title: HepG2 CD146oe3

city: Tianjin

first: Shuo

last: Qie

address: Huanhuxi Road, Tiyuanbei, Hexi District

department: Pathology

institute: Tianjin Medical University Cancer Institute & hospital

description: Library name: CD146oe3

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Supplementary files format and content: Excel file includes FPKM values for each Sample
Supplementary files format and content: Txt file includes raw counts for each Sample

growth_protocol: Hep3B cells were cultured in DMEM with 10% FBS plus 1% penicillin/streptomycin, whereas liver cancer HepG2 cells were maintained in MEM with 10% FBS supplemented with 1% penicillin/streptomycin and 1% sodium pyruvate. All cells were cultured in an incubator at 37˚C in an atmosphere containing 5% CO2.

extract_protocol:
Knockdown of CD146 was performed using Tet-on-induced Control shRNA or CD146 shRNA in Hep3B cells; while overexpression of CD146 was introduced into HepG2 cells via pLVX or CD146 vector.
Total RNA was extracted from biological samples using TRIzol Reagent (Invitrogen). 1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: Liver cancer


title: Young 3

status: Public on Aug 11 2026

type: RNA

city: Saint Louis

first: Victoria

middle: A.

last: Church

state: MO

address: 660 Euclid

country: USA

institute: Washington University School of Medicine

description: vc2,  N1

hyb_protocol: Labeled RNA was hybridized at 48 °C for 42 h at 60 rpm on an Affymetrix GeneChip™ human miRNA 4.0 array

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner G3000 7G with standard setting to capture signal intensities for the miRNAs.

data_processing: The raw intensity of miRNA microarray data was imported into Affymetrix Expression Console software (v1.4.1.46) for signal pre-processing including background correction utilizing the robust multi-array average (RMA) algorithm, median polish summarization from probe to probe set level of signal values, and the quantile method to normalize across multiple arrays and then calculate the log2 scale expression signals of miRNAs. Removal of unwanted variations correction of microarray data was performed by following the manual of the RUV package. The RUV III function was used to globally adjust the microarray data matrix using both negative controls and replicates. And the negative controls were the spike-in controls found on many microarray platforms. The significantly differentially expressed miRNAs between young and old samples in basal ganglia regions were identified by limma method with the adjusted p value < 0.05.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: cortex, non-diseased

label_protocol: Flashtag™ Biotin HSR RNA labeling kit

extract_protocol: Qiagen FFPE Rneasy extraction kit

treatment_protocol: FFPE human brain sections

tag: age

value: 19 yr

tag: gender

value: female


title: Young 1

description: vc3, N1

value: 9 yr


title: Young 2

description: vc1,  N1

value: 11 yr

value: male


title: HepG2 CD146oe2

type: SRA

country: China

description: Library name: CD146oe2

library_source: transcriptomic

treatment_protocol: Knockdown of CD146 was performed using Tet-on-induced Control shRNA or CD146 shRNA in Hep3B cells; while overexpression of CD146 was introduced into HepG2 cells via pLVX or CD146 vector.

tag: cell line

tag: cell type

tag: treatment


title: Skin; Control; P21 (postnatal day 21); control1

city: Suzhou

first: Yulong

last: He

address: 199 Ren-Ai Road

institute: Soochow University

description: Library name: sample1

data_processing:
Sequencing was performed on the BGISEQ /DNBSEQ platform with a read length of PE150 (BGI-Shenzhen, China)
Raw data filtered using SOAPnuke (v 2.3.2)
RNA-seq reads aligned to a reference genome using hisat2 (v 2.2.1)
The clean data was aligned to the reference gene set using Bowtie2 (v2.4.5) . Gene expression quantification was performed using RSEM (v1.3.1) software
Assembly: Mus_musculus：NCBI, GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes read counts for each sample

organism: Mus musculus

source_name: Skin

extract_protocol:
Total RNA was isolated from the ear skin tissues using Trizol (Invitrogen) according to the manufacturer's instructions
For library construction, total RNA was processed using mRNA enrichment. The mRNA was enriched using magnetic beads with Oligo(dT) to capture mRNA with a polyA tail. The obtained RNA was fragmented using a breaking buffer, and random N6 primers were used for reverse transcription. Subsequently, double-stranded cDNA was synthesized. The ends of the synthesized double-stranded DNA were blunted and 5' end-phosphorylated. A single-base overhang "A" was added to the 3' end, and a bubble-shaped adapter with a protruding "T" at the 3' end was ligated. The ligated products were PCR-amplified using specific primers. The PCR products were denatured to form single-stranded DNA, and single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries underwent quality control, and after passing, they were subjected to sequencing.

treatment_protocol: Ear skin tissues from the endothelial specific knockout and control mice were collected, and then snap‑frozen in liquid nitrogen.

tag: tissue

value: Skin

tag: genotype

value: Control

value: tamoxifen treatment


title: Metformin 2mM 24h Rep C

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

description: Library name: 24H2C

data_processing:
Raw reads were checked and trimmed by trimmomatic-0.39
Trimmed reads were mapped to the  whole genome using HISAT2
Reads counts for each gene with  htseq-count
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

molecule: polyA RNA

source_name: Bone marrow-derived macrophages (BMDMs)

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10 ng/ml mouse macrophage colony-stimulating factor (m-MCSF, PeproTech, USA), 10% fetal bovine serum (FBS, Gibco, USA), 0.1% penicillin/streptomycin (Gibco, USA), and 1% L-glutamine (Gibco, USA) for 7 days to achieve terminal differentiation into mature BMDMs.

extract_protocol:
Total RNA was isolated by the RNeasy Plus Mini Kit (Qiagen, Netherlands).
The Illumina Universal Plus mRNA-Seq kit was used for preparing RNA-seq libraries.

treatment_protocol: BMDM cells were treated with metformin (0.1mM and 2mM) for 24 hours.

value: Bone marrow-derived macrophages (BMDMs)

value: WT

value: 2mM metformin


title: Scm_OR_0-6hr_exp5_chrom1

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

country: Germany

institute: Max Planck Institute of Biochemistry

description: Library name: sample 31

library_source: genomic

data_processing:
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization) using STAR (Dobin et al., 2013). Only sequences that mapped uniquely to the genome with a maximum of two mismatches were considered for further analyses.
Bam files were used as inputs to run Bioconductor packages.
The proportion of D. pseudoobscura reads as compared to D. melanogaster reads in input and in samples was used to normalize the ChIP-seq datasets for histone marks in embryos. Reference samples for normalization with D. pseudoobscura chromatin are indicated. Other samples were normalized based on total read number per million reads. Normalization factor for each sample is indicated.
Assembly: dm6
Supplementary files format and content: Normalized bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: 0-6hr old embryos

growth_protocol: Drosophila embryos were grown on standard medium at 25˚C

extract_protocol:
Lysates were clarified from sonicated fixed nuclei. Histone/Protein-DNA complexes were isolated with antibody. D. pseudoobscura chromatin was spiked in before the addition of the antibody.
Libraries were prepared according to manufacturer's instructions.
ChIP-Seq

value: 0-6hr old embryos

value: OR

tag: antibodies

value: Scm (Gambetta et al., 2009)

tag: normalization factor


title: HepG2 pLVX3

description: Library name: pLVX3

value: pLVX


title: WT_2C_3 [RNA-Seq]

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

description:
Library name: WT_2C_3
WT_2C_3

data_processing:
And for each sample, ERCC (1:1000, 0.2μl/sample) were added as spike-in for further calibration.
Assembly: mm10
Supplementary files format and content: The count list calibrated by ERCC.

source_name: zygote

extract_protocol:
The oocytes were harvested from mature WT and Gdf9-cre Nat10 conditional knockout female mice 32-48h after PMSG and washed by 0.2% containing PBS for 3 times,
10 oocytes per sample were lysed in lysis buffer (containing 0.2% Triton X-100 and Recombination RNase Inhibitor) and prceeded for cDNA library constribution following the workflow of Smart-seq2

value: zygote


title: HepG2 CD146oe1

description: Library name: CD146oe1

value: Liver cancer


title: WT_2C_2 [RNA-Seq]

description:
Library name: WT_2C_2
WT_2C_2


title: Metformin 2mM 24h Rep B

description: Library name: 24H2B


title: HepG2 pLVX2

description: Library name: pLVX2


title: WT_2C_1 [RNA-Seq]

description:
Library name: WT_2C_1
WT_2C_1


title: Metformin 2mM 24h Rep A

description: Library name: 24H2A


title: HepG2 pLVX1

description: Library name: pLVX1


title: WT_Z1C_1 [RNA-Seq]

description:
Library name: WT_Z1C_1
WT_Z1C_1


title: WT_Z1C_2 [RNA-Seq]

description:
Library name: WT_Z1C_2
WT_Z1C_2


title: WT_Z1C_3 [RNA-Seq]

description:
Library name: WT_Z1C_3
WT_Z1C_3


title: Hep3B CD146 sh3

description: Library name: CD146 sh3

value: CD146 sh


title: WT_MII_3 [RNA-Seq]

description:
Library name: WT_MII_3
WT_MII_3

source_name: oocyte

value: oocyte


title: WT_MII_2 [RNA-Seq]

description:
Library name: WT_MII_2
WT_MII_2


title: WT_MII_1 [RNA-Seq]

description:
Library name: WT_MII_1
WT_MII_1


title: Metformin 0.1mM 24h Rep C

description: Library name: 24H0_1C

value: 0.1mM metformin


title: Hep3B CD146 sh2

description: Library name: CD146 sh2


title: WT_zFGO_2 [RNA-Seq]

description:
Library name: WT_zFGO_2
WT_zFGO_2


title: Metformin 0.1mM 24h Rep B

description: Library name: 24H0_1B


title: WT_zFGO_3 [RNA-Seq]

description:
Library name: WT_zFGO_3
WT_zFGO_3


title: Metformin 0.1mM 24h Rep A

description: Library name: 24H0_1A


title: Hep3B CD146 sh1

description: Library name: CD146 sh1


title: WT_zFGO_1 [RNA-Seq]

description:
Library name: WT_zFGO_1
WT_zFGO_1


title: Control Replicate C

description: Library name: CtlC


title: KO_ZMII_2 [RNA-Seq]

description:
Library name: KO_ZMII_2
KO_ZMII_2

value: Zp3-cre Nat10 cKO


title: Hep3B Con sh3

description: Library name: Con sh3

value: Con sh


title: Control Replicate B

description: Library name: CtlB


title: KO_ZMII_1 [RNA-Seq]

description:
Library name: KO_ZMII_1
KO_ZMII_1


title: Hep3B Con sh2

description: Library name: Con sh2


title: KO_ZMII_3 [RNA-Seq]

description:
Library name: KO_ZMII_3
KO_ZMII_3


title: Control Replicate A

description: Library name: CtlA


title: KO_ZFGO_3 [RNA-Seq]

description:
Library name: KO_ZFGO_3
KO_ZFGO_3


title: Hep3B Con sh1

description: Library name: Con sh1


title: KO_ZFGO_2 [RNA-Seq]

description:
Library name: KO_ZFGO_2
KO_ZFGO_2


title: mousePDAC iKras, smallRNAseq, +DOX, rep2

city: Houston

first: Ronald

middle: J

last: Parchem

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Bortoletto_2023_mpdac_miRNA_normalizedcounts.csv

data_processing:
Cutadapt (v3.5) for adapter trimming
Trimmed, high quality reads were mapped to Mmusculus (GRCm39) using STAR (v2.7.9a)
In R (v4.1.1), gene count matrices were built with GenomicAlignments tool (v1.28).
Count normalization and differential gene expression was performed using DESeq2 (3.14)
Assembly: GRCm39
Supplementary files format and content: comma-separated text files include normalized counts for each sample

source_name: mouse PDAC iKRAS

growth_protocol: Cells were seeded in 6 well plates in DMEM/F12 with 10% bovine serum albumin (BSA) in a humidified incubator at 37C at 5% CO2.

extract_protocol:
Cells were lysed and RNA was harvested directly into TRIzol and purfied using a miRNEasy microprep spin kit. RNA was eluted into RNAse free water.
Library was generated using Revvity (previously PerkinElmer) NEXTFLEX small RNA-seq kit V3. Breifly, total RNA was ligated to 3' and 5' adenylated adapters. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Fragments were ethanol purified and subject to PCR amplification. PCR products were gel purified (150 bp fragment) and library quality was assessed on the Agilent TapeStation 4150 system.

treatment_protocol: Cells were harvested when at 80% confluency.

value: mouse PDAC iKRAS

value: mouse pancreatic cancer cell line


title: KO_ZFGO_1 [RNA-Seq]

description:
Library name: KO_ZFGO_1
KO_ZFGO_1


title: PBIT_H3K9me3_1_S23

city: Pittsburgh

first: Niranjana

last: Natarajan

state: PA

address: 200 Lothrop street, BST1720

institute: university of pittsburgh

description: Library name: PBIT 2 - H3K9me3

data_processing:
CUT&RUN data analysis was performed using Partek Flow. Sequences were aligned to the mouse genome, and adapters were trimmed followed by peak calling using MACS and peak annotation. From the generated peaks, known motifs and de novo motifs were identified. Gene set enrichment and pathway analyses were performed with the annotated peak data.
Adapter sequences: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Library strategy: CUT&Run

source_name: primary bone marrow - derived macrophages

growth_protocol: Bone marrow cells were isolated from the femurs and tibias of C57BL/6 mice. The cells were cultured in DMEM containing 5.5 mM glucose and supplemented with 20% L929 conditioned medium.

extract_protocol:
CUT&RUN was performed according to manufacturer’s suggested protocol (Cell Signaling, #86652). Briefly, 100,000 BMDMs were plated per well, treated with epigenetic inhibitors and LPS as described above. Cells were trypsinized and harvested after treatment, permeabilized, and incubated with H3K4me3 and H3K9me3 antibodies overnight. Next, protein A-MNase was added to the cells after washing and incubated for 1 hour. Then, chromatin digestion was performed followed by release of digested chromatin and purification of digested DNA. Library preparation of CUT&RUN generated fragments was carried out followed by sequencing (~5million reads / sample).
CUTANA™ CUT&RUN Library Prep Kit was used for library construction, according to manufacturer's suggested protocol.

treatment_protocol: After the cells were 80% confluent, the culture was treated with 20mM n-octyl IOX1 or 20mM PB-IT (epigenetic inhibitors) for 8 hours, followed by 1ng/ml LPS for 24 hours.

value: macrophages

value: 20mM PB-IT and 1ng/ml LPS


title: KO_2C_2 [RNA-Seq]

description:
Library name: KO_2C_2
KO_2C_2


title: KO_2C_3 [RNA-Seq]

description:
Library name: KO_2C_3
KO_2C_3


title: mousePDAC iKras, smallRNAseq, +DOX, rep1


title: KO_Z1C_2 [RNA-Seq]

description:
Library name: KO_Z1C_2
KO_Z1C_2


title: KO_2C_1 [RNA-Seq]

description:
Library name: KO_2C_1
KO_2C_1


title: mousePDAC iKras, smallRNAseq, ethanol control, rep2

value: WT


title: KO_Z1C_3 [RNA-Seq]

description:
Library name: KO_Z1C_3
KO_Z1C_3


title: KO_Z1C_1 [RNA-Seq]

description:
Library name: KO_Z1C_1
KO_Z1C_1


title: KO_2C_3

description: Library name: KO_2C_3

data_processing:
Raw reads were trimmed with cutadapt v1.14 with parameters: cutadapt–trim-n -a GATCGGAAGAGCACACGTCTG-a AGAGCACACGTCTG <input.file>| cutadapt -u 3 -a A{100}–no-indels-e 0.16666666666666666 - | cutadapt -O 8–match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18–o <output.file>, and the trimmed reads were sequentially mapped to mouse or human rRNA sequences (mm9/hg19) using Bowtie2 v2.2.2 (ref. 89) with parameters –seedlen=23.
Assembly: mm10
Supplementary files format and content: The count list calibrated by ERCC.
Library strategy: Ribo-Seq

extract_protocol:
The zygotes were harvested from 6W mature WT and Zp3-cre Nat10 conditional knockout female mice 20h after hCG and lysed in 310 μl ice-cold lysis buffer for 10 min on ice.
The sample was then subjected to sequencing library preparation by CATS Small RNA-seq Kit (Diagenode, C05010048). CATS Small RNA-seq Kit utilizes a single-tube strategy based on polyadenylation, reverse transcription, template switch and PCR amplification, and DNA library was purified using AMPure XP (Beckman, A63882).

tag: Sex

value: female


title: PBIT_H3K9me3_1_S24

description: Library name: PBIT 3 - H3K9me3


title: KO_2C_1

description: Library name: KO_2C_1


title: mousePDAC iKras, smallRNAseq, ethanol control, rep1


title: KO_1C_3

description: Library name: KO_1C_3


title: PBIT_H3K9me3_1_S22

description: Library name: PBIT 1 - H3K9me3


title: IOX1_H3K9me3_1_S21

description: Library name: octyl IOX1 3 - H3K9me3

value: 20mM n-octyl-IOX1 and 1ng/ml LPS


title: KO_1C_2

description: Library name: KO_1C_2


title: satellite cells GFP+ 5dpi (from Pax3GFP/+ animals)

city: Creteil

first: Joana

last: Esteves de Lima

address: 8 rue du general sarrail

department: IMRB INSERM U955

country: France

institute: INSERM

description:
Library name: GFPplus_5dpi_PAX3plus
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were made using CellRanger software
The files barcode were uploaded in R studio and analysed with Seurat package.
Assembly: Mouse mm10
Supplementary files format and content: Processed files are barcode.tsv, features.tsv and matrix.mtx

source_name: skeletal muscle

extract_protocol:
Freshly and FACS-isolated PAX3⁺ (GFP+) and PAX3- (GFP-) satellite cells from biceps and recto femoris muscles  5 days-post-injury, were processed for scRNA-seq and 20 000 cells per condition were loaded into the 10× Chromium Chip with the Single Cell 3′ Reagent Kit v3.1.
Library Construction Kit 10x Library Construction Kit ref: 1000190

value: skeletal muscle

value: satellite cells (GFP+/PAX3+)

value: wild-type


title: LPS_H3K9me3_1_S17

description: Library name: LPS 2 - H3K9me3

value: 1ng/ml LPS


title: satellite cells GFP- 5dpi (from Pax3GFP/+ animals)

description:
Library name: GFPneg_5dpi_PAX3neg
10x Genomics

value: satellite cells (GFP-/PAX3-)


title: IOX1_H3K9me3_1_S20

description: Library name: octyl IOX1 2 - H3K9me3


title: IOX1_H3K9me3_1_S19

description: Library name: octyl IOX1 1 - H3K9me3


title: WT_1C_1

description: Library name: WT_1C_1

value: zygote


title: KO_1C_1

description: Library name: KO_1C_1


title: LPS_H3K9me3_1_S16

description: Library name: LPS 1 - H3K9me3


title: LPS_H3K9me3_1_S18

description: Library name: LPS 3 - H3K9me3


title: Hspa1a shRNA, biological replicate 2

city: Nanjing

first: Wang

last: Bo

state: Jiangsu

address: 121 Jiangjiayuan, Nanjing City

institute: The Second Affiliated Hospital of Nanjing Medical University

description:
Library name: CCCP_2
Column name in featureCounts_merged_count.annot.tsv: CCCP_2

data_processing:
Clean reads were aligned to the Mus musculus GRCm39 reference genome (Ensembl release 109) using HISAT2.
Gene-level fragment counts were quantified using featureCounts from the Subread package.
Differential expression analysis between Hspa1a shRNA and sh-NC samples was performed using DESeq2.
Assembly: Mus musculus GRCm39, Ensembl release 109
Supplementary files format and content: featureCounts_merged_count.annot.tsv is a tab-delimited annotated gene-level raw fragment count matrix. Rows represent Ensembl genes and columns G_1, G_2, G_3, CCCP_1, CCCP_2 and CCCP_3 contain counts for the six RNA-seq libraries; additional columns contain gene annotation.

source_name: bone marrow

growth_protocol: Bone marrow-derived monocyte/dendritic cell cultures were generated under granulocyte-macrophage colony-stimulating factor (GM-CSF)-driven differentiation conditions.

extract_protocol:
Total RNA was extracted using TRIzol and treated with DNase I. One microgram of total RNA per sample was used for library preparation.
Poly(A)+ RNA was enriched, fragmented and reverse-transcribed using random hexamer priming, followed by end repair, A-tailing, adapter ligation and PCR amplification. Library quality was assessed using an Agilent 2100 Bioanalyzer and Qubit fluorometry. Libraries were sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Knockdown cultures were treated with Hspa1a-targeting shRNA. Control cultures were treated with non-targeting control shRNA (sh-NC).

value: bone marrow

value: bone marrow-derived monocyte/dendritic cell culture

value: Hspa1a-targeting shRNA


title: V5_ph_wt_1-3hr_exp4_chrom1

description: Library name: sample 36

source_name: 1-3hr old embryos

value: 1-3hr old embryos

value: V5 (Cell Signalling (#D3H8Q))


title: Psc_ph_wt_1-3hr_exp4_chrom1

description: Library name: sample 30

value: DSHB (6E8)


title: WT_2C_3

description: Library name: WT_2C_3


title: WT_2C_2

description: Library name: WT_2C_2


title: WT_1C_2

description: Library name: WT_1C_2


title: V5_ph_deltaSAM_1-3hr_exp4_chrom1

description: Library name: sample 33


title: Hspa1a shRNA, biological replicate 3

description:
Library name: CCCP_3
Column name in featureCounts_merged_count.annot.tsv: CCCP_3


title: WT embryos, 36 hours post fertilization, biol rep 2

status: Public on Aug 12 2026

city: Lexington

first: Kaan Ihsan

last: Eskut

state: Kentucky

address: 195 Huguelet Dr.

department: Biology

institute: University of Kentucky

description:
Library name: hrs36_2
column name in raw counts:hrs36_2

data_processing:
RNA-seq reads from this study were aligned to the reference genome using HISAT2 v2.2.1
Gene expression was quantified from these alignments using StringTie v2.2.1
Assembly: UKy_Petmar_22M1.pri1.0
Supplementary files format and content: comma separated file with raw counts from stringtie v2.2.1

organism: Petromyzon marinus

source_name: Embryos

growth_protocol: Eggs and sperm were collected from mature adults by stripping gametes into crystallization dishes and containing 10% Holtfreter’s solution and incubated for 10 min to permit fertilization. After visually confirming activation, embryos were rinsed in distilled water to remove excess sperm and maintained in 10% Holtfreter’s solution at 18 °C throughout development.

extract_protocol:
Total RNA was extracted from two pools of approximately 100 snap frozen embryos for each condition, following the standard Trizol extraction protocol with the addition of 10 mM dithiothreitol(DTT) to the lysis reaction.
Library preparation and sequencing were conducted by Novogene using their "Plant and Animal Eukaryotic mRNA" pipeline.

value: Embryos

value: Wildtype


title: Psc_ph_deltaSAM_1-3hr_exp4_chrom1

description: Library name: sample 27


title: Hspa1a shRNA, biological replicate 1

description:
Library name: CCCP_1
Column name in featureCounts_merged_count.annot.tsv: CCCP_1


title: NT_H3K9me3_1_S15

description: Library name: control 3 - H3K9me3

value: macrophages

value: untreated


title: sh-NC control, biological replicate 1

description:
Library name: G_1
Column name in featureCounts_merged_count.annot.tsv: G_1

value: sh-NC


title: sh-NC control, biological replicate 2

description:
Library name: G_2
Column name in featureCounts_merged_count.annot.tsv: G_2


title: NT_H3K9me3_1_S14

description: Library name: control 2 - H3K9me3


title: input_ph_wt_1-3hr_exp4_chrom1

description: Library name: sample 23


title: DOWN4

city: Shanghai

first: Jing

last: Wang

address: No. 227 South Chongqing Road, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: Sample 12

data_processing:
Raw sequencing reads were aligned to the mouse reference genome using STAR. Gene-level read counts were generated using RSEM.
Assembly: Mouse mm10
Supplementary files format and content: Matrix files with gene counts and sample names

source_name: BALF

extract_protocol:
Cells were lysed directly without prior bulk RNA extraction. Full-length cDNA was synthesized and amplified from polyadenylated RNA using the SMART-Seq HT Kit (Takara Bio) according to the manufacturer’s instructions.
Samples exhibiting the expected cDNA size distribution were selected for sequencing library preparation, which were constructed from amplified cDNA using the TruePrep RNA Library Prep Kit V2 for Illumina (Vazyme) according to the manufacturer’s instructions.

value: BALF

value: Alveolar Macrophages


title: NT_H3K9me3_1_S13

description: Library name: control 1 - H3K9me3


title: DOWN1

description: Library name: Sample 9


title: DOWN2

description: Library name: Sample 10


title: UPSMALL4

description: Library name: Sample 8


title: sh-NC control, biological replicate 3

description:
Library name: G_3
Column name in featureCounts_merged_count.annot.tsv: G_3


title: PBIT_H3K4me3_1_S12

description: Library name: PBIT 3 - H3K4me3

value: 20mM PB-IT and 1ng/ml LPS


title: PBIT_H3K4me3_1_S11

description: Library name: PBIT 2 - H3K4me3


title: DOWN3

description: Library name: Sample 11


title: Pho_ph_wt_1-3hr_exp4_chrom1

description: Library name: sample 25

value: Pho (Papp and Mueller 2006)


title: UPSMALL3

description: Library name: Sample 7


title: WT embryos, 27 hours post fertilization, biol rep 1

description:
Library name: hrs27_1
column name in raw counts:hrs27_1


title: PBIT_H3K4me3_1_S10

description: Library name: PBIT 1 - H3K4me3


title: V5_ph_wt_1-3hr_exp1_chrom2

description: Library name: sample 18

tag: chip antibody


title: UPSMALL2

description: Library name: Sample 6


title: V5_ph_wt_1-3hr_exp1_chrom1

description: Library name: sample 17


title: UPSMALL1

description: Library name: Sample 5


title: WT embryos, 30 hours post fertilization, biol rep 1

description:
Library name: hrs30_1
column name in raw counts:hrs30_1


title: UPBIG4

description: Library name: Sample 4


title: IOX1_H3K4me3_1_S9

description: Library name: octyl IOX1 3 - H3K4me3

value: 20mM n-octyl-IOX1 and 1ng/ml LPS


title: V5_ph_deltaSAM_1-3hr_exp1_chrom1

description: Library name: sample 16


title: UPBIG3

description: Library name: Sample 3


title: IOX1_H3K4me3_1_S8

description: Library name: octyl IOX1 2 - H3K4me3


title: UPBIG2

description: Library name: Sample 2


title: UPBIG1

description: Library name: Sample 1


title: WT embryos, 45 hours post fertilization, biol rep 1

description:
Library name: hrs45_1
column name in raw counts:hrs45_1


title: V5_ph_KO_1-3hr_exp1_chrom1

description: Library name: sample 15


title: TGF2

description:
Library name: Sample 4
TGF2

data_processing:
Adapter sequences and low-quality reads were removed from the raw sequencing data using Skewer. Clean reads were aligned to the referance genome using STAR(2.5.3a). The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using StringTie (v1.3.1c). Differentially expression genes(DEGs) were determined by DEGseq2(v1.16.1).
Assembly: Mouse mm10
Supplementary files format and content: Matrix files with gene counts and sample names

source_name: Lung

extract_protocol:
Total RNA was isolated from each sample using RNAiso Plus (Takara Bio) according to the manufacturer’s instructions.
Strand-specific mRNA sequencing libraries were constructed from total RNA using the VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s instructions.

value: Lung

value: Primary lung fibroblasts


title: IOX1_H3K4me3_1_S7

description: Library name: octyl IOX1 1 - H3K4me3


title: TGF3

description:
Library name: Sample 5
TGF3


title: TGF1

description:
Library name: Sample 3
TGF1


title: Pho_ph_wt_1-3hr_exp1_chrom2

description: Library name: sample 14

value: Pho (Papp and Müller 2006)


title: LPS_H3K4me3_1_S6

description: Library name: LPS 3 - H3K4me3

value: 1ng/ml LPS


title: Control1

description:
Library name: Sample 1
Control1

value: Control


title: Pho_ph_wt_1-3hr_exp1_chrom1

description: Library name: sample 13

value: 1-3hr old embryos


title: LPS_H3K4me3_1_S5

description: Library name: LPS 2 - H3K4me3


title: input_ph_wt_1-3hr_exp1_chrom2

description: Library name: sample 12


title: LPS_H3K4me3_1_S4

description: Library name: LPS 1 - H3K4me3


title: input_ph_deltaSAM_1-3hr_exp4_chrom1

description: Library name: sample 20


title: Muscle, semaglutide + HIIT, 0.05 mg/kg injection + 60 min exercise, rep 3

city: Wuhan

first: Zhenghong

last: Kang

state: Hubei

address: 461 Luoyu Road, Hongshan District, Wuhan City, Hubei Province

department: School of Sports Medicine

institute: Wuhan Sports University

description: Library name: MHM3

data_processing:
Base calling was performed using CASAVA software. Raw sequencing data in FASTQ format were assessed for quality using FastQC.
Adapter sequences and low-quality reads were removed using Trimmomatic (version 0.36) with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
High-quality clean reads were aligned to the mouse reference genome (GRCm39) using STAR aligner (version 2.7.9a) with default parameters.
Gene-level read counts were generated using featureCounts (version 2.0.1) with default parameters against the mouse reference genome annotation (GENCODE).
Additionally, transcript assembly and expression quantification were performed using StringTie (version 2.1.4), and expression levels were normalized as FPKM and TPM values.
Assembly: GRCm39
Supplementary files format and content: Processed data are provided as a tab-delimited text file containing gene-level count matrix for all samples. Rows represent genes (annotated with Ensembl gene IDs and gene symbols), and columns represent individual samples. Values are raw read counts generated by featureCounts.

source_name: Muscle

growth_protocol: Eight-week-old male db/db mice were randomly assigned to four groups: sedentary control (CON), HIIT only, semaglutide only, and combined intervention (HIIT + semaglutide). HIIT was performed on a motorized treadmill, consisting of 10 bouts of 4-minute high-intensity running at 85-90% of maximal running speed interspersed with 2-minute active recovery at 50-60% of maximal speed, 5 days per week for 8 weeks. Semaglutide was administered via subcutaneous injection at a dose of 30 nmol/kg once daily for 8 weeks. The combined group received both interventions simultaneously.

extract_protocol:
Immediately after euthanasia, heart, kidney, hippocampus, liver, and soleus muscle were rapidly harvested, snap-frozen in liquid nitrogen, and stored at −80°C. Total RNA was extracted from each tissue sample using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's standard protocol. RNA quality and integrity were assessed using a NanoDrop spectrophotometer and an Agilent 2100 Bioanalyzer.
Stranded mRNA-seq libraries were constructed using poly(A) mRNA enrichment with oligo(dT) magnetic beads. Library preparation was performed following the standard protocol of the NEB Next Ultra RNA Library Prep Kit for Illumina. The constructed libraries were sequenced on the Illumina NovaSeq 6000 platform in paired-end 150 bp (PE150) mode. Library construction and sequencing services were provided by Qingke Biotechnology Co., Ltd.

value: Muscle

value: male

value: Eight-week-old

value: C57BL/KsJ db/db mice

value: HIIT Exercise AND Semaglutide injection


title: Control2

description:
Library name: Sample 2
Control2


title: Muscle, semaglutide + HIIT, 0.05 mg/kg injection + 60 min exercise, rep 2

description: Library name: MHM2

treatment_protocol: Eight-week-old male db/db mice were randomly assigned to four groups: sedentary control (CON), HIIT only, semaglutide only, and combined intervention (HIIT + semaglutide). HIIT was performed on a motorized treadmill, consisting of 10 bouts of 4-minute high-intensity running at 85-90% of maximal running speed interspersed with 2-minute active recovery at 50-60% of maximal speed, 5 days per week for 8 weeks. Semaglutide was administered via subcutaneous injection at a dose of 30 nmol/kg once daily for 8 weeks. The combined group received both interventions simultaneously.


title: Muscle, semaglutide + HIIT, 0.05 mg/kg injection + 60 min exercise, rep 1

description: Library name: MHM1


title: Muscle, semaglutide,0.05 mg/kg, rep2

description: Library name: MSEM2

value: Semaglutide injection


title: Muscle, semaglutide,0.05 mg/kg, rep3

description: Library name: MSEM3


title: input_ph_wt_1-3hr_exp1_chrom1

description: Library name: sample 11


title: NT_H3K4me3_1_S3

description: Library name: control 3 - H3K4me3

value: macrophages

value: untreated


title: Muscle, semaglutide,0.05 mg/kg, rep1

description: Library name: MSEM1


title: input_ph_deltaSAM_1-3hr_exp1_chrom2

description: Library name: sample 10


title: Muscle, exercised,60min, rep3

description: Library name: MHIIT3

value: HIIT Exercise


title: WT embryos, 48 hours post fertilization, biol rep 1

description:
Library name: hrs48_1
column name in raw counts:hrs48_1

value: Embryos

value: Wildtype


title: NT_H3K4me3_1_S2

description: Library name: control 2 - H3K4me3


title: input_ph_deltaSAM_1-3hr_exp1_chrom1

description: Library name: sample 9


title: NT_H3K4me3_1_S1

description: Library name: control 1 - H3K4me3


title: Muscle, exercised,60min, rep2

description: Library name: MHITT2


title: WT embryos, 39 hours post fertilization, biol rep 1

description:
Library name: hrs39_1
column name in raw counts:hrs39_1


title: input_ph_KO_1-3hr_exp1_chrom2

description: Library name: sample 8


title: Mammary Gland,Lactation,Goat-2

city: Cerdanyola del Vallès

first: Diego

middle: Alonso

last: Vargas Donayre

state: Barcelona

address: Carrer de la Vall Moronta

department: Plant and Animal Genomics

country: Spain

institute: Centre for Research in Agricultural Genomics (CRAG)

description: Library name: MG2

data_processing:
Raw reads with less than 100 bp and less than 85% of bases with Q>30 were discarded using Fastp. SILVA database rRNA database release 138.2 was used to eliminate rRNA contamination.
Filtered reads were mapped to the goat reference genome  with STAR and transcript structure recovery was conducted with StringTie. Novel lncRNAs were characterized with an internal protocol
Gene level estimated counts and offsets matrices were generated using tximport. Count data was normalized to CPM with edgeR. Genes with a CPM value greater than 0.5 in at least 3 samples in a tissue were considered as expressed. Null expressed genes were removed. Tissue-specificty of each gene was measured by the tau-index.
Assembly: ARS1.2
Supplementary files format and content: 33tissues_gene_counts.tsv.gz , tab-delimited text file includes raw gene count.
Supplementary files format and content: 33tissues_gene_length.tsv.gz , tab-delimited text file includes gene count offset.
Supplementary files format and content: 33tissues_CPM.tsv.gz , tab-delimited text file includes processed CPM
Supplementary files format and content: lncRNAs.gtf.gz , gtf file including novel lncRNA
Supplementary files format and content: 33tissues_tau.tsv.gz , tab-delimited text file includes tau-index for each expressed gene

organism: Capra hircus

source_name: Mammary Gland

extract_protocol:
RNA was extracted using the RiboPure™ Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
Strand-specific library construction was performed with VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina.

value: Mammary Gland


title: Muscle, db/db control group, rep2

description: Library name: MCON2

value: Normal rearing


title: PBIT_LPS_4_S16

description: Library name: PBIT 4

data_processing:
CLC genomics workbench was used to analyze transcriptomic data generated by RNA sequencing. The FASTQ files provided by Health Science Sequencing Core at UPMC Children’s Hospital were imported into CLC Genomics Workbench 22.
A sequencing QC report was generated to assess data quality. A PHRED score of less than 40 is considered optimal for downstream analysis.
The adapters present at the ends were trimmed. Forward - AGATCGGAAGAGCACACGTCTGAACTCCAGTCA Reverse - AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
The trimmed reads were aligned to the Mus musculus CLC reference genome version 86. The gene expression was calculated as reads per kilobase of transcript per million mapped reads (RPKM). Next, differential expression of genes in pairwise comparisons was calculated. Differentially expressed genes were identified with at least 2 log2 fold change and FDR-corrected p value <0.05.
Assembly: Mus musculus CLC reference genome version 86
Supplementary files format and content: tab delimited text file includes raw counts for each sample

extract_protocol:
RNA was isolated according to the manufacturer’s protocol (Qiagen RNeasy RNA isolation kit, #74106). Library prep and RNA sequencing was performed by the Health Science Sequencing core at UPMC Children’s hospital, Pittsburgh.
RNA quality was assessed by an Agilent TapeStation 2200 using the High Sensitivity RNA Tape (Agilent: 5567-5579). Samples (5.5 µl) were used for cDNA generation using the Takara Smart-Seq HT kit (Takara, #634438) with 15 cycles of cDNA amplification following manufactures instructions. Smart-Seq cDNA was assessed for quality on an Agilent TapeStation 2200 using the D5000 High sensitivity ScreenTape (Agilent, #5067-5592). All samples passed QC with full length cDNA were advanced to library preparation using Illumina Nextera XT kit (Illumina: FC-131-1096) with 12 PCR cycles. Libraries were pooled and sequenced on an Illumina NextSeq 500 using a High Output 150 v2.5 cycle flow cell (Illumina: 20024907), 2x75 bp, for an average of ~40 million reads per sample.

treatment_protocol: After the cells were 80% confluent, the culture was treated with 20mM n-octyl IOX1 or 20mM PB-IT (epigenetic inhibitors) for 8 hours, followed by 1ng/ml LPS for 24 hours prior to the collection of cells for RNA extraction.

value: 20mM PB-IT and 1ng/ml LPS


title: Muscle, exercised,60min, rep1

description: Library name: MHITT1


title: input_ph_KO_1-3hr_exp1_chrom1

description: Library name: sample 7


title: Muscle, db/db control group, rep1

description: Library name: MCON1


title: PBIT_LPS_3_S15

description: Library name: PBIT 3


title: Mutant, RL4

city: La Jolla

first: Rongbo

last: Li

state: CA

address: 9500 Gilman Drive

department: Pediatrics

institute: UC San DIego

description: Library name: Mutant, RL4

data_processing:
FASTQ files were aligned to the mouse reference genome mm10 using Cell Ranger v4.0.0 (10x Genomics). The filtered count matrices were loaded into Seurat, genes present in at least 3 cells and cells with a minimum of 200 detected genes were included in downstream analysis, cells with greater than 10% mitochondrial gene content were removed from the dataset. Furthermore, doublets were removed using the DoubleFinder v2.0.3 R package. UMI counts were normalized, scaled, and top variable features were identified using the SCTransform function. UMAP coordinates and cell clustering were determined by the Seurat functions RunUMAP, FindNeighbors, and FindClusters. Clusters were annotated using canonical markers and downstream differential gene expression analysis was performed using the FindMarkers function in Seurat V4. CellChat analysis were performed using the CellChat v2.1.2 R package.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix

extract_protocol:
Briefly, lungs were inflated with dissociation buffer containing Lysis Buffer (RPMI 1640 (Thermo Scientific) with 10 % FBS, 1 mM HEPES (Life Technology), 1 mM MgCl2 (Life Technology), 1 mM CaCl2 (Sigma), 0.525 mg/ml collagenase (Roche), 5 unit/ml dispase (Stemcell Technologies) and 0.25 mg DNase I (Roche)) and incubated at 37 °C shaking for 30 minutes. Following lung dissociation into a single cell suspension, red blood cells were lysed using ACK Lysis Buffer (Gibco). Cells were stained with BV510–CD45 (BioLegend, 103138, 1:100), APC–EpCAM (BioLegend, 118214, 1:100), and PE–CD31 (BioLegend, 102408, 1:100) in FACS buffer, and DAPI was used to eliminate dead cells. Three mice per genotype were pooled together into one FACS sample. Flow sorting was performed with a FACS Aria II (BD Biosciences) and FACS data was analyzed using FlowJo software.
Single cell library preparation was done following standard 10X Chromium Next GEM Single Cell 3’ v3 protocol.

value: Lung


title: PBIT_LPS_2_S14

description: Library name: PBIT 2


title: H2Aub1_ph_wt_1-3hr_exp1_chrom2

description: Library name: sample 6

value: H2Aub1 (Cell signaling (#8240))


title: PBIT_LPS_1_S13

description: Library name: PBIT 1


title: Control, RL1

description: Library name: Control, RL1

value: Control


title: Mutant, RL3

description: Library name: Mutant, RL3


title: RAW264.7 macrophages infected with M. abscessus PLJR962 vector control, 24 h after ATC induction, biological replicate 3

first: Dan

last: Luo

state: Shanghai

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

description:
Library name: PLJR962_KD3
Host–pathogen dual RNA-seq sample; group: PLJR962 control; pathogen reference strain: M. abscessus ATCC 19977; ATC induction after removal of extracellular bacteria; time point: 24 h after ATC induction; read length: paired-end 150 bp; strand-specific/directional library; columns in host and bacterial matrices: PLJR962_KD3.
Dual RNA-seq sample from RAW264.12 macrophages infected with Mycobacteroides abscessus.

data_processing:
Clean reads were obtained after quality control using fastp v0.19.7 with parameters: fastp -g -q 5 -u 50 -n 15 -l 150. Filtering removed adapter-containing reads, reads containing N, and low-quality reads where bases with Qphred ≤ 5 accounted for more than 50% of the read length.
Host clean reads were mapped to the mouse reference genome GRCm39 using HISAT2 v2.0.5 with default parameters. Host gene counts were generated using featureCounts v1.5.0-p3.
Bacterial clean reads were separately mapped to the M. abscessus ATCC 19977 reference genome using Bowtie2 v2.3.4.3 with default parameters. Bacterial gene counts were obtained using HTSeq-count/HTSeq v0.9.1.
Host differential expression analysis was performed using DESeq2 v1.20.0 with thresholds of |log2FC| ≥ 1 and adjusted P ≤ 0.05. Bacterial differential expression analysis was performed using edgeR with thresholds of |log2FC| ≥ 0.58 and FDR < 0.05.
Functional analysis included clusterProfiler for GO/KEGG enrichment and GSEA where applicable. Bacterial genes were annotated using eggNOG-mapper, followed by functional classification and enrichment analysis based on KEGG and COG databases. Additional prokaryotic analyses may include Rockhopper v2.0.3, GATK4, and SNPEff; representative differentially expressed genes were validated by RT-qPCR.
Assembly: Mus musculus reference genome GRCm39; Mycobacterium abscessus ATCC 19977 reference genome.
Supplementary files format and content: Tab-delimited text files include raw gene counts for each sample for the host and bacterial references.
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample for the host and bacterial references.

growth_protocol: RAW264.7 macrophages were seeded in 6-well plates at 1 × 10^6 cells per well and infected with M. abscessus MetRS_KD or PLJR962. For each biological replicate, cells from two wells were pooled.

extract_protocol:
Mixed host–pathogen total RNA was prepared using a modified TRIzol-based extraction protocol. Infected cells were lysed in TRIzol, and intact mycobacterial cells were pelleted by centrifugation. The host RNA-enriched TRIzol supernatant was retained, whereas the bacterial pellet was resuspended in fresh TRIzol and mechanically disrupted with 0.1-mm glass beads using a precooled Precellys homogenizer. Approximately 50% of the host RNA-containing supernatant was recombined with the bacterial lysate, and mixed host–pathogen total RNA was extracted according to the standard TRIzol protocol. RNA samples were treated with DNase I and purified using Hieff NGS RNA Cleaner. RNA integrity and quantity were assessed using an Agilent 2100 Bioanalyzer.
Qualified RNA samples were subjected to both eukaryotic and prokaryotic rRNA depletion, followed by strand-specific RNA-seq library construction. The workflow included RNA fragmentation, random-primer reverse transcription, second-strand cDNA synthesis with dUTP incorporation, end repair, A-tailing, adapter ligation, size selection, USER enzyme treatment, PCR amplification, and purification. Library quality was assessed using Qubit 2.0 Fluorometer, Agilent 2100 Bioanalyzer for insert size, and qRT-PCR for effective library concentration. Libraries were sequenced by Novogene using Illumina NovaSeq 6000 paired-end sequencing with PE150 reads.

treatment_protocol: After removal of extracellular bacteria, ATC was added to induce metS knockdown, and infected cells were incubated for an additional 24 h. Both MetRS_KD and PLJR962 control groups received ATC.

value: macrophage

value: PLJR962 vector control


title: H2Aub1_ph_deltaSAM_1-3hr_exp1_chrom2

description: Library name: sample 4

value: 1-3hr old embryos


title: octyl_IOX1_LPS_4_S12

description: Library name: octyl IOX1 4

value: 20mM n-octyl-IOX1 and 1ng/ml LPS


title: RAW264.7 macrophages infected with M. abscessus PLJR962 vector control, 24 h after ATC induction, biological replicate 1

description:
Library name: PLJR962_KD1
Host–pathogen dual RNA-seq sample; group: PLJR962 control; pathogen reference strain: M. abscessus ATCC 19977; ATC induction after removal of extracellular bacteria; time point: 24 h after ATC induction; read length: paired-end 150 bp; strand-specific/directional library; columns in host and bacterial matrices: PLJR962_KD1.
Dual RNA-seq sample from RAW264.10 macrophages infected with Mycobacteroides abscessus.


title: octyl_IOX1_LPS_3_S11

description: Library name: octyl IOX1 3


city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: LP_ATAC-NUP88-0h-2
library prep for ATAC-NUP88-0h-2 derived from ADLI-4-3-84-3-5__OCP_74G

data_processing:
STAR Suite v1.6.1
https://github.com/morphic-bio/STAR-suite
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: .bed, .narrowPeak and unstranded.bw

extract_protocol:
Paired-end libaries
ATAC-sequencing

value: iPSC

tag: editing strategy

value: Knock-in of inducible C-terminal degron

tag: altered gene_symbol

tag: time

tag: model system

tag: condition

value: DMSO

tag: parental cell_line


title: RAW264.7 macrophages infected with M. abscessus metS knockdown strain, 24 h after ATC induction, biological replicate 3

description:
Library name: MetRS_KD3
Host–pathogen dual RNA-seq sample; group: MetRS_KD; pathogen reference strain: M. abscessus ATCC 19977; ATC induction after removal of extracellular bacteria; time point: 24 h after ATC induction; read length: paired-end 150 bp; strand-specific/directional library; columns in host and bacterial matrices: MetRS_KD3.
Dual RNA-seq sample from RAW264.9 macrophages infected with Mycobacteroides abscessus.

value: metS knockdown strain


title: RAW264.7 macrophages infected with M. abscessus metS knockdown strain, 24 h after ATC induction, biological replicate 2

description:
Library name: MetRS_KD2
Host–pathogen dual RNA-seq sample; group: MetRS_KD; pathogen reference strain: M. abscessus ATCC 19977; ATC induction after removal of extracellular bacteria; time point: 24 h after ATC induction; read length: paired-end 150 bp; strand-specific/directional library; columns in host and bacterial matrices: MetRS_KD2.
Dual RNA-seq sample from RAW264.8 macrophages infected with Mycobacteroides abscessus.


title: RAW264.7 macrophages infected with M. abscessus metS knockdown strain, 24 h after ATC induction, biological replicate 1

description:
Library name: MetRS_KD1
Host–pathogen dual RNA-seq sample; group: MetRS_KD; pathogen reference strain: M. abscessus ATCC 19977; ATC induction after removal of extracellular bacteria; time point: 24 h after ATC induction; read length: paired-end 150 bp; strand-specific/directional library; columns in host and bacterial matrices: MetRS_KD1.
Dual RNA-seq sample from RAW264.7 macrophages infected with Mycobacteroides abscessus.


title: CFP4

city: Long Island City

first: Salsabiel

last: El Nagar

state: NY

address: 45-18 Ct Square W

institute: Mangrove Neuro

description: Library name: NesCFP_P1_L2S2

data_processing:
The Cell Ranger Single Cell software suite (10x Genomics) was used to align reads, and generate feature-barcode matrices. The reference genome used was the Genome Reference Consortium Mouse Build 38 (GRCm38, Gencode annotation mm10). Raw reads were processed using the Cell Ranger count program using default parameters.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 including barcodes, feature and matrix files for replicates.

source_name: Cerebellum

extract_protocol:
Nes-CFP and Atoh1-GFP; Nes-CFP mice were euthanized at P1 and the cerebella were dissected in cold HBSS. For Nes-CFP cerebella, only the posterior part was kept, posterior to the primary fissure.  Posterior cerebella or whole cerebella (Nes-CFP; Atoh1-GFP mice) were dissociated in Papain for 30 minutes at 37°C before being washed out in Ovalbumin Tumors were triturated by pipetting up and down using a P1000 and filtered through a 40µm cell strainer. Once the cells were dissociated, Nes-CFP cell pellets were washed with PBS. For each sample (4 samples, 1 cerebellum each), cells were counted using 0.2% Trypan on a hemocytometer and diluted before loading onto a 10X chip, targeting 10,000 viable cells per sample. Nes-CFP; Atoh1-GFP cell pellets were grouped together (3 cerebella for 1 sample) and the double positive population CFP+ GFP+ were sorted using BD FACS aria. Transgene negative, Nes-CFP and Atoh1-GFP cerebella were used as controls to set up the FACS settings. The scRNA-Seq of cell suspensions for the 5 samples was performed on a Chromium instrument (10X genomics) following the user guide manual for 3’ v3.1. Final libraries were sequenced on an Illumina NovaSeq6000 by the IGO core of MSKCC
10x library (3' scRNA-seq)

value: Cerebellum

value: NesCFP


title: H2Aub1_ph_KO_1-3hr_exp1_chrom1

description: Library name: sample 1

data_processing:
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization) using STAR (Dobin et al., 2013). Only sequences that mapped uniquely to the genome with a maximum of two mismatches were considered for further analyses.
Bam files were used as inputs to run Bioconductor packages.
The proportion of D. pseudoobscura reads as compared to D. melanogaster reads in input and in samples was used to normalize the ChIP-seq datasets for histone marks in embryos. Reference samples for normalization with D. pseudoobscura chromatin are indicated. Other samples were normalized based on total read number per million reads. Normalization factor for each sample is indicated.
Assembly: dm6
Supplementary files format and content: Normalized bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).

extract_protocol:
Lysates were clarified from sonicated fixed nuclei. Histone/Protein-DNA complexes were isolated with antibody. D. pseudoobscura chromatin was spiked in before the addition of the antibody.
Libraries were prepared according to manufacturer's instructions.
ChIP-Seq


title: H2Aub1_ph_KO_1-3hr_exp1_chrom2

description: Library name: sample 2


title: octyl_IOX1_LPS_2_S10

description: Library name: octyl IOX1 2

value: macrophages


title: CFP3

description: Library name: NesCFP_P1_L2S1


title: CFP1

description: Library name: NesCFP_P1_L1S1


title: CFP-GFP

description: Library name: Atoh1GFP_NesCFP_P1_L2S3

value: Atoh1GFP; NesCFP


title: NAT10 and Xrp1 KD rep2

last: Lin

address: 2005 Songhu Road, Yangpu District, Shanghai, China

department: College of Life Science

institute: Fudan University

description:
Library name: en_NAT10-RNAi Xrp1-RNAi_2
Column name in processed files:en_GD_Xrp1-2

data_processing:
The resulting cDNA library was sequenced using Illumina Novaseq6000
Reads were further filtered by fastp (version 0.18.0)
paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release109
Supplementary files format and content: csv files include FPKM for each sample
Supplementary files format and content: csv files include diff gene expression(NAT10-RNAi vs Control)
Supplementary files format and content: csv files include diff gene expression(NAT10-RNAi Xrp1-RNAi vs Control)

source_name: Wing disc

growth_protocol: All Drosophila stocks were maintained on standard cornmeal–yeast–agar–syrup food at 25 °C.

extract_protocol:
Total RNA from 100 dissected wing disc was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA quality was assessed on an Agilent 2100 Bioanalyzer(Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beadsThen the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA).

treatment_protocol: Wing discs were dissected from third instar larvae of the indicated genotypes in ice-cold PBS.

value: Wing disc

value: epithelial cells

value: en-GAL4 > UAS-NAT10-RNAi,Xrp1-RNAi


title: LPS_3_S7

description: Library name: LPS 3

value: 1ng/ml LPS


title: Kmt5a knockout MuSC H4K20me1

city: Madison

first: Jeonghye

middle: Hannah

last: Hwang

state: Wisconsin

address: 1111 Highland ave.

department: Department of Cell and Regenerative Biology

institute: University of Wisconsin-Madison

description: Library name: Kmt5a_KO_H4K20me1

data_processing:
Paired-end raw FASTQ reads were trimmed for adapter sequences and low-quality bases using Trim Galore (v0.6.10) with default parameters.
Trimmed reads were aligned to the mouse reference genome using Bowtie2 (v2.5.4) with the --very-sensitive preset. Alignment parameters were set to --no-mixed --no-discordant -X 1000 for high-confidence paired-end mapping and a maximum fragment length of 1000 bp.
Initial alignments were converted to BAM format and sorted using Samtools (v1.22.1).  Duplicates were identified and removed using Picard Tools (v3.4.0) MarkDuplicates.
Reads overlapping with ENCODE blacklist regions (ENCFF547MET) were removed using bedtools (v2.31.1) intersect. Only propery paired (-f 2) reads with a mapping quiality (MAPQ) score greater than 30 were kept. Reads mapping to the mitochondrial genome were excluded.
The filtered BAM files were converted to bigWig format using deepTools (v3.5.6) bamCoverage. The genome was binned into 10 bp windows, and signal intensity was RPKM normalized. A smoothing window of 30 bp was applied (--smoothLength 30) to reduce local noise.
Assembly: mm10
Supplementary files format and content: bigWig,  RPKM-normalized signal tracks for genome browser visualization
Library strategy: CUT&Tag

extract_protocol:
Freshly isolated MuSCs were bound to Concanavalin A magnetic beads and permeabilized. Cells were incubated overnight at 4 °C with primary antibodies, followed by secondary antibody incubation and binding of protein A–Tn5 transposase preloaded with sequencing adapters. Targeted tagmentation was performed at 37 °C in the presence of MgCl₂. DNA fragments were released by SDS and proteinase K treatment and purified by phenol–chloroform extraction followed by ethanol precipitation.
CUT&Tag DNA fragments were PCR-amplified using indexed i5 and i7 primers and NEBNext HiFi 2× PCR Master Mix. The number of amplification cycles was determined by qPCR to minimize PCR duplicates. Libraries were quantified using the Qubit dsDNA High Sensitivity Assay and fragment size distribution was assessed using an Agilent Bioanalyzer High Sensitivity DNA kit.

treatment_protocol: Muscle stem cells (MuSCs) were isolated from mouse skeletal muscle under quiescent or activated conditions. Quiescent MuSCs were freshly isolated from non-injured muscle, whereas activated MuSCs were isolated 2 days post-injury (2 dpi) following BaCl₂ injection into the tibialis anterior (TA) muscle. For conditional knockout samples, Kmt5a deletion was induced in adult mice using a tamoxifen-inducible Cre recombinase system prior to MuSC isolation. Cells were immediately processed for CUT&Tag.

value: skeletal muscle

value: muscle stem cell

value: Pax7CreERT2/+, Kmt5afl/fl

value: tamoxifen (for KO induction)


title: Activated MuSC H4K20me3 biol rep3

description: Library name: Act3_H4K20me3

value: WT

value: BaCl₂ injury


title: LPS_1_S5

description: Library name: LPS 1


title: Activated MuSC H4K20me3 biol rep1

description: Library name: Act1_H4K20me3


title: NAT10 KD rep2

description:
Library name: en_NAT10-RNAi_2
Column name in processed files:en_GD-2

value: en-GAL4 > UAS-NAT10-RNAi


title: Quiescent MuSC H4K20me3 biol rep3

description: Library name: Q3_H4K20me3


title: Quiescent MuSC H4K20me3 biol rep2

description: Library name: Q2_H4K20me3


title: Quiescent MuSC H4K20me3 biol rep1

description: Library name: Q1_H4K20me3


title: NAT10 KD rep1

description:
Library name: en_NAT10-RNAi_1
Column name in processed files:en_GD-1


title: control_2_S2

description: Library name: control 2

value: untreated


title: Control rep3

description:
Library name: en/+_3
Column name in processed files:en_w1118-3


title: Activated MuSC H4K20me1 biol rep1

description: Library name: Act1_H4K20me1


title: Quiescent MuSC H4K20me1 biol rep3

description: Library name: Q3_H4K20me1


title: control_1_S1

description: Library name: control 1


title: Control rep1

description:
Library name: en/+_1
Column name in processed files:en_w1118-1


title: PL1 cell line REP 2

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

description: Library name: PL1B

data_processing:
Raw read quality was assessed using FASTQC. Reads were aligned to the Mus musculus reference genome (GRCm38, GENCODE M25) using the STAR aligner with default settings. Gene-level quantification (raw counts, transcripts per million [TPM], and fragments per kilobase million [FPKM]) was performed using the RSEM algorithm. Differential gene expression analysis was conducted using the DESeq2.
Assembly: GRCm38, Genome Reference Consortium Mouse Build 38 Organism
Supplementary files format and content: text file contains trancripts per million for each sample

source_name: mouse LUSC

extract_protocol:
Total RNA was extracted from PL and PLA murine cell lines using the RNeasy Plus Universal Mini Kit (QIAGEN) according to the manufacturer’s instructions.
cDNA synthesis was performed using the SMARTer PCR cDNA Synthesis Kit (Clontech), followed by library preparation with the Nextera XT DNA Library Preparation Kit (Illumina), following standard protocols

value: mouse LUSC


title: NIH/3T3 cells KrasWT Dcp1aOE_1

description:
Library name: Dcp1aOE1
mRNA-seq
NIH3T3_KrasWT_mRNA_Dcp1aOE_normalizedcounts.csv
DCP1acl2

data_processing:
Reads were trimmed with cutadapt, and aligned to mm10 with STAR
Assembly: mm39
Supplementary files format and content: Common-separated values of normalized counts

source_name: pancreas

growth_protocol: 10% FBS+1xglutamax in DMEM/F12

extract_protocol:
Trizol total RNA extraction
illumina Truseq stranded mRNA

value: pancreas

value: fibroblast

value: KrasWT Dcp1aOE


title: HMC3_M3KO_rRNAfree_Rep3

first: Yi-Lan

last: Weng

state: Texas

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

description: rRNA depletion

data_processing:
Sequence read were trimmed using Trimmomatic.
The sequence reads were aligned to the human genome (hg38) using the STAR aligner.
Read count tables were then generated based on the STAR alignment to the hg39 transcriptome and subsequently normalized using DESeq2.
Assembly: hg38
Supplementary files format and content: METTL3KO_DEG.txt
Supplementary files format and content: METTL3KO_rRNAfree.TPM.txt

extract_protocol:
Total RNA was extracted using the Trizol reagent, followed by purification with Zymo RNA Clean and Concentrator.
The Smart-seq2 protocol (poly-A selection) was then applied to 100 ng of this RNA for sequencing library construction.  For rRNA-depleted RNA-seq, rRNA was depleted from 100 ng total RNA, followed by library construction using the NEBNext Ultra II Directional RNA Library Prep Kit.

value: microglial cell

value: METTL3 KO


title: PL12  cell line rep 2

description: Library name: PL12B


title: NIH/3T3 cells KrasWT_2

description:
Library name: WT2
mRNA-seq
NIH3T3_KrasWT_mRNA_Dcp1aOE_normalizedcounts.csv
WT2

value: KrasWT


title: PLA4 cell line rep  2

description: Library name: PLA4B


title: RAW264.7 macrophages infected with M. abscessus PLJR962 vector control, 24 h after ATC induction, biological replicate 2

description:
Library name: PLJR962_KD2
Host–pathogen dual RNA-seq sample; group: PLJR962 control; pathogen reference strain: M. abscessus ATCC 19977; ATC induction after removal of extracellular bacteria; time point: 24 h after ATC induction; read length: paired-end 150 bp; strand-specific/directional library; columns in host and bacterial matrices: PLJR962_KD2.
Dual RNA-seq sample from RAW264.11 macrophages infected with Mycobacteroides abscessus.

value: macrophage

value: PLJR962 vector control


title: octyl_IOX1_LPS_1_S9

description: Library name: octyl IOX1 1

value: macrophages

value: 20mM n-octyl-IOX1 and 1ng/ml LPS


title: NAT10 and Xrp1 KD rep3

description:
Library name: en_NAT10-RNAi Xrp1-RNAi_3
Column name in processed files:en_GD_Xrp1-3

value: Wing disc

value: epithelial cells

value: en-GAL4 > UAS-NAT10-RNAi,Xrp1-RNAi


title: LPS_4_S8

description: Library name: LPS 4

value: 1ng/ml LPS


title: PLA4 cell line rep  1

description: Library name: PLA4A


title: HMC3_M3KO_rRNAfree_Rep1

description: rRNA depletion


title: NAT10 and Xrp1 KD rep1

description:
Library name: en_NAT10-RNAi Xrp1-RNAi_1
Column name in processed files:en_GD_Xrp1-1


title: Wild-type MuSC H4K20me1

description: Library name: WT_H4K20me1

value: skeletal muscle

value: muscle stem cell

value: WT littermate

value: tamoxifen (for control)


title: Activated MuSC H4K20me3 biol rep2

description: Library name: Act2_H4K20me3

value: WT

value: BaCl₂ injury


title: WT embryos, 12 hours post fertilization, biol rep 2

description:
Library name: hrs12_2_1
column name in raw counts:hrs12_2_1

value: Embryos

value: Wildtype


title: control_4_S4

description: Library name: control 4

value: untreated


title: PLA cell line REP 1

description: Library name: HHPLAA

value: mouse LUSC


title: control_3_S3

description: Library name: control 3


title: NIH/3T3 KrasG12V, smallRNAseq, rep3

description: Bortoletto_2023_KVC_mirna_normalizedcounts.csv

data_processing:
Cutadapt (v3.5) for adapter trimming
Trimmed, high quality reads were mapped to Mmusculus (GRCm39) using STAR (v2.7.9a)
In R (v4.1.1), gene count matrices were built with GenomicAlignments tool (v1.28).
Count normalization and differential gene expression was performed using DESeq2 (3.14)
Assembly: GRCm39
Supplementary files format and content: comma-separated text files include normalized counts for each sample

extract_protocol:
Cells were lysed and RNA was harvested directly into TRIzol and purfied using a miRNEasy microprep spin kit. RNA was eluted into RNAse free water.
Library was generated using Revvity (previously PerkinElmer) NEXTFLEX small RNA-seq kit V3. Breifly, total RNA was ligated to 3' and 5' adenylated adapters. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Fragments were ethanol purified and subject to PCR amplification. PCR products were gel purified (150 bp fragment) and library quality was assessed on the Agilent TapeStation 4150 system.

value: mouse embryonic fibroblast line


title: HMC3_WT_rRNAfree_Rep3

description: rRNA depletion

value: microglial cell


title: Activated MuSC H4K20me1 biol rep2

description: Library name: Act2_H4K20me1


title: HMC3_WT_rRNAfree_Rep2

description: rRNA depletion


title: NIH/3T3 KrasG12V, smallRNAseq, rep2


title: Primary human keloid fibroblasts, ADSC-mitochondria treatment 24 h, rep2

city: Beijing

first: Wenjing

state: Beijing

address: No. 33 Ba-Da-Chu Road

department: Department of Plastic and Reconstructive Surgery

institute: Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Library name: mitoKF2

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: GRCh38
Supplementary files format and content: Tab‑delimited text file include gene‑count values for each sample.

source_name: Primary human keloid fibroblasts isolated from human keloid tissue

extract_protocol:
1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into a tissue grinding tube (tissue ≤ 30 mg, cells ≤ 1×10⁷). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the sample using a rotor–stator homogenizer, and incubate the lysate at room temperature for 5 min. 1.1.3 Centrifuge at 12,000× g for 3 min at room temperature, then transfer the supernatant onto the AllPrep DNA spin column. 1.1.4 Centrifuge at 12,000× g for 30 s at room temperature. Retain the flow-through in the collection tube for subsequent RNA purification. 1.1.5 Transfer the AllPrep DNA spin column into a new collection tube for DNA purification.  1.2 DNA Purification 1.2.1 Add 500 μL Buffer AW1 to the AllPrep DNA spin column, centrifuge at 10,000× g for 30 s, and discard the flow-through. 1.2.2 Add 500 μL Buffer AW2 to the AllPrep DNA spin column, centrifuge at 10,000× g for 30 s, and discard the flow-through. 1.2.3 Perform a dry spin at 16,000× g for 2 min. Transfer the AllPrep DNA spin column into a 1.5 mL microcentrifuge tube. 1.2.4 Add 50 μL Buffer EB onto the column membrane, and incubate at room temperature for 1 min. 1.2.5 Centrifuge at 16,000× g for 2 min to elute DNA.  1.3 RNA Purification 1.3.1 Add an equal volume of 70% ethanol to the flow-through collected in step 1.1.4 and mix thoroughly by pipetting. 1.3.2 Transfer up to 700 μL of the mixture onto an RNeasy spin column placed in a 2 mL collection tube. 1.3.3 Centrifuge at 10,000× g for 30 s and discard the flow-through. 1.3.4 Add 700 μL Buffer RW1 to the RNeasy spin column. Centrifuge at 10,000× g for 30 s and discard the flow-through. 1.3.5 Add 500 μL Buffer RPE to the RNeasy spin column. Centrifuge at 10,000× g for 30 s and discard the flow-through. 1.3.6 Add another 500 μL Buffer RPE to the RNeasy spin column. Centrifuge at 10,000× g for 30 s and discard the flow-through. 1.3.7 Centrifuge at 16,000× g for 2 min to dry the column membrane, then transfer the RNeasy spin column into a 1.5 mL microcentrifuge tube. 1.3.8 Add 35 μL RNase-free water onto the column membrane and incubate at room temperature for 1 min. 1.3.9 Centrifuge at 16,000× g for 2 min at room temperature to elute purified RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: ADSC-mitochondria treatment 24 h

tag: batch


title: Citeseq, CD45-cells, TET2cKO+IR_HTO

city: Chicago

first: Hua

middle: L

last: Liang

state: IL

department: Department of Radiation and Cellular Oncology

institute: University of Chicago

description:
Library name: TET2cKO+IR_HTO
HTO library of TET2cKO+IR

library_source: other

data_processing:
CITE-seq and Multiome files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10
Supplementary files format and content: CellRanger output files: WT_mRNA_barcodes.tsv.gz, WT_mRNA_features.tsv.gz, WT_mRNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: WT_HTO_barcodes.tsv.gz, WT_HTO_features.tsv.gz, WT_HTO_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: WT+IR_mRNA_barcodes.tsv.gz, WT+IR_mRNA_features.tsv.gz, WT+IR_mRNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: WT+IR_HTO_barcodes.tsv.gz, WT+IR_HTO_features.tsv.gz, WT+IR_HTO_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: TET2cKO_mRNA_barcodes.tsv.gz, TET2cKO_mRNA_features.tsv.gz, TET2cKO_mRNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: TET2cKO_HTO_barcodes.tsv.gz, TET2cKO_HTO_features.tsv.gz, TET2cKO_HTO_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: TET2cKO+IR_mRNA_barcodes.tsv.gz, TET2cKO+IR_mRNA_features.tsv.gz, TET2cKO+IR_mRNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: TET2cKO+IR_HTO_barcodes.tsv.gz, TET2cKO+IR_HTO_features.tsv.gz, TET2cKO+IR_HTO_matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: Tumor

extract_protocol:
CD45-cells sorted from mice. Single cells were encapsulated in  Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell 3’ GEM Library and Gel Bead kit (Garvan Weizmann Centre for Cellular Genomics).
The CITE-seq and hashing protocol described by Stoeckius et al was used to generate an antibody-derived tag (ADT) sequencing library, a hashtag oligo (HTO) library and a 3’ gene expression library (Stoeckius et al.,2017) https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf

value: Tumor

value: mixed sample (unimmunized, immunized)

tag: library type

value: HTO

tag: hto

value: B0301 anti-mouse Hashtag-1 (unimmunized mouse), B0302 anti-mouse Hashtag-2 (immunized mouse), B0303 anti-mouse Hashtag-3 (unimmunized mouse), B0304 anti-mouse Hashtag-4 (immunized mouse)


title: NIH/3T3 cells KrasWT Dcp1aOE_2

first: Ronald

last: Parchem

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
Library name: Dcp1aOE2
mRNA-seq
NIH3T3_KrasWT_mRNA_Dcp1aOE_normalizedcounts.csv
DCP1acl5

value: pancreas

tag: cell line

tag: cell type

value: fibroblast

value: KrasWT Dcp1aOE


title: HMC3_WT_rRNAfree_Rep1

description: rRNA depletion


title: Primary human keloid fibroblasts, ADSC-mitochondria treatment 24 h, rep1

description: Library name: mitoKF1

tag: tissue

value: Primary human keloid fibroblasts isolated from human keloid tissue

tag: treatment


title: Citeseq, CD45-cells, TET2cKO+IR_GEX

description:
Library name: TET2cKO+IR_mRNA
GEX library of TET2cKO+IR

value: mRNA


title: NIH/3T3 empty vector control, smallRNAseq, rep3

tag: genotype

value: WT


title: Primary human keloid fibroblasts, untreated, rep3

description: Library name: KF3


title: HMC3_M3KO_Rep5

description: polyA-seletion

value: METTL3 KO


title: Citeseq, CD45-cells, TET2cKO_HTO

description:
Library name: TET2cKO_HTO
HTO library of TET2cKO


title: NIH/3T3 empty vector control, smallRNAseq, rep2


title: HMC3_M3KO_Rep4

description: polyA-seletion


title: Citeseq, CD45-cells, TET2cKO_GEX

description:
Library name: TET2cKO_mRNA
GEX library of TET2cKO


title: NIH/3T3 empty vector control, smallRNAseq, rep1


title: Primary human keloid fibroblasts, untreated, rep1

description: Library name: KF1


title: HMC3_M3KO_Rep3

description: polyA-seletion


title: Citeseq, CD45-cells, WT+IR_HTO

description:
Library name: WT+IR_HTO
HTO library of WT+IR


title: NIH/3T3 KrasG12V, mRNAseq, rep3

data_processing:
Fastq files were downloaded from Basespace.
Trimmed, high quality reads were mapped to Mmusculus (GRCm39)  or Hsapien (GRCh38) using STAR (v2.7.9a)
In R (v4.1.1), raw data was corrected for batch effect (if present) using ComBat in sva. Gene count matrices were built with GenomicAlignments tool (v1.28).
Count normalization and differential gene expression was performed using DESeq2 (3.14)
Assembly: GRCm39 or GRCh38
Supplementary files format and content: comma-separated text files include normalized counts for each sample

extract_protocol:
mRNA: Cells were lysed and RNA was harvested directly into TRIzol and purfied using a RNEasy miniprep spin kit. RNA was eluted into RNAse free water. TSA: cells were fixed, TSA protocol was carried out (see publication). Biotinylated RNA was enriched and isolated in TRIzol.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strandsynthesis was performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. 3’ ends of fragments were adenylated and Adaptor with hairpin loop structure were ligated. Library fragments (~370-420 bp) were purified with AMPure XP system (Beckman Coulter, Beverly, USA). PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCRprimers and Index (X) Primer. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: PDCs, H3K27me3 CUT&Tag, rep3

first: Chunlong

last: Zhong

address: 150 Jimo Road

department: Department of Neurosurgery

institute: Shanghai East Hospital, School of Medicine, Tongji University

description: Library name: H3K27me3, rep3

data_processing:
Raw sequence reads underwent initial quality control using FastQC (v0.20.0)
Clean reads were obtained by removing adapter sequences, poly-N stretches, and low-quality reads. Quality-filtered reads were then mapped to the reference genome using BWA (v0.7.12)
Peak calling was performed using MACS2 (v2.1.0). Peaks were adjusted to a uniform size (500 bp) centered on peak summits
Motif discovery within these loci was conducted using HOMER (v4.9.1) with the command: findMotifsGenome.pl -len 8,10,12,14 -gc -size given -homer2 -dumpFasta.
Genomic annotation and identification of the nearest genes associated with peaks were performed using ChIPseeker.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

source_name: patient-derived glioma cells

growth_protocol: PDCs were maintained in DMEM/F12 medium supplemented with B27 (1:50, Gibco, USA), basic fibroblast growth factor (bFGF, PeproTech, USA) at 25 ng/mL, epidermal growth factor (EGF, PeproTech, USA) at 50 ng/mL, 10% fetal bovine serum (FBS, Gibco, USA), and 1% penicillin-streptomycin (Thermo, USA).

extract_protocol:
CUT&Tag was performed following previously established protocols using the CUT&Tag assay kit (Vazyme, TD904) (Kaya-Okur et al, 2019).
Approximately 1 × 105 PDCs were bound to ConA beads, followed by overnight incubation at 4°C with either a primary antibody or control IgG on a rotator. The next day, a secondary antibody was added and incubated for 60 minutes at room temperature, followed by pA/G-Tn5 transposome incubation and tagmentation in an activating buffer supplemented with magnesium. Adaptor-ligated DNA fragments were extracted and PCR-amplified using indexing primers (TD202, Vazyme). The amplified products were purified with VAHTS DNA Clean Beads (N411-01, Vazyme), and the DNA library's quantity and quality were assessed using a Qubit™ 4 Fluorometer and Bioanalyzer 2100 (Invitrogen). Libraries were sequenced on the Illumina platform by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), generating 150 bp paired-end reads.

treatment_protocol: 5 μM CX5461 treated for 24 hours

tag: cut&tag antibody

value: Anti-Histone H3 (trimethyl K27) (ab6002, Abcam)

value: patient-derived glioma cells

value: glioma cells

value: IDH/ATRX WT


title: HMC3_M3KO_Rep2

description: polyA-seletion

value: microglial cell


title: HMC3_M3KO_rRNAfree_Rep2

description: rRNA depletion


title: Citeseq, CD45-cells, WT+IR_GEX

description:
Library name: WT+IR_mRNA
GEX library of WT+IR


title: PDCs, H3K27me3 CUT&Tag, rep2

description: Library name: H3K27me3, rep2


title: HMC3_M3KO_Rep1

description: polyA-seletion


title: NIH/3T3 KrasG12V, mRNAseq, rep1

value: mouse embryonic fibroblast line


title: HMC3_WT_Rep5

description: polyA-seletion


title: Citeseq, CD45-cells, WT_HTO

description:
Library name: WT_HTO
HTO library of WT

value: Tumor


title: Citeseq, CD45-cells, WT_GEX

description:
Library name: WT_mRNA
GEX library of WT

value: mixed sample (unimmunized, immunized)


title: PDCs, H3K27me3 CUT&Tag, rep1

description: Library name: H3K27me3, rep1


title: Muscle, db/db control group, rep3

description: Library name: MCON3

data_processing:
Base calling was performed using CASAVA software. Raw sequencing data in FASTQ format were assessed for quality using FastQC.
Adapter sequences and low-quality reads were removed using Trimmomatic (version 0.36) with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
High-quality clean reads were aligned to the mouse reference genome (GRCm39) using STAR aligner (version 2.7.9a) with default parameters.
Gene-level read counts were generated using featureCounts (version 2.0.1) with default parameters against the mouse reference genome annotation (GENCODE).
Additionally, transcript assembly and expression quantification were performed using StringTie (version 2.1.4), and expression levels were normalized as FPKM and TPM values.
Assembly: GRCm39
Supplementary files format and content: Processed data are provided as a tab-delimited text file containing gene-level count matrix for all samples. Rows represent genes (annotated with Ensembl gene IDs and gene symbols), and columns represent individual samples. Values are raw read counts generated by featureCounts.

extract_protocol:
Immediately after euthanasia, heart, kidney, hippocampus, liver, and soleus muscle were rapidly harvested, snap-frozen in liquid nitrogen, and stored at −80°C. Total RNA was extracted from each tissue sample using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's standard protocol. RNA quality and integrity were assessed using a NanoDrop spectrophotometer and an Agilent 2100 Bioanalyzer.
Stranded mRNA-seq libraries were constructed using poly(A) mRNA enrichment with oligo(dT) magnetic beads. Library preparation was performed following the standard protocol of the NEB Next Ultra RNA Library Prep Kit for Illumina. The constructed libraries were sequenced on the Illumina NovaSeq 6000 platform in paired-end 150 bp (PE150) mode. Library construction and sequencing services were provided by Qingke Biotechnology Co., Ltd.

value: Muscle

tag: Sex

value: male

tag: age

value: Eight-week-old

value: C57BL/KsJ db/db mice

value: Normal rearing


title: NIH/3T3 empty vector control, mRNAseq, rep3


title: PDCs, IgG CUT&Tag, rep3

description: Library name: IgG, rep3

value: Rabbit IgG (#2729, Cell Signaling)


title: NIH/3T3 empty vector control, mRNAseq, rep2


title: PDCs, IgG CUT&Tag, rep2

description: Library name: IgG, rep2


title: NIH/3T3 empty vector control, mRNAseq, rep1


title: HMC3_WT_Rep3

description: polyA-seletion


title: 1702 - Female WT

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

institute: Indiana University

description: Library name: 1702

data_processing:
The sequencing data were processed using the Cell Ranger pipeline (v7.2.0, 10x Genomics) and aligned to the mouse reference genome GRCm38 (gex-mm10-2020-A)
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz - cellranger output required for SoupX
Supplementary files format and content: raw_feature_bc_matrix.tar.gz - cellranger output required for SoupX
Supplementary files format and content: analysis.tar.gz - cellranger output required for SoupX

source_name: Anterior cortex

extract_protocol:
Nuclei were isolated using the Singulator 100 system (S2 Genomics) as described before (DOI: 10.1101/2025.03.25.645306), with all steps performed on ice. Briefly, frozen tissue was processed in pre-chilled nucleus isolation cartridges with RNase inhibitor. The resulting nuclear suspension was pelleted by centrifugation, and the pellet was then purified through density gradient centrifugation using a 20% Nuclei Debris Removal Stock Solution in Nuclear Storage Reagent to remove myelin and other debris. Following a final wash and centrifugation step, the purified nuclei were resuspended in resuspension buffer (2% BSA in Nuclear Storage Reagent) for downstream applications.
Purified nuclei were stained with trypan blue and manually counted using a disposable hemocytometer (C-Chip, SKC, Inc., Covington, GA) under a 40x objective on an EVOS XL Core microscope. Each suspension was adjusted to 1,000 nuclei/μL and loaded onto a Chromium Chip G for GEM (gel bead-in-emulsion) generation and barcoding using the Chromium Controller (10x Genomics, Pleasanton, CA). Library preparation followed the manufacturer's protocol using the Chromium Next GEM Single Cell 3′ v3.1 Dual Index kit (10x Genomics) with SPRIselect magnetic bead purification (Beckman Coulter Life Sciences, Indianapolis, IN). cDNA and library integrity were evaluated using an Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA), and concentrations were measured using a Qubit Fluorometer with the dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Waltham, MA). Libraries were sequenced on an Illumina NovaSeq 6000 (v1.5 S2 flow cell) using a 28-10-10-91 read configuration.

value: Anterior cortex

value: F


title: HMC3_WT_Rep2

description: polyA-seletion

value: WT


title: 1699 - Male 5XFAD

description: Library name: 1699

value: M


title: mousePDAC iKras, mRNAseq, +DOX, rep3

source_name: mouse PDAC iKRAS

value: mouse PDAC iKRAS

value: mouse pancreatic cancer cell line


title: HMC3_WT_Rep1

description: polyA-seletion


title: PDCs, CX5461_G4 CUT&Tag, rep3

description: Library name: CX5461_G4, rep3

value: Anti-DNA G-quadruplex (G4) Antibody, clone BG4 (MABE918, Sigma-Aldrich)

value: patient-derived glioma cells

value: glioma cells

value: IDH/ATRX WT


title: mousePDAC iKras, mRNAseq, +DOX, rep2


title: PDCs, CX5461_G4 CUT&Tag, rep2

description: Library name: CX5461_G4, rep2


title: RPMI8226, exp1, GFP-KRAS, input 3, match to R5, R6

city: Bethesda

first: Ryan

middle: M

last: Young

state: MD

address: 9000 Rockvill Pike, Bld. 10, rm. 6N105

department: LYMB

institute: NIH/NCI

description: Library name: RPMI8226_GFP_KRAS_R3

data_processing:
Demultiplexing was performed with DRAGEN (v3.7.4, Illumina), and sequencing reads were aligned to the reference sgRNA library using Bowtie2 (v2.2.9).
Assembly: hg19
Supplementary files format and content: Normalized readcounts for each sgRNA in the Brunello sgRNA library are found in KRAS-stability-norm-counts.txt
Library strategy: CRISPR Screen

source_name: multiple myeloma cell line

growth_protocol: XG7 and RPMI 8226 cells stably expressing Cas9(26) ectopically expressing mNG-KRASG12D were transduced in triplicate with the Brunello sgRNA library. Following transduction, cells were selected with 1 μg/mL puromycin, and Cas9 expression was induced by 100 ng/mL doxycycline treatment. Cells were expanded for 7 days, after which 5×10⁷ cells were harvested and stored as the baseline (input) sample. The remaining ~8×10⁷ cells were stained with anti-Lyt2 antibody (BioLegend) at a 1:1000 dilution in PBS supplemented with 0.5% FBS for 20 min on ice. Cells were washed, resuspended at ~2×10⁷ cells/mL in PBS with 0.5% FBS, and sorted on a Sony MA900 cell sorter to isolate the top and bottom 5% of mNG–KRAS-expressing populations, yielding ~2×10⁶ cells per fraction.  Each biological replicate was independently sorted in two technical replicates.

extract_protocol:
Genomic DNA from sorted populations was extracted using the QIAamp DNA FFPE Advanced Kit (QIAGEN) according to the manufacturer’s protocol.
Genomic DNA from CRISPR screens was processed using a nested PCR strategy. In the first round, sgRNA sequences were amplified from genomic DNA, followed by a second round of PCR to append Illumina-compatible sequencing adapters. Each PCR reaction was performed with ExTaq DNA polymerase (Takara) for 18–20 cycles per round. Amplified products were size-selected using a 2% E-Gel SizeSelect agarose gel (Invitrogen) and quantified with the Qubit dsDNA High-Sensitivity Assay (Thermo Fisher Scientific).

value: multiple myeloma cell line

value: Cas9 clone


title: NIH/3T3 KrasG12V, smallRNAseq, rep1

city: Houston

value: mouse embryonic fibroblast line


title: 1646 - Male 5XFAD;PS19

description: Library name: 1646


title: Primary human keloid fibroblasts, untreated, rep2

description: Library name: KF2

value: Primary human keloid fibroblasts isolated from human keloid tissue

value: untreated


title: 1643 - Male PS19

description: Library name: 1643


title: RPMI8226, exp1, GFP-KRAS, input 2, match to R3, R4

description: Library name: RPMI8226_GFP_KRAS_R2


title: PDCs, CX5461_G4 CUT&Tag, rep1

description: Library name: CX5461_G4, rep1


title: 1636 - Male 5XFAD

description: Library name: 1636


title: mousePDAC iKras, mRNAseq, ethanol control, rep3


title: PDCs, Ctrl_G4 CUT&Tag, rep3

description: Library name: Ctrl_G4, rep3

value: Anti-DNA G-quadruplex (G4) Antibody, clone BG4 (MABE917, Sigma-Aldrich)

value: DMSO


title: Control, RL2

description: Library name: Control, RL2

data_processing:
FASTQ files were aligned to the mouse reference genome mm10 using Cell Ranger v4.0.0 (10x Genomics). The filtered count matrices were loaded into Seurat, genes present in at least 3 cells and cells with a minimum of 200 detected genes were included in downstream analysis, cells with greater than 10% mitochondrial gene content were removed from the dataset. Furthermore, doublets were removed using the DoubleFinder v2.0.3 R package. UMI counts were normalized, scaled, and top variable features were identified using the SCTransform function. UMAP coordinates and cell clustering were determined by the Seurat functions RunUMAP, FindNeighbors, and FindClusters. Clusters were annotated using canonical markers and downstream differential gene expression analysis was performed using the FindMarkers function in Seurat V4. CellChat analysis were performed using the CellChat v2.1.2 R package.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix

extract_protocol:
Briefly, lungs were inflated with dissociation buffer containing Lysis Buffer (RPMI 1640 (Thermo Scientific) with 10 % FBS, 1 mM HEPES (Life Technology), 1 mM MgCl2 (Life Technology), 1 mM CaCl2 (Sigma), 0.525 mg/ml collagenase (Roche), 5 unit/ml dispase (Stemcell Technologies) and 0.25 mg DNase I (Roche)) and incubated at 37 °C shaking for 30 minutes. Following lung dissociation into a single cell suspension, red blood cells were lysed using ACK Lysis Buffer (Gibco). Cells were stained with BV510–CD45 (BioLegend, 103138, 1:100), APC–EpCAM (BioLegend, 118214, 1:100), and PE–CD31 (BioLegend, 102408, 1:100) in FACS buffer, and DAPI was used to eliminate dead cells. Three mice per genotype were pooled together into one FACS sample. Flow sorting was performed with a FACS Aria II (BD Biosciences) and FACS data was analyzed using FlowJo software.
Single cell library preparation was done following standard 10X Chromium Next GEM Single Cell 3’ v3 protocol.

value: Lung

value: Control


title: RPMI8226, exp1, GFP-KRAS, input 1, match to R1, R2

description: Library name: RPMI8226_GFP_KRAS_R1


title: H2Aub1_ph_wt_1-3hr_exp1_chrom1

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

institute: Max Planck Institute of Biochemistry

description: Library name: sample 5

value: 1-3hr old embryos

tag: chip antibody

value: H2Aub1 (Cell signaling (#8240))

tag: normalization factor


title: WT embryos, 9 hours post fertilization, biol rep 2

first: Kaan Ihsan

last: Eskut

address: 195 Huguelet Dr.

institute: University of Kentucky

description:
Library name: hrs9_2
column name in raw counts:hrs9_2

data_processing:
RNA-seq reads from this study were aligned to the reference genome using HISAT2 v2.2.1
Gene expression was quantified from these alignments using StringTie v2.2.1
Assembly: UKy_Petmar_22M1.pri1.0
Supplementary files format and content: comma separated file with raw counts from stringtie v2.2.1

extract_protocol:
Total RNA was extracted from two pools of approximately 100 snap frozen embryos for each condition, following the standard Trizol extraction protocol with the addition of 10 mM dithiothreitol(DTT) to the lysis reaction.
Library preparation and sequencing were conducted by Novogene using their "Plant and Animal Eukaryotic mRNA" pipeline.

value: Embryos

value: Wildtype


title: mousePDAC iKras, mRNAseq, ethanol control, rep2

value: mouse PDAC iKRAS

value: mouse pancreatic cancer cell line

value: WT


title: 1629 - Female PS19

description: Library name: 1629

value: Anterior cortex

value: F


title: PDCs, Ctrl_G4 CUT&Tag, rep2

description: Library name: Ctrl_G4, rep2

value: patient-derived glioma cells

value: glioma cells

value: IDH/ATRX WT


title: H2Aub1_ph_deltaSAM_1-3hr_exp1_chrom1

description: Library name: sample 3


title: 1627 - Female 5XFAD;PS19

description: Library name: 1627


title: mousePDAC iKras, mRNAseq, ethanol control, rep1


title: RPMI8226, exp1, GFP-KRAS Low, R6

description: Library name: RPMI8226_GFP_KRAS_6L

value: multiple myeloma cell line

value: Cas9 clone


title: HU-rep2

city: Kanazawa

first: Santosh

middle: Kumar

last: Gothwal

address: Kakumamachi

country: Japan

institute: Kanazawa University

data_processing:
FastQC
Trim galore
STAR
Deseq2
Edge
Assembly: Grch38
Supplementary files format and content: comma-delimited texxt files include cpm values for combined sample

source_name: Blood

extract_protocol:
Raji cellls treated with DMSO, HU or Thy-Noc  were used for RNA-isolation kit (Takara Bio Japan).
Library construction was performed by Macrogen Japan (TruSeq stranded mRNA kit)

value: Blood

value: Raji

value: B-lymphoma

value: Hydroxyurea


title: PDCs, Ctrl_G4 CUT&Tag, rep1

description: Library name: Ctrl_G4, rep1

value: Anti-DNA G-quadruplex (G4) Antibody, clone BG4 (MABE917, Sigma-Aldrich)

value: DMSO


title: NIH/3T3 KrasG12V, mRNAseq, rep2

value: mouse embryonic fibroblast line


title: CFP2

description: Library name: NesCFP_P1_L1S2

data_processing:
The Cell Ranger Single Cell software suite (10x Genomics) was used to align reads, and generate feature-barcode matrices. The reference genome used was the Genome Reference Consortium Mouse Build 38 (GRCm38, Gencode annotation mm10). Raw reads were processed using the Cell Ranger count program using default parameters.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 including barcodes, feature and matrix files for replicates.

extract_protocol:
Nes-CFP and Atoh1-GFP; Nes-CFP mice were euthanized at P1 and the cerebella were dissected in cold HBSS. For Nes-CFP cerebella, only the posterior part was kept, posterior to the primary fissure.  Posterior cerebella or whole cerebella (Nes-CFP; Atoh1-GFP mice) were dissociated in Papain for 30 minutes at 37°C before being washed out in Ovalbumin Tumors were triturated by pipetting up and down using a P1000 and filtered through a 40µm cell strainer. Once the cells were dissociated, Nes-CFP cell pellets were washed with PBS. For each sample (4 samples, 1 cerebellum each), cells were counted using 0.2% Trypan on a hemocytometer and diluted before loading onto a 10X chip, targeting 10,000 viable cells per sample. Nes-CFP; Atoh1-GFP cell pellets were grouped together (3 cerebella for 1 sample) and the double positive population CFP+ GFP+ were sorted using BD FACS aria. Transgene negative, Nes-CFP and Atoh1-GFP cerebella were used as controls to set up the FACS settings. The scRNA-Seq of cell suspensions for the 5 samples was performed on a Chromium instrument (10X genomics) following the user guide manual for 3’ v3.1. Final libraries were sequenced on an Illumina NovaSeq6000 by the IGO core of MSKCC
10x library (3' scRNA-seq)

value: Cerebellum

value: NesCFP


title: GRKO, 6 months #12

city: Calgary

first: Paul

last: Gordon

state: AB

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

description: Library name: GRKO-6-12

data_processing:
Kallisto 0.48.0 pseudo-mapping with k-mer=31, against Danio rerio Ensembl transcriptome
Assembly: GRCz11
Supplementary files format and content: tab-delimited file containing the raw counts for each transcript (Ensembl identifiers)

organism: Danio rerio

source_name: ovary

extract_protocol:
RNA was extracted using Qiagen RNAeasy kit.
NEB UltraExpress RNA Library Prep Kit (pol;y dT capture)

value: ovary

value: nr3c1 -/- Female

value: 6 months post fertilisation


title: PDCs, CX5461_TOP2B CUT&Tag, rep3

description: Library name: CX5461_TOP2B, rep3

value: TOP2B(20549-2-AP, Proteintech)

value: patient-derived glioma cells


title: RPMI8226, exp1, GFP-KRAS High, R5

description: Library name: RPMI8226_GFP_KRAS_5H


title: 1705 - Female PS19

description: Library name: 1705

value: Anterior cortex

value: F


title: RPMI8226, exp1, GFP-KRAS Low, R5

description: Library name: RPMI8226_GFP_KRAS_5L

value: multiple myeloma cell line

value: Cas9 clone


title: GRKO, 6 months #10

description: Library name: GRKO-6-10


title: 1625 - Female 5XFAD;PS19

description: Library name: 1625


title: 1624 - Female 5XFAD

description: Library name: 1624


title: GRKO, 6 months #11

description: Library name: GRKO-6-11


title: PDCs, CX5461_TOP2B CUT&Tag, rep1

description: Library name: CX5461_TOP2B, rep1

value: glioma cells

value: IDH/ATRX WT


title: RPMI8226, exp1, GFP-KRAS Low, R4

description: Library name: RPMI8226_GFP_KRAS_4L


title: 1620 - Male PS19

description: Library name: 1620

value: M


title: GRKO, 6 months #5

description: Library name: GRKO-6-5


title: PDCs, Ctrl_TOP2B CUT&Tag, rep3

description: Library name: Ctrl_TOP2B, rep3

value: TOP2B(20549-1-AP, Proteintech)


title: 1619 - Male 5XFAD;PS19

description: Library name: 1619


title: PDCs, Ctrl_TOP2B CUT&Tag, rep2

description: Library name: Ctrl_TOP2B, rep2

value: DMSO


title: 1617 - Female WT

description: Library name: 1617

value: WT


title: RPMI8226, exp1, GFP-KRAS High, R4

description: Library name: RPMI8226_GFP_KRAS_4H


title: GRKO, 6 months #2

description: Library name: GRKO-6-2