last: Yu

state: Jiangsu

address: Xiyuan road 279

institute: Suzhou Polytechnic Institute of Agriculture

description: Library name: Sample5

data_processing:
The low-quality reads were removed and the clean reads were mapped to the reference genome of P. protegens Pf-5. The differential expressed genes (DEGs) between two samples were analysed using the DESeq2 with a threshold of |log2(Fold Change)| >1 and FDR < 0.05. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was applied to investigate the role of DEGs.
Assembly: GCA_000012265.1
Supplementary files format and content: CSV files including raw counts for each sample
Supplementary files format and content: CSV files including TPM for each sample

organism: Pseudomonas protegens

extract_protocol:
Total RNAs of Pf-5 and ΔgacA was extracted by the RNA isolation kit (Vazyme, R403-01).
RNA-seq library was constructed by using  ribosome-depleted, strand-specific library preparation methods.

value: gacA knockout


title: △gacA 3

description: Library name: Sample6


title: △gacA 1

description: Library name: Sample4


title: Pf-5 2

description: Library name: Sample2


title: Pf-5 3

description: Library name: Sample3


title: Pf-5 1

description: Library name: Sample1


title: Full-length mouse GZF1

type: protein

city: rehovot

first: irina

last: miodownik

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Microarray was self-hybridized on IDT duplex buffer on a temperature gradient

scan_protocol: GenePix 4400A array scanner. Multiple scans at different intensities were performed and the optimal per protein was selected for further analysis.

data_processing: For each probe area, the median of pixels was calculated. Then, the data was spatially detrended according to the local background.

molecule: protein

source_name: E coli

extract_protocol: Purified from E. coli or obtained commercially

tag: tag

value: FLAG-tagged protein


title: APP23het_late_M2_roi1

city: Heidelberg

first: Julius

last: Michel

address: Im Neueunheimer Feld 280

department: Neuroimmunology and brain tumor immunology

description: Raw data files include tab-separated values files containing x-y-z location for each transcript (txt format) and staining images of DAPI and PFTAA stained section (tiff format).Processed data include transcript assignment tables (*_results_assigned.txt), containing individual RNA molecules with spatial coordinates and their assignment to segmented cells, cell-by-gene count matrices (*_segmentation_counts.txt), providing the number of detected transcripts per gene for each segmented cell, and cell metadata tables (*_segmentation_cell_stats.csv), containing per-cell information such as cell ID, spatial location (centroid), area, and quality control metrics.

hyb_protocol: Resolve Biosciences’ Molecular Cartography platform for labeling, hybridization, and imaging with 99-plex combinatorial single molecule fluorescence in-situ hybridization

data_processing: The detection of cell boundaries was performed with QuPath v0.3.2. Gene expression counts were computed per cell and extracted using Resolve Bioscience plugin in the ImageJ2 toolkit.

source_name: cerebral cortex

extract_protocol: Mouse brain or human brain was dissected and right or left hemisphere immersed in Tissue-Tek® (Sakura) on dry ice bath and stored at -80.  The frozen brains were sectioned into 7 μm coronal slices on a cryostat at -20°C.

value: cerebral cortex

value: APP23 heterozygous

tag: braak stage

tag: apoe genotype

tag: caa stage according to thal


title: Full-length human CREB1

description: Obtained commercially (Origene, cat# TP760318)

value: GST-tagged protein


title: APP23wt_early_M2_roi1

scan_protocol: Resolve Biosciences’ Molecular Cartography platform for labeling, hybridization, and imaging with 99-plex combinatorial single molecule fluorescence in-situ hybridization

tag: tissue

value: APP23 wildtype


title: APP23wt_late_M2_roi1

label_protocol: Resolve Biosciences’ Molecular Cartography platform for labeling, hybridization, and imaging with 99-plex combinatorial single molecule fluorescence in-situ hybridization

tag: age


title: APP23het_late_M1_roi3

value: female


title: APP23het_late_M2_roi2


title: APP23wt_late_M1_roi1


title: APP23wt_early_M1_roi2


title: APP23wt_late_M1_roi2


title: APP23wt_early_M2_roi2


title: APP23wt_early_M1_roi1


title: APP23wt_late_M2_roi2


title: APP23het_late_M1_roi2


title: Full-length human ATF1

description: Obtained commercially (Prospec, cat# PKA-019)

value: HIS-tagged protein


title: APP23wt_early_M2_roi3


title: APP23het_early_M2_roi3


title: APP23wt_early_M1_roi3


title: APP23het_late_M1_roi1


title: APP23het_early_M1_roi3


title: APP23het_early_M2_roi1


title: APP23het_early_M2_roi2


title: APP23het_early_M1_roi1


title: Full-length human ETS1


title: Full-length human MITF

description: Obtained commercially (Origene, cat# TP761396)


title: SE50/110 ΔtreY, acarbose fermentation, 72 hr, rep 2

first: Feifei

last: Cai

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

description:
Library name: S72_6
Column name in raw_counts.txt: S72_6_count

data_processing:
Raw sequencing reads were filtered using fastp [2,3] with the following criteria: 1.Adapter sequences derived from sequencing primers were removed from the reads; 2. Bases at the 3′ end of reads with a quality score Q < 20 were trimmed; 3. Reads with a remaining length of < 25 bp after trimming were discarded; 4. Ribosomal RNA reads from the target species were removed.
Bowtie2 was utilized for genome mapping
Aligned fragments within each gene locus were quantified using StringTie software, followed by normalization with the trimmed mean of M values (TMM) method. Gene expression levels FPKM  were calculated using the edgeR software.
Assembly: GCA_900119315.1
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample

organism: Actinoplanes

source_name: Actinoplanes sp. SE50/110

growth_protocol: The acarbose fermentation medium contains 5% maltose, 3% glucose, 1% soya flour, 0.3% glutamate, 0.3% yeast (Angel Yeast Co., Ltd), 0.1% K2HPO4·3H2O, 0.05% FeCl3, and 0.25% CaCO3, pH 7.2. Actinoplanes sp. SE50/110 ΔtreY was cultured in 250 ml baffled flasks on rotary shaker at 30 ℃, 220 r.p.m

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing. One micrograms of RNA were used as input material for the RNA sample preparations.
RNA-seq strand-specific libraries were constructed using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit (Vazyme, China) according to the manufacturer’s instructions. Briefly, RNA was purified by magnetic beads after removal of rRNA. Then RNA was fragmented into small pieces using divalent cations for 8 min at 94°C. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. These cDNA fragments then go through the end repair process, addition of a single ‘A’ base, and ligation of the adapters. The products were purified and enriched by PCR to create the final cDNA library. Purified libraries were quantified and validated by Qubit® 3.0 Fluorometer and Agilent 2100 bioanalyzer to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot after the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 platform (Illumina, USA). The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).

tag: cell type

value: Actinoplanes sp. SE50/110

value: Acarbose fermentation medium


title: SE50/110 ΔtreY, acarbose fermentation, 72 hr, rep 3

description:
Library name: S72_8
Column name in raw_counts.txt: S72_8_count

tag: genotype


title: APP23het_early_M1_roi2


title: SE50/110 ΔtreY, acarbose fermentation, 72 hr, rep 1

description:
Library name: S72_3
Column name in raw_counts.txt: S72_3_count

tag: treatment


title: SE50/110 ΔtreY, acarbose fermentation, 64 hr, rep 2

description:
Library name: S64_6
Column name in raw_counts.txt: S64_6_count


title: SE50/110 ΔtreY, acarbose fermentation, 56 hr, rep 1

description:
Library name: S56_3
Column name in raw_counts.txt: S56_3_count


title: SE50/110 ΔtreY, acarbose fermentation, 64 hr, rep 1

description:
Library name: S64_3
Column name in raw_counts.txt: S64_3_count


title: SE50/110 ΔtreY, acarbose fermentation, 52 hr, rep 2

description:
Library name: S52_6
Column name in raw_counts.txt: S52_6_count


title: SE50/110 ΔtreY, acarbose fermentation, 48 hr, rep 1

description:
Library name: S48_3
Column name in raw_counts.txt: S48_3_count


title: SE50/110 ΔtreY, acarbose fermentation, 56 hr, rep 3

description:
Library name: S56_8
Column name in raw_counts.txt: S56_8_count


title: SE50/110 ΔtreY, acarbose fermentation, 56 hr, rep 2

description:
Library name: S56_6
Column name in raw_counts.txt: S56_6_count


title: SE50/110 ΔtreY, acarbose fermentation, 40 hr, rep 2

description:
Library name: S40_6
Column name in raw_counts.txt: S40_6_count


title: SE50/110 ΔtreY, acarbose fermentation, 40 hr, rep 3

description:
Library name: S40_8
Column name in raw_counts.txt: S40_8_count


title: SE50/110 ΔtreY, acarbose fermentation, 52 hr, rep 3

description:
Library name: S52_8
Column name in raw_counts.txt: S52_8_count


title: SE50/110 ΔtreY, acarbose fermentation, 52 hr, rep 1

description:
Library name: S52_3
Column name in raw_counts.txt: S52_3_count


title: SE50/110 ΔtreY, acarbose fermentation, 48 hr, rep 3

description:
Library name: S48_8
Column name in raw_counts.txt: S48_8_count


title: SE50/110 ΔtreY, acarbose fermentation, 40 hr, rep 1

description:
Library name: S40_3
Column name in raw_counts.txt: S40_3_count


title: SE50/110 ΔtreY, acarbose fermentation, 32 hr, rep 2

description:
Library name: S32_6
Column name in raw_counts.txt: S32_6_count


title: SE50/110 ΔtreY, acarbose fermentation, 24 hr, rep 3

description:
Library name: S24_8
Column name in raw_counts.txt: S24_8_count


title: SE50/110 ΔtreY, acarbose fermentation, 64 hr, rep 3

description:
Library name: S64_8
Column name in raw_counts.txt: S64_8_count


title: SE50/110 ΔtreY, acarbose fermentation, 32 hr, rep 1

description:
Library name: S32_3
Column name in raw_counts.txt: S32_3_count


title: SE50/110 ΔtreY, acarbose fermentation, 20 hr, rep 3

description:
Library name: S20_8
Column name in raw_counts.txt: S20_8_count


title: SE50/110 ΔtreY, acarbose fermentation, 20 hr, rep 1

description:
Library name: S20_3
Column name in raw_counts.txt: S20_3_count


title: SE50/110 ΔtreY, acarbose fermentation, 8 hr, rep 3

description:
Library name: S8_8
Column name in raw_counts.txt: S8_8_count


title: SE50/110 ΔtreY, acarbose fermentation, 20 hr, rep 2

description:
Library name: S20_6
Column name in raw_counts.txt: S20_6_count


title: SE50/110 ΔtreY, acarbose fermentation, 8 hr, rep 2

description:
Library name: S8_6
Column name in raw_counts.txt: S8_6_count


title: SE50/110 ΔtreY, acarbose fermentation, 24 hr, rep 1

description:
Library name: S24_3
Column name in raw_counts.txt: S24_3_count


title: SE50/110 ΔtreY, acarbose fermentation, 8 hr, rep 1

description:
Library name: S8_3
Column name in raw_counts.txt: S8_3_count


title: SE50/110 ΔtreY, acarbose fermentation, 16 hr, rep 2

description:
Library name: S16_6
Column name in raw_counts.txt: S16_6_count


title: SE50/110 ΔtreY, acarbose fermentation, 16 hr, rep 3

description:
Library name: S16_8
Column name in raw_counts.txt: S16_8_count


title: SE50/110 ΔtreY, acarbose fermentation, 24 hr, rep 2

description:
Library name: S24_6
Column name in raw_counts.txt: S24_6_count


title: 84K poplar, drought, 9 days, rep3

city: Heilongjiang

first: huijiao

last: li

address: No.26 Hexing Road, Xiangfang District

institute: Northeast Forestry University

description:
Library name: Sample 12
DT9

data_processing:
Quantification using Qubit 4.0, followed by sample pooling according to data ratio
Bridge PCR amplification on cBot to generate clusters
Sequencing on the NovaSeq X Plus platform.
Assembly: Populus_alba_x_Populus_glandulosa
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Populus alba x Populus glandulosa

source_name: leaf

extract_protocol:
Total RNA was extracted from tissue samples. The concentration and purity of the extracted RNA were detected using a Nanodrop 2000 spectrophotometer. A total of 1 ug of total RNA was used for the construction of sequencing libraries.
The products after adapter connection were purified and subjected to fragment size sorting. The sorted products were used for PCR amplification, and the final library was obtained after purification.

value: leaf

value: wild type

value: drought


title: 84K poplar, drought, 9 days, rep2

description:
Library name: Sample 11
DT9


title: SE50/110 ΔtreY, acarbose fermentation, 16 hr, rep 1

description:
Library name: S16_3
Column name in raw_counts.txt: S16_3_count


title: SE50/110 ΔtreY, acarbose fermentation, 48 hr, rep 2

description:
Library name: S48_6
Column name in raw_counts.txt: S48_6_count


title: 84K poplar, drought, 6 days, rep3

description:
Library name: Sample 9
DT6


title: 84K poplar, drought, 6 days, rep2

description:
Library name: Sample 8
DT6


title: Human SOX2 (37-118)


title: 84K poplar, drought, 3 days, rep2

description:
Library name: Sample 5
DT3


title: 84K poplar, drought, 3 days, rep3

description:
Library name: Sample 6
DT3


title: 84K poplar, drought, 0 days, rep1

description:
Library name: Sample 1
CK


title: 84K poplar, drought, 6 days, rep1

description:
Library name: Sample 7
DT6


title: 84K poplar, drought, 0 days, rep3

description:
Library name: Sample 3
CK


title: 84K poplar, drought, 9 days, rep1

description:
Library name: Sample 10
DT9


title: Jurkat-CCR5, CIMSS, Infected, rep 2

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

description: Library name: 11-CIMSS-Mock

data_processing:
Raw sequence data were processed using the nf-core RNA-Seq pipeline (version 3.18.0). Reads were aligned to the GRCh38 human reference genome using the STAR aligner and gene quantification was performed against the GENCODE v42 primary assembly annotation with RSEM to obtain gene expression counts.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file that includes counts/TPM for each gene and sample

growth_protocol: Jurkat-Tat-CCR5 (Jurkat-CCR5) cells were provided by Quentin Sattentau (Sir William Dunn School of Pathology, University of Oxford, Oxford, UK) and cultured in RPMI medium.

extract_protocol:
The cells were then lysed and RNA extracted using the RNeasy Plus Mini kit (Qiagen, #74134).
Isolated RNA was sent to Azenta Life Sciences (New Jersey, USA) for library preparation.

treatment_protocol: Jurkat-CCR5 cells were treated with 50 mM alkyl-CIMSS or 0.5% DMSO as a vehicle control before being either mock-infected or infected with HIV-1BaL for 8 hours.

tag: cell line

value: T lymphocyte

value: CIMSS-Infected


title: Jurkat-CCR5, CIMSS, Infected, rep 3

description: Library name: 12-CIMSS-Mock


title: 84K poplar, drought, 3 days, rep1

description:
Library name: Sample 4
DT3


title: Jurkat-CCR5, CIMSS, Mock, rep 3

description: Library name: 6-CIMSS-Mock

value: CIMSS-Mock


title: Jurkat-CCR5, DMSO, Mock, rep 3

description: Library name: 3-DMSO-Mock

value: DMSO-Mock


title: 84K poplar, drought, 0 days, rep2

description:
Library name: Sample 2
CK


title: KO_3_H3K4me3

city: New York

first: Jennifer

middle: C

last: Chan

state: New York

address: 1470 Madison Ave 9-201

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample 70
NEBNext Ultra II DNA Library Prep Kit for Illumina

data_processing:
Alignment using bowtie2 to the appropriate genome (mm10 or hg19)
Filtered using samtools (MAPQ>30)
Deduplicated using picard
Normalized for ecoli spike in
Bigwig files generated using deeptools bamCoverage and scaled based on ecoli spike in normalization factor
Supplementary files format and content: bigwig files
Library strategy: CUT&RUN

source_name: HeLa

extract_protocol:
Nuclei isolation using lysis buffer, 40um filtering, followed by overnight incubation with antibody indicated. Following Mnase cleavage in calcium buffer, reaction was stopped and DNA was purified using the Zymo ChIP DNA Clean and Concentrator Kit.
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: HeLa

tag: region

tag: group

tag: virus


title: KO_1_H3K4me3

description:
Library name: Sample 68
NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: antibody

tag: batch


title: KO_1_IgG

description:
Library name: Sample 67
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: IgG


title: Jurkat-CCR5, DMSO, Infected, rep 2

description: Library name: 9-DMSO-BaL

value: DMSO-Infected


title: Jurkat-CCR5, CIMSS, Infected, rep 1

description: Library name: 10-CIMSS-Mock


title: KO_3_H3K4me3Q5dop

description:
Library name: Sample 66
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: Jurkat-CCR5, CIMSS, Mock, rep 2

description: Library name: 5-CIMSS-Mock


title: Jurkat-CCR5, DMSO, Mock, rep 1

description: Library name: 1-DMSO-Mock


title: Jurkat-CCR5, DMSO, Infected, rep 1

description: Library name: 8-DMSO-BaL


title: Jurkat-CCR5, DMSO, Mock, rep 2

description: Library name: 2-DMSO-Mock


title: SE50/110 ΔtreY, acarbose fermentation, 32 hr, rep 3

description:
Library name: S32_8
Column name in raw_counts.txt: S32_8_count


title: KO_2_H3K4me3

description:
Library name: Sample 69
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: KO_2_H3K4me3Q5dop

description:
Library name: Sample 65
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: KO_1_H3K4me3Q5dop

description:
Library name: Sample 64
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: WT_3_H3K4me3

description:
Library name: Sample 63
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: WT


title: WT_1_H3K4me3

description:
Library name: Sample 61
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: WT_1_IgG

description:
Library name: Sample 60
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 461_IgG

description:
Library name: Sample 51
NEBNext Ultra II DNA Library Prep Kit for Illumina

source_name: Brain

value: Brain

value: subiculum

value: NP


title: 258_IgG

description:
Library name: Sample 49
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: WT_3_H3K4me3Q5dop

description:
Library name: Sample 59
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 461_H3K4me3Q5dop

description:
Library name: Sample 43
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 532_H3K4me3Q5dop

description:
Library name: Sample 46
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Parous


title: WT_2_H3K4me3Q5dop

description:
Library name: Sample 58
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 505_H3K4me3Q5dop

description:
Library name: Sample 45
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: WT_1_H3K4me3Q5dop

description:
Library name: Sample 57
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 616_IgG

description:
Library name: Sample 56
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 505_IgG

description:
Library name: Sample 53
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 560_H3K4me3Q5dop

description:
Library name: Sample 47
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 258_H3K4me3Q5dop

description:
Library name: Sample 41
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: WT_2_H3K4me3

description:
Library name: Sample 62
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 616_H3K4me3Q5dop

description:
Library name: Sample 48
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 560_IgG

description:
Library name: Sample 55
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 484_H3K4me3Q5dop

description:
Library name: Sample 44
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 442_H3K4me3Q5dop

description:
Library name: Sample 42
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 442_IgG

description:
Library name: Sample 50
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 484_IgG

description:
Library name: Sample 52
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: SLAMseq_KMS11_NSD2KO#12_Rep1

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

description: Library name: Sample 186

data_processing:
Raw sequencing reads (FASTQ files) were processed using the nf-core/slamseq pipeline (v1.0.0). Initial read quality was assessed with FastQC (v0.11.9). Adapters and low-quality sequences were trimmed using TrimGalore! (v0.6.4_dev). The core processing, including conversion-aware alignment, filtering, SNP masking, and quantification, was performed using Slamdunk (v0.4.3) with default parameters. Reads were aligned to the human genome reference (GRCh38), using gene and 3' UTR annotations derived from the UCSC Table Browser for GRCh38. Slamdunk was used to quantify reads at the gene level, specifically generating counts for total reads and counts for reads containing T>C conversions (indicative of newly synthesized RNA, defined in the analysis as reads with >2 T>C conversions). The submitted processed data files consist of these gene-level count matrices generated by Slamdunk.
Assembly: hg38
Supplementary files format and content: Each processed data file corresponds to a single experimental sample and is provided in comma-separated value (.csv) format. Within each file, rows represent individual transcripts identified by their RefSeq transcript ID. The columns contain transcript-level quantification and metric data generated by Slamdunk, including:
* readCount: Raw count of total reads mapping to the transcript.
* tcReadCount: Raw count of reads identified as containing T>C conversions (representing newly synthesized RNA, based on the pipeline's criteria, e.g., >2 T>C conversions per read).
* length: The length of the transcript.
* readsCPM: Reads Per Million mapped reads (calculated for total reads).
* conversionRate: The calculated T>C conversion rate for reads mapping to this transcript.
* Tcontent: The proportion of thymine bases within the transcript sequence.
* coverageOnTs: Coverage depth specifically over thymine bases.
* conversionsOnTs: Number of T>C conversions observed at thymine positions.
* multimapCount: Count related to multi-mapping reads assigned to the transcript.

growth_protocol: KMS-11 cells are cultured in RPMI-1640 supplemented with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
Cells were metabolically labeled with 100 µM 4-thiouridine (4sU) for 1 hour. Total RNA was extracted using TRIzol reagent followed by purification with the RNA Clean & Concentrator-5 kit (Zymo Research). 10 µg of RNA was then alkylated with iodoacetamide, followed by another cleanup using the RNA Clean & Concentrator-5 kit. 1 µg of the resulting RNA was used as input for library construction.
Sequencing libraries were prepared from 1 µg of alkylated total RNA using the QuantSeq 3’mRNA-Seq Library Prep FWD Kit for Illumina (Lexogen #015), following the manufacturer's protocol.

treatment_protocol: NSD2dTAG KMS-11 cells were treated with dTAGV-1 (100 nM) to induce NSD2 degradation. For specific experiments, NSD2-depleted cells were subsequently treated either with doxycycline (100 ng/ml) for reconstitution studies, or with the PRC2 inhibitors EPZ-6438 (200 nM) or MAK-658 (50 nM), or a DMSO vehicle control. The specific duration of each treatment varied according to the experimental condition and is indicated in the metadata associated with each sample.

value: NSD2 KO

value: No


title: SLAMseq_KMS11_NSD2KO#3_Rep1

description: Library name: Sample 185


title: SLAMseq_KMS11_NSD2KO#13_Rep1

description: Library name: Sample 187


title: Jurkat-CCR5, CIMSS, Mock, rep 1

description: Library name: 4-CIMSS-Mock


title: SLAMseq_KMS11_NSD2KOparental_Rep2

description: Library name: Sample 184


title: 532_IgG

description:
Library name: Sample 54
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: SLAMseq_KMS11_NSD2KOparental_Rep1

description: Library name: Sample 183


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_MAK_21d_Rep2

description: Library name: Sample 182

value: NSD2_dTAG knockin

value: dTAGv1 and MAK-658 for 21d


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_MAK_21d_Rep1

description: Library name: Sample 181


title: SLAMseq_KMS11_NSD2dTAG#11_MAK_21d_Rep2

description: Library name: Sample 180

value: MAK-658 for 21d


title: SLAMseq_KMS11_NSD2dTAG#11_MAK_14d_Rep2

description: Library name: Sample 172

value: MAK-658 for 14d


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_MAK_14d_Rep2

description: Library name: Sample 174

value: dTAGv1 and MAK-658 for 14d


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_EPZ_7d_Rep1

description: Library name: Sample 161

value: dTAGv1 and EPZ-6438 for 7d


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_MAK_21d_Rep2

description: Library name: Sample 158


title: SLAMseq_KMS11_NSD2dTAG#11_MAK_14d_Rep1

description: Library name: Sample 171


title: SLAMseq_KMS11_NSD2dTAG#11_EPZ_14d_Rep1

description: Library name: Sample 167

value: EPZ-6438 for 14d


title: SLAMseq_KMS11_NSD2dTAG#11_EPZ_7d_Rep1

description: Library name: Sample 159

value: EPZ-6438 for 7d


title: SLAMseq_KMS11_NSD2dTAG#11_EPZ_21d_Rep1

description: Library name: Sample 175

value: EPZ-6438 for 21d


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_EPZ_21d_Rep2

description: Library name: Sample 178

value: dTAGv1 and EPZ-6438 for 21d


title: SLAMseq_KMS11_NSD2dTAG#11_MAK_21d_Rep1

description: Library name: Sample 179


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_EPZ_21d_Rep1

description: Library name: Sample 177


title: SLAMseq_KMS11_NSD2dTAG#11_EPZ_21d_Rep2

description: Library name: Sample 176


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_EPZ_7d_Rep2

description: Library name: Sample 162


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_MAK_14d_Rep1

description: Library name: Sample 173


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_EPZ_14d_Rep1

description: Library name: Sample 169

value: dTAGv1 and EPZ-6438 for 14d


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_MAK_7d_Rep2

description: Library name: Sample 166

value: dTAGv1 and MAK-658 for 7d


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_EPZ_14d_Rep2

description: Library name: Sample 170


title: SLAMseq_KMS11_NSD2dTAG#11_MAK_7d_Rep2

description: Library name: Sample 164

value: MAK-658 for 7d


title: SLAMseq_KMS11_NSD2dTAG#11_EPZ_14d_Rep2

description: Library name: Sample 168


title: SLAMseq_KMS11_NSD2dTAG#11_MAK_7d_Rep1

description: Library name: Sample 163


title: SLAMseq_KMS11_NSD2dTAG#11_EPZ_7d_Rep2

description: Library name: Sample 160


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_MAK_7d_Rep1

description: Library name: Sample 165


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_MAK_21d_Rep1

description: Library name: Sample 157


title: SLAMseq_KMS11_NSD2dTAG#8_MAK_21d_Rep1

description: Library name: Sample 155


title: SLAMseq_KMS11_NSD2dTAG#8_MAK_21d_Rep2

description: Library name: Sample 156


title: SLAMseq_KMS11_NSD2dTAG#8_EPZ_21d_Rep1

description: Library name: Sample 151


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_MAK_14d_Rep2

description: Library name: Sample 150


title: SLAMseq_KMS11_NSD2dTAG#8_EPZ_21d_Rep2

description: Library name: Sample 152


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_EPZ_21d_Rep2

description: Library name: Sample 154


title: SLAMseq_KMS11_NSD2dTAG#8_EPZ_14d_Rep1

description: Library name: Sample 143


title: SLAMseq_KMS11_NSD2dTAG#8_MAK_14d_Rep1

description: Library name: Sample 147


title: SLAMseq_KMS11_NSD2dTAG#8_EPZ_14d_Rep2

description: Library name: Sample 144


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_EPZ_14d_Rep2

description: Library name: Sample 146


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_EPZ_14d_Rep1

description: Library name: Sample 145


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_EPZ_21d_Rep1

description: Library name: Sample 153


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_MAK_7d_Rep1

description: Library name: Sample 141


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_MAK_7d_Rep2

description: Library name: Sample 142


title: SLAMseq_KMS11_NSD2dTAG#8_MAK_7d_Rep1

description: Library name: Sample 139


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_MAK_14d_Rep1

description: Library name: Sample 149


title: SLAMseq_KMS11_NSD2dTAG#8_EPZ_7d_Rep1

description: Library name: Sample 135


title: SLAMseq_KMS11_NSD2dTAG#8_MAK_14d_Rep2

description: Library name: Sample 148


title: SLAMseq_KMS11_NSD2dTAG#8_EPZ_7d_Rep2

description: Library name: Sample 136


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_EPZ_7d_Rep1

description: Library name: Sample 137


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_Dox_21d_Rep2

description: Library name: Sample 134

value: NSD2_dTAG knockin and NSD2Y1179A reconstitution

value: dTAGv1 and Doxycycline for 21d


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_Dox_21d_Rep1

description: Library name: Sample 133


title: SNI no amputation, 14DPA, Replicate 3

city: Guelph

first: Samantha

last: Payne

state: ON

address: 50 Stone Road East

country: Canada

institute: University of Guelph

description:
Library name: Samle 29
Bulk RNA-seq of non-regenerated mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 14 days post-amputation (biological replicate 3).

data_processing:
RNA integrity and quantity were assessed using an Agilent 4200 TapeStation prior to library preparation.
Libraries were sequenced on an Illumina NextSeq 2000 using a single-end 1×50 bp configuration
Assembly: GRCm39 (Mus musculus)
Supplementary files format and content: Raw read counts were analyzed in RStudio (v2024.12.1).

source_name: distal left hindlimb regenerate digit, nail removed

extract_protocol:
After euthanasia, tissue distal to the metacarpophalangeal joint was collected, the nail was removed, and samples were stored at −80 degrees celsius. Frozen tissue was mechanically disrupted using rotational shearing blades, homogenized using QIAshredder columns, and total RNA was isolated with DNase treatment using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s instructions.
RNA-seq libraries were prepared from 500 ng of total RNA following poly(A) mRNA enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Strand-specific cDNA libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit, amplified for nine PCR cycles, and prepared according to the manufacturer’s protocol.

treatment_protocol: Spared nerve injury (SNI) mice received surgery in which the common peroneal and tibial branches of the sciatic nerve on the left hindlimb were transected. SHAM-operated mice underwent an identical surgical procedure without nerve transection. Five days following surgery mice underwent amputation through the third phalanx of the left hindlimb to induce regeneration of the digit tip.

tag: time

value: 14 days post amputation

value: SNI surgery denervation without amputation

tag: replicate

value: replicate 3


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_Dox_21d_Rep1

description: Library name: Sample 131

value: Doxycycline for 21d


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_Dox_21d_Rep2

description: Library name: Sample 132


title: SNI no amputation, 14DPA, Replicate 2

description:
Library name: Sample 28
Bulk RNA-seq of non-regenerated mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 14 days post-amputation (biological replicate 2).

value: distal left hindlimb regenerate digit, nail removed

value: replicate 2


title: SLAMseq_KMS11_NSD2dTAG#8_MAK_7d_Rep2

description: Library name: Sample 140

value: NSD2_dTAG knockin


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_EPZ_7d_Rep2

description: Library name: Sample 138

value: dTAGv1 and EPZ-6438 for 7d


title: SNI no amputation, 14DPA, Replicate 1

description:
Library name: Sample 27
Bulk RNA-seq of non-regenerated mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 14 days post-amputation (biological replicate 1).

value: replicate 1


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_Dox_14d_Rep2

description: Library name: Sample 126

value: Doxycycline for 14d


title: SNI amputation, 14DPA, Replicate 1

description:
Library name: Sample 24
Bulk RNA-seq of regenerated mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 14 days post-amputation (biological replicate 1).

value: SNI surgery denervation with amputation


title: SNI amputation, 14DPA, Replicate 2

description:
Library name: Sample 25
Bulk RNA-seq of regenerated mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 14 days post-amputation (biological replicate 2).


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_Dox_14d_Rep1

description: Library name: Sample 127

value: dTAGv1 and Doxycycline for 14d


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_Dox_14d_Rep1

description: Library name: Sample 125


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_21d_Rep1

description: Library name: Sample 129

value: dTAGv1 for 21d


title: SNI amputation, 14DPA, Replicate 3

description:
Library name: Sample 26
Bulk RNA-seq of regenerated mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 14 days post-amputation (biological replicate 3).


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_21d_Rep2

description: Library name: Sample 130


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_Dox_14d_Rep2

description: Library name: Sample 128


title: SNI no amputation, 7DPA, Replicate 2

description:
Library name: Sample 22
Bulk RNA-seq of non-regenerated mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 7 days post-amputation (biological replicate 2).

value: 7 days post amputation


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_14d_Rep2

description: Library name: Sample 124

value: dTAGv1 for 14d


title: SNI no amputation, 7DPA, Replicate 3

description:
Library name: Sample 23
Bulk RNA-seq of non-regenerated mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 7 days post-amputation (biological replicate 3).


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_14d_Rep1

description: Library name: Sample 123

value: NSD2_dTAG knockin and NSD2Y1179A reconstitution


title: SNI no amputation, 7DPA, Replicate 1

description:
Library name: Sample 21
Bulk RNA-seq of non-regenerated mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 7 days post-amputation (biological replicate 1).


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_Dox_7d_Rep1

description: Library name: Sample 121

value: dTAGv1 and Doxycycline for 7d


title: SNI amputation, 7DPA, Replicate 1

description:
Library name: Sample 18
Bulk RNA-seq of regenerated mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 7 days post-amputation (biological replicate 1).


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_Dox_7d_Rep2

description: Library name: Sample 122


title: SNI, 21DPA, Replicate 3

description:
Library name: Sample 17
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 21 days post-amputation (biological replicate 3).

value: 21 days post amputation

value: SNI surgery denervation


title: SNI amputation, 7DPA, Replicate 3

description:
Library name: Samle 20
Bulk RNA-seq of regenerated mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 7 days post-amputation (biological replicate 3).

value: replicate 3


title: SNI, 21DPA, Replicate 2

description:
Library name: Sample 16
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 21 days post-amputation (biological replicate 2).


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_Dox_7d_Rep2

description: Library name: Sample 120

value: Doxycycline for 7d