title: CAL-27_Empty vector_2

city: La Jolla

first: Sayuri

last: Miyauchi

address: 3855 Health Sciences Drive

institute: University of California, San Diego

data_processing:
Raw reads filtering was as follows: (1) Removed reads with adaptor contamination.
(2) Removed reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).
(3) Removed reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent  of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
Clean RNA-sequencing reads were mapped to the reference genome using STAR software.
Aligned read counts were further used for downstream differential gene expression analysis using DESeq2 software.
Assembly: hg19, mm10
Supplementary files format and content: csv files include FPKM values for each sample.

growth_protocol: CAL-27 cells were maintained in DMEM supplemented with 10% FBS. DC2.4 cells were maintained I RPMI 1640 supplemented with 10% FBS.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using Nextera DNA Flex Library Prep Kit following manufacturer's protocols.

value: Squamous cell carcinoma

value: HPV16 E5 positive


title: OP_12

status: Public on Jan 29 2024

type: SRA

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

library_source: transcriptomic

data_processing:
Adapter sequences and low quality reads were trimmed using the Timmomatic tool (v0.36) (options:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35)
High-quality reads were aligned to the reference human GRCh38.p13 primary assembly genome using HISAT v2.1.0
Uniqe reads were counted for known exons of each gene using Rsubread package (R) and Ensembl annotation (GRCh38.101)
TPM values calculated using kallisto v0.44.0
Assembly: GRCh38.p13 primary genome assembly
Supplementary files format and content: tab-delimited text files: Read_counts.txt — uniquely aligned read counts for genes

molecule: polyA RNA

organism: Homo sapiens

source_name: musculus vastus lateralis

extract_protocol:
A frozen muscle sample (~10-15 mg) was lysed by the RLT buffer (Qiagen, Germany) using a drill homogenizer and total RNA was extracted by a silica spin column (CleanRNA Standard, Evrogen, Russia). RNA concentration and integrity were evaluated by a fluorimetric assay (Qubit 4, ThermoScientific, USA) and capillary electrophoresis (TapeStation, Agilent, Germany), respectively.
Strand-specific libraries were prepared by the NEBNext Ultra II Directional RNA Library Preparation kit (NEB, USA)

tag: tissue

value: musculus vastus lateralis

tag: Sex

value: female

tag: age

tag: healthy/patient

value: patient


title: CAL-27_HPV16 E5_1

state: CA

country: USA

molecule: total RNA

tag: cell line

tag: cell type

tag: genotype

value: Empty vector control

tag: treatment


title: MG1655 glnG mice RNA_biol rep 1

city: STILLWATER

first: Tyrrell

last: Conway

state: OKLAHOMA

address: 307 Life sciences east, OKLAHOMA STATE UNIVERSITY

department: Microbiology and Molecular Genetics

institute: Oklahoma state university

description: RNA-Seq of colonized Escherichia coli MG1655 ∆glnG extracted from mouse cecal mucus

data_processing:
Sequencing reads were mapped to the reference genome (accession number:U00096.3) using bowtie2
SAM files were converted to BAM format and sorted and indexed them using SAMtools
The BAM files were then converted to base count (WIG) files
Using in-house script, normalized WIG files were generated by using a simple global normalization approach in which the count at each base location was multiplied by 1 billion and divided that value by the sum of base counts at all base locations in the file
Assembly: U00096.3
Supplementary files format and content: normWIG

organism: Escherichia coli str. K-12 substr. MG1655

source_name: mouse mucus from the cecum

growth_protocol: Wild type StrR  and ∆glnG StrR CamR cultures were grown on MOPS minimal medium with 0.2% glucose as sole carbon source and high(10 mM NH4Cl) or low nitrogen source( 3 mM NH4Cl) at 37°C  and agitation at 200 rpm. For exponential phase samples, culture samples were harvested during logarithmic phase (OD600=0.4-0.6). For stationary phase samples, culture samples were harvested 30 minutes after the culture entered the stationary phase. 5 ml of cultures were harvested into RNA-protect reagent (Qiagen) at 1:2 dilution and cells were pelleted by centrifugation at 5000rpm for 10 minutes. Cell pellets were stored at -80°C until RNA extraction. To extract RNA from colonized E. coli MG1655∆glnG StrR CamR , the mutant strain was fed to CD-1 male mice and allowed it to stably colonize for 9 days. The mice were then euthanized, cecum was taken out and cecal mucus was extracted and immediately homogenized in 500 µl Hanks salt solution (Thermo scientific), 500 µl PCA and 210 µl 20% SDS . The tubes were kept on ice until further processing for RNA extraction.

extract_protocol:
All in-vitro RNA samples were extracted using the Qiagen RNeasy Mini Kit, following manufacturer’s protocol. For in vivo samples, RNA samples were extracted using phenol chloroform extraction method. DNase treatment was done using DNAse I enzyme (Invitrogen, Cat no. AM2238). The samples were quantified using the Agilent Bioanalyzer (Agilent, Catalog no. G2939BA).
Approximately 100 ng of total RNA from each sample were processed at University of Bern for ribo-depletion with the Illumina Ribo-Zero Plus rRNA Depletion Kit (Illumina, Catalog no. 20037135). RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep kit. Libraries were sequenced on a NovaSeq™ 6000 system, using 1×100 bp single-end read length.

value: mouse mucus from the cecum

value: deltaglnG mutant


title: OP_11

value: male


title: SclCre;V617F;GFP-4

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Reads were mapped to the mouse genome mm10 with STAR (version 2.7.10a) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax=10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”). The mm10 genome reference was supplemented with CreERT2, induceable Homo_sapiens_JAK2_V617F construct and pEGFP sequences.
All subsequent analyses were performed using the R software (version 4.2.2) and Bioconductor 3.16 packages. The featureCounts function from the Bioconductor Rsubread package (version 2.0.1) was used to count the number of reads (5' ends) overlapping with the exons of each gene (Ensembl release 102) assuming an exon union model
Assembly: mm10
Supplementary files format and content: gene_counts.tsv.gz: gzipped text file with tab-separated RNA-seq read counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: 1. Ensembl ID, 2.-26. read counts per gene and sample. Counts on the CreERT2, pEGFP and Homo_sapiens_JAK2_V617F construct (exons 3 to 12 and exons 13 to 25 separately) are listed at the end of the file

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Bone marrow cells were harvested from sacrificed mice and FACS stained and sorted directly in RNA extraction buffer (PicoPure)

extract_protocol:
Bone-marrow long-term hematopoietic stem cells (HSC; Lin−Sca1+cKit+CD48−CD150+) were FACS sorted directly into PicoPure extraction buffer and frozen at -80°C after a lysis step. Overall the samples were processed in 2 batches, 2 weeks apart (resp. 2 and 4 weeks after tamoxifen induction)
RNA from all 25 c\frozen samples was extracted using the Picopure RNA isolation kit (Applied Biosystems). The quality and concentration of total RNA was determined on Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Pico Assay.
Unstranded RNA-seq libraries were prepared using the SMART-Seq v4 kit (Takara).

value: Bone marrow

value: HSCs (Lin-Sca1+cKit+CD48-CD150+)

tag: time

value: 2 weeks after tamoxifen induction


title: MG1655 invitro N-lim E phase RNA_biol rep 1

description: RNA-Seq of exponential phase Escherichia coli MG1655 wild type grown in vitro in MOPS minimal media containing low nitrogen

source_name: E. coli grown invitro culture

value: E. coli grown invitro culture

value: WT


title: U2AF1WT rep3

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

data_processing:
Adapter trimming with Trim Galore
QC with FastQC
CircRNA quantification with CIRI2
Assembly: hg19
*_BSJ are read counts for "back splice junction spanning" reads. These are the counts that define the expression level of each circRNA.
*_LIN are read counts for linear splicing at the same genomic location. These read counts define the expression level of linear spliced RNA from the same host gene as the circRNA. These reads do not define the circRNA expression, but help explain the linear expression from the host gene.

growth_protocol: Cells were incubated with 250 ng/mL doxycycline for 48 hours. Equal numbers of cells were plated with DMSO for a further 24 hours in the presence of doxycycline.

extract_protocol:
Total RNA was extracted using Trizol LS (Thermo Fisher, Waltham, MA) and RNeasy mini kit (Qiagen, Hilden, Germany). Genomic DNA was removed using Turbo DNA-Free Kit (Thermo Fisher).
Stranded libraries were generated using an input of 500ng total RNA and the TruSeq Stranded Total RNA kit with Ribo-Zero Gold, set A, RS-122–2301 (Illumina, San Diego, CA) according to the manufacturer's instructions.


title: U2AF1WT rep2


title: SclCre;V617F;IL-1b-/-GFP-2


title: CAL-27_HPV16 E5_2


title: OP_10


title: OP_15


title: CAL-27_Empty vector_1


title: OP_9


title: SclCre;V617F;GFP-1


title: SclCre;V617F;GFP-2


title: U2AF1WT rep1


title: SclCre;GFP-4

value: SclCre;GFP


title: U2AF1S34F rep3


title: OP_7


title: U2AF1S34F rep2


title: monocyte-derived macrophages, Zymosan_3h_Rep1

city: Los Angeles

first: Quen

last: Cheng

address: 10833 LeConte Ave

institute: UCLA

description:
Column header in processed data file: Zymo.3h.R1
Cheng_RNAseqCounts.csv

data_processing:
Samples were sequenced and base calls performed on Illumina HiSeq 2500
The low quality 3’ends of reads were trimmed (cutoff q=30), and remaining adapter sequences were removed using cutadapt. Processed reads were aligned to hg38 genome using STAR, and count tables were generated by the featureCount function in deepTools
Assembly: hg38
Supplementary files format and content: Raw count table provided (unnormalized)

source_name: monocyte-derived macrophage

growth_protocol: Peripheral blood mononuclear cells were obtained from healthy donors through the UCLA-CFAR Virology Core. Monocytes were isolated by negative bead selection using a Pan-Monocyte Isolation Kit (Miltenyi Biotec) and grown on tissue culture plates (Corning) in complete medium consisting of RPMI 1640 broth containing 10% fetal bovine serum (Gibco), 100 IU/ml penicillin streptomycin, 100 μg/ml streptomycin,  2 mM L-glutamine, and 10 ng/ml recombinant human M-CSF (R&D Systems 216-MC-100) at 37°C for seven days. Macrophages at Day 7 were confirmed to have >90% viability by Trypan-blue stain.

extract_protocol:
Cells were lysed using Qiagen RNeasy Micro Kit (Qiagen 74004), and RNA was extracted according to manufacturer’s protocol.
RNA-seq libraries were prepared using KAPA stranded mRNA-seq library kit per manufacturer’s instructions

treatment_protocol: Monocytes were rested in complete medium for 30-60 minutes after purification, then trained with the following ligands for 24 hours: zymosan (1 μg/mL, InvivoGen tlrl-zyn), ETSU b-glucan (10 mg/mL), depleted zymosan (10 mg /mL, InvivoGen tlrl-zyd), Pam3CSK4 (100 ng/mL, Invivogen tlrl-pms), or IFN-b (100 U/mL, PBL Assay Science 11415-1). After 24 hours of training, the medium was aspirated, cells were washed with warm HBSS, and fresh complete medium was added. On Day 4, medium was aspirated and fresh medium was added. On Day 7, the cells were stimulated with LPS (1 ng/mL, Millipore Sigma L6529) and analyzed for gene expression or cytokine release.

value: monocyte-derived macrophage

tag: training regimen

value: Zymosan

tag: timepoint

value: 3 hours

tag: replicate

value: Replicate 1

tag: assay

value: RNA-seq


title: U2AF1S34F rep1


title: monocyte-derived macrophages, Zymosan_1h_Rep1

description:
Column header in processed data file: Zymo.1h.R1
Cheng_RNAseqCounts.csv

value: 1 hour


title: monocyte-derived macrophages, Zymosan_3h_Rep2

description:
Column header in processed data file: Zymo.3h.R2
Cheng_RNAseqCounts.csv

value: Replicate 2


title: SclCre;GFP-3


title: monocyte-derived macrophages, Zymosan_1h_Rep2

description:
Column header in processed data file: Zymo.1h.R2
Cheng_RNAseqCounts.csv


title: SclCre;V617F;GFP-3


title: OP_6

value: musculus vastus lateralis

value: female

value: patient


title: SclCre;GFP-2


title: OP_5


title: Peri-Implantitis 10 [PI11]

city: Yangsan-si

first: Yeongjoo

last: Kim

country: South Korea

institute: Pusan National University

description:
raw_count.csv
lcpm_exp.csv

data_processing:
Reads from the acquired raw RNA-Seq dataset were adapter and quality trimmed with default parameters with Trimmomatic.
Trimmed reads were aligned to Hg38 human genome reference with Hisat2 and raw counts were calculated using StringTie.
Read count data table was CPM-normalized and log2 transformed after low count removal.
Assembly: Hg38 primary assembly
Supplementary files format and content: raw_count.csv
Supplementary files format and content: lcpm_exp.csv

source_name: gingiva

extract_protocol:
Collected healthy, periodontal and peri-implantal gingival tissue samples were sent to Macrogen (Seoul, Korea) for RNA extraction, library construction and RNA sequencing and quality check was performed using 2100 Bioanalyzer
NGS library construction was performed using Illumina Truseq stranded total RNA prep kit.

value: gingiva

tag: subject status

value: Peri-Implantitis


title: 5'-Asp KD

type: RNA

city: Philadelphia

first: Megumi

last: Shigematsu

state: PA

address: 1020 Locust St

institute: Thomas Jefferson University

description: 5'-Asp KD vs R-Luc ctrl KD

hyb_protocol: (Microarray and the subseqent data acquisition were performed by Mogene)

source_name: LNCaP

growth_protocol: LNCaP cells were cultured in IMEM containing L-Glutamine and 5% FBS.

extract_protocol: Total RNA was extracted by using TRIzol reagent.

treatment_protocol: LNCaP cells were transfected with 20 nM (5'-LysCUU and 5'-AspGUC) or 10 nM (3'-AspGUC) siRNA and were harvested after 72 hours.

value: LNCaP

value: 5'-Asp KD

value: R-Luc KD


title: SclCre;GFP-1

value: Bone marrow

value: HSCs (Lin-Sca1+cKit+CD48-CD150+)

value: 2 weeks after tamoxifen induction


title: monocyte-derived macrophages, Zymosan_0h_Rep1

description:
Column header in processed data file: Zymo.0h.R1
Cheng_RNAseqCounts.csv

value: monocyte-derived macrophage

value: Zymosan

value: 0 hours


title: OP_8


title: OP_4


title: Peri-Implantitis 9 [PI10]

description:
raw_count.csv
lcpm_exp.csv


title: monocyte-derived macrophages, Zymosan_0h_Rep2

description:
Column header in processed data file: Zymo.0h.R2
Cheng_RNAseqCounts.csv

value: RNA-seq


title: MEF, untreated, rep 1

city: Beijing

first: Wenqing

last: Liu

email: puyulwq@163.com, liuwq21@gamils.com

address: No. 5 Summer Palace Road, Haidian District, Beijing

country: China

institute: Peking University

description:
detect modification level of specific TAG sites in W392X in untreated MEF
targetseq-CFTRandmIDUA.xlsx

data_processing:
First, sequencing reads with the same unique molecular identifier (UMI) were grouped and UMI groups with less than 3 reads were discarded.
Then, PCR duplicates were removed by retaining the most consensus sequence in each UMI group.
Adapter sequences were further trimmed from deduplicated reads with Trim_galore software (version0.6.7) with default parameters.
The 10-nucleotide UMIs were removed by umi_tools (version 1.0.0).
The cleaned reads were mapped to the targeted sequences using PRAISE-tool and the deletion rate of target sites was calculated.
Assembly: GRCh38
Supplementary files format and content: First, sequencing reads with the same unique molecular identifier (UMI) were grouped and UMI groups with less than 3 reads were discarded. Then, PCR duplicates were removed by retaining the most consensus sequence in each UMI group. Adapter sequences were further trimmed from deduplicated reads with Trim_galore software (version0.6.7) with default parameters. The 10-nucleotide UMIs were removed by umi_tools (version 1.0.0). The cleaned reads were mapped to the targeted sequences using PRAISE-tool and the deletion rate of target sites was calculated.

source_name: embryo

growth_protocol: MEF cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. 16HBEge cells were grown under 5% CO2 at 37°C in MEM medium (Corning) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
total RNA was extracted from cells using TRIzol reagent (Life Technologies)
RNA libraries were prepared using modified eCLIP library construction, NEBNext Small RNA library kits (NEB) and SMARTer Stranded Total RNA-Seq kits (v3) - Pico Input mammalian (Takara) Library Prep Kit following manufacturer's protocols.

treatment_protocol: RESTART v3 expressing AAVs were packaged in PackGene Company. 16HBE cells were seeded at a density of 1x105 in 24-well plate (Corning). 24 hours after seeding, 16HBE cells (CFTR-R553X) were transduced by AAV2 at multiplicities of infection 1 x 105. The cell medium was changed 24 hours after transduction. A group of 16HBEge cells was treated with 100 µg/mL G418. 5 days after transduction and 18 hours after G418 treatment, whole cell patch clamp experiments were performed. Besides, MEFs were seeded into 100 mm culture dishes at a density of 1.5 x 105 cells and were transduced by AAVDJ at multiplicities of infection of 5 x 106, 24 hours after seeding. The cell medium was changed 48 hours after transduction, and cells were collected after 7 days.

value: embryo

value: MEF

value: a type of fibroblast prepared from mouse embryo


title: Peri-Implantitis 8 [PI8]

description:
raw_count.csv
lcpm_exp.csv


title: OP_3

value: musculus vastus lateralis

value: male


title: 3'-Asp KD

description: 3'-Asp KD vs R-Luc ctrl KD

scan_protocol: (Microarray and the subseqent data acquisition were performed by Mogene)

value: 3'-Asp KD


title: monocyte-derived macrophages, Untrained_3h_Rep2

description:
Column header in processed data file: Untrained.3h.R2
Cheng_RNAseqCounts.csv

value: Untrained

value: 3 hours

value: Replicate 2


title: MEF, RESTART v3-treated, rep 2

description:
detect modification level of specific TAG sites in W392X with RESTART v3 treatment
targetseq-CFTRandmIDUA.xlsx


title: colonic epithelium, Smad4 knockout, DSS treated, replicate 3

city: Hoboken

first: Thompson

last: Hui

state: New Jersey

address: McLean 327

department: Chemistry and Chemical Biology

institute: Stevens Institute of Technology

data_processing:
Raw sequencing reads were cleaned by Novogene using in-house Perl scripts
Clean reads were aligned to the mm9 reference genome using Hisat2
Aligned reads were quantified by featureCounts
The aligned reads were quantified for gene expression levels using featureCounts
Assembly: mm9
Supplementary files format and content: tab-delimited text file including raw counts for each file

source_name: colonic epithelium

growth_protocol: The mice were maintained on standared chow diet, temperature, and humidity controlled animal facility with 12 hour light/dark cycle

extract_protocol:
Epithelium was isolated from the whole colon using 5mM EDTA/PBS buffer and rocked for ~ one hour to seperate the epithelium from the mesenchyme. The isolated crypt epithelium was washed thrice with PBS, pelleted and solubilized in Trizol for RNA extraction. All the aforementioned processes were carried at 4 degrees Celsius. The quality for the RNA was confirmed by Novogene prior to sequencing.
The PolyA enrichment procedure was used for library preparation

treatment_protocol: Adult wild type and Smad4 knockout mice were admimistered 2.5% Dextran Sulphate Sodium ad libitum in drinking water for three days.

value: colonic epithelium

value: colonic epithelial cells

value: Smad4 knockout

value: DSS treated


title: 5'-Lys KD

description: 5'-Lys KD vs R-Luc ctrl KD

data_processing: (Microarray and the subseqent data acquisition were performed by Mogene)

value: LNCaP

value: 5'-Lys KD

value: R-Luc KD


title: Peri-Implantitis 7 [PI7]

description:
raw_count.csv
lcpm_exp.csv

value: gingiva

value: Peri-Implantitis


title: monocyte-derived macrophages, Untrained_1h_Rep2

description:
Column header in processed data file: Untrained.1h.R2
Cheng_RNAseqCounts.csv

value: monocyte-derived macrophage

value: 1 hour

value: RNA-seq


title: monocyte-derived macrophages, Untrained_0h_Rep2

description:
Column header in processed data file: Untrained.0h.R2
Cheng_RNAseqCounts.csv

value: 0 hours


title: OP_1

value: musculus vastus lateralis

value: female

value: patient


title: YP_7

value: male


title: MEF, RESTART v3-treated, rep 1

value: embryo

value: MEF

value: a type of fibroblast prepared from mouse embryo


title: LL2_CAF_rep2

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

institute: University of Southern Denmark

data_processing:
Aligned to mm10 using STAR (V2.5.0c)
Raw counttable was generated using HOMER
Normalised gene expression (RPKM) was analysed by HOMER
Differential gene expression analysis was analysed by DEseq2
Assembly: mm10
Supplementary files format and content: normalized gene count table as txt file

source_name: tumor

growth_protocol: Six commonly used murine cancer cells lines (B16-F10, Pan02, MC38, LL2, EO771.LMB, and CT26) were cultured in cell culture-treated flasks at 37 degrees celcius and 5% CO2. CT26 was cultured in RPMI 1640 + 10% FBS + 1% P/S. B16-F10, LL2, and Pan02 were cultured in DMEM + 10% FBS + 1% P/S. EO771.LMB was cultured in DMEM + 20% FBS + 1% P/S + 20mM HEPES. MC38 was cultured in DMEM + 10% FBS + 1% P/S + 1% HEPES + 1% non-essential amino acid supplement + 1% sodium pyruvate. All reagents from Gibco. 500000 cells were injected into the flank of mice and tumor growth was monitored.

extract_protocol:
At endpoint, tumors were excised from the mice and a tumor fragment was used for RNA isolation. RNA isolation was performed using the Rneasy Mini Kit (Qiagen) according to manufacturer's instructions.
PolyA enriched RNA, unstranded cDNA library, NEBNext library synthesis

value: tumor

value: cancer-associated fibroblasts

value: Engrafted tumor


title: Peri-Implantitis 6 [PI6]

description:
raw_count.csv
lcpm_exp.csv


title: monocyte-derived macrophages, Untrained_3h_Rep1

description:
Column header in processed data file: Untrained.3h.R1
Cheng_RNAseqCounts.csv

value: Untrained

value: 3 hours

value: Replicate 1


title: Peri-Implantitis 5 [PI5]

description:
raw_count.csv
lcpm_exp.csv

value: gingiva

value: Peri-Implantitis


title: YP_6


title: Peri-Implantitis 4 [PI4]

description:
raw_count.csv
lcpm_exp.csv


title: YP_5


title: LL2_CAF_rep1


title: Peri-Implantitis 3 [PI3]

description:
raw_count.csv
lcpm_exp.csv


title: MC38_CAF_rep2


title: monocyte-derived macrophages, Untrained_0h_Rep1

description:
Column header in processed data file: Untrained.0h.R1
Cheng_RNAseqCounts.csv

value: monocyte-derived macrophage

value: RNA-seq


title: MC38_CAF_rep1


title: monocyte-derived macrophages, ETSU_3h_Rep1

description:
Column header in processed data file: ETSU.3h.R1
Cheng_RNAseqCounts.csv

value: ETSU beta-glucan


title: YP_4

value: musculus vastus lateralis


title: Pan02_CAF_rep2


title: YP_3

value: patient


title: Peri-Implantitis 1 [PI1]

description:
raw_count.csv
lcpm_exp.csv


title: OP_2

value: female


title: monocyte-derived macrophages, ETSU_3h_Rep2

description:
Column header in processed data file: ETSU.3h.R2
Cheng_RNAseqCounts.csv

value: Replicate 2


title: Peri-Implantitis 2 [PI2]

description:
raw_count.csv
lcpm_exp.csv


title: YP_2

value: male


title: Periodontitis 10 [PT11]

description:
raw_count.csv
lcpm_exp.csv

value: Periodontitis


title: Pan02_CAF_rep1

value: tumor


title: monocyte-derived macrophages, ETSU_1h_Rep1

description:
Column header in processed data file: ETSU.1h.R1
Cheng_RNAseqCounts.csv

value: 1 hour


title: YP_1


title: YH_15

value: healthy


title: EO771_CAF_rep1

value: cancer-associated fibroblasts

value: Engrafted tumor


title: Periodontitis 8 [PT8]

description:
raw_count.csv
lcpm_exp.csv


title: EO771_CAF_rep2


title: monocyte-derived macrophages, ETSU_1h_Rep2

description:
Column header in processed data file: ETSU.1h.R2
Cheng_RNAseqCounts.csv


title: monocyte-derived macrophages, ETSU_0h_Rep1

description:
Column header in processed data file: ETSU.0h.R1
Cheng_RNAseqCounts.csv

value: 0 hours

value: Replicate 1


title: monocyte-derived macrophages, Untrained_1h_Rep1

description:
Column header in processed data file: Untrained.1h.R1
Cheng_RNAseqCounts.csv

value: Untrained


title: Periodontitis 7 [PT7]

description:
raw_count.csv
lcpm_exp.csv

value: gingiva


title: MC38_tumor_rep3

value: whole tumor


title: YH_14


title: monocyte-derived macrophages, ETSU_0h_Rep2

description:
Column header in processed data file: ETSU.0h.R2
Cheng_RNAseqCounts.csv

value: monocyte-derived macrophage

value: ETSU beta-glucan

value: RNA-seq


title: MC38_tumor_rep2


title: YH_13

value: musculus vastus lateralis


title: Periodontitis 6 [PT6]

description:
raw_count.csv
lcpm_exp.csv


title: monocyte-derived macrophages, Depleted_3h_Rep1

description:
Column header in processed data file: Depleted.3h.R1
Cheng_RNAseqCounts.csv

value: Depleted zymosan

value: 3 hours


title: MC38_tumor_rep1


title: EO771_tumor_rep3


title: monocyte-derived macrophages, Depleted_1h_Rep1

description:
Column header in processed data file: Depleted.1h.R1
Cheng_RNAseqCounts.csv


title: YH_11

value: male


title: Periodontitis 4 [PT4]

description:
raw_count.csv
lcpm_exp.csv

value: Periodontitis


title: monocyte-derived macrophages, Depleted_0h_Rep1

description:
Column header in processed data file: Depleted.0h.R1
Cheng_RNAseqCounts.csv


title: YH_10


title: Periodontitis 3 [PT3]

description:
raw_count.csv
lcpm_exp.csv


title: EO771_tumor_rep2

value: tumor


title: monocyte-derived macrophages, Depleted_3h_Rep2

description:
Column header in processed data file: Depleted.3h.R2
Cheng_RNAseqCounts.csv

value: Replicate 2


title: Periodontitis 9 [PT10]

description:
raw_count.csv
lcpm_exp.csv


title: Periodontitis 2 [PT2]

description:
raw_count.csv
lcpm_exp.csv


title: YH_9

value: female

value: healthy


title: YH_8


title: EO771_tumor_rep1

value: Engrafted tumor


title: Periodontitis 1 [PT1]

description:
raw_count.csv
lcpm_exp.csv


title: YH_7


title: Healthy control 10 [H10]

description:
raw_count.csv
lcpm_exp.csv

value: Healthy control


title: Pan01_tumor_rep1


title: Pan01_tumor_rep3


title: Pan01_tumor_rep2


title: Periodontitis 5 [PT5]

description:
raw_count.csv
lcpm_exp.csv


title: monocyte-derived macrophages, Depleted_0h_Rep2

description:
Column header in processed data file: Depleted.0h.R2
Cheng_RNAseqCounts.csv

value: 0 hours


title: YH_6


title: OP_31

value: patient


title: CD140a+ second trimester human fetal brain isolates

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

data_processing:
Cell Ranger to align reads to GRCh38
Genome_build: GRCh38
Supplementary_files_format_and_content: Output from cellRanger that can be imported into Seurat with Read10X

source_name: human fetal brain

extract_protocol:
Human brain samples were obtained under approved Institutional Review Board protocols from consenting patients at Strong Memorial Hospital at the University of Rochester.  Brain tissue was obtained from normal GW 18-24 cortical and/or VZ/SVZ dissections or adult white matter/cortex epileptic resections (18,19, and 27 years old for mRNA, 8, 20, 43, and 54 years old for miRNA).  Fetal GPC acquisition, dissociation and immunomagnetic sorting of A2B5+/PSA-NCAM- cells were as described (Windrem et al., 2004). GPCs were isolated from dissociated tissue using a dual immunomagnetic sorting strategy: depleting mouse anti-PSA-NCAM+ (Millipore, DSHB) cells, using microbead tagged rat anti-mouse IgM (Miltenyi Biotech), then selecting A2B5+ (clone 105; ATCC, Manassas, VA) cells from the PSA-NCAM- pool, as described (Windrem et al., 2004; Windrem et al., 2008). After sorting, cells were maintained for 1-14 days in DMEM-F12/N1 with 10 ng/ml bFGF and 20 ng/ml PDGF-AA. Alternatively  CD140a/PDGFRA-defined GPCs were isolated and sorted using MACS as described (Sim et al., 2011b), yielding an enriched population of CD140+ glial progenitor cells.
Single cells were then captured on a 10X genomics chromium controller utilizing V2 chemistry and libraries generated according to manufacturer’s instructions

value: human fetal brain

tag: cell type/population

value: CD140+ glial progenitor cells


title: Healthy control 9 [H9]

description:
raw_count.csv
lcpm_exp.csv

value: gingiva


title: A2B5+ second trimester human fetal brain isolates


title: Healthy control 8 [H8]

description:
raw_count.csv
lcpm_exp.csv


title: LL2_tumor_rep3

value: whole tumor


title: YH_5

value: musculus vastus lateralis


title: LL2_tumor_rep2


title: Healthy control 7 [H7]

description:
raw_count.csv
lcpm_exp.csv


title: Normal fetal CD140a+ CTX, 5

description:
mRNA expression of dissociated CD140a-sorted glial progenitor cells from normal fetal cortex
fetal_cd140a_5p

data_processing:
Basecalling was performed with Illumina CASAVA
Reads were trimmed and filtered with Trimmomatic; quality was evaluated with FASTQC before and after trimming.
Alignment of reads to the human genome was performed with STAR 2.4.0j to GRCh38.p2, with annotation from Gencode Genes release 22.
Read counts for reads overlapping genomic regions were counted with FeatureCounts from the Subread package.
Genome_build: GRCh38.p2, Gencode Genes annotation release 22
Supplementary_files_format_and_content: gene read counts from FeatureCounts

source_name: Dissociated cells from normal fetal CTX, sorted on CD140a

extract_protocol:
mRNA was extracted and purified with the Qiagen RNeasy kit, according to the manufacturer's instructions.
Libraries were created by first generating cDNA with the SMARTer Ultra Low RNA kit (Clontech) and then taking 1ng of the resulting cDNA for the NexteraXT DNA kit (Illumina), according to the manufacturers’ instructions.

treatment_protocol: Tissue samples were dissociated with papain, cultured in suspension plates in serum-free media, and sorted via MACS and FACS on A2B5 (adult normal samples) or CD140a (fetal normal samples).

tag: tissue source

value: cortex

tag: developmental stage

value: fetal

tag: cell sort marker

value: CD140a+ (PDGFRA)


title: monocyte-derived macrophages, Depleted_1h_Rep2

description:
Column header in processed data file: Depleted.1h.R2
Cheng_RNAseqCounts.csv

value: monocyte-derived macrophage

value: Depleted zymosan

value: 1 hour

value: RNA-seq


title: YH_3

tag: tissue

tag: Sex

value: female

value: healthy


title: YH_4

value: male

tag: age

tag: healthy/patient


title: Healthy control 6 [H6]

description:
raw_count.csv
lcpm_exp.csv

value: Healthy control


title: LL2_tumor_rep1

value: tumor

tag: cell line

tag: cell type

value: Engrafted tumor


title: Normal fetal CD140a+ CTX, 2

description:
mRNA expression of dissociated CD140a-sorted glial progenitor cells from normal fetal cortex
fetal_cd140a_2p


title: Normal fetal CD140a+ CTX, 4

description:
mRNA expression of dissociated CD140a-sorted glial progenitor cells from normal fetal cortex
fetal_cd140a_4p


title: YH_2


title: Healthy control 5 [H5]

description:
raw_count.csv
lcpm_exp.csv


title: BB16_tumor_rep2

tag: treatment


title: Normal fetal CD140a+ CTX, 1

description:
mRNA expression of dissociated CD140a-sorted glial progenitor cells from normal fetal cortex
fetal_cd140a_1p


title: Healthy control 3 [H3]

description:
raw_count.csv
lcpm_exp.csv


title: Healthy control 4 [H4]

description:
raw_count.csv
lcpm_exp.csv


title: Normal adult A2B5+ WM, 414

description:
mRNA expression of dissociated A2B5-sorted glial progenitor cells from normal adult white matter
adult_a2b5_414

source_name: Dissociated cells from normal adult WM (epileptic resection), sorted on A2B5

value: white matter

value: adult


title: Normal adult A2B5+ WM, 412

description:
mRNA expression of dissociated A2B5-sorted glial progenitor cells from normal adult white matter
adult_a2b5_412


title: BB16_tumor_rep1

value: whole tumor


title: Normal adult A2B5+ WM, 411

description:
mRNA expression of dissociated A2B5-sorted glial progenitor cells from normal adult white matter
adult_a2b5_411


title: Healthy control 2 [H2]

description:
raw_count.csv
lcpm_exp.csv

value: gingiva


title: CN,fastGRO2_ICRF_2

city: Dallas

first: Ram

last: Madabhushi

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
Raw FastGRO sequencing reads were processed as described previously. Briefly, reads were trimmed and poly-A sequences were removed using Cutadapt then aligned to the mm10 reference genome using BWA-ALN and filtered/sorted using  Samtools (q=10)
Sorted read files were converted to BAM files and normalized by counts per million (CPM) to create bigWig coverage files using deepTools BamCoverage
BAM files were also used to generate tag directories using HOMER
Tag directories were used to call transcripts with HOMER findpeaks (options: -style groseq -tssFold 6 -bodyFold 5 -pseudoCount 0.5 -minBodySize 500 -maxBodySize 100000) and corresponding FPKM values for known genes using HOMER analyzeRepeats.pl in RNA mode (analyzeRepeats.pl rna mm10 -count genes -strand both -rpkm   -condenseGenes)
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: GRO-seq

source_name: Mouse Cortical Neurons

growth_protocol: Dissociated cortical neurons from E16 Swiss-Webster mice (Charles River) were plated at a density of 5 million cells/plate in 10 cm plates. The plates were pre-coated with poly-D-lysine (0.5 mg/ml) overnight at 37°C, followed by washing twice with dH2O. Neurons were maintained in neurobasal media (GIBCO) supplemented with L-glutamine, penicillin/streptomycin, and B27. Etoposide (ETP, 50µM, Sigma E1383) was dissolved in DMSO. Cells were treated by adding drug directly to the culture media 30 minutes prior to collection

extract_protocol:
DIV13 primary cortical neurons (~20M cells per replicate) were washed twice with ice-cold PBS and collected in a 15 mL conical tube. Cells were incubated in 10 mL swelling buffer (10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 2 U/ml Superase-In (Invitrogen)) for 5 minutes on ice, washed with swelling buffer + 10% glycerol, and resuspended in 10 mL lysis buffer (10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 10% glycerol, 1% IGEPAL, 2 U/ml Superase-In) to isolate nuclei. Isolated nuclei were washed twice with lysis buffer and resuspended in 100 µl freezing buffer (50 mM Tris-HCl pH 8.3, 5 mM MgCl2, 0.1 mM EDTA, 40% glycerol). An equal volume of pre-warmed, 2X nuclear run-on reaction buffer (10 mM Tris-HCl pH 8, 5 mM MgCl2, 300 mM KCl, 1 mM DTT, 0.5 mM ATP, 0.5 mM GTP, 0.5 mM 4-thio-UTP (Trilink), 2 µM CTP, 200 U/ml Superase-in, 1% sarkosyl) was added, and the reaction was incubated for 7 minutes at 30°C. Nuclear run-on (NRO) RNA was extracted with TRIzol LS reagent (Invitrogen) following the manufacturer's instructions and precipitated with ethanol.
Precipitated NRO-RNA was resuspended in 100 µl dH2O, and concentration was determined using a Qubit 4.0 fluorimeter (Thermo). RNA (120-150 µg) was transferred to a new tube and 5 % - 10 % spike-in RNA derived from S2 cells was added. RNA was then fragmented using a bioruptor (Diagenode; high power, 30 seconds on/30 seconds off for 3 cycles) Fragmentation efficiency was analyzed by running fragmented and unfragmented RNA on an Agilent 4200 TapeStation instrument using High Sensitivity RNA ScreenTape following manufacturer's instructions. Fragmented RNA was incubated in biotinylation solution (20 mM Tris pH 7.5, 2 mM EDTA, 40% dimethylformamide, 200 µg/ml EZ-link PDP Biotin (Thermo)) for 2 hours at 25°C with rotation (800 rpm) in a dark room then purified via ethanol precipitation and resuspended in dH2O. M280 streptavidin Dynabeads (Invitrogen) were washed twice with 2 volumes of freshly prepared wash buffer (100 mM Tris pH 7.5, 10 mM EDTA, 1M NaCl, 0.1% Tween-20) and resuspended in 1 volume of wash buffer. Thereafter, biotinylated RNA was affinity purified via incubation with 100 µl washed Dynabeads for 15 minutes at 4°C. After binding, Dynabeads were washed three times with wash buffer pre-warmed at 65°C, and three times with wash buffer at room temperature. RNA was eluted with 100 mM DTT buffer and purified with RNA Clean and Purification kit (Zymo Research) with in-column DNase reaction to eliminate traces of genomic DNA.

treatment_protocol: Etoposide (ETP, 50µM, Sigma E1383) for 30 mins

value: Mouse Cortical Neurons

tag: genotype

value: WT

value: ICRF (ICRF, 20µM) for 30 mins


title: CN,fastGRO2_CON_2

value: CON


title: CN,fastGRO2_ICRF_1


title: CN,fastGRO2_CON_1


title: mM10

city: Davis

first: Sarah

middle: S

last: Wang

address: 1 Shields Ave

institute: University of California, Davis

library_source: genomic

data_processing:
Assembly: mm9
The CpG_Me pipeline (https://github.com/ben-laufer/CpG_Me) was used to perform all data processing steps.
Trim Galore was used to trim adapters and methylation bias.
FastQ Screen was used to screen for sample contamination.
Bismark was used align to the reference genome, remove PCR duplicates, calculate coverage, extract CpG methylation, and generate genome-wide cytosine reports (CpG count matrices).
Picard Tools was used to calculate insert size metrics.
MultiQC was used for quality control.
Supplementary files format and content: Bismark CpG methylation bedgraph files

molecule: genomic DNA

source_name: pancreatic ductal adenocarcinoma mouse organoid

growth_protocol: Mouse organoids were grown to 70-90% confluency in a 50 uL dome of 100% Matrigel overlaid with 500 uL of mouse complete media [DMEM F12 Advanced (Invitrogen), 10 mM HEPES pH 7.2-7.5 (Invitrogen), 1X GlutaMax (Invitrogen), 1X Penicillin/Streptomycin (Invitrogen), 0.5 uM A83-01 (Tocris), 0.05 ug/mL mEGF (Invitrogen), 0.1 ug/mL FGF-10 (Peprotech), 0.01 uM Gastrin I (Sigma), 0.1 ug/mL mNoggin (Peprotech), 1.25 mM N-aceylcysteine (Sigma), 10 mM Nicotinamide (Sigma), 1X B27 Supplement (Invitrogen), 10% R-spondin-conditioned media], in 4-6 wells of a 24-well plate.

extract_protocol:
Media was removed from Matrigel domes, and 4-6 wells of organoids were harvested in 1 mL of mouse splitting medium [DMEM F12 Advanced (Invitrogen), 10 mM HEPES pH 7.2-7.5 (Invitrogen), 1X GlutaMax (Invitrogen), 1X Penicillin/Streptomycin (Invitrogen)]. DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit per manufacturer's instructions.
Swift BioSciences Accel-NGS Methyl-Seq DNA Library Kit
Whole genome bisulfite sequencing (WGBS)

tag: tumor stage

value: metastasis

tag: mouse background

value: KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre

tag: metastatic site

value: peritoneum


title: mM6

value: pancreatic ductal adenocarcinoma mouse organoid


title: mM3P


title: BB16_tumor_rep3


title: MNase-seq_231_DOX_12h_BRG1_shRNA-rep3

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

data_processing:
Adapter sequences were removed with cutadapt v1.2.1.
Reads were mapped to the hg19 genome using Bowtie 1.2 with paramters -m 1 -X 2000 --chunkmbs 1024.
Mapped hits were filtered to retain only those with fragment size 120-170bp.
Signal tracks were generated after collapsing mononucleosome-sized fragments to their midpoint coordinate, with conversion to bedGraph via Bedtools v2.17.0 genomeCoverageBed followed by conversion to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: hg19
Supplementary files format and content: coverage tracks in bigWig format

growth_protocol: DMEM High glucose + 10% FBS

extract_protocol:
MNase digested DNAs were purified by Phenol-chloroform extraction with ethanol precipitation
MNase-seq libraries were prepared by NEXTFLEX Rapid DNA-Seq kit (PerkinElmer).

treatment_protocol: For transient GATA3 expression, DOX (1 µg/ml at final) was added to medium. For CHD4 knockdown, MDA-MB-231 cells were infected with lentiviruses encoding CHD4 shRNA. After overnight incubation, the meidum was replaced with fresh medium and the cells were further incubated for 2 days until DOX induction.

tag: passages

tag: time point


title: mM1

value: liver


title: MNase-seq_231_DOX_12h_BRG1_shRNA-rep2


title: nonPSC_4_IL17

first: Alexander

middle: Quinn

last: Wixom

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, and gene counting were completed using the 10x Genomics Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Further processing was performed through the Seurat v4 pipeline for QC, normalization, and utilization of Harmony to integrate the samples into a single object for tertiary analysis.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Extrahepatic bile duct

extract_protocol:
ECO from PSC (n=4) and non-PSC patients (n=4), all at passage 3, were treated with vehicle or human recombinant IL-17A (100 ng/mL) for 24 hours. The organoids underwent trypsin digestion followed by mechanical dissociation to obtain single cell suspensions in PBS + 0.1% BSA and were submitted to the Gene Analysis Core of the Medical Genome Facility (Mayo Clinic, Rochester, MN) for scRNA-seq analysis.
The cDNA master mix was prepared according to the manufacture’s instruction for Chromium Next GEM Single Cell 3’ Library and Gel Bead Kit (10x Genomics, Pleasanton, CA). The standard targeted cell recovery was set to ~3000 cells. The cell suspension and master mix thawed gel beads and partitioning oil were added to a Chromium Single Cell G chip. The filled chip was loaded into the Chromium Controller, where each sample was processed and the individual cells within the sample were partitioned into uniquely labeled GEMs (Gel Beads-In-Emulsion). The GEMs were collected from the chip and subjected to reverse transcription, GEM dissolution, and cDNA clean-up.  The resulting cDNA contained a pool of uniquely barcoded molecules. A portion of the pooled cDNA was used for library construction, where standard Illumina sequencing primers and a 10x Genomics unique i7 sample index were added to each cDNA pool. All cDNA pools and resulting libraries were measured using Qubit High Sensitivity assays (Thermo Fisher Scientific, Waltham, MA) and Agilent Bioanalyzer High Sensitivity chips (Agilent, Santa Clara, CA). Libraries were sequenced at between 40,000 and 50,000 fragment reads per cell following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit (Illumina, San Diego, CA). The flow cells were sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 HD using HiSeq 3000/4000 sequencing kit and HCS v3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7.

tag: patient diagnosis

value: non-PSC

value: Cholangiocytes

value: Extrahepatic bile duct

tag: strain

value: organoids

tag: passage

value: passage 3


title: YH_1

value: musculus vastus lateralis

value: male

value: healthy


title: MNase-seq_231_DOX_12h_BRG1_shRNA-rep1


title: mT23

value: tumor


title: CN,TOP2Bcc-seq_Input_2

data_processing:
Raw FASTQ sequencing reads were analyzed for quality control using FastQC, trimmed using Trimmomatic, and aligned to the mm10 reference genome (GRCm38.p6 assembly) using BWA-MEM.
BAM files were marked and filtered for duplicate reads using Sambamba and Samtools, respectively.
Peaks were called using MACS2 from biological duplicates and pseudo-replicates where each ChIP sample was normalized to input DNA.
MACS2-generated bedGraph files were converted to bigWig files using Kent Utils for individual replicates and pooled replicates
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
TOP2Bccs were isolated from sonicated lysates containing covalently bound proteins via native TOP2B ChIP. Prior to immunoprecipitation, 1% of each sample transferred to a clean tube to be used for input normalization. Samples were then incubated with anti-TOP2B antibody (1:50, H-8, sc-25330, RRID:AB_628384) overnight at 4°C followed by incubation with ChIP-grade protein A/G magnetic beads (Thermo) for 3 hours at 4°C. Antibody-conjugated beads were washed with low salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 150 mM NaCl), high salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 500 mM NaCl), LiCl buffer (10 mM Tris-HCl pH 8, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 0.25 M LiCl), and twice with TE buffer (50 mM Tris-HCl pH 8, 1 mM EDTA) for 5 minutes each with agitation at room temperature. Immunoprecipitated TOP2B-DNA complexes were eluted from the magnetic beads in 500 µl ChIP elution buffer (1% SDS, 0.1 M NaHCO3) and purified along with input DNA via phenol-chloroform extraction and ethanol precipitation. Precipitated DNA was washed with 70% ethanol and resuspended in TE buffer.
To prepare libraries for sequencing, immunoprecipitated DNA was first end-repaired, A-tailed, and ligated with paired-end, Illumina barcoded adapters (KAPA biosciences) according to the manufacturer’s instructions. Attempts to amplify libraries for sequencing after this step alone proved unsuccessful, implying the successful isolation of TOP2Bccs. Following the first round of adapter ligation, the 5’strand was digested with l exonuclease (NEB). The resulting 3’strand was used as a temple for 10 rounds of primer extension (cycling conditions: 95°C for 3 min, ten rounds of linear amplification (95°C for 1 min, 57°C for 1 min and 72 °C for 3 min), 95°C for 1 min, hold at 4°C) using primers against the ligated adapter in a solution containing 1X HiFi Phusion buffer (NEB), 0.8 mM dNTPs, 2 U Phusion DNA polymerase (NEB) and 40 nM of P7 extension primer (CAAGCAGAAGACGGCATACGA*G; *denotes phosphorothioate linkage). The resulting single-stranded products were purified using 0.8X Ampure XP beads (Beckman), eluted in 35 µl TE dH2O, and concentrated to a volume of 18 µl using a vacuum centrifuge (Eppendorf). The purified products were appended with ribo-G in 1X terminal deoxynucleotidyl transferase buffer (NEB), 20 U terminal deoxynucleotidyl transferase enzyme (NEB), and 4 mM of rGTP at 37 °C for 15 min followed by 0.8X Ampure XP bead clean-up and elution as before. The single-stranded, ribo-tailed products were ligated to double-stranded adapters with CCC overhang (oligo 1, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCCC; oligo 2, (Phosphate)GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG) as described previously2. Ligated products were used as templates for standard paired-end library amplification (KAPA biosciences) with an additional extension step prior to linear amplification to create double-stranded DNA templates (cycling conditions: 60°C for 3 min, 98°C for 30 sec, eleven cycles of amplification (98°C for 10 s, 65°C for 30 s, and 60°C for 30 s), 60°C for 5 min and hold at 4°C). The final PCR products were purified using 0.8X Ampure XP beads, eluted in 40 µl EB (Qiagen). DNA fragment size was assessed via Tapestation (Agilent) and additional Ampure XP bead clean-up steps were performed to obtain a final library size of 350-450 bp. DNA concentration was quantified by fluorometry (dsDNA high sensitivity Qubit assay, Thermo) to ensure equal DNA concentration for each replicate before replicates were pooled and sequenced on an Illumina NextSeq 500 instrument using V2.5 reagents to an average depth of 25-35 million reads per replicate.

value: Mouse Cortical Neurons

value: WT

value: Etoposide (ETP, 50µM) for 30 mins


title: mT19


title: MNase-seq_231_DOX_12h_CHD4_shRNA-rep3


title: nonPSC_4_CNT

description: 10x Genomics

value: vehicle


title: mT6

value: KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre


title: Healthy control 1 [H1]

description:
raw_count.csv
lcpm_exp.csv

value: gingiva

tag: subject status

value: Healthy control


title: nonPSC_5_IL17

description: 10x Genomics

tag: tissue


title: MNase-seq_231_DOX_12h_CHD4_shRNA-rep2


title: YH_12

data_processing:
Adapter sequences and low quality reads were trimmed using the Timmomatic tool (v0.36) (options:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35)
High-quality reads were aligned to the reference human GRCh38.p13 primary assembly genome using HISAT v2.1.0
Uniqe reads were counted for known exons of each gene using Rsubread package (R) and Ensembl annotation (GRCh38.101)
TPM values calculated using kallisto v0.44.0
Assembly: GRCh38.p13 primary genome assembly
Supplementary files format and content: tab-delimited text files: Read_counts.txt — uniquely aligned read counts for genes

extract_protocol:
A frozen muscle sample (~10-15 mg) was lysed by the RLT buffer (Qiagen, Germany) using a drill homogenizer and total RNA was extracted by a silica spin column (CleanRNA Standard, Evrogen, Russia). RNA concentration and integrity were evaluated by a fluorimetric assay (Qubit 4, ThermoScientific, USA) and capillary electrophoresis (TapeStation, Agilent, Germany), respectively.
Strand-specific libraries were prepared by the NEBNext Ultra II Directional RNA Library Preparation kit (NEB, USA)

tag: Sex


title: CN,TOP2Bcc-seq_Input_1


title: CN,TOP2Bcc-seq_ChIP_1


title: CN,TOP2Bcc-seq_ChIP_2


title: mT3

value: pancreatic ductal adenocarcinoma mouse organoid


title: CN,RNA-seq_in_Control_3

data_processing:
The generated fastq files were trimmed using Trimmomatic and aligned to the UCSC mouse reference genome assembly mm10 using TopHat.The aligned reads were processed by HTSeq-Count.
The TopHat program used the high-throughput short read aligner, Bowtie, to align the reads to the reference genome.
Assembly: mm10
Supplementary files format and content: Text file with vm4 TPM quantification for 3 biological reps

extract_protocol:
QIAgen RNAeasy
One microgram of total DNAse treated RNA is then prepared with the TruSeq Stranded mRNA Library Prep Kit from Illumina. Poly-A RNA is purified and fragmented before strand specific cDNA synthesis. cDNA are then a-tailed and indexed adapters are ligated. After adapter ligation, samples are PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200. Before being normalized and pooled, samples are quantified by Qubit then run on the Illumina NextSeq 500 using V2.5 reagents.


title: MNase-seq_231_DOX_12h_CHD4_shRNA-rep1


title: nonPSC_5_CNT

description: 10x Genomics

value: non-PSC


title: mP2

source_name: PanIN mouse organoid

value: PanIN mouse organoid

value: female

value: PanIN


title: MNase-seq_231_DOX_12h_control_shRNA-rep3


title: mP1

value: Trp53LSL-R172H; Pdx1-Cre


title: MNase-seq_231_DOX_12h_control_shRNA-rep2


title: nonPSC_3_IL17

description: 10x Genomics

value: Cholangiocytes

value: Extrahepatic bile duct

value: organoids

value: passage 3


title: nonPSC_2_CNT

description: 10x Genomics


title: nonPSC_2_IL17

description: 10x Genomics


title: PSC_9_IL17

description: 10x Genomics

value: primary sclerosing cholangitis (PSC)


title: MNase-seq_231_DOX_12h_control_shRNA-rep1


title: mN11

source_name: normal pancreatic ductal mouse organoid

value: normal pancreatic ductal mouse organoid

value: normal

value: Wild type


title: PSC_9_CNT

description: 10x Genomics

value: vehicle


title: CN,RNA-seq_in_Control_1

value: Mouse Cortical Neurons

value: WT


title: CN,fastGRO_ETP_2

value: Etoposide (ETP, 50µM) for 30 mins


title: mN5


title: MNase-seq_231_DOX_6h_control_shRNA-rep3


title: CN,fastGRO_ETP_1


title: CN,fastGRO_CON_2

value: CON


title: NFKBIE_vitro_rep3

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

description: NFKBIE-wt TCL1-355 TKO cells Targeted exon 2 of the NFKBIE gene by nucleofection-mediated delivery of a ribonucleoprotein complex containing recombinant Cas9 and a NFKBIE guide RNA Retrieved from in vitro colture

data_processing:
Basecalls performed using CASAVA (Illumina Inc.)
Transcript quantification was conducted with Salmon (v1.8)  mapped to the Mus musculus genome version GRCm39 and with reference gtf annotation version 103.
Read counts generated by Salmon were analysed by using DESeq2 package (Love, 2014) for detecting transcripts that were differentially expressed. An adjusted p-value cut off of 0.05 was decided as threshold for detection of DEGs.
Assembly: Mus musculus genome version GRCm39 and with reference annotation gtf version 103.
Supplementary files format and content: Tab-delimited text files include COUNTS values for each Sample

source_name: NFKBIE-ko TCL1-355 TKO cells

growth_protocol: Cells were thawed and cultured in RPMI-1640 supplemented with 10% heat-inactivated FBS, 100U/mL penicillin, 0.1mg/mL streptomycin, 2mM L-glutamine, and 1mM sodium pyruvate (Invitrogen) at a concentration of 0.5x106 per mL for 20 hours prior to CRISPR/Cas9 editing with the Alt-R system.

extract_protocol:
Total RNA was extracted with RNeasy Micro Kit (Quiagen) following manufacturer recommendations.
The RNA-seq libraries were prepared according to the standard Illumina protocol with the mRNA-seq Illumina TruSeq. cDNA libraries were checked for quality and quantified using the DNA-1000 kit (Agilent) on a 2100 Bioanalyzer.
RNA-Seq on a Illumina NovaSeq 6000 instrument, using a 150-bp, dual-indexed, paired-end sequencing configuration

treatment_protocol: A predesigned IDT cr-RNA (AGTGATTCACGAAGCCCCGT) was used for targeting the NFKBIE gene. To generate the Cas9 ribonucleoprotein (RNP) complexes, the cr-RNA (1.5 mM) was combined with 1.5 mM ATTO 550-labeled trans-activating cr-RNA, 0.75 mM recombinant Cas9 protein, and 1.5 mM Alt-R Cas9 electroporation enhancer in 5 mL of nuclease-free duplex buffer (IDT). The Cas9 RNP complex was then electroporated using the Amaxa Nucleofector II device and the Z-001 program into 6x106 leukemic cells resuspended in 100ml Mouse B cell Nucleofector solution (Lonza).

value: blood

value: TCL1-355 TKO

value: leukemia cell line


title: CN,RNA-seq_in_Control_2


title: MNase-seq_231_DOX_6h_control_shRNA-rep1


title: MNase-seq_231_DOX_6h_control_shRNA-rep2


title: CN,CTCF_Input_2

data_processing:
Raw FASTQ sequencing reads were analyzed for quality control using FastQC, trimmed using Trimmomatic, and aligned to the mm10 reference genome (GRCm38.p6 assembly) using BWA-MEM.
BAM files were marked and filtered for duplicate reads using Sambamba and Samtools, respectively.
Peaks were called using MACS2 from biological duplicates and pseudo-replicates where each ChIP sample was normalized to input DNA.
MACS2-generated bedGraph files were converted to bigWig files using Kent Utils for individual replicates and pooled replicates
IDR (irreproducible discovery rate thresholding was performed on MACS2 peak calls using an IDR threshold of 0.05.
Assembly: mm10
Supplementary files format and content: BED - IDR thresholded peaks

extract_protocol:
CTCF ChIP was performed for two biological replicates using a ChIP assay kit (MilliporeSigma) as described by the manufacturer. Briefly, DIV13 primary cortical neurons (~15M cells per replicate) were crosslinked with 1% formaldehyde for 10 minutes at 37°C, washed twice with ice-cold PBS, scraped, and resuspended in SDS lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS, protease and phosphatase inhibitor cocktail). Cells were sonicated to shear DNA to 200-500 bp using a bioruptor (Diagenode; high power, 30 seconds on/30 seconds off for 40 cycles). Samples were then centrifuged at 13,000 RPM for 10 minutes at 4°C to remove cellular debris, and the supernatant was diluted up to 2 mL in ChIP dilution buffer (16.7 mM Tris-HCl pH 8, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS). Prior to immunoprecipitation, 1% of each sample transferred to a clean tube to be used for input normalization. Samples were then incubated with anti-CTCF antibody (1:200, CST, #3418) overnight at 4°C followed by incubation with ChIP-grade protein A/G magnetic beads (Thermo) for 3 hours at 4°C. Antibody-conjugated beads were washed with low salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 150 mM NaCl), high salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 500 mM NaCl), LiCl buffer (10 mM Tris-HCl pH 8, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 0.25 M LiCl), and twice with TE buffer (50 mM Tris-HCl pH 8, 1 mM EDTA) for 5 minutes each with agitation at room temperature. Immunoprecipitated CTCF-DNA complexes were eluted from the magnetic beads in 500 µl ChIP elution buffer (1% SDS, 0.1 M NaHCO3). DNA-protein crosslinks for immunoprecipitated samples and input DNA were reversed via incubation with an additional 20 mM NaCl for 4 hours at 37°C and residual protein was digested with Proteinase K (NEB) for 1 hour at 45°C. DNA was precipitated using phenol/chloroform isolation and ethanol precipitation, washed with 70% ethanol, and resuspended in 50 µl TE buffer.
Samples were prepared for sequencing using a paired-end library preparation kit compatible with Illumina sequencing instruments (KAPA biosciences) according to the manufacturer’s instructions. Following library amplification, DNA fragment size was assessed via Tapestation (Agilent) to ensure a final library size of 350-450 bp. DNA concentration was quantified by fluorometry (dsDNA high sensitivity Qubit assay, Thermo) to ensure equal DNA concentration for each replicate before replicates were pooled and sequenced on an Illumina NextSeq 500 instrument using V2.5 reagents to an average depth of 25-35 million reads per replicate.


title: nonPSC_3_CNT

description: 10x Genomics

value: non-PSC


title: MNase-seq_231_DOX_3h_control_shRNA-rep3


title: NFKBIE_spleen_rep2

description: NFKBIE-wt TCL1-355 TKO cells Targeted exon 2 of the NFKBIE gene by nucleofection-mediated delivery of a ribonucleoprotein complex containing recombinant Cas9 and a NFKBIE guide RNA Retrieved from spleen


title: NFKBIE_spleen_rep3

value: Targeted exon 2 of the NFKBIE gene by nucleofection-mediated delivery of a ribonucleoprotein complex containing recombinant Cas9 and a NFKBIE guide RNA


title: MNase-seq_231_DOX_3h_control_shRNA-rep2


title: MNase-seq_231_DOX_3h_control_shRNA-rep1


title: NFKBIE_spleen_rep1


title: NFKBIE_peritoneal_rep4

description: NFKBIE-wt TCL1-355 TKO cells Targeted exon 2 of the NFKBIE gene by nucleofection-mediated delivery of a ribonucleoprotein complex containing recombinant Cas9 and a NFKBIE guide RNA Retrieved from peritoneal cavity


title: PSC_8_CNT

description: 10x Genomics

value: Cholangiocytes

value: Extrahepatic bile duct


title: PSC_6_CNT

description: 10x Genomics

value: organoids

value: passage 3


title: PSC_4_CNT

description: 10x Genomics

value: primary sclerosing cholangitis (PSC)


title: PSC_6_IL17

description: 10x Genomics


title: PSC_8_IL17

description: 10x Genomics


title: PSC_4_IL17

description: 10x Genomics


title: CN,CTCF_Input_1


title: MNase-seq_231_DOX_0h_control_shRNA-rep3


title: Exp16

city: Oeiras

first: Rui

last: Martins

address: Rua da Quinta Grande 6

department: Inflammation

country: Portugal

institute: Gulbenkian Institute for Molecular Medicine

data_processing:
Primary data analysis, including base calling and quality scoring is performed by real-time analysis (RTA) on the instrument during the sequencing run. The NextSeq 500 uses a new implementation of RTA called RTA 2.0
RNAseq reads were aligned to the mm39 genome using the GENCODE vM27 annotation to extract splice junction information. Alignment performed using STAR (v.2.5.2a) with parameters: --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${SAMPLE} --sjdbOverhang 99 --sjdbGTFfile ~/All/GRCm39/gencode.vM27.primary_assembly.annotation.gtf --runThreadN 8
Read summarization was performed by assigning uniquely mapped reads to genomic features using FeatureCounts (v.1.5.0-p1), with following parameters: -a ~/All/GRCm39/gencode.vM27.primary_assembly.annotation.gtf -o -Q20 --primary --ignoreDup -T 4
Gene expression tables were imported into the R programming language and environment (v.4.1.0) and normalized gene expression counts were obtained using the DESEq2 R package (v.1.32) package with the function counts using the option normalized = TRUE.
Assembly: mm39
Supplementary files format and content: Tab-delimited feature counts table with raw gene counts for every gene; one file per sample
Supplementary files format and content: Summary tab-separated table with summarized alignment data.
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: mRNA from Ex-Treg cells (GFP-, tdT+)

extract_protocol:
RNA extraction (QIAgen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Recipient Rag2-/- mice were non-lethally irradiated and reconstituted with mixed bone marrow (50% Foxp3GFP-tdT  or Foxp3GFP-Fth/-tdT and 50% C57BL/6 bone marrow) for 6 weeks. Engraftment was verified 6 weeks post transplatation and cells were collected for RNAseq analysis.

tag: tissue/cell type

value: Lymph node Ex-Treg

tag: age

value: 15,28 weeks old

value: BM donor:Foxp3Cre-GFPtdTfl/flFthfl/fl


title: CN,CTCF_ChIP_1

value: Mouse Cortical Neurons


title: CN,CTCF_ChIP_2

value: WT


title: NFKBIE_spleen_rep4

tag: cell line


title: Exp15

source_name: mRNA from Treg cells (GFP+, tdT+)

value: Lymph node Treg


title: MNase-seq_231_DOX_0h_control_shRNA-rep1


title: Exp14


title: Exp13


title: RNA-seq_Time_12h_CHD4_shRNA_rep2

data_processing:
Reads were filtered based on a mean base quality score >20.
Read pairs were mapped against the hg19 reference genome by STAR (version 2.5) with the following parameters: -- outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 -- outMultimapperOrder Random (other parameters at default settings).
Mapped read counts per gene were collected by Subread featureCounts (version 1.5.0-p1) with paramters -s2 -Sfr -p.
Coverage tracks were generated via STAR (version 2.5) inputAlignmentsFromBAM function with parameters --outWigStrand Stranded --outWigNorm None, then normalized by size factors reported by DESeq2 (v1.10.1), and converted to bigWig format by UCSC utility bedGraphToBigWig.
Assembly: hg19
Supplementary files format and content: coverage tracks in bigWig format
Supplementary files format and content: raw counts per gene in tab-delimited text format

extract_protocol:
RNAs were purified by the RNeasy kit (Qiagen).
RNA-seq libraries were generated by the TruSeq RNA library preparation kit.


title: RNA-seq_Time_12h_CHD4_shRNA_rep3


title: xbp1-s+bhlha15-me_batch-C

city: Cambridge

first: Yiqun

address: 1414 Massachusetts Avenue

institute: Harvard University

description: 10x Genomics, V3.1

data_processing:
The cellranger command line tool was used to map reads in the fastq files to reference transcriptomes with the "cellranger count" command
For libraries that include xbp1-s misexpression (ME-E-5 to ME-E-8), the reference transcriptome was modified: the mis-expressed, codon-optimized, xbp1-s sequence was appended to the reference transcriptome.
Assembly: dr99
Supplementary files format and content: All processed data are output from the "cellranger count" command. barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz can be collectively input into third-party packages to allow users to wrangle the barcode-feature matrix. The matrix contains only detected cell-associated barcodes. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). The filtered_feature_bc_matrix.h5 files contain the same detected cell-associated feature and barcode information in HDF5 format.

organism: Danio rerio

source_name: Whole embryo

growth_protocol: Zebrafish embryos were collected at 1-cell stage and cultured in standard E3 medium in a 27°C incubator until desired stages.

extract_protocol:
At desired developmental stages (8hpf or 12hpf), approximately 30 embryos per sample were de-chonrionated with pronase. For libraries prepared with 10x chromium Single Cell 3' V3 chemistry, embryos for each condition were transferred into a 2ml eppendorf tube containing ice-cold deyolking buffer buffer (55 mM NaCl, 1.8 mM KCl, 1.25 mM NaHCO3). Embryos were pipetted up and down gently with a p1000 tip then shook at 1200 rpm at 4°C for 20 sec in a Thermal shaker. The tubes were then spun down at 4 °C with 250 g for 4 min. Supernatant was discarded and 1 ml wash buffer (10 mM Tris pH 8.5, 110 mM NaCl, 3.5 mM KCl, 2.7 mM CaCl2) was used to resuspend the cell pellet. The tubes were centrifuged again at 4 °C with 250 g for 4 min. 1 ml DMEM (gibco, 11594426) with 0.1% BSA was used to resuspend cells. Centrifuging and DMEM resuspension was repeated twice more, with the last resuspension step using 300 – 500 μl DMEM with 0.05% BSA. Cell suspension was then passed through a 40 μm cell strainer. For libraries prepared with 10x chromium Single Cell 3' V3.1 chemistry, several modifications were made to the dissociation protocol described above. Briefly, after being transferred to 2ml Eppendorf tubes, embryos were first incubated in a protease solution (10 mg/ml BI protease [Sigma, P5380], 125 U/ml DNaseI, 2.5 mM EDTA in DPBS) on ice for 4min. Embryos were then washed with a stop solution (30% FBS, 0.875 mM CaCl2 in DPBS) and gently triturated (by pipetting) in Ringer’s solution. Centrifuging, resuspending, and filtering steps were then performed as in the previous protocol, but with the Ringer's solution used as the wash buffer.
Cells were encapsulted and libraries were constructed with 10X Chromium instrument with the Single Cell 3' Reagent Kits (V3 and V3.1)

treatment_protocol: 1-cell stage embryos were either injected with Cas9 and gRNA, injected with mRNA, or uninjected according to experimental conditions.

value: Whole embryo

value: TL/AB

tag: developmental stage

value: 8 hpf

value: xbp1-s+bhlha15 co-mis-expression in xbp1+atf6 double crispant


title: bhlha15-me_batch-C (50pg)

description: 10x Genomics, V3.1

value: bhlha15 mis-expression in xbp1+atf6 double crispant


title: xbp1-s-me_batch-C (70pg)

description: 10x Genomics, V3.1

value: xbp1-s mis-expression in xbp1+atf6 double crispant


title: CN,fastGRO_CON_1

tag: cell type

tag: treatment

value: CON


title: NFKBIE_vitro_rep1

value: blood

value: TCL1-355 TKO

value: leukemia cell line

value: Targeted exon 2 of the NFKBIE gene by nucleofection-mediated delivery of a ribonucleoprotein complex containing recombinant Cas9 and a NFKBIE guide RNA


title: NFKBIE_peritoneal_rep3


title: NFKBIE_peritoneal_rep2


title: NFKBIE_vitro_rep2


title: Exp11

tag: genotype


title: Exp10

value: Lymph node Ex-Treg


title: MOCK_spleen_rep4

description: NFKBIE-wt TCL1-355 TKO cells Retrieved from spleen

source_name: NFKBIE-wt TCL1-355 TKO cells

value: NFKBIE-wild type


title: MOCK_vitro_rep3

description: NFKBIE-wt TCL1-355 TKO cells Retrieved from in vitro colture


title: RNA-seq_Time_0h_CHD4_shRNA_rep1


title: MOCK_spleen_rep3


title: Exp9

value: 15,28 weeks old

value: BM donor:Foxp3Cre-GFPtdTfl/flFthfl/fl


title: Exp8

value: 17 weeks old

value: BM donor:Foxp3Cre-GFPtdTfl/fl


title: creb3l2-N-me (40pg)

description: 10x Genomics, V3

value: Whole embryo

value: creb3l2-N mis-expression in xbp1 crispant


title: mCherry-me_batch-C (120pg)

description: 10x Genomics, V3.1

value: TL/AB

value: 8 hpf

value: nls-mCherry mis-expression in xbp1+atf6 double crispant


title: RNA-seq_Time_12h_control_shRNA_rep3


title: creb3l1-N-me (40pg)

description: 10x Genomics, V3

value: creb3l1-N mis-expression in xbp1 crispant


title: MOCK_spleen_rep1


title: NFKBIE_peritoneal_rep1


title: MOCK_spleen_rep2


title: Exp6


title: RNA-seq_Time_12h_control_shRNA_rep2


title: RNA-seq_Time_12h_CHD4_shRNA_rep1


title: RNA-seq_Time_0h_CHD4_shRNA_rep3


title: Exp5

value: Lymph node Treg


title: RNA-seq_Time_0h_CHD4_shRNA_rep2


title: RNA-seq_Time_12h_control_shRNA_rep1


title: MOCK_peritoneal_rep3

description: NFKBIE-wt TCL1-355 TKO cells Retrieved from peritoneal cavity

value: blood


title: MOCK_peritoneal_rep2

value: TCL1-355 TKO


title: Exp4


title: RNA-seq_Time_0h_control_shRNA_rep2


title: creb3l2-full-me (40pg)

description: 10x Genomics, V3

value: creb3l2-full-length mis-exprerssion


title: Exp2


title: RNA-seq_Time_0h_control_shRNA_rep1


title: Exp3


title: RNA-seq_Time_0h_control_shRNA_rep3


title: mCherry-me (125pg)

description: 10x Genomics, V3

value: nls-mCherry mis-expression


title: mCherry-me (40pg)

description: 10x Genomics, V3

value: NLS-mCherry mis-expression in xbp1 crispant


title: xbp1+bhlha15-cr_batch-C

description: 10x Genomics, V3.1

value: 12 hpf

value: xbp1+bhlha15 double crispant


title: MOCK_vitro_rep1

value: leukemia cell line

value: NFKBIE-wild type


title: MOCK_peritoneal_rep1


title: bhlha15-cr_batch-C

description: 10x Genomics, V3.1

value: bhlha15 crispant


title: Exp1

value: 17 weeks old

value: BM donor:Foxp3Cre-GFPtdTfl/fl


title: xbp1-cr_batch-C

description: 10x Genomics, V3.1

value: Whole embryo

value: TL/AB

value: xbp1 crispant


title: atf6-N-me (40pg)

description: 10x Genomics, V3

value: 8 hpf

value: atf6-N mis-expression in xbp1 crispant


title: Ty1_ChIP-seq_Time_48h_rep1

data_processing:
Reads were filtered based on a mean base quality score >20.
Reads were mapped to hg19 genome using Bowtie 0.12.8 with parameters '-I 0 -X 2000 -m 1'.
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
Coverage tracks generated with Bedtools v2.17.0 genomeCoverageBed after converting paired-end reads to a single fragment, then format conversion via UCSC utility bedGraphToBigWig.
Peak calling was performed with HOMER v4.1 at default parameters.
Assembly: hg19
Supplementary files format and content: coverage tracks in bigWig format
Supplementary files format and content: peak calls in BED format

extract_protocol:
For ChIP, AMPure XP (Beckman Coulter) was used to purify DNAs.
ChIP-seq libraries were prepared by NEXTFLEX Rapid DNA-Seq kit (PerkinElmer).

tag: chip antibody

value: anti-Ty1 (MilliporeSigma BB2)


title: Ty1_ChIP-seq_Time_48h_rep2


title: MOCK_peritoneal_rep4

value: blood

value: TCL1-355 TKO


title: H2548

city: Cold Spring Harbor

first: David

middle: A.

last: Tuveson

address: 1 Bungtown Rd.

department: Cancer Center

institute: Cold Spring Harbor Laboratory

description:
Mouse ID H2548
tumor_cells_gene_barcode_matrix.h5
tumor_cells_annotation.csv
Monocle_epithelial_2021.rds
Seurat_epithelial_2021.rds

data_processing:
scRNA-seq reads were processed into FASTQ files and aligned to the mouse GRCm38 genome reference version 2.1.0 from 10X Genomics (cellranger-mm10-2.1.0) using Cellranger version 2.1.1 (10X Genomics) and default parameters.
Filtered gene barcode matrices from 10x CellRanger pipeline were used for further data analysis.
Cells first went throught basic quality filtering and pre-processing before merging, including minimum 500 genes, less than 15% mitochodiral UMIs, library size normalization, log1p transformation, followed by umi, percentage mitochodrial and percentage ribosomal gene expresion regression, and scaling.
Dataset merging was conducted using Seurat program (version 2). Highly varible genes (HVGs) were identified using Seurat method. The union of HVGs of each dataset was used for canonical correlation analysis in Seurat.
t-SNE dimensionality reduction was performed on integrated dataset and cell clustering was based on shared nearest neightbor modularity optimization method available in Seurat.
Monocle 2 program was used for construction of pseudotime trajectory.
Genome_build: mm10
Supplementary_files_format_and_content: The H5 files contain the filtered gene barcode matrix in H5 format. The tumor annotation CSV file and the Epithelial metadata CSV file contain information on each cell in the analysis. The Seurat RDS file contains the Seurat results. The Monocle RDS file contains the Monocle results.

source_name: KPC tumor

growth_protocol: KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre (KPC) mice were bred and allowed to grow until they developed palpable tumors 1-2 cm in diameter.

extract_protocol:
Single-cell barcoding and library preparation were performed using the 10X ChromiumTM version 2 chemistry, according to the manufacturer’s protocol.
cDNA and libraries were prepared using the 10X ChromiumTM version 2 chemistry, according to the manufacturer’s protocol.

treatment_protocol: Tumor specimens from KPC mice were minced and enzymatically digested in 5% FBS/DMEM supplemented with 2.5 mg/mL Collagenase D , 0.5 mg/mL Liberase DL, and 0.2 mg/mL DNase I for 1h at 37°C with agitation. Cell digests were strained through a 100 μm cell strainer. The cell suspension was spun down, and cell pellets were resuspended in ACK lysis buffer to eliminate red blood cells. After a 3 minute incubation on ice, the ACK was quenched with 5% FBS/DMEM. Cells were spun down, resuspended in PBS supplemented with 0.5% BSA. KPC tumor cells were enriched with Tumor Cell Isolation Kit, mouse (Miltenyi Biotech) by magnetic cell sorting (MACS), according to manufacturer’s instructions. Up to 12,000 cells were loaded per lane on 10X Chromium microfluidic chips for single cell capture.

tag: tissue origin

value: Pancreatic ductal adenocarcinoma


title: DC2.4_HPV16 E5_2

city: La Jolla

first: Sayuri

last: Miyauchi

address: 3855 Health Sciences Drive

institute: University of California, San Diego

data_processing:
Raw reads filtering was as follows: (1) Removed reads with adaptor contamination.
(2) Removed reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).
(3) Removed reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent  of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
Clean RNA-sequencing reads were mapped to the reference genome using STAR software.
Aligned read counts were further used for downstream differential gene expression analysis using DESeq2 software.
Assembly: hg19, mm10
Supplementary files format and content: csv files include FPKM values for each sample.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using Nextera DNA Flex Library Prep Kit following manufacturer's protocols.

value: Dendritic cell

value: HPV16 E5 positive


title: Ty1_ChIP-seq_Time_24h_rep2

tag: passages


title: DC2.4_HPV16 E5_1

value: Empty vector control


title: tyr-cr_batch-C

description: 10x Genomics, V3.1

value: 12 hpf

value: tyr crispant


title: MOCK_vitro_rep2

value: leukemia cell line

value: NFKBIE-wild type


title: Ty1_ChIP-seq_Time_24h_rep1

tag: time point


title: H2626

description:
Mouse ID H2626
tumor_cells_gene_barcode_matrix.h5
tumor_cells_annotation.csv
Monocle_epithelial_2021.rds
Seurat_epithelial_2021.rds


title: DC2.4_Empty vector_2


title: G7678

description:
Mouse ID G7678
tumor_cells_gene_barcode_matrix.h5
tumor_cells_annotation.csv
Monocle_epithelial_2021.rds
Seurat_epithelial_2021.rds


title: xbp1+atf6+creb3l2+creb3l1-cr_rep2

description: 10x Genomics, V3

value: xbp1+atf6+creb3l2 triple cirspant in creb3l1 mutant


title: Ty1_ChIP-seq_Time_12h_rep2


title: H2700

description:
Mouse ID H2700
tumor_cells_gene_barcode_matrix.h5
tumor_cells_annotation.csv
Monocle_epithelial_2021.rds
Seurat_epithelial_2021.rds


title: DC2.4_Empty vector_1


title: Ty1_ChIP-seq_Time_12h_rep1


title: xbp1+creb3l2+creb3l1-cr

description: 10x Genomics, V3

value: Whole embryo

value: xbp1+creb3l2 double crispant in creb3l1 mutant


title: xbp1+atf6+creb3l2+creb3l1-cr_rep1

description: 10x Genomics, V3

value: TL/AB


title: G6754

description:
Mouse ID G6754
tumor_cells_gene_barcode_matrix.h5
tumor_cells_annotation.csv
Monocle_epithelial_2021.rds
Seurat_epithelial_2021.rds


title: MB3296

description:
Mouse ID MB3296
tumor_cells_gene_barcode_matrix.h5
tumor_cells_annotation.csv
Monocle_epithelial_2021.rds
Seurat_epithelial_2021.rds


title: Ty1_ChIP-seq_Time_6h_rep2


title: creb3l1-cr

description: 10x Genomics, V3

value: creb3l1 crispant


title: #10_Parental

city: Essen

first: Laura

last: Godfrey

address: Hufelandstraße 55

country: Germany

institute: DKTK Partner Site Essen/Düsseldorf

description:
MEKi treatment naive
#10_Parental

data_processing:
Demultiplexing of the sequencing reads with Illumina CASAVA v. 2.17 or bcl2fastq 2.19
Adapter trimming using Skewer v. 0.1.116 or 0.2.2
Quasi-mapping with salmon v. 0.12
Converting transcript-level counts to gene-level counts and performing of differentially gene expression analysis using DESeq2 v.1.18
Genome_build: mm10
Supplementary_files_format_and_content: csv files of normalized read counts and differential gene expression analysis results

source_name: Primary cell lines derived from pancreatic cancer of a genetically engineered mouse model

growth_protocol: DMEM high-glucose medium containing 10% fetal bovine serum, 1% penicillin/streptomycin and 1% non-essential amino acids

extract_protocol:
RNA was isolated using the Maxwell® RSC simplyRNA Cells Kit (Promega) according to manufacturer’s instruction.
TruSeq Stranded mRNA Kit (Illumina) with 100 ng input RNA

treatment_protocol: To induce resistance, cells were treated with increasing doses of trametinib (LKT) until they grew in 100x of their IC50. One batch was cultivated with 100x IC50 of trametinib in the culture medium (termed resistant ) with medium exchange every 2-3 days on a regular basis. Another batch of each cell line was kept under drug withdrawal and samples were named according their passage number in drug-free medium (P5 and P12)

value: Pancreas

tag: group

value: Parental


title: Ty1_ChIP-seq_Time_6h_rep1

value: anti-Ty1 (MilliporeSigma BB2)


title: #10_P12

description:
MEKi resistant and drug withdrawal for 12 passages
#10_P12


title: creb3l1-hom_rep2

description: 10x Genomics, V3

tag: strain

value: creb3l1 homozygous mutant


title: MB3387

description:
Mouse ID MB3387
tumor_cells_gene_barcode_matrix.h5
tumor_cells_annotation.csv
Monocle_epithelial_2021.rds
Seurat_epithelial_2021.rds

value: Pancreatic ductal adenocarcinoma


title: Ty1_ChIP-seq_Time_3h_rep2


title: tlab_rep2

description: 10x Genomics, V3

value: uninjected wild-type


title: mT69a_KO1_Spdef_rep2

description: SPDEF KO clone of murine PDA organoids mT69a with SPDEF overexpression (Spdef)

data_processing:
The quality of the RNA-seq reads was first confirmed using FastQC version 0.11.8.
Reads were mapped to transcript annotation GENCODE M17 using STAR version 2.5.2b.
RSEM version 1.3.0 was used to calculate expression estimates per gene and per isoform.
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: The gene.results files are tab-delimited text files that include expected counts, TPM and FKPM values per gene for each sample as generated by RSEM. The isoforms.results files are tab-delimited text files that include expected counts, TPM and FKPM values per isoform for each sample as generated by RSEM.

source_name: KPC pancreatic ductal adenocarcinoma tumor

growth_protocol: Organoids were grown in a matrigel dome in mouse complete organoid medium. (Boj et al. 2015 PMID 25557080)

extract_protocol:
Organoids were harvested in Trizol (Invitrogen), total RNA was extracted using the TRIzol Plus RNA Purification Kit (ThermoFisher) per manufacturer’s instructions. RNA samples were treated on column with PureLink DNase (ThermoFisher). The quality of purified RNA samples was determined using a Bioanalyzer 2100 (Agilent) with an RNA 6000 Nano Kit.
Libraries for RNA-Seq were prepared with the TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat (Illumina) following manufacturer instructions.

value: mT69a murine PDA organoids

tag: genetic manipulation

value: Spdef knock-out

tag: over-expression vector

value: SPDEF-OE


title: Ty1_ChIP-seq_Time_3h_rep1


title: tlab_rep1

description: 10x Genomics, V3

tag: tissue

value: 12 hpf


title: #6_P12

description:
MEKi resistant and drug withdrawal for 12 passages
#6_P12


title: #6_Resistant

description:
MEKi resistant
#6_Resistant

value: Resistant


title: Ty1_ChIP-seq_Time_0h_rep2


title: mT69a_KO1_Empty_rep2

description: SPDEF KO clone of murine PDA organoids mT69a without SPDEF overexpression (Empty)

value: Empty


title: tyr-cr_rep2

description: 10x Genomics, V3

value: tyr crispant


title: Ty1_ChIP-seq_Time_0h_rep1


title: #4_Resistant

description:
MEKi resistant
#4_Resistant


title: #4_P12

description:
MEKi resistant and drug withdrawal for 12 passages
#4_P12


title: creb3l2+creb3l1-cr

description: 10x Genomics, V3

value: Whole embryo

value: creb3l2 crispant generated in creb3l1 mutant


title: NSC_KO2

city: Singapore

first: Chin Tong

last: Ong

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
miRNA detection and annotation was performed using miRge3.0. Briefly, miRge3.0 pipeline would align the raw fastq reads against human specific small-RNA annotation libraries with the following commands: miRge3.0 -s -lib miRge3_Lib -on human -db miRBase -o output_dir -gff -trf -ai -cpu 12 -a AGATCGGAAGAGCACACGTCTGAACTCC.
Subsequently, raw miRNA read counts extracted from miR.Counts_Raw.csv file were used as input to perform differential analysis using DEseq2.
Supplementary files format and content: Tab-delimited Deseq output contains the differentially expressed miRNAs for wildtype and APOE-/- cells.

source_name: In-vitro neural stem cell line

growth_protocol: Isogenic control (XCL-1, SC-001-1V) and ApoE-/- NSCs (SC-001-ZOG-B-1V) were cultured and differentiated according to manufacturer’s protocols (XCell Science Inc). NSCs were seeded at a density of 0.04×10^6 cells/cm2 on poly-ornithine (20 µg/mL) & laminin (10 µg/mL)-coated plates in NSC maintenance media on Day 0 (D0). Cells were then replenished with neuronal induction media on Day 1, 3 and 5. On Day 6 (D6), neuronal precursor cells (NPCs) were harvested and replated on poly-ornithine/laminin-coated wells with similar density in neuronal maturation medium. Neurons were cultured for designated duration with media change every alternate Day.

extract_protocol:
Total RNA from biological replicates were isolated using RNAzol®RT (Sigma-Aldrich).
Small RNA sequencing were carried out by NovogeneAIT (Singapore), small RNA library preparation NovaSeq SE50.

treatment_protocol: Cells were untreated.

value: Neural stem cells

value: APOE double knockout

value: Passage 1-5


title: MB2383

description:
Mouse ID MB2383
tumor_cells_gene_barcode_matrix.h5
tumor_cells_annotation.csv
Monocle_epithelial_2021.rds
Seurat_epithelial_2021.rds


title: #4_Parental

description:
MEKi treatment naive
#4_Parental

value: Pancreas

value: Parental


title: mT6_KO1_Empty_rep2

description: SPDEF KO clone of murine PDA organoids mT6 without SPDEF overexpression (Empty)

value: mT6 murine PDA organoids


title: NSC_KO1


title: creb3l2-cr

description: 10x Genomics, V3

value: TL/AB

value: creb3l2 crispant


title: Skin, WT, S. aureus infected, rep 3

city: Baltimore

first: Alex

middle: Jea-Eun

last: Lee

state: MD

address: 1650 Orleans Street

institute: Johns Hopkins University

data_processing:
Clean reads were aligned to reference genes with Bowtie2
Assembly: GRCm38.p6
Supplementary files format and content: tab-separated values files include FPKM, TPM, and read counts values for each sample

source_name: skin

growth_protocol: S. aureus USA300 LAC4303 bacteria were streaked onto a tryptic soy agar (TSA) plate (tryptic soy broth [TSB] plus 1.5% bacto agar; BD Biosciences) and grown overnight at 37°C. Single colonies were picked and cultured in TSB at 37°C in a shaking incubator (240 rpm) overnight (18 hours), followed by a 1:50 subculture at 37°C for 2 hours to obtain mid-logarithmic growth phase bacteria. Bacteria were then pelleted, washed and resuspended in sterile PBS and the absorbance at 600 nm (A600) was measured to estimate the CFU (1×108 CFU/100 μL), which was verified by overnight culture on TSA plates.

extract_protocol:
Total RNA was extracted from about 60 mg of tissue per sample with Trizol (Invitrogen) according to the user manual instructions.
RNA libraries for RNA-seq were prepared using the DNBSEQ platform with a sequence length of PE100.

treatment_protocol: Dorsal fur of mice was shaved and depilated, followed by epicutenous infection using 1e8 S. aureus CFU for 7 days. A 10mm punch was then excised and sent for RNA purification and sequencing

value: Balb/c

value: skin

value: WT

value: S. aureus epicutaneous exposure


title: creb3l1-hom_rep1

description: 10x Genomics, V3

value: 12 hpf

value: creb3l1 homozygous mutant


title: NSC_CT2

value: wild type


title: mT69a_KO1_Spdef_rep1

value: mT69a murine PDA organoids

value: Spdef knock-out

value: SPDEF-OE


title: Skin, WT, S. aureus infected, rep 2


title: xbp1+atf6-cr

description: 10x Genomics, V3

value: Whole embryo

value: xbp1+atf6 double crispant


title: atf6+creb3l2+creb3l1-cr

description: 10x Genomics, V3

value: atf6+creb3l2 double crispant generated in creb3l1 mutant


title: Exp12

value: Lymph node Ex-Treg

value: 15,28 weeks old

value: BM donor:Foxp3Cre-GFPtdTfl/flFthfl/fl


title: #6_Parental

description:
MEKi treatment naive
#6_Parental

value: Pancreas

value: Parental


title: mT69a_KO1_Empty_rep1

value: Empty


title: mT69a_mRosa26_Empty_rep2

description: Rosa26 KO clone of murine PDA organoids mT69a without SPDEF overexpression (Empty)

value: mRosa26 knock-out


title: Skin, WT, S. aureus infected, rep 1

value: Balb/c

value: skin

value: WT

value: S. aureus epicutaneous exposure


title: mT6_KO1_Spdef_rep2

description: SPDEF KO clone of murine PDA organoids mT6 with SPDEF overexpression (Spdef)

value: mT6 murine PDA organoids


title: xbp1-cr

description: 10x Genomics, V3

value: TL/AB

value: 12 hpf

value: xbp1 crispant


title: D35 APOE_A

data_processing:
Reads were aligned to human reference genome (GRCh38.p13) using STAR (v2.5). HTSeq-count was used to identify read counts per gene. Differentially expressed genes (DEGs) were determined using DESeq2 (v1.22.1) on Galaxy platform. The data was visualised by Heatmap2 (v3.0.1). Gene Ontology analysis was performed using DAVID Functional Annotation Bioinformatics (v6.8).
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited Deseq output contains the differentially expressed genes for wildtype and APOE-/- cells.

source_name: In-vitro differentiated neurons, Day 35

extract_protocol:
Total RNA from biological replicates were isolated using RNAzol®RT (Sigma-Aldrich).
Poly-A and small RNA sequencing were carried out by NovogeneAIT (Singapore) NovaSeq PE150 according to company protocols.

value: Neurons

value: APOE double knockout

value: Day 35 after differentiation


title: mT6_mRosa26_Empty_rep2

description: Rosa26 KO clone of murine PDA organoids mT6 without SPDEF overexpression (Empty)


title: mT69a_mRosa26_Empty_rep1

value: mT69a murine PDA organoids


title: atf6-cr

description: 10x Genomics, V3

value: Whole embryo

value: atf6 crispant


title: mT6_KO1_Spdef_rep1

value: Spdef knock-out

value: SPDEF-OE


title: tyr-cr_rep1

description: 10x Genomics, V3

value: tyr crispant


title: Skin, Eosinophil KO, S. aureus infected, rep 3

value: Balb/c

value: eosinophil KO


title: D35 WT_A

value: wild type


title: D35 WT_B


title: #10_Resistant

description:
MEKi resistant
#10_Resistant

value: Pancreas

value: Resistant


title: NSC_CT1

value: Neural stem cells

value: Passage 1-5


title: D14 APOE_B

source_name: In-vitro differentiated neurons, Day 14

value: Day 14 after differentiation


title: Skin, Eosinophil KO, S. aureus infected, rep 2

value: skin

value: S. aureus epicutaneous exposure


title: #9_P12

description:
MEKi resistant and drug withdrawal for 12 passages
#9_P12


title: mT6_mRosa26_Empty_rep1

value: mT6 murine PDA organoids

value: mRosa26 knock-out

value: Empty


title: D35 APOE_B

value: Neurons

value: APOE double knockout

value: Day 35 after differentiation


title: D14 APOE_A


title: teratoma_rep3

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

description: RNA-Seq

data_processing:
Sequence reads were obtained and mapped to the human (hg19) genomes with Bowtie2.
The RPKM measure (read per kilo bases of exon model per million reads) was used to quantify the mRNA expression level of a gene from RNA-Seq data sets. The RBPM measure (read per base per million reads) was used to generate graph files.
Assembly: hg19
Supplementary files format and content: bedGraph

source_name: teratoma generated from H1 hESCs

growth_protocol: H1 hESCs were cultured on Matrigel-coated plates in serum-free E8 media at 37oC with 5% CO2 and passaged using EDTA. hESCs were dissociated using EDTA, and 1 million hESCs were injected subcutaneously into SCID-beige mice. Following a period of three to four weeks, mice were euthanized, and teratomas were cleaned and flash frozen.

extract_protocol:
RNA was harvest using RNeasy Qiagen kits.
Library preparation was performed using a New England Biolabs NEBNext Ultra II RNA Library Prep Kit for Illumina.

value: teratoma


title: #9_P5

description:
MEKi resistant and drug withdrawal for 12 passages
#9_P5


title: mT6_KO1_Empty_rep1

value: Spdef knock-out


title: Skin, Eosinophil KO, S. aureus infected, rep 1

value: Balb/c

value: eosinophil KO


title: teratoma_rep2

description: RNA-Seq


title: #9_Resistant

description:
MEKi resistant
#9_Resistant

value: Pancreas


title: D14 WT_B

value: wild type


title: D14 WT_A


title: teratoma_rep1

description: RNA-Seq


title: #9_Parental

description:
MEKi treatment naive
#9_Parental

value: Parental


title: Skin, Eosinophil KO, S. aureus infected, rep 4


title: #7_P12

description:
MEKi resistant and drug withdrawal for 12 passages
#7_P12


title: H1_hESC_teratoma_Input

description: Direct sequencing following sonication of x-linked chromatin

data_processing:
Sequence reads were obtained and mapped to the human (hg19) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Assembly: hg19
Supplementary files format and content: bedGraph

extract_protocol:
Teratoma tissue was rapidly frozen utilizing liquid nitrogen, and a section was excised using a razor blade. The tissue was then pulverized with liquid nitrogen using a mortar and pestle. The resulting crushed pellet was subsequently crosslinked with formaldehyde sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of adapters. PCR was performed using Phusion High Fidelity PCR master mix

tag: antibody


title: NSC APOE_B

value: Neural stem cells

value: Passage 1-5


title: H1_hESC_teratoma_H4K20me3_ChIP_rep2

description: Chromatin IP against H4K20me3

value: Anti-H4K20me3 antibody (Abcam; ab9053)


title: NSC APOE_A


title: #7_P5

description:
MEKi resistant and drug withdrawal for 12 passages
#7_P5


title: #7_Resistant

description:
MEKi resistant
#7_Resistant

value: Resistant


title: H1_hESC_teratoma_H4K20me1_ChIP_rep2

description: Chromatin IP against H4K20me1

value: Anti-H4K20me1 antibody (Abcam; ab9051)


title: H1_hESC_teratoma_H4K20me3_ChIP_rep1

description: Chromatin IP against H4K20me3


title: #7_Parental

description:
MEKi treatment naive
#7_Parental


title: NSC WT_A


title: NSC WT_B


title: Skin, WT, S. aureus infected, rep 4

value: skin

value: WT

value: S. aureus epicutaneous exposure


title: H1_hESC_teratoma_H3K9me3_ChIP_rep2

description: Chromatin IP against H3K9me3

value: Anti-H3K9me3 antibody (Abcam; ab8898)


title: #3_P5

description:
MEKi resistant and drug withdrawal for 5 passages
#3_P5


title: H1_hESC_teratoma_H4K20me1_ChIP_rep1

description: Chromatin IP against H4K20me1


title: H1_hESC_teratoma_H3K9me3_ChIP_rep1

description: Chromatin IP against H3K9me3


title: H1_hESC_teratoma_H3K4me3_ChIP_rep2

description: Chromatin IP against H3K4me3

value: Anti-H3K4me3 antibody (Millipore; 17-614)


title: Leaves at the tips of the branches (F2 stage) on July 23: Repeat 3

city: Changsha

first: Guolong

last: Wu

state: Hunan

address: South of Shaoshan Road No.498

institute: Central South University Forestry and Technology

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequenceflow-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 sing clc genomic benchwok (parameters- mismath cost: 2 insertion cost: 3 deleton cost-3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NOT PROVIDED
Supplementary files format and content: All_DEG.annot.xlsx

organism: Disanthus cercidifolius subsp. longipes

source_name: Leaves

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

value: Leaves

value: F2 stage


title: Leaves at the tips of the branches (F3 stage) on July 26: Repeat 1

value: F3 stage


title: Leaves at the tips of the branches (F3 stage) on July 26: Repeat 2


title: #3_Parental

description:
MEKi treatment naive
#3_Parental


title: Leaves at the tips of the branches (F3 stage) on July 26: Repeat 3


title: #3_P12

description:
MEKi resistant and drug withdrawal for 12 passages
#3_P12


title: H1_hESC_teratoma_H3K4me3_ChIP_rep1

description: Chromatin IP against H3K4me3

value: teratoma