title: Aorta_9240, 5 multiplexed samples

city: Nashville

first: Lindsey

middle: "Joey"

last: Stolze

state: TN

address: 1211 Medical Center Dr

institute: Vanderbilt University Medical Center

description: Library name: Sample_6

data_processing:
scRNA-seq samples were mapped to hg38 using CellRanger.
Demultiplexing was performed using scDemultiplex and validated with souporcell.
Further analysis was performed using primarily Seurat with a handful of other programs used for cell type annotations (SignacX, SingleR, Azimuth)
Assembly: hg38
Supplementary files format and content: Raw Feature bc matrices in 'h5' format following Cell Ranger mapping
Supplementary files format and content: Barcode file for demultiplexing

source_name: Aorta

extract_protocol:
Blood: Processed for PBMC isolation; Aorta & Adipose Tissue: Digested with Collagenase and then dissociated using MACS dissociator to obtain single cells.
10X Genomics Chromium platform

value: Aorta


title: Sh-Sy5y cells, Sirt6 ChIP, Replicate 2

status: Public on Nov 01 2025

type: SRA

city: Beer sheva

first: Debra

last: Toiber

state: Beer sheva

address: David Ben Gurion Blvd 1

department: Life Sciences

country: Israel

institute: Ben Gurion University of the Negev

description: Library name: Sh-Sy5y_Sirt6_ChIP_rep2

library_source: genomic

data_processing:
BWA Mapper, Samtools, bamCoverage_Genome, bedClip, bedGraphToBigWig
Trim Galore was used  with --length 25, we also used multiQC
macs3 peakcalling -g hs -f BED --nomodel p 0.01
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

organism: Homo sapiens

source_name: CNS

growth_protocol: DMEM, 10% fetal bovine serum, 2 mM L-glutamine, 1x penicillin/streptomycin. Cultured at 37 °C at 5% CO2, humidified atmosphere.

extract_protocol:
The cells were plated for all the experimental conditions at an equal confluence, fixed with 1% formaldehyde for 10 minutes, quenched, and collected. After, cell pellet resuspension in RIPA buffer, the lysates were sonicated using a vibracell needle sonicator (Sonics & Materials Inc, USA) to break the chromatin. Chromatin immunoprecipitations were carried out using anti-myc antibodies coated magnetic beads (MedChemExpress, Cat# HY-K0206) to isolate Sirt6-bound DNA.
Chip-seq libraries were prepared at the Crown Genomics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science starting from 1-20ng of DNA as previously described (Blecher-Gonen R et al. Nat. prot. (2013)). Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent). Sequencing was done on a Novaseq 6000 instrument (Illumina) using an SP 100 cycles kit, allocating 20M reads per sample (paired end sequencing).

treatment_protocol: untreated

tag: tissue

value: CNS

tag: cell line

tag: cell type

value: Neuroblastoma cell line

tag: treatment

value: cMyc-Sirt6 transduction


title: Sh-Sy5y cells, Sirt6 ChIP, Replicate 3

description: Library name: Sh-Sy5y_Sirt6_ChIP_rep3


title: PBMC_9240, 5 multiplexed samples

country: USA

description: Library name: Sample_5

library_source: transcriptomic single cell

molecule: polyA RNA

source_name: Blood

value: Blood

value: PBMC


title: Aorta_P3004_HiCMV

description: Library name: Sample_4


title: Sh-Sy5y cells, Sirt6 ChIP, Replicate 1

description: Library name: Sh-Sy5y_Sirt6_ChIP_rep1


title: Adipose_9240, 5 multiplexed samples

description: Library name: Sample_7

source_name: Adipose

value: Adipose


title: PBMC_8848, 5 multiplexed samples

description: Library name: Sample_1


title: TC-YIK cells, shControl_2

city: Suita

first: Satoshi

last: Nakagawa

state: Osaka

address: 2-15 Yamadaoka

department: Osaka University

country: Japan

institute: Department of Obstetrics and Gynecology

library_source: transcriptomic

data_processing:
ikra v 2.0.1
A gene expression table is generated from FASTQ files using ikra, which is an RNA-seq pipeline centered on salmon.
Assembly: hg38
Supplementary files format and content: tab-demilited text files includes raw counts for each sample

molecule: total RNA

source_name: TC-YIK

extract_protocol:
RNA was harvested using the RNeasy Mini Kit (QIAGEN) following the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Kit (Illumina) following the manufacturer's protocol.

value: TC-YIK

value: Small cell neuroendocrine carcinoma of the uterine cervix

tag: genotype

value: WT


title: TC-YIK cells, shControl_1


title: TC-YIK cells, shControl_3


title: Aorta_8967, 4 Multiplexed samples

description: Library name: Sample_2


title: HCSC-1 cells, shVRK1_2

value: VRK1 knockdown


title: 9_Lung 14R LN

city: Philadelphia

first: Aliia

middle: R

last: Fatkhullina

state: Pennsylvania

address: 3400 Civic Center Blvd Bldg 421

institute: University of Pennsylvania

data_processing:
Raw Fastq files were pseudo-aligned to the human GRCh38.p13 transcriptome using Kallisto
The gene counts were input to R and transcripts per million (tpm). Initial filtering removed genes with expression under 1 count per million (cpm)
Filtered gene counts were used as an input for differential expression analysis using limma/voom (edgeR)
Genes with an adjusted p-value (adj_pval) < 0.05 were considered significant for downstream analysis
Assembly: hg38
Supplementary files format and content: tsv files containing kallisto alignment output (estimated counts, TPM, and effective length) for each sample
Supplementary files format and content: comma separated variable file for raw counts

source_name: lymph node

extract_protocol:
RNA was extracted using TRIZOL protocol, RNA samples were purified using RNAclean XP beads (Beckman Coulter), and RNA concentration was measured with a NanoDrop Microvolume Spectrophotometer (Thermo Fisher).
1000-1500 ng of RNA was used as the starting material for cDNA library synthesis and tagmentation using the NEBNext Poly A kit (NEB) per the manufacturer’s instructions.

treatment_protocol: To study the regionalization of human gut-, and lung-draining lymph nodes the following lymph nodes were isolated: Intestine-draining: superior central, mesenteric, juxta-intestinal, ileocolic, caecum, ascending colon; lung-draining: right lower paratracheal (4R), subcarinal (7), right hilar (10R), right subsegmental (14R).

value: lymph node

tag: tissue location/area

value: lung

tag: Sex

value: Female

tag: age


title: TC-YIK cells, shVRK1_3


title: HCSC-1 cells, shControl_3


title: PBMC_BL_8967, 5 multiplexed samples

description: Library name: Sample_3


title: HCSC-1 cells, shControl_1


title: HCSC-1 cells, shVRK1_3


title: TC-YIK cells, shVRK1_1


title: TC-YIK cells, shVRK1_2


title: 5_Lung 10R LN

value: Male


title: 4_Lung 10R LN


title: SAMPLE 12_genomic DNA from SCC25_JQ1_3

type: genomic

city: guangzhong

first: yurui

last: liu

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou City, Guangdong Province

country: China

institute: Southern Medical University

hyb_protocol: Genomic DNA was bisulfite conversed, amplified, incubated, fragmented, precipitated, resuspended, and hybridized to a BeadChip from the Infinium MethylationEPIC Kit

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

data_processing:
BeadStudio software
The 'matrix signal intensities.txt' contains unmethylated and methylated signal intensities.

source_name: cell line

label_protocol: Standard Illumina Protocol

growth_protocol: SCC15 and SCC25 were seeded in 6-well plates maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol: Genomic DNA was extracted using the TIANamp Genomic DNA Kit(TIANGEN), and the quality was verified by spectrometry.

treatment_protocol: SCC15 and SCC25 were exposed to 0.5 μM JQ1 or DMSO for 48 h.

value: tumor cell line


title: 5_Lung 14R LN


title: 2_Lung 10R LN


title: 8_Lung 14R LN


title: SAMPLE 7_genomic DNA from SCC25_DMSO_1

value: DMSO


title: 9_Lung 7 LN


title: SAMPLE 9_genomic DNA from SCC25_DMSO_3


title: 4_Lung 14R LN


title: HCSC-1 cells, shVRK1_1


title: 8_Lung 10R LN


title: 7_Lung 7 LN


title: 5_Lung 7 LN


title: SAMPLE 11_genomic DNA from SCC25_JQ1_2


title: HCSC-1 cells, shControl_2


title: 9_Lung 10R LN


title: SAMPLE 4_genomic DNA from SCC15_JQ1_1


title: SAMPLE 1_genomic DNA from SCC15_DMSO_1


title: 3_Lung 14R LN


title: 1_Lung 14R LN


title: 6_Lung 10R LN


title: 3_Lung 7 LN


title: SAMPLE 5_genomic DNA from SCC15_JQ1_2


title: 2_Lung 7 LN


title: 4_Lung 7 LN


title: 7_Lung 14R LN


title: 7_Lung 10R LN


title: SAMPLE 10_genomic DNA from SCC25_JQ1_1


title: 8_Lung 4R LN


title: 5_Lung 4R LN


title: SAMPLE 3_genomic DNA from SCC15_DMSO_3


title: 1_Lung 10R LN


title: SAMPLE 8_genomic DNA from SCC25_DMSO_2


title: 3_Lung 10R LN


title: 2_Lung 4R LN


title: 1_Lung 4R LN


title: SAMPLE 6_genomic DNA from SCC15_JQ1_3


title: 8_Lung 7 LN


title: 1_Ascending Colon LN

value: large intestine


title: 6_Lung 7 LN


title: 2_Ascending Colon LN


title: 9_Lung 4R LN


title: SAMPLE 2_genomic DNA from SCC15_DMSO_2


title: 7_Caecum LN


title: 4_Caecum LN


title: 6_Caecum LN


title: 4_Lung 4R LN


title: 6_Lung 4R LN


title: 5_Caecum LN


title: 2_Caecum LN


title: 3_Caecum LN


title: 3_Lung 4R LN


title: 6_Ascending Colon LN


title: 7_Ileocolic (D) LN

value: small intestine


title: 7_Lung 4R LN


title: 7_Ascending Colon LN


title: 8_Ascending Colon LN


title: 9_Ascending Colon LN


title: 6_Ileocolic (D) LN


title: 4_Ascending Colon LN


title: 5_Ileocolic (D) LN


title: 9_Caecum LN


title: 8_Caecum LN


title: 3_Ileocolic (D) LN


title: 2_Ileocolic (D) LN


title: 5_Ascending Colon LN


title: 1_Caecum LN


title: 1_Ileocolic (D) LN


title: 9_Juxta-intestinal LN


title: 7_Juxta-intestinal LN


title: 9_Ileocolic (D) LN


title: 8_Juxta-intestinal LN


title: Patient 15 Class 1

type: RNA

city: Kamakura

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
24

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

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

source_name: primary pancratic cancer

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

extract_protocol: RNA samples were extracted from serum using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

value: primary pancratic cancer

tag: blood sample type

value: PVB

tag: timing of sample collection

value: intraoperative

tag: recurrence site

value: Lung


title: 5_Juxta-intestinal LN


title: Patient 16 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
26


title: Patient 9 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
23


title: 2_Juxta-intestinal LN


title: Pateint 15 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
25

value: PB


title: 4_Juxta-intestinal LN


title: 9_Mesenteric (B) LN


title: 7_Mesenteric (B) LN


title: Patient 16 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
27


title: Patient 14 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
22

value: No recurrence


title: Patient 14 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
21


title: Patient 11 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
11


title: 4_Mesenteric (B) LN


title: Patient 12 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
16


title: 8_Mesenteric (B) LN


title: 5_Mesenteric (B) LN


title: Patient 13 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
20


title: 6_Mesenteric (B) LN


title: Patient 12 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
15


title: Patient 13 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
19


title: Patient 11 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
12


title: 2_Mesenteric (B) LN


title: 3_Mesenteric (B) LN


title: Patient 10 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
10


title: Patient 10 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
9


title: 9_Superior (A) LN


title: 1_Mesenteric (B) LN


title: Patient 9 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
8


title: 8_Superior (A) LN


title: 6_Superior (A) LN


title: Pateint 8 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
6

value: Liver


title: 5_Superior (A) LN


title: 4_Superior (A) LN


title: right ventricle,snRNA-seq,nine years

city: Chengdu

first: Yuwei

last: Gou

address: No. 211, Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
Using the rna mkref command in the Celescope v1.8.0 software to build an index file for single-cell alignment against the Sscrofa11.1 genome with Ensembl release 105 gene annotation. Subsequently, employing the multi_rna command to align and quantify gene expression in snRNA-seq data, generating output files for downstream Seurat analysis.
Supplementary files format and content: The tar archive file includes the matrix.mtx file, which contains gene expression levels for each cell. The barcodes.tsv file lists unique identifiers (barcodes) associated with each cell in the experiment. The genes.tsv file provides detailed information about the genes.

organism: Sus scrofa

source_name: right ventricle

extract_protocol:
Right ventricle tissues were harvested from pig heart and were washed in pre-cooled PBSE (PBS buffer containing 2 mM EGTA). Nuclei isolation was carried out using GEXSCOPE® Nucleus Separation Solution (Singleron Biotechnologies, Nanjing, China) referring to the manufacturer's product manual. Isolated nuclei were re-suspended in PBSE to 106 nuclei per 400μl, fltered through a 40μm cell strainer, and counted with Trypan blue. Nuclei enriched in PBSE were stained with DAPI (1:1,000) (TermoFisher Scientifc, D1306). Nuclei were defined as DAPI-positive singlets.
The concentration of single nucleus suspension was adjusted to 3-4 × 105 nuclei/mL in PBS. Single nucleus suspension was then loaded onto a microfluidic chip (GEXSCOPE® Single Nucleus RNA-seq Kit, Singleron Biotechnologies) and snRNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies). The resulting snRNA-seq libraries were sequenced on the Illumina HiSeq X Ten system with 150-bp paired end reads.

value: right ventricle

value: female

value: nine years


title: Patient 8 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
5


title: Patient 7 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
4


title: Patient 7 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
3


title: Patient 6 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
2


title: right ventricle,snRNA-seq,6 months postpartum

value: 6 months postpartum


title: 3_Superior (A) LN

value: lymph node

value: Female


title: ventricle,snRNA-seq,Embryo period 70 days

source_name: ventricle

value: ventricle

value: Embryo period 70 days


title: Patient 5 Class 4

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.24

value: postoperatie


title: Patient 6 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
1


title: 2_Superior (A) LN

value: small intestine

value: Male


title: Patient 5 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.21

value: primary pancratic cancer

value: PVB


title: Patient 5 Class 2

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.22


title: Patient 5 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.23

value: intraoperative


title: IHMGECs, input, biol rep 1

city: Charlottesville

first: Yumeng

last: Zhang

state: Virginia

address: 1726 Webland Park

institute: University of Virginia

description: Library name: Sample 9

data_processing:
Single end demultiplexed fastq files were generated using bcl2fastq2 (Illumina, v2.20), from NextSeq550 v2.5 reagent’s bcl files.
Fastq files were imported batch wise, trimmed for adapter sequences followed by quality trimming using CLC Genomics Workbench (CLC Bio, v24.0.2).
Assembly: The imported high-quality reads were mapped against gene regions and transcripts annotated by ENSEMBL v110 GRCh38 using the Map Reads to Reference 1.9, peaks were called using the Transcription Factor ChIP-Seq Analysis tool v2.0 (CLC Genomics Workbench), where the maximum p-value for peak calling was 0.1.
Supplementary files format and content: Tab-delimited text file include center of peak, length and peak shape score for all samples.

source_name: Meibomian gland

growth_protocol: IHMGECs (CRL-3472, ATCC) were cultured in keratinocyte serum-free medium with 5 ng/ml epidermal growth factor (EGF) and 50 μg/ml bovine pituitary extract (BPE) according to ATCC instructions.

extract_protocol:
Chromatin immunoprecipitation (ChIP) assay was conducted following the manufacturer’s instructions for SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (9003, Cell Signaling)
For downstream NG-sequencing DNA library construction, we used the Kapa Roche HyperPlus kit (7962428001, Roche) to generate the ChIP-seq libraries, and then the samples were sequenced on the Illumina NextSeq 550 sequencer platform with the SE-75 sequencing protocol, following the manufacturer’s instructions.

treatment_protocol: IHMGECs were cultured on 10 cm culture dishes, and infected with pLenti-GFP or pLenti-Krox20 lentivirus upon 50% confluency; cells were collected when the cell density reached 80-90% (42-hours post infection; approximately 107 cells for each condition).

value: Meibomian gland

value: IHMGECs

value: epithelial cells

tag: antibody

tag: batch

value: batch 2


title: IHMGECs, input, biol rep 2

description: Library name: Sample 10


title: IHMGECs, pulldown by anti-Histone H3, biol rep 3

description: Library name: Sample 8

value: Rabbit anti-Histone H3 (D2B12) XP® (4620, Cell Signaling, 10 μL per immunoprecipitation)


title: 1_Superior (A) LN


title: IHMGECs, pulldown by anti-Histone H3, biol rep 2

description: Library name: Sample 7


title: SKOV3 cells, sh3_3

city: Chongqing

first: Min

last: Wang

address: No. 1 Yixueyuan Road

institute: Chongqing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Ovarian cancer cells

value: STXBP6 knockdown_3

value: Lentiviral transduction


title: IHMGECs, pulldown by anti-Histone H3, biol rep 1

description: Library name: Sample 6

value: batch 1


title: Patient 4 Class 4

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.20

value: PB

value: Other


title: 7_Superior (A) LN

value: lymph node

value: Female


title: IHMGECs, infected by pLenti-GFP, post 42 hour infection, pulldown by anti-Krox20, biol rep 2

description: Library name: Sample 5

value: Rabbit anti-EGR2 (KROX20) (MA5-38053, Thermo Fisher, 1:50)


title: Patient 4 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.19

value: primary pancratic cancer


title: SKOV3 cells, sh3_2


title: IHMGECs, infected by pLenti-GFP, post 42 hour infection, pulldown by anti-Krox20, biol rep 1

description: Library name: Sample 4


title: IHMGECs, infected by pLenti-Krox20, post 42 hour infection, pulldown by anti-Krox20, biol rep 2

description: Library name: Sample 2


title: SKOV3 cells, sh3_1


title: IHMGECs, infected by pLenti-Krox20, post 42 hour infection, pulldown by anti-Krox20, biol rep 1

description: Library name: Sample 1


title: Patient 4 Class 2

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.18

value: PVB

value: postoperatie


title: IHMGECs, input, biol rep 3

description: Library name: Sample 11

value: Meibomian gland


title: IHMGECs, infected by pLenti-Krox20, post 42 hour infection, pulldown by anti-Krox20, biol rep 3

description: Library name: Sample 3

value: IHMGECs


title: IHMGECs, infected by pLenti-Krox20, post 66 hour infection, biol rep 1

description:
Library name: Sample 17
Column name in raw_counts_All_Samples.txt: pLenti-Krox20, 66h, repeat 1

data_processing:
CLC Genomics Workbench (CLC Bio, v24.0.2).
Fastq files were imported batch wise, trimmed for adapter sequences followed by quality trimming using CLC Genomics Workbench (CLC Bio, v24.0.2).
Assembly: The imported high-quality reads were mapped against gene regions and transcripts annotated by ENSEMBL v110 GRCh38 using the RNA-Seq Analysis tool v2.8 (CLC Genomics Workbench), only matches to the reverse strand of the genes were accepted (using the strand-specific reverse option).
Supplementary files format and content: Tab-delimited text file include raw counts, RPKM, TPM, CPM for all samples.

extract_protocol:
mRNA from IHMGECs transduced with lentivirus (pLenti-Krox20 or pLenti-GFP) was extracted with TRI Reagent® (T9424, Sigma-Aldrich).
The RNA libraries were generated using the Illumina TruSeq® Stranded mRNA Library Prep Kit (20020594, Illumina).

treatment_protocol: Lentiviral particles were produced in HEK 293 cells transfected with psPAX2, pMD2.G, and pLenti-Krox20 or pLenti-GFP. IHMGECs were transduced with the generated lentivirus upon 30% confluency, and the mRNA profiles were analyzed 18-, 42- and 66-hours post-infection via bulk RNA-Seq.

value: epithelial cells

value: Krox20 overexpression

value: pLenti-Krox20 infection


title: IHMGECs, infected by pLenti-Krox20, post 66 hour infection, biol rep 3

description:
Library name: Sample 19
Column name in raw_counts_All_Samples.txt: pLenti-Krox20, 66h, repeat 3


title: IHMGECs, infected by pLenti-Krox20, post 66 hour infection, biol rep 2

description:
Library name: Sample 18
Column name in raw_counts_All_Samples.txt: pLenti-Krox20, 66h, repeat 2


title: SKOV3 cells, sh1_3

value: Ovarian cancer cells

value: STXBP6 knockdown_1


title: Patient 4 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.17

value: intraoperative


title: IHMGECs, infected by pLenti-GFP, post 66 hour infection, biol rep 2

description:
Library name: Sample 15
Column name in raw_counts_All_Samples.txt: pLenti-GFP, 66h, repeat 2

value: GFP overexpression

value: pLenti-GFP infection

value: batch 1


title: SKOV3 cells, sh1_1

value: Lentiviral transduction


title: Patient 3 Class 3

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.15

value: PB

value: No recurrence


title: IHMGECs, infected by pLenti-GFP, post 66 hour infection, biol rep 1

description:
Library name: Sample 14
Column name in raw_counts_All_Samples.txt: pLenti-GFP, 66h, repeat 1


title: Input HFD 6

city: Cologne

first: Sophie

middle: M

last: Steculorum

address: Gleueler Straße 50

department: Metabolism Research

country: Germany

institute: Max Planck Institute

description: Library name: Sample42

data_processing:
We applied the community-curated nfcore rnaseq analysis pipeline version 1.446.
The gene-level quantification was carried out using Salmon 0.14.147 using the reference genome GRCm38
To normalize the immuno-pulldown for each sample to its background, we divide the salmon gene count per sample using the formula countpulldowncountinpu
. The differential gene expression analysis based on the normalized counts was done using the DESeq2 1.26. R package90
Gene-ontology term analysis was carried out using the clusterProfiler 3.14.3 R package91. Olfactory receptors with a Padj < 0.001 compared to no odor samples were defined as significantly activated, as defined by Jiang et al (2015)
Assembly: The gene-level quantification was carried out using Salmon 0.14.147 using the reference genome GRCm38
Supplementary files format and content: comma-delimited text files includes raw salmon counts for each sample

organism: Mus musculus

source_name: Main olfactory epithelium

extract_protocol:
The olfactory epithelium was dissected on ice in buffer containing 1×HBSS (Gibco, with Ca2+ and Mg2+), 2.5 mM HEPES (pH 7.4), 35 mM glucose, 100 μg/ml cycloheximide, 5 mM sodium fluoride, 1 mM sodium orthovanadate, 1 mM sodium pyrophosphate, 1 mM beta-glycerophosphate. 4 epithelia were pooled for homogenization at 250 rpm for 10 times, and 9 times at 750 rpm on a rotating glass/teflon potter homogenizer (Potter S, Braun) at 4°C in 1 ml of buffer containing 150 mM KCl, 5 mM MgCl2, 10 mM HEPES, 100 nM Calyculin A, 2 mM DTT, 100 U RNasin (Promega), 100 μg cycloheximide, 1 tablet of Complete mini EDTA-free protease inhibitor cocktail/7 ml and 1 tablet PhosSTOP/5 ml. Samples were spun in 1.5-ml LoBind tubes (Eppendorf), and centrifuged at 2,000g for 10 min at 4°C. 90 μl 10% NP-40 (v/v) and 90 μl 300 mM DHPC (Avanti Polar Lipids) were added to the supernatant which was centrifuged again at 17,000g for 10 min at 4°C. The supernatant was transferred to a new LoBind tube, and mixed with 20 μl pS6 antibody (#2215, Cell Signaling). Protein A Dynabeads (Invitrogen, 100 μl per sample) were washed 3 times with 900 μl buffer containing 150 mM KCl, 5 mM MgCl2, 10 mM HEPES, 0.05% BSA (w/v) and 1% NP-40. After antibody binding, the mixture was added to the washed beads mixed by pipetting, followed by incubation for 1 h at 4°C on a rotator. After incubation, the ribosome-bound beads were washed 4 times with 700 μl buffer containing 350 mM KCl, 5 mM MgCl2, 10 mM HEPES, 1% NP-40, 2 mM DTT, 100 U/ml recombinant RNasin (Promega), 100 μg/ml cycloheximide, 5 mM sodium fluoride, 1 mM sodium orthovanadate, 1 mM sodium pyrophosphate, 1 mM beta-glycerophosphate. During the final wash, beads were placed onto the magnet and moved to room temperature. After removing supernatant, RNA was eluted by mixing the beads with 350 μl RLT (from Qiagen RNeasy kit). The eluted RNA was purified using RNeasy Micro kit (Qiagen).
For library preparation, the Illumina Nextera XT DNA sample preparation protocol was used, with 1 ng cDNA input

value: Main olfactory epithelium

value: Male

value: HFD odor exposure


title: Patient 3 Class 2

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.14

value: primary pancratic cancer

value: PVB

value: postoperatie


title: SKOV3 cells, shNC_3

value: NC


title: Patient 3 Class 4

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.16


title: IHMGECs, infected by pLenti-Krox20, post 42 hour infection, biol rep 3

description:
Library name: Sample 13
Column name in raw_counts_All_Samples.txt: pLenti-Krox20, 42h, repeat 3

value: Meibomian gland

value: IHMGECs

value: epithelial cells

value: Krox20 overexpression

value: pLenti-Krox20 infection


title: SKOV3 cells, shNC_2

value: Ovarian cancer cells


title: Input HFD 3

description: Library name: Sample40


title: Patient 3 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.13

value: intraoperative


title: Patient 2 Class 4

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.12

value: Other


title: Input HFD 2

description: Library name: Sample39


title: IHMGECs, infected by pLenti-Krox20, post 42 hour infection, biol rep 2

description:
Library name: Sample 12
Column name in raw_counts_All_Samples.txt: pLenti-Krox20, 42h, repeat 2

value: batch 1


title: Patient 2 Class 2

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.10


title: IHMGECs, infected by pLenti-Krox20, post 42 hour infection, biol rep 1

description:
Library name: Sample 11
Column name in raw_counts_All_Samples.txt: pLenti-Krox20, 42h, repeat 1


title: SKOV3 cells, shNC_1

value: Lentiviral transduction


title: IHMGECs, infected by pLenti-GFP, post 66 hour infection, biol rep 3

description:
Library name: Sample 16
Column name in raw_counts_All_Samples.txt: pLenti-GFP, 66h, repeat 3

value: GFP overexpression

value: pLenti-GFP infection


title: SKOV3 cells, sh1_2

value: STXBP6 knockdown_1


title: N196147_R1

city: New York

first: Madelyn

last: Espinosa-Cotton

state: New York

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Gene counts were generated by alignment to human transcriptome GRCh38 using STAR in RSEM.
Differential gene expression analysis was performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: txt file with count data from RSEM

source_name: pleura

extract_protocol:
Phase separation in OCT frozen tissue lysed in TRIzol was induced with 200 µL chloroform and RNA was extracted from the aqueous phase using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher catalog # A27828) on the KingFisher Flex Magnetic Particle Processor (Thermo Scientific catalog # 5400630) according to the manufacturer’s protocol
179-700 ng of total RNA with DV200 percentages varying from 3-78% underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 Reagent Kit (200 Cycles) (Illumina).

value: pleura


title: Input Bacon 5

description: Library name: Sample37

value: Main olfactory epithelium

value: Male

value: Bacon odor exposure


title: N196147_R2


title: LX-2 cells,TGF-β24h,TGFB2 BS

city: Wuhan

first: An

address: Aerodrome Road 13

institute: Huazhong University of Science and Technology

description:
Library name: TGFB2
Bisulfite-sequencing of LX-2 cells treated with human recombinant TGF beta, biological rep2

data_processing:
Raw reads were first processed with fastp (version 0.23.0) to remove the residual adaptor sequences and the reads with low quality scores.
Then the clean reads were mapped to the reference genome and the duplicated reads were removed using Bismark (version 0.22.3).
The depth and coverage on chromosomes were calculated with mosdepth (version 0.3.1) and RSeQC(version 4.0.0)
The methylation detection along the whole genome were conducted by Bismark which calculates the proportion of methylated reads at every genome site.
Assembly: hg38
Supplementary files format and content: Detection and annotation of methylation sites

growth_protocol: LX-2 cells were maintained in 1640 supplemented with 10% fetal bovine serum(FBS) and  1% antibiotics in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was harvested using TRIzol reagent(Invitrogen, cat. NO 15596026）, and a minimum of 2 μg of total RNA per sample was used for the construction of sequencing libraries .
PolyA+ RNA was then selected and the library was constructed using the EZ RNA Methylation™ Kit (ZYMO RESEARCH) and KC UMI RNA Library Kit (Wuhan SeqHealth Tech) according to the manufacturer’s instructions.

treatment_protocol: LX-2 was stimulated by 5ng/ml TGF-β1 (PeproTech, USA) and after 24 hours we extracted the total RNA.

value: cell line

value: hepatic stellate cells

value: WT

value: treated with human recombinant TGF-β1


title: Input HFD 1

description: Library name: Sample38

value: HFD odor exposure


title: Input Bacon 4

description: Library name: Sample36


title: N195995_R2


title: IHMGECs, infected by pLenti-GFP, post 42 hour infection, biol rep 2

description:
Library name: Sample 9
Column name in raw_counts_All_Samples.txt: pLenti-GFP, 42h, repeat 2

value: Meibomian gland

value: IHMGECs

value: epithelial cells


title: Patient 2 Class 1

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.9

value: primary pancratic cancer

value: PVB

value: intraoperative

value: Other


title: IHMGECs, infected by pLenti-GFP, post 42 hour infection, biol rep 1

description:
Library name: Sample 8
Column name in raw_counts_All_Samples.txt: pLenti-GFP, 42h, repeat 1

value: GFP overexpression

value: pLenti-GFP infection

value: batch 1


title: N195995_R1

value: pleura


title: LX-2 cells,TGF-β24h,TGFB1 BS

description:
Library name: TGFB1
Bisulfite-sequencing of LX-2 cells treated with human recombinant TGF beta, biological rep1


title: Input Bacon 3

description: Library name: Sample35

value: Main olfactory epithelium

value: Male

value: Bacon odor exposure


title: Input HFD 5

description: Library name: Sample41


title: LX-2 cells,con2 BS

description:
Library name: con 2
Bisulfite-sequencing of LX-2 cells untreated,biological rep2

value: cell line

value: hepatic stellate cells

value: WT

value: untreated


title: Input Bacon 2

description: Library name: Sample34


title: IHMGECs, infected by pLenti-Krox20, post 18 hour infection, biol rep 3

description:
Library name: Sample 7
Column name in raw_counts_All_Samples.txt: pLenti-Krox20, 18h, repeat 3

value: Meibomian gland

value: IHMGECs

value: Krox20 overexpression

value: pLenti-Krox20 infection


title: N195139_R2


title: LX-2 cells,con1 BS

description:
Library name: con1
Bisulfite-sequencing of LX-2 cells untreated,biological rep1


title: IHMGECs, infected by pLenti-Krox20, post 18 hour infection, biol rep 2

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.txt: pLenti-Krox20, 18h, repeat 2

value: epithelial cells


title: IHMGECs, infected by pLenti-Krox20, post 18 hour infection, biol rep 1

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.txt: pLenti-Krox20, 18h, repeat 1


title: Input Bacon 1

description: Library name: Sample33


title: N195139_R1


title: Input NCD 6

description: Library name: Sample32

value: NCD odor exposure


title: HUDEP-2,shMAZ,rep2

city: Guangzhou

first: Bo

last: Yang

state: Guangdong

address: Guangzhou, 510150, Guangdong Province, China.

institute: The Third Affiliated Hospital of Guangzhou Medical University

data_processing:
Approximately 16-20 million of Q30>90% trimmed and filtered high-quality 150-bp paired-end reads per sample generated by Fastp28 were mapped to the human genome (hg38) using the STAR29 with default parameters. Gene counts were overlapped with exons of RefFlat (UCSC, https://genome.ucsc.edu/) by featureCounts30. DESeq231 was used for differential gene expression analysis. Expression visualized tracks were generated with bigwig files performed by bamCoverage32 then displayed by igvtools (IGV 2.8.6).
Assembly: hg38
Supplementary files format and content: tabular,gene counts table

growth_protocol: The HUDEP-2 cell line was a kind gift of Dr. Yukio Nakamura (Cell Engineering Department, BioResource Center, RIKEN, Japan). HUDEP-2 cells were cultured in StemSpan SFEM Ⅰ (STEMCELL) medium containing 50 ng/ml SCF (R&D Systems) , 3 IU/ml EPO, 1 μg /ml Dexamethasone,1 μg /ml Doxycycline , 2 mM GlutaMAX (Gibco).

extract_protocol:
Total RNA was extracted from cells using TRIzol regent (Invitrogen) following the manufacturer’s instructions.
RNA-seq libraries were prepared from total RNA from cells using MGIEasy RNA sample preparation kit (MGI) and sequenced on BGISEQ (MGI)

treatment_protocol: Primers containing sequences of short hairpin RNAs (shRNAs) targeting MAZ or scrambled shRNAs were annealed and cloned into GV248 lentivirus vectors. Each GV248 plasmid then cotransfected with psPAX2(Addgene #12260) and pMD2.G(Addgene #12259) into HEK293T cells. Then the viruses were collected from supernatant of HEK293T after 48 h. HUDEP-2 cells were transduced with virus. EGFP+ cells were sorted by FACS for subsequent expansion.

value: Human Umbilical cord blood-Derived Erythroid Progenitor-2

value: MAZ knockdown


title: N190515_R2

source_name: peritoneum

value: peritoneum


title: IHMGECs, infected by pLenti-GFP, post 42 hour infection, biol rep 3

description:
Library name: Sample 10
Column name in raw_counts_All_Samples.txt: pLenti-GFP, 42h, repeat 3

value: GFP overexpression

value: pLenti-GFP infection

value: batch 1


title: N190515_R1


title: Input NCD 5

description: Library name: Sample31

value: Main olfactory epithelium

value: Male


title: HUDEP-2,shControl

value: control


title: IHMGECs, infected by pLenti-GFP, post 18 hour infection, biol rep 2

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.txt: pLenti-GFP, 18h, repeat 2


title: IHMGECs, infected by pLenti-GFP, post 18 hour infection, biol rep 3

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.txt: pLenti-GFP, 18h, repeat 3


title: Patient 1 Class 4

description:
Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.
No.8

value: primary pancratic cancer

value: PB

value: postoperatie

value: Other


title: N180316_R2

value: pleura


title: Input NCD 4

description: Library name: Sample30


title: N180316_R1


title: IHMGECs, infected by pLenti-GFP, post 18 hour infection, biol rep 1

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.txt: pLenti-GFP, 18h, repeat 1

value: Meibomian gland

value: IHMGECs


title: TBI_ND1_rep 3

city: 广州

first: shuo

last: zhang

address: 黄埔大道西601号

institute: 暨南大学

description:
Library name: Sample_3
mouse_TBI_ND1_7d_14d_rep3

data_processing:
Raw reads were processed with CeleScope v1.15.0 (Singleron) using default parameters. Barcodes and UMIs were extracted from R1 and error-corrected; adapters and poly-A tails were trimmed from R2. Clean reads were aligned to GRCm38/mm10 with STAR v2.6.1a and assigned to genes with FeatureCounts v2.0.1. Reads sharing identical cell barcode, UMI and gene were collapsed into a gene-level UMI count matrix. Quality control, normalization and clustering were performed with Scanpy v1.8.2 in Python 3.7. Cells with <200 genes, top 2 % gene counts, top 2 % UMIs, or >15 % mitochondrial reads were removed; genes detected in <5 cells were discarded, yielding 88 582 cells (median 1 518 genes and 3 285 UMIs per cell). Counts were normalized per-cell and log-transformed. The 2 000 most variable genes were selected (flavor='seurat'); PCA was run on the scaled matrix and the top 20 PCs were used for Harmony v1.0 batch correction. Louvain clustering (resolution 1.2) identified 26 clusters visualized with UMAP and t-SNE.
Assembly: Mouse mm10
Supplementary files format and content: Normal_EmptyDrops_CR_224538_matrix.tar, GFP_EmptyDrops_CR_matrix.tar, ND1_EmptyDrops_CR_matrix.tar — each archive contains gzip-compressed Matrix Market (MTX) files: sparse gene-cell UMI count matrix (genes × cells), cell barcodes (barcodes.tsv) and gene IDs with symbols (genes.tsv).

source_name: Brain cortical tissue

extract_protocol:
Adult male FVB mice were anesthetized with 1.25 % tribromoethanol i.p. and transcardially perfused with ice-cold artificial cerebrospinal fluid (ACSF). Cortices were micro-dissected in cold ACSF, stripped of meninges and white matter, then dissociated into single-cell suspensions using the Papain Dissociation System (Worthington Biochemical, #LK003176) following the manufacturer’s protocol. Viable cells (>85 %) were counted by trypan blue exclusion and kept on ice for downstream processing.
Single-cell suspensions (2-2.5 × 10^5 cells ml⁻¹ in ice-cold 0.04 % BSA/PBS) were loaded onto a 150 000-well SCOPE-chip™ microfluidic device (Scope Single-Cell Technologies). Gravity-driven Poisson loading yielded ≈7 000 single cells. Barcoded magnetic beads carrying cell-specific oligos and UMIs were introduced (one bead per well). After on-chip lysis, poly-adenylated mRNA was captured by oligo(dT) beads. Beads were pooled and reverse-transcribed using SuperScript IV (Thermo Fisher) followed by 12–14 cycles of PCR amplification (KAPA HiFi HotStart). Amplified cDNA (average 350 bp after tagmentation) was processed for tagmentation, end-repair, A-tailing and Illumina adapter ligation using the Nextera XT kit (Illumina). Libraries were quantified by Bioanalyzer (Agilent) and qPCR (KAPA Library Quantification kit) before sequencing.

value: Brain cortical tissue

value: primary cortical cells from adult male FVB mice

value: mixed cortical cell population

value: FVB/NJ

value: TBI, therapeutic virus treatment


title: Input NCD 3

description: Library name: Sample29

value: NCD odor exposure


title: IHMGECs, widetype

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.txt: wt

value: epithelial cells

value: WT

value: batch 1


title: TBI_GFP_rep 3

description:
Library name: Sample_2
mouse_TBI_GFP_control_7d_14d_rep3

value: TBI, control virus treatment


title: MSK_5467__R2

source_name: DSRCT

value: DSRCT

tag: patient

value: Male

tag: fusion protein_identified

value: Yes

tag: survival (years)

value: Not Available


title: Input NCD 2

description: Library name: Sample28

value: Main olfactory epithelium


title: tilapia liver tissues, negative control group3

city: wuxi

first: Yi-Fan

last: Tao

state: jiangsu

address: 9 Shanshui East Road

institute: Freshwater Fisheries Research Center

data_processing:
Raw data was first processing with cutadapt software (version 1.9) to remove reads that contain more than 5% N (N means base information cannot be determined) of all base; adaptor-polluted and low quality reads (more than 20% bases with a Q value<10).
Q20, Q30, GC-content of clean data were further calculated to verify sequence quality.
Then, we aligned clean reads to the Oreochromis niloticus reference genome by using HISAT package to obtain annotation information.
Assembly: Nile tilapia (8128)
Supplementary files format and content: Tab-delimited text file includes read counts and FPKM values for each Sample.

organism: Oreochromis niloticus

source_name: liver

growth_protocol: The fish maintaining a controlled water temperature of 28±1°C and a pH level of 7.6±0.2. Continuous aeration was diligently administered to sustain dissolved oxygen levels above 5 mg/L. The fish was fed twice a day (7:00, 17:00) with a pellet diet containing 5% palm oil.

extract_protocol:
Liver samples from 18 individuals (nine per Elo and NC groups) were processed for total RNA extraction using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). RNA integrity was assessed using a NanoDrop 2000 (Thermo, Wilmington, MA, USA) and an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Equal quantities of RNA from three replicate tanks per treatment group were pooled, forming six RNA libraries (Elo_1, Elo_2, Elo_3, NC_1, NC_2, NC_3).
About 10 μg total RNA from these mixed sample was purified by using oligo-dT magnetic beads and then prepared for constructing RNA-seq libraries by mRNA-Seq Sample Preparation Kit (Illumina, USA) (Qiang et al., 2017). Transcriptome sequencing was performed by using Illumina Novaseq™ 6000 (LC Sciences, USA) that generated about 150bp double-ended (PE150) raw reads.

treatment_protocol: elovl6 knockdown by antisense RNA.

value: liver

value: male

value: fed with palm oil diet


title: Input NCD 1

description: Library name: Sample27


title: MSK_5467__R1


title: tilapia liver tissues, negative control group2


title: HUDEP-2,shMAZ,rep1

value: Human Umbilical cord blood-Derived Erythroid Progenitor-2

value: MAZ knockdown


title: tilapia liver tissues, negative control group1


title: MSK_5456__R2


title: Input No Odour 6

description: Library name: Sample26

value: No Odor


title: MSK_5456__R1


title: tilapia liver tissues, elovl6 knockdown group3

value: elovl6 knockdown


title: MSK_5349__R2


title: IP MM2-8W

city: Indianapolis

first: Núria

last: Morral

state: IN

address: 975 West Walnut, IB130

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

description: Library name: Sample 34

data_processing:
To identify consensus peaks across different experimental conditions, the raw sequencing reads (fastq files) were aligned to the mouse reference genome (mm10/GRCm38, GENCODE M25) using the Burrows-Wheeler Aligner [29]. Broad peaks were then identified with MACS2 and peaks in ENCODE blacklist regions were subsequently removed
Assembly: mm10
Supplementary files format and content: bam, broad peaks identified by MACS2
Supplementary files format and content: tab delimited txt files; data show DB

source_name: Liver tissue

extract_protocol:
Tissue was minced in cold D-PBS and chromatin was immediately crosslinked with 1% methanol-free formaldehyde for 5 min. Cells were sonicated using Bioruptor UCD-300
Illumina TruSeq Nano DNA LT Library Prep Kit

value: Liver tissue

value: 8w - ChIP-Maternal obesity - male

tag: chip antibody

value: H3K9me3 (#17-625, Millipore)


title: IP MM1-8W

description: Library name: Sample 33

tag: tissue


title: tilapia liver tissues, elovl6 knockdown group2


title: Input No Odour 3

description: Library name: Sample24


title: MSK_5349__R1


title: IP CM4-8W

description: Library name: Sample 32

value: 8w - ChIP-Control diet  - male


title: IP CM3-8W

description: Library name: Sample 31


title: Input No Odour 2

description: Library name: Sample23


title: MSK_5338__R1


title: IP CM2-8W

description: Library name: Sample 30


title: Input No Odour 1

description: Library name: Sample22


title: iPS_lung_2022_3

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

description: Library name: lung organoids MPXV clade IIb 3

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 platform with the paired-end mode.
Illumina RTA version 4.12.2 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by cutadapt v4.6. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.11a with the GENCODE (release 44, GRCh38.p14) gtf file.
The uniquely and properly mapped reads were used for further analysis. Raw read counts were calculated using htseq-count v2.0.5 with the GENCODE gtf file. Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: iPS cell-derived lung organoids

growth_protocol: The human iPS cell line, 1383D6 (provided by Dr. Masato Nakagawa, Kyoto University),  was maintained on 0.5 μg/cm2 recombinant human laminin 511 E8 fragments (iMatrix-511, Cat# 892 012, Nippi) with StemFit AK02N medium (Cat# RCAK02N, Ajinomoto) containing 10 μM Y-27632 (Cat# 034-24024, FUJIFILM Wako Pure Chemical). For cell passaging, human iPS cell colonies were treated with TrypLE Select Enzyme (Cat# 12563029, Thermo Fisher Scientific) for 10 min at 37°C. To start the differentiation, human iPS cell colonies were treated with TrypLE Select Enzyme (Cat# 12563029, Thermo Fisher Scientific) for 10 min at 37°C. After centrifugation, cells were seeded onto Matrigel Growth Factor Reduced Basement Membrane (Cat# 354230, Corning)-coated cell culture plates (2.0×105 cells/4 cm2) and cultured for 2 days. The differentiation of the lung organoids was performed in serum-free differentiation (SFD) medium, composed of DMEM/F12 (3:1) (Cat# 044-29765, FUJIFILM Wako Pure Chemical and Cat# 11320033, Thermo Fisher Scientific) supplemented with N2 (Cat# 141-08941, FUJIFILM Wako Pure Chemical), B-27 Supplement Minus Vitamin A (Cat# 12587001, Thermo Fisher Scientific), ascorbic acid (50 μg/mL, Cat# ST-72132, STEMCELL Technologies), 1× GlutaMAX (Cat# 35050-061, Thermo Fisher Scientific), 1% monothioglycerol (Cat# 195-15791, FUJIFILM Wako Pure Chemical), 0.05% bovine serum albumin (Cat# 820024, Sigma-Aldrich), and 1× penicillin/streptomycin). During days 0-1 of differentiation, cells were cultured with SFD medium supplemented with 10 μM Y-27632 (Cat# 034-24024, FUJIFILM Wako Pure Chemical) and 100 ng/mL recombinant Activin A (Cat# 338-AC-01M, R&D Systems). During days 1–3 of differentiation, cells were cultured with SFD medium supplemented with 10 μM Y-27632 (Cat# 034-24024, FUJIFILM Wako Pure Chemical), 100 ng/mL recombinant Activin A (Cat# 338-AC-01M, R&D Systems), and 1% FBS. Between days 3–5 of differentiation, cells were cultured in SFD medium supplemented with 1.5 μM Dorsomorphin dihydrochloride (Cat# 047-33763, FUJIFILM Wako Pure Chemical) and 10 μM SB431542 (Cat# 037-24293, FUJIFILM Wako Pure Chemical) for 24 h, and then SFD medium supplemented with 10 μM SB431542 and 1 μM IWP2 (Cat# 04-0034, Stemolecule) for another 24 h. During days 5–12 of differentiation, cells were cultured with SFD medium supplemented with 3 μM CHIR99021 (Cat# 034-23103, FUJIFILM Wako Pure Chemical), 10 ng/mL human FGF10 (Cat# AF-100-26, PeproTech), 10 ng/mL human FGF7 (Cat# AF-100-19, PeproTech), 10 ng/mL human BMP4 (Cat# 120-05ET, PeproTech), 20 ng/mL human EGF (Cat# AF-100-15, PeproTech), and all-trans retinoic acid (Cat# R2625 ATRA, Sigma-Aldrich). On day 12 of differentiation, cells were dissociated and embedded in the Matrigel Growth Factor Reduced Basement Membrane to generate organoids. During days 12–20 of the differentiation, organoids were cultured in SFD medium containing 3 μM CHIR99021, 10 ng/mL human FGF10, 10 ng/mL human FGF7, 10 ng/mL human BMP4, and 50 nM ATRA. On day 20 of differentiation, organoids were recovered from the Matrigel gel, and the resulting suspension of organoids (small free-floating clumps) was seeded onto thin Matrigel-coated cell culture plates. During days 20–30 of differentiation, organoids were cultured in SFD medium containing 50 nM dexamethasone (Cat# S1322, Selleck Chemicals), 0.1 mM 8-bromo-cAMP (Cat# 1140/50, Tocris), and 0.1 mM IBMX (3-isobutyl-1-methylxanthine) (Cat# 095-03413, FUJIFILM Wako Pure Chemical).

extract_protocol:
Total RNA was isolated using ISOGENE (Cat# 319-90211, NIPPON GENE).
Library preparation was performed using an Illumina Stranded mRNA Prep Kit (Cat# 20040532, Illumina) according to the manufacturer’s instructions.

treatment_protocol: Human iPS cell-derived lung organoids were infected with MPXV (0.05 multiplicity of infection (MOI)) and cultured for 72 h. Three MPXV strains (clade Ia, clade IIa, and clade IIb) were used in this experiment.

tag: cell line

value: iPS cell-derived lung organoids

value: lung organoids

value: wild type

value: MPXV clade IIb infected

tag: time

value: 3 dpi


title: Ribo HFD 6

description: Library name: Sample21

library_source: other

molecule: other

value: Main olfactory epithelium

value: Male

tag: treatment

value: HFD odor exposure


title: Normal_rep 3

description:
Library name: Sample_1
mouse_normal_rep3

value: Brain cortical tissue

value: primary cortical cells from adult male FVB mice

tag: cell type

value: mixed cortical cell population

tag: genotype

value: FVB/NJ

value: health


title: MSK_5338__R2

value: DSRCT

tag: Sex

value: Yes


title: IP MM4-8W

description: Library name: Sample 36

value: Liver tissue

value: 8w - ChIP-Maternal obesity - male

value: H3K9me3 (#17-625, Millipore)


title: Ribo HFD 5

description: Library name: Sample20


title: IP MM3-8W

description: Library name: Sample 35


title: Input No Odour 4

description: Library name: Sample25

value: No Odor


title: iPS_lung_2022_2

description: Library name: lung organoids MPXV clade IIb 2

value: iPS cell-derived lung organoids

value: lung organoids

value: wild type


title: IP MF4-8W

description: Library name: Sample 28

value: 8w - ChIP-Maternal obesity  - female


title: iPS_lung_Lb_3

description: Library name: lung organoids MPXV clade IIa 3

value: MPXV clade IIa infected

value: 3 dpi


title: MSK_5326__R2

value: Male

value: Not Available


title: IP CM1-8W

description: Library name: Sample 29

value: 8w - ChIP-Control diet  - male


title: tilapia liver tissues, elovl6 knockdown group1

value: liver

value: elovl6 knockdown

value: male

value: fed with palm oil diet


title: iPS_lung_Lb_2

description: Library name: lung organoids MPXV clade IIa 2


title: iPS_lung_2022_1

description: Library name: lung organoids MPXV clade IIb 1

value: MPXV clade IIb infected


title: Ribo HFD 3

description: Library name: Sample19

value: Main olfactory epithelium

value: HFD odor exposure


title: Ribo Bacon 5

description: Library name: Sample16

value: Bacon odor exposure


title: MSK_5324__R2

value: DSRCT

value: Female

value: Yes


title: MSK_5325__R2


title: Ribo HFD 2

description: Library name: Sample18


title: MSK_5274__R2


title: MSK_5326__R1


title: MSK_5325__R1


title: Ribo HFD 1

description: Library name: Sample17


title: IP MF2-8W

description: Library name: Sample 26

value: Liver tissue

value: 8w - ChIP-Maternal obesity  - female

value: H3K9me3 (#17-625, Millipore)


title: iPS_lung_Congo_3

description: Library name: lung organoids MPXV clade Ia 3

value: iPS cell-derived lung organoids

value: lung organoids

value: wild type

value: MPXV clade Ia infected

value: 3 dpi


title: IP CF3-8W

description: Library name: Sample 23

value: 8w - ChIP-Control diet  - female


title: IP MF1-8W

description: Library name: Sample 25


title: iPS_lung_Lb_1

description: Library name: lung organoids MPXV clade IIa 1

value: MPXV clade IIa infected


title: MSK_5274__R1

value: Male


title: iPS_lung_Congo_1

description: Library name: lung organoids MPXV clade Ia 1


title: IP CF2-8W

description: Library name: Sample 22


title: MSK_5324__R1

value: Not Available


title: Ribo Bacon 3

description: Library name: Sample14

value: Main olfactory epithelium


title: MSK_5273__R2


title: IP CF4-8W

description: Library name: Sample 24


title: iPS_lung_mock1_3

description: Library name: lung organoids mock 3

value: mock


title: iPS_lung_Congo_2

description: Library name: lung organoids MPXV clade Ia 2


title: iPS_lung_mock1_2

description: Library name: lung organoids mock 2


title: MSK_5273__R1

value: DSRCT


title: Ribo Bacon 4

description: Library name: Sample15

value: Bacon odor exposure


title: IC CM1-8w

description: Library name: Sample 20

value: 8w - Input control-male


title: Ribo Bacon 2

description: Library name: Sample13


title: IP MF3-8W

description: Library name: Sample 27

value: Liver tissue


title: iPS_lung_mock1_1

description: Library name: lung organoids mock 1


title: Ribo Bacon 1

description: Library name: Sample12


title: IP CF1-8W

description: Library name: Sample 21


title: Ribo NCD 5

description: Library name: Sample10

value: NCD odor exposure


title: MSK_5272__R2

value: Yes


title: IC CF1-8W

description: Library name: Sample 19

value: 8w - Input control-female

value: H3K9me3 (#17-625, Millipore)


title: MTS P5D6, biol rep 4

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
Raw read quality check was performed using FastQC
Low-quality reads and adapter sequences were removed using Trimmomatic v.036
Filtered reads were mapped onto the S. viridis A10 genome available in the GenBank database (GCF_005286985.1) using Hisat2
Transcript expression was estimated using the featureCounts command from the R package Rsubread v. 1.16.1
DESeq2 v. 1.6.3 was used to perform the differential expression analysis. Transcripts with an adjusted p-value <0.05 and log2-fold-change >1 or <-1 were considered differentially expressed.
For GO enrichment analysis the PANZER annotation and the R cluster profile package were used.
Assembly: GCF_005286985.1
Supplementary files format and content: Tab delimited text files (.tsv) containing differential expression analysis results
Supplementary files format and content: Tab delimited text files (.tsv) containing raw counts data

organism: Setaria viridis

source_name: shoots

growth_protocol: Seeds of S. viridis were kept overnight at −80°C, followed by soaking in sulfuric acid for 15 min and rinsing under running water for seed scarification. They were surface-sterilized by soaking in 2% sodium hypochlorite solution containing 50 μL Tween-20 emulsifier for 15 min under low stirring and rinsed ten times with sterile Milli-Q water. The surface-sterilized S. viridis seeds were germinated on glass Petri dishes (150 x 20 mm) containing half-strength Murashige and Skoog salt (½ MS) medium (pH 5.7) and 10% agar in a growth chamber (Fitotron® HGC Weiss Technik) under a 12 h photoperiod (28°C, irradiance of 250 μmol.m-2.s-1 / 25°C, dark) and 75% relative humidity. Two days before the co-cultivation experiments, two seedlings of 5-day old S. viridis were transferred to each co-cultivation system, consisted of a small Petri dish (49 × 12 mm) containing LB solid media inside a larger Petri dish (150 × 15 mm) filled with ½ MS solid medium. One day before the inoculation in the co-cultivation system, bacterial isolates were grown on LB broth for 16 h. Then, each culture was diluted with water to 108 CFU.mL−1 and 20 μL were spread onto the small dish of the system.  As mock control, seedlings were grown in co-culture plates without bacterial inoculum. All plates were sealed with polyvinyl chloride, positioned at ~70° angle, and placed in the growth chamber in the same described conditions for seven days.

extract_protocol:
Total RNA extraction was performed using the SV Total RNA Isolation System kit (Promega) following the manufacturer’s instructions. RNA quality and integrity was determined using the Agilent RNA 6000 Nano kit (Agilent Technologies) and a Bioanalyzer 2100 equipment (Agilent Technologies). Quantification was performed using the Invitrogen Qubit™ RNA BR Assay kit (ThermoFisher Scientific) and a Qubit Fluorometer (ThermoFisher Scientific)
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina Inc.), following manufacturer’s recommendations.

value: shoots

value: plant cells

value: WT

value: MTS P5D6


title: MSK_5272__R1


title: Ribo NCD 4

description: Library name: Sample9


title: Ribo NCD 3

description: Library name: Sample8


title: IP MM5-3w

description: Library name: Sample 18

value: 3w - ChIP-Maternal obesity - male


title: Ribo NCD 2

description: Library name: Sample7

value: Male


title: MSK_5271__R2


title: IP MM4-3w

description: Library name: Sample 17


title: MTS P5D6, biol rep 3


title: MTS P5D6, biol rep 2


title: MSK_5271__R1


title: Ribo NCD 1

description: Library name: Sample6


title: MSK_5240B_R2

value: Female

value: No

value: Not Available


title: MSK_5240B_R1

value: DSRCT


title: CTB P6B8, biol rep 3

value: CTB P6B8


title: Ribo NCD 6

description: Library name: Sample11

value: Main olfactory epithelium


title: MTS P5D6, biol rep 1


title: IP MM1-3w

description: Library name: Sample 15

value: Liver tissue


title: Ribo No Odour 6

description: Library name: Sample5

value: No Odor


title: MSK_5240A_R2


title: CTB P6B8, biol rep 2


title: Ribo No Odour 4

description: Library name: Sample4


title: IP CM4-3w

description: Library name: Sample 13

value: 3w - ChIP-Control diet  - male


title: IP CM5-3w

description: Library name: Sample 14


title: CTB P6B8, biol rep 1


title: MSK_5240A_R1


title: AI2.2-A, biol rep 4


title: Ribo No Odour 3

description: Library name: Sample3


title: MSK_5238__R2


title: IP CM3-3w

description: Library name: Sample 12


title: Ribo No Odour 2

description: Library name: Sample2


title: IP CM1-3w

description: Library name: Sample 11


title: MSK_5238__R1


title: IP MM3-3w

description: Library name: Sample 16


title: Ribo No Odour 1

description: Library name: Sample1


title: IP MF6-3w

description: Library name: Sample 10

value: 3w - ChIP-Maternal obesity  - female


title: MSK_5218__R2

value: Yes


title: IP MF5-3w

description: Library name: Sample 9

value: H3K9me3 (#17-625, Millipore)


title: noise_fluoxetin2

city: Seongnam

first: Hyun-Ju

last: An

state: --- Select One ---

address: Seongnam-si, 13496

country: South Korea

institute: CHA university

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(using fastx_trimmer), then mapped to rn6 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Rattus norvegicus

source_name: Hippocampus

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Hippocampus

value: noise

value: Fluoxetine


title: AI2.2-A, biol rep 1

value: shoots

value: plant cells

value: WT


title: IP MF4-3w

description: Library name: Sample 8


title: Control, biol rep 4

value: Control


title: IP MF3-3w

description: Library name: Sample 7


title: MSK_5217__R2

value: Male

value: Not Available


title: Control, biol rep 3


title: fluoxetin1

value: no noise


title: Control, biol rep 2


title: MSK_5217__R1

value: DSRCT


title: Control, biol rep 1


title: AI2.2-A, biol rep 3


title: MSK_5114D_R1


title: noise1

value: DW


title: KLN205 tumors, sh3 Tmprss11b, biol rep 3

city: Dallas

first: Hari Shankar

last: Sunil

state: TX

address: NA6 300A, 6000 Harry Hines Blvd.

department: Molecular Biology

institute: UT Southwestern Medical Center

description: Library name: 7945

data_processing:
Fastq files were quality checked using fastqc (Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc;).
Read from each sample were mapped to the reference genome using STAR(v2.5.3a) (Dobin, Alexander et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England) vol. 29,1 (2013): 15-21.).
Read counts were generated using featureCounts (Liao Y, Smyth GK and Shi W. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30, 2014.).
The differential expression analysis was performed using edgeR (Robinson MD, McCarthy DJ, Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140.).
Assembly: mm10
Supplementary files format and content: Tab-delimited file includes CPM and TPM RNA abundance for KLN205 allografts expressing shRNAs: shControl or sh2 Tmprss11b or sh3 Tmprss11b. logFC, logCPM, LR, Pvalue, and FDR values are included for shControl vs mT11bsh2 (sh2 Tmprss11b) and shControl vs mT11bsh3 (sh3 Tmprss11b).

source_name: Subcutaneous LUSC allograft grown in DBA/2 mouse

growth_protocol: KLN205 murine lung squamous cell carcinoma cells were maintained in DMEM supplemented with 10% foetal bovine serum and 1% antibiotics-antimycotics in humidified atmosphere  with 5% CO2 at 37C. These cells were injected subcutaneously in the flanks of DBA/2 WT mice for tumorigenic assays.

extract_protocol:
30-50 mg tumor tissue chunks were homogenized using a polytron and total RNA was isolated using Trizol (Ambion by Life Technologies; 15596018), followed by additional cleanup and DNase digestion using RNeasy Mini Kit (Qiagen; 74104) and subsquently used for RNA-seq profiling.
Samples are run on the Agilent Tapestation 4200 to determine level of degradation thus ensuring  only high quality RNA is used (RIN Score 8 or higher).   Qubit® 4.0 Fluorimeter from ThermoFisher is used to determine the concentration prior to staring library prep.  One microgram of total DNAse treated RNA is then prepared with the TruSeq Stranded mRNA Library Prep Kit from Illumina.  Poly-A RNA is purified and fragmented before strand specific cDNA synthesis.  cDNA are then a-tailed and UDI adapters are ligated.   After adapter ligation, samples are PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200.  Before being normalized and pooled, samples are quantified by Qubit then run on the Illumina NextSeq 2000 on a P2-100 flowcell.

treatment_protocol: The cells were treated with 3µg/ml doxycycline for expression of the shRNAs. For tumorigenic studies, when the average tumor volume across all the study groups reached 100mm^3, mice were maintained on doxycycline water to induce the expression of the shRNAs for the duration of the experiment.

value: Murine LUSC

value: SMART inducible shRNA, sh3 Tmprss11b

value: Doxycycline, to induce shRNAs


title: control2


title: IP CF4-3w

description: Library name: Sample 4

value: Liver tissue

value: 3w - ChIP-Control diet  - female


title: AI2.2-A, biol rep 2


title: MSK_5114C_R2

value: No


title: IP CF3-3w

description: Library name: Sample 3

value: H3K9me3 (#17-625, Millipore)


title: MSK_5114C_R1


title: noise2

value: Hippocampus

value: noise


title: noise_fluoxetin1

value: Fluoxetine


title: MSK_5218__R1

value: Yes


title: fluoxetin2


title: control1


title: KLN205 tumors, sh3 Tmprss11b, biol rep 1

description: Library name: 7911

value: Subcutaneous LUSC allograft grown in DBA/2 mouse


title: IC CM1-3w

description: Library name: Sample 2

value: 3w - Input control-male


title: IC CF3-3w

description: Library name: Sample 1

value: 3w - Input control-female


title: IP CF6-3w

description: Library name: Sample 6


title: MSK_5114B_R2

value: Male


title: KLN205 tumors, sh2 Tmprss11b, biol rep 3

description: Library name: 7933

value: SMART inducible shRNA, sh2 Tmprss11b


title: Leaves, OE Pst R2

city: New Delhi

first: Jagadis

middle: Gupta

last: Kapuganti

state: Delhi

address: Indusind bank OMMON CAUSE HOUSE, 5,INSTITUTIONAL AREA, NELSON MANDELA ROAD, VASANT KUNJ, NEW DELHI-110070

country: India

institute: National Institute of Plant Genome Research

description: SHMT6 over expression (Pseudomonas syringae pv tomato (Pst) DC3000)

data_processing:
STAR aligner for mapping against Arabidopsis genome available at plant ensemble
Reference-based assembly was performed using stringtie
Differentially exprssed gene set were identified using Deseq
Differentially expressed set was used for gene ontology and pathway analysis
Assembly: Arabidopsis latest genome assembly was used for analysis (TAIR10.1)
Supplementary files format and content: gtf files report cov, FPKM, TPM

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Four-week-old soilrite and agropeat grown fully expanded leaves of Arabidopsis were used in this experiment

extract_protocol:
Total RNA from MgCl2 (mock) and Pseudomonas syringae pv tomato DC3000 expressing AvrRpm1 infected tissue was isolated by Qiagen plant RNA extraction kit (RNeasy Plant Mini Kit) with on-column DNase digestion according to the manufacturer’s instructions. RNA quantity was measured using Qubit® 4.0 fluorometer and quality were analyzed by using 1% agarose gel.
The paired-end sequencing library was prepared using KAPA mRNA HyperPrep Kit for Illumina (CAT #KK8581). The library preparation process was initiated with 500-1000 ng input. mRNA  enrichment was performed as per user manual and mRNA was subjected to fragmentation, first &  second-strand cDNA synthesis, end-repair, 3´ adenylating, adapter ligation, selective enrichment  of adapter-ligated DNA fragments through PCR amplification, followed by validation of Library  on Agilent 4150 tape station. The final library was pooled with other samples, denatured &  loaded on to flow cell. On the flow cell, cluster generation & sequencing was performed using  Illumina Novaseq 6000 platform to generate 2×150bp paired-end (PE) read.Quantity and quality of samples were checked by (QC) of library on Agilent Tape Station 4150. The amplified libraries were analyzed on TapeStation 4150 (Agilent Technologies) using  HSD100 ScreenTape® as per manufacturer's instructions.
The mean library size ranged from 450 to 475bp for all samples.
The libraries were sequenced on Illumina Novaseq6000 platform (2 x 150 bp chemistry) to generate ~8-10GB data/Sample

treatment_protocol: Suspension of avirulent Pseudomonas syringae pv tomato (Pst) DC3000 in 10 mM MgCl2 at OD600 = 0.04 is used for treatment and 10 mM MgCl2 used as mock

value: leaves

value: over expression


title: MSK_5114D_R2

value: DSRCT


title: MSK_5114B_R1


title: MF4-8W

description: Library name: Sample 32

data_processing:
Approximately 85% of reads were uniquely mapped to the mouse genome reference mm10 using STAR (Spliced Transcripts Alignment to a Reference). To evaluate the quality of the RNA-seq data, the number of reads that fell into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genes was determined using bamUtils. Low-quality mapped reads (including reads mapped to multiple positions) were excluded, and featureCounts was used to quantify gene expression.The data were filtered using a counts per million (cpm) cutoff with each gene of at least 15 raw reads in at least four of the samples, normalized using TMM (trimmed mean of M values) method, and subjected to differential expression analysis using edgeR.
Assembly: mm10
Supplementary files format and content: tab delimited txt files; data show DEGs

extract_protocol:
Qiagen midiprep
KAPA mRNA Hyperprep kit (3w) and Illumina Stranded mRNA Prep, Ligation kit (8w)

value: 8w - Maternal obesity - female


title: Leaves, OE Pst R1

value: Pseudomonas syringae pv tomato (Pst) DC3000


title: IP CF5-3w

description: Library name: Sample 5

value: Liver tissue

value: 3w - ChIP-Control diet  - female


title: KLN205 tumors, sh2 Tmprss11b, biol rep 2

description: Library name: 7910

value: Murine LUSC

value: Doxycycline, to induce shRNAs


title: MF3-8W

description: Library name: Sample 31


title: Leaves, shmt6 mutant Pst R2

description: shmt6 mutant (Pseudomonas syringae pv tomato (Pst) DC3000)

value: mutant


title: KLN205 tumors, sh3 Tmprss11b, biol rep 2

description: Library name: 7913

value: SMART inducible shRNA, sh3 Tmprss11b


title: MF2-8W

description: Library name: Sample 30


title: MSK_5113__R2

value: Yes


title: MF1-8W

description: Library name: Sample 29


title: KLN205 tumors, sh Control, biol rep 3

description: Library name: 7924

value: Subcutaneous LUSC allograft grown in DBA/2 mouse

value: SMART inducible shRNA, shControl


title: Leaves, shmt6 mutant Pst R1


title: MSK_5113__R1


title: Leaves, Col-0 Pst R1

description: Col-0 (Pseudomonas syringae pv tomato (Pst) DC3000)

value: WT


title: KLN205 tumors, sh Control, biol rep 2

description: Library name: 7918


title: CF4-8W

description: Library name: Sample 28

value: 8w - Control diet  - female


title: KLN205 tumors, sh Control, biol rep 1

description: Library name: 414_2


title: MSK_5102__R1

value: Female

value: No

value: Not Available


title: CF3-8W

description: Library name: Sample 27


title: Isotype control (jejunal LN)_cd169_1

city: Philadelphia

first: Aliia

last: Fatkhullina

address: 3400 Civic Center Blvd Bldg 421

institute: University of Pennsylvania

data_processing:
Raw Fastq files were pseudo-aligned to the mouse GRCm39 transcriptome using Kallisto
The gene counts were input to R and transcripts per million (tpm) were scaled by gene length
Initial filtering removed genes with higher than 2 counts per million (cpm) expression in isotype control (to filter out potential non-specific, non-CD169 genes), then genes that have a cpm > 2 were used for the analysis.
Filtered gene counts were used as an input for differential expression analysis using limma/voom (edgeR)
Genes with an adjusted p-value < 0.05 were considered significant for downstream analysis
Assembly: mm10
Supplementary files format and content: comma separated variable files with raw counts for each sample

source_name: lymph node

extract_protocol:
RNA was extracted using the Arcturus PicoPure RNA isolation kit (Applied Biosystems) according to the manufacturer’s instructions.
500-1000ng of RNA was used as the starting material for cDNA library synthesis and tagmentation using the NEBNext Poly A kit (NEB) per the manufacturer’s instructions.

treatment_protocol: RiboTag mice were crossed to a CD169-Cre recombinase-expressing mouse to activate the Rpl22HA allele in all tissues. Homozygous CD169RPL22HA mice lymph nodes were collected and used for the RiboTag immunoprecipitation.

value: lymph node

value: CD169 Cre KI/KI, Rpl22HA homozygous

value: cd169 macrophages


title: Leaves, OE MgCl2 R1

description: SHMT6 over expression (10 mM MgCl2)

value: leaves

value: over expression

value: 10 mM MgCl2


title: CF2-8W

description: Library name: Sample 26

value: Liver tissue


title: CF1-8W

description: Library name: Sample 25


title: MSK_5101__R2

value: DSRCT

value: Male


title: Spleen_cd169_3


title: MSK_5114A_R2

value: Yes


title: Leaves, shmt6 mutant MgCl2 R2

description: shmt6 mutant (10 mM MgCl2)

value: mutant


title: Spleen_cd169_2


title: KLN205 tumors, sh2 Tmprss11b, biol rep 1

description: Library name: 7908

value: Subcutaneous LUSC allograft grown in DBA/2 mouse

value: Murine LUSC

value: SMART inducible shRNA, sh2 Tmprss11b

value: Doxycycline, to induce shRNAs


title: Leaves, OE MgCl2 R2

description: SHMT6 over expression (10 mM MgCl2)


title: MSK_5114A_R1


title: MM4-8W

description: Library name: Sample 24

value: 8w - Maternal obesity  - male


title: MSK_5101__R1


title: Leaves, Col-0 Pst R2

value: WT

value: Pseudomonas syringae pv tomato (Pst) DC3000


title: Leaves, shmt6 mutant MgCl2 R1

description: shmt6 mutant (10 mM MgCl2)


title: Iliac LN_cd169_3

value: lymph node

value: CD169 Cre KI/KI, Rpl22HA homozygous


title: Spleen_cd169_1

value: cd169 macrophages


title: Leaves, Col-0 MgCl2 R1

description: Col-0 (10 mM MgCl2)

value: leaves


title: MSK_5100__R2

value: Not Available


title: MSK_5102__R2

value: Female

value: No


title: Leaves, Col-0 MgCl2 R2

description: Col-0 (10 mM MgCl2)

value: 10 mM MgCl2


title: MM3-8W

description: Library name: Sample 23

value: Liver tissue


title: MM2-8W

description: Library name: Sample 22


title: MSK_5100__R1

value: DSRCT

value: Male

value: Yes


title: MSK_5099__R1


title: Deep Cervical LN_cd169_3


title: Mediastinal (Lung) LN_cd169_3


title: LS174T-R_H3K4me3,LS174T resistant, H3K4me3 ChIP-seq

first: yao

middle: yu

last: Guo

address: 广州

institute: Sun-Yat san university

description: Library name: Sample12

data_processing:
Quality control: FastQC v0.11.8. Adapter trimming: Trim Galore v0.6.3.
RNA-seq alignment: STAR v2.7.9a to GRCh37 (hg19) reference genome.
ChIP-seq alignment: BWA-MEM v0.7.17 to GRCh37 (hg19) reference genome.Peak calling: MACS2 v2.1.2 for H3K27ac and H3K4me3 peaks.
Differential expression: DESeq2 v1.28.1 for RNA-seq data.
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text files containing raw counts and normalized expression values for RNA-seq

growth_protocol: LS174T and other commercial CRC cell lines were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). For ChIP-seq, chromatin was cross-linked with 1% formaldehyde, sonicated, and immunoprecipitated with H3K27ac (Abcam ab4729) or H3K4me3 (Millipore 07-473) antibodies.
RNA-seq libraries were prepared with TruSeq Stranded RNA HT kit with Ribo-Zero Gold (Illumina). ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina.

treatment_protocol: Resistant models were generated by chronic exposure to increasing concentrations of BI-2865 pan-KRAS inhibitor. For ChIP-seq experiments, cells were treated with 5μM BI-2865 or DMSO control for 24 hours.

value: human colorectal adenocarcinoma cell line

value: KRAS mutant (G12D)


title: MSK_5098__R2


title: MM1-8W

description: Library name: Sample 21

value: 8w - Maternal obesity  - male


title: CM4-8W

description: Library name: Sample 20

value: 8w - Control diet  - male


title: MSK_5099__R2


title: Celiac LN_cd169_3


title: LS174T-R_H3K4me3-input,LS174T resistant, H3K4me3-input ChIP-seq

description: Library name: Sample11


title: Super Cervical LN_cd169_3


title: MSK_5098__R1


title: CM3-8W

description: Library name: Sample 19


title: CM2-8W

description: Library name: Sample 18


title: LS174T-P_H3K4me3,LS174T parental, H3K4me3 ChIP-seq

description: Library name: Sample10

value: DMSO


title: LS174T-P_H3K4me3-input,LS174T parental, H3K4me3-input ChIP-seq

description: Library name: Sample9


title: MSK_5070__R2


title: Inguinal LN_cd169_3

value: lymph node


title: LS174T-R_H3K27ac LS174T resistant, H3K27ac ChIP-seq

description: Library name: Sample8


title: Liver LN_cd169_3

value: CD169 Cre KI/KI, Rpl22HA homozygous


title: CM1-8W

description: Library name: Sample 17


title: MSK_5070__R1


title: Ceco-colonic LN_cd169_3

value: cd169 macrophages


title: MSK_5040D_R2


title: LS174T-R_H3K27ac-input,LS174T resistant, H3K27ac-input ChIP-seq

description: Library name: Sample7


title: MF6 (2)

description: Library name: Sample 16

value: 3w - Maternal obesity - female


title: LS174T-P_H3K27ac,LS174T parental, H3K27ac ChIP-seq

description: Library name: Sample6


title: MF5 (2)

description: Library name: Sample 15


title: MSK_5040D_R1


title: LS174T-P_H3K27ac-input,LS174T parental, H3K27ac-input ChIP-seq

description: Library name: Sample5


title: Ileal LN_cd169_3


title: MSK_5040C_R2


title: MF4 (2)

description: Library name: Sample 14


title: Jejunal LN_cd169_3


title: MF3 (2)

description: Library name: Sample 13


title: MSK_5040C_R1


title: Duodenal LN_cd169_3


title: Iliac LN_cd169_2


title: MSK_5040B_R1


title: CF5 (2)

description: Library name: Sample 11

value: 3w - Control diet  - female


title: MSK_5040B_R2

value: Female


title: LS174T-P_rep1, LS174T parental, Biological Rep 1

description:
Library name: Sample1
Column_name_in_raw_counts_All_Samples.txt:P.1


title: CF3 (2)

description: Library name: Sample 9


title: ST_60T

city: Ramat Gan

first: Maya

last: Dadiani

state: Please Select

address: Tel Hashomer

institute: Sheba Medical Center

data_processing:
Illumina adapters and PolyA/T stretches were trimmed using cutadapt
reads were mapped to the human genome (GRCh38) using STAR v2.4.2a
Counting proceeded over genes annotated in Ensembl release 88, using HTSeq-count
Normalization with DESeq2 (1.10.1)
Assembly: GRCh38
Supplementary files format and content: DESeq2 Normalized counts

source_name: breast cancer tumor

extract_protocol:
FFPE tumor samples were macro-dissected to enrich for tumor cellularity. The 5 microns sections were deparaffinized at 90°C for 5 min. Total RNA was extracted using nucleic acid isolation kit (AllPrep® Qiagen) according to protocol instructions.
mRNA-seq libraries were constructed by Truseq RNA Sample preparation kit v2 (illumina).

treatment_protocol: Chemotherapy treatment included a standard-of-care sequential doxorubicin and cyclophosphamide followed by paclitaxel, and additional Herceptin for HER2+ patients

value: breast cancer tumor

value: post-treatment

tag: breast cancer_pathological_subtype

value: TNBC


title: MSK_5039__R1

value: DSRCT

value: Not Available


title: LS174T-R_rep1,LS174T resistant, Biological Rep 1

description:
Library name: Sample3
Column_name_in_raw_counts_All_Samples.txt:R.1


title: CF6 (2)

description: Library name: Sample 12

value: Liver tissue


title: ST_60N

source_name: Normal breast tumor adjacent

value: Normal breast tumor adjacent


title: LS174T-P_rep2, LS174T parental, Biological Rep 2

description:
Library name: Sample2
Column_name_in_raw_counts_All_Samples.txt:P.2

value: human colorectal adenocarcinoma cell line

value: KRAS mutant (G12D)


title: Mediastinal (Lung) LN_cd169_2


title: CF4 (2)

description: Library name: Sample 10


title: MSK_5039__R2

value: Male

value: Yes


title: MM4 (2)

description: Library name: Sample 7

value: 3w - Maternal obesity  - male


title: Inguinal LN_cd169_2

value: lymph node

value: CD169 Cre KI/KI, Rpl22HA homozygous


title: ST_58N


title: Super Cervical LN_cd169_2

value: cd169 macrophages


title: LS174T-R_rep2,LS174T resistant,Biological Rep 2

description:
Library name: Sample4
Column_name_in_raw_counts_All_Samples.txt:R.2


title: Celiac LN_cd169_2


title: MM5 (2)

description: Library name: Sample 8


title: MM1

description: Library name: Sample 5


title: MSK_5038C_R1


title: Ceco-colonic LN_cd169_2


title: MSK_5038D_R2


title: CM5 (2)

description: Library name: Sample 4

value: 3w - Control diet  - male


title: ST_60C

value: pre-treatment


title: Ileal LN_cd169_2


title: Liver LN_cd169_2


title: MSK_5038D_R1


title: ST_58T

value: breast cancer tumor


title: ST_57R

value: post-treatment


title: MM3 (2)

description: Library name: Sample 6


title: MSK_5038C_R2


title: ST_57N

value: TNBC


title: Deep Cervical LN_cd169_2


title: ST_58C


title: Iliac LN_cd169_1


title: ST_56T

value: ER+


title: MSK_5038B_R2

value: DSRCT


title: MSK_5015B_R2


title: ST_57T


title: CM4 (2)

description: Library name: Sample 3

value: Liver tissue


title: Jejunal LN_cd169_2


title: MSK_5038B_R1


title: ST_56N

value: Normal breast tumor adjacent


title: WT-CNV-3

city: Shanghai

first: Yue

last: Zou

address: Shanghai

institute: Eye & ENT Hospital, Fudan University

description: Library name: 7

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: retina

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: retina

value: control


title: CM3 (2)

description: Library name: Sample 2


title: MSK_5038A_R2

value: Male


title: Duodenal LN_cd169_2


title: CM1

description: Library name: Sample 1


title: ST_57C


title: Mediastinal (lung) LN_cd169_1


title: WT-CNV-4

description: Library name: 8


title: MSK_5015B_R1

value: Yes


title: Super Cervical LN_cd169_1


title: Lung, SNL LUSC GEMM, 11Months post Ad-Cre

description:
Library name: HHSE13_NT
Sequencing was actually performed using the Singular Genomics G4 platform

data_processing:
Sequencing of Visium libraries and FASTQ file generation was performed with the Singular Genomics G4 platform using an F3 flow cell.
Visium spatial transcriptomics reads were aligned to mm10 genome using 10x Genomics Space Ranger v2.0.1
Gene expression counts were quantified using Space Ranger default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of spots assigned to tissue
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: cloupe.cloupe: Loupe Browser file to visualize the spatial data
Supplementary files format and content: HSE13_NT-tissue_annotations.tsv: table indicating tissue annotations for each spot barcode
Supplementary files format and content: D1_hse13-nt.tif: Eosin-only Cytassist tissue image for Space Ranger input
Supplementary files format and content: V43A17-312-D1.json: Loupe alignment file for Space Ranger input
Supplementary files format and content: HSE13_NT__ROI.tiff: H&E image of the region used as Space Ranger input
Library strategy: Spatial Transcriptomics

source_name: Lung section with LUSC and LUAD, from SNL autochthonous mouse model

growth_protocol: Rosa26LSL-SOX2-IRES-GFP; Nkx2-1fl/fl ;Lkb1fl/fl (SNL) mice were provided by Dr. Trudy Oliver (Duke University).

extract_protocol:
Mice were euthanized by intraperitoneal administration of an overdose of Avertin at the indicated time-points. Lungs were inflated and perfused through the trachea with 4% paraformaldehyde (PFA), fixed overnight, washed in 1xPBS for 24-48h, then transferred to 70% ethanol and subsequently embedded in paraffin. Sections were cut and stained with H&E by the UTSW HistoPathology Core. The H&E slides were scanned at 40x magnification using the Leica Biosystems Aperio AT2 DX brightfield slide scanner. Regions of lung adenocarcinoma and lung squamous cell carcinoma morphology were annotated. The regions of interest for spatial transcriptomics were digitally annotated using QuPath (v.5.0.1) and exported as a TIFF image file. Tissue slides were decoverslipped, washed, and rehydrated following the 10x Genomics Visium CyAssist Tissue Preparation Guide (CG000518 rev. B). Slides were immersed in xylene then placed on a metal block cooled with dry and the coverslip was removed with a razor blade. Sections were washed and rehydrated by sequential immersions in xylene, 100% ethanol, 96% ethanol, and 70% ethanol, according to manufacturer recommendations. A region of the tissue outside of the region of interest was cut away for RNA quality control. RNA was isolated with the Qiagen RNeasy Mini Kit (cat: 74104), and quality was evaluated using the Agilent Technologies RNA 6000 Pico kit (cat: 5067-1513) with a DV200 assay in the Agilent 2100 BioAnalyzer.
Spatial transcriptomics libraries were prepared with the following the 10x Genomics Visium CyAssist Tissue Preparation kit and protocol according to manufacturer's guidelines.

treatment_protocol: Cre-expressing adenovirus (Adeno-Cre) was purchased from Viral Vector Core Facility (University of Iowa). Rosa26LSL-SOX2-IRES-GFP; Nkx2-1fl/fl ;Lkb1fl/fl (SNL) mice (males and females) 6- to 8-weeks of age were intratracheally administered Adeno-Cre virus at 1-10 x 10^8 pfu/mouse.

value: Rosa26LSL-Sox2-IRES-GFP; Nkx2-1 fl/fl; Lkb1fl/fl

value: Ad-Cre virus to initiate tumorigenesis


title: Liver LN_cd169_1

value: lymph node

value: CD169 Cre KI/KI, Rpl22HA homozygous


title: MSK_4943__R2

data_processing:
Gene counts were generated by alignment to human transcriptome GRCh38 using STAR in RSEM.
Differential gene expression analysis was performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: txt file with count data from RSEM

extract_protocol:
Phase separation in OCT frozen tissue lysed in TRIzol was induced with 200 µL chloroform and RNA was extracted from the aqueous phase using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher catalog # A27828) on the KingFisher Flex Magnetic Particle Processor (Thermo Scientific catalog # 5400630) according to the manufacturer’s protocol
179-700 ng of total RNA with DV200 percentages varying from 3-78% underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 Reagent Kit (200 Cycles) (Illumina).