title: 304_1.1_resistant 3

description:
Xenograft of metastatic cells in mice
SAM24353400

data_processing:
HTSeqGenie
Reads characterized by low nucleotide qualities (defined as having 70% of bases with quality scores below 23) or those matching rRNA and adapter sequences were excluded. The remaining reads were aligned to the human reference genome (human: GRCh38.p10) using GSNAP (2013-10-10-v2; PMID:20147302, 27008021) with a maximum allowance of two mismatches per 75-base sequence (utilizing parameters: '-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). Transcript annotation relied on the GENCODE genes database (human: GENCODE 27).
For the quantification of gene expression levels, the count of reads unambiguously mapping to the exons of each gene was computed. Differential gene expression was performed with relevant contrasts using the “voom” function of the limma package. A pre-filter was applied so that only genes with at least a median CPM (counts per million mapped reads) value of 10 in one were analyzed. P-values for other genes were left out and not included in downstream steps including the multiple testing correction. Counts were normalized using trimmed mean of M-values (TMM). Q-values were obtained by correcting P-values for multiple hypotheses using the Benjamini-Hochberg procedure. Genes were considered if they had a Q-value of less than 0.05 and were protein-coding.
Assembly: GRCh38.p10
Supplementary files format and content: tab delimited text file includes raw counts of each sample.
Supplementary files format and content: tab delimited text file includes normalized RPKM counts of each sample.

source_name: Pancreas

growth_protocol: PATU-8902 shNTC and shYAP/WWTR1 were maintained in vitro as a monolayer culture in RPMI medium supplemented with 10% Tet free fetal bovine serum, and L-glutamine (2 mM) at 37C in an atmosphere of 5% CO2 in air. Cell culture medium did not contain any antibiotics. The tumor cells were routinely subcultured twice weekly by trypsin-EDTA treatment. The cells growing in an exponential growth phase were harvested and counted for tumor inoculation. Animals: 40 Nu/Nu nude mice, female, 6-8 weeks, weighing approximately 20-22g, were used for each cell line. Animals were purchased from Beijing Vital River Laboratory Animal Technology Co., Ltd Tumor Inoculation: Each mouse was inoculated subcutaneously at the right flank with PA-TU-8902 tumor cells (5 x 106) in 0.2 ml of HBSS with Matrigel (1:1) for tumor development. Cells from the shYAP/WWTR1 resistant tumor were propagated in vitro to establish a cell line.  RNA-seq and ATAC-seq were performed on the resistance cell line generated from the collected tumor (under doxycycline treatment). Parental PATU-8902 cells transfected with shNTC and shYAP/WWTR1 were used as a control.

extract_protocol:
Cell lines were lysed on-plate for RNA isolation using the Qiagen RNeasy Plus Mini kit (Cat. No. 74034), and RNA concentration was determined using a NanoDrop 8000 (Thermo Fisher Scientific).  RNA integrity was confirmed using a “Bioanalyzer 2100 (Agilent Technologies).
About 500 ng of RNA was used for library synthesis using the TrueSeq RNA Sample Preparation kit v2 (Illumina). Size of the libraries was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies), and the concentration was determined by a qPCR-based method using the Library Quantification Kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate an average of 56 million single-end 50-base reads per sample.

value: Pancreas

value: Adenocarcinoma


title: mouse cortex, wt, PANDORA-seq, rep3

status: Public on Dec 17 2024

type: SRA

city: Salt Lake City

first: Qi

last: Chen

state: Utah

department: Department of Human Genetics

country: USA

institute: university of utah

library_source: transcriptomic

data_processing:
The raw reads were trimmed by performing SPORTS1.1.1 (parameters: sports.pl -M 1 -a -x GUUCAGAGUUCUACAGUCCGACGAUC -y AAGATCGGAAGAGCACACGTCT -l 15 -L 45 -s).
Assembly: mm39 (for mouse),
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

molecule: total RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

tag: tissue

value: cortex

tag: age

value: 6 months

tag: genotype

value: WT

tag: treatment

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: control, rep1

city: Nijmegen

first: Nicholas

last: Raun

address: Geert Grooteplein 10

country: Netherlands

institute: Radboudumc

data_processing:
Raw sequence reads were trimmed using Trimmomatic (version 0.39), removing low quality leading and tailing bases (below quality 3) and reads below 30 bases.
Trimmed reads were aligned to D. melanogaster genome (dm6) using STAR (version 2.7.5a). Reads were also aligned to C. elegans unc-84 gene (NC_003284.9).
Reads that aligned to multiple loci, or to one loci with >4 mismatches, and genes that mapped to Drosophila rRNA were removed.
Gene counts were obtained using using FeatureCounts from the Rsubread R package (version 2.4.2).
Assembly: dm6
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

organism: Drosophila melanogaster

source_name: Mushroom body

extract_protocol:
Fly heads were obtained from samples of 50-60 flies through flash freezing with liquid nitrogen, followed by vortexing and separation through a series of a sieves. Fly heads were then suspended in homogenization buffer and nuclei released into solution through chemical and physical agitation of the cell membrane. Anti-GFP bound beads were then used to isolate GFP-positive nuclei from the whole head homogenate to represent the mushroom body-specific fraction (MB). RNA was then isolated from MB-fractions using a PicoPure RNA Isolation Kit (Invitrogen:KIT0204) according to the manufacturer instructions.
RNA libraries were generated using the Tecan Universal Plus Total RNA-Seq library preparation kit (Tecan: 3061-A01) according to manufacturer instructions.

value: Mushroom body


title: 304_1.1_resistant 2

city: San Fransisco

first: Xiaosai

last: Yao

state: CA

address: 1 DNA Way

department: Oncology Bioinformatics

institute: Roche/Genentech

description:
Xenograft of metastatic cells in mice
SAM24353399

organism: Homo sapiens

tag: cell line

tag: cell type

value: Resistant to TEAD inhibitor GNE-7883


title: input, rep4

library_source: genomic

data_processing:
Raw sequence reads were trimmed using trimmomatic (version 0.39) to remove low quality leading and tailing bases (below quality 3).
Trimmed reads were aligned to D. melanogaster genome (dm6) using Bowtie (version 2.4.1), with the very-sensitive setting.
Reads that aligned to multiple loci, had a low mapping quality (<4), aligned to mitochondrial chromosomes, or scaffolds were removed.
ChIP peaks were identified with macs2 (version 2.2.71), using q<0.01.
Assembly: dm6
Supplementary files format and content: narrowPeak (except for input samples)

molecule: genomic DNA

extract_protocol:
Fly heads were obtained from samples of 50-60 flies through flash freezing with liquid nitrogen, followed by vortexing and separation through a series of a sieves. Fly heads were then suspended in homogenization buffer and nuclei released into solution through chemical and physical agitation of the cell membrane. Anti-GFP bound beads were then used to isolate GFP-positive nuclei from the whole head homogenate to represent the mushroom body-specific fraction (MB). Chromatin was isolated using the True ChIP-seq Kit (Diagenode: C01010132), according to manufacturer instructions. DNA was isolated using the MicroChIP DiaPure columns (Diagenode: C03040001).
ChIP libraries were generated using the MicroPlex Library Preparation Kit (Diagenode: C05010001).


title: mouse cortex, wt, PANDORA-seq, rep2


title: 304_1.1_resistant 1

description:
Xenograft of metastatic cells in mice
SAM24353398


title: H226_P_DMSO_KD_cd81_YAP_2

data_processing:
For each sequence library, raw reads were aligned on the hg38 human genome reference using Bowtie2  (v2.4.1) followed by alignments sorting (samtools v1.9) of resulting bam files with filtering out of unmapped  reads and keeping reads with mapping quality higher than 30. Duplicates were removed with Picard’s  (v2.23.9) MarkDuplicates function followed by indexation of resulting bam files with samtools. For each bam  file, genome coverage was computed with bedtools (v2.29.2) followed by generation of bigwig  (wigToBigWig v357) files. Peaks were called with macs2 (v2.7.1) for each treatment sample using their  corresponding IgG control. Downstream analyses were performed with DiffBind v3.11.1 with default  parameters, except for summits=250 in dba.count(). dba.contrast() and dba.analyzed() were used to  compute significant differential peaks with DESeq2.
Assembly: hg38.p10
Supplementary files format and content: bigWig, Macs2 peaks
Library strategy: CUT&RUN

source_name: Lung, Epithelial

growth_protocol: Cell lines were maintained in RPMI 1640 supplemented with 10% FBS and 2 mM L-glutamine in a humidified incubator maintained at 37 °C with 5% CO2. TEAD SMI resistant NF2 null NCI-H226 (i.e. NCI-H226_CL3) cells were generated by incubation with increasing concentrations of TEAD SMI over time (0.25 μM to 3 μM at bi-weekly with 0.1-0.5 μM increments), ensuring at least a 25% confluence at all times. For the knockdown cell lines generation, CRISPR transfection was conducted in H226 and H226-7883R cells. Cells were seeded at 2 × 10 6 cells per 10 cm plate and incubated for 24 hours. The cells were then electroporated with an RNP complex containing pre-designed Alt-R CRISPR-Cas9 gRNA (final concentration 44 µM) and Cas9 protein (final concentration 36 µM) purchased from IDT (Alt-R™ S.p. Cas9 Nuclease V3, Cat. #1081058). Two guide RNAs were used for FOSL1: sgFOSL1_1 (CAAGGCCTTCGACGTACCCC) and sgFOSL1_2 (GATTTTGCAGATGGGTCGGT) at a concentration of 22 µM each. Guide RNA for CD81 (TGATGACGCCAACAACGCCA) was used as a control. Three days post-electroporation, H226 cells were treated with DMSO in the background of CD81 and FOSL1 KD, and H226-7883R resistant cells were maintained in 1 µM GNE-7883 in the background of CD81 and FOSL1 KD. After 48 hours of treatment, 500k cells from each condition were processed for CUT&RUN.

extract_protocol:
H226/ H226-7883R cells were trypsinized into single-cell suspension with 0.05% Trypsin, EDTA 0.5 mM.  500k cells were used for each reaction.
We used the CUTANA ChIC/CUT&RUN Kit from Epicypher (#14- 1048) following manufacturer’s instructions. ConA Beads were briefly resuspended and 11 μl of beads per  reaction was transferred to a 1.5 ml tube. Beads were resuspended in 100 μl bead activation buffer per  reaction and washed 2✕. Then resuspended in 11 μl buffer per reaction and aliquoted 10 μl into 8-strip PCR  tubes, and kept on ice. Harvested cells were spun down at 600 × g for 3 min at room temperature. Cells  were then resuspended in 100 μl/reaction of wash buffer and aliquoted into 8 strip tubes with the 10 μl of  activated ConA beads. After 10 mins incubation, 50 μl of cold antibody buffer was added. YAP antibody  (CST Cat. #14074) was used at 1:50 dilution, TEAD1 antibody (BD Cat. #610923) or FOSL1 antibody  (ThermoFisher Cat. #PA5-66880) was added at 0.5 μg per reaction. Tubes were incubated on nutator  overnight at 4 °C. The next day, tubes were collected and washed 2✕ with 200 μl cell permeabilization  buffer. Beads were resuspended in 50 μl cell permeabilization buffer and 2.5 μl pAG-MNase was added.  After 10 min incubation at room temperature, beads were washed with another 200 μl cell permeabilization  buffer 2✕. Finally beads were resuspended in 50μl cell permeabilization buffer. 1 μl of 100 mM CaCl2 was  added to activate the enzyme. Tubes were then incubated for 2 h on nutator at 4 °C. Finally, the reaction  was stopped with 33 μl of stop master mix. DNA was then purified and quantified using a Qubit fluorometer.  For library preparation, we used the CUTANA CUT&RUN Library Prep Kit from Epicypher (#14-1001). End  Repair step, Adapter ligation and U-excision were performed following manufacturer’s instructions. We  used 1✕ SPRIselect beads for DNA cleanup. After indexing PCR, we then used 1✕ SPRIselect beads for  DNA cleanup prior to sequencing. Analysis of the library fragment size was done using Tapestation.  10 million Paired End Reads (PE) per sample.

value: Lung, Epithelial

value: Mesothelioma

value: Sensitive to TEAD inhibitor GNE-7883

tag: cutnrun antibody


title: Neutrophils, CUMS, replicate 3

city: Hangzhou

first: Xinjiang

last: Lu

address: Yuhangtang road No.866

country: China

institute: Zhejiang University

description: Total 6 bone marrow samples were analyzed in this study. 3 samples as negtive control, 3 samples as CUMS groups.

data_processing:
Demultiplexing and adapter trimming were performed with bcl2fastq v2.19. No quality trimming was performed for deposited fastq files.
Sequenced reads were quality trimmed using Cutadapt v1.16.5.
Reads were mapped to mm10 whole genome using HISAT2 v2.1 with default settings for paired-end reverse strand specific libraries.
featureCounts v1.6.4 and DESeq2 v2.11.40.6 were applied for differentially expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone marrow

extract_protocol:
Neutrophils were harvested from the bone marrow of mice subjected to the CUMS paradigm. Total RNA was extracted using TRIZOL Reagent according the manufacturer’s instructions (Invitrogen). RNA-seq transcriptome libraries were prepared using 1 μg of total RNA following TruSeq RNA Sample Prep Kit from Illumina (San Diego, CA, USA).
The DNA library was then sequenced using Illumina Novaseq 6000 with 2 × 150 bp read length.

treatment_protocol: The chronic unpredictable mild stress (CUMS) protocol involves the sequential application of various environmental stressors over a 4-week duration.

value: Bone marrow

value: Neutrophils

tag: Sex

value: male

value: CUMS


title: Neutrophils, CUMS, replicate 2


title: input, rep3


title: mouse cortex, wt, PANDORA-seq, rep5


title: H226_P_DMSO_KD_cd81_TEAD1_2


title: H226_P_DMSO_KD_FOSL1_FOSL1_2

value: ThermoFisher Cat. #PA5-66880)


title: input, rep2


title: shYAP+TAZ_sensitive 2

description:
Xenograft of metastatic cells in mice
SAM24353393


title: Neutrophils, CUMS, replicate 1


title: input, rep1


title: mouse cortex, wt, PANDORA-seq, rep1


title: Neutrophils, Control, replicate 3

value: Control


title: H226_R_7883_KD_FOSL1_FOSL1_1


title: H226_P_DMSO_KD_FOSL1_YAP_2


title: trxKD, naïve, me3, rep3

tag: chip antibody

value: H3K4me3 (Diagenode:C15410003)

value: naïve


title: H226_P_DMSO_KD_cd81_FOSL1_2


title: shNTC_sensitive 2

description:
Xenograft of metastatic cells in mice
SAM24353391

value: Pancreas

value: Adenocarcinoma


title: Set1KD, rep3


title: trxKD, naïve, me3, rep2


title: shYAP+TAZ_sensitive 3

description:
Xenograft of metastatic cells in mice
SAM24353394


title: Neutrophils, Control, replicate 2

value: WT


title: H226_R_7883_KD_cd81_FOSL1_1


title: Non_CD09, Control participants, Ileum tissue

city: Seoul

first: Yoonho

last: Lee

address: 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: University of Ulsan College of Medicine

data_processing:
The RNA sequencing reads were trimmed using Cutadapt (v.3.7) in paired-end mode.(parameter- Quality : 20 minimum length : 20)
The filtered reads were mapped to the reference genome GRCH38 using STAR software v2.7.9a(parameter- default)
Quantification of the gene expression levels was performed using RNA-SeQC v2.1.2(parameter- default)
Assembly: GRCH38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Ileum

extract_protocol:
RNA was extracted using Rneasy Plus Mini Kit (Qiagen, Tokyo, Japan).
The sequencing libraries were prepared with the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Globin (Illumina, CA, United States)

value: Ileum

value: Female

tag: disease state

value: Colon cancer


title: Neutrophils, Control, replicate 1


title: H226_R_7883_KD_cd81_YAP_1

value: Lung, Epithelial

value: Resistant to TEAD inhibitor GNE-7883


title: trxKD, naïve, me3, rep1

value: Mushroom body


title: trxKD, trained, me3, rep3

value: trained


title: Non_CD08, Control participants, Ileum tissue

value: Male


title: Bend3_StcE_5

city: Stanford

first: Sophia

middle: Michelle

last: Shi

state: California

address: 63 Abrams Court

institute: Stanford University

data_processing:
Trimmed reads were mapped to Mus Musculus mm10 reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads mapped to each gene
DESeq2 v1.32.0 was used for differential expression analysis
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM values for each sample

growth_protocol: bEnd.3 cells were cultured in high glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin and maintained in a humidified incubator containing 5% CO2 at 37ºC.

extract_protocol:
RNA was extracted using the RNeasy Plus Micro kit (Qiagen, 74034).
Poly-T oligo-attached magnetic beads were used to purify mRNA from total RNA. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for directional library generation.

treatment_protocol: bEnd.3 cells were treated with 5 nM StcE or an equal volume of saline in growth media for 16 h at 37ºC.

value: brain endothelial cells

value: StcE


title: shYAP+TAZ_sensitive 1

description:
Xenograft of metastatic cells in mice
SAM24353392

value: Sensitive to TEAD inhibitor GNE-7883


title: H226_R_7883_KD_cd81_TEAD1_1

value: Mesothelioma


title: H226_R_7883_KD_FOSL1_YAP_1


title: Non_CD07, Control participants, Ileum tissue


title: IPF IPFrc 2, ATAC-seq

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

data_processing:
The nf-core ataq-seq pipeline (v2.1.2) was used to perform alignment and downstream analysis. Briefly, pre-alignment quality control and adapter trimming of the FASTQ files was performed with the default parameters. The reads were then aligned to the human reference genome (GRCh38.86) and alignments from multiple libraries per sample were merged.
Assembly: GRCh38.86
Supplementary files format and content: bigWig files (ATAC-seq), raw and normlized count matrices (RNA-seq)

source_name: Lung

extract_protocol:
Matched bulk-ATAC and RNA-seq was performed on IPF- and control-derived airway organoids originating from three donors. For RNA-seq, cells were pelleted and lysed in RLT Plus buffer. Total RNA was extracted and purified on the MagMAX instrument (Thermo Fisher) using the MagMAX™ 96 Total RNA Isolation Kit following manufacturer’s instructions. Total RNA samples were normalized on the MicroLab STAR automated liquid platform (Hamilton). For ATAC-seq library prep was performed as previously described with minor adaptions. 70,000 cells of singularized AOs were lysed in lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1 % NP-40) for 5 min and centrifuged. Pelleted cells were transposed using Tagment DNA TDE1 Enzyme and Buffer Kit for 60 min at 37 °C with shaking. Afterwards, samples were purified using clean-up buffer (0.5 M NaCl, 400 mM EDTA, 1 % SDS, 2 mg/ml Proteinase K) and normal phase 2x AMPureXP (Beckman Coulter, #A63881) bead clean-up, followed by PCR amplification. Finally, amplified samples were purified using DNA Clean & Concentrator Kit (Zymo, #ZYM-D4029) and double-sided clean-up with AMPure beads.
For RNA-seq, a total RNA input of 250ng was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (#E7760), together with the NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490) and NEBNext Multiplex Oligos for Illumina (#E7600). RNA-seq libraries were processed on a Biomek i7 Hybrid instrument (Beckman Coulter) using 13 PCR cycles, following the manufacturer’s protocol, except for the use of Ampure XP beads (Beckman Coulter) for double-stranded cDNA purification and PCR clean-up. Final sequencing libraries were quantified by the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). All sequencing libraries were then normalized on the MicroLab STAR (Hamilton), pooled, and sequenced on an Illumina NovaSeq 6000 using an S2 Reagent Kit v1.5. ATAC-seq libraries were normalized on the MicroLab STAR (Hamilton), pooled and spiked in with PhiX Control v3 (Illumina). Libraries were sequenced on an Illumina NovaSeq 6000 using an S2 Reagent Kit v1.5 (#20028315; Read parameters: Rd1:101bp, Rd2: 8bp, Rd3: 8bp, Rd4:101bp) with an average sequencing depth of ~100 million reads passed filter per sample.

value: Lung

value: Airway epithelium

value: IPF

value: IPF-relevant cocktail


title: H226_P_DMSO_KD_FOSL1_FOSL1_1

value: ThermoFisher Cat. #PA5-66880)


title: Bend3_StcE_3

value: WT


title: trxKD, trained, me3, rep1

value: H3K4me3 (Diagenode:C15410003)


title: Bend3_StcE_2


title: Non_CD06, Control participants, Ileum tissue

value: Ileum

value: Colon cancer


title: H226_R_7883_KD_FOSL1_TEAD1_1

value: Lung, Epithelial

value: Resistant to TEAD inhibitor GNE-7883


title: shNTC_sensitive 1

description:
Xenograft of metastatic cells in mice
SAM24353390

value: Pancreas

value: Adenocarcinoma


title: H226_P_DMSO_KD_FOSL1_YAP_1


title: control, naïve, me3, rep3

value: Mushroom body

value: naïve


title: Bend3_StcE_6

value: brain endothelial cells

value: StcE


title: Bend3_StcE_1


title: control, naïve, me3, rep2


title: Non_CD05, Control participants, Ileum tissue

value: Male


title: Bend3_saline_5

value: saline


title: trxKD, trained, me3, rep2

value: trained


title: Non_CD03, Control participants, Ileum tissue

value: Female


title: Non_CD04, Control participants, Ileum tissue


title: Bend3_saline_4


title: H226_P_DMSO_KD_cd81_FOSL1_1

value: Mesothelioma

value: Sensitive to TEAD inhibitor GNE-7883

value: ThermoFisher Cat. #PA5-66880)


title: H226_P_DMSO_KD_FOSL1_TEAD1_1


title: control, trained, me3, rep3

value: H3K4me3 (Diagenode:C15410003)


title: H226_P_DMSO_KD_cd81_YAP_1


title: Bend3_saline_2

value: WT


title: Bend3_saline_3


title: Non_CD02, Control participants, Ileum tissue

value: Ileum

value: Colon cancer


title: control, naïve, me3, rep1


title: control, trained, me3, rep1


title: CD84, CD participants, Ileum tissue

value: Crohn's disease


title: control, trained, me3, rep2


title: Non_CD01, Control participants, Ileum tissue


title: H226_P_DMSO_KD_cd81_TEAD1_1

value: Lung, Epithelial


title: 7883RCL3_G7883-IgG_rep3

value: Resistant to TEAD inhibitor GNE-7883


title: Bend3_saline_1


title: P_G7883-IgG_rep3


title: trxKD, naïve, me1, rep3

value: Mushroom body

value: H3K4me1 (Diagenode:C15410194)

value: naïve


title: CD83, CD participants, Ileum tissue

value: Male


title: mouse cortex, wt, traditional sncRNA-seq, rep1

value: cortex

value: 6 months

value: The 15-50nt RNAs were sequenced with standard protocols.


title: Veh_M_ct62_35

city: Gainesville

first: Spencer

last: Procopio

state: FL

address: 1345 Center Drive

institute: University of Florida

data_processing:
HiPerGator
Alignment: hisat2 with reference Mus_musculus.GRCm38.97.chr.gtf
Deduplication: picard
Raw Counts: htseq
Assembly: mm10 (GRCm38)
Supplementary files format and content: .csv of raw counts from each sample

molecule: polyA RNA

source_name: mouse ventricle

extract_protocol:
Qiagen RNeasy Mini Kit
Preparation of poly-A tail selected RNA libraries (Illumina mRNA Prep kit (Illumina, Inc. CA, USA)) and whole transcriptome sequencing (Novaseq 6000 (Illumina, Inc. CA, USA)),

value: mouse ventricle

value: iCSBmal1 KO

value: Vehicle


title: trxKD, naïve, me1, rep2


title: CD82, CD participants, Ileum tissue


title: Veh_M_ct62_34


title: 7883RCL3_G7883-IgG_rep1

value: Mesothelioma


title: Veh_M_ct58_33


title: CD81, CD participants, Ileum tissue


title: trxKD, naïve, me1, rep1


title: Veh_M_ct58_32


title: trxKD, trained, me1, rep2

value: trained


title: Veh_M_ct54_30


title: P_G7883-IgG_rep1

value: Sensitive to TEAD inhibitor GNE-7883


title: CD78, CD participants, Ileum tissue

value: Ileum

value: Female


title: 7883RCL3_G7883-FOSL1_rep3

value: Lung, Epithelial

value: ThermoFisher Cat. #PA5-66880)


title: trxKD, trained, me1, rep1

value: Mushroom body


title: CD76, CD participants, Ileum tissue

value: Crohn's disease


title: Veh_M_ct50_26


title: control, naïve, me1, rep3

value: H3K4me1 (Diagenode:C15410194)

value: naïve


title: P_G7883-FOSL1_rep3


title: P_DMSO-FOSL1_rep3


title: control, rep4


title: CD75, CD participants, Ileum tissue

value: Male


title: P_DMSO-IgG_rep3


title: Veh_M_ct50_25


title: control, naïve, me1, rep2


title: 7883RCL3_G7883-FOSL1_rep1

value: Resistant to TEAD inhibitor GNE-7883


title: Veh_M_ct46_24


title: control, naïve, me1, rep1


title: CD71, CD participants, Ileum tissue


title: P_G7883-FOSL1_rep1


title: P_DMSO-IgG_rep1


title: trxKD, trained, me1, rep3


title: control, trained, me1, rep3


title: CD77, CD participants, Ileum tissue


title: CD70, CD participants, Ileum tissue


title: P_DMSO-FOSL1_rep1


title: CD68, CD participants, Ileum tissue


title: Veh_M_ct46_23


title: control, trained, me1, rep2


title: CD67, CD participants, Ileum tissue


title: Veh_M_ct42_21


title: Veh_M_ct54_29


title: control, trained, me1, rep1


title: shSPT2_2

city: Dalian

first: Jianxin

last: Wang

state: Liaoning

address: West Lushun South Road

institute: Dalian Medical University

data_processing:
hisat2 for sequence alignment
stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
samtools tools for related file processing
Assembly: hg38
Supplementary files format and content: gene_count_OVCAR-3.xlsx,gene_fpkm_OVCAR-3.xlsx

growth_protocol: Human ovarian cancer cell lines OVCAR-3 were purchased from the American Type Culture Collection. Cells were cultured at 37℃ in 5% CO2 with RPMI-1640 (Gibco) medium supplemented with 10% fetal bovine serum, 100 unit/mL penicillin and 100 mg/mL streptomycin

extract_protocol:
1. Freeze 2ml Eppendorf microcentrifuge tube with tissue sample and glass ball at -80°C and then grind the sample in the MM300 Mixer Mill at 30Hz for two minutes.2. Add 1 ml fresh TRIzol Reagent to the mechanically disrupted tissue sample, vortex well, and incubate the sample at room temperature for 5 minutes.3. Add 0.2 ml of chloroform to the microcentrifuge tube for homogenization. Vortex well, and incubate the sample at room temperature for 3 minutes.4. Centrifugate the sample at maximum speed on table microcentrifuge at 4°C for 5 minutes.5. Transfer the aqueous phase to a fresh 2 ml microcentrifuge tube. Add an equal volume of chloroform to the fresh microcentrifuge tube, vortex well. Spin at maximum speed on table microcentrifuge for 5 minutes.6. Transfer the aqueous phase to a fresh 2 ml microcentrifuge tube. Add an equal volume of isopropanol to the fresh microcentrifuge tube, vortex well. Spin at maximum speed on table microcentrifuge at 4°C for 10 minutes.7. Wash the pellet with 1.5 ml 70% ethanol. Spin at maximum speed on table microcentrifuge for 5 minutes.8. Dissolve the pellet in 400 μl 1xTE at 55°С well with vortex. Add an equal volume of 10 M LiCl to the solution and chill it at -20°C for several hours (or overnight).9. Spin the tube at maximum speed on table microcentrifuge at 4°C for 10 minutes. Carefully remove and discard the supernatant (contains DNA and small RNA < 200 nt).10. Wash pellet with 1.5 ml 70% ethanol, vortex well. Spin the tube at maximum speed on table microcentrifuge at 4°C for 10 minutes. Discard the ethanol, do not dry the pellet.11. Dissolve the pellet in 200-400 μl fresh RNase-free ddH2O or 1xTE.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The lentiviral vectors encoding short hairpin RNAs (GIPZ shRNAs) targeting ZDHHC15 and scrambled shRNA were purchased from Dharmacon (America). The plasmids were transiently transfected into cells with Lipofectamine 3000 (Invitrogen, CA) according to the manufacturer’s protocol. Cells were harvested and analyzed 36 h after transfection.

value: Ovarian cancer

value: Knowdown SPTLC2 gene


title: shSPT2_1


title: Veh_M_ct42_20

value: mouse ventricle

value: iCSBmal1 KO


title: CD66, CD participants, Ileum tissue


title: VSMCs, WT, day 5, biol rep 2

city: Tuebingen

first: Robert

last: Feil

address: Auf der Morgenstelle 34

department: Interfaculty Institute of Biochemistry

institute: University of Tuebingen

description:
Library name: vsmcwt2
10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v3.0.2
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: Matrix files

source_name: aorta

growth_protocol: Cells were grown in full medium at 37 °C and 6 % CO2 for 5 days.

extract_protocol:
Cells were detached with trypsin/EDTA. After addition of full medium and centrifugation, cells were resuspended in PBS with 0.04 % BSA and passed through a 30‑μm filter. The number of viable cells was determined using an automated cell counter.
Libraries were constructed according to the manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics). In short, 10 000 live cells were loaded onto a 10x Genomics microfluidic chip and encapsulated with barcoded oligo-dT-containing gel beads using 10x Genomics Chromium controller.

value: vascular smooth muscle cells

value: aorta

value: wild type


title: Veh_M_ct38_17

value: Vehicle


title: CD73, CD participants, Ileum tissue

value: Ileum


title: shControl_2

value: Negative Control


title: VSMCs, WT, day 5, biol rep 1

description:
Library name: vsmcwt1
10x Genomics


title: Veh_M_ct34_14


title: CD63, CD participants, Ileum tissue


title: IL33-treated LTBR-negative myeloid cells

city: New York

first: Masataka

last: Amisaki

state: NY

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Libraries were diluted to 10nM and clustered on a NovaSeq600 on a pair end read flow cell and sequenced for 28 cycles on R1 (10x barcode and the UMIs), followed by 8 cycles of I7 Index (sample Index), and 89 bases on R2 (transcript), obtaining about 100M clusters per sample.
Primary processing of sequencing images was done using Illumina’s Real Time Analysis software (RTA).
10x Genomics Cell Ranger Single Cell Software suite v3.0.2 was used to perform sample demultiplexing, alignment (mm10), filtering, UMI counting, single-cell 5’end gene counting and performing quality control using the manufacturer parameter.
Assembly: mm10
Supplementary files format and content: Compressed files containing sparse matrices in (MEX) & gzipped TSV files with feature (genes) and barcode sequences of detected cellular barcodes.

growth_protocol: Wild type C57BL/6J mice were injected orthotopically into the pancreas with 1e6 KPC tumor cells. Tumor tissues were harvested 14 days after tumor implantation.

extract_protocol:
Fluorescence activated cell sorting-purified lymhotoxin-beta-positive and -negative myeloid cells were loaded onto to the 10x Genomics Chromium platform to generate Gel Beads-in-Emulsion (GEM). Samples were incubated at 53 °C for 45 min in a C1000 Touch Thermal cycler to generate polyA cDNA barcoded at the 5’end. GEMs were broken and single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads. The cDNA was amplified for 16 cycles. 50ng of cDNA was enzymatically fragmented, end repaired, A-tailed, subjected to a double-sided size selection with SPRIselect beads and ligated to adaptors provided in the kit.
Single-cell RNA-seq libraries were prepared according to 10X Genomics specifications (Chromium Single Cell V(D)J User Guide PN-1000006), see above.

treatment_protocol: Mice were treated with 500 ug of recombinant mouse interleukin-33 every day for 7 days followed by every other days after post tumor implantation.

value: Pancreatic tumor

value: Tumor-infiltrating myeloid cells

value: Recombinant mouse IL33


title: Hey-A8 cells, shSPTLC2_2

data_processing:
hisat2 for sequence alignment
stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
samtools tools for related file processing
Assembly: hg38
Supplementary files format and content: gene_count.txt, gene_fpkm.txt

growth_protocol: Human ovarian cancer cell lines Hey-A8 were purchased from the American Type Culture Collection. Cells were cultured at 37℃ in 5% CO2 with RPMI-1640 (Gibco) medium supplemented with 10% fetal bovine serum, 100 unit/mL penicillin and 100 mg/mL streptomycin

value: Knockdown SPTLC2 gene


title: Veh_M_ct34_13


title: CD62, CD participants, Ileum tissue

value: Crohn's disease


title: IL33-treated LTBR-positive myeloid cells


title: KO_ATM

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

institute: Ewha Womans University

description: Adipose tissue macrophage (ATM) of hMRP8cre+;Hif-1αfl/fl;ApoE-/- mice

data_processing:
Basecalling was performed using CASAVA version 1.8.2.
The reads were aligned to mm9 genome assembly using TopHat version 2.0.9.
The FPKM values were calculated with Cufflinks version 2.2.1.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: tab deliminated gene expression values (FPKM) for each samples

source_name: Mus musculus

growth_protocol: Mice were fed with high-fat diet (D101511; Dyets Inc., Bethlehem, PA) during 12 weeks.

extract_protocol:
Visceral adipose tissue was harvested from WT or KO mice.   Afterwards, adipose tissue macrophages were sorted using F4/80 and CD11b antibodies with FACS machine (MoFlo XDP, Beckman Coulter, USA). Total RNA was extracted by RNeasy RNA isolation kit (Qiagen, Germany).
Sequencing libraries were manually generated for high-throughput sequencing. Poly(A) mRNA was purified using Oligotex Direct mRNA Mini Kit (Qiagen). Enriched mRNA was fragmented by incubating in 5X RNA Fragmentation Buffer (200 mM Tris-acetate (pH 8.1), 150 mM MgOAc, and 500 mM KOAc) at 82 °C for 5 min. cDNA was synthesized by using SuperScript III RT (Invitrogen) and random hexamers with incubation for 30 min at 55 °C. Approximately 500 ng of cDNA of each sample was repaired using the End-It DNA End-Repair Kit (Epicentre Biotechnologies), followed by addition of 3' A base for adaptor ligation. Overnight ligation of polished cDNA with Genomic DNA Adaptors (Illumina), amplification for 18 cycles, and isolation of about 200~500 bp from agarose gel were performed according to the manufacturer’s instructions.

tag: strain

value: visceral adipose tissue macrophage


title: Hey-A8 cells, shCON_2


title: WT_ATM

description: Adipose tissue macrophage (ATM) of hMRP8cre-;Hif-1αfl/fl;ApoE-/- mice


title: CD60, CD participants, Ileum tissue

value: Male


title: Veh_M_ct30_10


title: CD58, CD participants, Ileum tissue


title: PTCHD4si#2_3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0, and the levels of different transcipts were estimated using RSEM v1.2.15.
Differentially abundant RNAs were identified using the edgeR program.
RNAs showing altered expression with p <0.05 and >1.5-fold changes were considered differentially abundant.
Assembly: hg38
Supplementary files format and content: Raw Count

growth_protocol: Human WI-38 diploid fibroblasts (Coriell Institute) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% FBS, 1% antibiotics, and 1% non-essential amino acids (Gibco). Cells were maintained in an incubator at 37 °C and 5% CO2and tested negative for mycoplasma.

extract_protocol:
Total RNA was extracted using a single-step liquid phase separation procedure and the TriPure isolation reagent (Sigma-Aldrich).
Total RNA was extracted from WI-38 cells (~PDL40), 48 h after transfection with siCtrl, siPTCHD4 #1 or siPTCHD4 #2, and sent to Quick Biology (Quick Biology, Pasadena) for further mRNA purification and analysis

treatment_protocol: Silencing interventions were performed by transfecting 50 nM of siRNAs using Lipofectamine (RNAiMax, Invitrogen) following the manufacturer’s instructions.  A non-targeting siRNA pool was purchased from Horizon Discovery (cat. D-001206-14-20).

value: Fetal Lung Fibroblast

value: PTCHD4 silencing Type 2


title: CD65, CD participants, Ileum tissue


title: Hey-A8 cells, shCON_1

value: Ovarian cancer


title: TSCL1_WT

city: Nanjing

first: Zhongyu

last: Zou

state: Jiangsu

address: 101 Longmian Road, Jiangning Campus, Nanjing Medical University, Nanjing, Jiangsu Province, China

institute: Nanjing Medical University

description:
Library name: Sample 3
Column name in raw_counts_All_Samples: TSCL1_WT

data_processing:
The RNA-seq reads of the mRNA were trimmed using Fastp, with rRNA sequences filtered by SortmeRNA , and analysed by Hisat2, featureCounts using mouse reference genome (GRCm38).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample
Library strategy: Ribo-Seq

source_name: testis

extract_protocol:
The mouse testes nuclei were obtained through the Sucrose density gradient , and MicroSpin S-400 Columns were used for purification of ribosome-protected fragments (RPFs) after Nuclease and RNase Inhibitor treatment.
Purify RPFs RNA samples using modified RNA Clean& Concentrator-25 Kit.After enrichment using Oligo (dT) beads, the RNA was fragmented and reverse-transcribed into cDNA using random primers, followed by purification using the QiaQuick PCR extraction kit. After end repair, poly(A) addition and ligation to Illumina sequencing adapters, the ligation products were size-selected using agarose gel electrophoresis, PCR-amplified and sequenced using HiSeq2500 (Illumina) by Gene Denovo Biotechnology.

value: testis


title: TSCL1_Lnc_KO2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples: TSCL1_Lnc_KO2


title: TSCL1_Lnc_KO1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples: TSCL1_Lnc_KO1


title: shControl_1


title: PTCHD4si#2_2


title: Veh_M_ct22_5

value: mouse ventricle

value: iCSBmal1 KO


title: CD56, CD participants, Ileum tissue

value: Female


title: CD61, CD participants, Ileum tissue


title: PTCHD4si#2_1


title: CD4 T cells CCR6highCCR2Positive, ST, D2

city: Bethesda

first: Farhat

last: Parween

state: MD

address: 10 Center Drive

department: NIAID

institute: NIH

description:
Library name: Sample 20
Column name in all.tpm CCR6posCCR2pos_ST_D2_AB3280
Column name in raw_counts.txt CCR6posCCR2pos_ST_D2_AB3280.sorted.dedup.bam

data_processing:
Adapter trimming was done using trimmomatic
alignment to the human reference genome was done with STAR
duplicate reads were removed using Picard MarkDuplicates tool; and number of reads per gene per sample were counted using the featureCounts software from the subread packag
Differential gene expression analysis was done in R (v4.2.1) using DESeq2 package
Assembly: GRCh38
Supplementary files format and content: txt file includes raw counts
Supplementary files format and content: txt file inclused tmp counts

source_name: Human Blood

growth_protocol: After purification by FACS, human primary CD4+ T cells were cultured overnight in RPMI media supplemented with 10 % FBS

extract_protocol:
Extraction of total RNA was done from all samples using RNeasy mini kit (Qiagen). 50 ng total RNA input per sample for construction of sequencing library
library preparation was completed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® using manufacturer's protocol

treatment_protocol: For ST(stimulated samples) cells were treated with PMA for three hours

value: Human Blood

value: Primary cells

value: CD4 T cells

value: PMA-Stimulated


title: Veh_M_ct30_11

value: Vehicle


title: CD54, CD participants, Ileum tissue

value: Ileum


title: Veh_M_ct38_16


title: PTCHD4si#1_3

value: PTCHD4 silencing Type 1


title: CD4 T cells CCR6high, ST, D2

description:
Library name: Sample 19
Column name in all.tpm CCR6high_ST_D2_AB3279
Column name in raw_counts.txt CCR6high_ST_D2_AB3279.sorted.dedup.bam


title: Veh_M_ct26_8


title: Veh_M_ct18_3


title: CD52, CD participants, Ileum tissue

value: Crohn's disease


title: PTCHD4si#1_2


title: CD57, CD participants, Ileum tissue


title: Veh_M_ct26_7


title: CD51, CD participants, Ileum tissue


title: Hey-A8 cells, shSPTLC2_1

value: Knockdown SPTLC2 gene


title: CD4 T cells CCR6 negative, ST, D2

description:
Library name: Sample 17
Column name in all.tpm CCR6neg_ST_D2_AB3277
Column name in raw_counts.txt CCR6neg_ST_D2_AB3277.sorted.dedup.bam


title: Veh_M_ct18_2


title: CD50, CD participants, Ileum tissue


title: PTCHD4si#1_1


title: Veh_F_ct62_458


title: CD4 T cells Naïve, ST, D2

description:
Library name: Sample 16
Column name in all.tpm Naive_ST_D2_AB3276
Column name in raw_counts.txt Naive_ST_D2_AB3276.sorted.dedup.bam


title: Veh_F_ct62_457


title: CD49, CD participants, Ileum tissue


title: CTRLsi_3

value: Control


title: CTRLsi_2

value: Fetal Lung Fibroblast


title: CD4 T cells CCR6highCCR2Positive, NS, D2

description:
Library name: Sample 15
Column name in all.tpm CCR6posCCR2pos_NS_D2_AB3275
Column name in raw_counts.txt CCR6posCCR2pos_NS_D2_AB3275.sorted.dedup.bam

value: NS


title: CD48, CD participants, Ileum tissue

value: Male


title: Veh_F_ct58_453


title: CTRLsi_1


title: Veh_M_ct22_4


title: CD4 T cells CCR6high, NS, D2

description:
Library name: Sample 14
Column name in all.tpm CCR6high_NS_D2_AB3274
Column name in raw_counts.txt CCR6high_NS_D2_AB3274.sorted.dedup.bam


title: CD46, CD participants, Ileum tissue


title: Veh_F_ct58_452


title: IP_IR_3

data_processing:
Data analysis was performed by Eclipsebio.
Clusters were identified using the peak caller CLIPper.  Each peak was normalized against the paired input sample.
Only m6A peaks that meet a cutoff of log2 fold change ≥3 and -log10(p-value) ≥3 were considered.
Reproducible peaks among triplicates were identified using the tool IDR
Clusters are found using the peak calling tool CLIPper. The clusters identified in the IP sample are then normalized against a paired input sample. A peak is defined as a cluster with log2 fold enrichment ≥ 3 and p-value ≤ 0.001. The table below shows information about each peak. The log2 fold change refers to the fold enrichment in eCLIP versus the paired input determined by Yates' Chi-square Test or Fisher's Exact Test.
Assembly: hg38
Supplementary files format and content: m6A peaks

extract_protocol:
Total RNA was extracted using a single-step liquid phase separation procedure and the TriPure isolation reagent (Sigma-Aldrich).
Sample preparation for the m6A-eCLIP analysis was performed with the m6A-eCLIP Kit (EclipseBio)

treatment_protocol: Total RNA from proliferating (PDL22) and senescent (10 Gy IR, harvested 10 days later) WI-38 cells was chemically fragmented into 100 nucleotides or smaller fragments, followed by UV crosslinking and magnetic immunoprecipitation with an m6A antibody. After immunoprecipitation, isolated RNA fragments were subjected to library preparation including adapter ligation, reverse transcription, and PCR amplification

value: m6A IP IR


title: CD45, CD participants, Ileum tissue


title: CD4 T cells CCR6low, ST, D2

description:
Library name: Sample 18
Column name in all.tpm CCR6low_ST_D2_AB3278
Column name in raw_counts.txt CCR6low_ST_D2_AB3278.sorted.dedup.bam


title: Veh_F_ct54_448

value: mouse ventricle


title: CD44, CD participants, Ileum tissue


title: Veh_F_ct54_447

value: iCSBmal1 KO


title: CD4 T cells CCR6low, NS, D2

description:
Library name: Sample 13
Column name in all.tpm CCR6low_NS_D2_AB3273
Column name in raw_counts.txt CCR6low_NS_D2_AB3273.sorted.dedup.bam


title: IP_IR_1


title: CD4 T cells CCR6 negative, NS, D2

description:
Library name: Sample 12
Column name in all.tpm CCR6neg_NS_D2_AB3272
Column name in raw_counts.txt CCR6neg_NS_D2_AB3272.sorted.dedup.bam


title: CD42, CD participants, Ileum tissue


title: CD4 T cells Naïve, NS, D2

description:
Library name: Sample 11
Column name in all.tpm Naive_NS_D2_AB3271
Column name in raw_counts.txt Naive_NS_D2_AB3271.sorted.dedup.bam


title: Veh_F_ct50_444


title: Veh_F_ct50_445


title: CD4 T cells CCR6highCCR2Positive, ST, D1

description:
Library name: Sample 10
Column name in all.tpm CCR6high_NS_D1_AB3264
Column name in raw_counts.txt CCR6posCCR2pos_ST_D1_AB3270.sorted.dedup.bam


title: IP_Prol_3

value: m6A IP Proliferating


title: CD41, CD participants, Ileum tissue


title: CD4 T cells CCR6high, ST, D1

description:
Library name: Sample 9
Column name in all.tpm CCR6high_ST_D1_AB3269
Column name in raw_counts.txt CCR6high_ST_D1_AB3269.sorted.dedup.bam

value: Human Blood


title: Veh_F_ct46_439


title: IP_Prol_2


title: CD40, CD participants, Ileum tissue


title: IP_Prol_1


title: Veh_F_ct46_438


title: CD39, CD participants, Ileum tissue

value: Female


title: Input_IR_3

value: Input IR


title: CD38, CD participants, Ileum tissue


title: Input_IR_2


title: IP_IR_2


title: CD4 T cells CCR6 negative, ST, D1

description:
Library name: Sample 7
Column name in all.tpm CCR6neg_ST_D1_AB3267
Column name in raw_counts.txt CCR6neg_ST_D1_AB3267.sorted.dedup.bam

value: Primary cells

value: CD4 T cells

value: PMA-Stimulated


title: CD4 T cells Naïve, ST, D1

description:
Library name: Sample 6
Column name in all.tpm Naive_ST_D1_AB3266
Column name in raw_counts.txt Naive_ST_D1_AB3266.sorted.dedup.bam


title: CD37, CD participants, Ileum tissue

value: Ileum


title: Veh_F_ct42_433

value: Vehicle


title: CD4 T cells CCR6highCCR2Positive, NS, D1

description:
Library name: Sample 5
Column name in all.tpm CCR6posCCR2pos_NS_D1_AB3265
Column name in raw_counts.txt CCR6posCCR2pos_NS_D1_AB3265.sorted.dedup.bam


title: CD36, CD participants, Ileum tissue

value: Crohn's disease


title: Input_IR_1


title: Veh_F_ct38_429


title: Input_Prol_3

value: Input Proliferating


title: CD35, CD participants, Ileum tissue


title: Veh_F_ct38_427


title: CD4 T cells CCR6high, NS, D1

description:
Library name: Sample 4
Column name in all.tpm CCR6high_NS_D1_AB3264
Column name in raw_counts.txt CCR6high_NS_D1_AB3264.sorted.dedup.bam


title: Veh_F_ct34_423


title: Input_Prol_2

value: Fetal Lung Fibroblast


title: CD34, CD participants, Ileum tissue


title: Input_Prol_1


title: CD33, CD participants, Ileum tissue


title: CD4 T cells CCR6low, NS, D1

description:
Library name: Sample 3
Column name in all.tpm CCR6low_NS_D1_AB3263
Column name in raw_counts.txt CCR6low_NS_D1_AB3263.sorted.dedup.bam

value: NS


title: CD4 T cells CCR6low, ST, D1

description:
Library name: Sample 8
Column name in all.tpm CCR6low_ST_D1_AB3268
Column name in raw_counts.txt CCR6low_ST_D1_AB3268.sorted.dedup.bam


title: CD4 T cells CCR6 negative, NS, D1

description:
Library name: Sample 2
Column name in all.tpm CCR6neg_NS_D1_AB3262
Column name in raw_counts.txt CCR6neg_NS_D1_AB3262.sorted.dedup.bam


title: Veh_F_ct34_422


title: CD4 T cells Naïve, NS, D1

description:
Library name: Sample 1
Column name in all.tpm Naive_NS_D1_AB3261
Column name in raw_counts.txt Naive_NS_D1_AB3261.sorted.dedup.bam


title: NCI-H226_CL3, NCI-H226, HTO

description: DNA-seq

data_processing:
Cellranger + ArchR
scMultiome data processing of sequencing reads was performed using our Single Cell Multiome ATAC + Gene Expression (ARCSeq) - 10X Cellranger (v2.0.0) bioinformatics pipeline which implements the CellRanger ARC seq (cellranger-arc count ) workflow (cellranger-arc_2.0.0) using the GRCh38 genome reference. ATAC-seq (atac_fragments.tsv.gz) and scRNA-seq (raw_feature_bc_matrix.h5) matrices were generated from fastq files. Approximately 200 million read pairs were generated for ATAC and Gene expression data types with more than 92% mapping to the human genome.
The cell hashing (hashed-tag oligonucleotide (HTO)) (.hashing.tsv) feature count matrix was generated with  cumulus_feature_barcoding (https://github.com/lilab-bcb/cumulus_feature_barcoding) (v0.11.1). This  barcode count matrix was then used to demultiplex the scRNAseq data using a DropleUtils (v1.21.0)-based  workflow with the emptyDrops(test.ambient = TRUE, by.rank=30000) and hashedDrops(  doublet.nmads=3, doublet.min=2, confident.nmads=1, confident.min=1) key steps and parameters. At this  point, 13,587 raw cells with valid barcodes were kept for downstream analyses.   ATAC-seq data was processed with ArchR v1.0.3. Briefly, low quality cells were removed (minTSS>4 and  minFrags>1000) and arrow files were generated followed by generation of Tile and Gene Score matrices  using a tile size of 500 bp. Doublets were identified and filtered out using ArchR’s addDoubletScores()  function with default parameters.  Filtered ATACSeq data was merged with the demultiplexed scRNAseq data which yielded a total of 4,952  cells and was assessed for quality (SI) before moving forward. Cells were clustered using the previously  generated 500 bp peaks tile matrix (addIterativeLSI(), addClusters() and addUMAP()) . Resulting clusters  were visualized and labeled according to their experimental conditions using the following names:  Sensitive_side, Sensitive_DMSO, Sensitive_GNE7883 and Resistant_side and Resistant_main. Peaks  were generated using addReproduciblePeakSet() with macs2. Peaks were annotated with  addPeakAnnotations()(using public databases from chipatlas.org; encodeproject.org) followed by  addDeviationsMatrix().  The peaks.mtx.gz and gex.mtx.gz files contains processed peaks and gene expression count data for the 4 HTOs (LIB5456248_SAM24416358.hashing_parsed.tsv.gz) relevant to this study.
Assembly: GRCh38.p10
Supplementary files format and content: peaks.mtx.gz
Supplementary files format and content: gex.mtx.gz
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: LIB5456248_SAM24416358.hashing_parsed.tsv.gz
Supplementary files format and content: NOTE: Final output: gex.mtx.gz: columns = single-cell barcodes           rows = features     gex_features.tsv: row names of gex.mtx.gz     gex_peaks_barcodes.tsv: column names of gex.mts.gz AND peaks.mtx.gz              peaks.mtx.gz: ArchR peaks where columns = single-cell barcodes                                     rows = peak features     peaks_features.tsv: row names of peaks.mtx.gz
Supplementary files format and content: NOTE: Output of cellranger: barcodes.tsv.gz: single-cell barcodes. corresponds to column names of matrix.mtx.gz matrix.mtx.gz: raw gene and peak counts where column names = barcodes.tsv.gz                                          row names = features.tsv.gz *gene and peak features concatenated together in the same file.
Library strategy: DNA-seq

growth_protocol: Cell lines were maintained in RPMI 1640 supplemented with 10% FBS and 2 mM L-glutamine in a humidified incubator maintained at 37 °C with 5% CO2. TEAD SMI resistant NF2 null NCI-H226 (i.e. NCI-H226_CL3) cells were generated by incubation with increasing concentrations of TEAD SMI over time (0.25 μM to 3 μM at bi-weekly with 0.1-0.5 μM increments), ensuring at least a 25% confluence at all times.

extract_protocol:
The multiplexed single-cell Multiome (scMultiome) assay was performed following the TEA-seq 71 protocol with some modifications. Briefly, the cells were cultured and treated with different compounds in 6-well plates. Upon harvesting, the cells were trypsinized to single cell suspension, washed once by PBS.
Samples from different conditions were labeled by the TotalSeq-A cell hashing antibodies with different hashtags (Biolegend) by incubating on ice for 20 minutes. After washing twice by PBS, the samples were pool together and permeabilized by the isotonic permeabilization buffer (20 mM Tris-HCl pH 7.4, Rnase Inhibitor 1 U/μL, 150 mM NaCl, 3 mM MgCl2, 0.01% digitonin) on ice for 15 minutes. Then the samples were washed with the isotonic buffer without digitonin, counted and immediately proceeded to the tagmentation step. We followed the standard protocol of 10X Multiome assay (10X Genomics) for  sample tagmentation and droplet generation. When performing the pre-amp PCR and cDNA amplification, 1μl of 100μM HTO additive primer (5’ GTGACTGGAGTTCAGACGTGTGCTC-3’) was added to help amplify the HTO. After cDNA amplification, save the supernatant from the 0.6X SPRI beads cleanup step to build the HTO libraries. The HTO library construction is following the standard cell hashing protocol.  For each 10X channel, 3 types of libraries were constructed: ATAC, GEX and HTO. The 3 types of libraries were sequenced on Illumina NovaSeq and NextSeq sequencers with roughly 30K, 20K and 2K raw reads per cell, respectively.

value: Lung, Epithelial

value: Mesothelioma


title: H226_P_DMSO_KD_FOSL1_TEAD1_2

value: Sensitive to TEAD inhibitor GNE-7883


title: CD32, CD participants, Ileum tissue

value: Male


title: Veh_F_ct30_417

value: mouse ventricle

value: iCSBmal1 KO


title: MCF10A AKT3OE 2

city: Dallas

first: Rolf

last: Brekken

state: TX

address: 6000 Harry Hines Blvd

institute: The University of Texas Southwestern Medical Center

data_processing:
Raw RNAseq reads were aligned against to the human genome release GRCh38/hg38 using HISAT2
exons were counted using RSubread.featureCounts
Libraries were filtered to remove gene counts of less than 1 CPM across all libraries and normalized.
Assembly: hg38
Supplementary files format and content: csv file

growth_protocol: Cells were plated on 10 cm dishes, grown in DMEM/F12 medium supplemented with 5% horse serum, 20 ng/mL of EGF, 0.5 μg/mL of hydrocortisone, 100 ng/mL cholera toxin, 10 μg/mL of insulin, 100 U/mL of penicillin and 100 μg/mL of streptomycin until cell densities of 70% were achieved.

extract_protocol:
Total RNA was extracted from cells using QIAGEN RNeasy Mini kit and stored at -80ºC
1 μg total RNA per sample were subjected to library generation using the TruSeq stranded total RNA sample preparation kit, according to the manufacturer's protocol (Illumina).

treatment_protocol: MCF10A cells were exposed to retro-virus-containing supernatant supplemented with 5 μg/mL prot-amine sulfate overnight. Infected cells were selected with 1 μg/mL puromycin.

value: immortalized epithelial cell

value: AKT3 overexpression


title: Veh_F_ct30_418


title: NCI-H226_CL3, NCI-H226, ATAC

description: ATAC-seq

library_source: genomic single cell

data_processing:
Cellranger + ArchR
scMultiome data processing of sequencing reads was performed using our Single Cell Multiome ATAC + Gene Expression (ARCSeq) - 10X Cellranger (v2.0.0) bioinformatics pipeline which implements the CellRanger ARC seq (cellranger-arc count ) workflow (cellranger-arc_2.0.0) using the GRCh38 genome reference. ATAC-seq (atac_fragments.tsv.gz) and scRNA-seq (raw_feature_bc_matrix.h5) matrices were generated from fastq files. Approximately 200 million read pairs were generated for ATAC and Gene expression data types with more than 92% mapping to the human genome.
The cell hashing (hashed-tag oligonucleotide (HTO)) (.hashing.tsv) feature count matrix was generated with  cumulus_feature_barcoding (https://github.com/lilab-bcb/cumulus_feature_barcoding) (v0.11.1). This  barcode count matrix was then used to demultiplex the scRNAseq data using a DropleUtils (v1.21.0)-based  workflow with the emptyDrops(test.ambient = TRUE, by.rank=30000) and hashedDrops(  doublet.nmads=3, doublet.min=2, confident.nmads=1, confident.min=1) key steps and parameters. At this  point, 13,587 raw cells with valid barcodes were kept for downstream analyses.   ATAC-seq data was processed with ArchR v1.0.3. Briefly, low quality cells were removed (minTSS>4 and  minFrags>1000) and arrow files were generated followed by generation of Tile and Gene Score matrices  using a tile size of 500 bp. Doublets were identified and filtered out using ArchR’s addDoubletScores()  function with default parameters.  Filtered ATACSeq data was merged with the demultiplexed scRNAseq data which yielded a total of 4,952  cells and was assessed for quality (SI) before moving forward. Cells were clustered using the previously  generated 500 bp peaks tile matrix (addIterativeLSI(), addClusters() and addUMAP()) . Resulting clusters  were visualized and labeled according to their experimental conditions using the following names:  Sensitive_side, Sensitive_DMSO, Sensitive_GNE7883 and Resistant_side and Resistant_main. Peaks  were generated using addReproduciblePeakSet() with macs2. Peaks were annotated with  addPeakAnnotations()(using public databases from chipatlas.org; encodeproject.org) followed by  addDeviationsMatrix().  The peaks.mtx.gz and gex.mtx.gz files contains processed peaks and gene expression count data for the 4 HTOs (LIB5456248_SAM24416358.hashing_parsed.tsv.gz) relevant to this study.
Assembly: GRCh38.p10
Supplementary files format and content: peaks.mtx.gz
Supplementary files format and content: gex.mtx.gz
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: LIB5456248_SAM24416358.hashing_parsed.tsv.gz
Supplementary files format and content: NOTE: Final output: gex.mtx.gz: columns = single-cell barcodes           rows = features     gex_features.tsv: row names of gex.mtx.gz     gex_peaks_barcodes.tsv: column names of gex.mts.gz AND peaks.mtx.gz              peaks.mtx.gz: ArchR peaks where columns = single-cell barcodes                                     rows = peak features     peaks_features.tsv: row names of peaks.mtx.gz
Supplementary files format and content: NOTE: Output of cellranger: barcodes.tsv.gz: single-cell barcodes. corresponds to column names of matrix.mtx.gz matrix.mtx.gz: raw gene and peak counts where column names = barcodes.tsv.gz                                          row names = features.tsv.gz *gene and peak features concatenated together in the same file.


title: NCI-H226_CL3, NCI-H226, GEX

description: scRNA-seq


title: CD31, CD participants, Ileum tissue

value: Female


title: MCF10A AKT3OE 1


title: Veh_F_ct42_434


title: CD30, CD participants, Ileum tissue


title: MCF10A Control 3

value: Control Vector


title: Veh_F_ct26_414


title: Veh_F_ct26_412


title: CD29, CD participants, Ileum tissue


title: NCI-H226 G7883 CL3

description: Exome-seq

data_processing:
Genome Analysis Toolkit (GATK) Best Practices recommendations,
Reads were aligned to GRCh38 using BWA (v0.7.15-r1140). In  accordance with the Genome Analysis Toolkit (GATK) Best Practices recommendations, Picard Tools  v2.18 was employed to eliminate redundant reads, and base score recalibration was carried out using  GATK (v4.1.4.1).
Copy numbers were determined using the GATK best practices for detecting copy ratio alterations (GATK  4.2.6.1, Article#11682 & Article#11683). In short, exome capture regions underwent preprocessing using  PreprocessIntervals with a padding of 250 bp. Overlapping intervals were merged. Reads were then  counted in each of the resulting intervals for all samples using CollectReadCounts. GATK CNV supports  single sample panel of normals by using CreateReadCountPanelOfNormals (-minimum-interval-median  percentile 5) to create a single-sample projection which can be used for denoising via DenoiseReadCounts.  The denoising process standardizes reads to the PoN median count and centers the data around 1. The  denoised read counts are then grouped into contiguous segments using a Gaussian-kernel binary  segmentation algorithm via ModelSegements (default settings, without allelic count data). The mean  log2(copy number) value is then assigned to the genes within that segment and used for gene-level copy  number comparisons. The parental line was used to generate the PoN and denoise the read counts from  the resistant lines.
Starting from the processed read alignments described above, variant calling using MuTect2 (from GATK  v4.1.4.1), Strelka (v.1.0.15; https://doi.org/10.1038/s41592-018-0051-x) and LoFreq (v2.1.3.1;  https://doi.org/10.1093/nar/gks918) was performed. MuTect2 was executed by using gatk Mutect2 followed by FilterMutectCalls. Strelka variants were obtained by running the software with default bwa parameters. For LoFreq, sensitive and resistant bam files were first processed with the indelqual command followed by the somatic command to generate variant calls. Here we specifically investigated  for mutations potentially present in the TEAD1, TEAD2, TEAD3, TEAD4, FOSL1, YAP1 and WWTR1  genes. Obtained variants from all three callers were annotated with transvar (v.2.5.10.20211024;  https://doi.org/10.1038/nmeth.3622). For each of the seven genes of interest, the transvar output was  filtered to keep only the transcripts associated with the canonical uniprot accession identifiers. The  predicted mutations (position and nature of amino acid modification) on the protein sequences were used  for protein structural analysis.
Assembly: GRCh38.p10
Library strategy: Exome-seq

extract_protocol:
H226/ H226-7883R cells were trypsinized into single-cell suspension with 0.05% Trypsin, EDTA 0.5 mM.  500k cells were used for each reaction.
DNA from both the tumor sensitive and tumor TEADi-resistant cell lines were extracted and fragmented  into 200 bp fragments. Whole exome was captured using Agilent Sureselect Human All Exon V7  (S31285117) and sequenced on a HiSeq1 system (Illumina) using a 2 x 75 bp configuration which yielded  an average of 86 million reads per library.

value: Resistant to TEAD inhibitor GNE-7883


title: MCF10A Control 2


title: NCI-H226 DMSO (83)

description: Exome-seq


title: CD28, CD participants, Ileum tissue

data_processing:
The RNA sequencing reads were trimmed using Cutadapt (v.3.7) in paired-end mode.(parameter- Quality : 20 minimum length : 20)
The filtered reads were mapped to the reference genome GRCH38 using STAR software v2.7.9a(parameter- default)
Quantification of the gene expression levels was performed using RNA-SeQC v2.1.2(parameter- default)
Assembly: GRCH38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

value: Ileum


title: Resistant_GNE-7883_rep3

data_processing:
HTSeqGenie
Reads characterized by low nucleotide qualities (defined as having 70% of bases with quality scores below 23) or those matching rRNA and adapter sequences were excluded. The remaining reads were aligned to the human reference genome (human: GRCh38.p10) using GSNAP (2013-10-10-v2; PMID:20147302, 27008021) with a maximum allowance of two mismatches per 75-base sequence (utilizing parameters: '-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). Transcript annotation relied on the GENCODE genes database (human: GENCODE 27).
For the quantification of gene expression levels, the count of reads unambiguously mapping to the exons of each gene was computed. Differential gene expression was performed with relevant contrasts using the “voom” function of the limma package. A pre-filter was applied so that only genes with at least a median CPM (counts per million mapped reads) value of 10 in one were analyzed. P-values for other genes were left out and not included in downstream steps including the multiple testing correction. Counts were normalized using trimmed mean of M-values (TMM). Q-values were obtained by correcting P-values for multiple hypotheses using the Benjamini-Hochberg procedure. Genes were considered if they had a Q-value of less than 0.05 and were protein-coding.
Assembly: GRCh38.p10
Supplementary files format and content: tab delimited text file includes raw counts of each sample.
Supplementary files format and content: tab delimited text file includes normalized RPKM counts of each sample.

extract_protocol:
Cell lines were lysed on-plate for RNA isolation using the Qiagen RNeasy Plus Mini kit (Cat. No. 74034), and RNA concentration was determined using a NanoDrop 8000 (Thermo Fisher Scientific).  RNA integrity was confirmed using a “Bioanalyzer 2100 (Agilent Technologies).
About 500 ng of RNA was used for library synthesis using the TrueSeq RNA Sample Preparation kit v2 (Illumina). Size of the libraries was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies), and the concentration was determined by a qPCR-based method using the Library Quantification Kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate an average of 56 million single-end 50-base reads per sample.


title: MCF10A Control 1


title: Veh_F_ct22_408

value: Vehicle


title: CD27, CD participants, Ileum tissue

value: Crohn's disease


title: Veh_F_ct22_409


title: H226_resistant_7883_YAP_rep2

data_processing:
ChIP-seq results were analyzed using the ENCODE ChIP-seq pipeline (v2.2.1)
ChIP-seq reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.4.3)
Aligned reads were then filtered for quality and duplicates using samtools (v1.9) and Picard (Broad Institute - v2.20.7).
The SPP peak caller was used to call ChIP-seq peaks for FOSL1 and YAP
Peak sets were filtered using a list of genomic regions that contain anomalous, unstructured, or experiment independent high signal
Assembly: hg38.p10
Supplementary files format and content: bigWig - .bigwig
Supplementary files format and content: bed - narrowPeak.gz

extract_protocol:
NCI-H226 mesothelioma cells (20 x 106) were double crosslinked with 50mM DSG (disuccinimidyl glutarate, #C1104 - ProteoChem) for 30-minutes followed by 10-minutes of 1% formaldehyde. Formaldehyde was quenched by the addition of glycine. Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0). Nuclei were sheared with Covaris sonicator using the following setup: Fill level – 10, Duty Cycle – 15, PIP – 350, Cycles/Burst – 200, Time – 8-minutes). Sheared chromatin was immunoprecipitated overnight with the following antibodies: FOSL1 (PA5-66880 – Invitrogen), YAP (14074S – Cell Signaling). Antibody chromatin complexes were pulled down with Protein A magnetic beads and washed twice in IP wash buffer I. (1% Triton, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer II. (1% Triton, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer III. (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC) and once in TE buffer (10 mM EDTA and 200 mM Tris, pH 8.0). DNA was eluted from the beads by vigorous shaking for 20-minutes in elution buffer (100mM NaHCO3, 1% SDS). DNA was de-crosslinked overnight at 65C and purified with MinElute PCR purification kit (Qiagen).
DNA was quantified by Qubit and equal amounts (2ng) of DNA was used for sequencing library construction with the Ovation Ultralow Library System V2 (Tecan) using 15 PCR cycles according to the manufacturer’s recommendations.

treatment_protocol: Parental cells were treated with TEAD SMI for 48-hours (1uM) in the acute treatment paradigm, while resistant cells were cultured in the presence of the TEAD SMI (2.5uM).


title: CD26, CD participants, Ileum tissue

extract_protocol:
RNA was extracted using Rneasy Plus Mini Kit (Qiagen, Tokyo, Japan).
The sequencing libraries were prepared with the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Globin (Illumina, CA, United States)


title: Resistant_GNE-7883_rep2


title: Resistant_GNE-7883_rep1


title: Resistant_DMSO_rep3


title: H226_parental_7883_YAP_rep2


title: CD25, CD participants, Ileum tissue


title: Veh_F_ct18_404

data_processing:
HiPerGator
Alignment: hisat2 with reference Mus_musculus.GRCm38.97.chr.gtf
Deduplication: picard
Raw Counts: htseq
Assembly: mm10 (GRCm38)
Supplementary files format and content: .csv of raw counts from each sample


title: Veh_F_ct18_403


title: CD24, CD participants, Ileum tissue


title: Resistant_DMSO_rep2


title: Tam_M_ct62_596

value: Tamoxifen


title: Tam_M_ct58_594


title: Tam_M_ct62_598


title: H226_resistant_7883_FOSL1_rep2

value: ThermoFisher Cat. #PA5-66880)


title: H226_parental_YAP_rep2


title: Resistant_DMSO_rep1


title: CD23, CD participants, Ileum tissue


title: CD22, CD participants, Ileum tissue


title: H226_parental_7883_FOSL1_rep2


title: Sensitive_GNE-7883_rep2


title: Tam_M_ct54_556


title: Sensitive_GNE-7883_rep3


title: Sensitive_GNE-7883_rep1


title: Tam_M_ct54_555


title: CD21, CD participants, Ileum tissue


title: H226_resistant_7883_YAP_rep1


title: H226_parental_FOSL1_rep2


title: CD19, CD participants, Ileum tissue


title: Tam_M_ct58_562


title: H226_parental_7883_YAP_rep1


title: CD20, CD participants, Ileum tissue


title: Sensitive_DMSO_rep3


title: H226_resistant_7883_FOSL1_rep1


title: CD17, CD participants, Ileum tissue


title: Tam_M_ct50_549


title: Sensitive_DMSO_rep1


title: CD16, CD participants, Ileum tissue


title: Tam_M_ct46_543


title: H226_parental_YAP_rep1


title: CD15, CD participants, Ileum tissue


title: Tam_M_ct50_550


title: TEB-029;N2

city: Krems

first: Christine

last: Hafner

address: Dr.-Karl-Dorrek-Straße 30

country: Austria

institute: Karl Landsteiner University of Health Sciences

description:
SS02024
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

data_processing:
On average, 12 million and 7.6 million reads per sample were generated for allergic and healthy individuals, respectively. Reads in fastq format were generated using the Illumina bcl2fastq command line tool (v2.19.1.403).
Reads were trimmed and filtered using cutadapt version 2.8 to trim polyA tails, remove reads with N’s and trim bases with a quality of less than 30 from the 3’ ends of the reads. On average, 7 million and 5 million reads were left after this procedure for allergic and healthy individuals, respectively.
Trimmed reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations  using STAR aligner version 2.6.1a in 2-pass mode. Raw reads per gene were counted by STAR.
Differential gene expression was calculated using DESeq2 version 1.22.2.
Assembly: Genome version GRCh38 with Gencode 29 annotations
Supplementary files format and content: Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv: File containing raw counts per gene from ReadsPerGene.out.tab generated by STAR aligner (allergic samples); Columns: GeneType, GeneSymbol Ensembl Gene ID , sampleIDs with raw counts (all integer numbers)
Supplementary files format and content: Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv:File containing raw counts per gene from ReadsPerGene.out.tab generated by STAR aligner (nonallergic samples); Columns: GeneType, GeneSymbol Ensembl Gene ID , sampleIDs with raw counts (all integer numbers)
Supplementary files format and content: Allergic_vst_transf_counts_GeneSymbols_GeneTypes.tsv: File containing variance-stabilizing-transformed count data (allergic samples), generated by DESeq2 function vst . Columns: GeneType, GeneSymbol, Ensembl Gene ID, sampleIDs with vst transformed counts
Supplementary files format and content: Nonllergic_vst_transf_counts_GeneSymbols_GeneTypes.tsv: File containing variance-stabilizing-transformed count data (nonallergic samples), generated by DESeq2 function vst . Columns: GeneType, GeneSymbol, Ensembl Gene ID, sampleIDs with vst transformed counts
Supplementary files format and content: Allergic_paired_T15.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (allergic samples; provocation 15 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Allergic_paired_T30.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (allergic samples; provocation 30 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Allergic_paired_T60.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (allergic samples; provocation 60 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Allergic_paired_T120.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (allergic samples; provocation 120 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Non-allergic_paired_T15.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (non-allergic samples; provocation 15 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Non-allergic_paired_T30.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (non-allergic samples; provocation 30 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Non-allergic_paired_T60.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (non-allergic samples; provocation 60 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Non-allergic_paired_T120.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (non-allergic samples; provocation 120 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)

source_name: Nasal mucosa

extract_protocol:
The nasal scrapings were immediately transferred to lysis buffer (RLT buffer, RNeasy micro kit, Qiagen, Germany) and kept on ice until total RNA was isolated using the protocol as described by the manufacturer. The RNA quality and concentration was determined by 2100 Bioanalyser instrument (Agilent).
Sequencing libraries from total RNA were prepared at the Core Facility Genomics, Medical University of Vienna, using the QuantSeq FWD protocol (Lexogen). 21 PCR cycles were used for library prep, as determined by qPCR according to the library prep manual. Libraries were QC-checked on a Bioanalyzer 2100 (Agilent) using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay (Invitrogen). Pooled libraries were sequenced on a NextSeq500 instrument (Illumina) in 1x75bp single-end sequencing mode.

value: Nasal mucosa

value: Non-allergic

value: Birch pollen extract

tag: time point

value: 30 min

value: male

tag: date of_sample_acquisition


title: Tam_M_ct46_588

value: mouse ventricle


title: Peripheral blood NK cells, hashtagged, Donor2

first: M. Kazim

last: Panjwani

address: 408 E 69th St

institute: MSKCC

description:
sex: XY
10x Genomics

data_processing:
The software Cell Ranger (version 5.0.1; 10x Genomics) was used for demultiplexing and alignment using default parameters. Velocyto (version 0.17.17) performed counting of spliced and un-spliced RNA molecules. Pre-processing and quality control of the data was carried out using the Python software package SCANPY (version 1.8.1). Cells that expressed low gene numbers, reading depth (counts) or high mitochondrial or ribosomal gene percentage were removed, the borders for these parameters were adapted according to the experiment. Cell cycle and mitochondrial genes were regressed out. SCANPY was also used to perform dimensionality reduction and clustering. The neighborhood graphs were based on 40 principal components and 80 neighbors. Clustering was performed using the Leiden algorithm with resolution r = 1.1. UMAP dimensionality reduction was computed using SCANPY’s default parameters. The software tool scvelo (version 0.2.2) was used to compute RNA velocities within a deterministic model.
Assembly: hg38
Supplementary files format and content: Cellranger raw output tab-separated value and matrix files (barcodes.tsv, features.tsv, matrix.mtx).
Supplementary files format and content: H5AD files.

source_name: Peripheral Blood Natural Killer Cells

extract_protocol:
PBMCs were isolated from peripheral blood via Ficoll density separation, and cryopreserved until use. Thawed PBMCs were labeled for FACS with anti-CD3, CD56, NKG2A, NKG2A, NKp30, and DAPI, and sorted on a BD Aria into seven populations: CD56bright NKG2A+NKG2C-, CD56bright NKG2A+NKG2C+, CD56dim NKG2A+NKG2C-, CD56dim NKG2A+NKG2C+, CD56dim NKG2A-NKG2C-, CD56dim NKG2A-NKG2C+NKp30hi, CD56dim NKG2A-NKG2C+NKp30-. Sorted populations were labeled with unique hashtag oligos according to manufacturer's protocol (TotalSeq-B, Biolegend), and 3,000 cells of each populations were pooled together for a total of 21,000 cells per sample from each donor. The samples were submitted to the MSKCC Integrated Genomics Operation in a solution of 0.04% BSA in PBS without calcium or magnesium.
Single-cell sample preparation, library prep, cDNA synthesis, and sequencing for Single Cell Gene Expression 3' v3 and Feature Barcoding performed by IGO according to the manufacturer's kit instructions.

value: Peripheral Blood Natural Killer Cells

value: Male

tag: donor

tag: disease status

value: healthy


title: Peripheral blood NK cells, hashtagged, Donor1

description:
sex: XX
10x Genomics

value: Female


title: CD14, CD participants, Ileum tissue


title: Tam_M_ct42_586

extract_protocol:
Qiagen RNeasy Mini Kit
Preparation of poly-A tail selected RNA libraries (Illumina mRNA Prep kit (Illumina, Inc. CA, USA)) and whole transcriptome sequencing (Novaseq 6000 (Illumina, Inc. CA, USA)),

value: iCSBmal1 KO


title: H226_parental_7883_FOSL1_rep1

value: Lung, Epithelial

value: Mesothelioma

value: Sensitive to TEAD inhibitor GNE-7883


title: TEB-029;N1

description:
SS02023
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Saline nasal spray

value: 15 min


title: Tam_M_ct42_537

value: Tamoxifen


title: Sensitive_DMSO_rep2


title: Bulk RNA-seq of post-treatment liver tumor of patient P41 (R/CR)

first: Chen

last: Dong

state: Zhejiang

address: Shilongshan Street No.18, Xihu District

institute: Westlake University

data_processing:
For scRNA-seq samples, reads were aligned and quantified using the Cell Ranger Single-Cell toolkit (v.6.1.2) against the GRCh38 human reference genome (refdata-gex-GRCh38-2020-A). Preliminary filtered raw count data generated from Cell Ranger were used for downstream analysis. Further quality control was applied to filter out low-quality cells with either (1) <500 expressed genes, (2) >6,000 expressed genes, (3) >20% mitochondrial UMI counts, or <1% hemoglobin UMI counts (sum of UMI counts of HBA1, HBA2 and HBB genes) and filter out genes detected in less than 3 cells. Scrublet (v.0.2.3) was applied to each sequencing library to remove potential doublets with default setting.
For 10X dCODE dextramer experiments, data
For scTCR-seq samples, reads were aligned and quantified using Cell Ranger Single-Cell toolkit (v.6.1.2) with the manufacturer-supplied human VDJ reference genome (refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0). For each sample, the output file all_contig_annotations.csv, containing TCR α- and β-chain complementarity determining region 3 (CDR3) amino acid sequence, was used for downstream analysis. These files were combined using scirpy (v.0.11.0) and quality control was performed with the following criterions: 1) low-confidence, non-productive chains or those with UMIs < 2 were discarded; 2) cells with more than four productive chains: two VJ and two VDJ chains were discarded; 3) cells with only one VD or only one VDJ chain were discarded; 4) for T cells with two α- or β- chains assembled, the α-β pair showing the highest expression level (UMIs) was defined as the domain α- β pair in the corresponding T cells. For each patient, T cells comprising the same VJ and VDJ CDR3 amino acid sequences for each patient were considered as having originated from the same clone and were therefore identified as clonal cells.
For bulk RNA-seq samples, we applied FastQC (v.0.11.9) to determine the quality of the raw sequencing data. Adapters, low quality bases and reads were removed using 'Trim Galore' (v.0.6.5). Then, the expression levels of transcripts were quantified by Salmon (v.1.9.1). The gene expression levels of genes, including raw count and transcript per million (TPM), were generated by tximport (v.1.18.0) with the inputs from Salmon.
Assembly: hg38
Supplementary files format and content: csv and txt files for TCR summary, and deCODE dextramer summary.
Supplementary files format and content: h5ad files for expression matrices

source_name: HBV+ HCC

extract_protocol:
To perform single-cell sequencing, single-cell suspensions from tumor and blood samples were stained with antibodies against CD45 and sorted using a BD FACSAriaTM III instrument. Based on FACS analysis, single cells were sorted into 15 ml tubes (Nest) and manually counted under a microscope. To perform bulk RNA analysis, small fragments of tumor tissues were first preserved in RNAlater RNA stabilization reagent (QIAGEN) immediately after surgical resection, and stored on ice to prevent RNA degradation. The RNA was then extracted from the tumor tissue samples using the RNeasy Mini Kit (QIAGEN), following the manufacturer's specifications. The concentration of RNA was quantified using the NanoDrop instrument (Thermo), and the quality of RNA was evaluated using the fragment analyzer (AATI).
To construct scRNA-seq libraries, the concentration of single cell suspensions was adjusted to 1,000 cells/ul, and cells were loaded between 5,000 and 20,000 cells/reaction using 10X Chromium Single Cell 5' and human variable, diversity, and joining (VDJ) (10X Genomics). All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina NovaSeq 6000 sequencer with 150-bp paired-end reads. The bulk RNA-seq libraries were constructed using the NEBNext Poly (A) mRNA Magnetic Isolation Module kit (NEB) and the NEBNext Ultra RNA Library Prep Kit for Illumina Paired-end Multiplexed Sequencing Library (NEB). Finally, the samples were sequenced on the Illumina Hiseq 4000 sequencer with 150 bp paired-end reads.
10x Chromium Single cell 5’ + VDJ library; 10x Chromium Single cell 5’ + VDJ library + deCODE dextramer library; bulk RNA-seq

treatment_protocol: All patients included in this study were pathologically diagnosed with HBV-infected hepatocellular carcinoma and received lenvatinib (12 mg/day for bodyweight ≥ 60 kg or 8 mg/day for bodyweight < 60 kg) orally once daily and a PD-1 inhibitor intravenously on day 1 of a 21-day treatment cycle. The anti-PD-1 antibodies and their single-dose infusion were sintilimab 200 mg, pembrolizumab 200 mg, tislelizumab 200 mg, or toripalimab 240 mg.

value: liver tumor

tag: patient

tag: response

value: CR, responder

tag: library type

value: Bulk RNA-seq

value: anti-PD-1 plus lenvatinib combination therapy


title: Bulk RNA-seq of post-treatment liver tumor of patient P40 (R/CR)

tag: tissue


title: TEB-028;N2

description:
SS02022
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Nasal mucosa

value: Non-allergic

value: Birch pollen extract

value: 60 min

value: male

tag: age


title: CD11, CD participants, Ileum tissue

value: Ileum

value: Male

value: Crohn's disease


title: TEB-028;N1

description:
SS02021
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

tag: treatment


title: Tam_M_ct38_584

value: mouse ventricle

tag: genotype

value: iCSBmal1 KO


title: H226_parental_FOSL1_rep1

first: Xiaosai

last: Yao

address: 1 DNA Way

institute: Roche/Genentech

value: Lung, Epithelial

tag: cell line

tag: cell type

value: Mesothelioma

value: Sensitive to TEAD inhibitor GNE-7883

value: ThermoFisher Cat. #PA5-66880)


title: Bulk RNA-seq of post-treatment liver tumor of patient P35 (R/CR)

value: liver tumor

value: CR, responder


title: TEB-027;N2

description:
SS02020
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: 30 min

tag: Sex

value: female


title: Bulk RNA-seq of post-treatment liver tumor of patient P18 (R/CR)

value: Bulk RNA-seq

value: anti-PD-1 plus lenvatinib combination therapy


title: Tam_M_ct34_526

value: Tamoxifen


title: Bulk RNA-seq of post-treatment liver tumor of patient P38 (R/CR)


title: Bulk RNA-seq of post-treatment liver tumor of patient P36 (R/PR)

value: PR, responder


title: Tam_M_ct30_599


title: TEB-027;N1

description:
SS02019
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Nasal mucosa

value: Non-allergic

value: Saline nasal spray

value: 15 min


title: CD12, CD participants, Ileum tissue

value: Ileum

value: Female

value: Crohn's disease


title: Tam_M_ct30_580

value: mouse ventricle

value: iCSBmal1 KO


title: CD08, CD participants, Ileum tissue


title: CD07, CD participants, Ileum tissue

value: Male


title: Bulk RNA-seq of post-treatment liver tumor of patient P31 (R/PR)

value: liver tumor


title: CD06, CD participants, Ileum tissue


title: CD05, CD participants, Ileum tissue


title: TEB-025;N2

description:
SS02016
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Birch pollen extract

value: 60 min


title: Tam_M_ct38_531


title: TEB-025;N1

description:
SS02015
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: female


title: CD09, CD participants, Ileum tissue


title: CD18, CD participants, Ileum tissue


title: Bulk RNA-seq of post-treatment liver tumor of patient P27 (R/PR)

value: Bulk RNA-seq

value: anti-PD-1 plus lenvatinib combination therapy


title: CD10, CD participants, Ileum tissue


title: Tam_M_ct26_514

value: Tamoxifen


title: TEB-024;N2

description:
SS02014
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Nasal mucosa


title: Tam_M_ct34_582


title: CD03, CD participants, Ileum tissue


title: Bulk RNA-seq of post-treatment liver tumor of patient P5 (R/PR)

value: PR, responder


title: Bulk RNA-seq of post-treatment liver tumor of patient P3 (R/PR)


title: Bulk RNA-seq of post-treatment liver tumor of patient P32 (R/PR)


title: Tam_M_ct22_576


title: TEB-026;N1

description:
SS02017
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Non-allergic

value: Saline nasal spray


title: Tam_M_ct26_578


title: CD04, CD participants, Ileum tissue

value: Ileum


title: Tam_M_ct18_574


title: TEB-024;N1

description:
SS02013
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: 15 min


title: Bulk RNA-seq of post-treatment liver tumor of patient P26 (NR/PD)

value: PD, non-responder


title: Tam_M_ct22_507

value: mouse ventricle


title: TEB-023;N2

description:
SS02012
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: male


title: Bulk RNA-seq of post-treatment liver tumor of patient P16 (NR/PD)


title: RS-2

description:
Library name: RS-2
Column name in raw_counts_All_Samples: RS-2

data_processing:
After filtering the raw sequencing data to obtain clean data, the reads were aligned to the reference genome using HISAT2. Transcriptome assembly was performed using StringTie, resulting in both known and novel transcripts. Coding potential of the novel transcripts was predicted using tools such as CPC and CNCI, identifying newly predicted lncRNAs. Subsequently, expression analyses were conducted for both mRNAs and lncRNAs in the samples.
Assembly: NCBI_GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

extract_protocol:
Total RNA was extracted from the samples, and ribosomal RNA was removed to maximize the retention of both coding and non-coding RNAs.
The resulting RNA was randomly fragmented into short fragments. These RNA fragments were used as templates to synthesize the first strand of cDNA using random hexamer primers. Subsequently, buffer, dNTPs (with dUTP replacing dTTP), RNase H, and DNA polymerase I were added to synthesize the second strand of cDNA. The double-stranded cDNA was then purified using a QiaQuick PCR kit and eluted with EB buffer.After end repair and addition of an adenine (A) base to the 3' ends, sequencing adapters were ligated. The second strand of cDNA was selectively degraded using Uracil-N-Glycosylase (UNG) to retain only the strand with dUTP incorporation. Size selection of the fragments was performed using agarose gel electrophoresis, followed by PCR amplification.

value: testis

value: mouse round spermatids

value: WT


title: TEB-023;N1

description:
SS02011
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv


title: RS-1

description:
Library name: RS-1
Column name in raw_counts_All_Samples: RS-1


title: Bulk RNA-seq of post-treatment liver tumor  of patient P34 (NR/SD)

value: liver tumor

value: SD, non-responder


title: TEB-022;N2

description:
SS02010
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Birch pollen extract

value: 120 min

value: female


title: Tam_F_ct62_569

value: iCSBmal1 KO

value: Tamoxifen


title: TEB-022;N1

description:
SS02009
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Nasal mucosa

value: Non-allergic


title: Bulk RNA-seq of post-treatment liver tumor of patient P1 (NR/SD)

value: Bulk RNA-seq

value: anti-PD-1 plus lenvatinib combination therapy


title: CD45+CD3+CD8+ immune cells from post-treatment tumor of patient P3 (R/PR)

value: PR, responder

value: CD45+CD3+CD8+ immune cells

value: scRNA-seq & scTCR-seq & deCODE-Dextramer-seq


title: Tam_F_ct62_568

value: mouse ventricle


title: PAC-3

description:
Library name: PAC-3
Column name in raw_counts_All_Samples: PAC-3

value: testis

value: mouse pachytene spermatocytes


title: PAC-2

description:
Library name: PAC-2
Column name in raw_counts_All_Samples: PAC-2

value: WT


title: TEB-018;N2

description:
SS02008
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv


title: CD45+CD8- immune cells from post-treatment tumor of patient P3 (R/PR)

value: liver tumor

value: CD45+ immune cells exclude CD45+CD3+CD8+ cells


title: RS-3

description:
Library name: RS-3
Column name in raw_counts_All_Samples: RS-3

value: mouse round spermatids


title: PAC-1

description:
Library name: PAC-1
Column name in raw_counts_All_Samples: PAC-1


title: Tam_F_ct58_595


title: TEB-018;N1

description:
SS02007
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Saline nasal spray

value: 15 min

value: female


title: Tam_F_ct54_559

value: iCSBmal1 KO

value: Tamoxifen


title: CD45+CD3+CD8+ immune cells from post-treatment blood of patient P3 (R/PR)

value: blood


title: Tam_F_ct54_558


title: ES-3

description:
Library name: ES-3
Column name in raw_counts_All_Samples: ES-3

value: mouse elongation spermatids


title: CD45+ immune cells from post-treatment tumor of patient P3 (R/PR)

value: PR, responder

value: CD45+ immune cells

value: anti-PD-1 plus lenvatinib combination therapy


title: TEB-017;N2

description:
SS02006
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Nasal mucosa

value: Non-allergic

value: Birch pollen extract

value: 120 min


title: ES-2

description:
Library name: ES-2
Column name in raw_counts_All_Samples: ES-2

value: testis

value: WT


title: CD45+CD3+CD8+ immune cells from post-treatment adjacent normal liver tissue of patient P3 (R/PR)

value: adjacent normal liver tissue

value: CD45+CD3+CD8+ immune cells

value: scRNA-seq & scTCR-seq & deCODE-Dextramer-seq


title: TEB-017;N1

description:
SS02005
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Saline nasal spray

value: 15 min

value: female


title: platelet-derived extracellular vesicles 5

city: Jacksonville

first: DeLisa

last: Fairweather

address: 4500 San Pablo Rd S

department: Cardiovascular Medicine

institute: Mayo Clinic

description: Library name: PEV_10

data_processing:
Cutadapt, miRDeep2 mapper, miRDeep2 module, edgeR
Assembly: hg38
Supplementary files format and content: Processed data is log2 normalized counts

source_name: Plasma

extract_protocol:
QIAseq miRNA Library Kit
Illumina cBot, HiSeq 3000/4000 PE Cluster Kit

value: Plasma


title: TEB-015;N2

description:
SS02004
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: 30 min


title: Tam_M_ct18_502

value: mouse ventricle

value: iCSBmal1 KO

value: Tamoxifen


title: ES-1

description:
Library name: ES-1
Column name in raw_counts_All_Samples: ES-1

value: mouse elongation spermatids


title: TEB-015;N1

description:
SS02003
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Nasal mucosa

value: Non-allergic


title: TEB-026;N2

description:
SS02018
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Birch pollen extract


title: platelet-derived extracellular vesicles 4

description: Library name: PEV_9


title: Tam_F_ct50_554


title: Tam_F_ct50_591


title: CD45+CD8- immune cells from post-treatment adjacent normal liver tissue of patient P3 (R/PR)

value: PR, responder

value: CD45+ immune cells exclude CD45+CD3+CD8+ cells

value: anti-PD-1 plus lenvatinib combination therapy


title: TEB-014;N2

description:
SS02002
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: 60 min


title: Tam_F_ct46_601


title: Tam_F_ct46_589


title: platelet-derived extracellular vesicles 3

description: Library name: PEV_8


title: platelet-derived extracellular vesicles 2

description: Library name: PEV_7


title: Tam_F_ct58_565


title: CD45+CD3+CD8+ immune cells from post-treatment tumor of patient P16 (NR/PD)

value: liver tumor

value: PD, non-responder

value: CD45+CD3+CD8+ immune cells

value: scRNA-seq & scTCR-seq & deCODE-Dextramer-seq


title: CD45+CD3+CD8+ immune cells from pre-treatment blood of patient P3 (R/PR)

value: blood


title: TEB-014;N1

description:
SS02001
Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Saline nasal spray

value: 15 min

value: female


title: TEB-013;N1

description:
SS01021
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Allergic


title: CD45+CD3+ immune cells from post-treatment tumor of patient P16 (NR/PD)

value: CD45+CD3+ immune cells


title: CD45+CD8- immune cells from post-treatment tumor of patient P16 (NR/PD)


title: Tam_F_ct42_542

value: mouse ventricle

value: iCSBmal1 KO

value: Tamoxifen


title: CD45+CD3+CD8+ immune cells from post-treatment blood of patient P16 (NR/PD)


title: premenopausal platelet-derived extracellular vesicles 5

description: Library name: pmPEV_5

value: Plasma


title: CD45+CD3+CD8+ immune cells from on-treatment blood of patient P3 (R/PR)

value: PR, responder


title: premenopausal platelet-derived extracellular vesicles 4

description: Library name: pmPEV_4


title: TEB-013;N2

description:
SS01022
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Nasal mucosa

value: Birch pollen extract

value: 120 min