title: ATAC_H9_mature

data_processing:
QC: FastQC v0.11.5. Sequenced reads were then trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
RNAeq Alignment: TopHat v2.1.1 for RNASeq, Bowtie2 for ATACseq
RNAseq normalization: Cufflinks v2.2.1
ATACseq sorting, normalization, and visualization: MACS2
Assembly: hg19
Supplementary files format and content: RNASeq: Normalized Counts in .csv
Supplementary files format and content: ATACseq: genome browser tracks in .bedGrap

extract_protocol:
The cells were washed with 1× PBS and lysed in TRIzol (Invitrogen, 15596026) following the manufacturer's protocol for RNAseq. The cells were washed with 1× PBS and nuclear DNA was extract  using Qiagen PCR DNA purification kit (Qiagen, 28106).
For RNAseq, the quality of RNA samples was assessed using the 2100 Bioanalyzer (Agilent Technologies), and 1,000 ng of total RNA was used to generate cDNA libraries using the Next Ultra II RNA Library Prep Kit (New England BioLabs, E7770) following the manufacturer's instructions. For ATACseq,  DNA was directly amplified using NEBNext Q5 Hot Start HiFi PCR Master Mix (New England BioLabs, M0543L) and Nextera primers for library preparation.

value: Hepatocyte-like cells


title: Lib13_SkinWound

status: Public on Dec 31 2025

type: SRA

city: New York

first: Dr. Shruti

last: Naik

state: NY

address: 1425 Madison Ave

department: Immunology and Immunotherapy

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: 13.F30810W.SW
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

library_source: other

data_processing:
The final library was sequenced on Illumina® Nextseq™ with a P1 reagent kit (600 cycles). The sequencing was performed with 30% PhiX spike-in.
QIIME2 pipeline (version: 2024.5) (PMID: 31341288) was used for training the classifier and for all downstream analysis of 16s data. Paired end demultiplexed FASTQ files were first imported into QIIME2 workflow, using import function with data type set to ‘SampleData[PairedEndSequencesWithQuality]’ and input format set to ‘PairedEndFastqManifestPhred33V2’. The data was denoised with DADA2 (PMID: 27214047) to trim and truncate reads to remove low quality reads. Output from DADA2 denoising included representative sequences, features table and DADA2 denoising stats.
New classifier was trained specifically for V1-V3 region of Bacterial genome using Silva 138 database (PMID: 23193283). The representative sequences were then tabulated to generate read counts using feature table function to generate feature counts tabulations based on the sample metadata. The representative reads / sequences were also aligned to the custom classifier generated for V1-V3 region and output taxonomic classifications were generated. The taxonomy data was then used to tabulate read counts and an output taxa bar plot was generated using the condition column from metadata to group the samples.
The taxonomy and feature data output from QIIME2 was then imported into an R programming environment and mia package (doi:10.18129/B9.bioc.mia) was used for subsequent analysis. ImportQIIME2 function was used to import the data into R. The imported microbiome data was stored in TreeSummarizedExperiment object in R.
Feature table and Taxonomic mapping were extracted from TreeSummarizedExperiment object in R.
Assembly: V1-V3 bacterial genomic region
Supplementary files format and content: Feature table with raw read counts (no normalization) stored in .csv file format.
Supplementary files format and content: Taxonomic mapping for features found in the read counts file, stored in .csv file format.
Library strategy: 16S rRNA-seq

molecule: other

organism: human skin metagenome

source_name: Skin wound

extract_protocol:
ZymoBIOMICS® DNA Miniprep Kit (Zymo Research, Irvine, CA) was used for low biomass samples such as skin swabs, as it permits for a lower elution volume, resulting in more concentrated DNA samples.
Bacterial 16S ribosomal RNA gene targeted sequencing was performed using the Quick-16S™ NGS Library Prep Kit (Zymo Research, Irvine, CA). The bacterial 16S primers amplified the V1-V3 region of the 16S rRNA gene. These primers have been custom-designed by Zymo Research to provide the best coverage of the 16S gene while maintaining high sensitivity.  The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned with the Select-a-Size DNA Clean & Concentrator™ (Zymo Research, Irvine, CA), then quantified with TapeStation®(Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA).

tag: tissue

value: Skin wound

tag: injury time

tag: Sex

value: f

tag: site

value: finger

tag: injury type

value: scratch

tag: age


title: Cerebellum nucleus PostNB, replicate 4

city: Urbana

first: Boxuan

last: Zhao

state: IL

address: 505 S Goodwin Ave

institute: UIUC

description:
Library name: cseq34.1 CN_Post_nb
cseq34_CN1
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode

data_processing:
Raw sequencing data was processed using Cell Ranger (v7.1.0) with custom genome references including SynBar and Cre genes. Nuclear libraries were processed using force-cells parameter of actual loaded amount, while synaptosomal libraries used expect-cells parameter of actual loaded amount. Barcode sequences were extracted from filtered nuclear and unfiltered synaptosomal BAM files using custom Python scripts. Sequences were collapsed using Hamming distance 1 within samples to account for sequencing errors.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

organism: Mus musculus

source_name: Cerebellum

extract_protocol:
After perfusion with ice-cold PBS, target brain regions (right one-third cerebellum or bilateral pons) were dissected, homogenized in SET buffer (sucrose, Tris-HCl, EDTA, protease and RNase inhibitors), and centrifuged to separate nuclear (P1) and synaptosomal (S1) fractions. Nuclei were isolated from P1 by brief rinsing and resuspension in nuclear lysis buffer, followed by homogenization (cerebellum) or gentle mixing (pons), dilution, incubation on ice, filtration, centrifugation, washing, and staining with SiR-DNA in washing and staining buffer prior to flow cytometry. Synaptosomes were isolated from S1 by centrifugation to obtain synaptosomal pellet (P2), which was resuspended in washing and staining buffer, blocked with Fc receptor blocker, stained with anti-V5-Alexa Fluor 647 and anti-HA-PE antibodies, washed, and incubated with CellBrite 405 membrane dye. Nuclei were sorted by DNA content (SiR-DNA) and GFP expression, while synaptosomes were sorted based on scatter profiles, membrane integrity (CellBrite 405), and double-positivity for V5 and HA, and all sorted samples were collected into tubes containing appropriate collection buffers for downstream processing.
Libraries were generated using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, Chromium Next GEM Chip G, and 10x Chromium Controller (10x Genomics) according to manufacturer's protocol with modifications. For each experiment, approximately 20,000-30,000 individually sorted GFP-positive nuclei or double-positive synaptosomes were loaded into each channel of the chip. For nuclear libraries, cDNA was amplified, size-selected using SPRIselect beads to separate transcriptome and barcode components, and independently constructed into mRNA libraries and barcode libraries. Synaptosome libraries were constructed using barcode-specific amplification without template switching oligonucleotides.

value: Cerebellum

tag: genotype

tag: library type

value: NB


title: NPC cells, BIHi269-B, control, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

description:
Library name: 269B_10um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_269B_10um_DRUG_06B

library_source: transcriptomic

data_processing:
The DNB library was then paired-end sequenced on the DNBSEQ-500 platform (DNBSEQ Technology, BGI, Beijing, China) with a read length of 150 bp. After removing of the sequencing adapters, the resulting FASTQ files were finally filtered for the desired length of 150 bp and for quality scores of Phred+33. FASTQ files were aligned to the human genome (GeneCode GRCh38.p14_47) using STAR v2.7.11a with the following settings: --runThreadN 36 --outReadsUnmapped Fastx --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --seedSearchStartLmax 75 --outFilterMatchNmin 250 --alignSoftClipAtReferenceEnds No --outSAMattrIHstart 0 --alignEndsType EndToEnd --twopassMode Basic. The resulting *.bam file was sorted and indexed using samtools v1.17.
The sorted *.bam file was passed to StringTie v2.2.1 with the following settings: -u -p 36. The resulting *.gtf files were merged using stringtie merge and normalized read counts (TPM and FPKM) were generated using stringtie ballgown. The read counts of all experimental samples were then concatenated into a single table: output.tpm.csv and output.fpkm.csv.
Assembly: GeneCode GRCh38.p14_47
Supplementary files format and content: Stringtie ballgown output files: *.cov.refs.ballgown.gtf => contains details of the transcripts that StringTie assembles from RNA-Seq data in the GTF format; *.gene_abund.ballgown.tab => contains gene abundance counts as normalized FPKM and TPM values as a CSV table; *.out.ballgown.gtf => This is a file listing all the transcripts in the reference annotation that are fully covered, end to end, by reads. The output format is a GTF file as described above. Each line of the GTF is corresponds to a gene or transcript in the reference annotation.
Supplementary files format and content: FPKM_joined.tab, FPKM_joined.csv, TPM_joined.tab, TPM_joined.csv => fused tables with all the samples of the experiment in CSV and EXCEL format provided as TPM and FPK values.

molecule: polyA RNA

organism: Homo sapiens

source_name: NPC generated from iPSC

growth_protocol: Neuronal Progenitor Cells (NPCs) were generated from iPSCs from controls and of patients with MT-ATP6 mutations using a protocol described by Zink et al., 2021 (https://doii.org/10.21769/BioProtoc.3939). NPCs were then maintained on Geltrex [Thermo Fisher Scientific, Gibco, #A1413302]-coated 6-well plates at 37°C and 5% CO2 with media changes every other day according to the published protocol from Reinhardt et al., 2013 (https://doi.org/10.1371/journal.pone.0059252) and Zink et al., 2021. NPCs were maintained in 4.5 mM glucose-containing media consisting of the following components: 0.5x Neurobasal without glucose [Thermo Fisher Scientific, Waltham, MA, USA, Gibco, A2477501], 0.5x DMEM/F12 without glucose [Elabscience, EP-CM-L0128], 0.5x N2 [Thermo Fisher Scientific, Gibco, #17502-048], 0.5x B27 without vitamin A [Thermo Fisher Scientific, Gibco #12587010], 2 mM L-Glutamine [Invitrogen, 25030-02425], 1x MycoZap Plus-CL [Lonza, Basel, Switzerland, #VZA-2012] with the addition of 0.5 µM PMA [Miltenyi Biotech, #130-104-465], 3 µM CHIR 99021 [Cayman Chemical, Ann Arbor, MI, USA, #13122], 150 µM ascorbic acid [Sigma-Aldrich, St. Louis, MO, USA, #A92902], 0.115 mM sodium pyruvate [Thermo Fisher Scientific, Gibco, #11360070]  and 4.5 mM glucose [Sigma-Aldrich, #G-5400].

extract_protocol:
RNA was purified using the NucleoSpin RNA Plus kit (Macherey-Nagel, Düren, Germany, #740984) and eluted in 30 µL RNase-free H2O. The RNA concentration was measured using the NanoDrop 2000 photometer and aliquots of 1-2 µg RNA were snap-frozen in liquid nitrogen and stored at -80°C.
The construction of the eukaryotic strand-specific transcriptome library was performed according to the „DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing“ protocol of the  Beijing Genetics Institute (BGI). Briefly, 500 ng total RNA was enriched for polyA-carrying molecules using oligo-dT beads. The RNA was then fragmented and the first cDNA strand was synthesized using random primers. Second strand cDNA was synthesized using dUTP instead of dTTP and the synthesized cDNA was subjected to end repair and 3' adenylation. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments, which were then amplified by PCR. After quality control, the library was circularized and amplified to produce DNA nanoballs (DNBs).

treatment_protocol: NPCs were seeded at a density of 500,000 cells/well in neural progenitor medium containing 4.5 mM glucose on Geltrex-coated or Matrigel-coated 6-well plates and incubated at 37°C and 5% CO2 with medium change every other day. After reaching 70% confluence, the medium was supplemented with 0.1% DMSO (vehicle) or 1 µM or 10 µM Sildenafil (Selleckchem, Cologne, Germany, #S4684) dissolved in 0.1% DMSO and incubated at 37°C and 5% CO2 for 6 or 24 hours (in triplicates). Control cells were grown without additives (in triplicate). At the end of the incubation period, the medium was aspirated and the cells were washed twice with Dulbecco's Phosphate-Buffered Saline (DPBS). Cells were then rapidly scraped in 1 mL DPBS. The cell suspension was collected in a 1.5 mL Eppendorf tube and centrifuged at 8,000 x g for 5 minutes at 4°C. The supernatant was aspirated and the cell pellet was flash-frozen in liquid nitrogen and stored at -80°C.

value: NPC generated from iPSC

tag: cell line

tag: cell type

value: Neuronal precursor cells (NPCs)

value: wildtype

tag: treatment

tag: biological replicate


title: Lib13_ContralateralSkin

description:
Library name: 13.F30810W.CS
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

source_name: Contralateral skin

value: Contralateral skin


title: ATAC_H1_mature

city: Guangzhou

first: Jian

last: Tu

state: Guangdong

address: #58 Zhongshan second road

country: China

institute: The First Affliated Hospitap of Sun Yat-sen University

library_source: genomic

molecule: genomic DNA


title: Cerebellum synaptosome PostNB, replicate 3

description:
Library name: cseq31 Syn_Post_nb
cseq31_Spost
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: ATAC_H9_HPC

value: Hepatic progenitor cells


title: Lib12_SkinWound

description:
Library name: 12.F2487W.SW
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: cut


title: NPC cells, BIHi269-B, control, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: 269B_10um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_269B_10um_DRUG_06A


title: NPC cells, BIHi267-B, MILS patient, vehicle [0.1% DMSO] treated for 24 hours, replicate 3

description:
Library name: 267B_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_267B_DMSO_24C

value: m.9176T>G (heteroplasmy 98.0%)

value: 0.1% DMSO for 24 hours


title: Cerebellum synaptosome PreNB, replicate 3

description:
Library name: cseq31 Syn_Pre_nb
cseq31_Spre
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: ATAC_H1_HPC


title: Pons nucleus PreNB, replicate 3

description:
Library name: cseq31 PN_Pre_nb
cseq31_PN
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode

source_name: Pons

value: Pons


title: Pons nucleus mRNA, replicate 3

description:
Library name: cseq31 PN_mRNA
cseq31_PN
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence

library_source: transcriptomic single cell

value: mRNA


title: Lib11B_SkinWound

description:
Library name: 11.F2383W.B.SW
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.


title: NPC cells, BIHi267-B, MILS patient, vehicle [0.1% DMSO] treated for 24 hours, replicate 2

description:
Library name: 267B_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_267B_DMSO_24B


title: ATAC_H9_endoderm

value: Definitive endoderm


title: NPC cells, BIHi267-B, MILS patient, vehicle [0.1% DMSO] treated for 24 hours, replicate 1

description:
Library name: 267B_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_267B_DMSO_24A


title: ATAC_H1_mature_2

value: Hepatocyte-like cells


title: ATAC_H1_endoderm


title: Cerebellum nucleus PostNB, replicate 3

description:
Library name: cseq31 CN_Post_nb
cseq31_CN
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode


title: Lib12_ContralateralSkin

description:
Library name: 12.F2487W.CS
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: f


title: NPC cells, BIHi267-B, MILS patient, vehicle [0.1% DMSO] treated for 6 hours, replicate 3

description:
Library name: 267B_DMSO_06C
Column_name in FPKM_joined.tab: FPKM_267B_DMSO_06C

value: 0.1% DMSO for 6 hours


title: Lib11B_ContralateralSkin

description:
Library name: 11.F2383W.B.CS
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: finger


title: ATAC_H9_hESC

value: HESC


title: Cerebellum nucleus mRNA, replicate 3

description:
Library name: cseq31 CN_mRNA
cseq31_CN
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence

value: Cerebellum


title: ATAC_H1_hESC_2


title: Lib11_ContralateralSkin

description:
Library name: 11.F2382W.Control
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.


title: Lib11_SkinWound

description:
Library name: 11.F2382W.SW
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: Skin wound


title: NPC cells, BIHi267-B, MILS patient, vehicle [0.1% DMSO] treated for 6 hours, replicate 2

description:
Library name: 267B_DMSO_06B
Column_name in FPKM_joined.tab: FPKM_267B_DMSO_06B

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)


title: Cerebellum synaptosome PostNB, replicate 2

description:
Library name: cseq25 Syn_Post_nb
cseq25_Spost
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.

value: NB


title: Lib10_SkinWound

description:
Library name: 10.F36724AA.SW
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: puncture


title: ATAC_H1_hESC_1


title: RUES2_D21

molecule: total RNA

tag: time


title: Pons nucleus PreNB, replicate 2

description:
Library name: cseq25 PN_Pre_nb
cseq25_PN
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode


title: Lib10_ContralateralSkin

description:
Library name: 10.F36724AA.CS
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: Contralateral skin


title: NPC cells, BIHi267-B, MILS patient, untreated for 24 hours, replicate 3

description:
Library name: 267B_basal_24C
Column_name in FPKM_joined.tab: FPKM_267B_basal_24C

value: m.9176T>G (heteroplasmy 98.0%)

value: no additives for 24 hours


title: Cerebellum synaptosome PreNB, replicate 2

description:
Library name: cseq25 Syn_Pre_nb
cseq25_Spre
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: NPC cells, BIHi267-B, MILS patient, untreated for 24 hours, replicate 2

description:
Library name: 267B_basal_24B
Column_name in FPKM_joined.tab: FPKM_267B_basal_24B


title: RUES2_D9

value: Hepatic progenitor cells


title: Pons nucleus mRNA, replicate 2

description:
Library name: cseq25 PN_mRNA
cseq25_PN
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence

value: Pons

value: mRNA


title: RUES2_D4

value: Definitive endoderm


title: Lib1A_SkinWound

description:
Library name: 1.0629M35A.SW
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: m


title: NPC cells, BIHi267-B, MILS patient, untreated for 24 hours, replicate 1

description:
Library name: 267B_basal_24A
Column_name in FPKM_joined.tab: FPKM_267B_basal_24A


title: Lib1B_ContralateralSkin

description:
Library name: 1.0629M35A.CSx
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.


title: RUES2_D0


title: NPC cells, BIHi267-B, MILS patient, untreated for 6 hours, replicate 3

description:
Library name: 267B_basal_06C
Column_name in FPKM_joined.tab: FPKM_267B_basal_06C

value: no additives for 6 hours


title: Cerebellum nucleus mRNA, replicate 2

description:
Library name: cseq25 CN_mRNA
cseq25_CN
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence


title: HES2_D21

value: Hepatocyte-like cells


title: Lib1A_ContralateralSkin

description:
Library name: 1.0629M35A.CS
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: finger


title: NPC cells, BIHi267-B, MILS patient, vehicle [0.1% DMSO] treated for 6 hours, replicate 1

description:
Library name: 267B_DMSO_06A
Column_name in FPKM_joined.tab: FPKM_267B_DMSO_06A

value: 0.1% DMSO for 6 hours


title: Cerebellum synaptosome PostNB, replicate 1

description:
Library name: cseq1 Syn_Post_nb
cseq1_Spost
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.

value: Cerebellum


title: NPC cells, BIHi267-B, MILS patient, untreated for 6 hours, replicate 1

description:
Library name: 267B_basal_06A
Column_name in FPKM_joined.tab: FPKM_267B_basal_06A

value: NPC generated from iPSC


title: Cerebellum synaptosome PreNB, replicate 1

description:
Library name: cseq1 Syn_Pre_nb
cseq1_Spre
single-synaptosome RNA-seq (ssRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode
Since only the neuronal barcodes, and not the mRNA, were sequenced for the synaptosomes, the feature.tsv files for the ssRNA-seq samples are empty.


title: Lib9_SkinWound

description:
Library name: 9.F20721H.SW
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: Skin wound

value: f

value: hand

value: cut


title: NPC cells, BIHi267-B, MILS patient, untreated for 6 hours, replicate 2

description:
Library name: 267B_basal_06B
Column_name in FPKM_joined.tab: FPKM_267B_basal_06B

value: Neuronal precursor cells (NPCs)

value: m.9176T>G (heteroplasmy 98.0%)


title: HES2_D4


title: NPC cells, BIHi267-B, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 3

description:
Library name: 267B_1um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_267B_1um_DRUG_24C


title: Pons nucleus PreNB, replicate 1

description:
Library name: cseq1 PN_Pre_nb
cseq1_PN
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode

value: NB


title: HES2_D9

value: Hepatic progenitor cells


title: HES2_D0

value: HESC


title: Lib9_ContralateralSkin

description:
Library name: 9.F20721H.CS
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: Contralateral skin


title: Pons nucleus mRNA, replicate 1

description:
Library name: cseq1 PN_mRNA
cseq1_PN
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence

value: Pons

value: mRNA


title: Lib1B_SkinWound

description:
Library name: 1.0629M35A.SWx
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: m

value: puncture


title: H9_D21

value: Hepatocyte-like cells


title: NPC cells, BIHi267-B, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 1

description:
Library name: 267B_1um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_267B_1um_DRUG_24A


title: Lib8_ContralateralSkin

description:
Library name: 8.M26720SA.C
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: finger


title: Lib8_SkinWound

description:
Library name: 8.M26720SA.Wound
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.


title: NPC cells, BIHi267-B, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 2

description:
Library name: 267B_1um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_267B_1um_DRUG_24B

value: NPC generated from iPSC


title: Cerebellum nucleus PostNB, replicate 1

description:
Library name: cseq1 CN_Post_nb
cseq1_CN
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode

value: Cerebellum


title: Cerebellum nucleus PostNB, replicate 2

description:
Library name: cseq25 CN_Post_nb
cseq25_CN
single-nucleus RNA-seq (snRNA-seq)
Neuronal barcode (NB)
NB library: read 1 file contains cell barcode and UMI; read 2 file contains neuronal barcode


title: H9_D9


title: Cerebellum nucleus mRNA, replicate 1

description:
Library name: cseq1 CN_mRNA
cseq1_CN
single-nucleus RNA-seq (snRNA-seq)
polyA RNA
mRNA: read 1 file contains cell barcode and UMI; read 2 file contains transcript sequence


title: H9_D4

value: Definitive endoderm


title: NPC cells, BIHi267-B, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: 267B_1um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_267B_1um_DRUG_06B


title: Lib7_ContralateralSkin

description:
Library name: 7.714M26SA.Control
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: forehead

value: blister


title: EAE_Spleen_DC_CLEC16A_KO_library

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description:
Library name: EAE_Spleen_DC_CLEC16A_KO
Dendritic Cells Isolated by FACS sorting from the spleens of EAE induced CLEC16A condition knockout mice

data_processing:
scRNA-Seq data was demultiplexed and quantified using the Cellranger multi function (GRCm38 reference genome), generating a count matrix for each scRNA-Seq sample; cells with more than 500 genes detected and less than 25% mitochondrial contents were retained for analysis.
Assembly: GRCm38
Supplementary files format and content: RDS format of Seurat Objects, which contains the metadata information and the count matrix for all the libraries

source_name: Spleen

extract_protocol:
For single cell RNA-sequencing, CNS cells from n=3 Control EAE and n=3 CLEC16AGFAP EAE (Day 23) were hashed before FACS sorting using multiplex 3’ Cell Plex Set Kit A (#100261, 10x Genomics).  After sorting and washing,  astrocytes from 6 samples were pooled and loaded into one well of a 10X Chromium Next GEM Chip G (10X Genomics).
Single-cell libraries were further generated using the Single Cell 3’ Reagent Kit v3.1 chemistry (10x Genomics) using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (PN-1000128) according to the manufacturer’s protocol. The generated scRNA-seq libraries were sequenced by NOVA-Seq S1 at the Broad Institute.

value: Spleen

value: Dendritic Cells

value: CLEC16A Knockout


title: H9_D0


title: EAE_CNS_DC_CLEC16A_KO_library

description:
Library name: EAE_CNS_DC_CLEC16A_KO
Dendritic Cells Isolated by FACS sorting from the brains of EAE induced CLEC16A condition knockout mice

source_name: CNS

value: CNS


title: Lib6_SkinWound

description:
Library name: 6.M33713W.SW
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: Skin wound

value: hand

value: cut


title: NPC cells, BIHi267-B, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 3

description:
Library name: 267B_10um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_267B_10um_DRUG_24C

value: Neuronal precursor cells (NPCs)

value: m.9176T>G (heteroplasmy 98.0%)


title: Lib7_SkinWound

description:
Library name: 7.714M26SA.Wound
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: m


title: NPC cells, BIHi267-B, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 2

description:
Library name: 267B_10um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_267B_10um_DRUG_24B


title: Lib5_SkinWound

description:
Library name: 5.M38712WH.Skin.wound
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: knee

value: scratch


title: Lib6_ContralateralSkin

description:
Library name: 6.M33713W.CS
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: Contralateral skin


title: Lib5_ContralateralSkin

description:
Library name: 5.M38712WH.Control
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.


title: H1_D4


title: 3h_NAA_Stem_3

city: Olomouc

first: Ales

last: Pecinka

address: Šlechtitelů 31

country: Czech Republic

institute: Institute of Experimental Botany of the AS CR

data_processing:
Illumina RTA3 was used for basecalling and .cbcl files were converted to .fastq using bcl2fastq2 Conversion Software v2.20
Sequenced reads were trimmed for adaptor sequence and low-quality sequence and then mapped to Morex v2 whole genome using hisat2 v2.0.5 with default parameters. Hisat2 output was converted and sorted by samtools view and samtools sort, respectively.
The number of reads falling in the exons of transcripts were counted using subread v1.5.2 with parameters -p -t exon -g Parent.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated in Excel using standard formula. In short number of reads falling in the exons were normalized by the size of transcript and by the size of the library.
Genome_build: Morex V2 by Masher et al. 2019
Supplementary_files_format_and_content: Tab-delimited text file including RAW counts for each Sample
Supplementary_files_format_and_content: Excel table including RAW counts for each Sample, calculated MEAN, SD and FPKM values

organism: Hordeum vulgare

source_name: Crown

growth_protocol: Barley grains were washed for 30sec in 70% EtOH, surface sterilized for 5 min in 3% sodium hypochloride soultion then extensively rinsed in distilled water. Grains were placed on wet filter paper containing 50 µM NPA (Naphthylphthalamic acid, inhibitor of polar auxin transport) in sealed Petri dishes, vernalized for 3 days at 4°C. Germination was induced by transfering petri dished in controlled condition (13h/11h; 16°C/13°C; day/night). After 3 days, germinated seedlings with 2cm-long roots are transfered to a mini-hydropony system containg ½ Hoagland + 50 µM NPA and grown in the same conditions as for germination. After 3 days, the solution was changed to ½ Hoagland containing 50 µM 1-NAA (1-Naphthaleneacetic acid). After 24h of treatments, plantlets were transfered to  ½ Hoagland.

extract_protocol:
Crowns (2 mm-long junction between roots and stem) were excised from roots and stem, and flash frozen in liquid nitrogen. Each samples represent a pool of 5 crowns. RNA was harvested using Trizol reagent protocol modified for starch-rich samples (Wang et al. 2012. Isolation of High Quality RNA from Cereals Seeds containing high levels of starch. Phytochemical analysis: PCA. 23. 159-63. 10.1002/pca.1337). An additional DNAseI treatment was performed before further proceeding. 1 µg of total RNA was used for the construction of sequencing libraries with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, after mRNA enrichment with Poly(A) mRNA Magnetic Isolation Module. Fragment sizes were around 300-400 bp. Libraries were indxed using NEBNext Multiplex Oligos for Illumin (96 Unique Dual Index Primer Pairs). Sequencing was performed on a NovaSeq6000 platform on S1 flow-cell with 2x150bp pair-ended reads.
RNA libraries were prepared using standard NEB protocols for Illumina sequencing

treatment_protocol: Seedlings were grown in hydropony in ½ Hoagland containg 50 µM synthetic auxin (1-NAA), crowns were harvested before treatment, then after 30 min, 1h and 3h.

tag: cultivar

value: Golden Promise

value: 2mm-long junction roots/stem

value: 3 h after 1-NAA induction


title: H1_D0

value: HESC


title: H1_D9

value: Hepatic progenitor cells


title: Lib4_SkinWound

description:
Library name: 4.F35712WH.B.SW.B
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: f

value: finger


title: NPC cells, BIHi267-B, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: 267B_1um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_267B_1um_DRUG_06C

value: NPC generated from iPSC


title: NPC cells, BIHi267-B, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: 267B_10um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_267B_10um_DRUG_06C


title: 3h_NAA_Stem_2


title: NPC cells, BIHi267-B, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: 267B_10um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_267B_10um_DRUG_06B


title: Lib4_ContralateralSkin

description:
Library name: 4.F35712WH.B.Control.B
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.


title: 3h_NAA_Stem_1


title: NPC cells, BIHi267-B, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: 267B_10um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_267B_10um_DRUG_06A


title: DMSO-treated

type: RNA

city: Hachioji-shi

first: Takahio

last: Ohashi

state: Tokyo

address: 7-1, Minamiosawa 4-chome

country: Japan

institute: Zenyaku Kogyo Co., Ltd.

hyb_protocol: Following fragmentation and labeling, 2.3 µg of sense-strand cDNA were hybridized for 16 hr at 45°C on Clariom S Human Array (Thermo Fisher Scientific). Arrays were washed and stained using the GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: RMA

label: biotin

source_name: MDA-MB-468 cells following 6-hour DMSO treatment

label_protocol: A total of 250 ng of total RNA per sample was used. Fragmentation and labeling of cDNA were performed using the GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: MDA-MB-468 cells were cultured in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) and 100 μg/mL kanamycin sulfate (Thermo Fisher Scientific) at 37 °C in a 5% CO2 incubator.

extract_protocol: RNA was harvested using the RNAeasy Mini Kit (QIAGEN).

treatment_protocol: MDA-MB-468 cells were exposed to adriamycin (HY-15142, Nacalai Tesque) or paclitaxel (Merck) at concentrations of 10 to 140 nM and 2 to 320 nM, respectively, to establish drug-resistant cell lines. Surviving cells were designated as adriamycin-resistant and paclitaxel-resistant MM468 cells.

value: Breast Cancer cell


title: NPC cells, BIHi267-B, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: 267B_1um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_267B_1um_DRUG_06A


title: Lib3_ContralateralSkin

description:
Library name: 3.F35712WH.ControlA
V1V3 16S rRNA sequencing of contralateral control skin. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.


title: H1_D21

value: Hepatocyte-like cells


title: ZSTK3744-treated

source_name: MDA-MB-468 cells following 6-hour ZSTK3744 (1 μM) treatment


title: Lut_3

city: Shanghai

first: qian

last: yu

address: 1665 Kong Jiang Road

institute: Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: Sample6

data_processing:
DNBs were transformed to single end 50 bases reads and sequencing on BGISEQ-500 platform (BGI-Shenzhen, China).
We used SOAPnuke (v1.5.2) to filter reads and generate FASTQ format
Then aligned clean reads to the reference mouse genome using the Bowtie2 (v2.2.5) with default parameters
calculated gene expression level with RSEM (v1.2.12)
Assembly: mm9
Supplementary files format and content: In GO analysis and pathway analysis, DEGs were classified according to official classification with the GO or KEGG annotation results and phyper (a function of R) was performed in GO and pathway functional enrichment.
Supplementary files format and content: processed data.xlsx

source_name: Cornea

extract_protocol:
Isolated the whole cornea, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 days vehicle-control treated or luteolin -control treated after benzalkonium chloride (BAC)-induced experimental dry eye model and then isolated the whole cornea

value: Cornea

value: multiple

value: 10 days luteolin -control treated after benzalkonium chloride (BAC)-induced experimental dry eye model


title: Lib3_SkinWound

description:
Library name: 3.F35712WH.A.SW
V1V3 16S rRNA sequencing of skin wound. Natural acute skin wounds from healthy volunteers were collected at New York University Langone Health under protocols approved by the Institutional Review Board (IRB #s23-00620). For each participant, wounded and contralateral skin sites were washed with soap one hour prior to sampling. Swabs were collected using the BD ESwab™ collection and transport system. Ambient air samples served as internal controls.

value: Skin wound


title: 40d_per01_gut_2

city: Beijing

first: Pengfei

last: Lv

address: No. 2, Old Summer Palace West Road

institute: China agricultural university

description: Library name: old_per01_gut_2

data_processing:
Raw sequencing data were processed and quality-controlled using fastp (default parameters). Subsequently, RNA-seq reads were mapped to the Drosophila melanogaster (dm6) reference genome (https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/) using hisat2 with default parameters. RNA-seq counts were generated using featureCounts, and differential expression analysis was performed using the R package DESeq2 with a threshold of FDR < 0.05 and |log2(fold change)| > 1.
Assembly: dm6
Supplementary files format and content: The CSV file contains the raw read counts for each sample.

organism: Drosophila melanogaster

source_name: gut

growth_protocol: Mated males were collected and maintained at 20 flies per vial at 25°C under 60% humidity and a 12-hour light/12-hour dark cycle. Flies were transferred to new vials every other day.

extract_protocol:
Following collection at ZT8 from age-appropriate flies, head and gut samples were dissected in 1X PBS, homogenized in TRIzol Reagent (Vazyme, Cat# R401-01), and subsequently processed for RNA extraction and RNA-seq analysis.
Following quality control, eukaryotic mRNA was enriched using oligo(dT) beads that bind to the poly-A tail via A-T complementarity. The mRNA was then fragmented, and first-strand cDNA was synthesized using random hexamers. Second-strand cDNA was generated using buffer, dNTPs, and DNA polymerase I, followed by purification with AMPure XP beads. The purified double-stranded cDNA underwent end repair, A-tailing, and sequencing adapter ligation. Fragments of appropriate size were selected again with AMPure XP beads, and the final cDNA library was amplified via PCR.

value: gut

value: Day 40


title: 40d_per01_gut_1

description: Library name: old_per01_gut_1


title: 40d_per01_gut_3

description: Library name: old_per01_gut_3


title: Lut_2

description: Library name: Sample5


title: NPC cells, BIHi267-B, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 1

description:
Library name: 267B_10um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_267B_10um_DRUG_24A

value: Neuronal precursor cells (NPCs)

value: m.9176T>G (heteroplasmy 98.0%)


title: 40d_orco2_gut_3

description: Library name: old_orco2_gut_3


title: Group 9

city: Isparta

first: Berrin

last: Ozdil

address: Cunur

department: Histology and Embryology

country: Turkey

institute: Suleyman Demirel University

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: GAPDH
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., test groups/control group) ratios.

label: SYBR Green

source_name: Glioblastoma test

label_protocol: PCR assays were performed using the cell lines and the Roche custom  panel following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the  Roche cDNA kit. Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: astrocytic cell line

tag: activation agent

value: cancerous cell test

value: 72 hrs


title: Group 8

description: Test


title: 1h_NAA_Stem_1

value: Golden Promise

value: 2mm-long junction roots/stem

value: 1h after 1-NAA induction


title: Lut_1

description: Library name: Sample4


title: Veh_3

description: Library name: Sample3

value: 10 days vehicle-control treated after benzalkonium chloride (BAC)-induced experimental dry eye model


title: Group 7

description: Test


title: 40d_orco2_gut_1

description: Library name: old_orco2_gut_1


title: 05h_NAA_Stem_2

value: 30 min after 1-NAA induction


title: Veh_2

description: Library name: Sample2


title: Group 6

description: Test


title: 05h_NAA_Stem_1


title: Group 5

description: Test


title: Veh_1

description: Library name: Sample1


title: 40day_w1118_gut_2

description: Library name: old_w1118_gut_2


title: 1h_NAA_Stem_3


title: PPSKO3

description: Library name: Sample6

growth_protocol: no

extract_protocol:
Corneal keratocytes were sorted by FACS, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Prrx1-creERT;Ptch1 and ctrl mice (10 weeks-old) were gave 3 dose of TAM and then sorted keratocytes from cornea

value: Keratocytes

value: Stromal cells

value: 3 dose of TAM treat for 1 month


title: Group 4

description: Test


title: 1h_NAA_Stem_2


title: Group 3

description: Test


title: 40day_w1118_gut_1

description: Library name: old_w1118_gut_1


title: 0h_NPA_Stem_2

value: before induction (control)


title: 40d_orco2_gut_2

description: Library name: old_orco2_gut_2


title: PPSKO1

description: Library name: Sample4

value: Cornea


title: 40day_orco2_head_2

description: Library name: old_orco2_head_2

source_name: head

value: head


title: PPSKO2

description: Library name: Sample5


title: Group 2

description: Test

source_name: Glioblastoma

value: cancerous cell


title: 0h_NPA_Stem_1


title: 05h_NAA_Stem_3


title: HD11 cells, Dextran 3

city: Yangzhou

first: Xuming

last: Hu

state: Jiangsu

address: No.48 East Wenhui Road

department: College of Animal Science and Technology

institute: Yangzhou University

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5)
The clean data were mapped to the reference genome by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5)
The expression level of genes was calculated by RSEM (v1.3.1)
Assembly: GCF_000002315.6_GRCg6a
Supplementary files format and content: txt file includes raw counts, TPMs, FPKMs for each Sample
Supplementary files format and content: The Excel file includes FPKM values for each Sample

organism: Gallus gallus

growth_protocol: The chicken macrophage cell line HD11 were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) with 5% foetal bovine serum (FBS) at 41°C in 5% CO2 and 95% humidity.

extract_protocol:
Total RNA was extracted from chicken cells or tissues using RNA-easy™ Isolation Reagent (Vazyme, Nanjing, China) according to the ‘manufacturer’s recommendations
The mRNA Library for RNA-seq was preparated by BGI Genomics Co.,Ltd

value: macrophages

value: Dextran


title: PPSWT3

description: Library name: Sample3


title: 40day_w1118_head_2

description: Library name: old_w1118_head_2

value: Day 40


title: 40day_w1118_gut_3

description: Library name: old_w1118_gut_3

value: gut


title: PPSWT2

description: Library name: Sample2


title: Astrocyte

description: Control

source_name: Astrocyte

value: astrocytic cell line

value: control cell

value: 72 hrs


title: HD11 cells, Dextran 2


title: 40day_w1118_head_1

description: Library name: old_w1118_head_1


title: HD11 cells, Dextran 1


title: PPSWT1

description: Library name: Sample1


title: 0h_NPA_Stem_3

value: Golden Promise

value: 2mm-long junction roots/stem


title: 3day_orco2_head_2

description: Library name: young_orco2_head_2

value: Day 3


title: KO_3

description: Library name: Sample6

extract_protocol:
Corneal Epithelial cells were separate by EDTA treatment, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Prrx1-creERT;Ptch1 and ctrl mice (10 weeks-old) were gave 3 dose of TAM and then separated Epithelial cells from cornea

value: Epithelial cells

value: 3 dose of TAM treat for 2 months


title: HD11 cells, Control 3

value: Control


title: 3day_orco2_head_1

description: Library name: young_orco2_head_1


title: FvADS-1,ketoconazole,rep2

city: Tianjin

first: Yajing

last: Yin

address: No. 409 Guangrong Road

institute: Tianjin University of Commerce

description:
Library name: sample8
column name in FPKMs_allSamples.xls:FvADS-1_ketoconazole_rep2

data_processing:
Sequencing was performed on the DNBSEQ‑G400 platform. Raw reads were filtered using BGI’s in‑house software SOAPnuke (v1.4.0; parameters: ‑l 15 ‑q 0.2 ‑n 0.1) to remove adapter‑contaminated reads, reads with >5% unknown bases (N), and low‑quality reads. Clean reads were then aligned to the reference genome using HISAT2 (v2.1.0; parameters: ‑‑dta ‑‑phred64 ‑‑unstranded ‑‑new‑summary ‑x index ‑1 read_r1 ‑2 read_r2).
Assembly: GCF_000149555.1_ASM14955v1
Supplementary files format and content: Microsoft excel files include FPKM values for each sample

organism: Fusarium verticillioides

source_name: deletion

growth_protocol: 107 conidia were inoculated in YPD liquid medium and cultured at 28°C with shaking (200 rpm) for 20 h.

extract_protocol:
The mycelia were treated with or without 2 μg/mL KTC for 16 h. After harvest, the mycelia were finely grounded into powder in liquid nitrogen. RNA was extracted according to standard TRIzol method (Invitrogen, Carlsbad, CA, United States), followed by high-throughput RNA sequencing (RNA-seq) analysis of the samples that passed quality control.
The library was constructed from total RNA by mRNA enrichment or rRNA depletion, followed by fragmentation, reverse transcription, and double‑stranded cDNA synthesis. After end‑repair, A‑tailing, and bubble adapter ligation, the products were PCR‑amplified and converted into single‑stranded circular DNA for sequencing.

treatment_protocol: Then the mycelia were treated with or without 2 μg/mL KTC for 16 h.

value: deletion

value: FvADS-1 deletion

value: ketoconazole


title: FvADS-1,ketoconazole,rep1

description:
Library name: sample7
column name in FPKMs_allSamples.xls:FvADS-1_ketoconazole_rep1


title: HD11 cells, Control 2


title: 40day_orco2_head_1

description: Library name: old_orco2_head_1

value: head


title: KO_2

description: Library name: Sample5

value: Cornea


title: FvADS-1,control,rep2

description:
Library name: sample6
column name in FPKMs_allSamples.xls:FvADS-1_control_rep2

value: control


title: KO_1

description: Library name: Sample4


title: HD11 cells, Control 1

value: macrophages


title: 3day_w1118_head_1

description: Library name: young_w1118_head_1


title: Group 1

description: Test

source_name: Astrocyte test

value: control cell test


title: FvADS-1,control,rep1

description:
Library name: sample5
column name in FPKMs_allSamples.xls:FvADS-1_control_rep1


title: WT_M3

first: Zhan

last: Ding

address: 300 Feng Lin Road

institute: CAS Center for Excellence in Molecular Plant Sciences

data_processing:
The adapter sequences were removed from raw reads by cutadapt (version 1.15).
Clean reads from RNA-seq were quality filtered, and then mapped to the human genome (hg38) and Drosophila melanogaster genome (dm6) by STAR.
Assembly: dm6
Supplementary files format and content: Supplementary files format and content: tab-delimited text files include TPM values for mRNA samples.

source_name: whole body

extract_protocol:
Total RNAs from the human and Drosophila cells and tissues were isolated by TRIzol (Sigma) and treated with RNase-free DNase I (Invitrogen). For RT-PCR, reverse transcription was performed using PrimeScript RT reagent Kit with gDNA Eraser (TaKaRa) and the obtained cDNA was amplified by 2×Hieff PCR Master Mix (Yeasen). the construction of cDNA libraries and sequencing were performed using Illumina HiseqXten-PE150 by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole body

tag: strain

value: control strain

value: male


title: WT_3

description: Library name: Sample3


title: Drosophila heads,WT,29˚C

first: jianquan

last: Ni

address: Shuangqing Road 30

institute: Tsinghua University

description:
Library name: control_29
Column name in gene_count.xls: control

data_processing:
reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat (v2.2.1).
Assembly: dm6
Supplementary files format and content: txt file includes raw count for each sample
Supplementary files format and content: txt file includes FPKM for each sample

source_name: brain

growth_protocol: Flies were kept in 25 ℃ for nomal conditions, while flies were kept in 18 ℃ and transferred to 29 ℃ after cross to induce the conditional overexpression of histone H1.

extract_protocol:
RNA was extracted by Trizol approach. 1 μg total RNA was used for the construction of sequencing libraries.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: Flies were kept in standard recipe food with 4g/L concentration of Levodopa for the treatment of Levodopa for 7 days. To conditionally overexpress H1, the Elav-temperature sensitive driver crossed with H1 overexpression strain under 18 ℃, the progenis were transferred to 29 ℃ for 7 days.

value: brain

value: Wilde type


title: Drosophila heads,Levodopa,29˚C

description:
Library name: Levodopa_29
Column name in gene_count_29.xls:Levodopa

value: Levodopa, 29˚C


title: WT_2

description: Library name: Sample2

value: Epithelial cells


title: WT_M2


title: FvWT,ketoconazole,rep2

description:
Library name: sample4
column name in FPKMs_allSamples.xls:FvWT_ketoconazole_rep2

source_name: WT

value: WT


title: WT_M1


title: WT_1

description: Library name: Sample1

value: 3 dose of TAM treat for 2 months


title: FvWT,control,rep2

description:
Library name: sample2
column name in FPKMs_allSamples.xls:FvWT_control_rep2


title: Lung tissue, HE3

city: Zhuzhou

first: Ziyu

last: He

state: Hunan

address: Tianyuan district

institute: Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)
(1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12)
Differential expression analysis was performed using the DESeq (v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO and KEGG enrichment analysis of annotated different expressed gene was performed by Phyper based on Hypergeometric test.
The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni
Assembly: Mus_musculus NCBI GCF_000001635.26_GRCm38.p6
Supplementary files format and content: excel files include read count values for each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Lung

value: Exercise slow down the hypoxia-induced pulmonary hypertension


title: Drosophila heads,Levodopa,25˚C

description:
Library name: Levodopa
Column name in all.fpkm_anno.xls: Levodopa

value: Levodopa, 25˚C


title: FvWT,control,rep1

description:
Library name: sample1
column name in FPKMs_allSamples.xls:FvWT_control_rep1


title: 3day_w1118_head_2

description: Library name: young_w1118_head_2

value: head

value: Day 3


title: Lung tissue, HE2


title: Lung tissue, HE1


title: 7_5

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

description: Library name: 7_5

data_processing:
reads were quality filterred by rcorrector and Trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Physcomitrium patens_v6.1
Supplementary files format and content: sf files generated by Salmon software, include TPM values

organism: Physcomitrium patens

source_name: Physcomitrium patens chloronema

growth_protocol: Cultures were grown for 1 month at 22 °C under 16/8-h light/dark periods at a light intensity of 75 µmol m-2 s-1

extract_protocol:
RNeasy Plant MiniKit (Qiagen)
KAPA HyperPrep kit (Roche)

treatment_protocol: Modified Knop medium with 1% Plant Agar and 300mM NaCl

value: Physcomitrium patens chloronema

value: Grandsen 2004

tag: batch


title: 7_4

description: Library name: 7_4

tag: tissue


title: WT_F1

value: female


title: w1118, D10, ZT4, GFP, CUT&RUN, Rep 3

city: West Lafayette

first: Sarah

last: McGovern

state: IN

address: Department of Biochemistry

department: Biochemistry

institute: Purdue University

data_processing:
Read trimming with Trimmomatic version 0.39
Alignment with Bowtie2 version 2.5.1, dovetail mates considered concordant
Indexing, generation of BAM files using Samtools version 1.8
CPM-normalized bigWigs generated with deepTools version 3.5.4
Assembly: BDGP6.46
Supplementary files format and content: bigWig files, CPM-normalized

source_name: outer photoreceptors

growth_protocol: Flies were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle. 200 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated ZTs (ZT4, ZT12, ZT16).

extract_protocol:
Photoreceptor nuclei were immunoenriched using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by CUT&RUN (dx.doi.org/10.17504/protocols.io.zcpf2vn). For CUT&RUN, 1 ug of either anti-GFP antibody (Abcam ab6556), or IgG (EpiCypher CUTANA IgG Negative Control Antibody) was used.  MNase digestion was performed for 5 min using 1 ug of antibody.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina. Modifications to the library preperation were made to preserve short DNA fragments generated in TF CUT&RUN (dx.doi.org/10.17504/protocols.io.bagaibse).
CUT&RUN

value: outer photoreceptors

tag: time (zt)

tag: antibody

value: GFP

value: M


title: KO_M3

value: whole body

value: enox deletion strain

tag: Sex

value: male


title: Lung tissue, Hy3


title: 7_2

description: Library name: 7_2


title: Lung tissue, Hy4


title: KO_M2


title: FvWT,ketoconazole,rep1

description:
Library name: sample3
column name in FPKMs_allSamples.xls:FvWT_ketoconazole_rep1

value: ketoconazole


title: w1118, D10, ZT4, GFP, CUT&RUN, Rep 2


title: KO_M1


title: KO_F3


title: Drosophila heads,H1 overexpression,29˚C

description:
Library name: H1OE_29
Column name in gene_count_29.xls: H1OE

value: brain

value: H1 overexpression

value: H1 overexpression, 29˚C


title: 3_2

description: Library name: 3_2


title: WT_F3

value: control strain


title: 3_3

description: Library name: 3_3


title: Lung tissue, Hy2

value: Lung

value: WT

value: Exercise slow down the hypoxia-induced pulmonary hypertension


title: w1118, D10, ZT4, IgG, CUT&RUN, Rep 3

value: IgG


title: Lung tissue, Hy1


title: w1118, D10, ZT4, IgG, CUT&RUN, Rep 2


title: WT_F2


title: 3_1

description: Library name: 3_1

value: Physcomitrium patens chloronema

value: Grandsen 2004


title: KO_F2

value: female


title: Drosophila heads,WT,25˚C

description:
Library name: control
Column name in all.fpkm_ano.xls: control

value: Wilde type

value: No, 25˚C


title: Lung tissue, C3


title: 11_6

description: Library name: 11_6


title: Lung tissue, C2


title: CYCGFP, D50, ZT16, GFP, CUT&RUN, Rep 3

value: outer photoreceptors

value: GFP

value: M

value: w; PBac{y[+mDint2] w[+mC]=cyc-GFP.FPTB}VK00037/+; P{w[+mC]=[UAS-GFP-Msp3 00KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]/+


title: w1118, D10, ZT4, IgG, CUT&RUN, Rep 1


title: KO_F1

value: whole body

value: enox deletion strain


title: 11_4

description: Library name: 11_4


title: F16_M3

value: enox-Motif deletion strain

value: male


title: 11_2

description: Library name: 11_2


title: Lung tissue, C1

value: Lung


title: 1_6

description: Library name: 1_6

value: WT


title: F16_M2


title: CYCGFP, D50, ZT16, GFP, CUT&RUN, Rep 2


title: UN_fibroblast_rep 3

city: Shenzhen

first: Jiajie

last: Lin

address: 3025# Shennan Road

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

data_processing:
Reads containing adaptor contamination, low-quality reads and those with an unknown base ratio of more than 5% were filtered out using SOAPnuke (v1.5.6) to generate clean reads. The clean reads were then mapped to GRCm38 using HISAT2 (v2.0.4). RSEM (v1.3.1) was employed to calculate the expression level of gene, and differentially expressed genes were analyzed using the DESeq2(v1.4.5) with |log2Fold Change| > 1 and Q value < 0.05.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes read counts for each sample

source_name: Fibroblast

extract_protocol:
Total RNA was extracted from mouse tendon entheseal fibroblasts using TRIzol according to the manufacturer’s instructions. RNA integrity was evaluated using the Agilent Bioanalyzer 2100 system.
cDNA library was constructed and paried-end 150-base reads were generated by the Beijing Genomics Institute using the BGISEQ-500 platform

value: Fibroblast

value: un-diseased


title: CYCGFP, D50, ZT16, IgG, CUT&RUN, Rep 3

value: IgG


title: w1118, D10, ZT4, GFP, CUT&RUN, Rep 1


title: F16_M1


title: F16_F3


title: 1_4

description: Library name: 1_4

value: Physcomitrium patens chloronema

value: Grandsen 2004


title: UN_fibroblast_rep 1


title: 1_5

description: Library name: 1_5


title: CYCGFP, D50, ZT16, GFP, CUT&RUN, Rep 1


title: CYCGFP, D50, ZT16, IgG, CUT&RUN, Rep 2


title: NTS_fibroblast_rep 3

value: diseased


title: F16_F2

value: female


title: CYCGFP, D50, ZT16, IgG, CUT&RUN, Rep 1

value: outer photoreceptors


title: CYCGFP, D50, ZT12, GFP, CUT&RUN, Rep 3

value: GFP


title: F16_F1


title: NTS_fibroblast_rep 2


title: METTL3Mut rescue, HAT1-ChIP, rep2

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

institute: UC-Riverside

data_processing:
Raw reads were aligned to human hg38 reference genome using Bowtie2 (v2.4.5)
Genome coverage bigwig files for Integrative Genomics Viewer visualization were generated by deeptools (v3.5.1)48 bamCoverage using scale factors for the normalization
Heat maps were generated by deeptools (v3.5.1) computeMatrix and plotHeatmap.
Metegene profile was generated by deeptools (v3.5.1) computeMatrix and plotProfile
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
the cells were crosslinked with 1% formaldehyde at room temperature for 10 min with gentle shaking, and quenched with 125 mM glycine for 10 min. After washing with ice-cold PBS buffer for three times, the cells were resuspended in cell lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.5% NP-40, protease inhibitors) at 4°C on a rotator for 20 min. After centrifugation at 3000 g for 3 min, the pellets were resuspended in RIPA buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, protease inhibitors) and rotated at 4°C for 20 min, followed by a brief sonication on a Qsonica Sonicator q125 (42% amplitude, 10s on/10s off, 80 s). After incubation for another 20 min, cell lysate was sonicated on a Covaris S220 Sonicator for 6 min with a peak incident power of 140 W, a duty cycle of 10.1% and 200 cycles per burst at 4°C. After centrifugation at 4°C for 10 min, 50 µL of supernatant was saved as “Input” sample, and the rest of supernatant was subjected to IP experiment.
The DNA-sequencing library was prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions.

treatment_protocol: HEK293T and METTL3-/- cells were plated in 100 mm dishes at ~35% confluency a day before transfection. On the next day, the cells were transfected with empty vector, wild-type or D395A METTL3 plasmid.

value: Human embryonic kidney

tag: chip antibody

value: HAT1 (Invitrogen, 18HCLC)


title: NTS_fibroblast_rep 1


title: CYCGFP, D50, ZT12, IgG, CUT&RUN, Rep 3

tag: age

value: M

value: w; PBac{y[+mDint2] w[+mC]=cyc-GFP.FPTB}VK00037/+; P{w[+mC]=[UAS-GFP-Msp3 00KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]/+


title: METTL3Mut rescue, HAT1-ChIP, rep1


title: splenic CD4+CD25+ Treg cells, KI3

first: Weiqi

last: Zhang

address: 280 South Chongqing Road, Shanghai, China

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.6).
Assembly: GRCm38
Supplementary files format and content: csv file includes raw counts for each sample

source_name: spleen

extract_protocol:
Total RNA was extracted using TRIzol reagent (Ambion)
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. The PCR reaction system and program are configured and set up to amplify the product. The corresponding library quality control protocol will be selected depending upon product requirements. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: spleen

value: splenic CD4+CD25+ Treg cells

tag: genotype

value: Foxp3V408M Knock-in


title: METTL3WT rescue, HAT1-ChIP, rep2


title: Donor 4 MePyr [metabolism_panel]

city: Rochester

first: Adebowale

last: Bamidele

state: Minnesota

address: Medicine, 200 First Street SW, Guggenheim 10

department: Medicine

institute: Mayo Clinic

hyb_protocol: Total RNA  was hybridized with the NanoString nCounter Human Autoimmune Profiling Panel, which includes Reporter and Capture probe pairs for targeted immune-related gene transcripts. Hybridization was performed according to the manufacturer's protocol (NanoString Technologies), involving  hybridization at 65°C for 16 hours (without enzymatic amplification). The Reporter Probes carry fluorescent barcodes for digital counting, while the biotin-labeled Capture Probes facilitate immobilization on a streptavidin-coated cartridge. No additional labeling was performed.

scan_protocol: Post-hybridization processing and data collection were performed using the nCounter Prep Station and Digital Analyzer.

data_processing: Raw RCC files were imported into nSolver Analysis Software, and data were background-corrected, normalized to internal positive controls and housekeeping genes, and log2-transformed before analysis.

source_name: naïve CD4 T cells

growth_protocol: Human naive cells were differentiated into effector Th1 cells in cRPMI 1640 media (RPMI 1640 + L-Glutamine [Gibco] supplemented with 10% FCS, 10 mmol/L HEPES pH 7.4, 1 mmol/L sodium pyruvate, 2 mmol/L L-glutamine, 1% non-essential amino acids, penicillin, streptomycin, and 50 µmol/L β-mercaptoethanol)

extract_protocol: Total RNA was extracted with Rneasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.

value: Th1 cells

value: MePyr

tag: sample group

value: Test


title: splenic CD4+CD25+ Treg cells, KI2


title: CYCGFP, D50, ZT12, GFP, CUT&RUN, Rep 2


title: UN_fibroblast_rep 2

value: Fibroblast

value: un-diseased


title: CYCGFP, D50, ZT12, IgG, CUT&RUN, Rep 2

value: IgG


title: Donor 3 MePyr [metabolism_panel]


title: Donor 2 MePyr [metabolism_panel]


title: METTL3WT rescue, HAT1-ChIP, rep1

tag: cell line


title: splenic CD4+CD25+ Treg cells, WT3

tag: cell type

value: Wild-type


title: METTL3 knockout, HAT1-ChIP, rep2


title: splenic CD4+CD25+ Treg cells, WT2

tag: treatment


title: CYCGFP, D50, ZT12, IgG, CUT&RUN, Rep 1


title: splenic CD4+CD25+ Treg cells, KI1


title: Donor 1 MePyr [metabolism_panel]


title: Donor 4 LY2090314 [metabolism_panel]


title: CYCGFP, D50, ZT12, GFP, CUT&RUN, Rep 1


title: CYCGFP, D50, ZT4, GFP, CUT&RUN, Rep 3


title: METTL3 knockout, HAT1-ChIP, rep1


title: HEK293T, HAT1-ChIP, rep2


title: splenic CD4+CD25+ Treg cells, WT1


title: Donor 2 LY2090314 [metabolism_panel]


title: Donor 3 LY2090314 [metabolism_panel]


title: Donor 1 LY2090314 [metabolism_panel]


title: CYCGFP, D50, ZT4, IgG, CUT&RUN, Rep 3


title: HEK293T, HAT1-ChIP, rep1


title: HDAC3 KO3

first: Zhimin

address: No. 1 Qinghuayuan Street

department: School of Medicine

data_processing:
Basecalling using Real-Time Analysis software (RTA 2.7.7)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2
Fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated using RSEM (Li,B et al. BMC Bioinfomatics, 2011).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
total RNA was extracted using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Alveolar macrophages were sorted from degiested lung tissue from Hdac3fl/fl mice or Cd11c-CreHdac3fl/fl mice using FACS

value: alveolar macrophages


title: CYCGFP, D50, ZT4, GFP, CUT&RUN, Rep 2

value: outer photoreceptors


title: METTL3 knockout, Input


title: HDAC3 KO2


title: CYCGFP, D50, ZT4, IgG, CUT&RUN, Rep 2


title: Donor 3 Vehicle [metabolism_panel]

value: Vehicle

value: Control


title: HDAC3 KO1


title: Donor 4 Vehicle [metabolism_panel]


title: CYCGFP, D50, ZT4, GFP, CUT&RUN, Rep 1

value: GFP


title: HEK293T, Input

value: Human embryonic kidney


title: UCMSC-2

city: Kunming

first: Lihua

last: Qiu

state: Yunnan

address: Puxin Road

institute: Kunming University

data_processing:
Trimmomatic v.0.36
Sequence reads were trimmed for adaptor sequence/low-gualty sequence using Trimmomatic v.0.36
Trimmed seauence reads were maped to GRCh38/hg38 using HISAT2 v2.1.0
Assembly: human NCBI genome build 38 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: primary cell

extract_protocol:
RNA was harvested using RNAiso Easy kit (Takara).  2 ug of total RNA was used for the construction of seguencing libraries
RNA libraries for RNA-seg were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit following manufacturer's protocols

value: primary cell

value: UCMSC


title: Donor 2 Vehicle [metabolism_panel]


title: ctrl3


title: Patient_3_Metastasis_SRS

first: liu

last: tianxiang

address: No.94 Weijin Road, Nankai District

institute: Nankai University

description:
Library name: M3_SRS
M3

data_processing:
LRS: Two major steps were performed to obtain full-length non-chimeric (FLNC) reads: (i) Poly(A) tails and concatemers were identified and removed to refine high-quality full-length (FL) reads; (ii) The resulting FL reads were clustered to generate high-confidence transcript isoforms. The processed FLNC reads were then aligned using pbmm2 with the ISOSEQ preset. Aligned BAM files were subsequently sorted and indexed with samtools, and data from multiple SMRT cells of the same sample were merged prior to clustering.Sorted bam files from long read were quantified using isoquant
SRS: Raw sequencing reads were maaped using STAR. The resulting alignments were subsequently sorted and indexed with samtools. Gene-level counts were then obtained using featurecounts.Transcript-level counts were quantified using stringtie.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw trancript and gene counts from Isoquant for each LRS sample
Supplementary files format and content: tab-delimited text file includes raw trancript and gene counts from stringtie2 for each SRS sample

source_name: omentum

extract_protocol:
Total RNA was extracted using TRIeasyTM Total RNA Extraction Reagent according to the manufacturer’s instruction.
LRS:Using the Iso-Seq Express 2.0 kit, polyadenylated RNA molecules were enriched with Oligo(dT) primers and reverse-transcribed to synthesize cDNA, followed by PCR amplification to generate barcoded cDNA. The Kinnex Full-Length RNA kit was then used to amplify the cDNA and introduce sticky ends, allowing concatenation of eight cDNA fragments in series while ligating barcoded adapters at both ends. Damage repair was performed, and exonuclease treatment was applied to remove incompletely ligated fragments, yielding the final sequencing library. After quantification, the library templates of a certain concentration and volume and enzyme complexes were loaded into the nanopores of the PacBio Revio sequencing system for single-molecule real-time (SMRT) sequencing.
SRS:Eukaryotic mRNA was enriched using Oligo(dT) magnetic beads. The enriched mRNA was then fragmented using fragmentation buffer. Using the fragmented mRNA as a template, first- and second-strand cDNA were synthesized and subsequently purified. The purified double-stranded cDNA underwent end repair, A-tailing, adapter ligation, and fragment size selection to obtain cDNA fragments of approximately 350 bp. Finally, PCR amplification was performed to generate the cDNA library.The double-stranded cDNA was then denatured at high temperature to produce single-stranded DNA, followed by the addition of a circularization primer to form a single-stranded circular library. The constructed libraries were quality-checked using Qubit 3.0 and Agilent 2100 systems. Libraries that passed quality assessment were sequenced on a high-throughput sequencing platform with a PE150 strategy.

value: omentum


title: CYCGFP, D50, ZT4, IgG, CUT&RUN, Rep 1

value: M

value: w; PBac{y[+mDint2] w[+mC]=cyc-GFP.FPTB}VK00037/+; P{w[+mC]=[UAS-GFP-Msp3 00KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]/+


title: ctrl2


title: CYCGFP, D10, ZT16, GFP, CUT&RUN, Rep 3


title: Donor 1 Vehicle  [metabolism_panel]

value: Th1 cells


title: CYCGFP, D10, ZT16, IgG, CUT&RUN, Rep 3


title: Control_br 2

city: Changsha

first: Jianying

address: NO.72 Xiangya Road

department: Xiangya School of Stomatology

institute: Central South University

description: Gene expression of S.mutans UA159 without LSOS treatment

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions..  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with GeneSpring GX v11.5.1  (Agilent) using default parameters (GE1_1100_Jul11 and Grid: 060191_D_F_20130915) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Streptococcus mutans

source_name: bacterial cells, control_replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted by resuspending cells in lysis buffer (30 mM Tris-HCl, 1 mM EDTA, 20 mg/mL lysozyme, pH 8.0) and incubating at 37°C with gentle agitation for 30 min. RNA was purified using RNeasy Mini kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: S. mutans UA159 was cultured to mid-logarithmic phase (OD600 = 0.5) with or without LSOS treatment  (0 or 2.5 mM), and cells were harvested by centrifugation.

value: S. mutans UA159


title: ctrl1


title: LSOS treatment_br 1

description: Gene expression of S.mutans UA159 with LSOS treatment

source_name: bacterial cells, LSOS treated_replicate 1


title: Control_br 1

source_name: bacterial cells, control_replicate 1


title: CYCGFP, D10, ZT16, IgG, CUT&RUN, Rep 2


title: CYCGFP, D10, ZT16, GFP, CUT&RUN, Rep 2


title: Patient_1_Metastasis_SRS

description:
Library name: M1_SRS
M1


title: skin cells-8, STAT5A-NC

value: skin cells

value: CON


title: ES (H9)

value: embryonic stem cells


title: UCMSC-1


title: 4mWT_skin [replicate_4]

city: Tokyo

first: Jiancheng

last: Liang

state: Bunkyo

department: Graduate school of Agricultural and Life Sciences

institute: The University of Tokyo

data_processing:
Raw reads with low-quality bases and adapters were removed using BBTools (parameters: minlen=50 qtrim=rl trimq=20 ref=adapters.fa ktrim=r k=25 mink=11 hdist=1 tbo tpe). STAR for genome mapping and alignment to the Danio rerio GRCz11 reference genome (Ensembl.Danio.rerio.GRCz11.112), (parameters: STAR –genomeDir --runThreadN 16  --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate --readFilesCommand gunzip -c). RSEM for quantifying the expression (parameters: rsem-calculate-expression --alignments --paired-end -p 30 --append-names --estimate-rspd). DESeq2 for differential expression analysis.
Assembly: Ensembl.Danio.rerio.GRCz11.112
Supplementary files format and content: tab-delimited text file includes expected counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

organism: Danio rerio

source_name: Skin

extract_protocol:
Zebrafish were euthanized using Tricaine, dissected, and gathered the corresponding organs kept in NucleoProtect RNA (TAKARA) solution. Total RNA was extract using NucleoSpin RNA Clean-up Kit (TAKARA) following the manufacturer's protocols and verified the RNA quality and concentration using TapeStation RNA ScreenTape (Agilent).
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep Kit following the manufacture’s protocols.

value: Skin

value: 4 month

value: WT


title: fibroblast-8-STAT5A-KO

value: fibroblast


title: CYCGFP, D10, ZT16, GFP, CUT&RUN, Rep 1

value: outer photoreceptors


title: 4mWT_intestine [replicate_4]

source_name: Intestine

value: Intestine


title: UCMSC-3


title: Patient_3_Primary_tumor _SRS

description:
Library name: P3_SRS
P3

source_name: ovary

value: ovary


title: CYCGFP, D10, ZT16, IgG, CUT&RUN, Rep 1

value: IgG


title: 4mWT_muscle [replicate_4]

source_name: Muscle

value: Muscle


title: Patient_2_Primary_tumor _SRS

description:
Library name: P2_SRS
P2


title: skin cells-50, STAT5A-KO

value: primary cell


title: 4mWT_heart [replicate_4]

source_name: Heart

value: Heart


title: CYCGFP, D10, ZT12, GFP, CUT&RUN, Rep 3

value: GFP

value: M

value: w; PBac{y[+mDint2] w[+mC]=cyc-GFP.FPTB}VK00037/+; P{w[+mC]=[UAS-GFP-Msp3 00KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]/+


title: Patient_2_Metastasis_SRS

description:
Library name: M2_SRS
M2

value: omentum


title: LSOS treatment_br 2

source_name: bacterial cells, LSOS treated_replicate 2

value: S. mutans UA159


title: CYCGFP, D10, ZT12, IgG, CUT&RUN, Rep 3


title: Patient_1_Primary_tumor _SRS

description:
Library name: P1_SRS
P1


title: 4mWT_gills [replicate_4]

source_name: Gills

value: Gills


title: skin cells-80, STAT5A-NC

value: skin cells

value: CON


title: Patient_3_Normal_tissue_SRS

description:
Library name: N3_SRS
N3


title: IL6_TY52156_3

city: Nanjing

first: Hongwei

address: No. 22, Hankou Road

institute: Nnanjing University

data_processing:
RNA-seq raw files (fastq, SE50) were aligned to the  version of the GRCh38 reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
HISAT2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: GRCh38
Supplementary files format and content: Bedgraph files contain the gene expression tags counts and p-value.

growth_protocol: HaCaT were cultured under IL-6 or IL-6 plus TY52156 for 24 hours.

extract_protocol:
Total cellular RNA was extracted using the RNA Rapid Extraction Kit (Vazyme, Nanjing, China) and total tissue RNA was extracted using Trizol (Vazyme), according to the reagent instructions.
The RNA-seq library preparation was followed by the instructions of BGI_Shenzhen (Shenzhen, China)

treatment_protocol: The cancer cachexia model was constructed according to the literature, in brief, a cell suspension containing a certain number of tumor cells was prepared by resuspension in PBS and injected subcutaneously into the unilateral flank of mice at a dose of 500,000 cells/100ul per mouse.  It took approximately 2 to 3 weeks for the cachexia phenotype to appear.

value: Skin

value: HaCaT


title: CYCGFP, D10, ZT12, GFP, CUT&RUN, Rep 2

value: outer photoreceptors


title: IL6_TY52156_2


title: Patient_2_Normal_tissue_SRS

description:
Library name: N2_SRS
N2


title: IL6_TY52156_1


title: CYCGFP, D10, ZT12, IgG, CUT&RUN, Rep 2


title: Patient_1_Normal_tissue_SRS

description:
Library name: N1_SRS
N1


title: CYCGFP, D10, ZT12, GFP, CUT&RUN, Rep 1


title: 4mWT_brain [replicate_4]

source_name: Brain

value: Brain

value: 4 month

value: WT


title: 4mWT_skin [replicate_3]


title: IL6_3


title: Ad-lncRNA-ITGA2-3

city: Xi'an

first: XIAN

last: GUO

address: Xinyi Road

institute: Air Force Medical University

description: Library name: Ad-lncRNA-ITGA2-3

data_processing:
The reads were aligned to the human genome hg19 for all the samples. RNA-seq: differential gene expression analysis was performed using DESeq2 package in R .
Assembly: hg19
Supplementary files format and content: xslx files include FPKM values for each Sample

source_name: human aortic smooth muscle cell

extract_protocol:
Refer to the instruction manual of Trizol (Invitrogen, CA, USA) to extract total RNA.RNA contamination was assessed by 1.5% agarose gel.
The mRNA was purified from the total RNA using poly‐T oligo‐attached magnetic beads. Sequencing libraries were generated from the purified mRNA using the V AHTS Universal V6 RNA-seq Library Kit for MGI (V azyme, Nanjing, China) following the manufacturer's recommendations with unique index codes.

value: human aortic smooth muscle cell


title: CYCGFP, D10, ZT12, IgG, CUT&RUN, Rep 1

source_name: outer photoreceptors

value: IgG


title: 4mWT_muscle [replicate_3]

value: Muscle


title: Ad-lncRNA-ITGA2-2

description: Library name: Ad-lncRNA-ITGA2-2


title: IL6_1


title: 4mWT_intestine [replicate_3]

value: Intestine


title: CYCGFP, D10, ZT4, GFP, CUT&RUN, Rep 3

value: GFP

value: M


title: skin cells-80, STAT5A-KO

value: primary cell


title: 4mWT_eyes [replicate_4]

source_name: Eyes

value: Eyes


title: IL6_2


title: 4mWT_heart [replicate_3]

value: Heart


title: CYCGFP, D10, ZT4, IgG, CUT&RUN, Rep 3

value: w; PBac{y[+mDint2] w[+mC]=cyc-GFP.FPTB}VK00037/+; P{w[+mC]=[UAS-GFP-Msp3 00KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]/+


title: Ad-lncRNA-ITGA2-1

description: Library name: Ad-lncRNA-ITGA2-1


title: Ad-GFP-3

description: Library name: Ad-GFP-3

value: Ad-GFP