title: shXBP1.cl18.day24.rep2

description: Library name: SAM24405142


title: shXBP1.cl18.day0.rep3

status: Public on Jan 07 2025

type: SRA

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

country: USA

institute: Genentech Inc.

description: Library name: SAM24405140

library_source: transcriptomic

data_processing:
Bulk RNA-seq experiment was processed using the HTSeqGenie pipeline in BioConductor[85]. First, reads with low nucleotide qualities (70% of bases with quality<23) or matches to rRNA and adapter sequences were removed.
The remaining reads were aligned to the human reference genome GRCh37/hg19 using GSNAP (v.2013-10-10-v2)[86], allowing a maximum of two mismatches per 75 base-sequence (parameters: ‘-M2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 –pairmax-rna=200000 –clip-overlap’).
Transcript annotation was based on the Gencode genes database[87]. To quantify gene expression levels, the number of reads mapping unambiguously to the exons of each gene was calculated.
The resulting count matrix was analysed in R (v.4.1.3; 03 November 2023) using the edgeR package (v.3.32.1)[88]. The count matrix was filtered to remove low expressed genes by keeping the features with at least 15 counts, considering library size differences, in more than the minimum number of samples of the experimental design. The resulting filtered count matrix was then log2-transformed and TMM-normalized with edgeR::cpm(log=T) and edgeR::calcNormFactors(method= “TMM”).
For exploratory data analysis, the matrix was further filtered to the most variable genes selected using projection score[89] to focus on the major contributors to the variance in transcriptional state. This matrix was then scaled using base:scale() for posterior exploration.
Differential expression analyses were conducted using limma (v.3.46.0)[90]. To identify significantly interacting genes between gene silencing backgrounds and time points, a polynomial spline model with three degrees of freedom was used for the design matrix. A large number of genes were significantly interacting and a more stringent false discovery rate adjusted p-value of 10−12 was used to perform exploratory data analysis.
Assembly: Human reference genome GRCh37/hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TMM normalized counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Plasmacytoma

growth_protocol: AMO1 shIRE1 cl.1, cl.3 or shXBP1 cl.1, cl.18 cells grown in biological triplicates in T-75 flasks in RPMI 10% FBS

extract_protocol:
RNA from 1x106 cell was first extracted with RNeasy Plus kit (Qiagen), per manufacturer’s protocol. Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies).
Truseq Stranded mRNA kit (Illumina) was used with an input of 100 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

treatment_protocol: 0.2 ug/ml Doxycycline (Dox) for 0, 24, 48 or 72h

tag: tissue

value: Plasmacytoma

tag: cell line

tag: cell type

value: Tumor Plasma cell

tag: genotype

value: AMO-1 XBP1 sh4,6,7 Clone 18

tag: treatment

value: No treatment


title: shXBP1.cl1.day72.rep3

description: Library name: SAM24405137

value: AMO-1 XBP1 sh4,6,7 Clone 1

value: 0.2 ug/ml Dox 72h


title: shXBP1.cl1.day48.rep1

description: Library name: SAM24405132

value: 0.2 ug/ml Dox 48h


title: shXBP1.cl1.day72.rep1

description: Library name: SAM24405135


title: shXBP1.cl1.day0.rep2

description: Library name: SAM24405127


title: shIRE1.cl3.day72.rep3

description: Library name: SAM24405125

value: AMO-1 IRE1 sh7,8,9 Clone 3


title: shIRE1.cl3.day72.rep2

description: Library name: SAM24405124


title: shXBP1.cl1.day0.rep1

description: Library name: SAM24405126


title: shXBP1.cl1.day0.rep3

description: Library name: SAM24405128


title: shXBP1.cl1.day24.rep3

description: Library name: SAM24405131

value: 0.2 ug/ml Dox 24h


title: shIRE1.cl3.day72.rep1

description: Library name: SAM24405123


title: shIRE1.cl3.day48.rep2

description: Library name: SAM24405121


title: shIRE1.cl3.day48.rep3

description: Library name: SAM24405122


title: shXBP1.cl18.day24.rep1

description: Library name: SAM24405141


title: shXBP1.cl1.day48.rep2

description: Library name: SAM24405133


title: shXBP1.cl1.day48.rep3

description: Library name: SAM24405134


title: shXBP1.cl18.day72.rep3

description: Library name: SAM24405149


title: shIRE1.cl3.day48.rep1

description: Library name: SAM24405120


title: shIRE1.cl3.day24.rep1

description: Library name: SAM24405117


title: shIRE1.cl3.day24.rep2

description: Library name: SAM24405118


title: shIRE1.cl3.day0.rep3

description: Library name: SAM24405116


title: shIRE1.cl3.day24.rep3

description: Library name: SAM24405119


title: shIRE1.cl1.day72.rep1

description: Library name: SAM24405111

value: AMO-1 IRE1 sh7,8,9 Clone 1


title: shIRE1.cl1.day24.rep2

description: Library name: SAM24405106


title: shIRE1.cl3.day0.rep1

description: Library name: SAM24405114


title: shIRE1.cl3.day0.rep2

description: Library name: SAM24405115


title: shIRE1.cl1.day0.rep3

description: Library name: SAM24405104


title: shIRE1.cl1.day24.rep1

description: Library name: SAM24405105


title: shIRE1.cl1.day48.rep1

description: Library name: SAM24405108


title: shIRE1.cl1.day0.rep2

description: Library name: SAM24405103


title: shIRE1.cl1.day48.rep2

description: Library name: SAM24405109


title: shIRE1.cl1.day24.rep3

description: Library name: SAM24405107


title: shIRE1.cl1.day0.rep1

description: Library name: SAM24405102


title: HEPM, R157S, 6h, rep1

city: Nanjing

first: yucheng

last: jiang

address: No.140 Hanzhong Road, Nanjing

country: China

institute: Nanjing medical university

description: Library name: R157S_1

data_processing:
After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq6000 platform using NovaSeq Reagent Kit.
Assembly: Tthe expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: cell line

growth_protocol: HEPM cells in α-MEM (Gibco, C12440500BT) supplemented with 10% FBS and 1% PS at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA samplewas used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions . The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected or cDNA target fragments of 300-400bp use magnetic beads followed by PCR amplified for 10-15 PCR cycles.

value: cell line

value: HEPM

value: Human embryonic palatal mesenchymal cells

value: MSX1 R157S overexpression

value: plasmid transfection

tag: batch


title: HEPM, R157K, 6h, rep1

description: Library name: R157K_1

value: MSX1 R157K overexpression


title: HEPM, R157K, 6h, rep3

description: Library name: R157K_3


title: HEPM, R157K, 6h, rep2

description: Library name: R157K_2


title: HEPM, R157S, 6h, rep3

description: Library name: R157S_3


title: HEPM, R157S, 6h, rep2

description: Library name: R157S_2


title: HEPM, R157F, 6h, rep3

description: Library name: R157F_3

value: MSX1 R157F overexpression


title: HEPM, R157F, 6h, rep1

description: Library name: R157F_1


title: HEPM, MSX1, 6h, rep3

description: Library name: MSX1_3

value: WT MSX1 overexpression


title: shIRE1.cl1.day72.rep3

description: Library name: SAM24405113

value: Plasmacytoma

value: Tumor Plasma cell


title: shIRE1.cl1.day48.rep3

description: Library name: SAM24405110


title: HEPM, R157F, 6h, rep2

description: Library name: R157F_2


title: HEPM, MSX1, 6h, rep1

description: Library name: MSX1_1


title: HEPM, MSX1, 6h, rep2

description: Library name: MSX1_2


title: shIRE1.cl1.day72.rep2

description: Library name: SAM24405112


title: Carboplatin resistant OVCAR-3 (Biological replicate 3)

city: Bangalore

first: Ramray

last: Bhat

state: Karnataka

address: CV Raman Rd

department: Developmental Biology & Genetics

country: India

institute: Indian Institute of Science

description: Library name: Sample 6 [O3.A13.C]

data_processing:
RNA-Seq data was processed using the nf-core RNA-Seq pipeline (version v3.14.0) (Ewels et al., 2020). The bam files obtained from the nf-core RNA-Seq pipeline were then used to generate an expression matrix using featureCounts v2.0.1. (Liao et al., 2014). CPM counts for plotting were generated using EdgeR after TMM normalization (Robinson et al., 2010).
Assembly: hg38
Supplementary files format and content: .tsv file containing raw counts for each sample
Supplementary files format and content: .tsv file containing CPM counts for each sample

source_name: ovary

growth_protocol: OVCAR-3 and res OVCAR-3 cells were maintained in RPMI-1640 medium (AL162A; HiMedia) supplemented with 20% FBS (10270; Gibco) and incubated in a humidified incubator with 5% carbon dioxide at 37 °C.

extract_protocol:
Cells were lysed using a Trizol reagent (Takara, Japan). RNA was isolated by the chloroform-isopropanol extraction method. All reagents were molecular grade and purchased from Merck.
The libraries were prepared from 500 ng of intact RNA using QIAseq Stranded RNA Lib Kit (Qiagen, Cat. No. 180451) according to the manufacturer’s protocol and the library QC was done using Agilent D1000 screentape (Agilent, Cat No. 5067-5582) and Qubit DNA HS (Thermo, Q33230).

value: ovary

value: cancerous

value: Carboplatin resistant


title: Carboplatin resistant OVCAR-3 (Biological replicate 2)

description: Library name: Sample 5 [O3.A13.B]


title: Carboplatin resistant OVCAR-3 (Biological replicate 1)

description: Library name: Sample 4 [O3.A13.A]


title: HUVEC_NaPBA_LPS_Nigericin3

city: Shanghai

first: Jian

last: Xu

address: 180 Fenglin Road

institute: Zhongshan hospital

description: Library name: Sample15

data_processing:
Raw data of FASTQ format were firstly processed through in-house perl scripts and obtained clean data. Then, map the clean reads to the silva database to remove the rRNA. Paired-end clean reads were aligned to the reference genome using Hisat2. Featurecount was used to count the reads numbers mapped to each gene. EdgeR was used for differential expression analysis. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: mm10; GRCh38
Supplementary files format and content: Gene counts or fpkm for each sample.

molecule: polyA RNA

source_name: HUVEC

extract_protocol:
Total RNA was extracted using TRIzol reagent. Total RNA was qualified and quantified: (1) RNA purity and concentration were examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
Libraries were constructed by enriching mRNA with polyT, synthesizing cDNA, adding adapters, and amplifying via PCR. Libraries were sequenced on an Illumina NovaSeq 6000 platform, generating paired-end 150 bp reads.

value: HUVEC

value: WT

value: Na-PBA+LPS+Nigericin


title: OVCAR-3 (Biological replicate 3)

description: Library name: Sample 3 [O3.C]


title: HUVEC_NaPBA_LPS_Nigericin2

description: Library name: Sample14


title: OVCAR-3 (Biological replicate 2)

description: Library name: Sample 2 [O3.B]


title: HUVEC_LPS_Nigericin1

description: Library name: Sample10

value: LPS+Nigericin


title: HUVEC_LPS_Nigericin2

description: Library name: Sample11


title: HUVEC_CON3

description: Library name: Sample9

value: Vehicle


title: HUVEC_CON2

description: Library name: Sample8


title: Knee OA synovium_fibro_2

city: Bunkyo-ku

first: Junya

last: Miyahara

state: Tokyo

address: Hongo 7-3-1

department: Sensory & Motor system Medicine, Graduate School of Medicine

country: Japan

institute: The University of Tokyo

description: Library name: OA_syn_fibro_2

library_source: transcriptomic single cell

data_processing:
Library was sequenced using Novaseq6000 (Illumina) with 28/91-bp paired-end reads and about 50,000 reads per cell on average.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Synovium

extract_protocol:
Synovial tissues  were collected surgically. Immediately after collection, they were removed from bone and adipose tissues using surgical scissors, and cryopreserved by CryoStor CS10 (HemaCare Corporation) at -80℃. Cryopreserved synovial tissues were enzymatically treated and resuspended at a concentration of 1,000 cells/µL. Cell viability, confirmed at approximately 80%, was assessed using the trypan blue exclusion method with automated counting by LUNA-FL (Logos Biosystems).
The cell suspension was prepared according to the protocol of Chromium Next GEM Single Cell 3ʹ Reagent Kits (v3.1 10X Genomics), and a single cell emulsion was produced using Chromium Controller (10X Genomics).

value: Synovium

tag: disease state

value: osteoarthritis (OA)


title: TYK-nu_Wildtype_Biological_Replicate_2

city: Baltimore

first: Michael

last: Topper

address: 1650 Orleans St.

institute: Johns Hopkins University, Sidney Kimmel Comprehensive Cancer Center

description:
Library name: Sample2
Processed data file name matches condition. Processed data file is gene level quantification derived from Salmon with ENSG name, length, effective length, transcript per million, and number of reads provided as individual columns.

data_processing:
Raw FASTQ files were first assessed for quality metrics using FastQC.
Trimmomatic was used to remove adapters and low-quality reads from raw FASTQ files.
Processed FASTQ files were aligned using Salmon with GENCODE transcript fasta file (version 44) used as reference.
Salmon-processed files were used as input for tximport followed by DESeq2  for differential expression analysis.
Assembly: gencode.v44.fasta
Supplementary files format and content: Individual sample tab delimited text files from Salmon quantification with ENSG ID, length, TPM, and read number provided as individual columns within each text file.

source_name: TYK-nu

growth_protocol: TYK-nu WT and ZNFX1 KO cells were cultured in RPMI-1640 (Corning) supplemented with 10% FBS (Sigma) and 1% penicillin-streptomycin (Sigma).To ensure cell line integrity, all cell lines were thawed at frequent intervals and not used beyond 40 passages. Cell lines were cultured at 37ºC with 5% CO2. Cell lines were regularly tested for mycoplasma.

extract_protocol:
RNA was isolated from cell pellets using the RNeasy kit according to manufacturers instructions (Qiagen). Quality and quantity of RNA was monitored using the Bioanalyzer RNA High Sensitivity kit on a Model 2100 BioAnalyzer (Agilent). All RNA samples had a RIN score of 9 or greater.
500 ng of total RNA was used for library construction with the TruSeq Stranded Total RNA Library kit according to manufacturers instructions (Illumina). Quality and quantity of the resulting cDNA was monitored using the Bioanalyzer DNA High Sensitivity kit (Agilent). Bulk RNA libraries were sequenced on an Illumina Novaseq 6000 X instrument using 150bp paired-end dual indexed reads and 1% of PhiX control. Depth of coverage was targeted to a total of 50 million reads (25 million pairs) per library.

treatment_protocol: Cells were not drug treated.

value: TYK-nu

value: Ovarian cancer cell line

value: Wildtype


title: TYK-nu_ZNFX1_KO_Biological_Replicate_1

description:
Library name: Sample4
Processed data file name matches condition. Processed data file is gene level quantification derived from Salmon with ENSG name, length, effective length, transcript per million, and number of reads provided as individual columns.

value: ZNFX1 Knockout


title: TYK-nu_ZNFX1_KO_Biological_Replicate_2

description:
Library name: Sample5
Processed data file name matches condition. Processed data file is gene level quantification derived from Salmon with ENSG name, length, effective length, transcript per million, and number of reads provided as individual columns.


title: TYK-nu_Wildtype_Biological_Replicate_1

description:
Library name: Sample1
Processed data file name matches condition assessed. Processed data file represents gene level quantification data derived from Salmon with ENSG name, length, effective length, transcript per million, and number of reads provided as individual columns within the file.


title: Knee OA synovium_infla_2

description: Library name: OA_syn_infla_2


title: Knee OA synovium_fibro_1

description: Library name: OA_syn_fibro_1


title: Knee non-OA synovium_5

description: Library name: non-OA_syn_5

data_processing:
Sequencing was performed by Novaseq6000 (Illumina) with two 150-bp paired-end reads and about 10 million reads per sample on average.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Synivial tissues were collected surgically. Immediately after collection, they were removed from bone and adipose tissues using surgical scissors, crushed with a bead homogenizer, and dissolved in TRI Reagent (Molecular Research Center).Total RNA was extracted using Direct-zol RNA MicroPrep Kit (ZYMO RESEARCH).
Library was prepared using the NEBNext Ultra II RNA Library Prep Kit (Illumina) according to each specimen protocol.

value: non-osteoarthritis (OA)


title: Knee OA synovium_infla_1

description: Library name: OA_syn_infla_1


title: Knee non-OA synovium_3

description: Library name: non-OA_syn_3


title: Knee non-OA synovium_4

description: Library name: non-OA_syn_4


title: OVCAR-3 (Biological replicate 1)

description: Library name: Sample 1 [O3.A]


title: HUVEC_LPS_Nigericin3

description: Library name: Sample12


title: Knee non-OA synovium_1

description: Library name: non-OA_syn_1


title: Knee OA synovium_36

description: Library name: OA_syn_36


title: HUVEC_NaPBA_LPS_Nigericin1

description: Library name: Sample13


title: Knee OA synovium_35

description: Library name: OA_syn_35


title: Knee OA synovium_33

description: Library name: OA_syn_33


title: Knee OA synovium_34

description: Library name: OA_syn_34


title: TYK-nu_ZNFX1_KO_Biological_Replicate_3

description:
Library name: Sample6
Processed data file name matches condition. Processed data file is gene level quantification derived from Salmon with ENSG name, length, effective length, transcript per million, and number of reads provided as individual columns.


title: Knee OA synovium_28

description: Library name: OA_syn_28


title: Knee OA synovium_27

description: Library name: OA_syn_27


title: HUVEC_CON1

description: Library name: Sample7


title: Knee OA synovium_31

description: Library name: OA_syn_31


title: Knee OA synovium_32

description: Library name: OA_syn_32


title: TYK-nu_Wildtype_Biological_Replicate_3

description:
Library name: Sample3
Processed data file name matches condition. Processed data file is gene level quantification derived from Salmon with ENSG name, length, effective length, transcript per million, and number of reads provided as individual columns.


title: Knee OA synovium_29

description: Library name: OA_syn_29


title: Knee OA synovium_25

description: Library name: OA_syn_25


title: Knee OA synovium_24

description: Library name: OA_syn_24


title: Knee OA synovium_21

description: Library name: OA_syn_21


title: Knee OA synovium_23

description: Library name: OA_syn_23


title: Knee non-OA synovium_2

description: Library name: non-OA_syn_2


title: Knee OA synovium_18

description: Library name: OA_syn_18


title: Knee OA synovium_26

description: Library name: OA_syn_26


title: Knee OA synovium_19

description: Library name: OA_syn_19


title: Knee OA synovium_17

description: Library name: OA_syn_17


title: Knee OA synovium_16

description: Library name: OA_syn_16


title: Knee OA synovium_20

description: Library name: OA_syn_20


title: Knee OA synovium_15

description: Library name: OA_syn_15


title: Knee OA synovium_30

description: Library name: OA_syn_30


title: Knee OA synovium_12

description: Library name: OA_syn_12


title: Knee OA synovium_10

description: Library name: OA_syn_10


title: Knee OA synovium_13

description: Library name: OA_syn_13


title: Knee OA synovium_8

description: Library name: OA_syn_8


title: Knee OA synovium_9

description: Library name: OA_syn_9


title: Knee OA synovium_4

description: Library name: OA_syn_4


title: Knee OA synovium_3

description: Library name: OA_syn_3


title: Knee OA synovium_1

description: Library name: OA_syn_1


title: Knee OA synovium_6

description: Library name: OA_syn_6


title: Knee OA synovium_7

description: Library name: OA_syn_7


title: Knee OA synovium_2

description: Library name: OA_syn_2


title: mRNA_10_V2D7

city: Hamburg

last: Spohn

address: Martinistr. 52

department: Bioinformatics Core

country: Germany

institute: UKE Hamburg

data_processing:
Raw data from Illumina NovaSeq 6000 have been demultiplexed using bcl2fastq v2.20.0.422.
Quality of the raw reads was inspected by FastQC v0.11.8 and MultiQC v1.9.
Low quality read ends and adapters were removed by fastp v0.23.2.
STAR v.2.7.10a was employed for read mapping and genewise counting based on Ensembl annotation 110.
For normalization of the raw counts and determination of differentially expressed genes DESeq2 v1.36.0 was applied.
Assembly: GRCh38
Supplementary files format and content: Tab-separated raw counts
Supplementary files format and content: Tab-separated normalized counts

source_name: Whole blood

extract_protocol:
RNA was isolated from PAXgene blood RNA tubes using Qiagen's BloodRNA Kit following the manufacturer's instructions.
Library prepararation was performed using the TruSeq stranded mRNA library prep assay, according to the manufacturer’s instructions.

value: Whole blood

tag: cohort

value: mRNA

tag: participant id

tag: time point

tag: vaccine v1

tag: vaccine v2

tag: batch id


title: mRNA_09_V2D7


title: Knee OA synovium_14

description: Library name: OA_syn_14


title: mRNA_07_V2D7


title: mRNA_08_V2D7


title: mRNA_05_V2D7


title: mRNA_06_V2D7


title: Knee OA synovium_22

description: Library name: OA_syn_22


title: mRNA_04_V2D7


title: mRNA_03_V2D7


title: mRNA_02_V2D7


title: mRNA_10_V2D3


title: mRNA_08_V2D3


title: mRNA_07_V2D3


title: Knee OA synovium_11

description: Library name: OA_syn_11


title: mRNA_06_V2D3


title: mRNA_01_V2D7


title: mRNA_01_V2D3


title: mRNA_02_V2D3


title: mRNA_09_V2D1


title: mRNA_05_V2D3


title: Knee OA synovium_5

description: Library name: OA_syn_5


title: mRNA_08_V2D1


title: mRNA_06_V2D1


title: mRNA_02_V2D1


title: mRNA_07_V2D1


title: mRNA_08_V2D0


title: mRNA_05_V2D1


title: mRNA_01_V2D1


title: mRNA_05_V2D0


title: mRNA_09_V2D0


title: mRNA_07_V2D0


title: mRNA_03_V2D0


title: mRNA_04_V2D0


title: mRNA_06_V2D0


title: mRNA_09_V1D7


title: mRNA_10_V1D7


title: mRNA_08_V1D7


title: mRNA_07_V1D7


title: mRNA_03_V1D7


title: mRNA_01_V1D7


title: mRNA_02_V1D7


title: mRNA_04_V1D7


title: mRNA_09_V1D3


title: mRNA_07_V1D3


title: mRNA_06_V1D3


title: mRNA_05_V1D3


title: mRNA_04_V1D3


title: mRNA_08_V1D3


title: mRNA_03_V1D3


title: mRNA_10_V1D3


title: mRNA_02_V1D3


title: mRNA_06_V1D7


title: mRNA_05_V1D7


title: mRNA_08_V1D1


title: mRNA_01_V2D0


title: mRNA_09_V1D1


title: mRNA_07_V1D1


title: mRNA_06_V1D1


title: mRNA_02_V1D1


title: mRNA_04_V1D1


title: mRNA_05_V1D1


title: mRNA_03_V1D1


title: mRNA_09_V1D0


title: mRNA_10_V1D0


title: mRNA_08_V1D0


title: mRNA_01_V1D1


title: mRNA_07_V1D0


title: mRNA_06_V1D0


title: mRNA_04_V1D0


title: mRNA_02_V1D0


title: MVA-ST_15_V2D7

value: MVA-ST

value: MVA-SARS-2-ST (MD)


title: MVA-ST_12_V2D7


title: MVA-ST_11_V2D7


title: mRNA_10_V1D1


title: MVA-ST_13_V2D7


title: MVA-ST_10_V2D7


title: MVA-ST_09_V2D7


title: MVA-ST_06_V2D7

value: MVA-SARS-2-ST (LD)


title: MVA-ST_08_V2D7


title: mRNA_01_V1D3


title: MVA-ST_07_V2D7


title: MVA-ST_05_V2D7


title: MVA-ST_04_V2D7


title: MVA-ST_02_V2D7


title: MVA-ST_03_V2D7


title: MVA-ST_14_V2D7


title: MVA-ST_15_V2D1


title: MVA-ST_13_V2D1


title: MVA-ST_01_V2D7


title: MVA-ST_09_V2D1


title: MVA-ST_08_V2D1


title: MVA-ST_07_V2D1


title: MVA-ST_12_V2D1


title: MVA-ST_11_V2D1


title: MVA-ST_05_V2D1


title: MVA-ST_06_V2D1


title: MVA-ST_02_V2D1


title: MVA-ST_04_V2D1


title: MVA-ST_10_V2D1


title: MVA-ST_14_V2D1


title: MVA-ST_14_V2D0


title: MVA-ST_01_V2D1


title: MVA-ST_12_V2D0


title: MVA-ST_13_V2D0


title: MVA-ST_10_V2D0


title: MVA-ST_11_V2D0


title: MVA-ST_09_V2D0


title: MVA-ST_06_V2D0


title: MVA-ST_03_V2D0


title: MVA-ST_08_V2D0


title: MVA-ST_04_V2D0


title: MVA-ST_07_V2D0


title: MVA-ST_05_V2D0


title: MVA-ST_02_V2D0


title: MVA-ST_01_V2D0


title: MVA-ST_14_V1D7


title: MVA-ST_15_V1D7


title: MVA-ST_10_V1D7


title: MVA-ST_09_V1D7


title: MVA-ST_12_V1D7


title: MVA-ST_03_V2D1


title: MVA-ST_11_V1D7


title: MVA-ST_07_V1D7


title: MVA-ST_08_V1D7


title: MVA-ST_15_V2D0


title: MVA-ST_06_V1D7


title: MVA-ST_04_V1D7


title: MVA-ST_01_V1D7


title: MVA-ST_03_V1D7


title: MVA-ST_05_V1D7


title: MVA-ST_14_V1D3


title: MVA-ST_12_V1D3


title: MVA-ST_11_V1D3


title: MVA-ST_15_V1D3


title: MVA-ST_10_V1D3


title: MVA-ST_08_V1D3


title: MVA-ST_09_V1D3


title: MVA-ST_07_V1D3


title: MVA-ST_05_V1D3


title: MVA-ST_04_V1D3


title: MVA-ST_13_V1D7


title: MVA-ST_02_V1D7


title: MVA-ST_01_V1D3


title: MVA-ST_02_V1D3


title: MVA-ST_03_V1D3


title: MVA-ST_13_V1D1


title: MVA-ST_15_V1D1


title: MVA-ST_14_V1D1


title: MVA-ST_12_V1D1


title: MVA-ST_10_V1D1


title: MVA-ST_11_V1D1


title: MVA-ST_08_V1D1


title: MVA-ST_07_V1D1


title: MVA-ST_13_V1D3


title: MVA-ST_06_V1D1


title: MVA-ST_03_V1D1


title: MVA-ST_05_V1D1


title: MVA-ST_02_V1D1


title: MVA-ST_06_V1D3


title: MVA-ST_14_V1D0


title: MVA-ST_09_V1D1


title: MVA-ST_13_V1D0


title: MVA-ST_15_V1D0


title: MVA-ST_11_V1D0


title: MVA-ST_12_V1D0


title: MVA-ST_10_V1D0


title: MVA-ST_09_V1D0


title: MVA-ST_08_V1D0


title: MVA-ST_07_V1D0


title: MVA-ST_06_V1D0


title: MVA-ST_04_V1D0


title: MVA-ST_03_V1D0


title: MVA-ST_02_V1D0


title: MVA-ST_01_V1D0


title: MVA-S_09_V2D7

value: MVA-S

value: MVA-SARS-2-S (HD)


title: MVA-S_06_V2D1

value: MVA-SARS-2-S (LD)


title: MVA-S_08_V2D1


title: MVA-S_03_V2D1


title: MVA-S_06_V2D7


title: MVA-ST_01_V1D1


title: MVA-S_07_V2D1


title: MVA-S_02_V2D1


title: MVA-S_01_V2D7


title: MVA-S_07_V2D7


title: MVA-S_01_V2D1


title: MVA-S_03_V2D7


title: MVA-S_04_V2D7


title: MVA-S_05_V2D1


title: MVA-S_05_V2D7


title: MVA-S_02_V2D7


title: MVA-S_08_V2D7


title: MVA-S_12_V2D0


title: MVA-ST_04_V1D1


title: MVA-S_06_V2D0


title: MVA-S_04_V2D1


title: MVA-S_12_V2D1


title: MVA-S_09_V2D1


title: MVA-S_03_V2D0


title: MVA-S_08_V2D0


title: MVA-S_09_V2D0


title: MVA-S_04_V2D0


title: MVA-ST_05_V1D0


title: MVA-S_12_V2D7


title: MVA-S_02_V2D0


title: MVA-S_01_V2D0


title: MVA-S_08_V1D7


title: MVA-S_05_V2D0


title: MVA-S_05_V1D7


title: MVA-S_04_V1D7


title: MVA-S_06_V1D3


title: MVA-S_03_V1D3


title: MVA-S_04_V1D3


title: MVA-S_07_V1D3


title: MVA-S_09_V1D7


title: MVA-S_07_V1D7


title: MVA-S_12_V1D1


title: MVA-S_12_V1D7


title: MVA-S_09_V1D1


title: MVA-S_08_V1D1


title: MVA-S_12_V1D3


title: MVA-S_07_V1D1


title: MVA-S_06_V1D1


title: MVA-S_02_V1D3


title: MVA-S_03_V1D7


title: MVA-S_02_V1D7


title: MVA-S_09_V1D3


title: MVA-S_03_V1D1


title: MVA-S_02_V1D1


title: MVA-S_01_V1D3


title: MVA-S_04_V1D1


title: MVA-S_06_V1D7


title: MVA-S_08_V1D3


title: MVA-S_05_V1D3


title: MVA-S_12_V1D0


title: MVA-S_09_V1D0


title: MVA-S_03_V1D0


title: MVA-S_06_V1D0


title: MVA-S_05_V1D0


title: MVA-S_02_V1D0


title: MVA-S_01_V1D0


title: MVA-S_07_V1D0


title: ChAd/mRNA_08_V2D7

value: ChAd/mRNA

value: ChAdOx1 nCoV-19


title: MVA-S_08_V1D0


title: MVA-S_04_V1D0


title: ChAd/mRNA_04_V2D7


title: MVA-S_05_V1D1


title: ChAd/mRNA_05_V2D7


title: ChAd/mRNA_06_V2D7


title: ChAd/mRNA_03_V2D7


title: ChAd/mRNA_02_V2D7


title: ChAd/mRNA_01_V2D7


title: ChAd/mRNA_06_V2D3


title: ChAd/mRNA_03_V2D3


title: ChAd/mRNA_04_V2D3


title: ChAd/mRNA_07_V2D3


title: ChAd/mRNA_02_V2D3


title: ChAd/mRNA_05_V2D3


title: MVA-S_01_V1D1


title: ChAd/mRNA_01_V2D3


title: ChAd/mRNA_06_V2D1


title: ChAd/mRNA_08_V2D1


title: ChAd/mRNA_07_V2D1


title: ChAd/mRNA_05_V2D1


title: ChAd/mRNA_07_V2D7


title: ChAd/mRNA_04_V2D1


title: ChAd/mRNA_01_V2D1


title: ChAd/mRNA_06_V2D0


title: ChAd/mRNA_05_V2D0


title: ChAd/mRNA_07_V2D0


title: ChAd/mRNA_08_V2D0


title: ChAd/mRNA_02_V2D0


title: ChAd/mRNA_01_V2D0


title: Whole body 7 dpf sox10 mutant embryos - biol rep 3

city: Cincinnati

first: Lindsey

last: Barske

state: Ohio

address: 3333 Burnet Ave

department: Human Genetics

institute: Cincinnati Children's Hospital

description:
Library name: 7 dpf Mutant 3
bulk RNA-seq

data_processing:
The data was processed through the Galaxy project using Trimmomatic (version 0.39)
Sequences were pseudoaligned and quantified at TPM values using Kallisto.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text file includes TPM values for each transcript at 45 hpf, 4 dpf and 7 dpf

organism: Danio rerio

source_name: whole body

extract_protocol:
RNA was extracted using the RNAqueous-4PCR Total RNA Isolation Kit (Invitrogen)
150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high-sensitivity spectrofluorometric measurement was poly-A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.

value: whole body

tag: time

value: 7 dpf


title: ChAd/mRNA_06_V1D7


title: ChAd/mRNA_08_V1D7


title: Whole body 7 dpf sox10 mutant embryos - biol rep 1

description:
Library name: 7 dpf Mutant 1
bulk RNA-seq


title: ChAd/mRNA_05_V1D7


title: Whole body 7 dpf wild-type embryos - biol rep 3

description:
Library name: 7 dpf WT 3
bulk RNA-seq

value: WT


title: Whole body 7 dpf wild-type embryos - biol rep 2

description:
Library name: 7 dpf WT 2
bulk RNA-seq


title: ChAd/mRNA_04_V1D7


title: ChAd/mRNA_02_V1D7


title: Whole body 7 dpf wild-type embryos - biol rep 1

description:
Library name: 7 dpf WT 1
bulk RNA-seq


title: ChAd/mRNA_03_V1D7


title: Whole body 4 dpf sox10 mutant embryos  - biol rep 3

description:
Library name: 4 dpf Mutant 3
bulk RNA-seq

value: 4 dpf


title: ChAd/mRNA_01_V1D7


title: Whole body 4 dpf sox10 mutant embryos  - biol rep 2

description:
Library name: 4 dpf Mutant 2
bulk RNA-seq


title: ChAd/mRNA_04_V2D0


title: ChAd/mRNA_03_V2D1


title: ChAd/mRNA_08_V1D3


title: ChAd/mRNA_03_V2D0


title: Whole body 4 dpf wild-type embryos - biol rep 3

description:
Library name: 4 dpf WT 3
bulk RNA-seq


title: Whole body 4 dpf sox10 mutant embryos  - biol rep 1

description:
Library name: 4 dpf Mutant 1
bulk RNA-seq


title: Whole body 4 dpf wild-type embryos - biol rep 2

description:
Library name: 4 dpf WT 2
bulk RNA-seq


title: ChAd/mRNA_06_V1D3


title: ChAd/mRNA_05_V1D3


title: HEK-293-PRCCTFE3120-C1, Doxy(+)

type: RNA

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Urology

institute: Kumamoto University

description: Gene expression data from HA-PRCC-TFE3 doxycycline-inducible HEK293 cell line with doxyxycline

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0 array in an Affymetrix GeneChip® Hybridisation Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The processed array was scanned using the GeneChip® Scanner 3000 7G.

data_processing: The scan data is processed using GeneChip™ Command Console™ (GCC) software for further analysis.

label: biotin

source_name: HEK293 cell, PRCC-TFE3 expressing

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HA-PRCC-TFE3-inducible HEK293 cell lines which express HA-PRCC-TFE3 in a doxycycline-dependent manner were cultured with DMEM supplemented with 10% FCS, 100 U/ml penicillin, 100 microg/ml streptomycin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HA-PRCC-TFE3-inducible HEK293 cells were cultured with or without 0.2 microg/ml of doxycycline for 24hr.

value: Human embryonic kidney cell line


title: ChAd/mRNA_07_V1D7


title: Whole body 7 dpf sox10 mutant embryos - biol rep 2

description:
Library name: 7 dpf Mutant 2
bulk RNA-seq


title: Whole body 4 dpf wild-type embryos - biol rep 1

description:
Library name: 4 dpf WT 1
bulk RNA-seq


title: Whole body 45 hpf sox10 mutant embryos - biol rep 2

description:
Library name: 45 hpf Mutant 2
bulk RNA-seq

value: 45 hpf


title: ChAd/mRNA_02_V1D3


title: ChAd/mRNA_04_V1D3


title: Whole body 45 hpf sox10 mutant embryos - biol rep 3

description:
Library name: 45 hpf Mutant 3
bulk RNA-seq


title: ChAd/mRNA_03_V1D3


title: Whole body 45 hpf sox10 mutant embryos - biol rep 1

description:
Library name: 45 hpf Mutant 1
bulk RNA-seq


title: Whole body 45 hpf wild-type embryos - biol rep 3

description:
Library name: 45 hpf WT 3
bulk RNA-seq


title: ChAd/mRNA_01_V1D3


title: ChAd/mRNA_06_V1D1


title: ChAd/mRNA_08_V1D1


title: ChAd/mRNA_07_V1D3


title: HEK-293-PRCCTFE3120-C1, Doxy(-)

description: Gene expression data from HA-PRCC-TFE3 doxycycline-inducible HEK293 cell line without doxycycline

source_name: HEK293 cell


title: ChAd/mRNA_05_V1D1


title: ChAd/mRNA_07_V1D1


title: Zebrafish_ac4C

city: Fuzhou

first: lele

last: Yang

address: Fujian Medical University, 1 Xuefubei Road, Minhou, Fuzhou, Fujian province, China

institute: Fujian Medical University

data_processing:
The raw ac4C-RIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for ac4C-modification peak calling and the significant methylation was identified by exomepeak2 , and the ac4C peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the ac4C peaks contained the consensus of ac4C motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of ac4C regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: danRer10 or WBcel235
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels and ac4C status changes for each gene.

source_name: Animal organ cells

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: Animal organ cells

value: Wild type

tag: rip antibody

value: anti-ac4C  (Abcam  catalog No. ab252215)


title: Whole body 45 hpf wild-type embryos - biol rep 1

description:
Library name: 45 hpf WT 1
bulk RNA-seq


title: Zebrafish Lateral Ectoderm 7.5 hpf 4

city: Klosterneuburg

first: Stefania

last: Tavano

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (ISTA)

description: NovaSeq S4 XP 150-bp pair end sequencing

data_processing:
FastQC (quality control)
Trimmomatic (adapter & quality trimming; parameters: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:19)
FastQC (controlling trimming results)
salmon (Alignment; used flags: --seqBias --qcBias)
R - DESeq2 (differential gene expression analysis; DESEq2, apeglm, tximport, genefilter, GenomicRanges)
R - EnhancedVolcano & biomaRt (visualization)
Assembly: Danio rerio GRCz11
Supplementary files format and content: tab delimited text file with gene name, gene length, effective length, tpm and number of reads for each sample

source_name: Lateral Ectoderm

growth_protocol: Embryos were kept at 28.5 C until dissociation

extract_protocol:
Cells were subjected to RNA extraction using RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer instructions
Complete cDNA synthesis and library preparation were performed using SMART-Seq v3 protocol with Nextera UDI adapters. Libraries were then quantified by qPCR (KAPA Biosysytems).

treatment_protocol: Embryo were injected with 125 pg of PAmCherry1 mRNA at 1-cell stage. At 6 hours post fertilization (hpf), embryos were mounted for up-right imaging and a 444 x 220 x 58.5 µm volume was photoactivated using a 405 nm laser either at the animal pole or on the lateral side. The photoactivation process was composed of 10 cycles of 28 sec per embryo in a time window of approximately 90 min. After photoactivation, embryos were transferred in Ca2+-free Ringer solution and dissociated by gently pipetting using a P-1000 pipette to obtain a single-cell suspension. 5000 PAmCherry1+ cells were sorted in 150 µl of RTL plus lysis buffer (RNeasy Plus Micro Kit, QIAGEN) with 1% of 2-mercaptoethanol.

value: Lateral Ectoderm

value: WT (Tg(Sebox::eGFP) embryos)

value: 1-cell stage injection of PAmCherry1 mRNA, Photoactivation, FACS


title: ChAd/mRNA_04_V1D1

value: Whole blood


title: ChAd/mRNA_02_V2D1


title: Whole body 45 hpf wild-type embryos - biol rep 2

description:
Library name: 45 hpf WT 2
bulk RNA-seq


title: Zebrafish_input

value: none (input)


title: ChAd/mRNA_03_V1D1


title: ChAd/mRNA_08_V1D0


title: Leaf, Cool, 495, rep 3

city: Poznan

first: Rocco

middle: Fabrizio

last: Notarnicola

state: Wielkopolskie

address: ul, Uniwersytetu Poznańskiego 6

department: Evolutionary Biology

country: Poland

institute: Adam Mickiewicz University

data_processing:
Raw reads were trimmed for adapters and low-quality base calls (PHRED < 20) using Trim Galore! (Babraham Bioinformatics) with default settings.
Trimmed reads were inspected using MultiQC (Ewels et al., 2016).
An index was constructed with Kallisto using a fasta file of transcripts defined in our trancsriptome assembly. Transcript quantification was performed with Kallisto (Bray et al., 2016) on those transcripts.
Assembly: W. ceracea genome assembly will be uploaded on DRYAD upon manuscript submission
Supplementary files format and content: tsv: plaintext file of the abundance estimates. It does not contains bootstrap estimates.
Supplementary files format and content: h5: HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length.
Supplementary files format and content: count_matrix.csv: csv file containing raw gene counts for each gene and each sample generated by the tximport R package and function with the 'lengthScaledTPM' algorithm.

organism: Wahlenbergia ceracea

source_name: Leaf

growth_protocol: F3 seeds were germinated in seed raising mix in 14 × 8.5 × 5 cm pots in the glasshouse under 28/20 ºC to maximise germination and establishment (Notarnicola et al., 2022; Arnold et al., 2022). Subsequently, plants were grown under controlled conditions (28/20 ºC, 60 % relative humidity, 14-hour photoperiod, 1200 µmol s-1 m-2) using a Growth Capsule GC (Photon Systems Instruments, Brno, Czech Republic). Individual plants were transplanted into individual pots (6.5 × 6.5 × 16 cm) and supplemented with slow-release fertilizer (Osmocote Plus, Scotts Australia). We randomly arranged three replicate plants for each line in three blocks (one replicate per block) that were equivalent in each of 2 capsules. Plants were bottom watered as needed and supplemented with liquid fertiliser every two weeks (Yates Thrive, Yates Australia).

extract_protocol:
Total RNA was extracted from snap-frozen and ground leaf tissue using the Spectrum Plant Total RNA Kit (Merck, New Jersey, USA) with on-column DNase I digestion.
The construction of cDNA libraries was conducted with 250 ng RNA input using the Illumina stranded mRNA prep ligation protocol, as per manufacturer’s instructions except that reaction volumes were scaled by one-half and 12 PCR cycles were used for library amplification.

treatment_protocol: Two weeks after transplantation, plants were subject to either cool (24/15 ºC day/night, optimal for growth and flowering of post-seedling plants; Arnold et al., 2022) or warm temperatures (30/20 ºC day/night). Plants grown at 30 ºC have reduced fitness (seed number and viability) but are not sterile nor undergo photoinhibition [Fv/Fm (maximum PSII efficiency) > 0.70; Notarnicola et al., 2021]. Experimental design: 12 lines x 3 replicates x 2 growth temperatures = 72 individuals (Figure S1). We let the plants grow for a further two weeks by which time they had produced new leaves acclimated to the respective temperature conditions. We took two ~1 mg leaf tissue per plant from the two youngest, fully-expanded, healthy leaves. Leaves were harvested in a randomized order between 11:00 and 16:30, and immediately flash-frozen in liquid nitrogen and stored at -80 ºC. Time of harvesting and developmental stage were recorded for each sample (‘nonflowering’ n = 56; ‘early bud’ n = 16).

value: Leaf

value: Cool

tag: tolerance

value: Tolerant

tag: flowering state

value: Early bud


title: Zebrafish Lateral Ectoderm 7.5 hpf 1

tag: tissue


title: Leaf, Cool, 491, rep 3

value: Non-flowering


title: ChAd/mRNA_02_V1D1

value: ChAd/mRNA

value: ChAdOx1 nCoV-19


title: Zebrafish Lateral Ectoderm 7.5 hpf 2


title: ChAd/mRNA_05_V1D0


title: Zebrafish Animal Ectoderm 7.5 hpf 4

source_name: Animal Ectoderm

value: Animal Ectoderm


title: ChAd/mRNA_06_V1D0


title: Leaf, Cool, 483, rep 3


title: Zebrafish Animal Ectoderm 7.5 hpf 3


title: Zebrafish Lateral Ectoderm 7.5 hpf 3


title: ChAd/mRNA_04_V1D0


title: ChAd/mRNA_03_V1D0


title: ChAd/mRNA_02_V1D0


title: Leaf, Cool, 479, rep 3


title: ChAd/mRNA_01_V1D1


title: ChAd/mRNA_07_V1D0


title: Leaf, Warm, 477, rep 3

value: Warm

value: Sensitive


title: patient 076 primary tumor sample 1

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

data_processing:
Adapter sequences and low quality read ends were trimmed off using Cutadapt v2.8
Trimmed reads were mapped against the human reference (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters --dta --strandness RF -k 5
Secondary alignments were filtered out using samtools (v 1.10)
Mapped reads were summarized using featureCounts (v 2.0.0) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh38.100)
Assembly: UCSC GRCh38
Supplementary files format and content: Comma-separated text file containing raw count values for each sample

source_name: tumor of the oral cavity

extract_protocol:
RNA from patient-derived samples was isolated according to an acid guanidinium thiocyanate-phenol-chloroform extraction method (PMID: 2440339). The TRIzol incubation time for patient samples was increased to 10min and the samples were regularly resuspended at room temperature
Library preparation based on ribosome depletion were conducted by Genewiz (Leipzig, Germany)

value: tumor of the oral cavity

tag: disease

value: OSCC

tag: Sex

value: male

tag: age

tag: cluster


title: ChAd/mRNA_01_V1D0


title: Zebrafish Animal Ectoderm 7.5 hpf 1

tag: genotype

value: WT (Tg(Sebox::eGFP) embryos)

tag: treatment


title: WT-AA rep3

city: Kaifeng

first: Xiaohong

last: Zhu

address: Jinming Street

institute: Henan University

data_processing:
HiSeq2500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Seedlings were grown vertically on 1/2 MS medium with 1% sucrose and 1.2% agar.

extract_protocol:
Total RNA was isolated usingTRIzol for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ten day old seedlings were transferred from MS plates to 9-well plate containing 1mL 1/2 liquid MS medium per well and treated with 50uM antimycin for 5 hours.

value: whole seedling

value: ten day old

value: wildtype Col-0

value: AA treatment


title: patient 077 metastasis 1

source_name: metastasis of the lymph node

value: metastasis of the lymph node

value: female


title: patient 075 primary tumor sample 1


title: Leaf, Warm, 487, rep 3

value: Leaf

value: Late bud


title: patient 075 primary tumor sample 2


title: patient 074 primary tumor sample 1

source_name: tumor

value: tumor


title: Leaf, Cool, 467, rep 3

value: Cool

value: Tolerant

value: Non-flowering


title: Leaf, Cool, 457, rep 3

value: Sensitive


title: WT-AA rep2


title: Leaf, Warm, 439, rep 3

value: Warm


title: patient 072 metastasis 3

value: OSCC


title: WT-AA rep1


title: patient 072 metastasis 2


title: Leaf, Cool, 495, rep 2


title: patient 072 primary tumor sample 2

source_name: tumor of the jaw

value: tumor of the jaw


title: patient 072 metastasis 1


title: patient 071 primary tumor sample 1

source_name: tumor of the tongue

value: tumor of the tongue

value: male


title: Leaf, Warm, 487, rep 2


title: Leaf, Cool, 483, rep 2


title: crf6-2-AA rep3

value: whole seedling

value: ten day old

value: crf6 mutant


title: patient 068 primary tumor sample 1


title: WT-CK rep2

value: wildtype Col-0

value: mock  control


title: patient 070 primary tumor sample 1


title: WT-CK rep1


title: patient 067 primary tumor sample 1


title: patient 065 primary tumor sample 1


title: patient 066 primary tumor sample 1

value: tumor of the oral cavity


title: patient 064 metastasis 2

value: metastasis of the lymph node

value: female


title: Leaf, Warm, 491, rep 3

value: Leaf


title: Leaf, Warm, 477, rep 2


title: patient 070 primary tumor sample 2


title: patient 064 metastasis 1


title: crf6-2-AA rep2

value: AA treatment


title: patient 066 primary tumor sample 2


title: crf6-2-CK rep3


title: Leaf, Cool, 467, rep 2

value: Cool

value: Tolerant

value: Non-flowering


title: Leaf, Warm, 479, rep 3

value: Warm


title: patient 060 primary tumor sample 1

value: tumor of the jaw

value: OSCC


title: crf6-2-CK rep2


title: crf6-2-AA rep1


title: patient 062 primary tumor sample 1

source_name: tumor of the cheek

value: tumor of the cheek

value: male


title: WT-CK rep3

value: whole seedling

value: ten day old


title: patient 059 primary tumor sample 1


title: Leaf, Warm, 439, rep 2

value: Sensitive


title: patient 064 primary tumor sample 1

value: tumor


title: patient 059 metastasis 1


title: patient 058 primary tumor sample 1

value: tumor of the tongue


title: crf6-2-CK rep1

value: crf6 mutant

value: mock  control


title: SnRK1aOX-AA rep3

value: SnRK1a overexpression line


title: patient 056 primary tumor sample 1

value: female


title: patient 057 primary tumor sample 1

value: tumor of the oral cavity


title: patient 054 primary tumor sample 2


title: patient 055 primary tumor sample 1


title: patient 063 primary tumor sample 1


title: Leaf, Warm, 457, rep 3

value: Leaf


title: SnRK1aOX-AA rep1

value: AA treatment


title: Leaf, Warm, 491, rep 2

value: Warm

value: Tolerant

value: Non-flowering


title: patient 052 primary tumor sample 1

value: tumor of the jaw

value: OSCC


title: patient 053 primary tumor sample 1

value: male


title: patient 054 primary tumor sample 1


title: patient 051 primary tumor sample 1


title: Leaf, Cool, 483, rep 1

value: Cool


title: Leaf, Cool, 485, rep 3


title: SnRK1aOX-CK rep3

value: whole seedling

value: ten day old


title: Leaf, Warm, 479, rep 2


title: patient 050 primary tumor sample 1


title: SnRK1aOX-CK rep2


title: patient 049 metastasis 1

value: metastasis of the lymph node


title: Leaf, Cool, 475, rep 3

value: Sensitive

value: Early bud


title: Leaf, Cool, 495, rep 1


title: SnRK1aOX-CK rep1

value: SnRK1a overexpression line

value: mock  control


title: SnRK1aOX-AA rep2


title: patient 048 primary tumor sample 1

value: tumor of the oral cavity


title: Leaf, Cool, 467, rep 1

value: Leaf


title: patient 047 primary tumor sample 1


title: jmj15-2-AA rep3

value: jmj15 mutant

value: AA treatment


title: patient 046 primary tumor sample 1

value: female


title: Leaf, Cool, 437, rep 3


title: patient 047 metastasis 1


title: patient 044 primary tumor sample 1


title: patient 046 metastasis 1


title: jmj15-2-CK rep1


title: Leaf, Warm, 457, rep 2

value: Warm

value: Non-flowering


title: jmj15-2-CK rep3


title: patient 042 primary tumor sample 1

value: tumor of the jaw

value: OSCC


title: jmj15-2-CK rep2


title: patient 046 metastasis 2


title: Leaf, Cool, 485, rep 2

value: Cool

value: Tolerant


title: patient 042 metastasis 3

value: male


title: patient 049 primary tumor sample 1


title: Leaf, Warm, 495, rep 3


title: patient 043 primary tumor sample 1


title: patient 045 primary tumor sample 1


title: Leaf, Warm, 491, rep 1


title: patient 042 primary tumor sample 2


title: jmj15-2-AA rep2

value: whole seedling

value: ten day old


title: jmj15-2-AA rep1


title: patient 041 primary tumor sample 1

value: tumor of the tongue


title: patient 042 metastasis 2

value: metastasis of the lymph node


title: snrk1a-2-AA rep3

value: snrk1a mutant


title: patient 042 metastasis 1


title: Leaf, Warm, 479, rep 1


title: patient 040 primary tumor sample 1


title: Leaf, Warm, 483, rep 3


title: patient 037 primary tumor sample 3

value: tumor of the oral cavity


title: snrk1a-2-CK rep2

value: mock  control


title: patient 038 primary tumor sample 2


title: Leaf, Warm, 457, rep 1

value: Leaf

value: Sensitive


title: patient 036 primary tumor sample 1


title: snrk1a-2-CK rep1


title: Leaf, Cool, 475, rep 2


title: patient 034 primary tumor sample 3

value: female


title: snrk1a-2-AA rep1

value: AA treatment


title: snrk1a-2-AA rep2


title: patient 037 primary tumor sample 2


title: Leaf, Warm, 495, rep 2

value: Warm

value: Non-flowering


title: patient 037 primary tumor sample 4

value: OSCC


title: patient 037 primary tumor sample 1


title: Leaf, Cool, 487, rep 3

value: Cool


title: patient 034 primary tumor sample 2

value: tumor of the jaw


title: patient 034 metastasis 1


title: patient 034 primary tumor sample 1


title: 30D cortical organoid, meth-treated, batch 2, sample 3

city: La Jolla

first: Tariq

last: Rana

state: California

address: 3147 Biomedical Sciences Wy

department: Pediatrics

institute: UC San Diego School of Medicine

description: Library name: M3-B2

data_processing:
Chromium single-cell 3′ RNA-seq libraries were aligned to GRCh38 using the 10x Genomics Cell Ranger 8.0.1 pipeline following default settings.
Assembly: GRCh38-2024-A
Supplementary files format and content: features.tsv.gz: zipped tab separted value files containing gene information.
Supplementary files format and content: barcodes.tsv.gz: zipped tab separted value files containing cell barcode information
Supplementary files format and content: matrix.mtx.gz: zipped matrix file containing gene counts per cell

source_name: cortical organoid

growth_protocol: H9 hESCs (WA09) from WiCell was cultured on a feeder layer of irradiated mouse embryonic fibroblasts or under feeder-free matrigel coated conditions following previously established protocols. Feeder-dependent H9 hESCs were detached from their feeder layer using 1 mg/ml collagenase (dissolved in DMEM-F12 medium) for 15–20 min at 37 °C in CO2 incubator and 0.5 mg/ml dispase (dissolved in DMEM-F12 medium) for an additional 15 min at 37 °C in CO2 incubator. Wells were washed with media to collect floating undifferentiated hESCs and colonies were dissociated using Accumax or Versene solution at 37 °C for 10 min to generate a single-cell suspension. At day 0, embryoid bodies were formed using the hanging drop method with 4500 cells/drop in DMEM/F12 media supplemented with 20% knockout serum replacement (KOSR), bFGF (4 ng/ml), MEM nonessential amino acids (MEM-NEAA, 1%, vol/vol), and glutamine (200 mM, 1%, vol/vol) or grown in microwell plates. After 2 days of hanging drop culture, embryoid bodies were transferred to sterile petri dishes with refreshed media. After 6 days in culture, embryoid bodies were transferred to new petri dishes containing neural induction media consisting of DMEM/F12, N2 supplement (1%, vol/vol), MEM-NEAA (1%, vol/vol), glutamine (200 mM, 1%, vol/vol), and heparin (1 μg/ml) until day 11. At day 11, organoids were transferred to Matrigel droplets (30 μl) and cultured in 1:1 mixture of DMEM/F12 and Neurobasal medium supplemented with B-27 without vitamin A (1%, vol/vol), N2 (1%, vol/vol), NEAA (1%, vol/vol), insulin, beta-mercaptoethanol, and glutamine (200 mM, 1%, vol/vol). Twenty organoids were then transferred to stir flask bioreactors (125 ml) containing magnetic shaft and stirring speed was maintained 50–60 rpm. For long term growth on day 15 in 75–100 ml of cerebral organoid differentiation media with vitamin A. Media was changed every 3 days.

extract_protocol:
scRNA-seq was performed on eight untreated and six METH-treated organoids. Organoids were manually dissociated into single-cell suspension using the Milteny Biotec Neural Tissue Dissociation Kit (P) (Milteny Biotec, 130–092–628) following manufacturer’s instructions. Briefly, organoids were washed with PBS and cut into small pieces using a scalpel. Tissues were resuspended in warmed enzyme mix 1 containing papain and rotated for 15 min at 37 °C. Enzyme mix 2 was added and tissues were mechanically dissociated using a wide-tipped pipet. Cell suspensions were passed through a 40 μm cell strainer and centrifuged to pellet. Cell concentrations and viability were assessed by trypan blue staining.
scRNA-seq libraries were generated using the 10x Genomics Chromium Single-cell 3′ Library & Gel Bead Kit V2 (10x Genomics, PN-120237) at the UCSD Institute for Genomic Medicine Genomic Center. Libraries were generated from organoid single-cell suspensions following manufacturer’s protocol.

treatment_protocol: Organoids were treated with 5 μM METH dissolved in organoid culture media every other day for 1 week before fixing for immunostaining or dissociation for scRNA-seq.

value: cortical organoid

tag: cell line

value: 5 uM methamphetamine

tag: batch


title: 30D cortical organoid, meth-treated, batch 2, sample 2

description: Library name: M2-B2


title: patient 038 primary tumor sample 1

value: male


title: patient 035 primary tumor sample 1


title: Leaf, Warm, 467, rep 3

value: Tolerant


title: 30D cortical organoid, meth-treated, batch 2, sample 1

description: Library name: M1-B2


title: patient 029 primary tumor sample 1


title: snrk1a-2-CK rep3

value: whole seedling

value: ten day old


title: Zebrafish Animal Ectoderm 7.5 hpf 2

value: Animal Ectoderm

value: WT (Tg(Sebox::eGFP) embryos)

value: 1-cell stage injection of PAmCherry1 mRNA, Photoactivation, FACS


title: patient 005 primary tumor sample 2

value: tumor


title: patient 028 primary tumor sample 1

value: female


title: Leaf, Cool, 477, rep 3

value: Leaf

value: Sensitive


title: patient 032 primary tumor sample 1

value: tumor of the cheek


title: 30D Cortical organoid, meth-treated, batch 1, sample 1

description: Library name: M1-B1


title: patient 027 primary tumor sample 1

value: OSCC


title: patient 031 primary tumor sample 1

value: tumor of the oral cavity


title: patient 027 primary tumor sample 2


title: 30D Cortical organoid, meth-treated, batch 1, sample 3

description: Library name: M3-B1


title: patient 027 metastasis 2

value: metastasis of the lymph node


title: Leaf, Cool, 437, rep 2

value: Cool

value: Non-flowering


title: Leaf, Cool, 475, rep 1

value: Early bud


title: Leaf, Warm, 467, rep 2

value: Warm

value: Tolerant


title: patient 027 metastasis 1

value: male


title: 30D Cortical organoid, untreated, batch 2, sample 5

description: Library name: NT6-B2

value: cortical organoid

value: no treatment


title: patient 026 primary tumor sample 1

value: tumor of the jaw


title: 30D Cortical organoid, untreated, batch 2, sample 4

description: Library name: NT5-B2


title: Leaf, Cool, 485, rep 1


title: Leaf, Warm, 483, rep 2


title: patient 024 primary tumor sample 1


title: patient 025 primary tumor sample 1

value: tumor of the tongue


title: Leaf, Cool, 437, rep 1


title: patient 023 primary tumor sample 1


title: 30D Cortical organoid, untreated, batch 2, sample 3

description: Library name: NT4-B2


title: patient 021 primary tumor sample 1

value: female


title: patient 019 primary tumor sample 1


title: Leaf, Cool, 487, rep 2

value: Leaf


title: patient 020 primary tumor sample 1


title: 30D Cortical organoid, untreated, batch 2, sample 1

description: Library name: NT1-B2


title: patient 018 primary tumor sample 1


title: patient 016 primary tumor sample 1


title: Leaf, Warm, 485, rep 3


title: 30D Cortical organoid, untreated, batch 1, sample 3

description: Library name: NT3-B1


title: Leaf, Cool, 439, rep 3

value: Sensitive


title: patient 017 primary tumor sample 1


title: patient 015 primary tumor sample 2


title: 30D Cortical organoid, untreated, batch 1, sample 2

description: Library name: NT2-B1


title: Leaf, Cool, 477, rep 2


title: patient 014 primary tumor sample 1


title: patient 015 primary tumor sample 1


title: 30D Cortical organoid, untreated, batch 1, sample 1

description: Library name: NT1-B1


title: patient 013 primary tumor sample 1


title: Leaf, Warm, 483, rep 1


title: Leaf, Warm, 475, rep 3


title: patient 012 primary tumor sample 1


title: PAX351_RNAseq

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

institute: Robert Bosch Center for Tumor Diseases

data_processing:
Paired end sequencing reads were mapped to the reference genome assembly hg38 using STAR (star/2.7.3a). Reverse (sense strand) reads were quantified using htseq-count (htseq/0.9.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: PDX

growth_protocol: AsPC1 (RPMI, 10% FBS, 1% Pen-Strep), HPAFII and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep), PaTu8988s (DMEM, 20% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C. PDX models were generated as described in PMID: 36889906.

extract_protocol:
Cells were washed twice with PBS after removing cell culture medium and total RNA was extracted from cells by adding 700 µL of QIAzol, incubated for 5 min on rocker, scraped and transferred to a new tube. 140 µL chloroform was added to the samples, vortexed for 15 sec, incubated for 3 min at room temperature, and centrifuged. Aqueous phase was transferred to a new tube and mixed with an equal volume of isopropanol. Samples were incubated at -20°C overnight and centrifuged. RNA pellet was washed twice with 70% ethanol and the pellet was air-dried at room temperature for 5-10 min. 50 µL of RNAse-free water was used to resuspend the pellet.
Before RNA-sequencing, RNA integrity was validated by gel electrophoresis and libraries were prepped using 500 ng following supplier’s protocol TruSeq Stranded mRNA Library Prep Kit (Illumina, 20020595). The library fragment size was determined by TapeStation.
cDNA_oligo_dT

value: PDX

tag: cell type

value: PDAC


title: patient 022 primary tumor sample 1

value: tumor of the oral cavity

value: OSCC


title: 30D Cortical organoid, untreated, batch 2, sample 2

description: Library name: NT2-B2


title: patient 011 primary tumor sample 2


title: patient 011 primary tumor sample 1


title: Leaf, Warm, 467, rep 1


title: patient 010 primary tumor sample 1


title: patient 009 primary tumor sample 1


title: PAX330_RNAseq


title: Leaf, Warm, 495, rep 1


title: PAX326_RNAseq


title: patient 006 primary tumor sample 1


title: Leaf, Cool, 439, rep 2

value: Cool


title: patient 004 metastasis 2

value: metastasis of the lymph node


title: Leaf, Cool, 491, rep 2

value: Non-flowering


title: patient 004 primary tumor sample 1


title: PAX308_RNAseq


title: PAX298_RNAseq


title: Leaf, Cool, 487, rep 1


title: Leaf, Warm, 437, rep 3

value: Warm

value: Early bud


title: patient 004 metastasis 1

value: male


title: patient 001 primary tumor sample 2


title: patient 003 primary tumor sample 1


title: patient 001 primary tumor sample 1


title: patient 001 metastasis 2


title: PAX297_RNAseq


title: patient 002 primary tumor sample 1


title: PAX295_RNAseq


title: PAX300_RNAseq


title: patient 008 primary tumor sample 1


title: patient 001 metastasis 1


title: PAX280_RNAseq


title: PAX265_RNAseq


title: patient 007 primary tumor sample 1


title: patient 005 primary tumor sample 1

value: tumor


title: RNA_RRP001_Pt31_Screening_Tissue

city: Plymouth Meeting

first: Elisabeth

last: Gillespie

state: PA

address: 660 W Germantown Pike, Suite 110

institute: Inovio Pharmaceuticals

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv

data_processing:
Data were processed as per ImmunoID Next Analysis Pipeline from Personalis (www.personalis.com)
Aligment was perfomred with STAR (Spliced Transcripts Aligment to a Refernce)
Normalized gene and transcript expression were derived from propietery tools from Personalis and Salmon
Immune repertorie analysis was conducted with MIXCR
Raw count  normalization was conducted in EdgeR
Assembly: hs37d5
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing TCR sequences and  counts for each sample

source_name: Tissue

extract_protocol:
Dual isolation of nucleic acids was performed utilizing the AllPrep DNA/RNA FFPE Tissue kit (Qiagen).
Libraries were prepared using the Stranded RNA Sequencing kit (Kapa Biosystems).

tag: individual

value: Orophraryngeal biopsy

value: Female

value: Screening


title: RNA_RRP001_Pt30_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv

value: Male


title: Leaf, Warm, 475, rep 2

value: Leaf


title: RNA_RRP001_Pt32_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: PAX277_RNAseq


title: Leaf, Warm, 437, rep 2

value: Sensitive


title: Leaf, Cool, 457, rep 2


title: PAX242_RNAseq

value: PDX


title: Leaf, Cool, 491, rep 1

value: Tolerant


title: PAX232_RNAseq

value: PDAC


title: Leaf, Cool, 439, rep 1


title: PAX252_RNAseq


title: Leaf, Warm, 487, rep 1


title: RNA_RRP001_Pt30_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: Leaf, Warm, 485, rep 1


title: RNA_RRP001_Pt26_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: Leaf, Warm, 485, rep 2


title: Leaf, Cool, 477, rep 1


title: 30D Cortical organoid, meth-treated, batch 1, sample 2

description: Library name: M2-B1

value: cortical organoid

value: 5 uM methamphetamine


title: RNA_RRP001_Pt31_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: Leaf, Cool, 479, rep 1

value: Cool


title: RNA_RRP001_Pt19_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: RNA_RRP001_Pt26_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: RNA_RRP001_Pt25_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: RNA_RRP001_Pt25_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: Leaf, Cool, 479, rep 2

value: Non-flowering


title: RNA_RRP001_Pt18_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: PAX139_RNAseq


title: Leaf, Warm, 477, rep 1

value: Warm


title: PaTu8988s_siNT5_Rep3_RNAseq

source_name: cell line

value: cell line


title: RNA_RRP001_Pt32_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: RNA_RRP001_Pt23_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: PAX217_RNAseq


title: RNA_RRP001_Pt19_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: RNA_RRP001_Pt15_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: PaTu8988s_siNT5_Rep2_RNAseq


title: RNA_RRP001_Pt17_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: RNA_RRP001_Pt23_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: RNA_RRP001_Pt15_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: PAX208_RNAseq


title: RNA_RRP001_Pt17_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: Leaf, Cool, 457, rep 1


title: RNA_RRP001_Pt18_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: RNA_RRP001_Pt12_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: PaTu8988s_siNT5_Rep1_RNAseq


title: RNA_RRP001_Pt12_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: Leaf, Warm, 439, rep 1


title: RNA_RRP001_Pt11_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: PaTu8988s_siGATA6_Rep3_RNAseq


title: RNA_RRP001_Pt11_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: RNA_RRP001_Pt8_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: Leaf, Warm, 437, rep 1

value: Early bud


title: RNA_RRP001_Pt8_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: PaTu8988s_siGATA6_Rep2_RNAseq


title: RVSMC Vector Input2

city: Beijing

first: Jiaqi

last: Huang

address: Xueyuan Road 38

institute: Peking University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the sequences, in which reads with the same sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
Assembly: Rn5
Supplementary files format and content: Differentially methylated RNA sites

organism: Rattus norvegicus

source_name: primary rat vascular smooth smucle cells

extract_protocol:
MeRIP experiments, high-throughput sequencing and data analysis were conducted by Seqhealth Technology Co., Ltd. (Wuhan, China). Briefly, total RNA was extracted from control or Mettl3-overexpressing rat primary VSMCs using TRIzol Reagent (Invitrogen, cat. No. 15596026). One hundred micrograms of total RNA were used for the meRIP experiment. Briefly, 20 mM ZnCl2 was added to total RNA and incubated at 94°C for 5 min until the RNA fragments were mainly distributed in 100-200 nt. Then, 10% of the RNA fragments were saved as “input”, and the remaining fragments were used for m6A immunoprecipitation (IP). The specific anti-m6A antibody (Synaptic Systems, 202003) was applied for m6A IP.
The stranded RNA sequencing library was constructed by using the KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog No. DR08502, Wuhan Seqhealth Co., Ltd., China) with five PCR cycles. The kit eliminates duplication bias in PCR and sequencing steps. Then, ribosomal cDNA was removed by a SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian; 634413; TaKaRa/Clontech, Japan), and ten PCR cycles were added.
The library products corresponding to 200-500 bp were enriched, quantified and finally sequenced on a DNBSEQ-T7 sequencer (MGI Tech Co., Ltd., China) with a PE150 model.

value: control


title: RNA_RRP001_Pt7_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv

value: Orophraryngeal biopsy


title: PaTu8988s_siGATA6_Rep1_RNAseq


title: RNA_RRP001_Pt7_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: RNA_RRP001_Pt6_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv

value: Female


title: AsPC1_siNT5_Rep3_RNAseq


title: RVSMC Vector IP2

value: primary rat vascular smooth smucle cells

value: anti-m6A antibody (Synaptic Systems, 202003)


title: Leaf, Warm, 475, rep 1

value: Leaf


title: RNA_RRP001_Pt2_Week52_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv

value: Male


title: RNA_RRP001_Pt6_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv

value: Screening


title: AsPC1_siNT5_Rep2_RNAseq


title: RVSMC Vector input1


title: RVSMC Vector IP1


title: RNA_RRP001_Pt1_Week47_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: RNA_RRP001_Pt2_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: AsPC1_siNT5_Rep1_RNAseq


title: RVSMC OE Mettl3 input2


title: AsPC1_siGATA6_Rep3_RNAseq


title: RNA_RRP001_Pt1_Screening_Tissue

description:
rrp_tcr_counts.csv
rrp_raw_counts.csv


title: RNA_RRP001_Pt32_Week26_PBMC

source_name: PBMC

value: PBMC


title: RNA_RRP001_Pt32_Week11_PBMC


title: RVSMC OE Mettl3 input1


title: RNA_RRP001_Pt32_Week52_PBMC


title: AsPC1_siGATA6_Rep1_RNAseq

value: PDAC


title: RVSMC OE Mettl3 IP1


title: RNA_RRP001_Pt31_Week26_PBMC


title: RNA_RRP001_Pt32_Week9_PBMC


title: AsPC1_siGATA6_Rep2_RNAseq


title: RNA_RRP001_Pt32_Day0_PBMC


title: Patient_4_PAX265_scFFPEseq

data_processing:
Reads were mapped to hg38 genome and Chromium_Human_Transcriptome_Probe_Set_v1.0.1 probe set using CellRanger v8.0 multi pipeline. We applied three quality control measures on the filtered feature barcode matrix file. Cells with mitochondrial genes <20%, UMI counts per cell ranging from 100-100000 and cells expressing >200 genes with sum of counts for each gene with more than 3 counts were used for further analysis.
Assembly: hg38
Supplementary files format and content: barcodes, features, and matrix

source_name: PDAC primary tumor from 25 um FFPE section

extract_protocol:
FFPE sections (2 x 25 µm) from each patient sample were collected and single-cell suspensions were isolated by combining mechanical dissociation with enzymatic degradation using Tumor Dissociation Kit (Miltenyi Biotech, Germany) following the manufacturer’s protocol. Briefly, FFPE tissue sections were deparaffinized and rehydrated with Xylene and ethanol washes. The samples were then scraped from the slide and transferred to C tube containing the dissociation mix (1x Buffer S, Enzyme D, G, RNase inhibitor). The gentleMACS program 37_FFPE_1 on the gentleMACS Octo Dissociator with heaters was run for both the samples. Each cell suspension was transferred to a new 15 mL tube on ice after being passed through a 30 μm strainer. The C tube was rinsed with 1 mL of ice cold Buffer F to minimize any cell loss. The filtered cell suspension was centrifuged at 850 g at 4°C for 5 min. The supernatant was aspirated and the cell pellet was resuspended in 0.5 mL of resuspension buffer which was further used for single-cell RNA sequencing.
Each cell suspension was subjected to probe-based multiplexed sequencing using 10X Chromium Fixed RNA Kit, Human Transcriptome (4 reactions x 4 BC PN-1000475) with a cell recovery target of 6000 following the user guide (CG000527). Libraries were sequenced on an Illumina NextSeq 2000 with paired-end dual-indexing (28 cycles Read 1, 10 cycles i7, 10 cycles i5, 90 cycles Read 2).

value: Not applicable


title: RNA_RRP001_Pt31_Week52_PBMC


title: RNA_RRP001_Pt31_Week9_PBMC


title: RNA_RRP001_Pt31_Week6_PBMC


title: RNA_RRP001_Pt31_Screening_PBMC


title: RNA_RRP001_Pt30_Week52_PBMC


title: Patient_1_PAX295_scFFPEseq

value: PDAC primary tumor from 25 um FFPE section


title: GoPDX5_leChROseq

library_source: other

data_processing:
Paired end 66 bp sequencing reads were mapped to hg38 genome using proseq2.0 pipeline (https://github.com/Danko-Lab/proseq2.0.git). Briefly, -SE, -G, --UMI1=6.
Assembly: hg38
Supplementary files format and content: merged plus strand bigwig file from each condition
Supplementary files format and content: merged minus strand bigwig file from each condition

molecule: other

growth_protocol: PDX samples were generated as previosuly described in PMID: 36889906.

extract_protocol:
Length-extension Chromatin Run-On and sequencing (leChRO-seq) was performed as outlined PMID: 30349114 and PMID: 37279184
Adapter design was adapted from Illumina TruSeq small RNA library prep kit with added 6XN UMIs.

value: PDX


title: GoPDX4_leChROseq


title: GoPDX8_leChROseq


title: L36pl_GW870086_Rep3_RNAseq


title: GoPDX15_leChROseq


title: RNA_RRP001_Pt30_Week9_PBMC


title: L36pl_GW870086_Rep2_RNAseq


title: RNA_RRP001_Pt30_Week11_PBMC


title: RNA_RRP001_Pt32_Week6_PBMC


title: RNA_RRP001_Pt30_Week6_PBMC


title: PaTu8988s_siNT5_Pol2_Rep3_ChIPseq

library_source: genomic

data_processing:
Paired or single end sequencing reads were mapped to the reference genome assembly hg38 using bowtie2/2.5.0. PCR duplicates were removed with samtools markdup and replicates were merged using samtools merge (samtools/1.18). Bigwig files for individual and merged bam files were generated removing blacklist regions using reads per genomic content (RPGC) normalization with bamCoverage (deeptools/3.3.2) . MACS2 callpeak (python/3.10.11) was used to call the significant peaks with --broad cutoff 0.05 for histone marks and non-broad cutoff of 0.05 for transcription factors while using input files from respective conditions as background.
Assembly: hg38
Supplementary files format and content: merged bigiwg file for each conditiion
Supplementary files format and content: 3 column bed file

molecule: genomic DNA

growth_protocol: AsPC1 (RPMI, 10% FBS, 1% Pen-Strep), HPAFII and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep), PaTu8988s (DMEM, 20% FBS, 1% Pen-Strep), GöCDX5 (keratinocyte-SFM media, 10% FBS, 1% Pen-Strep, recombinant epidermal growth factor, bovine pituitary extract) were maintained in humidified 5% CO2 incubator at 37C. GöCDX5, a GöPDX5-derived cell line, was thawed on collagen coated plates and after the first trypsinization were transferred to a normal cell culture plate. PDX models were generated as described in PMID: 36889906.

extract_protocol:
Chromatin immunoprecipitation was performed by crosslinking cells with 1% formaldehyde for 20 min and quenched by 1.25 M glycine for 5 min. Cells were lysed with lysis buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 0.5% v/v NP-40, 1% v/v Triton X-100, 10 mM NaF). Nuclear pellets were resuspended and sonicated in sonication buffer (150 mM NaCl, 20 mM EDTA, 50 mM Tris-HCl, 1% v/v NP-40, 0.5% v/v sodium deoxycholate, 10 mM NaF, 0.1% SDS) using a Bioruptor Pico (Diagenode) and a cycle setting of 30 sec on/off until fragment sizes around 200-500 bp was reached. Protease and phosphatase inhibitors were added to both lysis and sonication buffers. Samples were precleared by 50% slurry of sepharose resuspended in sonication buffer. Antibodies were added and incubated rotating overnight. Sepharose beads coupled with Protein A (rabbit antibodies) or Protein G (mouse or goat antibodies) were added to samples and incubated for 2 hr, washed, de-crosslinked, RNAse A and proteinase K treated, and DNA was extracted. For GATA6 and Pol II ChIP of PDX tumors, 5 mm3 samples were thawed on ice in a petri dish, washed three times with PBS, cut into small pieces and transferred to a 15 mL falcon. Samples were fixed with 1% formaldehyde rotating on wheel for 20 min and quenched with 1.25 M glycine for 5 min. Samples were washed three times with PBS, resuspended in RPMI 1640 with 210 µg liberase TH per sample and transferred to gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) and incubated (step 1: spin 50 rpm 20 min; step 2: spin 1000 rpm 30 min; step 3: spin -1000 rpm 30 min). Samples were centrifuged and transferred to a new tube and washed three times with lysis buffer, resuspending the nuclear pellet each time. ChIP was continues as described above for cell lines. For H3K27ac ChIP of PDX tumors, 5 mm3 samples were homogenized on dry ice using the Sciences BioMasher II Micro Tissue Homogenizer. ChIP was carried out for the powdered tissue as described for cell lines.
ChIP DNA was quantified with Qubit using the Qubit 1X dsDNA High Sensitivity Kit and libraries were prepped per supplier’s protocol using the MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001). The library fragment size was determined by TapeStation using the High Sensitivity D1000 Sample Buffer and High Sensitivity D1000 ScreenTape.


title: RNA_RRP001_Pt30_Screening_PBMC


title: PaTu8988s_siNT5_Pol2_Rep2_ChIPseq


title: RNA_RRP001_Pt29_Week52_PBMC


title: RNA_RRP001_Pt29_Week11_PBMC


title: L36pl_Dex_Rep3_RNAseq


title: L36pl_Dex_Rep2_RNAseq


title: RVSMC OE Mettl3 IP2


title: RNA_RRP001_Pt29_Week9_PBMC


title: PaTu8988s_siNT5_Pol2_Rep1_ChIPseq


title: RNA_RRP001_Pt29_Week6_PBMC


title: RNA_RRP001_Pt29_Screening_PBMC


title: L36pl_Dex_Rep1_RNAseq


title: PaTu8988s_siGATA6_Pol2_Rep2_ChIPseq


title: RNA_RRP001_Pt28_Week26_PBMC


title: L36pl_DMSO_Rep3_RNAseq


title: RNA_RRP001_Pt28_Week11_PBMC


title: RNA_RRP001_Pt28_Week9_PBMC


title: L36pl_DMSO_Rep2_RNAseq


title: RNA_RRP001_Pt28_Week6_PBMC


title: RNA_RRP001_Pt28_Day0_PBMC


title: RNA_RRP001_Pt27_Week52_PBMC


title: PaTu8988s_Input_Rep2_ChIPseq


title: PaTu8988s_Input_Rep1_ChIPseq


title: L36pl_GW870086_Rep1_RNAseq


title: L36pl_DMSO_Rep1_RNAseq


title: RNA_RRP001_Pt27_Week11_PBMC


title: L36pl_BI653048_Rep3_RNAseq


title: RNA_RRP001_Pt29_Week26_PBMC


title: RNA_RRP001_Pt27_Day0_PBMC


title: RNA_RRP001_Pt27_Week9_PBMC


title: RNA_RRP001_Pt26_Week26_PBMC


title: RNA_RRP001_Pt26_Week52_PBMC


title: PaTu8988s_HNF4A_Rep1_ChIPseq


title: L36pl_BI653048_Rep1_RNAseq


title: PaTu8988s_HNF4A_Rep2_ChIPseq


title: L36pl_BI653048_Rep2_RNAseq


title: PaTu8988s_GATA6_Rep2_ChIPseq


title: RNA_RRP001_Pt28_Week52_PBMC


title: L36pl_AZD9567_Rep3_RNAseq


title: PaTu8988s_siGATA6_Pol2_Rep1_ChIPseq


title: RNA_RRP001_Pt26_Day0_PBMC


title: RNA_RRP001_Pt26_Week6_PBMC


title: PaTu8988s_GATA6_Rep1_ChIPseq


title: L36pl_AZD9567_Rep2_RNAseq


title: PaTu8988s_siGATA6_Pol2_Rep3_ChIPseq


title: RNA_RRP001_Pt25_Week52_PBMC


title: RNA_RRP001_Pt25_Week26_PBMC


title: RNA_RRP001_Pt25_Week11_PBMC


title: PaTu8988s_CDX2_Rep1_ChIPseq


title: RNA_RRP001_Pt25_Week9_PBMC


title: PaTu8988s_CDX2_Rep2_ChIPseq


title: RNA_RRP001_Pt26_Week11_PBMC


title: HPAFII_siNT5_Rep3_RNAseq

value: HPAFII


title: RNA_RRP001_Pt25_Week6_PBMC


title: L36pl_NELFE_Rep2_ChIPseq


title: L36pl_AZD9567_Rep1_RNAseq


title: RNA_RRP001_Pt25_Screening_PBMC


title: RNA_RRP001_Pt24_Week11_PBMC


title: RNA_RRP001_Pt24_Week52_PBMC


title: RNA_RRP001_Pt24_Week26_PBMC


title: HPAFII_siNT5_Rep2_RNAseq


title: HPAFII_siNT5_Rep1_RNAseq


title: RNA_RRP001_Pt24_Week9_PBMC


title: RNA_RRP001_Pt26_Week9_PBMC


title: GoPDX8_Input_ChIPseq


title: HPAFII_siGATA6_Rep3_RNAseq


title: RNA_RRP001_Pt24_Week6_PBMC


title: GoPDX8_H3K27ac_ChIPseq


title: HPAFII_siGATA6_Rep2_RNAseq


title: RNA_RRP001_Pt24_Day0_PBMC


title: GoPDX5_Input_ChIPseq


title: RNA_RRP001_Pt23_Week26_PBMC


title: patient 030 primary tumor sample 1

value: tumor of the tongue

value: OSCC

value: female


title: RNA_RRP001_Pt23_Week11_PBMC


title: AsPC1_GW870086_Rep3_RNAseq

value: cell line


title: RNA_RRP001_Pt23_Day0_PBMC


title: GoPDX5_H3K27ac_ChIPseq


title: RNA_RRP001_Pt23_Week6_PBMC


title: AsPC1_siNT5_Pol2_Rep3_ChIPseq


title: RNA_RRP001_Pt22_Week52_PBMC


title: L36pl_NELFE_Rep1_ChIPseq


title: RNA_RRP001_Pt22_Week11_PBMC


title: AsPC1_siNT5_Pol2_Rep2_ChIPseq


title: RNA_RRP001_Pt22_Week9_PBMC


title: AsPC1_GW870086_Rep2_RNAseq


title: RNA_RRP001_Pt22_Week26_PBMC


title: AsPC1_siNT5_Pol2_Rep1_ChIPseq


title: RNA_RRP001_Pt22_Week6_PBMC


title: RNA_RRP001_Pt22_Day0_PBMC


title: AsPC1_siNT5_NELFE_Rep2_ChIPseq


title: RNA_RRP001_Pt21_Week52_PBMC


title: AsPC1_Dex_Rep2_RNAseq


title: RNA_RRP001_Pt21_Week26_PBMC


title: RNA_RRP001_Pt21_Week11_PBMC


title: AsPC1_Dex_Rep1_RNAseq


title: RNA_RRP001_Pt21_Week9_PBMC


title: AsPC1_DMSO_Rep3_RNAseq


title: RNA_RRP001_Pt21_Week6_PBMC


title: AsPC1_siNT5_NELFE_Rep1_ChIPseq


title: HPAFII_siGATA6_Rep1_RNAseq


title: RNA_RRP001_Pt20_Week52_PBMC


title: AsPC1_siNT5_H3K4me3_Rep1_ChIPseq


title: RNA_RRP001_Pt21_Day0_PBMC


title: AsPC1_DMSO_Rep2_RNAseq


title: AsPC1_GW870086_Rep1_RNAseq


title: RNA_RRP001_Pt20_Week26_PBMC


title: AsPC1_siNT5_H3K27ac_Rep3_ChIPseq


title: RNA_RRP001_Pt20_Week11_PBMC


title: AsPC1_DMSO_Rep1_RNAseq


title: RNA_RRP001_Pt20_Week9_PBMC


title: AsPC1_Dex_Rep3_RNAseq


title: RNA_RRP001_Pt23_Week9_PBMC


title: AsPC1_siNT5_H3K27ac_Rep2_ChIPseq


title: RNA_RRP001_Pt20_Screening_PBMC


title: RNA_RRP001_Pt20_Week6_PBMC


title: AsPC1_BI653048_Rep3_RNAseq


title: AsPC1_BI653048_Rep2_RNAseq


title: AsPC1_siNT5_BRD4_Rep2_ChIPseq


title: RNA_RRP001_Pt18_Week52_PBMC


title: RNA_RRP001_Pt18_Week9_PBMC


title: AsPC1_siNT5_H3K27ac_Rep1_ChIPseq


title: AsPC1_siNT5_H3K4me3_Rep2_ChIPseq


title: RNA_RRP001_Pt18_Week11_PBMC


title: AsPC1_BI653048_Rep1_RNAseq


title: AsPC1_siGATA6_Pol2_Rep3_ChIPseq


title: AsPC1_siNT5_BRD4_Rep1_ChIPseq


title: RNA_RRP001_Pt17_Week52_PBMC


title: AsPC1_AZD9567_Rep3_RNAseq


title: RNA_RRP001_Pt18_Screening_PBMC


title: RNA_RRP001_Pt17_Week26_PBMC


title: RNA_RRP001_Pt17_Week11_PBMC


title: AsPC1_siGATA6_Pol2_Rep2_ChIPseq


title: AsPC1_AZD9567_Rep2_RNAseq


title: RNA_RRP001_Pt17_Week9_PBMC


title: AsPC1_siGATA6_Pol2_Rep1_ChIPseq


title: RNA_RRP001_Pt17_Week6_PBMC


title: AsPC1_AZD9567_Rep1_RNAseq


title: RNA_RRP001_Pt16_Week52_PBMC


title: RNA_RRP001_Pt16_Week26_PBMC


title: AsPC1_siGATA6_H3K4me3_Rep2_ChIPseq


title: L36pl_siTP63_Rep2_PROseq

description: contains 2% mouse spike in (NIH3T3 cells)

data_processing:
Paired end 66 bp sequencing reads were mapped to hg38 genome using proseq2.0 pipeline (https://github.com/Danko-Lab/proseq2.0.git). Briefly, -PE, --map5=TRUE, --opposite-strand=TRUE, --UMI1=6, --UMI2=6. Discriminative regulatory element detection (dREG) was generated via https://dreg.dnasequence.org.
Assembly: hg38
Supplementary files format and content: merged plus strand bigwig file from each condition
Supplementary files format and content: merged minus strand bigwig file from each condition
Supplementary files format and content: dREG peaks for control condition

growth_protocol: AsPC1 (RPMI, 10% FBS, 1% Pen-Strep) and L36pl (phenol red free MEM, 10% FBS, 1% Pen-Strep) were maintained in humidified 5% CO2 incubator at 37C.

extract_protocol:
Quick Precision Run-On and sequencing (qPRO-seq) was performed as outlined (doi: 10.1101/2020.05.18.102277) with 1 million cells in triplicates and spike in by cell number of 20,000 (2%) NIH 3T3 cells.
Libraries consisted of a maximum of 25% primer dimers as determined by TapeStation. Adapter design was adapted from Illumina TruSeq small RNA library prep kit with added 6XN UMIs.


title: L36pl_siTP63_Rep3_PROseq


title: AsPC1_siGATA6_H3K4me3_Rep1_ChIPseq


title: RNA_RRP001_Pt16_Week9_PBMC


title: L36pl_siTP63_Rep1_PROseq


title: RNA_RRP001_Pt16_Day0_PBMC


title: RNA_RRP001_Pt18_Week6_PBMC


title: RNA_RRP001_Pt15_Week52_PBMC


title: L36pl_Ctrl_Rep3_PROseq


title: RNA_RRP001_Pt15_Week26_PBMC


title: AsPC1_siGATA6_H3K27ac_Rep3_ChIPseq


title: AsPC1_siGATA6_H3K27ac_Rep2_ChIPseq


title: RNA_RRP001_Pt15_Week11_PBMC


title: RNA_RRP001_Pt15_Week9_PBMC


title: L36pl_Ctrl_Rep2_PROseq


title: AsPC1_siGATA6_H3K27ac_Rep1_ChIPseq


title: RNA_RRP001_Pt15_Week6_PBMC


title: L36pl_Ctrl_Rep1_PROseq


title: AsPC1_Input_Rep2_ChIPseq


title: RNA_RRP001_Pt15_Day0_PBMC


title: RNA_RRP001_Pt14_Week52_PBMC


title: RNA_RRP001_Pt17_Day0_PBMC


title: L36pl_CDK9i_Rep3_PROseq


title: RNA_RRP001_Pt14_Week11_PBMC


title: RNA_RRP001_Pt14_Week26_PBMC


title: AsPC1_Input_Rep1_ChIPseq


title: L36pl_CDK9i_Rep2_PROseq


title: RNA_RRP001_Pt14_Week6_PBMC


title: L36pl_CDK9i_Rep1_PROseq


title: RNA_RRP001_Pt16_Week11_PBMC


title: RNA_RRP001_Pt12_Week26_PBMC


title: AsPC1_HNF4A_Rep1_ChIPseq


title: AsPC1_siGATA6_Rep3_PROseq


title: RNA_RRP001_Pt12_Week11_PBMC


title: RNA_RRP001_Pt12_Week9_PBMC


title: RNA_RRP001_Pt12_Day0_PBMC


title: AsPC1_GATA6_Rep2_ChIPseq


title: AsPC1_GATA6_Rep1_ChIPseq


title: AsPC1_siGATA6_Rep2_PROseq


title: RNA_RRP001_Pt11_Week26_PBMC


title: AsPC1_siGATA6_Rep1_PROseq


title: RNA_RRP001_Pt11_Week11_PBMC


title: AsPC1_CDX2_Rep2_ChIPseq


title: RNA_RRP001_Pt11_Day0_PBMC


title: AsPC1_Ctrl_Rep2_PROseq


title: RNA_RRP001_Pt11_Week6_PBMC


title: RNA_RRP001_Pt10_Week52_PBMC


title: AsPC1_HNF4A_Rep2_ChIPseq


title: AsPC1_CDX2_Rep1_ChIPseq


title: AsPC1_Ctrl_Rep1_PROseq


title: RNA_RRP001_Pt14_Day0_PBMC


title: RNA_RRP001_Pt10_Week11_PBMC


title: a375 g[9]nt RNA-seq rep2

city: Cambridge

first: Fadi

middle: John

last: Najm

state: Massachusetts

address: 415 Main Street 6043

department: Epigenomics

institute: Broad Institute

data_processing:
Fastqs were processed using Kallisto v0.46.1 with default parameters. GTF and transcriptome index were taken from https://github.com/pachterlab/kallisto-transcriptome-indices/releases.
Assembly: hg38
Supplementary files format and content: .h5 files that contain raw counts and TPM normalized counts

source_name: skin

growth_protocol: Jurkat cells were continuously cultured in RPMI 1640 supplemented with 10% FBS and penicilin/streptomycin. A375 cells were cultured in GlutaMAX High Glucose DMEM (Gibco) + 10% FBS supplemented with 1% penicillin/streptomycin

extract_protocol:
RNA was isolated with Qiagen RNeasy Plus Micro kit according to the manufacturer's protocol and ensuring RIN values were greater than 7.
Libraries were prepared first with Poly-A enrichment using magnetic oligo(dT)-beads (Invitrogen), then ligated to RNA adaptors for sequencing.

treatment_protocol: CRISPRi guide

value: skin

value: Melanoma


title: AsPC1_CDK9i_Rep3_PROseq


title: RNA_RRP001_Pt10_Week6_PBMC


title: liver, high-fat diet, treatment with 100 mg propiconazole per kg body weight for 10 weeks, replicate 6

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: Library name: G4_151

data_processing:
Sequencing reads that contained adapters and/or had low quality, aligned to rRNA were filtered off before mapping.
The tool Salmon (version 1.10.0) was used to map the cleaned reads to the GRCm39 mouse genome assembly-based transcriptome sequences as annotated by the GENCODE consortium (release M33). Salmon parameters used: -i ./salmon_index_M33  --libType A --seqBias --numBiasSamples 10000000 --gcBias --biasSpeedSamp 5 --validateMappings --numGibbsSamples 100
The Salmon-obtained transcript abundance estimates and lengths were imported in R using the package tximeta to estimate gene level counts.
Assembly: GRCm39
Supplementary files format and content: Matrix table (TxiMeta.GeneLevel.counts.GEO.txt) with raw gene counts for every gene and every sample (gene level counts were calculated from the Salmon-obtained transcript abundance estimates)
Supplementary files format and content: R-object (gse.counts.annotated.v2.Rdata; exported tximeta object) containing gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was not transformed nor scaled (i.e. countsFromAbundance = "no"), and can be used for subsequent analysis in edgeR or DESeq2.
Supplementary files format and content: R object (gse.lengthScaledTPM.annotated.v2.Rdata; exported tximeta object) containing scaled gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was scaled using library size and transcript gene length (i.e. countsFromAbundance = "lengthScaledTPM"), and these scaled counts can be used for subsequent analysis in limma (voom function).

organism: Mus musculus

source_name: liver

growth_protocol: Six- to seven-week-old male wildtype C57BL/J mice were purchased from Envigo. Mice were housed individually at the animal facility of Wageningen University under specific pathogen-free conditions and housed on a 12:12 hour light-dark cycle. Mice had ad libitum access to food and water throughout the study. Normal bedding and cage enrichment were provided. The experiment received approval from the central committee on animal experimentation and the local animal welfare committee of Wageningen University (AVD10400202115283, 2021.W-0016.006).

extract_protocol:
Total RNA was isolated using Trizol and further purified using Rneasy columns. Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.
Library construction and RNA sequencing on BGISEQ-500 were conducted at Beijing Genomics Institute (BGI) for pair-end 100bp runs. At BGI, Genomic DNA was removed with two digestions using Amplification grade DNAse I (Invitrogen). The RNA was sheared and reverse transcribed using random primers to obtain cDNA, which was used for library construction. The library quality was determined by using Bioanalyzer 2100 (Agilent Technologies). Then, the library was used for sequencing with the sequencing platform BGISEQ-500 (BGI).

treatment_protocol: After two weeks of acclimatization, mice (in the age of eight to nine weeks) were randomly divided into four groups (N = 15) and placed on a HFD (45% energy derived from fat; D12451, Research Diets, USA) for 20 weeks to induce MASLD, obesity and insulin resistance. After 10 weeks on HFD, mice were subsequently treated with either vehicle or three doses of propiconazole through oral gavage (100 µl olive oil + 6.5% EtOH) three times per week. The administrated doses of propiconazole were calculated to achieve daily doses of 0.04, 30, or 100 mg/kg bw/day propiconazole (Sigma-Aldrich, purity ≥98.0%). Prior to starting the administration of propiconazole, two mice per group with atypical growth curves (either fast or slow body weight gainers) were excluded from analysis, finally resulting in 13 mice per group. Body weight and food intake were assessed weekly. Five mice (three mice in the control group and two mice in the 100 mg/kg bw/day dose group) were prematurely euthanized during the study period due to problems emerging shortly after the oral gavage. These mice were inspected after sacrifice, and it was concluded that problems were likely caused by the technical aspects of the procedure. Mice were euthanized after 20 weeks of HFD and 10 weeks of administration of propiconazole or vehicle. Mice were euthanized three days after the final administration of propiconazole at Zeitgeber Time (ZT) 8. Mice were anesthetized with isoflurane inhalation followed by blood collection by orbital puncture and euthanized by cervical dislocation. Livers were weighed, and subsequently snap frozen in liquid nitrogen. Samples were stored at -80 °C before further analyses. Samples from 6 mice per treatment group were used for RNA-sequencing.

value: liver

tag: strain

tag: background diet

value: high-fat diet (45% energy derived from fat; D12451, Research Diets, USA)

value: propiconazole

tag: dose (mg/kg_body_weight)

tag: mouseid

value: male

tag: section day_(day1_or_day2)

value: Day 1


title: RNA_RRP001_Pt11_Week52_PBMC

value: PBMC

value: Male

tag: time


title: AsPC1_CDK9i_Rep2_PROseq

tag: tissue

value: PDAC


title: RNA_RRP001_Pt10_Week9_PBMC


title: a375 20nt RNA-seq rep1


title: liver, high-fat diet, treatment with 100 mg propiconazole per kg body weight for 10 weeks, replicate 5

description: Library name: G4_150

value: Day 2


title: a375 20nt RNA-seq rep2


title: a375 Safe Harbor RNA-seq rep2


title: AsPC1_CDK9i_Rep1_PROseq


title: RNA_RRP001_Pt11_Week9_PBMC


title: RNA_RRP001_Pt10_Week26_PBMC


title: RNA_RRP001_Pt7_Week52_PBMC


title: L36pl_siTP63_Rep2_H3K4me3_HiChIP

data_processing:
HiChIP data were analyzed using the HiC-Pro pipeline. Briefly, sequencing reads were mapped with HiC-Pro/3.1.01 and FitHiChIP/11.0 was utilized to generate bedpe file format. For HiC-Pro, we used MIN_CIS_DIST = 20000 and BIN_SIZE = 2000. We generated an in-house script (https://github.com/bhc-rbct/Filter-A2A-loops-for-active-genes.git) which extracts the active TSS of target genes using a cell line specific H3K4me3 bed file (anchor 1) which interacts with (enhancer) regions of interest (anchor 2). Resulting bedpe files and .hic files (generated from hicpro2juicebox.sh) were used to generate aggregate peak analysis (APA) plots and contact maps utilizing the Tinker Box platform (Morgan et al. manuscript in preparation, https://docs.axiotl.com/). Counts per million were used to normalize samples.
Assembly: hg38
Supplementary files format and content: All-to-all bedpe files for each condition
Supplementary files format and content: bedpe files of control AsPC1 or L36pl cells for active TSS regions to intergenic open (ATAC positive) and active (H3K27ac positive) regions in each cell line.

extract_protocol:
H3K4me3 HiChIP was performed as previously described with a few modifications (PMID: 32051612, PMID: 33658703). Briefly, cells were trypsinized, counted, and 10 million cells were used for each condition. Pertinent modifications are digestion was carried out by incubating with 200 U each of MboI, DpnII, and HinfI (NEB) at 37°C for 2 hr and samples were sonicated for 8 cycles 30 sec on/off. 6 µg of H3K4me3 and Protein A beads were added to the samples. DNA was purified as described above for ChIP-seq and on-bead libraries were prepped using MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001).
Libraries were prepped using MicroPlex Library Preparatioin Kit v3 (Diagenode, C05010001).


title: AsPC1_Ctrl_Rep3_PROseq


title: RNA_RRP001_Pt7_Week26_PBMC


title: a375 Safe Harbor RNA-seq rep1


title: liver, high-fat diet, treatment with 100 mg propiconazole per kg body weight for 10 weeks, replicate 2

description: Library name: G4_144


title: RNA_RRP001_Pt7_Week11_PBMC


title: a375 g[9]nt RNA-seq rep1


title: L36pl_siTP63_Rep1_H3K4me3_HiChIP


title: Jurkat sg8 RNA-seq rep2

source_name: peripheral blood

value: peripheral blood

value: Jurkat

value: T lymphoblast


title: liver, high-fat diet, treatment with 100 mg propiconazole per kg body weight for 10 weeks, replicate 1

description: Library name: G4_142


title: Jurkat sg8 RNA-seq rep1


title: RNA_RRP001_Pt7_Week9_PBMC


title: L36pl_siNT5_Rep1_H3K4me3_HiChIP


title: liver, high-fat diet, treatment with 100 mg propiconazole per kg body weight for 10 weeks, replicate 4

description: Library name: G4_148


title: L36pl_CDK9i_Rep2_H3K4me3_HiChIP


title: RNA_RRP001_Pt7_Week6_PBMC


title: Jurkat sg4 RNA-seq rep4


title: liver, high-fat diet, treatment with 30 mg propiconazole per kg body weight for 10 weeks, replicate 6

description: Library name: G3_137


title: RNA_RRP001_Pt7_Day0_PBMC


title: Jurkat sg4 RNA-seq rep3


title: liver, high-fat diet, treatment with 30 mg propiconazole per kg body weight for 10 weeks, replicate 5

description: Library name: G3_136


title: RNA_RRP001_Pt6_Week52_PBMC

value: Female


title: liver, high-fat diet, treatment with 100 mg propiconazole per kg body weight for 10 weeks, replicate 3

description: Library name: G4_145


title: L36pl_CDK9i_Rep1_H3K4me3_HiChIP


title: liver, high-fat diet, treatment with 30 mg propiconazole per kg body weight for 10 weeks, replicate 3

description: Library name: G3_131


title: RNA_RRP001_Pt10_Screening_PBMC

value: Screening


title: liver, high-fat diet, treatment with 30 mg propiconazole per kg body weight for 10 weeks, replicate 4

description: Library name: G3_132


title: RNA_RRP001_Pt6_Week26_PBMC


title: AsPC1_siNT5_Rep2_H3K4me3_HiChIP

value: cell line


title: L36pl_siNT5_Rep2_H3K4me3_HiChIP


title: AsPC1_siNT5_Rep1_H3K4me3_HiChIP


title: Jurkat Safe Harbor RNA-seq rep3


title: liver, high-fat diet, treatment with 30 mg propiconazole per kg body weight for 10 weeks, replicate 1

description: Library name: G3_127


title: AsPC1_siGATA6_Rep2_H3K4me3_HiChIP


title: Jurkat Safe Harbor RNA-seq rep2


title: RNA_RRP001_Pt6_Week6_PBMC


title: RNA_RRP001_Pt6_Day0_PBMC


title: liver, high-fat diet, treatment with 0.04 mg propiconazole per kg body weight for 10 weeks, replicate 6

description: Library name: G2_122


title: AsPC1_siGATA6_Rep1_H3K4me3_HiChIP


title: RNA_RRP001_Pt4_Week52_PBMC


title: Jurkat sg4 RNA-seq rep2


title: AsPC1_CDK9i_Rep2_H3K4me3_HiChIP


title: liver, high-fat diet, treatment with 0.04 mg propiconazole per kg body weight for 10 weeks, replicate 5

description: Library name: G2_121