title: UUATAC-seq datasets of Chicken_Spleen

description: single-nucleus ATAC profile of Chicken_Spleen

data_processing:
The FASTQ files generated by MGI sequencer were split by the T7 index using the software splitBarcode (version 0.1.6, https://github.com/MGI-tech-bioinformatics/splitBarcode). Reads with barcode base quality lower than 10 or more than two mismatches per index were removed. Then the cell barcode was tagged into the query name of each reads using Drop-Seq tools  (version 2.5.1, https://github.com/broadinstitute/Drop-seq). The cell barcode of each read pair consists of four components: T7 index, Hy AS barcode, Hy B barcode and Tn5 barcode (128, 768, 8 and 192 indexes, respectively). We corrected each barcode to its original sequence if only one base was mismeasured in each barcode component. Bam files with tagged barcodes were split by Tn5 barcodes and then merged by tissue information. Different samples were marked by different Tn5 barcodes. Subsequently, reads were aligned to reference genomes of chicken (galGal6) using BWA (version 0.7.15, https://github.com/lh3/bwa) with default parameters in paired-end mode to obtain the bam file.
To deal with the Tn5 insertion bias, we performed the function alignmentSieve of deepTools (version 3.5.1, https://github.com/deeptools/deepTools) to shift each read. Next, paired-reads with mapping quality higher than 30 were converted to fragments. And then nonduplicate fragments with length range from 10bp to 1000bp were extracted. We generated one fragment file for each tissue.
Assembly: galGal6
Supplementary files format and content: BED files recording coordinates of fragments captured by UUATAC-seq

organism: Gallus gallus

extract_protocol:
Whole organs were then dissected in the following order: air sac, pancreas, ileum, duodenum, heart, ovary, spleen, brainstem, lung, glandular stomach, muscular stomach, cecum, cloaca, brain, bowel, kidney, cerebellum and liver. Except for bone marrow, the samples were quickly transferred into cold DPBS, washed and then manually pulverized using a mortar and pestle within a liquid nitrogen bath. The pulverized tissues were suspended in 1mL of Nuclear Isolation Buffer (NIB) and followed by incubation for 1.5-3 min to isolate the nuclei. The bone marrow cell suspension was centrifuged at 350 × g for 5 min, and the pellet was directly resuspended in 1 mL of NIB for 2min incubation. The suspension of each tissue was transferred to 15 mL centrifuge tubes pre-filled with 5mL of WB (wash buffer, 0.2% BSA, 3 mM MgCl2 in DPBS), filtered through 40 μm strainers and centrifuged at 650 × g for 5 min at 4°C. We resuspended the nuclei in 1 mL of WB and filtered the suspension through 20 μm size strainers, pelleted at 650 × g for 5 min and resuspended in the appropriate amount of DPBS to give a final concentration of 25,000 nuclei per microlitre.
Library preparations were performed with the UUATAC-seq protocol

treatment_protocol: After decapitation, a bloodletting procedure was employed to drain the entire blood volume.

value: Spleen

tag: breed

value: Huxu

value: Wild-type

value: Adult

value: Female


title: 2AF atrial fibrillation

status: Public on Jul 14 2025

type: SRA

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry road

department: Cardiovascular Medicine

country: USA

institute: Stanford University

library_source: genomic

data_processing:
The sequencing quality was evaluated using FastQC (0.11.9) before and after adapter trimming to ensure PHRED < 30 via TrimGalore (0.4.4). Sequenced reads were aligned to the CT- and GA-converted human hg38 (GRCh38.p12) genome assemblies using Bismark [42] to quantify the relative alignment of methylated and unmethylated CpGs, respectively.
Assembly: GRCh38.p12
Supplementary files format and content: The R package methylKit (1.8.0) was used for this purpose, and statistical significance of differential methylation was assumed based on an over-correction adjusted Chi-squared test.

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
A total of 15 mL of peripheral venous blood was collected in EDTA vacuettes through venipuncture from AF patients (at hospitalization time and before any treatment administration) and from HS. Blood samples were centrifuged at 1900 x g 10 min at + 4°C within 1 hour and aliquots of plasma were stored at -80°C for long-term storage. Peripheral blood mononuclear cells (PBMCs) were isolated via density centrifugation using Ficoll-Paque™ PLUS (Cytiva) according to the manufacturer’s protocol. CD4+ T cells were purified starting from 5x107/mL of  PBMCs by negative immunomagnetic selection using EasySep™ Human CD4+ T Cell Isolation Kit (STEMCELL Technologies) as previously described.
To perform genome-wide DNA methylation analysis, genomic DNA from 10 AF patients and 11 HS (set population) were analyzed by RRBS at the Genomix4Life S.r.l. (Baronissi, Salerno, Italy). DNA concentrations for each sample was assayed with Qubit fluorometer (Thermo Fisher Scientific) and its quality assessed with the TapeStation 4200 system (Agilent Technologies, Inc.). Indexed libraries were prepared starting from 100 ng/ea purified DNA with Ovation RRBS Methyl-Seq System (Tecan Group Ltd.) according to the manufacturer’s instructions. Libraries were quantified using the TapeStation 4200 system (Agilent Technologies, Inc.) and Qubit fluorometer (Thermo Fisher Scientific), then pooled such that each index-tagged sample was present in equimolar amounts. The pooled samples were subject to cluster generation and sequencing using an Illumina NextSeq 550Dx (Illumina, Inc.) in a 2x76 paired-end format.

tag: tissue

value: peripheral blood

tag: cell type

value: pBMC

tag: phenotype

value: atrial fibrillation


title: Male Homo Hypothalamus, mouse P60

city: Bethesda

first: Timothy

last: Petros

state: Maryland

address: 35 Convent Drive, Bg 35 Room 3B-1002

institute: NICHD

description:
Library name: P60_Hom_Hypothalamus_male
10x Genomics Multiome

library_source: transcriptomic single cell

data_processing:
The raw sequencing data were processed using Cell Ranger ARC (v2.0.0) pipeline. The cellranger-arc mkfastq command was used to generate the demultiplexed FASTQ files from BCL files. The sequencing reads were aligned to mouse (GRCm38/mm10) reference genome using cellranger-arc count.  Reads with de-duplicated and valid cell barcodes were used to build gene-by-barcode matrices by cellranger-arc count per genotype.
Assembly: GRCm38/mm10
Supplementary files format and content: cellranger filtered_feature_bc_matrix.h5

molecule: nuclear RNA

organism: Mus musculus

source_name: Hypothalamus

extract_protocol:
Embryonic brain dissections: Pregnant dams were anesthetized with an i.p. injection of Euthasol, E13.5 embryos were removed and placed in ice-cold carbogenated artificial cerebral spinal fluid (ACSF, in mM: 87 NaCl, 26 NaHCO3, 2.5 KCl, 1.25 NaH2PO4, 0.5 CaCl2, 7 MgCl2, 10 glucose, 75 sucrose, saturated with 95% O2, 5% CO2, pH 7.4). Embryonic tails were cut for genotyping. MGE and hypothalamus were dissected from individual brains in ice-cold ACSF, transferred to individual 0.5 mL Eppendorf tubes, then flash frozen on dry ice and stored at -80°C. Adult brain dissections:  The somatosensory cortex and hypothalamus were dissected, transferred to 1.5 mL Eppendorf tubes, then flash frozen on dry ice and stored at -80°C. Frozen E13.5 and P60 tissue from Nkx2.1-Cre;H3.3K4M;sun1-GFP mice were mechanically lysed, washed and filtered to generate single nuclei suspensions for the 10x Genomics Multiome assay as previously described. These suspensions were then sorted via flow cytometry to harvest ~100,000 GFP+ nuclei. Nuclei solutions were centrifuged in a bucket centrifuge at 500 g for 5 minutes at 4 degree. Supernatant was removed and nuclei reconstituted in 1x Nuclei buffer at a density of 3,000 nuclei/μL. 5 μL of this solution was then used for the 10x Genomics Single Cell Multiome Assay per manufacturer’s protocol.
Joint libraries for scRNA-seq and scATAC-seq were created using 10X Genomics Single Cell Multiome ATAC + Gene Expression kit (1000285) by following manufacturer’s protocols.

value: Hypothalamus

tag: Sex

value: male

tag: genotype

value: Homo

tag: age


title: 18S reads obtained from sample S003 (Run 1 - Replicate 3)

city: Pisa

first: Giulio

last: Petroni

address: Via A. Volta n°4/6

department: Department of Biology

country: Italy

institute: University of Pisa

description:
Library name: S003_18S
Full-length 18S rRNA gene sequencing

data_processing:
Primer-trimmed sequences delivered by CD Genomics (Shirley, NY, USA) were put through the DADA2 pipeline in R: quality filtering, dereplication, denoising and chimera removal
The resulting ASV table and sequences were imported in QIIME2 (2022.2) for taxonomic classification using a Naive Bayes classifier trained on the reference database EUKARYOME (v1.9)
Supplementary files format and content: dna-sequences.fasta: text file containing the ASV IDs and sequences
Supplementary files format and content: feature_table.tsv: TSV text file containing the ASV abundances in each sample
Supplementary files format and content: taxonomy.tsv: TSV text file containing the taxonomic classification of the ASVs

organism: activated sludge metagenome

source_name: mixed microbial community

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Kit (QIAGEN, Hilden, Germany)
PacBio Full-Length Amplicon Library Preparation using the SMRTbell Prep Kit 3.0 protocol

value: mixed microbial community


title: UUATAC-seq datasets of Chicken_Ovary

city: Hangzhou

first: Guoji

last: Guo

state: Zhejiang

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

country: China

institute: Center for Stem Cell and Regenerative Medicine

description: single-nucleus ATAC profile of Chicken_Ovary

library_source: genomic single cell

source_name: Ovary

value: Ovary

tag: developmental stage


title: Male WT Hypothalamus, mouse P60

description:
Library name: P60_WT_Hypothalamus_male
10x Genomics Multiome

value: WT


title: 1AF atrial fibrillation


title: Male WT Cortex, mouse P60

description:
Library name: P60_WT_Cortex_male
10x Genomics Multiome

source_name: Cortex

value: Cortex


title: 18S reads obtained from sample S101 (Run 2 - Replicate 1)

description:
Library name: S101_18S
Full-length 18S rRNA gene sequencing


title: UUATAC-seq datasets of Chicken_Pancreas

description: single-nucleus ATAC profile of Chicken_Pancreas

source_name: Pancreas

value: Pancreas


title: 18S reads obtained from sample S002 (Run 1 - Replicate 2)

description:
Library name: S002_18S
Full-length 18S rRNA gene sequencing


title: UUATAC-seq datasets of Chicken_MuscularStomach

description: single-nucleus ATAC profile of Chicken_MuscularStomach

source_name: Muscular stomach

value: Muscular stomach


title: Female Homo Cortex, mouse P60

description:
Library name: P60_Hom_Cortex_female
10x Genomics Multiome

value: female


title: NSC_IgG_CT

city: New York

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

description: Library name: NSC_IgG_CT

data_processing:
Cleaned reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.4.5) with the parameters: --local --sensitivie --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Peak calling was performed using MACS2 (v2.7.1) with options -p 0.00001 -f BAMPE --keep-dup all.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files were generated using bamCoverage from deepTools, and bigwig files were analyzed using plotProfile and plotHeatmap. Peaks annotation were implemented by R package "ChIPseeker".
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: Neural stem cells

extract_protocol:
NSCs were crosslinked, bound to ConA beads, incubated with anti-H3K27ac antibody, and treated with pre-loaded pA-Tn5 adapter complex.
Libraries were prepared by NEBNext HiFi 2x PCR Master Mix.

value: Neural stem cells

tag: cell line


title: Female Homo Hypothalamus, mouse P60

description:
Library name: P60_Hom_Hypothalamus_female
10x Genomics Multiome


title: UUATAC-seq datasets of Chicken_Lung

description: single-nucleus ATAC profile of Chicken_Lung

source_name: Lung

value: Lung

value: Huxu

value: Wild-type


title: 18S reads obtained from sample S001 (Run 1 - Replicate 1)

description:
Library name: S001_18S
Full-length 18S rRNA gene sequencing


title: αLPs from fetal liver of WT mice

city: Nanjing

first: Jiarui

last: Li

state: Jiangsu

address: Xianlin road #138

institute: Nanjing University of Chinese Medicine

description:
Library name: Sample 1
xiaoshu-fetal liver αLPs

data_processing:
The raw gene expression data were converted to Seurat data using the Seurat (v4.0) R toolkit.
Low quality cells with unique feature counts < 200 or > 4500 and > 20% mitochondrial counts were removed by quality control.
αLPs from the FL (8884 cells) or BM (7067 cells) populations were retained for subsequent analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: fetal liver

extract_protocol:
To obtain Lin−CD45+CD127+Flt3−α4β7+CD25− αLPs subsets from fetal liver and bone marrow of WT B6  mice, the  mononuclear cells (MNCs) were incubated with anti-CD45 mAbs for 30 min at 4°C. Subsequently, MNCs were incubated with anti-PE beads for 60 min at 4°C. Nextly, MNCs were incubated with the indicated antibodies for 30 min at 4°C. 7AAD was added to the MNCs suspension, which was subsequently sorted using a FACSAria Fusion (BD Biosciences, San Diego, USA). The purity of the sorted cell populations was >  90%. Purified live cells were labelled with 0.4% Trypan blue to determine their viability (> 90% before processing for scRNA-seq).
Single-cell barcode scRNA-seq libraries were generated using the Chromium Single Cell 3’ Library (v2 chemistry; Nugen) according to the manufacturer’s standard protocol. The libraries were sequenced on a NovaSeq 6000 (Illumina). Gene-barcode matrices were generated by counting UMIs and filtering non-cell-associated barcodes.

value: fetal liver

value: lymphocytes

value: 6-8 weeks old

value: B6 WT

tag: treatment

value: no

tag: batch


title: NSC_TMut_CT_rep2

description: Library name: NSC_TMut_CT_rep2


title: UUATAC-seq datasets of Chicken_Liver

description: single-nucleus ATAC profile of Chicken_Liver

source_name: Liver

value: Liver

value: Adult

value: Female


title: NSC_TMut_CT_rep1

description: Library name: NSC_TMut_CT_rep1


title: Female WT Cortex, mouse P60

description:
Library name: P60_WT_Cortex_female
10x Genomics Multiome

value: WT


title: UUATAC-seq datasets of Chicken_Kidney

description: single-nucleus ATAC profile of Chicken_Kidney

source_name: Kidney

value: Kidney


title: 18S reads obtained from sample AS02 (Inoculum - Replicate 2)

description:
Library name: AS02_18S
Full-length 18S rRNA gene sequencing

value: mixed microbial community


title: 18S reads obtained from sample AS03 (Inoculum - Replicate 3)

description:
Library name: AS03_18S
Full-length 18S rRNA gene sequencing


title: Female WT Hypothalamus, mouse P60

description:
Library name: P60_WT_Hypothalamus_female
10x Genomics Multiome

value: Hypothalamus


title: 18S reads obtained from sample AS01 (Inoculum - Replicate 1)

description:
Library name: AS01_18S
Full-length 18S rRNA gene sequencing


title: NSC_TFoCa_CT_rep2

description: Library name: NSC_TFoCa_CT_rep2


title: UUATAC-seq datasets of Chicken_Ileum

description: single-nucleus ATAC profile of Chicken_Ileum

source_name: Ileum

value: Ileum


title: NSC_TFoCa_CT_rep1

description: Library name: NSC_TFoCa_CT_rep1

value: Neural stem cells


title: ITS reads obtained from sample SS32 (Run 3 - Replicate 3)

description:
Library name: SS32_ITS
Full-length ITS sequencing

data_processing:
Primer-trimmed sequences delivered by CD Genomics (Shirley, NY, USA) were put through the DADA2 pipeline in R: quality filtering, dereplication, denoising and chimera removal
The resulting ASV table and sequences were imported in QIIME2 (2022.2) for taxonomic classification using a Naive Bayes classifier trained on the reference database UNITE (v10)
Supplementary files format and content: dna-sequences.fasta: text file containing the ASV IDs and sequences
Supplementary files format and content: feature_table.tsv: TSV text file containing the ASV abundances in each sample
Supplementary files format and content: taxonomy.tsv: TSV text file containing the taxonomic classification of the ASVs


title: UUATAC-seq datasets of Chicken_Heart

description: single-nucleus ATAC profile of Chicken_Heart

source_name: Heart

value: Heart


title: ITS reads obtained from sample SS22 (Run 3 - Replicate 2)

description:
Library name: SS22_ITS
Full-length ITS sequencing


title: Male Homo MGE, mouse E13.5

description:
Library name: E13.5_Hom_MGE_male
10x Genomics Multiome

source_name: MGE

value: MGE

value: male

value: Homo


title: UUATAC-seq datasets of Chicken_GrandularStomach

description: single-nucleus ATAC profile of Chicken_GrandularStomach

source_name: Grandular stomach

value: Grandular stomach

value: Huxu

value: Wild-type


title: NSC_WT_CT_rep1

description: Library name: NSC_WT_CT_rep1


title: NSC_WT_CT_rep2

description: Library name: NSC_WT_CT_rep2


title: 16S reads obtained from sample SS32 (Run 3 - Replicate 3)

description:
Library name: SS32_16S
Full-length 16S rRNA gene sequencing

data_processing:
Primer-trimmed sequences delivered by CD Genomics (Shirley, NY, USA) were put through the DADA2 pipeline in R: quality filtering, dereplication, denoising and chimera removal
The resulting ASV table and sequences were imported in QIIME2 (2022.2) for taxonomic classification using a Naive Bayes classifier trained on the reference database MiDAS 4 (v5.3)
Supplementary files format and content: dna-sequences.fasta: text file containing the ASV IDs and sequences
Supplementary files format and content: feature_table.tsv: TSV text file containing the ASV abundances in each sample
Supplementary files format and content: taxonomy.tsv: TSV text file containing the taxonomic classification of the ASVs


title: UUATAC-seq datasets of Chicken_Duodenum

description: single-nucleus ATAC profile of Chicken_Duodenum

source_name: Duodenum

value: Duodenum


title: Male WT MGE, mouse E13.5

description:
Library name: E13.5_WT_MGE_male
10x Genomics Multiome


title: Female Homo Hypothalamus, mouse E13.5

description:
Library name: E13.5_Hom_Hypothalamus_female
10x Genomics Multiome

value: female


title: 16S reads obtained from sample SS22 (Run 3 - Replicate 2)

description:
Library name: SS22_16S
Full-length 16S rRNA gene sequencing


title: UUATAC-seq datasets of Chicken_Cloaca

description: single-nucleus ATAC profile of Chicken_Cloaca

source_name: Cloaca

value: Cloaca

value: Adult


title: 16S reads obtained from sample SS12 (Run 3 - Replicate 1)

description:
Library name: SS12_16S
Full-length 16S rRNA gene sequencing


title: UUATAC-seq datasets of Chicken_Cerebellum

description: single-nucleus ATAC profile of Chicken_Cerebellum

source_name: Cerebellum

value: Cerebellum

value: Female


title: Female Homo MGE, mouse E13.5

description:
Library name: E13.5_Hom_MGE_female
10x Genomics Multiome


title: CutTag_HDAC1_V5 control_mitosis_rep2

city: Beijing

first: Yan

last: Song

state: 北京

address: No.5 Yiheyuan Road

institute: Peking University

description: Library name: CutTag_HDAC1_V5 control_mitosis_rep2

data_processing:
Raw FASTQ reads were trimmed using Trim Galore (v0.6.10, with parameters --paired --quality 20 --stringency 3 -j 4).
Trimmed reads were mapped to Drosophila reference genome (version: dm6) using Bowtie2 (v2.5.1) very-sensitive-local mode
Picard tools were used to remove duplicate reads. Reads with a low mapping quality score were further filtered using Samtool
Assembly: dm6
Supplementary files format and content: bigwig files were generated using bamCoverage (--binSize 50 --normalizeUsing RPKM --extendReads)
Library strategy: CUT&Tag

organism: Drosophila melanogaster

source_name: larval brain

growth_protocol: Flies were reared and crossed according to standard procedures.

extract_protocol:
Larval brains were dissected and dissociated into single cells, then the cells were arrested by ConA beads, and the proteins of interest were combined by the specific primary antibody, followed by secondary antibody and Tn5 transposase. To obtain interphase and mitosis cells, the dissociated cells were fixed with 0.5% formaldehyde for 8min and quenched by Glycine., then stained with pH3 (phospho-histone H3) and DAPI before ConA beads incubation.
CUT&Tag libraries were prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) complemented with TruePrep Index Kit V2 for Illumina (Vazyme). 2w-100w cells were used as starting materials. Libraries were amplified using 10-20 cycles on the thermocycler. Post-amplification libraries were purified using VAHTS DNA Clean Beads (Vazyme).

value: larval brain

value: type II NSC

value: WT


title: CutTag_HDAC1_HDAC1_V5_interphase_rep2

description: Library name: CutTag_HDAC1_HDAC1_V5_interphase_rep2


title: CutTag_HDAC1_HDAC1_V5_mitosis_rep2

description: Library name: CutTag_HDAC1_HDAC1_V5_mitosis_rep2


title: Female WT Hypothalamus, mouse E13.5

description:
Library name: E13.5_WT_Hypothalamus_female
10x Genomics Multiome

source_name: Hypothalamus

value: Hypothalamus


title: CutTag_HDAC1_V5 control_interphase_rep2

description: Library name: CutTag_HDAC1_V5 control_interphase_rep2


title: UUATAC-seq datasets of Chicken_Cecum

description: single-nucleus ATAC profile of Chicken_Cecum

source_name: Cecum

value: Cecum


title: Male Homo Hypothalamus, mouse E13.5

description:
Library name: E13.5_Hom_Hypothalamus_male
10x Genomics Multiome


title: Female WT MGE, mouse E13.5

description:
Library name: E13.5_WT_MGE_female
10x Genomics Multiome

value: MGE


title: 16S reads obtained from sample S102 (Run 2 - Replicate 2)

description:
Library name: S102_16S
Full-length 16S rRNA gene sequencing

source_name: mixed microbial community

value: mixed microbial community


title: Male WT Hypothalamus, mouse E13.5

description:
Library name: E13.5_WT_Hypothalamus_male
10x Genomics Multiome

value: male


title: UUATAC-seq datasets of Chicken_BrainStem

description: single-nucleus ATAC profile of Chicken_BrainStem

source_name: Brain stem

value: Brain stem


title: CutTag_HDAC1_HDAC1_V5_mitosis_rep1

description: Library name: CutTag_HDAC1_HDAC1_V5_mitosis_rep1


title: UUATAC-seq datasets of Chicken_Brain

description: single-nucleus ATAC profile of Chicken_Brain

source_name: Brain

value: Brain

value: Huxu


title: 16S reads obtained from sample S101 (Run 2 - Replicate 1)

description:
Library name: S101_16S
Full-length 16S rRNA gene sequencing


title: CutTag_HDAC1_HDAC1_V5_interphase_rep1

description: Library name: CutTag_HDAC1_HDAC1_V5_interphase_rep1


title: Male Homo Hypothalamus, mouse P60

description:
Library name: P60_Hom_Hypothalamus_male
10x Genomics Multiome

data_processing:
The raw sequencing data were processed using Cell Ranger ARC (v2.0.0) pipeline. The cellranger-arc mkfastq command was used to generate the demultiplexed FASTQ files from BCL files. The sequencing reads were aligned to mouse (GRCm38/mm10) reference genome using cellranger-arc count. The cellranger-arc count command was used to generate peak-by-barcode (snATAC-seq) matrices.
Assembly: GRCm38/mm10
Supplementary files format and content: cellranger atac_fragments.tsv.gz
Supplementary files format and content: cellranger atac_peak_annotation.tsv

value: Homo


title: UUATAC-seq datasets of Chicken_Bowel

description: single-nucleus ATAC profile of Chicken_Bowel

source_name: Bowel

value: Bowel

value: Wild-type


title: Male Homo Cortex, mouse P60

description:
Library name: P60_Hom_Cortex_male
10x Genomics Multiome

source_name: Cortex

value: Cortex


title: CutTag_HDAC1_V5 control_mitosis_rep1

description: Library name: CutTag_HDAC1_V5 control_mitosis_rep1


title: 16S reads obtained from sample S002 (Run 1 - Replicate 2)

description:
Library name: S002_16S
Full-length 16S rRNA gene sequencing


title: UUATAC-seq datasets of Chicken_AirSac

description: single-nucleus ATAC profile of Chicken_AirSac

source_name: Air sac

value: Air sac

value: Adult


title: Male WT Cortex, mouse P60

description:
Library name: P60_WT_Cortex_male
10x Genomics Multiome


title: 16S reads obtained from sample S001 (Run 1 - Replicate 1)

description:
Library name: S001_16S
Full-length 16S rRNA gene sequencing


title: CutTag_HDAC1_V5 control_interphase_rep1

description: Library name: CutTag_HDAC1_V5 control_interphase_rep1

value: larval brain


title: 16S reads obtained from sample S003 (Run 1 - Replicate 3)

description:
Library name: S003_16S
Full-length 16S rRNA gene sequencing


title: 16S reads obtained from sample S103 (Run 2 - Replicate 3)

description:
Library name: S103_16S
Full-length 16S rRNA gene sequencing


title: T3.5, 2 hours before ovulation, animal 15, scRNAseq

city: Celbridge

first: Lais

last: Barbosa Latorraca

state: Kildare

address: UCD Lyons Farm

department: Agriculture and Food Science

country: Ireland

institute: University College Dublin

description:
Library name: T3.5_RNAseq
Oocyte collected from dominant follicle 2 hours before ovulation

data_processing:
Trim Galore (version 0.6.6) was used to trim raw sequence reads by removing adapter contamination and poor-quality reads with less than 20 Phred score. Only reads with a minimum 20 bp sequence length after trimming were retained for further processing. The data was mapped to the ARS-UCD 1.2 bovine genome using Hista2. Raw counts were quantified using SeqMonk software (version 11.0.10; Babraham Institute; https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Assembly: ARS-UCD 1.2
Supplementary files format and content: Tab-Delimited Text file containing raw read counts for each sample and gene esembl ID on the first column

molecule: polyA RNA

organism: Bos taurus

source_name: Oocyte

extract_protocol:
PCR tubes containing single oocyte samples snap-frozen in PBS + RLT-Plus Buffer at the collection day were transported in dry ice to the Babraham Institute, UK. Oocyte lysates were thawed and transferred to a 96-well plate and incubated with Dynabeads (MyOne Streptavidin C1, Life Technologies) annealed to Smart-seq2 oligo-dTs to capture polyadenylated mRNA. The remaining lysate containing the DNA was transferred to a new 96 well-plate for a subsequent bisulphite conversion analysis. The beads containing the mRNA were diluted in reverse transcription master mix using SuperScript™ II Reverse Transcriptase (Invitrogen) and reverse transcription was performed to produce cDNA.
cDNA was amplified using KAPA HiFi HotStart ReadyMix (Roche), purified with Ampure XP beads with a 1:0.9 ratio, and eluted into 20 μL of water. Amplified cDNA was quantified using a High Sensitivity DNA Assay chip (Agilent Technologies), and libraries were prepared using the Nextera XT Kit (Illumina) with ~300 pg of cDNA in two different replicates. A total of 15 oocytes were sequenced on the NextSeq500 HighOutput 75 bp Single End with a sequence depth of ~2 million reads.

value: Oocyte

tag: experimental group

value: DF (dominant follicle)

value: 2 hours before ovulation


title: 16S reads obtained from sample AS02 (Inoculum - Replicate 2)

description:
Library name: AS02_16S
Full-length 16S rRNA gene sequencing


title: 16S reads obtained from sample AS01 (Inoculum - Replicate 1)

description:
Library name: AS01_16S
Full-length 16S rRNA gene sequencing


title: T3.2, 2 hours before ovulation, animal 12, scRNAseq

description:
Library name: T3.2_RNAseq
Oocyte collected from dominant follicle 2 hours before ovulation


title: T3.4, 2 hours before ovulation, animal 14, scRNAseq

description:
Library name: T3.4_RNAseq
Oocyte collected from dominant follicle 2 hours before ovulation


title: ATAC_NSC-rep1

description: Library name: ATAC_NSC-rep1

data_processing:
Raw FASTQ reads were trimmed using Trim Galore (v0.6.10, with parameters --paired --quality 20 --stringency 3 -j 4).
Trimmed reads were mapped to Drosophila reference genome (version: dm6) using Bowtie2 (v2.5.1) very-sensitive-local mode.
Picard tools were used to remove duplicate reads.
Mitochondrial and low-quality reads were filterer out using Samtools (v1.6).
Assembly: dm6
Supplementary files format and content: bigwig files were generated using bamCoverage (--binSize 50 --normalizeUsing RPKM --extendReads)

extract_protocol:
Larval brains were dissected and dissociated into single cells, then the cells were arrested by ConA beads, and the proteins of interest were combined by the specific primary antibody, followed by secondary antibody and Tn5 transposase. To obtain interphase and mitosis cells, the dissociated cells were fixed with 0.5% formaldehyde for 8min and quenched by Glycine., then stained with pH3 (phospho-histone H3) and DAPI before ConA beads incubation.
ATAC-seq libraries were prepared using Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme). 1w-9w cells were used as starting materials. Libraries were amplified using 14 cycles on the thermocycler. 200-2000 bp DNA was purified to construct library.

value: type II NSC

value: WT


title: Female Homo Cortex, mouse P60

description:
Library name: P60_Hom_Cortex_female
10x Genomics Multiome

value: female


title: Female Homo Hypothalamus, mouse P60

description:
Library name: P60_Hom_Hypothalamus_female
10x Genomics Multiome

value: Hypothalamus


title: ATAC_NSC-rep2

description: Library name: ATAC_NSC-rep2


title: ATAC_progenitor-rep1

description: Library name: ATAC_progenitor-rep1

value: progenitors


title: 16S reads obtained from sample AS03 (Inoculum - Replicate 3)

description:
Library name: AS03_16S
Full-length 16S rRNA gene sequencing

value: mixed microbial community


title: Female WT Cortex, mouse P60

description:
Library name: P60_WT_Cortex_female
10x Genomics Multiome


title: T3.3, 2 hours before ovulation, animal 13, scRNAseq

description:
Library name: T3.3_RNAseq
Oocyte collected from dominant follicle 2 hours before ovulation


title: CutTag_GAF_Osa overexpression_rep2

value: Osa-V5 overexpression


title: Male WT Hypothalamus, mouse P60

description:
Library name: P60_WT_Hypothalamus_male
10x Genomics Multiome

value: male


title: ATAC_progenitor-rep2

description: Library name: ATAC_progenitor-rep2


title: CutTag_GAF_WT_control_rep2


title: Male Homo Hypothalamus, mouse E13.5

description:
Library name: E13.5_Hom_Hypothalamus_male
10x Genomics Multiome

value: Homo


title: T2.4, 19 to 23 hours before ovulation, animal 10, scRNAseq

description:
Library name: T2.4_RNAseq
Oocytre collected from dominant follicle 19 to 23 hours after estrus detection

value: 19 to 23 hours after estrus detection


title: T2.3, 19 to 23 hours before ovulation, animal 9, scRNAseq

description:
Library name: T2.3_RNAseq
Oocytre collected from dominant follicle 19 to 23 hours after estrus detection


title: CutTag_GAF_IgG_control_rep2


title: Male Homo MGE, mouse E13.5

description:
Library name: E13.5_Hom_MGE_male
10x Genomics Multiome

value: MGE


title: T2.2, 19 to 23 hours before ovulation, animal 8, scRNAseq

description:
Library name: T2.2_RNAseq
Oocytre collected from dominant follicle 19 to 23 hours after estrus detection


title: Male WT MGE, mouse E13.5

description:
Library name: E13.5_WT_MGE_male
10x Genomics Multiome


title: Male WT Hypothalamus, mouse E13.5

description:
Library name: E13.5_WT_Hypothalamus_male
10x Genomics Multiome


title: CutTag_GAF_Osa overexpression_rep1


title: CutTag_GAF_WT_control_rep1


title: T1.5, 24 hours before ovulation, animal 5, scRNAseq

description:
Library name: T1.5_RNAseq
Oocyte collected from dominant follicle 24 hours before ovulation

value: 24 hours before ovulation


title: Female Homo MGE, mouse E13.5

description:
Library name: E13.5_Hom_MGE_female
10x Genomics Multiome


title: Female WT Hypothalamus, mouse P60

description:
Library name: P60_WT_Hypothalamus_female
10x Genomics Multiome


title: T1.6, 24 hours before ovulation, animal 6, scRNAseq

description:
Library name: T1.6_RNAseq
Oocyte collected from dominant follicle 24 hours before ovulation


title: Female Homo Hypothalamus, mouse E13.5

description:
Library name: E13.5_Hom_Hypothalamus_female
10x Genomics Multiome


title: CutTag_Osa_V5 control_rep2


title: T1.4, 24 hours before ovulation, animal 4, scRNAseq

description:
Library name: T1.4_RNAseq
Oocyte collected from dominant follicle 24 hours before ovulation


title: Female WT Hypothalamus, mouse E13.5

description:
Library name: E13.5_WT_Hypothalamus_female
10x Genomics Multiome


title: Female WT MGE, mouse E13.5

description:
Library name: E13.5_WT_MGE_female
10x Genomics Multiome


title: T3.1, 2 hours before ovulation, animal 11, scRNAseq

description:
Library name: T3.1_RNAseq
Oocyte collected from dominant follicle 2 hours before ovulation


title: T1.2, 24 hours before ovulation, animal 2, scRNAseq

description:
Library name: T1.2_RNAseq
Oocyte collected from dominant follicle 24 hours before ovulation


title: T1.3, 24 hours before ovulation, animal 3, scRNAseq

description:
Library name: T1.3_RNAseq
Oocyte collected from dominant follicle 24 hours before ovulation


title: CutTag_Osa_Osa-V5_rep1


title: NSC_TMut_RNAseq_rep1

description: Library name: NSC_TMut_RNAseq_rep1

library_source: transcriptomic

data_processing:
Adaptors were trimmed using trim galore (v0.6.5) and trimmed reads were mapped to the mouse genome (mm39) using STAR (v2.7.3a) with default parameters. Gene counts were extracted from mapped reads using featureCounts with --largestOverlap parameter. Raw counts were used to identify differentially expressed genes with DESeq2 (FDR <0.05 and fold-change >1.5), following the standard package documentation.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files.
Assembly: mm39
Supplementary files format and content: CSV

source_name: Neural stem cells

extract_protocol:
RNA was extracted from NSCs using Omega EZNA Total RNA kit.
Libraries were prepared by Novogene (https://en.novogene.com/).

value: Neural stem cells

value: Tet-TMut


title: CutTag_GAF_IgG_control_rep1

value: larval brain


title: CutTag_H3K27ac_mitosis_rep2


title: T2.1, 19 to 23 hours before ovulation, animal 7, scRNAseq

description:
Library name: T2.1_RNAseq
Oocytre collected from dominant follicle 19 to 23 hours after estrus detection

value: Oocyte

value: DF (dominant follicle)


title: gcn4∆,H2O2,Replicate3

city: Faridabad

first: Anil

last: Thakur

state: Haryana

address: Pali Faridabad

department: Biotechnology

country: India

institute: Regional Centre For Biotechnology

description:
Library name: CGAR22
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is CGAR22
H2O2_gcn4_vs_WT_AllReplicates_Counts.tsv
H2O2_gcn4_vs_WT_AllReplicates_FPKM.tsv

data_processing:
Quality assessment of raw FASTQ reads was performed using FastQC v0.11.9 with default parameters. Reads were preprocessed using Fastp v0.20.1 with the following parameters: --qualified_quality_phred 30, --unqualified_percent_limit 30, and -e 30. Quality was reassessed post-preprocessing using FastQC, and results were summarized using MultiQC.  The reference genome of Nakaseomyces glabratus (GCF_000002545.3) was indexed using STAR v2.7.9a. Processed reads were aligned to the indexed reference genome using STAR with the following alignment parameters:  --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outFilterMismatchNoverReadLmax 0.1 --outSAMattributes NH HI AS NM MD --outFilterScoreMinOverLread 0.5 --outFilterMatchNminOverLread 0.5 To ensure accurate gene quantification, rRNA and tRNA features were removed from the annotation GTF file. Gene-level counts were obtained from the sorted BAM alignment files using FeatureCounts v2.0.1.  For differential expression analysis, gene counts were processed using DESeq2. The following parameters were applied:  Threshold for statistical significance: --alpha 0.05 p-value adjustment method: Benjamini-Hochberg (BH) Regularized log transformation (rlog) in DESeq2 was used for clustering and principal component analysis (PCA). Differentially expressed genes were determined using an adjusted p-value ≤ 0.05 and a log2 fold change threshold of ±1.5.
Assembly: Nakaseomyces glabratus (GCF_000002545.3)
Supplementary files format and content: TSV file format includes the raw count value for each listed sample
Supplementary files format and content: TSV file format  includes the FPKM for each listed sample

organism: Nakaseomyces glabratus

source_name: N. glabratus cells

growth_protocol: The cells were grown overnight at 30°C and the secondary culture of around 0.1 was set in 50 ml SD (minimal media) and was grown till log phase at 30°C.

extract_protocol:
The RNA was extracted by utilising a hybrid method combining the classic acid-phenol extraction method (Schmitt et al., 1990). Then, finally, eluting using an RNA extraction kit by Qiagen (Cat. No. 74104).The extracted RNA quality was verified via gel electrophoresis, qRT-PCR, Qubit fluorometer (Thermofisher #Q33238) using RNA HS assay kit (Thermofisher #Q32851), Nanodrop 1000 and RIN values from an Agilent screen tape station.
The library preparation used Trueseq standard total RNA (Illumina #20020597). Similarly, the final libraries were quantified using a Qubit fluorometer, and the tape station measured the insert size. The prepared library was sequenced by paired-end sequencing on an Illumina platform.

treatment_protocol: The treatment of both 3-Amino triazole (3AT), which causes histidine auxotrophy and ultimately amino acid starvation and Hydrogen peroxide (H2O2) as a ROS agent for oxidative stress was given at the log phase O.D. in a concentration of 5 mM and 10 mM, respectively, for 30 minutes. 30 min was chosen as it corresponds to a strong eIF2α-Phosphorylation time point, which is mediated by Gcn2 kinase.

value: N. glabratus cells

value: GCN4 delete, Bg2 Phototrophic

value: 10 mM H2O2


title: NSC_TMut_RNAseq_rep2

description: Library name: NSC_TMut_RNAseq_rep2


title: CutTag_Osa_V5 control_rep1

value: type II NSC

value: WT


title: CutTag_Osa_Osa-V5_rep2


title: NSC_TFoCa_RNAseq_rep1

description: Library name: NSC_TFoCa_RNAseq_rep1

value: Tet-TFoCa


title: NSC_TFoCa_RNAseq_rep2

description: Library name: NSC_TFoCa_RNAseq_rep2


title: skeletal muscle DNA from young vehicle  control 9

type: genomic

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

hyb_protocol: DNA underwent bisulfite conversion using the Zymo EZ DNA methylation Kit (Zymo). At least 150 ng of bisulfite converted DNA was processed using a custom mammalian array and the 285k Illumina Mouse Methylation BeadChip.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: MammalMethylClock in R-package. Limma R-package (v.3.50.3) with adjustment for unknown cofounders performed with RUBV-seq R-package (v.1.28.0)

label: Cy3 and Cy5

source_name: tibalias anterior

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from skeletal muscle tissue samples using QIAamp DNA Micro kits (Qiagen #56304) according to standard procedures.

treatment_protocol: Chemical injury via barium chloride injection in the tibalias anterior muscle of young and old mice. The contralateral tibalias anterior was injected with PBS and served as the control within mice.

value: tibalias anterior

value: Control


title: CutTag_H3K27ac_interphase_rep2


title: skeletal muscle DNA from young vehicle  control 10

value: male


title: WT,H2O2,Replicate2

description:
Library name: AR20
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is AR20
H2O2_gcn4_vs_WT_AllReplicates_Counts.tsv
H2O2_gcn4_vs_WT_AllReplicates_FPKM.tsv

value: WT, Bg2 Phototrophic


title: skeletal muscle DNA from young vehicle  injury 9

value: Injury


title: skeletal muscle DNA from young vehicle  control 6


title: gcn4∆,H2O2,Replicate2

description:
Library name: AR24
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is AR24
H2O2_gcn4_vs_WT_AllReplicates_Counts.tsv
H2O2_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: skeletal muscle DNA from young vehicle  control 7


title: skeletal muscle DNA from young vehicle  control 8


title: T1.1, 24 hours before ovulation, animal 1, scRNAseq

description:
Library name: T1.1_RNAseq
Oocyte collected from dominant follicle 24 hours before ovulation

value: 24 hours before ovulation


title: gcn4∆,H2O2,Replicate1

description:
Library name: AR21
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is AR21
H2O2_gcn4_vs_WT_AllReplicates_Counts.tsv
H2O2_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: WT,H2O2,Replicate1

description:
Library name: AR18
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is AR18
H2O2_gcn4_vs_WT_AllReplicates_Counts.tsv
H2O2_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: CutTag_H3K27ac_mitosis_rep1


title: NSC_WT_RNAseq_rep1

description: Library name: NSC_WT_RNAseq_rep1

value: Neural stem cells


title: skeletal muscle DNA from young vehicle  injury 8


title: gcn4∆,3AT,Replicate3

description:
Library name: CGAR16
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is CGAR16
3AT_gcn4_vs_WT_AllReplicates_Counts.tsv
3AT_gcn4_vs_WT_AllReplicates_FPKM.tsv

value: GCN4 delete, Bg2 GCN4 delete

value: 5 mM 3AT


title: CutTag_HDAC1-V5_GAF-RNAi_rep1

value: larval brain

value: HDAC1-V5, GAF-RNAi


title: CutTag_HDAC1-V5_WT control_rep2


title: NSC_WT_RNAseq_rep2

description: Library name: NSC_WT_RNAseq_rep2


title: CutTag_H3K27ac_interphase_rep1


title: gcn4∆,3AT,Replicate2

description:
Library name: AR15
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is AR15
3AT_gcn4_vs_WT_AllReplicates_Counts.tsv
3AT_gcn4_vs_WT_AllReplicates_FPKM.tsv

value: N. glabratus cells


title: NK Cells treated by Virus 2206 [5ADB.ATGCGCAG_TATGCAGT]

city: Boston

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
The sample is aligned to GRCm38 transcriptome and quantified using Kallisto
Assembly: GRCm38
Supplementary files format and content: gzipped abundance.tsv output from Kallisto

source_name: GBM-bearing mice (C57BL/6)

extract_protocol: Brains were isolated, minced, and digested. Brain cells suspensions were separated using 33% Percoll. Microglia, monocytes, and T Cells were FACS-Sorted and RNA was extracted using the PicoPure RNA Isolation Kit.

tag: strain

value: Male

value: 8 weeks old


title: skeletal muscle DNA from young vehicle  injury 6


title: gcn4∆,3AT,Replicate1

description:
Library name: AR13
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is AR13
3AT_gcn4_vs_WT_AllReplicates_Counts.tsv
3AT_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: skeletal muscle DNA from old vehicle control  5


title: NSC_WT_RNAseq_rep3

description: Library name: NSC_WT_RNAseq_rep3


title: NK Cells treated by Virus 2206 [5ADB.TACGCTGC_TATGCAGT]


title: CutTag_HDAC1-V5_WT control_rep1

value: type II NSC


title: CutTag_HDAC1-V5_GAF-RNAi_rep2


title: NK Cells treated by Virus 2206 [5ADB.CGGAGCCT_TATGCAGT]


title: CutTag_HDAC1_HDAC1-V5_rep2


title: skeletal muscle DNA from young vehicle  injury 7

value: WT


title: skeletal muscle DNA from young vehicle  injury 10


title: skeletal muscle DNA from old vehicle control  2


title: WT,3AT,Replicate3

description:
Library name: CGAR12
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is CGAR12
3AT_gcn4_vs_WT_AllReplicates_Counts.tsv
3AT_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: CD8 T Cells treated by Virus 2206 [5ADB.GCGTAGTA_TATGCAGT]


title: CutTag_HDAC1_V5 control_rep2


title: skeletal muscle DNA from old vehicle control  15


title: skeletal muscle DNA from old vehicle control  4


title: WT,3AT,Replicate2

description:
Library name: AR10
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is AR10
3AT_gcn4_vs_WT_AllReplicates_Counts.tsv
3AT_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: skeletal muscle DNA from young vehicle  injury 5


title: CutTag_HDAC1_HDAC1-V5_rep1


title: skeletal muscle DNA from old vehicle control  3


title: gcn4∆, GCN4 gene deleted, Untreated/Control,  Replicate3

description:
Library name: CGAR7
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is CGAR7
Control_gcn4_vs_WT_AllReplicates_Counts.tsv
Control_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: CutTag_HDAC1_V5 control_rep1


title: CutTag_H3K27ac_IgG control_rep2


title: CD4 T Cells treated by Virus 2206 [5ADB.TCGACGTC_CTCCTTAC]


title: CD4 T Cells treated by Virus 2206 [5ADB.TGCAGCTA_CTCCTTAC]


title: WT,3AT,Replicate1

description:
Library name: AR9
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is AR9
3AT_gcn4_vs_WT_AllReplicates_Counts.tsv
3AT_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: CD8 T Cells treated by Virus 2206 [5ADB.ACTCGCTA_TATGCAGT]


title: CD4 T Cells treated by Virus 2206 [5ADB.CGATCAGT_CTCCTTAC]


title: gcn4∆, GCN4 gene deleted, Untreated/Control, Replicate1

description:
Library name: AR5
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is AR5
Control_gcn4_vs_WT_AllReplicates_Counts.tsv
Control_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: CutTag_H3K27ac_WT_rep2


title: CD8 T Cells treated by Virus 2206 [5ADB.GGAGCTAC_TATGCAGT]


title: gcn4∆, GCN4 gene deleted, Untreated/Control,  Replicate2

description:
Library name: AR6
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is AR6
Control_gcn4_vs_WT_AllReplicates_Counts.tsv
Control_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: WT, Untreated/Control, Replicate3

description:
Library name: CGAR4
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is CGAR4
Control_gcn4_vs_WT_AllReplicates_Counts.tsv
Control_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: skeletal muscle DNA from old vehicle control  14


title: CutTag_H3K27ac_HDAC1-RNAi_rep2


title: skeletal muscle DNA from old vehicle control  12


title: CutTag_H3K27ac_IgG control_rep1


title: skeletal muscle DNA from old vehicle control  11


title: WT, Untreated/Control, Replicate2

description:
Library name: AR2
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is AR2
Control_gcn4_vs_WT_AllReplicates_Counts.tsv
Control_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: NK Cells treated by Virus Empty [5ADB.ATGCGCAG_CTCCTTAC]


title: NK Cells treated by Virus Empty [5ADB.TACGCTGC_CTCCTTAC]


title: Macrophage treated by Virus 2206 [5ADB.ACTGAGCG_CTCCTTAC]


title: CutTag_H3K27ac_HDAC1-RNAi_rep1


title: CutTag_H3K27ac_NSC_rep3


title: skeletal muscle DNA from old vehicle injury  4


title: WT, Untreated/Control, Replicate1

description:
Library name: AR1
Column name in both AllReplicates_Count. Tsv and AllReplicates_FPKM.tsv is AR1
Control_gcn4_vs_WT_AllReplicates_Counts.tsv
Control_gcn4_vs_WT_AllReplicates_FPKM.tsv


title: skeletal muscle DNA from old vehicle control  10


title: Macrophage treated by Virus 2206 [5ADB.CCTAAGAC_CTCCTTAC]


title: skeletal muscle DNA from old vehicle injury  5


title: Macrophage treated by Virus 2206 [5ADB.TAGCGCTC_CTCCTTAC]


title: NK Cells treated by Virus Empty [5ADB.CGGAGCCT_CTCCTTAC]


title: CutTag_H3K27ac_WT_rep1


title: CutTag_H3K27ac_progenitor_rep3

value: neural progenitor

value: Erm overexpression


title: CD4,KO,infected, oligo

city: Xiamen City

first: GUO

last: FU

address: No. 4221, Xiang'an South Road, Xiang'an District, Xiamen, Fujian Province

institute: Xiamen University

description:
Library name: KO. Oligo
BGI C4 single-cell RNA-seq

data_processing:
Raw sequencing data were processed using Cell Ranger (version 3.0.2) with default parameters for alignment, UMI quantification, and generation of the gene expression matrix.
Assembly: mm10 (Mouse Genome, GRCm38)
Supplementary files format and content: Processed files: Gene expression matrix in Matrix Market Exchange format (.mtx),Cell barcodes: barcodes.tsv ,Gene annotations: genes.tsv

source_name: spleen

extract_protocol:
Single-cell suspensions were prepared from harvested lung and spleen tissues. Samples were processed using mechanical dissociation and enzymatic digestion to ensure viable single-cell isolation. Dead cells and debris were removed using density gradient centrifugation.
Single-cell RNA-seq libraries were constructed using the BGI C4 single-cell sequencing platform. The libraries were generated following the C4 protocol, which uses droplet-based single-cell capture, UMI barcoding, and cDNA synthesis. Libraries were then sequenced on the BGI DNBSEQ-G400 instrument.

value: spleen

value: 6-8 weeks old

value: CD4+ T cells

value: LCMV-clone 13

tag: time

value: 21 days


title: CD4,WT,infected, oligo

description:
Library name: WT, oligo
BGI C4 single-cell RNA-seq

value: male


title: skeletal muscle DNA from old vehicle control  13

value: tibalias anterior

value: Control


title: CutTag_IgG control_progenitor_rep3

value: larval brain


title: skeletal muscle DNA from old vehicle injury  15

value: Injury


title: UUATAC-seq datasets of MouseMale_Thymus_A

description: single-nucleus ATAC profile of MouseMale_Thymus_A

data_processing:
The FASTQ files generated by MGI sequencer were split by the T7 index using the software splitBarcode (version 0.1.6, https://github.com/MGI-tech-bioinformatics/splitBarcode). Reads with barcode base quality lower than 10 or more than two mismatches per index were removed. Then the cell barcode was tagged into the query name of each reads using Drop-Seq tools  (version 2.5.1, https://github.com/broadinstitute/Drop-seq). The cell barcode of each read pair consists of four components: T7 index, Hy AS barcode, Hy B barcode and Tn5 barcode (128, 768, 8 and 192 indexes, respectively). We corrected each barcode to its original sequence if only one base was mismeasured in each barcode component. Bam files with tagged barcodes were split by Tn5 barcodes and then merged by tissue information. Different samples were marked by different Tn5 barcodes. Subsequently, reads were aligned to reference genomes of mouse (mm10) using BWA (version 0.7.15, https://github.com/lh3/bwa) with default parameters in paired-end mode to obtain the bam file.
To deal with the Tn5 insertion bias, we performed the function alignmentSieve of deepTools (version 3.5.1, https://github.com/deeptools/deepTools) to shift each read. Next, paired-reads with mapping quality higher than 30 were converted to fragments. And then nonduplicate fragments with length range from 10bp to 1000bp were extracted. We generated one fragment file for each tissue.
Assembly: mm10
Supplementary files format and content: BED files recording coordinates of fragments captured by UUATAC-seq

source_name: Thymus

extract_protocol:
Whole organs were then dissected in the following order: small intestine, large intestine, spleen, pancreas, lymph nodes (inguinal lymph nodes, abdominal aortic lymph nodes, axillary lymph nodes, cervical lymph nodes), stomach, thyroid gland, brain, heart, lung, thymus, kidney, adrenal gland, bladder, prostate, testis, liver, muscle, bone marrow and spinal cord. Except for bone marrow, the samples were quickly transferred into cold DPBS, washed and then manually pulverized using a mortar and pestle within a liquid nitrogen bath. The pulverized tissues were suspended in 1mL of Nuclear Isolation Buffer (NIB) and followed by incubation for 1.5-3 min to isolate the nuclei. The bone marrow cell suspension was centrifuged at 350 × g for 5 min, and the pellet was directly resuspended in 1 mL of NIB for 2min incubation. The suspension of each tissue was transferred to 15 mL centrifuge tubes pre-filled with 5mL of WB (wash buffer, 0.2% BSA, 3 mM MgCl2 in DPBS), filtered through 40 μm strainers and centrifuged at 650 × g for 5 min at 4°C. We resuspended the nuclei in 1 mL of WB and filtered the suspension through 20 μm size strainers, pelleted at 650 × g for 5 min and resuspended in the appropriate amount of DPBS to give a final concentration of 25,000 nuclei per microlitre.
Library preparations were performed with the UUATAC-seq protocol

treatment_protocol: After anaesthetization with 1% (i.p.) sodium pentobarbital, mice were weighed, shaved, and given transcardial perfusion with 20-30 mL of PBS.

value: Thymus

value: Wild-type

value: 8 weeks


title: skeletal muscle DNA from old vehicle injury  3


title: skeletal muscle DNA from old vehicle injury  14


title: skeletal muscle DNA from old vehicle injury  13


title: CutTag_GAF_progenitor_rep3


title: UUATAC-seq datasets of MouseMale_Testis_A

description: single-nucleus ATAC profile of MouseMale_Testis_A

source_name: Testis

value: Testis

value: Male


title: skeletal muscle DNA from old vehicle control  1

value: WT


title: skeletal muscle DNA from old vehicle injury 2


title: CD4,WT,infected

description:
Library name: WT
BGI C4 single-cell RNA-seq


title: CD8 T Cells treated by Virus Empty [5ADB.GCGTAGTA_CTCCTTAC]

value: 8 weeks old


title: CD4,KO,infected

description:
Library name: KO
BGI C4 single-cell RNA-seq

value: spleen


title: CutTag_GAF_NSC_rep3

source_name: larval brain

value: type II NSC


title: skeletal muscle DNA from old vehicle injury  12


title: skeletal muscle DNA from old vehicle injury  10


title: CD8 T Cells treated by Virus Empty [5ADB.GGAGCTAC_CTCCTTAC]


title: UUATAC-seq datasets of MouseMale_Thymus_B

description: single-nucleus ATAC profile of MouseMale_Thymus_B


title: CutTag_IgG control_NSC_rep3


title: CD4 T Cells treated by Virus Empty [5ADB.TCGACGTC_AGAGGATA]


title: UUATAC-seq datasets of MouseMale_Testis_B

description: single-nucleus ATAC profile of MouseMale_Testis_B


title: CutTag_GAF_progenitor_rep2

value: neural progenitor

value: Erm overexpression


title: CD8 T Cells treated by Virus Empty [5ADB.ACTCGCTA_CTCCTTAC]


title: Macrophage treated by Virus Empty [5ADB.CCTAAGAC_AGAGGATA]


title: CutTag_H3K27ac_progenitor_rep2


title: UUATAC-seq datasets of MouseMale_Spleen_B

description: single-nucleus ATAC profile of MouseMale_Spleen_B

source_name: Spleen

value: Spleen


title: CD4 T Cells treated by Virus Empty [5ADB.TGCAGCTA_AGAGGATA]


title: CutTag_H3K27ac_NSC_rep2


title: skeletal muscle DNA from old vehicle injury  1

value: male


title: Macrophage treated by Virus Empty [5ADB.ACTGAGCG_AGAGGATA]


title: CutTag_GAF_NSC_rep2


title: CutTag_IgG control_NSC_rep2


title: CD4 T Cells treated by Virus Empty [5ADB.CGATCAGT_AGAGGATA]


title: UUATAC-seq datasets of MouseMale_Prostate_B

description: single-nucleus ATAC profile of MouseMale_Prostate_B

source_name: Prostate

value: Prostate


title: UUATAC-seq datasets of MouseMale_Spleen_A

description: single-nucleus ATAC profile of MouseMale_Spleen_A


title: CutTag_IgG control_progenitor_rep2


title: UUATAC-seq datasets of MouseMale_Pancreas_B

description: single-nucleus ATAC profile of MouseMale_Pancreas_B

source_name: Pancreas

value: Pancreas


title: Monocytes Treated By Virus [ATCTCAGG_TCGCATAA]


title: UUATAC-seq datasets of MouseMale_Prostate_A

description: single-nucleus ATAC profile of MouseMale_Prostate_A


title: Monocytes Treated By Control [GCTCATGA_TCGCATAA]


title: Macrophage treated by Virus Empty [5ADB.TAGCGCTC_AGAGGATA]


title: CutTag_H3K27ac_NSC_rep1

value: larval brain


title: Monocytes Treated By Virus [GTAGAGGA_TCGCATAA]


title: UUATAC-seq datasets of MouseMale_Muscle_A

description: single-nucleus ATAC profile of MouseMale_Muscle_A

source_name: Muscle

value: Muscle


title: CutTag_H3K27ac_progenitor_rep1


title: UUATAC-seq datasets of MouseMale_Muscle_B

description: single-nucleus ATAC profile of MouseMale_Muscle_B


title: UUATAC-seq datasets of MouseMale_Pancreas_A

description: single-nucleus ATAC profile of MouseMale_Pancreas_A


title: UUATAC-seq datasets of MouseMale_Lung_A

description: single-nucleus ATAC profile of MouseMale_Lung_A

source_name: Lung

value: Lung


title: CutTag_GAF_NSC_rep1


title: CutTag_GAF_progenitor_rep1


title: Monocytes Treated By Virus [CGAGGCTG_TCGCATAA]


title: CutTag_IgG control_progenitor_rep1


title: CutTag_IgG control_NSC_rep1


title: UUATAC-seq datasets of MouseMale_Liver_B

description: single-nucleus ATAC profile of MouseMale_Liver_B

source_name: Liver

value: Liver

value: Wild-type


title: UUATAC-seq datasets of MouseMale_Lung_B

description: single-nucleus ATAC profile of MouseMale_Lung_B

value: 8 weeks


title: skeletal muscle DNA from old senolytic control 13

value: tibalias anterior

value: Control


title: skeletal muscle DNA from old senolytic control 3

value: WT


title: UUATAC-seq datasets of MouseMale_Liver_A

description: single-nucleus ATAC profile of MouseMale_Liver_A

value: Male


title: skeletal muscle DNA from old senolytic control 2


title: CutTag_His modification_H3K14ac_progenitor_rep1


title: UUATAC-seq datasets of MouseMale_Kidney_B

description: single-nucleus ATAC profile of MouseMale_Kidney_B

source_name: Kidney

value: Kidney


title: Microglia Treated By Virus [TCCTGAGC_TCGCATAA]

value: 8 weeks old


title: skeletal muscle DNA from old senolytic control 15


title: Microglia Treated By Virus [TAGGCATG_TCGCATAA]


title: Monocytes Treated By Control [CTCTCTAC_TCGCATAA]


title: skeletal muscle DNA from old senolytic control 14


title: Monocytes Treated By Control [AAGAGGCA_TCGCATAA]


title: UUATAC-seq datasets of MouseMale_Kidney_A

description: single-nucleus ATAC profile of MouseMale_Kidney_A


title: skeletal muscle DNA from old senolytic injury 15

value: Injury


title: Microglia Treated By Control [AGGCAGAA_TCGCATAA]


title: skeletal muscle DNA from old senolytic control 12


title: CutTag_His modification_H3K14ac_NSC_rep1

value: type II NSC


title: Microglia Treated By Control [GGACTCCT_TCGCATAA]


title: CutTag_His modification_H3K4me_progenitor_rep1

value: neural progenitor

value: Erm overexpression


title: UUATAC-seq datasets of MouseMale_Heart_B

description: single-nucleus ATAC profile of MouseMale_Heart_B

source_name: Heart

value: Heart


title: UUATAC-seq datasets of Gecko_Skin

description: single-nucleus ATAC profile of Gecko_Skin

data_processing:
The FASTQ files generated by MGI sequencer were split by the T7 index using the software splitBarcode (version 0.1.6, https://github.com/MGI-tech-bioinformatics/splitBarcode). Reads with barcode base quality lower than 10 or more than two mismatches per index were removed. Then the cell barcode was tagged into the query name of each reads using Drop-Seq tools  (version 2.5.1, https://github.com/broadinstitute/Drop-seq). The cell barcode of each read pair consists of four components: T7 index, Hy AS barcode, Hy B barcode and Tn5 barcode (128, 768, 8 and 192 indexes, respectively). We corrected each barcode to its original sequence if only one base was mismeasured in each barcode component. Bam files with tagged barcodes were split by Tn5 barcodes and then merged by tissue information. Different samples were marked by different Tn5 barcodes. Subsequently, reads were aligned to reference genomes of Eublepharis macularius (MPM_Emac_v1.0) using BWA (version 0.7.15, https://github.com/lh3/bwa) with default parameters in paired-end mode to obtain the bam file.
To deal with the Tn5 insertion bias, we performed the function alignmentSieve of deepTools (version 3.5.1, https://github.com/deeptools/deepTools) to shift each read. Next, paired-reads with mapping quality higher than 30 were converted to fragments. And then nonduplicate fragments with length range from 10bp to 1000bp were extracted. We generated one fragment file for each tissue.
Assembly: MPM_Emac_v1.0
Supplementary files format and content: BED files recording coordinates of fragments captured by UUATAC-seq

organism: Eublepharis macularius

source_name: Skin

extract_protocol:
Whole organs were then dissected in the following order: ovary, liver, fat, pancreas, lung, kidney, small bladder, esophagus, skin, muscles, stomach, large bladder, intestine, cloaca, tail root, tail tip, eyes, tongue, brain, and heart. All samples were quickly transferred into cold DPBS, washed and then manually pulverized using a mortar and pestle within a liquid nitrogen bath. The pulverized tissues were suspended in 1mL of Nuclear Isolation Buffer (NIB) and followed by incubation for 1.5-3 min to isolate the nuclei. The suspension of each tissue was transferred to 15 mL centrifuge tubes pre-filled with 5mL of WB (wash buffer, 0.2% BSA, 3 mM MgCl2 in DPBS), filtered through 40 μm strainers and centrifuged at 650 × g for 5 min at 4°C. We resuspended the nuclei in 1 mL of WB and filtered the suspension through 20 μm size strainers, pelleted at 650 × g for 5 min and resuspended in the appropriate amount of DPBS to give a final concentration of 25,000 nuclei per microlitre.
Library preparations were performed with the UUATAC-seq protocol

treatment_protocol: The leopard gecko was anesthetized by intraperitoneal injection of 1% (i.p.) sodium pentobarbital.

value: Skin

value: Adult

value: Female


title: CutTag_His modification_H3K4me_NSC_rep1

value: larval brain


title: skeletal muscle DNA from old senolytic control 11

value: male


title: UUATAC-seq datasets of MouseMale_Heart_A

description: single-nucleus ATAC profile of MouseMale_Heart_A

value: Wild-type

value: 8 weeks


title: skeletal muscle DNA from old senolytic control 1

value: tibalias anterior

value: Control


title: Microglia Treated By Control [TAAGGCGA_TCGCATAA]

value: Male


title: skeletal muscle DNA from old senolytic injury 2

value: WT


title: skeletal muscle DNA from old senolytic injury 3


title: Microglia Treated By Virus [CGTACTAG_TCGCATAA]

value: 8 weeks old


title: UUATAC-seq datasets of Gecko_Heart

description: single-nucleus ATAC profile of Gecko_Heart


title: CD8 T Cells Treated By Virus [ATCTCAGG_TAAGGCTC]


title: skeletal muscle DNA from old vehicle injury  11

value: Injury


title: CutTag_His modification_H3K27ac_progenitor_rep1


title: UUATAC-seq datasets of Gecko_Tongue

description: single-nucleus ATAC profile of Gecko_Tongue

source_name: Tongue

value: Tongue


title: skeletal muscle DNA from old senolytic injury 13


title: skeletal muscle DNA from old senolytic control 4


title: CD8 T Cells Treated By Virus [GTAGAGGA_TAAGGCTC]


title: skeletal muscle DNA from old senolytic injury 14


title: CutTag_His modification_H3K27ac_NSC_rep1

value: type II NSC


title: UUATAC-seq datasets of MouseMale_Stomach

description: single-nucleus ATAC profile of MouseMale_Stomach

source_name: Stomach

value: Stomach


title: CD8 T Cells Treated By Control [AAGAGGCA_TAAGGCTC]


title: UUATAC-seq datasets of Gecko_TailRoot

description: single-nucleus ATAC profile of Gecko_TailRoot

source_name: Tail root

value: Tail root


title: UUATAC-seq datasets of MouseMale_Bladder_B

description: single-nucleus ATAC profile of MouseMale_Bladder_B

source_name: Bladder

value: Bladder


title: skeletal muscle DNA from old senolytic injury 12

source_name: tibalias anterior


title: UUATAC-seq datasets of Gecko_Stomach

description: single-nucleus ATAC profile of Gecko_Stomach

value: Adult


title: skeletal muscle DNA from old senolytic injury 11


title: CD8 T Cells Treated By Virus [CGAGGCTG_TAAGGCTC]

source_name: GBM-bearing mice (C57BL/6)


title: skeletal muscle DNA from old senolytic injury 4


title: CD8 T Cells Treated By Control [CTCTCTAC_TAAGGCTC]


title: UUATAC-seq datasets of Gecko_SmallBladder

description: single-nucleus ATAC profile of Gecko_SmallBladder

source_name: Small bladder

value: Small bladder

value: Female


title: CutTag_His modification_IgG control_progenitor_rep1

source_name: larval brain

value: larval brain

value: neural progenitor

value: Erm overexpression


title: UUATAC-seq datasets of MouseMale_Bladder_A

description: single-nucleus ATAC profile of MouseMale_Bladder_A

value: Wild-type

value: 8 weeks


title: CD8 T Cells Treated By Control [GCTCATGA_TAAGGCTC]

value: Male


title: CutTag_His modification_IgG control_NSC_rep1

value: WT


title: CutTag_GAF_interphase_rep1


title: UUATAC-seq datasets of Gecko_Ovary

description: single-nucleus ATAC profile of Gecko_Ovary

source_name: Ovary

value: Ovary


title: UUATAC-seq datasets of MouseMale_Telencephalon

description: single-nucleus ATAC profile of MouseMale_Telencephalon

source_name: Telencephalon

value: Telencephalon


title: UUATAC-seq datasets of Gecko_TailTip

description: single-nucleus ATAC profile of Gecko_TailTip

source_name: Tail tip

value: Tail tip


title: UUATAC-seq datasets of Gecko_Muscle

description: single-nucleus ATAC profile of Gecko_Muscle

source_name: Muscle

value: Muscle


title: UUATAC-seq datasets of MouseMale_LargeIntestine

description: single-nucleus ATAC profile of MouseMale_LargeIntestine

source_name: Large intestine

value: Large intestine


title: skeletal muscle DNA from old senolytic injury 1

value: tibalias anterior

value: male

value: Injury


title: UUATAC-seq datasets of Gecko_Lung

description: single-nucleus ATAC profile of Gecko_Lung

source_name: Lung

value: Lung

value: Adult


title: CutTag_IgG_rep3

value: larval brain

value: type II NSC


title: UUATAC-seq datasets of Gecko_Liver

description: single-nucleus ATAC profile of Gecko_Liver

source_name: Liver

value: Liver

value: Female


title: CutTag_GAF_GAF-RNAi_rep3

value: GAF RNAi


title: UUATAC-seq datasets of MouseMale_Hypothalamus

description: single-nucleus ATAC profile of MouseMale_Hypothalamus

source_name: Hypothalamus

value: Hypothalamus

value: Wild-type

value: 8 weeks

value: Male


title: UUATAC-seq datasets of MouseMale_Cerebellum

description: single-nucleus ATAC profile of MouseMale_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: CD4 T Cells Treated By Virus [CGTACTAG_TAAGGCTC]

value: 8 weeks old


title: CutTag_GAF_mitosis_rep2

value: WT


title: CutTag_GAF_WT_rep3


title: UUATAC-seq datasets of MouseMale_BrainStem

description: single-nucleus ATAC profile of MouseMale_BrainStem

source_name: Brain stem

value: Brain stem


title: CutTag_GAF_interphase_rep2


title: UUATAC-seq datasets of MouseFemale_Uterus

description: single-nucleus ATAC profile of MouseFemale_Uterus

source_name: Uterus

extract_protocol:
Whole organs were then dissected in the following order: small intestine, large intestine, spleen, pancreas, lymph nodes (inguinal lymph nodes, abdominal aortic lymph nodes, axillary lymph nodes, cervical lymph nodes), stomach, thyroid gland, brain, heart, lung, thymus, kidney, adrenal gland, ovary, uterus, bladder, liver, muscle, bone marrow and spinal cord. Except for bone marrow, the samples were quickly transferred into cold DPBS, washed and then manually pulverized using a mortar and pestle within a liquid nitrogen bath. The pulverized tissues were suspended in 1mL of Nuclear Isolation Buffer (NIB) and followed by incubation for 1.5-3 min to isolate the nuclei. The bone marrow cell suspension was centrifuged at 350 × g for 5 min, and the pellet was directly resuspended in 1 mL of NIB for 2min incubation. The suspension of each tissue was transferred to 15 mL centrifuge tubes pre-filled with 5mL of WB (wash buffer, 0.2% BSA, 3 mM MgCl2 in DPBS), filtered through 40 μm strainers and centrifuged at 650 × g for 5 min at 4°C. We resuspended the nuclei in 1 mL of WB and filtered the suspension through 20 μm size strainers, pelleted at 650 × g for 5 min and resuspended in the appropriate amount of DPBS to give a final concentration of 25,000 nuclei per microlitre.
Library preparations were performed with the UUATAC-seq protocol

value: Uterus


title: UUATAC-seq datasets of Gecko_Eye

description: single-nucleus ATAC profile of Gecko_Eye

source_name: Eye

value: Eye


title: UUATAC-seq datasets of MouseMale_BoneMarrow

description: single-nucleus ATAC profile of MouseMale_BoneMarrow

source_name: Bone marrow

value: Bone marrow


title: CutTag_GAF_GAF-RNAi_rep2


title: 37 Planktonic  0% Rep3

city: Oberlin

first: Lisa

last: Ryno

state: Ohio

address: 119 Woodland St

department: Chemistry and Biochemistry

institute: Oberlin College

description: Library name: Sample 23

data_processing:
RNA-Seq data quality control, alignment, quantification, and statistics calculations were done using the workflow, using the reference genome and annotation of E. coli strain MG1655 from NCBI (genome sequence GenBank ID U00096.3; assembly ID GCA_000005845.2). Adapter sequences were trimmed with scythe v0.994, and low-quality ends were trimmed with sickle v1.33.5,17 HISAT2 v2.2.2.1 was used to align reads to the reference genome.20 Salmon v1.10.2 was used to quantify the expression of transcripts.35
Assembly: GCA_000005845
Supplementary files format and content: Tab-delimited text file of raw counts for each sample

organism: Escherichia coli

growth_protocol: PHL628 E coli cells were grown in either LB or M9 media supplemented with rhamnose or no additional sugar or 0.5% glucose, respectively. Cells were grown at 28 or 37 C for 48 h and harvested as biofilm cells or planktonic (swimming) cells.

extract_protocol:
RNA was harvested using RNAprotect (Qiagen) and Rneasy Plus kit (Qiagen). 1 µg or greater was sent for sequencing. rRNA removal by using Ribo-Zero Plus rRNA Depletion Kit (Illumina)
rRNA depleted samples were quantified and used for library preparation using the KAPA mRNA HyperPrep Kits (Roche). Following the library preparation, the final concentration of all of the libraries was measured using the Qubit dsDNA HS Assay Kit (Life Technologies), and the average library size was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies)

value: planktonic

tag: temperature

value: 37 °C

value: control


title: UUATAC-seq datasets of MouseMale_SpinalCord

description: single-nucleus ATAC profile of MouseMale_SpinalCord

source_name: Spinal cord

value: Spinal cord


title: UUATAC-seq datasets of Gecko_Esophagus

description: single-nucleus ATAC profile of Gecko_Esophagus

source_name: Esophagus

value: Esophagus

value: Adult

value: Female


title: UUATAC-seq datasets of MouseFemale_Telencephalon

description: single-nucleus ATAC profile of MouseFemale_Telencephalon

value: Telencephalon

value: Wild-type


title: CutTag_IgG_interphase_rep2

value: larval brain

value: type II NSC


title: CutTag_IgG_interphase_rep1


title: UUATAC-seq datasets of Gecko_Pancreas

description: single-nucleus ATAC profile of Gecko_Pancreas

source_name: Pancreas

value: Pancreas


title: CD4 T Cells Treated By Virus [TAGGCATG_TAAGGCTC]

source_name: GBM-bearing mice (C57BL/6)

value: Male

value: 8 weeks old


title: UUATAC-seq datasets of MouseMale_Pituitary

description: single-nucleus ATAC profile of MouseMale_Pituitary

source_name: Pituitary

value: Pituitary

value: 8 weeks


title: UUATAC-seq datasets of MouseMale_SmallIntestine

description: single-nucleus ATAC profile of MouseMale_SmallIntestine

source_name: Small intestine

value: Small intestine


title: CutTag_GAF_mitosis_rep1

source_name: larval brain

value: WT


title: UUATAC-seq datasets of MouseMale_LymphNode

description: single-nucleus ATAC profile of MouseMale_LymphNode

source_name: Lymph node

value: Lymph node


title: UUATAC-seq datasets of Gecko_Brain

description: single-nucleus ATAC profile of Gecko_Brain

source_name: Brain

value: Brain


title: 37 Planktonic  0.5%Ara Rep2

description: Library name: Sample 20

value: planktonic

value: 37 °C

value: arabinose


title: CD4 T Cells Treated By Virus [TCCTGAGC_TAAGGCTC]


title: CD4 T Cells Treated By Control [AGGCAGAA_TAAGGCTC]


title: CD4 T Cells Treated By Control [GGACTCCT_TAAGGCTC]


title: UUATAC-seq datasets of Gecko_Kidney

description: single-nucleus ATAC profile of Gecko_Kidney

source_name: Kidney

value: Kidney

value: Adult

value: Female


title: CutTag_GAF_WT_rep1

value: larval brain


title: CD4 T Cells Treated By Control [TAAGGCGA_TAAGGCTC]


title: UUATAC-seq datasets of MouseFemale_SmallIntestine

description: single-nucleus ATAC profile of MouseFemale_SmallIntestine

value: Wild-type


title: UUATAC-seq datasets of Gecko_Intestine

description: single-nucleus ATAC profile of Gecko_Intestine

source_name: Intestine

value: Intestine


title: RNA_Osa overexpression rep2

data_processing:
Raw FASTQ reads were trimmed using Trim Galore (v0.6.10, with parameters --paired --quality 20 --stringency 3 -j 4).
Trimmed reads were aligned to Drosophila genome (Version: dm6) using HISAT2 (v2.2.1) and processed with Samtools (v1.6) to generate bam files.
FeatureCounts (v2.0.3) was used to generate raw count matrix for ncbiRefSeq genes.
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvest using Discover-sc WTA Kit V2 (Vazyme). 1-2k cells are used for the extraction of RNA used to construct sequencing libraries.
RNA libraries for RNA-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocols.

value: type II NSC

value: Osa overexpression


title: 28 Planktonic  0.5%Ara Rep2

description: Library name: Sample 18

value: 28 °C


title: RNA_Osa_control rep2


title: 28 Planktonic  0% Rep2

description: Library name: Sample 17

value: control


title: 37 Planktonic  0.5%Ara Rep3

description: Library name: Sample 24


title: 28 Planktonic  0.5%Ara Rep3

description: Library name: Sample 22


title: UUATAC-seq datasets of Gecko_Cloaca

description: single-nucleus ATAC profile of Gecko_Cloaca

source_name: Cloaca

value: Cloaca


title: CutTag_GAF_WT_rep2

value: WT


title: CutTag_IgG_rep2


title: 37 Planktonic  0.5%Ara Rep1

description: Library name: Sample 16


title: RNA_Osa_control rep1


title: RNA_HDAC1_control rep2


title: UUATAC-seq datasets of MouseFemale_LymphNode

description: single-nucleus ATAC profile of MouseFemale_LymphNode

value: Lymph node

value: 8 weeks


title: RNA_HDAC1-RNAi rep2

value: HDAC1 RNAi


title: 28 Planktonic  0% Rep1

description: Library name: Sample 13

value: planktonic


title: UUATAC-seq datasets of MouseFemale_SpinalCord

description: single-nucleus ATAC profile of MouseFemale_SpinalCord

value: Spinal cord


title: RNA_HDAC1-RNAi rep1


title: CutTag_IgG_rep1


title: UUATAC-seq datasets of MouseFemale_Stomach

description: single-nucleus ATAC profile of MouseFemale_Stomach

source_name: Stomach

value: Stomach


title: UUATAC-seq datasets of Gecko_Adipose

description: single-nucleus ATAC profile of Gecko_Adipose

source_name: Adipose

value: Adipose

value: Adult


title: UUATAC-seq datasets of MouseFemale_Pituitary

description: single-nucleus ATAC profile of MouseFemale_Pituitary

value: Pituitary

value: Female


title: UUATAC-seq datasets of MouseFemale_Hypothalamus

description: single-nucleus ATAC profile of MouseFemale_Hypothalamus

source_name: Hypothalamus

value: Hypothalamus

value: Wild-type


title: UUATAC-seq datasets of MouseFemale_LargeIntestine

description: single-nucleus ATAC profile of MouseFemale_LargeIntestine

source_name: Large intestine

value: Large intestine


title: RNA_GAF-RNAi rep3

value: larval brain

value: type II NSC

value: GAF RNAi


title: 37 Planktonic  0% Rep2

description: Library name: Sample 19

value: 37 °C

value: control


title: 28 Planktonic  0% Rep3

description: Library name: Sample 21

value: 28 °C


title: UUATAC-seq datasets of MouseFemale_Pancreas

description: single-nucleus ATAC profile of MouseFemale_Pancreas

value: Pancreas

value: 8 weeks


title: UUATAC-seq datasets of MouseFemale_Heart

description: single-nucleus ATAC profile of MouseFemale_Heart

source_name: Heart

value: Heart


title: CutTag_GAF_GAF-RNAi_rep1


title: RNA_Osa overexpression rep1

value: Osa overexpression


title: UUATAC-seq datasets of MouseFemale_Ovary

description: single-nucleus ATAC profile of MouseFemale_Ovary

source_name: Ovary

value: Ovary


title: 28 Biofilm  0% Rep3

description: Library name: Sample 9

value: biofilm


title: RNA_GAF-RNAi rep2


title: 37 Planktonic  0% Rep1

description: Library name: Sample 15

value: planktonic


title: RNA_GAF_control rep2

value: WT


title: 28 Planktonic  0.5%Ara Rep1

description: Library name: Sample 14

value: arabinose


title: RNA_GAF-RNAi rep1


title: RNA_GAF_control rep1


title: UUATAC-seq datasets of MouseFemale_Muscle

description: single-nucleus ATAC profile of MouseFemale_Muscle

source_name: Muscle

value: Muscle

value: Wild-type

value: Female


title: UUATAC-seq datasets of MouseFemale_Spleen

description: single-nucleus ATAC profile of MouseFemale_Spleen

source_name: Spleen

value: Spleen


title: UUATAC-seq datasets of MouseFemale_Liver

description: single-nucleus ATAC profile of MouseFemale_Liver

source_name: Liver

value: Liver


title: UUATAC-seq datasets of MouseFemale_AdrenalGland

description: single-nucleus ATAC profile of MouseFemale_AdrenalGland

source_name: Adrenal gland

value: Adrenal gland


title: 37 Biofilm  0% Rep3

description: Library name: Sample 11

value: 37 °C

value: control


title: 28 Biofilm  0.5%Ara Rep3

description: Library name: Sample 10

value: 28 °C


title: UUATAC-seq datasets of MouseFemale_Lung

description: single-nucleus ATAC profile of MouseFemale_Lung

source_name: Lung

value: Lung

value: 8 weeks


title: 37 Biofilm  0.5%Ara Rep3

description: Library name: Sample 12


title: RNA_HDAC1_control rep1

source_name: larval brain

value: larval brain

value: type II NSC


title: UUATAC-seq datasets of MouseFemale_BrainStem

description: single-nucleus ATAC profile of MouseFemale_BrainStem

source_name: Brain stem

value: Brain stem


title: RNA_GAF_control rep3


title: 37 Biofilm  0% Rep1

description: Library name: Sample 3

value: biofilm


title: UUATAC-seq datasets of MouseFemale_Bladder

description: single-nucleus ATAC profile of MouseFemale_Bladder

source_name: Bladder

value: Bladder


title: 37 Biofilm  0% Rep2

description: Library name: Sample 7


title: 37 Biofilm  0.5%Ara Rep2

description: Library name: Sample 8

value: arabinose


title: WT_BM

city: Shapingba

first: Wen

last: Luo

state: Chongqing

address: No. 83, Xinqiao  street

institute: Xinqiao Hospital, Third Military Medical University

description: Library name: Sample 2

data_processing:
The Cell Ranger toolkit (version 6.1.2) provided by 10x Genomics was used to align reads to the mouse reference genome (mm10) and generate a unique molecular identifier (UMI) matrix. After UMI matrix generation, the doublet score of each cell was predicted using Scrublet. Seurat (v4.3.0) on R (v4.2.1) was used for downstream analysis. For samples from either the tumor microenvironment or bone marrow, cells with 500–50,000 UMIs, 200-5,000 genes, less than 10% mitochondrial gene counts, and less than a 0.2 doublet score were kept as high-quality cells. For samples from the TME, following rigorous quality filtering, we obtained a total of 20,854 high-quality single-cell transcriptomic data, comprising 10,383 cells from the S100a8-KO group and 10,471 cells from the WT group, for further analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample
Supplementary files format and content: Tab-separated values fles and matrix fles

source_name: bone marrow

growth_protocol: Natural growth.

extract_protocol:
CD45+ cells in tumor-free bone marrow, or  LLC tumor, both from S100a8-cKO and WT mice were sorted.
Approximately 1 x 10^6 from three mice were pooled and loaded onto a 10x Genomics Chromium instrument, according to the manufacturer's protocol.

treatment_protocol: No treatment.

value: bone marrow


title: 28 Biofilm  0.5%Ara Rep2

description: Library name: Sample 6


title: UUATAC-seq datasets of MouseFemale_BoneMarrow

description: single-nucleus ATAC profile of MouseFemale_BoneMarrow

source_name: Bone marrow

value: Bone marrow

value: Wild-type


title: 37 Biofilm  0.5%Ara Rep1

description: Library name: Sample 4


title: UUATAC-seq datasets of MouseFemale_Kidney

description: single-nucleus ATAC profile of MouseFemale_Kidney

source_name: Kidney

value: Kidney

value: Female


title: KO_BM

description: Library name: Sample 1

value: S100a8fl/flVav-Cre+/-(S100a8 conditional knock out in hematopoietic system)


title: 28 Biofilm  0.5%Ara Rep1

description: Library name: Sample 2


title: LLCKOT3

description: Library name: Sample 3

source_name: llc tumor

value: llc tumor

value: LLC


title: UUATAC-seq datasets of MouseFemale_Cerebellum

description: single-nucleus ATAC profile of MouseFemale_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: LLCT4

description: Library name: Sample 4


title: UUATAC-seq datasets of MouseFemale_Thymus

description: single-nucleus ATAC profile of MouseFemale_Thymus

source_name: Thymus

value: Thymus


title: 28 Biofilm  0% Rep2

description: Library name: Sample 5

value: 28 °C

value: control


title: 16hex_rep3

status: Public on Jul 13 2025

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
The adapter sequence and low-quality reads were removed using trimmomatic (v0.38).
Trimmed reads were mapped to reference genome hg38 using Kallisto (v0.46.2).
The count matrix data from Kallisto was loaded into R software (v4.2.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using illumina TruSeq RNA Library Prep Kit following manufacturer's protocols.

value: iPSC derived NS/PCs


title: CTRL_rep3

value: non


title: CTRL_rep2


title: CTRL_rep1


title: KO-DLN

city: Nanning

first: Wang

last: Xi

state: Guangxi

address: 100 University East Road, Nanning City, Guangxi

department: School of Medicine

institute: Guangxi University

description:
Library name: sample2
10X Genomics

data_processing:
Alignment, barcode assignment and unique molecular identifier (UMI) counting. The Cell Ranger 1.3 Single-Cell software suite (10xGenomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
Assembly: mm10

source_name: spleen and lymph node

extract_protocol:
Mice were immunized with MOG/CFA to induce EAE. CD4+ YFP+ cells from spleen at the peak of disease were sorted on an AriaIII cell sorter into 15-ml tubes containing complete media, counted, and placed on ice. All samples were spun down at 500g for 10 min. The supernatant was removed, and cells were resuspended in 100 μl of 1 × PBS (Thermo Fisher Scientific) plus 0.04% BSA (Amresco). The cells were counted and checked for viability using a Luna dual fluorescence cell counter (Logos Biosystems). Cell counts ranged from 2× 105 to 4× 105 cells per millilitre and viability was greater than 98%.
Libraries were prepared using the Chromium single cell 3′ v2 library and gel bead kit (10x Genomics). The complementary DNA content of each sample after cDNA amplification of 12 cycles was quantified and quality checked using a high-sensitivity DNA chip with a 2100 Bioanalyzer (Agilent Technologies) to determine the number of PCR amplification cycles to yield sufficient library for sequencing. After library quantification and quality checking by DNA 1000 chip (Agilent Technologies), during the library construction ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: spleen and lymph node

value: primary cell

value: FACS sorted CD4+YFP+ cells


title: WT-DLN

description:
Library name: sample1
10X Genomics


title: 28 Biofilm  0% Rep1

description: Library name: Sample 1

value: biofilm


title: S1-END-seq_U2OS_ishScr_E1

city: BETHESDA

first: Benura

last: Azeroglu

address: National Cancer Institute, NIH, Building 37, Room 1108 37 Convent Drive

institute: NIH

description: Library name: Library 53

data_processing:
We developed a Python script, "getTelomereENDseq," to analyze gzipped FASTQ files for the presence of telomeric motifs in DNA sequences on a command-line environment using a Linux-based operating system and the statistical environment RStudio. The script identifies sequences containing G-rich and C-rich telomeric repeats, quantifies their occurrences, and calculates their relative frequencies. It takes a gzipped FASTQ file as input, and the minimum number of telomeric repeats is required. It generates two output files: one with sequences containing G-rich motifs and another with sequences containing C-rich motifs. For this study, we used a minimum of 4 consecutive TTAGGG repeats for G-rich reads and a minimum of 4 consecutive CCCTAA repeats for C-rich reads.
Assembly: hg19, mm10
Supplementary files format and content: The .txt files contain reads corresponding to the G- and C-strands.

growth_protocol: Human, mouse, and dog cell lines were grown in DMEM medium supplemented with 10% fetal bovine serum (FBS) and 0.5 mg/ml penicillin, streptomycin and L-glutamine (Gibco) and cultured at 37°C and 5%CO2. HeLa cells used in this study were HeLa1.2.11. G292 cells were grown in McCoy medium supplement with 15% FBS and 0.5 mg/ml penicillin, streptomycin and L-glutamine (Gibco). Cell lines were tested for mycoplasma contamination.

extract_protocol:
Cells were washed with PBS, treated with Trypsin/EDTA, and neutralized with growth media. After pelleting and resuspending in neutralization buffer, cells were processed for END-seq or S1-END-seq. For S1-END-seq, cells were embedded in agarose plugs, lysed with Proteinase K, treated with RNase A, and equilibrated in S1 nuclease buffer. S1 nuclease was added to the plugs, incubated on ice for 15 minutes, then at 37°C for 20 minutes before terminating the reaction with EDTA.
For S1/END-seq, plugs were processed through the standard END-seq protocol.

value: wild-type

value: 1 μg/ml of doxycycline for 72 hours


title: S1-END-seq_U2OS_ishScr_E2

description: Library name: Library 54


title: S1-END-seq_U2OS_ishPOT1-2_E2

description: Library name: Library 52

value: POT1 knockdown


title: S1-END-seq_U2OS_ishPOT1-1_E2

description: Library name: Library 50


title: S1-END-seq_U2OS_ishPOT1-2_E1

description: Library name: Library 51


title: S1-END-seq_U2OS_E3

description: Library name: Library 44


title: S1-END-seq_U2OS_E5

description: Library name: Library 46


title: S1-END-seq_U2OS_E4

description: Library name: Library 45


title: S1-END-seq_U2OS_E6

description: Library name: Library 47


title: S1-END-seq_U2OS-BLMKO-TRF1-Fok1

description: Library name: Library 55

value: BLM  knockout and TRF1 Fok1 overexpression

value: 1 μg/ml of doxycycline and 0.6 μM of 4-hydroxytamoxifen (4-OHT) for 24 hours


title: S1-END-seq_U2OS_ishPOT1-1_E1

description: Library name: Library 49


title: S1-END-seq_U2OS-TRF1-Fok1

description: Library name: Library 56

value: TRF1 Fok1 overexpression


title: S1-END-seq_U2OS_E7

description: Library name: Library 48


title: zebrafish embryo, 34C 40A polyA 8h 1

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

description: Library name: 34C_40A_polyA_8h_1

library_source: other

data_processing:
constant sequences were trimmed
reporter 3'UTR sequences were aligned against the full set of 90,000 reporter sequences
number of unique molecular identifiers (UMIs) that match each reporter sequence were counted
Assembly: the full set of 90,000 reporter sequences
Supplementary files format and content: tab-delimited text files include readcount for each reporter in each sample

molecule: other

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Total RNA was isolated using tri-reagent (Sigma T9424) and quantified using nanodrop
We used a two-step RNA-Seq library construction approach that specifically targeted the variable 3′UTR region of reporters. In the first step, total-RNA was reverse-transcribed with Maxima RT (Thermo Fisher) and a gene-specific primer that matched the 20nt downstream 3′UTR universal adaptor. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step, resulting cDNA was amplified by 18 cycles of PCR with primers that matched the 20nt upstream 3′UTR universal adaptor and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing adaptors,  resulting in the final RNA-Seq library.

treatment_protocol: 1 pg mRNA from reporters injection at 1-cell stage

value: whole embryo


title: zebrafish embryo, 34C 40A polyA 8h 2

description: Library name: 34C_40A_polyA_8h_2


title: S1-END-seq_U2OS_E1

description: Library name: Library 42


title: zebrafish embryo, 34C 40A polyA 7h 1

description: Library name: 34C_40A_polyA_7h_1


title: S1-END-seq_U2OS-BLMKO

description: Library name: Library 41

value: BLM knockout


title: 16hex_rep2


title: S1-END-seq_U2OS_E2

description: Library name: Library 43


title: S1-END-seq_SUMS1

description: Library name: Library 40


title: zebrafish embryo, 34C 40A polyA 6h 2

description: Library name: 34C_40A_polyA_6h_2


title: zebrafish embryo, 34C 40A polyA 7h 2

description: Library name: 34C_40A_polyA_7h_2


title: S1-END-seq_GM847

description: Library name: Library 38


title: zebrafish embryo, 34C 40A polyA 6h 1

description: Library name: 34C_40A_polyA_6h_1


title: S1-END-seq_G292

description: Library name: Library 37


title: zebrafish embryo, 34C 40A polyA 5h 1

description: Library name: 34C_40A_polyA_5h_1


title: 16hex_rep1


title: zebrafish embryo, 34C 40A polyA 1h 1

description: Library name: 34C_40A_polyA_1h_1


title: END-seq_U2OS_ishPOT1-2_E1

description: Library name: Library 25


title: END-seq_U2OS-BLMKO-TRF1_Fok1

description: Library name: Library 28


title: zebrafish embryo, 34C 40A polyA 3h 1

description: Library name: 34C_40A_polyA_3h_1


title: END-seq_U2OS_ishPOT1-1_E2

description: Library name: Library 24


title: zebrafish embryo, 34C 40A polyA 3h 2

description: Library name: 34C_40A_polyA_3h_2


title: zebrafish embryo, 34C 0A total 75h2

description: Library name: 34C_0A_total_75h2


title: zebrafish embryo, 34C 0A total 85h2

description: Library name: 34C_0A_total_85h2


title: END-seq_U2OS-TRF1_Fok1

description: Library name: Library 29


title: zebrafish embryo, 34C 40A polyA 1h 2

description: Library name: 34C_40A_polyA_1h_2


title: END-seq_U2OS-BLMKO

description: Library name: Library 27

value: BLM  knockout


title: zebrafish embryo, 34C 0A total 85h1

description: Library name: 34C_0A_total_85h1


title: zebrafish embryo, 34C 0A total 65h1

description: Library name: 34C_0A_total_65h1


title: zebrafish embryo, 34C 0A total 75h1

description: Library name: 34C_0A_total_75h1


title: zebrafish embryo, 34C 0A total 65h2

description: Library name: 34C_0A_total_65h2


title: END-seq_U2OS_ishScr_E2

description: Library name: Library 22


title: zebrafish embryo, 34C 40A polyA 5h 2

description: Library name: 34C_40A_polyA_5h_2


title: S1-END-seq_SAOS2

description: Library name: Library 39


title: END-seq_U2OS_E5

description: Library name: Library 20


title: S1-END-seq_HeLa

description: Library name: Library 36

source_name: HeLa

value: HeLa


title: END-seq_U2OS_E4

description: Library name: Library 19


title: END-seq_U2OS_ishPOT1-2_E2

description: Library name: Library 26


title: zebrafish embryo, 34C 0A total 35h2

description: Library name: 34C_0A_total_35h2


title: zebrafish embryo, 34C 0A total 55h1

description: Library name: 34C_0A_total_55h1


title: zebrafish embryo, 34C 0A total 35h1

description: Library name: 34C_0A_total_35h1


title: END-seq_U2OS_E3

description: Library name: Library 18


title: END-seq_U2OS_E2

description: Library name: Library 17


title: END-Seq_U2OS_T7_E1

description: Library name: Library 7

value: in vitro T7 exonuclease treatement for 30 mins


title: zebrafish embryo, 34C 0A total 05h2

description: Library name: 34C_0A_total_05h2


title: zebrafish embryo, 34C 0A total 15h1

description: Library name: 34C_0A_total_15h1


title: zebrafish embryo, 34C 0A total 05h1

description: Library name: 34C_0A_total_05h1


title: END-seq_HeLa-ishPOT1

description: Library name: Library 3


title: END-seq_U2OS_ishPOT1-1_E1

description: Library name: Library 23


title: END-Seq_U2OS_NT_E1

description: Library name: Library 4


title: zebrafish embryo, 34C 0A polyA 85h 1

description: Library name: 34C_0A_polyA_85h_1


title: zebrafish embryo, 34C 0A polyA 75h 2

description: Library name: 34C_0A_polyA_75h_2


title: MEC1 cells, gDNA_rep5

first: Gue-ho

last: Hwang

state: MA

address: 300 Longwood Ave

institute: Boston Children's hospital

data_processing:
Barcode sequences extracted from NGS data using edlib module in Python.
Barcodes were connected with diffusion DNA sequence using the barocode-diffustion DNA combination list that was analyzed using Nanopore sequencing data for plasmid library.
The comparative expressions were analyzed comparing the number of barcodes between mRNA and gDNA NGS data.
Assembly: Do not use reference sequence.
Supplementary files format and content: Tab delimited text file includes raw counts for each sample
Library strategy: Amplicon sequencing

source_name: Chronic lymphocytic leukemia

growth_protocol: MEC1 was cultured in IMDM media supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptomycin and 5 g/ml Blasticidin

extract_protocol:
gDNA was extracted using mini AllPrep DNA/RNA extraction kit (Qiagen).
Reverse trasncription and PCR as described in  Kribelbauer-Swietek et al (provided during the revision process)

treatment_protocol: Plasmid library was delivered using Neon Transfection System.

value: Chronic lymphocytic leukemia

value: chronic B cell leukemia


title: END-seq_U2OS_ishScr_E1

description: Library name: Library 21


title: zebrafish embryo, 34C 0A total 55h2

description: Library name: 34C_0A_total_55h2


title: MEC1 cells, gDNA_rep4


title: zebrafish embryo, 34C 0A polyA 75h 1

description: Library name: 34C_0A_polyA_75h_1


title: END-seq_HeLa-ishScr

description: Library name: Library 2


title: zebrafish embryo, 34C 0A polyA 65h 2

description: Library name: 34C_0A_polyA_65h_2


title: MEC1 cells, gDNA_rep3


title: MEC1 cells, gDNA_rep2


title: zebrafish embryo, 34C 0A polyA 65h 1

description: Library name: 34C_0A_polyA_65h_1


title: zebrafish embryo, 34C 0A polyA 55h 1

description: Library name: 34C_0A_polyA_55h_1


title: MEC1 cells, gDNA_rep1


title: END-seq_U2OS_E1

description: Library name: Library 16


title: MEC1 cells, mRNA_rep5

extract_protocol:
mRNA was extracted using mini AllPrep DNA/RNA extraction kit (Qiagen).
Reverse transcription and PCR as described in  Kribelbauer-Swietek et al (provided during the revision process)


title: zebrafish embryo, 34C 0A polyA 55h 2

description: Library name: 34C_0A_polyA_55h_2


title: MEC1 cells, mRNA_rep4


title: zebrafish embryo, 34C 0A total 15h2

description: Library name: 34C_0A_total_15h2


title: zebrafish embryo, 34C 0A polyA 35h 1

description: Library name: 34C_0A_polyA_35h_1


title: zebrafish embryo, 34C 0A polyA 15h 2

description: Library name: 34C_0A_polyA_15h_2


title: MEC1 cells, mRNA_rep2


title: MEC1 cells, mRNA_rep1


title: MEC1 cells, mRNA_rep3


title: zebrafish embryo, 34C 0A polyA 85h 2

description: Library name: 34C_0A_polyA_85h_2


title: END-seq_SAOS2_E3

description: Library name: Library 15


title: zebrafish embryo, 34C 0A polyA 05h 2

description: Library name: 34C_0A_polyA_05h_2


title: END-seq_SAOS2_E2

description: Library name: Library 14


title: zebrafish embryo, 34C 0A polyA 05h 1

description: Library name: 34C_0A_polyA_05h_1


title: END-seq_SAOS2_E1

description: Library name: Library 13


title: END-seq_G292_E3

description: Library name: Library 12


title: zebrafish embryo, 22C 40A total validation set 9h 2

description: Library name: 22C_40A_total_v_9h_2


title: zebrafish embryo, 22C 40A total validation set 9h 1

description: Library name: 22C_40A_total_v_9h_1


title: zebrafish embryo, 22C 40A total validation set source

description: Library name: 22C_40A_total_v_source


title: zebrafish embryo, 22C 40A total validation set 7h 2

description: Library name: 22C_40A_total_v_7h_2


title: END-seq_G292_E1

description: Library name: Library 10


title: END-Seq_U2OS_T7_E3

description: Library name: Library 9


title: zebrafish embryo, 22C 40A total validation set 7h 1

description: Library name: 22C_40A_total_v_7h_1


title: END-Seq_U2OS_T7_E2

description: Library name: Library 8


title: zebrafish embryo, 34C 0A polyA 35h 2

description: Library name: 34C_0A_polyA_35h_2


title: zebrafish embryo, 22C 40A total validation set 5h 2

description: Library name: 22C_40A_total_v_5h_2


title: END-Seq_U2OS_NT_E3

description: Library name: Library 6


title: zebrafish embryo, 22C 40A total validation set 3h 2

description: Library name: 22C_40A_total_v_3h_2


title: END-Seq_U2OS_NT_E2

description: Library name: Library 5


title: zebrafish embryo, 22C 40A total validation set 5h 1

description: Library name: 22C_40A_total_v_5h_1


title: END-seq_mESC_E14_Pot1a_dTAG_Pot1bKO

description: Library name: Library 35

source_name: mESC

value: mESC

value: POT1a depleted and POT1b knockout

value: 0.5 µM dTAG-13  for 72 hrs


title: END-seq_mESC_E14_Pot1bKO

description: Library name: Library 34

value: POT1b knockout


title: zebrafish embryo, 34C 0A polyA 15h 1

description: Library name: 34C_0A_polyA_15h_1


title: zebrafish embryo, 22C 40A total validation set 1h 2

description: Library name: 22C_40A_total_v_1h_2


title: zebrafish embryo, 22C 40A total validation set 3h 1

description: Library name: 22C_40A_total_v_3h_1


title: END-seq_mESC_E14

description: Library name: Library 32

value: wild-type


title: zebrafish embryo, 22C 40A total validation set 1h 1

description: Library name: 22C_40A_total_v_1h_1


title: zebrafish embryo, 22C 40A total validation set 15h 1

description: Library name: 22C_40A_total_v_15h_1


title: END-seq_MEFs

description: Library name: Library 30

source_name: MEFs

value: MEFs


title: END-seq_Mouse-Spleen

description: Library name: Library 31

source_name: spleen

value: spleen


title: zebrafish embryo, 22C 40A total validation set 13h 2

description: Library name: 22C_40A_total_v_13h_2


title: END-seq_mESC_E14_Pot1a_dTAG

description: Library name: Library 33

value: POT1a depleted


title: zebrafish embryo, 22C 40A total validation set 15h 2

description: Library name: 22C_40A_total_v_15h_2