title: HCT116_24h_rep2


title: Evs-FBMSC1

status: Public on May 13 2025

type: SRA

city: Xi'an

first: Beibei

last: Yu

address: No. 157, Xiwu Road, Xincheng District, Xi'an City, Shaanxi Province

country: China

institute: The Second Affiliated Hospital, Xi’an Jiaotong University

library_source: transcriptomic

data_processing:
CLC Genomics Workbench w 11.0.1
Assembly: Mmul_10
Supplementary files format and content: TPM

molecule: total RNA

organism: Macaca mulatta

source_name: whole blood

extract_protocol:
A NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs, USA, Catalog #: E7530L) was used according to the manufacturer's guidelines to construct sequencing libraries and incorporate index codes for sample identification
he prepared libraries were sequenced on an Illumina platform using the paired-end 150 strategy at the Novogene Bioinformatics Technology Co. Ltd., Beijing, China. The sequencing process converted the original fluorescence images into raw data, which were then processed in FASTQ format, capturing both nucleotide sequences and their corresponding quality scores

tag: tissue

value: whole blood

tag: genotype

value: WT

tag: treatment

value: Evs-FBMSC


title: HCT116_0h_rep1

city: BALTIMORE

first: Marikki

last: Laiho

state: Maryland

address: 1550 Orleans St

department: Department of Radiation Oncology and Molecular Radiation Sciences

country: USA

institute: Johns Hopkins University

data_processing:
Reads were analyzed using STAR aligner and Salmon, respectively for alignment to reference genome and quantification at the gene level
Assembly: GRCh38
Supplementary files format and content: xlsx, gene expression (TPM) table

molecule: polyA RNA

organism: Homo sapiens

source_name: colon

growth_protocol: McCoy's 5a Medium + 10% FBS

extract_protocol:
Trizol extraction protocol
rRNA was removed using the Ribo-Zero kit. mRNA was fragmented randomly using fragmentation buffer, and cDNA was synthesized using random hexamer primers, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second strand synthesis. Double-stranded cDNA library construction was completed by size selection and PCR enrichment.

treatment_protocol: Cells were treated with DMSO (control) or treated with BMH-21, 1 microM for 24 hours.

value: colon

tag: cell line

tag: cell type

value: Human colorectal carcinoma cell line

value: control


title: BR2DM25T1SuGA_RNAseq_4.5 hours_DM25

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

description:
Library name: BR2DM25T7uGA
BR2DM25T1SuGA

data_processing:
The NASA GeneLab RNA-Seq pipeline was utilized to perform a STAR alignment of reads to the REL606 (NCBI Reference Sequence: NC_012967.1) genome for transcriptomic analysis
Feature counts (v2.0.6) was used to generate a counts table of reads per gene for each sample.
DESeq2 (v1.40.2) was used for read count normalization and differential gene expression analysis.
Assembly: REL606 (NCBI Reference Sequence: NC_012967.1)
Supplementary files format and content: Comma separated file includes normalized counts per million values for each sample

organism: Escherichia coli

growth_protocol: cultures were grown at 25C for 24 hours

extract_protocol:
Samples were collected at 4.5 or 6.5 or 24 hours depending on culture media. Cultures were concentrated with CP SELECT (0.20 µm) device. Frozen cell pellets were sent on dry ice to Azenta GeneWiz for RNA extraction, ribosomal depletion, library preparation and 2x150 base pair, paired-end sequencing.
Ribosomal RNA-depleted libraries were constructed at Azenta GeneWiz

treatment_protocol: Cuttures were rotataed at 20rpm vertically, horizontially, or  static with no rotation. Cultures were grown in Davis Minimal media with 25mg/L glucose or in 2000mg/L glucose.

tag: time

value: 4.5 hours

tag: media

value: simulated microgravity


title: SKOV3 cells, normoxia-mitomycinC, biological rep3

type: RNA

city: Warsaw

first: Aleksandra

last: Gawrylak

email: aklemba@gmail.com, agawrylak@wim.mil.pl

address: Szaserów 128

country: Poland

institute: Military Institute of Medicine – National Research Institute

description: Gene expression data from SKOV3 ovarian cancer cells treated with mitomycin C in normoxia.

hyb_protocol: GeneChip Hybridization Oven was used for HTA 2.0 microarrays hybridization at 45°C for 16h. Then chips were washed and stained in the Affymetrix fluidics Station 450.

scan_protocol: The microarrays were scanned with GeneChip Scanner 3000 7G (Affymetrix) according to WT labeling protocol.

data_processing: HTA 2.0 microarray scans were visually inspected with the Affymetrix GeneChip Command Console (AGCC) version 4.0, generating CEL files with processed pixel intensity values for each probe on the arrays. The CEL files (n=16, 1 GB of data) were then imported to the Transcriptome Analysis Console 4.0 software (Affymetrix) for probe set summarization with the robust multi-array average (RMA) algorithm including background adjustment, quantile normalization, and a log2 transformation of the data, that was later used in the gene-level and the exon-level analysis.

label: biotin

label_protocol: Briefly, the first step of the WT (Whole-Transcript) Sense Target Labelling protocol was incorporation of T7 promoter tags to all RNA strands with (N63’ ends) to enable DNA strand synthesis. Once RNA molecules were replaced, cRNA (non-labeled antisense RNA) was synthesized by in vitro transcription (IVT) overnight. 3’ bias was prevented by linear transcription of all RNA strands. Purified cRNA was used as a template to produce single-stranded sense strand DNA (ss-DNA) by reverse transcription reaction with random primers and dNTP mix (with dUTP included).  The cRNA was eliminated with RNaseH digestion.  The resulting ss-DNA with unnatural dUTP (uracil residues) was fragmented with uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1. The 3’ ends of ss-DNA fragments were biotin-coupled using the DNA labeling reagent (Biotin-11-dXTP) by deoxynucleotidyl transferase.

growth_protocol: Human ovarian cancer cell line SKOV3 was cultured in RPMI-1640 GlutaMaxTM medium supplemented with 10% Fetal Bovine Serum (FBS). SKOV3 cells seeded in T-25 flask in 5ml medium were incubated for 24h in normoxic conditions.

extract_protocol: Total RNA was extracted from the SKOV3 cells incubated with or without MMC under normoxia or hypoxia using Direct-zol TM RNA Miniprep Kit. Genomic DNA was removed with TURBO DNA-free kit.

treatment_protocol: After 24h medium was changed to preconditioned medium (incubated in normoxia or hypoxia for 24h before the experiment), with or without mitomycin C (MMC) and the flasks were incubated for the following 72h before material RNA collection.

value: Ovary; Ascites

value: mitomycin C

tag: stress

value: normoxia


title: C18_iHO_2_others

city: bunkyo-ku

first: Masato

last: Miyoshi

address: yushima

department: Gastroenterology

country: Japan

institute: Tokyo Medical and Dental University

description:
Library name: C18_iHO_2_others
C18_iHO_2_R

data_processing:
The TruSeq Stranded mRNA protocol was used for the preparation of RNA-seq libraries and sequenced on a Illumina NovaSeq X, as paired-end, 101 base pairs reads.
Read count extraction and normalization were performed using salmon v1.2.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts

extract_protocol:
Total RNA was extracted by RNeasy Micro (QIAGEN, Venlo, Netherlands).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: iPSC


title: PBS injection3

value: PBS injection


title: SKOV3 cells, normoxia-mitomycinC, biological rep2

source_name: SKOV3 ovarian cancer cells treated with mitomycin C in normoxia


title: Evs-FBMSC3


title: BR2DM25T1SA_RNAseq_4.5 hours_DM25

description:
Library name: BR2DM25T7SA
BR2DM25T1SA

value: static


title: C18_iHO_2_grape

description:
Library name: C18_iHO_2_grape
C18_iHO_2_P


title: BR2DM25T1RA_RNAseq_4.5 hours_DM25

description:
Library name: BR2DM25T7RA
BR2DM25T1RA

value: rotating


title: PBS injection2


title: C18_iHO_1_others

description:
Library name: C18_iHO_1_others
C18_iHO_1_R


title: SKOV3 cells, normoxia-control, biological rep4

description: Gene expression data from SKOV3 ovarian cancer control cells cultured in normoxia.


title: PBS injection1


title: BR2DM2000T0B_RNAseq_0 hours_DM2000

description:
Library name: BR2DM2KT0B
BR2DM2000T0B

value: 0 hours


title: C18_iHO_1_grape

description:
Library name: C18_iHO_1_grape
C18_iHO_1_P


title: SKOV3 cells, normoxia-mitomycinC, biological rep1


title: BR2DM2000T0A_RNAseq_0 hours_DM2000

description:
Library name: BR2DM2KT0A
BR2DM2000T0A


title: SKOV3 cells, normoxia-control, biological rep3

source_name: SKOV3 ovarian cancer control cells cultured in normoxia


title: Lifr eKO 1

status: Public on May 12 2025

city: Sagamihara

first: Junya

last: Ito

state: Kanagawa

address: 1-17-71 Fuchinobe, Chuo-ku

department: School of Veterinary Medicine

institute: Azabu university

description: Library name: Sample 4

data_processing:
The FASTQ files were processed for removal of adaptor sequences, trimmed and quality-based filtered using fastp v0.23.2
The trimmed reads were removed ribosomal RNA using SortMeRNA v4.3.6
The removed reads were mapped onto the reference genome of Mus musculus (GRCm39) using STAR v2.7.10a
Mapped reads were counted using RSEM v1.3.3.
Differential expression analysis was performed in R v4.2.1 using the EdgeR v 3.38.4 package.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include raw count values for each sample

organism: Mus musculus

source_name: uterus

extract_protocol:
RNA was isolated using RNeasy plus mini kit (Qiagen).
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: uterus

value: Lifr conditional knockout


title: Lifr eKO 3

description: Library name: Sample 6


title: Control 2

description: Library name: Sample 2

value: WT


title: Lifr eKO 2

description: Library name: Sample 5


title: Control 3

description: Library name: Sample 3


title: Human_A549, 8 hours post infection, rep2

city: Guangzhou

first: Alvaro

last: Castells-Garcia

state: Guandong

address: 106 Zhongshan Er Road, Yuexiu district

department: Medical Research Department

institute: Guandong Peoples Hospital

data_processing:
Genes read counting was performed using STAR while transcript per million (TPM) quantification was performed using Kallisto (Bray, N.L., et al., Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol, 2016. 34(5): p. 525-7).
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text file includes TPM (transcripts per million) for each sample.

growth_protocol: A549 cells (Lung Carcinoma, American Type Culture Collection, ATCC CRL-185) were cultured in F-12K (Kaighn's) Medium (Gibco, Thermo Fisher Scientific, #21127022) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific, #10270106), 1% Penicillin–Streptomycin (Thermo Fisher Scientific, #15140122). Cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Three biological replicates were prepared by condition. Oligo(dT)-attached magnetic beads were used to purify mRNA, and cDNA was generated using random hexamer-primed reverse transcription synthesis. The product was validated using the Agilent Technologies 2100 bioanalyzer.
Samples were processed and 50 base reads were generated on BGIseq500 platform (BGI-Shenzhen, China). The sequencing reads were filtered with SOAPnuke (v1.5.2) and mapped to a modified version of the reference human genome (GRCh38/hg38) containing also the viral genome HSV-1 genome (HSV-1 strain KOS, GenBank accession code JQ673480.1) using STAR (v2.5.2a).

treatment_protocol: After media wash, cells were infected with HSV-1 (KOS strain, JQ673480.1) at a multiplicity of infection (MOI) of 3 for 1 h at 37°C in a humidified incubator with 5% CO2, then, the medium was removed and replaced by fresh DMEM medium (supplemented with 2% FBS). At 1, 3 and 8 hours post infection, cells were harvested. We generated 3 biological replicates for mock, 1, 3 and 8 hpi of approximately 10 million cells each.  Non infected cells had their media replaced by fresh DMEM+2% FBS media, without HSV-1 infection.

value: 8 hpi, HSV-1


title: Human_A549, 8 hours post infection, rep3


title: Human_A549, 8 hours post infection, rep1


title: Control 1

description: Library name: Sample 1


title: Human_A549, 1 hour post infection, rep3

value: 1 hpi, HSV-1


title: Human_A549, 3 hours post infection, rep2

value: 3 hpi, HSV-1


title: Human_A549, 3 hours post infection, rep3


title: Human_A549, 1 hour post infection, rep1


title: Human_A549, 1 hour post infection, rep2


title: Human_A549, non infected, rep3


title: circRNA Microarray Service for 8 human samples_42

city: Shaanxi

first: Peini

last: Xue

address: Department of Pulmonary and Critical Care Medicine, Tangdu Hospital,

institute: Fourth Military Medical University

description: Gene expression profile of early-stage lung adenocarcinoma (59-year-old male)

hyb_protocol: 1.65 μg of Cy3-labeled cRNA was fragmented and hybridized to Agilent Human circRNA Array slides (Agilent-072363) for 17 hours at 65 °C in a rotating hybridization oven. Slides were washed using Agilent Gene Expression Wash Buffers and dried by centrifugation according to the Agilent protocol.

scan_protocol: Arrays were scanned immediately after washing using the Agilent Microarray Scanner (G2505C) at 3鈥糾 resolution with default settings for the one-color 8x60K format.

data_processing: Raw images were processed using Agilent Feature Extraction Software (v10.7.3.1) with default protocol settings. Processed signal intensities were background-subtracted and normalized. Features flagged as non-uniform or saturated were excluded.

source_name: plasma from lung adenocarcinoma patient

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 μg of total RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s instructions. Labeled cRNA was purified with RNeasy columns (Qiagen), and dye incorporation and yield were assessed using a NanoDrop spectrophotometer.

growth_protocol: Not applicable (plasma was collected directly from donors without culture).

extract_protocol: Total RNA, including circRNAs, was extracted from 2–4 mL of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen) according to the manufacturer’s instructions. RNA quantity was measured using a Qubit Fluorometer (Thermo Fisher Scientific), and RNA quality was assessed using an Agilent Bioanalyzer when needed.

treatment_protocol: Peripheral blood was drawn from early-stage lung adenocarcinoma patients and healthy controls into EDTA tubes. Plasma was isolated within 2 hours by centrifugation at 1,600 × g for 10 minutes at 4 °C, followed by a second centrifugation at 16,000 × g for 10 minutes to remove debris. Plasma was aliquoted and stored at −80 °C until RNA extraction. No treatment or stimulation was applied.

tag: age

tag: gender

value: male

tag: Stage

value: T2N0M0 IIA


title: Human_A549, non infected, rep2


title: SKOV3 cells, normoxia-control, biological rep1

value: control


title: RENCA cells with NDUFA4L2 stably re-expressed (rescue), replicate 3

city: Nashville

first: w. Kimryn

middle: N.

last: Rathmell

state: TN

address: 1161 21st Avenue South

institute: Vanderbilt University Medical Center

description: Library name: Res_3

library_source: genomic

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality. GC content distribution detects potential AT/GC separation, which affects subsequent gene expression quantification. In view of random fragmentation and biological law of G/C-A/T content, G and C, A and T should be respectively equal, and the content should be stable throughout the entire sequencing process for non-stranded library(Parkhomchuk et al., 2009) (If the library is strand-specific, AT separation or GC separation may occur). A large variation of sequencing error in the first 6-7 bases is allowed considering the use of random primer in library construction, in which it is normal that the first few bases have certain preference in existing high-throughput sequencing technology. The sequencing reads/raw reads often contain low quality reads or reads with adapters, which will affect the quality of downstream analysis. To avoid this, it is necessary to filter the raw reads and obtain the clean reads.
Perform alignments with HISAT2 to the reference. HISAT2(Mortazavi et al., 2008) uses a graph-based alignment and has succeeded HISAT and TOPHAT2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads. Besides one global GFM index, HISAT2 also includes a large set of small GFM indexes that collectively cover the whole genome. These small indexes (local indexes), combined with multiple alignment strategies, enabled effective alignment of RNA-seq reads, particularly, reads spanning multiple exons. Mapped regions can be classified as exons, introns, or intergenic regions. Exon-mapped reads should be the most abundant type of read when the reference genome is well-annotated. Intron-reads may be derived from pre-mRNA contamination or intron-retention from alternative splicing. Reads mapped to intergenic regions are mainly attributed to weak annotation of the reference genome.
Assembly: mm10
Supplementary files format and content: Gene expression quantification analysis in xls format. After the gene expression is quantified, statistical analysis of the expression data is required to screen the genes whose expression levels are significantly different in different conditions.

molecule: genomic DNA

source_name: Kidney Tumor

growth_protocol: RENCA cells (ATCC CRL-2947) were grown in RPMI supplemented with 10% FBS, 1% penicillin/streptomycin, 1% l-glutamine, 1% HEPES, 1% sodium pyruvate, and 1% MEM amino acid.

extract_protocol:
Total RNA was isolated from samples using TRIzol Reagent (Invitrogen, USA) and purified using RNeasy Mini Kit (QIAGEN, Germany).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: The following CRISPR guides were used for single-guide scaffold PX458. For NDUFA4L2: forward, CACCGAGATGGCAGGAACTAGTCTA; for reverse, aaacTAGACTAGTTCCTGCCATCTC. NDUFA4L2 KO clones were grown from single-cell colonies and screened for effective KO using qPCR. For re-expression, an NDUFA4L2 3rd-generation lentiviral expression vector were designed with a puromycin resistance cassette and purchased from Vectorbuilder Inc. Lentiviral supernatants were used immediately to infect target cells. 48-72hrs after transduction, cells were selected using 1.5ug/mL puromycin.

value: Kidney Tumor

value: RENCA

value: Cancer Cell

value: NDUFA4L2 +/+

value: NDUFA4L2 expressed via Lentivirus


title: Human_A549, 3 hours post infection, rep1


title: circRNA Microarray Service for 8 human samples_6

description: Gene expression profile of healthy control (41-year-old female)

source_name: plasma from healthy control

value: female


title: circRNA Microarray Service for 8 human samples_48

description: Gene expression profile of early-stage lung adenocarcinoma (56-year-old female)

value: T1bN0M0 IA


title: circRNA Microarray Service for 8 human samples_2

description: Gene expression profile of early-stage lung adenocarcinoma (53-year-old female)


title: circRNA Microarray Service for 8 human samples_44

description: Gene expression profile of healthy control (41-year-old male)


title: circRNA Microarray Service for 8 human samples_4

description: Gene expression profile of healthy control (40-year-old female)


title: circRNA Microarray Service for 8 human samples_3

description: Gene expression profile of early-stage lung adenocarcinoma (60-year-old male)

value: T1cN0M0 IA


title: circRNA Microarray Service for 8 human samples_5

description: Gene expression profile of healthy control (45-year-old female)


title: RENCA cells with NDUFA4L2 knocked out, replicate 1

description: Library name: KO_1

value: NDUFA4L2 -/-

value: NDUFA4L2 knocked out


title: RENCA cells with NDUFA4L2 knocked out, replicate 3

description: Library name: KO_3


title: RENCA cells with NDUFA4L2 knocked out, replicate 2

description: Library name: KO_2


title: RENCA cells with NDUFA4L2 stably re-expressed (rescue), replicate 1

description: Library name: Res_1


title: RENCA cells expressing empty vector, replicate 2

description: Library name: EVP_2

value: WT

value: Empty Vector


title: RENCA cells expressing empty vector, replicate 1

description: Library name: EVP_1


title: SKOV3 cells, normoxia-control, biological rep2

value: Ovary; Ascites

value: normoxia


title: RENCA cells with NDUFA4L2 stably re-expressed (rescue), replicate 2

description: Library name: Res_2


title: Ythdf24OHT-6D-2

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

description: Library name: FRAS240094890-1r

data_processing:
RNA was extracted with RNeasy Mini Kit (QIAGEN, 74104)
The construction and sequencing of the cDNA library were both completed by Novogene Co., Ltd. cDNA library was pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
Sequencing reads were aligned to mouse genome reference (mm39) using STAR (Spliced Tran_x0002_scripts Alignment to a Reference)
Assembly: mm39
Supplementary files format and content: space-delimited text file of raw counts for each samples

source_name: Small intestine

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (QIAGEN, 74104) according to the manufacturer’s instruction.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Small intestine


title: Ythdf2ISCEtOH-4d

description: Library name: FRAS240297443-1r

value: EtOH


title: RENCA cells expressing empty vector, replicate 3

description: Library name: EVP_3


title: Ythdf2EtOH-6D-1

description: Library name: FRAS240094887-1r


title: Ythdf2EtOH-6D-2

description: Library name: FRAS240094888-1r


title: Ythdf24OHT-6D-1

description: Library name: FRAS240094889-1r


title: Human_A549, non infected, rep1


title: RNA_L2C_A485+Dux_rep3

city: Hangzhou

first: Lieying

last: Xiao

state: 浙江省

address: Nongshenghuan Building E, Zhejiang University, Hangzhou, Zhejiang

institute: Zhejiang University

data_processing:
RNA-seq reads were aligned to the mouse genome (mm10) with Hisat2 (version 2.2.1)(Kim et al., 2015) after removing adaptor sequences and low-quality reads by Trim_Galore(version 4.0; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The read counts and normalized FPKM values for each gene were calculated with featureCounts (version 2.0.1)(Kim et al., 2015) and cufflinks (version 2.2.1)(Trapnell et al., 2010). To quantify the repetitive sequences, TEtranscripts (version 2.2.3)(Jin et al., 2015) was used to calculate the read counts based on RepeatMasker annotation from the UCSC genome annotation database. To calculate the read counts of Obox4, trimmed sequencing reads were also mapped to the reference Obox4 mRNA sequence by Magic-BLAST(Boratyn et al., 2019). The read counts were normalized by total reads and gene length for estimation of FPKM.
Assembly: mm10
Supplementary files format and content: gene expression FPKM table for RNA-seq data

source_name: late 2-cell mouse embryos

growth_protocol: Female BDF1 mice (C57BL/6 × DBA2, Beijing Vital River Laboratory Animal Technology), aged 8-10 weeks, were super-ovulated with an injection of 7.5 IU of pregnant mare’s serum gonadotropin (PMSG) (San-Sheng Pharmaceutical, 110914564), followed by an injection of 7.5 IU of human chorionic gonadotropin (hCG) (San-Sheng Pharmaceutical, 110911282) 48 hours later. After hCG injection, females were mated with BDF1 stud male mice. Zygotes were collected from the oviduct 20 hours post-hCG, and the surrounding cumulus cells were removed using hyaluronidase (Sigma-Aldrich, H4272). Embryos were cultured in KSOM (Millipore, MR-016D) and incubated at 37°C with 5% CO2 in humidified air.

extract_protocol:
For embryos, the zona pellucidae of the embryos were removed with Acid Tyrode's solution (Sigma, T1788). Then the embryos were lysed in lysis buffer containing RNase inhibitor.
The Smart-seq2 procedure was performed as previously described with minor modifications(Picelli et al., 2014). For stacc-seq, the library was prepared following the protocol as descripted before (Liu et al., 2020).

treatment_protocol: A485 (Selleck, S8740) dissolved in dimethyl sulfoxide (DMSO) (Sigma-Aldrich, D2650) was added to KSOM at a final concentration of 1 μM. To transiently inhibit p300/CBP in minor ZGA, embryos were cultured in A485 during post-hCG injection: 22 h~37 h. Embryos were washed at least three times in KSOM to remove A485. In the control group, an equivalent amount of DMSO (0.1%) was added. For DUX rescue embryos, Dux-Flag mRNA (15 ng/μl or 100 ng/μl) was injected into cytoplasm of M1C, E2C and M2C embryos (23 h, 37 h and 42h post hCG injection) with a Piezo-drill (Eppendorf) and Eppendorf Transferman 4r micromanipulators. Samples were injected at 5–10 pl per zygote or 2C embryo.

value: late 2-cell mouse embryos

value: A485 with Dux overexpression


title: RNA_L2C_A485+Dux_rep4


title: RNA_L2C_A485+Dux_rep1


title: RNA_L2C_A485+Dux_rep2


title: RNA_L2C_A485_rep2


title: RNA_L2C_A485_rep3


title: RNA_L2C_A485_rep1


title: RNA_L2C_DMSO_rep3

value: DMSO


title: RNA_L2C_DMSO_rep1


title: RNA_L2C_DMSO_rep2


title: RNA_L2C_DMSO_rep4


title: RNA_E2C_A485+Dux_rep3

source_name: early 2-cell mouse embryos

value: early 2-cell mouse embryos


title: Ythdf2ISC4OHT-4d

description: Library name: FRAS240297444-1r


title: RNA_E2C_A485+Dux_rep1


title: RNA_E2C_A485_rep3


title: RNA_E2C_A485_rep2


title: RNA_E2C_A485_rep4


title: RNA_E2C_A485_rep1


title: RNA_E2C_DMSO_rep4


title: RNA_E2C_DMSO_rep3


title: ATAC_L2C_A485_rep1

data_processing:
Stacc–seq, ChIP-seq and ATAC-seq sequencing reads were aligned to the mouse genome (mm10) with Bowtie2 (version 2.2.5)(Langmead and Salzberg, 2012) after removing adaptor sequences and low-quality reads by Trim_Galore (version 4.0). Low-mapping-quality (MapQ < 20) reads and PCR duplicates were filtered with Samtools (version 1.10)(Li et al., 2009) and Picard (version 2.23; https://broadinstitute.github.io/picard/). For downstream analysis, read counts were normalized to RPKM in a 100-bp window using ‘bamCoverage’ from deepTools (version 3.5.3)(Ramírez et al., 2016).
Assembly: mm10
Supplementary files format and content: Bigwig for Stacc-seq, ChIP-seq and ATAC-Seq signals

extract_protocol:
For embryos, the zona pellucidae of the embryos were removed with Acid Tyrode's solution (Sigma, T1788). Then the embryos were lysed in lysis buffer containing RNase inhibitor.
For ChIP-seq, the library was prepared following the protocol as descripted before (Brind'Amour et al., 2015). For ATAC-seq,  the library was prepared following the protocol as descripted before (Buenrostro et al., 2013; Wu ET AL., 2016). The Stacc–seq procedure was performed as previously described with minor modifications(Ji et al., 2023; Liu et al., 2020).


title: ATAC_L2C_A485_rep2


title: RNA_E2C_DMSO_rep1


title: ATAC_E2C_A485_rep2


title: ATAC_E2C_DMSO_rep2


title: RNA_L2C_A485_rep4


title: ATAC_E2C_A485_rep1


title: ATAC_E2C_DMSO_rep1


title: H3K27ac_E2C_input


title: H3K27ac_L2C_input


title: H3K27ac_L2C_A485+Dux_rep1


title: H3K27ac_L2C_DMSO_rep2


title: H3K27ac_L2C_A485_rep2


title: H3K27ac_L2C_DMSO_rep1


title: RNA_E2C_A485+Dux_rep4


title: RNA_E2C_A485+Dux_rep2


title: H3K27ac_L2C_A485_rep1


title: H3K27ac_E2C_A485+Dux_rep2


title: H3K27ac_E2C_A485+Dux_rep1


title: H3K27ac_E2C_DMSO_rep1


title: H3K27ac_E2C_A485_rep2


title: Pol2_L2C_A485+Dux_rep2


title: H3K27ac_E2C_DMSO_rep2


title: Pol2_L2C_A485+Dux_rep1


title: H3K27ac_E2C_A485_rep1


title: ATAC_L2C_DMSO_rep2


title: RNA_E2C_DMSO_rep2


title: ATAC_L2C_DMSO_rep1


title: Pol2_L2C_A485_rep1


title: Pol2_L2C_A485_rep2


title: Pol2_E2C_A485_rep2


title: Pol2_E2C_A485_rep1


title: H3K27ac_L2C_A485+Dux_rep2


title: Pol2_E2C_A485+Dux_rep2


title: Pol2_L2C_DMSO_rep1


title: p300_L2C_A485+Dux_rep2

data_processing:
Stacc–seq, ChIP-seq and ATAC-seq sequencing reads were aligned to the mouse genome (mm10) with Bowtie2 (version 2.2.5)(Langmead and Salzberg, 2012) after removing adaptor sequences and low-quality reads by Trim_Galore (version 4.0). Low-mapping-quality (MapQ < 20) reads and PCR duplicates were filtered with Samtools (version 1.10)(Li et al., 2009) and Picard (version 2.23; https://broadinstitute.github.io/picard/). For downstream analysis, read counts were normalized to RPKM in a 100-bp window using ‘bamCoverage’ from deepTools (version 3.5.3)(Ramírez et al., 2016).
Assembly: mm10
Supplementary files format and content: Bigwig for Stacc-seq, ChIP-seq and ATAC-Seq signals
Library strategy: Stacc-seq


title: Pol2_E2C_DMSO_rep1


title: p300_L2C_A485+Dux_rep1


title: p300_L2C_A485_rep1


title: p300_L2C_A485_rep2


title: p300_L2C_DMSO_rep1


title: p300_E2C_A485+Dux_rep2


title: p300_E2C_A485+Dux_rep1


title: p300_L2C_DMSO_rep2


title: p300_E2C_A485_rep2


title: p300_E2C_DMSO_rep1


title: p300_L1C_A485_rep1

source_name: late 1-cell mouse embryos

value: late 1-cell mouse embryos


title: p300_L1C_DMSO_rep2


title: p300_L1C_DMSO_rep1


title: p300_L1C_A485_rep2


title: SD3 brain, WT, rep1, scRNAseq

city: New York

first: Mary

middle: Elizabeth

last: Ughetta

state: NY

address: 1 Gustave L. Levy Pl

institute: Mount Sinai

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using the Cell Ranger software V7.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: brain tissue

extract_protocol:
Animals were euthanized and brain tissue containing the main tumor bulk was dissected on ice. Tissue piece was diced with scalpel blades and dissociated into single cell suspension using papain digestion (Miltenyi Neural Tissue Dissociation Kit (P) 130-092-628). The cell suspension was pelleted and resuspended in 7 ml of HBSS (without Ca/Mg), mixed with 1.2 ml of fetal bovine serum (FBS) and 3.6 ml of 100% Percoll (GE Healthcare). Percoll cell suspension was overlaid with 1 ml of DMEM containing 10% FBS and spun at 800g for 15 min, and pellet was collected in a new 15 ml tube and resuspended in 0.5 ml of FACS buffer ((Hibernate-E low fluorescence (BrainBits) with 0.2% BSA and 20 μg/ml DNase (Worthington)). Red blood cells (RBCs) were removed by incubating with RBC lysis buffer (BioLegend) for 10 mins at room temperature. The final cell suspension was submitted for single cell sequencing with the 10X Genomics system at the Mount Sinai Genomics core facility.
GEM formation, cDNA amplification and library preparation was performed according to the manufacture’s instructions (Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns PN-1000268; Chromium Next GEM Chip G Single Cell Kit, 48 rxns PN-1000120). Barcoding libraries was performed per User guide, CG000315 from 10x Genomics (Dual Index Kit TT Set A, 96 rxns PN-1000215).

value: brain tissue

value: GBM

value: Wild Type


title: Old_enrich_rep3

city: Shanghai

first: Yuanbo

last: Liu

address: 100 Hai Ke Rd.

institute: Shanghai Institute of Organic Chemistry

description: Counts3.csv, Counts4.csv

data_processing:
All sequencing reads were processed with Trim Galore (v0.6.6) with the parameters “--nextseq 30 --paired” to remove the adapter sequences (AGATCGGAAGAGC) from NovaSeq-platforms, and reads longer than 20 bp were kept. Reads that passed the quality control procedure were kept and mapped to the Mus musculus genome (GRCm39) and Drosophila melanogaster genome (dmel-all-chromosome-r6.36) using STAR (v2.7.6a) with default parameters, respectively. Uniquely mapped read pairs were counted against annotations from Mus musculus (Ensembl: GRCm39.104) and Drosophila melanogaster (Flybase: dmel-all-r6.36) using featureCounts (v2.0.1) with parameters “-p -B -C” and summarized as gene-level counts, respectively. We calculated transcript abundance based on the transcript fasta files downloaded from Ensembl release-104 (Mus_musculus.GRCm39.cdna.all.fa.gz and Drosophila_melanogaster.BDGP6.32.cdna.all.fa.gz) using Salmon with default parameters.
Assembly: GRCm39 and dmel_r6.36
Supplementary files format and content: Counts from featurecounts output and salmon output were merged into csv table with each gene or transcript in rows and each sample in columns.

source_name: liver

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa, catalog: 9108)
RNA libraries were prepared according to instructions of  Vazyme TruePrep® DNA Library Prep Kit for Illumina (TD501)

value: liver

tag: strain

tag: Sex

value: male

value: 18 month

tag: assay

value: capturing NCIN-capped RNAs


title: Old_enrich_rep2

description: Counts3.csv, Counts4.csv


title: Pol2_L2C_DMSO_rep2

value: WT


title: Pol2_E2C_A485+Dux_rep1


title: Pol2_E2C_DMSO_rep2


title: Old_input_rep3

description: Counts3.csv, Counts4.csv

value: capturing all-capped RNAs


title: Old_input_rep2

description: Counts3.csv, Counts4.csv


title: Young_enrich_rep1

description: Counts3.csv, Counts4.csv

value: 2 month


title: Young_enrich_rep2

description: Counts3.csv, Counts4.csv


title: Old_enrich_rep1

description: Counts3.csv, Counts4.csv


title: Old_input_rep1

description: Counts3.csv, Counts4.csv


title: Young_enrich_rep3

description: Counts3.csv, Counts4.csv


title: Young_input_rep3

description: Counts3.csv, Counts4.csv


title: p300_E2C_A485_rep1


title: Young_input_rep1

description: Counts3.csv, Counts4.csv


title: Figure3D_enrich_rep3


title: p300_E2C_DMSO_rep2


title: Figure3D_enrich_rep1


title: Figure3C_enrich_rep2


title: 92-6W

city: Dallas

first: David

last: Gerber

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Library name: Sample_00000000000284

data_processing:
Raw paired‑end FASTQ files were processed with MiXCR (vX.X) to assemble BCR heavy‑chain sequences, call clonotypes, and quantify clone counts and frequencies
Assembly: Not applicable—reads were not aligned to a whole‑genome assembly but instead processed for V(D)J annotation using the built‑in MiXCR IMGT reference.
Supplementary files format and content: Tab‑delimited text (.tsv) files, one per sample, with one row per BCR clonotype

source_name: Blood

extract_protocol:
Total RNA was isolated via poly‑A mRNA enrichment using oligo‑dT magnetic beads as part of the TruSeq Stranded mRNA kit workflow (oligo‑dT capture, wash, and elution)
Illumina TruSeq® Stranded mRNA Library Preparation protocol (poly‑A selection, mRNA fragmentation, first‑ and second‑strand cDNA synthesis, end repair and A‑tailing, UMI adapter ligation, two rounds of AMPure XP bead clean‑up, PCR amplification)

value: Blood

value: PBMCs

value: ipilimumab


title: 92-BL

description: Library name: Sample_00000000000285

value: BL


title: Female KO MTECs, naïve, biol rep 2

city: Orlando

first: Justine

middle: T.

last: Tigno-Aranjuez

state: FL

address: 6900 Lake Nona Blvd., BSBS Bldg, Rm 370

department: BSBS, Immunity and Pathogenesis Division

institute: University of Central Florida

description: Library name: Sample 14

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an FDR 0.1 and min fold change > 2 were called as differentially expressed genes for each comparison.
For k-means clustering, data was transformed and genes were ranked by standard deviation. Only to the top 2000 are used for clustering (3 clusters were used). Enrichment analysis was performed for each cluster using KEGG pathways. Enrichment p-value are calculated based on one-sided the hypergeometric test, which is then adjusted for multiple testing using the Benjamini-Hochberg procedure and converted to FDR(false discovery rate). FDR tells us how likely to observe the enrichment by chance. Due to increased statistical power, large pathways tend to have smaller FDRs. Fold Enrichment is defined as the percentage of genes in the list belonging to a pathway, divided by the corresponding percentage in the background. As a measure of effect size, Fold Enrichment indicates how drastically genes of a certain pathway is overrepresented. The background genes are filtered genes from the original gene list. The filtered genes are those that are passed a low filter in RNA-seq. A total of 343 gene sets are obtained from KEGG ( Kyoto Encyclopedia of Genes and Genomes ). Dabase version/date is Release 104.0 . For details on this KEGG type of database, please refer to: Kanehisa M, et al. , KEGG: kyoto encyclopedia of genes and genomes , Nucleic Acids Res. 2000 Jan 1;28(1):27-30 ( PubMed ID: 10592173 ). After the analysis is done, pathways are first filtered based on a FDR cutoff (0.05). Then the significant pathways are sorted by. FDR . Only the top 10 pathways are shown.
Assembly: Mus musculus GRCm38 reference genome
Supplementary files format and content: *.csv file contains raw counts for each sample

source_name: Murine tracheal airway epithelium cultures

growth_protocol: Murine tracheal airway epithelial cell cultures were generated as in Lauer et al. J Biol Chem. 2008 Sep 19;283(38):26283-96.

extract_protocol:
Rneasy mini kit as directed by manufacturer (Qiagen)
A. mRNA enrichment, mRNA fragmentation and random priming; B. First and second strand cDNA synthesis; C. End repair, 5' phosphorylation and dA-tailing; D. Adaptor ligation, PCR enrichment and sequencing

treatment_protocol: untreated or treated with 20 ug/ml house dust mite extract overnight

value: Primary

value: airway epithelial cells

value: LMAN1 KO


title: Figure3C_enrich_rep1


title: 90-BL

description: Library name: Sample_00000000000283


title: 90-3W

description: Library name: Sample_00000000000282


title: Figure3D_input_rep2


title: Figure3D_input_rep3


title: Figure3D_input_rep1


title: 74-2W

description: Library name: Sample_00000000000280


title: 74-BL

description: Library name: Sample_00000000000281


title: Figure3C_input_rep3


title: 60-BL

description: Library name: Sample_00000000000279


title: Figure3C_input_rep1


title: 60-2W

description: Library name: Sample_00000000000278


title: 386-BL

description: Library name: Sample_00000000000277

value: pembrolizumab


title: 386-6W

description: Library name: Sample_00000000000276


title: Young_input_rep2

description: Counts3.csv, Counts4.csv


title: 14d_WT_2

city: Bethesda

first: Zhaoyi

last: Peng

state: maryland

address: 49 CONVENT DR

department: National Institutes of Health

institute: Eunice Kennedy Shriver National Institute of Child Health and Human Development

description: RNA-seq of intestine replication 2 of WT_14D

data_processing:
For each sample, reads were identified and mapped onto the mm10 (Gencode M26) assembly of mouse genome using STAR software (v2.7.3).
Quantification of gene expression was determined by HTSeq software featurecounts v1.6.4 and gene annotations from Gencode release M26.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw couns for each sample

source_name: intestine

extract_protocol:
Total RNA from small intestinal crypts were isolated as described before and extracted by using Direct-zol™ RNA Miniprep (ZYMO Research) according to the manufacturer’s instructions. Then the RNA samples were sent to the NICHD Molecular Genomics Core for library preparation and sequencing.
Libraries was prepared using the illumina TruSeq total RNA prep kit with Ribo-zero kit at the step of ribodepletion

value: intestine


title: Figure3C_input_rep2


title: 14d_WT_1

description: RNA-seq of intestine replication 1 of WT_14D


title: 14d_KO_3

description: RNA-seq of intestine replication 3 of KO_2]14D

value: KO


title: 360-6W

description: Library name: Sample_00000000000274

value: nivolumab


title: 14d_KO_2

description: RNA-seq of intestine replication 2 of KO_14D


title: Figure3C_enrich_rep3

value: liver

value: male


title: Figure3D_enrich_rep2

value: capturing NCIN-capped RNAs


title: 7d_WT_3

description: RNA-seq of intestine replication 3 of WT_7D

value: WT


title: 14d_KO_1

description: RNA-seq of intestine replication 1 of KO_14D


title: 352-BL

description: Library name: Sample_00000000000271


title: 358-2W

description: Library name: Sample_00000000000272


title: 14d_WT_3

description: RNA-seq of intestine replication 3 of WT_14D


title: 352-6W

description: Library name: Sample_00000000000270


title: 7d_WT_2

description: RNA-seq of intestine replication 2 of WT_7D


title: 7d_WT_1

description: RNA-seq of intestine replication 1 of WT_7D


title: 360-BL

description: Library name: Sample_00000000000275


title: 7d_KO_3

description: RNA-seq of intestine replication 3 of KO_7D


title: 2d_WT_3

description: RNA-seq of intestine replication 3 of WT_2D


title: 350-6W

description: Library name: Sample_00000000000266


title: 7d_KO_2

description: RNA-seq of intestine replication 2 of KO_7D


title: 2d_WT_1

description: RNA-seq of intestine replication 1 of WT_2D


title: 346-BL

description: Library name: Sample_00000000000265


title: 358-BL

description: Library name: Sample_00000000000273


title: 346-6W

description: Library name: Sample_00000000000264


title: 7d_KO_1

description: RNA-seq of intestine replication 1 of KO_7D


title: 338-BL

description: Library name: Sample_00000000000263

value: ipilimumab+nivolumab


title: 2d_KO_3

description: RNA-seq of intestine replication 3 of KO_2D


title: 2d_KO_2

description: RNA-seq of intestine replication 2 of KO_2D


title: 336-BL

description: Library name: Sample_00000000000261

value: durvalumab


title: 2d_KO_1

description: RNA-seq of intestine replication 1 of KO_2D


title: 336-4W

description: Library name: Sample_00000000000260

value: Blood


title: 334-BL

description: Library name: Sample_00000000000259

value: PBMCs


title: 351-BL

description: Library name: Sample_00000000000269

value: pembrolizumab+other


title: [Smart-Seq2] neutrophil, Lig, rep3

first: Yuman

last: Li

address: No.22 , Zhongguancun South Avenue, Haidian District, Beijing

institute: Peking University School and Hospital of Stomatology

data_processing:
A cDNA library constructed by technology from the pooled RNA from peripheral blood neutrophils of mice was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis.
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus_musculus.GRCm38 V101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: peripheral blood

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. SMARTer cDNA synthesis starts with picogram amounts of total RNA. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribeTM Reverse Transcriptase reaches the 5' end of the mRNA, the enzyme's terminal transferase activity adds a few additional nucleotides to the 3' end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5' end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.
smart-seq2

value: peripheral blood

value: neutrophil

value: Lig


title: [Smart-Seq2] neutrophil, Lig, rep1


title: 329-2W

description: Library name: Sample_00000000000256


title: [Smart-Seq2] neutrophil, Ctrl, rep3

value: Ctrl


title: 334-6W

description: Library name: Sample_00000000000258


title: [Smart-Seq2] neutrophil, Ctrl, rep2


title: [Smart-Seq2] neutrophil, Ctrl, rep 1


title: 2d_WT_2

description: RNA-seq of intestine replication 2 of WT_2D


title: 328-4W

description: Library name: Sample_00000000000254


title: 338-3W

description: Library name: Sample_00000000000262


title: 327-BL

description: Library name: Sample_00000000000253

value: atezolizumab+other

value: BL


title: neutrophil, Lig, rep3

data_processing:
A cDNA library constructed by technology from the pooled RNA from bone marrow neutrophils of mice was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis.
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus_musculus.GRCm38 V101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: bone marrow

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: bone marrow


title: neutrophil, Lig, rep2


title: 326-BL

description: Library name: Sample_00000000000251

value: pembrolizumab


title: 327-6W

description: Library name: Sample_00000000000252


title: 326-6W

description: Library name: Sample_00000000000250


title: neutrophil, Ctrl, rep3


title: 320-BL

description: Library name: Sample_00000000000249

value: nivolumab


title: 310-BL

description: Library name: Sample_00000000000247


title: neutrophil, Ctrl, rep 1


title: neutrophil, Ctrl, rep2


title: neutrophil, Lig, rep1


title: [Smart-Seq2] neutrophil, Lig, rep2


title: 329-BL

description: Library name: Sample_00000000000257


title: 320-8W

description: Library name: Sample_00000000000248


title: 299-BL

description: Library name: Sample_00000000000245

value: atezolizumab


title: 299-4W

description: Library name: Sample_00000000000244


title: 310-8W

description: Library name: Sample_00000000000246


title: HSPCs, Ctrl, single-cell multiomics sequencing, scATAC-seq

description: 10X Genomics

data_processing:
The raw multiomic data was input into the CellRanger-ARC-2.0.0 pipeline to perform sequence alignment and generate single-cell feature counts. Reads were aligned to the GRCm38 (mm10) reference genome.  Subsequently, quality control and preprocessing steps were conducted using Seurat (v.4.0.3) and Signac (v.1.3.0). For scRNA-seq data, cells with a low number of features (<200) or a high fraction of mitochondrial genes (>25%) were filtered out. For scATAC-seq data, cells with low fragment counts (<1,000) or high fragment counts (>50,000) were excluded. Finally, the remaining cells obtained after the integration of scATAC and scRNA data were selected for downstream analysis.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

molecule: nuclear RNA

extract_protocol:
A single-cell nuclear suspension was prepared from the sorted cells, and cell counting and viability assessment were performed using Countstar. Cells with a viability of 0%-5% were considered for further analysis, and the cell concentration was adjusted to the desired concentration of 2000 cells/μl. Isolated nuclei from Lin-ckit+ cells were transposed and loaded onto the Chromium Next GEM Chip J (10X Genomics).
The cell chip was loaded onto a Chrome Controller, and the library was sequenced on a NovaSeq6000 platform (Illumina) following the manufacturer's instructions.
single-cell multiomics sequencing

value: HSPCs


title: HSPCs, Lig, single-cell multiomics sequencing, scATAC-seq

description: 10X Genomics


title: HSPCs, Lig, single-cell multiomics sequencing, scRNA-seq

description: 10X Genomics


title: HSPCs, Ctrl, single-cell multiomics sequencing, scRNA-seq

description: 10X Genomics


title: 299-3W

description: Library name: Sample_00000000000243


title: 351-6W

description: Library name: Sample_00000000000268


title: 299-3M

description: Library name: Sample_00000000000242


title: 299-2W

description: Library name: Sample_00000000000241


title: Tumor/stroma compartment - treated with anti-CD25- Second replicate

city: London

first: Gordon

last: Beattie

address: Gower Street

country: United Kingdom

institute: UCL

description: 10x genomics

data_processing:
Gene expression reads were aligned using a custom version of mm10 which included EGFRvIII and eGFP and counted using cellranger count (v6.0.1)
TCR reads were aligned to the 10x genomics GRCm38 VDJ reference dataset using cellranger vdj (v6.0.1)
Assembly: mm10
Supplementary files format and content: GEX data provided as raw count matrices in the .h5 format (i.e. "filtered_feature_bc_matrix.h5" output from cellranger)
Supplementary files format and content: TCR data provided in .csv output (i.e. "filtered_contig_annotations.csv" output from cellranger)

source_name: Brain tumor

extract_protocol:
Tumors were microdisected from the brain to avodi contamination with normal tissue and subsequently enzymatically digested to obtain a single cell suspension ready to perform single cell sorting
Single-cell suspensions were prepared and Live CD45-, Live CD45+CD3+ and Live CD45+CD11b+ populations were sorted. Cells were washed, counted and resuspended to a concentration of 1000 cells/uL in PBS 0.04% BSA. After this, cells were loaded and processed on the 10X Chromium Controller using the CG000331 Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) User guide, which enabled us to process the gene expression and immune profiling of the samples. Once the libraries were processed, they were pooled with a GEX 4:1 TCR ratio (as per 10X recommendation) and submitted for sequencing. Each library can be recognized by its unique sample index. Sample sequencing was performed at Novogene, using a Novaseq 6000 platform and PE150 sequencing strategy.

value: Brain tumor

value: Tumor and stromal cells

value: anti-CD25 - Treg depletion


title: Tumor/stroma compartment - untreated- Second replicate

description: 10x genomics

value: Untreated tumor


title: 350-BL

description: Library name: Sample_00000000000267

value: Blood

value: PBMCs


title: 299-10W

description: Library name: Sample_00000000000240


title: Myeloid compartment - Untreated- Second replicate

description: 10x genomics

value: Myeloid cells


title: 298-BL

description: Library name: Sample_00000000000239


title: Lymphoid compartmetn - Untreated - Used for TCRseq- Second replicate

description: 10x genomics

value: Lymphoid cells


title: 298-3W

description: Library name: Sample_00000000000238


title: Lymphoid compartment - Untreated- Second replicate

description: 10x genomics


title: 293-BL

description: Library name: Sample_00000000000235

value: other


title: 296-3W

description: Library name: Sample_00000000000236


title: 296-BL

description: Library name: Sample_00000000000237


title: Lymphoid compartment - treated with anti-CD25 - Second replicate

description: 10x genomics


title: Tumor/stroma compartment - untreated- First replicate

description: 10x genomics


title: Tumor/stroma compartment - treated with anti-CD25- First replicate

description: 10x genomics


title: 293-6W

description: Library name: Sample_00000000000234


title: Lymphoid compartment - treated with anti-CD25 - Used for TCRseq - Second replicate

description: 10x genomics


title: 285-3M

description: Library name: Sample_00000000000232


title: Myeloid compartment - treated with anti-CD25- First replicate

description: 10x genomics


title: 285-2W

description: Library name: Sample_00000000000231


title: Lymphoid compartmetn - Untreated - Used for TCRseq- First replicate

description: 10x genomics


title: Lymphoid compartment - treated with anti-CD25 - Used for TCRseq - First replicate

description: 10x genomics


title: 283-8W

description: Library name: Sample_00000000000229


title: Myeloid compartment - Untreated- First replicate

description: 10x genomics


title: 328-BL

description: Library name: Sample_00000000000255


title: 269-BL

description: Library name: Sample_00000000000228

value: nivolumab+other


title: Lymphoid compartment - treated with anti-CD25 - First replicate

description: 10x genomics


title: 269-6W

description: Library name: Sample_00000000000227


title: Lymphoid compartment - Untreated- First replicate

description: 10x genomics


title: Myeloid compartment - treated with anti-CD25- Second replicate

description: 10x genomics


title: Protoperithecia WT mat A rep2 [145]

city: Athens

first: Zachary

middle: A

last: Lewis

state: GA

address: 120 E. Green St.

department: Microbiology

institute: University of Georiga

description: Library name: 145-138_cDNA_WTmata_PP_Rep2_counts.txt

data_processing:
Illumina adaptors trimmed using Trim_Galore (0.6.7) and aligned to the N. crassa genome with STAR (2.7.10b)
Readcounts per gene were compiled using Subread (2.0.6)
Assembly: Neurospora crassa NC12
Supplementary files format and content: tab-deliminated text file of counts aligned to genes

organism: Neurospora crassa

source_name: Protoperithecia

growth_protocol: Mycelial samples were grown as disks in Vogel's Minimal Media + 1.5% sucrose overnight at 32C in a 50 mL flask. False perithecia and protoperithecial samples were grown on Synthetic Crossing Medium + 1% sucrose  overlain with cellophane  for 12 days at room temperature in constant darkness.

extract_protocol:
RNA was extracted from snap-frozen and ground tissue using TRIzol reagent
cDNA libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation kit (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: Protoperithecia

value: 12 days

value: WT  mat a

tag: medium

value: Synthetic Crossing Medium + 1% sucrose


title: Protoperithecia WT mat A rep3 [145]

description: Library name: 145-139_cDNA_WTmata_PP_Rep3_counts.txt


title: 261-BL

description: Library name: Sample_00000000000226

value: pembrolizumab

value: BL


title: Protoperithecia WT mat A rep1 [145]

description: Library name: 145-137_cDNA_WTmata_PP_Rep1_counts.txt


title: 285-BL

description: Library name: Sample_00000000000233

value: nivolumab


title: 261-6W

description: Library name: Sample_00000000000225


title: 260-BL

description: Library name: Sample_00000000000224

value: ipilimumab+nivolumab


title: Protoperithecia WT mata rep3 [145]

description: Library name: 145-136_cDNA_WTmatA_PP_Rep3_counts.txt

value: WT  mat A


title: Protoperithecia WT mata rep1 [145]

description: Library name: 145-134_cDNA_WTmatA_PP_Rep1_counts.txt


title: 257-BL

description: Library name: Sample_00000000000222


title: 249-BL

description: Library name: Sample_00000000000220


title: rep 1 mat a FalsePerithecia  delta set7 [145]

description: Library name: 145-131_cDNA_set7mata_FP_Rep1_counts.txt

source_name: False Perithecia

value: False Perithecia

value: delta set7  mat a


title: rep 2 mat a FalsePerithecia  delta set7 [145]

description: Library name: 145-133_cDNA_set7mata_FP_Rep3_counts.txt


title: 257-7W

description: Library name: Sample_00000000000221

value: Blood


title: 260-3W

description: Library name: Sample_00000000000223

value: PBMCs


title: 283-BL

description: Library name: Sample_00000000000230


title: 245-BL

description: Library name: Sample_00000000000218

value: pembrolizumab+other


title: 249-6W

description: Library name: Sample_00000000000219


title: rep 2 FalsePerithecia  delta set7 A [145]

description: Library name: 145-129_cDNA_set7matA_FP_Rep2_counts.txt

value: delta set7  mat A


title: 245-3M

description: Library name: Sample_00000000000217


title: 244-BL

description: Library name: Sample_00000000000216

value: other


title: Protoperithecia  WT mata  rep3 [144]

description: Library name: 144-139


title: Protoperithecia WT mat A rep2 [144]

description: Library name: 144-138


title: 244-6W

description: Library name: Sample_00000000000215


title: 237-BL

description: Library name: Sample_00000000000214


title: Protoperithecia WT mat A rep1 [144]

description: Library name: 144-137


title: Protoperithecia WT mata rep2 [145]

description: Library name: 145-135_cDNA_WTmatA_PP_Rep2_counts.txt


title: 237-6W

description: Library name: Sample_00000000000213


title: Protoperithecia WT mata rep3 [144]

description: Library name: 144-136


title: 234-BL

description: Library name: Sample_00000000000212


title: Protoperithecia WT mata rep2 [144]

description: Library name: 144-135


title: Protoperithecia WT mata rep1 [144]

description: Library name: 144-134


title: 234-6W

description: Library name: Sample_00000000000211


title: rep 2 mat a FalsePerithecia  delta set7 [144]

description: Library name: 144-133


title: FalsePerithecia  delta set7 mat A  rep3 [145]

description: Library name: 145-130_cDNA_set7matA_FP_Rep3_counts.txt


title: 230-6W

description: Library name: Sample_00000000000209


title: 230-BL

description: Library name: Sample_00000000000210


title: 227-BL

description: Library name: Sample_00000000000208


title: FalsePerithecia  delta set7 mat A  rep3 [144]

description: Library name: 144-130


title: rep 1 FalsePerithecia  delta set7 A [144]

description: Library name: 144-128


title: 225-6W

description: Library name: Sample_00000000000205


title: Mycelia  delta set7  24h  rep3

description: Library name: 141-99

source_name: Mycelia

value: Mycelia

value: 24 hr

value: Vogel's Minimal Medium + 1.5% sucrose


title: 225-BL

description: Library name: Sample_00000000000206


title: rep 1 FalsePerithecia  delta set7 A [145]

description: Library name: 145-128_cDNA_set7matA_FP_Rep1_counts.txt

value: 12 days


title: 227-6W

description: Library name: Sample_00000000000207


title: 221-BL

description: Library name: Sample_00000000000204


title: Mycelia  delta set7  24h  rep2

description: Library name: 141-98


title: 218-BL

description: Library name: Sample_00000000000202


title: Mycelia  delta set7  24h  rep1

description: Library name: 141-97


title: Huh7, Dakar, DMSO, rep2

city: Princeton

first: Jiayu

last: Zhang

state: NJ

address: 119 Lewis Thomas Laboratory, Washington Road

department: Molecular Biology

institute: Princeton

data_processing:
Raw sequencing reads were demultiplexed using Picard v2.21.1 (from within viralngs v.1.25.0) which merge also pair-end reads. The demultiplexed reads from two flowcell lanes were then merged using samtools v1.9. Analysis of SHAPE-MaP data was performed using RNAframework. Reads pre-processing and mapping was performed using the rf-map module (parameters: -ctn -cmn 0 -cqo -cq5 20 -b2 -mp ‘–very-sensitive-local’). The SHAPE mutational signal was then derived using the rf-count module (parameters: -m -rd). Data normalization was performed using the rf-norm module (parameters: -sm <3).
Assembly: YFV-17D-IC.fasta, YFV-Asibi.fasta, YFV-Dakar.fasta
Supplementary files format and content: YFVs genome sequence and normalized SHAPE reactivity of each nucleotide
Library strategy: SHAPE-MaP

organism: Yellow fever virus

source_name: Huh7 (host)

growth_protocol: Huh7 cells were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S) in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
cell pellets were lysed in 1 mL Trizol (Thermo Scientific), followed by the addition of 0.2 ml of chloroform. Aqueous phase was transferred to a new tube and mixed with one volume of 70% Ethanol and transferred to RNeasy mini column (QIAGEN) according to manufacturer instructions.
1.5 μg of total RNA was firstly subjected to ribosomal RNA depletion using HUMANV1 probes. Ribo-depleted RNA was purified by 0.8X RNAClean XP Beads (Beckman Coulter) and fragmented in RNA Fragmentation Buffer (NEB) at 94°C for 105s. After addition of the stop solution, fragmented RNA was purified with 2X RNAClean XP Beads (Beckman Coulter) and eluted in 9 μl nuclease-free H2O. Eluted RNA was then supplemented with 1 μl 50 μM random hexamers and 1 μl dNTPs (10 mM), then incubated at 70°C for 5 min and immediately transferred to ice for 1 min. Reverse transcription reactions were conducted in a final volume of 20 μl supplemented with 120mM MnCl2, SHAPE-RT buffer [50 mM Tris–HCl pH 8.0, 55 mM KCl], 0.1M DTT, 2U of SuperScript II (SSII, Thermo Scientific, Waltham, MA), and 2U of SUPERase•In (Thermo Scientific). Reactions were incubated at 25°C for 10 min to allow partial primer extension, followed by 3 h at 42°C. Followed by heat-inactivation of SSII at 75°C for 15 min. 0.1M EDTA was added in a final concentration of 6 mM to chelate Mn2+ ions and incubate at room temperature for 5 mins. Followed by addition of 6 mM final MgCl2, the resulting RNA:cDNA duplex then underwent second strand synthesis  using NEBNext® Ultra™ II Non-Directional RNA Second Strand Synthesis Module (NEB) according to manufacturer instructions. cDNA were then ligated with xGen Dual Index UMI Adapter (IDT) and were sequenced on Illumina NovaSeq 6000 SP 100 cycle flowcell.

treatment_protocol: Huh7 cells were infected at a MOI of 0.05. 2 (17D and Asibi) or 5 (Dakar) days post infection, cells were washed with PBS twice, trypsinized and resuspended in 1× PBS. 2A3 from a 500mM stock (in DMSO) was added at a final concentration of 100 mM. A corresponding amount of DMSO was added to the control sample. Samples were then incubated at 37°C in heat block with constant shaking for 15 min, followed by quenching of 2A3 by adding DTT at a final concentration of 0.5 M.

value: Huh7 (host)

value: Human hepatoma (host)

value: Dakar

value: DMSO

tag: flowcell lane

value: lane1 and lane2

tag: replicate


title: 221-8W

description: Library name: Sample_00000000000203

tag: tissue

value: nivolumab


title: Huh7, Dakar, DMSO, rep1


title: 218-6W

description: Library name: Sample_00000000000201

value: pembrolizumab


title: Huh7, Dakar, 2A3, rep2


title: Huh7, Dakar, 2A3, rep1


title: 211-BL

description: Library name: Sample_00000000000198

value: BL


title: 214-6W

description: Library name: Sample_00000000000199

value: Blood

value: durvalumab


title: Huh7, Asibi, DMSO, rep2

value: Asibi


title: rep 1 mat a FalsePerithecia  delta set7 [144]

description: Library name: 144-131

value: False Perithecia

tag: genotype

value: delta set7  mat a

value: Synthetic Crossing Medium + 1% sucrose


title: Huh7, Asibi, DMSO, rep1

tag: treatment


title: 211-3W

description: Library name: Sample_00000000000197

value: PBMCs


title: Huh7, Asibi, 2A3, rep2

tag: cell line


title: 209-BL

description: Library name: Sample_00000000000196

tag: cell type


title: 209-6W

description: Library name: Sample_00000000000195

tag: time


title: rep 2 FalsePerithecia  delta set7 A[ 144]

description: Library name: 144-129

value: delta set7  mat A


title: 208-BL

description: Library name: Sample_00000000000194


title: 208-6W

description: Library name: Sample_00000000000193


title: Huh7, 17D, DMSO, rep2


title: Huh7, Asibi, 2A3, rep1


title: Huh7, 17D, DMSO, rep1


title: 193-BL

description: Library name: Sample_00000000000192


title: 193-8W

description: Library name: Sample_00000000000191


title: Huh7, 17D, 2A3, rep1


title: 192-BL

description: Library name: Sample_00000000000190


title: Leaves_PL4xWD_4

city: Petit-bourg

first: Leny

last: Calvez

address: Station de Roujol

country: France

institute: CIRAD

description:
Library name: Sample 49
counts_leaves.csv

data_processing:
Raw sequencing read cleaning : trimmomatic software
Read aligment : MapSplice gapped alignment algorithm
Count reads : HTSeq-count Python tool
Assembly: Citrus clementina V1.0 Phytozome genome ID: 182 • NCBI taxonomy ID: 85681
Supplementary files format and content: counts_leaves.csv : file includes raw counts (RPKM) for each leaves samples
Supplementary files format and content: counts_roots.csv : file includes raw counts (RPKM) for each roots samples

organism: Citrus x latifolia

source_name: Leaves

growth_protocol: Plants were transplanted in 40L pots with the same substrate's amount containing (50% volcanic rock and 50% peat). The plants grown up for 2 years in an insect-proof greenhouse with natural photoperiod, day/night temperatures of 25-32°C and 22-28°C and a relative humidity between 70% and 98%. Daily irrigations and regular NPK fertilisations were applied.

extract_protocol:
Total RNA was extracted from 100 mg of leaves and roots frozen powder using the RNeasy® Plant Mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA quality and quantity were determine using a mySPEC microvolume spectrophotometer (VWR, Radnor, PA, USA). High purity RNA samples (OD260/OD280 values at 1.8-2.0) were used for library construction and sequencing. For each RNA sample, cDNA libraries were prepared for sequencing from 1 µg of total RNA using the Truseq Stranded mRNA kit (Illumina, San Diego, CA, USA) following the manufacturer’s protocol.

treatment_protocol: Trees were split in two group treatments as follow: (i) control plant set with trees under regular irrigation and (ii) and a drought stress set with trees subjected to water deficit condition by stopping the irrigation.

value: Leaves

tag: scion

value: Persian lime (Citrus latifolia)

tag: rootstock

value: tetraploid Swingle citrumelo 4475 (Citrus sinensis x Poncirus trifoliata)

value: Water deficit


title: 189-BL

description: Library name: Sample_00000000000188


title: Leaves_PL4xWD_1

description:
Library name: Sample 46
counts_leaves.csv


title: Huh7, 17D, 2A3, rep2

value: Huh7 (host)

value: Human hepatoma (host)


title: Leaves_PL4xWD_2

description:
Library name: Sample 47
counts_leaves.csv


title: 186-9M

description: Library name: Sample_00000000000185

value: nivolumab


title: 192-6W

description: Library name: Sample_00000000000189

value: pembrolizumab


title: Leaves_PL4xCtrl_2

description:
Library name: Sample 44
counts_leaves.csv

value: Control


title: 214-BL

description: Library name: Sample_00000000000200

value: Blood

value: BL


title: 186-BL

description: Library name: Sample_00000000000186


title: Leaves_PL4xCtrl_3

description:
Library name: Sample 45
counts_leaves.csv


title: 189-6W

description: Library name: Sample_00000000000187


title: Leaves_PL4xCtrl_1

description:
Library name: Sample 43
counts_leaves.csv


title: 186-6W

description: Library name: Sample_00000000000184


title: 186-3M

description: Library name: Sample_00000000000183


title: Leaves_PL2xWD_2

description:
Library name: Sample 33
counts_leaves.csv

value: diploid Swingle citrumelo 4475 (Citrus sinensis x Poncirus trifoliata)


title: Leaves_PL2xWD_1

description:
Library name: Sample 32
counts_leaves.csv


title: 185-BL

description: Library name: Sample_00000000000182


title: 185-6W

description: Library name: Sample_00000000000181


title: Leaves_PL2xWD_3

description:
Library name: Sample 35
counts_leaves.csv


title: 181-BL

description: Library name: Sample_00000000000180

value: ipilimumab+nivolumab


title: 181-6W

description: Library name: Sample_00000000000179


title: Leaves_PL2xCtrl_1

description:
Library name: Sample 29
counts_leaves.csv


title: 173-BL

description: Library name: Sample_00000000000178


title: Leaves_ML4xWD_4

description:
Library name: Sample 21
counts_leaves.csv

organism: Citrus x aurantiifolia

value: Mexican lime (Citrus aurantiifolia)


title: Leaves_ML4xWD_3

description:
Library name: Sample 20
counts_leaves.csv


title: Leaves_PL4xWD_3

description:
Library name: Sample 48
counts_leaves.csv


title: 172-Bl

description: Library name: Sample_00000000000176

value: atezolizumab

value: Bl


title: Leaves_ML4xWD_2

description:
Library name: Sample 19
counts_leaves.csv


title: 173-6W

description: Library name: Sample_00000000000177

value: PBMCs


title: Leaves_ML4xWD_1

description:
Library name: Sample 18
counts_leaves.csv

value: Leaves


title: 172-6W

description: Library name: Sample_00000000000175


title: 170-BL

description: Library name: Sample_00000000000174

value: avelumab


title: Leaves_ML4xCtrl_3

description:
Library name: Sample 17
counts_leaves.csv

value: tetraploid Swingle citrumelo 4475 (Citrus sinensis x Poncirus trifoliata)


title: Leaves_ML4xCtrl_2

description:
Library name: Sample 16
counts_leaves.csv


title: 167-BL

description: Library name: Sample_00000000000172


title: 167-6W

description: Library name: Sample_00000000000171


title: Leaves_ML2xWD_4

description:
Library name: Sample 7
counts_leaves.csv

value: Water deficit


title: 170-2W

description: Library name: Sample_00000000000173


title: Leaves_ML2xWD_3

description:
Library name: Sample 6
counts_leaves.csv


title: Leaves_ML4xCtrl_1

description:
Library name: Sample 15
counts_leaves.csv


title: Leaves_ML2xWD_2

description:
Library name: Sample 5
counts_leaves.csv


title: 146-6W

description: Library name: Sample_00000000000169

value: durvalumab


title: 146-6M

description: Library name: Sample_00000000000168


title: Leaves_PL2xCtrl_2

description:
Library name: Sample 31
counts_leaves.csv

value: Persian lime (Citrus latifolia)


title: Leaves_ML2xCtrl_3

description:
Library name: Sample 3
counts_leaves.csv


title: Leaves_ML2xWD_1

description:
Library name: Sample 4
counts_leaves.csv


title: 140-BL

description: Library name: Sample_00000000000166


title: 146-3M

description: Library name: Sample_00000000000167


title: 140-6W

description: Library name: Sample_00000000000165


title: 323-8W

description: Library name: Sample_00000000000164

value: nivolumab


title: Liver_Control_D912

city: Leipzig

first: Alexander

last: Jais

address: Philipp-Rosenthal-Straße 27

country: Germany

institute: Helmholtz Institute for Metabolic, Obesity, and Vascular Research (HI-MAG)

data_processing:
The trimmed reads were aligned to the reference genome using HISAT2 v2.0.5, which generated a database of splice junctions from the gene model annotation file to improve alignment quality.
Gene expression levels were quantified using featureCounts v1.5.0-p3, with results expressed in FPKM (Fragments Per Kilobase of transcript per Million mapped reads) to normalize for gene length and sequencing depth.
For differential gene expression analysis, DESeq2 was employed for groups with biological replicates. Criteria for differential expression included log2 fold change > 0.5 and adjusted p-value < 0.05.
Assembly: GRCm39 (mm39)
Supplementary files format and content: xlsx (Excel file containing FPKM values and DEG analysis)

extract_protocol:
RNeasy Mini Kit
Fragmentation was followed by the synthesis of the first strand cDNA using random hexamer primers, and the second strand cDNA was synthesized using dUTP to ensure strand specificity. The resulting cDNA libraries underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was confirmed using Qubit for quantification, real-time PCR, and bioanalyzer for size distribution.

treatment_protocol: High-fat diet feeding for 17 weeks (HFD, E15742-34 - corresponds to D12492, ssniff Spezialdiäten GmbH) containing 20kJ% carbohydrates, 20kJ% protein and 60kJ% fat from 8 weeks of age onwards)

value: liver

value: Control (CD19-Cre)

value: High fat diet (17 weeks)


title: Leaves_ML2xCtrl_1

description:
Library name: Sample 1
counts_leaves.csv

value: Control


title: Liver_Control_D911


title: 295-8W

description: Library name: Sample_00000000000162

value: Blood


title: Liver_PnocBKO_D386


title: 290-3M

description: Library name: Sample_00000000000161

value: pembrolizumab


title: Liver_PnocBKO_D180


title: Liver_PnocBKO_D088


title: 270-8W

description: Library name: Sample_00000000000159


title: 146-BL

description: Library name: Sample_00000000000170

value: BL


title: 266-8W

description: Library name: Sample_00000000000158


title: eWAT_Control_D912

data_processing:
The trimmed reads were aligned to the reference genome using HISAT2 v2.0.5, which generated a database of splice junctions from the gene model annotation file to improve alignment quality.
Gene expression levels were quantified using featureCounts v1.5.0-p3, with results expressed in FPKM (Fragments Per Kilobase of transcript per Million mapped reads) to normalize for gene length and sequencing depth.
For differential gene expression analysis, DESeq2 was employed for groups with biological replicates. Criteria for differential expression included log2 fold change > 0.5 and adjusted p-value < 0.05.
Assembly: GRCm39 (mm39)
Supplementary files format and content: xls (tab-delimited text file containing FPKM values and DEG analysis)
Supplementary files format and content: xlsx (Excel file containing FPKM values and DEG analysis)

source_name: epididymal (eWAT) adipose tissue

extract_protocol:
RNeasy Lipid Tissue Mini Kit
Fragmentation was followed by the synthesis of the first strand cDNA using random hexamer primers, and the second strand cDNA was synthesized using dUTP to ensure strand specificity. The resulting cDNA libraries underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was confirmed using Qubit for quantification, real-time PCR, and bioanalyzer for size distribution.

value: epididymal (eWAT) adipose tissue


title: eWAT_Control_D911


title: 254-27W

description: Library name: Sample_00000000000157


title: eWAT_Control_D087


title: Leaves_ML2xCtrl_2

description:
Library name: Sample 2
counts_leaves.csv

value: Mexican lime (Citrus aurantiifolia)

value: diploid Swingle citrumelo 4475 (Citrus sinensis x Poncirus trifoliata)


title: 252-3M

description: Library name: Sample_00000000000156

value: PBMCs

value: pembrolizumab+other


title: 223-TOX

description: Library name: Sample_00000000000153


title: 216-3M

description: Library name: Sample_00000000000152

value: ipilimumab+nivolumab


title: eWAT_PnocBKO_D180


title: 224-8W

description: Library name: Sample_00000000000154


title: eWAT_PnocBKO_D088


title: 304-8W

description: Library name: Sample_00000000000163


title: eWAT_PnocBKO_D386


title: ileum, D0, digoxin 3

city: West Haven

first: Aman

last: Kumar

state: CT

address: 840 West Campus Drive

institute: Yale Universitry

data_processing:
A positive control (PhiX library) provided by Illumina was included in every lane at a concentration of 0.3% to monitor sequencing quality in real time.
Signal intensities were converted to individual base calls using Real Time Analysis (RTA) software (Illumina). Primary analysis (sample de-multiplexing and alignment to the mouse genome) was performed using Illumina's CASAVA 1.8.2 software suite. Low-quality reads were trimmed, and adaptor contamination was removed using Trim Galore v0.5.0. Trimmed reads were mapped to the mouse reference genome (GRCm38) using HISAT2 v2.1.033. Gene expression levels were quantified using StringTie v1.3.3b34 with gene models (M15) from the GENCODE project. Differentially expressed genes were identified using DESeq235.
Assembly: mm10
Supplementary files format and content: tab-separated value file includes normalized (TPM) counts for each sample

source_name: terminal ileum

growth_protocol: C57BL/6N mice purchased from Taconic Biosciences were maintained under 12hr light dark cycle in conventional room

extract_protocol:
Approximately 2cm of terminal ileum was dissected and submerged in Tissue protect reagent (Qiagen), and kept at -80C. RNA was extracted using  RNeasy Plus Universal mini kit (Qiagen #73404) and RNA concentration was measured and stored at -80C until ready for sequencing.
mRNA was purified from approximately 1000 ng of total RNA with oligo-dT beads and sheared by incubation at 94°C in the presence of Mg2+ (Kapa mRNA HyperPrep).  Following first-strand synthesis with random primers, second strand synthesis and A-tailing were performed with dUTP for generating strand-specific sequencing libraries. Adapters containing 3’ dTMP overhangs were ligated to library insert fragments, and library amplification was used to select and amplify fragments carrying the appropriate adapter sequences at both ends. Strands marked with dUTP are not amplified. Indexed libraries that meet appropriate cut-offs for both were quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent TapeStation. Samples with a yield of ≥0.5 ng/ul were used for sequencing.
Sample concentrations were normalized to 2.0 nM and loaded onto an Illumina NovaSeq flow cell at a concentration that yields 30 million post-filtering clusters per sample. Samples were sequenced using 100bp paired-end sequencing according to Illumina protocols.

treatment_protocol: Mice were treated with digoxin or PBS(5%DMSO) for two days and sacrificed 12hr-post the last drug dose (ZT12).

value: terminal ileum

value: WT

value: Digoxin


title: 213-8M

description: Library name: Sample_00000000000150

value: durvalumab


title: ileum, D0, digoxin 2


title: 205-3M

description: Library name: Sample_00000000000149


title: 279-3W

description: Library name: Sample_00000000000160


title: ileum, D0, digoxin 1


title: Liver_Control_D909

value: liver


title: 203-BL

description: Library name: Sample_00000000000148

value: nivolumab


title: ileum, D0, PBS control 3

value: PBS


title: 215-6W

description: Library name: Sample_00000000000151


title: 203-8W

description: Library name: Sample_00000000000147


title: ileum, D0, PBS control 2


title: 202-8W

description: Library name: Sample_00000000000146


title: ileum, D0, PBS control 1


title: 196-8W

description: Library name: Sample_00000000000145


title: siNONO_3-mRNA

city: Urumuqi

first: chao

last: peng

state: Xinjiang

address: tianchi road 91

institute: people's hospital of xinjiang uygur autonomous region

data_processing:
Illumina Novaseq 6000 system for 150 nt paired-end sequencing.
Raw reads containing more than 2-N bases were first discarded. Adaptors and low-quality bases were then trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.013). The short reads less than 16nt were also dropped.
clean reads were aligned to the mRatBN7.2 genome by HISAT2 (32), allowing 4 mismatches. Unique mapped reads were used for gene reads number counts and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
edgeR was used to the DEG analysis with FC>2 or < 0.5, FDR <= 0.05.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include gene FPKM values for each Sample

organism: Rattus

source_name: cardiac musculus

growth_protocol: The rat cardiac fibroblasts cells line (Procell Science & Technology Co., Ltd., China) were cultured at 37℃ with 5% CO2 in a complete medium for rat cardiac fibroblasts.

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA, and the quality and quantity of the purified RNA were determined by measuring the absorbance at wavelengths 260nm/280nm (A260/A280) using Nanodrop One (Thermo). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1 μg of total RNA was used for RNA-seq library construction by KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (#KK8544). Polyadenylated mRNAs were purified by VAHTS mRNA capture Beads (N401-01) and then fragmented. Fragmented mRNAs were converted into double-stranded cDNAs. Following end repair and poly-A tailing, the cDNAs were ligated to Diluted Roche Adaptor (KK8726). The ligation product was purified and size fractionated to 300-500bps, amplified, purified, quantified, and sequenced after storage at -80℃.

treatment_protocol: NONO siRNA transfection of the cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48h for RT-qPCR and western blotting analysis.

value: cardiac musculus

value: fibroblasts cells

value: transfected with GENE_NONO siRNA


title: 155-2W

description: Library name: Sample_00000000000144

value: Blood

value: pembrolizumab


title: 233-8W

description: Library name: Sample_00000000000155


title: eWAT_Control_D909

value: epididymal (eWAT) adipose tissue

value: Control (CD19-Cre)

value: High fat diet (17 weeks)


title: 153-6W

description: Library name: Sample_00000000000143

value: PBMCs


title: 126-3M

description: Library name: Sample_00000000000142

value: ipilimumab+nivolumab


title: siNONO_1-mRNA


title: siCtrl_2-mRNA

value: transfected with empty vector


title: siCtrl_1-mRNA


title: siCtrl_3-mRNA


title: 125-6-8W

description: Library name: Sample_00000000000141


title: H9C2_Input_2-mRNA

data_processing:
Illumina Novaseq 6000 system for 150 nt paired-end sequencing.
The reads were aligned onto the genome with HISAT2, the unique alignment on the genome was finally obtained, and the alignment results of PCR duplicates were removed. Peak calling was then performed using two software programs, Piranha and ABLIRC, which have been described in previous studies
The process of peak calling was as follows: firstly, the whole genome was scanned with 5bp as a window and 5bp as a step from each chromosome. Identification of peaks was required that the depth of the first window to be 2.5 times for 8 consecutive windows on the genome, or a medium depth greater than 50. A peak ended when the 8 consecutive windows were less than 4% of the peak's maximum depth.
the reads on each gene were randomly distributed to each gene for 500 times, and the frequency of peak depth of each peak was counted, so as to conduct significance analysis on identified peak and screen out the peak with significant peak (p<0.05) or peak with maximum depth of a certain degree (≥10).
The locations of these peaks was further analyzed for abundance differences with the input samples as a control, and the peaks with IP abundance greater than 4 times (adjustable parameter) of input abundance were screened out as the final combination peak.
The target genes of IP were finally determined by the peaks and the binding motifs of IP proteins were called by HOMER software
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include gene FPKM values for each Sample

tag: antibody


title: 325-BL

description: Library name: Sample_00000000000122

value: BL


title: 323-3M

description: Library name: Sample_00000000000119


title: 319-6W

description: Library name: Sample_00000000000117


title: 325-6W

description: Library name: Sample_00000000000121


title: H9C2_NONO_IP_2-mRNA

value: anti-NONO


title: H9C2_Input_1-mRNA


title: 319-BL

description: Library name: Sample_00000000000118


title: 323-BL

description: Library name: Sample_00000000000120


title: 317-BL

description: Library name: Sample_00000000000116

value: durvalumab


title: 317-2W

description: Library name: Sample_00000000000115


title: H9C2_NONO_IP_1-mRNA


title: TTKL32

first: Gabriella

middle: Alves

last: Sidhu

state: Ontario

address: The Laurene O. Paterson Building, Western Science Centre

department: Biology

country: Canada

institute: Western University

description:
Library name: 106
column name in L3_processed_counts.csv: 106

data_processing:
RNAseq reads were aligned to the BDGP6 assembly of the Drosophila melanogaster genome using HISAT2 (version 2.2.1)
Gene count data was extracted with featureCounts (version 2.0.1) with the BDGP6.46.110 genome assembly
Differentially expressed genes were detected with DEseq2 (version 1.40.2).
Salmon (version 1.10.1) estimated the number of transcripts expressed from the endogenous transcription factor loci and UAS transcription factor constructs using the BDGP6 assembly of the Drosophila melanogaster transcriptome supplemented with files of the UAS constructs used (Supplemental data S1).
Assembly: BDGP6 assembly of Drosophila melanogaster genome.
Supplementary files format and content: csv files include raw counts for each Sample

organism: Drosophila melanogaster

source_name: wing imaginal disc

extract_protocol:
Total RNA was extracted from the tissues using the Quagen RNeasy mini kit.
Sequencing services were executed with the DNBseq sequencing technology, featuring cPAS and DNA Nanoballs (DNBTM) technology.

value: wing imaginal disc

tag: developmental stage

value: late third larval

value: y w; apnull/apGAL4; M{UASttk3XHA}

tag: batch


title: TTKL35

description:
Library name: 109
column name in L3_processed_counts.csv: 109


title: TTKL34

description:
Library name: 108
column name in L3_processed_counts.csv: 108


title: SISAL35

description:
Library name: 104
column name in L3_processed_counts.csv: 104

value: y w; apnull/apGAL4; M{UASsisA3XHA}


title: TTKL31

description:
Library name: 105
column name in L3_processed_counts.csv: 105


title: 313-BL

description: Library name: Sample_00000000000114


title: 306-BL

description: Library name: Sample_00000000000112


title: SISAL33

description:
Library name: 102
column name in L3_processed_counts.csv: 102


title: siNONO_2-mRNA

value: cardiac musculus

value: fibroblasts cells


title: 306-6W

description: Library name: Sample_00000000000111

value: Blood


title: SISAL34

description:
Library name: 103
column name in L3_processed_counts.csv: 103


title: SISAL32

description:
Library name: 101
column name in L3_processed_counts.csv: 101


title: SISAL31

description:
Library name: 100
column name in L3_processed_counts.csv: 100


title: 313-3W

description: Library name: Sample_00000000000113


title: 305-BL

description: Library name: Sample_00000000000110


title: 122-3M

description: Library name: Sample_00000000000140

value: nivolumab


title: TTKL33

description:
Library name: 107
column name in L3_processed_counts.csv: 107


title: MYBL32

description:
Library name: 518
column name in L3_processed_counts.csv: 518

value: y w; apnull/apGAL4; M{UASmyb}


title: 304-BL

description: Library name: Sample_00000000000108


title: 304-3M

description: Library name: Sample_00000000000106


title: MYBL34

description:
Library name: 520
column name in L3_processed_counts.csv: 520


title: MYBL33

description:
Library name: 519
column name in L3_processed_counts.csv: 519


title: 302-BL

description: Library name: Sample_00000000000105


title: MYBL31

description:
Library name: 516
column name in L3_processed_counts.csv: 516


title: 304-6M

description: Library name: Sample_00000000000107


title: CADL33

description:
Library name: 113
column name in L3_processed_counts.csv: 113

value: y w; apnull/apGAL4; M{UAScad3XHA}


title: 290-BL

description: Library name: Sample_00000000000102

value: pembrolizumab


title: CADL35

description:
Library name: 115
column name in L3_processed_counts.csv: 115


title: 290-6W

description: Library name: Sample_00000000000101

value: PBMCs


title: CADL31

description:
Library name: 111_CAD
column name in L3_processed_counts.csv: 111_CAD


title: 289-6M

description: Library name: Sample_00000000000099


title: APL35

description:
Library name: 510
column name in L3_processed_counts.csv: 510

value: y w; apnull/apGAL4; P{UASap}


title: 305-6W

description: Library name: Sample_00000000000109

value: ipilimumab+nivolumab


title: 295-BL

description: Library name: Sample_00000000000103

value: BL


title: CADL32

description:
Library name: 112
column name in L3_processed_counts.csv: 112


title: 289-4W

description: Library name: Sample_00000000000098


title: 284-BL

description: Library name: Sample_00000000000097

value: atezolizumab


title: APL33

description:
Library name: 508
column name in L3_processed_counts.csv: 508


title: 284-3W

description: Library name: Sample_00000000000096


title: APL34

description:
Library name: 509
column name in L3_processed_counts.csv: 509


title: 279-BL

description: Library name: Sample_00000000000095


title: APL31

description:
Library name: 511
column name in L3_processed_counts.csv: 511


title: 302-6W

description: Library name: Sample_00000000000104


title: CADL34

description:
Library name: 114
column name in L3_processed_counts.csv: 114


title: ConL35

description:
Library name: 62
column name in L3_processed_counts.csv: 62

value: y w; apnull/apGAL4


title: 279-3M

description: Library name: Sample_00000000000094


title: 289-BL

description: Library name: Sample_00000000000100


title: 278-6W

description: Library name: Sample_00000000000092

value: nivolumab+other


title: ConL36

description:
Library name: 63
column name in L3_processed_counts.csv: 63

value: wing imaginal disc

value: late third larval


title: ConL34

description:
Library name: 61_AP_Mutant
column name in L3_processed_counts.csv: 61_AP_Mutant


title: WTL36

description:
Library name: 116
column name in L3_processed_counts.csv: 116

value: y w


title: ConL33

description:
Library name: 60
column name in L3_processed_counts.csv: 60


title: WTL37

description:
Library name: 117
column name in L3_processed_counts.csv: 117


title: APL32

description:
Library name: 507
column name in L3_processed_counts.csv: 507


title: 273-2W

description: Library name: Sample_00000000000086


title: 278-BL

description: Library name: Sample_00000000000093


title: 274-6W

description: Library name: Sample_00000000000088


title: 277-6W

description: Library name: Sample_00000000000090

value: durvalumab


title: 264-BL

description: Library name: Sample_00000000000083


title: WTL32

description:
Library name: 54
column name in L3_processed_counts.csv: 54


title: 274-BL

description: Library name: Sample_00000000000089


title: ConL31

description:
Library name: 58_AP_Mutant
column name in L3_processed_counts.csv: 58_AP_Mutant


title: ConL32

description:
Library name: 59_AP_mutant
column name in L3_processed_counts.csv: 59_AP_mutant


title: 270-BL

description: Library name: Sample_00000000000085


title: 277-BL

description: Library name: Sample_00000000000091


title: 273-BL

description: Library name: Sample_00000000000087


title: WTL34

description:
Library name: 56_AP_WT
column name in L3_processed_counts.csv: 56_AP_WT


title: WTL33

description:
Library name: 55_AP_WT
column name in L3_processed_counts.csv: 55_AP_WT


title: WTL35

description:
Library name: 57_AP_WT
column name in L3_processed_counts.csv: 57_AP_WT


title: WTL31

description:
Library name: 53_AP_WT
column name in L3_processed_counts.csv: 53_AP_WT


title: 264-6W

description: Library name: Sample_00000000000082


title: 266-BL

description: Library name: Sample_00000000000084


title: TTKE34

description:
Library name: 544
column name in E3_processed_counts.csv: 544

value: early third larval

value: y w; apnull/apGAL4; M{UASttk3XHA}


title: 263-6W

description: Library name: Sample_00000000000080

value: Blood


title: 263-BL

description: Library name: Sample_00000000000081


title: TTKE35

description:
Library name: 545
column name in E3_processed_counts.csv: 545


title: 262-BL

description: Library name: Sample_00000000000079


title: TTKE33

description:
Library name: 543
column name in E3_processed_counts.csv: 543


title: TTKE32

description:
Library name: 542
column name in E3_processed_counts.csv: 542


title: TTKE31

description:
Library name: 541
column name in E3_processed_counts.csv: 541


title: SISAE34

description:
Library name: 550
column name in E3_processed_counts.csv: 550

value: y w; apnull/apGAL4; M{UASsisA3XHA}


title: 262-6W

description: Library name: Sample_00000000000078


title: 259-BL

description: Library name: Sample_00000000000077


title: SISAE33

description:
Library name: 548
column name in E3_processed_counts.csv: 548


title: SISAE32

description:
Library name: 547
column name in E3_processed_counts.csv: 547


title: 254-6W

description: Library name: Sample_00000000000073

value: nivolumab


title: 254-BL

description: Library name: Sample_00000000000075


title: 254-3W

description: Library name: Sample_00000000000071


title: 254-6M

description: Library name: Sample_00000000000072


title: MYBE33

description:
Library name: 533
column name in E3_processed_counts.csv: 533

value: y w; apnull/apGAL4; M{UASmyb}


title: 259-6W

description: Library name: Sample_00000000000076

value: PBMCs

value: pembrolizumab


title: MYBE32

description:
Library name: 532
column name in E3_processed_counts.csv: 532


title: 252-6W

description: Library name: Sample_00000000000069

value: pembrolizumab+other


title: 252-BL

description: Library name: Sample_00000000000070

value: BL


title: SISAE31

description:
Library name: 546
column name in E3_processed_counts.csv: 546


title: CADE35

description:
Library name: 540
column name in E3_processed_counts.csv: 540

value: y w; apnull/apGAL4; M{UAScad3XHA}


title: 248-6W

description: Library name: Sample_00000000000067


title: 248-BL

description: Library name: Sample_00000000000068


title: MYBE31

description:
Library name: 531
column name in E3_processed_counts.csv: 531


title: CADE34

description:
Library name: 539
column name in E3_processed_counts.csv: 539


title: CADE33

description:
Library name: 538
column name in E3_processed_counts.csv: 538


title: 242-BL

description: Library name: Sample_00000000000066


title: 242-6W

description: Library name: Sample_00000000000065


title: 254-9M

description: Library name: Sample_00000000000074


title: CADE31

description:
Library name: 536
column name in E3_processed_counts.csv: 536


title: CADE32

description:
Library name: 537
column name in E3_processed_counts.csv: 537


title: MYBE34

description:
Library name: 535
column name in E3_processed_counts csvt: 535