title: HepG2_DNA_Replicate_3_R1

city: Boston

first: Gue-ho

last: Hwang

state: MA

address: 300 Longwood Ave

institute: Boston Children's hospital

description: Library name: 18_22KMWCLT3_CGGCTATG-TATAGCCT

data_processing:
To quantify the different 6000 CRE in our STARR-Seq library and define their mRNA and DNA ratios, we first created a Kallisto index using the 200bp sequences as the reference and setting the Kmer length parameter equal to 23. To count the sequences in each R1 and R2 fastq file, we used the Kallisto Quant command, which allowed for unstranded alignments to accommodate the CRE unstranded library.
After aligning each sample, we used the generated Kallisto BAM files to keep only alignments from reads containing the 3’homology arm (TAGAGCATGCACCGG or the reverse complement GGCCGAATTCGTCGA). Finally, we generate a final count matrix containing the mRNA and DNA counts for our three replicates for each cell type used to test the library activity potential (GM12878, K562, HepG2).  considered to the final mRNA/DNA ratio calculation only sequences with non-zero DNA count across all the cell types and replicates.
The STARR-Seq activity was analyzed using the “mpra” package (v1.14.0) in R (v4.1.2). This methodology utilizes the “voom” framework60 for precision weighting and the well-established “limma” methodology for differential expression analysis. Barcode counts for each synthetic sequences were aggregated by summation, normalization was set to “TRUE”, and the model_type parameter was set to “indep_groups”. Activity is reported as log2 fold change (log2FC, RNA compared to DNA). Error bar ranges were calculated as log2FC ± 2 * log2FC / t-statistic
Assembly: Kallisto reference was create using sequences from DHS regions extracted using the HG38 genome and DNA-Diffusion sequences created using this training sequences set
Supplementary files format and content: Excel file with different tabs. The first  has the  raw counts for each sample,replicate, type (RNA or DNA) for each of the 6000 tested sequences. Second tab the sequence metadata and the third tab the Vromm analysis with LFC and SE for each tested  sequence after filtering the ones present ( > 0 counts) in all the replicates.

source_name: Liver

extract_protocol:
Electroporated cells, collected post 6 hours were subjected to RNA and DNA isolation using TRIzol reagent (Cat#15596026). Isolated RNA was then DNase treated using TURBO DNA-free™ Kit (Cat# AM1907). cDNA was further prepared using SuperScript™ IV Reverse Transcriptase (Cat# 18090010).
STARR-Seq (Other) Pair-ended. Region of interest was amplified from the isolated DNA using the forward primer TTGCCTTTCTCTCCACAGGT and reverse primer GATGAGTTTGGACAAACCACAAC. While region of interest from the reverse transcribed RNA was amplified using the forward primer TAGAGCATGCACCGG and reverse primer GATGAGTTTGGACAAACCACAAC. Amplified fragments were then gel purified before preparing the sequencing library using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®(Cat# 7645S). Libraries thus prepared post-quality control were multiplexed and sequenced.

treatment_protocol: The plasmid library with an appropriate complexity was then electroporated using a Neon™ NxT Electroporation System, into cell lines of interest (K562, HepG2 and Gm12878) grown and maintained at 70% confluency. The number of cells (8X107 cells per replicate) and the amount of plasmids (20 ug plasmid per 1X 107 cells) were estimated according to Neumayr et al (2).

value: Liver


title: lung, ECV30W, 3 months, SAMPLE 25

status: Public on Oct 07 2025

type: RNA

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

hyb_protocol: Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarrays were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Mus musculus

source_name: lung

label_protocol: manufacturer's instructions

extract_protocol: Total RNA extracted using manufacturer's instructions

tag: tissue

value: lung

tag: time

value: 3 months

tag: treatment


title: lung, Control, 3 months, SAMPLE 22

value: Control


title: H3K9me3_500_1

type: SRA

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

country: USA

institute: Mayo Clinic

library_source: genomic

data_processing:
Fastq files of pair-end reads were mapped with Bowtie 1.1.2  using parameters -k 1 -m 1 -e 70 -l 51 --best to the human reference genome hg19.
HOMER 4.8.2 was used to identify peaks for each sample against the background using default parameters.
Occupancy profiles were generated by HOMER in bedGraph format and converted to bigWig format using bedGraphToBigWig provided by UCSC.
Genome_build: hg19
Supplementary_files_format_and_content: peak calls in bed format;  bigwig files for occupancy profile.

molecule: genomic DNA

organism: Homo sapiens

source_name: OCI-Ly1 Cells

growth_protocol: OCI-Ly1 cells were cultured in IMDM+10%FBS with Penn-strep

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature before termination with 0.125 M glycine. Cells were then lysed in ChIP buffer (0.6% SDS, 10 mM EDTA, and 50 mM Tris-HCl, pH 8.1) and cross-linked chromatin was sonicated to obtain DNA fragments of 300–800 bp. Chromatin was then centrifuged (10 min, 4°C, 13,000 rpm) and the supernatant was diluted 6-fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8, and 167 mM NaCl) with protease inhibitors (Roche Diagnostics). Diluted chromatin was incubated with 5 μg of primary antibody overnight at 4C under agitation. Antibodies were pelleted using 50 μL of dynabeads (ThermoFisher Scientific). Beads were sequentially washed once with the ChIP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 150 mM NaCl), the ChIP wash buffer 2 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 500 mM NaCl), the ChIP wash buffer 3 (0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid, 1 mM EDTA, 10 mM Tris pH 8), and finally the ChIP wash buffer 4 (10 mM Tris-HCl, 1 mM EDTA). Chromatin was eluted using ChIP Elution Buffer (1% SDS, 100mM NaHCO3). The cross-link between protein and DNA was reversed by heat incubation (65°C, overnight), and proteins were then digested with proteinase K. DNA was recovered by phenol-chloroform extraction and ethanol precipitation in presence of 20 µg of glycogen (Sigma Aldrich).
ChIP-seq libraries were prepared using NEBNext DNA library preparation reagents (E6040); the protocol and reagents concentrations described in the Illumina Multiplex ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. Libraries were quantified by Qubit (Invitrogen), and sequenced using a HiSeq 2000 (Illumina) to generate 50 bp single end reads.

treatment_protocol: Indicated concentration of JIB-04 were added to the cells for 48 hours and cells were processed for chip-seq

tag: cell type

value: DLBCL cell line

tag: cell line

tag: chip-antibody

value: Abcam, Ab8898


title: Input_150_2

value: none (input)


title: lung, ECV18W, 3 months, SAMPLE 24


title: NT2 cells, HYDIN2 knockdown, rep1

city: Pune

first: Yash

middle: Lahu

last: Kuber

state: Maharashtra

address: Nccs, inside pune university, ganeshkhind

department: Biotechnology

country: India

institute: National center for cell science

description: Library name: Sample 2

library_source: transcriptomic

data_processing:
The raw reads were filtered using Trimmomatic for quality scores and adapters. Filtered reads were aligned to the Human genome (hg38) using STAR aligner to quantify reads mapped to each transcript. Total number of uniquely mapped reads were counted using feature counts. The uniquely mapped reads were then subjected to differential gene expression using DeSeq2.
Assembly: GRCh38
Supplementary files format and content: Delimited text file with read counts of all samples.

growth_protocol: NT2 cells were grown in Dulbecco's Modified Essential medium supplemented with 10% FBS, maintained in humidified incubator at 37C with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy Mini Kit (cat #74104).
A modified NEBNext RNA ultra II directional protocol is used to prepare the libraries for total RNA sequencing.

value: human embryonal carcinoma

tag: genotype

value: HYDIN2 knockdown


title: H3K9me3_500_2


title: lung, ECV18W, 3 months, SAMPLE 23


title: H3K9me3_150_1


title: HepG2_DNA_Replicate_2_R1

description: Library name: 17_22KMWCLT3_TAATGCGC-GTACTGAC

library_source: other

molecule: other


title: HepG2_DNA_Replicate_1_R1

description: Library name: 16_22KMWCLT3_CTGAAGCT-CAGGACGT


title: GM12878_DNA_Replicate_3_R1

description: Library name: 15_22KMWCLT3_GAATTCGT-TAATCTTA

source_name: Lymphoblastoid

value: Lymphoblastoid


title: H3K9me2_500_2

value: Abcam ab1220


title: H3K9me2_150_2


title: GM12878_DNA_Replicate_2_R1

description: Library name: 14_22KMWCLT3_ATTCAGAA-AGGCGAAG


title: H3K9me2_150_1


title: GM12878_DNA_Replicate_1_R1

description: Library name: 13_22KMWCLT3_GAGATTCC-GGCTCTGA


title: lung, CS, 3 months, SAMPLE 20

value: CS


title: H3K9me2_500_1


title: K562_DNA_Replicate_3_R1

description: Library name: 12_22KMWCLT3_CGCTCATT-CCTATCCT

source_name: lymphoblast cells

value: lymphoblast cells


title: lung, ECV18W, 3 months, SAMPLE 17


title: lung, ECV30W, 3 months, SAMPLE 21


title: lung, CS, 3 months, SAMPLE 18


title: H3K9me3_150_2


title: K562_DNA_Replicate_1_R1

description: Library name: 10_18_22KMWCLT3_ATTACTCG-TATAGCCT


title: DMSO_H3K9me2_1

value: DMSO


title: lung, ECV30W, 6 Months, SAMPLE 15

value: 6 Months


title: 70SG: 19 months, synaptosomes

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

description:
70SG
20180323_356_CC_counts_RPMs_RPKMs.xls

data_processing:
Sequence information was converted to FASTQ format using bcl2FastQ v2.19.
Per sample, the reads were mapped to the Mus musculus genome GRCm38 and respective annotation Release 85 [PMID: 29155950] using tophat2 v2.1 [PMID: 23618408] (parameters: --no-coverage-search --no-convert-bam --no-novel-juncs --no-novel-indels -T).
Read counts were introduced into the statistical environment R in order to calculate RPMs (reads per million mappable reads) and RPKMs (reads per kilobase and million mappable reads). For calculation of RPKMs lengths of transcripts were taken from featureCounts output.
Assembly: GRCm38.85
Supplementary files format and content: xls file contains a three tabs for each read counts, RPMs and RPKMs per Gene and sample

source_name: brain - cortex

growth_protocol: Tissue from wild-type C57BL/6 mice was obtained from the Leibniz Institute on Aging, Fritz Lipmann Institute Jena and from Janvier facility. Mice were housed in standard cages and fed standard lab chow and water ad libitum. Euthanasia was carried out by cervical dislocation in accordance with the European Council Directive of 22 September 2010 (2010/63/EU). The scientific purposes of the experiments were approved by the local authorities and supervised by the local veterinary (Anzeige N. O_AC_04, O_AC_08, O_AC_10 and O_AC_23-27).

extract_protocol:
Synaptosome samples were processed for RNA extraction according to (Smalheiser et al., 2014), and RNA was then extracted from the appositely prepared synaptosome samples and from TH samples through acidic phenol-chloroform extraction according to (Chomczynski, 1993). The synaptosomes were diluted in synaptosomal RNA buffer (50 mM Hepes, pH 7.5, 125 mM NaCl, 100 mM sucrose, 2 mM K acetate, 10 mM EDTA) containing protease inhibitors (1 tablet/10 mL, Roche, Cat. N. 11836170001), 160 U/mL Superase-In (Invitrogen, Cat.N. AM2694), 160 U/mL Rnase-OUT (Invitrogen, Cat. N. 10777019), quickly pelleted at 20.000 g for 20 min and rinsed twice in 4 × volume of synaptosomal RNA buffer and spundown again 20.000 g for 20 minutes. They were then resuspended in 100 μL of synaptosomal RNA buffer and RNA was extracted with standard Trizol protocol (Chomczynski & Sacchi, 1987) using Qiazol lysis reagent (Qiagen Cat. N. 79306).
Libraries were prepared from 10 ng of input material (total RNA) using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara, Cat. N. 635006) following the manufacturer's instructions.

treatment_protocol: Synaptosomes were extracted from cerebral cortices of 3 weeks-, 5 months- and 18/19 months-old mice as previously described (Gray & Whittaker, 1962; Moczulska et al., 2014). Briefly, the cortex was dissected and transferred to ice-cold synaptosomal buffer (10 mM HEPES, 1 mM EDTA, 2 mM EGTA, 0.5 mM DTT, 0.32 M sucrose, pH 7) containing protein inhibitors (1 tablet/10 mL, Roche). Samples were homogenized using a pestle (Sigma-Aldrich) with 12 strokes on ice. The homogenate was then centrifuged for 10min at 1.000g at 4°C and the supernatant was centrifuged again for 40min at 10.000g at 4°C. The obtained pellet, that contains the synaptosomes, was then resuspended in ice-cold synaptosomal buffer and layered over a discontinuous sucrose gradient (0.8M/1M/1.18M sucrose). The samples were then centrifuged for 2h at 50.512g at 4°C (Beckman Coulter Optima XPN-80 ultracentrifuge). The interface between 1M and 1.18M was withdrawn (synaptosome sample) and stored at -80°C.

value: brain - cortex

tag: strain

tag: age

value: 19 months

tag: fraction

value: synaptosomes

tag: Sex

value: male


title: K562_DNA_Replicate_2_R1

description: Library name: 11_22KMWCLT3_TCCGGAGA-ATAGAGGC


title: 69SG: 19 months, synaptosomes

description:
69SG
20180323_356_CC_counts_RPMs_RPKMs.xls


title: lung, Control, 3 months, SAMPLE 16

value: lung

value: 3 months


title: DMSO_H3K9me2_2

value: DLBCL cell line


title: HepG2_RNA_Replicate_3_R1

description: Library name: 9_22KMWCLT3_AGCGATAG-TATAGCCT

value: Liver


title: HepG2_RNA_Replicate_2_R1

description: Library name: 8_22KMWCLT3_TCTCGCGC-GTACTGAC


title: 68SG: 19 months, synaptosomes

description:
68SG
20180323_356_CC_counts_RPMs_RPKMs.xls


title: lung, ECV18W, 6 Months, SAMPLE 14


title: lung, Control, 6 Months, SAMPLE 13

value: Control


title: HepG2_RNA_Replicate_1_R1

description: Library name: 7_22KMWCLT3_TCCGCGAA-CAGGACGT


title: lung, ECV30W, 3 months, SAMPLE 19


title: GM12878_RNA_Replicate_3_R1

description: Library name: 6_22KMWCLT3_AGCGATAG-TAATCTTA


title: lung, Control, 6 Months, SAMPLE 12


title: 67SG: 19 months, synaptosomes

description:
67SG
20180323_356_CC_counts_RPMs_RPKMs.xls


title: 70TH: 19 months, total homogenate

description:
70TH
20180323_356_CC_counts_RPMs_RPKMs.xls

value: total homogenate


title: GM12878_RNA_Replicate_1_R1

description: Library name: 4_22KMWCLT3_TCCGCGAA-GGCTCTGA


title: lung, ECV18W, 6 Months, SAMPLE 10


title: lung, CS, 6 Months, SAMPLE 11


title: lung, ECV18W, 6 Months, SAMPLE 8


title: 69TH: 19 months, total homogenate

description:
69TH
20180323_356_CC_counts_RPMs_RPKMs.xls


title: 68TH: 19 months, total homogenate

description:
68TH
20180323_356_CC_counts_RPMs_RPKMs.xls


title: GM12878_RNA_Replicate_2_R1

description: Library name: 5_22KMWCLT3_TCTCGCGC-AGGCGAAG


title: K562_RNA_Replicate_3_R1

description: Library name: 3_22KMWCLT3_AGCGATAG-CCTATCCT


title: lung, CS, 6 Months, SAMPLE 7


title: K562_RNA_Replicate_2_R1

description: Library name: 2_22KMWCLT3_TCTCGCGC-ATAGAGGC


title: lung, ECV30W, 6 Months, SAMPLE 6


title: K562_RNA_Replicate_1_R1

description: Library name: 1_22KMWCLT3_TCCGCGAA-TATAGCCT


title: 49SG: 18 months, synaptosomes

description:
49SG
20170531_259_CC_counts_RPMs_RPKMs.xls

value: 18 months


title: lung, Control, 6 Months, SAMPLE 5


title: 47SG: 18 months, synaptosomes

description:
47SG
20170531_259_CC_counts_RPMs_RPKMs.xls


title: Bulk_RNA_KPTN_tumor2

city: San Antonio

first: Pei

last: Wang

state: TX

address: 7703 Floyd Curl Dr

institute: UT Health San Antonio

description: Library name: KPTN_tumor2

data_processing:
Raw sequencing data were aligned to reference genome GRCh38 using TopHat 2.1.1. Gene expression reads were quantified using HTSeq 0.11.1. For tumor tissue samples, in order to separate human and mice transcripts, the raw reads were aligned to a concatenated human (GRCh38) and mouse (GRCm38) genome. Reads for which multiple alignments shared the top score were discarded to remove those aligned to both the human and mouse genome
Assembly: GRCh38 and GRCm38
Supplementary files format and content: tab-delimited files containing raw read counts for each samples

source_name: pancreas

growth_protocol: Engineered human primary pancreatic acinar cells were cultred as 3D organoid in serum free advanced DMEM/F-12 media supplemented with Wnt3a conditioned medium (50%), recombinant human R-Spondin 1 (500 ng/ml), Noggin (200 ng/ml), FGF10 (100 ng/ml), EGF (50 ng/ml), PGE II (1 nM), A83-01 (0.5 µM), Nicotinamide (10 mM), Penicillin/Streptomycin (1 mM), HEPES (10 mM), GlutaMax (1X).

extract_protocol:
Cell pellets of cultured organoids were collected and stored in Trizol for total RNA extraction using Zymo Direct-zol RNA Miniprep Kit (Zymo Research, Irvine, CA, R2063) following manufacturer’s instructions. Tumor tissues were flash frozen in liquid nitrogen and ground into fine powder with the addition of Trizol, followed by RNA extraction using Zymo Direct-zol RNA Miniprep Kit.
Indexed cDNA libraries were prepared using the Illumina® Stranded mRNA Prep Ligation kit (Illumina, San Diego, CA, 20040532) following manufacturer’s instructions.

value: pancreas

value: primary acinar

value: KPTN

value: xenograft tansplantation


title: Bulk_RNA_KPTN_tumor3

description: Library name: KPTN_tumor3


title: stp2Δ/zcf25Δ HQN II

first: Enrico

last: Garbe

address: Albert-Einstein-Straße 10

department: (Epi-)Genetics of Fungal Infections

institute: HKI Jena

description: Sample 47

data_processing:
Fastq files were assessed for sequence quality using FastQC (version 0.11.9) and a genome index from file C_albicans_SC5314_A22_current_chromosomes.fasta fom http://www.candidagenome.org/ was created with bowtie2 (version 2.4.2). Mapping of reads to the index was performed with bowtie2. Reads were counted and assigned to the corresponding genome using function featureCounts of R package Rsubread (version 2.2.6). Contrasts were calculated using R package DESeq2 (version 1.28.1). R version 4.0.4 was used.
Assembly: C_albicans_SC5314_A22_current_chromosomes.fasta
Supplementary files format and content: Raw.Counts.ZCF.csv, Comma separated text file containing counts of all samples

organism: Candida albicans

source_name: liquid culture

growth_protocol: C. albicans were generally maintained on YPD agar plates and ON cultures prepared in liquid SD minimal medium (30°C) for experimental use on the subsequent day.

extract_protocol:
Total RNA was isolated from C. albicans cells using phenol-chlororform extraction as previously reported (https://doi.org/10.1128/mbio.03142-21): "For total RNA isolation, cells were resuspended in 440 μL acetate EDTA buffer (50 mM sodium acetate, 10 mM EDTA) with 10% SDS, and 440 μL of acid-phenol-chloroform with isoamyl alcohol (Ambion, Germany) was added. The suspension was thoroughly mixed, incubated for 5 min at 65°C, frozen at −20°C for 30 min, and subsequently thawed at 65°C for 5 min. The phases were separated via 4 min of centrifugation at 16,000 × g, the upper aqueous phase was transferred, and a 1/10 volume of sodium acetate (pH 5.3) and 1 volume of 2-propanol were added to precipitate the RNA for at least 30 min at −20°C. The supernatant was discarded after 10 min of centrifugation at 12,000 × g, and the RNA pellet was washed twice with 80% ethanol and finally solved in 300 μL nuclease-free H2O. The quality and quantity of the RNA were assessed using 2100 bioanalyzer (Agilent Technologies, CA, USA) and Nanodrop (Thermo Fisher Scientific, MA, USA) measurements."
Sequencing libraries were prepared as previously reported (https://doi.org/10.1128/msystems.00539-22): "A total amount of 0.4 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs [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) oligonucleotide-attached magnetic beads. Fragmentation was carried out by Covaris sonication. First-strand cDNA was synthesized using random hexamer primers and Moloney murine leukemia virus (M-MuLV) reverse transcriptase (RNase H−). Subsequently, second-strand cDNA synthesis was performed using dTTP. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. Afterward, the 3′ ends of DNA fragments were adenylated. Next, an NEBNext adaptor with hairpin loop structure was ligated for hybridization. To select cDNA fragments of preferentially 250 to 300 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, MA, USA). Then, 3 μL User enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then, PCR was performed with Phusion high-fidelity DNA polymerase, universal PCR primers, and index (X) primer. At last, PCR products were purified (AMPure XP system), and library quality and quantity were assessed by Qubit and real-time PCR. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using a cBot-HS PE cluster kit (Illumina) according to the manufacturer’s instructions."

treatment_protocol: Cells from ON-cultures were harvested and transferred to fresh SD medium (Starting OD 0.3) and incubated (30°C) until early log-phase (OD 1) was reached. Cells were then harvested, washed and transferred to indicated test medium (OD 0.3) and incubated for 4 h at 30°C. cells were then collected and snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: liquid culture

value: yeast cell

tag: c-source

value: Hydroquinone


title: stp2Δ/zcf25Δ HQN III

description: Sample 48


title: Bulk_RNA_KPT_tumor3

description: Library name: KPT_tumor3

value: KPT


title: 76SG: 5 months, synaptosomes

description:
76SG
20170531_259_CC_counts_RPMs_RPKMs.xls

value: brain - cortex

value: 5 months

value: synaptosomes


title: stp2Δ/zcf25Δ HQN I

description: Sample 46


title: 67TH: 19 months, total homogenate

description:
67TH
20180323_356_CC_counts_RPMs_RPKMs.xls

value: 19 months

value: male


title: zcf25Δ HQN III

description: Sample 45


title: Bulk_RNA_KPT_tumor1

description: Library name: KPT_tumor1


title: 74SG: 5 months, synaptosomes

description:
74SG
20170531_259_CC_counts_RPMs_RPKMs.xls


title: 75SG: 5 months, synaptosomes

description:
75SG
20170531_259_CC_counts_RPMs_RPKMs.xls


title: lung, Control, 6 Months, SAMPLE 3

value: lung

value: 6 Months


title: lung, CS, 6 Months, SAMPLE 2

value: CS


title: lung, ECV18W, 6 Months, SAMPLE 1


title: lung, ECV30W, 6 Months, SAMPLE 4


title: zcf25Δ HQN II

description: Sample 44


title: zcf25Δ HQN I

description: Sample 43


title: RMC-4998-R LU65, Replicate 3

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
LU65 cells were chronically treated with RMC-4998 starting from their IC50s.
The treatment dose was doubled in every next passage for 4-6 passages and then maintained at constant dose of 200 nM of RMC-4998.

value: epithelial cells

value: KRAS G12C

value: Maintained in drug


title: 62SG: 3 weeks, synaptosomes

description:
62SG
20170531_259_CC_counts_RPMs_RPKMs.xls

value: 3 weeks


title: lung, ECV30W, 6 Months, SAMPLE 9


title: 72SG: 5 months, synaptosomes

description:
72SG
20170531_259_CC_counts_RPMs_RPKMs.xls


title: 48SG: 18 months, synaptosomes

description:
48SG
20170531_259_CC_counts_RPMs_RPKMs.xls

value: 18 months


title: 46SG: 18 months, synaptosomes

description:
46SG
20170531_259_CC_counts_RPMs_RPKMs.xls


title: RMC-4998-R LU65, Replicate 1


title: stp2Δ HQN II

description: Sample 41

value: liquid culture


title: RMC-4998-R LU65, Replicate 2


title: Bulk_RNA_KPTN_tumor1

description: Library name: KPTN_tumor1

value: pancreas

value: primary acinar

value: KPTN

value: xenograft tansplantation


title: Bulk_RNA_KPT_tumor2

description: Library name: KPT_tumor2

value: KPT


title: LU65-P, replicate 3

value: No treatment


title: 61SG: 3 weeks, synaptosomes

description:
61SG
20170531_259_CC_counts_RPMs_RPKMs.xls

value: brain - cortex

value: synaptosomes


title: 60SG: 3 weeks, synaptosomes

description:
60SG
20170531_259_CC_counts_RPMs_RPKMs.xls

value: male


title: LU65-P, replicate 2


title: stp2Δ HQN I

description: Sample 40

value: yeast cell

value: Hydroquinone


title: 59SG: 3 weeks, synaptosomes

description:
59SG
20170531_259_CC_counts_RPMs_RPKMs.xls


title: WT HQN III

description: Sample 39

value: wild type


title: LU65-P, replicate 1

value: epithelial cells

value: KRAS G12C


title: 49TH: 18 months, total homogenate

description:
49TH
20170911_285_CC_counts_RPMs_RPKMs.xls

value: total homogenate


title: WT HQN I

description: Sample 37


title: WT HQN II

description: Sample 38


title: WM793, siRNA control, replicate 3

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

data_processing:
Illumina basecalling.
Standard Illumina bioinformatics analysis were used to generate fastq files, followed by quality assessment [MultiQC].
Rsubread was used for mapping to the hg38 genome and creating a matrix of RNA-Seq counts
edgeR was used for all downstream preprocessing steps
Assembly: hg38
Supplementary files format and content: rpkm on edgeR normalized data with all samples

growth_protocol: WM793 melanoma cell line was cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Eurobio, CVFSVF00-01), 2 mM glutamine (Thermo Fisher Scientific, 25030-024), non-essential amino acids (Thermo Fisher Scientific, 11140-035), 1 mM sodium pyruvate (Thermo Fisher Scientific, 11360-039), and penicillin/streptomycin (Thermo Fisher Scientific, 15140-122). Cells were cultured in a humidified atmosphere at 37°C and routinely checked for mycoplasma contamination.

extract_protocol:
Total RNA extraction was carried out using the Nucleospin RNA extraction kit (Macherey Nagel, 740955) according to the manufacturer’s protocol.For RNA sequencing (RNAseq) analysis, libraries were constructed using 600 ng of total RNA per sample with the TruSeq Stranded mRNA kit (Illumina), following the manufacturer’s guidelines. The process involved capturing PolyA mRNA using oligo-dT beads, synthesizing double-stranded cDNA, ligating adapters, amplifying libraries, and sequencing. Sequencing was performed using the NextSeq500 Illumina sequencer with 75 bp paired-end reads.
Standard Illumina protocol, paired-end sequencing
Sequencing was performed using a NovaSeq Illumina device (Illumina).

treatment_protocol: Cells were seeded in 6-well plate wells 24 hours prior to transfection. Subsequently, cells were transfected with 25nM (or 50nM as specified) siRNAs targeting CASP3 (Qiagen, 1027417, SI02654603; Horizon Discovery, L-004307-00-0005; Sigma-Aldrich, SASI_Hs01_00139105). The negative control used was a non-targeting siRNA (Sigma-Aldrich, SIC001-10NMOL). Cells were transfected for 48 hours prior to analysis.

value: melanoma

value: Control


title: 47TH: 18 months, total homogenate

description:
47TH
20170911_285_CC_counts_RPMs_RPKMs.xls

value: 18 months


title: stp2Δ HQN III

description: Sample 42

value: liquid culture


title: 48TH: 18 months, total homogenate

description:
48TH
20170911_285_CC_counts_RPMs_RPKMs.xls


title: stp2Δ/zcf25Δ CAT III

description: Sample 36

value: Catechol


title: stp2Δ/zcf25Δ CAT II

description: Sample 35


title: stp2Δ/zcf25Δ CAT I

description: Sample 34


title: 76TH: 5 months, total homogenate

description:
76TH
20170911_285_CC_counts_RPMs_RPKMs.xls

value: 5 months


title: WM793, siRNA Caspase 3, replicate 2

value: Caspase 3 knock-down


title: zcf25Δ CAT III

description: Sample 33


title: zcf25Δ CAT II

description: Sample 32


title: 75TH: 5 months, total homogenate

description:
75TH
20170911_285_CC_counts_RPMs_RPKMs.xls


title: 46TH: 18 months, total homogenate

description:
46TH
20170911_285_CC_counts_RPMs_RPKMs.xls


title: 5_440796-T WES

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: No. 3, Qingchun East Rd

department: Sir Run Run Shaw Hospital

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the hg38 reference genome using BWA (v2.2.1) with the default parameter settings.
GATK MuTect2 pipeline was used to identify the somatic mutations
Maftools was exploited for annotation of somatic mutations
Assembly: GRCh38(hg38, v34)
Supplementary files format and content: The Variant Call Format (VCF) for each pair of samples (BRCA and normal samples) generated by MuTect2 software was used to record the somatic mutations

source_name: BRCA sample ID:440796, belong to HER-2 subtype

extract_protocol:
Genomic DNA was prepared fosr exome sequencing using the Agilent SureSelect Human All Exon V6 kit with the following steps: Initially, 0.4 μg of high-quality genomic DNA was randomly sheared to a mean size of 180-280 base pairs using a Covaris S220 sonicator. Any remaining DNA overhangs were made blunt by exonuclease and polymerase treatment.
Subsequently, the DNA fragments underwent end repair and phosphorylation, followed by the addition of a single 'A' base (A-tailing) and ligation with paired-end adaptors at the 3' ends. Fragments with adaptors on both ends were amplified via PCR. Post-PCR, the library was hybridized with biotinylated probes in solution and then captured using streptavidin-coated magnetic beads to selectively enrich for gene exons. The captured libraries were subjected to an additional PCR to incorporate index tags, preparing them for sequencing. The PCR products were purified with the AMPure XP system, and DNA concentration was determined using a Qubit®3.0 Flurometer. The library size distribution was assessed with NGS3K/Caliper, and the library was quantified by real-time PCR to a final concentration of 3 nM. Ultimately, the DNA library was sequenced on an Illumina platform to achieve paired-end 150 base pair reads.


title: zcf25Δ CAT I

description: Sample 31


title: 72TH: 5 months, total homogenate

description:
72TH
20170911_285_CC_counts_RPMs_RPKMs.xls


title: stp2Δ CAT III

description: Sample 30


title: 5_440796-N WES

source_name: Paracancerous sample of BRCA sample ID:440796


title: 74TH: 5 months, total homogenate

description:
74TH
20170911_285_CC_counts_RPMs_RPKMs.xls


title: 3_440634-N WES

source_name: Paracancerous sample of BRCA sample ID:440634


title: WM793, siRNA control, replicate 1


title: 60TH: 3 weeks, total homogenate

description:
60TH
20170911_285_CC_counts_RPMs_RPKMs.xls

value: 3 weeks


title: 4_440601-T WES

source_name: BRCA sample ID:440601, belong to TNBC subtype


title: stp2Δ CAT I

description: Sample 28


title: stp2Δ CAT II

description: Sample 29


title: 59TH: 3 weeks, total homogenate

description:
59TH
20170911_285_CC_counts_RPMs_RPKMs.xls

value: brain - cortex


title: WM793, siRNA control, replicate 2


title: Bulk_RNA_KPTN_organoid6

description: Library name: KPTN_organoid6

value: pancreas

value: primary acinar

value: KPTN

value: 3D organoid culture


title: WT CAT III

description: Sample 27

value: yeast cell

value: wild type


title: 4_440601-N WES

source_name: Paracancerous sample of BRCA sample ID:440601


title: WM793, siRNA Caspase 3, replicate 1


title: 2120RL

city: Madison

first: Hugo

last: Lee

state: WI

address: 440 Henry Mall

institute: University of Wisconsin-Madison

library_source: transcriptomic single cell

data_processing:
Cell Ranger mkfastq v6.1.2
Cell Ranger count v6.1.2
Cell Ranger aggr v6.1.2
Assembly: mm10
Supplementary files format and content: Gene expression matrix, barcodes, features

source_name: pancreatic islets

growth_protocol: Housed under a 12:12-hr light/dark cycle, with unrestricted access to food and drinking water in an animal housing facility accredited by the Association for Assessment and Accreditation of Laboratory Animal Care.

extract_protocol:
Islets were isolated using the standard collagenase/protease digestion method. The pancreatic duct was cannulated and distended with 4°C collagenase/protease solution. Islets were separated from the exocrine tissue using Histopaque-1077. Hand-picked islets were cultured overnight at 37°C in RPMI-1640 media containing 10% FBS and 1% Penicillin/Streptomycin. Cells were dissociated using accutase digestion.
RNA libraries were prepared for sequencing using standard 10X Genomics protocols

treatment_protocol: To induce Cre recombinase activity, tamoxifen was dissolved in sterilized corn oil  by shaking overnight at 37°C. The solution was protected from light, and10 mg/ml tamoxifen was administrated via intraperitoneal injection twice every 24 hours in five consecutive days.

value: pancreatic islets

value: dispersed islet cells

value: tamoxifen injection to induce deletion


title: Bulk_RNA_KPTN_organoid5

description: Library name: KPTN_organoid5


title: WT CAT I

description: Sample 25


title: 62TH: 3 weeks, total homogenate

description:
62TH
20170911_285_CC_counts_RPMs_RPKMs.xls

value: total homogenate

value: male


title: WT CAT II

description: Sample 26

value: liquid culture


title: 12_431003-N WES

source_name: Paracancerous sample of BRCA sample ID:431003


title: 61TH: 3 weeks, total homogenate

description:
61TH
20170911_285_CC_counts_RPMs_RPKMs.xls


title: 12_431003-T WES

source_name: BRCA sample ID:431003, belong to TNBC subtype


title: 11_430299-T WES

source_name: BRCA sample ID:430299, belong to TNBC subtype


title: stp2Δ/zcf25Δ SC III

description: Sample 24

value: Proteinogenic amino acids


title: Bulk_RNA_KPTN_organoid2

description: Library name: KPTN_organoid2


title: Bulk_RNA_KPTN_organoid4

description: Library name: KPTN_organoid4


title: 2118R


title: 2119L


title: 3_440634-T WES

source_name: BRCA sample ID:440634, belong to HER-2 subtype


title: 2117N


title: Bulk_RNA_KPTN_organoid1

description: Library name: KPTN_organoid1


title: stp2Δ/zcf25Δ SC I

description: Sample 22


title: 10_430223-T WES

source_name: BRCA sample ID:430223, belong to TNBC subtype


title: stp2Δ/zcf25Δ SC II

description: Sample 23


title: zcf25Δ SC III

description: Sample 21


title: RPE1 cells, 48 hour DMSO, replicate B

city: Toronto

first: Daniel

last: Durocher

state: ON

address: 600 University

country: Canada

institute: Lunenfeld Tanenbaum Research Institute

description:
Library name: Untreated Replicate B
Replicate B

data_processing:
mRNA-seq reads were aligned with Salmon
Differential gene expression changes were calculated with DESeq2
Gene set enrichment analyses were first performed with clusterProfiler, Reactome pathway analysis (ReactomePA) and enrichplot Bioconductor packages in RStudio or using the Enrichr webtool
To perform DNA motif analysis on AZD1775-regulated genes, the iRegulon package (1.3) was used in Cytoscape 3
Assembly: human genome assembly GRCh38.p13 cDNA
Supplementary files format and content: tab-delimited text file with raw counts and TPM for each Sample

molecule: polyA RNA

source_name: Eye; Pigmented epithelium;Retina

extract_protocol:
Total RNA was prepared using DirectZol RNA MiniPrep kits (Zymo Research)
cDNA libraries were constructed using Truseq Stranded Total RNA library kits with Ribo-Zero Gold rRNA depletion (Illumina)

value: Eye; Pigmented epithelium;Retina

value: TP53-knockout; PAC-knockout


title: RPE1 cells, 48 hour DMSO, replicate A

description:
Library name: Untreated Replicate A
Replicate A


title: 11_430299-N WES

source_name: Paracancerous sample of BRCA sample ID:430299


title: 6_429752-T WES

source_name: BRCA sample ID:429752, belong to Luminal A subtype


title: zcf25Δ SC I

description: Sample 19


title: zcf25Δ SC II

description: Sample 20


title: 10_430223-N WES

source_name: Paracancerous sample of BRCA sample ID:430223


title: Bulk_RNA_KPTN_organoid3

description: Library name: KPTN_organoid3

source_name: pancreas


title: Bulk_RNA_KPT_organoid5

description: Library name: KPT_organoid5

value: KPT


title: Bulk_RNA_KPT_organoid6

description: Library name: KPT_organoid6


title: Bulk_RNA_KPT_organoid4

description: Library name: KPT_organoid4


title: stp2Δ SC III

description: Sample 18

source_name: liquid culture


title: Bulk_RNA_KPT_organoid3

description: Library name: KPT_organoid3


title: 8_428258-N WES

source_name: Paracancerous sample of BRCA sample ID:428258


title: stp2Δ SC II

description: Sample 17


title: HCC-Normal

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: HCC-Normal

extract_protocol:
The tissues were cut into small pieces in prechilled phosphate-buffered saline (PBS) and digested with 200 U/ml collagenase type II (Worthington, 43J14367B) in a 37°C water bath with mild shaking. The single-cell suspension was filtered with a 40 μm cell strainer and collected by centrifugation at 400 × g for 5 min. The supernatant was discarded, and the cell pellets were resuspended in 1 ml of 10% FBS/DMEM
scRNA-Seq library preparation for 10x Genomics single-cell 5′ and suspensions were loaded on a Chromium Single-Cell Controller (10x Genomics) to generate a single-cell and gel bead emulsion (GEM).The scRΝΑ-seq libraries were prepared using a single-cell 5’ solution v2 reagent kit (Chromium, 1000006) according to the protocol provided with the 10x Genomics Chromium Single-Cell Immune Profiling Solution.Briefly, FACS-sorted Cd45+ immune cells (90-95% viability) were encapsulated into droplets. Following the RT step, the droplets were disrupted and the barcoded cDNAs were purified with DynaBeads and subjected to 14 cycles of PCR amplification (98°C for 45 s; [98°C for 20 s, 67°C for 30 s, and 72°C for 1 min] x 14 cycles; 72°C for 1 min). The resulting amplified cDNAs were sufficient to construct 5’ gene expression libraries and T/B cell receptor (TCR/BCR)-enriched libraries. The cDNAs from the single-cell transcriptomes (50 ng) were fragmented, subjected to two rounds of size selection with SPRI beads (average size 450 bp).

value: HCC-Normal


title: HCC-Lymph node1

description: 10x Genomics

source_name: HCC-Lymph node1

value: HCC-Lymph node1


title: 8_428258-T WES

source_name: BRCA sample ID:428258, belong to Luminal B subtype


title: RPE1 cells, 48 hour 250nM AZD1775, replicate B

description:
Library name: Treated Replicate B
Replicate B


title: 6_429752-N WES

source_name: Paracancerous sample of BRCA sample ID:429752


title: RPE1 cells, 48 hour 250nM AZD1775, replicate A

description:
Library name: Treated Replicate A
Replicate A


title: Bulk_RNA_KPT_organoid2

description: Library name: KPT_organoid2

value: pancreas

value: primary acinar


title: HCC-Lymph node2

description: 10x Genomics

source_name: HCC-Lymph node2

value: HCC-Lymph node2


title: stp2Δ SC I

description: Sample 16

value: yeast cell


title: 440796_T

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the hg38 reference genome using HISAT2 (v2.2.1) with the default parameter settings.
Gene expression was determined using stringtie (v2.0) with the default parameter settings.
Transcripts per Million (TPM) were calculated for representing the expression of each gene.
Assembly: GRCh38(hg38, v34)
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: BRCA sample ID:440796, belong to HER-2 subtype

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was extracted from the total RNA using magnetic beads that had poly-T oligos attached to them. The mRNA was then subjected to fragmentation facilitated by divalent cations at an increased temperature within a First Strand Synthesis Reaction Buffer (5X). For the synthesis of the first strand of cDNA, a random hexamer primer and M-MuLV Reverse Transcriptase devoid of RNase H activity were employed. The creation of the second strand of cDNA was followed up using DNA Polymerase I and RNase H. The residual overhangs on the DNA fragments were transformed into blunt ends with the help of exonuclease and polymerase enzymes.
Subsequently, the 3' ends of the DNA fragments were adenylated, and adapters with a hairpin loop were attached to prepare the fragments for hybridization. To isolate cDNA fragments that were predominantly 370 to 420 base pairs in length, the AMPure XP system was used to purify the library fragments. PCR amplification was then conducted using Phusion High-Fidelity DNA polymerase in conjunction with Universal PCR primers and an Index (X) Primer. Finally, the PCR products were subjected to purification using the AMPure XP system, and the library's quality was determined with the Agilent Bioanalyzer 2100 system.


title: WT SC III

description: Sample 15

value: wild type


title: 440796_N

source_name: Paracancerous sample of BRCA sample ID:440796


title: HCC-Portal aorta metastasis

description: 10x Genomics

source_name: HCC-Portal aorta metastasis

value: HCC-Portal aorta metastasis


title: Screen_culture4_tumor2

description: Library name: culture4_tumor2

data_processing:
Count summary and statistical analysis of sgRNA enrichment from raw fastq data was performed using MAGeCK software v0.5.9.5 .
Assembly: N.A.
Supplementary files format and content: tab-delimited files containing raw counts of all sgRNAs detected in the library for each sample
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA was extracted using Zymo Genomic DNA Clean & Concentrator-25 kit.
The collected gDNA containing sgRNA library sequences was subject to a two-step PCR protocol for library amplification and sample indexing.

treatment_protocol: A pooled CRISPR knockout library was introduced into KPT organoids using lentivirus transduction. The transduced cells were maintained as 3D organoid cultures or transplanted into immunodeficient mice (NOD/SCID/gamma).

value: xenograft tansplantation


title: HCC-Tumor

description: 10x Genomics

source_name: HCC-Tumor

value: HCC-Tumor


title: Screen_culture4_tumor1

description: Library name: culture4_tumor1


title: 440634_T

source_name: BRCA sample ID:440634, belong to HER-2 subtype


title: Screen_culture4_organoid

description: Library name: culture4_organoid

value: 3D organoid culture


title: 440634_N

source_name: Paracancerous sample of BRCA sample ID:440634


title: ICC-Lymph node

description: 10x Genomics

source_name: ICC-Lymph node

value: ICC-Lymph node


title: WT SC II

description: Sample 14

value: liquid culture


title: WT SC I

description: Sample 13

value: Proteinogenic amino acids


title: stp2Δ/zcf25Δ SD III

description: Sample 12

value: Glucose


title: Bulk_RNA_KPT_organoid1

description: Library name: KPT_organoid1


title: 440601_T

source_name: BRCA sample ID:440601, belong to TNBC subtype


title: ICC-Metastasis3

description: 10x Genomics


title: ICC-Normal

description: 10x Genomics

source_name: ICC-Normal

value: ICC-Normal


title: Screen_culture3_tumor2

description: Library name: culture3_tumor2

source_name: pancreas

value: KPT


title: Screen_culture4_ctrl

description: Library name: culture4_ctrl


title: zcf25Δ SD III

description: Sample 9

source_name: liquid culture


title: 440601_N

source_name: Paracancerous sample of BRCA sample ID:440601


title: stp2Δ/zcf25Δ SD I

description: Sample 10


title: Screen_culture3_tumor1

description: Library name: culture3_tumor1


title: ICC-Metastasis2

description: 10x Genomics


title: ICC-Metastasis1

description: 10x Genomics


title: ICC-Tumor

description: 10x Genomics

source_name: ICC-Tumor

value: ICC-Tumor


title: 431003_T

source_name: BRCA sample ID:431003, belong to TNBC subtype


title: stp2Δ/zcf25Δ SD II

description: Sample 11


title: WM793, siRNA Caspase 3, replicate 3

value: melanoma

value: Caspase 3 knock-down


title: Screen_culture3_organoid

description: Library name: culture3_organoid

value: pancreas

value: primary acinar


title: 431003_N

source_name: Paracancerous sample of BRCA sample ID:431003


title: Screen_culture2_tumor2

description: Library name: culture2_tumor2


title: Screen_culture3_ctrl

description: Library name: culture3_ctrl


title: zcf25Δ SD II

description: Sample 8

value: yeast cell


title: stp2Δ SD III

description: Sample 6


title: 430223_T

source_name: BRCA sample ID:430223, belong to TNBC subtype


title: zcf25Δ SD I

description: Sample 7


title: Screen_culture2_tumor1

description: Library name: culture2_tumor1


title: stp2Δ SD II

description: Sample 5


title: Screen_culture2_organoid

description: Library name: culture2_organoid


title: 430223_N

source_name: Paracancerous sample of BRCA sample ID:430223


title: Screen_culture2_ctrl

description: Library name: culture2_ctrl


title: stp2Δ SD I

description: Sample 4


title: WT SD III

description: Sample 3

value: wild type


title: Screen_culture1_tumor1

description: Library name: culture1_tumor1


title: 429752_N

source_name: Paracancerous sample of BRCA sample ID:429752


title: WT SD II

description: Sample 2


title: 428258_T

source_name: BRCA sample ID:428258, belong to Luminal B subtype


title: 2N5

city: Mitaka

first: Atsuyoshi

last: Shimada

state: Tokyo

address: 5-4-1 Shimorenjaku

department: Health Sciences

country: Japan

institute: Kyorin University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Ver.2.0 Microarray (Agilent, G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and 074809_D_F_20200916) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization was performed using Agilent GeneSpring GX 14.9, and baseline transformation was applied using the median of all samples.

source_name: LPS 24 h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Micro kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoVue spectrophotometer and was monitored by Hokkaido System Science with the Bioanalyzer (Agilent).

value: brain

tag: gender

value: male

value: 7 days


title: Screen_culture1_organoid

description: Library name: culture1_organoid

value: 3D organoid culture


title: Screen_culture1_ctrl

description: Library name: culture1_ctrl


title: 428258_N

source_name: Paracancerous sample of BRCA sample ID:428258


title: 430299_N

source_name: Paracancerous sample of BRCA sample ID:430299


title: ChIPseq_CD19_CAR_T_Control_JUNB_IP_1

status: Public on Oct 06 2025

city: Dallas

first: Chen

last: Yao

state: Texas

address: 5901 FOREST PARK RD, NS6 218

institute: UT Southwestern Medical Center

description:
Library name: Sample 15
Chipmentation

data_processing:
ScRNAseq: Fastq files of gene expression and Hashtag libraries were aligned to mm10 using cellranger count (Cell Ranger v6.0.0), which perform filtering, barcode counting, and UMI counting at the same time.
Multiome: Cell versus gene matrix of UMI counts for gene expression assay and cell versus fragment matrix for ATAC assay were generated from fastq files aligned to mm10 using cellranger-arc (v 2.0.0).
ChIP-Seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. ChIP-seq reads were mapped to the mouse genome (build mm10) with Bowtie 1.1.1. Peaks were identified using MACS (v 1.4.3; default p-value threshold of 1E-5) .
Assembly: mm10
Supplementary files format and content: ScRNA-Seq: matrix H5 files
Supplementary files format and content: SCATAC-Seq: tab-separated values files
Supplementary files format and content: ChIP-Seq: BigWig files (Narrow peaks expet for input files)

source_name: T cells from spleen

extract_protocol:
CAR T cells isolated from spleen were sorted for scRNA-Seq or multiome anallysis.
We used Chromium Next GEM Single Cell 5' Kit (10x Genomics) to generate scRNA-Seq libraries according to the manufacturer’s protocol. We used Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits (10x Genomics) to generate scRNA-Seq and scATAC-Seq libraries according to the manufacturer’s protocol. ChIP-Seq was performed according to the published chipmentation protocol (Schmidl, C., Rendeiro, A. F., Sheffield, N. C., & Bock, C. (2015).http://doi.org/10.1038/nmeth.3542).

value: T cells from spleen

value: in vitro

value: CAR T cells

value: WT

tag: batch


title: 2M5


title: 2K5

source_name: saline 24 h


title: ChIPseq_CD19_CAR_T_Control_JUNB_IP_2

description:
Library name: Sample 16
Chipmentation


title: ChIPseq_CD19_CAR_T_BACH2OE_JUNB_IP_1

description:
Library name: Sample 17
Chipmentation


title: ChIPseq_CD19_CAR_T_BACH2OE_BACH2_IP_2

description:
Library name: Sample 14
Chipmentation


title: ChIPseq_CD19_CAR_T_BACH2OE_IgG_IP_2

description:
Library name: Sample 12
Chipmentation


title: ChIPseq_CD19_CAR_T_BACH2OE_BACH2_IP_1

description:
Library name: Sample 13
Chipmentation


title: 429752_T

source_name: BRCA sample ID:429752, belong to Luminal A subtype


title: 2I5


title: Screen_culture1_tumor2

description: Library name: culture1_tumor2

value: xenograft tansplantation


title: 430299_T

source_name: BRCA sample ID:430299, belong to TNBC subtype


title: ChIPseq_CD19_CAR_T_BACH2OE_IgG_IP_1

description:
Library name: Sample 11
Chipmentation


title: 2G5


title: ChIPseq_CD19_CAR_T_Control_IgG_IP_1

description:
Library name: Sample 9
Chipmentation


title: ChIPseq_CD19_CAR_T_Control_IgG_IP_2

description:
Library name: Sample 10
Chipmentation


title: 2H5


title: CD8+ T Palmitate 3 (RNA-seq)

city: Milano

first: Teresa

last: Manzo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: IEO

data_processing:
Adaptors removed with TrimGalore v 0.6.10
Genome index created with Salmon v 1.10.0 with GRCm39 (release 109) with default parameters
Read calling with Salmon v 1.10.0 with default parameters
Processing with tximport
Assembly: GRCm39 (release 109)
Supplementary files format and content: Salmon quantification files, plain-text, tab-delimited for each sample
Supplementary files format and content: plain-text, tab-delimited matrix with read counts from DESeq (v 1.42.0) with tximport (v 1.30.0)

source_name: Immune T cells

growth_protocol: CD8+ T cells were extracted from mouse pancreas, spleen and lymph nodes

extract_protocol:
Total RNA was harvested using RNeasy Mini kits (Qiagen)
RNA Libraries were constructed using SMARTER mRNA-Seq kit according to manufacturer's instructions

treatment_protocol: Cells kept in complete T cell media and supplemented with Palmitate (100 μM)

value: CD8+ T Cell

value: Palmitate


title: CD8+ T Control 3 (RNA-seq)

value: Control


title: WT SD I

description: Sample 1

source_name: liquid culture

value: liquid culture

value: Glucose


title: CD8+ T Palmitate 1 (RNA-seq)


title: CD8+ T Control 2 (RNA-seq)


title: ChIPseq_CD19_CAR_T_BACH2OE_JUNB_IP_2

description:
Library name: Sample 18
Chipmentation


title: CD8+ T Control 1 (RNA-seq)


title: CD8+ T Palmitate 2 (RNA-seq)


title: CD8+ T Palmitate 2 (ATAC-seq)

data_processing:
Adaptors removed with TrimGalore v 0.6.10
Sequences aligned on mm10 with Bowtie2 aligner(v2.5.1) with default except "very-sensitive-1000"
Duplicated reads removed with Picard (v 2.23.8)
Peak calling with MACS2 (v 2.2.8) with FDR < 0.01
Read quantification with csaw (v 1.32.0) followed by edgeR (v 3.40.2)
Assembly: mm10
Supplementary files format and content: MACS2 peak quantification files, plain-text, bed format
Supplementary files format and content: plain-text, tab-delimited matrix with peak-based ATAC-Seq peak read counts csaw and edgeR

extract_protocol:
Tagmented DNA was isolated using 2x SPRI Beads (Beckman Coulter) and amplified through PCR. Fragments smaller than 600 bp were isolated via negative size selection using 0.65x SPRI Beads (Beckman Coulter) and purified using 1.8x SPRI Beads (BeckmanCoulter).
Libraries were created following a modified protocol from Buenrostro et al. In summary, 50,000 FACS-purified CD8+ T cells per subset were washed with PBS and suspended in 50 μl of lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.1%IPEGALCA-630).


title: CD8+ T Palmitate 3 (ATAC-seq)


title: CD8+ T Control 2 (ATAC-seq)


title: CD8+ T Control 3 (ATAC-seq)


title: CD8+ T Control 1 (ATAC-seq)


title: EG251-EpCAM-Obese

city: Chapel Hill

first: Stephen

middle: D

last: Hursting

state: North Carolina

address: 215B MHRC

institute: University of North Carolina - Chapel Hill

description: Library name: EG251-EpCAM

data_processing:
Raw data were converted to fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software, allowing one mismatch for index sequence identification
Adapters were trimmed and low-quality reads were filtered using Trimmomatic
Spliced Transcripts Alignment to a Reference (STAR) aligned reads to the reference GRCm38 mouse genome and produced a counts matrix
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Colon

growth_protocol: Apc-null;KrasG12D/+;Trp53-null;Smad4-null;tdTomato organoids grew in the submucosal space of control or obese mice for 4 weeks.

extract_protocol:
RNA was isolated from EpCAM+-enriched cell populations using the RNeasy micro kit (Qiagen).
RNA sequencing libraries were prepared using a NEBNext Ultra II RNA library prep kit

treatment_protocol: Tumors were collected four weeks after organoid transplant, cut into 2-4 mm pieces, and stored on ice in Leibovitz’s L-15 media (Corning). Tumors were dissociated into single-cell suspensions using a mouse tumor dissociation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) and a gentleMACS dissociator (Miltenyi Biotec). Resulting suspensions were sequentially filtered using 70 µm and 30 µm filters, centrifuged, and resuspended in RPMI 1640 media (Gibco). CD45+ cells were removed using CD45 MicroBeads (Miltenyi Biotec) and EpCAM+ cells were subsequently enriched from the CD45- fraction using CD326 (EpCAM) MicroBeads (Miltenyi Biotec) per manufacturer’s instructions. Cell fractions were centrifuged and pelleted cells were lysed with lysis buffer (Qiagen, Hilden, Germany) and stored at -80°C.

value: Colon

value: EpCAM+ tumor cells

value: Obese


title: EG250-EpCAM-Obese

description: Library name: EG250-EpCAM


title: EG243-EpCAM-Obese

description: Library name: EG243-EpCAM


title: EG195-EpCAM-Obese

description: Library name: EG195-EpCAM


title: 2L5

value: brain


title: EG189-EpCAM-Obese

description: Library name: EG189-EpCAM


title: 2J5

value: male


title: EG235-EpCAM-Control

description: Library name: EG235-EpCAM


title: EG175-EpCAM-Control

description: Library name: EG175-EpCAM


title: EG186-EpCAM-Obese

description: Library name: EG186-EpCAM


title: EG171-EpCAM-Control

description: Library name: EG171-EpCAM


title: EG227-EpCAM-Control

description: Library name: EG227-EpCAM


title: EG226-EpCAM-Control

description: Library name: EG226-EpCAM


title: EG167-EpCAM-Control

description: Library name: EG167-EpCAM


title: EG164-EpCAM-Control

description: Library name: EG164-EpCAM


title: EG229-EpCAM-Control

description: Library name: EG229-EpCAM


title: Ctrl

city: TianJin

first: Xiao Tong

last: Ma

state: TianJin

address: Blood hospital, 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow cells

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Leukemia stem cells were isolated from bone marrow of Twist1-/- MLL-AF9 and Twist1+/+ MLL-AF9 AML mice 14 days after transplantation. At 14 days after transplantation, leukemia stem cells were isolated from bone marrow of Hoxa9 knockdown and control MLL-AF9+ AML mice treated with doxycycline.

value: Bone marrow cells

value: leukemia stem cells

value: wild type

value: FACS-sorted leukemia stem cells (Lin-cKit+Sca1-CD127-CD34+CD16/32+)


title: shControl


title: shHoxa9

value: Hoxa9 knockdown


title: mnase_mock_r3

city: Berlin

first: Manuel

last: Neumann

address: Philippstr. 13

institute: HU Berlin

description: Library name: MNASE_6

data_processing:
Quality of raw reads was assesed with FastQC (version 0.11.9)
Raw Reads were mapped to the Arabidopsis genome using STAR (version 2.7.9a) with default parameters
bigWig files were generated using DeepTools with the command “bamCoverage” (version 3.5.1) with parameters -bs 1 --skipNonCoveredRegions
Assembly: TAIR10
Supplementary files format and content: bigWig, narrowPeak (except for mock samples)

organism: Arabidopsis thaliana

source_name: the aerial part of 10 day old seedlings

growth_protocol: AP1 inducible transgenic seedlings were grown on ½ MS medium for 10 days at 22℃ and 60% humidity under long-day conditions (16hr light, 8hr dark) and then treated with dex or mock solutions

extract_protocol:
Tissue was ground into powders, resuspended in NIB (10 mM Tris–HCl, 80 mM KCl, 10 mM EDTA, 0.5 M sucrose, 1 mM spermidine and 1 mM spermine) and filtered through a 55 μm mesh. Nuclei pellet was washed three times with NWB (NIB containing 0.5% of freshly prepared Triton X 100).
Chromatin was digested by MNase in MNB (10% sucrose, 50 mM Tris–HCl pH 7.5, 4 mM MgCl2 and 1 mM CaCl2) and reaction was stopped by EDTA. DNA was purified using phenol, phenol: chloroform mixture (1:1), chloroform, respectively and then precipitated by ethanol and NaOAc. Based on DNA distribution pattern, samples containing approximately 20% nucleosome dimers and 80% mononucleosomes were selected for library preparation. NEB Next Ultra II DNA Library Prep Kit was used for library preparation.

treatment_protocol: Treatment was done by spraying an equal amount of dex or mock solution on seedlings. Dex solution is prepared by mixing 25 μl 20 mM dexamethasone dissolved in DMSO and 8 μl Silwet in 50 ml water, and the mock solution is prepared by mixing 25 μl DMSO and 8 μl Silwet in 50 ml water. After treatment, seedlings were transferred back to their normal growth condition.

value: the aerial part of 10 day old seedlings

value: mixed cell types of the aerial part of seedlings

value: mock


title: Twist1 KO

value: Twist1 KO


title: CD8+ T Palmitate 1 (ATAC-seq)

value: CD8+ T Cell

value: WT

value: Palmitate


title: mnase_dex_r3

description: Library name: MNASE_3

value: Dexamethasone


title: mnase_mock_r2

description: Library name: MNASE_5


title: mnase_dex_r2

description: Library name: MNASE_2


title: mnase_mock_r1

description: Library name: MNASE_4


title: EG239-EpCAM-Obese

description: Library name: EG239-EpCAM

value: Colon

value: EpCAM+ tumor cells


title: ap1tet_h8_mock_rna_r2

growth_protocol: AP1 inducible transgenic seedlings were grown on ½ MS medium for 10 days and then treated with dex or mock solutions. Tissues were collected 2, 8, 24 and 48 hours after treatment. Plants were grown at 22℃ and 60% humidity and under long-day conditions (16hr light, 8hr dark)

extract_protocol:
RNA was extracted using TRIzol reagent following the product introduction.
RNA-seq libararies for AP1wt were constructed by the TruSeq Stranded mRNA kit from Illumina. Libraries for AP1tet were generated by the Novogene sequencing company.


title: chip_ap1-hist_r1

description: Library name: ChIP-seq_1

data_processing:
Quality of raw reads was assesed with FastQC (version 0.11.9)
Raw read were timmed with Trimmomatic v0.36 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
Trimmed Reads were mapped to the Arabidopsis genome using bowtie2 (version 2.4.4) with default parameters
Peak calling on aligend reads was done using MACS3 (version 3.0.0b1) with defaults parameters except: -g 101274395 -q 0.1 --mfold 1 50
bigWig files were generated using DeepTools with the command “bamCoverage” (version 3.5.1) with parameters -bs 1 --skipNonCoveredRegions
Assembly: TAIR10
Supplementary files format and content: bigWig, narrowPeak (except for mock and background samples)

growth_protocol: Plants were grown at 22℃ and 60% humidity and under long-day conditions (16hr light, 8hr dark).

extract_protocol:
1.5 g inflorescences were used for each replicate. Plant tissues were fixed in formaldehyde, and ChIP-seq was done according to the published protocol (Kaufmann, K., Muiño, J.M., Østerås, M., Farinelli, L., Krajewski, P., and Angenent, G.C. (2010a) with modifications. The first immunoprecipitation was done with AP1 antibody from rabbit and protein A Dynabeads. The first elution was done using non-denaturing acidic elution buffer. The second immunoprecipitation was done with H3 mouse monoclonal antibody and anti mouse IgG beads.
Libraries were prepared suing the ThruPlex DNA-Seq kit (TaKaRa).

tag: chip antibody

value: AP1 native antibody


title: mnase_dex_r1

description: Library name: MNASE_1


title: chip_ap1-hist_r2

description: Library name: ChIP-seq_2


title: ap1tet_h8_mock_rna_r1


title: ap1tet_h8_dex_rna_r2


title: ap1tet_h8_dex_rna_r1


title: ap1tet_h2_dex_rna_r2


title: ap1tet_h2_dex_rna_r1


title: ap1tet_h2_mock_rna_r1


title: ap1tet_h24_mock_rna_r2


title: ap1tet_h24_dex_rna_r2


title: ap1tet_h24_mock_rna_r1


title: ap1_h8_dex_rna_r2


title: ap1tet_h24_dex_rna_r1


title: ap1_h8_mock_rna_r2


title: ap1_h2_mock_rna_r1


title: ap1_h2_mock_rna_r2


title: ap1_h2_dex_rna_r2


title: ap1_h8_mock_rna_r1


title: ap1_h2_dex_rna_r1


title: ap1_h8_dex_rna_r1


title: ap1_h24_mock_rna_r1


title: ap1_h24_mock_rna_r2


title: ap1tetmut_h24_mock_atac_r2

description:
ap1tetmut_h24_mock_atac.bw
ap1tetmut_h24_mock_atac_peaks.narrowPeak

data_processing:
Quality of raw reads was assesed with FastQC (version 0.11.9)
Reads were mapped to the Arabidopsis genome using bowtie2 (version 2.4.4) with default parameters
Peak calling on aligend reads was done using MACS3 (version 3.0.0b1) with defaults parameters except: -g 101274395 -q 0.1 --mfold 1 50
bigWig files were generated using DeepTools with the command “bamCoverage” (version 3.5.1) with parameters -bs 1 --skipNonCoveredRegions
Assembly: TAIR10
Supplementary files format and content: bigWig, narrowPeak (except for mock samples)

extract_protocol:
Plant nuclei were isolated using gentleMACS dissociator in Honda buffer, and then nuclei were sorted by cell cytometry. Nuclei isolation details have been published (Sunaga‐Franze, D.Y., Muino, J.M., Braeuning, C., Xu, X., Zong, M., Smaczniak, C., Yan, W., Fischer, C., Vidal, R., Kliem, M., Kaufmann, K., and Sauer, S. (2021). Single‐nucleus RNA sequencing of plant tissues using a nanowell‐based system. Plant J. 108: 859–869.). 50000 nuclei were used for ATAC-seq. ATAC-seq was done following a published protocol (Buenrostro, J.D., Wu, B., Chang, H.Y., and Greenleaf, W.J. (2015a). ATAC-seq: A method for assaying chromatin accessibility genome-wide. Curr. Protoc. Mol. Biol. 2015: 21.29.1-21.29.9.)
ATAC-seq library was done following a published protocol (Buenrostro, J.D., Wu, B., Chang, H.Y., and Greenleaf, W.J. (2015a). ATAC-seq: A method for assaying chromatin accessibility genome-wide. Curr. Protoc. Mol. Biol. 2015: 21.29.1-21.29.9.)

value: Mock


title: ap1_h24_dex_rna_r2


title: ap1tetmut_h24_dex_atac_r2

description:
ap1tetmut_h24_dex_atac.bw
ap1tetmut_h24_dex_atac_peaks.narrowPeak


title: ap1tetmut_h24_dex_atac_r1


title: ap1_h8_mock_atac_r1

description:
ap1_h8_mock_atac.bw
ap1_h8_mock_atac_peaks.narrowPeak


title: ap1_h8_dex_atac_r1

description:
ap1_h8_dex_atac.bw
ap1_h8_dex_atac_peaks.narrowPeak


title: ap1_h48_mock_atac_r2

description:
ap1_h48_mock_atac.bw
ap1_h48_mock_atac_peaks.narrowPeak


title: ap1tet_h2_mock_rna_r2


title: ap1_h48_mock_atac_r1


title: ap1_h48_dex_atac_r2

description:
ap1_h48_dex_atac.bw
ap1_h48_dex_atac_peaks.narrowPeak


title: ap1_h48_dex_atac_r1


title: ap1_h2_mock_atac_r2

description:
ap1_h2_mock_atac.bw
ap1_h2_mock_atac_peaks.narrowPeak


title: ap1_h2_mock_atac_r1


title: ap1_h2_dex_atac_r2

description:
ap1_h2_dex_atac.bw
ap1_h2_dex_atac_peaks.narrowPeak


title: ap1_h24_dex_rna_r1


title: ap1_h24_mock_atac_r1

description:
ap1_h24_mock_atac.bw
ap1_h24_mock_atac_peaks.narrowPeak


title: ap1_h24_mock_atac_r2


title: ap1_h2_dex_atac_r1


title: ap1_stagemix-flower_tet-mut_dm_chip_r2

description:
ap1_stagemix-flower_tet-mut_dm_chip_r2
ap1_stagemix-flower_tet-mut_dm_chip.bw
ap1_stagemix-flower_tet-mut_dm_chip_peaks.narrowPeak

source_name: inflorescence

extract_protocol:
2.5 to 3 g of seedlings and around 1g inflorescence were collected for ChIP-seq. Plant tissues were fixed in formaldehyde, and ChIP-seq was done according to the published protocol (Kaufmann, K., Muiño, J.M., Østerås, M., Farinelli, L., Krajewski, P., and Angenent, G.C. (2010a). Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat. Protoc. 5: 457–472.). Nuclei lysate was incubated with native SEP3 antibody for 1 hour, and 50 µl Dynabeads protein A (Thermo Fisher) was then added for immunoprecipitation.
Libraries were prepared suing the ThruPlex DNA-Seq kit (TaKaRa).

value: inflorescence

value: floral cells

value: GFP antibody


title: ap1_stagemix-flower_tet-mut_dm_chip_r1

description:
ap1_stagemix-flower_tet-mut_dm_chip_r1
ap1_stagemix-flower_tet-mut_dm_chip.bw
ap1_stagemix-flower_tet-mut_dm_chip_peaks.narrowPeak


title: ap1_h24_dex_atac_r1

description:
ap1_h24_dex_atac.bw
ap1_h24_dex_atac_peaks.narrowPeak


title: ap1_h8_dex_atac_r2


description:
ap1_stagemix-flower_tet-mut_cirspr_chip_r3_s1
ap1_stagemix-flower_tet-mut_cirspr_chip.bw
ap1_stagemix-flower_tet-mut_cirspr_chip_peaks.narrowPeak


title: ap1_stagemix-flower_tet-mut_sm_chip_r2

description:
ap1_stagemix-flower_tet-mut_sm_chip_r2
ap1_stagemix-flower_tet-mut_sm_chip.bw
ap1_stagemix-flower_tet-mut_sm_chip_peaks.narrowPeak


title: ap1tetmut_h2_mock_chip_r2

description:
ap1tetmut_h2_mock_chip_r2_s1
ap1tetmut_h2_mock_chip.bw


title: ap1tetmut_h24_mock_atac_r1


description:
ap1_stagemix-flower_tet-mut_cirspr_chip_r2_s1
ap1_stagemix-flower_tet-mut_cirspr_chip.bw
ap1_stagemix-flower_tet-mut_cirspr_chip_peaks.narrowPeak


title: ap1_h8_mock_atac_r2


title: ap1tetmut_h2_dex_chip_r2

description:
ap1tetmut_h2_dex_chip_r2_s1
ap1tetmut_h2_dex_chip.bw
ap1tetmut_h2_dex_chip_peaks.narrowPeak


title: ap1tetmut_h2_mock_chip_r1

description:
ap1tetmut_h2_mock_chip_r1_s1
ap1tetmut_h2_mock_chip.bw


title: ap1tetmut_h24_mock_chip_r1

description:
ap1tetmut_h24_mock_chip_r1
ap1tetmut_h24_mock_chip.bw


title: ap1tetmut_h24_dex_chip_r2

description:
ap1tetmut_h24_dex_chip_r2
ap1tetmut_h24_dex_chip.bw
ap1tetmut_h24_dex_chip_peaks.narrowPeak


title: ap1tetmut_h2_dex_chip_r1

description:
ap1tetmut_h2_dex_chip_r1_s1
ap1tetmut_h2_dex_chip.bw
ap1tetmut_h2_dex_chip_peaks.narrowPeak


title: ap1_h8_mock_chip_r2

description:
ap1_h8_mock_chip_r2_s1
ap1_h8_mock_chip.bw


title: ap1_h8_mock_chip_r1

description:
ap1_h8_mock_chip_r1_s1
ap1_h8_mock_chip.bw


title: ap1tetmut_h24_dex_chip

description:
ap1tetmut_h24_dex_chip_r1
ap1tetmut_h24_dex_chip.bw
ap1tetmut_h24_dex_chip_peaks.narrowPeak


title: ap1_h8_dex_chip_r2

description:
ap1_h8_dex_chip_r2_s1
ap1_h8_dex_chip.bw
ap1_h8_dex_chip_peaks.narrowPeak


title: ap1_h2_mock_chip_r2

description:
ap1_h2_mock_chip_r2_s1
ap1_h2_mock_chip.bw


title: ap1_h2_dex_chip_r2

description:
ap1_h2_dex_chip_r2_s1
ap1_h2_dex_chip.bw
ap1_h2_dex_chip_peaks.narrowPeak


title: ap1_h24_dex_atac_r2


title: ap1_h2_dex_chip_r1

description:
ap1_h2_dex_chip_r1_s1
ap1_h2_dex_chip.bw
ap1_h2_dex_chip_peaks.narrowPeak


title: ap1_h8_dex_chip_r1

description:
ap1_h8_dex_chip_r1_s1
ap1_h8_dex_chip.bw
ap1_h8_dex_chip_peaks.narrowPeak


title: ap1_stagemix-flower_tet-mut_sm_chip_r3

description:
ap1_stagemix-flower_tet-mut_sm_chip_r3
ap1_stagemix-flower_tet-mut_sm_chip.bw
ap1_stagemix-flower_tet-mut_sm_chip_peaks.narrowPeak


title: ap1_h2_mock_chip_r1

description:
ap1_h2_mock_chip_r1_s1
ap1_h2_mock_chip.bw


title: ap1_h24_mock_chip_r2

description:
ap1_h24_mock_chip_r2_s1
ap1_h24_mock_chip.bw


title: ap1_h24_dex_chip_r1

description:
ap1_h24_dex_chip_r1_s1
ap1_h24_dex_chip.bw
ap1_h24_dex_chip_peaks.narrowPeak


title: CRSwNP_NP_6, Nasal polyps, scRNAseq

city: Boston

first: Guanrui

last: Liao

state: Massachusetts

address: 3 Blackfan Circle

institute: BIDMC

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger v3.1.0 (10X Genomics).
Assembly: GRCh38-3.0.0
Supplementary files format and content: Compressed files containing tab-seperated values files and matrix files

source_name: Nasal polyps

extract_protocol:
Each sample was received directly from surgeons and promptly delivered to the laboratory on ice. Upon arrival at the laboratory, the samples were immediately processed. The ethmoid sinus mucosa was removed from the bone and nasal polyps were left intact and were minced into small pieces by scissors on ice. The minced tissues were placed into a C tube (Miltenyi Biotec, Bergisch Gladbach, Germany) within a solution of RPMI 1640 (Gibco, Grand Island, NY) containing 10% fetal bovine serum (FBS), 0.02 mg/ml DNase I (Millipore Sigma, St. Louis, MO), and 4 mg/ml collagenase type IV (Thermo Fisher Scientific). The mixture was homogenized using the gentleMACS Dissociator (Miltenyi Biotec) and incubated at 37°C for total of 30 minutes (15 minutes, 2 times) with rotated using MACSmix Tube Rotator (Miltenyi Biotec). Between and after the two incubations, they were also homogenized in a gentleMACS Dissociator. Finally, the samples were filtered through a 70-μm cell strainer and spun down at 500g for 5 min. Red blood cells (RBC) were lysed using the RBC Lysis Solution (BioLegend, San Diego, CA) for 4 min at room temperature. Cells were then washed with ice-cold PBS and spun down at 500g for 5 min at 4°C before resuspension in RPMI containing 10% FBS. The cell suspension was filtered through 40-μm Flowmi Cell Strainers (Millipore Sigma) and counted to adjust concentration to 1,000 cells per μl. In all samples, the process up to this point was completed within 3 hours to minimize cell dissociation artifacts.
The single cell suspension was loaded onto the Chromium Controller (10x Genomics) using the Chromium single cell 3’ Reagent Kit v3 (10X Genomics), and scRNA-seq libraries generated in accordance with the manufacturer’s protocols.

value: Nasal polyps

tag: disease state

value: Chronic rhinosinusitis


title: ap1_h24_dex_chip_r2

description:
ap1_h24_dex_chip_r2_s1
ap1_h24_dex_chip.bw
ap1_h24_dex_chip_peaks.narrowPeak

value: the aerial part of 10 day old seedlings


title: ap1_h24_mock_chip_r1

description:
ap1_h24_mock_chip_r1_s1
ap1_h24_mock_chip.bw

value: mixed cell types of the aerial part of seedlings


title: CRSwNP_Eth_4, Ethmoid sinus, scRNAseq

source_name: Ethmoid sinus

value: Ethmoid sinus


title: CRSwNP_Eth_5, Ethmoid sinus, scRNAseq


title: CRSwNP_NP_1, Nasal polyps, scRNAseq


title: CRSwNP_Eth_2, Ethmoid sinus, scRNAseq


title: CRSwNP_NP_2, Nasal polyps, scRNAseq


title: CRSwNP_Eth_6, Ethmoid sinus, scRNAseq


title: CRSwNP_NP_3, Nasal polyps, scRNAseq


title: CRSwNP_Eth_3, Ethmoid sinus, scRNAseq


title: CRSwNP_Eth_1, Ethmoid sinus, scRNAseq


title: CRSsNP_Eth_5, Ethmoid sinus, scRNAseq


title: CRSsNP_Eth_1, Ethmoid sinus, scRNAseq


title: CRSsNP_Eth_2, Ethmoid sinus, scRNAseq


title: Control_4, Ethmoid sinus, scRNAseq

value: healthy


title: Control_3, Ethmoid sinus, scRNAseq


title: Control_2, Ethmoid sinus, scRNAseq


title: MS023 (1uM) 3hr (13)

city: Bronx

first: David

last: Shechter

state: New York

address: 1300 Morris Park Ave

department: Biochemistry

institute: Albert Einstein College of Medicine

data_processing:
nf-core/nascent:v2.1.1
subread FeatureCounts v2.0.1
Assembly: hg38
Supplementary files format and content: .txt - merged condition featureCounts for genes
Supplementary files format and content: .csv - DESeq2 output for genes per condition

growth_protocol: Per sample, approximately 10 million A549 cells were treated in T182 flasks.

extract_protocol:
At the conclusion of the treatment, media was aspirated and cells were rinsed with 10mL of ice-cold PBS, scraped, and collected into 15mL conical tubes on ice. Cells were collected by centrifugation at 1,000xg at four degrees C for 5 minutes. PBS was aspirated and pellets were resuspended in 10mL ice-cold permeabilization buffer. Cells were incubated in permeabilization buffer for five minutes before being centrifuged at 1,000xg at four degrees for five minutes. Permeabilization buffer was aspirated and permeabilized cells were resuspended in 100uL freezing buffer and snap frozen before being stored at -80C. When preparing for the run on step, frozen permeabilized cells were thawed on ice. Run-on master mix was warmed to 37C and 100uL of 2x run-on master mix was added to 100uL of frozen cells before being placed in a 30C water bath for five minutes with slight agitation after 2.5 minutes of incubation. After five minutes of run-on, 500uL of Trizol LS was added and samples were vortexed until homogenized to stop the reaction. 130uL of chloroform was added, samples were vortexed for 15 seconds, and tubes were centrifuged at 15,000xg for five minutes at 4C. The aqueous phase was transferred to a new Eppendorf tube and RNA was precipitated using 2.5 volumes of 100% ethanol for 10 minutes before being centrifuged at 15,000xg for 20 minutes at 4C. The pellet was washed with 75% EtoH, centrifuged again, and ethanol removed completely before resuspending the RNA pellet in 19uL of DEPC-treated water. Sample quality was assessed by nanodrop and Tapestation before proceeding to RNA fragmentation with Ambion RNA fragmentation reagent (Ambion AM8740) for 4 minutes at 72C before adding stop solution to the reaction. Free NTPs were removed using a p30 column.
Nascent RNA was enriched using streptavidin-coated Dynabeads (Thermo Fisher #65305), washed 2X with 500uL of ice cold high-salt wash buffer using a magnet. Beads were then washed 2X with 500uL binding buffer and 1X with low-salt wash buffer. Buffer was removed and beads were resuspended in 300uL of Trizol to dissociate nascent RNA from the beads. All buffers were made according to Mahat, 2016. 60uL of chloroform was added and vortexed.  The mixture was centrifuged at 15,000xg for five minutes at 4C. The aqueous phase was removed and moved to a separate tube before repeating the nascent RNA enrichment and wash steps. After the second round of purification, nascent RNA was precipitated with 1.25uL glycoblue and 2.5 volumes of 100% ethanol before centrifugation at 15,000xg for 20 minutes at 4C. Ethanol was removed and the RNA pellet was washed with 75% ethanol. RNA was centrifuged again  before removing the 75% ethanol completely. Pellets were resuspended in 5uL DEPC treated H2O and taken directly into library preparation using the NEBNext Ultradirectional II RNA sequencing kit (NEB #E7760S) following the manufacturer's instructions.

treatment_protocol: 1micromolar (uM) GSK591, 1micromolar (um) MS023, or 100nM Dexamethasone (Dex) were applied to cells in 0.01% DMSO final concentration for the indicated time

value: 1uM MS023 3hours in 0.01% DMSO


title: D3-M-H

city: Dongguan

first: Kai

last: Cui

address: No.1 Xincheng Avenue,Songshan Lake Science and Technology Industrial Park

institute: Guangdong Medical University

description:
Library name: Sample4
D3-M-H_FPKM

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: The reference genome sequences and gene model annotation files were downloaded from genome websites (e.g., UCSC, NCBI, ENSEMBL). The reference genome was indexed using Hisat2 (v2.2.1), and the clean data were then aligned to the reference genome using the same software.
Expression Quantification: Transcript sequences in fasta format were generated from the known GFF annotation file. Using this as a reference, HTSeq (v0.6.1) was employed to estimate gene and isoform expression levels from the pair-end clean data.
Differential Expression Analysis: Differential expression analysis was performed using the DESeq2 Bioconductor package, which utilizes a negative binomial model. Padj ≤ 0.05 was set as the threshold to identify differentially expressed genes.
GO and KEGG Enrichment Analysis: GOSeq (v1.34.1) was used to identify significantly enriched Gene Ontology (GO) terms (padj ≤ 0.05) among the differentially expressed genes, and topGO was used for visualization. In-house scripts were used to perform KEGG pathway enrichment analysis on the significant differentially expressed genes.
Novel Transcript Prediction: Assembled transcriptomes were compared to known transcripts using Cuffcompare (from Cufflinks v2.2.1) to predict novel transcripts.
Alternative Splicing Analysis: Differential alternative splicing events were detected from the HISAT2 alignment BAM files using rMATS v4.1.0.
SNV Analysis: SNV calling was performed using Samtools v0.1.19 (mpileup command) and Bcftools v0.1.19.
Differential Exon Usage (DEU) Analysis: Changes in relative exon usage were analyzed using the Bioconductor package DEXSeq (V 1.21.1).
Principal Component Analysis (PCA): Principal Component Analysis was performed using R language with FPKM values as input to visualize sample-to-sample distances and overall data variance.
Assembly: GRCh38 (hg38)
Supplementary files format and content: all.fpkm_anno.txt

source_name: T cell

extract_protocol:
1 μg total RNA was used for the following library preparation. The total RNA was isolated from cells using TRIzol reagent according to the manufacturer's instructions, and its quality and quantity were verified prior to use.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: T cell

tag: cell subtype

value: Mock T cells

value: co-cultured with HGC-27


title: D3-C-A

description:
Library name: Sample1
D3-C-A_FPKM

value: CAR-T cells

value: co-cultured with AGS


title: D3-M-A

description:
Library name: Sample2
D3-M-A_FPKM


title: D3-C-H

description:
Library name: Sample3
D3-C-H_FPKM


title: Control_1, Ethmoid sinus, scRNAseq

tag: tissue


title: GSK591 (1uM) 3hr (12)

value: 1uM GSK591 3hours in 0.01% DMSO


title: MS023 (1uM) 3hr (14)


title: GSK591 (1uM) + Dex (100nM) 15min (7)

value: 1uM GSK591 and 100nM Dexamethasone for 15min in 0.01% DMSO


title: MS023 (1uM) 15min (6)

value: 1uM MS023 15min in 0.01% DMSO


title: CRSsNP_Eth_3, Ethmoid sinus, scRNAseq


title: CRSsNP_Eth_4, Ethmoid sinus, scRNAseq


title: GSK591 (1uM) 15min (3)

value: 1uM GSK591 15min in 0.01% DMSO


title: GSK591 (1uM) 15min (4)


title: Untreated 15min (1)

value: Untreated 15min in 0.01% DMSO


title: Untreated 15min (2)


title: MS023 1week + Dex 15min (28)

data_processing:
nf-core/nascent:v2.1.1
subread FeatureCounts v2.0.1
Assembly: hg38
Supplementary files format and content: .txt

value: 1uM MS023 1week + 100nM Dexamethasone 15min in 0.01% DMSO


title: Control_5, Ethmoid sinus, scRNAseq


title: MS023 1week + Dex 15min (27)


title: MS023 (1uM) 15min (5)


title: GSK591 (1uM) 3hr (11)


title: MS023 1week + Dex 3hrs (29)

value: 1uM MS023 1week + 100nM Dexamethasone 3hrs in 0.01% DMSO


title: MS023 1week (26)

value: 1uM MS023 1week in 0.01% DMSO


title: MS023 1week + Dex 3hrs (30)


title: MS023 1week (25)


title: GSK591 1week + Dex 3hrs (24)

value: 1uM GSK591 1week + 100nM Dexamethasone 3hrs in 0.01% DMSO


title: GSK591 1week + Dex 3hrs (23)


title: MS023 (1uM) + Dex (100nM) 15min (9)

value: 1uM MS023 and 100nM Dexamethasone for 15min in 0.01% DMSO


title: GSK591 1week (20)

value: 1uM GSK591 1week in 0.01% DMSO


title: GSK591 1week (19)


title: GSK591 1week + Dex 15min (22)

value: 1uM GSK591 1week + 100nM Dexamethasone 15min in 0.01% DMSO


title: MS023 (1uM) + Dex (100nM) 15min (10)


title: GSK591 (1uM) + Dex (100nM) 15min (8)


title: GSK591 1week + Dex 15min (21)


title: MS023 4days (18)

value: 1uM MS023 4days in 0.01% DMSO


title: MS023 4days (17)


title: oocyte-1

city: Haining

first: Xinyu

last: Xiang

address: 718 East Haizhou Road

description: Library name: oocyte-1

data_processing:
sRNA-seq data processing: FastQC v0.11.8 was applied for raw reads quality control. The NEB adapter sequence (AGATCGGAAGA) was trimmed from the 3′ ends of raw FASTQ files using Cutadapt v2.9. Reads shorter than 16 bases after trimming were discarded (-m 16), as well as those lacking adaptors (--trimmed-only). Small RNA sequences with a minimum length of 23 bases were defined as piRNAs for downstream analysis to exclude miRNAs and siRNAs. For alignment, reads were mapped to the axolotl genome or transposon consensus sequences with STAR v2.7.0e with the following parameters: up to 1000 multimapped reads permitted (--outFilterMultimapNmax 1000), a maximum of three mismatches allowed (--outFilterMismatchNmax 3), and minimum of 15 matched bases required (--outFilterMatchNmin 15). All multimapped reads were exported (--outSAMmultNmax -1) were included for quantification over genes or transposons, with each read contributing 1/n to the counts.
EM-seq data processing: Raw sequencing reads were quality-checked with FastQC v0.11.8 and processed using Trim Galore v0.6.7 with Cutadapt v3.4 to remove low-quality bases and adapter sequences (--quality 20 --length 25 --trim-n --clip_R2 5). To increase sequencing coverage and depth, the three replicates were merged for downstream analysis. Trimmed paired-end reads were aligned to the axolotl genome with standard pipeline from Bismark v0.24.0 with Bowtie2 v2.4.2, allowing up to 1 bp mismatch and permitting multimapping, with a random alignment reported for ambiguous mappings (-N 1 --ambig_bam). The mapped reads were deduplicated by deduplicate_bismark. CpG methylation data were then extracted using bismark_methylation_extractor with default parameters. The methylation coverage data generated by Bismark v0.24.0 was imported into SeqMonk v1.48.1 for quantification and visualization.
Assembly: AmexG_v6.0-DD from https://www.axolotl-omics.org
Supplementary files format and content: For sRNA-seq, transposon counts normalized by RPKM are included. For EM-seq, bismark deduplicated and methylation coverage extracted data are included.

organism: Ambystoma mexicanum

source_name: oocyte

growth_protocol: All lines were bred and maintained at the Research Institute of Molecular Pathology (IMP) facilities.

extract_protocol:
For sRNA-seq, RNA was extracted from two testis and two oocyte samples of the white axolotl strain using lysis reagent (QIAzol, 79306), following the manufacturer’s protocol. For EM-seq, DNA was extracted from three sperm samples of the white axolotl strain using Monarch HMW DNA Extraction Kit (NEB, T3050L) and solubilized in 10mM Tris, pH 9.0, 0.5 mM EDTA.
For sRNA-seq, total RNA was size-selected for 15-40 nt fragments using 15% Novex TBE-urea gel (Invitrogen, EC68855BOX). RNA fragments were purified from the gel and resuspended in 10 μl nuclease-free water. Library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7330L) according to the manufacturer’s protocol. Sequencing was performed on an Illumina HiSeq2500 platform in 50-bp single-end read mode. For EM-seq, libraries were prepared using the NEBnext Enzymatic Methyl-seq kit (NEB, E7120L) according to the manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq2000 platform in 150-bp paired-end read mode.

treatment_protocol: Handling and surgical procedures adhered to local ethics committee guidelines, and animal experiments were conducted with approval from the Magistrate of Vienna.

value: oocyte


title: GSK591 4days (15)

value: 1uM GSK591 4days in 0.01% DMSO


title: HUCCT1_CRISPR_Clone_22b

city: Austin

first: Sergio

last: Gradilone

address: 801 16th Avenue NE

department: The Hormel Institute

institute: University of Minnesota

data_processing:
The University of Minnesota Research Informatics at MSI  analyzed the RNA Seq output. 2 x 75bp FastQ paired-end reads for 6 samples  were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Quality control on raw sequence data for each sample was performed with FastQC
Sequencing reads were mapped to the human reference genome (hg38, UCSC) using Hisat2.
Genes differentially expressed between HuCCT1 AQP1 KO (Clone 22 ) and HuCCT1 WT (clone 1)  were calculated using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: Homo_sapiens (hg38)
Supplementary files format and content: GradiloneRawCount.txt

growth_protocol: The human cholangiocarcinoma cell line, HuCCT1, was cultured using the following media: DMEM-F12, 10% FBS, 1% L-glutamine, and 1% pen/strep. Cells were cultured in plastic flasks with media at 37°C and 5% CO2.

extract_protocol:
The analysis of differential gene expression between the HuCCT1 AQP1 KO (Clone 22 )and HuCCT1 WT (clone 1) cell lines was conducted using the RNA-seq technique. Total RNA was obtained using the Qiagen RNeasy kit, following the manufacturer's instructions.
RNA libraries were prepared for sequencing using Illumina TruSeq stranded mRNA Protocols at the University of Minnesota Genomic Center (UMGC)

tag: clone

value: AQP1 KO


title: GSK591 4days (16)

tag: treatment


title: HUCCT1_CRISPR_Clone_22c


title: oocyte-2

description: Library name: oocyte-2


title: HUCCT1_CRISPR_Clone_22a


title: testis-2

description: Library name: testis-2

source_name: testis

value: testis


title: HUCCT1_CRISPR_Clone_1b

value: WT


title: GSK591 2days (12)

value: 1uM GSK591 2days in 0.01% DMSO


title: HUCCT1_CRISPR_Clone_1a


title: testis-1

description: Library name: testis-1


title: MS023 2days (14)

value: 1uM MS023 2days in 0.01% DMSO


title: Dex + MS023 3hrs (10)

value: 100nM Dexamethasone + 1uM MS023 3hrs in 0.01% DMSO


title: HUCCT1_CRISPR_Clone_1c


title: CTRL_9, PanCK+ ROI1

description: CRS Q3 Normalization.xlsx

data_processing:
Probes from the Nanostring CTA panel were mapped and counted using the Nanostring GeoMx Data Analysis software pipeline. Thereafter, the data underwent quality control and normalization steps with the ‘Geomx-Tools' software from Nanostring
Assembly: GRCh38-3.0.0
Supplementary files format and content: Comma-separated values files including normalized gene counts for each sample

extract_protocol:
Samples collected for Nanostring GeoMx-Digital Spatial Profiling were fixed in 10% neutral buffered formalin at room temperature for 24-48 hours at a volume 10 times greater than the tissue volume. The specimens were then washed in 1xPBS, dehydrated, and paraffin-embedded at the Stanford Histology Core, and sectioned onto Fisher Superfrost Plus microscope slides (Fisher, 12-500-15) at 5um. Slides were deparaffinized and prepared according to the official Nanostring GeoMx-NGS RNA Manual Slide Preparation protocol.
The Nanostring DSP Human CTA detection probe cocktail was then applied to the slides and incubated overnight (~18 hrs) at 37°C. Each ROI was uniquely indexed using Illumina’s i5 x  i7 dual-indexing system. In total, 4 µL of collected sample was used in a PCR reaction with 1 µM of i5 primer, 1 µM i7 primer, and 1 x Nanostring library prep PCR Master Mix. PCR reaction conditions were 37 °C for 30 min, 50 °C for 10 min, 95 °C for 3 min, 18 cycles of 95 °C for 15 s, 65 °C for 60 s, 68 °C for 30 s, and final extension of 68 °C for 5 min. Then the product was purified with two rounds of AMPure XP beads (Beckman Coulter) at 1.2 x bead-to-sample ratio

value: Ethmoid sinus

value: healthy


title: CTRL_9, PanCK+ ROI2

description: CRS Q3 Normalization.xlsx


title: Dex + MS023 3hrs (9)


title: Dex + GSK591 3hrs (8)

value: 100nM Dexamethasone + 1uM GSK591 3hrs in 0.01% DMSO


title: CTRL_8, PanCK+ ROI2

description: CRS Q3 Normalization.xlsx


title: CTRL_8, PanCK+ ROI1

description: CRS Q3 Normalization.xlsx


title: CTRL_7, PanCK+ ROI1

description: CRS Q3 Normalization.xlsx


title: Dexamethasone 3hrs (5)

value: 100nM Dexamethasone 3hrs in 0.01% DMSO


title: CTRL_7, PanCK+ ROI2

description: CRS Q3 Normalization.xlsx


title: Dexamethasone 3hrs (6)


title: Dex + GSK591 3hrs (7)


title: MS023 2days (13)


title: Dexamethasone 15min (4)

value: 100nM Dexamethasone 15min in 0.01% DMSO


title: CTRL_6, PanCK+ ROI2

description: CRS Q3 Normalization.xlsx


title: CTRL_6, PanCK+ ROI1

description: CRS Q3 Normalization.xlsx


title: GSK591 2days (11)


title: Dexamethasone 15min (3)


title: B cells, IL-4+Bryostatin1-3

city: Bunkyo-ku

first: Naoki

last: MORITA

address: 1-1-1 Yayoi

institute: The University of Tokyo

data_processing:
The DNA nanoball (DNB) was prepared by the DNBSEQ-G400RS High-throughput Sequencing Kit (MGI Tech)
The generated DNB was sequenced using DNBSEQ G 400 under the condition of 2 × 100 bp.
After removing the adaptor sequences in cutadapt. We used the sickle to remove base pairs with a quality score of less than 20 and pair leads with a quality score of less than 40.
The hisat2 was used to map the sequenced read to the reference sequence and output the data in sam format.
The samtools were used to convert sam format to bam format, which was then sorted and indexed.
Assembly: The featureCounts were used to count the reads that mapped to the genomic region of the reference sequence, followed by Reads Per Kilobase Million (RPKM) normalization and Transcripts Per Million (TPM) to correct for the total number of reads and genomic length between samples.
Supplementary files format and content: Excel file contains raw counts for each samples

source_name: B cell

growth_protocol: B cells were cultured in in RPMI 1640 medium containing 10% FBS, 500 µg / mL penicillin, and 50 µM 2-mercaptoethanol with 500 ng /mL anti-mouse CD40 Ab

extract_protocol:
RNA was isolated from cells by the Fast Gene RNA isolation kit (NIPPON Genetics)
Libraries were prepared according to the manual using the MGIEasy RNA Directional Library Prep Set (MGI Tech)

treatment_protocol: 5 ng / mL IL-4 with or without 0.8 nM Bryostatin 1

value: B cell

value: IL-4 + Bryostatin 1


title: Untreated 15min (1)

value: Untreated 15min in 0.01% DMSO


title: CRSwNP_8, PanCK+ ROI2

description: CRS Q3 Normalization.xlsx

source_name: Nasal poylps

value: Nasal poylps

value: Chronic rhinosinusitis


title: Untreated 15min (2)


title: CRSwNP_8, PanCK+ ROI1

description: CRS Q3 Normalization.xlsx


title: CRSwNP_9, PanCK+ ROI2

description: CRS Q3 Normalization.xlsx


title: B cells, IL-4+Bryostatin1-2


title: B cells, IL-4+Bryostatin1-1


title: B cells, IL-4-2


title: B cells, IL-4-3


title: B cells, IL-4-1


title: CRSwNP_6, PanCK+ ROI1

description: CRS Q3 Normalization.xlsx


title: CRSwNP_5, PanCK+ ROI2

description: CRS Q3 Normalization.xlsx


title: CRSwNP_4, PanCK+ ROI1

description: CRS Q3 Normalization.xlsx


title: CRSwNP_4, PanCK+ ROI2

description: CRS Q3 Normalization.xlsx


title: hevg2-nhp5-dpi35

city: Galveston

first: Jacquelyn

last: Turcinovic

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

hyb_protocol: Purified RNA samples were hybridized with the NHP_Immunology_V2 reporter and capture codesets containing ~779 targets (Nanostring Technologies) for ~24h at 65˚C.

scan_protocol: Hybridized samples were loaded onto a nCounter SPRINT microfluidics cartridge that was immediately run on a Nanostring nCounter SPRINT Profiler to determine fluorescent counts for each target.

data_processing: Raw RCC files were processed in nSolver v4.0 to generate background-thresholded counts matrices. Count matrices were analysed in R using the limma package.

organism: Chlorocebus aethiops

source_name: Circulating whole blood

growth_protocol: None; samples from in vivo model

extract_protocol: Samples inactivated in AVL were extracted with the QIAGEN RNeasy Kit according to the manufacturer's protocol. Samples inactivated in TRIzol LS were extracted according to the manufacturer's protocol.

treatment_protocol: Each animal was challenged with 5e5 PFU HeV

tag: nhp

tag: dpi

tag: timepoint

value: >10 DPI

tag: agent


title: CRSwNP_9, PanCK+ ROI1

description: CRS Q3 Normalization.xlsx


title: CTRL_9, CD45+ ROI2

description: CRS Q3 Normalization.xlsx


title: CTRL_9, CD45+ ROI1

description: CRS Q3 Normalization.xlsx


title: CTRL_8, CD45+ ROI2

description: CRS Q3 Normalization.xlsx


title: hevg2-nhp5-dpi28


title: CTRL_7, CD45+ ROI2

description: CRS Q3 Normalization.xlsx


title: CRSwNP_7, PanCK+ ROI1

description: CRS Q3 Normalization.xlsx


title: CTRL_7, CD45+ ROI1

description: CRS Q3 Normalization.xlsx


title: CRSwNP_6, PanCK+ ROI2

description: CRS Q3 Normalization.xlsx


title: hevg2-nhp5-dpi14


title: hevg2-nhp5-dpi21


title: CRSwNP_7, PanCK+ ROI2

description: CRS Q3 Normalization.xlsx


title: CTRL_8, CD45+ ROI1

description: CRS Q3 Normalization.xlsx


title: hevg2-nhp5-dpi10

value: 10 DPI


title: hevg2-nhp5-dpi07

value: 7 DPI


title: hevg2-nhp5-dpi04

value: 4 DPI


title: CTRL_6, CD45+ ROI2

description: CRS Q3 Normalization.xlsx


title: CTRL_6, CD45+ ROI1

description: CRS Q3 Normalization.xlsx


title: CRSwNP_9, CD45+ ROI2

description: CRS Q3 Normalization.xlsx


title: hevg2-nhp4-dpi35


title: hevg2-nhp4-dpi14


title: hevg2-nhp4-dpi28


title: hevg2-nhp4-dpi21


title: hevg2-nhp4-dpi10


title: CRSwNP_5, PanCK+ ROI1

description: CRS Q3 Normalization.xlsx


title: CRSwNP_8, CD45+ ROI1

description: CRS Q3 Normalization.xlsx


title: CRSwNP_7, CD45+ ROI2

description: CRS Q3 Normalization.xlsx


title: hevg2-nhp4-dpi07


title: hevg2-nhp4-dpi04


title: CRSwNP_5, CD45+ ROI2

description: CRS Q3 Normalization.xlsx


title: CRSwNP_6, CD45+ ROI2

description: CRS Q3 Normalization.xlsx


title: CRSwNP_6, CD45+ ROI1

description: CRS Q3 Normalization.xlsx


title: CRSwNP_7, CD45+ ROI1

description: CRS Q3 Normalization.xlsx


title: CRSwNP_4, CD45+ ROI2

description: CRS Q3 Normalization.xlsx


title: hevg2-nhp3-dpi35


title: hevg2-nhp3-dpi28


title: hevg2-nhp4-dpi00

value: Baseline