title: BV-2 transfected with control miRNA mimic (cel-miR-67)_sample3

city: Tokorozawa

first: Yusuke

last: Mizohata

address: Namiki 3-2

institute: National Defense Medical College

data_processing:
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.39 tool.
The sequence reads were aligned to the Mouse reference genome (mm10) using STAR 2.7.10b.
The aligned reads were subjected to downstream analyses using StrandNGS v4.0 software.
The read counts allocated for each gene and transcript (RefSeq Database 2018.02.25) were quantified using a Transcripts Per Million (TPM) method.
Assembly: mm10
Supplementary files format and content: An excel file include raw counts and TPM quantified value for each Sample.

growth_protocol: The culture mediums were as follows: for Neuro-2A, Minimum essential medium (11095098, Thermo), 1× Non-Essential Amino Acids (11140050, Thermo), 1 mM sodium pyruvate (11360070, Thermo), 10% deactivated fetal bovine serum (FBS) (SH30910.03, HyClone, Tokyo, Japan) and 100 U/mL Penicillin-Streptomycin (PS) (15140122, Thermo); for BV-2, Dulbecco's modified Eagle medium (DMEM) (high glucose) (11965092, Thermo), 10% deactivated FBS and 100 U/mL PS; for primary cultured astrocytes, DMEM/F12 (11320082, Thermo), 15% deactivated FBS and 100 U/mL PS. All cells were cultured at 37°C, 5% CO2.

extract_protocol:
Extraction of RNA from cultured cells was performed using the miRNeasy Mini Kit (217004, Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions.
RNA-Seq libraryies for RNA-Seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module following manufacture's protocols.

treatment_protocol: Equal amounts of three custom miRNA mimics (miR-199a-3p, miR-99b-3p and miR-140-5p) (Horizon) (Supplementary Table 16) and Dharmafect 1 (T-2001, Horizon) were mixed to form a complex using PS-free serum-free medium. The mimic-Dharmafect1 complex was then diluted with complete medium to 25 nM. For the control mimic, cel-miR-67 was used (Horizon). After cultivation in PS-free medium (37°C, 5% CO2, 24 h), the cells were incubated in a transfection medium for 24 h. Cell seeding was conducted at 6.0×105 cells/mL for Neuro-2A cells, at 9.0×105 cells/mL for primary astrocytes and at 3.0×105 cells/mL for BV-2 cells.

tag: cell line

value: Microglia

value: Not genetically modified.

value: Control miRNA mimic transfection (24 h)


title: ST-wildtype-1

status: Public on Dec 09 2025

type: SRA

city: College Station

first: Ling

last: Yang

state: TX

address: 206 Olsen Blvd, Reynolds HSC  Rm159

country: USA

institute: Texas A&M university

description: Library name: WT1

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: S. Typhimurium 14028 reference genome (NC_016856.1)
Supplementary files format and content: TSV files include FPKM values for each Sample

molecule: total RNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: ATCC 14028S

growth_protocol: Single coloby of each bacteria strain was innoclated in 5mL fresh LB, and cultured at 37℃ overnignt

extract_protocol:
RNA were extracted by using QIANGEN Rneasy mini kit following the manufacturing guidelines
libraries were prepared with the TruSeq Stranded Total RNA kit

tag: strain

tag: genotype

value: wildtype


title: mRNAseq_OAL_rep3

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description:
Library name: Sample 21
mRNAseq_OWT_rep3

data_processing:
cutadapt
STAR alignment (RNA-seq)
BWA-mem alignment (ATAC-seq, ChIP-seq)
featureCount, gene-level extraction (RNA-seq), macs2 peak-calling (ATAC-seq,ChIP-seq)
Assembly: mm10
Supplementary files format and content: text file

molecule: polyA RNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
RNA was purified with TRIzol TM Reagent (Invitrogen, 15596026) and Direct-zol RNA microprep (Zymo R2060)
RNA-seq libraries were constructed using SMARTer Standard total RNA-seq kit v2
The engineered hyperactive Tn5 transposase that is preloaded with DNA adapters thus removing the need for a separate annealing step.
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Bone marrow

tag: cell type

value: Hematopoietic stem cell

value: WT

tag: treatment

value: control


title: 64T-Tumour_B-FOV_16

type: RNA

city: Clayton

first: Andrew

last: Pattison

state: Vic

address: Wellington Rd

department: Anatomy and developmental biology

country: Australia

institute: Monash University

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_16.rds

hyb_protocol: NanoString®ISH probes were prepared by incubation at 95 °C for 2 min and immediately transferred to ice. The ISH probe mix (1 nM ISH probe, 40% formamide, 2.5% dextran sulfate, 0.2% BSA, 100 μg ml–1 salmon sperm DNA, 2× SSC, 0.1 U μl–1 SUPERase•In (ThermoFisher) in DEPC H2O) was then pipetted into the chamber, and adhesives supplied with the chambers were applied to the chamber ports. Hybridization occurred at 37 °C overnight after sealing the chamber to prevent evaporation. Following ISH probe hybridization, tissue sections were washed twice in a buffer comprising 50% formamide (VWR) in 2× SSC at 37 °C for 25 min, washed twice with 2× SSC for 2 min each at room temperature and then blocked with 100 mM NHS-acetate for 15 min. After blocking, the hydrophobic barrier was removed with a blade and a custom-made flow cell was attached to the slide.

scan_protocol: Slides 1–3 were processed using the CosMx Human Universal Cell Characterization Panel Version 1 under the NanoString Technology Access Program. FFPE tissue sections were hybridized with transcript-specific probes targeting 1000 genes. Cell segmentation was performed using immunofluorescence markers DAPI, CD298/B2M, PanCK, CD45, and CD3. Slides were mounted into the CosMx Spatial Molecular Imager (SMI) flow cell and flushed with 1.5 ml of reporter wash buffer (1× SSPE, 0.5% Tween 20, 0.1 U μl–1 SUPERase•In, 0.1% Proclin 950, DEPC-treated water) to remove air bubbles. A low-resolution whole-slide image was acquired for field-of-view (FOV) placement. RNA detection began with 100 μl of Reporter 1 flowed at 200 μl min–1 for 15 minutes, followed by 1 ml of reporter wash buffer at 750 μl min–1 to remove unbound probes. Imaging buffer (80 mM glucose, 0.6 U ml–1 pyranose oxidase, 18 U ml–1 catalase, 1:1,000 Proclin 950, 500 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% Tween 20, DEPC-treated water) was then introduced, and eight Z-stack images (800 nm step size) were acquired per FOV. Fluorophores were UV-cleaved (385 nm, 116 J cm–2, 500 ms) and removed with 200 μl of strip wash buffer (0.0033× SSPE, 0.5% Tween 20, 1:1,000 Proclin 950). This procedure was repeated for 16 reporter pools and cycles, with multiple iterations to enhance sensitivity. Morphology staining was performed on the same instrument using NanoString buffer W for 30 minutes, followed by a 1-hour incubation with an antibody cocktail (CD298, CD45, CD3, PanCK), wash with 8 ml of reporter wash buffer, and final imaging in imaging buffer.

data_processing:
Flat files generated as described in: He et a., Nature Biotechnology 2022;40(12):1794-806. Each sample/slide/FOV combination is provided as a seurat saved in R Data Serialization (RDS) format. To obtain the metadata provided including cell identites:
Processed data: AtoMx computed gene-level probe counts with corresponding XY coordinates

organism: Homo sapiens

label_protocol: Tissue was digested with Protease Plus (ACD Bio) spiked with Proteinase K (ThermoFisher), ranging from 1 to 5 μg ml–1 depending on tissue type, at 40 °C for 15–30 min. Tissue sections were rinsed twice with DEPC H2O, incubated in 1:400 diluted fiducials (Bangs Laboratories) in 2× saline sodium citrate and Tween (0.001% Tween 20, Teknova) for 5 min at room temperature and washed with 1× PBS (ThermoFisher) for 5 min. After digestion and fiducial placement, tissue was fixed with 10% neutral-buffered formalin for 1 min to maintain soft tissue morphology, washed twice with Tris-glycine buffer (0.1 M glycine (Sigma), 0.1 M Tris-base (FisherScientific) in DEPC H2O) for 5 min and then washed with 1× PBS for 5 min. Fixed tissue was blocked using 100 mM N-succinimidyl (acetylthio) acetate (NHS-acetate, ThermoFisher) diluted in NHS-acetate buffer (0.1 M NaP + 0.1% Tween pH 8.0 in DEPC H2O) for 15 min at room temperature and washed in 2× saline sodium citrate (SSC) for 5 min. An adhesive SecureSeal Hybridization Chamber (Grace Bio-Labs) was placed over tissue.

extract_protocol: To perform in situ hybridization on tissue sections, the slides were baked in an oven overnight at 37 °C and then at 60 °C for at least 2 h. Tissue sections were dewaxed twice in xylene (Millipore) for 5 min, twice in ethanol (Pharmco) for 2 min and then the slides were baked at 60 °C for 5 min. Tissue sections were subjected to the target retrieval step using the RNAscope Target Retrieval kit (ACD Bio) and heated at 100 °C in a pressure cooker for 15–30 min. After target retrieval, tissue sections were rinsed with diethyl pyrocarbonate (DEPC)-treated water (DEPC H2O, ThermoFisher), washed in ethanol for 3 min and dried at room temperature for 30 min. On the dried slide, a hydrophobic barrier line was drawn around the tissue section using an ImmEdge Pen (Vector).

treatment_protocol: Tissue microarrays were constructed at the Monash Histology Platform. 2mm cores were dissected from formalin fixed paraffin embedded clinical samples using a Micro Tissue Arrayer, MTA-1 (Beecher Instruments, USA). Core placement was guided by the histopathological annotation of tissue blocks, excluding overly necrotic areas, as defined by an expert anatomical pathologist (Dr David Nickless). Donor cores were arranged into TMA recipient blocks and reannealed at 45 degrees for 3 hours. 4um sections were collected onto slides. To aid in field of view (FOV) placement, the first and last slide in each series of sequential sections was stained with haematoxylin and eosin (H&E) and digitised at 40X magnification on the Aperio AT slide scanner.

value: Colon tumour,FFPE

tag: donor

tag: Sex

value: F

tag: age at diagnosis

tag: primary tumour location

value: caecum

tag: total cells

tag: mmr status

value: pMMR

tag: sidedness

value: RHS


title: 150T-Tumour_A-FOV_16

description:
raw data files:
Run5654_Tumor_A_exprMat_file.csv.gz
Run5654_Tumor_A_fov_positions_file.csv.gz
Run5654_Tumor_A_metadata_file.csv.gz
Run5654_Tumor_A_tx_file.csv.gz
Run5654_Tumor_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
150T-Tumour_A-FOV_16.rds

value: transverse


title: HD11 cells, MARCO knockout, KO2

city: Yangzhou

first: Xuming

last: Hu

state: Jiangsu

address: No.48 East Wenhui Road

department: College of Animal Science and Technology

country: China

institute: Yangzhou University

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

organism: Gallus gallus

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

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

value: macrophages

value: MARCO knockout


title: mRNAseq_OAL_rep2

description:
Library name: Sample 20
mRNAseq_OWT_rep2


title: BV-2 transfected with control miRNA mimic (cel-miR-67)_sample1

country: Japan


title: mRNAseq_OAL_rep1

description:
Library name: Sample 19
mRNAseq_OWT_rep1


title: HD11 cells, MARCO knockout, KO1


title: 67T-Run5850.2186.2-FOV_16

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_16.rds

scan_protocol: Slides 4–5 were processed using the CosMx Human Universal Cell Characterization Panel Version 1 under the NanoString Technology Access Program. FFPE tissue sections were hybridized with probes targeting 1000 genes. Cell segmentation was performed using DAPI, CD298/B2M, PanCK, and CD45. Slides were loaded into the CosMx SMI flow cell and flushed with 1.5 ml of reporter wash buffer (1× SSPE, 0.5% Tween 20, 0.1 U μl–1 SUPERase•In, 0.1% Proclin 950, DEPC-treated water) to remove bubbles. A low-resolution whole-slide image was acquired to guide FOV placement. RNA detection involved flowing 100 μl of Reporter 1 at 200 μl min–1 for 15 minutes, washing with 1 ml of reporter wash buffer at 750 μl min–1, then adding imaging buffer (80 mM glucose, 0.6 U ml–1 pyranose oxidase, 18 U ml–1 catalase, 1:1,000 Proclin 950, 500 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% Tween 20, DEPC-treated water) before imaging. Eight Z-stacks were acquired per FOV (800 nm step size), followed by UV cleavage of fluorophores (385 nm, 116 J cm–2, 500 ms) and washing with 200 μl of strip wash buffer (0.0033× SSPE, 0.5% Tween 20, 1:1,000 Proclin 950). This 16-cycle hybridization and imaging process was repeated for improved sensitivity. Morphology staining was performed by incubating with blocking buffer (NanoString buffer W) for 30 minutes, applying a cocktail of CD298, CD45, CD3, and PanCK antibodies for 1 hour, washing with 8 ml of reporter wash buffer, and imaging in imaging buffer.

value: M

value: sigmoid

value: LHS


title: BV-2 transfected with 3 mixed miRNA mimic (miR-199a-3p, miR-99b-3p and miR-140-5p)_sample2

value: Microglia

value: Not genetically modified.

value: 3 mixed miRNA mimic transfection (24 h)


title: HD11 cells, MARCO wild type, C2

value: MARCO wild type


title: BV-2 transfected with 3 mixed miRNA mimic (miR-199a-3p, miR-99b-3p and miR-140-5p)_sample3


title: 67T-Run5850.2186.1-FOV_16

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.1-FOV_16.rds


title: BV-2 transfected with 3 mixed miRNA mimic (miR-199a-3p, miR-99b-3p and miR-140-5p)_sample1


title: mRNAseq_OCR_rep4

description:
Library name: Sample 18
mRNAseq_OCR_rep4

value: Bone marrow

value: Hematopoietic stem cell

value: WT

value: CR treatment


title: mRNAseq_OCR_rep2

description:
Library name: Sample 16
mRNAseq_OCR_rep2


title: mRNAseq_OCR_rep3

description:
Library name: Sample 17
mRNAseq_OCR_rep3


title: 73N-Normal_A-FOV_16

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
73N-Normal_A-FOV_16.rds

value: Colon tumour,FFPE


title: HD11 cells, MARCO wild type, C3


title: Primary astrocyte transfected with control miRNA mimic (cel-miR-67)_sample3

source_name: Primary astrocyte

value: Primary astrocyte

value: Astrocyte

value: Control miRNA mimic transfection (24 h)


title: HD11 cells, MARCO wild type, C1

value: macrophages


title: mRNAseq_OCR_rep1

description:
Library name: Sample 15
mRNAseq_OCR_rep1


title: 137T-3461G-FOV_16

description:
raw data files:
3461G_exprMat_file.csv.gz
3461G_fov_positions_file.csv.gz
3461G_metadata_file.csv.gz
3461G_tx_file.csv.gz
3461G-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
137T-3461G-FOV_16.rds

scan_protocol: Slides 6–9 were processed using the CosMx Human Universal Cell Characterization Panel Version 2 at the Central Facility for Genomics, Griffith University. FFPE tissue sections were hybridized with probes targeting 1000 genes. Cell segmentation was performed using DAPI, CD298/B2M, PanCK, CD45, and CD68. Slides were loaded into the CosMx SMI flow cell and washed with 1.5 ml of reporter wash buffer (1× SSPE, 0.5% Tween 20, 0.1 U μl–1 SUPERase•In, 0.1% Proclin 950, DEPC-treated water) to remove bubbles. A low-resolution image of the entire slide was acquired to allow FOV placement. RNA readout was initiated by flowing 100 μl of Reporter 1 at 200 μl min–1 and incubating for 15 minutes, followed by washing with 1 ml of reporter wash buffer at 750 μl min–1. Imaging buffer (80 mM glucose, 0.6 U ml–1 pyranose oxidase, 18 U ml–1 catalase, 1:1,000 Proclin 950, 500 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% Tween 20, DEPC-treated water) was applied before acquisition of eight Z-stack images per FOV (800 nm step size). Fluorophores were UV-cleaved (385 nm, 116 J cm–2, 500 ms) and removed using 200 μl of strip wash buffer (0.0033× SSPE, 0.5% Tween 20, 1:1,000 Proclin 950). Sixteen hybridization cycles were performed and repeated multiple times to enhance sensitivity. Morphology staining was completed on the same instrument by incubating with blocking buffer (NanoString buffer W) for 30 minutes, applying a cocktail of CD298, CD45, CD3, and PanCK antibodies for 1 hour, washing with 8 ml of reporter wash buffer, and adding imaging buffer prior to image acquisition.

value: F

value: rectal

value: pMMR


title: HD11 cells, MARCO knockout, KO3

value: MARCO knockout


title: mRNAseq_OCRRF_rep2

description:
Library name: Sample 14
mRNAseq_OCRRF_rep2

value: CR refeed


title: BV-2 transfected with control miRNA mimic (cel-miR-67)_sample2

value: Microglia

value: Not genetically modified.


title: 46T-148191A-FOV_16

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
46T-148191A-FOV_16.rds

value: hepatic flexure

value: RHS


title: Huh-7 cell, Control, biol rep3

city: Changchun

first: Wei

last: Huang

state: Jilin

address: Xinmin Street No. 1163

department: Modern biology

institute: nstitute of Frontier Medical Science, Jilin University

description:
Library name: CK3
Column name in raw_counts_all_Samples.txt: CK3

data_processing:
The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and PE 100/150 bases reads are generated on G400/T7/T10 platform (BGI-Shenzhen, China).
The raw data was filtered with SOAPnuke (v1.5.2)  by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT (v2.1.0).
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5)
The expression level of genes was calculated by RSEM (v1.2.8)
Assembly: Reference Genome Version: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Liver

growth_protocol: Huh-7 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Cells were maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from cells using TRIzol™ Reagent (Thermo Fisher Scientific) according to the manufacturer's instructions.  A minimum of 5 μg of total RNA with high integrity was used as input for subsequent sequencing library preparation.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

treatment_protocol: Huh-7 cells were transfected with an ALKBH5 overexpression plasmid using the Neon Transfection System (Thermo Fisher Scientific). The electroporation parameters were set as follows: 1250 V pulse voltage, 20 ms pulse width, and 3 pulses. Following electroporation, the cell suspension was immediately transferred to pre-warmed complete culture medium. Cells were then incubated for 60 hours under standard growth conditions (37°C, 5% CO2) post-transfection prior to RNA extraction.

value: Liver

value: Hepatocellular carcinoma

value: Untreated


title: Huh-7 cell, Control, biol rep2

description:
Library name: CK2
Column name in raw_counts_all_Samples.txt: CK2

value: WT


title: Primary astrocyte transfected with control miRNA mimic (cel-miR-67)_sample2

value: Primary astrocyte


title: 280T-120131-FOV_16

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
280T-120131-FOV_16.rds

value: Colon tumour,FFPE

value: caecum


title: Primary astrocyte transfected with control miRNA mimic (cel-miR-67)_sample1

value: Astrocyte

value: Control miRNA mimic transfection (24 h)


title: 130T-10501A-FOV_16

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
130T-10501A-FOV_16.rds

value: F

value: rectum upper

value: LHS


title: mRNAseq_OCRRF_rep1

description:
Library name: Sample 13
mRNAseq_OCRRF_rep1

value: Bone marrow

value: Hematopoietic stem cell

value: CR refeed


title: Huh-7 cell, Control, biol rep1

description:
Library name: CK1
Column name in raw_counts_all_Samples.txt: CK1


title: Huh-7 cell, oeALKBH5, biol rep3

description:
Library name: A3
Column name in raw_counts_all_Samples.txt: A3

value: ALKBH5 overexpression


title: mRNAseq_YAL_rep4

description:
Library name: Sample 12
mRNAseq_YWT_rep4

value: control


title: Primary astrocyte transfected with 3 mixed miRNA mimic (miR-199a-3p, miR-99b-3p and miR-140-5p)_sample3

value: 3 mixed miRNA mimic transfection (24 h)


title: 64T-Tumour_B-FOV_15

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_15.rds

value: pMMR

value: RHS


title: 150T-Tumour_A-FOV_15

description:
raw data files:
Run5654_Tumor_A_exprMat_file.csv.gz
Run5654_Tumor_A_fov_positions_file.csv.gz
Run5654_Tumor_A_metadata_file.csv.gz
Run5654_Tumor_A_tx_file.csv.gz
Run5654_Tumor_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
150T-Tumour_A-FOV_15.rds

value: transverse


title: Huh-7 cell, oeALKBH5, biol rep2

description:
Library name: A2
Column name in raw_counts_all_Samples.txt: A2

value: Liver

value: Hepatocellular carcinoma

value: Untreated


title: Primary astrocyte transfected with 3 mixed miRNA mimic (miR-199a-3p, miR-99b-3p and miR-140-5p)_sample1

value: Primary astrocyte

value: Astrocyte

value: WT


title: mRNAseq_YAL_rep3

description:
Library name: Sample 11
mRNAseq_YWT_rep3


title: Huh-7 cell, oeALKBH5, biol rep1

description:
Library name: A1
Column name in raw_counts_all_Samples.txt: A1


title: Neuro-2A transfected with control miRNA mimic (cel-miR-67)_sample3

value: Neuron

value: Not genetically modified.

value: Control miRNA mimic transfection (24 h)


title: mRNAseq_YAL_rep2

description:
Library name: Sample 10
mRNAseq_YWT_rep2

value: Bone marrow

value: Hematopoietic stem cell


title: 67T-Run5850.2186.2-FOV_15

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_15.rds

value: Colon tumour,FFPE

value: M

value: sigmoid

value: LHS


title: 67T-Run5850.2186.1-FOV_15

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.1-FOV_15.rds

value: pMMR


title: fibroblast, CSE treatment, 72h, rep3

city: Shanghai

first: Jin

last: Liu

state: Huangpu district

address: 833 Zhizaoju Road

institute: Shanghai Ninth People’s Hospital

data_processing:
For  orbital fibroblasts sequencing, the sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05 (or FDR ≤ 0.001).
For PBMCs sequencing, raw fastq data were subjected to quality control using fastp-0.12.4. Alignment was performed using hisat2-2.2.0, referencing the GRCh38 human genome, which included ERCC spike sequences. Sorted SAM files were processed using GATK4-4.2.6.0, and transcript assembly and abundance estimation were carried out using stringtie-2.2.1. Batch effects were corrected using ERCC spike-in as references, employing the R package RUVSeq-1.30.0 for normalization.
Assembly: hg38
Supplementary files format and content: For orbital fibroblasts sequencing, tab-delimited text file includes raw counts for each cell sample
Supplementary files format and content: For PBMCs sequencing, tab-delimited text file includes ERCC counts for each Sample

source_name: orbital fibroblast

extract_protocol:
For cell RNA extraction, Add 600 μL TRIzol to one cell sample. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification.Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
For orbital fibroblast cell bulk RNA-seq, the libraries were sequenced on an MGISEQ-2000RS system. For PBMCs sequencing, the total RNA was mixed with ERCC RNA Spike-in Mix (4456740, Invitrogen) in proportion for transcriptome library construction. The sequencing library was prepared using the RNA-seq Library Prep Kit for MGI (NRM605, Vazyme) and sequenced in batches on the DNBSEQ-T7 platform.

value: orbital fibroblast

value: thyroid eye disease (TED)


title: mRNAseq_YCR_rep4

description:
Library name: Sample 8
mRNAseq_YCR_rep4

value: CR treatment


title: 73N-Normal_A-FOV_15

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
73N-Normal_A-FOV_15.rds


title: fibroblast, CSE treatment, 72h, rep2


title: 7T-3461G-FOV_15

description:
raw data files:
3461G_exprMat_file.csv.gz
3461G_fov_positions_file.csv.gz
3461G_metadata_file.csv.gz
3461G_tx_file.csv.gz
3461G-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7T-3461G-FOV_15.rds

value: ascending

value: RHS


title: mRNAseq_YCR_rep3

description:
Library name: Sample 7
mRNAseq_YCR_rep3


title: Neuro-2A transfected with control miRNA mimic (cel-miR-67)_sample1


title: fibroblast, CSE treatment, 72h, rep1


title: Neuro-2A transfected with 3 mixed miRNA mimic (miR-199a-3p, miR-99b-3p and miR-140-5p)_sample3

value: 3 mixed miRNA mimic transfection (24 h)


title: mRNAseq_YCR_rep2

description:
Library name: Sample 6
mRNAseq_YCR_rep2

value: WT


title: fibroblast, CSE treatment, 48h, rep3


title: 46T-148191A-FOV_15

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
46T-148191A-FOV_15.rds

value: F

value: hepatic flexure


title: Neuro-2A transfected with 3 mixed miRNA mimic (miR-199a-3p, miR-99b-3p and miR-140-5p)_sample2

value: Neuron

value: Not genetically modified.


title: 280T-120131-FOV_15

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
280T-120131-FOV_15.rds

value: caecum


title: Primary astrocyte transfected with 3 mixed miRNA mimic (miR-199a-3p, miR-99b-3p and miR-140-5p)_sample2

value: Primary astrocyte

value: Astrocyte


title: mRNAseq_YCR_rep1

description:
Library name: Sample 5
mRNAseq_YCR_rep1

value: Bone marrow

value: Hematopoietic stem cell


title: mRNAseq_YCRRF_rep4

description:
Library name: Sample 4
mRNAseq_YCRRF_rep4

value: CR refeed


title: fibroblast, CSE treatment, 48h, rep2

value: orbital fibroblast


title: Neuro-2A transfected with 3 mixed miRNA mimic (miR-199a-3p, miR-99b-3p and miR-140-5p)_sample1


title: 92T-10501A-FOV_15

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
92T-10501A-FOV_15.rds

value: Colon tumour,FFPE

value: dMMR


title: 64T-Tumour_B-FOV_14

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_14.rds

value: pMMR


title: PS19_vector_6MPI_5 [ACSS2.WT.6MPI.R5]

city: Philadelphia

first: Shuo

last: Zhang

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Demultiplexed FASTQs were aligned to the reference genome using STAR
Gene level read counts were prepared using featureCounts or HTSeq.
Unwanted variation was estimated by RUVr.
Differential expressed genes were called using DESeq2 with Wald test
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: dorsal Hippocampus

growth_protocol: Primary hippomcapal neurons culture were cultured in neural basal medium with 2% B27, 1x Glutamax, and 1x Penicillin/Streptomycin.

extract_protocol:
Total RNA was extracted using Trizol-chloroform following RNA purification using RNeasy mini-kit, Qiagen.
130 ng input RNA was used to make libraries using the NEB kit E7490.

treatment_protocol: Cells were treated with 1.5xE6 PhP.eb.upACSS2 or PhP.eB-vector at 5DIV for 48 hours before 1x PBS wash on 7DIV and treatment with hAD-tau or PBS. Aged and 10 months old C57BL6 mice were treated with retro-orbital injection of PhP.eb.upACSS2 or PhP.eB-vector. Aged mice treated at 21-22 months of age with 1.5 xE11 viral genome (vg) and tissue harvested 30 min post remote context recall after 2 months of viral treatment. 10 months old mice treated with 1.2 xE11 vg for 2 weeks and tissue harvested 30 min after acquisition of fear conditioning.2.5 month old PS 19 mice were treated with 1.5 xE10 vg PhP.eb.upACSS2 or PhP.eB-vector for 1 month (1mpi) or 6 month (6 mpi) and euthanized 30 min post 24-hour contextual recall.

value: dorsal Hippocampus

tag: age

value: 8.5-9 months old

value: male


title: mRNAseq_YAL_rep1

description:
Library name: Sample 9
mRNAseq_YWT_rep1

value: WT

value: control


title: Neuro-2A transfected with control miRNA mimic (cel-miR-67)_sample2

value: Neuron

value: Control miRNA mimic transfection (24 h)


title: fibroblast, CSE treatment, 48h, rep1

value: thyroid eye disease (TED)


title: PS19_vector_6MPI_4 [ACSS2.WT.6MPI.R4]


title: mRNAseq_YCRRF_rep3

description:
Library name: Sample 3
mRNAseq_YCRRF_rep3


title: fibroblast, CSE treatment, 24h, rep3


title: PS19_vector_6MPI_3 [ACSS2.WT.6MPI.R3]


title: 150T-Tumour_A-FOV_14

description:
raw data files:
Run5654_Tumor_A_exprMat_file.csv.gz
Run5654_Tumor_A_fov_positions_file.csv.gz
Run5654_Tumor_A_metadata_file.csv.gz
Run5654_Tumor_A_tx_file.csv.gz
Run5654_Tumor_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
150T-Tumour_A-FOV_14.rds

value: F

value: transverse

value: RHS


title: fibroblast, CSE treatment, 24h, rep1


title: 67T-Run5850.2186.2-FOV_14

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_14.rds

value: M

value: sigmoid

value: LHS


title: PS19_vector_6MPI_2 [ACSS2.WT.6MPI.R2]


title: mRNAseq_YCRRF_rep1

description:
Library name: Sample 1
mRNAseq_YCRRF_rep1

value: Bone marrow

value: Hematopoietic stem cell

value: CR refeed


title: 142N-Run5850.2186.1-FOV_14

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142N-Run5850.2186.1-FOV_14.rds

value: Colon tumour,FFPE

value: ascending

value: dMMR


title: Endothelial cells (DAPI-, CD31+, CD45-) from B16-OVA-VEGFC tumors from Ifnγr1WT (Cre minus) mice

city: New York

first: Amanda

last: Lund

state: New York

address: 522 First Ave

institute: NYU Langone Health

description:
Library name: Cre-minus
10x Genomics

library_source: transcriptomic single cell

data_processing:
The barcoded processing, gene counting were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin tumor

extract_protocol:
Tumors were harvested and digested with 220 U ml–1 collagenase IV (Invitrogen, 17104019) and 80 U ml–1 DNASE I (Sigma-Aldrich, 04536282001) for 30 min at 37°C. Digests were then passed through a metallic mesh and a 70-μm pore filter. Single cell suspensions were stained for Live/Dead with DAPI, CD45 (FITC), CD31(PE)
Libraries were prepared using single cell 3′ reagent kits v3.1 (Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1, 16 rxns PN-1000121; 10x Genomics)

value: Skin tumor

value: B16F10-OVALBUMIN/ VEGFC

value: Endothelial cell


title: fibroblast, CSE treatment, 12h, rep3

value: orbital fibroblast


title: PS19_vector_6MPI_1 [ACSS2.WT.6MPI.R1]

value: dorsal Hippocampus

value: 8.5-9 months old

value: male


title: Endothelial cells (DAPI-, CD31+, CD45-) from B16-OVA-VEGFC tumors from Ifnγr1iProx1 (Cre plus) mice

description:
Library name: Cre-plus
10x Genomics


title: 73N-Normal_A-FOV_14

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
73N-Normal_A-FOV_14.rds

value: pMMR


title: fibroblast, CSE treatment, 12h, rep2

value: thyroid eye disease (TED)


title: fibroblast, CSE treatment, 12h, rep1


title: Unc119_KO-3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101 base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse reference genome sequences (mm10) using TopHat, version 2.1.1.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Retina

extract_protocol:
Total RNAs from the mouse retina were isolated using TRIzol RNA extraction reagent (Invitrogen).
Sequencing libraries were constructed with the TruSeq stranded mRNA Library Prep kit (Illumina).

value: Retina


title: PS19_upACSS2_6MPI_5 [ACSS2.OE.6MPI.R5]


title: 7T-3461G-FOV_14

description:
raw data files:
3461G_exprMat_file.csv.gz
3461G_fov_positions_file.csv.gz
3461G_metadata_file.csv.gz
3461G_tx_file.csv.gz
3461G-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7T-3461G-FOV_14.rds

value: M

value: RHS


title: fibroblast, CSE treatment, 24h, rep2


title: 46T-148191A-FOV_14

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
46T-148191A-FOV_14.rds

value: F

value: hepatic flexure


title: mRNAseq_YCRRF_rep2

description:
Library name: Sample 2
mRNAseq_YCRRF_rep2

value: Bone marrow

value: Hematopoietic stem cell

value: WT

value: CR refeed


title: fibroblast, CSE treatment, 8h, rep3


title: fibroblast, CSE treatment, 8h, rep2


title: Unc119_KO-1


title: Unc119_KO-2


title: 280N-120131-FOV_14

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
280N-120131-FOV_14.rds

value: Colon tumour,FFPE

value: caecum


title: Unc119_WT-3


title: fibroblast, CSE treatment, 8h, rep1

value: orbital fibroblast


title: PS19_upACSS2_6MPI_4 [ACSS2.OE.6MPI.R4]

value: dorsal Hippocampus


title: 92T-10501A-FOV_14

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
92T-10501A-FOV_14.rds

value: dMMR


title: PS19_upACSS2_6MPI_2 [ACSS2.OE.6MPI.R2]

value: 8.5-9 months old

value: male


title: PS19_upACSS2_6MPI_1 [ACSS2.OE.6MPI.R1]


title: Unc119_WT-1


title: 118T-Tumour_A-FOV_13

description:
raw data files:
Run5654_Tumor_A_exprMat_file.csv.gz
Run5654_Tumor_A_fov_positions_file.csv.gz
Run5654_Tumor_A_metadata_file.csv.gz
Run5654_Tumor_A_tx_file.csv.gz
Run5654_Tumor_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
118T-Tumour_A-FOV_13.rds

value: pMMR


title: fibroblast, CSE treatment, 6h, rep2

value: thyroid eye disease (TED)


title: PS19_vector_1MPI_4 [ACSS2.WT.1MPI.R4]

value: 3.5 months old


title: 64T-Tumour_B-FOV_13

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_13.rds

value: RHS


title: Unc119_WT-2

value: Retina


title: fibroblast, CSE treatment, 6h, rep3


title: Itln-1_knockout_HDM_3

city: Changsha

first: Shiyue

last: He

state: other

address: Changsha, China

institute: Xiangya Hospital, Central South University

data_processing:
According to the position information of gene alignment on the reference genome, the number of reads covered by each gene (including the new predicted gene) from inception to termination was counted. reads with a comparison mass value lower than 10 were filtered out, and reads without paired comparison were compared to reads in multiple regions of the genome. The featureCounts tool in subread is used in this part of the analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts of each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: lung

growth_protocol: All mice were in groups of 4-5 animals per cage, maintaining a temperature range of 23° to 25°C with 40-60% humidity. All mice were exposed to a 12-hour light/dark cycle and allowed free access to water and standard laboratory pellets.

extract_protocol:
RNA is extracted from tissues or cells using standard extraction methods, followed by rigorous quality control of RNA samples, primarily through Agilent 2100 bioanalyzer: Accurate detection of RNA integrity.
Total RNA was used as input material for the RNA sample preparations. 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 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, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system.

treatment_protocol: For HDM induced asthma model, mice were anesthetized by isoflurane inhalation followed by sensitized with 20 μg HDM in 50 μl PBS by intratracheal administration on day 1, 3 and 5. From days 11-14, mice were continuously challenged with 20 μg HDM by intratracheal administration.

value: lung


title: 67T-Run5850.2186.2-FOV_13

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_13.rds

value: M

value: sigmoid

value: LHS


title: 142N-Run5850.2186.1-FOV_13

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142N-Run5850.2186.1-FOV_13.rds

value: F

value: ascending


title: PS19_upACSS2_6MPI_3 [ACSS2.OE.6MPI.R3]


title: PS19_vector_1MPI_3 [ACSS2.WT.1MPI.R3]


title: fibroblast, control, rep3


title: Itln-1_knockout_HDM_2


title: fibroblast, CSE treatment, 6h, rep1


title: 73N-Normal_A-FOV_13

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
73N-Normal_A-FOV_13.rds

value: Colon tumour,FFPE


title: PS19_vector_1MPI_2 [ACSS2.WT.1MPI.R2]


title: WT_HDM_3

value: WT


title: PS19_vector_1MPI_1 [ACSS2.WT.1MPI.R1]

value: dorsal Hippocampus


title: 7T-3461G-FOV_13

description:
raw data files:
3461G_exprMat_file.csv.gz
3461G_fov_positions_file.csv.gz
3461G_metadata_file.csv.gz
3461G_tx_file.csv.gz
3461G-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7T-3461G-FOV_13.rds


title: PS19_upACSS2_1MPI_5 [ACSS2.OE.1MPI.R5]

source_name: whole Hippocampus

value: whole Hippocampus


title: fibroblast, control, rep2

value: orbital fibroblast


title: WT_HDM_2


title: WT_HDM_1


title: PS19_upACSS2_1MPI_4 [ACSS2.OE.1MPI.R4]

value: male


title: PS19_vector_1MPI_5 [ACSS2.WT.1MPI.R5]


title: 280N-120131-FOV_13

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
280N-120131-FOV_13.rds

value: caecum

value: pMMR


title: PS19_upACSS2_1MPI_3 [ACSS2.OE.1MPI.R3]

value: 3.5 months old


title: 130T-10501A-FOV_13

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
130T-10501A-FOV_13.rds

value: rectum upper


title: PS19_upACSS2_1MPI_2 [ACSS2.OE.1MPI.R2]


title: p14_sham_4

first: zheng

last: sixie

address: 1678 Dongfang Road

institute: Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong Univerisity School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced of library size (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. 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: FPKM

growth_protocol: The postnatal  mice were breastfed by the motherand were housed in groups of 5-6 per cage, fed under the same conditions with free access to food and water, maintained in the 12h: 12h day: night cycle.

extract_protocol:
Lung tissue  was rapidly removed from executed mice and flash frozen in -80℃ refrigerator , 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® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The P7 mice were anesthetized using 4% isoflurane, then were performed with a midline laparotomy to expose the abdominal aorta (AA) and inferior vena cava (IVC). After puncturing through the AA into the IVC with a needle of 11-0 nylon thread, a hemostatic compression for 2 min with the surrounding connective tissue was performed. At last, the abdominal wall was closed, and the pups were returned to their mother.  The mice in Sham group underwent the same procedure except for the puncture step.

value: Sham operated


title: Itln-1_knockout_HDM_1

value: lung


title: 64T-Tumour_B-FOV_12

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_12.rds

value: RHS


title: p14_sham_3


title: PS19_upACSS2_1MPI_1 [ACSS2.OE.1MPI.R1]


title: p14_sham_2


title: 118T-Tumour_A-FOV_12

description:
raw data files:
Run5654_Tumor_A_exprMat_file.csv.gz
Run5654_Tumor_A_fov_positions_file.csv.gz
Run5654_Tumor_A_metadata_file.csv.gz
Run5654_Tumor_A_tx_file.csv.gz
Run5654_Tumor_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
118T-Tumour_A-FOV_12.rds

value: M


title: 67T-Run5850.2186.2-FOV_12

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_12.rds

value: sigmoid

value: LHS


title: M4_vector_10m [M4_vector_10m]

value: 10 months old


title: M5_vector_10m [M5_vector_10m]


title: p14_sham_1


title: fibroblast, control, rep1

value: thyroid eye disease (TED)


title: M3_vector_10m [M3_vector_10m]


title: 142N-Run5850.2186.1-FOV_12

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142N-Run5850.2186.1-FOV_12.rds

value: Colon tumour,FFPE

value: F

value: ascending

value: dMMR


title: 7N-Normal_A-FOV_12

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7N-Normal_A-FOV_12.rds


title: p14_ipf_5

value: WT

value: fistula surgery


title: 46T-148191A-FOV_13

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
46T-148191A-FOV_13.rds

value: hepatic flexure

value: pMMR


title: p14_sham_5


title: p14_ipf_4


title: Parkinson’s Disease [JM-PK9]

city: Sant Joan d'Alacant

first: Marina

last: Guillot Fernández

state: Alicante

address: Av. Don Santiago Ramón y Cajal, s/n

country: Spain

institute: Instituto de Neurociencias

description: Gene expression data

hyb_protocol: Labeled cRNA was hybridized to the Clariom S Array (Human, Affymetrix) following the manufacturer’s guidelines.

scan_protocol: The Clariom S Array (Human, Affymetrix) was scanned using the GeneChip® Scanner 3000 7G according to the manufacturer's instructions

data_processing:
Raw .CEL files were processed using the R computing environment (version 4.4.2) and BioConductor packages. Quality control was performed with the oligo package and the Transcriptome Analysis Console (TAC) software (version 4.0.3, ThermoFisher Scientific). Robust Multi-array Average (RMA) normalization was applied to adjust for background noise and normalize expression levels. Probes not mapping to known genes were excluded, and lowly expressed genes were filtered out. Differential expression analysis was performed using the limma package, with multiple testing correction applied via the False Discovery Rate (FDR) method.
Normalized log2-transformed gene expression values were obtained after RMA normalization and background correction.

label: biotin

source_name: Parkinson’s Disease

label_protocol: Biotin-labeled cRNA was generated for hybridization using the standard Affymetrix protocol.

growth_protocol: Not applicable. Human peripheral blood samples were collected from Parkinson’s disease (PD) patients and healthy controls.

extract_protocol: Peripheral Blood Mononuclear Cells (PBMCs) were isolated from whole blood using BD Vacutainer® CPT™ Cell Preparation Tubes with Sodium Heparin, following the manufacturer’s instructions. RNA extraction was performed using TRI Reagent (Applied Biosystems), and RNA integrity was assessed with the Agilent 2100 Bioanalyzer.

treatment_protocol: No treatment was applied. Samples were obtained from de novo and drug-naïve PD patients and age- and sex-matched healthy controls.

value: Female

tag: Stage

value: Hoehn II


title: Parkinson’s Disease [JM-PK7]

description: Gene expression data

value: Male


title: Parkinson’s Disease [JM-PK5]

description: Gene expression data


title: Parkinson’s Disease [JM-PK3]

description: Gene expression data

value: Hoehn I


title: 7T-3461G-FOV_12

description:
raw data files:
3461G_exprMat_file.csv.gz
3461G_fov_positions_file.csv.gz
3461G_metadata_file.csv.gz
3461G_tx_file.csv.gz
3461G-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7T-3461G-FOV_12.rds

value: M

value: RHS


title: Parkinson’s Disease [JM-PK4]

description: Gene expression data


title: p14_ipf_3

value: lung


title: 280T-120131-FOV_12

description:
raw data files:
120131_exprMat_file.csv.gz
120131_fov_positions_file.csv.gz
120131_metadata_file.csv.gz
120131_tx_file.csv.gz
120131-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
280T-120131-FOV_12.rds

value: caecum


title: Parkinson’s Disease [JM-PK8]

description: Gene expression data


title: M6_upACSS2_10m [M6_upACSS2_10m]

value: dorsal Hippocampus

value: 10 months old

value: male


title: p14_ipf_2


title: p14_ipf_1


title: M4_upACSS2_10m [M4_upACSS2_10m]


title: Parkinson’s Disease [JM-PK29]

description: Gene expression data


title: 74T-10501A-FOV_12

description:
raw data files:
10501A_exprMat_file.csv.gz
10501A_fov_positions_file.csv.gz
10501A_metadata_file.csv.gz
10501A_tx_file.csv.gz
10501A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
74T-10501A-FOV_12.rds

value: Colon tumour,FFPE

value: descending colon

value: LHS


title: Parkinson’s Disease [JM-PK6]

description: Gene expression data


title: M5_upACSS2_10m [M5_upACSS2_10m]


title: M1_vector_10m [M1_vector_10m]


title: CIH groupn replicate3

city: 泉州

first: 清石

last: 陈

state: 福建省

address: 福建省泉州市鲤城区中山北路34号

institute: 医科大学附属第二医院

data_processing:
miRNA sequencing and data analysis Using miRBase, reads from the reference genome were compared to mature sequences of known miRNAs with a maximum of one mismatch allowed. The range of matches was 2 nt upstream and 5 nt downstream. The readings that were found were regarded as known miRNAs. Based on the biological characteristics of miRNA, the potential precursor sequences were found by the Illumina Genome Analyzer IIx program by comparing readings with genome location data. RNA-fold (version 2.1.7) and the read distribution on the precursor sequence were used to evaluate energy information for the precursor structure using a Bayesian model[19]. This model took into account features related to miRNA synthesis, mature sequence characteristics, star sequences, and loops, and consequently predicted novel miRNA. Each sample's miRNA expression levels were counted, and the transcript per million (TPM) approach was then used to standardize the result[20]. DESeq2 is suitable for biological repetition studies, whereas differential expression analysis between sample groups may be utilized to acquire DE miRNA sets between two biological scenarios[21]. DE miRNAs between two samples can be identified in research without biological replication by using EdgeR[22]. In our current study, DESeq2 was used to compare the relative expression levels of the two (groups) samples, and the DE miRNAs were categorized as either upregulated or downregulated. The fold change (FC) and P value in expression were used to determine the screening threshold for the identification of DE miRNAs, which was as follows: |log2 (FC)|≥2, P-value<0.05. To lower the false discovery rate (FDR) and correct the P values used in the identification of DE miRNAs, the Benjamini Hochberg technique was applied. 2.5. GO annotation and KEGG pathway enrichment analysis For the target genes identified by exosome-derived miRNAs, we carried out KEGG pathway enrichment analysis and GO analysis to get more insight into the biological functions of the genes. The categories of biological process (BP), molecular function (MF), and cellular component (CC) were present. The important routes all have a p-value of less than 0.05. 2.6. Construction of a ceRNA Interaction Network To construct the miRNA-mRNA network, 8 significantly differentially expressed miRNAs were chosen using Arraystar's in-house miRNA target prediction software, which was developed using TargetScan and miRanda. Next, we constructed a competitive endogenous RNA (ceRNA) network using Cytoscape 2.8.3 with eight selected miRNAs and targeted genes. Pearson's correlation coefficient was set at (r) > 0.97.
Assembly: mm9
Supplementary files format and content: xlsx

source_name: pancreatic tissues

growth_protocol: We used our previously published approach to establish the CIH model[18]. Simply put, we took 18 mice mentioned above and randomly divided them into 2 groups. There were 9 mice in the CIH group and 9 mice in the control group, and the dead mice were excluded as the experiment progressed. Finally, 3 mice in each group were randomly selected for experiment. All the mice that were allocated to the CIH group were kept in specially designed, commercially available chambers(ProOx-100-CIH-M, Shanghai TOW Intelligent Technology Co., Ltd). The system pumps pure nitrogen into the chamber and reduces O2 to 6% in 60 seconds. Then, the control system permits rapid oxygen replenishment, which causes O2 to reoxidize quickly to 21% in 60 seconds. For a total of eight weeks, this 2-minute CIH cycle is repeated thirty times every hour for eight hours each day. In the control group, the tube of the experimental device was directly connected to the indoor air during the entire experiment. Following eight weeks of exposure to CIH, all mice were put to sleep with isoflurane anesthesia and then euthanized by cervical dislocation performed by a qualified practitioner. After that, the tissues of the pancreas were harvested and sectioned by two well-experienced pathologists.

extract_protocol:
To screen for differentially expressed miRNAs, total RNA was extractedusing mirVana™ miRNA Isolation Kit （Cat #. AM1561, Austin TX,US ）following the manufacturer's instructions and checked for a RIN number (RNA Integrity Number, RNA integrity test, from 0 to 10, the higher the score RNA, the better the integrity) to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Qualified total RNA was further purified by RNA Clean XP Kit (Beckman Coulter, Inc Kraemer Boulevard Brea, CA, USA). Then, the total RNA was subjected to quality inspection by NanoDrop ND-2000 spectrophotometer and Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). The quality-qualified RNA was subsequently subjected to library construction. According to the experimental instructions, the purified total RNA was subjected to rRNA removal, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, terminal repair, 3ʹ end plus A, ligation linker, enrichment and the like to complete the sequencing sample library. Double-end sequencing was performed using an Illumina NovaSeq 6000 (Illumina, USA).Sequencing results were filtered by Seqtk to exclude unqualified Reads with the low overall quality, sequencing primers, and low-end quality. Using edge R to perform differential gene analysis between samples, the P value is obtained and a multihypothesis test is performed. The threshold of the P value is determined by controlling FDR (False Discovery Rate), and the corrected P value is q value. At the same time, we calculate the differential expression multiple based on the FPKM (Fragments per kilobase of exon model per Million mapped reads) value, which is Fold-change. The differential miRNA screening conditions are as follows: (a) q-value ≤ 0.05, (b) Fold-change ≥ 2. miRNAs with P values (Transcripts per million value, formula: number of reads on a miRNA × 106/total number of reads) greater than 10 were selected for further verification. The sequencing experiments and analyses were completed by Shanghai Biotechnology Corporation.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135-155 bp PCR amplified fragments (corresponding to 15-35 nt small RNAs).

treatment_protocol: Tissues from  pancreati tissues and promptly cooled at -80℃ refrigerator.

value: pancreatic tissues

value: CIH


title: 64T-Tumour_B-FOV_11

description:
raw data files:
Run5629_Tumor_B_exprMat_file.csv.gz
Run5629_Tumor_B_fov_positions_file.csv.gz
Run5629_Tumor_B_metadata_file.csv.gz
Run5629_Tumor_B_tx_file.csv.gz
Run5629_Tumor_B-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
64T-Tumour_B-FOV_11.rds

value: F

value: pMMR


title: M3_upACSS2_10m [M3_upACSS2_10m]


title: M2_vector_10m [M2_vector_10m]


title: CIH group replicate2

address: 福建省泉州市鲤城区中山北路34号


title: 118T-Tumour_A-FOV_11

description:
raw data files:
Run5654_Tumor_A_exprMat_file.csv.gz
Run5654_Tumor_A_fov_positions_file.csv.gz
Run5654_Tumor_A_metadata_file.csv.gz
Run5654_Tumor_A_tx_file.csv.gz
Run5654_Tumor_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
118T-Tumour_A-FOV_11.rds


title: M2_upACSS2_10m [M2_upACSS2_10m]


title: 67T-Run5850.2186.2-FOV_11

description:
raw data files:
Run5850_2186_2_exprMat_file.csv.gz
Run5850_2186_2_fov_positions_file.csv.gz
Run5850_2186_2_metadata_file.csv.gz
Run5850_2186_2_tx_file.csv.gz
Run5850_2186_2-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
67T-Run5850.2186.2-FOV_11.rds

value: sigmoid


title: CIH group replicate1

address: 福建省泉州市鲤城区中山北路34号


title: 46T-148191A-FOV_12

description:
raw data files:
148191A_exprMat_file.csv.gz
148191A_fov_positions_file.csv.gz
148191A_metadata_file.csv.gz
148191A_tx_file.csv.gz
148191A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
46T-148191A-FOV_12.rds

value: hepatic flexure


title: M1_upACSS2_10m [M1_upACSS2_10m]


title: Control group replicate3

address: 福建省泉州市鲤城区中山北路34号

value: Control


title: 142N-Run5850.2186.1-FOV_11

description:
raw data files:
Run5850_2186_1_exprMat_file.csv.gz
Run5850_2186_1_fov_positions_file.csv.gz
Run5850_2186_1_metadata_file.csv.gz
Run5850_2186_1_tx_file.csv.gz
Run5850_2186_1-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
142N-Run5850.2186.1-FOV_11.rds

value: ascending

value: dMMR


title: Control group replicate2

address: 福建省泉州市鲤城区中山北路34号


title: 7N-Normal_A-FOV_11

description:
raw data files:
Run5654_Normal_A_exprMat_file.csv.gz
Run5654_Normal_A_fov_positions_file.csv.gz
Run5654_Normal_A_metadata_file.csv.gz
Run5654_Normal_A_tx_file.csv.gz
Run5654_Normal_A-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7N-Normal_A-FOV_11.rds

value: M

value: RHS


title: 7T-3461G-FOV_11

description:
raw data files:
3461G_exprMat_file.csv.gz
3461G_fov_positions_file.csv.gz
3461G_metadata_file.csv.gz
3461G_tx_file.csv.gz
3461G-polygons.csv.gz
This study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Cabrini Research Governance Office (CRGO 04-19-01-15 and 04-15-05-17) and the Monash University Human Research Ethics Committee (MUHREC ID 2518). Fresh and archival tissue specimens from treatment naïve patients receiving treatment for CRC at Cabrini Hospital, Malvern, Australia were obtained. All patients provided written informed consent. Clinical information including patient and tumour characteristics, were obtained from the prospectively maintained, clinician-led Cabrini Monash University Department of Surgery colorectal neoplasia database (CMCND)
processed data file:
7T-3461G-FOV_11.rds


title: Control group replicate1

address: 福建省泉州市鲤城区中山北路34号


title: M11_vector_Aged [ACSS2.WT.R11]

value: whole Hippocampus

value: 22-23 months old


title: M12_vector_Aged [ACSS2.WT.R12]

value: male


title: M10_vector_Aged [ACSS2.WT.R10]


title: Ca_h3k4_2

city: Shanxi

first: wenbin

last: ren

address: 56 Xinjian South Road, Yingze District, Taiyuan City

institute: Shanxi Medical University

library_source: genomic

data_processing:
The raw sequencing data were examined using the illumina analysis pipeline.
Using Bowtie2, the data were aligned to the Mus musculus reference genome (University of California, Santa Cruz, mm10).
The data were further analyzed through the ChIP-seq analysis based on the model (MACS) program (https://github.com/taoliu/MACS).
The enriched binding peaks were identified after normalization with the control input.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

source_name: embryo

growth_protocol: DMEM, UltraPure™ distilled water (Invitrogen, USA), 1 mM glucose, 0.1 mM nonessential amino acids, 0.1 mM glutamate, 15% FBS, 0.1 mM β-mercaptoethanol (Life Technologies, USA), 1000 U/ml leukemia inhibitory factor (Millipore, USA)  Cells were cultured at 37C at 5% CO2.

extract_protocol:
C57BL/6 mESCs were seeded into culture dishes precoated with MEFs cultured in DMEM supplemented with 0.1 mM nonessential amino acids, 0.1 mM glutamate, and 10% fetal bovine serum (FBS) (Invitrogen, USA) overnight.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 30 cycles on the thermocycler. Post amplification libraries were size selected at 250-500bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Folate power (Sigma–Aldrich, USA) was dissolved in Dulbecco’s modified Eagle’s medium (DMEM) 10X without folic acid (Sigma–Aldrich, USA) and with 3.7%. filtered sodium hydrogen carbonate (Beijing ChemicalReagent Company, China). The final concentration of 4 mg/L folate as a normal control while the folatedeficient group was treated simply by DMEM without folate.

value: embryo

value: mouse embryonic stem cells

value: folate deficiency

value: neurodevelopment


title: M9_vector_Aged [ACSS2.WT.R9]