title: m6A_IP_iCKO

data_processing:
For total RNA-seq, the resulting FASTQ files were aligned to the mm10 mouse reference genome employing HISAT2 version 2.2.1, The abundance of transcripts was quantified using the HTSeq-count tool, with expression levels reported in counts per million (CPM) to normalize for sequencing depth and gene length. Subsequently, differential expression analysis of transposable element transcripts was performed using the DESeq2 package
For ChIP-seq, the resulting FASTQ files were quality-trimmed with Trim Galore v0.6.4_dev and aligned to the mm10 genome using Bowtie2 v2.3.5.1. Genome coverage visualizations were created bigwig files with deeptools v3.5.5 bamCompare
For MeRIP-seq, the resulting FASTQ files were quality-trimmed with Trim Galore v0.6.4_dev and aligned to the mm10 genome using HISAT2 version 2.2.1. Genome coverage visualizations were created bigwig files with deeptools v3.5.5 bamCompare
Assembly: mm10
Supplementary files format and content: Total RNA-seq files are in txt format, containing the results of transcriptomic analysis statistics. ChIP- and MeRIP-seq files are in bigwig format.
Library strategy: MeRIP-seq

extract_protocol:
For MeRIP-seq, m6A target RNA enrichment was performed using the EpiMark® N6-Methyladenosine kit (E1610S, NEB), and the m6A immunoprecipitated and input RNAs were constructed to NGS libraries using SMARTer Stranded Total RNA-Seq Kit (635008, TAKARA).
Total RNA was extracted using a RNAsimple Total RNA Kit (DP419, TIANGEN)；genomic DNA was extracted with nuclei dilution buffer (20 mM Tris Cl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% NP40, 1% SDS, and 1×PI).


title: Liver, Pre-TXP, Patient3-Pre-TXP, TCR

status: Public on Aug 20 2025

type: SRA

city: Cincinnati

first: Erica

last: DePasquale

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology

country: USA

institute: Cincinnati Children's Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing and FASTQ generation using CellRanger version 6.0.0
Generate single-cell expression matrix using CellRanger version 6.0.0
Process BCR and TCR data using CellRanger version 6.0.0
Quality control and filtering using R 4.3.2
Create Seurat objects using Seurat version 5.0.1
Normalization using SCTransform version 0.4.1
Sample integration, clustering, and sub-clustering using Seurat version 5.0.1
Predict cell-cell interactions using CellPhoneDB and Seurat version 5.0.1
Assembly: NCBI Genome assembly GRCh38
Supplementary files format and content: Cell Ranger output files for GEX samples: tab-separated barcodes.tsv.gz, features.tsv.gz, and matrix.tsv.gz
Supplementary files format and content: Cell Ranger output files for BCR and TCR samples: comma-separated clonotypes.csv and filtered_contig_annotations.csv

molecule: total RNA

organism: Homo sapiens

source_name: Liver

extract_protocol:
Liver core biopsies were thawed, minced into 1-2mm pieces with a sharp scissors, and gently digested at 4C in RPMI+10% FBS containing 100mg/mL soy trypsin inhibitor (Roche, cat #10109886001), 250U DNase I (Roche, cat #4536282001), 5mM CaCl2, 25ug/mL collagenase A from clostridium histolyticum (Roche, cat #10103586001), and 25ug/mL collagenase type IV from clostridium histolyticum (Worthington, LS004186). Digestion was performed for 3min on ice with intermittent inversion and gentle pipetting with wide-bore pipet tips. The cell suspension was filtered via a pre-primed 30mm cell strainer, then centrifuged at 300g for 5 min at 4C. Trypan blue exclusion was used to determine cell viability and concentration. Cells were resuspended at 1,000cell/mL per the 10x Genomics Chromium protocol and immediately prepared for single-cell barcoding.
Samples were processed for single-cell sequencing following the Chromium Next GEM Single Cell V(D)J Reagent Kit, version 1.1 or 1.2 protocols. Briefly, cells were uniquely barcoded by using 10x fluidics (10x Genomics Single Cell Controller) to combine each individual cell with an individual barcoded Single Cell 5’ Gel Bead creating a Gel Beads-in-Emulsion (GEMs) solution (10x Genomics, PN-1000165 and PN-1000120). An average of 17,400 cells were loaded to achieve an estimated recovery of 10,000 cells per biopsy. GEM gel beads were dissolved and cDNA was synthesized from the resulting tagged mRNA transcripts over 14 amplification cycles; 50ng of cDNA was used for the construction of each library.

treatment_protocol: Baseline immunosuppression and rejection treatment meta data columns describe treatments the patients received prior to the biospy. No treatments were applied after sample collection. Abbreviations: ATG: anti-thymocyte globulin, MMF: mycophenolate mofetil, TAC: tacrolimus, RAPA: rapamycin.

tag: tissue

value: Liver

tag: library type

value: mRNA

tag: baseline immunosuppression

tag: rejection treatment


title: m6A_IP_WT

city: shanghai

first: Junhao

last: Xiong

address: *800 Rd dongchuan

country: China

institute: shanghai jiao tong university

library_source: transcriptomic

organism: Mus musculus

source_name: Heart

growth_protocol: The animals were maintained under the standard photoperiod conditions (12-hour light/dark cycle).

treatment_protocol: Mice were treated with I/R or 25mg/kg tamoxifen

value: Heart

tag: Sex

value: Male

tag: strain

tag: genotype

value: WT

tag: treatment

value: treatment with tamoxifen


title: AE9a mBM c-Kit+ cells, C-176-2

city: Shanghai

first: Yue

last: Sun

address: 131 Dongan Road

institute: Institutes of Biomedical Sciences, Medical College of Fudan University

data_processing:
The raw pair-end RNA-seq FASTQ data were trimmed to remove low-quality bases and adaptor sequences by Trim Galore (v0.5.0) with default settings.
The clean RNA-seq FASTQ data were mapped to mouse reference genome mm10 using Hisat2 (v2.1.0) with default parameters
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: BM c-Kit+ cells

growth_protocol: Mouse bone marrow cells were maintained in SFEM supplemented with 100ng/mL mSCF, 50ng/mL mTPO, 50ng/mL mFLT3 and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
A total of 300 c-Kit+ cells per group were sorted using FACS and lysed directly with Smart-seq2 lysis buffer (Vazyme, Cat. TD502).
The RNA from the sorted cells was reverse-transcribed and amplified following the SMART-Seq2 protocol to generate sufficient cDNA. After quantifying the cDNA, 5 ng of cDNA was utilized to construct the cDNA library using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat. TD502).
SMART-seq2

treatment_protocol: Cells were treated with DMSO or 1μM C-176 for 48 hours.

tag: cell type

value: BM c-Kit+ cells


title: AE9a mBM c-Kit+ cells, C-176-1


title: Liver, Pre-TXP, Patient3-Pre-TXP, GEX

description: 10x Genomics


title: m6A_input_iCKO

value: TRIM28 iCKO


title: Liver, Pre-TXP, Patient2-Pre-TXP, BCR

description: 10x Genomics


title: AE9a mBM c-Kit+ cells, DMSO-3

value: DMSO


title: m6A_input_WT


title: Liver, Pre-TXP, Patient2-Pre-TXP, TCR

description: 10x Genomics


title: iCKO_rep3

data_processing:
For total RNA-seq, the resulting FASTQ files were aligned to the mm10 mouse reference genome employing HISAT2 version 2.2.1, The abundance of transcripts was quantified using the HTSeq-count tool, with expression levels reported in counts per million (CPM) to normalize for sequencing depth and gene length. Subsequently, differential expression analysis of transposable element transcripts was performed using the DESeq2 package
For ChIP-seq, the resulting FASTQ files were quality-trimmed with Trim Galore v0.6.4_dev and aligned to the mm10 genome using Bowtie2 v2.3.5.1. Genome coverage visualizations were created bigwig files with deeptools v3.5.5 bamCompare
For MeRIP-seq, the resulting FASTQ files were quality-trimmed with Trim Galore v0.6.4_dev and aligned to the mm10 genome using HISAT2 version 2.2.1. Genome coverage visualizations were created bigwig files with deeptools v3.5.5 bamCompare
Assembly: mm10
Supplementary files format and content: Total RNA-seq files are in txt format, containing the results of transcriptomic analysis statistics. ChIP- and MeRIP-seq files are in bigwig format.

extract_protocol:
Total RNA was extracted using a RNAsimple Total RNA Kit (DP419, TIANGEN)；genomic DNA was extracted with nuclei dilution buffer (20 mM Tris Cl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% NP40, 1% SDS, and 1×PI).
For total RNA-seq, the libraries were constructed with TIANSeq Fast RNA Library Prep Kit (NR102, TIANGEN).
Total RNA was extracted using a RNAsimple Total RNA Kit (DP419, TIANGEN)；genomic DNA was extracted with nuclei dilution buffer (20 mM Tris Cl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% NP40, 1% SDS, and 1×PI).


title: AE9a mBM c-Kit+ cells, DMSO-2


title: iCKO_rep2


title: AE9a mBM c-Kit+ cells, DMSO-1


title: Liver, Pre-TXP, Patient2-Pre-TXP, GEX

description: 10x Genomics


title: Liver, Pre-TXP, Patient1-Pre-TXP, BCR

description: 10x Genomics


title: WT mBM c-Kit+ cells, C-176-3


title: Liver, Pre-TXP, Patient1-Pre-TXP, TCR

description: 10x Genomics


title: iCKO_rep1


title: WT_rep3


title: Colorectal mucosa 3

type: RNA

city: Osaka

first: Norikatsu

last: Miyoshi

address: 3-1-69, Ohtemae, Chuo-ku

department: Innovative Oncology Research and Regenerative Medicine

country: Japan

institute: Osaka International Cancer Institute

description:
0614_Normal
Gene expression for clinical colorecal mucosa tissue

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. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Clinical tissue

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.

growth_protocol: The human colorectal tumor cell lines were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 1% GlutaMAX, and 1% penicillin/streptomycin/amphotericin B. Primary cultured cells were established according to a previous ¬report (2018 BBRC, Fujino, et al) and cultured in modified stem cell culture medium.

extract_protocol: Total RNA was prepared using an RNA Purification Kit (Qiagen,  Hilden, Germany)

treatment_protocol: No treatment

value: Colorectal mucosa

tag: cancer

value: No

tag: material

value: Tissue


title: Liver, Pre-TXP, Patient1-Pre-TXP, GEX

description: 10x Genomics


title: Colorectal mucosa 5

description:
713YS_Normal
Gene expression for clinical colorecal mucosa tissue


title: Colorectal mucosa 2

description:
SM_Normal
Gene expression for clinical colorecal mucosa tissue


title: WT mBM c-Kit+ cells, C-176-1


title: Colorectal mucosa 4

description:
420IY_Normal
Gene expression for clinical colorecal mucosa tissue


title: Liver, Pre-TXP, Patient4-Pre-TXP, GEX

description: 10x Genomics


title: Primary cultured colorectal cancer cells 8

description:
iCC1225AK
Gene expression for primary cultured colorectal cancer cells

source_name: Primary clutured cell

value: Yes

value: Cell


title: Colorectal mucosa 1

description:
Oh_Normal
Gene expression for clinical colorecal mucosa tissue


title: Primary cultured colorectal cancer cells 7

description:
iCC0622
Gene expression for primary cultured colorectal cancer cells


title: WT mBM c-Kit+ cells, DMSO-3


title: 7d-1

city: Suzhou

first: Hu

last: ya'nan

state: Jiangsu

address: 199 Ren-Ai Road, Suzhou Industrial Park

department: Department of Cell Biology

institute: Medical College of Soochow University

data_processing:
Sequence reads were trimmed for adapters sequence/low-quality sequence using fastp (version 0.18.0)
Trimmed sequence reads were mapped to Ensembl_release106 using HISAT2. 2.4
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
Read count extraction and normalization were performed using RSEM software
Assembly: Ensembl_release106
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: brain

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen) according to the user guide for RNA-seq analysis.
Total RNA was extracted, and the eukaryotic mRNA was enriched by Oligo (dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversely transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs).

value: brain

tag: cell line

value: glioblastoma

value: YFSS in neural differentiation media for 7d


title: WT_rep1


title: Primary cultured colorectal cancer cells 9

description:
iCC160602
Gene expression for primary cultured colorectal cancer cells


title: IR_rep3

tag: protocol

value: IR

value: Ischemia 45min and perfusion 24 h


title: 5d-2

value: YFSS in neural differentiation media for 5d


title: WT mBM c-Kit+ cells, DMSO-2


title: IR_rep2

value: Heart

value: Male


title: WT mBM c-Kit+ cells, DMSO-1

value: WT


title: WT mBM c-Kit+ cells, C-176-2

value: BM c-Kit+ cells


title: Primary cultured colorectal cancer cells 5

description:
iCC0603
Gene expression for primary cultured colorectal cancer cells


title: IR_rep1


title: Liver_ADAL_WT14

city: Sendai

first: Fan-Yan

last: Wei

address: Seiryo-machi 4-1

institute: Tohoku University

data_processing:
Sequence reads were trimmed using FASTP on Galaxy platform, following by mapping-based estimation of transcript abundance using Salmon quant on Galaxy platform.
Assembly: Mus_musculus.GRCm38.cds.all.fa
Supplementary files format and content: tubular text files include TPM values for each samples

extract_protocol:
RNA was extracted using TRIzol following the manufacturer's instruction
Total RNA was send to the company, where they perform library construction using automated library preparation kit following the manufacturer's instruction

value: Liver

value: ADAL WT


title: 3d-2

value: YFSS in neural differentiation media for 3d


title: 7d-2


title: Liver_ADAL_WT13


title: Sham_rep3

value: Sham

value: chest-opening surgery but not with I/R


title: Primary cultured colorectal cancer cells 2

description:
iCC1605243D
Gene expression for primary cultured colorectal cancer cells

value: Yes


title: Liver_ADAL_WT4


title: 1d-2

value: YFSS in neural differentiation media for 1d


title: Primary cultured colorectal cancer cells 6

description:
iCC0614
Gene expression for primary cultured colorectal cancer cells

value: Cell


title: Sham_rep1


title: Liver_ADAL_WT3


title: Primary cultured colorectal cancer cells 3

description:
iCC0129MF
Gene expression for primary cultured colorectal cancer cells


title: Primary cultured colorectal cancer cells 4

description:
iCC0524
Gene expression for primary cultured colorectal cancer cells


title: 0d-2

value: brain

value: glioblastoma

value: DMSO in neural differentiation media


title: Liver_ADAL_WT2


title: 5d-1


title: 3d-1


title: CTR, replicate 2

city: Barcelona

first: Daniel

last: Toro Ruiz

address: C/Casanova 143

department: Dept Biomedical Sciences

country: Spain

institute: Universitat de Barcelona

description: 10x genomics

data_processing:
Transcriptome and barcode libraries were sequenced on a NovaSeq 6000. Barcode filtering and sequence alignment were performed using the CellRanger pipeline (http://10xgenomics.com, version 7.0.1). Reads were aligned to the mouse reference genome (reference 'refdata-gex-mm10-2020').
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: neocortex

extract_protocol:
Mouse brains at E15.5 were collected and sectioned in 300 μm under a vibratome in ice-cold Leibowitz medium with 5% FBS. The rostal region of cortex for both hemisphere were collected using a scalpel. The tissues were transferred into a dissociation Buffer, EBSS, and were subsequently dissociated into a single cell suspension with Worthington Kit and manually Papain dissociation system according to the manufacturer’s instructions.
For experiments utilizing the 10x Genomics platform, the following reagents were used: Chromium Single Cell Next GEM Single Cell 3’ GEM kit v3.1 (PN-1000130), Library Construction Kit (PN-1000196), Chromium Next GEM Single Cell 3′ Gel Bead Kit v3.1 (PN-1000129) and Dual Index Kit TT Set A (PN-1000215),  according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits v3.1 User Guide.

treatment_protocol: Administration of 0.2mg/ml doxycycline in the drinking water of pregnant females for 4d (E10.5 to E14.5)

value: neocortex

value: Cortical neurons

value: 0.2mg/ml doxycycline


title: Liver_ADAL_WT1


title: 0d-1


title: i4F-Nes, replicate 2

description: 10x genomics


title: CTR, replicate 1

description: 10x genomics


title: Sham_rep2

value: Heart

value: Male


title: Liver_ADAL_KO17

value: ADAL KO


title: i4F-Nes, replicate 1

description: 10x genomics


title: Astrocyte, BD NR 3, rep2

city: Daejeon

first: Dayeon

last: Kim

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

data_processing:
The sequenced reads were mapped to the human genome (hg38/GRCh38) using STAR 2.7.9.
The mapped reads were annotated and quantified using RSEM.
DESeq2 was used for normalization and differential analysis.
Assembly: hg38/GRCh38
Supplementary files format and content: csv file includes TPM values

source_name: Astrocyte

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) following the munufacturer's instructions.
RNA libraries for RNA-seq were prepared using NEBNext ultra II directional RNA library prep kit according to manufacturer’s instructions.

value: Astrocyte


title: Liver_ADAL_KO16

value: Liver


title: Colorectal cancer cell line 6

description:
SW480
Gene expression for colorecal cancer cell line

source_name: Cell line

value: Colorectal cancer cell line


title: VCAM1+CD163+CCR3+ general macrophages_from normal  bone marrow_repeat 6

city: Plainsboro

first: Yong

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

data_processing:
The library pools were denatured and sequenced on Illumina NovaSeq 6000 using the S Prime flowcells as pair-end 65 nt reads according to the manufacturer’s protocol.  Raw sequencing reads were filtered by Illumina NovaSeq Control Software, only the Pass-Filter (PF) reads were de-multiplexed allowing 1 mismatch and used for further analysis.
Demultiplexed raw sequence files (FASTQ) were analyzed using the Partek® Flow® software package. Raw reads were aligned using STAR version 2.7.3a. Gene counts were obtained by quantifying against the mm10-Ensembl Transcripts release 100_v2 annotation model. Downstream data analysis was conducted using the DESeq2 package (1.40.2) in R (version 4.3.1).
Assembly: mm10-Ensembl Transcripts release 100_v2
Supplementary files format and content: tab-delimited text file includes gene expression raw counts for each sample

source_name: Bone

extract_protocol:
Bone marrow cells were flushed out from the mouse femur and tibia with PBS containing 2% of FBS. Red blood cells were removed with RBC lysis buffer.The cell suspension was filtered through a 70-μm strainer and stained with live dye and antibodies.
General macrophages were sorted by F4/80 and CD11b from single live bone marrow cells; Niche-specific macrophages were sorted by VCAM1, CD163, and CCR3 from single live bone marrow cells.
Total RNA were extracted using RNAeasy micro kit from Qiagen
The integrity of total RNA samples were assessed on Bioanalyzer 2100 using RNA 6000 Pico chip (Agilent Technologies, CA).  Messenger RNA was enriched from these samples using QIAseq FastSelect - rRNA HMR Kit (Qiagen, CA), fragmented and converted to cDNA and Illumina sequencing library using the PrepX RNA-seq library preparation protocol on the Apollo 324TM NGS Library Prep System (Takara Bio, CA).

value: Bone

value: Macrophage

tag: sorting markers

value: VCAM1, CD163, CCR3_

tag: group

value: Normal


title: Astrocyte, BD NR 3, rep1


title: Colorectal cancer 1

description:
Oh_Tumor
Gene expression for clinical colorecal cancer tissue

value: Colorectal cancer

value: Yes

value: Tissue


title: Liver_ADAL_KO15


title: Colorectal cancer 2

description:
SM_Tumor
Gene expression for clinical colorecal cancer tissue


title: Colorectal cancer 4

description:
614_Tumor
Gene expression for clinical colorecal cancer tissue


title: Primary cultured colorectal cancer cells 1

description:
iCC1605242D
Gene expression for primary cultured colorectal cancer cells

value: Cell


title: Astrocyte, BD NR 2, rep2


title: Colorectal cancer cell line 5

description:
HT29
Gene expression for colorecal cancer cell line


title: Astrocyte, BD NR 2, rep1


title: VCAM1+CD163+CCR3+ general macrophages_from normal  bone marrow_repeat 4


title: Liver_ADAL_KO5


title: VCAM1+CD163+CCR3+ general macrophages_from normal  bone marrow_repeat 5


title: Liver_ADAL_KO6


title: Colorectal cancer 5

description:
622_Tumor
Gene expression for clinical colorecal cancer tissue


title: Astrocyte, BD NR 1, rep2


title: VCAM1+CD163+CCR3+ general macrophages_from metastatic bone marrow_repeat 3

value: Bone Metatasis


title: Astrocyte, BD NR 1, rep1


title: Colorectal cancer cell line 4

description:
Caco2
Gene expression for colorecal cancer cell line


title: Colorectal cancer cell line 3

description:
RKO
Gene expression for colorecal cancer cell line


title: VCAM1+CD163+CCR3+ general macrophages_from metastatic bone marrow_repeat 2


title: Hippocampus, DE8, Day3

city: Harbin

first: Wenchao

last: Fu

state: Chongqing

address: Second Hospital of Harbin Medical University, Xuefu Road, Nangang District, Harbin City, Heilongjiang Province, China

institute: Harbin Medical University

description:
Library name: Sample 32
The rat model was subjected to 72-hour sleep deprivation prior to cardiac arrest induction via asphyxiation. Mechanical cardiopulmonary resuscitation (CPR) with epinephrine administration was initiated at 8.5 minutes post-arrest. Post-resuscitation management included initial electroacupuncture (EA) intervention delivered within 1 hour following return of spontaneous circulation (ROSC), followed by daily EA sessions for 3 consecutive days.

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequenceflow-quality sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benvhwork
Assembly: mm10
Supplementary files format and content: Allsamples_FPKM.txt
Supplementary files format and content: Allsamples_counts.txt

organism: Rattus norvegicus

source_name: Hippocampus

growth_protocol: All rats were housed under controlled environmental conditions (temperature: 22±1°C, humidity: 50±5%) with ad libitum access to standard rodent chow and sterilized water

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Cardiac arrest was induced in rats through asphyxiation, with mechanical chest compressions combined with epinephrine injection administered for cardiopulmonary resuscitation at 8.5 minutes following cardiac arrest cessation

value: Hippocampus

value: Sleep deprivation+Cardiac arrest +Electroacupuncture

tag: batch


title: Soleus_ADAL_WT14

source_name: Soleus

value: Soleus

value: ADAL WT


title: Soleus_ADAL_WT13


title: Astrocyte, BD LR 3, rep2


title: VCAM1+CD163+CCR3+ general macrophages_from metastatic bone marrow_repeat 1


title: Colorectal cancer cell line 2

description:
HCT116
Gene expression for colorecal cancer cell line


title: Astrocyte, BD LR 3, rep1


title: Colorectal cancer cell line 1

description:
DLD1
Gene expression for colorecal cancer cell line


title: Soleus_ADAL_WT4


title: Hippocampus, DE6, Day3

description:
Library name: Sample 30
The rat model was subjected to 72-hour sleep deprivation prior to cardiac arrest induction via asphyxiation. Mechanical cardiopulmonary resuscitation (CPR) with epinephrine administration was initiated at 8.5 minutes post-arrest. Post-resuscitation management included initial electroacupuncture (EA) intervention delivered within 1 hour following return of spontaneous circulation (ROSC), followed by daily EA sessions for 3 consecutive days.


title: Soleus_ADAL_WT3


title: Astrocyte, BD LR 2, rep2


title: Hippocampus, DE5, Day3

description:
Library name: Sample 29
The rat model was subjected to 72-hour sleep deprivation prior to cardiac arrest induction via asphyxiation. Mechanical cardiopulmonary resuscitation (CPR) with epinephrine administration was initiated at 8.5 minutes post-arrest. Post-resuscitation management included initial electroacupuncture (EA) intervention delivered within 1 hour following return of spontaneous circulation (ROSC), followed by daily EA sessions for 3 consecutive days.


title: Astrocyte, BD LR 2, rep1


title: CD11b+F4/80+ general macrophages_from normal bone marrow_repeat 1


title: Soleus_ADAL_WT1


title: Soleus_ADAL_WT2


title: Hippocampus, DE3, Day3

description:
Library name: Sample 27
The rat model was subjected to 72-hour sleep deprivation prior to cardiac arrest induction via asphyxiation. Mechanical cardiopulmonary resuscitation (CPR) with epinephrine administration was initiated at 8.5 minutes post-arrest. Post-resuscitation management included initial electroacupuncture (EA) intervention delivered within 1 hour following return of spontaneous circulation (ROSC), followed by daily EA sessions for 3 consecutive days.


title: Hippocampus, DE4, Day3

description:
Library name: Sample 28
The rat model was subjected to 72-hour sleep deprivation prior to cardiac arrest induction via asphyxiation. Mechanical cardiopulmonary resuscitation (CPR) with epinephrine administration was initiated at 8.5 minutes post-arrest. Post-resuscitation management included initial electroacupuncture (EA) intervention delivered within 1 hour following return of spontaneous circulation (ROSC), followed by daily EA sessions for 3 consecutive days.


title: WT_rep2

value: Heart

value: Male

value: WT

value: treatment with tamoxifen


title: Astrocyte, BD LR 1, rep2

value: Astrocyte


title: Soleus_ADAL_KO17

value: ADAL KO


title: CD11b+F4/80+ general macrophages_from metastatic bone marrow_repeat 3

value: Bone

value: Macrophage


title: Soleus_ADAL_KO16


title: Hippocampus, DE2, Day3

description:
Library name: Sample 26
The rat model was subjected to 72-hour sleep deprivation prior to cardiac arrest induction via asphyxiation. Mechanical cardiopulmonary resuscitation (CPR) with epinephrine administration was initiated at 8.5 minutes post-arrest. Post-resuscitation management included initial electroacupuncture (EA) intervention delivered within 1 hour following return of spontaneous circulation (ROSC), followed by daily EA sessions for 3 consecutive days.


title: Hippocampus, DE7, Day3

description:
Library name: Sample 31
The rat model was subjected to 72-hour sleep deprivation prior to cardiac arrest induction via asphyxiation. Mechanical cardiopulmonary resuscitation (CPR) with epinephrine administration was initiated at 8.5 minutes post-arrest. Post-resuscitation management included initial electroacupuncture (EA) intervention delivered within 1 hour following return of spontaneous circulation (ROSC), followed by daily EA sessions for 3 consecutive days.


title: Astrocyte, BD LR 1, rep1


title: Astrocyte, control3, rep2


title: Hippocampus, DE1, Day3

description:
Library name: Sample 25
The rat model was subjected to 72-hour sleep deprivation prior to cardiac arrest induction via asphyxiation. Mechanical cardiopulmonary resuscitation (CPR) with epinephrine administration was initiated at 8.5 minutes post-arrest. Post-resuscitation management included initial electroacupuncture (EA) intervention delivered within 1 hour following return of spontaneous circulation (ROSC), followed by daily EA sessions for 3 consecutive days.


title: CD11b+F4/80+ general macrophages_from normal bone marrow_repeat 3

value: Normal


title: CD11b+F4/80+ general macrophages_from metastatic bone marrow_repeat 1


title: Soleus_ADAL_KO15


title: Hippocampus, DA8, Day3

description:
Library name: Sample 24
Following 72-hour sleep deprivation, cardiac arrest was induced in rats via asphyxiation, with mechanical cardiopulmonary resuscitation (CPR) initiated at 8.5 minutes post-arrest using standardized chest compressions.

value: Sleep deprivation+Cardiac arrest


title: Astrocyte, control3, rep1


title: All live cells from primary tumor

description: 10x Genomics

data_processing:
Raw sequencing reads were filtered by Illumina NovaSeq Control Software and only the Pass-Filter (PF) reads were used for further analysis. After sample demultiplexing, raw PF reads were processed through the CellRanger software (10X Genomics Inc., CA) to obtain the gene expression levels in single cells and quality control matrices for each sample.
Downstream analysis was performed using Seurat packages.
Assembly: mm10
Supplementary files format and content: tab-seperarated values files and matrix files

source_name: Mammary gland

growth_protocol: Breast cancer cell E0771 was injected into female albino B6 mice, through caudal artery to develop bone metastatic tumor and into mammary gland to develop primary tumor. Bone metastatic tumor and primary tumor were dissociated with  Collagenase/hyaluronidase in DMEM (Stemcell # 07912) and DNase I using the gentleMACS™ Octo Dissociator with Program 37C_m_TDK_1. Red blood cells were removed with RBC lysis buffer. The cell suspension was filtered through a 70-μm strainer and stained with live dye and antibodies.  To characterize bone metastasis niche, bone marrow cells were flushed out from the mouse femur and tibia with PBS containing 2% of FBS. Red blood cells were removed with RBC lysis buffer.The cell suspension was filtered through a 70-μm strainer and stained with live dye.

extract_protocol:
Single cell suspension samples were examined on Attune flow cytometer for cell density and viability. For each sample, 15,000 sorted cells were resuspended in 15 ul of PBS containing 0.5% BSA for library preparation.
Around 15,000 cells from each sample were loaded into each channel of the 10X Genomics Chromium X system using the Chromium Single Cell 3’ v3.1 Reagent Kits (10X Genomics Inc., CA) to generate and amplify cDNA from individual cells. The amplified cDNA samples were purified with Ampure XP magnetic beads (Beckman Coulter, CA), quantified by Qubit fluorometer (Invitrogen, CA), and examined on Bioanalyzer with High Sensitivity DNA chips (Agilent, CA) for size distribution. Illumina sequencing libraries were generated from the amplified cDNA samples using the Illumina Tagment DNA Enzyme and Buffer kit (Illumina, CA). These libraries were examined by Qubit and Bioanalyzer, then pooled at equal molar amount and sequenced on Illumina NovaSeq 6000 S Prime flowcells as 28+94 nt pair-end reads following the standard Illumina protocol.

treatment_protocol: Niche bone marrow cells (GFP-mCherry+) and distal bone marrow cells (GFP-mCherry-) were isolated from live bone marrow of the bone metastatic mice. Normal bone marrow (GFP-mCherry-) were isolated from live bone marrow of the healthy control mice. For bone metastasis tumor, CD45 negative live cells were sorted from bone metastatic tumor. All live cells were sorted from primary tumor.

value: Mammary gland

value: Tumor + mesenchymal stromal + immune cells

value: All Live

tag: disease

value: Primary tumor


title: Soleus_ADAL_KO6

tag: tissue


title: CD11b+F4/80+ general macrophages_from normal bone marrow_repeat 2


title: Astrocyte, control2, rep2


title: Hippocampus, DA7, Day3

description:
Library name: Sample 23
Following 72-hour sleep deprivation, cardiac arrest was induced in rats via asphyxiation, with mechanical cardiopulmonary resuscitation (CPR) initiated at 8.5 minutes post-arrest using standardized chest compressions.

value: Hippocampus


title: Astrocyte, control2, rep1


title: CD45 negative live cells  from bone metastatic tumor

description: 10x Genomics

value: Tumor+ mesenchymal stromal + erythroblast cells

value: CD45 negative live

value: Bone metastatic tumor


title: Hippocampus, DA6, Day3

description:
Library name: Sample 22
Following 72-hour sleep deprivation, cardiac arrest was induced in rats via asphyxiation, with mechanical cardiopulmonary resuscitation (CPR) initiated at 8.5 minutes post-arrest using standardized chest compressions.


title: GC_ADAL_WT14

source_name: gastrocnemius (GC) muscle

value: gastrocnemius (GC) muscle

value: ADAL WT


title: Normal bone marrow cells from normal bone marrow

description: 10x Genomics

value: Bone marrow cells

value: GFP-mCherry-


title: CD11b+F4/80+ general macrophages_from metastatic bone marrow_repeat 2

value: Bone Metatasis


title: Hippocampus, DA5, Day3

description:
Library name: Sample 21
Following 72-hour sleep deprivation, cardiac arrest was induced in rats via asphyxiation, with mechanical cardiopulmonary resuscitation (CPR) initiated at 8.5 minutes post-arrest using standardized chest compressions.


title: GC_ADAL_WT13


title: Hippocampus, DA4, Day3

description:
Library name: Sample 20
Following 72-hour sleep deprivation, cardiac arrest was induced in rats via asphyxiation, with mechanical cardiopulmonary resuscitation (CPR) initiated at 8.5 minutes post-arrest using standardized chest compressions.


title: Astrocyte, control1, rep1

value: Astrocyte


title: Niche bone marrow cells from metastatic bone marrow

description: 10x Genomics

value: Bone

value: GFP-mCherry+


title: GC_ADAL_WT4


title: Tin protoporphyrin rep3

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

description: Library name: SHSY5Y_SnPorph_3

data_processing:
The adapters were trimmed with fastp 0.21.1 (Chen et al., 2018).
Reads were mapped with STAR 2.7.7a (Dobin et al., 2013).
Count matrix was generated with featureCount tool from ssubread-2.0.1 aligner (Liao et al., 2013, 2014).
Assembly: GENCODE release 37 GRCh38.primary assembly.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

growth_protocol: Neuroblastoma SH-SY5Y cells were grown in 6-well plates in 2 mL medium per well up to 80% confluence. The medium consisted of DMEM/F12 (Thermo Fisher Scientific) containing 10% FBS (Thermo Fisher Scientific), 100 U/mL penicillin, and 100 μg/mL streptomycin (Thermo Fisher Scientific).

extract_protocol:
Cells were lysed with the QIAzol Lysis Reagent (Qiagen, Germany). RNA isolation was performed using miRNeasy Micro Kit (Qiagen, Germany) according to the manufacturer's protocol. Nanodrop ND-1000 (Thermo Fisher Scientific, USA) was used to assess quantity and purity of the extracted RNA. Total RNA samples were also QC-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
Libraries for mRNA sequencing were prepared from total RNA samples using MGIEasy RNA Library Prep Set (MGI Tech Co., China).

treatment_protocol: The samples were prepared and added as follows: 10 uL of the stock solution in DMSO was added to the well to have the final concentrations equal to 5 uM HPPE, zinc or tin protoporphyrin; 10 uL DMSO was used for the control well. The medium was removed after 5h incubation, the cells were washed with DPBS tree times and lysed.

value: Tin protoporphyrin


title: GC_ADAL_WT3


title: Hippocampus, DA3, Day3

description:
Library name: Sample 19
Following 72-hour sleep deprivation, cardiac arrest was induced in rats via asphyxiation, with mechanical cardiopulmonary resuscitation (CPR) initiated at 8.5 minutes post-arrest using standardized chest compressions.

value: Sleep deprivation+Cardiac arrest


title: Replicate III HTO

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

country: Germany

institute: Leibniz Institute for Immunotherapy

description:
Sequenced with both NovaSeq and NextSeq 2000
p123_A5_library_run_1_2_matrix.mtx.gz
p123_A5_library_run_1_2_features.tsv.gz
p123_A5_library_run_1_2_barcodes.tsv.gz
SeuratObj_raw_merged_2023-03-24.rds
SeuratObj_clustered_2023-04-12.rds
SeuratObj_reclustered_SingleR-Stem-TA_2023-04-19.rds

library_source: other

data_processing:
Sequencing of libraries on NovaSeq 6000 and NextSeq 2000, producing bcl files
Demultiplexing of bcl files with Illumina Dragon bclconvert version 3.8.4
Mapping to mouse genome with cellranger v.7.0.0 using default parameters
Demultiplexing of treatments using HTOs with Seurat (version 4.0.5), identification of doublets via Cell Hashing and scDblFinder (version 1.8.0)
Normalization, scaling, finding variable features and PCA with Seurat, integration of batches with Harmony (version 0.1.0)
Clustering with Seurat
Annotation with SingleR (version 1.8.1)
Assembly: refdata-gex-mm10-2020-A:ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz, ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M23/gencode.vM23.primary_assembly.annotation.gtf.gz
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for each library, mRNA and HTO combined
Supplementary files format and content: Seurat objects, raw/unfiltered and filtered/processed (dimensionality reduction, clustering, annotation…), as well as reclustered subset based on Stem/TA cells
Supplementary files format and content: monocle was used to subset Stem and TA cells

molecule: protein

source_name: small intestine

extract_protocol:
Intestinal organoids were washed with PBS, resuspended in TrypLE Express Enzyme and digested for 10 minutes at 37°C. Afterwards the reaction was stopped by adding PBS + 0,5% FBS and passed through a 100µm strainer. The single cells were stained with EpCAM-BUV395 and respective Hashing antibodies (TotalSeq B). Live/dead staining was performed with Propidiumiodid. Single cells were sorted by FACS as live/dead- EpCAM+ single cells and directly processed for scRNA-seq
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 and 3’ Feature Barcode Kit (Dual Index)
Oligo-dT priming of full length poly adenylated mRNA, Capture Sequence 1 and 2 for Feature Barcoding library, followed by enzymatic fragmentation, P5,P7 i5,i7 are added via EndRepair, A-tailing and Adaptor Ligation

value: small intestine

value: intestinal organoids

value: intestinal epithelial cells

value: mixed sample (WT, STING GT)

value: mixed sample (control, DAT, ICA)

tag: library type

value: HTO


title: Replicate II HTO

description:
Sequenced with both NovaSeq and NextSeq 2000
p123_A3_library_run_1_2_matrix.mtx.gz
p123_A3_library_run_1_2_features.tsv.gz
p123_A3_library_run_1_2_barcodes.tsv.gz
SeuratObj_raw_merged_2023-03-24.rds
SeuratObj_clustered_2023-04-12.rds
SeuratObj_reclustered_SingleR-Stem-TA_2023-04-19.rds


title: Hippocampus, DA2, Day3

description:
Library name: Sample 18
Following 72-hour sleep deprivation, cardiac arrest was induced in rats via asphyxiation, with mechanical cardiopulmonary resuscitation (CPR) initiated at 8.5 minutes post-arrest using standardized chest compressions.

value: Hippocampus


title: Hippocampus, DA1, Day3

description:
Library name: Sample 17
Following 72-hour sleep deprivation, cardiac arrest was induced in rats via asphyxiation, with mechanical cardiopulmonary resuscitation (CPR) initiated at 8.5 minutes post-arrest using standardized chest compressions.


title: Tin protoporphyrin rep2

description: Library name: SHSY5Y_SnPorph_2


title: GC_ADAL_WT2

value: gastrocnemius (GC) muscle


title: Tin protoporphyrin rep1

description: Library name: SHSY5Y_SnPorph_1


title: Soleus_ADAL_KO5

value: Soleus

value: ADAL KO


title: Replicate I HTO

description:
Sequenced with both NovaSeq and NextSeq 2000
p123_A2_library_run_1_2_matrix.mtx.gz
p123_A2_library_run_1_2_features.tsv.gz
p123_A2_library_run_1_2_barcodes.tsv.gz
SeuratObj_raw_merged_2023-03-24.rds
SeuratObj_clustered_2023-04-12.rds
SeuratObj_reclustered_SingleR-Stem-TA_2023-04-19.rds


title: Astrocyte, control1, rep2


title: Hippocampus, CE8, Day3

description:
Library name: Sample 16
Cardiac arrest was induced in rats through asphyxiation. Mechanical CPR with epinephrine was initiated at 8.5 minutes post-arrest. Post-resuscitation management included electroacupuncture intervention (delivered within 1 hour post-ROSC) and daily EA sessions for 72 hours, with standardized parameters: 2/15 Hz alternating frequency, 1.5 mA intensity, and 30-minute duration per session at zusanli (ST36) and Pericardium 6 (PC6) acupoints.

value: Cardiac arrest+Electroacupuncture


title: GC_ADAL_WT1

value: ADAL WT


title: Replicate III GEX

molecule: polyA RNA

value: mRNA


title: Zinc protoporphyrin rep2

description: Library name: SHSY5Y_ZnPorph_2

value: Zinc protoporphyrin


title: Hippocampus, CE7, Day3

description:
Library name: Sample 15
Cardiac arrest was induced in rats through asphyxiation. Mechanical CPR with epinephrine was initiated at 8.5 minutes post-arrest. Post-resuscitation management included electroacupuncture intervention (delivered within 1 hour post-ROSC) and daily EA sessions for 72 hours, with standardized parameters: 2/15 Hz alternating frequency, 1.5 mA intensity, and 30-minute duration per session at zusanli (ST36) and Pericardium 6 (PC6) acupoints.


title: Distal bone marrow cells from metastatic bone marrow

description: 10x Genomics

value: Bone

value: Bone marrow cells

value: GFP-mCherry-

value: Bone Metatasis


title: GC_ADAL_KO17


title: Replicate II GEX

value: small intestine

value: intestinal organoids


title: Zinc protoporphyrin rep1

description: Library name: SHSY5Y_ZnPorph_1


title: Hippocampus, CE6, Day3

description:
Library name: Sample 14
Cardiac arrest was induced in rats through asphyxiation. Mechanical CPR with epinephrine was initiated at 8.5 minutes post-arrest. Post-resuscitation management included electroacupuncture intervention (delivered within 1 hour post-ROSC) and daily EA sessions for 72 hours, with standardized parameters: 2/15 Hz alternating frequency, 1.5 mA intensity, and 30-minute duration per session at zusanli (ST36) and Pericardium 6 (PC6) acupoints.


title: Replicate I GEX

value: intestinal epithelial cells

value: mixed sample (WT, STING GT)


title: HPPE rep3

description: Library name: SHSY5Y_HPPE_3

value: HPPE


title: GC_ADAL_KO16


title: WT, rep5

city: Cologne

first: Ulrike

last: Göbel

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Bioinformatics Core Facility

institute: CECAD Research Center

data_processing:
Merging: The two raw fastq files (from two sequencer lanes) derived from each biological sample were merged by simple concatenation (following the advice of the sequencing center).
Trimming: The merged fastq files were 3-trimmed by two rounds of cutadapt v 3.2, removing the Illumina TruSeq adapter and poly-A runs of length >= 18. Exact cutadapt call for one sample:  cutadapt --cores=3 --minimum-length=35 --nextseq-trim=20 --overlap=10  -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC [merged fastq.gz files of a given Sample]  | cutadapt --cores=3 --minimum-length=35 --nextseq-trim=20  --overlap=10 -a 'A{18}' -o [merged and trimmed fastq.gz file of a given Sample] -
Read Alignment: subread-buildindex and subread-align (both v 2.0.1) were used to build an index of the Mus_musculus GRCm38 genome (Ensembl version 100) plus the ERCC92 spike-in sequences and  to align the trimmed reads against the index. Exact subread-align call for one sample: subread-align -T 4 -t 0 --multiMapping -B 5 --sortReadsByCoordinates -i [index built by subread-index] -r [merged and trimmed fastq.gz file of a given Sample] -a Mus_musculus.GRCm38.100.gtf -o [bam file containing the read alignments of a given Sample]
Read Counting: featureCounts v 2.01 was used to count the reads per gene, using  Mus_musculus.GRCm38.100.gtf (Ensembl version 100) as gene annotation. Exact featureCounts call for one sample: featureCounts -a Mus_musculus.GRCm38.100.ERCC.gtf.gz -o [output file containing the counts for a given sample] -F "GTF" -t "exon" -g "gene_id" --minOverlap 20 -M --primary -O --fraction -J -Q 30 -T 4 --verbose [bam file containing the read alignments of a given Sample]. The per-sample count output files were subsequently combined into table featureCounts_from_merged_and_trimmed_reads.tsv, using R-4.0.0.
Assembly: mm10 (Mus_musculus GRCm38, Ensembl version 100)
Supplementary files format and content: tab-delimited text file, where the first column lists the Ensembl gene ID, and the remaining columns contain the raw featureCounts read counts for the individual samples, with column names connected to samples as listed in the SAMPLES section

source_name: colon

extract_protocol:
Total RNA was extracted with the Direct-zol RNA Miniprep Kit by using RNAzol® RT. For each mouse, 2μg total RNA (OD260/280 = 1.8-2.1, OD260/230 > 1.5 and RIN > 7) was used.
Lexogen 3’ QuantSeq Kit (FWD protocol)

value: colon

value: WT


title: GC_ADAL_KO6

value: gastrocnemius (GC) muscle


title: Zinc protoporphyrin rep3

description: Library name: SHSY5Y_ZnPorph_3


title: WT, rep4


title: Hippocampus, CE4, Day3

description:
Library name: Sample 12
Cardiac arrest was induced in rats through asphyxiation. Mechanical CPR with epinephrine was initiated at 8.5 minutes post-arrest. Post-resuscitation management included electroacupuncture intervention (delivered within 1 hour post-ROSC) and daily EA sessions for 72 hours, with standardized parameters: 2/15 Hz alternating frequency, 1.5 mA intensity, and 30-minute duration per session at zusanli (ST36) and Pericardium 6 (PC6) acupoints.

value: Hippocampus


title: GC_ADAL_KO5

value: ADAL KO


title: Hippocampus, CE3, Day3

description:
Library name: Sample 11
Cardiac arrest was induced in rats through asphyxiation. Mechanical CPR with epinephrine was initiated at 8.5 minutes post-arrest. Post-resuscitation management included electroacupuncture intervention (delivered within 1 hour post-ROSC) and daily EA sessions for 72 hours, with standardized parameters: 2/15 Hz alternating frequency, 1.5 mA intensity, and 30-minute duration per session at zusanli (ST36) and Pericardium 6 (PC6) acupoints.

value: Cardiac arrest+Electroacupuncture


title: HPPE rep1

description: Library name: SHSY5Y_HPPE_1


title: WT, rep3


title: Control rep3

description: Library name: SHSY5Y_Ctrl_3

value: DMSO


title: Hippocampus, CE2, Day3

description:
Library name: Sample 10
Cardiac arrest was induced in rats through asphyxiation. Mechanical CPR with epinephrine was initiated at 8.5 minutes post-arrest. Post-resuscitation management included electroacupuncture intervention (delivered within 1 hour post-ROSC) and daily EA sessions for 72 hours, with standardized parameters: 2/15 Hz alternating frequency, 1.5 mA intensity, and 30-minute duration per session at zusanli (ST36) and Pericardium 6 (PC6) acupoints.


title: Liver_ADKWT_12_1

value: Liver

value: ADK WT


title: Liver_ADKWT_6_2


title: GC_ADAL_KO15


title: WT, rep2


title: Hippocampus, CE1, Day3

description:
Library name: Sample 9
Cardiac arrest was induced in rats through asphyxiation. Mechanical CPR with epinephrine was initiated at 8.5 minutes post-arrest. Post-resuscitation management included electroacupuncture intervention (delivered within 1 hour post-ROSC) and daily EA sessions for 72 hours, with standardized parameters: 2/15 Hz alternating frequency, 1.5 mA intensity, and 30-minute duration per session at zusanli (ST36) and Pericardium 6 (PC6) acupoints.


title: Hippocampus, CA8, Day3

description:
Library name: Sample 8
Cardiac arrest was induced in rats through asphyxiation, with mechanical chest compressions combined with epinephrine injection administered for cardiopulmonary resuscitation at 8.12 minutes following cardiac arrest cessation

value: Cardiac arrest


title: Liver_ADKWT_8_6


title: Control rep1

description: Library name: SHSY5Y_Ctrl_1


title: Liver_ADKWT_5_4


title: Control rep2

description: Library name: SHSY5Y_Ctrl_2


title: Hippocampus, CE5, Day3

description:
Library name: Sample 13
Cardiac arrest was induced in rats through asphyxiation. Mechanical CPR with epinephrine was initiated at 8.5 minutes post-arrest. Post-resuscitation management included electroacupuncture intervention (delivered within 1 hour post-ROSC) and daily EA sessions for 72 hours, with standardized parameters: 2/15 Hz alternating frequency, 1.5 mA intensity, and 30-minute duration per session at zusanli (ST36) and Pericardium 6 (PC6) acupoints.


title: XBP1IEC-KO;Casp8IEC-KO;MLKLKO, rep5


title: Hippocampus, CA7, Day3

description:
Library name: Sample 7
Cardiac arrest was induced in rats through asphyxiation, with mechanical chest compressions combined with epinephrine injection administered for cardiopulmonary resuscitation at 8.11 minutes following cardiac arrest cessation


title: HPPE rep2

description: Library name: SHSY5Y_HPPE_2


title: Liver_ADKWT_5_2


title: tcf25_ko_S_rep1

city: Changsha

first: Xiaomin

last: Shang

state: Hunan Province

address: 172 Tongzipo Road

department: Department of Parasitology

institute: Central South University

description: Library name: sample7

data_processing:
RNA-seq reads were trimmed by trim-galore.
The resulting data was aligned to genome using Hisat2.
The Samtools was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
Using Picard, PCR duplicates were removed from the sequencing data.
Read counts  were obtained using FeatureCounts. The BAM alignment files were processed with bamCoverage to generate BigWig coverage files.
Assembly: Pf 3D7 v64
Supplementary files format and content: FPKM values for all Plasmodium falciparum samples were compiled in an Excel file.

organism: Plasmodium falciparum

growth_protocol: Parasites were cultured in medium containing 0.5% Albumax II with O type fresh red blood cells, and a gas phase with 5% O2, 5 % CO2 at 37 °C.

extract_protocol:
The RNA was extracted with the TransZol Up Plus RNA kit. 500ng of  total RNA was used  for the construction of sequencing libraries.
Libraries were constructed ollowing the manufacturer's protocols.

treatment_protocol: Parasites were tightly synchronized by percoll or sorbitol.

tag: developmental stage

value: schizont

value: protozoa

value: tcf25 knockout


title: Hippocampus, CA6, Day3

description:
Library name: Sample 6
Cardiac arrest was induced in rats through asphyxiation, with mechanical chest compressions combined with epinephrine injection administered for cardiopulmonary resuscitation at 8.10 minutes following cardiac arrest cessation


title: XBP1IEC-KO;Casp8IEC-KO;MLKLKO, rep3


title: tcf25_ko_R_rep2

description: Library name: sample6

value: ring


title: Liver_ADKWT_1_3


title: XBP1IEC-KO;Casp8IEC-KO;MLKLKO, rep2


title: Hippocampus, CA5, Day3

description:
Library name: Sample 5
Cardiac arrest was induced in rats through asphyxiation, with mechanical chest compressions combined with epinephrine injection administered for cardiopulmonary resuscitation at 8.9 minutes following cardiac arrest cessation


title: WT, rep1


title: tcf25_ko_R_rep1

description: Library name: sample5


title: Hippocampus, CA4, Day3

description:
Library name: Sample 4
Cardiac arrest was induced in rats through asphyxiation, with mechanical chest compressions combined with epinephrine injection administered for cardiopulmonary resuscitation at 8.8 minutes following cardiac arrest cessation


title: WT_S_rep2

description: Library name: sample4

value: normal


title: tcf25_ko_S_rep2

description: Library name: sample8


title: Hippocampus, CA3, Day3

description:
Library name: Sample 3
Cardiac arrest was induced in rats through asphyxiation, with mechanical chest compressions combined with epinephrine injection administered for cardiopulmonary resuscitation at 8.7 minutes following cardiac arrest cessation


title: XBP1IEC-KO;Casp8IEC-KO;MLKLKO, rep1


title: WT_S_rep1

description: Library name: sample3


title: XBP1IEC-KO;Casp8IEC-KO;MLKLKO, rep4


title: Liver_ADKKO_8_4

value: ADK KO


title: XBP1IEC-KO;Casp8IEC-KO, rep4


title: Liver_ADKKO_11_1


title: WT_R_rep2

description: Library name: sample2


title: Hippocampus, CA2, Day3

description:
Library name: Sample 2
Cardiac arrest was induced in rats through asphyxiation, with mechanical chest compressions combined with epinephrine injection administered for cardiopulmonary resuscitation at 8.6 minutes following cardiac arrest cessation


title: XBP1IEC-KO;Casp8IEC-KO, rep3


title: Liver_ADKKO_6_3


title: WT_R_rep1

description: Library name: sample1


title: Liver_ADKKO_12_5


title: XBP1IEC-KO;Casp8IEC-KO, rep2


title: 1d-1

value: brain

value: glioblastoma

value: YFSS in neural differentiation media for 1d


title: TCF25_rep2

description: Library name: sample4

library_source: genomic

data_processing:
ChIP-seq reads were trimmed by trim-galore.
The resulting data was aligned to genome using Bowtie2.
The Samtools was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
BAM files were converted to BigWig format using bamCoverage from the deepTools
The MACS2 peak-calling algorithm was applied to find target genes.
Assembly: Pf 3D7 v64
Supplementary files format and content: All samples were visualized using BigWig files.

molecule: genomic DNA

extract_protocol:
The DNA was extracted with the MinElute PCR purification kit.
Libraries were prepared with the VAHTS Universal DNA Library Prep Kit for Illumina V4 (Vazyme) following manufacturer's instructions.

value: HA antibodies


title: Brain_ADKWT_12_1

source_name: Brain

value: Brain


title: Liver_ADKKO_1_4

source_name: Liver


title: XBP1IEC-KO;Casp8IEC-KO, rep1

value: colon


title: Sham-P7-2

first: Zheng

last: WANG

state: Shanghai

address: Shanghai Dongfang Road No.1678 Shanghai Children's Medical Center

institute: Shanghai Jiaotong University

description: Library name: Sample 11

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rat whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Bray N, Pimentel H, Melsted P, et al., Near-optimal RNA-Seq quantification, 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm38(mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: left ventricular myocardiocytes

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 ml USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads (PE150) were generated.

value: left ventricular myocardiocytes


title: TCF25_rep1

description: Library name: sample3


title: XBP1IEC-KO, rep5


title: Sham-P7-1

description: Library name: Sample 10


title: XBP1IEC-KO;Casp8IEC-KO, rep5


title: Colorectal cancer 3

description:
524_Tumor
Gene expression for clinical colorecal cancer tissue

value: Colorectal cancer

value: Yes

value: Tissue


title: Input_rep2

description: Library name: sample2


title: Brain_ADKWT_8_6

value: ADK WT


title: XBP1IEC-KO, rep4


title: Liver_ADKKO_6_4

value: Liver


title: Input_rep1

description: Library name: sample1

value: schizont

value: protozoa


title: Brain_ADKWT_6_2


title: Hippocampus, CA1, Day3

description:
Library name: Sample 1
Cardiac arrest was induced in rats through asphyxiation, with mechanical chest compressions combined with epinephrine injection administered for cardiopulmonary resuscitation at 8.5 minutes following cardiac arrest cessation

value: Hippocampus

value: Cardiac arrest


title: XBP1IEC-KO, rep3


title: ABS-P7-2

description: Library name: Sample 8


title: Brain_ADKWT_5_4


title: ABS-P7-1

description: Library name: Sample 7


title: Sham-P7-3

description: Library name: Sample 12


title: Brain_ADKWT_5_2


title: B16 cells, Fam222B-siRNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: B16 cells, Fam222B-siRNA

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: B16 cells were maintained with DMEM containing 5%FBS.

extract_protocol: RNA samples were extracted from cells using Tri reagent (Cosmo Bio Co.).

treatment_protocol: B16 cells were preincubated in 5% FBS-DMEM for 24 h and then each siRNA was introduced into B16 cells using the Lipofectamine RNAiMAX. After 48 h of incubation, total RNA was isolated.

value: melanoma cell line B16


title: Sham-P3-3

description: Library name: Sample 6


title: Brain_ADKWT_1_3


title: XBP1IEC-KO;Casp8IEC-KO;TNFR1IEC-KO, rep5


title: XBP1IEC-KO, rep1


title: XBP1IEC-KO;Casp8IEC-KO;TNFR1IEC-KO, rep4


title: XBP1IEC-KO, rep2


title: ABS-P7-3

description: Library name: Sample 9


title: ABS-P3-3

description: Library name: Sample 3


title: XBP1IEC-KO;Casp8IEC-KO;TNFR1IEC-KO, rep3


title: Brain_ADKKO_11_1

value: ADK KO


title: Sham-P3-1

description: Library name: Sample 4


title: XBP1IEC-KO;Casp8IEC-KO;TNFR1IEC-KO, rep2


title: Brain_ADKKO_8_4


title: ABS-P3-2

description: Library name: Sample 2


title: Ts12S-1

city: Lanzhou

first: QI

last: Wang

state: Gansu

address: Yintan Road Street

department: College of Animal Science and Technology

institute: Gansu Agricultural University

description: Library name: Sample 7

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads  without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oncorhynchus mykiss

source_name: spleen tissues

growth_protocol: Fish weighing (130 ± 5.0) g were selected and temporarily reared for two weeks in a flow-through aquaculture system with DO of 8.5 ± 0.1 mg/L, water temperature of 12 ± 0.1℃.

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

treatment_protocol: Two weeks after rainbow trout were suspended, healthy rainbow trout were randomly divided into three groups, including normoxia, moderate hypoxia, and severe hypoxia groups, the oxygen levels were maintained at 8.5 ± 0.1, 4.5 ± 0.1, and 3.0 ± 0.1 mg/L, respectively, and the low oxygen environment was created by mixing oxygen and nitrogen.

value: spleen tissues

tag: time point

value: severe hypoxia stress


title: Ts12S-2

description: Library name: Sample 8


title: Tm12S-3

description: Library name: Sample 6

value: moderate hypoxia stress


title: Tm12S-2

description: Library name: Sample 5


title: ABS-P3-1

description: Library name: Sample 1


title: Ts12S-3

description: Library name: Sample 9


title: Brain_ADKKO_6_4

value: Brain


title: Sham-P3-2

description: Library name: Sample 5


title: B16 cells, Control-siRNA

source_name: B16 cells, control-siRNA

value: Control-siRNA


title: XBP1IEC-KO;Casp8IEC-KO;TNFR1IEC-KO, rep1

value: colon


title: Brain_ADKKO_12_5


title: Brain_ADKKO_6_3


title: Tm12S-1

description: Library name: Sample 4


title: WT/Untreated/WUT-2

city: Orlando

first: Vandana

last: Sekhar

state: Florida

address: 6900 Lake Nona Blvd, Burnett School Of Biomed Sciences

institute: University of Central Florida (UCF)

description: Library name: WUT-2

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).Sequence quality was examined using the FastQC [1] software.
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt [2] ) were aligned to reference genome using Hisat2 software [3] . The transcript abundances for each sample was estimated with StringTie [4] , and the FPKM [8] value for gene and transcript level were calculated with R package Ballgown
Sequencing Type Paired-end Reference Genome Rnor6 Annotation Ensembl
Assembly: Reference Genome Rnor6
Supplementary files format and content: csv files include FPKM values for each sample

source_name: hepatoma cell line

growth_protocol: Rat hepatoma cells (McARH-7777) were obtained from American Type Culture Collection (ATCC) and cultured in Dulbecco's modified Eagle's medium (Life Technologies) supplemented with 10% FBS (Life Technologies) and 1% penicillin-streptomycin (Sigma Co) in 5% CO2.

extract_protocol:
Trizol extraction was used to collect the total RNA from cells
1. Total RNA is enriched by oligo (dT) magnetic beads (rRNA removed); 2. RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific. The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method. To sequence the libraries on the Illumina NovaSeq 6000 instrument, the barcoded libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified in situ, and subsequently sequenced for 150 cycles for both ends on Illumina NovaSeq 6000 instrument.

treatment_protocol: WT and KO cells untreated and treated with 0.4mM BSA-Oleic acid for 1 h and collected 24 h post treatment.

value: hepatoma cell line

value: Wildtype

value: untreated


title: Casp8IEC-KO, rep5


title: CS-3

description: Library name: Sample 3

value: 0 h

value: control


title: Casp8IEC-KO, rep4


title: WT/Untreated/WUT-1

description: Library name: WUT-1


title: Brain_ADKKO_1_4


title: CS-2

description: Library name: Sample 2


title: CS-1

description: Library name: Sample 1


title: Casp8IEC-KO, rep3


title: WT/Treated/WTT-1

description: Library name: WTT-1

value: 0.4mM BSA-Oleic acid treatment


title: WT/Treated/WTT-2

description: Library name: WTT-2


title: KO/Untreated/KUT-1

description: Library name: KUT-1

value: SVIP KO


title: Casp8IEC-KO, rep2


title: H3K27me3.nos-White.3 [ChIP-seq]

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

data_processing:
Sequencing adapters were removed using Trim Galore! (v0.6.4, ‑‑paired ‑‑stringency 6 ).
The resulting reads were mapped to their respective reference genome using Bowtie2 (v2.4.2), reporting at most one hit for each read .
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, ‑‑binSize 1 ‑‑ignoreForNormalization chrM ‑‑normalizeUsing CPM  ‑‑exactScaling ‑‑scaleFactor s ‑‑skipNonCoveredRegions ‑‑minMappingQuality 50 --extendReads --centerReads), where the scale factor, s, was set to the number of uniquely mapped reads divided by all mapped reads.
Assembly: dm6
Supplementary files format and content: BigWig with read coverage per position across the genome.

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Flies were kept at standard condition at 25°C

extract_protocol:
100 ovary pairs were manually dissected into Schneider media and cross-linked in 1% formaldehyde/PBS for 10 min at room temperature with agitation
Libraries were prepared following the manufacturer’s instructions with 2S™ Plus DNA Library Kit 24 rxn from IDT

value: ovary

value: Nanos Gal4 VP16-expressed dsRNA-white BDSC_35573

tag: antibody

value: Histone H3K27me3 antibody _Rabbit_Millipore 07-449


title: KO/Untreated/KUT-2

description: Library name: KUT-2


title: Casp8IEC-KO, rep1


title: input.nos-White.1 [ChIP-seq]

value: none (input)


title: 12 SU iPSC line 3

city: Bangkok

first: Chanatip

last: Metheetrairut

state: Bangkok

address: 2 Wanglang Rd.

department: Department of Biochemistry, Faculty of Medicine Siriraj Hospital

country: Thailand

institute: Mahidol University

description: Culture iPS cells were harvested for total RNA by miRNeasy mini kit (Qiagen). miRNA expression were examined by nCounter® miRNA Expression Assay (Human v3 miRNA panel).

hyb_protocol: Labeled samples were hybridized to the miRNA Capture ProbeSet at 65C overnight.

scan_protocol: Samples were examined on the two nCounter® Analysis System instruments according to the manufacturer’s protocol (NanoString Technologies): samples were immobilized on the sample cartridge on the nCounter® Prep Station instrument; then the reporter code counts (RCC) were performed by the nCounter® Digital Analyzer instrument. Data were exported as RCC files.

data_processing: Exported RCC files were processed with the nSolver® Analysis Software ver. 4.0.70 (NanoString Technologies). Initially, Imaging QC, Binding Density, QC, Positive Control Linearity QC, Positive Control Limit of Detection QC, and Ligation QC were done. Reads were normalized with the geometric mean of positive control counts and to the geometric mean of the top 100 expressed miRNAs. miRNAs were considered to be expressed if their normalized counts were above the 95% CI of normalized counts of negative control probes (>31.12).

label: biotin

source_name: iPSC line

label_protocol: 100 ng of total RNA were labeled by hybridization to the miRNA CodeSet in the nCounter® miRNA Expression Assay according to the manufacturer's protocol.

growth_protocol: Cells were cultured on Matrigel-coated wells (Matrigel (BD Biosciences) diluted in DMEM:F-12 (Gibco) at the ratio of 1:50) in Essential 8 medium (Gibco) at 37C with 5% CO2.

extract_protocol: Cells were lysed by QIAzol Lysis Reagent (Qiagen). RNA extraction was performed according to the manufacturer’s protocol of the miRNeasy mini kit (Qiagen).

treatment_protocol: All iPSC lines were cultured until passage 35. They were then lysed by QIAzol Lysis Reagent (Qiagen) and stored at -80C until RNA extraction.

tag: iPSc derived from

value: exfoliated renal epithelial cells


title: KO/Treated/KT-2

description: Library name: KT-2

tag: genotype


title: input.nos-E(z).1 [ChIP-seq]

value: Nanos Gal4 VP16-expressed dsRNA-E(z) BDSC_33659


title: 11 SU iPSC line 2


title: KO/Treated/KT-1

description: Library name: KT-1

tag: treatment


title: H3K27me3.nos-White.2 [ChIP-seq]


title: Cis7d Group rep.4 [scRNA-seq]

city: Nanjing

first: Bingquan

last: Deng

address: Nanjing Medical University, No.109 Longmian Avenue, Jiangning District

institute: Nanjing Medical University

description: 10x Genomics

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software（version2.20）
Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline(version 6.1.1) and scRNA-seq data were aligned to GRCm38 reference genome
The Cell Ranger output was loaded into Seurat(version 3.1.1) be used to Dimensional reduction, clustering, and analysis of scRNA-seq data
Cells were captured from 11 samples and screened by control threshold of gene expressed >200 and mitochondrial-DNA <70%
Marker genes that expressed in more than 10% of the cells in a cluster (the average log(Fold Change) ≥0.26, P value ≤0.01) were selected
Assembly: GRCm38
Supplementary files format and content: tsv and mtx include barcodes, genes and matrix for each Sample

source_name: kidney

extract_protocol:
Single-cell suspensions were loaded to 10x Chromium to capture more than 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3)
The cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) at a minimum depth of 90,000 reads per cell

treatment_protocol: 3/7 days after intraperitoneal injection of 20mg/kg (body weight) cisplatin, Sham group injected with the same volume of normal saline

value: kidney

tag: Sex

value: male

tag: age

value: 8-10 weeks old

tag: strain

value: 7 days after intraperitoneal injection of cisplatin


title: 09 ST iPSC line 3

value: peripheral blood T cells


title: Cis7d Group rep.2 [scRNA-seq]

description: 10x Genomics


title: Cis7d Group rep.3 [scRNA-seq]

description: 10x Genomics


title: 08 ST iPSC line 2


title: 10 SU iPSC line 1


title: H3K27me3.nos-White.1 [ChIP-seq]


title: 07 ST iPSC line 1


title: LS10, Lung, Sham air inhalation, Rep1

city: Minneapolis

first: Allison

middle: M.

last: Haaning

state: MN

address: 117 Pleasant St. SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

data_processing:
Adaptor sequences were trimmed from raw reads using Trimmomatic (v 0.33), and quality of raw and trimmed reads was assessed with FastQC (v 0.11.7).
Ribosomal RNA (rRNA) contamination, which was low in all samples (<= 1%), was quantified by aligning a subsample of 10,000 reads pairs from each sample to rRNA sequences from the SILVA database (release 132).
Trimmed reads were aligned to the Rattus norvegicus reference genome (mRatBN7.2, Ensembl release109) using HISAT2 (v 2.1.0). Reads with mapping quality <60 were removed.
Raw counts were generated using the featureCounts tool from the Subread package (v 1.6.2).
For each tissue raw counts were imported into R (v 4.3.0). Genes shorter than 200 bp or with very low expression (<1 CPM in at least 50% of samples) were pruned from the counts matrix before differential expression testing with EdgeR (v 4.0.5). CPM and log2 CPM values in the processed dataset were generated using the EdgeR cpm function (normalized.lib.sizes = TRUE, and prior.count = 1 for log2 CPM).
Assembly: mRatBN7.2, Ensembl release109
Supplementary files format and content: Brain_Processed_Data_for_GEO_Submission.xlsx contains three tabs with raw counts, CPM, and log2 CPM values after filtering out genes that were very short (< 200bp) or with very low expression (<1 CPM in at least 50% of brain samples).
Supplementary files format and content: Lung_Processed_Data_for_GEO_Submission.xlsx contains three tabs raw counts, CPM, and log2 CPM values after filtering out genes that were very short (< 200bp) or with very low expression (<1 CPM in at least 50% of lung samples).

source_name: Lung

growth_protocol: Male Sprague Dawley rats (8 weeks, 250–275 g) were obtained from Hilltop Laboratories (Scottdale, PA) and housed in an AAALAC approved facility at WVU. All procedures were approved by the WVU Institutional Animal Care and Use Committee (protocol 1602000621) and conformed to the most current National Institutes of Health (NIH) Guidelines for the Care and Use of Laboratory Animals. Housing conditions included 12:12 h light:dark cycle, 20–26 °C, 30–70% relative humidity, acclimatization for 48–72 h prior to any procedure and ad libitum access to food and water.

extract_protocol:
Tissue was harvested 24h after exposure. Euthanasia was performed via exsanguination under deep anesthesia (5% induction, 2% maintenance with isoflurane gas) followed by organ removal. Whole tissues  (brain and lung) were snap frozen in liquid nitrogen and stored at −80 °C. Lung and brain tissue was sent to the University of Minnesota Genomics Center (UMGC) for isolation of total RNA using an RNAeasy Plus Universal kit (Qiagen, Germantown, MD), according to manufacturer’s instructions.
Libraries were prepared by the UMGC. RNA was quantified using a RiboGreen assay (Thermo Fisher, Waltham, MA), and quality was assessed by capillary electrophoresis using a Tapestation (Agilent, Santa Clara, CA). All samples had an RNA integrity number (RIN) >= 8. Libraries were prepared using a TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA), and next-generation sequencing was performed using a Novaseq 6000 (Illumina) to generate 150 bp read pairs.

treatment_protocol: Rats were randomly assigned to sham-control or treatment groups (n=10/group). The treatment group was exposed to a mixture of carbon black (target concentration = 6 mg/m3) and naphthalene vapor (target concentration = 10 PPM) for 6 h/day for 3 consecutive days  (CBN), and the sham-control group was exposed to HEPA filtered air only. The exposure chamber was 22″ × 20″ × 20″ (wdh) with an approximate volume of 144 L. The airflow through the chamber was approximately 28 LPM during exposures.

value: Lung

value: 8 weeks

value: Sprague Dawley

value: Sham air inhalation for 6 hrs/day for 3 consectuve days


title: H3K27me3.nos-E(z).3 [ChIP-seq]


title: 06 SK iPSC line 3

value: hair follicle keratinocytes


title: LS9, Lung, Sham air inhalation, Rep7


title: 05 SK iPSC line 2


title: Cis3d Group rep.4 [scRNA-seq]

description: 10x Genomics

value: 3 days after intraperitoneal injection of cisplatin


title: H3K27me3.nos-E(z).2 [ChIP-seq]

value: ovary


title: LS6, Lung, Sham air inhalation, Rep6


title: Cis3d Group rep.3 [scRNA-seq]

description: 10x Genomics


title: H3K27me3.nos-E(z).1 [ChIP-seq]


title: 04 SK iPSC line 1


title: LS5, Lung, Sham air inhalation, Rep3


title: input.nos-White.1.2 [ChIP-seq]

value: Nanos Gal4 VP16-expressed dsRNA-white BDSC_35573


title: LS4, Lung, Sham air inhalation, Rep2


title: Cis3d Group rep.1 [scRNA-seq]

description: 10x Genomics


title: Cis3d Group rep.2 [scRNA-seq]

description: 10x Genomics


title: input.nos-Kipf.1.2 [ChIP-seq]

value: Nanos Gal4 VP16-expressed shRNA-Kipferl VDRC_314048


title: LCN8, Lung, CBN inhalation, Rep5

value: Carbon black nanoparticles and naphthalene (CBN) inhalation for 6 hrs/day for 3 consecutive days


title: Sham Group rep.3 [scRNA-seq]

description: 10x Genomics

value: Intraperitoneal injection of normal saline


title: H3K27me3.nos-White.3.2 [ChIP-seq]

value: Histone H3K27me3 antibody _Rabbit_Cell signaling (C36B11) mAB#9733


title: Old_GF

city: Gainesville

first: Adam

last: Wong

address: 1881 Natrual Area Drive, Steinmetz Hall

department: Entomology and Nematology Department

institute: University of Florida

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: BDGP 6.28
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Adult brain

extract_protocol:
Fly brain dissection and tissue dissociation were conducted before 11 AM. Fly brains were dissected in ice-cold Schneider’s Drosophila medium (Gibco), with twenty brains pooled for each sample. The dissected brains were immediately incubated with 1.2 mg/mL Dispase (Sigma-Aldrich) and 0.6 mg/mL Collagenase (Invitrogen) in a shaking incubator (Eppendorf) at 25°C and 500 rpm for 75 minutes. Following the incubation, the samples were washed three times with ice-cold Dulbecco’s phosphate-buffered saline (DPBS, Gibco) and resuspended in 50 µm DPBS with 0.04% bovine serum albumin (BSA, Sigma). The cell suspension was then passed through a 35 µm cell strainer (Falcon) to remove debris. Cell number and viability were assessed simultaneously using an epifluorescence microscope (Leica) and an Automated Cell Counter (LUNA) to ensure the cell viability to exceed 90%.
Single-cell libraries were prepared using the Chromium Single Cell 3’ Reagent Kit v2 (10x Genomics) in accordance with the manufacturer’s manual.

value: Adult brain

value: Canton-S

value: Axenic


title: LCN6, Lung, CBN inhalation, Rep3

value: male


title: Old_CV

description: 10X Genomics

value: Conventional


title: H3K27me3.nos-White.2.2 [ChIP-seq]


title: LCN7, Lung, CBN inhalation, Rep4

value: Lung


title: 03 SF iPSC line 3

value: dermal fibroblasts


title: Cis7d Group rep.1 [scRNA-seq]

description: 10x Genomics

value: kidney

value: 8-10 weeks old

value: 7 days after intraperitoneal injection of cisplatin


title: Sham Group rep.2 [scRNA-seq]

description: 10x Genomics


title: 02 SF iPSC line 2


title: 01 SF iPSC line 1


title: Young_CV

description: 10X Genomics


title: H3K27me3.nos-White.1.2 [ChIP-seq]


title: Sham Group rep.1 [scRNA-seq]

description: 10x Genomics


title: RNAseq of porcine: skin woundDay_0_ID1323

city: Santa Cruz

first: Ksenia

last: Zlobina

state: California

address: 1156 High Street

department: Applied Mathematics

institute: University of California Santa Cruz

description:
Library name: A_1_1323_1
A_1_1323

data_processing:
The folowings prepared by Novogene: Raw Data, as well as gene counts in raw and normalized format: gene_count.txt and  gene_fkpm.txt
Assembly: Sus scrofa
Supplementary files format and content: gene_count.txt - the readcount list with the annotation of each gene
Supplementary files format and content: gene_fpkm.txt - the FPKM list with the annotation of each gene

organism: Sus scrofa domesticus

source_name: Skin wound tissue

extract_protocol:
mRNA was extracted from these samples with the RNeasy fibrous tissue mini kit (Qiagen)
>200ng mRNA/sample were sent to Novogene for RNA sequencing. The followings were done by Novogene: 1. RNA Sample QC 2. Library Preparation (Poly-A Enrichment) 3. Sequencing (Illumina – PE150 – 20M Paired Reads)

value: Skin wound tissue

tag: time

tag: anumal id


title: Young_GF

description: 10X Genomics


title: Rhino.nos-White.2 [ChIP-seq]

value: ovary

value: Rhino polyclonal antibody_Rabbit_Eurogentec (Mohn et al, 2014)


title: H3K27me3.nos-Kipf.2.2 [ChIP-seq]

value: Nanos Gal4 VP16-expressed shRNA-Kipferl VDRC_314048


title: H3K27me3.nos-Kipf.1.2 [ChIP-seq]


title: RNAseq of porcine: skin woundDay_4_ID1328_Wound_F_edge

description:
Library name: E_51_F_E_1
E_51_F_E

tag: location

value: edge

tag: wound id


title: LCN5, Lung, CBN inhalation, Rep2

value: 8 weeks

value: Sprague Dawley

value: Carbon black nanoparticles and naphthalene (CBN) inhalation for 6 hrs/day for 3 consecutive days


title: BS7, Brain, Sham air inhalation, Rep7

value: Brain

value: Sham air inhalation for 6 hrs/day for 3 consectuve days


title: MASLD CosMX Slide2 (Sample 3, Sample 4)

city: Tsu city

first: Naoto

last: Fujiwara

state: Mie

address: 2-174 Edobashi

institute: Mie University

description: CosMx spatial transcriptome of MASLD biopsies (F2), Samples 3 and 4.

scan_protocol: Samples were processed following NanoString's standard protocol (CosMx SMI Instrument User Manual, MAN-10161-02-1)

data_processing: Raw spatial transcriptomics data were processed, normalized, and batch-corrected using Harmony implemented in Seurat v5. Cell segmentation was performed based on morphological markers (DAPI, pan-CK, CD45, CK8/18). Cells with total RNA counts ≥50 and detected probes ≥30 were included in downstream analyses.

source_name: Liver biopsy

label_protocol: CosMx Human Universal Cell Characterization Panel

extract_protocol: Samples were processed following NanoString's standard protocol (Manual Slide Preparation, MAN-10159-02).

value: Liver biopsy


title: Rhino.nos-E(z).2 [ChIP-seq]

value: Nanos Gal4 VP16-expressed dsRNA-E(z) BDSC_33659


title: Rhino.nos-White.1 [ChIP-seq]

value: Nanos Gal4 VP16-expressed dsRNA-white BDSC_35573


title: RNAseq of porcine: skin woundDay_4_ID1328_Wound_F_center

description:
Library name: E_52_F_C_1
E_52_F_C

value: center


title: BS6, Brain, Sham air inhalation, Rep6

value: male


title: LCN4, Lung, CBN inhalation, Rep1

value: Lung


title: RNAseq of porcine: skin woundDay_5_ID1323_Wound_B_center

description:
Library name: F_56_B_C_1
F_56_B_C


title: Rhino.nos-E(z).1 [ChIP-seq]


title: BS2, Brain, Sham air inhalation, Rep2


title: RNAseq of porcine: skin woundDay_5_ID1323_Wound_K_edge

description:
Library name: F_57_K_E_1
F_57_K_E


title: RNAseq of porcine: skin woundDay_0_ID1328

description:
Library name: A_6_1328_1
A_6_1328


title: RNAseq of porcine: skin woundDay_4_ID1328_Wound_G_center

description:
Library name: E_54_G_C_1
E_54_G_C


title: Brain Microphysiological Systems, Week 13, run29 W13 2-1

city: Baltimore

first: Lena

last: Smirnova

address: 615 N. Wolfe St

department: Environmental Health & Engineering

institute: Johns Hopkins University

description:
Library name: DA33
Column name in counts.csv: DA33

data_processing:
Samples were processed with the nf-core/rnaseq pipeline v3.14.0 run with Nextflow 23.10.1
Raw sequence reads were trimmed for adaptors and low-quality bases using Trim Galore v0.6.7 with Cutadapt v5.0 (quality cutoff Q=20, auto-detecting adapters).
Trimmed reads were aligned to the GRCh38 reference genome using STAR v2.7.10a (default alignment settings, splice-aware).
Transcript-level quantification was performed using Salmon v1.10.1 in alignment-based mode (--libType auto, kmer size 31).
Gene-level counts were generated using featureCounts from Subread v2.0.1
Assembly: GRCh38
Supplementary files format and content: Comma-delimited text file includes the raw counts for each sample

source_name: Brain Microphysiological Systems

growth_protocol: NIBSC8 hiPSCs were maintained in mTESR-Plus medium at 37°C, 5% CO₂, and 5% O₂. NPCs were generated using neural induction medium and aggregated into 3D organoids under gyratory shaking. Organoids were cultured in brain differentiation medium for up to 14 weeks.

extract_protocol:
RNA was extracted using the Quick-RNA Microprep Kit. RNA quality was assessed using TapeStation and Qubit.
RNA libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit using 500 ng of RNA per sample, following manufacturer’s protocol.

treatment_protocol: Organoids were collected and snap frozen for RNA extraction.

tag: cell line

value: Brain Microphysiological Systems

tag: cell type

value: neural organoid

value: Control

value: at week 13 post differentiation

tag: batch


title: input.nos-White.2 [ChIP-seq]

tag: tissue

value: ovary

value: none (input)


title: BS1, Brain, Sham air inhalation, Rep1

value: 8 weeks


title: Brain Microphysiological Systems, Week 13 run29 W13 1-2

description:
Library name: DA32
Column name in counts.csv: DA32


title: BCN5, Brain, CBN inhalation, Rep5

value: Sprague Dawley


title: input.nos-E(z).2 [ChIP-seq]


title: RNAseq of porcine: skin woundDay_5_ID1325_Wound_B_edge

description:
Library name: F_63_B_E_1
F_63_B_E

value: Skin wound tissue

value: edge


title: Brain Microphysiological Systems, Week 13, run29 W13 1-1

description:
Library name: DA31
Column name in counts.csv: DA31


title: H3K9me3.nos-White.2 [ChIP-seq]

value: Histone H3K9me3 antibody _Rabbit_active motif 39161


title: RNAseq of porcine: skin woundDay_5_ID1324_Wound_K_center

description:
Library name: F_62_K_C_1
F_62_K_C


title: BS3, Brain, Sham air inhalation, Rep3

value: Brain

value: Sham air inhalation for 6 hrs/day for 3 consectuve days


title: H3K9me3.nos-White.1 [ChIP-seq]

value: Nanos Gal4 VP16-expressed dsRNA-white BDSC_35573


title: RNAseq of porcine: skin woundDay_5_ID1324_Wound_K_edge

description:
Library name: F_61_K_E_1
F_61_K_E


title: MASLD CosMX Slide1 (Sample 1, Sample 2)

description: CosMx spatial transcriptome of MASLD biopsies (F2), Samples 1 and 2

hyb_protocol: Samples were processed following NanoString's standard protocol (Manual Slide Preparation, MAN-10159-02)

value: Liver biopsy


title: BCN3, Brain, CBN inhalation, Rep3

value: male

value: Carbon black nanoparticles and naphthalene (CBN) inhalation for 6 hrs/day for 3 consecutive days


title: Brain Microphysiological Systems, Week 12, LD_W12_3

description:
Library name: DA30
Column name in counts.csv: DA30

value: Brain Microphysiological Systems

value: at week 12 post differentiation


title: RNAseq of porcine: skin woundDay_1_ID1323_Wound_L_center

description:
Library name: B_10_L_C_1
B_10_L_C

value: center


title: H3K9me3.nos-E(z).2 [ChIP-seq]

value: Nanos Gal4 VP16-expressed dsRNA-E(z) BDSC_33659


title: H3K9me3.nos-E(z).1 [ChIP-seq]

value: ovary


title: Brain Microphysiological Systems, Week 13, run29 W13 2-2

description:
Library name: DA34
Column name in counts.csv: DA34

value: neural organoid

value: Control

value: at week 13 post differentiation


title: Brain Microphysiological Systems, Week 12, LD_W12_1

description:
Library name: DA28
Column name in counts.csv: DA28


title: BCN2, Brain, CBN inhalation, Rep2

value: 8 weeks

value: Sprague Dawley


title: Brain Microphysiological Systems, Week 12, LD_W12_2

description:
Library name: DA29
Column name in counts.csv: DA29


title: BCN1, Brain, CBN inhalation, Rep1


title: RNAseq of porcine: skin woundDay_5_ID1324_Wound_B_center

description:
Library name: F_60_B_C_1
F_60_B_C

value: Skin wound tissue


title: Brain Microphysiological Systems, Week 8, LD_W8_3

description:
Library name: DA27
Column name in counts.csv: DA27

value: at week 8 post differentiation


title: RNAseq of porcine: skin woundDay_5_ID1324_Wound_B_edge

description:
Library name: F_59_B_E_1
F_59_B_E

value: edge


title: Brain Microphysiological Systems, Week 8, LD_W8_2

description:
Library name: DA26
Column name in counts.csv: DA26


title: WT, -Mg, batch2, rep2

city: Bethesda

first: Hernan

middle: A

last: Lorenzi

state: Maryland

address: 8 Center Dr, Bldg 8A

department: National Institutes of Diabetes and Digestive and Kidney Diseas

institute: National Institutes of Health

data_processing:
Libraries were sequenced using a HiSeq 2500 sequencer to generate single-end reads.
Sequencing reads were quality trimmed and sequencing adapters removed with fastp (v0.23.2). Trimmed reads were then mapped to the GenBank B. pertussis Tohama I assembly GCF_000195715.1 with STAR (v2.7.10a) and quantification of fragments per gene was carried out with the featureCounts tool from Subread software (v2.0.1) by counting reads falling within gene features.
Assembly: GCF_000195715.1
Supplementary files format and content: Tab-delimited test file with raw read counts per sample per gene.
Supplementary files format and content: BigWig files with RNA-Seq reads mapped to GCF_000195715.1 assembly.

organism: Bordetella pertussis Tohama I

growth_protocol: Bordetella pertussis strains were grown at 37˚C in Bordet Gengou media containing streptomycin (50 µ/mL) in the absence or presence of 50 mM MgSO4. After 3 days, cells were scraped from plates and resuspended in PLB medium without MgSO4 to obtain an initial OD600 between 0.1 and 0.2.  Cells were then incubated at 37°C with shaking at 250 rpm until mid-log phase (OD600 ~ 0.5).

extract_protocol:
Culture aliquots of 7 ml were collected by centrifugation, and total RNA was isolated by the hot-phenol method (Moon et al. 2021).  Total RNA was treated with DNase (Turbo DNA-free kit; Life Technologies, Inc.) for 1 h at 37° C, followed by phenol extraction and ethanol precipitation. rRNA wasremoved using the RiboZero kit.
Strand-specific Illumina DNA libraries were prepared for Illumina sequencing using the ScriptSeq 2.0 kit (Illumina).

tag: batch number

value: wild type

value: without Mg


title: 16s microbiome data for patient 16 as JEB sample at week 12, rep 2

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

description: Library name: 1985set2_264_AP16Week12-2

data_processing:
Cutadapt v3.5 was used to trim forward and reverse primers from sequences. Reads were also trimmed and filtered for quality using DADA2 v1.32.0, with the following changes from default parameters: acceptable lengths were set to between 100 (minLen) and 1600 bp (maxLen), minimum quality score (minQ) set to 3, maxEE of 2, and rm.phix as FALSE
Error rates were estimated using PacBioErrfun, which is recommended for analysis of PacBio circular consensus reads. To follow, reads were separated into ASVs using dada2’s divisive partitioning machine learning approach. For both error modeling and divisive partitioning, band size was increased to 32 for sequence alignment in order to accommodate for increased rate of insertions and deletions in PacBio sequences.19 Chimeric sequences were identified and removed using the de novo approach included within dada2, with minFoldParentAbundance increased to 3.5.
Assembly: hg38
Supplementary files format and content: Excel file include count value
Library strategy: 16s microbiome

source_name: skin

extract_protocol:
Genomic DNA was extracted using a Maxwell 16 LEV Blood DNA Kit (Promega, Madison, WI) implemented on a Maxwell 16 Instrument, following the manufacturer’s instructions with minor modifications
Genomic DNA was prepared for sequencing on a PacBio Revio sequencer using a two-stage PCR protocol, similar to that described for Illumina amplicon library preparation.15 In the first stage of PCR, DNA was PCR amplified with primers 27F and 1492R (TTTCTGTTGGTGCTGATATTGCAGRGTTYGATYMTGGCTCAG and ACTTGCCTGTCGCTCTATCTTC RGYTACCTTGTTACGACTT, respectively) using domain-level bacterial primers as described by PacBio.
The underlined regions, however, represent Oxford Nanopore Universal sequences for tailing PCR primers’ linker sequences. In the second stage of PCR, amplicons from the first stage were used as a template and amplified with primers that contained PacBio Kinnex adapter sequences, combinatorial dual indices, and the ONT linker sequences at the 3’ ends of the primers . Library preparation was performed using a two-stage PCR amplification protocol but with primers targeting the full 16S rRNA gene

value: skin


title: WT, -Mg, batch2, rep1


title: 16s microbiome data for patient 16 as JEB control at week 12

description: Library name: 1985set2_265_AP16Week12-C


title: RNAseq of porcine: skin woundDay_5_ID1323_Wound_K_center

description:
Library name: F_58_K_C_1
F_58_K_C


title: 16s microbiome data for patient 16 as JEB sample at week 12, rep 1

description: Library name: 1985set2_263_AP16Week12-1


title: WT, -Mg, batch1, rep2


title: RNAseq of porcine: skin woundDay_5_ID1325_Wound_B_center

description:
Library name: F_64_B_C_1
F_64_B_C


title: BCN4, Brain, CBN inhalation, Rep4

value: Brain

value: male

value: Carbon black nanoparticles and naphthalene (CBN) inhalation for 6 hrs/day for 3 consecutive days


title: 16s microbiome data for patient 16 as JEB control at week 8

description: Library name: 1985set2_262_AP16Week8-C


title: RNAseq of porcine: skin woundDay_5_ID1325_Wound_K_edge

description:
Library name: F_65_K_E_1
F_65_K_E


title: WT, -Mg, batch3, rep3


title: Brain Microphysiological Systems, Week 8, 24_VC_2

description:
Library name: DA14
Column name in counts.csv: DA14

value: Brain Microphysiological Systems

tag: time point


title: Brain Microphysiological Systems, Week 8, 24_VC_3

description:
Library name: DA15
Column name in counts.csv: DA15


title: RNAseq of porcine: skin woundDay_5_ID1323_Wound_B_edge

description:
Library name: F_55_B_E_1
F_55_B_E


title: 16s microbiome data for patient 16 as JEB sample at week 8, rep 2

description: Library name: 1985set2_261_AP16Week8-2


title: WT, -Mg, batch1, rep1


title: WT, -Mg, batch3, rep2


title: 16s microbiome data for patient 16 as JEB sample at week 8, rep 1

description: Library name: 1985set2_260_AP16Week8-1


title: RNAseq of porcine: skin woundDay_4_ID1328_Wound_G_edge

description:
Library name: E_53_G_E_1
E_53_G_E


title: 16s microbiome data for patient 16 as JEB sample at week 4, rep 1

description: Library name: 1985set2_258_AP16Week4-1


title: Brain Microphysiological Systems, Week 8, 24_VC_1

description:
Library name: DA13
Column name in counts.csv: DA13


title: WT, -Mg, batch3, rep1


title: 16s microbiome data for patient 16 as JEB sample at week 4, rep 2

description: Library name: 1985set2_259_AP16Week4-2


title: Brain Microphysiological Systems, Week 8, LD_W8_1

description:
Library name: DA25
Column name in counts.csv: DA25


title: mutant, -Mg, batch3, rep3


title: mutant, -Mg, batch3, rep2


title: MITF_SETD6_Control2 cells

city: Be'er Sheva

first: Dan

last: Levy

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben-Gurion University

description: Library name: Sample 13

data_processing:
Trim Galore v0.4.5 (length= 25, q- 25)
FastQC v0.12.0 was used for reads quality control
BWA Mapper (v0.7.12,  t=20, B= 5) aligned paired-end reads to reference human genome assembly hg38 and to  spike-in control (Escherichia coli) reference genome assembly
SAMtools removed PCR duplicates and created coordinate-sorted BAM files
Bigwig files were created by bamCoverage
Reads that refer to off-chromosome locations were removed with BedClip v377 and sorted by Bedtools v2.30.0
Bigwig files of each sample and corresponding IgG control were created with bedGraphToBigWig v2.8 by deepTools.
Peak calling results by Macs2 and SEACR  are presented as bed files
Assembly: GRCh38
Supplementary files format and content: bed files and bigwig files
Library strategy: CUT&Run

growth_protocol: SKmel147 cells  were maintained in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum (FBS), penicillin-streptomycin , 2 mg/ml L-glutamine and non-essential amino acids.

extract_protocol:
EpiCypher CUT&RUN Protocol
EpiCypher library kit protocol

value: SETD6 CT Cells


title: RNAseq of porcine: skin woundDay_6_ID1326_Wound_B_edge

description:
Library name: G_67_B_E_1
G_67_B_E


title: RNAseq of porcine: skin woundDay_6_ID1326_Wound_B_center

description:
Library name: G_68_B_C_1
G_68_B_C

value: center


title: MITF_SETD6_Control1 cells

description: Library name: Sample 12


title: MITF_SETD6_KO1 cells

description: Library name: Sample 14

value: SETD6 KO Cells