title: Untreated IκBα SOFNF-kB  rep1

description:
M3_CT1
RNAseq_INDs_ikBa_gene_quantification.txt (col. 11)

source_name: Untreated HT29 IκBα mutant associating with p65 and p50 rep1


title: MOCK, WVC1, scRNAseq

status: Public on May 18 2025

type: SRA

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

country: USA

institute: Columbia University

library_source: transcriptomic single cell

data_processing:
Single cell RNA-Seq FASTQ files were aligned to the human reference genome using CellRanger software (v 5.0.1) to generate raw count matrices for all the 4 different experimental conditions, named as MOCK, 1dpi, 3dpi and 6 dpi
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separeted values files and matrix files (Standard Cell Ranger Output)

molecule: total RNA

organism: Homo sapiens

source_name: Human Ariway Epithelium

growth_protocol: Tracheal basal cells isolated from a de-identified human lung specimen was expanded in PneumaCULT-Ex expansion media (StemCell Technologies, MA) and seeded on collagen-coated 24-well transwells. Once the cells reached confluence, media in the upper chamber of the transwell was removed and the media in the bottom chamber will be changed to PneumaCULT-ALI media (StemCell Technologies, MA) containing compounds including retinoic acid to induce cell differentiation. Differentiation efficiency on ALI day 21 was evaluated by measuring markers for ciliated cell (FOXJ1, ac-Tubulin), secretory cell (MUC5AC, CC10), and basal cells (TP63, KRT5) using immunofluorescence analysis.

extract_protocol:
Cells were removed at days 1, 3, and 6 days post-infection by adding 1 mL of accutase solution (Sigma A6964-100mL) into the basolateral side of the transwell. Cells were incubated at 37 degrees Celsius for 30 minutes until cells were detached.
Cells were centrifuged at 4 degrees celsius at 350 rpm for 5 minutes, were resuspended, and processed for scRNA-Seq on a 10× Genomics Chromium Controller using 5′ Next GEM v1.1 reagents (10× Genomics, Inc) according to the manufacturer’s protocol.

treatment_protocol: All ALI cultures were infected following BSL-3 guidelines. Specifically, ALI-differentiated cells at day 21 were inoculated on the apical surface by SARS- CoV-2 (“Seattle strain”, NR-52281) at a previously tested multiplicity of infection (MOI) of 0.1. After 2 hours, the virus-containing media in the apical chamber was removed and cells will be washed with PBS and continue to grow for 1, 3, and 6 days (days post infection, dpi). Mock infection condition will be performed in parallel using the same reagents without virus. Infection efficiency was determined by plaque assay (titer) performed on Vero-6 cells.

tag: tissue

value: Human Ariway Epithelium

tag: treatment

value: MOCK


title: P-OO-9M-3

city: WuHan

first: Yi-Xuan

last: Tu

state: HuBei

address: 1 Shizishan Rd

department: College of Life Science and Technology

country: China

institute: Huazhong agricultural university

description: Library name: sample6

library_source: transcriptomic

data_processing:
FastQC was used to check the quality of the raw sequence fastq files. High-quality pruning was performed using fastp. Paired end reads were mapped to the reference genome of Ensembl (GRCm39) using HISAT2. And SAMtools is used to sort and index aligned BAM files. Reads were counted using the featureCounts program in the Subread.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: ovary

extract_protocol:
A reverse transcription system was prepared and first-strand cDNA was synthesized using SMART-SeqII amplification technology. A PCR amplification system was prepared for preamplification of cDNA. The corresponding detection methods were selected to check the quality of cDNA.
Qualified amplification products were used for post-library renewal using the transposase method. According to the product requirements, the corresponding detection method was selected to check the quality of the library. After denaturing the PCR product to a single strand, the cyclization reaction system was prepared and the reaction program was set to obtain a single stranded circular product, and the uncyclized linear DNA molecules were digested.

value: ovary

tag: Sex

value: female

tag: cell type

value: oocytes

tag: strain

value: polished rice


title: Untreated IκBα SOFNF-kB  rep2

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

description:
M3_CT2
RNAseq_INDs_ikBa_gene_quantification.txt (col. 12)

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads. Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped toGrCh38 whole genome using STAR with default parameters except for the number of allowed mismatches which was set to 1.
Obtained BAM files with uniquely mapped reads were considered for further analysis. Raw gene expression was quantified using featureCounts tool from subRead software
DESeq2 R package was run to infer differentially expressed genes accross samples. Comparisons between treatment conditions per cell type were considered
Assembly: GRCh38
Supplementary files format and content: txt file generated from featureCounts containing all samples counts in separate columns

source_name: Untreated HT29 IκBα mutant associating with p65 and p50 rep2

growth_protocol: Starting material was freshly cells from HT29 WT, HT29 N108A mutant and HT29 triple mutant which were treated with 0.067 ug/mL, 0.04 ug/mlL and 1 ug/mL with doxycicline for 16h, respectively.

extract_protocol:
Direct RNA isolation with RNeasy Mini Kit (Qiagen Cat. No. 74106)
Samples were processed to obtain cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina NextSeq500 sequencer.

tag: cells

tag: origin

value: IκBalpha triple H84, E85, E86 to A mutant

tag: phenotype

value: untreated

value: human colorectal adenocarcinoma


title: Doxy-treated IκBα SOFPCR2  rep2

description:
108_D2
RNAseq_INDs_ikBa_gene_quantification.txt (col. 10)

source_name: Doxy-treated HT29 IκBα mutant specifically binding to PRC2 rep2

value: IκBalpha N108A mutant

value: doxycicline inducible


title: P-OO-9M-2

description: Library name: sample5


title: Doxy-treated IκBα SOFPCR2  rep1

description:
108_D1
RNAseq_INDs_ikBa_gene_quantification.txt (col. 9)

source_name: Doxy-treated HT29 IκBα mutant specifically binding to PRC2 rep1


title: Asexual Trophozoite-stage tRNA, biol rep2

city: Stockholm

first: Sherwin

last: Chan

address: Solnavagen 9

country: Sweden

institute: Karolinska Institutet

description:
Library name: T2-tRNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file

library_source: other

data_processing:
Basecalls were performed using Generate FASTQ v 2.0.1 for NextSeq output
UMI was extracted using UMI_tools v1.1.2.  Sequence reads were trimmed for adaptor sequence using fastx_toolkit v0.0.14
Trimmed reads were mapped to the reference using Bowtie2 v2.2.1 with sensitive local mode
UMI  deduplication was performed using UMI_tools v1.1.2. Read counts were then extracted from htseq-count v0.9.1
Assembly: In-house curated tRNA reference including both Plasmodium falciparum and homo sapiens tRNA sequences
Supplementary files format and content: tab-delimited text files (tabular) of raw count for each Sample

molecule: other

organism: Plasmodium falciparum

growth_protocol: infected red blooc cells were grown in RPMI 1640 supplemented with 10% pooled human serum, cultured at 37C at 5% CO2, 5% O2

extract_protocol:
MirVana miRNA isolation kit (invitrogen), small RNA purification according to manufacturer's instruction, for periodate treatment, the RNA was treated in 100 mM NaOAc/HOAc, pH 4.8 and freshly prepared 50 mM NaIO4 at room temperature for 30 mins and then column purified. The recovered RNA was treated again in 60 mM sodium borate, pH 9.5 at 45°C for 90 min before final column purification
library was constructed using TGIRT3 modular kit (InGex), 100ng small RNA was used as input, RNA-Seq, single-end 120 cycles

tag: cell line

value: Infected red blood cell

tag: genotype

value: complete medium


title: 3dpi rep3

city: 杭州市

first: li

last: yucong

state: 浙江省

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

data_processing:
fastaq RNA-seq data adapter trimming by fastap
RNA-seq data quality control
Quantification of feature counts to obtain raw counts by STAR  methods
Assembly: smed_20140614_60aa_genes-noref.gtf
Supplementary files format and content: fuzhao_Count_gene.matrix.csv
Supplementary files format and content: fuzhao_TPM_gene.matrix.csv

organism: Schmidtea mediterranea

source_name: whole body

extract_protocol:
RNA was harvested using TRIGene Reagent(Genstar Cat#ZP118-101S). 400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA SMARTER Library Prep Kit for Illumina following manufacturer's protocols.

value: whole body

value: WT

value: lethal irradiation

tag: time

value: Day 3


title: 3dpi rep2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: 3dpi rep1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: P-OO-9M-1

description: Library name: sample4


title: WT rep3

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生

value: no treatment

value: Day 0


title: Asexual Schizont-stage tRNA, biol rep2

description:
Library name: S2-tRNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: B-OO-9M-3

description: Library name: sample3

value: ovary

value: black rice


title: Asexual ring-stage tRNA, biol rep2

description:
Library name: R2-tRNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: Asexual Schizont-stage tRNA, biol rep1

description:
Library name: S1-tRNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: Untreated IκBα SOFPCR2  rep1

description:
108_CT1
RNAseq_INDs_ikBa_gene_quantification.txt (col. 7)

source_name: Untreated HT29 IκBα mutant specifically binding to PRC2 rep1


title: Untreated IκBα SOFPCR2  rep2

description:
108_CT2
RNAseq_INDs_ikBa_gene_quantification.txt (col. 8)

source_name: Untreated HT29 IκBα mutant specifically binding to PRC2 rep2


title: B-OO-9M-2

description: Library name: sample2

value: female

value: oocytes


title: WT rep2

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Internal melanocytes

city: Brookline

first: Swathy

last: Babu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: SORT-seq from internal melanocytes

data_processing:
BWA was used to align paired-end read to danRer11.
Count tables were generated using MapAndGo.
Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0
Assembly: danRer11
Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat
Library strategy: SORT-seq

molecule: polyA RNA

organism: Danio rerio

source_name: Internal melanocytes

growth_protocol: mitfa-/-; roy-/- zebrafish injected with mitfa:GFP were Raised to adulthood to obtain tissues

extract_protocol:
Respective tissues were mechanically dissociated, digested in TrypLE for 45 min (Invitrogen, 12563011), 40uM filtered, spun down, and resuspended in FACs buffer (dPBS Mg+/Ca+ free, with 2% FBS, pen/strep).
Cells were heat-lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification, library preparation was done following the CEL-Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina).

value: Internal melanocytes

value: melanocytes

value: mitfa-/-; roy-/- fish injected with mitfa:GFP


title: B-OO-9M-1

description: Library name: sample1


title: Asexual Trophozoite-stage tRNA, biol rep1

description:
Library name: T1-tRNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: WT rep1

address: 浙江省杭州市西湖区墩余路600号西湖大学云谷校区E8120

institute: 西湖大学生命科学学院博士研究生


title: Asexual ring-stage tRNA, biol rep3

description:
Library name: R3-tRNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: Cutaneous melanocytes

description: SORT-seq from cutaneous melanocytes

source_name: Cutaneous melanocytes

value: Cutaneous melanocytes


title: Asexual ring-stage tRNA, biol rep1

description:
Library name: R1-tRNA
fastq files from four lanes of the same flow cells were concatenated into one fastq file


title: hmr-5pifq 21℃ w/ suc rep2

status: Public on May 17 2025

city: Riverside

first: Meng

last: Chen

state: CA

address: 2150 Batchelor Hall, 900 University Ave.

institute: University of California, Riverside

data_processing:
The raw reads were mapped to the Araport11 genome using STAR version 2.7.7a
The number of reads mapped uniquely to each annotated gene was counted using FeatureCounts version 2.0.1
Transcript levels were measured in fragments per kilobase per million total mapped fragments (FPKM). Differentially expressed genes were identified using DEseq2 v1.35.0 with a fold change of two and P < 0.01
Assembly: Araport11
Supplementary files format and content: Comma-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: 4-d-old seedlings

growth_protocol: Arabidopsis seeds were surface-sterilized and plated on half-strength Murashige and Skoog media either with or without 1% (w/v) sucrose. Seeds were stratified in the dark at 4 ˚C for 5 days before treatment of specific light and temperature in an LED chamber.

extract_protocol:
100 mg seedlings were collected by flash freezing in liquid nitrogen at the indicated time point. Plant tissues were ground to a fine powder in liquid nitrogen, and total RNA was extracted using Quick-RNA MiniPrep kit with on-column DNase I digestion (Zymo Research).
Library construction was performed by Novogene. Ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, enzyme digestion to remove UTP-containing second strand cDNA, amplification, and purification. The libraries were subjected to paired-end 150 bp sequencing using NovaSeq 6000

treatment_protocol: Seedlings were initially grown under 50 μmol m−2 s−1 red light at 21 °C for 2 days (48h) to induce germination. Subsequently, they were either maintained in the same conditions or transferred to 27 °C under the same light conditions for two additional days (48h). For sucrose treatment, media were supplemented with 1% (w/v) sucrose

value: 4-d-old seedlings

value: 21C with sucrose treatment


title: hmr-5pifq 21℃ w/ suc rep3


title: hmr-5pifq 27℃ w/ suc rep1

value: 27C with sucrose treatment


title: hmr-5pifq 27℃ w/ suc rep2


title: hmr-5pifq 27℃ w/ suc rep3


title: hmr-5 27℃ w/ suc rep3


title: hmr-5 21℃ w/ suc rep1


title: hmr-5 27℃ w/ suc rep1


title: hmr-5 21℃ w/ suc rep2


title: hmr-5 27℃ w/ suc rep2


title: hmr-5 27℃ w/o suc rep3

value: 27C without sucrose treatment


title: hmr-5 27℃ w/o suc rep2


title: hmr-5 21℃ w/o suc rep3

value: 21C without sucrose treatment


title: hmr-5 21℃ w/ suc rep3


title: hmr-5 21℃ w/o suc rep2


title: hmr-5 27℃ w/o suc rep1


title: Human scar processed with Visium spatial transcriptomics

city: Tucson

first: Kellen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

description: Library name: Visium-Scar

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation of mkfastq
Then aligned against the mm10 (mouse) genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 10,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin.
Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis.
Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Highly variable genes were identified, and cells were scaled by regression to the fraction of mitochondrial transcripts. Aggregated data was then evaluated using uniform manifold approximation and projection (UMAP) analysis
Assembly: mm10 (mouse)
Supplementary files format and content: filtered feature matrix
Library strategy: Spatial Transcriptomics

source_name: Human tissue section

growth_protocol: Freshly isolated murine cells from murine or human skin or healed scars.

extract_protocol:
Tissue was enzymatically digested, cells were collected and washed. These cellular suspensions were then submitted for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA).
cDNA was fragmented followed by end repair and A-tailing at 65°C for 30min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA libraries were sequenced on a HiSeq 4000 Illumina platform aiming for 50,000 reads per cell.

treatment_protocol: Murine wounds were either given mechanical strain or not, in either knockout or wildtype mice, or treated with FAKI, then submitted for scRNA-seq analysis.

value: Human tissue section

value: all cells


title: Neural retina, double cKO (Rho-Cre/Mfn1flx/flx/Mfn2flx/flx) rep4

city: Madison

first: Ryo

last: Hagimori

state: WI

address: 425-G Henry Mall

department: Department of Medical Genetics

institute: University of Wisconsin-Madison

description: Library name: Sample8

data_processing:
NetworkAnalyst 3.0
Assembly: mm10
Supplementary files format and content: csv file includes raw counts and TPM for each sample

source_name: Neural retina

extract_protocol:
Total RNA was extracted from neural retinas with an RNeasy Plus Universal Mini kit (Qiagen, Hilden, Germany) following the Manufacturer’s protocols.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) following manufacturer’s instructions.

value: Neural retina

value: double cKO

value: 1 month old


title: Neural retina, double cKO (Rho-Cre/Mfn1flx/flx/Mfn2flx/flx) rep3

description: Library name: Sample7


title: Human skin processed with Visium spatial transcriptomics

description: Library name: Visium-Skin


title: Neural retina, Control (cre-/-) rep4

description: Library name: Sample4

value: cre-/-


title: Neural retina, double cKO (Rho-Cre/Mfn1flx/flx/Mfn2flx/flx) rep2

description: Library name: Sample6


title: Neural retina, Control (cre-/-) rep3

description: Library name: Sample3


title: Neural retina, double cKO (Rho-Cre/Mfn1flx/flx/Mfn2flx/flx) rep1

description: Library name: Sample5


title: Neural retina, Control (cre-/-) rep2

description: Library name: Sample2


title: Neural retina, Control (cre-/-) rep1

description: Library name: Sample1


title: Co-culture of murine macrophages and fibroblasts in 3D collagen scaffold with mechanical strain

description: Library name: Co-S

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation of mkfastq
Then aligned against the mm10 (mouse) genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 10,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin.
Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis.
Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Highly variable genes were identified, and cells were scaled by regression to the fraction of mitochondrial transcripts. Aggregated data was then evaluated using uniform manifold approximation and projection (UMAP) analysis
Assembly: mm10 (mouse)
Supplementary files format and content: filtered feature matrix

source_name: freshly isolated cells from co-cultured in vitro scaffold


title: Mechanically strained incision in WT mouse from parabiotic mice with FAKI GFP cells

description: Library name: Strain-FAKI-GFP

source_name: freshly isolated cells from scar tissue

value: freshly isolated cells from scar tissue


title: Mechanically strained incision in Lyz2-Cre+Ptk2-flox knockout mouse

description: Library name: Strain-KO


title: Incision with no additional mechanical strain from parabiotic mice GFP cells

description: Library name: NoStrain-GFP


title: hmr-5pifq 21℃ w/ suc rep1


title: Mechanically strained incision in wildtype mouse

description: Library name: Strain-WT


title: Incision with no additional mechanical strain

description: Library name: NoStrain-WT


title: Mechanically strained incision in wildtype mouse from parabiotic mice GFP cells

description: Library name: Strain-GFP


title: B34 neuron

city: Nanjing

first: Guo

last: Zhang

address: Xianlin street 163

institute: Nanjing University

description: Library name: Sample 2

data_processing:
We analyed sequencing data using software HISAT2 and the reference genome AplCal3.0 (GCF_000002075.1), and obtained read counts for each gene sample using the featureCounts tool.
Assembly: AplCal3.0 (GCF_000002075.1)
Supplementary files format and content: csv file includes raw counts for each sample

organism: Aplysia californica

source_name: single neuron cell

extract_protocol:
The ganglion was fixed using ethyl alcohol for approximately 1-2 minutes. Subsequently, the cells surrounding the target neuron was carefully removed using forceps. The target neuron was then isolated carefully using scissors and forceps. Once isolated, the single neuron was transferred into a tube containing RNAase inhibitor and lysis buffer.
RNA libraries for RNA-seq were prepared using TAKARA mRNA-Seq Library Prep Kit following manufacture's protocols.

value: single neuron cell

value: WT

value: ethanol fix


title: B20 neuron

description: Library name: Sample 1


title: Unwounded murine skin

description: Library name: WT_unwounded

source_name: freshly isolated cells from skin tissue

value: freshly isolated cells from skin tissue


title: NC rep2

city: WuXi

first: Guoshui

last: Tao

address: No. 8, Zhongnan West Road, Wuxi City, Jiangsu Province

institute: WuXi Traditional Chinese Medicine Hospital

description: Library name: DZ-2

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence（Clean Data）for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.0.5.
we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used TPM to standardize the expression. Then difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.
we mapped all the genes to Terms in the Gene Ontology database and calculated the numbers of differentially enriched genes in each Term. Using topGO to perform GO enrichment analysis on the differential genes, calculate P-value by hypergeometric distribution method (the standard of significant enrichment is P-value <0.05), and find the GO term with significantly enriched differential genes to determine the main biological functions performed by differential genes. ClusterProfiler (3.4.4) software was used to carry out the enrichment analysis of the KEGG pathway of differential genes, focusing on the significant enrichment pathway with P-value <0.05.
Assembly: GCF_026167765.1_ASM2616776v1_genomic
Supplementary files format and content: txt file include TPM values for each Sample

organism: Staphylococcus aureus

source_name: strain

growth_protocol: A single colony of the Staphylococcus aureus strain was selected and inoculated into 5 mL of broth medium. The culture was cultured at 37°C with a speed of 200 revolutions per minute (rpm) for 24 hours.

extract_protocol:
total RNA was extracted with RNAprep pure Cell/Bacteria Kit (Tiangen Biotech; Beijing; China)
RNA libraries for RNA-seq were prepared using VAHTS Universal V10 RNA-seq Library Prep Kit ollow ing manufacturer's protocols.

treatment_protocol: Three sterilized 250 mL conical flasks were filled with 43.75 mL of broth medium, to which 6.25 mL of the EO working solution and 43 μL of the bacterial suspension were added, and the contents were mixed well. Another three sterilized 250 mL conical flasks were prepared with 50 mL of broth medium and 43 μL of the bacterial solution each, followed by thorough mixing. The flasks were cultured at 200 rpm and 37°C for 5 hours.

value: strain


title: EO rep3

description: Library name: HFY-3


title: NC rep3

description: Library name: DZ-3


title: NC rep1

description: Library name: DZ-1


title: hmr-5 21℃ w/o suc rep1

value: 4-d-old seedlings


title: Same as above but also with FAKI treatment

description: Library name: Co-FAKI

value: freshly isolated cells from co-cultured in vitro scaffold


title: 53

city: Los Angeles

first: Matteo

last: Pellegrini

address: 610 Charles E. Young Dr S

institute: University of California, Los Angeles

description:
Library name: 53
Targeted bisulfite sequencing

library_source: genomic

data_processing:
Reads were trimmed using fastp with TruSeq adapters trimmed and options --length_required 40 --trim_front1 5 --trim_tail1 5 --trim_front2 5 --trim_tail2 5 --trim_poly_g --qualified_quality_phred 20.
Alignment to the Xenopus tropicalis reference genome (XENTR_10.0) was performed with BisulfiteBolt (v1.6.0) Align (default options). PCR duplicates were removed with samtools (v1.11) markdup (option: -r).
BSBolt CallMethylation (arguments: -BQ 10 -MQ 20 -IO -CG) and BSBolt AggregateMatrix (arguments: -min-coverage 100 -min-sample 1.0 -CG) were used to create the methylation matrix. Data processing code is available at github.com/ronanbennett/xenopus-aging
Assembly: Xenopus tropicalis genome (version XENTR_10.0)
Supplementary files format and content: A tab-separated matrix containing CpG site methylation levels (decimal value between 0 and 1). Rows represent CpGs, columns represent frogs.

molecule: genomic DNA

organism: Xenopus tropicalis

source_name: hindlimb webbing

growth_protocol: 192 Xenopus tropicalis frogs were housed at the National Xenopus Resource (RRID: SCR_013731) in multi-rack recirculating aquatic systems with a constant temperature of 25°C and 12 hr light /12 hr dark cycle.

extract_protocol:
Disposable biopsy punches were used to collect tissue (VWR 21,909–140) from the hindlimb webbing of each of the 187 adult frogs in the dataset. For the 5 tadpoles, the entire organism was used for DNA extraction.
500 nanograms of purified DNA per sample was sonicated using a Covaris R230. Fragmented DNA was subject to end-repair, dA-tailing and ligation to pre-methylated unique-dual-indexed custom adapters (Integrated DNA Technologies). Pooled samples (16 samples per pool) were subject to hybridization with biotinylated oligonucleotide probes (synthesized by Integrated DNA Technologies) complementary to the previously identified age-associated regions in the presence of Xenopus Hybloc DNA (Applied Genetics Laboratories - Melbourne, FL, US). Captured fragments were then treated with bisulfite (Zymo Lightning), then amplified and purified according to (Morselli et al. 2023). Samples were subject to QC, normalized and combined in two pools of 96 samples, and each sequenced on NovaSeq6000 (SP lanes) as paired-end 150 bases.

treatment_protocol: All animals have a Nigerian strain genetic background (NXR_1018). Some frogs in the dataset are transgenic; this information is given in the strain annotation.

value: hindlimb webbing

tag: age (days,_approximate_for_tadpoles)


title: 55

description:
Library name: 55
Targeted bisulfite sequencing


title: 58

description:
Library name: 58
Targeted bisulfite sequencing


title: 60

description:
Library name: 60
Targeted bisulfite sequencing


title: 56

description:
Library name: 56
Targeted bisulfite sequencing


title: 57

description:
Library name: 57
Targeted bisulfite sequencing


title: 59

description:
Library name: 59
Targeted bisulfite sequencing


title: 54

description:
Library name: 54
Targeted bisulfite sequencing


title: 50

description:
Library name: 50
Targeted bisulfite sequencing


title: 52

description:
Library name: 52
Targeted bisulfite sequencing


title: 51

description:
Library name: 51
Targeted bisulfite sequencing


title: Mechanically strained incision

description: Library name: WT_strain


title: 49

description:
Library name: 49
Targeted bisulfite sequencing


title: EO rep2

description: Library name: HFY-2


title: 47

description:
Library name: 47
Targeted bisulfite sequencing


title: EO rep1

description: Library name: HFY-1


title: 48

description:
Library name: 48
Targeted bisulfite sequencing


title: 46

description:
Library name: 46
Targeted bisulfite sequencing


title: 45

description:
Library name: 45
Targeted bisulfite sequencing


title: 44

description:
Library name: 44
Targeted bisulfite sequencing


title: 43

description:
Library name: 43
Targeted bisulfite sequencing


title: 42

description:
Library name: 42
Targeted bisulfite sequencing


title: OE_Rep1

city: Málaga

first: Vitor

last: Amorim-Silva

address: Av. Louis Pasteur, 49

institute: University of Malaga

description:
Library name: Sample 10
Column name in ALL_SAMPLES_FPKM_VitC_RNAseq.xlsx: OE_1

data_processing:
The reads were quality filtered and trimmed using Trimmomatic version 0.36 (Bolger, Lohse, & Usadel, 2014) with paired-end mode options: -threads 8 -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36.
The resulting reads were then aligned to the TAIR10 version of the Arabidopsis thaliana genome sequence (https://www.arabidopsis.org/) using Hisat2 version 2.1.0 (Kim, Langmead, & Salzberg, 2015). These read alignments (in BAM format) were used for transcript quantification with the cuffdiff program of the Cufflinks version 2.2.1 package (Trapnell et al., 2013). The resulting read alignments were visualized and clustered using Tablet software (Milne et al., 2013) and CummeRbund R package version 2.23.0 (Goff, Trapnell, & Kelley, 2014). To determine DEGs, a False Discovery Rate (q-value) cutoff of ≤ 0,05 was set.
Assembly: Reads were then aligned to the TAIR10 version of the Arabidopsis thaliana genome sequence (https://www.arabidopsis.org/)
Supplementary files format and content: xlsx file includes FPKM values for each sample

source_name: Arabidopsis rosettes

growth_protocol: Four-weeks old plant rosettes grown under short day photoperiod (8-h light/16-h darkness cycle, 22±1ᵒC, 300±70 μmol photons m-2 s-1) were collected 30 minutes after the lights turned on and flash-frozen in liquid nitrogen.

extract_protocol:
RNA from three independent replicates per genotype, where each replicate was composed of 8 randomized rosettes, was extracted with Trizol following the manufacturer’s protocol. RNA quality and integrity were validated using the Bioanalyzer 2100 (Agilent Technologies Santa Clara, CA, USA), being the RNA integrity number (RIN) >8.0 for all biological replicates.
Paired-end Illumina mRNA libraries were generated using the TruSeq stranded mRNA according to the manufacturer’s instructions (Illumina Inc., San Diego, CA, USA) for the mutant and control lines. Libraries were sequenced in an Illumina NextSeq550 platform, and 2 x 75 bp paired-end reads were generated.

treatment_protocol: No treatment

value: Arabidopsis rosettes

tag: developmental stage

value: Four-weeks old

value: vtc2/OE-VTC2 L15

value: No treatment


title: vtc4_Rep1

description:
Library name: Sample 7
Column name in ALL_SAMPLES_FPKM_VitC_RNAseq.xlsx: vtc4_1


title: vtc4_Rep2

description:
Library name: Sample 8
Column name in ALL_SAMPLES_FPKM_VitC_RNAseq.xlsx: vtc4_2


title: vtc4_Rep3

description:
Library name: Sample 9
Column name in ALL_SAMPLES_FPKM_VitC_RNAseq.xlsx: vtc4_3


title: vtc2_Rep3

description:
Library name: Sample 6
Column name in ALL_SAMPLES_FPKM_VitC_RNAseq.xlsx: vtc2_3


title: OE_Rep2

description:
Library name: Sample 11
Column name in ALL_SAMPLES_FPKM_VitC_RNAseq.xlsx: OE_2


title: OE_Rep3

description:
Library name: Sample 12
Column name in ALL_SAMPLES_FPKM_VitC_RNAseq.xlsx: OE_3


title: 41

description:
Library name: 41
Targeted bisulfite sequencing


title: vtc2_Rep1

description:
Library name: sample 4
Column name in ALL_SAMPLES_FPKM_VitC_RNAseq.xlsx: vtc2_1


title: vtc2_Rep2

description:
Library name: Sample 5
Column name in ALL_SAMPLES_FPKM_VitC_RNAseq.xlsx: vtc2_2


title: 75

description:
Library name: 75
Targeted bisulfite sequencing


title: 39

description:
Library name: 39
Targeted bisulfite sequencing


title: 40

description:
Library name: 40
Targeted bisulfite sequencing


title: WT_Rep2

description:
Library name: Sample 2
Column name in ALL_SAMPLES_FPKM_VitC_RNAseq.xlsx: WT_2


title: WT_Rep1

description:
Library name: Sample 1
Column name in ALL_SAMPLES_FPKM_VitC_RNAseq.xlsx: WT_1


title: 73

description:
Library name: 73
Targeted bisulfite sequencing


title: siControl_no_induction_3

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description: Library name: siControl_no_induction_3

data_processing:
RNA-seq libraries were sequenced on an Illumina NovaSeq 6000 (2x150)
Reads were trimmed using cutadapt (v1.16) to remove adapters
Reads were aligned to the hg38 genome using STAR (v2.5.2a)
Gene counts were calculated using featureCounts (v1.6.2)
Differentially expressed genes were identified using Degust (https://degust.erc.monash.edu/)
Assembly: hg38
Supplementary files format and content: tab-delimited file with raw counts for every sample and gene
Supplementary files format and content: bigwig files

source_name: RPE-1 cells

growth_protocol: RPE-1/Tet-PLK4 GFP-CETN were grown in DMEM/high glucose with Glutamine (Cytiva or Gibco) at 37°C with 5% CO2.

extract_protocol:
RNA was isolated with the Monarch Total RNA isolation miniprep kit (New England Biolabs)
Libraries were generated using the Nugen Universal Plus mRNA-seq library construction kit (part no. 0508)

treatment_protocol: Cells were treated with small interfering RNAs using Lipofectamine RNAiMAX Transfection Reagent (ThermoFisher Scientific). PLK4 was induced with 1µg/mL doxycycline (Sigma-Aldrich).

value: RPE-1 cells

value: RPE-1 cells with Cetn2 tagged with GFP to identify centrioles, and PLK4 under control of the rtTA, doxycycline inducible promoter

value: expression of scramble siRNA and no induction of PLK4


title: 72

description:
Library name: 72
Targeted bisulfite sequencing


title: siControl_no_induction_2

description: Library name: siControl_no_induction_2


title: VFO__52R__Cohort_Female_organoids__33360.D__Carrier-Mutant__d120

city: Baltimore

first: Jennifer

last: Erwin

state: MD

address: 855 N Wolf St.

institute: Lieber Institute for Brain Development

description:
Library name: 52R
Column name in count files: 52R

data_processing:
SPEAQeasy pipeline (PMID: 33932985) with the following parameters nextflow $ORIG_DIR/main.nf \     --input $input_path \     --output $output_path \     --sample "paired" \     --reference "hg38" \     --strand "reverse" \     --strand_mode "declare" \     --use_star \     --annotation "/dcs04/lieber/ds2b/projects/SPEAQeasyAnnotation" \     -with-report execution_reports/JHPCE_run.html \     -profile jhpce \     -resume
Assembly: hg38
Supplementary files format and content: GZIP compressed raw counts for genes or exons (*__counts.tsv.gz)
Supplementary files format and content: GZIP compressed info for genes or exons (*__rowData.tsv.gz)
Supplementary files format and content: GZIP compressed sample metrics info (*__colData.tsv.gz)
Supplementary files format and content: Metadata table (xdp_bulkrnaseq_metadata.tsv)

source_name: Ventral forebrain organoid

extract_protocol:
Zymo Direct-zol RNA kit or Zymo Quick-DNA/RNA Microprep Plus Kit
Illumina TruSeq Stranded Total RNA Gold Kit

value: Ventral forebrain organoid

tag: differentiation cohort

value: Carrier-Mutant

tag: day of_maturation

tag: extraction kit

tag: disease status

value: patient

tag: rin

tag: individual


title: siControl_no_induction_1

description: Library name: siControl_no_induction_1

tag: treatment


title: 4

description:
Library name: 4
Targeted bisulfite sequencing

tag: tissue


title: 3

description:
Library name: 3
Targeted bisulfite sequencing

tag: strain


title: 5

description:
Library name: 5
Targeted bisulfite sequencing


title: 2

description:
Library name: 2
Targeted bisulfite sequencing


title: WT_Rep3

description:
Library name: Sample 3
Column name in ALL_SAMPLES_FPKM_VitC_RNAseq.xlsx: WT_3

value: WT


title: VFO__36N__Cohort_C__33363.D__XDP__d90

description:
Library name: 36N
Column name in count files: 36N

value: C

value: XDP


title: VFO__40N__Cohort_C__33363.D-3C2__DELTA-SVA-XDP__d120

description:
Library name: 40N
Column name in count files: 40N

value: DELTA-SVA-XDP

value: healthy


title: 38

description:
Library name: 38
Targeted bisulfite sequencing


title: 36

description:
Library name: 36
Targeted bisulfite sequencing


title: VFO__38N__Cohort_C__33362.C__Control__d120

description:
Library name: 38N
Column name in count files: 38N

value: Control


title: 74

description:
Library name: 74
Targeted bisulfite sequencing

value: hindlimb webbing


title: VFO__39N__Cohort_C__33363.D__XDP__d120

description:
Library name: 39N
Column name in count files: 39N


title: 35

description:
Library name: 35
Targeted bisulfite sequencing


title: 32

description:
Library name: 32
Targeted bisulfite sequencing


title: VFO__34N__Cohort_C__33363.D-3C2__DELTA-SVA-XDP__d60

description:
Library name: 34N
Column name in count files: 34N


title: VFO__35N__Cohort_C__33362.C__Control__d90

description:
Library name: 35N
Column name in count files: 35N


title: 34

description:
Library name: 34
Targeted bisulfite sequencing


title: 31

description:
Library name: 31
Targeted bisulfite sequencing


title: 33

description:
Library name: 33
Targeted bisulfite sequencing


title: VFO__33N__Cohort_C__33363.D__XDP__d60

description:
Library name: 33N
Column name in count files: 33N


title: VFO__50N__Cohort_Female_organoids__33360.A__Carrier-Mutant__d120

description:
Library name: 50N
Column name in count files: 50N


title: VFO__31N__Cohort_C__33363.D-3C2__DELTA-SVA-XDP__d30

description:
Library name: 31N
Column name in count files: 31N


title: VFO__32N__Cohort_C__33362.C__Control__d60

description:
Library name: 32N
Column name in count files: 32N


title: VFO__29N__Cohort_C__33362.C__Control__d30

description:
Library name: 29N
Column name in count files: 29N


title: 29

description:
Library name: 29
Targeted bisulfite sequencing


title: 30

description:
Library name: 30
Targeted bisulfite sequencing


title: VFO__47N__Cohort_Female_organoids__33360.A__Carrier-Mutant__d90

description:
Library name: 47N
Column name in count files: 47N


title: 1-Web-Punches

description:
Library name: 1-Web-Punches
Targeted bisulfite sequencing


title: 25

description:
Library name: 25
Targeted bisulfite sequencing


title: VFO__27N__Cohort_B__33109.2B__XDP__d120

description:
Library name: 27N
Column name in count files: 27N

value: B


title: VFO__28N__Cohort_B__33109.2B-3A12__DELTA-SVA-XDP__d120

description:
Library name: 28N
Column name in count files: 28N


title: VFO__37N__Cohort_C__33363.D-3C2__DELTA-SVA-XDP__d90

description:
Library name: 37N
Column name in count files: 37N


title: 37

description:
Library name: 37
Targeted bisulfite sequencing


title: 23

description:
Library name: 23
Targeted bisulfite sequencing


title: 22

description:
Library name: 22
Targeted bisulfite sequencing


title: VFO__26__Cohort_B__33114.C__Control__d120

description:
Library name: 26
Column name in count files: 26


title: VFO__24N__Cohort_B__33109.2B__XDP__d90

description:
Library name: 24N
Column name in count files: 24N


title: VFO__25N__Cohort_B__33109.2B-3A12__DELTA-SVA-XDP__d90

description:
Library name: 25N
Column name in count files: 25N


title: VFO__22N__Cohort_B__33109.2B-3A12__DELTA-SVA-XDP__d60

description:
Library name: 22N
Column name in count files: 22N


title: 114

description:
Library name: 114
Targeted bisulfite sequencing


title: VFO__23N__Cohort_B__33114.C__Control__d90

description:
Library name: 23N
Column name in count files: 23N


title: 113

description:
Library name: 113
Targeted bisulfite sequencing


title: 21

description:
Library name: 21
Targeted bisulfite sequencing


title: VFO__21N__Cohort_B__33109.2B__XDP__d60

description:
Library name: 21N
Column name in count files: 21N


title: 111

description:
Library name: 111
Targeted bisulfite sequencing


title: 110

description:
Library name: 110
Targeted bisulfite sequencing


title: 112

description:
Library name: 112
Targeted bisulfite sequencing


title: VFO__19N__Cohort_B__33109.2B-3A12__DELTA-SVA-XDP__d30

description:
Library name: 19N
Column name in count files: 19N


title: 109

description:
Library name: 109
Targeted bisulfite sequencing


title: VFO__20__Cohort_B__33114.C__Control__d60

description:
Library name: 20
Column name in count files: 20


title: VFO__18N__Cohort_B__33109.2B__XDP__d30

description:
Library name: 18N
Column name in count files: 18N


title: VFO__17N__Cohort_B__33114.C__Control__d30

description:
Library name: 17N
Column name in count files: 17N


title: 108

description:
Library name: 108
Targeted bisulfite sequencing


title: VFO__16N__Cohort_A__33109.2G-2F2__DELTA-SVA-XDP__d120

description:
Library name: 16N
Column name in count files: 16N

value: A


title: 107

description:
Library name: 107
Targeted bisulfite sequencing


title: 106

description:
Library name: 106
Targeted bisulfite sequencing


title: VFO__15N__Cohort_A__33109.2G-1A4__DELTA-SVA-XDP__d120

description:
Library name: 15N
Column name in count files: 15N


title: VFO__14N__Cohort_A__33109.2G__XDP__d120

description:
Library name: 14N
Column name in count files: 14N


title: 105

description:
Library name: 105
Targeted bisulfite sequencing


title: 101

description:
Library name: 101
Targeted bisulfite sequencing


title: VFO__12N__Cohort_A__33109.2G-2F2__DELTA-SVA-XDP__d90

description:
Library name: 12N
Column name in count files: 12N


title: 103

description:
Library name: 103
Targeted bisulfite sequencing


title: 100

description:
Library name: 100
Targeted bisulfite sequencing


title: NT-2

city: Shanghai

first: Shuo

last: Zhu

address: No. 500 of Zhennan Road

institute: Tongji University

description:
Library name: NT-2
Column name in gene_FPKM.xlsx: NT-2

data_processing:
The original image data files obtained from high-throughput sequencing were converted into raw data through base calling analysis using CASAVA. Raw reads were quality-checked, and clean reads were obtained after filtering out the low-quality reads (average base quality < 20) or reads containing more than 5 ambiguous bases (N). These clean reads were aligned to the C. albicans SC5314 reference genome using HISAT2 software. Gene expression levels were quantified using FeatureCounts, and FPKM values were calculated to compare gene expression differences across samples.
Assembly: https://www.ncbi.nlm.nih.gov/genome/21? genome_assembly_id=294796
Supplementary files format and content: xslx. file include FPKM values for each Sample

organism: Candida albicans

extract_protocol:
For each sample, 1 mL of the culture was collected for RNA extraction using the Column Fungal RNA Extraction Kit (KANLANG, KL-10112BTN), following strict sterile and enzyme-free protocols.
RNA integrity was assessed using the Agilent 4150 system, and only samples meeting quality thresholds were used for cDNA library construction. Sequencing was performed on the DNBSEQ-T7 (MGI) platform. After the sample passes quality control, eukaryotic mRNA is enriched using Oligo(dT)-attached magnetic beads. The mRNA is then randomly fragmented by adding a fragmentation buffer. Using the mRNA as a template, the first strand of cDNA is synthesized with random hexamer primers. Subsequently, the second strand of cDNA is synthesized by adding buffer, dNTPs, and DNA polymerase I. The double-stranded cDNA is purified using AMPure XP beads. The purified double-stranded cDNA then undergoes end repair, A-tailing, and adapter ligation, followed by size selection with AMPure XP beads. Finally, PCR amplification is performed to enrich the final cDNA library.

treatment_protocol: The overnight-cultured SC5314 was adjusted to 2×10⁶ cells/mL and incubated with or without NT-a9 (4×MIC) or FLC (4×MIC) at 30°C with shaking at 200 rpm for 12 hours, with three replicates per group

tag: cell type

value: fungi, Candida albicans

value: NT-a9(4×MIC), biol rep2


title: 104

description:
Library name: 104
Targeted bisulfite sequencing


title: 24

description:
Library name: 24
Targeted bisulfite sequencing


title: 102

description:
Library name: 102
Targeted bisulfite sequencing


title: VFO__53R__Cohort_A__33109.2G__XDP__d90

description:
Library name: 53R
Column name in count files: 53R


title: VFO__8N__Cohort_A__33109.2G-2F2__DELTA-SVA-XDP__d60

description:
Library name: 8N
Column name in count files: 8N


title: NT-1

description:
Library name: NT-1
Column name in gene_FPKM.xlsx: NT-1

value: NT-a9(4×MIC), biol rep1


title: FLC-3

description:
Library name: FLC-3
Column name in gene_FPKM.xlsx: FLC-3

value: FLC(4×MIC), biol rep3


title: 99

description:
Library name: 99
Targeted bisulfite sequencing


title: NT-3

description:
Library name: NT-3
Column name in gene_FPKM.xlsx: NT-3

value: NT-a9(4×MIC), biol rep3


title: 97

description:
Library name: 97
Targeted bisulfite sequencing


title: 7

description:
Library name: 7
Targeted bisulfite sequencing


title: VFO__9__Cohort_A__33113.2I__Control__d90

description:
Library name: 9
Column name in count files: 9

value: Ventral forebrain organoid


title: VFO__13N__Cohort_A__33113.2I__Control__d120

description:
Library name: 13N
Column name in count files: 13N


title: 6

description:
Library name: 6
Targeted bisulfite sequencing


title: 98

description:
Library name: 98
Targeted bisulfite sequencing


title: 65

description:
Library name: 65
Targeted bisulfite sequencing


title: FLC-1

description:
Library name: FLC-1
Column name in gene_FPKM.xlsx: FLC-1

value: FLC(4×MIC), biol rep1


title: 8

description:
Library name: 8
Targeted bisulfite sequencing


title: FLC-2

description:
Library name: FLC-2
Column name in gene_FPKM.xlsx: FLC-2

value: FLC(4×MIC), biol rep2


title: VFO__7N__Cohort_A__33109.2G-1A4__DELTA-SVA-XDP__d60

description:
Library name: 7N
Column name in count files: 7N


title: Ctrl-3

description:
Library name: Ctrl-3
Column name in gene_FPKM.xlsx: Ctrl-3

value: WT

value: Control, biol rep3


title: 63

description:
Library name: 63
Targeted bisulfite sequencing


title: 62

description:
Library name: 62
Targeted bisulfite sequencing


title: 120

description:
Library name: 120
Targeted bisulfite sequencing

value: tubb2b GFP


title: Ctrl-2

description:
Library name: Ctrl-2
Column name in gene_FPKM.xlsx: Ctrl-2

value: Control, biol rep2


title: VFO__2N__Cohort_A__33109.2G__XDP__d30

description:
Library name: 2N
Column name in count files: 2N

value: XDP

value: patient


title: VFO__4N__Cohort_A__33109.2G-2F2__DELTA-SVA-XDP__d30

description:
Library name: 4N
Column name in count files: 4N

value: DELTA-SVA-XDP

value: healthy


title: 116

description:
Library name: 116
Targeted bisulfite sequencing

value: hindlimb webbing


title: Ctrl-1

description:
Library name: Ctrl-1
Column name in gene_FPKM.xlsx: Ctrl-1

value: fungi, Candida albicans

value: Control, biol rep1


title: VFO__3N__Cohort_A__33109.2G-1A4__DELTA-SVA-XDP__d30

description:
Library name: 3N
Column name in count files: 3N

value: A


title: HCT116 cells, no 4sU labeling,rep3

city: Guangzhou

first: Hui

last: Wang

state: GuangDong

address: 190 Kaiyuan Avenue, Huangpu District

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH, CAS

description: Library name: noFn_no4sU_3

data_processing:
Raw data was demultiplexed at first to different samples by fastq-multx (v1.4.2) according to the specific barcode. Reads were then trimmed using Trim Galore (v0.6.10) and R1 was selected for subsequent analysis, the 35 bp polyA sequence at the 5’ end of R1 was cut by cutadapt (v4.9).Trimmed reads were mapped to the human genome (GRCh38, Ensembl v113) using STAR (v2.7.11a) with Gencode annotation of the human genome (v44). GRAND-SLAM (v2.0.7b) software was used to analysis the labeling RNA and the conversion of T to C base with default parameter.
Assembly: GRCh38, Ensembl v113
Supplementary files format and content: tsv file includes raw counts, length and every base counts (A/T/G/C) for each sapmles produced by GRAND-SLAM software.

source_name: HCT116 cells

extract_protocol:
Total RNAs were extracted using the TRNzol Universal Reagent Kit (TIANGEN, DP424), and 50 ng input RNA was used for cDNA libraries preparion.
RNA libraries for SLAM-seq were prepared according to VASA-seq protocols

value: HCT116 cells

value: colorectal cancer cells


title: 13

description:
Library name: 13
Targeted bisulfite sequencing

value: tlx3 F0


title: VFO__1N__Cohort_A__33113.2I__Control__d30

description:
Library name: 1N
Column name in count files: 1N

value: Ventral forebrain organoid

value: Control


title: 28

description:
Library name: 28
Targeted bisulfite sequencing

value: gtpbp2 F1 KO


title: 119

description:
Library name: 119
Targeted bisulfite sequencing


title: VFO__5N__Cohort_A__33113.2I__Control__d60

description:
Library name: 5N
Column name in count files: 5N


title: 118

description:
Library name: 118
Targeted bisulfite sequencing


title: 27

description:
Library name: 27
Targeted bisulfite sequencing


title: HCT116 cells, no 4sU labeling,rep1

description: Library name: noFn_no4sU_1


title: 20

description:
Library name: 20
Targeted bisulfite sequencing


title: 26

description:
Library name: 26
Targeted bisulfite sequencing


title: VFO__6N__Cohort_A__33109.2G__XDP__d60

description:
Library name: 6N
Column name in count files: 6N


title: 115

description:
Library name: 115
Targeted bisulfite sequencing


title: 61

description:
Library name: 61
Targeted bisulfite sequencing


title: CFU-E, 2-DG  treated 3, 24h (RNAseq)

city: zhengzhou

first: Hengchao

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

data_processing:
The original data were filtered and compared with the reference genome, which can be downloaded from the Ensemble database (http://www.ensembl.org/index.html,human genome build GRCh38.87). Using HISAT2 version 2.2.1 (http://daehwankimlab.github.io/hisat2/) to read the counts for each gene in each sample and gene expression was assessed by StringTie (https://ccb.jhu.edu/software/stringtie/). TPM (Transcripts Per Kilobase of exon model per Million mapped reads) was calculated to evaluate the expression level, and DESeq2 version 1.38.3 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) was packaged to identify differentially expressed genes from the data. Gene ontology (GO) enrichment analysis and visualization of DEGs was performed using the Metascape (www.metascape.org/) online tool with q < 0.05.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

source_name: Cord blood

growth_protocol: CD34+ cells were puriﬁed from cord blood by positive selection using the magnetic-activated cell sorting magnetic beads system, according to the manufacturer’sinstructions. The purity of isolated CD34+ cells was 95% to 98%. The cell culture procedure was comprised of 3 phases. Composition ofthe base culture medium was Iscove’sModiﬁed Dulbecco’s Medium, 2%human peripheral blood plasma, 3% human AB serum, 200 mg/mL Holo-human transferrin, 3 IU/mL heparin, and 10 mg/mL insulin. In the ﬁrst phase(day 0 to day 6), CD34+ cells at a concentration of 105/mL were cultured inthe presence of 10 ng/mL stem cell factor, 1 ng/mL IL-3, and 3 IU/mL erythropoietin. In the second phase (day 7 to day 11), IL-3 was omitted from the culture medium. In the third phase that lasted until day 21, the cell concentration was adjusted to 106/mL on day 11 and to 5 3 106/mL on day 15, respectively, the medium for this phase was the base medium plus 3 IU/mL erythropoietin, and the concentration of transferrin was adjusted to 1mg/mL. The cells were cultured at 37°C in the presence of 5% CO2.

extract_protocol:
Experiment procedure before sequencing: 2 million cells were collected and washed twice with PBS. RNA was extracted from cell culture using RNA extract kits (74104, Qiagen) according to the manufacturer’s instruction.
RNA was extracted and used as cDNA input, cDNA library was prepared by Illumina Truseq DNA library kit, and sequenced on Illumina NovaSeq 6000.

treatment_protocol: Here, we set 2.5mM 2-DG dosing which was an inhibitor of glycolysis to inhibit lactate level. After treated with 2.5mM 2-DG for 24h, we performed a RNA-seq of DMSO and 2-DG treated CFU-E cells.

value: Cord blood

value: Erythroid cells


title: HCT116 cells, 4sU labeling,rep3

description: Library name: noFn_4sU_3


title: 64

description:
Library name: 64
Targeted bisulfite sequencing


title: HCT116 cells, 4sU labeling,rep2

description: Library name: noFn_4sU_2


title: CFU-E, 2-DG  treated 2, 24h (RNAseq)

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: 17

description:
Library name: 17
Targeted bisulfite sequencing


title: 19

description:
Library name: 19
Targeted bisulfite sequencing


title: HCT116 cells, no 4sU labeling,rep2

description: Library name: noFn_no4sU_2


title: 16

description:
Library name: 16
Targeted bisulfite sequencing


title: 18

description:
Library name: 18
Targeted bisulfite sequencing


title: HCT116 cells, 4sU labeling,rep1

description: Library name: noFn_4sU_1


title: 15

description:
Library name: 15
Targeted bisulfite sequencing


title: CFU-E, 2-DG  treated 1, 24h (RNAseq)

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: 14

description:
Library name: 14
Targeted bisulfite sequencing


title: HCT116 cells infected by Fn, no 4sU labeling,rep3

description: Library name: Fn_no4sU_3


title: CFU-E, Control 3, 24h (RNAseq)

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

value: DMSO


title: 164

description:
Library name: 164
Targeted bisulfite sequencing


title: HCT116 cells infected by Fn, no 4sU labeling,rep2

description: Library name: Fn_no4sU_2


title: CFU-E, Control 2, 24h (RNAseq)

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: 161

description:
Library name: 161
Targeted bisulfite sequencing


title: 162

description:
Library name: 162
Targeted bisulfite sequencing


title: CFU-E, Control 1, 24h (RNAseq)

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: HCT116 cells infected by Fn, no 4sU labeling,rep1

description: Library name: Fn_no4sU_1


title: 157

description:
Library name: 157
Targeted bisulfite sequencing


title: CFU-E, Control, 24h (CUT&Tag)

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

data_processing:
Trim Galore version 0.6.6 was used to remove adapter and low-quality reads. Align paired-end reads using Bowtie2 version 2.5.1 with options: “--end-to-end --very-sensitive”. Peak calling uses MACS2 version 2.1.1 with threshold: q<0.01, and the differential binding sites of H3K4me3 were calculated using the DiffBind version 3.8.4 with the parameter log2foldchange >=1 and FDR <0.05 (https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/diffbind.html). Scatterplots, correlation plots, and heatmaps are displayed using deepTools version 2.5.7. Annotation of peaks is performed using an R package ChIPseeker version 1.34.1(https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/ ChIPseeker.html). The CUT&Tag peak/region <1000bp from the nearest TSS was defined as the promoter. Hypergeometric Optimization of Motif Enrichment (HOMER) version 4.11 (http://homer.ucsd.edu/homer/) was used to search for the binding motif.
Assembly: GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Cells were harvested, counted and centrifuged for 3 min at 600×g at room temperature. 1×105 cells were washed twice in 500μL wash buffer by gentle pipetting. Concanavalin A coated magnetic beads were prepared as the kit manual described, 10 µL of activated beads were added per sample and incubated at RT for 10 min. According to the kit instructions, cells were sequentially incubated with ConA Beads, primary antibody (anti-H3K14la antibody, secondary antibody (Goat anti-Rabbit IgG) and Hyperactive PG-TN5/PA-TN5 Transposon and then fragmented. The fragmented DNA was extracted from the samples and amplified by PCR.
CUT&Tag libraries were constructed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD901, Vazyme, China) and sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated.

treatment_protocol: Here, we set 2.5mM 2-DG dosing which was an inhibitor of glycolysis to inhibit lactate level. After treated with 2.5mM 2-DG for 24h, we performed a H3K14la CUT&Tag of DMSO and 2-DG treated CFU-E cells.

tag: antibody

value: IgG


title: HCT116 cells infected by Fn, 4sU labeling 2 hours,rep3

description: Library name: Fn_4sU_3


title: 163

description:
Library name: 163
Targeted bisulfite sequencing


title: CFU-E, 2-DG  treated 2, 24h (CUT&Tag)

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: 159

description:
Library name: 159
Targeted bisulfite sequencing


title: 158

description:
Library name: 158
Targeted bisulfite sequencing


title: 152

description:
Library name: 152
Targeted bisulfite sequencing


title: CFU-E, 2-DG  treated 3, 24h (CUT&Tag)

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: MINS7d_4

city: Sapporo

first: Makishi

last: Maeda

address: South1 West 16 291

department: Anesthesiology

country: Japan

institute: Sapporo Medical University School of Medicine

description: Library name: MINS7d-4

data_processing:
Sequencing was performed on the NovaSeq 6000 (Illumina) platform in a 2 × 150 bp paired‐end configuration with over 20 million reads per samples.
The sequenced reads were trimmed using cutadapt and mapped to the reference genome (mm10, Ensembl version 111) using the STAR aligner.
Assembly: mm10, Ensembl version 111
Supplementary files format and content: tsv files include raw, tpm , FPKM values for each Sample

source_name: myocardium

extract_protocol:
Total RNA was extracted from the left ventricle using TRIzol reagent (Thermo Fisher Scientific) and treated with a Turbo DNase-free kit (Thermo Fisher Scientific)
The sequencing libraries for RNA-seq  were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs; #E7760), according to the manufacturer's instructions.

value: myocardium

value: post-abdominal surgery

tag: time point

tag: Sex

value: male


title: HCT116 cells infected by Fn, 4sU labeling 2 hours,rep2

description: Library name: Fn_4sU_2

tag: cell line


title: 155

description:
Library name: 155
Targeted bisulfite sequencing

value: hindlimb webbing


title: HCT116 cells infected by Fn, 4sU labeling 2 hours,rep1

description: Library name: Fn_4sU_1


title: 156

description:
Library name: 156
Targeted bisulfite sequencing


title: 154

description:
Library name: 154
Targeted bisulfite sequencing


title: 153

description:
Library name: 153
Targeted bisulfite sequencing


title: MINS7d_3

description: Library name: MINS7d-3


title: MINS7d_2

description: Library name: MINS7d-2


title: CFU-E, 2-DG  treated 1, 24h (CUT&Tag)

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: 160

description:
Library name: 160
Targeted bisulfite sequencing


title: 149

description:
Library name: 149
Targeted bisulfite sequencing


title: 151

description:
Library name: 151
Targeted bisulfite sequencing


title: CFU-E, Control 3, 24h (CUT&Tag)

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: CFU-E, Control 2, 24h (CUT&Tag)

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: MINS7d_1

description: Library name: MINS7d-1


title: 150

description:
Library name: 150
Targeted bisulfite sequencing


title: 76

description:
Library name: 76
Targeted bisulfite sequencing


title: 10

description:
Library name: 10
Targeted bisulfite sequencing

value: sox3 F0


title: 148

description:
Library name: 148
Targeted bisulfite sequencing


title: CFU-E, Control 1, 24h (CUT&Tag)

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: MINS24h_4

description: Library name: MINS24h-4


title: 84

description:
Library name: 84
Targeted bisulfite sequencing


title: 81

description:
Library name: 81
Targeted bisulfite sequencing


title: THP-1 cells,H37rv,3

city: chongqing

first: yusheng

last: yang

address: Department of Orthopedic, Southwest Hospital, Army Medical University

data_processing:
In brief, poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.
Subsequently, the mRNA was fragmented into small pieces using divalent cations at 94℃ for 8 min. The cleaved RNA fragments were then used to generate first-strand cDNA with reverse transcriptase and random primers. This was followed by the synthesis of second-strand cDNA using DNA Polymerase I and RNase H.
The resulting cDNA fragments underwent an end repair process, the addition of a single ‘A’ base, and ligation of the adapters.
The products were then purified and enriched with PCR to create the final cDNA library. The purified libraries were quantified using a Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the molar concentration. Clusters were generated by cBot with the library diluted to 10 pM and then sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
Assembly: mm9
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

growth_protocol: The THP-1 cell lines were purchased from ATCC and maintained in 1640 medium (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA) and 1% Penicillin & Streptomycin solution (Solarbio, CHN) in a 5% CO2 atmosphere at 37℃.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, GER).
Paired-end libraries were synthesized using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following the TruSeq™ RNA Sample Preparation Guide.

treatment_protocol: Cells were seeded in 24-well plates with phorbol myristate (PMA, Sigma Aldrich, USA) at a concentration of 100 ng/ml. Adherent THP-1 cells were infected with H37Rv at an MOI of 1 for 4 hours, and then washed three times with PBS to remove bacteria. Experiments involving live H37Rv were performed in a P2+ facility.

value: Tohoku Hospital Pediatrics-1

value: Infected with H37rv


title: MINS24h_3

description: Library name: MINS24h-3


title: THP-1 cells,H37rv,2


title: MINS24h_2

description: Library name: MINS24h-2


title: 78

description:
Library name: 78
Targeted bisulfite sequencing


title: 82

description:
Library name: 82
Targeted bisulfite sequencing


title: 79

description:
Library name: 79
Targeted bisulfite sequencing


title: MINS3h_4

description: Library name: MINS3h-4


title: THP-1 cells,H37rv,1


title: 71

description:
Library name: 71
Targeted bisulfite sequencing

value: WT Superman


title: 70

description:
Library name: 70
Targeted bisulfite sequencing


title: THP-1 cells,control 3


title: 77

description:
Library name: 77
Targeted bisulfite sequencing


title: MINS24h_1

description: Library name: MINS24h-1


title: THP-1 cells,control 2


title: 69

description:
Library name: 69
Targeted bisulfite sequencing


title: MINS3h_3

description: Library name: MINS3h-3


title: 68

description:
Library name: 68
Targeted bisulfite sequencing


title: 66

description:
Library name: 66
Targeted bisulfite sequencing


title: THP-1 cells,control 1


title: 67

description:
Library name: 67
Targeted bisulfite sequencing


title: MINS3h_2

description: Library name: MINS3h-2


title: WAALPRE

city: Burwood

first: Danielle

last: Hiam

state: Vic

address: 221 Burwood Hwy

department: IPAN

country: Australia

institute: Deakin University

data_processing:
Reads underwent quality check with FastQC (v0.11.9); Kallisto (v0.46.1) was used to map reads to the human reference genome (HomoSapien GRCh38) and to generate transcript counts.
Assembly: HomoSapien GRCh38
Supplementary files format and content: 3col.tsv- Long format of aligned raw gene counts
Supplementary files format and content: GeneCounts_ RAW DATA.xlsx- Wide format of aligned raw gene counts

source_name: Skeletal Muscle

extract_protocol:
RNA was extracted using AllPrep RNA/RNA/miRNA universal kit (Qiagen) according to manufacturer instructions
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol

treatment_protocol: 27 Pre-menopausal, untrained females (aged 23.5 ± 4.8) underwent a 12-week resistance training program. Skeletal muscle biopsies were collected before (PRE) and after (POST) the training program to quantify the effect of resistance training on the transcriptome

value: vastus lateralis muscle

value: Skeletal Muscle

value: Female

tag: age of_donor

value: PRE


title: 147

description:
Library name: 147
Targeted bisulfite sequencing

value: OLIG2 F1

tag: age (days,_approximate_for_tadpoles)


title: MINS3h_1

description: Library name: MINS3h-1


title: 146

description:
Library name: 146
Targeted bisulfite sequencing


title: 80

description:
Library name: 80
Targeted bisulfite sequencing


title: TEOCPRE


title: SOBRPOST

value: POST


title: 143

description:
Library name: 143
Targeted bisulfite sequencing


title: MINS0h_3

description: Library name: MINS0h-3


title: 142

description:
Library name: 142
Targeted bisulfite sequencing


title: MINS0h_2

description: Library name: MINS0h-2


title: 141

description:
Library name: 141
Targeted bisulfite sequencing

value: CMV MEM GFP


title: 139

description:
Library name: 139
Targeted bisulfite sequencing


title: 138

description:
Library name: 138
Targeted bisulfite sequencing


title: 144

description:
Library name: 144
Targeted bisulfite sequencing


title: 145

description:
Library name: 145
Targeted bisulfite sequencing


title: 137

description:
Library name: 137
Targeted bisulfite sequencing


title: 140

description:
Library name: 140
Targeted bisulfite sequencing


title: SOBRPRE


title: SICEPOST


title: SHVAPOST


title: MINS0h_1

description: Library name: MINS0h-1


title: MINS0h_4

description: Library name: MINS0h-4


title: SHVAPRE


title: 136

description:
Library name: 136
Targeted bisulfite sequencing


title: Young_Male_4_VGAT

city: Oklahoma City

first: Ana Luiza

last: Drumond-Bock

state: OK

address: 825 NE 13th St.

department: Aging & Metabolism Research Program

institute: Oklahoma Medical Research Foundation

description:
Library name: Young_Male_4_VGAT
VGAT_NuTRAP.csv, column_T

data_processing:
Using a high-performance computing (HPC) cluster, fastq files were submitted to pre-alignment quality control (QC) analysis (Ewels et al., 2016), after which adaptors were removed and reads were trimmed for poly-G and Q<20 (Krueger et al., 2023).
Reads were aligned to the mouse genome assembly mm39 using STAR v2.7.10b (Dobin, 2022; Dobin et al., 2013) and quantification was performed using featureCounts (Liao et al., 2014), and post alignment QC reports generated.
Assembly: Mus_musculus.GRCm39.111
Supplementary files format and content: Raw feature counts

source_name: Brain

growth_protocol: Experimental mice were aged naturally within our colony.

extract_protocol:
Mice were anesthetized with isoflurane and rapidly decapitated. To minimize activity induced transcriptomic changes, the brain was immediately removed and placed in ice-cold choline chloride cutting solution. 600 µm-thick horizontal brain slices were collected, accounting for the entire rostral-caudal length of the ventral midbrain. Sections were moved onto a pre-chilled collection block, where the surrounding tissue (such as the pons, hippocampus, and cortex) was removed. Remaining bilateral midbrain portions (containing the substantia nigra pars compacta [SNc] and the ventral tegmental area [VTA]) were collected into Eppendorf tubes and flash-frozen for RNA preservation. All samples were stored in -80oC freezer until the time of TRAP and mRNA isolation. midbrain slices were placed in 200 µl of ice-cold homogenization buffer (50mM Tris, pH 7.4; 12mM MgCl2; 100mM KCl; 1% NP-40; 1 mg/ml sodium heparin; 1mM DTT) supplemented with 100 μg/mL cycloheximide (Millipore, cat# C4859–1ML), 200 units/ml RNaseOUT Recombinant Ribonuclease Inhibitor (ThermoFisher, cat# 10777019), and 1× cOmplete, EDTA-free Protease Inhibitor Cocktail (Milipore, cat# 11836170001). Homogenization used a cordless motor pestle (Kimble #749520-0090 and #749540). After initial homogenization, an additional 500 µl of buffer was added to the samples, washing the pestle in between pulses. Homogenate solution volume was then brought to a total of 1.5 ml and centrifuged at 12,000 g for 10 min at 4oC. After centrifugation, 100 µl of the supernatant was removed and set aside on ice (“input fraction”). The remaining supernatant (~900 µl of “positive fraction”) was transferred into a fresh tube and incubated with 1 µl anti-GFP antibody (Abcam, cat# ab290). Both input and positive samples were placed in an end-over-end rotating mixer and incubated for 1 h at 4oC. Pre-washed Dynabeads protein G (Invitrogen, cat# 10003D; 30 µl per sample) were then added to the positive fraction and the final solution incubated overnight (~16 h) in a rotating mixer at 4oC. Positive tubes were then placed in a DynaMag-2 magnet and supernatant removed and saved as the “negative fraction”. The magnetic beads bound with GFP-labelled polyribosomes/mRNAs, were washed with high-salt buffer (50mM Tris, pH 7.5; 12mM MgCl2; 300mM KCl; 1% NP-40; 100 μg/ml cycloheximide; 2mMDTT) three times. After the final wash, Dynabeads were separated from the GFP-labelled polyribosomes/mRNAs by adding 350 µl of Buffer RLT (Qiagen) and 3.5 µl of 2-β mercaptoethanol, proceeding with incubation in a benchtop ThermoMixer (Eppendorf) for 10 min at 22oC. The eluted solution (“positive fraction”), free of magnetic beads, was placed in a fresh tube. mRNA isolation was carried out using RNeasy Mini kit (#74104, QIAGEN), following manufacturer’s suggested protocol. Isolated mRNA was then quantified with a Nanodrop spectrophotometer (ThermoFisher, model# ND-ONEC-W) and its quality measured in a 4150 Tapestation analyzer (Agilent, model# G2992AA) using HSRNA ScreenTape (Agilent, cat# 5067-5579).
Directional mRNA libraries were prepared using NEBNext Ultra II Kit for Illumina (NEB, cat# E7760L) in accordance to the manufacturer’s directions, and following previously established protocol (Chucair-Elliott et al., 2020; Ocanas et al., 2022). In summary, each sample of both positive and input fractions (ranging 3.5-35 ng of mRNA) were individually captured by poly-A RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, cat# NEBE7490L). mRNA was then eluted from oligo-dT beads, fragmented using a thermal cycler at 94°C for 15 min, and first and second strands of cDNA were individually synthesized following manufacturer’s guidance (NEB, cat# E7760L). The final double-stranded cDNA was purified with the use of SPRISelect Beads (Beckman Coulter, cat# B23318) and eluted in 50 µl 0.1x TE buffer. Next, adaptor ligation was performed using 100-fold dilution of the NEBNext adaptor in dilution buffer (NEB, cat# E6609L), and PCR of the ligated products was conducted using the NEBNext Ultra II Q5 Master Mix (NEB, cat#7760L) and unique index primers (NEB, cat# E6609L), both provided with aforementioned kits, in accordance to manufacture’s protocol (14 cycles). Purified libraries were then quantified using HS dsDNA Qubit kit (ThermoFisher, cat# Q33230). Library integrity, verified in a 4150 Tapestation analyzer (Agilent, model# G2992AA) using HS D1000 ScreenTape (Agilent, cat# 5067-5584), revealed an average peak size of 332bp. Libraries for each sample were then pooled at 5 nM concentration and sequenced by the OMRF[Author’s institution] Clinical Genomics Center using the Illumina NovaSeq 6000 system (S4 PE150).

value: Brain

tag: group

value: Young

value: Male

tag: genotype

value: VGAT;NuTRAP

tag: age

value: 7 months

tag: cell

tag: batch


title: Young_Male_3_VGAT

description:
Library name: Young_Male_3_VGAT
VGAT_NuTRAP.csv, column_S


title: 134

description:
Library name: 134
Targeted bisulfite sequencing

value: hindlimb webbing


title: 135

description:
Library name: 135
Targeted bisulfite sequencing


title: Young_Male_2_VGAT

description:
Library name: Young_Male_2_VGAT
VGAT_NuTRAP.csv, column_O

value: 8.5 months


title: SELAPRE


title: SELAPOST


title: 133

description:
Library name: 133
Targeted bisulfite sequencing


title: 132

description:
Library name: 132
Targeted bisulfite sequencing


title: Young_Male_1_VGAT

description:
Library name: Young_Male_1_VGAT
VGAT_NuTRAP.csv, column_E

value: 9 months


title: 131

description:
Library name: 131
Targeted bisulfite sequencing


title: Old_Male_3_VGAT

description:
Library name: Old_Male_3_VGAT
VGAT_NuTRAP.csv, column_J

value: Old

value: 21 months


title: 95

description:
Library name: 95
Targeted bisulfite sequencing


title: SADIPOST

value: vastus lateralis muscle


title: PABRPOST

value: Skeletal Muscle


title: 130

description:
Library name: 130
Targeted bisulfite sequencing


title: Old_Male_2_VGAT

description:
Library name: Old_Male_2_VGAT
VGAT_NuTRAP.csv, column_I


title: 94

description:
Library name: 94
Targeted bisulfite sequencing


title: 93

description:
Library name: 93
Targeted bisulfite sequencing


title: PABRPRE

value: Female


title: 91

description:
Library name: 91
Targeted bisulfite sequencing


title: Old_Male_1_VGAT

description:
Library name: Old_Male_1_VGAT
VGAT_NuTRAP.csv, column_D


title: OLMOPOST


title: 92

description:
Library name: 92
Targeted bisulfite sequencing


title: 90

description:
Library name: 90
Targeted bisulfite sequencing


title: 88

description:
Library name: 88
Targeted bisulfite sequencing


title: Young_Female_5_VGAT

description:
Library name: Young_Female_5_VGAT
VGAT_NuTRAP.csv, column_Q


title: Young_Female_6_VGAT

description:
Library name: Young_Female_6_VGAT
VGAT_NuTRAP.csv, column_R


title: OLMOPRE

value: PRE


title: 87

description:
Library name: 87
Targeted bisulfite sequencing


title: NAWOPOST


title: 89

description:
Library name: 89
Targeted bisulfite sequencing


title: 127

description:
Library name: 127
Targeted bisulfite sequencing

value: TYR


title: Young_Female_3_VGAT

description:
Library name: Young_Female_3_VGAT
VGAT_NuTRAP.csv, column_H


title: NAWOPRE


title: 128

description:
Library name: 128
Targeted bisulfite sequencing


title: Young_Female_4_VGAT

description:
Library name: Young_Female_4_VGAT
VGAT_NuTRAP.csv, column_P


title: 129

description:
Library name: 129
Targeted bisulfite sequencing


title: 125

description:
Library name: 125
Targeted bisulfite sequencing


title: NAHIPOST

value: POST


title: 126

description:
Library name: 126
Targeted bisulfite sequencing


title: 124

description:
Library name: 124
Targeted bisulfite sequencing


title: NAHIPRE


title: Young_Female_2_VGAT

description:
Library name: Young_Female_2_VGAT
VGAT_NuTRAP.csv, column_G


title: 123

description:
Library name: 123
Targeted bisulfite sequencing


title: 122

description:
Library name: 122
Targeted bisulfite sequencing


title: 121

description:
Library name: 121
Targeted bisulfite sequencing

value: tubb2b GFP


title: Young_Female_1_VGAT

description:
Library name: Young_Female_1_VGAT
VGAT_NuTRAP.csv, column_F

value: Brain


title: 192

description:
Library name: 192
Targeted bisulfite sequencing

value: SUPERMAN F8


title: 191

description:
Library name: 191
Targeted bisulfite sequencing


title: Old_Female_5_VGAT

description:
Library name: Old_Female_5_VGAT
VGAT_NuTRAP.csv, column_N


title: 190

description:
Library name: 190
Targeted bisulfite sequencing


title: Old_Female_4_VGAT

description:
Library name: Old_Female_4_VGAT
VGAT_NuTRAP.csv, column_M


title: KACOPRE


title: 188

description:
Library name: 188
Targeted bisulfite sequencing


title: Old_Female_3_VGAT

description:
Library name: Old_Female_3_VGAT
VGAT_NuTRAP.csv, column_L


title: 187

description:
Library name: 187
Targeted bisulfite sequencing


title: Old_Female_2_VGAT

description:
Library name: Old_Female_2_VGAT
VGAT_NuTRAP.csv, column_K


title: JOSAPOST


title: 186

description:
Library name: 186
Targeted bisulfite sequencing


title: JOSAPRE


title: 185

description:
Library name: 185
Targeted bisulfite sequencing


title: 8-Tadpole

description:
Library name: 8-Tadpole
Targeted bisulfite sequencing


title: Old_Female_1_VGAT

description:
Library name: Old_Female_1_VGAT
VGAT_NuTRAP.csv, column_C

value: 24 months


title: 184

description:
Library name: 184
Targeted bisulfite sequencing


title: 6-Tadpole

description:
Library name: 6-Tadpole
Targeted bisulfite sequencing


title: Young_Male_4_DAT

description:
Library name: Young_Male_4_DAT
DAT_NuTRAP.csv, column_O

value: Young

value: Male

value: DAT;NuTRAP


title: 183

description:
Library name: 183
Targeted bisulfite sequencing

value: hindlimb webbing

value: NIGERIAN F8


title: JESIPRE


title: JESIPOST


title: 181

description:
Library name: 181
Targeted bisulfite sequencing


title: Young_Male_5_DAT

description:
Library name: Young_Male_5_DAT
DAT_NuTRAP.csv, column_P

value: 9 months


title: 7-Tadpole

description:
Library name: 7-Tadpole
Targeted bisulfite sequencing


title: 180

description:
Library name: 180
Targeted bisulfite sequencing


title: LAJUPRE


title: LAJUPOST


title: JANIPRE


title: JANIPOST


title: 189

description:
Library name: 189
Targeted bisulfite sequencing


title: 179

description:
Library name: 179
Targeted bisulfite sequencing


title: JAMIPOST


title: 178

description:
Library name: 178
Targeted bisulfite sequencing


title: 177

description:
Library name: 177
Targeted bisulfite sequencing


title: Young_Male_1_DAT

description:
Library name: Young_Male_1_DAT
DAT_NuTRAP.csv, column_C

value: 10.5 months


title: 176

description:
Library name: 176
Targeted bisulfite sequencing


title: JAMIPRE

value: vastus lateralis muscle


title: Young_Male_3_DAT

description:
Library name: Young_Male_3_DAT
DAT_NuTRAP.csv, column_N


title: 175

description:
Library name: 175
Targeted bisulfite sequencing


title: Old_Male_5_DAT

description:
Library name: Old_Male_5_DAT
DAT_NuTRAP.csv, column_U

value: Old

value: 21 months


title: 174

description:
Library name: 174
Targeted bisulfite sequencing


title: ISURPOST

value: Skeletal Muscle

value: Female


title: Old_Male_4_DAT

description:
Library name: Old_Male_4_DAT
DAT_NuTRAP.csv, column_T


title: 182

description:
Library name: 182
Targeted bisulfite sequencing


title: 172

description:
Library name: 172
Targeted bisulfite sequencing


title: 173

description:
Library name: 173
Targeted bisulfite sequencing


title: ISURPRE

value: PRE


title: Old_Male_3_DAT

description:
Library name: Old_Male_3_DAT
DAT_NuTRAP.csv, column_I


title: 170

description:
Library name: 170
Targeted bisulfite sequencing


title: HAMEPOST

value: POST


title: 169

description:
Library name: 169
Targeted bisulfite sequencing


title: Old_Male_2_DAT

description:
Library name: Old_Male_2_DAT
DAT_NuTRAP.csv, column_H

value: Brain


title: Young_Male_2_DAT

description:
Library name: Young_Male_2_DAT
DAT_NuTRAP.csv, column_F

value: 8 months


title: HAMEPRE


title: 167

description:
Library name: 167
Targeted bisulfite sequencing


title: 168

description:
Library name: 168
Targeted bisulfite sequencing


title: Old_Male_1_DAT

description:
Library name: Old_Male_1_DAT
DAT_NuTRAP.csv, column_G


title: GEYOPOST


title: 165

description:
Library name: 165
Targeted bisulfite sequencing


title: GEYOPRE


title: 14-Tadpole

description:
Library name: 14-Tadpole
Targeted bisulfite sequencing

source_name: whole tadpole

value: whole tadpole

value: ZBTB14 KO


title: Young_Female_5_DAT

description:
Library name: Young_Female_5_DAT
DAT_NuTRAP.csv, column_S

value: Young


title: 15-Tadpole

description:
Library name: 15-Tadpole
Targeted bisulfite sequencing


title: 4-Tadpole

description:
Library name: 4-Tadpole
Targeted bisulfite sequencing

value: Superman F9 WT


title: GAVAPRE


title: Young_Female_3_DAT

description:
Library name: Young_Female_3_DAT
DAT_NuTRAP.csv, column_Q

value: DAT;NuTRAP


title: 2-Tadpole

description:
Library name: 2-Tadpole
Targeted bisulfite sequencing


title: FLTHPRE


title: 171

description:
Library name: 171
Targeted bisulfite sequencing

value: hindlimb webbing

value: NIGERIAN F8


title: TMD8,DMSO, rep3

city: Xiamen

first: jiazhen

last: lin

state: Fujian

address: No. 2000 of Xiang an East road

institute: Xiamen uniersity

description: Library name: DMSO3 FPKM

data_processing:
3.RNAseq analysis method
3.1 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).
3.2 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.
3.3 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) [5] (or DEGseq[6] or PoissonDis[7])with Q value ≤ 0.05 (or FDR ≤ 0.001).
3.4 Gene Annotation
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Assembly: hg38
Supplementary files format and content: processed data excel file include FPKM values for each sample

source_name: Lymphoma tissue

growth_protocol: The incubator condition was set at 37℃ with 5% CO2. TMD8 cell line was cultured in RPMI-1640 (Hyclone, Thermo Scientific, Logan, UT, USA) adding 10% fetal bovine serum (Gibco, Thermo Scientific, Grand Island, NY, USA).

extract_protocol:
1.1 Cell Sample Lysis
Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells).
1.2 Sample Purification
1.2.1 Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃.
1.2.2 Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking；
1.2.3 Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity).
1.2.4 Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h.
1.2.5 Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting.
1.2.6 Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃)。
1.2.7 Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min.
1.2.8 Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
2.mRNA Library Preparation
2.1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2.2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
2.3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
2.4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
2.5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
2.6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
2.7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
2.8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
2.9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: TMD8 cells were treated with 375nM chidamide, 1µM anlotinib, or 375nM chidamide combined with 1µM anlotinib for 24h, and then first lysed with TRIzol reagent (Invitrogen, NY, USA) and further extracted following the manufacturer's guidelines.

value: Lymphoma tissue

value: Lymphoma cell line

value: double-hit lymphoma with TP53 mutation

value: DMSO


title: Young_Female_2_DAT

description:
Library name: Young_Female_2_DAT
DAT_NuTRAP.csv, column_E

value: 9 months


title: EVZAPOST

value: vastus lateralis muscle

value: Skeletal Muscle

value: Female


title: TMD8,DMSO, rep2

description: Library name: DMSO2 FPKM


title: Young_Female_1_DAT

description:
Library name: Young_Female_1_DAT
DAT_NuTRAP.csv, column_D

value: Brain


title: 166

description:
Library name: 166
Targeted bisulfite sequencing


title: EVZAPRE

value: PRE


title: TMD8,DMSO, rep1

description: Library name: DMSO1 FPKM


title: Old_Female_4_DAT

description:
Library name: Old_Female_4_DAT
DAT_NuTRAP.csv, column_M

value: Old

value: 21 months


title: Old_Female_3_DAT

description:
Library name: Old_Female_3_DAT
DAT_NuTRAP.csv, column_L


title: TMD8,D, rep3

description: Library name: D3 FPKM

value: Chidamide combined with anlotinib


title: ELWAPOST

value: POST


title: ELWAPRE


title: Young_Female_4_DAT

description:
Library name: Young_Female_4_DAT
DAT_NuTRAP.csv, column_R

value: Young

value: DAT;NuTRAP


title: VitC Dam&ChIC Dam-scFv-K27me3/H2AK119Ub (KIN10644.index48)

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Library name: KIN10644.index48
damchic_damk27_h2ak119ub.h5ad.gz

data_processing:
Dam&ChIC data processing is largely based on the workflow and scripts described in Rooijers et al., 2019 and Markodimitraki et al., 2020 (available at: https://github.com/KindLab/scDamAndTools), but adapted to allow for computational separation of scDamID and sortChIC derived reads and further processing of sortChIC reads.
All reads are demultiplexed by comparing their sample barcode (e.g. single-cell barcode) located at the start of each read (R1 in case of paired-end sequenced libraries) conform to the read layout of 5′-[3 nt UMI][8 nt barcode]TC[gDNA]-3′ for scDamID and 5′-[3 nt UMI][8 nt barcode]WN[gDNA]-3′ for sortChIC reads, to a reference list of barcodes and zero mismatches between the observed barcode and reference are allowed. Sample barcodes and UMIs are trimmed off the reads to only retain gDNA sequences. The UMI sequences were appended to the read name for downstream processing. Per sample barcode, scDamID and sortChIC reads remain mixed at this point.
After preprocessing, the reads were aligned to a reference genome using bowtie2 (v. 2.4.1) with parameters: ‘‘--seed 42 --very-sensitive -N 1’’. Before alignment a ‘GA’ dinucleotide was prepended to the reads that has effectively been digested off scDamID fragments during DpnI gDNA digestion. For human samples, reads were aligned to reference genome hg19 (GRCh37) and mouse samples to mm10 (GRCm38). For allele-specific processing for X-chromosome inactivation experiments, data were aligned to reference genomes generated by imputing 129S1/SvImJ and CAST/EiJ single nucleotide polymorphisms obtained from the Sanger Mouse Genomes project (Keane et al., 2011) onto the mm10 reference genome. The reads were assigned to either genotype by aligning reads to both references. Reads that aligned with lower edit distance (SAM tag ‘NM’) or higher alignment score (SAM tag ‘AS’) in case of equal edit distance to one of the genotypes were assigned to that genotype. Reads aligning with equal edit distance and alignment score to both genotypes were considered of ‘ambiguous’ genotype. Reads that yielded an alignment with mapping quality (BAM field ‘MAPQ’) lower than 10 were discarded.
Following read alignment with ‘GA’ prepended dinucleotide, reads were considered scDamID in case of perfect alignment on genomic GATC motifs. Residual reads were considered sortChIC and their original sequences (i.e., without prepended GA dinucleotide) were realigned using hisat2 (v. 2.1.0) with parameters: ‘‘--seed 42 --no-spliced-alignment --mp '2,0' --sp '4,0'”. These sortChIC-considered reads were further pruned given MNase’s strong adenine or thymidine-nucleotide cut preference; only sortChIC reads were kept that lead with an ‘A’ or ‘T’ base. In addition, we observed that a larger fraction of sortChIC reads (i.e., that do not map on a genomic GATC motif) are ‘TC’-dinucleotide leading in Dam&ChIC libraries than in sortChIC libraries and hence decided to exclude TC-leading reads from Dam&ChIC-derived sortChIC libraries.
Assembly: GRCm38
Supplementary files format and content: H5AD

source_name: Inner cell mass derived

growth_protocol: Human haploid KBM7 cells were cultured in suspension in IMDM medium (10% FBS and 1% Pen/Strep). Human HT-1080 cells were cultured in DMEM medium (10% FBS and 1% Pen/Strep). Mouse F1 hybrid Cast/EiJ x 129SvJ embryonic stem cells (mESCs; a kind gift from the Joost Gribnau laboratory) were cultured on a monolayer of irradiated feeders (MEFs) in CM+/+ (G-MEM + 10% FBS, 1% Pen/Strep, 1× GlutaMAX (Gibco), 1× NEVitaminC, 1× sodium pyruvate, 0.1 mM 2-ME and 1000 U/ml ESGROmLIF (EMD Millipore, ESG1107))

extract_protocol:
double thymidine block: cells received 2 mM thymidine for 15 hours, followed by 9 hours of release, followed by a second thymidine block for 13 hours.
MN was activated thorugh 2mM CaCl2 for 30min at 4C at inactivated by EGTA addition. Cells were lysed (protK + NP40), fragments end-repaired (Klenow) and adenine methylated sites were cut (DpnI). Dam and ChIC fragemnts are ligated to blunt end adaptors containing a cell barcode and unique molecular identifier and a T7 promoter. After pooling DNA is amplified by in vitro transcription, before rundom hexamer based reverse transcription and final indexing PCR for sequencing.

treatment_protocol: Dam-POI induction: For Kbm7 cells 0.5 nM Shield-1 was added to stabilize the protein at the indicated timepoint. For mESCs 1mM IVitaminC was added 24h prior to induction, to ensure protein degradation.

value: Inner cell mass derived

value: ESC

value: VitaminC differentiation

value: 129S1/SvImJ x CAST/Eij


title: VitC Dam&ChIC Dam-scFv-K27me3/H2AK119Ub (KIN10644.index46)

description:
Library name: KIN10644.index46
damchic_damk27_h2ak119ub.h5ad.gz


title: VitC Dam&ChIC Dam-scFv-K27me3/H2AK119Ub (KIN10644.index47)

description:
Library name: KIN10644.index47
damchic_damk27_h2ak119ub.h5ad.gz


title: ELSCPOST


title: VitC Dam&ChIC Dam-scFv-K27me3/H2AK119Ub (KIN10644.index45)

description:
Library name: KIN10644.index45
damchic_damk27_h2ak119ub.h5ad.gz


title: 1-Tadpole

description:
Library name: 1-Tadpole
Targeted bisulfite sequencing

value: whole tadpole

value: Superman F9 WT


title: TMD8,D, rep1

description: Library name: D1 FPKM

value: Lymphoma tissue

value: Lymphoma cell line

value: double-hit lymphoma with TP53 mutation


title: Old_Female_2_DAT

description:
Library name: Old_Female_2_DAT
DAT_NuTRAP.csv, column_K

value: Brain

value: Female


title: Cortical neurons, mir-92a, 5d, biol rep 4

city: Berlin

first: Seija

last: Lehnardt

state: Berlin

address: Charitéplatz 1

department: Institute of Cell Biology and Neurobiology, and Department of Neurology

country: Germany

institute: Charité – Universitätsmedizin Berlin

data_processing:
Bulk RNA-seq reads were mapped to the mouse genome (GRCm38) with STAR version-2.7.3a
Reads were assigned to genes using FeatureCounts SUBREAD version-v2.0.0 with the following parameters: -t exon -g gene_id -s 2
Assembly: GRCm38, version M12 (Ensembl 87)
Supplementary files format and content: tab-delimited file includes raw counts for each Sample

source_name: cortical neurons

growth_protocol: Cortical neurons were maintained in Neurobasal medium supplemented with 2% B27 supplement, 1% L-Glutamine and antibiotics in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA kit according to manufacturer’s instructions.

value: cortical neurons

value: WT

value: miRNA incubation

tag: time

value: 5 d

tag: experiment batch


title: ELSCPRE

value: vastus lateralis muscle

value: Skeletal Muscle

tag: treatment

value: PRE


title: TMD8,C, rep3

description: Library name: C3 FPKM

tag: tissue

value: Chidamide


title: Cortical neurons, mir-92a, 5d, biol rep 3


title: COGRPRE