title: Cells isolated from Ptf1a-CreERTM mouse; 4-Hydroxytamoxifen treatment for 1 day

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 6651 SPH1, 1415 Washington Heights

department: Environmental Health Sciences

institute: University of Michigan

description: Library name: CA2-D1

data_processing:
RNA-sequencing fastq reads were transferred to the University of Michigan Great Lakes computational cluster for pseudoalignment to the mouse genome (Gencode version M35) using Salmon v1.9.0 to generate a counts per sample matrix.
Assembly: Gencode version M35
Supplementary files format and content: Salmon Pseudocounts

source_name: primary pancreatic acinar cells

growth_protocol: Cells were cultured in 1x Waymouth’s media (Gibco, 11220035) supplemented with 0.4 mg/mL soybean trypsin inhibitor (Gibco, 17075-029), 1 ug/mL dexamethasone (Sigma, D4902), and 0.5% gentamicin (Lonza, 17-519L). Cultures were maintained in humidified atmosphere at 37C with 5% CO2.

extract_protocol:
RNA isolation from cells using Qiagen RNeasy Plus Mini Kit (Cat. 74134) using manufacturer's instructions. A minimum of 23 ng/uL of RNA was submitted to GENEWIZ from Azenta Life Sciences.
ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation per manufacturer's protocol. RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Acinar cells were isolated from KrasLSL-G12D/+;Ptf1a-CreERTM/+ pancreas (n=3 individual pancreata; labeled as KC2, KC3, and KC5). Cells were were treated with 4-hydroxytamoxifen (2uM; Cayman Chemical; dissolved in 100% ethanol) over three days to induce KrasG12D (labeled as -D1, -D2, -D3). This was compared with vehicle treatment for one day in culture (labeled as -V). Control acinar cells from Ptf1a-CreERTM/+ pancreas (n=1; labeled as CA2) were also treated with vehicle (V) or 4-hydroxytamoxifen (D1) as a reference.

value: primary pancreatic acinar cells

value: 2uM 4-hydroxytamoxifen


title: apocrine gland anal sac adenocarcinoma (AGASAC), 16

status: Public on Dec 15 2025

type: RNA

city: Berlin

first: Alexander

middle: F. H.

last: Haake

address: Robert-von-Ostertag-Straße 15

department: Department of Veterinary Medicine

country: Germany

institute: Freie Universität Berlin

hyb_protocol: 150 to 250 ng of total RNA was hybridised to the nCounter Canine IO Panel XT CodeSets (NanoString Technologies, Inc., Seattle, WA, USA). Hybridised samples were processed following the manufacturer’s protocols (protocol ID: MAN-10023-11, MAN-10056-06) and loaded onto the nCounter MAX Analysis System’s (NanoString) Prep Station for purification and immobilization on sample cartridges.

scan_protocol: Samples were transferred to the nCounter MAX Digital Analyzer (NanoString) for data collection following the manufacturer’s user manual (protocol ID: MAN-C0035-08).

data_processing: Following the workflow described in the manufacturer’s user manuals (MAN-C0019-08, MAN-C0011-04), the reporter library files (RLF) and reporter code count (RCC) files were imported into the nSolverTM 4.0 Analysis Software. Quality control and normalisation followed default settings.

molecule: total RNA

organism: Canis lupus familiaris

source_name: archival FFPE tumour tissue

extract_protocol: Total RNA was extracted utilising the PureLinkTM FFPE Total RNA Isolation Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA).

tag: Sex

value: male

tag: breed

value: Appenzeller Sennenhund

tag: age (years)


title: AnR SD-1

type: SRA

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

country: USA

institute: University of South Carolina

description:
Library name: S57
AR_SD#1

library_source: transcriptomic

data_processing:
RNA-Seq
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by cutadapt (v 2.8) with parameters -m 75 -q 30
Reads were aligned to genome human GRCh38.p13 primary assembly genome , utilizing STAR (v 2.7.10a) with parameter --outFilterMismatchNoverReadLmax 0.01 --outFilterMultimapNmax 1
Read counts over annotated genes were obtained using featureCount (subreads | version: 2.0.3) with parameters -T 12 -B -O --fraction -s 2 -p --countReadPairs -d 50 -D 800 -g gene_id
Assembly: GRCh38.p13
Supplementary files format and content: comma-delimited text files include human gene counts for each sample

organism: Homo sapiens

source_name: cell line

growth_protocol: Cells were frown either in 2D ( standard) culture conditions or in suspension cultures on poly hema coated plates

extract_protocol:
RNA extraction using Qiagen's RNeasy plus mini kit , cat# 74134
Sequencing libraries were generated using NEBNext UltraExpress® RNA Library Prep Kit

treatment_protocol: OV90 parental ( anoikis sensitive) and adapted resistant lines were treated with vehicle ( DMSO) or 500nM SNX631 for 4 days in attached cultures. Adapted resistant OV90 cells were also either treated for 4 days in attached 2D culture followed by switch to suspension culture on polyhema coated plates for 24 hrs. Cells were either treated with vehicle or SNX631 ( 500nM) in attached culture, followed, by either  treatmet with DMSO or SNX631 ( 500nM) in suspension alone or continued treatment of SNX631 in both attached and suspension culture. DMSO serves as control everywhere.

tag: tissue

value: cell line

tag: cell line

value: OV90 adapted anoikis resistant

tag: cell type

value: ovarian cancer

tag: genotype

value: WT

tag: treatment


title: A1_Naïve monocytes

first: Michael

middle: S.

last: Diamond

state: MO

address: 425 S. Euclid Ave

department: Immunology and Pathology

institute: Washington University School of Medicine

description: Library name: A1

data_processing:
RNA-seq reads were aligned to the Mus musculus reference genome (GRCm39) using HISAT2 (v2.2.1). Gene-level quantification was performed with featureCounts from the Subread package (v2.0.6) using Ensembl annotations (Mus_musculus_Ensemble_107_new). Across samples, the median mapping rate was ~94%. Raw counts were imported into R (v4.4.0) for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: tsv files include raw gene counts for all samples

molecule: polyA RNA

organism: Mus musculus

source_name: infiltrating monocytes

extract_protocol:
Three days after MA30 infection, mice were anesthetized with ketamine/xylazine (100 and 10 mg/kg via intraperitoneal injection, respectively), and 100 μL of CD45.2 antibody (APC; clone 104; Biolegend) was administered at a 1:10 dilution in PBS by retroorbital injection to identify intravascular cells. Two min later, mice were euthanized and then perfused with sterile PBS. Lungs were digested in 50 μL of Liberase Tm (5 mg/mL, Roche) and 12.5 μl of DNase I (10 mg/mL, Sigma-Aldrich) in 5 mL of HBSS at 37°C for 35 min. Single-cell suspensions were pre-incubated with Fc block antibody (BioLegend) in PBS + 2% heat-inactivated FBS + 1 mM EDTA for 20 min at 4°C. Cells were then divided into two groups for sorting. For interstitial macrophages, cells were stained with antibodies against CD45 (PE-Cy7; clone 30-F11; Biolegend), MHCII (BV421; clone M5; Biolegend), CD88 (PE; clone 20/70; Biolegend), and CX3CR1 (BV510; clone SA011F11; Biolegend). For classical monocytes, cells were stained with antibodies against CD45 (PE-Cy7; clone 30-F11; Biolegend), Ly6G (BV510; clone 1A8; Biolegend), Ly6C (PE; clone HK1.4; Biolegend), and CD115 (BV421; clone AFS98; Biolegend). All samples were stained with fixable viability dye (zombie green), True-Stain Monocyte Blocker (5 μL per sample), and Brilliant Stain Buffer Plus (10 μL per sample). All antibodies were used at a dilution of 1:200, with the exceptions of MHCII BV421, CD88 PE, and Ly6C, which were used at 1:100, and the viability dye, which was used at 1:2,000. Following incubation in PBS + 2% heat-inactivated FBS + 1 mM EDTA for 20 min at 4°C, cells were sorted on a MACSQuant Tyto instrument (Miltenyi Biotec).
Following cell sorting, RNA was extracted using the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA purity was confirmed using a NanoPhotometer® spectrophotometer (IMPLEN). RNA concentration and quality were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies). One µg of RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using a random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 µL of USER Enzyme (NEB) was added with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR with Phusion High-Fidelity DNA polymerase, Universal PCR primers and an Index Primer. Finally, PCR products were purified (AMPure XP system), and the library quality was assessed on an Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform, and paired-end reads were generated.

treatment_protocol: For MA30 challenge experiments, 24-week-old Hu-FcgR Tg male mice were administered different doses of S309, S309-GA-AFUC, or isotype control by intraperitoneal injection depending on the experimental question. To assess for differences in virological protection, mice were administered 6 mg/kg of antibody -24 h and then harvested at 4 dpi. The antibody dose was increased to account for the enhanced viral infection in the MA30 model compared to B.1.351. For evaluation of lung ventilatory function and histopathology, mice were administered a lower 1 mg/kg dose of antibody at -24 h and then harvested at 7 dpi, which facilitated differences in disease progression between treatment groups. At day 0 (one day after mAb treatment), mice were inoculated intranasally with 6 x 105 FFU of SARS-CoV-2 MA30 in a final volume of 50 μL. Lungs, nasal turbinates and nasal washes (collected in 1 mL of 0.5% bovine serum albumin in PBS) were collected at 4 dpi for virological and flow cytometric analyses.

value: infiltrating monocytes

value: Hu-FcgR Tg

value: naive

tag: infection status


title: apocrine gland anal sac adenocarcinoma (AGASAC), 15

value: male, neutered

value: English Cocker Spaniel


title: Pancreatic cancer, patient 3235, whole transcriptome

city: Chapel Hill

first: Jen Jen

last: Yeh

state: NC

address: 450 West Dr, CB7295

institute: University of North Carolina at Chapel Hill

description: Library name: rnaseq_3235

data_processing:
BCL files were converted to FASTQ files using bcl2fastq2 conversion software 2.20.0
Salmon (v1.5.2) was used to derive normalized counts (TPM)
For samples sequenced at Tempus, kallisto (v0.44.0) was used to derive normalized counts (TPM)
Assembly: GENCODE Release 38 (GRCh38.p13) for whole transcriptome; GENCODE Release 37 (GRCh37) for exome capture
Supplementary files format and content: csv files include TPM values per sample

source_name: PDAC

extract_protocol:
Total RNA was extracted from FFPE samples using Rneasy FFPE Kit (Qiagen, 73504).
KAPA RNA HyperPrep Kit with RiboErase (Roche) per manufacturer protocol for whole-transcriptome RNA-seq; sequencing done at Tempus for exome capture

value: PDAC

tag: individual

value: patient 3235


title: apocrine gland anal sac adenocarcinoma (AGASAC), 13

value: female, neutered

value: Tibetan Terrier


title: Cells isolated from KrasG12D;Ptf1a-CreERTM mouse #5; 4-Hydroxytamoxifen treatment for 3 days

description: Library name: KC5-D3

value: primary pancreatic acinar cells

value: KrasLSL-G12D/+; Ptf1aCre-ERTM/+


title: AnR DD-2

description:
Library name: S50
AR_DD#2

value: DMSO


title: apocrine gland anal sac adenocarcinoma (AGASAC), 10

value: female

value: Cairn Terrier


title: AnR DD-1

description:
Library name: S49
AR_DD#1

value: cell line

value: OV90 adapted anoikis resistant


title: Pancreatic cancer, patient 3212, whole transcriptome

description: Library name: rnaseq_3212

value: patient 3212


title: AnR SNX-4

description:
Library name: S48
AnR_SNX#4

value: ovarian cancer

value: WT


title: Cells isolated from KrasG12D;Ptf1a-CreERTM mouse #5; 4-Hydroxytamoxifen treatment for 2 days

description: Library name: KC5-D2

value: 2uM 4-hydroxytamoxifen


title: AR SNX-3

description:
Library name: S47
AnR_SNX#3


title: Cells isolated from KrasG12D;Ptf1a-CreERTM mouse #5; vehicle treated for 1 day

description: Library name: KC5-V

value: vehicle (ethanol)


title: Pancreatic cancer, patient 3199, whole transcriptome

description: Library name: rnaseq_3199

value: patient 3199


title: apocrine gland anal sac adenocarcinoma (AGASAC), 9

value: male

value: Mixed-breed


title: Cells isolated from KrasG12D;Ptf1a-CreERTM mouse #3; 4-Hydroxytamoxifen treatment for 3 days

description: Library name: KC3-D3


title: AnR DD-3

description:
Library name: S51
AR_DD#3


title: AnR SNX-1

description:
Library name: S45
AnR_SNX#1


title: Pancreatic cancer, patient 3196, whole transcriptome

description: Library name: rnaseq_3196

value: PDAC

value: patient 3196


title: apocrine gland anal sac adenocarcinoma (AGASAC), 29

description: re-analysis of GSM8152091

value: male, neutered

value: Shih Tzu


title: Pancreatic cancer, patient 3193, whole transcriptome

description: Library name: rnaseq_3193

value: patient 3193


title: Cells isolated from KrasG12D;Ptf1a-CreERTM mouse #3; 4-Hydroxytamoxifen treatment for 2 days

description: Library name: KC3-D2

value: primary pancreatic acinar cells

value: KrasLSL-G12D/+; Ptf1aCre-ERTM/+


title: AnR DMSO-5

description:
Library name: S44
AnR_Ctrl#4

value: cell line

value: DMSO


title: Pancreatic cancer, patient 3232, whole transcriptome

description: Library name: rnaseq_3232

value: patient 3232


title: hepatoid gland adenoma (HGA), 3

description: re-analysis of GSM8152088

value: female

value: Jack Russell Terrier-mix


title: Cells isolated from KrasG12D;Ptf1a-CreERTM mouse #3; 4-Hydroxytamoxifen treatment for 1 day

description: Library name: KC3-D1

value: 2uM 4-hydroxytamoxifen


title: Pancreatic cancer, patient 3172, whole transcriptome

description: Library name: rnaseq_3172

value: patient 3172


title: Pancreatic cancer, patient 3220, whole transcriptome

description: Library name: rnaseq_3220

value: patient 3220


title: AnR DMSO-4

description:
Library name: S43
AnR_Ctrl#3

value: OV90 adapted anoikis resistant

value: ovarian cancer

value: WT


title: hepatoid gland adenoma (HGA), 2

description: re-analysis of GSM8152087

value: female, neutered

value: Beagle


title: Cells isolated from KrasG12D;Ptf1a-CreERTM mouse #5; 4-Hydroxytamoxifen treatment for 1 day

description: Library name: KC5-D1


title: Pancreatic cancer, patient 3165, whole transcriptome

description: Library name: rnaseq_3165

value: PDAC

value: patient 3165


title: Pancreatic cancer, patient 3144, whole transcriptome

description: Library name: rnaseq_3144

value: patient 3144


title: hepatoid gland adenoma (HGA), 1

description: re-analysis of GSM8152086

value: Boxer-mix


title: Cells isolated from KrasG12D;Ptf1a-CreERTM mouse #3; vehicle treated for 1 day

description: Library name: KC3-V

value: primary pancreatic acinar cells

value: KrasLSL-G12D/+; Ptf1aCre-ERTM/+

value: vehicle (ethanol)


title: AnR DMSO-3

description:
Library name: S42
AnR_Ctrl#2

value: cell line

value: DMSO


title: Cells isolated from KrasG12D;Ptf1a-CreERTM mouse #2; 4-Hydroxytamoxifen treatment for 3 days

description: Library name: KC2-D3

value: 2uM 4-hydroxytamoxifen


title: AnR DMSO-2

description:
Library name: S41
AnR_Ctrl#1


title: AnR SNX-2

description:
Library name: S46
AnR_SNX#2


title: hepatoid gland adenoma (HGA), 12

description: re-analysis of GSM8152090

value: male, neutered

value: Groenendael


title: Cells isolated from KrasG12D;Ptf1a-CreERTM mouse #2; 4-Hydroxytamoxifen treatment for 2 days

description: Library name: KC2-D2


title: Pancreatic cancer, patient 3127, whole transcriptome

description: Library name: rnaseq_3127

value: patient 3127


title: AnS SNX-4

description:
Library name: S40
AnS_SNX#4

value: OV90 parental

value: ovarian cancer


title: Pancreatic cancer, patient 3109, whole transcriptome

description: Library name: rnaseq_3109

value: patient 3109


title: Cells isolated from KrasG12D;Ptf1a-CreERTM mouse #2; 4-Hydroxytamoxifen treatment for 1 day

description: Library name: KC2-D1


title: apocrine gland anal sac adenocarcinoma (AGASAC), 14

description: re-analysis of GSM8152085

value: Mixed-breed


title: AnS SNX-3

description:
Library name: S39
AnS_SNX#3

value: WT


title: apocrine gland anal sac adenocarcinoma (AGASAC), 27

description: re-analysis of GSM8152089

value: Pug


title: Pancreatic cancer, patient 3071, whole transcriptome

description: Library name: rnaseq_3071

value: PDAC

value: patient 3071


title: Cells isolated from Ptf1a-CreERTM mouse; vehicle treated for 1 day

description: Library name: CA2-V

value: primary pancreatic acinar cells


title: apocrine gland anal sac adenocarcinoma (AGASAC), 11

description: re-analysis of GSM8152083

value: Munsterlander


title: Cells isolated from KrasG12D;Ptf1a-CreERTM mouse #2; vehicle treated for 1 day

description: Library name: KC2-V

value: KrasLSL-G12D/+; Ptf1aCre-ERTM/+

value: vehicle (ethanol)


title: Pancreatic cancer, patient 3039, whole transcriptome

description: Library name: rnaseq_3039

value: patient 3039


title: AnS SNX-1

description:
Library name: S37
AnS_SNX#1

value: cell line


title: Gata1_8C_CUTnRUN_rep2

city: Martinsried

first: Siwat

last: Ruangroengkulrith

state: Bavaria

address: Am Klopferspitz 18

department: Totipotency

institute: Max Planck Institute of Biochemistry

description: Library name: CUT and RUN Sample 2

library_source: genomic

data_processing:
Low quality reads were trimmed out using TrimGalore (version 0.6.2) (https://github.com/FelixKrueger/TrimGalore) using parameters: --paired --quality 20 --length 20.
Read mapping to mm10 genome was done using Bowtie2 (version 2.3.5.1) using parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant.
Unmapped reads and reads with low mapping quality (Q<30) were removed. PCR duplicated reads were identified and discarded using the MarkDuplicates command from Picard (version 2.18.27) (http://broadinstitute.github.io/picard/) with parameters: VALIDATION_STRINGENCY=LENIENT.
The bigwig files were generated using bamCoverage command from deepTools (version 3.5.4) using parameters: --normalizeUsing RPKM --binSize 1 --ignoreForNormalization chrM. Peak calling for CUT&Tag, ATAC-seq, and ChIP-seq datasets were done using MACS2’s callpeak function (version 2.2.9) with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Run

molecule: genomic DNA

source_name: preimplantation embryo

growth_protocol: Frozen zygotes from B6CBAF1 mouse strain (Janvier-lab) were used for CUT&RUN experiments of GATA1. Zygotes were thawed according to a manual of kits of frozen zygotes and cultured in potassium-supplemented simplex-optimized medium (KSOM) with Lumox dish (Sarstedt). Eight-cell stage embryos were collected after thawing at 44-46 hours (56-58 hpf).

extract_protocol:
CUT&RUN was performed according to the published protocol (Hayashi and Inoue, 2023) with a few modifications. 8-cell embryos were treated with acidic Tyrode to remove the zona pellucida, and washed through 0.15% BSA in PBS on a microplate (NuncTM MicrowellTM Minitrays). Embryos were incubated in antibody buffer (20 mM HEPES-NaOH (pH 7.5), 150 mM NaCl, 0.5 mM Spermidine, 0.02% Digitonin, 2 mM EDTA and 1x Protease inhibitor cocktail (Roche) with primary antibody (1:100 dilution) overnight at 4°C on a nutator. Embryos were washed three times through antibody buffer and further incubated with secondary antibody (1:100 dilution) for 1 hour at room temperature. After incubation, embryos were washed three times through cold Dig-Wash buffer (20 mM HEPES-NaOH (pH 7.5), 150 mM NaCl, 0.5 mM Spermidine, 0.02% Digitonin, and 1x Protease inhibitor cocktail), followed by incubation in Dig-Wash buffer for 20 min at room temperature. Embryos were further incubated with cold Dig-Wash buffer containing homemade pAG-MNase (500 ng/µl) for 1.5 h on ice with gentle nutation. Embryos were washed twice through cold Dig-Wash buffer and incubated for 20 min at room temperature with gentle nutation. Embryos were transferred into a 1.5 mL tube containing 50 µL of the wash buffer and then captured by Bio-Mag Plus Concanavalin A-coated beads. After removing the supernatant, 180 µL of cold Dig-wash buffer was added, and MNase reaction was carried out in the presence of 2 mM CaCl2 for 20 min on ice. The reaction was stopped by adding 20 µL of 10XSTOP buffer (1700 mM NaCl, 500 mM EDTA, 22 mM EGTA, 0.02% digitonin, 250 μg/mL RNase A, 500 μg/mL glycogen). The protein–DNA complexes were then released by 20 min incubation at 37°C with shaking at 1000 rpm. The supernatant was transferred into a new 1.5 ml of DNA LoBind Tube (Eppendorf) and then deproteinized. The DNA was purified by phenol-chloroform extraction and followed by ethanol precipitation. DNA libraries were prepared using a NEBNext Ultra II DNA library preparation kit for Illumina (New England Biolabs) according to the manufacturer's instructions
Purified DNA libraries were sequenced on a AVITI (Element Biosciences) with paired-end reads.

value: preimplantation embryo

value: 8-cell embryo

tag: chip antibody

value: Abcam, ab11852


title: AnS DMSO-3

description:
Library name: S36
AnS_Ctrl#3

value: OV90 parental

value: DMSO


title: Gata1_8C_CUTnRUN_rep1

description: Library name: CUT and RUN Sample 1


title: hepatoid gland adenoma (HGA), 5

description: re-analysis of GSM8152081

value: female

value: Border Collie-mix


title: Pancreatic cancer, patient 3027, whole transcriptome

description: Library name: rnaseq_3027

value: patient 3027


title: Pancreatic cancer, patient 3030, whole transcriptome

description: Library name: rnaseq_3030

value: patient 3030


title: ATAC_8C_Nr5a2_Klf5_dKD_rep2

description: Library name: ATAC Sample 16

data_processing:
Low quality reads were trimmed out using TrimGalore (version 0.6.2) (https://github.com/FelixKrueger/TrimGalore) using parameters: --paired --quality 20 --length 20.
Read mapping to mm10 genome was done using Bowtie2 (version 2.3.5.1) using parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant.
Unmapped reads and reads with low mapping quality (Q<30) were removed. PCR duplicated reads were identified and discarded using the MarkDuplicates command from Picard (version 2.18.27) (http://broadinstitute.github.io/picard/) with parameters: VALIDATION_STRINGENCY=LENIENT.
The bigwig files were generated using bamCoverage command from deepTools (version 3.5.4) using parameters: --normalizeUsing RPKM --binSize 1 --ignoreForNormalization chrM. Peak calling for CUT&Tag, ATAC-seq, and ChIP-seq datasets were done using MACS2’s callpeak function (version 2.2.9) with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: Frozen zygotes from B6CBAF1 mouse strain (Janvier-lab) were used for CUT&Tag experiments of NR5A2, KLF5 GATA6, and H3K27ac. Zygotes were thawed according to a manual of kits of frozen zygotes and cultured in potassium-supplemented simplex-optimized medium (KSOM) with Lumox dish (Sarstedt). Two-cell, four-cell, eight-cell, morula were collected after thawing at 22-24 hours (34-36 hpf), 29-31 hours (41-43 hpf), 44-46 hours (56-58 hpf), and 61-61 hours (71-72 hpf), respectively. Zygotes from natural mating were used for siRNA knockdown experiment. Females mice (3-5 weeks old B6129F1 strain) were injected with PMSG (5IU) followed by hCG injection 46-48 hours later for superovulation, before mating with B6CBAF1 male mice. Zygotes were after 19 hours post hCG injection. Embryos were then cultured in KSOM with Lumox dish (Sarstedt).

extract_protocol:
Omni ATAC-seq was performed as described previously (Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017)). Zona pellucida was removed by treatment with acidic Tyrode. Embryos were transferred into 1.5 ml of DNA LoBind Tube (Eppendorf) with 200 μl of PBS and were spun at 500×g at 4°C for 5 min to remove supernatant. 50 μl of ATAC-Resuspension buffer (RSB) (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20 and 0.01% Digitonin was added into tube and incubated for 3 min on ice. After incubation, 200 μl of ATAC-RSB containing 0.1% Tween-20 was further added into the tube to wash out lysis. Nuclei were spun at 500×g at 4°C for 10 min to remove supernatant. Nuclei were incubated with 50 μl of transposition mixture (10 mM Tris-HCl (pH 7.6), 5 mM MgCl2, 10% Dimethyl formamide, 33% PBS, 0.1 % Tween-20, 0.01% Digitonin and 95 nM Tn5-adaptor complex) at 37°C for 30 min with 1000 rpm mixing. The samples were then deproteinized and further purified by phenol-chloroform and followed by ethanol precipitation. The DNA was amplified 50 µl of reaction with 1×NEBNext HF 2×PCR Master mix (NEB) and 0.25 µM barcoded primers using the following PCR program: 72 °C for 5 min; 98°C for 30 sec; 15 cycles of 98°C for 10 sec, 63°C for 30 sec and 72 °C for 1 min; final extension at 72 °C for 5 min and hold at 4°C. After PCR reaction, libraries were purified by 1.1×AMPure XP magnetic beads (Beckman Coulter) and were eluted in 20 μl of RNase-free water.
Purified DNA libraries were sequenced on a NextSeq 500 (Illumina), Novaseq 6000 (Illumina), or AVITI (Element Biosciences) with paired-end reads.

treatment_protocol: For siRNA knockdown, isolated zygotes (8-9 hpf) were microinjected with siRNAs against targets Nr5a2 (5 µM), Klf5 (10 µM) or control (15 µM). As a control of successful injection 150 ng/µl H2B-EGFP was co-injected. The siRNA targeting control and Nr5a2 were ordered as Silencer select from Life technologies. Predesigned siRNAs were obtained from following vendors: Klf5 (#160900, Silencer pre-designed siRNA, Life technologies); To test Gata6 KD efficiency, 100 M of siRNA targeting Gata6 (#158651, Silencer pre-designed siRNA, Life technologies) was injected into zygotes. The injected embryos were cultured in KSOM using lumox dishes (35 mm, Sarstedt) under 5% O2, 5% CO2, 90% N2.

value: Nr5a2 and Klf5 KD


title: AnS DMSO-2

description:
Library name: S35
AnS_Ctrl#2

value: ovarian cancer

value: WT


title: apocrine gland anal sac adenocarcinoma (AGASAC), 12

description: re-analysis of GSM8152084

value: Eurasier


title: apocrine gland anal sac adenocarcinoma (AGASAC), 8

description: re-analysis of GSM8152082

value: female, neutered

value: Shepherd


title: ATAC_8C_Nr5a2_Klf5_dKD_rep1

description: Library name: ATAC Sample 15


title: hepatoid gland adenoma (HGA), 4

description: re-analysis of GSM8152080

value: male

value: Husky


title: AnS DMSO-1

description:
Library name: S34
AnS_Ctrl#1

value: cell line


title: Pancreatic cancer, patient 2977, whole transcriptome

description: Library name: rnaseq_2977

value: PDAC

value: patient 2977


title: ATAC_8C_Klf5_KD_rep2

description: Library name: ATAC Sample 14

value: preimplantation embryo

value: 8-cell embryo

value: Klf5 KD


title: apocrine gland anal sac adenocarcinoma (AGASAC), 7

description: re-analysis of GSM8152079

value: Shepherd-mix


title: 39 RNA

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Library name: 39 RNA

library_source: transcriptomic single cell

data_processing:
Raw reads were demultiplexed and single-nucleus gene expression and peak enrichment were quantified simultaneously using CellRanger-arc count (10X Genomics). Single cells were filtered to ensure data used in the downstream analysis is high quality: cells with >10% mitochondrial expression, indicative of dead or dying cells; cells with low numbers of genes expressed (<1000 genes) or low total UMI RNA counts (<2000 UMI counts); and cells with low peak numbers (<200 peaks) or total ATAC counts (<500 counts) were removed. Clustering was performed on the RNA-seq data, anticipating that gene expression would have a higher dynamic range than open chromatin, using the Seurat package in R. Single - droplet multiplets were detected using the union of two independent methods: Scrublet (https://doi.org/10.1016/j.cels.2018.11.005) and DoubletDetection (http://doi.org/10.5281/zenodo.2678041). Following determination of cell types, we re-called peaks separately for each cell type using Seurat, merging peaks across all cell types to obtain a more complete measurement of the open chromatin peaks for rarer cell types.
Assembly: hg38
Supplementary files format and content: Aggregated_atac_fragments.tsv.gz: gzipped tab-separated text file, ATAC-seq fragment alignments
Supplementary files format and content: barcodes.tsv.gz: gzipped tab-separated text file, barcodes for combined multi-sample and multi-omics matrix.
Supplementary files format and content: features.tsv.gz: gzipped tab-separated text file, feature names for combined multi-sample and multi-omics matrix.
Supplementary files format and content: matrix.mtx.gz: gzipped tab-separated text file, Matrix Market format, expression matrix for combined multi-sample and multi-omics matrix.
Supplementary files format and content: recall_peaks.bed: peak coordinates of re-analyzed peak calls
Supplementary files format and content: sample_numbering_manifest.txt: manifest matching cell barcode suffixes in Aggregated_atac_fragments.tsv.gz and barcodes.tsv.gz to sample IDs
Supplementary files format and content: seurat_object.rds: Seurat object with analyzed data

source_name: Dentate gyrus

extract_protocol:
The dentate gyrus was isolated from Fresh Frozen blocks of 36 participants representing 5 diagnostic groups (YA, NCI, MCI, AD and SA). Tissue was then immediately moved to homogenization; For each sample, a separate homogenizer and douncing pestles (loose and tight) were used. Each sample was homogenized in 1ml pre-chilled lysis buffer (0.1% NP-40 Alternative (or NP-40), 10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 40U/mL of RNAse inhibitor) by mechanical douncing for 20 times with the loose pestle followed by 20 times with the tight pestle to obtain a single cell suspension. Cell suspensions were then incubated on ice for 5 minutes. The homogenate was then filtered through 70 µm filters (Milentyi Biotec 130-041-407) and 40 µm filters (Milentyi Biotec 130-041-406), moved to 1.5 ml tubes and centrifuged at 4C for 5 minutes at 500 RCF.   Supernatants were removed and the nuclei pellet was washed 3 times with wash buffer (10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2), 0.01% BSA, 40U/mL of RNAse inhibitor). After the last wash, supernatants were removed, and the nuclei pellet was resuspended in resuspension buffer and mixed with 900 µl of Sucrose Cushion buffer. To remove the additional debris, resuspended nuclei were then loaded above a 3 Sucrose Cushion gradient (2.7 ml Nuclei PURE 2M Sucrose Cushion Solution with 300 μl Nuclei PURE Sucrose Cushion Buffer) and the sucrose gradient containing the nuclei was Centrifuged at 13,000 rcf for 45 min at 4°C. The supernatant was then carefully removed and the samples were immediately processed following the Single Cell protocol from 10x Genomics.
The 10X Genomics Multiome library preparation and sequencing was done at Northwestern University NUseq facility core with the support of NIH Grant (1S10OD025120). Nuclei number was analyzed using Nexcelom Cellometer Auto2000 with AOPI fluorescent staining method. The nuclei were first undergone transposition with ATAC enzyme for one hour at 37°C.  we loaded 16,000 transposed nuclei into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip J (10X Genomics, PN-1000230), and according to the manufacturer’s protocol, single cell gel beads were generated in the emulsion (GEM). Barcoded DNA and cDNA were PCR amplified and subjected to library construction. The single nuclei ATAC-seq library was generated using the Chromium Next GEM Single Cell Multiome ATAC + Gene expression kit (10X Genomics, PN-1000281) and single Index Kit N Set A (10X Genomics, PN-1000212) according to the manufacturer’s manual. In addition, the amplified cDNA was used for the gene expression library using dual Index Kit TT Set A (10X Genomics, PN-1000215). Quality control for the constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively. For the snATAC-seq library, the multiplexed libraries were pooled and sequenced on Illumina Novaseq sequencer with 100 cycles kits using the following read length: 50 bp Read1 and 49 bp Read2. For the snRNA-seq library, the libraries were sequenced on Illumina Novaseq sequencer with 100 cycles kits using the following read length: 28 bp Read 1 for cell barcode and UMI and 90 bp Read 2 for transcript expression. The targeted sequencing depth for snATAC-seq and snRNA-seq is 25,000 and 20,000 reads per cell, respectively.

value: Dentate gyrus

tag: diagnosis

value: MCI

tag: age at_death

tag: pmi


title: AnS SNX-2

description:
Library name: S38
AnS_SNX#2

value: OV90 parental


title: ATAC_8C_Klf5_KD_rep1

description: Library name: ATAC Sample 13


title: apocrine gland anal sac adenocarcinoma (AGASAC), sublumbal lymph node metastasis from 5

description: re-analysis of GSM8152078

value: female

value: Labrador Retriever


title: Pancreatic cancer, patient 2924, whole transcriptome

description: Library name: rnaseq_2924

value: patient 2924


title: ATAC_8C_Nr5a2_KD_rep2

description: Library name: ATAC Sample 12

value: Nr5a2 KD


title: Pancreatic cancer, patient 2976, whole transcriptome

description: Library name: rnaseq_2976

value: patient 2976


title: apocrine gland anal sac adenocarcinoma (AGASAC), 5

description: re-analysis of GSM8152077


title: apocrine gland anal sac adenocarcinoma (AGASAC), 4

description: re-analysis of GSM8152075

value: male, neutered

value: Mixed-breed


title: Pancreatic cancer, patient 2447, whole transcriptome

description: Library name: rnaseq_2447

value: patient 2447


title: Pancreatic cancer, patient 2236, whole transcriptome

description: Library name: rnaseq_2236

value: PDAC

value: patient 2236


title: 38 RNA

description: Library name: 38 RNA

value: YA


title: ATAC_8C_NT_ctrl_rep2

description: Library name: ATAC Sample 10

value: preimplantation embryo

value: 8-cell embryo

value: NT siRNA control KD


title: ATAC_8C_Nr5a2_KD_rep1

description: Library name: ATAC Sample 11


title: apocrine gland anal sac adenocarcinoma (AGASAC), sublumbal lymph node metastasis from 3

value: female, neutered

value: Shepherd-mix


title: apocrine gland anal sac adenocarcinoma (AGASAC), 3


title: H358 cells, T16, rep3 lane4

city: TORONTO

first: Xin

last: Xu

state: Ontario

address: 101 COLLEGE ST EAST TOWER 11-601D

country: Canada

institute: Princess Margaret Cancer Center

description: Library name: H358_T16_rep3 lane4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore
Trimmed sequence reads were mapped to the guide library by using Bowtie2
The BAM files produced were used to calculate the counts with the MAGeCK “count” function with default parameters.
The altered guides were identified by the “test” function.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts
Library strategy: CRISPR Screen

growth_protocol: H358 dCasRx-METTL3 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. Lentivirus-mediated sgRNAs were transduced into cells prior to selection by 10 μg/mL blasticidin.

extract_protocol:
The genomic DNA was purified from both T0 and T16 samples with gSYNC DNA extraction kit (Geneaid, GS300).
Sequencing libraries were generated by an in house optimized protocol from genomic DNA.

value: human lung cancer

value: Day 16

value: no treatment


title: 37 ATAC

description: Library name: 37 ATAC

library_source: genomic single cell

value: Dentate gyrus


title: 39 ATAC

description: Library name: 39 ATAC

value: MCI


title: ATAC_8C_NT_ctrl_rep1

description: Library name: ATAC Sample 9


title: 37 RNA

description: Library name: 37 RNA


title: H3K27ac_8C_Nr5a2_Klf5_dKD_rep3

description: Library name: CUT and Tag Sample 37

data_processing:
Low quality reads were trimmed out using TrimGalore (version 0.6.2) (https://github.com/FelixKrueger/TrimGalore) using parameters: --paired --quality 20 --length 20.
Read mapping to mm10 genome was done using Bowtie2 (version 2.3.5.1) using parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant.
Unmapped reads and reads with low mapping quality (Q<30) were removed. PCR duplicated reads were identified and discarded using the MarkDuplicates command from Picard (version 2.18.27) (http://broadinstitute.github.io/picard/) with parameters: VALIDATION_STRINGENCY=LENIENT.
The bigwig files were generated using bamCoverage command from deepTools (version 3.5.4) using parameters: --normalizeUsing RPKM --binSize 1 --ignoreForNormalization chrM. Peak calling for CUT&Tag, ATAC-seq, and ChIP-seq datasets were done using MACS2’s callpeak function (version 2.2.9) with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed as described previously with few modifications (Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun 10, 1930 (2019)). Embryos with intact zona pellucida were incubated with ice-cold extraction buffer (25 mM HEPES-NaOH (pH 7.4), 50 mM NaCl, 3 mM MgCl2, 300 mM sucrose and 0.5% Triton X-100) on ice for 6-7 min and were washed three times through with ice-cold extraction buffer without TritonX-100. Pre-extracted embryos were immediately lightly fixed by Dulbecco’s phosphate- buffered saline (DPBS) with 0.1% formaldehyde for 2 min at room temperature. Embryos were incubated in antibody buffer (20 mM HEPES-NaOH (pH7.5), 150 mM NaCl, 0.5 mM Spermidine, 0.1% BSA, 2 mM EDTA and 1x Protease inhibitor cocktail (Roche) with primary antibody (1:100 dilution) overnight at 4°C on nutator. Embryos were washed three times through antibody buffer and further incubated with secondary antibody (1:100 dilution) for 1.5 hours at room temperature. Cells were washed three times through Wash buffer (20 mM HEPES-NaOH (pH7.5), 150 mM NaCl, 0.5 mM Spermidine and 1x Protease inhibitor cocktail (Roche)) and further incubated with homemade pA-Tn5 or pAG-Tn5 adaptor complex (1:250 dilution) for 1.5 hours at room temperature. Embryos were washed three times through Wash-300 buffer (20 mM HEPES-NaOH (pH7.5), 300 mM NaCl, 0.5 mM Spermidine and 1x Protease inhibitor cocktail (Roche)). Embryos were transferred into 1.5 ml of DNA LoBind Tube (Eppendorf) with 200 µl of Tagmentation buffer (10 mM MgCl2 in Wash-300) and incubated at 37°C for 1 hour. The samples were then deproteinized and reverse-crosslinked. The DNA was purified by phenol-chloroform and followed by ethanol precipitation. The DNA was amplified 50 µl of reaction with 1×Q5 High-Fidelity Master mix (NEB) and 0.25 µM barcoded primers using the following PCR program: 72 °C for 5 min; 98°C for 30 sec; 15 cycles of 98°C for 10 sec and 63°C for 10 sec; final extension at 72 °C for 1 min and hold at 4°C. After PCR reaction, libraries were purified by 1.1×AMPure XP magnetic beads (Beckman Coulter) and were eluted in 20 µl of RNase-free water.
Purified DNA libraries were sequenced on a NextSeq 500 (Illumina), Novaseq 6000 (Illumina), or AVITI (Element Biosciences) with paired-end reads.

value: Nr5a2 and Klf5 KD

value: Active motif, 39133


title: 36 ATAC

description: Library name: 36 ATAC

value: HA


title: apocrine gland anal sac adenocarcinoma (AGASAC), sublumbal lymph node metastasis from 2

description: re-analysis of GSM8152074

value: male, neutered

value: Border Collie


title: H358 cells, T16, rep2 lane4

description: Library name: H358_T16_rep2 lane4


title: H3K27ac_8C_Nr5a2_Klf5_dKD_rep2

description: Library name: CUT and Tag Sample 36


title: H358 cells, T16, rep1 lane4

description: Library name: H358_T16_rep1 lane4


title: H358 cells, T0, rep3 lane4

description: Library name: H358_T0_rep3 lane4

value: Day 0


title: apocrine gland anal sac adenocarcinoma (AGASAC), 2

description: re-analysis of GSM8152073


title: 36 RNA

description: Library name: 36 RNA


title: H3K27ac_8C_Nr5a2_Klf5_dKD_rep1

description: Library name: CUT and Tag Sample 35


title: apocrine gland anal sac adenocarcinoma (AGASAC), sublumbal lymph node metastasis from 1

description: re-analysis of GSM8152072

value: Rhodesian Ridgeback


title: Pancreatic cancer, patient 3009, whole transcriptome

description: Library name: rnaseq_3009

value: PDAC

value: patient 3009


title: apocrine gland anal sac adenocarcinoma (AGASAC), 1

description: re-analysis of GSM8152071


title: 38 ATAC

description: Library name: 38 ATAC

value: YA


title: H358 cells, T0, rep2 lane4

description: Library name: H358_T0_rep2 lane4


title: Xenium spatial transcriptomics from intestinal epithelial cells of Yersini pseudotuberculosis infected mice rep1

city: Philadlephia

first: Daniel

last: Beiting

state: Pennsylvania

address: 380 S. University Avenue

institute: University of Pennsylvania

description: Xenium probe base, imaging based, spatial RNA quantification using Xenium 5k mouse probe panel

data_processing: Transcript processing occurs through Xenium on Board Analysis provides processed transcript information derived from raw images. According to 10X Genomics, the transcripts file (transcripts.parquet) contains data used to evaluate transcript quality and localization within the image coordinate system of the morphology images. Information is provided in parquet and .zarr format. Each row corresponds to a single decoded transcript and includes the following columns: transcript_id, cell_id, overlaps_nucleus, feature_name, x_location, y_location, z_location, qv, fov_name, nucleus_distance, codeword_index, codeword_category, and is_gene. The transcript.zarr file is used with Xenium Explorer

label: hybrid probe

source_name: mouse small intestine ileum

label_protocol: Manufacturer protocols were followed for 10X Xenium transcriptomic profiling. https://cdn.10xgenomics.com/image/upload/v1741380245/CG000760_XeniumPrime_GeneExpression_optionalCellSegmentation__UserGuide_RevC.pdf

extract_protocol: Spatially resolved transcriptomic profiling was carried out using the 10x Genomics Xenium platform and the pre-designed Xenium Prime 5K Mouse Gene Expression Panel. Infected and naive mice were euthanized and the small intestine isolated and flushed before 5 cm of the terminal ileum was Swiss rolled. Tissues were fixed in 10% neutral buffered formalin for 18-24 hours prior to paraffin embedding. Sections were cut following embedding and placed per manufacturer guidelines onto Xenium slides.

tag: mouse strain

value: Yersinia pseudotuberculosis

value: clinical isolate strain 32777, serogroup O5

value: 1-2e8 CFU

value: oral gavage

value: Xenium spatial Transcriptomics Mouse 5k probe set

value: fixed swiss roll of intestinal tissue

value: female

tag: age

value: 7.5 weeks


title: H3K27ac_8C_Klf5_KD_rep3

description: Library name: CUT and Tag Sample 34

value: preimplantation embryo

value: 8-cell embryo

value: Klf5 KD

value: Active motif, 39133


title: H358 cells, T0, rep1 lane4

description: Library name: H358_T0_rep1 lane4

value: human lung cancer

value: Day 0

value: no treatment


title: apocrine gland anal sac adenocarcinoma (AGASAC), sublumbal lymph node metastasis from 4

description: re-analysis of GSM8152076

value: male, neutered

value: Mixed-breed


title: H3K27ac_8C_Klf5_KD_rep2

description: Library name: CUT and Tag Sample 33


title: 35 ATAC

description: Library name: 35 ATAC

value: Dentate gyrus

value: YA


title: Xenium spatial transcriptomics from intestinal epithelial cells of Yersini pseudotuberculosis infected mice rep2

value: Yersinia pseudotuberculosis

value: clinical isolate strain 32777, serogroup O5

value: 1-2e8 CFU


title: Xenium spatial transcriptomics from intestinal epithelial cells of Naive mice rep2

value: Xenium spatial Transcriptomics Mouse 5k probe set

value: fixed swiss roll of intestinal tissue


title: H3K27ac_8C_Klf5_KD_rep1

description: Library name: CUT and Tag Sample 32


title: H358 cells, T16, rep3 lane3

description: Library name: H358_T16_rep3 lane3

value: Day 16


title: Xenium spatial transcriptomics from intestinal epithelial cells of Naive mice rep1

value: female

value: 7.5 weeks


title: 34 ATAC

description: Library name: 34 ATAC

value: AD


title: 34 RNA

description: Library name: 34 RNA


title: H3K27ac_8C_Nr5a2_KD_rep3

description: Library name: CUT and Tag Sample 31

value: preimplantation embryo

value: 8-cell embryo

value: Nr5a2 KD

value: Active motif, 39133


title: 33 ATAC

description: Library name: 33 ATAC

value: MCI


title: Mouse_Lung_Flu_d30

city: Basel

first: Carolyn

last: King

address: Hebelstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel

hyb_protocol: Processing and acquisition (with cell segmentation) was performed by Functional Genomics Center Zurich, following the user guides GC000760, GC000749 and GC00582 using Xenium in situ 5K gene expression kit (10 Genomics).

scan_protocol: Xenium

data_processing:
Probability-based segmentation was performed using Proseg. Analysis steps such as finding HVGs, PCA, cell annotation and clustering were done with bioconductor R packages as in sc-RNAseq processing.
Object metadata (tsv) and expected counts (rds) based on Proseg segmentation

label: Xenium label

source_name: influenza infected lung

extract_protocol: Lungs were fixed with 4% methanol-free PFA for 24 hours at 4°C, washed with PBS and paraffinized using Tissue Processing Center (TPC 15 Trio, Medite) and embedded in paraffin using TES station machine  (Tissue Embedding Station, Medite). FFPE blocks were kept  at 4°C and 5μm sections and placement of sections were performed according to the protocol CG000578 (10X Genomics), handled by the histology facility of Basel.

treatment_protocol: Mouse sacrificed at day 30 after influenza (PR8) infection

value: Lung

tag: infection

value: Influenza PR8

tag: timepoint

value: Day 30 p.i.


title: 33 RNA

description: Library name: 33 RNA

value: Dentate gyrus


title: H3K27ac_8C_Nr5a2_KD_rep2

description: Library name: CUT and Tag Sample 30


title: H358 cells, T16, rep1 lane3

description: Library name: H358_T16_rep1 lane3

value: human lung cancer

value: no treatment


title: Mouse_Lung_Flu_d14

label_protocol: Xenium Prime 5K Mouse Pan Tissue & Pathways Panel

treatment_protocol: Mouse sacrificed at day 14 after influenza (PR8) infection

value: Day 14 p.i.


title: H3K27ac_8C_Nr5a2_KD_rep1

description: Library name: CUT and Tag Sample 29


title: H358 cells, T0, rep3 lane3

description: Library name: H358_T0_rep3 lane3

value: Day 0


title: 32 ATAC

description: Library name: 32 ATAC

value: YA


title: 35 RNA

description: Library name: 35 RNA


title: Xenium Image-Based Spatial Transcriptomics of Post-Treatment Tumor from Patient 20

type: other

city: Los Angeles

first: Jason

middle: Michael

last: Link

state: CA

address: 650 Charles E Young Dr S

department: Surgery

institute: University of California, Los Angeles

scan_protocol: Xenium 5K Prime With Full Cell Segmentation

data_processing: Xenium Onboard Analyzer Standard

molecule: other

source_name: Pancreatic adenocarcinoma

treatment_protocol: Patients were treated with neoadjuvant FOLFIRINOX and nivolumab before tumors were resected

value: Neoadjuvant treatment with FOLFIRINOX and nivolumab


title: H358 cells, T0, rep2 lane3

description: Library name: H358_T0_rep2 lane3


title: H3K27ac_8C_NT_ctrl_rep3

description: Library name: CUT and Tag Sample 28

value: NT siRNA control KD


title: 32 RNA

description: Library name: 32 RNA


title: Xenium Image-Based Spatial Transcriptomics of Post-Treatment Tumor from Patient 15


title: H3K27ac_8C_NT_ctrl_rep2

description: Library name: CUT and Tag Sample 27


title: 31 ATAC

description: Library name: 31 ATAC

value: HA


title: H358 cells, T0, rep1 lane3

description: Library name: H358_T0_rep1 lane3


title: H3K27ac_8C_NT_ctrl_rep1

description: Library name: CUT and Tag Sample 26

value: preimplantation embryo


title: Xenium Image-Based Spatial Transcriptomics of Post-Treatment Tumor from Patient 11


title: 31 RNA

description: Library name: 31 RNA


title: H358 cells, T16, rep2 lane2

description: Library name: H358_T16_rep2 lane2

value: Day 16


title: H358 cells, T16, rep2 lane3

description: Library name: H358_T16_rep2 lane3


title: Xenium Image-Based Spatial Transcriptomics of Post-Treatment Tumor from Patient 09


title: ZNF626_Macaque_Unbound_2

city: Palo Alto

first: Zheng

last: Zuo

address: Stanford

department: Genetics

institute: Stanford university

description:
Library name: Spec_seq_sample_ZNF626_Macaque_Unbound_2
ZNF626(Macaque).rep2.csv

library_source: other

data_processing:
Counting the number of Bound and Unbound reads for each sample. The negative logarithmic ratio of Bound and Unbound reads can be calculated as the relative binding energy for each binding sites.
Cross comparison between replicate samples reveals the resolution of each sample, usually around 0.2kT for individual site.
The motif or specificity profile can be constructed by regression of binding energy values of select sequences, e.g., some reference site and all of its single/double variants. TFCookbook package, which contains all necessary codes to analyze the TF-DNA motif profile, can be accessed through https://github.com/zeropin/zeropin/TFCookbook.
Assembly: human genome hg38
Supplementary files format and content: For each sample, the associated csv file (linked to the corresponding *bound sample records) contains the bound and unbound reads, calculated relative bindng energy, library type, and the number of mismatches to some reference site for individual binding site. The data analysis protocol for each ZFP can be accessed through Github https://github.com/zeropin/ZFPCookbook

organism: Macaca

source_name: Recombinant protein

growth_protocol: We used the NEB PURExpress or E. coli(BL21) system to produce N-terminal HALO tagged ZFP constructs and noticed better success rates than previously used SUMO-tagged constructs.

extract_protocol:
The bound and unbound fractions of each sample were cut separately as thin gel slice, extracted by acrylamide gel extraction buffer (soaking a 55C for more than 30mins). Each fraction of DNA pool was purified and further amplified by uniquely indexed Illumina primers set for at least 12 cycles (annealing temperature 52C, extension time 30s). All samples were pooled together for Illumina Novaseq.
Synthetic DNA library was prepared by ordering 20 degenrate ologos containing triply randomized sites within the putative ZNF626 binding site (54bp long). Reversed PE2 primer was used to anneal and extend the ssDNA library to make dsDNA library.

treatment_protocol: We ran EMSA to physically separate DNA bound by ZNF626(Human) or ZNF626(Macaque) from unbound DNA. The EMSA condition is 10% Tris-glycine gel, 170V for 1h in cold room.

value: Recombinant protein

tag: fraction

value: unbound


title: ZNF626_Macaque_Bound_2

description:
Library name: Spec_seq_sample_ZNF626_Macaque_Bound_2
ZNF626(Macaque).rep2.csv

value: bound


title: Xenium Image-Based Spatial Transcriptomics of Post-Treatment Tumor from Patient 10


title: 30 ATAC

description: Library name: 30 ATAC

value: AD


title: H358 cells, T16, rep1 lane2

description: Library name: H358_T16_rep1 lane2


title: 30 RNA

description: Library name: 30 RNA


title: ZNF626_Macaque_Unbound_1

description:
Library name: Spec_seq_sample_ZNF626_Macaque_Unbound_1
ZNF626(Macaque).rep1.csv


title: H358 cells, T0, rep3 lane2

description: Library name: H358_T0_rep3 lane2


title: 29 ATAC

description: Library name: 29 ATAC


title: spt5-S1-15D , KY3594 , Rep1

city: Pittsburgh

first: Karen

middle: M.

last: Arndt

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

description:
Library name: spt5_S1_15D_KY3594_Rep1
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D

data_processing:
Reads were aligned to the hydrid genome of S. cerevisiae and S. pombe with HISAT2 version 2.2.1.
PCR duplicates were removed from the aligned reads using Samtools markdup.
The filtered hybrid alignment files were separated into S. cerevisiae and spike-in files.
S. pombe read counts from featureCounts were input into DESeq2 estimateSizeFactors() to get spike-in size factors.
The inverse of size factors was applied as spike-in normalization, and bigWig files were generated using bamCoverage.
Assembly: S. cerevisiae SacCer3
Assembly: S. pombe ASM294v2
Supplementary files format and content: bigWig, spike-in normalized 4tU-seq signal

organism: Saccharomyces cerevisiae

growth_protocol: All yeast cultures, including spike-in cells, were grown to mid-log phase in YPD+Trp media at 30ºC.

extract_protocol:
Total RNA was extracted using hot acid phenol extraction method. From 50 µg total RNA input, 4tU-labeled RNA was biotinylated with10 µg/mL MTSEA Biotin-XX (Biotium, 90066) for 30 minutes. The biotinylated RNA was purified and bound to magnetic MyOne Streptavidin C1 beads (Invitrogen, 65001) for 15 minutes. The RNA was eluted off the beads and concenrated using RNeasy MinElute cleanup kit (Qiagen, 74204). 100 ng of RNA was used for library construction.
Libraries were prepared using Universal Plus Total RNA-seq with NuQuant kit (Tecan, 0361-A01), UPlus Total RNA AnyDeplete module (Tecan, 0370-A01) and UPlus Total AnyDeplete Custom Probe Mix for S. cerevisiae (Tecan, S02714).

treatment_protocol:
4tU was added to the mid-log culture (or after the indicated treatment) at a final concentration of 5 mM for 5 min at RT before quenching the 4tU labeling reaction by adding 1/2 volume -20 degrees cold methanol.
For auxin inducible degron, the mid-log culture was treated with 5 µM 5-phenyl-indole-3-acetic acid (5-Ph-IAA) or equivalent amount of vehicle (DMSO) for 45 minutes.
For anchor-away experiments, the mid-log culture was treated with 1 µg/mL rapamycin or equivalent amount of vehicle (DMSO) for 1 hour.

tag: strain

tag: batch


title: Weighted 6

city: Notre Dame

first: Alice

last: Burchett

state: IN

address: 2030 McCourtney Hall East

institute: University of Notre Dame

description:
Library name: Sample 12
Column name in count_matrix.csv: Weighted-6_S28_L008

data_processing:
Create genome index using STAR  (version 2.7.2) using GENCODE gene annotation files.
Align files to generate gen count matrix using STAR 2.7.2
Assembly: Gene annotation file here: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M33/gencode.vM33.chr_patch_hapl_scaff.basic.annotation.gff3.gz and FASTA file here:https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M33/GRCm39.genome.fa.gz
Supplementary files format and content: CSV including with raw counts for each sample.

growth_protocol: RAW274.7 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1X pen/strep.

extract_protocol:
RNA was extracted using the Zymo RNA Extraction Kit.
Illumina directional RNA library prep with mRNA enrichment

treatment_protocol: Cells were seeded atop a cell culture insert with 0.4 um pore size (CellQuart, 9300412) and placed in a 6-well plate. Agarose cushions were made from 1% (w/v) agarose (Bio-Rad, 1613100) dissolved in complete culture medium and formed with custom 3-D printed cylindrical molds to match the size of the cell culture insert. These serve as a media reservoir to prevent nutrient deprivation and protect the cells from direct contact with the rigid weight. The agarose cushions were submerged in culture medium and placed in the incubator for 24 hours before use to equilibrate CO2 and oxygen within the gels. After cells had adhered to the cell culture insert (overnight), the agarose cushion was placed on top, and a custom 3-D printed PLA weight was placed on top of the agarose. The mass of the weight is such that it applies 0.14 kPa of compressive stress distributed across the insert membrane area. For the control condition, only the agarose cushion was placed on the cells. After the addition of the agarose (control) or agarose + weight (compressed), the cells were placed in a standard incubator for 24 hours, after which the RNBA was isolated and submitted for RNA sequencing.

tag: cell line

value: Macrophage

value: Compressed


title: ZNF626_Macaque_Bound_1

description:
Library name: Spec_seq_sample_ZNF626_Macaque_Bound_1
ZNF626(Macaque).rep1.csv

tag: tissue

tag: cell type


title: 29 RNA

description: Library name: 29 RNA

value: Dentate gyrus


title: Weighted 5

description:
Library name: Sample 11
Column name in count_matrix.csv: Weighted-5_S27_L008

tag: treatment


title: H358 cells, T0, rep2 lane2

description: Library name: H358_T0_rep2 lane2

value: human lung cancer

tag: genotype


title: H358 cells, T0, rep1 lane2

description: Library name: H358_T0_rep1 lane2

value: no treatment


title: mouse lineage-ckit+ cells, Afg3l2-WT, rep2

type: protein

city: Indianapolis

first: Bin

last: Guo

state: Indiana

address: 950 W. Walnut Street

department: Microbiology & Immunology

institute: Indiana University

description: Instrument model: Bruker timsTOF Pro/Pro2 . Column ID_REF in the matrix table contains UniProtKB accession numbers

data_processing: The data was log-transformed using log2(x+1), missing values were replaced with 0, and processed with limma (3.58.1).

molecule: protein

source_name: Bone Marrow

label_protocol: Mass spectrometry analysis can obtain the mass-to-charge ratio and signal intensity of peptides in the sample, as well as the mass-to-charge ratio and signal intensity of fragment ions after peptide fragmentation. The information at the peptide level is usually called the primary spectrum, and the information of peptide fragment ions is called the secondary spectrum. The information contained in the spectrum is very complex, and the database is needed to correctly parse the peptide sequence potentially contained in the spectrum. Before searching, a theoretical secondary spectrum database is constructed based on the protein sequences in the database. Then the secondary spectrum generated by the mass spectrometry is searched and compared with the theoretical secondary spectrum, and the correctly matched theoretical peptide sequence is obtained after algorithm scoring and filtering. Through the identified protein-specific peptides, the protein information contained can be identified.

growth_protocol: Fresh separation

extract_protocol: The sample was grinded with liquid nitrogen into cell powder and then transferred to a 5-mL centrifuge tube. After that, four volumes of lysis buffer (8 M urea, 1% protease inhibitor cocktail) was added to the cell powder, followed by sonication three minutes on ice using a high intensity ultrasonic processor (Scientz). (Note: For PTM experiments, inhibitors were also added to the lysis buffer, e.g. 3 μM TSA and 50 mM NAM for acetylation, 1% phosphatase inhibitor for phosphorylation). The remaining debris was removed by centrifugation at 12,000 g at 4 °C for 10 min. Finally, the supernatant was collected and the protein concentration was determined with BCA kit according to the manufacturer’s instructions.

treatment_protocol: PBS wash

value: Bone Marrow

value: Primary cells

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: Afg3l2 WT


title: Weighted 4

description:
Library name: Sample 10
Column name in count_matrix.csv: Weighted-4_S26_L008


title: H358 cells, T16, rep3 lane2

description: Library name: H358_T16_rep3 lane2


title: 28 RNA

description: Library name: 28 RNA


title: mouse lineage-ckit+ cells, Afg3l2-WT, rep1


title: mouse lineage-ckit+ cells, Afg3l2-KO, rep3

value: Afg3l2 KO


title: H358 cells, T16, rep2 lane1

description: Library name: H358_T16_rep2 lane1


title: Weighted 2

description:
Library name: Sample 8
Column name in count_matrix.csv: Weighted-2_S24_L008


title: 27 RNA

description: Library name: 27 RNA

value: HA


title: H358 cells, T16, rep1 lane1

description: Library name: H358_T16_rep1 lane1


title: mouse lineage-ckit+ cells, Afg3l2-KO, rep2


title: Xenium Image-Based Spatial Transcriptomics of Post-Treatment Tumor from Patient 01

value: Neoadjuvant treatment with FOLFIRINOX and nivolumab


title: H358 cells, T0, rep3 lane1

description: Library name: H358_T0_rep3 lane1

value: Day 0


title: H358 cells, T16, rep3 lane1

description: Library name: H358_T16_rep3 lane1

value: Day 16


title: mouse lineage-ckit+ cells, Afg3l2-KO, rep1


title: Agarose 6

description:
Library name: Sample 6
Column name in count_matrix.csv: Agarose-6_S22_L008

value: Control


title: 26 RNA

description: Library name: 26 RNA


title: H358 cells, T0, rep2 lane1

description: Library name: H358_T0_rep2 lane1


title: H358 cells, T0, rep1 lane1

description: Library name: H358_T0_rep1 lane1


title: mouse lineage-ckit+ cells, Afg3l2-WT, rep3


title: 25 ATAC

description: Library name: 25 ATAC

value: YA


title: Agarose 5

description:
Library name: Sample 5
Column name in count_matrix.csv: Agarose-5_S21_L008


title: UPX overexpressed,PhiV-1 infection,rep_3

city: Hangzhou

first: Tong

last: Jiajing

address: Xiasha

country: China

institute: Zhejiang University of Technology

description: Library name: Treatment-2-3

data_processing:
Reads were trimmed for low quality and adaptors using Cutadapt.
Trimmed reads were aligned to a combined E. coli MG1655 + phiV-1 reference genome using Bowtie2.
HTSeq was used to estimat gene expression levels from the pair-end clean data.
Assembly: Combined E. coli MG1655(GenBank: U00096.3) + Escherichia phage phiV-1(GenBank: MT542512.1) reference genome
Supplementary files format and content: csv files include raw count for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Escherichia coli

source_name: E. coli MG1655 culture

extract_protocol:
Total RNA was isolated using the TRIzol methods, including chloroform phase separation, isopropanol precipitation, ethanol washing, and TURBO DNase treatment. RNA quality (RIN>6.5) was identified prior to bacterial rRNA depletion and preparation of strand-specific sequencing libraries.
Libraries were sequenced on an Illumina platform, and trimmed reads were aligned to a combined E. coli MG1655 + phiV-1 reference genome for gene-level quantification and differential expression analysis.

treatment_protocol: E. coli MG1655 cultures were grown in LB at 37 °C with shaking (200 rpm) to an OD₆₀₀ of 0.5 and subsequently infected with Escherichia phage phiV-1 at an MOI of 3. After infected for 20 minutes, culture samples were rapidly quenched and collected by centrifugation at 4 °C, and stored at −80 °C.

value: E. coli MG1655 culture

value: UPX overexpressed

value: Escherichia phage phiV-1 infected


title: 28 ATAC

description: Library name: 28 ATAC

value: Dentate gyrus

value: AD


title: Weighted 3

description:
Library name: Sample 9
Column name in count_matrix.csv: Weighted-3_S25_L008

value: Macrophage

value: Compressed


title: Agarose 4

description:
Library name: Sample 4
Column name in count_matrix.csv: Agarose-4_S20_L008


title: DMSO_input

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
ChIP-Seq reads were aligned to the Drosophila melanogaster BDGP6 genome with BWA (0.7.5a-r405). The output SAM files were converted to BAM using SAMtools view (0.1.19) and the number of Drosophila mapped reads were counted with SAMtools flagstat for later normalization. Drosophila reads were filtered out and BAM files sorted with SAMtools prior to alignment to the Human GRCh37 genome. Human mapped files were converted to BAM, counted with flagstat, filtered with SAMtools, and then any reads mapping to the Duke Encode blacklist regions were excluded using Bedtools (2.17.0). Finally, the Drosophila mapped reads were quality checked for overlap by aligning to the Human GRCh37 genome. The final normalised read counts for each ChIP-Seq sample were calculated by dividing the total number of Human mapped reads by the total number of Drosophila mapped reads.
Assembly: Human GRCh37 genome and Drosophila melanogaster BDGP6 genome
Supplementary files format and content: bigwig files of reads mapped to human GRCh37

source_name: HEK293T (ATCC, CRL-3216)

growth_protocol: HEK293T cells (ATCC, CRL-3216) were grown in DMEM (Sigma, D6429) containing 10% FBS (Sigma, F7524), 1% penicillin G-streptomycin (Sigma, P0781) and 1% L-glutamine (Sigma, G7513). Cells were grown on 15 cm plates to approximately 80-90% confluency on the day of harvest.

extract_protocol:
Chromatin-bound proteins were crosslinked to DNA by addition of 37% formaldehyde to a concentration of 1% (w/v) followed by gentle rocking on ice (10 min). The reaction was quenched by addition of glycine (125 mM) solution and followed by gentle rocking at room temperature (10 min). Cells were washed twice with PBS before being physically scraped into 5 mL PBS. This suspension was centrifuged (4°C, 800 rpm, 10 min). The supernatant was discarded and pelleted cells were then resuspended in 500 µL of ChIP SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8.1, supplemented with fresh Roche complete protease inhibitor cocktail (2× concentration)) before incubation on ice (10 min). Lysates were diluted with ChIP dilution buffer (500 µL, 0.01% SDS, 1.1% Triton™ X-100, 1.2 mM EDTA, 16.7 mM Tris pH 8.1, 167 mM NaCl) and transferred to Bioruptor Plus TPX tubes suitable for sonication. Chromatin fragmentation was accomplished by 30 minutes of sonication using a Bioruptor ® Plus set to ‘HIGH’ mode (15 s on / 15 s off). The sonicated chromatin was centrifuged (13,000 rpm, 4 °C, 10 min), the supernatant was collected. A 20 µL aliquot of sonicated chromatin was taken for quantification and the rest snap-frozen for storage at -80°C. Fresh elution buffer (220 µL, 0.1 M NaHCO3, 1% SDS), was added to an aliquot and NaCl solution (12.5 µL, 4 M) was added to each sample and shaken overnight on an Eppendorf ThermoMixer F1.5 set to 65°C, 1400 rpm. Proteins were digested with Proteinase K (Thermo Fisher, 2 µL) and shaken (1400 rpm, 45°C, 4 h). For RNA degradation, RNase A (Thermo Fisher, 1.0 µL) was added and shaken (1400 rpm, 37 °C, 30 min). Samples were then mixed with PB binding buffer (Qiagen, 1.0 mL) and sodium acetate solution (10 µL, 3 M, pH 5.2). DNA was purified with MinElute PCR Purification columns (Qiagen) and eluted with nuclease-free water (20 µL). Chromatin fragmentation was assessed by Agilent 2200 TapeStation System Automated Electrophoresis and D1000 DNA ScreenTape analysis and ~200 bp was considered acceptable. The concentration of purified DNA was quantified by Qubit 2.0 fluorometer (Invitrogen) and dsDNA Broad Range Assay kit (Thermo Fisher). A pre-determined amount of chromatin (detailed in Supplementary Table 5) was taken from each sample and diluted with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris, 167 mM NaCl, pH 8.1) to achieve a final volume of 1.0 mL in 2.0 mL Eppendorf DNA LoBind safe-lock microcentrifuge tubes (Thermo Fisher). This fixed amount of Human chromatin was combined with an antibody of interest according to the details in Supplementary Table 5. Drosophila melanogaster chromatin (Active Motif, 10 ng) and Drosophila-specific histone variant H2Av antibody (Active Motif, 1 µg) was added to each reaction as a spike-in control for downstream normalization. For ChIP-Seq determining H3K9acOH, the Drosophila chromatin (5 ng) and antibody (0.5 µg) was reduced. These chromatin/antibody reactions were rotated overnight (4 °C), antibody-bound DNA was pulled down by magnetic Protein G Dynabeads (Thermo Fisher). Beads (50 µL) were added to each sample along with ChIP dilution buffer (500 µL) and incubated on the end-over-end rotator (4 °C, 2 h). After the supernatant was removed by utilizing a magnetic rack, the samples were washed using low salt wash buffer (500 µL, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.1, 150 mM NaCl), high salt wash buffer (500 µL, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.1, 500 mM NaCl), LiCl wash buffer (500 µL, 1% Igepal, 1 mM EDTA, 10 mM Tris, 250 mM LiCl, 1% sodium deoxycholate, pH 8.1), and two rounds of TE wash (500 µL, 10 mM, 1 mM EDTA, Tris pH 8.0) using sample rotary machine (4°C, 5 min). Fresh elution buffer was added to the beads (120 µL) and shaken (1400 rpm, room temperature, 15 min). The supernatant was collected; the elution process was repeated and the eluates were pooled.
All libraries were prepared and sequenced (single-end) by the US NCI CCR Genomics Core following Illumina recommended protocols for the NextSeq 500 75 cycle High output platform.

treatment_protocol: HEK293T cells were treated with 0.04% dimethyl sulfoxide (DMSO) (Sigma, D2650) for 4 hours

value: HEK293T (ATCC, CRL-3216)

value: Human embryonic kidney

tag: secondary chip_antibody

value: Drosophila spike-in (histone variant H2Av, Active Motif, 61686)

value: Dimethylsulfoxide (DMSO) for 4 hours


title: UPX overexpressed,PhiV-1 infection,rep_1

description: Library name: Treatment-2-1


title: Agarose 3

description:
Library name: Sample 3
Column name in count_matrix.csv: Agarose-3_S19_L008


title: Agarose 2

description:
Library name: Sample 2
Column name in count_matrix.csv: Agarose-2_S18_L008


title: 24 RNA

description: Library name: 24 RNA


title: 24 ATAC

description: Library name: 24 ATAC


title: vector,PhiV-1 infection,rep_3

description: Library name: Treatment-1-3

value: WT


title: 27 ATAC

description: Library name: 27 ATAC

value: HA


title: Weighted 1

description:
Library name: Sample 7
Column name in count_matrix.csv: Weighted-1_S23_L008


title: 26 ATAC

description: Library name: 26 ATAC


title: TMD8, DMSO, rep3

city: Xiamen

first: jiazhen

last: lin

state: Fujian

address: No. 2000 of Xiang an East road

institute: Xiamen uniersity

description: Library name: DMSO3A FPKM

data_processing:
3.RNAseq analysis method 3.1 Data filtering The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com). 3.2 RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. 3.3 Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) [5] (or DEGseq[6] or PoissonDis[7])with Q value ≤ 0.05 (or FDR ≤ 0.001). 3.4 Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Assembly: hg38
Supplementary files format and content: processed data excel file include FPKM values for each sample

source_name: Lymphoma tissue

growth_protocol: The incubator condition was set at 37℃ with 5% CO2. TMD8 cell line was cultured in RPMI-1640 (Hyclone, Thermo Scientific, Logan, UT, USA) adding 10% fetal bovine serum (Gibco, Thermo Scientific, Grand Island, NY, USA).

extract_protocol:
1.1 Cell Sample Lysis Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells). 1.2 Sample Purification 1.2.1 Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃. 1.2.2 Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking； 1.2.3 Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity). 1.2.4 Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h. 1.2.5 Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting. 1.2.6 Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃)。 1.2.7 Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min. 1.2.8 Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
2.mRNA Library Preparation 2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: TMD8 cells were treated with 375nM chidamide, 1µM selinexor, or 375nM chidamide combined with 1µM selinexor for 24h, and then first lysed with TRIzol reagent (Invitrogen, NY, USA) and further extracted following the manufacturer's guidelines.

value: Lymphoma tissue

value: Lymphoma cell line

value: double-hit lymphoma with TP53 mutation

value: DMSO


title: 23 RNA

description: Library name: 23 RNA


title: DMSO_H3K9ac

tag: chip antibody

value: H3K9ac (Abcam, ab4441)


title: 22 ATAC

description: Library name: 22 ATAC

tag: diagnosis

value: MCI


title: DMSO_H3K4me3

value: H3K4me3 (Cell Signaling, 9751S)


title: 25 RNA

description: Library name: 25 RNA

value: Dentate gyrus

value: YA

tag: age at_death


title: UPX overexpressed,PhiV-1 infection,rep_2

description: Library name: Treatment-2-2

value: E. coli MG1655 culture

value: UPX overexpressed

value: Escherichia phage phiV-1 infected


title: Agarose 1

description:
Library name: Sample 1
Column name in count_matrix.csv: Agarose-1_S17_L008

value: Macrophage

value: Control


title: TMD8, DMSO, rep1

description: Library name: DMSO1A FPKM


title: rhesus fetal kidney scRNA-seq Sample 628

city: Cincinnati

first: Kairavee

last: Thakkar

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Library name: Sample 628

data_processing:
For all rhesus samples, count matrices from raw FASTQ files were generated using cellranger (v6.0.1) and rhesus reference genome (Mmul assembly 10). To remove ambient mRNA, we applied the SoupX protocol on the count matrices with automatic calculation of the contamination fraction. Post ambient mRNA removal, we used DoubletFinder to remove doublet cells using the parameters recommended by the authors of DoubletFinder. Rhesus genes were translated to human orthologs (using hg19, Ensmbl release 75). The intersection of genes observed between the human scRNA-seq datasets (see the next section in Methods) and the human orthologs observed in rhesus scRNA-seq datasets were considered for all downstream analyses.
Cell type annotation and subclustering can be found in the supplemental methods.
Assembly: Mmul assembly 10
Supplementary files format and content: Seurat object (Rds format) containing gene expression and metadata is provided.

organism: Macaca mulatta

source_name: kidney

extract_protocol:
Samples 600 and 628 were manually dissected cortical tissue from two donor kidneys were kept on ice and dissociated using cold-active enzyme mixture enhanced by repeated trituration with a 1ml pipette and vigorous shaking between each step. Cell suspensions were filtered, red blood cells lysed, and the final pellet was washed before loading into the 10x chromium apparatus. Samples 623, 627, and 632 were vortexed in cold Bacillus licheniformis (B lich) B mix to generate a cortically-biased cell suspension, and after filtration, processed as previously described.
Cell viability and concentration were determined with a hemocytometer using trypan blue. 16,000 cells were loaded into the 10x Genomics controller (10x Genomics 3' version 3) to target recovery of 10,000. Excess dissected cortex was frozen in liquid nitrogen.

value: kidney

value: cortical tissue

value: cortically-enriched kidney cells


title: vector,PhiV-1 infection,rep_2

description: Library name: Treatment-1-2

value: WT


title: 23 ATAC

description: Library name: 23 ATAC

value: HA

tag: pmi


title: vector,PhiV-1 infection,rep_1

description: Library name: Treatment-1-1


title: DMSO_H3K9acOH

value: HEK293T (ATCC, CRL-3216)

value: Human embryonic kidney

value: H3K9acOH (in house)

value: Drosophila spike-in (histone variant H2Av, Active Motif, 61686)

value: Dimethylsulfoxide (DMSO) for 4 hours


title: TMD8, DMSO, rep2

description: Library name: DMSO2A FPKM

value: Lymphoma tissue

value: Lymphoma cell line

value: double-hit lymphoma with TP53 mutation

value: DMSO


title: 22Rv1 cells, T16, rep2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore
Trimmed sequence reads were mapped to the guide library by using Bowtie2
The BAM files produced were used to calculate the counts with the MAGeCK “count” function with default parameters.
The altered guides were identified by the “test” function.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts
Library strategy: CRISPR screen

growth_protocol: 22Rv1-dCasRx-METTL3 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

value: human prostate cancer

value: no treatment


title: 22 RNA

description: Library name: 22 RNA

value: Dentate gyrus

value: MCI


title: rhesus fetal kidney scRNA-seq Sample 632

description: Library name: Sample 632

value: kidney

value: cortical tissue


title: 22Rv1 cells, T16, rep3


title: TMD8, SC, rep3

description: Library name: SC3A FPKM

value: Chidamide combined with selinexor


title: 22Rv1 cells, T16, rep1


title: DMSO_H3_total

value: Total H3 (Abcam, ab1791)


title: rhesus fetal kidney scRNA-seq Sample 627

description: Library name: Sample 627

value: cortically-enriched kidney cells


title: rhesus fetal kidney scRNA-seq Sample 600

description: Library name: Sample 600


title: 22Rv1 cells, T0, rep2


title: 21 RNA

description: Library name: 21 RNA


title: TMD8, SC, rep1

description: Library name: SC1A FPKM


title: TMD8, S, rep2

description: Library name: S2A FPKM

value: Chidamide


title: 21 ATAC

description: Library name: 21 ATAC


title: 22Rv1 cells, T0, rep3


title: TMD8, S, rep3

description: Library name: S3A FPKM


title: 19 ATAC

description: Library name: 19 ATAC

value: SA


title: rhesus fetal kidney scRNA-seq Sample 623

description: Library name: Sample 623


title: TMD8, C, rep3

description: Library name: C3A FPKM

value: selinexor


title: Control (normal/unmodified ASCs)

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: D

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6, while the FASTQ file generation and de-multiplexing utilised bcl2fastq conversion software v2.15.0.4.
Sequenced reads were mapped using the align function in the Rsubread package (version 1.29.6) with default parameters.
Gene-level counts were obtained using the featureCounts function from the Rsubread package using the in-built hg38 annotation.
Data were TMM normalized using the edgeR (version 3.22.5) and limma (version 3.36.5) packages and transformed to log2 counts per million.
Genome_build: hg38
Supplementary_files_format_and_content: a tab-delimited text file with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene for each sample.

source_name: Subcutaneous fat tissue

growth_protocol: ASCs were grown in DMEM+10% FBS+1% Penicillin+1% Streptomycin

extract_protocol:
Total RNA from transduced and control cells was isolated using RNeasy lipid tissue mini kit (Qiagen) accroding to the manufacture's instruction.
An input of 100ng of total RNA were prepared and indexed separately for Illumina sequencing using the TruSeq RNA sample Prep Kit (Illumina) as per manufacturer’s instruction. Each library was quantified using the Agilent Tapestation and the Qubit™ DNA BR assay kit for Qubit 3.0® Fluorometer (Life technologies).  The indexed libraries were pooled and diluted to 1.5pM for paired end sequencing (2x 81 cycles) on a NextSeq 500 instrument using the v2 150 cycle High Output kit (Illumina) as per manufacturer’s instructions.

treatment_protocol: CAV-1 over expression or knocdown were performed by lentiviral overexpression of human CAV-1 or shRNA targetting CAV-1 respectively

value: Untreated control cells

tag: growth conditions

value: 37C, 5% CO2, DMEM+10% FBS+1% Penicillin+1% Streptomycin

value: Mesenchymal stem cells


title: GFP overexpressing ASCs

description: C

value: GFP overexpression


title: TMD8, SC, rep2

description: Library name: SC2A FPKM

value: Lymphoma tissue

value: Lymphoma cell line

value: double-hit lymphoma with TP53 mutation


title: Organoid Day 14

city: Atlanta

first: Alejandro

last: de Janon

state: GA

address: 225 North Ave NW

department: Biomedical Engineering

institute: Georgia Institute of Technology

description: Library name: Sample 2

data_processing:
Alignment was performed using PIPSeeker software V 3.2.0 (https://www.fluentbio.com)
FASTQ files were aligned to a custom reference containing the human genome (GRCh38) using PIPseeker software, version 3.2.0 (Fluent Biosciences). The resulting count matrices were converted to Seurat objects using the Read10X() function. Individual samples were merged into a single Seurat object, and standard Seurat pipelines were applied for quality control and downstream analysis. Quality filtering excluded cells with fewer than 200 or more than 10,000 detected genes (nFeature_RNA), more than 10% mitochondrial gene content (percent.mt), or total RNA counts (nCount_RNA) outside the range of 300 to 100,000. Following filtering, Seurat was used to perform normalization, dimensionality reduction, clustering, and visualization. Cluster-specific markers were identified, cell types were assigned based on canonical marker expression, and UMAP coordinates were calculated for embedding.
Assembly: GRCh38.p13
Supplementary files format and content: tab-separated values files and matrix files

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: Cells cultured in Vascular Cellular Basal Media supplemented with 5 ng/ml VEGF, 5 ng/ml EGF, 5 ng/ml FEF, 15 ng/ml IGF-1, 10 mM L-glutamine, 0.75 U/ml heparin sulfate, 1 µg/ml hydrocortisone, and 50 µg/ml ascorbic acid

extract_protocol:
Single-cell RNA sequencing (scRNA-seq) of VMOs was performed using the PIPseq pipeline (PIPseq T20 3’ Single-Cell RNA kit v4.0, Fluent BioSciences). Organoids collected at D3 and D14 were digested in TrypLE for 20-60 minutes at 37°C with vigorous pipetting every 20 minutes. The resulting cell suspension was filtered through a 40 µm cell strainer (Greiner Bio-One) to remove undigested Matrigel and large cell clumps. The Dead Cell Removal Microbubble Kit (Akadeum Life Sciences) was used to separate viable from dead cells based on buoyancy. Viable cells were then spun down to the required concentration and submitted to core facilities for processing according to the manufacturer’s protocol.
The PIPSeq T20 kits were used to capture mRNA, synthesize cDNA, and construct libraries. Libraries that passed QC were sequenced in paired-end mode using a 138-cycle NovaSeq X SP kit (Illumina), with read lengths specified by the user guide. The resulting FASTQ files underwent QC preprocessing.

value: Bone Marrow Mesenchymal Stem Cell

value: Human Umbilical Vein Endothelial Cells

value: 14 days culture time


title: TMD8, S, rep1

description: Library name: S1A FPKM


title: 20 ATAC

description: Library name: 20 ATAC

data_processing:
Raw reads were demultiplexed and single-nucleus gene expression and peak enrichment were quantified simultaneously using CellRanger-arc count (10X Genomics). Single cells were filtered to ensure data used in the downstream analysis is high quality: cells with >10% mitochondrial expression, indicative of dead or dying cells; cells with low numbers of genes expressed (<1000 genes) or low total UMI RNA counts (<2000 UMI counts); and cells with low peak numbers (<200 peaks) or total ATAC counts (<500 counts) were removed. Clustering was performed on the RNA-seq data, anticipating that gene expression would have a higher dynamic range than open chromatin, using the Seurat package in R. Single - droplet multiplets were detected using the union of two independent methods: Scrublet (https://doi.org/10.1016/j.cels.2018.11.005) and DoubletDetection (http://doi.org/10.5281/zenodo.2678041). Following determination of cell types, we re-called peaks separately for each cell type using Seurat, merging peaks across all cell types to obtain a more complete measurement of the open chromatin peaks for rarer cell types.
Assembly: hg38
Supplementary files format and content: Aggregated_atac_fragments.tsv.gz: gzipped tab-separated text file, ATAC-seq fragment alignments
Supplementary files format and content: barcodes.tsv.gz: gzipped tab-separated text file, barcodes for combined multi-sample and multi-omics matrix.
Supplementary files format and content: features.tsv.gz: gzipped tab-separated text file, feature names for combined multi-sample and multi-omics matrix.
Supplementary files format and content: matrix.mtx.gz: gzipped tab-separated text file, Matrix Market format, expression matrix for combined multi-sample and multi-omics matrix.
Supplementary files format and content: recall_peaks.bed: peak coordinates of re-analyzed peak calls
Supplementary files format and content: sample_numbering_manifest.txt: manifest matching cell barcode suffixes in Aggregated_atac_fragments.tsv.gz and barcodes.tsv.gz to sample IDs
Supplementary files format and content: seurat_object.rds: Seurat object with analyzed data

value: Dentate gyrus


title: shHIF1a

city: Tainan

first: Jie

middle: ning

last: Li

state: Please select an option below

address: No1. University road

department: Department of Medical Laboratory Science and Biotechnology

country: Taiwan

institute: National Cheng Kung University

description: MDA-MB-231 cells infected with shHIF-1a.  Three independent biological replicates within the same experimental group were equally pooled to generate a representative sample for microarray analysis.

hyb_protocol: Hybridization was performed on the Affymetrix GeneChip miRNA 4.0 Array for 16 hours at 48°C and 60 rpm in the GeneChip Hybridization Oven 645.

scan_protocol: Arrays were washed and stained using the GeneChip Fluidics Station 450 and scanned with the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw CEL files were imported into Transcriptome Analysis Console (TAC) software (Thermo Fisher Scientific) for analysis. Background correction was performed using the DABG (Detection Above Background) model. Probe-level intensities were summarized into probeset-level expression values using the RMA (Robust Multi-array Average) median polish algorithm. Importantly, between-array quantile normalization was ntentionally omitted to preserve the biological signal of global expression shifts observed between conditions. The final processed data represent log2-transformed signal intensities.

label: biotin

label_protocol: Biotin-labeled RNA was prepared using the FlashTag Biotin HSR RNA Labeling Kit (Thermo Fisher Scientific) according to the manufacturer's instructions.

growth_protocol: MCF-7 cells were cultured using low-glucose DMEM medium supplemented with 10% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO₂. MDA-MB-231 cells were cultured using high-glucose DMEM medium supplemented with 10% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO₂

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: MCF-7 cells were transfected with pcDNA3.1, HIF-1alpha or HLH-truncated HIF1alpha plasmids for 72 hours. MDA-MB-231 cells were stablely knockdown with GFP or HIF-1aplha.

value: breast

value: pooled RNA from 3 independent biological replicates


title: TMD8, C, rep2

description: Library name: C2A FPKM


title: CAV1 knockdown ASCs

description: A

value: Knockdown of CAV1


title: HIF1a

description: MCF-7 cells overexpressed with HIF1-a.  Three independent biological replicates within the same experimental group were equally pooled to generate a representative sample for microarray analysis.

tag: transfection period

value: 72 hours


title: HLH

description: MCF-7 cells overexpressed with HLH-truncated HIF1-a.  Three independent biological replicates within the same experimental group were equally pooled to generate a representative sample for microarray analysis.


title: pcDNA 3.1

description: MCF-7 cells overexpressed with pcDNA 3.1.   Three independent biological replicates within the same experimental group were equally pooled to generate a representative sample for microarray analysis.


title: 19 RNA

description: Library name: 19 RNA

value: SA


title: GFP

description: MDA-MB-231 cells infected with shGFP.  Three independent biological replicates within the same experimental group were equally pooled to generate a representative sample for microarray analysis.


title: TMD8, C, rep1

description: Library name: C1A FPKM

value: selinexor


title: Organoid Day 3

description: Library name: Sample 1

value: 3 days culture time


title: 22Rv1 cells, T0, rep1

value: human prostate cancer

value: no treatment


title: V. cholerae C6706 cells grown in Brain Heart Infusion containing extracts, replicate 3

status: Public on Dec 14 2025

city: Lawrence

first: Luis Caetano

last: Antunes

state: KS

address: 1200 Sunnyside Avenue

institute: University of Kansas

description: Library name: Extract_3

data_processing:
Read quality was assessed using FastQC v0.12.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC v1.14. Reads were then mapped against the V. cholerae C6706 reference genome (GCF_015482825.1) using STAR software v2.7.10b (parameter: --quantMode GeneCounts). Raw counts were normalized and the differentially expressed genes were determined with DESeq2 R package (Log2 fold-change ≥1, p-adjusted <0.05).
Assembly: GCF_015482825.1
Supplementary files format and content: xlsx file with normalized counts for each sample

organism: Vibrio cholerae C6706

source_name: bacterial cells

growth_protocol: V. cholerae C6706 was grown overnight in LB medium at 37°C with shaking (200 rpm). The culture was diluted 1:200 in BHI broth containing either a control extract or an extract from E. citroniae WAL17108 and incubated at 37°C with shaking (200 rpm). After approximately 3 hours of growth (mid-log phase), cells were processed as described below.

extract_protocol:
Bacterial RNA was stabilized using RNAprotect Bacteria Reagent (Qiagen) according to the manufacturer’s instructions. Bacterial cells were pelleted by centrifugation, and total RNA was isolated using the SV Total RNA Isolation System (Promega), following the manufacturer’s recommendations. RNA samples were treated with Turbo DNase (2 U/μL; Life Technologies) to eliminate residual DNA, followed by an additional purification step using the SV Total RNA Isolation System (Promega), according to the manufacturer’s recommendations. RNA concentration and purity were assessed using an ND-1000 NanoDrop spectrophotometer (Thermo Fisher Scientific). Absence of DNA contamination in the RNA was checked by quantitative Real-Time PCR.
RNA sequencing (RNA-seq) was performed on an Illumina NextSeq 2000 platform using a P1 flow cell, as single reads (100 bp), at The University of Kansas Genome Sequencing Core.

value: bacterial cells

value: WT

value: E. citroniae extracts


title: CAV1 overexpressing ASCs

description: B

value: Overexpression of CAV1

value: 37C, 5% CO2, DMEM+10% FBS+1% Penicillin+1% Streptomycin

value: Mesenchymal stem cells


title: V. cholerae C6706 cells grown in Brain Heart Infusion containing extracts, replicate 2

description: Library name: Extract_2


title: V. cholerae C6706 cells grown in Brain Heart Infusion, replicate 3

description: Library name: Control_3

value: No addition


title: V. cholerae C6706 cells grown in Brain Heart Infusion, replicate 2

description: Library name: Control_2


title: V. cholerae C6706 cells grown in Brain Heart Infusion containing extracts, replicate 1

description: Library name: Extract_1


title: lefko1 72 h rep1

city: Athens

first: Anastasios

last: Alatzas

address: IERA ODOS 75

country: Greece

institute: Agricultural University of Athens

description: Library name: L1

data_processing:
Raw sequencing data were filtered using SOAPnuke software (version 1.5.6)
The clean reads were mapped onto the Arabidopsis reference genome (TAIR10) by means of HISAT2 software (version 2.2.1)
Clean reads were aligned to the reference gene set using Bowtie2 (version 2.4.5)
Gene expression level was calculated with RSEM (version 1.3.1)
DEGs were identified with DESeq2 (version 1.34.0)
Alternative splicing and differential alternative splicing were detected by using rMAT (version 3.2.5)
Assembly: Arabidopsis_thaliana_3702.arabidopsis.TAIR10.v2201
Supplementary files format and content: .txt files include the FPKM values of the samples

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were germonated in MS medium in the dark for 5 days

extract_protocol:
Total RNA was extracted by using the phenol-sodium dodecyl sulfate (SDS) extraction method and treated with DNase
The cDNA libraries were constructed and sequenced in DNBSEQ platform (BGI, Hong Kong)

treatment_protocol: The dark-grown seedlings were transfered to light and sampling was performed at 10min, 60min, 3h, 24h and 72h

value: seedlings

value: light 72 h


title: lefko1 24 h rep1

description: Library name: K1

value: light 24 h


title: lefko1 24 h rep3

description: Library name: K3


title: lefko1 3 h rep3

description: Library name: J3

value: light 3 h


title: lefko1 3 h rep1

description: Library name: J1


title: lefko1 72 h rep2

description: Library name: L2


title: lefko1 60 min rep3

description: Library name: I3

value: light 60 min


title: V. cholerae C6706 cells grown in Brain Heart Infusion, replicate 1

description: Library name: Control_1


title: lefko1 10 min rep3

description: Library name: H3

value: light 10 min


title: lefko1 10 min rep2

description: Library name: H2


title: lefko1 3 h rep2

description: Library name: J2


title: lefko1 0 min rep3

description: Library name: G3

value: dark


title: lefko1 60 min rep2

description: Library name: I2