title: T3MINUSDOXP2_rep1

data_processing:
For RNA-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Gene annotation from Ensembl (v107) was used, and featureCounts (v2.0.3) was employed to count mapped reads for genomic features. For MeRIP-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Hisat2 (v2.2.1). Samtools view (v1.18) was used to separate stranded reads with “-d XS:+” and “-d XS:-”. Strand-specific genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1). Differentially methylated peaks were identified by exomePeak2 (v1.10.0). Homer (v4.11) was used to infer enriched motifs on peaks that lost m6A upon METTL3 loss with the parameter “-rna -len 4,5,6”. Gene Ontology analysis was performed using DAVID (v2024q2). For the enrichment of m6A on TEs, m6A reads were aligned directly to the TE consensus sequence9, allowing for discordant paired reads to increase mapping rates. For CUT&Tag, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. Duplicated reads were removed using MarkDuplicates from Picard (v3.0.0). SICER2 (v1.0.2) was used to call differentially enriched peaks of H3K27me3 with the parameter “-g 600”. Genome coverage bigwig files for visualization, heatmaps, and aggregation plots were generated using bamCompare from Deeptools (v3.5.1) with spike-in normalization. For ATAC-seq, Raw reads were trimmed using Trim Galore (v0.6.10), filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs. Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. MACS2 (v2.2.7.1) was used to call accessible peaks. Csaw was utilized to identify differentially accessible peaks using the TMM (trimmed mean of M-values) method, following a previously established pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For RNA-seq and MeRIP-seq, total RNA was extracted with TRIzol reagent. CUT&Tag was performed according to the manufacturer’s protocol (Vazyme, TD904). For ATAC-seq, 50,000 cells were collected and washed twice in pre-cold PBS without DNase. Nuclei were isolated, lysed, and incubated with Tn5 transposase according to the manufacturer’s protocol (Vazyme, TD501). Transposed DNA was isolated using a DNA Clean & Concentrator kit (Zymo).
For RNA-seq, Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). For MeRIP-seq, The NEBNext® Ultra™ II RNA Library Prep Kit (NEB, E7770) was used to construct libraries for both the input and IP samples. For CUT&Tag, Library preparation and amplification was followed by manufacturer’s protocol (Vazyme, TD904). For ATAC-seq, Libraries were prepared by amplifying DNA for 12 cycles using the TruePrep DNA Library Prep Kit (Vazyme). After amplification, libraries were purified using VAHTS DNA Clean Beads (Vazyme).

value: trophoblast stem cell

value: KO

value: wo DOX P2


title: dCas9-p300 WT, GDO

status: Public on Nov 11 2025

type: SRA

city: Houston

first: Isaac

middle: B

last: Hilton

state: Texas

address: 6500 Main St., BRC Rm 660

country: USA

institute: Rice University

description:
Guide-derived oligonucleotide (GDO)
GDO library: read1 file contains cell barcode and UMI; read2 file contains Guide Derived Tag reads

library_source: other

data_processing:
Cell Ranger Count v7.1.0 was used to perform count matrix generation using default parameters. Human (GRCh38) 2020-A was used for the transcriptome reference. Cells with less than 10% mitochondrial reads and between 750 and 7000 genes detected were kept for analysis. Resulting processed matrices were used for all downstream analyses.
Each of the sequencing datasets was processed using Seurat. Cells with greater than 10% mitochondrial transcripts, or less than 4000 total RNA transcripts were removed. For each gRNA in the library, expression levels were gathered for all genes within 1Mb of the gRNA target site. For each gRNA-target gene pairing, the FindMarkers() function was used to calculate the log2() fold changes in expression using the following parameters: ident.1 = gRNA_Cells, ident.2 = Control_Cells, min.pct = 0, min.cells.feature = 0, min.cells.group = 0, features = target_gene, logfc.threshold = 0. Violin plots were created using Seurat on the top few hits by adjusted p-value for each dataset analyzed. To make the violin plots, cells were divided into those with the gRNA present and those without, and the resulting expression levels for the target gene for each set of cells were visualized.
SCEPTRE was implemented as described previously. Our processed count matrices were used along with single-cell metadata as covariates to fit the SCEPTRE model. We tested gRNA-response pairs for differential expression for all genes within 1MB upstream and 1Mb downstream of the gRNA of interest. SCEPTRE p-values were adjusted with the Benjamini-Hochberg procedure and target genes were identified if they were significantly below a threshold value of 10% FDR.
Assembly: Human (GRCh38) 2020-A
Supplementary files format and content: individual files corresponding to each sample are outputs of 10X Genomics Cloud pipeline and SCEPTRE
Library strategy: Perturb-seq

molecule: other

organism: Homo sapiens

growth_protocol: K562 (ATCC, CRL-243) were cultured in  ATCC-recommended RPMI media supplemented with 10% FBS (Sigma-Aldrich) and 1% pen/strep (100units/ mL penicillin, 100µg/ mL streptomycin; Gibco) at 37° C and 5% CO2.

extract_protocol:
Cells were harvested and prepared as per the 10X Genomics Single Cell Protocols Cell Preparation Guide. ~10,000 cells were captured per lane using a 10X Chromium device. One lane was used per construct (dCas9-p300 WT and dCas9-p300 I1417N). Cells were captured using a 10X Chromium chip using the Chromium Next GEM Single Cell 3’ Reagents Kit v.3 with Feature Barcoding Technology for CRISPR screening.
Final libraries were sequenced using a NovaSeq 6000 for each p300 screen. Gene expression and CRISPR Guide Capture transcript libraries were pooled at a 4:1 ratio for sequencing.

treatment_protocol: Monoclonal K562 cell lines expressing the construct of interest were generated by transducing cells (8ug/mL) at a range of %v/v and performing flow cytometry 2 days later. Wells receiving dilutions with ~40% mCherry+ were selected and plated for monoclonal lines by limiting dilution. Monoclonal lines were transduced (10ug/mL) with varying titers to assess viral copy number. Library transduction with a 1.5%v/v was selected for the scCRISPRa experiment. For this experiment, 500k cells were transduced with virus containing the gRNA library. Cells were spun out of polybrene-containing media and replaced with standard K562 culture media. At 2 days post-transduction, 1ug/mL puromycin was added to the culture. 9 days after transduction, cells were collected for scRNA-seq.

tag: cell line

tag: cell type

value: imortalized myelogenous leukemia cell line

tag: library type

value: GDO

tag: treatment

value: Monoclonal line expressing dCas9-p300 WT transduced with lentiviral sgRNA at MOI ~20


title: HyperTRIBE_Mex3a_gg8tTA_omptTA_rep2

city: New York

first: Rachel

last: Duffié

state: NY

address: Jerome L Greene Sciene Building

department: Biochemistry and Molecular Biophysics

institute: Columbia University

description:
Library name: TetOMexHT_rep2_Red_Sept19
gg8tTA;OMPtTA cells with point mutations in Mex3a-HyperTRIBE-domain associated RNAs
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv

library_source: transcriptomic

data_processing:
libraries were quality checked with fastqc, then cutadapt was used to remove adapter sequences
libraries were aligned with STAR, and bioinformatic steps were followed as described in Rahman et al. 2018 (PMID: 30013039)
sorted sam file was converted to a matrix using MySQL
perl script from PMID 30013039 used to identify editing sites compared to internal control RNA Seq samples with output of bedgraph
postprocessing using bedtools intersect to identify high confidence editing sites. Custom R script used to generate weighted average for given transcript across replicates
Assembly: mm10
Supplementary files format and content: csv with transcript per million data for each library

molecule: total RNA

organism: Mus musculus

source_name: Main olfactory epithelium

growth_protocol: mice had access to food and water ad libitum

extract_protocol:
cells were isolated using papain enzymatic treatment (Worthington), RNA was extracted using TRIzol reagent, followed by standard 1-Bromo-3-chloropropane/isopropanol methods
libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara) using 10ng of RNA as input

tag: tissue

value: Main olfactory epithelium

value: sorted immature and mature OSN

tag: genotype


title: M2M3_HET_862373_SCV

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description:
Library name: DSP-1001660020554-A-C04
FFPE spatial transcriptome sequencing

data_processing:
FASTQ files were trimmed, stitched, aligned and deduplicated using the NanoString GeoMx NGS pipeline (version 2.3.3.10).
Generated DCC files were processed with the R GeoMxTools package (version 3.8.0).
Differential gene expression analysis was performed using Iimma (version 3.60.1) on quantile-normalized data.
Assembly: mm10
Supplementary files format and content: NS3 DE tables.xlsx (differential expression tables)
Library strategy: Spatial Transcriptomics

source_name: delB/delB adult superior caval vein

extract_protocol:
Formalin-fixed paraffin embedded E17.5 fetusses were sectioned at 5 µm. The samples were prepared according to the GeoMx Manual Slide Preparation User Manual, MAN-10150-3 using rabbit-anti-HCN4 (Merck Millipore AB5805), goat-anti-cTnI (Hytest 4T21/2) and Sytox Green Nucleic Acid Stain (Thermo Fisher Scientific S7020) antibodies and the GeoMx Whole Transcriptome Atlas Mouse RNA Probes for NGS (Bruker Spatial Biology).
Spatial transcriptome sequence libraries were constructed and sequencing using the NextSeq2000 (P2.100).

value: delB/delB adult superior caval vein

value: heterozygous mutant


title: 28-mo, male, replicate1

city: Boston

first: Dogacan

last: Yucel

state: MA

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description: RRBS

library_source: genomic

data_processing:
FASTQ files were mapped using mm10 assembly.
Bam files were processed using bismark to identify differentially methylated regions between samples.
Assembly: mm10
Supplementary files format and content: processed data includes bismark coverage and BedGraph files.

molecule: genomic DNA

source_name: Heart

extract_protocol:
Cardiomyocyte nuclei were isolated and purified using MACS.
250 ng of DNA was used to generate libraries according to Zymo-seq RRBS Library Kit.

value: Heart

value: Cardiomyocytes

value: Wildtype


title: dCas9-p300 WT

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

molecule: polyA RNA

value: mRNA


title: 28-mo, female, replicate2

description: RRBS


title: HyperTRIBE_InternalControl_Mex3a_gg8tTA_omptTA_rep2

description:
Library name: TetOMexHT_rep2_Neg_Sept19
internal control for HyperTRIBE experiment of same replicate (same mouse, so same genetic SNPs)
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv

value: sorted mCherry- cells from Main olfactory epithelium


title: HyperTRIBE_Mex3a_gg8tTA_omptTA_rep1

description:
Library name: TetOMexHT_rep1_Red_Sept19
gg8tTA;OMPtTA cells with point mutations in Mex3a-HyperTRIBE-domain associated RNAs
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv


title: M2M3_HET_862373_RA

description:
Library name: DSP-1001660020554-A-C02
FFPE spatial transcriptome sequencing

source_name: delB/+ adult right atrium

value: delB/+ adult right atrium


title: HyperTRIBE_InternalControl_Mex3a_gg8tTA_omptTA_rep1

description:
Library name: TetOMexHT_rep1_Neg_Sept19
internal control for HyperTRIBE experiment of same replicate (same mouse, so same genetic SNPs)
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv


title: L2HGDH IP

city: Birmingham

first: Sunil

last: Sudarshan

state: AL

address: FOT 1120 -  510 20th Street South

institute: University of Alabama at Birmingham

data_processing:
LC Sciences company sequenced and analyzed the data. Below is how they analyzed the data.
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor conatmination, low quality bases and undetermined bases.
We used bowtie to map reads to the genome ofHomo sapiens(Version: v101) with default parameters
Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software
MEME and HOMER were used forde novoand known motif finding followed by localization of the motif with respect to peak summit by perl scripts in house
Called peaks were annotated by intersection with gene architecture using ChIPseeker
Then StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)×exon_length(kB)])
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR
Assembly: Ensembl GRCh38 Release 101
Supplementary files format and content: bigWig
Library strategy: MeRIP-Seq

source_name: 786-O L2HGDH

extract_protocol: RCC cells with high basal L-2HG were stably transduced with control vector (CV) or L2HGDH cDNA.  RNA was then extracted from high L-2HG cells (CV) and low L-2HG Cells (L2HGDH).  m6A methylated RNA was then immunprecipiated followed by RNAseq (MeRIP).

value: 786-O L2HGDH


title: CV Input

source_name: 786-O Control Vector

value: 786-O Control Vector


title: 4-mo, male, replicate1

description: RRBS


title: HyperTRIBE_gg8tTA_omptTA_rep3

description:
Library name: TetOHT_rep3_Red_Sept19
gg8tTA;OMPtTA cells with point mutations in HyperTRIBE-domain associated RNAs
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv

value: gg8tTA; OMPtTA; tetO-HyperTRIBE_mCherry


title: WT3_LA_Aur

description:
Library name: DSP-1001660036294-A-D03
FFPE spatial transcriptome sequencing

data_processing:
FASTQ files were trimmed, stitched, aligned and deduplicated using the NanoString GeoMx NGS pipeline (version 2.3.3.10).
Generated DCC files were processed with the R GeoMxTools package (version 3.8.0).
Differential gene expression analysis was performed using Iimma (version 3.60.1) on quantile-normalized data.
Assembly: mm10
Supplementary files format and content: NS2 DE tables.xlsx (differential expressiom tables)
Library strategy: Spatial Transcriptomics

source_name: wild-type E17.5 left atrial appendage

value: wild-type E17.5 left atrial appendage

value: wild-type


title: WT3_SAN

description:
Library name: DSP-1001660036294-A-D04
FFPE spatial transcriptome sequencing

source_name: wild-type HCN4+ E17.5 sinus node

value: wild-type HCN4+ E17.5 sinus node


title: HyperTRIBE_InternalControl_gg8tTA_omptTA_rep3

description:
Library name: TetOHT_rep3_Neg_Sept19
internal control for HyperTRIBE experiment of same replicate (same mouse, so same genetic SNPs)
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv


title: HyperTRIBE_InternalControl__Mex3a_gg8tTA_omptTA_rep3

description:
Library name: TetOMexHT_rep3_Neg_Sept19
internal control for HyperTRIBE experiment of same replicate (same mouse, so same genetic SNPs)
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv


title: 4-mo, female, replicate2

description: RRBS


title: Human, inhalation injury, convalescence, the day before discharged, M3 and N3

city: ShangHai

first: Chenru

last: Wei

address: NO.168,Changhai Road,Yangpu District ,Shanghai,China

country: China

institute: the first  Affiliated Hospital of Naval Medical University

description: Sample name: II-C-3

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
 MT% < 30%;
 Cell Gene Number < 10000;
 Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Supplementary files format and content: GRCh38Ensembl100
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: circulating blood

extract_protocol:
Cells from each sample were used for single-cell isolation using BD Rhapsody Single-Cell Analysis System (BD Biosciences). Before single-cell isolation, all cells were labeled and annotated by sample tag using a BD Single-Cell Multiplexing Kit. Finally, multiple samples were mixed together.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: circulating blood

value: myeloid and lymphocyte cell

value: PBMCs;neutrophil;T cell; B cell

tag: m or n

value: myeloid replication3 and lymphocyte replication3

tag: condition

value: inhalation injury

tag: time


title: 4-mo, female, replicate1

description: RRBS

value: Heart


title: WT3_LA

description:
Library name: DSP-1001660036294-A-D02
FFPE spatial transcriptome sequencing

source_name: wild-type E17.5 left atrium

value: wild-type E17.5 left atrium


title: WT2_SAN

description:
Library name: DSP-1001660036294-A-D01
FFPE spatial transcriptome sequencing


title: Human, inhalation injury, progressive stage, day 3 post hospital, M3 and N3

description: Sample name: II-P-3

value: progressive stage, day 3 post hospital


title: WT2_LA

description:
Library name: DSP-1001660036294-A-C11
FFPE spatial transcriptome sequencing


title: HyperTRIBE_InternalControl_gg8tTA_omptTA_rep2

description:
Library name: TetOHT_rep2_Neg_Sept19
internal control for HyperTRIBE experiment of same replicate (same mouse, so same genetic SNPs)
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv

value: Main olfactory epithelium


title: HyperTRIBE_gg8tTA_omptTA_rep1

description:
Library name: TetOHT_rep1_Red_Sept19
gg8tTA;OMPtTA cells with point mutations in HyperTRIBE-domain associated RNAs
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv

value: sorted immature and mature OSN


title: cell line, shMsln #1, rep2

city: Shanghai

first: Haiou

last: Liu

address: No.128, Shengyang road, Yangpu distinct, Shanghai, P. R. China.

institute: Fudan University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: Comma-Separated csv file include TPM values for each sample.

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MSLN knockdown


title: 28-mo, female, replicate1

description: RRBS

value: Cardiomyocytes

value: Wildtype


title: L2HGDH Input

value: 786-O L2HGDH


title: 4-mo, male, replicate2

description: RRBS


title: M2M3_HET_862373_SAN

description:
Library name: DSP-1001660020554-A-C03
FFPE spatial transcriptome sequencing

source_name: delB/+ adult sinus node

value: delB/+ adult sinus node

value: heterozygous mutant


title: Human, traumatic lung injury, convalescence, the day before discharged, M3 and N3

description: Sample name: TLI-C-3

value: traumatic lung injury


title: HyperTRIBE_InternalControl_gg8tTA_omptTA_rep1

description:
Library name: TetOHT_rep1_Neg_Sept19
internal control for HyperTRIBE experiment of same replicate (same mouse, so same genetic SNPs)
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv

value: sorted mCherry- cells from Main olfactory epithelium

value: gg8tTA; OMPtTA; tetO-HyperTRIBE_mCherry


title: CV IP

value: 786-O Control Vector


title: WT1_SAN

description:
Library name: DSP-1001660036294-A-C10
FFPE spatial transcriptome sequencing

value: wild-type HCN4+ E17.5 sinus node

value: wild-type


title: cell line, shMsln #1, rep1


title: HyperTRIBE_Mex3a_gg8tTA_rep2

description:
Library name: RNA_TetOMexHT_gg8tta_rep2_Red_Jan20
gg8tTA cells with point mutations in Mex3a associated RNAs
TetOMexHT_gg8tTA_Clonetech_tpm.csv

value: sorted immature OSN

value: gg8tTA; tetO-Mex3a_HyperTRIBE_mCherry


title: cell line, shcontrol, rep3

value: Control


title: Human, traumatic lung injury, progressive stage, day 3 post hospital, M3 and N3

description: Sample name: TLI-P-3

value: circulating blood

value: myeloid and lymphocyte cell

value: PBMCs;neutrophil;T cell; B cell

value: myeloid replication3 and lymphocyte replication3

value: progressive stage, day 3 post hospital


title: HyperTRIBE_gg8tTA_omptTA_rep2

description:
Library name: TetOHT_rep2_Red_Sept19
gg8tTA;OMPtTA cells with point mutations in HyperTRIBE-domain associated RNAs
TetOMexHT_TetOHT_Neg_gg8tTA_omptTA_tpm.csv

value: Main olfactory epithelium

value: sorted immature and mature OSN


title: Human, traumatic lung injury, acute stage, day 1 post hospital admission, M3 and N3

description: Sample name: TLI-A-3


title: HyperTRIBE_InternalControl_Mex3a_gg8tTA_rep2

description:
Library name: RNA_TetOMexHT_gg8tta_rep2_Neg_Jan20
internal control for HyperTRIBE experiment of same replicate (same mouse, so same genetic SNPs)
TetOMexHT_gg8tTA_Clonetech_tpm.csv


title: cell line, shcontrol, rep2


title: cell line, shMsln #1, rep3

value: MSLN knockdown


title: WT1_LA

description:
Library name: DSP-1001660036294-A-C08
FFPE spatial transcriptome sequencing

value: wild-type E17.5 left atrium


title: Human, inhalation injury, convalescence, the day before discharged, M2 and N2

description: Sample name: II-C-2

value: myeloid replication2 and lymphocyte replication2

value: inhalation injury


title: cell line, shcontrol, rep1


title: WT2_LA_Aur

description:
Library name: DSP-1001660036294-A-C12
FFPE spatial transcriptome sequencing

value: wild-type E17.5 left atrial appendage


title: Human, inhalation injury, acute stage, day 1 post hospital admission, M3 and N3

description: Sample name: II-A-3


title: Human, traumatic lung injury, convalescence, the day before discharged, M2 and N2

description: Sample name: TLI-C-2

value: traumatic lung injury


title: HOM3_SAN_HCN4pos

description:
Library name: DSP-1001660036294-A-C06
FFPE spatial transcriptome sequencing

source_name: delB/delB HCN4-high E17.5 sinus node

value: delB/delB HCN4-high E17.5 sinus node

value: homozygous mutant


title: Tumor tissues, shMsln #1, rep3

source_name: tumor tissue

value: tumor tissue


title: MOLM-13, shControl, biol rep 4 (RNA-seq)

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

description: Library name: MOLM-13 cells shControl biological replicate 4

data_processing:
Reads were mapped to the hg38 genome build using minimap2 and filtered with a long-read mapq>50.
Differentially expressed genes were identified using Stringtie to generate transcript counts, followed by DESeq2 with an adj. p-value <.05.
Differential isoform usage was performed by IsoformSwitchAnalyzeR with a q-value >.05.
Assembly: hg38
Supplementary files format and content: countmatrix and tpmmatrix (tab) files

extract_protocol:
RNA extraction was carried out using Qiagen’s RNeasy Mini Kit (Qiagen, Germantown, Maryland) following manufacturer’s instructions.
Long-read RNA sequencing was performed by CD Genomics, Shirley, NY using cDNA libraries prepared using the ONT SQK-PCS109 + SQK-PBK004 kits.

treatment_protocol: PTBP1 knockdown and control MOLM-13 cells were treated with doxycycline for 9 days.

value: acute myeloid leukemia

value: WT

value: 9 days of doxycycline


title: Tumor tissues, shMsln #1, rep4


title: Human, inhalation injury, progressive stage, day 3 post hospital, M2 and N2

description: Sample name: II-P-2

value: circulating blood

value: myeloid and lymphocyte cell

value: PBMCs;neutrophil;T cell; B cell


title: HOM3_LA_Aur

description:
Library name: DSP-1001660036294-A-C05
FFPE spatial transcriptome sequencing

source_name: delB/delB E17.5 left atrial appendage

value: delB/delB E17.5 left atrial appendage


title: MOLM-13, shControl, biol rep 3 (RNA-seq)

description: Library name: MOLM-13 cells shControl biological replicate 3


title: Human, inhalation injury, acute stage, day 1 post hospital admission, M2 and N2

description: Sample name: II-A-2


title: Tumor tissues, shMsln #1, rep2


title: HOM3_LA

description:
Library name: DSP-1001660036294-A-C04
FFPE spatial transcriptome sequencing

source_name: delB/delB E17.5 left atrium

value: delB/delB E17.5 left atrium


title: WT1_LA_Aur

description:
Library name: DSP-1001660036294-A-C09
FFPE spatial transcriptome sequencing

value: wild-type


title: HOM2_SAN_HCN4neg

description:
Library name: DSP-1001660036294-A-C03
FFPE spatial transcriptome sequencing

source_name: delB/delB HCN4-low E17.5 sinus node

value: delB/delB HCN4-low E17.5 sinus node


title: MOLM-13, shControl, biol rep 1 (RNA-seq)

description: Library name: MOLM-13 cells shControl biological replicate 1


title: Tumor tissues, shcontrol, rep4

value: Control


title: Human, inhalation injury, convalescence, the day before discharged, M1 and N1

description: Sample name: II-C-1

value: myeloid replication1 and lymphocyte replication1

value: inhalation injury


title: HOM2_SAN_HCN4pos

description:
Library name: DSP-1001660036294-A-C02
FFPE spatial transcriptome sequencing


title: MOLM-13, shPTBP1, biol rep 4 (RNA-seq)

description: Library name: MOLM-13 cells shPTBP1 biological replicate 4

value: PTBP1 KD


title: Human, traumatic lung injury, progressive stage, day 3 post hospital, M1 and N1

description: Sample name: TLI-P-1

value: traumatic lung injury

value: progressive stage, day 3 post hospital


title: HOM3_SAN_HCN4neg

description:
Library name: DSP-1001660036294-A-C07
FFPE spatial transcriptome sequencing

value: homozygous mutant


title: HOM2_LA_Aur

description:
Library name: DSP-1001660036294-A-C01
FFPE spatial transcriptome sequencing


title: Tumor tissues, shcontrol, rep3

value: tumor tissue


title: MOLM-13, shPTBP1, biol rep 3 (RNA-seq)

description: Library name: MOLM-13 cells shPTBP1 biological replicate 3

value: acute myeloid leukemia


title: Human, inhalation injury, progressive stage, day 3 post hospital, M1 and N1

description: Sample name: II-P-1


title: Tumor tissues, shcontrol, rep2


title: HOM2_LA

description:
Library name: DSP-1001660036294-A-B12
FFPE spatial transcriptome sequencing


title: Tumor tissues, shcontrol, rep1


title: Human, traumatic lung injury, progressive stage, day 3 post hospital, M2 and N2

description: Sample name: TLI-P-2

value: myeloid replication2 and lymphocyte replication2


title: MOLM-13, shPTBP1, biol rep 2 (RNA-seq)

description: Library name: MOLM-13 cells shPTBP1 biological replicate 2

value: 9 days of doxycycline


title: MOLM-13, shPTBP1, biol rep 1 (RNA-seq)

description: Library name: MOLM-13 cells shPTBP1 biological replicate 1


title: Healthy-3, Human, healthy, M3 and N3

description: Sample name: Healthy-3

value: circulating blood

value: myeloid and lymphocyte cell

value: myeloid replication3 and lymphocyte replication3

value: healthy


title: HOM1_SAN_HCN4neg

description:
Library name: DSP-1001660036294-A-B11
FFPE spatial transcriptome sequencing


title: intervene group rep6

city: Yangzhou

first: Tianfeng

last: Huang

address: 98 Nantong West Road

institute: Northern Jiangsu People's Hospital

data_processing:
Reads were aligned to the mouse genome Hisat2. The reads mapped the genome were calculated using featureCounts.
Assembly: GRCm39
Supplementary files format and content: read counts table (01.dat_count.csv) and fpkm table (01.dat_fpkm.csv)

source_name: thalamus

extract_protocol:
The total RNA of the sample was isolated and purified by TRIzol (Invitrogen, 114 CA, USA).
The mRNA captured by oligo(dT) magnetic beads was fragmented at high temperature and reverse transcribed into cDNA. Next, the second strand of cDNA was synthesized by RNase H digestion, and the ends of the double-stranded DNA were aligned to form flat ends. Then, an A base was added at each end of the double-stranded DNA so that it could be ligated to the junction with a T base at the end of the double-stranded DNA. Finally, magnetic beads were used for the selection of fragment sizes and purification so that fragments could be formed into 300 bp±50 bp fragments.

value: thalamus

value: tissue

value: WT

value: Coll IV+remodelin


title: Tumor tissues, shMsln #1, rep1

value: MSLN knockdown


title: HOM1_SAN_HCN4pos

description:
Library name: DSP-1001660036294-A-B10
FFPE spatial transcriptome sequencing

value: delB/delB HCN4-high E17.5 sinus node


title: Human, traumatic lung injury, convalescence, the day before discharged, M1 and N1

description: Sample name: TLI-C-1

value: PBMCs;neutrophil;T cell; B cell

value: myeloid replication1 and lymphocyte replication1

value: traumatic lung injury


title: HyperTRIBE_InternalControl_Mex3a_gg8tTA_rep1

description:
Library name: RNA_TetOMexHT_gg8tta_rep1_Neg_Jan20
internal control for HyperTRIBE experiment of same replicate (same mouse, so same genetic SNPs)
TetOMexHT_gg8tTA_Clonetech_tpm.csv

source_name: Main olfactory epithelium

value: Main olfactory epithelium

value: sorted mCherry- cells from Main olfactory epithelium

value: gg8tTA; tetO-Mex3a_HyperTRIBE_mCherry


title: MOLM-13, shControl, biol rep 2 (RNA-seq)

description: Library name: MOLM-13 cells shControl biological replicate 2

value: acute myeloid leukemia

value: 9 days of doxycycline


title: intervene group rep5


title: Healthy-2, Human, healthy, M2 and N2

description: Sample name: Healthy-2

value: circulating blood

value: myeloid and lymphocyte cell

value: myeloid replication2 and lymphocyte replication2


title: HOM1_LA_Aur

description:
Library name: DSP-1001660036294-A-B09
FFPE spatial transcriptome sequencing

value: delB/delB E17.5 left atrial appendage

value: homozygous mutant


title: HUDEP-2_sg1617_Ery_CPC_rep2

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

description: Library name: sample12

data_processing:
The sequenced POD5 files were basecalled using Dorado (v0.5.1) on a GPU node with the DNA super accuracy model, generating FASTQ files.
Raw sequencing reads were trimmed using Cutadapt (v4.4)  with the parameters -m 200 -q 20 -u 30 -M 150000.
Trimmed reads were mapped to the human genome and analyzed for chromatin interactions using the Nextflow Pore-C pipeline (v23.10.0) with parameter --cutter NlaIII.
Assembly: hg38
Supplementary files format and content: pairs format
Library strategy: Capture-C

extract_protocol:
After ligation, DNA was subjected to proteinase K and pronase digestion, followed by purification using phenol:chloroform:isoamyl alcohol (25:24:1, v/v). Enriched and amplified DNA was then purified using a custom-prepared SPRIselect bead solution, optimized for 3–4 kb DNA by modifying the stock buffer.
After two rounds of enrichment, DNA was processed using the Ligation Sequencing Kit V14 (Oxford Nanopore Technologies, SQK-LSK114). Finally, 200 fmol of DNA libraries were loaded onto a pre-rinsed PromethION flow cell (Oxford Nanopore Technologies, FLO-PRO114M).

value: human erythroid progenitor cells

value: sg1617 editing


title: intervene group rep4

value: thalamus

value: tissue

value: WT

value: Coll IV+remodelin


title: TLI-A-2，Human, traumatic lung injury, acute stage, day 1 post hospital admission, M2 and N2

description: Sample name: TLI-A-2

value: PBMCs;neutrophil;T cell; B cell

value: traumatic lung injury


title: HUDEP-2_sg1617_Ery_CPC_rep1

description: Library name: sample11


title: TLI-A-1, Human, traumatic lung injury, acute stage, day 1 post hospital admission, M1 and N1

description: Sample name: TLI-A-1

value: myeloid replication1 and lymphocyte replication1


title: intervene group rep3


title: HUDEP-2_Ery_CPC_rep2

description: Library name: sample10

value: wild-type


title: HyperTRIBE_Mex3a_gg8tTA_rep1

description:
Library name: RNA_TetOMexHT_gg8tta_rep1_Red_Jan20
gg8tTA cells with point mutations in Mex3a associated RNAs
TetOMexHT_gg8tTA_Clonetech_tpm.csv

value: Main olfactory epithelium

value: sorted immature OSN

value: gg8tTA; tetO-Mex3a_HyperTRIBE_mCherry


title: HUDEP-2_Ery_CPC_rep1

description: Library name: sample9


title: intervene group rep2


title: Healthy-1, Human, healthy, M1 and N1

description: Sample name: Healthy-1

value: circulating blood

value: myeloid and lymphocyte cell

value: healthy


title: HET6_SAN_HCN4pos

description:
Library name: DSP-1001660036294-A-B06
FFPE spatial transcriptome sequencing

source_name: delB/+ HCN4-high E17.5 sinus node

value: delB/+ HCN4-high E17.5 sinus node

value: heterozygous mutant


title: HUDEP-2_sg1617_CBS_CPC_rep2

description: Library name: sample8

value: human erythroid progenitor cells

value: sg1617 editing


title: HET6_LA_Aur

description:
Library name: DSP-1001660036294-A-B05
FFPE spatial transcriptome sequencing

source_name: delB/+  E17.5 left atrial appendage

value: delB/+  E17.5 left atrial appendage


title: II-A-1, Human, inhalation injury, acute stage, day 1 post hospital admission, M1 and N1

description: Sample name: II-A-1

value: inhalation injury


title: HUDEP-2_sg1617_CBS_CPC_rep1

description: Library name: sample7


title: exp9_combinedRNA

first: Liying

last: Jiang

address: 279 zhouzhugong road

institute: Shanghai University of Medicine and Health Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 (Kim et al., 2015;Pertea et al., 2016).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample ...

source_name: pregnant female

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogen) and determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).
Next-generation libraries of mRNA-seq were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).

tag: Sex

value: female

value: peripheral blood

value: lymphocyte

tag: disease state

value: gestational diabetes (GDM)


title: intervene group rep1

value: thalamus

value: tissue

value: WT

value: Coll IV+remodelin


title: HET6_LA

description:
Library name: DSP-1001660036294-A-B04
FFPE spatial transcriptome sequencing

source_name: delB/+  E17.5 left atrium

value: delB/+  E17.5 left atrium


title: exp8_combinedRNA


title: exp7_combinedRNA


title: HUDEP-2_EnhKO_CBS_CPC_rep2

description: Library name: sample6

value: enhancer knockout


title: model group rep6

value: Coll IV


title: model group rep5


title: exp4_combinedRNA


title: model group rep3


title: HUDEP-2_EnhKO_CBS_CPC_rep1

description: Library name: sample5


title: model group rep4


title: HET5_SAN_HCN4pos

description:
Library name: DSP-1001660036294-A-B02
FFPE spatial transcriptome sequencing

value: delB/+ HCN4-high E17.5 sinus node


title: HET5_SAN_HCN4neg

description:
Library name: DSP-1001660036294-A-B03
FFPE spatial transcriptome sequencing

source_name: delB/+ HCN4-low E17.5 sinus node

value: delB/+ HCN4-low E17.5 sinus node

value: heterozygous mutant


title: HET6_SAN_HCN4neg

description:
Library name: DSP-1001660036294-A-B07
FFPE spatial transcriptome sequencing


title: model group rep2


title: HOM1_LA

description:
Library name: DSP-1001660036294-A-B08
FFPE spatial transcriptome sequencing

value: delB/delB E17.5 left atrium

value: homozygous mutant


title: exp3_combinedRNA


title: HET4_SAN_HCN4neg

description:
Library name: DSP-1001660036294-A-B01
FFPE spatial transcriptome sequencing


title: exp1_combinedRNA


title: HUDEP-2_CBS_CPC_rep1

description: Library name: sample3

value: human erythroid progenitor cells

value: wild-type


title: HET3_SAN_HCN4neg

description:
Library name: DSP-1001660036294-A-A11
FFPE spatial transcriptome sequencing


title: model group rep1


title: con7_combinedRNA

value: female

value: peripheral blood

value: Control


title: OPC, 5day, BAF155 ChIP

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

data_processing:
Following ChIP-seq sequencing, raw reads were obtained and filtered to remove junctions using Cutadapt.
Trimmomatic was then used to remove low quality reads, followed by quality control by FastQC.
The clean data were decontaminated and aligned to the reference genome using Bowtie2.
Peak-calling: MACS2. Peak filtering: IDR. Peak annotation: ChIPseeker. High-quality mapped reads with a mean Phred quality score (MPAQ) of 30 or greater were used for subsequent analysis.
Assembly: Rnor_6.0 - rn6
Supplementary files format and content: bigwig

organism: Rattus norvegicus

source_name: Rat OPC

growth_protocol: Primary rat OPCs isolated from mix glial culture by the addition of 0.04% EDTA in PBS and repetitive rocking, and cultured with OPC proliferation medium for 1 day then with differentiation medium for 4 days.

extract_protocol:
ChIP-seq sample were prepared on day 1 and day 5 after purification of OPC by addition of 1% formaldehyde for 10 min, followed by quenching using 0.125 M glycine. cell membranes were disrupted with lysis buffer to release the nuclear material. The chromatin was sheared into small fragments, usually ranging from 200 to 1000 base pairs, through ultrasonic fragmentation. This was followed by enriching the protein-DNA complexes using the BAF155 antibody (Cell Signaling Technology, catalog number 11956). The BAF155 antibody was bound to Protein A+G magnetic beads (Magna ChIP™, catalog number 16-663), and the sonicated samples were incubated overnight with the antibody-bound beads. After incubation, unbound material was removed, and DNA fragments were released from the immunoprecipitation complexes.
The purified DNA underwent end repair and splice addition, followed by amplification using PCR to generate a sequencing library. Once the library was tested and validated, it was sequenced using the Illumina HiSeq platform.

tag: strain

value: Sprague Dawley

value: Rat OPC

tag: chip antibody

value: 1 day with OPC proliferation medium, 4 day with OPC differentiation medium


title: control group rep6

value: thalamus

value: tissue

value: WT

value: saline


title: con6_combinedRNA

value: lymphocyte


title: OPC, 1day, Input

value: 1 day with OPC proliferation medium


title: control group rep5


title: HET3_LA_Aur

description:
Library name: DSP-1001660036294-A-A09
FFPE spatial transcriptome sequencing

value: delB/+  E17.5 left atrial appendage

value: heterozygous mutant


title: con5_combinedRNA


title: OPC, 1day, BAF155 ChIP

value: BAF155 antibody (Cell Signaling Technology, catalog number 11956)


title: HUDEP-2_CBS_CPC_rep2

description: Library name: sample4

value: human erythroid progenitor cells


title: control group rep4


title: HET3_LA

description:
Library name: DSP-1001660036294-A-A08
FFPE spatial transcriptome sequencing

value: delB/+  E17.5 left atrium


title: con4_combinedRNA

value: female


title: H3K27me3_sciCUTnTag_40daysold_chip2_(240320_SL_Dm6_gut_H3K27me3_40doC2_240313)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Library name: H3K27me3_sciCUTnTag_40daysold_chip2
iCell8 Chip 2 of SciCUT&Tag targeting H3K27me3 in 40 days old Drosophila gut

data_processing:
*library strategy: sciCUT&Tag
Single cell data from the iCell8 system. Bulk data processing: 1. We trimmed adapters from the 29 bp reads using cutadapt 4.1 with parameters: --nextseq-trim 20 -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z 2. We aligned the bulk reads to dm6 using Bowtie2 2.4.4 with parameters: --very-sensitive-local --soft-clipped-unmapped-tlen --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 1000 3. We extracted properly paired alignments to generate a fragment bed files using bedtools bamtobed -bedpe 4. We constructed tracks in bigwig format as the fraction of each count at each base pair multiplied by the size of the reference sequence so if the counts were uniformly distributed there would be one count at each base pair using bedtools genomecov.
Assembly: dm6
Supplementary files format and content: bw
Library strategy: sciCUT&Tag

organism: Drosophila melanogaster

source_name: Drosophila 40 days old gut

value: Drosophila 40 days old gut

tag: antibody

value: H3K27me3, Cell Signaling Technology cat # 9733 BC


title: HET2_SAN_HCN4neg

description:
Library name: DSP-1001660036294-A-A07
FFPE spatial transcriptome sequencing

value: delB/+ HCN4-low E17.5 sinus node


title: control group rep3


title: HET4_SAN_HCN4pos

description:
Library name: DSP-1001660036294-A-A12
FFPE spatial transcriptome sequencing

value: delB/+ HCN4-high E17.5 sinus node


title: con2_combinedRNA

value: peripheral blood

value: Control


title: OPC, 5day, Input

value: Sprague Dawley

value: Rat OPC

value: 1 day with OPC proliferation medium, 4 day with OPC differentiation medium


title: HET2_LA_Aur

description:
Library name: DSP-1001660036294-A-A05
FFPE spatial transcriptome sequencing


title: control group rep2

value: thalamus

value: tissue

value: WT

value: saline


title: H3K27me3_sciCUTnTag_15daysold_chip2_(240320_SL_Dm6_gut_H3K27me3_15doC2_240313)

description:
Library name: H3K27me3_sciCUTnTag_15daysold_chip2
iCell8 Chip 2 of SciCUT&Tag targeting H3K27me3 in 15 days old Drosophila gut

source_name: Drosophila 15 days old gut

value: Drosophila 15 days old gut


title: HET2_SAN_HCN4pos

description:
Library name: DSP-1001660036294-A-A06
FFPE spatial transcriptome sequencing

value: heterozygous mutant


title: control group rep1


title: N2A_Input_hemin

city: Beijing

first: Liye

last: Hu

address: #10 YouAnMenWai XiTouTiao, Fengtai District

institute: Capital medical university

data_processing:
Raw data was performed using fastp-0.23.2.
Clean reads are aligned to the reference sequence by using SOAP2.21 aligner. No more than 2 mismatches are allowed in the alignment.
Callpeak was generated using MACS-1.4.2 with p<0.005.
Differential peaks were generated using MAnorm software with |M_value_rescaled|>1并且-log10(p-value)>5.
Assembly: mm10
Supplementary files format and content: wig, bed

source_name: brain

growth_protocol: DMEM, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using VCX150 (Sonics).
5ng of purified ChIP DNA was used to generate the sequencing library using a NEB kit and sequenced with the Illumina HiSeq X Ten. DNA-end repair, 3’-dA overhang and ligation of methylated sequencing adaptors use Paired-End DNA Sample Prep kit (Illumina). PCR amplification was size selected at 100-300bp. Qualified library for sequencing.

treatment_protocol: control: DMSO, drug:15 μM Hemin for 12 hours

value: brain

value: neuroblast

value: IgG

value: hemin


title: H3K27me3_sciCUTnTag_40daysold_chip1_(240322_SL_Dm6_gut_H3K27me3_40doC1_240313)

description:
Library name: H3K27me3_sciCUTnTag_40daysold_chip1
iCell8 Chip 1 of SciCUT&Tag targeting H3K27me3 in 40 days old Drosophila gut

value: Drosophila 40 days old gut

value: H3K27me3, Cell Signaling Technology cat # 9733 BC


title: sci-mtChIL-seq, NIH3T3-14, MyoD-RNAPolII (D24,D72)

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
The cell barcodes were made by modifing index sequences using seqkit (version 0.16.1)  and they were assigned to read sequences by umi_tools (version 1.1.1).
Adapter sequences were trimmed using Trim Galore (version 0.6.10) with the default options.
The paired-reads were mapped to the mm10 using bowtie2 (version 2.3.5.1) with the default options.
The reads uniquely mapped to autosome or sex chromosomes were extracted.
Duplicates were remove by R package GenomicRanges (version 1.54.1).
Assembly: mm10
Supplementary files format and content: The processed data fromat is BED. These indicate the position of unique fragments and column 3 indicates cell barcode.
Library strategy: sci-mtChIL-seq

source_name: NIH3T3 TetOn3G/MyoD cells

extract_protocol:
Trunks at E10.5 and E11.5 and limbs at E12.5, E13.5, and E14.5 were dissected from the embryos and cut into small pieces approximately 1 mm square and cell were isolated with protease treatment. Cell line were isolated with protease treatment.
A total of 10-30k biotinylated cells per well were combined in 96-well avidin-coated plates and stained with primary antibody (1st Ab) and sci-ChIL probe. Tn5 transposition via Tn5 transposase integrates the sci-ChIL probe’s indexed DNA into the genome around the primary antibody of the cell (cells are indexed with a unique sci-ChIL probe per well). The cells in the 96-well plate are then pooled, and 25 cells per well are added to another 96-well plate with a cell sorter, so that cells with different primary indexes are placed in the wells. The integrated regions are then amplified as RNA by in vitro transcription using T7 RNA polymerase. Transcribed RNA is purified and converted to cDNA for sequencing library preparation; a second index is added by PCR prior to sequencing. PCR is performed with a set of primers with unique i5 and i7 sequences per well. A library with a different primary index and the same secondary index was generated for each well. Overall, a library of approximately 2400 cells with different primary and secondary indices is produced. One single-target sequence includes one set of 96 sci-ChIL probes with T5 barcodes, and two sets of multi-target sequences is used.

value: NIH3T3 TetOn3G/MyoD cells

value: The Myod1 gene was inserted downstream of the TRE3G promoter in NIH3T3 cells expressing Tet-On 3G transactivator from the CMV promoter.

value: D0 cell were changing the culture medium to DMEM supplemented with 2% horse serum for 24h (D24) or 72h (D72)


title: HET3_SAN_HCN4pos

description:
Library name: DSP-1001660036294-A-A10
FFPE spatial transcriptome sequencing

value: delB/+ HCN4-high E17.5 sinus node


title: con1_combinedRNA

value: female

value: peripheral blood

value: lymphocyte

value: Control


title: H3K27me3_sciCUTnTag_15daysold_chip1_(240322_SL_Dm6_gut_H3K27me3_15doC1_240313)

description:
Library name: H3K27me3_sciCUTnTag_15daysold_chip1
iCell8 Chip 1 of SciCUT&Tag targeting H3K27me3 in 15 days old Drosophila gut


title: HET2_LA

description:
Library name: DSP-1001660036294-A-A04
FFPE spatial transcriptome sequencing

value: delB/+  E17.5 left atrium


title: N2A_Input_vehicle

value: DMSO


title: H3K27me3_sciCUTnTag_1dayold_chip2_(240320_SL_Dm6_gut_H3K27me3_1doC2_240313)

description:
Library name: H3K27me3_sciCUTnTag_1dayold_chip2
iCell8 Chip 2 of SciCUT&Tag targeting H3K27me3 in 1 day old Drosophila gut

source_name: Drosophila 1 day old gut

value: Drosophila 1 day old gut


title: HET1_SAN_HCN4neg

description:
Library name: DSP-1001660036294-A-A03
FFPE spatial transcriptome sequencing

value: delB/+ HCN4-low E17.5 sinus node

value: heterozygous mutant


title: sci-mtChIL-seq, NIH3T3-13, MyoD-RNAPolII (MyoDminus,D0)

value: MyoDminus:Cell were grown without doxyxycline. D0:Cell induced MyoD for 24 h after the addition of doxycycline.


title: H3K27me3_sciCUTnTag_1dayold_chip1_(240322_SL_Dm6_gut_H3K27me3_1doC1_240313)

description:
Library name: H3K27me3_sciCUTnTag_1dayold_chip1
iCell8 Chip 1 of SciCUT&Tag targeting H3K27me3 in 1 day old Drosophila gut


title: N2A_H3K9me3_hemin

value: brain

value: neuroblast

value: hemin


title: HET1_SAN_HCN4pos

description:
Library name: DSP-1001660036294-A-A02
FFPE spatial transcriptome sequencing


title: sci-mtChIL-seq, NIH3T3-12, H3K27ac-RNAPolII (D24,D72)

value: NIH3T3 TetOn3G/MyoD cells


title: Pc_CUTAC_40daysold_rep4_(240911_SL_Dm_masked_transposons_rDNA_40do_Pc_721)

description:
Library name: Pc_CUTAC_40daysold_rep4
CUTAC targeting Pc in 40 days old Drosophila gut

data_processing:
*library strategy: Cleavage under targets and Tagmentation (Cut-and-Tag)
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the dm6 Drosophia melanogaster reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the dm6 alignments.
4. We used bedtools 2.30.0 "genomecov" to make a normalized count dm6 track which is the fraction of counts at each base pair scaled by the size of the dm6 reference sequence (137567484) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .dm6.bw)
Assembly: dm6_masked_transposons.fa.gz
Supplementary files format and content: bw

value: Drosophila 40 days old gut

value: Pc antibody clone Pc7759.  Gift from Judith Kassis


title: N2A_H3K9me3_vehicle


title: sci-mtChIL-seq, NIH3T3-11, H3K27ac-RNAPolII (MyoDminus,D0)

value: The Myod1 gene was inserted downstream of the TRE3G promoter in NIH3T3 cells expressing Tet-On 3G transactivator from the CMV promoter.


title: DelB_WT_3_SAN

description:
Library name: DSP-1001660020586-A-F06
FFPE spatial transcriptome sequencing

data_processing:
FASTQ files were trimmed, stitched, aligned and deduplicated using the NanoString GeoMx NGS pipeline (version 2.3.3.10).
Generated DCC files were processed with the R GeoMxTools package (version 3.8.0).
Differential gene expression analysis was performed using Iimma (version 3.60.1) on quantile-normalized data.
Assembly: mm10
Supplementary files format and content: NS1 DE tables.xlsx (differential expression tables)
Library strategy: Spatial Transcriptomics

source_name: wild-type HCN4+ E17.5 sinus node

value: wild-type HCN4+ E17.5 sinus node

value: wild-type


title: Visium retina (Anolis carolinensis), biological replicate 2

city: Aarhus C

first: Christian

last: Damsgaard

address: C F Møllers Alle 3

department: Department of Biology

country: Denmark

institute: Aarhus University

description:
Library name: 22
10x Genomics Visium Spatial Gene Expression v1, 55 µm resolution

data_processing:
Visium: Raw BCL files were converted to FASTQ using bcl2fastq. FASTQ files were processed with SpaceRanger v3.1.1 using the count pipeline and species-specific reference genomes (AnoCar3.1, TaeGut1, Cliv_2.1, GRCg7b). The outputs include filtered_feature_bc_matrix, spatial coordinates, histology images, and QC metrics. Chromium: FASTQ files were processed with CellRanger v7.1.0 using the count pipeline and the Taeniopygia guttata (TaeGut1) reference genome. The outputs include the filtered_feature_bc_matrix. No additional filtering, ambient RNA removal (e.g., SoupX), doublet removal, or further QC was performed before deposition.
Assembly: Anolis carolinensis — AnoCar3.1 Taeniopygia guttata — TaeGut1 Columba livia — Cliv_2.1 Gallus gallus — GRCg7b
Supplementary files format and content: Each sample is provided as a single compressed tar archive (sampleID.tar.gz). For Visium: contains filtered_feature_bc_matrix/ (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz), spatial/ (tissue_positions.csv, scalefactors_json.json), histology image (.tif), and QC metrics (metrics_summary.csv). For Chromium: contains filtered_feature_bc_matrix/ (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz) and optional per-cell metadata (metadata.csv if available).
Library strategy: spatial transcriptomics

organism: Anolis carolinensis

source_name: Eye

extract_protocol:
Retinas were dissected from freshly euthanized adult animals. For Visium libraries, eyes were embedded in OCT, cryosectioned (10 µm), and mounted on 10x Genomics Visium slides. For Chromium single-cell libraries, retinas were enzymatically and mechanically dissociated into single cells following the 10x Genomics recommended protocol.
Spatial transcriptomics libraries were prepared using the 10x Genomics Visium Spatial Gene Expression kit v1 (poly-A capture, 55 µm spot resolution). Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3′ v3 chemistry. All libraries were sequenced on an Illumina HiSeq 4000 with paired-end 2 × 150 bp reads.

value: Eye


title: Pc_CUTAC_40daysold_rep3_(240911_SL_Dm_masked_transposons_rDNA_40do_Pc_720)

description:
Library name: Pc_CUTAC_40daysold_rep3
CUTAC targeting Pc in 40 days old Drosophila gut


title: DelB_WT_3_RA

description:
Library name: DSP-1001660020586-A-F05
FFPE spatial transcriptome sequencing

source_name: wild-type E17.5 right atrium

value: wild-type E17.5 right atrium


title: Visium retina (Anolis carolinensis), biological replicate 1

description:
Library name: 21
10x Genomics Visium Spatial Gene Expression v1, 55 µm resolution


title: sci-mtChIL-seq, NIH3T3-10, H3K27me3-RNAPolII (D24,D72)

value: D0 cell were changing the culture medium to DMEM supplemented with 2% horse serum for 24h (D24) or 72h (D72)


title: Pc_CUTAC_40daysold_rep2_(240911_SL_Dm_masked_transposons_rDNA_40do_Pc_719)

description:
Library name: Pc_CUTAC_40daysold_rep2
CUTAC targeting Pc in 40 days old Drosophila gut


title: DelB_WT_2_SAN

description:
Library name: DSP-1001660020586-A-F04
FFPE spatial transcriptome sequencing


title: Visium retina (Gallus gallus), biological replicate 1

description:
Library name: 43
10x Genomics Visium Spatial Gene Expression v1, 55 µm resolution

organism: Gallus gallus


title: DelB_WT_2_RA

description:
Library name: DSP-1001660020586-A-F03
FFPE spatial transcriptome sequencing


title: sci-mtChIL-seq, NIH3T3-8, Brg1-RNAPolII (D24,D72)


title: sci-mtChIL-seq, NIH3T3-9, H3K27me3-RNAPolII (MyoDminus,D0)


title: sci-mtChIL-seq, NIH3T3-7, Brg1-RNAPolII (MyoDminus,D0)


title: Pc_CUTAC_40daysold_rep1_(240911_SL_Dm_masked_transposons_rDNA_40do_Pc_718)

description:
Library name: Pc_CUTAC_40daysold_rep1
CUTAC targeting Pc in 40 days old Drosophila gut


title: w_H3K4me3_R1_(240525_BT_Dm_3074)

description: wildtype wing disc H3K4me3

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the dm6 Drosophia melanogaster reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the dm6 alignments.
4. We used bedtools 2.30.0 "genomecov" to make a normalized count dm6 track which is the fraction of counts at each base pair scaled by the size of the dm6 reference sequence (137567484) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .dm6.bw)
Assembly: dm6
Supplementary files format and content: bw
Library strategy: CUT&Tag

source_name: wing imaginal disc

extract_protocol:
readme_extract_protocol.txt
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: wing imaginal disc

value: male

value: wildtype

value: anti-H3K4me3 Epicypher 13-0060


title: DelB_WT_1_SAN

description:
Library name: DSP-1001660020586-A-F02
FFPE spatial transcriptome sequencing


title: w_H3K4me1_R1_(240525_BT_Dm_3072)

description: wildtype wing disc H3K4me1

value: anti-H3K4me1 Epicypher 13-0057


title: Pc_CUTAC_15daysold_rep4_(240911_SL_Dm_masked_transposons_rDNA_15do_Pc_725)

description:
Library name: Pc_CUTAC_15daysold_rep4
CUTAC targeting Pc in 15 days old Drosophila gut

value: Drosophila 15 days old gut


title: Pc_CUTAC_15daysold_rep3_(240911_SL_Dm_masked_transposons_rDNA_15do_Pc_724)

description:
Library name: Pc_CUTAC_15daysold_rep3
CUTAC targeting Pc in 15 days old Drosophila gut


title: sci-mtChIL-seq, NIH3T3-6, Myog-RNAPolII (D24,D72)


title: DelB_WT_1_RA

description:
Library name: DSP-1001660020586-A-F01
FFPE spatial transcriptome sequencing


title: w_H3K27ac_R1_(240525_BT_Dm_3069)

description: wildtype wing disc H3K27ac

value: anti-H3K27ac Epicypher 13-0058


title: sci-mtChIL-seq, NIH3T3-5, Myog-RNAPolII (MyoDminus,D0)

value: MyoDminus:Cell were grown without doxyxycline. D0:Cell induced MyoD for 24 h after the addition of doxycycline.


title: w_H3K4me2_R1_(240525_BT_Dm_3068)

description: wildtype wing disc H3K4me2

value: anti-H3K4me2 Epicypher 13-0027


title: w_RNAPII-S2p_R1_(240525_BT_Dm_3067)

description: wildtype wing disc RNAPII-S2p

value: anti-RNAPII-S2p CST E1Z3G


title: Pc_CUTAC_15daysold_rep2_(240911_SL_Dm_masked_transposons_rDNA_15do_Pc_723)

description:
Library name: Pc_CUTAC_15daysold_rep2
CUTAC targeting Pc in 15 days old Drosophila gut

value: Pc antibody clone Pc7759.  Gift from Judith Kassis


title: sci-mtChIL-seq, NIH3T3-3, MyoD-RNAPolII (MyoDminus,D0)

value: NIH3T3 TetOn3G/MyoD cells

value: The Myod1 gene was inserted downstream of the TRE3G promoter in NIH3T3 cells expressing Tet-On 3G transactivator from the CMV promoter.


title: DelB_HOM_6_RA

description:
Library name: DSP-1001660020586-A-E10
FFPE spatial transcriptome sequencing

source_name: delB/delB E17.5 right atrium

value: delB/delB E17.5 right atrium

value: homozygous mutant


title: DelB_HOM_6_SAN_Hcn4pos

description:
Library name: DSP-1001660020586-A-E12
FFPE spatial transcriptome sequencing

value: wild-type HCN4+ E17.5 sinus node

value: wild-type


title: Pc_CUTAC_15daysold_rep1_(240911_SL_Dm_masked_transposons_rDNA_15do_Pc_722)

description:
Library name: Pc_CUTAC_15daysold_rep1
CUTAC targeting Pc in 15 days old Drosophila gut


title: DelB_HOM_6_SAN_Hcn4neg

description:
Library name: DSP-1001660020586-A-E11
FFPE spatial transcriptome sequencing

source_name: delB/delB HCN4-low E17.5 sinus node

value: delB/delB HCN4-low E17.5 sinus node


title: w_Mxc_R1_(240525_BT_Dm_3065)

description: wildtype wing disc Mxc

value: wing imaginal disc

value: male

value: anti-Mxc


title: Pc_CUTAC_1dayold_rep4_(240911_SL_Dm_masked_transposons_rDNA_1do_Pc_729)

description:
Library name: Pc_CUTAC_1dayold_rep4
CUTAC targeting Pc in 1 day old Drosophila gut

value: Drosophila 1 day old gut


title: sci-mtChIL-seq, NIH3T3-2, H3K4me3-RNAPolII (D24,D72)

value: D0 cell were changing the culture medium to DMEM supplemented with 2% horse serum for 24h (D24) or 72h (D72)


title: 12XWT_H3K27ac_R3_(240525_BT_Dm_3063)

description: short histone array wing disc H3K27ac

value: short histone array

value: anti-H3K27ac Epicypher 13-0058


title: DelB_HOM_5_SAN_Hcn4pos

description:
Library name: DSP-1001660020586-A-E09
FFPE spatial transcriptome sequencing

source_name: delB/delB HCN4-high E17.5 sinus node

value: delB/delB HCN4-high E17.5 sinus node


title: DelB_HOM_5_RA

description:
Library name: DSP-1001660020586-A-E07
FFPE spatial transcriptome sequencing


title: Pc_CUTAC_1dayold_rep2_(240911_SL_Dm_masked_transposons_rDNA_1do_Pc_727)

description:
Library name: Pc_CUTAC_1dayold_rep2
CUTAC targeting Pc in 1 day old Drosophila gut


title: sci-mtChIL-seq,  embryo-26, MyoD-RNAPolII

source_name: embroy

tag: developmental stage

value: embroy

value: MyoD-RNAPolII


title: sci-mtChIL-seq, NIH3T3-1, H3K4me3-RNAPolII (MyoDminus,D0)

value: NIH3T3 TetOn3G/MyoD cells

value: MyoDminus:Cell were grown without doxyxycline. D0:Cell induced MyoD for 24 h after the addition of doxycycline.


title: 12XWT_H3K4me3_R2_(240525_BT_Dm_3062)

description: short histone array wing disc H3K4me3

value: anti-H3K4me3 Epicypher 13-0060


title: RNAPIIS5P_CUTAC_40daysold_rep4_(231223_SL_Dm_masked_transposons_S5P_40do_592)

description:
Library name: RNAPIIS5P_CUTAC_40daysold_rep4
CUTAC targeting RNA Polymerase II S5P in 40 days old Drosophilia gut

value: Drosophila 40 days old gut

value: RNAP2Ser5P Cell Signaling Technology cat# 13523


title: RNAPIIS5P_CUTAC_40daysold_rep3_(231223_SL_Dm_masked_transposons_S5P_40do_591)

description:
Library name: RNAPIIS5P_CUTAC_40daysold_rep3
CUTAC targeting RNA Polymerase II S5P in 40 days old Drosophilia gut


title: 12XWT_H3K4me3_R1_(240525_BT_Dm_3061)

description: short histone array wing disc H3K4me3


title: 12XWT_H3K4me1_R1_(240525_BT_Dm_3059)

description: short histone array wing disc H3K4me1

value: anti-H3K4me1 Epicypher 13-0057


title: Pc_CUTAC_1dayold_rep1_(240911_SL_Dm_masked_transposons_rDNA_1do_Pc_726)

description:
Library name: Pc_CUTAC_1dayold_rep1
CUTAC targeting Pc in 1 day old Drosophila gut

value: Pc antibody clone Pc7759.  Gift from Judith Kassis


title: DelB_HOM_4_SAN_Hcn4pos

description:
Library name: DSP-1001660020586-A-E06
FFPE spatial transcriptome sequencing

value: homozygous mutant


title: 12XWT_H3K4me2_R1_(240525_BT_Dm_3060)

description: short histone array wing disc H3K4me2

value: wing imaginal disc

value: male

value: anti-H3K4me2 Epicypher 13-0027


title: sci-mtChIL-seq, NIH3T3-4, MyoD-RNAPolII (D24,D72)

value: The Myod1 gene was inserted downstream of the TRE3G promoter in NIH3T3 cells expressing Tet-On 3G transactivator from the CMV promoter.

value: D0 cell were changing the culture medium to DMEM supplemented with 2% horse serum for 24h (D24) or 72h (D72)


title: sci-mtChIL-seq,  embryo-25, H3K27me3-RNAPolII, H3K4me3-RNAPolII

value: H3K27me3-RNAPolII, H3K4me3-RNAPolII


title: DelB_HOM_4_SAN_Hcn4neg

description:
Library name: DSP-1001660020586-A-E05
FFPE spatial transcriptome sequencing

value: delB/delB HCN4-low E17.5 sinus node


title: RNAPIIS5P_CUTAC_40daysold_rep2_(231223_SL_Dm_masked_transposons_S5P_40do_590)

description:
Library name: RNAPIIS5P_CUTAC_40daysold_rep2
CUTAC targeting RNA Polymerase II S5P in 40 days old Drosophilia gut


title: RNAPIIS5P_CUTAC_15daysold_rep4_(231223_SL_Dm_masked_transposons_S5P_15do_641)

description:
Library name: RNAPIIS5P_CUTAC_15daysold_rep4
CUTAC targeting RNA Polymerase II S5P in 15 days old Drosophilia gut

value: Drosophila 15 days old gut


title: DelB_HOM_5_SAN_Hcn4neg

description:
Library name: DSP-1001660020586-A-E08
FFPE spatial transcriptome sequencing


title: DelB_HOM_4_RA

description:
Library name: DSP-1001660020586-A-E04
FFPE spatial transcriptome sequencing

value: delB/delB E17.5 right atrium


title: sci-mtChIL-seq,  embryo-19, H3K27me3-RNAPolII, H3K4me3-RNAPolII

value: embroy


title: sci-mtChIL-seq,  embryo-23, MyoD-RNAPolII

value: MyoD-RNAPolII


title: Pc_CUTAC_1dayold_rep3_(240911_SL_Dm_masked_transposons_rDNA_1do_Pc_728)

description:
Library name: Pc_CUTAC_1dayold_rep3
CUTAC targeting Pc in 1 day old Drosophila gut

value: Drosophila 1 day old gut


title: RNAPIIS5P_CUTAC_15daysold_rep3_(231223_SL_Dm_masked_transposons_S5P_15do_628)

description:
Library name: RNAPIIS5P_CUTAC_15daysold_rep3
CUTAC targeting RNA Polymerase II S5P in 15 days old Drosophilia gut


title: sci-mtChIL-seq,  embryo-24, MyoD-RNAPolII


title: sci-mtChIL-seq,  embryo-22, H3K27me3-RNAPolII, H3K4me3-RNAPolII


title: 12XWT_H3K9me3_R2_(240525_BT_Dm_3058)

description: short histone array wing disc H3K9me3

value: short histone array

value: anti-H3K9me3 Abcam ab8898


title: DelB_HOM_3.2_SAN_Hcn4pos

description:
Library name: DSP-1001660020586-A-E03
FFPE spatial transcriptome sequencing

value: delB/delB HCN4-high E17.5 sinus node


title: sci-mtChIL-seq,  embryo-21, MyoD-RNAPolII


title: RNAPIIS5P_CUTAC_15daysold_rep1_(231223_SL_Dm_masked_transposons_S5P_15do_626)

description:
Library name: RNAPIIS5P_CUTAC_15daysold_rep1
CUTAC targeting RNA Polymerase II S5P in 15 days old Drosophilia gut

value: RNAP2Ser5P Cell Signaling Technology cat# 13523


title: 12XWT_H3K9me3_R1_(240525_BT_Dm_3057)

description: short histone array wing disc H3K9me3


title: RNAPIIS5P_CUTAC_1dayold_rep4_(231223_SL_Dm_masked_transposons_S5P_1do_595)

description:
Library name: RNAPIIS5P_CUTAC_1dayold_rep4
CUTAC targeting RNA Polymerase II S5P in 1 day old Drosophilia gut


title: DelB_HOM_3.2_SAN_Hcn4neg

description:
Library name: DSP-1001660020586-A-E02
FFPE spatial transcriptome sequencing

value: homozygous mutant


title: 12XWT_RNAPII-S2p_R1_(240525_BT_Dm_3055)

description: short histone array wing disc RNAPII-S2p

value: wing imaginal disc

value: anti-RNAPII-S2p CST E1Z3G


title: 12XWT_RNAPII-S2p_R2_(240525_BT_Dm_3056)

value: male


title: sci-mtChIL-seq, embryo-15, H3K4me3-RNAPolII, MyoD-RNAPolII

value: H3K4me3-RNAPolII, MyoD-RNAPolII


title: RNAPIIS5P_CUTAC_15daysold_rep2_(231223_SL_Dm_masked_transposons_S5P_15do_627)

description:
Library name: RNAPIIS5P_CUTAC_15daysold_rep2
CUTAC targeting RNA Polymerase II S5P in 15 days old Drosophilia gut


title: DelB_HOM_3.2_RA

description:
Library name: DSP-1001660020586-A-E01
FFPE spatial transcriptome sequencing


title: 12XWT_Mute_R2_(230704_BT_Dm_BT2000_mute)

description: short histone array wing disc Mute

value: anti-Mute


title: DelB_HOM_2.2_SAN_Hcn4pos

description:
Library name: DSP-1001660020586-A-D09
FFPE spatial transcriptome sequencing


title: 12XWT_Mxc_R3_(240525_BT_Dm_3053)

description: short histone array wing disc Mxc

value: anti-Mxc


title: DelB_HOM_3.1_SAN_Hcn4pos

description:
Library name: DSP-1001660020586-A-D12
FFPE spatial transcriptome sequencing


title: sci-mtChIL-seq,  embryo-18, H3K27me3-RNAPolII, H3K4me3-RNAPolII

value: H3K27me3-RNAPolII, H3K4me3-RNAPolII


title: sci-mtChIL-seq,  embryo-17, H3K4me3-RNAPolII


title: RNAPIIS5P_CUTAC_1dayold_rep1_(231223_SL_Dm_masked_transposons_S5P_1do_558)

description:
Library name: RNAPIIS5P_CUTAC_1dayold_rep1
CUTAC targeting RNA Polymerase II S5P in 1 day old Drosophilia gut


title: sci-mtChIL-seq, embryo-13, MyoD-RNAPolII


title: DelB_HOM_3.1_SAN_Hcn4neg

description:
Library name: DSP-1001660020586-A-D11
FFPE spatial transcriptome sequencing

value: delB/delB HCN4-low E17.5 sinus node


title: sci-mtChIL-seq, embryo-16, H3K4me3-RNAPolII, MyoD-RNAPolII


title: 12XWT_Mute_R3_(240525_BT_Dm_3052)

description: short histone array wing disc Mute


title: RNAPIIS5P_CUTAC_40daysold_rep1_(231223_SL_Dm_masked_transposons_S5P_40do_589)

description:
Library name: RNAPIIS5P_CUTAC_40daysold_rep1
CUTAC targeting RNA Polymerase II S5P in 40 days old Drosophilia gut

value: Drosophila 40 days old gut


title: 12XWT_Mxc_R1_(230704_BT_Dm_BT1998_268)

description: short histone array wing disc Mxc


title: DelB_HOM_3.1_RA

description:
Library name: DSP-1001660020586-A-D10
FFPE spatial transcriptome sequencing

value: delB/delB E17.5 right atrium


title: w_Mute_R1_(240222_BT_Dm_2579_mute)

description: wildtype wing disc Mute

value: wildtype


title: HeLa siAMD1 siSCR cells, plate 2

city: Derio

first: Arkaitz

last: Carracedo

address: Bizkaia Science and Technology Park, building 801A

country: Spain

institute: CIC bioGUNE

description:
2x125 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_HeLa_siAMD.txt
HeLa_noDOX_2

data_processing:
RNA-seq  reads were aligned usig Vast-tools v2.5.1 to identify alternative splicing events.
Aligned reads from single and paired datasets were merged with Vast-tools v2.5.1.
Differentially spliced events were identified using Matt v.1.3.0 with a minimum abs(deltaPSI) > 10% and a Wilcoxon p-value < 0.01 after excluding events with PSIRANGE_ALL = NA and LENGTH= 0.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text file includes PSI values for each sample

source_name: HeLa

growth_protocol: DNEM, 15% fetal bovine serum, 2 mM glutamine, 1 x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was extracted using NucleoSpin RNA isolation kit from Macherey-Nagel.
RNA libraries were prepared using Illumina Stranded mRNA Library Prep Kit following manufacture's protocol.

treatment_protocol: Mice in a mixed background were housed under controlled environmental conditions, such as time-controlled lighting on standard 12:12 light: dark cycles, controlled temperature at 22 ± 2ºC and 30-50% relative humidity. Mice were fed regular chow diet ad libitum and fasted for 6 h prior to tissue harvest (9 am-3 pm) to prevent metabolic alterations due to immediate food intake.

value: HeLa

value: Cervical carcinoma

value: Control


title: 12XWT_H3K27ac_R2_(230704_BT_Dm_BT1997_217)

description: short histone array wing disc H3K27ac

value: short histone array

value: anti-H3K27ac Epicypher 13-0058


title: RNAPIIS5P_CUTAC_1dayold_rep3_(231223_SL_Dm_masked_transposons_S5P_1do_560)

description:
Library name: RNAPIIS5P_CUTAC_1dayold_rep3
CUTAC targeting RNA Polymerase II S5P in 1 day old Drosophilia gut

value: Drosophila 1 day old gut

value: RNAP2Ser5P Cell Signaling Technology cat# 13523


title: RNAPIIS5P_CUTAC_1dayold_rep2_(231223_SL_Dm_masked_transposons_S5P_1do_559)

description:
Library name: RNAPIIS5P_CUTAC_1dayold_rep2
CUTAC targeting RNA Polymerase II S5P in 1 day old Drosophilia gut


title: DelB_HOM_2.2_SAN_Hcn4neg

description:
Library name: DSP-1001660020586-A-D08
FFPE spatial transcriptome sequencing

value: homozygous mutant


title: sci-mtChIL-seq, embryo-14, MyoD-RNAPolII

value: embroy

value: MyoD-RNAPolII


title: 12XWT_Mxc_R2_(230704_BT_Dm_BT1999_269)

description: short histone array wing disc Mxc

value: wing imaginal disc

value: male


title: 12XWT_uH2A_R2_(230704_BT_Dm_BT1996_H106)

description: short histone array wing disc uH2A

value: anti-uH2A CST D27C4


title: DelB_HOM_2.2_RA

description:
Library name: DSP-1001660020586-A-D07
FFPE spatial transcriptome sequencing


title: HeLa siAMD1 siSCR cells, plate 4

description:
2x125 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_HeLa_siAMD.txt
HeLa_noDOX_4


title: DelB_HOM_2.1_SAN_Hcn4pos

description:
Library name: DSP-1001660020586-A-D06
FFPE spatial transcriptome sequencing

value: delB/delB HCN4-high E17.5 sinus node


title: sci-mtChIL-seq, embryo-12, H3K27me3-RNAPolII


title: 12XWT_H3K9me2_R3_(230704_BT_Dm_BT1994_H1)

description: short histone array wing disc H3K9me2

value: anti-H3K9me2 EMD Millipore 05-1249


title: 12XWT_RNAPII-S5p_R2_(230704_BT_Dm_BT1993_P51)

description: short histone array wing disc RNAPII-S5p

value: anti-RNAPII-S5p CST D9N5I


title: sci-mtChIL-seq, embryo-11, MyoD-RNAPolII


title: HeLa siAMD1 cells, DOX 48 hours, plate 1

description:
2x125 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_HeLa_siAMD.txt
HeLa_48H_1

value: Doxycycline (100 ng/mL) for 48 hours


title: sci-mtChIL-seq, embryo-08, H3K27me3-RNAPolII


title: DelB_HOM_1.2_SAN_Hcn4neg

description:
Library name: DSP-1001660020586-A-D02
FFPE spatial transcriptome sequencing

value: delB/delB HCN4-low E17.5 sinus node


title: HeLa siAMD1 siSCR cells, plate 1

description:
2x125 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_HeLa_siAMD.txt
HeLa_noDOX_1

value: HeLa

value: Cervical carcinoma


title: DelB_HOM_2.1_SAN_Hcn4neg

description:
Library name: DSP-1001660020586-A-D05
FFPE spatial transcriptome sequencing


title: sci-mtChIL-seq, embryo-10, H3K27me3-RNAPolII, H3K4me3-RNAPolII, MyoD-RNAPolII


title: DelB_HOM_2.1_RA

description:
Library name: DSP-1001660020586-A-D04
FFPE spatial transcriptome sequencing

value: delB/delB E17.5 right atrium


title: HeLa siAMD1 cells, DOX 48 hours, plate 4

description:
2x125 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_HeLa_siAMD.txt
HeLa_48H_4


title: sci-mtChIL-seq, embryo-09, H3K27me3-RNAPolII


title: DelB_HOM_1.2_SAN_Hcn4pos

description:
Library name: DSP-1001660020586-A-D03
FFPE spatial transcriptome sequencing


title: DelB_HOM_1.2_RA

description:
Library name: DSP-1001660020586-A-D01
FFPE spatial transcriptome sequencing


title: 12XWT_H3K9me2_R2_(230628_BT_Dm_BT1965_H1)

description: short histone array wing disc H3K9me2

value: short histone array


title: sci-mtChIL-seq, embryo-07, H3K4me3-RNAPolII, MyoD-RNAPolII

value: H3K4me3-RNAPolII, MyoD-RNAPolII


title: 12XWT_Mute_R1_(230522_BT_Dm_BT1945_mute)

description: short histone array wing disc Mute

value: anti-Mute


title: sci-mtChIL-seq, embryo-06, H3K27me3-RNAPolII


title: mid_organoids8644018

city: London

first: George

middle: Thomas

last: Hall

address: Zayed Centre for Research, 20 Guilford Street

department: UCL Great Ormond Street Institute of Child Health

country: United Kingdom

institute: University College London

library_source: transcriptomic single cell

data_processing:
Spatial transcriptomics: Raw intensities files were processed using 10X Genomics' SpaceRanger v2.1.0. Fastq files were generated with `mkfastq`, and processed files with `count`.
Single cell Transcriptomics:Fastq files were processed using 10X Genomics CellRanger 3.1.0 with "cellranger count". For fetal midbrain samples, the paths to the multiple FASTQ files generated from the library subdivisions were specified in the "--fastqs" argument.
Assembly: Spatial transcriptomics: 10X Genomics' genome build: GRCh38-2020-A. Single-cell transcriptomics: Pre-built human reference 3.0.0, GRCh38 (Ensembel release 93)
Supplementary files format and content: Spatial transcriptomics: Spaceranger count spatial directory. Paraphrased from https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs: aligned_fiducials.jpg: shows which fiducial spots on the slide were detected by spaceranger; detected_tissue_image.jpg: shows the section of tissue detected by spaceranger; scalefactors_json.json: relative scales of user-supplied images; spatial_enrichment.csv: Moran's I values for each expressed feature; tissue_hires_image.png: high-resolution image of the tissue; tissue_lowres_image.png: low-resolution image of the tissue; tissue_positions.csv: table with information about each spot; barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene expression matrix files.
Supplementary files format and content: Single-cell transcriptomics: CellRanger count output with the files accounting for filtered feature-barcode matrices for each GEM well in "gz" compressed format.

source_name: 3D in vitro models at day 120 of differentiation (Pool 3)

extract_protocol:
For spatial transcriptomics: Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat. For single-cell transcriptomics: samples were dissociated, treated with papain, equilibrated with 02:C02, minced, PBS wahed, dissociated again, triturated and finally pelleted
For spatial transcriptomics: Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction. For single-cell transcriptomics: single cell suspensions were prepared and processed using the Chromium Single Cell 3’ Reagent Kits v3

value: Organoids

value: Control1-3D, Control2-3D, Patient1-3D, Patient2-3D

value: Dopaminergic lineage


title: DelB_HOM_1.1_SAN_Hcn4pos

description:
Library name: DSP-1001660020586-A-C12
FFPE spatial transcriptome sequencing

value: homozygous mutant


title: mid_organoids8644017

source_name: 3D in vitro models at day 120 of differentiation (Pool 2)


title: sci-mtChIL-seq, embryo-04, H3K27me3-RNAPolII, H3K4me3-RNAPolII

value: embroy

value: H3K27me3-RNAPolII, H3K4me3-RNAPolII


title: sci-mtChIL-seq, embryo-05, H3K4me3-RNAPolII, MyoD-RNAPolII


title: 12XWT_H3K27ac_R1_(230522_BT_Dm_BT1940_217)

description: short histone array wing disc H3K27ac

value: wing imaginal disc

value: male

value: anti-H3K27ac Epicypher 13-0058


title: DelB_HOM_1.1_SAN_Hcn4neg

description:
Library name: DSP-1001660020586-A-C11
FFPE spatial transcriptome sequencing


title: 12XWT_uH2A_R1_(230522_BT_Dm_BT1943_H106)

description: short histone array wing disc uH2A

value: anti-uH2A CST D27C4


title: 12XWT_H3K36me3_R1_(230522_BT_Dm_BT1942_283)

description: short histone array wing disc H3K36me3

value: anti-H3K36me3 Epicypher 13-0058


title: DelB_HOM_1.1_RA

description:
Library name: DSP-1001660020586-A-C10
FFPE spatial transcriptome sequencing


title: mid_organoids8644016

source_name: 3D in vitro models at day 120 of differentiation (Pool 1)

value: Control1-3D, Control2-3D, Patient1-3D, CrisprPatient2-3D


title: HeLa siAMD1 cells, DOX 48 hours, plate 2

description:
2x125 paired-end sequence reads
INCLUSION_LEVELS_FULL_hg38-8_HeLa_siAMD.txt
HeLa_48H_2

value: HeLa

value: Cervical carcinoma

value: Doxycycline (100 ng/mL) for 48 hours


title: mid_organoids8643922

source_name: 2D and 3D in vitro models at day 70 of differentiation (Pool 3)

value: 2D, Organoids

value: Control1-3D, Control2-2D, Patient1-3D, Patient2-3D


title: sci-mtChIL-seq, embryo-03, MyoD-RNAPolII

value: MyoD-RNAPolII


title: 12XWT_H3K27me3_R1_(230522_BT_Dm_BT1939_H128)

description: short histone array wing disc H3K27me3

value: short histone array

value: anti-H3K27me3 CST C36B11


title: TSPCs, VLDLR_Pos_3

city: 北京市

first: 美莲

last: 蔡

state: 北京市

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心

data_processing:
Data comparison, gene quantification, and cell identification were performed using CellRanger, the official 10X Genomics software.
DNASTAR Lasergene v15.0 (DNASTAR, Madison, WI)
Illunina’s bcl bcl2fastq v1.8.4 software (Illumina,San Diego, CA) was used to convert the resulting base calling (bcl) to FASTQ files. Mapping RNA-seq reads on the mouse genome were performed using DNASTAR Lasergene v15.0 (DNASTAR, Madison, WI) and reported using FPKM (fragments per kilobase of exon per pillion fragments mapped).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Tendon

growth_protocol: Col1α1+Vldlr+ and Col1α1+Vldlr- tendon stem/progenitor cells were sorted by flow cytometry.  Then the cells were maintained in DMEM supplemented with 20% fetal bovine serum(FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA were extracted using Trizol (Takara, 9109). 1 μg of total RNA were used to prepare the sequencing library
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Tendon

value: Col1{alpha}1+Vldlr+ TSPCs

value: tendon stem/progenitor cells


title: TSPCs, VLDLR_Pos_2

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心


title: 12XWT_H3K9me2_R1_(230522_BT_Dm_BT1936_H1)

description: short histone array wing disc H3K9me2

value: wing imaginal disc

value: anti-H3K9me2 EMD Millipore 05-1249


title: mid_organoids8643921

source_name: 2D and 3D in vitro models at day 70 of differentiation (Pool 2)

value: Control1-3D, Control2-2D, Patient1-3D, CrisprPatient2-3D

value: Dopaminergic lineage


title: sci-mtChIL-seq, embryo-01, MyoD-RNAPolII

value: embroy


title: mid_organoids8643920

source_name: 2D and 3D in vitro models at day 70 of differentiation (Pool 1)

value: Control1-2D, Control2-3D, Patient1-3D, Patient2-3D


title: mid_organoids8644114

source_name: 2D and 3D in vitro models at day 40 of differentiation (Pool 3)


title: 12XWT_RNAPII-S5p_R1_(230522_BT_Dm_BT1933_P51)

value: male

value: anti-RNAPII-S5p CST D9N5I


title: w_RNAPII-S5p_R1_(230404_BT_Dm_BT1781_P51)

description: wildtype wing disc RNAPII-S5p

value: wildtype


title: TSPCs, VLDLR_Neg_3

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心

value: Col1{alpha}1+Vldlr- TSPCs


title: sc-ChIL-seq, SP2-3, mix

data_processing:
The cell barcodes were made by modifing index sequences using seqkit (version 0.16.1)  and they were assigned to read sequences by umi_tools (version 1.1.1).
Adapter sequences were trimmed using Trim Galore (version 0.6.10) with the default options.
The paired-reads were mapped to the mm10 using bowtie2 (version 2.3.5.1) with the default options.
The reads uniquely mapped to autosome or sex chromosomes were extracted.
Duplicates were remove by R package GenomicRanges (version 1.54.1).
Assembly: mm10
Supplementary files format and content: The processed data fromat is BED. These indicate the position of unique fragments and column 3 indicates cell barcode.
Library strategy: sci-ChILseq

value: Mix (H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3, H3K36me3, H3.1/3.2, and RNA PolII)


title: w_H3K9me2_R1_(230404_BT_Dm_BT1778_H1)

description: wildtype wing disc H3K9me2


title: sc-ChIL-seq, SP2-2, mix


title: mid_organoids8644113

source_name: 2D and 3D in vitro models at day 40 of differentiation (Pool 2)

value: 2D, Organoids


title: TSPCs, VLDLR_Neg_2

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心


title: Gastrocnemius, SAM486A, 5

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-10_Gastro_SAM486A.txt
Gastro_SAM486A_10

source_name: Gastrocnemius

value: Gastrocnemius

value: Musculoskeletal

value: SAM486A (10 mg/kg/day) intraperitoneally for 8 days

value: Male


title: rel1 strain, V8, Replicate #3

city: Nanchang

first: Fanglin

last: Zheng

state: Jiangxi

address: 1519 Dongyue Avenue, Nanchang County, Jiangxi Province

department: The First Affiliated Hospital of Nanchang University

institute: Nanchang University

description: Library name: Sample 9

data_processing:
The clean reads were mapped to the reference strain JEC21α genome using HISAT2.
FPKM  of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Differential expression analysis was performed using the DESeq2.
The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).
Assembly: ASM9104v1 (JEC21α)
Supplementary files format and content: Tab-delimited text fle includes raw counts for each Sample
Supplementary files format and content: Text files include FPKM values for each Sample

organism: Cryptococcus deneoformans

source_name: Yeast and hyphae cells

growth_protocol: The wild type XL280 strain was cultured under mating repressing (YPD) and mating inducing (V8) conditions for 24 h respectively, the rel1 deletion mutant was cultured under mating inducing (V8) condition for 24 h.

extract_protocol:
RNA was extracted using a commercial Ultrapure RNA kit (CWBIO, CW0581S) according to the manufacturer’s protocol. 1.0 μg of total RNA was used for the construction of sequencing libraries.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit following the manufacturer’s instructions. The libraries were sequenced on an Illumina Novaseq 6000  platform and 150 bp paired-end reads were generated.

value: Yeast and hyphae cells

value: MATalpha, rel1::NEO

value: Mating inducing


title: TSPCs, VLDLR_Neg_1

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心

value: Tendon

value: tendon stem/progenitor cells


title: w_H3K9me3_R1_(220819_BT_Dm_BT1175_H28)

description: wildtype wing disc H3K9me3

source_name: wing imaginal disc

value: wing imaginal disc

value: anti-H3K9me3 Abcam ab8898


title: mid_organoids8644112

source_name: 2D and 3D in vitro models at day 40 of differentiation (Pool 1)

value: Control1-2D, Control2-3D, Patient1-3D, Patient2-3D

value: Dopaminergic lineage


title: w_H3K9me1_R1_(230404_BT_Dm_BT1777_H126)

description: wildtype wing disc H3K9me1

value: male

value: wildtype

value: anti-H3K9me1 Epicypher 13-0029


title: HUDEP-2_CBS_MCC_rep2

description: Library name: sample2

data_processing:
Adaptor sequences were trimmed from raw sequencing data using Cutadapt (v4.4).
The trimmed reads were then processed with HiC-Pro (v 3.1.0) without specifying the GENOME_FRAGMENT parameter.
The interaction loops were subsequently called using hichipper (v0.7.7) and converted into longrange file format for visulization.
Assembly: hg38
Supplementary files format and content: bedpe format
Library strategy: Capture-C

source_name: cell line

extract_protocol:
After two rounds of enrichment with biotin-labeled probes and stringent washing, DNA was directly amplified on Strepavidin beads.
Libraries were amplified using Herculase II Fusion DNA Polymerase and size selected with SPRIselect beads.

value: cell line

value: human erythroid progenitor cells


title: sci-mtChIL-seq, embryo-02, H3K4me3-RNAPolII

value: embroy


title: rel1 strain, V8, Replicate #2

description: Library name: Sample 8


title: TSPCs, VLDLR_Pos_1

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心

value: Col1{alpha}1+Vldlr+ TSPCs


title: Gastrocnemius, SAM486A, 4

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-10_Gastro_SAM486A.txt
Gastro_SAM486A_9

value: Gastrocnemius

value: Musculoskeletal

value: SAM486A (10 mg/kg/day) intraperitoneally for 8 days

value: Male


title: w_H3K27me3_R1_(220819_BT_Dm_BT1173_H128)

description: wildtype wing disc H3K27me3

value: anti-H3K27me3 CST C36B11


title: rel1 strain, V8, Replicate #1

description: Library name: Sample 7

value: Yeast and hyphae cells

value: MATalpha, rel1::NEO

value: Mating inducing


title: w_uH2A_R1_(220406_BT_Hs_BT827_H106)

description: wildtype wing disc uH2A

value: wing imaginal disc

value: anti-uH2A CST D27C4


title: Gastrocnemius, SAM486A, 3

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-10_Gastro_SAM486A.txt
Gastro_SAM486A_8


title: XL280 strain, V8, Replicate #2

description: Library name: Sample 5

value: MATalpha, wild type


title: Gastrocnemius, SAM486A, 1

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-10_Gastro_SAM486A.txt
Gastro_SAM486A_6


title: HUDEP-2_CBS_MCC_rep1

description: Library name: sample1


title: sc-ChIL-seq, SP2-1, mix

value: Mix (H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3, H3K36me3, H3.1/3.2, and RNA PolII)


title: w_H3K36ne3_R1_(220406_BT_Hs_BT826_H4)

description: wildtype wing disc H3K36me3

value: male

value: wildtype

value: anti-H3K36me3 Epicypher 13-0058


title: w_RNAPII_(220119_BT_Dm_BT542_P222)

description: wildtype wing disc RNAPII

value: anti-RNAPII Covance MMS-126R


title: Visium retina (Columba livia), biological replicate 1

description:
Library name: 42
10x Genomics Visium Spatial Gene Expression v1, 55 µm resolution

organism: Columba livia

source_name: Eye

value: Eye


title: Gastrocnemius, Veh,  5

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-10_Gastro_SAM486A.txt
Gastro_Vehicle_5

value: Gastrocnemius

value: Control


title: Gastrocnemius, Veh,  3

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-10_Gastro_SAM486A.txt
Gastro_Vehicle_3

value: Musculoskeletal


title: 8h-PD-2

city: Hannover

first: Felix

last: Polten

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hanover Medical School

description:
Library name: N6512
N6512_quant sf

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422.
Raw data were processed and quality-controlled using the nf-core/rnaseq RNA sequencing analysis pipeline (version 3.9, SciLifeLab).
Normalization and differential expression analysis was performed on the internal Galaxy (version 20.05) instance of the RCU Genomics, Hannover Medical School, Germany with DESeq2 (Galaxy Tool Version 2.11.40.6) with default settings except for “Output normalized counts table”, which was set to “Yes” and all additional filters were disabled (“Turn off outliers replacement”, “Turn off outliers filtering”, and “Turn off independent filtering” set “Yes”).
Assembly: Genome reference and annotation data were obtained from https://www.gencodegenes.org/ (Homo sapiens, GRCh38.p14; release 46).
Supplementary files format and content: .gz are processed raw files as described above
Supplementary files format and content: .xlsx are processed pairwise comparisons as indicated

source_name: Human coronary artery endothelial cells

extract_protocol:
HCAECs were grown in 6 cm plates (Thermo Fisher Scientific , 3 × 105 cells per plate), stimulated for 8 hours, and lysed in RLT buffer (Qiagen).
The New England Biolabs NEBNext Poly(A) mRNA Magnetic Isolation Module was used for mRNA enrichment from 500 ng total RNA per sample. cDNA libraries were generated following the New England Biolabs NEB Next Ultra II workflow with 8 cycles of PCR. A DNA purification step was introduced at the end of the procedure using 1.2× Agencourt AMPure XP beads (Beckman Coulter). Fragment length distribution was monitored with the Bioanalyzer High Sensitivity DNA Analysis kit (Agilent). Libraries were quantified using the Qubit dsDNA HS Assay (Thermo Fisher Scientific). Individually barcoded libraries were pooled, denatured, diluted to 1.8 pmol l–1, and sequenced with an Illumina NextSeq 550 High Output Flowcell Kit (75 cycles) (20024906; Illumina), using the following settings: 38 bp each as sequence reads 1 and 2; 8 bp each as index reads 1 and 2. Samples obtained an average sequencing depth of 27 million reads.

value: Human coronary artery endothelial cells


title: Gastrocnemius, Veh,  4

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-10_Gastro_SAM486A.txt
Gastro_Vehicle_4

value: Male


title: 8h-PD-3

description:
Library name: N6513
N6513_quant sf


title: Single-cell RNA-seq retina (Taeniopygia guttata), biological replicate 6

description:
Library name: 40
10x Genomics Chromium Single Cell 3′ v3

data_processing:
Visium: Raw BCL files were converted to FASTQ using bcl2fastq. FASTQ files were processed with SpaceRanger v3.1.1 using the count pipeline and species-specific reference genomes (AnoCar3.1, TaeGut1, Cliv_2.1, GRCg7b). The outputs include filtered_feature_bc_matrix, spatial coordinates, histology images, and QC metrics. Chromium: FASTQ files were processed with CellRanger v7.1.0 using the count pipeline and the Taeniopygia guttata (TaeGut1) reference genome. The outputs include the filtered_feature_bc_matrix. No additional filtering, ambient RNA removal (e.g., SoupX), doublet removal, or further QC was performed before deposition.
Assembly: Anolis carolinensis — AnoCar3.1 Taeniopygia guttata — TaeGut1 Columba livia — Cliv_2.1 Gallus gallus — GRCg7b
Supplementary files format and content: Each sample is provided as a single compressed tar archive (sampleID.tar.gz). For Visium: contains filtered_feature_bc_matrix/ (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz), spatial/ (tissue_positions.csv, scalefactors_json.json), histology image (.tif), and QC metrics (metrics_summary.csv). For Chromium: contains filtered_feature_bc_matrix/ (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz) and optional per-cell metadata (metadata.csv if available).

organism: Taeniopygia guttata

source_name: Retina

value: Retina


title: XL280 strain, YPD, Replicate #2

description: Library name: Sample 2

source_name: Yeast cells

value: Yeast cells

value: Mating repressing


title: Gastrocnemius, SAM486A, 2

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-10_Gastro_SAM486A.txt
Gastro_SAM486A_7

value: SAM486A (10 mg/kg/day) intraperitoneally for 8 days


title: 8h-BRK+PD-3

description:
Library name: N6515
N6515_quant sf


title: 8h-VEGFA-3

description:
Library name: N6516
N6516_quant sf


title: XL280 strain, V8, Replicate #3

description: Library name: Sample 6

value: Yeast and hyphae cells

value: Mating inducing


title: Single-cell RNA-seq retina (Taeniopygia guttata), biological replicate 5

description:
Library name: 39
10x Genomics Chromium Single Cell 3′ v3


title: XL280 strain, YPD, Replicate #1

description: Library name: Sample 1

value: MATalpha, wild type


title: 8h-BRK+PD-2

description:
Library name: N6514
N6514_quant sf


title: Gastrocnemius, Veh,  2

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-10_Gastro_SAM486A.txt
Gastro_Vehicle_2


title: OPC, Hippocampus, GABA, repeat3

data_processing:
Clean reads after filtering were aligned to the reference genome with HISAT.
Bowtie2 were used to align the clean reads to the reference genes.
Differential expression analysis was performed using DESeq2.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: xlsx file includes normalized read count.

source_name: Hippocampus

growth_protocol: For Cultured OPC, OPC were isolated and cultured in OPC proliferation medium for 2 days, followed by 200 uM GABA or 200 uM Glutamate treatment for 24 h, then subjected to RNA sample collection by Trizol.

extract_protocol:
For acute-isolated OPC, Mice were anesthetized and transcardially perfused with ice-cold HBSS. The brains were isolated with the meninges removed, followed by dissection of the cortex and hippocampus, which were then minced and digested by 1% papain. OPCs were isolated from the resulting cell suspension via immunopanning and directly lysed on the panning plate by Trizol.
Poly-A selected method was used to prepare the RNA-seq library. Sequencing was performed on the DNBSEQ platform with SE50 sequencing length

value: Hippocampus

value: Cultured OPC

value: wild type

value: GABA treatment


title: XL280 strain, V8, Replicate #1

description: Library name: Sample 4


title: XL280 strain, YPD, Replicate #3

description: Library name: Sample 3


title: Single-cell RNA-seq retina (Taeniopygia guttata), biological replicate 4

description:
Library name: 38
10x Genomics Chromium Single Cell 3′ v3


title: 8h-VEGFA-2

description:
Library name: N6505
N6505_quant sf


title: Gastrocnemius, Veh,  1

description:
2x150 paired-end sequence reads
INCLUSION_LEVELS_FULL_mm10-10_Gastro_SAM486A.txt
Gastro_Vehicle_1


title: 8h-BRK-3

description:
Library name: N6511
N6511_quant sf


title: 8h-Kontrolle-3

description:
Library name: N6510
N6510_quant sf


title: 8h-BRK+PD-1

description:
Library name: N6503
N6503_quant sf


title: KO rep3

first: Haibo

last: Zhou

state: Shanghai

address: Shangdong Middle street

institute: Renji Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using HISAT2 (Kim et al., 2015;Pertea et al., 2016).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using StringTie(Pertea et al., 2016).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample.

source_name: Bone marrow

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogen) and determined by Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).
Next-generation libraries of mRNA-seq were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

value: Bone marrow

value: Primary hematopoietic stem cell

value: Hematopoietic stem cell


title: 8h-VEGFA-1

description:
Library name: N6504
N6504_quant sf


title: KO rep1


title: OPC, Hippocampus, GABA, repeat1


title: OPC, Hippocampus, repeat3


title: OPC, Hippocampus, repeat2


title: Single-cell RNA-seq retina (Taeniopygia guttata), biological replicate 2

description:
Library name: 36
10x Genomics Chromium Single Cell 3′ v3


title: WT rep3


title: 8h-BRK-2

description:
Library name: N6501
N6501_quant sf


title: OPC, Hippocampus, repeat1

description: Hip


title: Single-cell RNA-seq retina (Taeniopygia guttata), biological replicate 1

description:
Library name: 34
10x Genomics Chromium Single Cell 3′ v3


title: Visium retina (Taeniopygia guttata), biological replicate 4

description:
Library name: 28
10x Genomics Visium Spatial Gene Expression v1, 55 µm resolution

value: Eye