title: AC_211_R30

description: Isolated transgenes from Round 30 (E30) of rtTA-3G VLPs, to identify transgene substitutions.

data_processing:
Raw FASTQ files were aligned to transgene reference sequences (FASTA) with minimap2. Any mate-pair issues were fixed in the output .sam files with the samtools fixmate command before reads were sorted (samtools sort) and reformatted (samtools mpileup). VarScan 2.3.9 was used to call for variants with command mpileup2snp with arguments --min-coverage 10000 --min-reads2 15 --min-var-freq 0.00025 --p-value 0.01. Further annotation was performed with vcf-annotator using default commands, aligning to transgene reference sequences (GenBank format).
Assembly: ATGTCTAGACTGGACAAGAGCAAAGtcataaactctgctctggaattactcaatggagtcggtatcgaaggcctgacgacaaggaaactcgctcaaaagctgggagttgagcagcctaccctgtactggcacgtgaagaacaagcgggccctgctcgatgccctgccaatcgagatgctggacaggcatcatacccactcctgccccctggaaggcgagtcatggcaagactttctgcggaacaacgccaagtcataccgctgtgctctcctctcacatcgcgacggggctaaagtgcatctcggcacccgcccaacagagaaacagtacgaaaccctggaaaatcagctcgcgttcctgtgtcagcaaggcttctccctggagaacgcactgtacgctctgtccgccgtgggccactttacactgggctgcgtattggaggaacaggagcatcaagtagcaaaagaggaaagagagacacctaccaccgattctatgcccccacttctgaaacaagcaattgagctgttcgaccggcagggagccgaacctgccttccttttcggcctggaactaatcatatgtggcctggagaaacagctaaagtgcgaaagcggcgggccgaccgacgcccttgacgattttgacttagacatgctcccagccgatgcccttgacgactttgaccttgatatgctgcctgctgacgctcttgacgattttgaCCTTGACATGCTCCCCGGGTAA
Supplementary files format and content: .vcf file (openable in Excel) containing analysis of mutation calls.
Library strategy: Amplicon sequencing


title: Cpt1a_Spc_KO_MHV68_replicate_6

status: Public on Apr 03 2025

type: SRA

city: Columbus

first: Jhonny

last: Rodriguez Lopez

state: Ohio

address: Holly Ave 1383 203A

department: Internal medicine

country: USA

institute: The Ohio State University

description:
Library name: Sample 6
TruSeq Stranded Total RNA With Illumina Ribo-Zero Plus

library_source: transcriptomic

data_processing:
Raw sequencing reads underwent quality assessment and alignment to the mouse reference genome GRCm38 using the Cell Ranger pipeline v7.1.0 (10X Genomics).
The reference datasets used were refdata-gex-mm10-2020-A and Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10 provided by 10x Genomics.
A unique molecular identifier (UMI) count matrix was generated as the output of Cell Ranger, which was then used to create a Seurat object for downstream analysis.
Quality control metrics included filtering cells based on gene expression counts and mitochondrial RNA content.
The single cell RNA seq was further analyzed for normalization, scaling, and identification of highly variable genes to create clusters of cells based on expression profiles.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Processed data files include raw counts, and normalized counts, containing information on cell, respectively.

molecule: total RNA

organism: Mus musculus

source_name: Mouse Lung

extract_protocol:
Total RNA was extracted from mouse lung tissue using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions, including DNase treatment to remove genomic DNA.
RNA-Seq libraries were prepared with the TruSeq Stranded Total RNA kit (Illumina, SanDiego, CA) following manufacturer’s protocol. Mitochondrial and rRNA were depleted from total RNA by Ribo-Zero Plus followed by RNA fragmentation and cDNA synthesis. Blunt ended cDNA fragments were A-tailed followed by ligation of indexed sequencing adapters. PCR amplification allowed enrichment of DNA with adapters ligated to both ends and was followed by library quantity and quality control by Qubit and Agilent DNA 1000 TapeStation. Final libraries were normalized to 10nM pooled and diluted. Flowcells for NextSeq 500 were loaded with 1.6pM denatured library for automated cluster formation and 2x75 paired end sequencing, approximately 60 million reads per sample.

treatment_protocol: Mice were infected with MHV68. No additional treatments were applied before RNA extraction.

tag: tissue

value: Mouse Lung

tag: cell type

value: Lung cell types

tag: genotype

value: Spc-KO

tag: treatment


title: Donor_Y_F3

city: Lund

first: Anna

last: Konturek-Ciesla

state: Skane

address: Klinikgatan 26, BMC B12

department: Laboratory Medicine

country: Sweden

institute: Lund University

description: Artificially single-ended: sequenced as paired-end, the sample barcode was sequenced in R1 and this information was moved to the headers/file names of the R2 sequences. Only these complete R2 files are included. The data originates from a forward-stranded library.

data_processing:
The cDNA library was paired-end sequenced on an Illumina NovaSeq X Plus, using a 10B Illumina kit (100 cycles), with a sequencing depth of 10 million reads per sample and the following read configuration: R1=26 cycles; i7=6 cycles and R2=60 cycles.
Read 1 was used to identify the sample barcode, and this information was moved to the headers of the R2 sequences. Read 2 was mapped to the Mouse GRCm38 reference genome using the STARsolo v.2.7.10b package.
Reads that mapped to multiple locations on the reference genome were discarded.
Generation of the count table was carried out using the STARsolo v.2.7.10b package.
Downstream analyses were performed using R v.4.2.1, including normalization and differential gene expression using DESeq2 v.1.36.0 package. Differentially expressed genes were identified based on adjusted p-value <0.1.
Assembly: mouse GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts of all samples

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
Donor and host MPP Ly cells (Lineage-cKIT+SCA-1+IL7Ra-FLT3+CD150-) were isolated from the BM of each recipient by fluorescence-activated cell sorting (FACS) 16 weeks after CD45.2-saporin treatment. Two hundred MPP Ly cells were directly sorted into TRIzol reagent.
mRNA was reverse transcribed, barcoded with CEL-seq2 primers, pooled, and amplified with in vitro transcription. The resulting amplified RNA was fragmented and used to generate cDNA sequencing libraries with Truseq Small RNA adapters (Illumina).

treatment_protocol: Young ex vivo expanded HSCs were transplanted into young (3 months) and aged (16 months) mice treated with G-CSF/AMD3100. 20 weeks after transplantation, mice were treated with CD45.2-saporin to deplete host BM cells.

value: Bone marrow

value: MPP Ly

tag: cell origin

value: donor

tag: recipient

value: young


title: Cpt1a_Flox_MHV68_replicate_4

description:
Library name: Sample 4
TruSeq Stranded Total RNA With Illumina Ribo-Zero Plus


title: AC_213_R8_2

city: Camperdown

first: Graham

middle: Gregory

last: Neely

state: NSW

address: John Hopkins Drive

country: Australia

institute: Charles Perkins Centre, The University of Sydney

description: Isolated transgenes from Round 8 (E8) of tTA VLPs, to identify transgene substitutions. [Campaign 1]

data_processing:
Raw FASTQ files were aligned to transgene reference sequences (FASTA) with minimap2. Any mate-pair issues were fixed in the output .sam files with the samtools fixmate command before reads were sorted (samtools sort) and reformatted (samtools mpileup). VarScan 2.3.9 was used to call for variants with command mpileup2snp with arguments --min-coverage 10000 --min-reads2 15 --min-var-freq 0.00025 --p-value 0.01. Further annotation was performed with vcf-annotator using default commands, aligning to transgene reference sequences (GenBank format).
Assembly: ATGGCTAGATTAGATAAAAGTAAAGTGATTAACagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgcgtacagccgcgcgcgtacgaaaaacaattacgggtctaccatcgagggcctgctcgatctcccggacgacgacgcccccgaagaggcggggctggcggctccgcgcctgtcctttctccccgcgggacacacgcgcagactgtcgacggcccccccgaccgatgtcagcctgggggacgagctccacttagacggcgaggacgtggcgatggcgcatgccgacgcgctagacgatttcgatctggacatgttgggggacggggattccccgggtccgggatttaccccccacgactccgccccctacggcgctctggatatggccgacttcgagtttgagcagatgtttaccgatgcccttggaattgacgagtacggtgggtag
Supplementary files format and content: .vcf file (openable in Excel) containing analysis of mutation calls.
Library strategy: Amplicon sequencing

organism: Semliki Forest virus

extract_protocol:
Total RNA from VLP supernatant extracted. RT-PCR to amplify transgene sequences (amplicons used for library construction).
Samples were sequenced with Novogene using their ‘Microbial PCR Product Whole Genome Sequencing’ strategy. Amplicons underwent fragmentation prior to PCR-free library preparation and sequencing using NovaSeq PE250 technology.

tag: cell line


title: Brain _Midday_Female1

city: Edinburgh

first: Violeta

last: Trejo-Reveles

address: Old College, South Bridge, Edinburgh

country: United Kingdom

institute: The University of Edinburgh

description: Library name: 5BA

data_processing:
Raw fastq files were processed by trimming using trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) with the following parameters: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10; SLIDINGWINDOW:10:30; LEADING:28; TRAILING:28; MINLEN:75. After trimming the quality of the reads was checked using FASTQC
Reads were aligned using STAR aligner version 2.7.11a (https://github.com/alexdobin/STAR), with the ENSEMBL green anole (Anolis carolinensis) genome and gtf (AnoCar2.0v2, Anolis_carolinensis.AnoCar2.0v2.112.gtf) as references. BAM files were counted using featurecounts (https://subread.sourceforge.net/).
Assembly: AnoCar2.0v2
Supplementary files format and content: csv files contain ether raw counts for each sample

organism: Anolis carolinensis

source_name: Brain

growth_protocol: Twenty-four free-living adult green anole lizards (Anolis carolinensis; twelve of each sex) were captured in the breeding season, in May 2024, on the urban campus of Trinity University in San Antonio, Texas, USA, during daylight hours. Green anole lizards were collected by using a dental floss loop attached to an extendable fishing pole or by hand and were transported individually to the Trinity University vivarium in cotton bags. On the day of capture, the body mass of each anole was measured to the nearest 0.1 g using a Pesola spring scale and snout-vent length measured to the nearest mm using a clear plastic ruler (Males: range 52-69mm, average 62mm; Females: range 51-57mm, average 55mm). Each individual was given a unique identification number on the lower jaw using a non-toxic permanent marker.

extract_protocol:
RNAeasy kit
Library construction performed by BGI Genomics

treatment_protocol: Each anole was  randomly assigned to one of three treatment groups: Midday, Midnight, or ALAN. Sex was determined by the presence of hemipenes and the size of the dewlap; four anoles of each sex were assigned to each treatment group

value: Brain

tag: Sex

value: Female

value: WT

value: Midday

tag: batch


title: Th17, KO, Rep3

city: South San Francisco,

first: Saiyu

last: Hang

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Sequencing reads were aligned to the Mus musculus genome (version mm10) using STAR alignment software tools. Calculation of read counts was carried out using featureCounts. Gene expression normalization was performed using DESeq2
Assembly: mm10
Supplementary files format and content: .txt includes raw counts for each sample

extract_protocol:
Total RNA extraction and purification were performed using the RNeasy mini kit (Qiagen) following the manufacturer’s instructions.
The purified RNA samples were then sent to Harvard Biopolymers Core for library preparation and deep sequencing.

value: KO


title: Donor_Y_F1


title: AC_211_R25

description: Isolated transgenes from Round 25 (E25) of rtTA-3G VLPs, to identify transgene substitutions.


title: Th17, KO, Rep2


title: AC_211_R20

description: Isolated transgenes from Round 20 (E20) of rtTA-3G VLPs, to identify transgene substitutions.


title: Brain _Midday_Male2

description: Library name: 2BA

value: male


title: Th17, KO, Rep1


title: Donor_A_F9

value: aged


title: Brain _Midday_Male1

description: Library name: 1BA


title: Brain _Midday_Male3

description: Library name: 3BA


title: Th17, Control, Rep3


title: AC_211_R10

description: Isolated transgenes from Round 10 (E10) of rtTA-3G VLPs, to identify transgene substitutions.


title: Donor_A_F7


title: AC_211_R5

description: Isolated transgenes from Round 5 (E5) of rtTA-3G VLPs, to identify transgene substitutions.


title: Donor_A_F6


title: Th17, Control, Rep2


title: Donor_A_F10


title: kideny,24h,rep2

city: Taigu

first: libo

last: gu

state: shanxi

address: No. 1 Xianming South Road

department: College of Animal Science

country: China

institute: Shanxi Agricultural University

description: Library name: ZK3-2

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic [1]. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. After removing adaptor and low quality sequences, the clean reads were assembled into expressed sequence tag clusters (contigs) and de novo assembled into transcripts by Trinity [2] (vesion: 2.4) with paired-end method. The longest transcript was choose as a unigene based on the similarity and length for subsequent analyses.
Assembly: The function of the unigenes was annotated by alignment of the unigenes with the NCBI  non-redundant (NR), Swiss-Prot, evolutionary genealogy of genes
Supplementary files format and content: include FPKM values for each Sample

organism: Tachysurus ussuriensis

source_name: kidney

extract_protocol: Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol. RNA  purity and quantification were evaluated NanoDrop 2000 spectrophotometer (Thermo Scientific,  USA).

value: kidney

tag: time


title: kideny,24h,rep1

description: Library name: ZK3-1


title: AC_211_RA

description: Isolated transgenes from Round A (amplification) of rtTA VLPs, to identify transgene substitutions.


title: AC_150_R1

description: Isolated transgenes from Round 2 of eGFP-LUC VLPs, to identify transgene substitutions.

data_processing:
Raw FASTQ files were aligned to transgene reference sequences (FASTA) with minimap2. Any mate-pair issues were fixed in the output .sam files with the samtools fixmate command before reads were sorted (samtools sort) and reformatted (samtools mpileup). VarScan 2.3.9 was used to call for variants with command mpileup2snp with arguments --min-coverage 10000 --min-reads2 15 --min-var-freq 0.00025 --p-value 0.01. Further annotation was performed with vcf-annotator using default commands, aligning to transgene reference sequences (GenBank format).
Assembly: ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTCAGGATCCGGAGCCACGAACTTCTCTCTGTTAAAGCAAGCAGGAGACGTGGAAGAAAACCCCGGGCCCATGGAAGATGCCAAAAACATTAAGAAGGGCCCAGCGCCATTCTACCCACTCGAAGACGGGACCGCCGGCGAGCAGCTGCACAAAGCCATGAAGCGCTACGCCCTGGTGCCCGGCACCATCGCCTTTACCGACGCACATATCGAGGTGGACATTACCTACGCCGAGTACTTCGAGATGAGCGTTCGGCTGGCAGAAGCTATGAAGCGCTATGGGCTGAATACAAACCATCGGATCGTGGTGTGCAGCGAGAATAGCTTGCAGTTCTTCATGCCCGTGTTGGGTGCCCTGTTCATCGGTGTGGCTGTGGCCCCAGCTAACGACATCTACAACGAGCGCGAGCTGCTGAACAGCATGGGCATCAGCCAGCCCACCGTCGTATTCGTGAGCAAGAAAGGGCTGCAAAAGATCCTCAACGTGCAAAAGAAGCTACCGATCATACAAAAGATCATCATCATGGATAGCAAGACCGACTACCAGGGCTTCCAAAGCATGTACACCTTCGTGACTTCCCATTTGCCACCCGGCTTCAACGAGTACGACTTCGTGCCCGAGAGCTTCGACCGGGACAAAACCATCGCCCTGATCATGAACAGTAGTGGCAGTACCGGATTGCCCAAGGGCGTAGCCCTACCGCACCGCACCGCTTGTGTCCGATTCAGTCATGCCCGCGACCCCATCTTCGGCAACCAGATCATCCCCGACACCGCTATCCTCAGCGTGGTGCCATTTCACCACGGCTTCGGCATGTTCACCACGCTGGGCTACTTGATCTGCGGCTTTCGGGTCGTGCTCATGTACCGCTTCGAGGAGGAGCTATTCTTGCGCAGCTTGCAAGACTATAAGATTCAATCTGCCCTGCTGGTGCCCACACTATTTAGCTTCTTCGCTAAGAGCACTCTCATCGACAAGTACGACCTAAGCAACTTGCACGAGATCGCCAGCGGCGGGGCGCCGCTCAGCAAGGAGGTAGGTGAGGCCGTGGCCAAACGCTTCCACCTACCAGGCATCCGCCAGGGCTACGGCCTGACAGAAACAACCAGCGCCATTCTGATCACCCCCGAAGGGGACGACAAGCCTGGCGCAGTAGGCAAGGTGGTGCCCTTCTTCGAGGCTAAGGTGGTGGACTTGGACACCGGTAAGACACTGGGTGTGAACCAGCGCGGCGAGCTGTGCGTCCGTGGCCCCATGATCATGAGCGGCTACGTTAACAACCCCGAGGCTACAAACGCTCTCATCGACAAGGACGGCTGGCTGCACAGCGGCGACATCGCCTACTGGGACGAGGACGAGCACTTCTTCATCGTGGACCGGCTGAAGAGCCTGATCAAATACAAGGGCTACCAGGTAGCCCCAGCCGAACTGGAGAGCATCCTGCTGCAACACCCCAACATCTTCGACGCCGGGGTCGCCGGCCTGCCCGACGACGATGCCGGCGAGCTGCCCGCCGCAGTCGTCGTGCTGGAACACGGTAAAACCATGACCGAGAAGGAGATCGTGGACTATGTGGCCAGCCAGGTTACAACCGCCAAGAAGCTGCGCGGTGGTGTTGTGTTCGTGGACGAGGTGCCTAAAGGACTGACCGGCAAGTTGGACGCCCGCAAGATCCGCGAGATTCTCATTAAGGCCAAGAAGGGCGGCAAGATCGCCGTGTCGACTGTTTAA
Supplementary files format and content: .vcf file (openable in Excel) containing analysis of mutation calls.
Library strategy: Amplicon sequencing


title: Th17, Control, Rep1


title: NSG pancreatic cells 17

city: Bergen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

data_processing:
All analysis were carried out using CLC Genomics Workbench (version 12.0.2) and CLC Genomics Server (version 11.0.2).
Adapter and quality trimming was done by “Trim Reads” tool from CLC Genomics Workbench. While adapters are often removed directly by the sequencer, part of the adapter region may be included in the sequenced reads. Such adapters artefacts were removed by identifying read-through adapter sequences, whereby the 3’ end of one read includes the reverse complement of the adapter from the other read.
Further, reads were trimmed based on quality scores and ambiguous nucleotides, e.g. due to stretches of Ns. A maximum of 2 ambiguous nucleotides were allowed in a read.
The QC reports were generated by “QC for Sequencing Reads” tool from CLC Genomics Workbench scores as emitted by the base-caller.
Read mapping and gene quantification were done by “RNA-seq Analysis” tool from CLC Genomics Workbench.
Principal Component Analyses (PCA) were performed on the gene expression profile using the “PCA for RNA-seq” tool from CLC Genomic Workbench.
Assembly: ENSEMBL Mus musculus GRCm38
Supplementary files format and content: xlsx file include normalized TPM values for each sample

source_name: Pancreatic islet cells

extract_protocol:
Pancreas were digested with collagenase, islets extracted with histopaque gradient, and mRNA extracted using the Qiagen RNeasy Micro Kit (50)
QIAseq Stranded mRNA Select Kit with FastSelect rRNA depletion(QIAGEN) and further proccesed with standard illumina protocols

tag: strain

value: NOD scid gamma

tag: age

value: 6 weeks


title: F_SEQ029

description: Isolated transgenes from Round E3 of co-packaged SRF-VP64/eGFP-LUC VLPs, to observe transgene proportion.

data_processing:
Up to 40 fmol of each DNA library was loaded on ONT Flongle flow cells (R9.4.1 chemistry, #FLO-FLG001) in a MinION Mk1B Sequencer (ONT, #MIN-101B) fitted with a Flongle Adapter (ONT, #ADP-FLG001). Sequencing was performed using MinKNOW (ONT, version 4.2.8) using default parameters and the following inputs: kit used, SQK-LSK110; 0.5 hours between MUX scans; basecalling, disabled. A minimum 2 x 104 raw reads were obtained per flow cell. Raw FAST5 files were basecalled using Guppy (version 4.5.2) with the minimum q-score filter set to 7.0. Quality-filtered basecalled reads (in FASTQ format) were processed using EPI2ME Desktop Agent (ONT, version 3.3.0.1031). Sequence reference files were uploaded into the program with the Fasta Reference Upload workflow (v2021.07.15). For each sample, all reads were aligned to reference files using the Fastq Custom Alignment workflow (v2021.03.25) using default parameters.
Assembly: ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTCAGGATCCGGAGCCACGAACTTCTCTCTGTTAAAGCAAGCAGGAGACGTGGAAGAAAACCCCGGGCCCATGGAAGATGCCAAAAACATTAAGAAGGGCCCAGCGCCATTCTACCCACTCGAAGACGGGACCGCCGGCGAGCAGCTGCACAAAGCCATGAAGCGCTACGCCCTGGTGCCCGGCACCATCGCCTTTACCGACGCACATATCGAGGTGGACATTACCTACGCCGAGTACTTCGAGATGAGCGTTCGGCTGGCAGAAGCTATGAAGCGCTATGGGCTGAATACAAACCATCGGATCGTGGTGTGCAGCGAGAATAGCTTGCAGTTCTTCATGCCCGTGTTGGGTGCCCTGTTCATCGGTGTGGCTGTGGCCCCAGCTAACGACATCTACAACGAGCGCGAGCTGCTGAACAGCATGGGCATCAGCCAGCCCACCGTCGTATTCGTGAGCAAGAAAGGGCTGCAAAAGATCCTCAACGTGCAAAAGAAGCTACCGATCATACAAAAGATCATCATCATGGATAGCAAGACCGACTACCAGGGCTTCCAAAGCATGTACACCTTCGTGACTTCCCATTTGCCACCCGGCTTCAACGAGTACGACTTCGTGCCCGAGAGCTTCGACCGGGACAAAACCATCGCCCTGATCATGAACAGTAGTGGCAGTACCGGATTGCCCAAGGGCGTAGCCCTACCGCACCGCACCGCTTGTGTCCGATTCAGTCATGCCCGCGACCCCATCTTCGGCAACCAGATCATCCCCGACACCGCTATCCTCAGCGTGGTGCCATTTCACCACGGCTTCGGCATGTTCACCACGCTGGGCTACTTGATCTGCGGCTTTCGGGTCGTGCTCATGTACCGCTTCGAGGAGGAGCTATTCTTGCGCAGCTTGCAAGACTATAAGATTCAATCTGCCCTGCTGGTGCCCACACTATTTAGCTTCTTCGCTAAGAGCACTCTCATCGACAAGTACGACCTAAGCAACTTGCACGAGATCGCCAGCGGCGGGGCGCCGCTCAGCAAGGAGGTAGGTGAGGCCGTGGCCAAACGCTTCCACCTACCAGGCATCCGCCAGGGCTACGGCCTGACAGAAACAACCAGCGCCATTCTGATCACCCCCGAAGGGGACGACAAGCCTGGCGCAGTAGGCAAGGTGGTGCCCTTCTTCGAGGCTAAGGTGGTGGACTTGGACACCGGTAAGACACTGGGTGTGAACCAGCGCGGCGAGCTGTGCGTCCGTGGCCCCATGATCATGAGCGGCTACGTTAACAACCCCGAGGCTACAAACGCTCTCATCGACAAGGACGGCTGGCTGCACAGCGGCGACATCGCCTACTGGGACGAGGACGAGCACTTCTTCATCGTGGACCGGCTGAAGAGCCTGATCAAATACAAGGGCTACCAGGTAGCCCCAGCCGAACTGGAGAGCATCCTGCTGCAACACCCCAACATCTTCGACGCCGGGGTCGCCGGCCTGCCCGACGACGATGCCGGCGAGCTGCCCGCCGCAGTCGTCGTGCTGGAACACGGTAAAACCATGACCGAGAAGGAGATCGTGGACTATGTGGCCAGCCAGGTTACAACCGCCAAGAAGCTGCGCGGTGGTGTTGTGTTCGTGGACGAGGTGCCTAAAGGACTGACCGGCAAGTTGGACGCCCGCAAGATCCGCGAGATTCTCATTAAGGCCAAGAAGGGCGGCAAGATCGCCGTGTCGACTGTTTAA; ATGCTCCCTACCCAGGCTGGCGCTGCTGCCGCTCTGGGCAGAGGCTCTGCTCTGGGAGGCTCTCTGAACCGGACCCCTACCGGCAGACCTGGAGGCGGCGGCGGCACCCGGGGCGCCAACGGAGGCAGAGTGCCTGGCAATGGCGCTGGTCTGGGCCCAGGCCGGCTGGAAAGAGAGGCCGCTGCCGCCGCCGCCACAACCCCTGCTCCAACCGCCGGCGCTCTGTATAGCGGATCCGAGGGCGATTCCGAGTCTGGCGAGGAAGAGGAACTGGGCGCTGAGCGGAGAGGCCTGAAGAGATCCCTGTCTGAGATGGAAATCGGCATGGTGGTGGGCGGACCTGAGGCCTCCGCTGCTGCTACAGGAGGCTACGGCCCTGTGTCTGGCGCCGTGTCCGGCGCCAAGCCTGGCAAGAAAACCCGCGGAAGAGTCAAGATCAAGATGGAATTCATCGACAACAAGCTGAGAAGATACACCACCTTCTCCAAGAGGAAAACAGGCATCATGAAGAAGGCCTACGAGCTGTCTACCCTGACAGGCACCCAGGTGCTGCTGCTGGTGGCTTCTGAGACTGGACACGTGTACACCTTTGCCACACGGAAACTGCAACCTATGATCACCTCTGAAACCGGAAAGGCCCTGATCCAGACCTGCCTGAATTCTCCAGATTCCCCTCCTAGATCTGATCCTACCACAGATCAGCGGATGTCTGCCACCGGATTTGAGGAAACCGACCTGACCTACCAAGTGTCCGAGTCCGACTCCTCTGGCGAGACAAAGGACACCCTCAAGCCATCAGGAAGTGGGAAGCGTCCTGCTGCTACAAAAAAAGCTGGACAGGCTAAGAAAAAAAAAGGCTCTGATGCACTGGATGATTTTGATCTCGATATGCTGGGAAGCGATGCCCTTGATGACTTTGATCTGGACATGCTGGGATCCGATGCTCTTGACGACTTCGACTTGGATATGTTGGGGTCCGATGCACTTGATGATTTTGACCTTGACATGCTGTAA; ATGAAGTGCCTTTTGTACTTAGCCTTTTTATTCATTGGGGTGAATTGCAAGTTCACCATAGTTTTTCCACACAACCAAAAAGGAAACTGGAAAAATGTTCCTTCTAATTACCATTATTGCCCGTCAAGCTCAGATTTAAATTGGCATAATGACTTAATAGGCACAGCCTTACAAGTCAAAATGCCCAAGAGTCACAAGGCTATTCAAGCAGACGGTTGGATGTGTCATGCTTCCAAATGGGTCACTACTTGTGATTTCCGCTGGTATGGACCGAAGTATATAACACATTCCATCCGATCCTTCACTCCATCTGTAGAACAATGCAAGGAAAGCATTGAACAAACGAAACAAGGAACTTGGCTGAATCCAGGCTTCCCTCCTCAAAGTTGTGGATATGCAACTGTGACGGATGCCGAAGCAGTGATTGTCCAGGTGACTCCTCACCATGTGCTGGTTGATGAATACACAGGAGAATGGGTTGATTCACAGTTCATCAACGGAAAATGCAGCAATTACATATGCCCCACTGTCCATAACTCTACAACCTGGCATTCTGACTATAAGGTCAAAGGGCTATGTGATTCTAACCTCATTTCCATGGACATCACCTTCTTCTCAGAGGACGGAGAGCTATCATCCCTGGGAAAGGAGGGCACAGGGTTCAGAAGTAACTACTTTGCTTATGAAACTGGAGGCAAGGCCTGCAAAATGCAATACTGCAAGCATTGGGGAGTCAGACTCCCATCAGGTGTCTGGTTCGAGATGGCTGATAAGGATCTCTTTGCTGCAGCCAGATTCCCTGAATGCCCAGAAGGGTCAAGTATCTCTGCTCCATCTCAGACCTCAGTGGATGTAAGTCTAATTCAGGACGTTGAGAGGATCTTGGATTATTCCCTCTGCCAAGAAACCTGGAGCAAAATCAGAGCGGGTCTTCCAATCTCTCCAGTGGATCTCAGCTATCTTGCTCCTAAAAACCCAGGAACCGGTCCTGCTTTCACCATAATCAATGGTACCCTAAAATACTTTGAGACCAGATACATCAGAGTCGATATTGCTGCTCCAATCCTCTCAAGAATGGTCGGAATGATCAGTGGAACTACCACAGAAAGGGAACTGTGGGATGACTGGGCACCATATGAAGACGTGGAAATTGGACCCAATGGAGTTCTGAGGACCAGTTCAGGATATAAGTTTCCTTTATACATGATTGGACATGGTATGTTGGACTCCGATCTTCATCTTAGCTCAAAGGCTCAGGTGTTCGAACATCCTCACATTCAAGACGCTGCTTCGCAACTTCCTGATGATGAGAGTTTATTTTTTGGTGATACTGGGCTATCCAAAAATCCAATCGAGCTTGTAGAAGGTTGGTTCAGTAGTTGGAAAAGCTCTATTGCCTCTTTTTTCTTTATCATAGGGTTAATCATTGGACTATTCTTGGTTCTCCGAGTTGGTATCCATCTTTGCATTAAATTAAAGCACACCAAGAAAAGACAGATTTATACAGACATAGAGATGAACCGACTTGGAAAGTA
Supplementary files format and content: .xlsx file containing analysis of mapped read proportions.
Library strategy: Amplicon sequencing

extract_protocol:
Total RNA from VLP supernatant extracted. RT-PCR to amplify transgene sequences (amplicons used for library construction).
Sequencing samples were prepared following the recommendations found within the ONT protocol ‘Amplicons by Ligation’ (version ACDE_9110_v110_revV_10Nov2020). DNA concentrations were determined using the Qubit™ dsDNA HS Assay Kit (ThermoFisher, #Q32851) and 200 fmol of DNA was processed using the NEBNext Companion Module for ONT Ligation Sequencing (NEB, #E7180). Sequencing adapters were ligated onto sequences with the Ligation Sequencing Kit (ONT, #SQK-LSK110).


title: kideny,0h,rep2

description: Library name: ZK0-2


title: AC_150_RA

description: Isolated transgenes from Round 1 of eGFP-LUC VLPs, to identify transgene substitutions.


title: F_SEQ028

description: Isolated transgenes from Round E2 of co-packaged SRF-VP64/eGFP-LUC VLPs, to observe transgene proportion.


title: kideny,24h,rep3

description: Library name: ZK3-3


title: kideny,0h,rep1

description: Library name: ZK0-1


title: NSG pancreatic cells 16


title: NSG pancreatic cells 15


title: AC_150_RP

description: Isolated transgenes from Round P (packaging) of eGFP-LUC VLPs, to identify transgene substitutions.


title: F_SEQ027

description: Isolated transgenes from Round E1 of co-packaged SRF-VP64/eGFP-LUC VLPs, to observe transgene proportion.


title: Naive-ALPS-8799

city: Durham

first: Kirit

last: Singh

state: NC

address: Room 215, Sands Building, 303 Research Drive

department: Biomedical Engineering

institute: Duke University

description: Library name: Naive-ALPS-8799

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using fastp v.0.23.1. UMI-based de-duplication was performed using fastp v.0.23.1 simultaneously. Trimmed and de-duplicated reads were then mapped to the Homo sapiens GRCh38 with ERCC genes 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.
Assembly: 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.
Supplementary files format and content: tab-delimited .COUNT txt files
Supplementary files format and content: tab-delimited TPM .csv files

organism: Homo sapiens

source_name: Processed hPBMCs

growth_protocol: Cryopreserved PBMCs were then thawed into PrimeXV T-cell expansion media (FujiFilm) supplemented with 3% of human platelet lysate (hPL, Compass Biomedical) and pelleted at 300g for 10 min. The cell pellet was re-suspended in PrimeXV/3% hPL to a concentration of 1 x 106 cells/ml and 1 x 106 cells plated per well of a G-Rex 6M six well plate (Wilson-Wolf). For each sample, two wells were set up. One was supplemented with IL-2 at 300 IU/ml (BioTechne, BT-002-AFL) and the other was supplemented with IL-7 at 20ng/ml (PeproTech, 200-07). The cells were activated with 100µl a-CD3/a-CD8 nanoparticles (TransAct, Miltenyi, 130-111-160) according to the manufacturers protocol. The plates were incubated at 37⁰C and 5% CO2.

extract_protocol:
PolyA selection for mRNA species performed per vendor methods
30 million paired-end reads per sample for gene expression analysis

value: Processed hPBMCs

value: Sorted CD8+ T cells

value: Naïve


title: NSG pancreatic cells 14


title: Naive-ALPS-8041

description: Library name: Naive-ALPS-8041


title: F_SEQ026

description: Isolated transgenes from Round A (amplification) of co-packaged SRF-VP64/eGFP-LUC VLPs, to observe transgene proportion.


title: AC_213_R4_2

description: Isolated transgenes from Round 4 (E4) of tTA VLPs, to identify transgene substitutions. [Campaign 1]


title: NSG pancreatic cells 13

value: 12 weeks


title: gill,24h,rep2

description: Library name: ZG3-2

source_name: gill

value: gill


title: gill,24h,rep1

description: Library name: ZG3-1


title: OVNR1H3oe3

city: Hefei

first: Yifan

last: Feng

state: Anhui

address: Jixi Road 218

institute: The Anhui Medical University

description: Library name: Sanple 12

data_processing:
Bridge amplification. Bridge PCR amplification was performed on the cBot instrument to generate clusters.
The Illumina sequencing platform uses a 2*150 sequencing mode for Sequencing by Synthesis. Four fluorescently labeled dNTPs, DNA polymerase, and adapter primers are added to the flow cell for amplification. During the extension of the complementary strand in each sequencing cluster, the addition of each fluorescently labeled dNTP releases a corresponding fluorescence. The sequencer captures the fluorescence signals, and computer software converts the light signals into sequencing peaks, thereby obtaining the sequence information of the target fragments.
The image data of sequencing fragments obtained by the high-throughput sequencer are converted into sequence data (reads) through CASAVA base calling, and the files are in fastq format, which mainly contains the sequence information of the sequencing fragments and their corresponding sequencing quality information. The raw data are in fastq format files, which include the base sequences of the reads and their sequencing quality values. Each read is represented by four lines of information: the first line is the unique identifier of the read in Illumina sequencing, the second line is the base sequence, the third line is a + sign followed by the omitted read identifier, and the fourth line is the base quality value.
Assembly: For each sample, the results of reads aligned to the reference genome were used by the StringTie software to assemble transcripts in the sample based on the known transcript location information file as a guide. Transcripts with expression levels equal to 0 were filtered out, and the StringTie-assembled transcripts from all samples were reassembled.
Supplementary files format and content: xls file includes raw counts for each sample

source_name: cell line

extract_protocol:
Total RNA was extracted from cell samples, and a total of 1 μg of RNA was required for mRNA sequencing library construction.
1.mRNA Enrichment  For eukaryotic mRNA, enrichment was performed using Oligo (dT) magnetic beads to isolate poly(A)-tailed mRNA.  2.mRNA Fragmentation  The enriched mRNA was randomly fragmented into short fragments of approximately 200 bp using chemical or enzymatic methods.  3.Strand-Specific cDNA Synthesis  First-strand cDNA was synthesized using fragmented mRNA as a template and random primers for reverse transcription.  During second-strand cDNA synthesis, dTTP in the dNTP mix was replaced with dUTP to enable strand specificity.  4.Adapter Ligation  Double-stranded cDNA was purified using AMPure XP beads.  The cDNA ends were repaired and A-tailed using an End Repair Mix.  Sequencing adapters were ligated to the A-tailed cDNA.  5.Second-Strand cDNA Digestion  USER enzyme was used to digest the second-strand cDNA (containing dUTP), ensuring the final library contained only first-strand cDNA.  6.PCR Enrichment  The cDNA library was amplified by PCR for approximately 15 cycles using primers complementary to the sequencing adapters to enrich the final library.  7.Library Quality Control and Quantification  The quality of the library was assessed using an Agilent Bioanalyzer or similar instrument to confirm the expected fragment size distribution (~200-500 bp).  The library concentration was quantified using qPCR or a fluorometric method (e.g., Qubit) to ensure optimal concentration for sequencing.

value: cell line

value: Ovarian cancer


title: NSG pancreatic cells 12


title: kideny,0h,rep3

description: Library name: ZK0-4


title: F_SEQ030

description: Isolated transgenes from Round E4 of co-packaged SRF-VP64/eGFP-LUC VLPs, to observe transgene proportion.


title: Naive-ALPS-7590

description: Library name: Naive-ALPS-7590


title: NSG pancreatic cells 11


title: OVNR1H3oe2

description: Library name: Sanple 11


title: gill,0h,rep2

description: Library name: ZG0-2


title: OVNR1H3oe1

description: Library name: Sanple 10


title: NSG pancreatic cells 10


title: gill,0h,rep1

description: Library name: ZG0-1


title: gill,24h,rep3

description: Library name: ZG3-4


title: NSG pancreatic cells 9

value: 24 weeks


title: OVNR1H3oenc3

description: Library name: Sanple 9


title: D14-IL-7-ALPS-8041

description: Library name: D14-IL-7-ALPS-8041


title: Naive-ALPS-7906

description: Library name: Naive-ALPS-7906


title: NSG pancreatic cells 8


title: HG-SIG3

city: Lanzhou

first: Xiaoxia

last: Hu

address: No. 222 South Tianshui Road, Lanzhou 730000, Gansu Province, P.R.China

institute: The Second Hospital & Clinical Medical School, Lanzhou University Lanzhou, China

description: Library name: Sample9

data_processing:
SOAPnuke(V2.1.0) was used to filter the sequencing data.
HSAT2(V2.1.0) was used to compare clean reads with the reference genome, and Bowtie2 (V2.3.5)was used to align the quality controlled sequence to thereference transcription sequence.
Using RSEM, the bowtie2 comparison results were used for statistics, and the number of Reads compared to each transcript of each sample was obtained, and FPKM (Fragments Per Kilobase Per Million bases) conversion was performed.
Assembly: mm10
Supplementary files format and content: .xls file includes raw counts for each Sample

extract_protocol:
extract protocol：Total RNA was extracted using the Trizol(Invitrogen, CA, USA) library construction protocol：RNA-seq library preparation using a standard mRNA-Seq protocol with oligo(dT) selection and random hexamer priming.
Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription.followed by a second-strand cDNA synthesis and purified using AMPure XP Beads.Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to endcDNA repair. The cDNA fragments obtained from previous steps were amplified byPCR, and products were purified by Ampure XP Bead, get the final library.After the library was constructed, Qubit 2.0 was used for preliminaryquantification, and the library was diluted to 1.5 ng/pL. Then Agilent 2100 BioAnalyzerwas used to detect the insert size ofthe library. Qrt-pcr was used to accurately quantify the effective concentration of the library to ensure the quality of the library.


title: F_SEQ025

description: Isolated transgenes from Round P (packaging) of co-packaged SRF-VP64/eGFP-LUC VLPs, to observe transgene proportion.


title: OVNR1H3oenc2

description: Library name: Sanple 8


title: HG-SIG2

description: Library name: Sample8


title: D14-IL-7-ALPS-7590

description: Library name: D14-IL-7-ALPS-7590


title: NSG pancreatic cells 7


title: OVNR1H3oenc1

description: Library name: Sanple 7


title: gill,0h,rep3

description: Library name: ZG0-4


title: OVNR1H3si3

description: Library name: Sanple 6


title: D14-IL-2-ALPS-9256

description: Library name: D14-IL-2-ALPS-9256


title: HG3

description: Library name: Sample6


title: NSG pancreatic cells 5

value: 40 weeks


title: D14-IL-7-ALPS-9256

description: Library name: D14-IL-7-ALPS-9256


title: D14-IL-7-ALPS-8799

description: Library name: D14-IL-7-ALPS-8799


title: OVNR1H3si2

description: Library name: Sanple 5


title: HG2

description: Library name: Sample5


title: D14-IL-2-ALPS-8799

description: Library name: D14-IL-2-ALPS-8799


title: OVNR1H3si1

description: Library name: Sanple 4


title: NSG pancreatic cells 4


title: HG1

description: Library name: Sample4


title: NSG pancreatic cells 3


title: D14-IL-2-ALPS-8041

description: Library name: D14-IL-2-ALPS-8041


title: OVNR1H3sinc3

description: Library name: Sanple 3


title: D14-IL-7-ALPS-7906

description: Library name: D14-IL-7-ALPS-7906


title: D14-IL-2-ALPS-7906

description: Library name: D14-IL-2-ALPS-7906


title: HG-SIG1

description: Library name: Sample7


title: NSG pancreatic cells 6


title: D14-IL-2-ALPS-7590

description: Library name: D14-IL-2-ALPS-7590


title: OVNR1H3sinc2

description: Library name: Sanple 2


title: NSG pancreatic cells 2


title: NC2

description: Library name: Sample2


title: NSG pancreatic cells 1


title: NC1

description: Library name: Sample1


title: OVNR1H3sinc1

description: Library name: Sanple 1


title: BG01 cells, anti-M8nAb, 24h, biol rep 1

status: Public on Apr 02 2025

city: Seoul

first: Jong-Hoon

last: Kim

address: 145 Anam-ro, Seongbuk-gu

department: Biotechnology

country: South Korea

institute: Korea University

data_processing:
Data were processed using Illumina HiSeq 1500.
Briefly, raw reads were filtered through several steps; removing reads with adaptors, removing reads when unknown bases are more than 10%, and have low quality. After filtering, the remaining reads are stored as FASTQ format.
We checked read quality for each sample using FastQC v0.11.9.
Raw reads were trimmed using Trimmomatic. Trimmed reads were aligned to the human genome (GRCh38.p14) according to the STAR 2-pass method.
Duplicated reads were eliminated using Picard Markduplicate and filtered reads were then processed for variant calling using the GATK. This process include realignment of insertion and deletion, recalibration of base quality score, and haplotypecaller.
According to Ensembl gene set, the reads aligned to the genes using HTseq.
FPKM (fragments per kilo base of exon per million mapped reads) for each sample were calculated by RNAnorm.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

growth_protocol: BG01 human embryonic stem cells were maintained in mTeSR supplemented with antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated from BG01 cells treated with isotype IgG or anti-M8nAb using Trizol reagent according to the manufacturer's instructions.
Libraries were prepared for RNA-seq by using Illumina RNA-seq platform. All procedures were proceeded by Beijing Genomics Institute (BGI) corporation.

treatment_protocol: Cells were treated with isotype IgG (normal mouse IgG for control) or anti-M8nAb (anti-MFG-e8 neutralizing antibody) for 12 hours or 24 hours.

value: Human embryonic stem cells

value: anti-M8nAb for 24 hours


title: BG01 cells, Isotype IgG, 24h, biol rep 1

value: Isotype IgG for 24 hours


title: BG01 cells, anti-M8nAb, 24h, biol rep 2


title: BG01 cells, anti-M8nAb, 12h, biol rep 2

value: anti-M8nAb for 12 hours


title: AC_211_R15

description: Isolated transgenes from Round 15 (E15) of rtTA-3G VLPs, to identify transgene substitutions.


title: BG01 cells, Isotype IgG, 24h, biol rep 2


title: BG01 cells, anti-M8nAb, 12h, biol rep 1


title: BG01 cells, Isotype IgG, 12h, biol rep 1

value: Isotype IgG for 12 hours


title: NC3

description: Library name: Sample3


title: Chip with HP1BP3, SET siRNA

city: Minato-Ku

first: Mitsuru

last: Okuwaki

state: Tokyo

address: 5-9-1 Shirokane, Minato-ku

country: Japan

institute: Kitasato University

library_source: genomic

data_processing:
FASTQ files were pre-processedusing fastp (Galaxy Version 0.23.2+galaxy0).
Reads were aligned to the hg38 human genome using Bowtie 2(Galaxy Version 2.5.3+galaxy1, --very-sensitive).
To remove multi-mapped, PCR-duplicated, andmitochondrial reads, samtools was used: samtools sort (Galaxy Version 2.0.5), samtoolsview (Version 1.18, -e 'rname != "chrM"' -F 0x4 -q 40), samtoolsfixmate (Version 1.18, -m), and samtools markdup (Galaxy Version 1.15.1+galaxy2,-r).
For visualization on IGV (Integrative Genomics Viewer, version2.8.7), aligned reads (BAM files) were converted to bigWig files using thebamCoverage function of deepTools (normalized as CPM (Counts Per Million),Galaxy Version 3.5.4+galaxy0).
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: HeLa S3

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% FBS at 37°C in an incubator containing 5% CO2.

extract_protocol:
The fixed cells were suspended in lysis buffer and extensively sonicated. The length of DNA extracted from the cell extracts were confirmed to be between 200 and 500 base pairs.
The purified DNA (50 ng) was used for library construction using ChIP-Seq library preparation kit (ThruPLEX DNA-Seq kit, Takara Bio) according to the manufacturers’ instruction

treatment_protocol: HeLa cells were transfected with control siRNA, NPM1 siRNA, and SET siRNA. The cells were replated to fresh dishes 24 h post siRNA transfection and incubated additional 48 h. Then, the cells were fixed with 0.5% formardehyde and Chip assay was conducted.

value: HeLa S3

tag: antibody

value: SET siRNA


title: BG01 cells, Isotype IgG, 12h, biol rep 2


title: Chip with HP1BP3, NPM1 siRNA

value: NPM1 siRNA


title: Chip with H1.2, control siRNA

value: control siRNA


title: Chip with HP1BP3, control siRNA


title: Input DNA


title: BBS2_ATMi_2

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5690 rosemont boulevard

country: Canada

institute: HMR

data_processing:
Base-calling and feature count were done using HISAT2.
Assembly: HG19
Supplementary files format and content: excel file containing the count extracted from HISAT2.

source_name: DIV15 RPCs

growth_protocol: Briefly, iPSCs were dissociated using TrypLE (Gibco™ Express Enzyme (1X), no phenol red, CAT# 12604013) and platted on growth factor reduced Matrigel (Corning #356231), in StemFit™ Basic04CT (Complete Type) Culture Medium (CAT# ASB04CT) with adding ROCK inhibitor (Y-27632;10 µM, Cayman Chemical #10005583) for 24 hrs then the media has changed without ROCK inhibitor. Upon confluency, cells were differentiated with CI media: DMEM-F12 medium (Invitrogen) containing 1% N2, 2% B27, 10 ng/ml IGF1 (PeproTech, Cat#100-11), and 5 ng/ml bFGF (PeproTech, Cat#AF-100-18B), Heparin (Sigma, Cat#H3149), and 30 ng/ml COCO (R&D System, Cat#3047-CC-050) 36.

extract_protocol:
RNA was extracted using the standard procedure of Qiagen columns and assayed for RNA integrity
cDNA was prepared according to the manufacturer's instructions (NEB library) and sequenced using the Illumina platform

value: DIV15 RPCs

value: ATMi


title: BBS1_ATMi_2


title: BBS2_ATMi_1


title: BBS2_C2i_1


title: BBS1_ATMi_1


title: BBS1_2


title: BBS1_C2i_2


title: BBS2_1


title: BBS1_1


title: BBS1_C2i_1


title: CTL2_1

value: CTL


title: BBS2_C2i_2


title: CTL1_1


title: CTL2_2


title: Chip with H1.2, SET siRNA


title: Chip with H1.2, NPM1 siRNA


title: CTL1_2


city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description: Library name: TSA-seq CENPB in H1 cells, condition2 - conditionE - anti-CENPB, Bio rep 1, Tech rep 1

data_processing:
TSA_Seq_v1_protocol: Chen et al. 2018 (doi:10.1083/jcb.201807108), TSA Seq v2 and modifications related to application of TSA-Seq to adherent cells, see Zhang et al. 2019 (doi: https://doi.org/10.1101/824433)
Assembly: GRCh38
Supplementary files format and content: File type: normalized counts (bw) Description: Bigwig file format

source_name: stem cell

growth_protocol: H1-ESC (WA01), HFF-hTert-Clone 6 cells and HCT116 were obtained thorough the 4D Nucleome Consortium and were cultured according to the 4DN SOPs (https://www.4dnucleome.org/cell-lines.html). K562 cells were obtained from the ATCC and were cultured according to the ENCODE Consortium protocol (http://genome.ucsc.edu/ENCODE/protocols/cell/human/K562_protocol.pdf).

extract_protocol:
Nucleolar and PCH TSA-Seq was performed using either Condition C (labeling with 1:3000 tyramide biotin, 50% sucrose and 0.0015% hydrogen peroxide) or Condition E (labeling with 1:300 tyramide biotin, 50% sucrose and 0.0015% hydrogen peroxide) with the following minor modification: 150ul of Dynabeads M-270 streptavidin (Invitrogen, catalog no. 65306) was used to purify the biotinylated DNA. LMNB1 TSA-seq was performed using Condition AI for HFFc6, H1, and K562 and Condition A for HCT116 cells. POL1RE and MKI67IP TSA-Seq, raw sequencing reads were mapped to the Telomere-to-Telomere (version 1.1).
Libraries were constructed using Illumina’s TruSeq DNA PCR-free Library Preparation kit (350 bp), and fragments were size-selected by sample-purifying beads. 150 bp paired-end sequencing was performed using the Illumina HiSeq X Ten sequencing system.

treatment_protocol: Lamin B1 TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition AI (1:10000 tyramide-biotin, 20 minute reaction) on k562 cells replicate 1

value: stem cell

value: Stem cell derived cell line

value: anti-CENP-B

tag: target

value: CENPB protein

tag: donor sex

value: male

tag: donor lifestage

value: embryonic

tag: donor health_status

value: healthy

value: condition2 - conditionE - anti-CENPB

tag: experiment url

tag: experiment replicate_info

value: Bio rep 1, Tech rep 1

tag: biosample url


description: Library name: TSA-seq CENPB in H1 cells, condition2 - conditionE - anti-CENPB, Bio rep 2, Tech rep 1

tag: tissue

tag: cell type

tag: treatment

value: Bio rep 2, Tech rep 1


title: C666-1, ctrl5

city: Huai'an

first: Xingchen

last: Dong

state: Jiangsu Province

address: No.1 Huanghe West Road

department: Department of Otorhinolaryngology

institute: Huai'an No.1 People's Hospital

description: Library name: ctrl5

data_processing:
Raw data were quality controlled and filtered using fastp (v0.20.0)
Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 (v2.1.0)
Gene expression levels were quantified using featureCounts (v2.0.0)
Differential expression analysis was performed using DESeq2 (v1.30.0), with genes having |log2FC|> 1.5 and padj<0.05 considered significantly differentially expressed
GO and KEGG enrichment analyses were performed using clusterProfiler (v3.18.0)
Assembly: GRCh38/hg38
Supplementary files format and content: Comma-delimited text files containing raw counts data for each sample

source_name: nasopharyngeal carcinoma

growth_protocol: C666-1 cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum and 1% penicillin-streptomycin. All cells were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent. RNA concentration and purity were determined by spectrophotometry, and RNA integrity was detected using an Agilent 2100 Bioanalyzer, ensuring RIN values >8.0.
The NEBNext Ultra RNA Library Prep Kit for Illumina was used to construct mRNA libraries. Steps included mRNA enrichment, RNA fragmentation, cDNA first and second strand synthesis, end repair, adapter ligation, fragment selection, and PCR amplification.

treatment_protocol: C666-1 cells were treated with 2nM BAY2402234 dissolved in DMSO for 48 hours. The control group received an equal volume of DMSO (final concentration <0.1%).

value: nasopharyngeal carcinoma

tag: cell line

value: nasopharyngeal carcinoma cells

tag: genotype

value: WT

value: DMSO(final concentration <0.1%)


title: C666-1, ctrl3

description: Library name: ctrl3


title: endometrium_control_1

type: RNA

city: Chapel Hill

first: Melinda

middle: S

last: Yates

address: 160 Medical Drive

institute: University of North Carolina at Chapel Hill

description: Gene expression data from benign endometrium in control mouse

hyb_protocol: Following fragmentation, ss-DNA were hybridized according to GeneChip WT Pico Reagent Kit User Guide (Pub. No. MAN0017893 B.0) on GeneChip Mouse Genome Array.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with RMA-Sketch algorithm using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Control mouse 20B benign endometrium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA in GeneChip WT Pico Reagent Kit User Guide (Pub. No. MAN0017893 B.0)

extract_protocol: Total RNA was extracted using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) according to manufacturer's instructions.

treatment_protocol: Harvested uterine tissue from Msh2KO and control mice were embedded in optimal cutting temperature compound (OCT) and rapidly frozen on dry ice. Tissue sections were fixed in 70% ethanol then microdissected using laser-capture microdissection technology, which enabled isolation of regions of interest.

value: microdissected endometrial glands

value: Control

tag: tissue category

value: Benign


title: endometrium_control_2

source_name: Control mouse 50 benign endometrium


title: C666-1, ctrl1

description: Library name: ctrl1


title: Lichen planus 5

city: Paris

first: Chloé

last: Grolleau

address: 1 avenue Claude Vellefaux

department: Hopital saint Louis

country: France

institute: INSERM U1342, eq 16

description: Library name: LP5

library_source: transcriptomic single cell

data_processing:
All provided R1 and R2 FASTQ files are already demultiplexed by sample index.
Data pre-processing (read quality control, extraction, alignment, deduplication and assignment) was performed from raw FASTQ files to count matrices using Cytonaut v1.4 (https://cytonaut-scipio.bio) with Cytonaut's pre-processing module v6.12.6.
Detection of cell-associated barcodes was done for each sample by applying the distance-based knee method of UMI-tools double-checked by manual inspection.
The provided processed data is composed of one count matrix per sample at full sequencing depth.
Data post-processing (filtering, normalization, HVG, batch correction, PCA, 2D embedding, clustering, DGE) was performed using Seurat v4.3.0.1 and cell annotation was performed manually based on markers found in the literature for cell types typically present in the human skin. Pseudo-time analysis was performed using Monocle v3.0.
Assembly: The reference genome sequences and annotations are based on Ensembl release v99 for human species (GRCh38). Unique Genome Name in Cytonaut v6.7.0: Human_Scipio_2022_A; Species: Homo_sapiens; Genome Source: ensembl; Genome Version: GRCh38; Genome Link: ftp.ensembl.org//pub/release-99/fasta/homo_sapiens/dna/; Annotation Source: ensembl; Annotation Version: 99; Annotation Link: ftp.ensembl.org//pub/release-99/gtf/homo_sapiens/
Supplementary files format and content: Tab Separated Values (TSV format) including all count matrix information (genes in first column, then one column per cell-associated barcode)

source_name: skin

extract_protocol:
5 patients with active cutaneous lichen planus were recruited for this study and contributed for 4mm skin biopsies. 4 healthy controls were recruited for skin biopsy from plastic breast surgery waste. The study was approved by the by our institutional ethic committee (Comité de Protection des Personnes Ile de France IV), and all patients were consented. Skin biopsies were transferred in NaCl 9‰ and immediately digested for 4h30 at 37°C using whole skin dissociation kit (Miltenyi) according to the manufacturer protocol. Single cell suspension obtained was then processed with Asteria kit (Scipio Bioscience) with 30,000 cells input in 2 kits for each sample to generate 3' enriched cDNA with corresponding cell barcode.
The cell barcoded cDNA was fragmented, end-repaired then adapter was ligated to the extremities using NEBNext Ultra II FS DNA libary kit for illumina. Selective amplification of cDNA fragment containing the cell barcode was done with custum P5-R1 library primer from Asteria kit and indexed P7-R2 primier from NEBNext Mulitplex Oligos kit. Libraries were sequenced on the illumina NovaSeq 6000 sequencer to generate paired-end read. 25 bases for read1 and 70 bases for read2. read1 contains cell barcode and read2 contains 3' sequence of cDNA.

value: skin


title: C666-1, ctrl4

description: Library name: ctrl4


title: C666-1, BAY4

description: Library name: BAY4

value: 2nM BAY2402234 dissolved in DMSO


title: C666-1, BAY5

description: Library name: BAY5


title: endometrium_control_3

source_name: Control mouse 424 benign endometrium


title: endometrium_Msh2KO_2

description: Gene expression data from benign endometrium in Msh2KO mouse

source_name: Msh2KO mouse 26 benign endometrium


title: tumor_Msh2KO_7

description: Gene expression data from endometrial tumors developed in Msh2KO mouse

source_name: Msh2KO mouse 369 uterine tumor

value: Tumor


title: C666-1, BAY3

description: Library name: BAY3


title: C666-1, BAY1

description: Library name: BAY1


title: endometrium_control_4

source_name: Control mouse 1006 benign endometrium


title: endometrium_Msh2KO_3

source_name: Msh2KO mouse 40A benign endometrium


title: endometrium_Msh2KO_5

source_name: Msh2KO mouse 403 benign endometrium


title: C666-1, ctrl2

description: Library name: ctrl2


title: tumor_Msh2KO_2

source_name: Msh2KO mouse 31 uterine tumor


title: endometrium_Msh2KO_6

source_name: Msh2KO mouse 420 benign endometrium


title: tumor_Msh2KO_5

source_name: Msh2KO mouse 10 uterine tumor


title: tumor_Msh2KO_3

source_name: Msh2KO mouse 39 uterine tumor


title: SOC97T-O MAF

city: Goyang-si

first: Mi Rim

last: Lee

address: 323, Ilsan-ro

institute: National Cancer Center Research Institute

description: Library name: SOC97T-O

library_source: other

data_processing:
Raw sequencing reads were assessed using FastQC for quality control. Low-quality reads and adapter sequences were removed using Trimmomatic. Clean reads were aligned to the human reference genome (GRCh38) using BWA-MEM. Picard was used to mark PCR duplicates, and GATK was used for base recalibration and quality score adjustment.
Somatic variant calling was performed using Mutect2 (GATK) on matched tumor-normal BAM file pairs. Filtering was conducted using germline resource (af-only-gnomad.vcf) and additional filters to remove false positives. Filtered somatic variants were annotated with SnpEff, dbSNP, and the 1000 Genomes Project database. Additional annotations were added using in-house scripts with databases such as ESP6500, ClinVar, dbNSFP, and ACMG.
mutation annotation format file generated using the R package maftools for downstream visualization and analysis
Assembly: GRCh38
Supplementary files format and content: OSCC organoid_maftools.maf

molecule: other

source_name: oral squamous cell carcinoma

extract_protocol:
Genomic DNA was extracted from cell lines using standard phenol-chloroform extraction or commercial kits, followed by RNase treatment. DNA concentration and purity were measured using PicoGreen (Thermo Fisher Scientific), and integrity was confirmed by agarose gel electrophoresis.
To generate standard exome capture libraries, we used the Agilent SureSelectXT Low Input Target Enrichment protocol for Illumina paired-end sequencing with 1 μg of input genomic DNA. DNA was diluted in EB Buffer and sheared to 150–200 bp using the Covaris LE220 focused-ultrasonicator. Fragmented DNA underwent end-repair, A-tailing, and ligation with Agilent adapters. After PCR amplification and purification, libraries were quantified using the Agilent TapeStation with DNA Screentape D1000. For exome capture, 250 ng of DNA library was hybridized with SureSelect all exon capture probes and subjected to post-capture wash, amplification, and purification. Final libraries were quantified by qPCR (KAPA Library Quantification Kit) and TapeStation.

value: oral squamous cell carcinoma

value: organoid


title: tumor_Msh2KO_6

source_name: Msh2KO mouse 21B uterine tumor


title: SOC119T-O MAF

description: Library name: SOC119T-O


title: tumor_Msh2KO_4

source_name: Msh2KO mouse 41 uterine tumor


title: SOC99T-O MAF

description: Library name: SOC99T-O


title: SOC88T-O MAF

description: Library name: SOC88T-O


title: endometrium_Msh2KO_4

source_name: Msh2KO mouse 41A benign endometrium


title: SOC70T-O MAF

description: Library name: SOC70T-O


title: endometrium_Msh2KO_1

source_name: Msh2KO mouse 8 benign endometrium


title: tumor_Msh2KO_1

source_name: Msh2KO mouse 17 uterine tumor


title: SOC26T-O MAF

description: Library name: SOC26T-O


title: SOC23T-O MAF

description: Library name: SOC23T-O


title: SOC34T-O MAF

description: Library name: SOC34T-O


title: SOC68T-O MAF

description: Library name: SOC68T-O


title: SOC44T-O MAF

description: Library name: SOC44T-O


title: SOC22T-O MAF

description: Library name: SOC22T-O


title: SOC49T-O MAF

description: Library name: SOC49T-O


title: SOC42T-O MAF

description: Library name: SOC42T-O


title: SOC65T-O MAF

description: Library name: SOC65T-O


title: SOC14T-O MAF

description: Library name: SOC14T-O


title: SOC17T-O MAF

description: Library name: SOC17T-O


title: SOC6T-O MAF

description: Library name: SOC6T-O


title: SOC63T-O MAF

description: Library name: SOC63T-O


title: SOC50T-O MAF

description: Library name: SOC50T-O


title: OC182T-O MAF

description: Library name: OC182T-O


title: OC179T-O MAF

description: Library name: OC179T-O


title: OC139T-O MAF

description: Library name: OC139T-O


title: OC133T-O MAF

description: Library name: OC133T-O


title: OC109T-O MAF

description: Library name: OC109T-O


title: OC80T-O MAF

description: Library name: OC80T-O


title: OC84T-O MAF

description: Library name: OC84T-O


title: OC71T-O MAF

description: Library name: OC71T-O


title: OC59T-O MAF

description: Library name: OC59T-O


title: OC53T-O MAF

description: Library name: OC53T-O


title: OC60T-O MAF

description: Library name: OC60T-O


title: OC44T-O MAF

description: Library name: OC44T-O


title: OC37T-O MAF

description: Library name: OC37T-O


title: OC25T-O MAF

description: Library name: OC25T-O


title: OC40T-O MAF

description: Library name: OC40T-O


title: R1797D

city: Madison

first: Tracy

last: Hagemann

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin-Madison

data_processing:
Base calling was performed using Bcl2fastq (v2.20.0.422), read trimming with Skewer (Jiang et al., 2014), read alignment with STAR (Dobin et al., 2013), expression estimation with RSEM (Li and Dewey, 2011), and differential expression estimation with EdgeR (Robinson et al., 2010).
Assembly: Rn7
Supplementary files format and content: tab-deliminated text file including rsem counts for each sample
Supplementary files format and content: tab-deliminated text file including TPM for each sample

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
RNA was prepared using Trizol (Invitrogen) according to the manufacturer's protocol.
Libraries were prepared using TruSeq Stranded mRNA Reagent with polyA enrichment.

value: hippocampus

tag: Sex

value: female

tag: background strain


title: R1790C

tag: age


title: OC15T-O MAF

description: Library name: OC15T-O


title: SOC119T-O RNA-seq

description:
Library name: SOC119T-O
SOC119T-O

data_processing:
Raw FASTQ files were quality checked using FastQC.
Adapter trimming was performed using Trimmomatic.
Trimmed reads were aligned to the human reference genome (GRCh38) using HISAT2 and Bowtie2.
Transcript assembly and quantification were performed using StringTie.
Assembly: GRCh38
Supplementary files format and content: organoid_count_data.csv file contains gene-level read counts. Rows are genes, columns are sample IDs matching the library name.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.


title: R1796A

value: Gfap+/+


title: R1789B


title: R1790B


title: R1790A


title: OC144T-O MAF

description: Library name: OC144T-O


title: SOC99T-O RNA-seq

description:
Library name: SOC99T-O
SOC99T-O


title: R1797C


title: OC122T-O MAF

description: Library name: OC122T-O


title: SOC97T-O RNA-seq

description:
Library name: SOC97T-O
SOC97T-O


title: OC62T-O MAF

description: Library name: OC62T-O


title: SOC88T-O RNA-seq

description:
Library name: SOC88T-O
SOC88T-O


title: OC56T-O MAF

description: Library name: OC56T-O


title: R1789A


title: R1781I

value: male


title: SOC68T-O RNA-seq

description:
Library name: SOC68T-O
SOC68T-O


title: SOC70T-O RNA-seq

description:
Library name: SOC70T-O
SOC70T-O


title: R1781H


title: R1781G


title: R1781F


title: OC38T-O MAF

description: Library name: OC38T-O


title: R1781D


title: R1781E


title: SOC63T-O RNA-seq

description:
Library name: SOC63T-O
SOC63T-O


title: s71-D-Hip


title: s70-C-Hip


title: R1781C


title: s70-A-Hip


title: SOC23T-O RNA-seq

description:
Library name: SOC23T-O
SOC23T-O


title: R1781A


title: s70-B-Hip


title: SOC42T-O RNA-seq

description:
Library name: SOC42T-O
SOC42T-O


title: SOC14T-O RNA-seq

description:
Library name: SOC14T-O
SOC14T-O


title: SOC34T-O RNA-seq

description:
Library name: SOC34T-O
SOC34T-O


title: OC182T-O RNA-seq

description:
Library name: OC182T-O
OC182T-O


title: SOC44T-O RNA-seq

description:
Library name: SOC44T-O
SOC44T-O


title: s69-D-Hip


title: SOC49T-O RNA-seq

description:
Library name: SOC49T-O
SOC49T-O


title: s69-B-Hip


title: SOC17T-O RNA-seq

description:
Library name: SOC17T-O
SOC17T-O


title: s69-C-Hip


title: s69-A-Hip


title: OC174T-O RNA-seq

description:
Library name: OC174T-O
OC174T-O


title: SOC6T-O RNA-seq

description:
Library name: SOC6T-O
SOC6T-O


title: SOC65T-O RNA-seq

description:
Library name: SOC65T-O
SOC65T-O


title: OC144T-O RNA-seq

description:
Library name: OC144T-O
OC144T-O


title: s66-B-Hip


title: OC139T-O RNA-seq

description:
Library name: OC139T-O
OC139T-O


title: s66-A-Hip


title: s66-D-Hip


title: SOC22T-O RNA-seq

description:
Library name: SOC22T-O
SOC22T-O


title: SOC50T-O RNA-seq

description:
Library name: SOC50T-O
SOC50T-O


title: s65-C-Hip


title: s65-A-Hip


title: OC133T-O RNA-seq

description:
Library name: OC133T-O
OC133T-O


title: OC109T-O RNA-seq

description:
Library name: OC109T-O
OC109T-O


title: s65-B-Hip


title: s64-B-Hip


title: OC84T-O RNA-seq

description:
Library name: OC84T-O
OC84T-O


title: OC122T-O RNA-seq

description:
Library name: OC122T-O
OC122T-O


title: OC60T-O RNA-seq

description:
Library name: OC60T-O
OC60T-O


title: SOC26T-O RNA-seq

description:
Library name: SOC26T-O
SOC26T-O


title: s64-A-Hip


title: shPDE12_1

city: beijing

first: Li-Na

last: Zhang

address: College of Chemistry and Life Science

institute: Beijing University of Technology

description:
Library name: sample 4
SH group, replicate biosample 1

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

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


title: OC56T-O RNA-seq

description:
Library name: OC56T-O
OC56T-O


title: shNC_1

description:
Library name: sample 1
NC group, replicate biosample 1

value: shNC


title: OC71T-O RNA-seq

description:
Library name: OC71T-O
OC71T-O


title: OC62T-O RNA-seq

description:
Library name: OC62T-O
OC62T-O


title: OC53T-O RNA-seq

description:
Library name: OC53T-O
OC53T-O


title: shNC_3

description:
Library name: sample 3
NC group, replicate biosample 3


title: shNC_2

description:
Library name: sample 2
NC group, replicate biosample 2


title: shPDE12_3

description:
Library name: sample 6
SH group, replicate biosample 3


title: shPDE12_2

description:
Library name: sample 5
SH group, replicate biosample 2


title: HHst.28 NTN1-GFP negative optic fissure cells, replicate 5

city: Midlothian

first: Joe

last: Rainger

state: Scotland

address: Easter Bush Campus

department: The Division of Functional Genetics and Development

institute: The Roslin Institute

data_processing:
Sequencing quality was evaluated using FASTQC (version 0.11.4). Sequencing adaptors were trimmed using Cutadapt (Martin, 2011) (version 1.16) and Trimmgalore (version 0.4.1). Trimmed sequences were aligned to the chicken genome (GRCg6a) using STAR (version 2.7.1a) to generate binary alignment and map (BAM) files, which were then coordinate sorted and indexed using Samtools.
A count matrix of transcripts annotated in Ensembl (version 105) was subsequently generated from BAM files using featureCounts of the Subread package.
Assembly: GRCg6a
Supplementary files format and content: tab-delimited file of count matrix containing the transcript raw counts, aligned to genes enlisted on Ensembl (version 105), of each sample.

organism: Gallus gallus

source_name: Optic fissure

growth_protocol: Optic fissure tissue from gene edited NTN1-T2A-GFP Hy-Line chicken embryos at Hamburger-Hamilton stage 28 were pooled for each biological replicate.

extract_protocol:
Dissociated GFP+ve and GFP-ve cells were immediately processed for total RNA isolation using PicoPure RNA isolation kit (Articus, Thermo), applying the DNaseI step.
Libraries were prepared from 7 ng of total-RNA samples using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB), according to the provided protocol.

treatment_protocol: Optic fissure tissue was dissected and cells were dissociated. Dissociated cells were separated into GFP positive (GFP+ve) and GFP negative (GFP-ve) populations using a Bigfoot cell sorter.

value: Optic fissure

tag: developmental stage

value: Hamburger-Hamilton stage 28

value: GFPneg

value: Heterozygous for NTN1T2A-eGFP/+


title: OC44T-O RNA-seq

description:
Library name: OC44T-O
OC44T-O


title: OC59T-O RNA-seq

description:
Library name: OC59T-O
OC59T-O


title: HHst.28 NTN1-GFP negative optic fissure cells, replicate 4


title: OC40T-O RNA-seq

description:
Library name: OC40T-O
OC40T-O


title: HHst.28 NTN1-GFP negative optic fissure cells, replicate 3


title: OC38T-O RNA-seq

description:
Library name: OC38T-O
OC38T-O


title: OC37T-O RNA-seq

description:
Library name: OC37T-O
OC37T-O


title: OC25T-O RNA-seq

description:
Library name: OC25T-O
OC25T-O


title: HHst.28 NTN1-GFP negative optic fissure cells, replicate 1

description: The separate count matrices of the two technical replicates of the sample, as well as the merged count matrix, were provided.


title: OC80T-O RNA-seq

description:
Library name: OC80T-O
OC80T-O


title: HHst.28 NTN1-GFP negative optic fissure cells, replicate 2


title: OC15T-O RNA-seq

description:
Library name: OC15T-O
OC15T-O


title: N3

city: Shijiazhuang

first: Jia'xiang

last: Wu

address: Shijiazhuang 050011,China

institute: The Fourth Hospital of Hebei Medical University

description: Library name: Sample 6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time, Q20, Q3 0 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired- end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The circRNA were detected and identified using find_ circ (Memczak et al.,2013) and CIRI2 (Gao et al.,2017). Circos software was used to construct the circos figure.
The raw counts were first normalized using TPM (Zhou et al.,2010) Normalized expression level=(readCount*1,000,000)/libsize (libsize is the sum of circRNA readcount).
Assembly: Homo_sapiens.GRCh38 version108
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Adjacent normal

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, the linear RNA was digested with 3U of RNase R (Epicentre, USA) per µg of RNA. The sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250-300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 ul USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 ° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High- Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5 ng/ul, and the insert size of the library is detected by 5Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2 nM) to ensure the quality of the library. After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis).

value: Adjacent normal


title: HHst.28 NTN1-GFP positive optic fissure cells, replicate 5

value: GFPpos


title: HHst.28 NTN1-GFP positive optic fissure cells, replicate 4


title: HHst.28 NTN1-GFP positive optic fissure cells, replicate 3


title: Normal N treated roots of WT rep3

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

data_processing:
RNA-seq reads were mapped to the P. trichocarpa genome v.3.1 using TopHat.
Differentially expressed genes (DEGs) were identified using the DESeq2 package in R. Fold change ≥ 2 and FDR < 0.05 were required for DEGs to be considered significant.
Gene Ontology (GO) enrichment analysis was carried out using the AmiGO Term Enrichment Tool (http://bioinfo.cau.edu.cn/agriGO/index.php) with a Fisher’s exact test result with corrected P < 0.05 considered significantly enriched.
Assembly: Ptrichocarpa_533_v4.0.fa
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Populus ussuriensis

source_name: root

growth_protocol: Clonally propagated in vitro Populus ussuriensis plants were maintain in woody plant medium (WPM) with 25 g/L sucrose and 6 g L-1 agar with 16 h/8 h day/night photoperiod at 24-26 ℃.

extract_protocol:
Roots were  harvested before total RNA extraction using the method of CTAB. Library construction and sequencing were performed by Biomarker Technologies (Beijing, China) and Bioacme Technologies (Wuhan, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Selected top one internodes of in vitro propagated WT and PuHox52-OE plants, which were grown on WPM for 6 d to develop consistently, and then choose consistently developed plants for the subsequent normal-N and low-N for 3 wks.

value: root

value: tissue seedling

tag: time

value: WT

value: Normal N


title: Normal N treated roots of PuHox52-OE rep1


title: A13098-NSC-Control-04h

city: McAllen

first: Satish

last: Kumar

state: Texas

address: 5300 North L Street (MBMRF-2.219)

department: Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine

institute: University of Texas Rio Grande Valley

description: Library name: Sample 24

data_processing:
Raw fastq sequence files were generated and demultiplexed using Illumina bcl2fastq software (Illumina, Inc., San Diego, CA, USA).
The aligned reads were filtered based on read quality metrics and only high-quality aligned sequencing reads were retained and quantified using NGS software v4.1 (Strand Life Sciences Pvt. Ltd., Bangalore, India).
The aligned reads were filtered based on read quality metrics and only high-quality aligned sequencing reads were retained and quantified using NGS software v4.1 (Strand Life Sciences Pvt. Ltd., Bangalore, India).
The gene expression values as raw counts of sequencing reads were obtained and log2 transformation and ‘DESeq’ normalization was applied.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of raw sequencing read counts formatted as genes-vs-samples matrix table.

source_name: iPSC-derived neural stem cells

growth_protocol: Existing validated iPSCs were differentiated into a highly uniform population of NSCs using a commercially available Gibco PSC neural induction medium (Thermo Fisher Scientific, Waltham, MA, USA) and following the manufacturer's instructions. Briefly, the iPSCs maintained in feeder-free conditions were dissociated and then seeded as 50 – 200 µm size cell aggregates in a Geltrex (Thermo Fisher Scientific, Waltham, MA, USA) coated tissue culture vessel and mTeSR-1 medium (Stem Cell Technologies Inc., Cambridge, MA, USA) supplemented with 10 µM ROCK inhibitor Y27632 (ATCC, Manassas, VA, USA). The iPSCs were seeded at a cell density that reached 15-25%  cell confluency after 24 hours when the cell culture medium was switched to Gibco PSC neural induction medium (Thermo Fisher Scientific, Waltham, MA, USA). Thereafter medium was changed every other day. On day 7, the differentiated NSCs were dissociated with Stem Pro Accutase (Thermo Fisher Scientific, Waltham, MA, USA) and then reseeded in a Geltrex-coated six-well tissue culture plate(s), and at a cell density of 0.1 million/cm2. The seeded NSCs were cultured in an NSC expansion medium containing 50% Neurobasal medium, 50% Advanced DMEM/F12, and 1X neural induction supplement (all from Thermo Fisher Scientific, Waltham, MA, USA) until reaching confluence. The NSC expansion medium was supplemented with 5 µM ROCK inhibitor Y27632 (ATCC, Manassas, VA, USA) for the first 24 hours. The generated NSCs from passage one were used for characterization and all downstream Mojave Type A rattlesnake venom stress challenge experiments.

extract_protocol:
Total RNA from both control and venom-challenged NSCs was extracted using a commercially available RNeasy Mini Kit (Qiagen, Germantown, MD, USA) and by following the manufacturer’s instructions. RNA quality and quantity were assessed using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and an Agilent 2200 TapeStation system (Agilent, Santa Clara, CA, USA).
1 µg of high-quality total RNA per sample and the reagents supplied in Illumina Stranded mRNA sample preparation kit v2 (Illumina, Inc., San Diego, CA, USA) were used to prepare mRNA sequencing libraries.

treatment_protocol: Validated, low-passage NSCs were seeded in Geltrex (Thermo Fisher Scientific, Waltham, MA, USA) -coated tissue culture vessel at a cell density that reached 70 – 80 % confluency in 24 hours. During the first 24 hours, the NSCs were cultured in the NSC expansion medium consisting of 50% Neurobasal medium, 50% Advanced DMEM/F12, and 1X neural induction supplement (all from Thermo Fisher Scientific, Waltham, MA, USA) along with 5 µM ROCK inhibitor Y27632 (ATCC, Manassas, VA, USA). Subsequently, when the cells reached 70-80% confluency, the medium was replaced with the NSC expansion medium containing vehicle-control (phosphate buffered saline), 10 µg/mL, and 30 µg/mL Mojave Type A rattlesnake venom (obtained from National Natural Toxins Research Center/NNTRC, Kingsville, USA), respectively. Half of the NSC cultures for each treatment (i.e., vehicle-control, 10 µg/mL, and 30 µg/mL venom challenge) were harvested after 4 hours, and the other half after 24 hours.

value: iPSC-derived neural stem cells

value: neural stem cell

value: vehicle-treated for 04 hours (Control)


title: C3

description: Library name: Sample 3

source_name: Esophageal squamous cell carcinoma

value: Esophageal squamous cell carcinoma


title: C2

description: Library name: Sample 2


title: Normal N treated roots of PuHox52-OE rep2


title: HHst.28 NTN1-GFP positive optic fissure cells, replicate 1


title: N2

description: Library name: Sample 5


title: A13098-NSC-MRV10µg/ml-04h

description: Library name: Sample 22

value: 10 µg/mL Mojave Type A rattlesnake venom 04 hours


title: A13098-NSC-MRV30µg/ml-04h

description: Library name: Sample 23

value: 30 µg/mL Mojave Type A rattlesnake venom for 04 hours


title: C1

description: Library name: Sample 1


title: Normal N treated roots of WT rep1


title: N1

description: Library name: Sample 4


title: AF16_day_9_r3

city: Hamilton

first: Bhagwati

middle: P

last: Gupta

state: ON

address: 1280 main street W, Life Sciences Building LSB322

department: Biology

institute: McMaster University

description:
Library name: AF16_day_9_r3
Reads_AF16d1369.xlsx column: M
d9r3
AF16_day_9_r3.tabular

data_processing:
RNA sample quality was vetted for inclusion based on Bioanalyzer RIN scores
MultiQC was used to aggregate multiple results into a single report (Ewels et al. 2016).
Reads were aligned to the genome using RNA STAR, set to paired-end sequences and default settings (Dobin et al. 2013).
To count hits per gene, featureCounts was used with default settings for paired-end reads (Liao, et al. 2014).
Assembly: C. briggsae CB4 (Ross et al. 2011), with WS279 for annotation
Supplementary files format and content: Excel file (.xlsx) containing gene read counts, obtained from Featurecounts

organism: Caenorhabditis briggsae

source_name: Whole organism (hermaphrodite)

growth_protocol: Worms were grown and maintained according to established methods (Wood 1988). Cultures were propagated on the Nematode Growth Medium (NGM) plates seeded with E. coli OP50 bacteria and maintained at 20 °C. C. briggsae AF16 wild-type strain was obtained from the Caenorhabditis Genetic Center (CGC). Age-synchronized populations were obtained by two successive rounds of bleaching of young gravid adults by standard methods using NaOCl and NaOH (Stiernagle 2006). Animals were left to pass through larval stages and live to specified ages: day 1, 3, 6, 9 of adulthood. Every second day, adults and larvae were column separated by washing in an upright 15 mL tube filled with M9 for 5 minutes to achieve size separation, after which the water column was pipetted off to remove larvae. This was repeated at least 3 more times to increase removal of larvae. Worms were pipetted on fresh seeded plates, and remaining larvae were removed with a platinum worm pick and burned.

extract_protocol:
RNA was isolated using Trizol-reagent (Sigma, USA, Catalog Number T9424), chloroform, and isopropanol (Chomczynski and Sacchi 1987).
cDNA libraries were constructed from 100–200 ng RNA using an Illumina-specific commercial kit (TruSeq RNA Sample Preparation Kit v2, Set A, Catalog number RS-122-2001).

value: Whole organism (hermaphrodite)

value: Day 9 adult


title: A13098-NSC-MRV30µg/ml-24h

description: Library name: Sample 20

value: 30 µg/mL Mojave Type A rattlesnake venom for 24 hours


title: AF16_day_9_r2

description:
Library name: AF16_day_9_r2
Reads_AF16d1369.xlsx column: L
d9r2
AF16_day_9_r2.tabular


title: A13098-NSC-MRV10µg/ml-24h

description: Library name: Sample 19

value: 10 µg/mL Mojave Type A rattlesnake venom 24 hours


title: AF16_day_9_r1

description:
Library name: AF16_day_9_r1
Reads_AF16d1369.xlsx column: K
d9r1
AF16_day_9_r1.tabular


title: AF16_day_6_r3

description:
Library name: AF16_day_6_r3
Reads_AF16d1369.xlsx column: J
d6r3
AF16_day_6_r3.tabular

value: Day 6 adult


title: HHst.28 NTN1-GFP positive optic fissure cells, replicate 2

value: Optic fissure

value: Hamburger-Hamilton stage 28

value: Heterozygous for NTN1T2A-eGFP/+


title: Normal N treated roots of PuHox52-OE rep3

value: root

value: tissue seedling


title: AF16_day_6_r2

description:
Library name: AF16_day_6_r2
Reads_AF16d1369.xlsx column: I
d6r2
AF16_day_6_r2.tabular


title: A13097-NSC-MRV30µg/ml-04h

description: Library name: Sample 17


title: A13097-NSC-MRV10µg/ml-04h

description: Library name: Sample 16


title: A13097-NSC-Control-04h

description: Library name: Sample 18


title: A13097-NSC-Control-24h

description: Library name: Sample 15

value: vehicle-treated for 24 hours (Control)


title: Normal N treated roots of WT rep2

value: WT

value: Normal N


title: AF16_day_6_r1

description:
Library name: AF16_day_6_r1
Reads_AF16d1369.xlsx column: H
d6r1
AF16_day_6_r1.tabular


title: A13098-NSC-Control-24h

description: Library name: Sample 21

value: iPSC-derived neural stem cells

value: neural stem cell


title: A13097-NSC-MRV30µg/ml-24h

description: Library name: Sample 14


title: AF16_day_3_r2

description:
Library name: AF16_day_3_r2
Reads_AF16d1369.xlsx column: F
d3r2
AF16_day_3_r2.tabular

value: Day 3 adult


title: AF16_day_3_r1

description:
Library name: AF16_day_3_r1
Reads_AF16d1369.xlsx column: E
d3r1
AF16_day_3_r1.tabular


title: AF16_day_1_r3

description:
Library name: AF16_day_1_r3
Reads_AF16d1369.xlsx column: D
d1r3
AF16_day_1_r3.tabular

value: Day 1 adult


title: A13062-NSC-MRV30µg/ml-04h

description: Library name: Sample 11

value: 30 µg/mL Mojave Type A rattlesnake venom for 04 hours


title: A13062-NSC-Control-04h

description: Library name: Sample 12

value: vehicle-treated for 04 hours (Control)


title: A13062-NSC-MRV10µg/ml-04h

description: Library name: Sample 10

value: 10 µg/mL Mojave Type A rattlesnake venom 04 hours


title: AF16_day_3_r3

description:
Library name: AF16_day_3_r3
Reads_AF16d1369.xlsx column: G
d3r3
AF16_day_3_r3.tabular

value: Whole organism (hermaphrodite)


title: A13097-NSC-MRV10µg/ml-24h

description: Library name: Sample 13

value: 10 µg/mL Mojave Type A rattlesnake venom 24 hours


title: 16-L30-Out-rpt3

city: Würzburg

first: Laura

last: Jenniches

address: Josef-Schneider-Straße 2/D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
demultiplexed, filtered by transposon tag (up to 1 mismatch)
Adapter removal: BBDuk (BBMap v38.94)
Alignment/Quantification: Bio-TraDIS pipeline (v1.4.5)
Assembly: CP037923.1, CP037924.1
Supplementary files format and content: TraDIS_counts.csv: count table with all non-zero insertion sites, insertion sites are assigned to genes
Library strategy: Tn-Seq

organism: Shigella flexneri

growth_protocol: Sub-libraries of over-night cultures (LB, 37°C, 220rpm)  from the Shigella flexneri Tn5 Libraries were pooled to generate 3 replicate sub-libraries containing ~10.000 or ~30.000 mutants/each. The resulting sub-libraries (Min) were used to infect replicate wells containing ~500 BO enteroids at MOI 200 as described above. After infection, enteroids were lysed in 0.1% Na-deoxycholate by extensive pipetting. Intracellular bacterial populations were enriched ON at 37°C in 2ml LB (Out). A diluted culture of the inoculum was also enriched and used as the input reference (Inp). A 1.5ml portion of the bacterial culture was used to extract genomic DNA.

extract_protocol:
gDNA isolation was performed using the GenElute Bacterial gDNA kit (Sigma; NA2110-1KT)
TraDIS library (Barquist et al., 2016 Bioinformatics)

tag: strain

value: pool of EZ-Tn5 transposase mutants

value: enriched intracellular bacteria


title: AF16_day_1_r2

description:
Library name: AF16_day_1_r2
Reads_AF16d1369.xlsx column: C
d1r2
AF16_day_1_r2.tabular


title: A13062-NSC-Control-24h

description: Library name: Sample 9


title: AF16_day_1_r1

description:
Library name: AF16_day_1_r1
Reads_AF16d1369.xlsx column: B
d1r1
AF16_day_1_r1.tabular


title: A13062-NSC-MRV30µg/ml-24h

description: Library name: Sample 8

value: 30 µg/mL Mojave Type A rattlesnake venom for 24 hours


title: 15-L30-Out-rpt2


title: A00208-NSC-Control-04h

description: Library name: Sample 6


title: 14-L30-Out-rpt1


title: 12-L30-Inp-rpt2

value: enriched input


title: A00208-NSC-MRV10µg/ml-04h

description: Library name: Sample 4


title: A00208-NSC-MRV30µg/ml-04h

description: Library name: Sample 5


title: 13-L30-Inp-rpt3


title: 11-L30-Inp-rpt1


title: A00208-NSC-Control-24h

description: Library name: Sample 3


title: 10-L30-Min-rpt2

value: input library


title: A00208-NSC-MRV30µg/ml-24h

description: Library name: Sample 2


title: Colo357-siSOX9, rep3

city: Moscow

first: Liya

last: Kondratyeva

address: Ulitsa Miklukho Maklaya, 16/10

country: Russia

institute: Institute of bioorganic chemistry of the Russian Academy of Sciences

description: Library name: 24_TCGGCA

data_processing:
Raw reads were mapped to a human reference genome (hg38) using HISAT2 (Galaxy Version 2.1.0 + galaxy 5, usegalaxy.org, accessed on May 25, 2022). FeatureCounts (Galaxy Version 1.6.4 + galaxy 1, usegalaxy.org, accessed on May 25, 2022) was used to  count the reads of the annotated GENCODE version 33 genes.
Assembly: hg38
Supplementary files format and content: .txt format, matrix table with featureCounts read counts

source_name: pancreas

growth_protocol: PANC-1 cells were maintained in Dulbecco’s modified Eagle medium/Ham’s F12 (DMEM/F12, 1:1) containing 10% fetal calf serum, 2 mM L-glutamine, 100 U/mL penicillin and 100 μg/mL streptomycin. Colo357 cells were maintained in RPMI 1640 medium con-taining 10% fetal calf serum, 2 mM L-glutamine, 55 nM 2-mercaptoethanol, 100 U/mL penicillin, and 100 μg/mL streptomycin. All cells were cultured at 37 °C in a humidified atmosphere with 95% air and 5% CO2.

extract_protocol:
Total RNA from each sample was extracted using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany). The yield of RNA was first quantified by measuring total RNA concentration using a Qubit™ 2.0 fluorometer (Thermo Fisher Scientific, USA) with Qubit™ RNA HS Assay Kit (Thermo Fisher Scientific). The quality of the extracted RNA was estimated using the Agilent High Sensitivity RNA Screen Tape using the TapeStation 2200 (Agilent Technologies, Santa Clara, CA, USA). PolyA RNA isolation was performed with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA).
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Bi-olabs) and the NEBNext Multiplex Oligos for Illumina (Index Primers Set 3, 4) were used to prepare the libraries.

treatment_protocol: Human SOX9 targeting siRNAs were synthesized by Syntol (Syntol JSC, Moscow, Russia). Sense sequences of the SOX9 siRNAs are shown in Supplementary Table S2. Three differ-ent SOX9 siRNA duplexes were tested individually and in a combination. SiRNA trans-fections were performed using the Lipofectamine RNAiMAX reagent (Invitrogen), accord-ing to the manufacturer’s protocol. Pancreatic cancer cells seeded in 6-well plates were transfected with 10 nM siSOX9 pooled duplexes and control 10 nM siNeg. To achieve the best depletion of the SOX9 protein, transfection was performed twice: 24 h after seeding the cells and 48 h after the first transfection. Seventy-two hours after the first transfection, cells were harvested for further analysis.

value: pancreas

value: pancreatic cancer cell

value: Colo357 SOX9 knockdown

tag: batch


title: 8-L10-Out-rpt3


title: 9-L30-Min-rpt1


title: Colo357-siNeg, rep3

description: Library name: 23_TCGAAG

value: siNeg


title: 5-L10-Inp-rpt3


title: 4-L10-Inp-rpt2


title: Colo357-siNeg, rep2

description: Library name: 21_TCATTC


title: Colo357-siSOX9, rep1

description: Library name: 20_TATAAT


title: PANC1-siSOX9, rep3

description: Library name: 12_TAATCG

value: PANC1 SOX9 knockdown


title: Colo357-siNeg, rep1

description: Library name: 19_TACAGC


title: A13062-NSC-MRV10µg/ml-24h

description: Library name: Sample 7

value: iPSC-derived neural stem cells

value: neural stem cell


title: 1-L10-Min-rpt1


title: PANC1-siNeg, rep3

description: Library name: 11_CCAACA


title: PANC1-siSOX9, rep2

description: Library name: 10_CATTTT


title: Donor2, Bay-60 6583 treated M2

city: Frederick

first: Jun

last: Yang

state: MD

address: P. O. Box B

institute: Leidos Biomedical

description:
Library name: D2_Ar2b
10X Genomics

data_processing:
Sequence data were processed with Cell Ranger V6.0.1 (10X Genomics). The resulting count matrices followed the standard pipeline with default parameters.
Assembly: Homo Sapiens-hg38
Supplementary files format and content: Matrix files

source_name: Macrophage

extract_protocol:
M2 macrophages (4x10^6 cells) were seeded in 60 mm petri dishes and cultured at 37 °C for more than 16 h in D10 media. The cells were polarized with IL-6, BAY60-6583 or IL-27 for 3 days and then washed with the warmed PBS three times followed by incubation with 2.5 mL of trypsin-EDTA (0.25%) (QBI) at 37 °C for 15 min in a CO2 (5%) incubator. After the incubation, 5 mL of warm D10 was added per dish and the cells were detached by flushing the media. Cells were washed three times with D10 media and cell viability, and cell number were determined using Cellometer Auto 20000 (Nexcellom Bioscience, Lawrence, MA) with the ViaStain AOPI Staining Solution (Nexcellom Bioscience).  The cell viability was 98% ~ 100 %. Each cell was resuspended at 1200 cells/µL in D10
The scRNA sequence libraries were constructed using the Chromium Next GEM Single Cell 5’ Reagent Kit V2 (Dual Index) (10x Genomics, Pleasanton, CA) following the Vendor’s instruction. Briefly, 16.5 µL of cell suspension were mixed with 16.5 µL of master mix containing reverse transcription (RT) reagent and template switch oligos. The single cells generation and barcoding followed by cDNA synthesis was run on the Chromium Chip K in the 10x Chromium Controller (10x Genomics). The cDNA was amplified by 14 cycles reaction. Based on Agilent 2100 Bioanalyzer (Agilent Biotechnology, Santa Clara, CA) and Qubit 4 analysis (Thermo Fisher). The scRNA sequence libraries contained a single peak of DNA between 300-1000bp, with an average fragment size of 400-500bp.

value: Macrophage


title: PANC1-siSOX9, rep1

description: Library name: 8_CAGGCG


title: Donor2, IL6 treated M2

description:
Library name: D2_IL6
10X Genomics


title: PANC1-siNeg, rep2

description: Library name: 9_CATGGC


title: PANC1-siNeg, rep1

description: Library name: 7_CACTCA


title: Donor2, IL27 treated M2

description:
Library name: D2_IL27
10X Genomics


title: Donor2, M2

description:
Library name: D2_M
10X Genomics

value: M-CSF


title: A00208-NSC-MRV10µg/ml-24h

description: Library name: Sample 1


title: 6-L10-Out-rpt1


title: 3-L10-Inp-rpt1


title: Colo357-siSOX9, rep2

description: Library name: 22_TCCCGA


title: JJ012 PPP1R3C ko, rep3

city: Durham

first: Makoto

last: Nakagawa

address: 308 Research Drive

department: Department of Orthopaedic Surgery

institute: Duke University

description: Library name: JJ012_PTGKO_3

data_processing:
The quality check and trimming of raw FASTQ data were performed using the fastp software.
Read mapping was conducted with HISAT2 (v2.0.5) using the Homo sapiens (human) genome assembly GRCh38 (hg38) as the reference.
The number of reads mapped to each gene was quantified using featureCounts (v1.5.0-p3).
TMM normalization and differential gene expression analysis were performed using the R packages edgeR (v4.2.2) and limma (v3.60.2), respectively.
Assembly: hg38
Supplementary files format and content: csv file includes the raw counts for each sample.

source_name: Cell line

growth_protocol: High-glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S). Cells were cultured at 37°C in a humidified incubator in an atmosphere of 95% air and 5% CO2.

extract_protocol:
Total RNA was isolated using Direct-zol RNA Miniprep Plus Kit (Zymo Research) according to the manufacturer’s protocol.
The library was prepared for sequencing using standard Illumina protocols. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Dox inducible HT1080−PPP1R3C−HA cells and JJ012−PPP1R3C−HA cells were treated with Dox 1 µg/ml for 72 h.

value: Cell line

value: Human Chondrosarcoma

value: PPP1R3C ko


title: JJ012 PPP1R3C ko, rep2

description: Library name: JJ012_PTGKO_2


title: Donor1, Bay-60 6583 treated M2

description:
Library name: D1_Ar2b
10X Genomics


title: JJ012 Non-Targeting, rep3

description: Library name: JJ012_nonT_3

value: control (Non-Targeting)


title: 7-L10-Out-rpt2

value: pool of EZ-Tn5 transposase mutants

value: enriched intracellular bacteria


title: Donor1, IL27 treated M2

description:
Library name: D1_IL27
10X Genomics


title: Donor1, M2

description:
Library name: D1_M
10X Genomics


title: JJ012 PPP1R3C ko, rep1

description: Library name: JJ012_PTGKO_1


title: Donor1, IL6 treated M2

description:
Library name: D1_IL6
10X Genomics


title: 2-L10-Min-rpt2


title: dialout_rep_14

first: Alexis

last: Caulier

state: Massachusetts

address: 1 Blackfan street

department: Oncology/Hematology

institute: Boston Children's Hospital

description: demultiplexed with BCL Convert

data_processing:
Files were demultiplexed with BCL convert then aligned with Cellranger with GRCh38 genome
Assembly: GRCh38
Supplementary files format and content: h5 matrix, gene expression counts stored in $`Gene Expression`
Supplementary files format and content: h5 matrix, peak counts stored in $`Peaks`
Supplementary files format and content: h5 matrix, CROPseq counts
Library strategy: 10x ATAC + GEX Multiome

source_name: Hematopoietic cells

growth_protocol: Erythroid media

extract_protocol: Chromium Single Cell Multiome ATAC + Gene Expression

value: Hematopoietic cells

value: erythroid cells


title: dialout_rep_16

description: demultiplexed with BCL Convert


title: JJ012 Non-Targeting, rep2

description: Library name: JJ012_nonT_2


title: dialout_rep_13

description: demultiplexed with BCL Convert


title: JJ012−PPP1R3C−HA, Dox 1 µg/ml for 72 h, rep3

description: Library name: JJ012_Dox72_3

value: Dox 1 µg/ml for 72 h


title: JJ012−PPP1R3C−HA, Dox 0 µg/ml, rep3

description: Library name: JJ012_ctrl_3

value: Dox 0 µg/ml


title: JJ012−PPP1R3C−HA, Dox 1 µg/ml for 72 h, rep1

description: Library name: JJ012_Dox72_1


title: dialout_rep_9

description: demultiplexed with BCL Convert


title: dialout_rep_7

description: demultiplexed with BCL Convert


title: JJ012−PPP1R3C−HA, Dox 0 µg/ml, rep1

description: Library name: JJ012_ctrl_1


title: dialout_rep_10

description: demultiplexed with BCL Convert


title: HT1080−PPP1R3C−HA, Dox 1 µg/ml for 72 h, rep3

description: Library name: HT_Dox72_3

value: Human Fibrosarcoma


title: HT1080−PPP1R3C−HA, Dox 1 µg/ml for 72 h, rep1

description: Library name: HT_Dox72_1


title: dialout_rep_4

description: demultiplexed with BCL Convert


title: JJ012−PPP1R3C−HA, Dox 0 µg/ml, rep2

description: Library name: JJ012_ctrl_2


title: dialout_rep_5

description: demultiplexed with BCL Convert


title: dialout_rep_6

description: demultiplexed with BCL Convert


title: dialout_rep_3

description: demultiplexed with BCL Convert


title: JJ012 Non-Targeting, rep1

description: Library name: JJ012_nonT_1


title: HT1080−PPP1R3C−HA, Dox 0 µg/ml, rep3

description: Library name: HT_ctrl_3


title: HT1080−PPP1R3C−HA, Dox 0 µg/ml, rep1

description: Library name: HT_ctrl_1


title: dialout_rep_12

description: demultiplexed with BCL Convert