title: DND41_GSI_Res_sustained_scRNA

first: Robert

middle: Babak

last: Faryabi

address: Room 553 BRB II/III, 421 Curie Boulevard

description: sustained high-dose GSI-resistant cell

data_processing:
FASTQ file generation and alignment to GRCh38 were performed using Cell Ranger v2.1.1 with default arguments.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell x gene unnormalized count matrices in matrix market format.

source_name: DND-41 cell line

growth_protocol: Cells were cultured in RPMI 1,640 supplemented with 10% fetal bovine serum , 2mM Lglutamine, 100U/mL and 100 μgmL−1 penicillin/streptomycin, 100mM nonessential amino acids, 1mM sodium pyruvate and 0.1mM of 2-mercaptoethanol. All cells were grown at 37 degree C and 5% CO2 with media refreshed every 3-4 days. Cells were regularly tested for mycoplasma contamination.

extract_protocol:
Prior to single–cell transcriptomic profiling, cells were washed with 1 x PBS and stained with DAPI and live cells were sorted on BD FACS Aria II using 100 μm nozzle. Cells were washed twice with RPMI, counted and single-cell RNA-seq was performed using 10X Genomics Single Cell 3’ Library and Gel Bead Kit v2 following the manufacturer’s instruction.
Briefly, Cells were loaded onto independent channels of a Chromium Controller (10X Genomics) for targeted recovery of 3,000 cells/condition. Complementary DNA was synthesized and amplified with PCR for 13 ycles. Amplified cDNA was assessed for QC and quantified on Agilent TapeStation using High sensitivity D5000 chip and subsequently used for library construction. Libraries were quantified using KAPA Library Quantification Kits for Illumina platform and pair-end sequenced on NextSeq 550 using 150 cycles High Output kit.

treatment_protocol: DND41 treatment-naïve cells were cultured in the presence of 10, 20, 40, 80, 125 nM gamma-secretase inhibitor (GSI) compound E with concentration increasing every week for six weeks and maintained in 125 nM GSI. To generate sustained high-dose GSI-resistant cells, DND41 treatment-naïve cells were cultured in the presence of 125 nM GSI for at least six weeks. Short-term DMSO/GSI treatment was performed on treatment-naïve DND41 cells with 125 nM DMSO/GSI for 24 hours.

value: T-cell acute lymphoblastic leukemia

tag: drug treatment

value: Gamma Secretase Inhibitor


title: Patient 15

status: Public on Jan 15 2020

type: protein

city: Groningen

first: Sanne

last: Arjaans

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

hyb_protocol: Two sequential bead-based immobilization and washing steps eliminated unbound or non-specifically bound proteins and the unbound SOMAmer reagents, leaving only protein target-bound SOMAmer reagents.

scan_protocol: SOMAmers are hybridized to complementary sequences on a microarry chip and quantified by fluorescence.

data_processing: The amount of each SOMAmer measured was quantitatively proportional to the protein concentration in the original sample. The relative fluorescent units provided by the company are included in the sample tables. Statistical analysis output is available on the series record.

label: Photocleavable linker

molecule: protein

organism: Homo sapiens

source_name: Plasma

label_protocol: SOMAmers are labeled with a fluorophore, photocleavable linker, and biotin.

extract_protocol: Blood was placed into an EDTA-plasma tube, which was centrifuged after phlebotomy. The supernatant was removed, aliquoted and stored at −80°C until assay.

tag: tissue

value: Plasma

tag: gender

value: Female

tag: bpd

value: Severe


title: HEK293T_7_OTA100

type: SRA

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

description: processed data file: HEK293T_rawCounts.txt

library_source: transcriptomic

data_processing:
Adaptor removal (Cutadapt - v1.8.1)
Alignment (tophat - 2.0.14)
Counting (featureCounts - 1.4.6)
Genome_build: hg38
Supplementary_files_format_and_content: txt files containing raw counts obtained after Counting with featureCounts

molecule: total RNA

source_name: HEK293-T_100 nM OTA

growth_protocol: HK-2 and HEK293-T were cultivated in DMEM/F12 media with 5% FCS. Prior to incubation with OTA, cells were incubated for 24h with serum-free media.

extract_protocol:
Total RNA was isolated with TriZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
rRNA were removed using RiboMinus (Life Technologies) according to the manufacturer's instructions. RNA was fragmented (w/ Tris-acetate, Potassium acetate and Magnesium acetate) and precipitated (w/ 100% Ethanol, Ammonium acetate and glycogen).
Resulting RNAs were used to generate cDNA libraries using Illumina index adapters.  10nM of pools of up to 10 libraries were used for cluster generation (Illumina cBot). Paired end sequencing (2x100bp) was performed on Illumina HiScanHQ and HiSeq 2000.

treatment_protocol: Cells were incubated for 48h with 0, 10 or 100nM OTA in serum-free media.

tag: cell line

tag: tissue source

value: Kidney

tag: cell type

value: Human embryonic kidney cell line

tag: treatment

value: 100 nM OTA


title: 5k_CART_cells

city: Philadelphia

first: Wenliang

last: Wang

state: PENNSYLVANIA

address: 421 Curie Boulevard

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
make fastq files with mkfastq from Cell Ranger ATAC pipeline version 1.1.0
analysis with count from Cell Ranger ATAC pipeline version 1.1.0
integration site analysis with epiVIA
Genome_build: hg38

molecule: genomic DNA

source_name: Bulk human T cells from peripheral blood.

growth_protocol: Bulk human T cells were activated with anti-CD3 and anti-CD28 monoclonal-antibody-coated polystyrene beads for 24 hours and subsequently transduced with a lentiviral vector encoding a  CD19-specific CAR with 4-1BB/CD3ζ domains. T cell expansion was carried out for 9 days as previously described , followed by cryopreservation.

extract_protocol:
T cells were thawed and checked for purity based on cell-surface expression of CD3, CD4, CD8 and CAR via flow cytometry. For scATAC-seq experiments, the first experiment on ~5000 CD8+CAR+ T cells  were isolated using bead-based positive selection, according to the manufacturer’s instructions (Miltenyi Biotech), while in the second experiment on ~1000 cells, they were FACS sorted with CD8 and CAR.
scATAC-seq was carried out using the Chromium platform and following the standard protocols provided by 10X Genomics: 1) “Chromium Single Cell ATAC Reagent Kits” and 2) “Nuclei Isolation for Single Cell ATAC Sequencing.” Libraries were paired-end sequenced (50 bp + 50 bp) on a NextSeq 550 (Illumina).
scATAC-seq

value: PBMC


title: Patient 19

value: Moderate


title: HEK293T_8_OTA100


title: DND41_GSI_Res_ascending_scRNA

state: Pennsylvania

department: Pathology

description: ascending-dose GSI-resistant cells

molecule: polyA RNA


title: Patient 14

value: Male


title: HEK293T_6_OTA100


title: Patient 13

value: Mild


title: DND41_GSI_scRNA

description: short-term GSI treated cells


title: Patient 12


title: DND41_DMSO_scRNA

description: untreated cells

value: DMSO


title: HEK293T_4_Ctrl

source_name: HEK293-T_0 nM OTA

value: 0 nM OTA


title: Methylation data from Astrocytoma tissue 3

type: genomic

city: New York City

first: Matija

last: Snuderl

state: NY

address: 240 E 38th St

institute: New York University Langone Medical Center

description:
Astrocytoma_3
RD-14-24
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

hyb_protocol: The DNA is bisulfite-converted using the EZ-96 DNA Methylation Kit from Zymo Research. After bisulfite conversion, the DNA then undergoes restoration using the Illumina Infinium HD FFPE DNA Restore Kit. The DNA then undergoes a whole-genome overnight amplification. The amplified DNA is then enzymatically fragmented using end-point fragmentation. The DNA is then isolated and precipitated in isopropanol and re-suspended in Illumina RA1 buffer. The re-suspended DNA is then denatured at 95⁰C, and the resulting single-stranded DNA is dispensed directly onto the Illumina Array for hybridization. The DNA hybridizes with the array overnight in an oven at 48⁰C. After hybridization, the BeadChips are then washed with Illumina PB1 buffer to remove any unhybridized and non-specifically hybridized DNA.

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting.

data_processing: The Minfi R package was used to analyze the data. Data was preprocessed, quantile normalized and poor samples and probes were removed based on mean detection Pvalues per sample. 'dmpFinder' was used to identify the differentially methylated probes between MPNSTs and DMs. qvalue < 0.01 are considered significant.

label: Cy5 and Cy3

source_name: IDH Mutant Astrocytoma sample

label_protocol: Standard Illumina Protocol.

extract_protocol: Using a Promega Maxwell 16 instrument, DNA was extracted from formalin-fixed paraffin-embedded (FFPE) specimens with the Maxwell® 16 FFPE Plus LEV DNA Purification Kit.

tag: disease state

value: Astrocytoma

tag: genotype/variation

value: IDH Mutant

value: Astrocytoma tissue


title: Methylation data from TCGA AML tissue 2

description:
AML_2
TCGA-AB-3002
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

source_name: IDH Mutant AML sample

value: AML

value: AML tissue


title: Methylation data from TCGA AML tissue 5

description:
AML_5
TCGA-AB-2926
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 11

value: Plasma


title: Infected bradyzoite foreskin fibroblast (1 week) replicate 3

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
The human and toxoplasma genomes were combined. Reads were aligned to this combined genome by Rsubread version 1.24.1
Reads counts were summarized using the Rsubread featureCounts function.  Human genes were identified by Entrez Gene ID and NCBI annotation. Toxoplasma genes were identified using annotation available through ToxoDB (http://toxodb.org/toxo/)
Genome_build: hg38 (Homo sapien), ME49 (Toxoplasma gondii)
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Entrez Gene ID (human)/ToxoDB ID (Toxoplasma), total gene length (total base count of all exons) and the number of reads mapping to that gene

organism:
Toxoplasma gondii
Homo sapiens

source_name: Foreskin

growth_protocol: Parasites were lysised and incoluated (or not) onto confluent HFF (host cells) at an MOI of 0.2 in either D1 ot iM media for 24 hours or 1 week.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen)
100ng of total RNA was prepared and indexed separately for IlluminaTM sequencing using the TruSeq RNA sample Prep Kit (Illumina) as per manufacturer’s instruction.  Each library was quantified using the Agilent Tapestation and the Qubit™ DNA BR assay kit for Qubit 3.0® Fluorometer (Life technologies).  The indexed libraries were pooled and diluted to 1.5pM for paired end sequencing (2x 81 cycles) on a NextSeq 500 instrument using the v2 150 cycle High Output kit (Illumina) as per manufacturer’s instructions (generating 80bp paired-ends)

treatment_protocol: host cells were washed with PBS and dislodged with trypsin before being FACS sorted for the presence of mCherry.

tag: infection

value: Infected

tag: toxoplasma stage

value: Bradyzoite

tag: toxoplasma strain

value: Prugniaud - Toxofilin-Cre (Koshy et al., 2010)

tag: incubation time

value: 1 week

tag: incubation media

value: iM - RPMI-HEPES  supplemented with 5% v/v fetal calf serum at pH 8.1-8.2


title: HEK293T_2_Ctrl

value: Kidney

value: Human embryonic kidney cell line


title: HEK293T_3_Ctrl


title: Methylation data from TCGA AML tissue 4

description:
AML_4
TCGA-AB-2907
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 10

value: Male


title: Methylation data from TCGA AML tissue 1

description:
AML_1
TCGA-AB-2973
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: HEK293T_5_OTA100

value: 100 nM OTA


title: Infected bradyzoite foreskin fibroblast (1 week) replicate 1


title: HEK293T_1_Ctrl


title: Patient 9

value: Female


title: Infected bradyzoite foreskin fibroblast (1 week) replicate 2


title: Infected tachyzoite foreskin fibroblast (24 hours) replicate 3

value: Tachyzoite

value: 24 hours

value: D1 - Dulbecco's Modified Eagle medium supplemented with 1% v/v fetal calf serum and 1% v/v Glutamax


title: Patient 8

value: Moderate


title: AS033

city: Changchun

first: yu

last: zheng

address: 2699 Qianjin Street

department: Jilin University

country: China

institute: National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun

data_processing:
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this  gene.
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010)
Genome_build: mm10

organism: Mus musculus

source_name: Whole blood

extract_protocol:
Total RNA was isolated with TRIzol. RNA degradation and contamination were assayed on 1% agarose gels, and RNA purity was verified using a NanoPhotometer spectrophotometer. Concentration were measured using a Qubit RNA Assay Kit and a Qubit 2.0 Fluorometer. RNA integrity was assessed using an RNA Nano 6000 Assay Kit and a Bioanalyzer 2100 system. 3 μg RNA per qualified sample was used as input material for RNA library preparation. Sequencing libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina, and unique index codes were added to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four groups ((1) RSV-F, (2) RSV-F + Alhydrogel, (3) RSV-F + AS02, and (4) RSV-F + AS03) were analyzed in the transcriptome sequencing experiment. 14 days after the last vaccination, blood samples from three mice in each group were collected.

tag: strain

value: BALB/c

value: Whole blood

tag: age at the first immunization

value: post natal day 20

tag: vaccine and adjuvant

value: RSV-F + AS03


title: Infected tachyzoite foreskin fibroblast (24 hours) replicate 2

value: Infected


title: Patient 7

tag: tissue

value: Plasma

value: Mild


title: Infected tachyzoite foreskin fibroblast (24 hours) replicate 1

value: Prugniaud - Toxofilin-Cre (Koshy et al., 2010)


title: Methylation data from TCGA AML tissue 8

description:
AML_8
TCGA-AB-2977
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

value: AML

value: IDH Mutant

value: AML tissue


title: AS031


title: Patient 6

tag: gender


title: Infected bradyzoite (Myr1 KO) foreskin fibroblast replicate 3

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
The human and toxoplasma genomes were combined. Reads were aligned to this combined genome by Rsubread version 1.27.4
Reads counts were summarized for human genes by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: hg38 (Homo sapien), ME49 (Toxoplasma gondii)
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

growth_protocol: Parasites were lysised and incoluated (or not) onto confluent HFF (host cells) at an MOI of 0.2 in iM media for 1 week.

treatment_protocol: host cells were washed with PBS and dislodged with trypsin before being FACS sorted on the absence (bystander) or presence (infected) of mCherry.

tag: toxoplasma genetic modification

value: Myc regulation 1 (Myr1) knock-out


title: Patient 5

value: Male

tag: bpd

value: Severe


title: AS023

value: RSV-F + AS02


title: AS032


title: Patient 4

value: Female


title: Infected bradyzoite (Myr1 KO) foreskin fibroblast replicate 2


title: AS022


title: AS021


title: Patient 3


title: Methylation data from SNUC tissue 8

description:
SNUC_8
RD-17-159
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

source_name: IDH Mutant SNUC sample

value: SNUC

value: SNUC tissue


title: genomic DNA from azacytidine-treated Malme-3M

city: Aurora

first: Eduardo

last: Davila

state: Colorado

department: Medicine

institute: University of Colorado Anschutz Medical Campus

hyb_protocol: Sodium bisulfite treated genomic DNA was amplified, fragmented and hybridized to the Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged by the BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio Software 2011.1 (Illumina)

source_name: Malme-3M cells were treated with 50 µM azacytidine for 72 hours

label_protocol: Standard Illumina Protocol

growth_protocol: All cell lines were cultured at 37°C in a humid environment with 5% CO2

extract_protocol: Genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega) according to the manufacturer's instructions

treatment_protocol: 500,000 Mb3429, C32 and Malme-3M cells were treated with 2 µM NU7441, 50 µM EPZ-6438 and 50 µM azacytidine respectively in 6-well flat-bottom plates containing 3 ml of culture medium for 72 hours.

value: melanoma

tag: cell line


title: AL3

value: BALB/c

value: Whole blood

value: post natal day 20

value: RSV-F + Alhydrogel


title: Infected bradyzoite (WT) foreskin fibroblast replicate 2

value: Infected

value: Wild-type


title: Methylation data from SNUC tissue 7

description:
SNUC_7
RD-17-158
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: 12yGSSCB

city: Urbana

first: Ann

middle: Marie

last: Kemper

state: IL

address: 1008 W Hazelwood Dr

institute: University of Illinois

description: gelded male

data_processing:
Quality control on all 56 samples (112 paired-end files) was performed using fastp (version 0.19.5) and summarized using MultiQC (version 1.6)
All fastq files were trimmed using Trimmomatic(version 0.38) in paired end mode to trim any remaining adaptors, then trim leading or trailing bases with quality scores below 28, then discarding a read pair if either read was shorter than 30 bases
Salmon (version 0.11.3) was used to quasi-map reads in paired-end mode to quantify transcript abundance (with additional arguments –seqBias --gcBias –numBootstraps=30) to the EquCab3.0 genome assembly utilizing NCBI Annotation Release 103
R package tximport was used to estimate gene-level counts from transcript-level quantification.   For the articular cartilage tissue (AC0), two individual horses had two samples taken at slightly different locations (ACD vs. ACS) in the stifle joint.  Gene-level counts for the ACD and ACS samples from the same horse were added together at the gene-level as they looked extremely similar to each other.
Reads were filtered and normalized (TMM) using edgeR, surrogate variables were calculated and counts were corrected using sva, and DE analysis performed using limma-trend
Genome_build: EquCab3.0
Supplementary_files_format_and_content: tab-delimited files with normalized log2(cpm) values for 54 of 56 samples

organism: Equus caballus

source_name: subcondral bone

extract_protocol:
Samples were collected immediately following euthanasia and were flash frozen in liquid nitrogen or placed in RNAlater (Qiagen, Valencia, CA) at 4°C for 24-48 hours prior to storage at -80°C. Frozen samples were pulverized and placed in TRIzol reagent (Invitrogen, Carlsbad, CA) prior to mechanical homogenization. RNA extraction was performed on spin columns using the RNeasy Micro Kit (Qiagen, Valencia, CA) per manufacturer instructions.
Standard library preparation and sequencing (100 base-pair, paired-end) on an Illumina Hi-Seq sequencer (90 samples on a Hi-Seq 2500, 22 samples on a Hi-Seq 4000)

tag: age

value: 12 years

tag: Sex

value: neuter

value: subcondral bone

tag: location

value: femoropatellar joint

tag: individual


title: Patient 1

value: Plasma

value: Male


title: AL4


title: Methylation data from SNUC tissue 2

description:
SNUC_2
RD-17-152
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

tag: disease state

tag: genotype/variation

value: IDH Mutant


title: Infected bradyzoite (Myr1 KO) foreskin fibroblast replicate 1

tag: infection

tag: toxoplasma strain

value: Prugniaud - Toxofilin-Cre (Koshy et al., 2010)

value: Myc regulation 1 (Myr1) knock-out


title: AL1


title: Methylation data from SNUC tissue 5

description:
SNUC_5
RD-17-155
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

value: SNUC

value: SNUC tissue


title: Patient 2

value: Severe


title: Infected bradyzoite (WT) foreskin fibroblast replicate 1


title: Methylation data from SNUC tissue 4

description:
SNUC_4
RD-17-154
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: 12yGSAC0

description: gelded male

source_name: articular cartilage

value: articular cartilage


title: Methylation data from SNUC tissue 6

description:
SNUC_6
RD-17-156
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: Bystander bradyzoite (Myr1 KO) foreskin fibroblast replicate 3

value: Bystander


title: RSV-F6

value: BALB/c

value: Whole blood

value: post natal day 20

value: RSV-F


title: Methylation data from SNUC tissue 3

description:
SNUC_3
RD-17-153
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: genomic DNA from NU7441-treated Mb3429

source_name: Mb3429 cells were treated with 2 µM NU7441 for 72 hours

value: melanoma


title: 12yGHSCB

description: gelded male

value: 12 years

value: neuter

value: subcondral bone

value: tarsocrural joint


title: genomic DNA from DMSO-treated Mb3429

source_name: Mb3429 cells were treated with DMSO for 72 hours


title: Bystander bradyzoite (Myr1 KO) foreskin fibroblast replicate 2


title: RSV-F4


title: genomic DNA from C32

source_name: normal C32 cells


title: 12yGHAC0

description: gelded male


title: Bystander bradyzoite (Myr1 KO) foreskin fibroblast replicate 1


title: RSV-F2


title: genomic DNA from Malme-3M

source_name: normal Malme-3M cells


title: Methylation data from SNUC tissue 1

description:
SNUC_1
RD-17-151
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

value: IDH Mutant


title: Methylation data from Oligodendroglioma tissue 20

description:
Oligodendroglioma_20
RD-16-657
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

source_name: IDH Mutant Oligodendroglioma sample

value: Oligodendroglioma

value: Oligodendroglioma tissue


title: genomic DNA from SK-MEL-28

source_name: normal SK-MEL-28 cells


title: 12yGFSCB

description: gelded male

value: metatarsophalangeal joint


title: Methylation data from Oligodendroglioma tissue 17

description:
Oligodendroglioma_17
RD-16-628
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: Bystander bradyzoite (WT) foreskin fibroblast replicate 3

value: Prugniaud - Toxofilin-Cre (Koshy et al., 2010)

value: Wild-type


title: 08yFSSCB

value: 8 years

value: female

value: femoropatellar joint


title: SRCAP_KO

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

data_processing:
RNA-seq was performed using a BGISEQ-500 platform and the raw reads were filtered for adaptor sequence, masked for low-complexity or low-quality sequence.  Clean reads were mapped to mm10 using HISAT/Bowtie2 tool.Gene expression level was qantified by RSEM and FPKM was calculated.RNA-seq analysis was completed by BGI company(Shenzhen,China)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: ISC cells

growth_protocol: Primary Lgr5+ ISCs were isolated from tamoxifen treated Srcapflox/flox; Lgr5-Cre+ mice (Srcap KO) and Srcap+/+; Lgr5-Cre+ mice (Srcap WT). No in vitro culture were done.

extract_protocol:
Total RNA isolated using Trizol reagent (Ambion). Single-ended 50 bp reads (59 million per sample on average) were generated using a BGISEQ-500 platform (BGI America Co., Cambridge, MA).
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).

treatment_protocol: Crypts were isolated from Lgr5GFP mice.For ISC isolation, the crypts were dissociated into individual cells with 1x TrypLE express supplemented with 0.8 kU/ml DNaseI (Roche) followed by sorting according to GFP intensity

value: Intestinal stem cell

tag: genotype

value: Srcap knockout


title: SRCAP_WT

value: wild type


title: 08yFHSCB


title: Bystander bradyzoite (WT) foreskin fibroblast replicate 1

value: Bystander


title: Bystander bradyzoite (WT) foreskin fibroblast replicate 2


title: 08yFHAC0

value: articular cartilage


title: 04wCSSCB

value: 4 weeks

value: male


title: FSF_epi_3

city: Cambridge

first: Douglas

middle: A.

last: Melton

state: MA

address: 7 Divinity Ave.

institute: Harvard University

description:
Mexican axolotl
processed data file: matrix.TMM.EXPR.matrix

data_processing:
Illumina Casava1.7 software used for basecalling.
Adapters and reads were trimmed using Trimmomatic to a minimum length of 100 bp and aligned to the axolotl transcriptome from Whited et al. (2017) using Kallisto.
Un-normalized counts were fed into DESeq2 for differential expression analysis.
Genome_build: axolotl transcriptome (Whited et al. 2017)
Supplementary_files_format_and_content: matrix.TMM.EXPR.matrix: Tab-delimited text file includes TMM-normalized TPM values for each sample.

organism: Ambystoma mexicanum

source_name: axolotl limb

extract_protocol:
Regenerating tissue was isolated from limbs at 5 dpa. Epidermis and stump tissues were separate dissociated, DAPI stained, and FACS sorted based on cell cycle content. RNA was extracted using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE. More details can be found in Tsai et al. (2019).
cDNA was synthesized with the NuGEN Ovation RNA-seq System V2, mechanically sheared to approximately 200 bp, and libraries were prepped using the Wafergen PrepX Complete ILMN DNA Library kit and the Apollo 324 NGS Library Prep System.

value: Axolotl limb

tag: cell population

value: Epithelial cells of full thickness skin

tag: time point

value: 5 days post-amputation (dpa)


title: FSF_epi_2


title: 08yFFSCB

value: subcondral bone


title: 04wCHSCB

value: tarsocrural joint


title: 08yFFAC0

value: metatarsophalangeal joint


title: 04wCSAC0


title: FSF_epi_1


title: genomic DNA from EPZ-6438-treated C32

source_name: C32 cells were treated with 50 µM EPZ-6438 for 72 hours

value: melanoma


title: 04wCHAC0


title: FSF_4N_3

value: Dividing cells in stump


title: Methylation data from Oligodendroglioma tissue 18

description:
Oligodendroglioma_18
RD-16-649
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

value: Oligodendroglioma

value: IDH Mutant

value: Oligodendroglioma tissue


title: genomic DNA from RPMI7951

source_name: normal RPMI7951 cells


title: 04wCFSCB


title: 03dFSACS

value: 3 days

value: female

value: femoropatellar joint


title: 03dFSSCB


title: FSF_4N_2


title: Infected bradyzoite (WT) foreskin fibroblast replicate 3

value: Infected

value: Prugniaud - Toxofilin-Cre (Koshy et al., 2010)

value: Wild-type


title: 03dFSACD

value: articular cartilage


title: 04wCFAC0

value: 4 weeks

value: male


title: Methylation data from Oligodendroglioma tissue 16

description:
Oligodendroglioma_16
RD-16-144
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: FSF_4N_1

value: Axolotl limb

value: 5 days post-amputation (dpa)


title: 03wCSSCB

value: 3 weeks

value: subcondral bone


title: 03dFHSCB

value: tarsocrural joint


title: FSF_2N_2

value: Non-dividing cells in stump


title: 03wCHSCB


title: Methylation data from Breast Cancer tissue 5

description:
Breast_Cancer_5
RD-16-141
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

source_name: IDH Mutant Breast Cancer sample

value: Breast Cancer

value: IDH Mutant

value: Breast Cancer tissue


title: 03wCSAC0


title: 03dFFSCB

value: 3 days

value: female

value: metatarsophalangeal joint


title: Methylation data from Breast Cancer tissue 3

description:
Breast_Cancer_3
RD-16-139
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: Methylation data from Breast Cancer tissue 4

description:
Breast_Cancer_4
RD-16-140
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: Methylation data from Breast Cancer tissue 1

description:
Breast_Cancer_1
RD-16-137
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: 03dFHAC0


title: Methylation data from Breast Cancer tissue 2

description:
Breast_Cancer_2
RD-16-138
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: FSF_2N_1


title: Methylation data from Astrocytoma tissue 31

description:
Astrocytoma_31
RD-16-656
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

source_name: IDH Mutant Astrocytoma sample

value: Astrocytoma

value: Astrocytoma tissue


title: 03wCHAC0

value: articular cartilage


title: 03wCFSCB


title: FSF_2N_3


title: hyphae, WT_Pos_3

city: Montreal

first: Donald

last: Sheppard

state: QC

address: 1001 Boulevard Decarie, Research Institute, E03.3126

department: Microbiology and Immunology

country: Canada

institute: McGill University

data_processing:
Raw reads from the FASTQ files were aligned to the Aspergillus fumigatus Af293 (ASM265v1) genome and transcriptome using STAR (v.2.6.1a)
The transcript level quantification was performed with Salmon (v0.6.0) quant adjusting for both sequencing and GC bias
The quantification matrix was imported to R environment using lengthScaledTPM from txtimport
Samples normalization by library depth was calculated with EdgeR (v3.26.8) and low expression transcripts (less than 50 reads in 2 replicates of a condition) were removed in R enviroment
Normalized counts were transformed to log2 counts per million (CPM) reads using limma voom (v3.40.6)
Genome_build: Aspergillus fumigatus Af293 (ASM265v1)
Supplementary_files_format_and_content: txt files contaning (i) raw counts produce by Salmon and (ii)  Normalized log2 CPM counts produced by limma voom

organism: Aspergillus fumigatus

source_name: Aspergillus fumigatus hyphae

growth_protocol: A. fumigatus hyphae were pre-grown in 50ml liquid AMM at a concentration of 1 x 10e6 conidia/ml and cultured for 10 hours at 37°C

extract_protocol:
The resulting fungal biomass was crushed under liquid nitrogen before extracting RNA using a RNeasy minikit (Qiagen) as per the manufacturer’s instructions
Libraries were prepared according to the manufacturer's instructions accompanying the NEBNext® Ultra™ II RNA Library Prep Kit (NEB)

treatment_protocol: Fungal cultures were treated with 20 µg/ml doxycycline or dH2O for 30 minutes.

tag: strain

value: Wild-type parent

tag: treatment

value: Doxycycline

value: hyphae


title: 01wCSSCB

value: 1 week

value: male

tag: tissue

value: femoropatellar joint


title: Methylation data from Astrocytoma tissue 30

description:
Astrocytoma_30
RD-16-653
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: hyphae, WT_Pos_2


title: 01wCSACS


title: hyphae, WT_Pos_1


title: 03wCFAC0

value: 3 weeks


title: 02wCSSCB

value: 2 weeks

value: subcondral bone


title: Methylation data from Astrocytoma tissue 26

description:
Astrocytoma_26
RD-17-207
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

value: IDH Mutant


title: 01wCSACD


title: Methylation data from Astrocytoma tissue 28

description:
Astrocytoma_28
RD-16-147
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: hyphae, WT_Neg_3

value: No Doxycycline


title: Methylation data from Astrocytoma tissue 27

description:
Astrocytoma_27
RD-17-268
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: 01wCHSCB

value: tarsocrural joint


title: 02wCSAC0


title: Methylation data from Astrocytoma tissue 29

description:
Astrocytoma_29
RD-16-646
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.


title: 02wCHSCB


title: hyphae, WT_Neg_2


title: 01wCHAC0


title: hyphae, WT_Neg_1


title: 01wCFSCB


title: 03dFFAC0

value: 3 days

value: female


title: hyphae, brlA_Pos_3

value: Mutant


title: 02wCFSCB

value: metatarsophalangeal joint


title: hyphae, brlA_Pos_2


title: 02wCFAC0

value: articular cartilage


title: 01wCFAC0


title: Methylation data from Oligodendroglioma tissue 19

description:
Oligodendroglioma_19
RD-16-652
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

value: Oligodendroglioma

value: Oligodendroglioma tissue


title: 02wCHAC0


title: iMDK_1

description:
mRNA-seq
processed data file: matrix.TMM.EXPR.matrix

data_processing:
Illumina Casava1.7 software used for basecalling.
Adapters and reads were trimmed using Trimmomatic to a minimum length of 100 bp and aligned to the axolotl transcriptome from Whited et al. (2017) using Kallisto.
Un-normalized counts were fed into DESeq2 for differential expression analysis.
Genome_build: axolotl transcriptome (Whited et al. 2017, GSE92429)
Supplementary_files_format_and_content: matrix.TMM.EXPR.matrix: Tab-delimited text file includes TMM-normalized TPM values for each sample.

source_name: regenerating axolotl limb

extract_protocol:
Total RNA from regenerating limb tissue was isolated using a standard Trizol extraction protocol.
mRNA was isolated with oligo-DT beads and cDNA libraries were generated with Illumina's Nextera XT kit.

treatment_protocol: Limbs were treated with iMDK or DMSO beginning immediately post-amputation up until the collection point at 11 dpa.

value: Regenerating axolotl limb

value: iMDK

value: 11 days post-amputation (dpa)


title: hyphae, brlA_Pos_1

value: Doxycycline

value: hyphae


title: iMDK_3


title: iMDK_2


title: hyphae, brlA_Neg_2


title: 01dCSAC0

value: 1 day

value: male

value: femoropatellar joint


title: 01dCSSCB

value: subcondral bone


title: hyphae, brlA_Neg_3

value: No Doxycycline


title: 01dCHAC0

value: tarsocrural joint


title: 01dCHSCB


title: DMSO_2

value: DMSO


title: DMSO_3


title: 01dCFSCB


title: hyphae, brlA_Neg_1

value: Mutant


title: SCAP_RNAseq

city: Mutilva

first: Alejandro

last: Toledo-Arana

state: Navarra

address: Avenidad de Pamplona 123

department: IDAB

country: Spain

institute: CSIC

data_processing:
RNA sequencing and preliminary data analysis was carried out by the Stab Vida company.
RNA-seq reads from the S. simiae CCM 7213T, S. capitis SK14 and S. epidermidis RP62A samples were aligned with the Rockhopper program (Tjaden, B., 2015, Genome Biol, 16, 1) using the complete genome sequences from S. simiae NCTC13838 (NZ_LT906460.1), S. capitis AYP1020 (NZ_CP007601.1) and S. epidermidis RP62A (NC_002976.3) as references, respectively.
The wiggle read coverage (.wig) files from the plus and minus strands were converted to BigWig (.bw) files with the wig2BigWig program.
The .bw files were loaded into a public web server based on Jbrowse (http://rnamaps.unavarra.es/).
Genome_build: S. simiae NCTC13838 (NZ_LT906460.1), S. capitis AYP1020 (NZ_CP007601.1) and S. epidermidis RP62A (NC_002976.3)
Supplementary_files_format_and_content: BigWig files representing read coverage

organism: Staphylococcus capitis

source_name: Staphylococcus capitis SK14

growth_protocol: Bacteria were grown in TSB glucose at 37ºC and 200 rpm until exponential phase was reached.

extract_protocol:
Total RNAs were extracted as previously described (Toledo-Arana et al, 2009, Nature 459, 950–956)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth phase

value: Exponential phase


title: SEPI_RNAseq

organism: Staphylococcus epidermidis

source_name: Staphylococcus epidermidis RP62A


title: DMSO_1


title: 01dCFAC0

source_name: articular cartilage

value: articular cartilage

value: metatarsophalangeal joint


title: SSIM_RNAseq

organism: Staphylococcus simiae

source_name: Staphylococcus simiae CCM 7213T

value: CCM 7213T


title: WT32-TAU-11M

status: Public on Jan 14 2020

city: Leuven

first: Bart

last: De Strooper

address: O&N4 Herestraat 49

department: Centre for Brain and Disease research

country: Belgium

institute: VIB - KU Leuven

data_processing:
Cellranger (version 3.1.0)
Genome_build: human genome database (hg38, ensembl version 84) and mouse database (mm10, ensembl version 84) and rat genome (Rnor_6.0)
Supplementary_files_format_and_content: *.pkl: Raw gene expression counts per cell in a gzipped tab separated values file )*.p.
Supplementary_files_format_and_content: meta.data.tsv.gz: meta data contating information about each cells and cluster assigments using UMAP
Supplementary_files_format_and_content: expr.filtered.SeuratNorm.tsv.gz: Seurat (Version 3.1.1)  filtered and normliased count tables

source_name: hippocampus

extract_protocol:
Single cell suspension and Flow Cytometry enriching for CD11b+/CD45+ cells
10X Genomics V2 chemistry

tag: mouse strain

value: TAU

value: WT


title: WT1-APP-11M

value: APP


title: WT4-APP-4M


title: TG31-TAU-11M

value: TG


title: WT2-TAU-4M


title: TG4-APP-4M


title: WT31-TAU-11M


title: MG-OSK

type: RNA

city: Kobe-City

first: Shuichi

last: Fujiwara

country: Japan

institute: Kobe University

description: Gene expression by transducing OCT3/4, SOX2, KLF4

hyb_protocol: 0.6 μμg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μμl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μμl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters(protocol GE1_1200_Jun14 and Grid: 072363_D_F_20180928) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: MG-63, OSK

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from cultured cells using an RNeasy mini kit (Qiagen, Valencia, CA, USA)

treatment_protocol: We designed the polycistronic retroviral vector encoding OCT3/4, SOX2, and KLF4 in the pMX retroviral vector (pMX-OSK). Concomitantly, pMX with GFP (pMX-GFP) was used as a control vector. To produce retroviral particles, Plat-A cells (in DMEM with 10 % FBS without antibiotics) were transfected with the retroviral vector (pMX-OSK or pMX-GFP) using the FuGene HD transfection reagent (Promega, Madison, WI, USA) according to the manufacturer's instructions.

value: osteosarcoma


title: MG-cont

description: Gene expression without gene transduction

source_name: MG-63, parental


title: TG32-TAU-11M


title: PAS-seq Lane1

city: Boston

first: Michael

middle: Demian

last: Blower

address: 185 Cambridge St CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

description:
PAS-Seq
SupplementalTable5.txt

data_processing:
Library strategy: PAS-seq
Base calls were generated using Illumina software
reads were collapsed to unique using a custom Perl script (Schwart and Blower. JCB. 2014)
reads were aligned to X. laevis transcripts using Bowtie and counted using a custom Perl script or reads were aligned to X. laevis 9.2 genome sequence using Tophat2 and counted agains gene models using Cufflinks.
PAS-seq 5' linker sequences (CGG TCT CGG CAT TCC TGC TGA ACC GCT CTT CCG ATC TGG G) were trimmed form all reads using the fasx toolkit. Trimmed sequences longer than 30nts were retained for analysis.
PAS-Seq Reads were aligned to the Xl9_2 genome using Bowtie2. Alignments were filtered to retain only reads with two nonteplated As.
Genome_build: Xl9_2
Supplementary_files_format_and_content: Supplemental Table 2: Measures of RNA stability during oocyte maturation derived from sucrose density gradient sequencing.
Supplemental Table 3: Fraction of each mRNA present in polyribosome fraction of sucrose density gradient during oocyte maturation.
Supplemental Table 5: Genomic locations of polyadenylation sites derived from PAS-seq experiment.

organism: Xenopus laevis

source_name: PAS-Seq

extract_protocol:
Trizol, Zymo clean and concentrate, Exiqon LNA dT kit.
NEB

treatment_protocol: oocyte extracts were separated using sucrose density gradients. PG90 = 90 minutes after progesterone addition.

value: oocyte

tag: developmental stage

value: StageVI oocyte


title: MIImRNP_2

description:
mRNP fraction from sucrose density gradient
SupplementalTable2.txt
SupplementalTable3.txt

data_processing:
Base calls were generated using Illumina software
reads were collapsed to unique using a custom Perl script (Schwart and Blower. JCB. 2014)
reads were aligned to X. laevis transcripts using Bowtie and counted using a custom Perl script or reads were aligned to X. laevis 9.2 genome sequence using Tophat2 and counted agains gene models using Cufflinks.
PAS-seq 5' linker sequences (CGG TCT CGG CAT TCC TGC TGA ACC GCT CTT CCG ATC TGG G) were trimmed form all reads using the fasx toolkit. Trimmed sequences longer than 30nts were retained for analysis.
PAS-Seq Reads were aligned to the Xl9_2 genome using Bowtie2. Alignments were filtered to retain only reads with two nonteplated As.
Genome_build: Xl9_2
Supplementary_files_format_and_content: Supplemental Table 2: Measures of RNA stability during oocyte maturation derived from sucrose density gradient sequencing.
Supplemental Table 3: Fraction of each mRNA present in polyribosome fraction of sucrose density gradient during oocyte maturation.
Supplemental Table 5: Genomic locations of polyadenylation sites derived from PAS-seq experiment.

value: MII oocyte


title: MIIpolysome_2

description:
polysome fraction from sucrose density gradient
SupplementalTable2.txt
SupplementalTable3.txt


title: IntmRNP_2

source_name: mRNP fraction from sucrose density gradient

value: Interkinesis oocyte


title: MG-GFP

description: Gene expression by transducing GFP

source_name: MG-63, GFP


title: Mimonosome_2

description:
monosome fraction from sucrose density gradient
SupplementalTable2.txt
SupplementalTable3.txt

value: MI oocyte


title: Mipolysome_2

source_name: polysome fraction from sucrose density gradient


title: MImRNP_2


title: Intmonosome_2

source_name: monosome fraction from sucrose density gradient


title: TG2-TAU-4M

tag: age


title: PG90polysome_2

value: Stage VI oocyte 90 minutes after progesterone


title: PG90monosome_2


title: PG90mRNP_2


title: noPGpolysome_2

value: Stage VI oocyte


title: noPGmonosome_2


title: MIImonosome_1


title: MIImRNP_1


title: noPGmRNP_2


title: TG1-APP-11M


title: Intpolysome_1


title: Genomic DNA from CR-XenoCSC from patient #21

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

description:
X200526210157_R08C01
Cancer stem cells isolated from xenograft established from patient #21 colorectal tumor

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to IInfinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: HiScan scanner (Illumina)

data_processing:
Signal intensities files were extracted using the minfi Bioconductor package.
Veronese_GEO_submission_matrix_signal.txt contains Unmethylated and methylated signal intensities

label: Cy3 and Cy5

source_name: CR-XenoCSC from patient #21

growth_protocol: Tumor samples were mechanically and enzymatically digested with collagenase and hyaluronidase for 1 hour at 37 °C. The obtained digests were cultured in ultralow adhesion flasks to select CSCs that do not undergo anoikis positively. The culture medium was based on serum-free Advanced DMEM/F12, supplemented with EGF and bFGF, to induce differentiated tumor cells to cell death. Cells were cultured in these conditions for several passages (3-4 months depending on the parental tumor histological grading and the number of CSCs in tumor specimens) and expanded by both enzymatic and mechanical dissociation. Then cells were characterized and eventually sorted for the expression of putative CSC markers. Finally, CR-CSCs were tested for their tumorigenic potential by subcutaneous injection in NOD/SCID mice. Cells were maintained at 37 °C in a 5% CO2 humidified incubator.

extract_protocol: Genomic DNA was extracted using the Dneasy Blood & Tissue kit (Qiagen) according to the manufactirer's instructions

tag: subject status

value: Colorectal cancer patient

tag: subject id

value: patient #21

tag: Sex

value: Male

tag: cell type

value: Colorectal cancer stem cells from xenograft tumor


title: PAS-seq Lane2

description:
PAS-Seq
SupplementalTable5.txt


title: Mimonosome_1


title: Mipolysome_1


title: IntmRNP_1


title: PG90monosome_1


title: PG90polysome_1


title: PG90mRNP_1


title: Genomic DNA from CR-XenoCSC from patient #14

description:
X200526210157_R02C01
Cancer stem cells isolated from xenograft established from patient #14 colorectal tumor

source_name: CR-XenoCSC from patient #14

value: patient #14

value: Female


title: Intmonosome_1


title: MImRNP_1


title: noPGmRNP_1


title: MIImonosome_2


title: noPGpolysome_1


title: Genomic DNA from CR-XenoCSC from patient #11

description:
X200526210157_R05C01
Cancer stem cells isolated from xenograft established from patient #11 colorectal tumor

source_name: CR-XenoCSC from patient #11

value: patient #11


title: Genomic DNA from CR-XenoCSC from patient #8

description:
X200526210157_R06C01
Cancer stem cells isolated from xenograft established from patient #8 colorectal tumor

source_name: CR-XenoCSC from patient #8

value: patient #8


title: PAX 300

city: Scottsdale

first: michael

middle: thomas

last: barrett

state: Arizona

address: 13400 east shea boulevard

institute: mayo clinic arizona

data_processing:
OMNI ATAC-seq data were analyzed using the HiChIP pipeline developed by the Mayo Bioinformatics Core
Paired-end reads were mapped to the HG38 genome reference using Burrows-Wheeler Alignment tool (BWA) (27). Pairs of reads with one or both reads uniquely mapped were retained and duplicates removed using Picard MarkDuplicates command (http://broadinstitute.github.io/picard/).
Peaks were identified using the Model-based Analysis of ChIP-Seq (MACS2) software package at FDR <=1%
For data visualization, BEDTools in combination with in-house scripts were used to generate normalized tag density profiles at a window size of 200 bp and step size of 20 bp.
Differential analysis of chromatin accessibility was performed using the DiffBind package
Raw read counts were normalized using the trimmed mean of M values (TMM) method, and sites with fold changes >=2 and FDR <=0.05 in the DiffBind test were extracted to represent differential chromatin accessibility sites.
Genome_build: hg38
Supplementary_files_format_and_content: bed

source_name: flow sorted nuclei_PDAC_PDX

extract_protocol:
Approximately 50,000 flow sorted nuclei were utilized for OMNI ATAC-seq following the protocol by Corces et al. (Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods 2017;14:959-62).
Nuclei were subjected to transposition reaction following cell lysis and washing steps. The transposition reaction was performed at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. DNA was purified and indexed ATAC-seq libraries amplified by PCR. The enrichment of accessible regions in each library was determined by real-time PCR targeting known highly accessible and closed chromatin sites and expressed as fold difference. Libraries passing this quality control step were sequenced to 51 base pairs from both ends on an Illumina HiSeq 4000 instrument at the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.

value: pancreatic ductal adenocarcinoma (PDAC)

tag: tissue type

value: patient derived xenografts (PDXs)

value: DNA content flow sorted


title: PAX 265

source_name: flow sorted nuclei_ASCP_PDX

value: adenosquamous cancer of the pancreas (ASCP) tumor


title: PAX 139


title: PAX 297


title: noPGmonosome_1

value: oocyte


title: Genomic DNA from CR-CSC from patient #8

description:
X200516380136_R06C01
Cancer stem cells isolated from patient #8 colorectal tumor

source_name: CR-CSC from patient #8

value: Colorectal cancer stem cells


title: mut.48h.r2

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

description: mRNA-Seq

data_processing:
Reads were Illumina adapter trimmed using Cutadapt v1.9.1
Reads were aligned against GRCh38 and Ensembl release 89 transcript annotations using STAR v2.5.2a via the transcript quantification software RSEM v1.2.31.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using bedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.

source_name: RPB1 K1268R mutant, 48h, r2

growth_protocol: Cells were seeded and transfected in DMEM (Thermo Fisher Scientific, 11965118) supplemented with 10% v/v TET-free FBS (Clontech, 631106) and 2 mM L-glutamine, with addition of 10 ng/μl Doxycycline. On day 2, cells were transfected with RPB1 siRNAs, and re-seeded on day 3 in DMEM (Thermo Fisher Scientific, 11965118) supplemented with 10% v/v TET-free FBS (Clontech, 631106), 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 100 μg/ml hygromycin, 15 μg/ml blasticidin and with addition of 500 ng/μl Doxycycline.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen, 74104) according to the manufacture’s instruction including the on-column DNase treatment. 2μg total RNA was used for oligo(dT) purification.
KAPA mRNA HyperPrep kit

tag: cell line

value: Flp-In T-REx HEK293

tag: mutational status

value: RPB1 K1268R mutant

value: UV irradiated (20 J/m2)

tag: collection time

tag: replicate


title: mut.48h.r1

description: mRNA-Seq

source_name: RPB1 K1268R mutant, 48h, r1


title: mut.48h.r3

description: mRNA-Seq

source_name: RPB1 K1268R mutant, 48h, r3


title: Genomic DNA from CR-XenoCSC from patient #12

description:
X200526210157_R04C01
Cancer stem cells isolated from xenograft established from patient #12 colorectal tumor

source_name: CR-XenoCSC from patient #12

value: Colorectal cancer patient

value: patient #12


title: mut.24h.r2

description: mRNA-Seq

source_name: RPB1 K1268R mutant, 24h, r2


title: Intpolysome_2

value: Interkinesis oocyte


title: mut.24h.r3

description: mRNA-Seq

source_name: RPB1 K1268R mutant, 24h, r3


title: Genomic DNA from CR-CSC from patient #21

description:
X200516380136_R08C01
Cancer stem cells isolated from patient #21 colorectal tumor

source_name: CR-CSC from patient #21

value: patient #21

value: Male


title: Genomic DNA from CR-XenoCSC from patient #9

description:
X200526210157_R07C01
Cancer stem cells isolated from xenograft established from patient #9 colorectal tumor

source_name: CR-XenoCSC from patient #9

value: patient #9

value: Female

value: Colorectal cancer stem cells from xenograft tumor


title: mut.UNT.r3

description: mRNA-Seq

source_name: RPB1 K1268R mutant, untreated, r3

value: untreated


title: mut.8h.r2

description: mRNA-Seq

source_name: RPB1 K1268R mutant, 8h, r2


title: mut.3h.r2

description: mRNA-Seq

source_name: RPB1 K1268R mutant, 3h, r2


title: mut.3h.r1

description: mRNA-Seq

source_name: RPB1 K1268R mutant, 3h, r1


title: mut.3h.r3

description: mRNA-Seq

source_name: RPB1 K1268R mutant, 3h, r3


title: mut.8h.r1

description: mRNA-Seq

source_name: RPB1 K1268R mutant, 8h, r1


title: Genomic DNA from CR-CSC from patient #11

description:
X200516380136_R05C01
Cancer stem cells isolated from patient #11 colorectal tumor

source_name: CR-CSC from patient #11

value: patient #11


title: mut.8h.r3

description: mRNA-Seq

source_name: RPB1 K1268R mutant, 8h, r3


title: Genomic DNA from CR-CSC from patient #9

description:
X200516380136_R07C01
Cancer stem cells isolated from patient #9 colorectal tumor

source_name: CR-CSC from patient #9


title: mut.UNT.r2

description: mRNA-Seq

source_name: RPB1 K1268R mutant, untreated, r2


title: wt.48h.r1

description: mRNA-Seq

source_name: RPB1 wild-type, 48h, r1

value: RPB1 wild-type


title: wt.48h.r2

description: mRNA-Seq

source_name: RPB1 wild-type, 48h, r2


title: wt.48h.r3

description: mRNA-Seq

source_name: RPB1 wild-type, 48h, r3


title: Genomic DNA from CR-XenoCSC from patient #13

description:
X200526210157_R03C01
Cancer stem cells isolated from xenograft established from patient #13 colorectal tumor

source_name: CR-XenoCSC from patient #13

value: patient #13


title: wt.24h.r2

description: mRNA-Seq

source_name: RPB1 wild-type, 24h, r2


title: wt.24h.r1

description: mRNA-Seq

source_name: RPB1 wild-type, 24h, r1


title: wt.24h.r3

description: mRNA-Seq

source_name: RPB1 wild-type, 24h, r3


title: mut.UNT.r1

description: mRNA-Seq

source_name: RPB1 K1268R mutant, untreated, r1


title: PAX 217

source_name: flow sorted nuclei_ASCP_PDX

value: adenosquamous cancer of the pancreas (ASCP) tumor

value: patient derived xenografts (PDXs)

value: DNA content flow sorted


title: wt.8h.r3

description: mRNA-Seq

source_name: RPB1 wild-type, 8h, r3

value: Flp-In T-REx HEK293


title: PAX 295

source_name: flow sorted nuclei_PDAC_PDX

value: pancreatic ductal adenocarcinoma (PDAC)


title: wt.UNT.r2

description: mRNA-Seq

source_name: RPB1 wild-type, untreated, r2


title: wt.UNT.r1

description: mRNA-Seq

source_name: RPB1 wild-type, untreated, r1


title: wt.UNT.r3

description: mRNA-Seq

source_name: RPB1 wild-type, untreated, r3


title: wt.3h.r2

description: mRNA-Seq

source_name: RPB1 wild-type, 3h, r2

value: UV irradiated (20 J/m2)


title: wt.3h.r3

description: mRNA-Seq

source_name: RPB1 wild-type, 3h, r3


title: wt.3h.r1

description: mRNA-Seq

source_name: RPB1 wild-type, 3h, r1


title: wt.8h.r2

description: mRNA-Seq

source_name: RPB1 wild-type, 8h, r2


title: wt.8h.r1

description: mRNA-Seq

source_name: RPB1 wild-type, 8h, r1


title: CSB-KO_plus_mut_3h_r2

description:
Nascent RNA
TT-Seq

data_processing:
Sequenced reads were aligned against human genome version GRCh38 using STAR v2.5.2a with Ensembl release 89 transcript annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using bedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.

source_name: RPB1 mutant, CSB KO, 3h, r2

extract_protocol:
RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) accordingly to the manufacturer’s instructions. As a control for equal sample preparation, we spiked-in S. cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) 4-thiouracil (4TU)-labelled RNA. S. cerevisiae were grown in YPD medium overnight, diluted to an OD600 of 0.1, and grown to mid-log phase (OD600 of 0.8) and labelled with 5 mM 4TU (Sigma-Aldrich, 440736) for 6 min. Total RNA was extracted using the PureLink RNA Mini kit (Thermo Fisher Scientific, 12183020) following the enzymatic protocol. For purification of 4SU labelled RNA, 100 μg mammalian 4SU labelled RNA was spiked-in 1/100 of 4TU-labelled S. cerevisiae RNA. The 101 μg RNA was fragmented by addition of 20 μL 1 M NaOH to fragment RNA and left on ice for 20 min. Fragmentation was stopped by addition of 80 μL 1 M Tris pH 6.8 and cleaned up twice with Micro Bio-Spin™ P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues were carried out in a total volume of 250 μl, containing 10 mM Tris-HCl [pH 7.4], 1 mM EDTA and 5mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol:chloroform extraction, denatured by 10 min incubation at 65°C and added to 200 μL μMACS Streptavidin MicroBeads (Miltenyi, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads applied to a μColumn in the magnetic field of a μMACS magnetic separator. Beads were washed twice with pull-out wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). 4SU-RNA was eluted twice by addition of 100 mM DTT and RNA cleaned up using the RNeasy MinElute kit (Qiagen, 74204).
Libraries were prepared using the KAPA RNA HyperPrep Kit using 5 min 65°C fragmentation incubation to anneal primers but to prevent further fragmentation of the samples. Library purifications with Ampure beads were performed with 0.95x and 1x bead-to-sample volumes to retain smaller cDNA fragments.

treatment_protocol: Nascent RNA labelling by addition of 1 mM 4-thiourdine to cell media for 15 min prior to harvest

value: RPB1 K1268R mutant

tag: csb status

value: CSB knock-out


title: CSB-KO_plus_mut_24h_r2

description:
Nascent RNA
TT-Seq

source_name: RPB1 mutant, CSB KO, 24h, r2


title: CSB-KO_plus_mut_24h_r1

description:
Nascent RNA
TT-Seq

source_name: RPB1 mutant, CSB KO, 24h, r1


title: CSB-KO_plus_mut_UNT_r1

description:
Nascent RNA
TT-Seq

source_name: RPB1 mutant, CSB KO, untreated, r1


title: CSB-KO_plus_mut_UNT_r2

description:
Nascent RNA
TT-Seq

source_name: RPB1 mutant, CSB KO, untreated, r2


title: Genomic DNA from CR-XenoCSC from patient #5

description:
X200526210157_R01C01
Cancer stem cells isolated from xenograft established from patient #5 colorectal tumor

source_name: CR-XenoCSC from patient #5

value: Colorectal cancer patient

value: patient #5


title: CSB-KO_plus_wt_24h_r2

description:
Nascent RNA
TT-Seq

source_name: RPB1 WT, CSB KO, 24h, r2


title: CSB-KO_plus_mut_3h_r1

description:
Nascent RNA
TT-Seq

source_name: RPB1 mutant, CSB KO, 3h, r1


title: CSB-KO_plus_wt_24h_r1

description:
Nascent RNA
TT-Seq

source_name: RPB1 WT, CSB KO, 24h, r1


title: Genomic DNA from CR-CSC from patient #13

description:
X200516380136_R03C01
Cancer stem cells isolated from patient #13 colorectal tumor

source_name: CR-CSC from patient #13

value: Male

value: Colorectal cancer stem cells


title: CSB-KO_plus_wt_UNT_r2

description:
Nascent RNA
TT-Seq

source_name: RPB1 WT, CSB KO, untreated, r2


title: CSB-KO_plus_wt_3h_r1

description:
Nascent RNA
TT-Seq

source_name: RPB1 WT, CSB KO, 3h, r1


title: CSB-KO_plus_wt_3h_r2

description:
Nascent RNA
TT-Seq

source_name: RPB1 WT, CSB KO, 3h, r2


title: Genomic DNA from CR-CSC from patient #5

description:
X200516380136_R01C01
Cancer stem cells isolated from patient #5 colorectal tumor

source_name: CR-CSC from patient #5


title: Genomic DNA from CR-CSC from patient #14

description:
X200516380136_R02C01
Cancer stem cells isolated from patient #14 colorectal tumor

source_name: CR-CSC from patient #14

value: patient #14

value: Female


title: CSB-KO_plus_wt_UNT_r1

description:
Nascent RNA
TT-Seq

source_name: RPB1 WT, CSB KO, untreated, r1

value: untreated


title: mut_24h_r1

description:
Nascent RNA
TT-Seq

source_name: RPB1 mutant, CSB WT, 24h, r1

value: CSB wild-type


title: MIIpolysome_1

description:
polysome fraction from sucrose density gradient
SupplementalTable2.txt
SupplementalTable3.txt

value: oocyte

value: MII oocyte


title: Genomic DNA from CR-CSC from patient #12

description:
X200516380136_R04C01
Cancer stem cells isolated from patient #12 colorectal tumor

source_name: CR-CSC from patient #12

value: patient #12


title: mut_3h_r1

description:
Nascent RNA
TT-Seq

source_name: RPB1 mutant, CSB WT, 3h, r1


title: mut_3h_r2

description:
Nascent RNA
TT-Seq

source_name: RPB1 mutant, CSB WT, 3h, r2


title: mut_UNT_r2

description:
Nascent RNA
TT-Seq

source_name: RPB1 mutant, CSB WT, untreated, r2


title: mut_UNT_r1

description:
Nascent RNA
TT-Seq

source_name: RPB1 mutant, CSB WT, untreated, r1


title: wt_UNT_r1

description:
Nascent RNA
TT-Seq

source_name: RPB1 WT, CSB WT, untreated, r1

value: RPB1 wild-type


title: wt_3h_r2

description:
Nascent RNA
TT-Seq

source_name: RPB1 WT, CSB WT, 3h, r2

value: Flp-In T-REx HEK293


title: wt_24h_r2

description:
Nascent RNA
TT-Seq

source_name: RPB1 WT, CSB WT, 24h, r2


title: wt_UNT_r2

description:
Nascent RNA
TT-Seq

source_name: RPB1 WT, CSB WT, untreated, r2


title: wt_3h_r1

description:
Nascent RNA
TT-Seq

source_name: RPB1 WT, CSB WT, 3h, r1


title: wt_24h_r1

description:
Nascent RNA
TT-Seq

source_name: RPB1 WT, CSB WT, 24h, r1


title: wtC_UNT_r2

description:
Nascent RNA
TT-Seq

data_processing:
Library strategy: TT-seq
Sequenced reads were aligned against human genome version GRCh38 using STAR v2.5.2a with Ensembl release 89 transcript annotations.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using bedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.

source_name: WT, siControl, untreated, r2

tag: sirna

value: siControl


title: wtR_3h_r1

description:
Nascent RNA
TT-Seq

source_name: WT, siRPB1+Dox, 3h, r1

tag: treatment

value: UV irradiated (20 J/m2)


title: wtR_3h_r3

description:
Nascent RNA
TT-Seq

source_name: WT, siRPB1+Dox, 3h, r3


title: wtR_45min_r2

description:
Nascent RNA
TT-Seq

source_name: WT, siRPB1+Dox, 45min, r2


title: wtR_3h_r2

description:
Nascent RNA
TT-Seq

source_name: WT, siRPB1+Dox, 3h, r2


title: wtC_45min_r2

description:
Nascent RNA
TT-Seq

source_name: WT, siControl, 45min, r2


title: wtC_UNT_r1

description:
Nascent RNA
TT-Seq

source_name: WT, siControl, untreated, r1


title: wtR_UNT_r3

description:
Nascent RNA
TT-Seq

source_name: WT, siRPB1+Dox, untreated, r3


title: wtC_UNT_r3

description:
Nascent RNA
TT-Seq

source_name: WT, siControl, untreated, r3


title: wtR_UNT_r2

description:
Nascent RNA
TT-Seq

source_name: WT, siRPB1+Dox, untreated, r2


title: wtR_UNT_r1

description:
Nascent RNA
TT-Seq

source_name: WT, siRPB1+Dox, untreated, r1


title: wtR_45min_r3

description:
Nascent RNA
TT-Seq

source_name: WT, siRPB1+Dox, 45min, r3


title: wtC_3h_r2

description:
Nascent RNA
TT-Seq

source_name: WT, siControl, 3h, r2


title: wtC_45min_r1

description:
Nascent RNA
TT-Seq

source_name: WT, siControl, 45min, r1


title: wtC_3h_r3

description:
Nascent RNA
TT-Seq

source_name: WT, siControl, 3h, r3


title: wtR_45min_r1

description:
Nascent RNA
TT-Seq

source_name: WT, siRPB1+Dox, 45min, r1


title: wtC_3h_r1

description:
Nascent RNA
TT-Seq

source_name: WT, siControl, 3h, r1


title: mutR_UNT_r3

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siRPB1+Dox, untreated, r3

value: RPB1 K1268R mutant


title: mutR_UNT_r2

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siRPB1+Dox, untreated, r2


title: mutR_45min_r3

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siRPB1+Dox, 45min, r3


title: mutR_UNT_r1

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siRPB1+Dox, untreated, r1


title: mutR_45min_r2

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siRPB1+Dox, 45min, r2


title: mutR_3h_r2

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siRPB1+Dox, 3h, r2


title: mutR_45min_r1

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siRPB1+Dox, 45min, r1


title: mutR_3h_r3

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siRPB1+Dox, 3h, r3


title: mutC_UNT_r3

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siControl, untreated, r3


title: mutR_3h_r1

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siRPB1+Dox, 3h, r1


title: mutC_3h_r1

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siControl, 3h, r1


title: mutC_UNT_r1

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siControl, untreated, r1


title: mutC_3h_r3

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siControl, 3h, r3


title: mutC_3h_r2

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siControl, 3h, r2


title: mutC_UNT_r2

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siControl, untreated, r2


title: wtC_45min_r3

description:
Nascent RNA
TT-Seq

source_name: WT, siControl, 45min, r3


title: mutC_45min_r2

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siControl, 45min, r2


title: mutC_45min_r3

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siControl, 45min, r3


title: MOUSE4531_antiGM1_boneMacromet

city: NEW YORK

first: Ashley

middle: M

last: Laughney

state: New York

address: 413 East 69th Street

department: Physiology, Biophysics and Systems Biology

institute: Weill Cornell Medicine

description: Barcoded single cells

data_processing:
InDrop v2 RNA-seq data was processed from raw fastq files to count matrices with SEQC v0.2.1 (see https://github.com/ambrosejcarr/seqc.git)
Genome_build: hg38 annotation restricted to transcribed, polyadenylated RNA of length > 200 nucleotides
Supplementary_files_format_and_content: csv of cells x genes unnormalized

source_name: early stage RAS-mutant human lung adenocarcinoma (H2087-LCC) (see Malladi et al.2016, Cell)

growth_protocol: Animal experiments were performed in accordance with protocols approved by the MSKCC Institutional Animal Care and Use Committee. 1x105 H2087-LCC2 cells expressing a lentiviral TK-green fluorescent protein(GFP)-luciferase (TGL) construct and the antibiotic resistance marker Blasticidin in 100 µl of PBS, were injected into the left cardiac ventricle of 6-7 week-old female athymic NCR nu/nu mice (Charles River) to ensure systemic dissemination of tumour cells. Metastatic colonization was then measured weekly using bioluminescence imaging (BLI).

extract_protocol:
Cancer cells were freshly derived from DTCs, incipient and spontaneous metastatic outbreak in vivo immediately following sacrifice of animals +/- BLI-detected metastases. Ex-vivo BLI was performed on harvested organs to confirm the absence or to define the precise location of macrometastatic lesions. Organs were resected under sterile conditions and mechanically dissociated using a gentleMACS dissociator (Miltenyl Biotec) and placed in culture medium containing a 1:1 mixture of DMEM/Ham’s F12 medium supplemented with 0.125% collagenase III and 0.1% hyaluronidase. Minced samples were incubated at 37°C for 1 h, with gentle rocking to produce single cell suspensions. After collagenase treatment, cells were briefly centrifuged, re-suspended in 0.25% trypsin, and incubated for a further 15 min at 37°C. Cells were then re-suspended in their culture conditions and allowed to grow to confluence on a 15-cm dish in selection media containing blasticidin to select for tumour cells and exclude host cells. scRNA-seq assays were performed after a single passage from the primary dissociation.   Single cell suspensions were similarly derived from metastatic outbreaks in NK cell-depleted mice, but were processed immediately for scRNA-seq without antibiotic selection. Cell suspensions were subsequently flow sorted with a BD FACSAria II cell sorter fitted with a 100 µm nozzle to enrich for viable, GFP-positive single cells according to forward and side scattering, fluorescent protein expression, and DAPI exclusion. Cells were sorted directly into RPMI media with 10% FBS, washed thrice and re-suspended in PBS containing 0.04% BSA for single cell encapsulation.
Sequencing libraries were prepared following the InDrop v2 protocol (see Zilinonis et al. 2017, Nature Protocols)

treatment_protocol: NK cell depleted-outbreaks were achieved by twice-weekly intra-peritoneal injection of 100μl of anti-asialo-GM1 antibody (Wako Chemicals Cat. 98610001) 30 days after H2087-LCC2 cells were inoculated in mice.

value: H2087 Bone macrometastasis generated by NK cell depletion identified by BLI

tag: tissue

tag: passages

tag: nk cell depletion

value: Yes


title: MOUSE4737_antiGM1_kidneyMacromet

description: Barcoded single cells

value: H2087 Kidney macrometastasis generated by NK cell depletion identified by BLI

value: early stage RAS-mutant human lung adenocarcinoma (H2087-LCC) (see Malladi et al.2016, Cell)


title: MOUSE4544_antiGM1_kidneyMacromet

description: Barcoded single cells


title: MOUSE4531_antiGM1_kidneyMacromet

description: Barcoded single cells


title: MOUSE4766_lungMacromet

description: Barcoded single cells

value: H2087 Lung macrometastasis identified by BLI

value: No


title: MOUSE4770_lungMacromet

description: Barcoded single cells


title: MOUSE4768_lungMacromet

description: Barcoded single cells


title: mutC_45min_r1

description:
Nascent RNA
TT-Seq

source_name: K1268R mutant, siControl, 45min, r1


title: MOUSE4774_02_lungIncipientMet

description: Barcoded single cells

value: H2087 Lung incipient metastasis identified by ex vivo BLI


title: MOUSE4774_01_lungIncipientMet

description: Barcoded single cells


title: mut_24h_r2

description:
Nascent RNA
TT-Seq

source_name: RPB1 mutant, CSB WT, 24h, r2


title: MOUSE4585_kidneyDTC

description: Barcoded single cells

value: H2087 DTCs isolated from BLI-negative kidney


title: MOUSE4548_antiGM1_boneMacromet

description: Barcoded single cells


title: MOUSE4737_antiGM1_boneMacromet

description: Barcoded single cells


title: 47_input_active_TNF60min_rep2

city: Tokyo

first: Yoshiki

last: Higashijima

address: 1-5-45 Yushima, Bunkyo

department: Medical Research Institute

institute: Tokyo Medical and Dental University

description: ChIP-seq data of human endothelial cells through TNF-induced inflammatory signaling

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Sequence reads (36-bp single read) from ChIP for histones, KDM7A, UTX, and p65 were mapped to the human reference genome hg19, by using the Illumina alignment program, ELAND. Only sequence reads that mapped uniquely to the reference genome were used for further analysis.
The mapped sequence reads were extended to 500-2000 bp and converted to the continuous signal data in wig format.  Wig files were converted to bigwig files using UCSC wigToBigWig program.
Genome_build: human NCBI genome build 37 (hg19)
Supplementary_files_format_and_content: bigwig

source_name: human umblical vein endothelial cells

growth_protocol: HUVECs were purchased from Lonza Japan Ltd. (Tokyo, Japan) and cultured and passaged every 2 or 3 days in EBM-2 complete medium composed of EBM-2 Basal Medium (Lonza) supplemented with EGM-2 SingleQuot Kit Suppl. & Growth Factors (Lonza) and 3% fetal bovine serum (FBS) (Thermo Fisher Scientific, Waltham, MA). We sub-cultured HUVECs when they reached 80 to 90% confluence to avoid excessive floaters. HUVECs were used within passage 4 to 7 for all experiments in this work. Human monocyte cell line U937 was purchased from JCRB Cell Bank (Osaka, Japan) and grown and passaged every 2 or 3 days in RPMI1640 (Thermo Fisher Scientific) supplemented with 1% penicillin/streptomycin (Wako, Osaka, Japan) and 10% FBS. All cells were cultured at 37 ºC and 5% CO2 in a humidified incubator.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (Kanki et al., 2011; Kanki et al., 2017). In brief, 10 million HUVECs were cross-linked with 1% formaldehyde (Wako) for 10 min. For p65 and FLAG ChIP analysis, cells were fixed with 2 mM EGS (ethylene glycol bis [succinimidyl succinate]) (Thermo Fisher Scientific) for 1 hr prior to formaldehyde fixation. After neutralization by using 0.2 M glycine, cells were collected, re-suspended in 2 ml SDS lysis buffer composed of 10 mM Tris-HCl; pH8.0 (Thermo Fisher Scientific), 150 mM NaCl (Thermo Fisher Scientific), 1% SDS (Sigma-Aldrich), 1mM EDTA; pH 8.0 (Thermo Fisher Scientific), cOmplete™ EDTA-free Protease Inhibitor Cocktail (Sigma-Aldrich), and fragmented by the Picoruptor (40 cycles for histones and p65, and 20 cycles for FLAG, 30 sec on/30 sec off; Diagenode, Liege Science Park, Belgium). Sonicated solution was diluted by ChIP dilution buffer (20 mM Tris-HCl; pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100 (Sigma-Aldrich)) up to 10.3 ml, which was used for immunoprecipitation (10 ml) and the rest 300 μl as a non-immunoprecipitated chromatin (INPUT). Specific antibody was bound with magnetic Dynabeads M-280 and applied to diluted sonicated solution for immunoprecipitation. Antibodies against H3K4me3, H3K27ac, H3K9me2, H3K27me3 (MAB Institute, Inc. Hokkaido, Japan), p65 (abcam for ChIP-Seq and Santa Cruz Biotechnology Inc for ChIP-PCR), and FLAG (Sigma-Aldrich) were used. Prepared DNA was quantified using NanoDrop 2000 (Thermo Fisher Scientific) and more than 10 ng of DNA was processed for qPCR or sequence.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: 80-90% confluent HUVECs plates were washed with PBS once and then serum starved in EBM-2 Basal Medium containing 0.5% FBS for 16 hrs. HUVECs were stimulated with or without 10 ng/ml TNF-α (Peprotech, Rocky Hill, NJ) for indicated periods thereafter.

tag: antibody used for chip

tag: donor

value: pooled from multiple donors

value: HUVECs


title: 49_H3K4me3_TNF60min_rep2


title: 48_H3K4me3_TNF0min_rep2


title: 50_H3K27ac_TNF0min_rep2


title: 46_input_active_TNF0min_rep2


title: 44_H3K27ac_TNF0min_rep1


title: 45_H3K27ac_TNF60min_rep1


title: 43_H3K4me3_TNF60min_rep1


title: mut.24h.r1

description: mRNA-Seq

source_name: RPB1 K1268R mutant, 24h, r1


title: 42_H3K4me3_TNF0min_rep1


title: 40_input_active_TNF0min_rep1


title: MOUSE4587_kidneyDTC

description: Barcoded single cells


title: 51_H3K27ac_TNF60min_rep2


title: Emp_rep1

first: SRIGANESH

last: JAMMULA

state: UK

address: University of Cambridge, Li Ka Shing Centre, Robinson Way

institute: CRUK CI

data_processing:
Sequencing data is aligned to human (mm9) genome in a reference guided manner by HISAT2
Differentially expressed genes were identified using DESeq2.
Genome_build: GRCh37
Supplementary_files_format_and_content: list of genes with rpkm values

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying theTruSeq RNA Sample Preparation Kit v2 ( RS-122-2001 )

treatment_protocol: total RNA extracted with Rneasy Plus Micro Kit Qiagen processed for mRNA library preparation

value: ovarian carcinoma cell line


title: B10_C20_rep2

source_name: shPRMT1 #5_CDDP_2


title: B10_rep2

source_name: shPRMT1 #5_UT_2


title: B6_rep2

source_name: shPRMT1 #1_UT_2


title: Emp_C20_rep2


title: B8_rep2

source_name: shPRMT1 #3_UT_2


title: B6_rep1

source_name: shPRMT1 #1_UT_1


title: B8_rep1

source_name: shPRMT1 #3_UT_1


title: B6_C20_rep1

source_name: shPRMT1 #1_CDDP_1


title: Emp_rep2


title: B6_C20_rep2

source_name: shPRMT1 #1_CDDP_2


title: B8_C20_rep2

source_name: shPRMT1 #3_CDDP_2


title: B10_rep1

source_name: shPRMT1 #5_UT_1


title: 41_input_active_TNF60min_rep1


title: B10_C20_rep1

source_name: shPRMT1 #5_CDDP_1


title: Emp_C20_rep1


title: B8_C20_rep1

source_name: shPRMT1 #3_CDDP_1


title: Diapaused ICM rep1

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

data_processing:
Reads were aligned using Bowtie (Langmead et al., 2009) version 0.12.5, to version mm9 of the mouse genome. Paramaters were adjusted to allow for two mismatches in the initial eighteen bases. To account for reads crossing splice junctions, we aligned the remaining reads to a set of sequences taken from upstream of the donor site and downstream of the acceptor site of every splice junction annotated in version 58 of the Ensembl gene annotations (Hubbard et al., 2009). For the purpose of analysis we used only reads aligned uniquely to the genome, and took the additional precaution of filtering out any reads overlapping low complexity regions or simple repeats as defined by the UCSC genome brower RepeatMasker track
After summarizing the expression of each gene by the number of reads aligned unambiguously within any of its exons, the DESeq package was used to perform differential expression analysis
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited file of gene-level transcript per million (TPM) for each sample.

source_name: Mouse embryo

growth_protocol: All embryos were recovered from C57BL/6 females (Charles River). The day of the vaginal plug was considered day 0.5. The third day following detection of a vaginal plug was referred to as day 3.5. Embryonic diapause was induced by intraperitoneal injection of tamoxifen and subcutaneous administration of 0.5 mg of Depo Provera on day 3.5 (MacLean Hunter and Evans, 1999). Diapause blastocysts were harvested 5 days later. Day 3.5 and diapause blastocysts were flushed from the uterus of superovulated pregnant females. For the isolation of ICM, the zona pellucida was first removed from day 3.5 embryos by incubation in acid Tyrode’s solution.  To remove the trophoectoderm through immune-surgery, blastocysts were placed in a rabbit anti-mouse polyclonal antibody (Rockland Immunochemicals) for 20 min at 37 C, followed by guinea pig serum complement for 20–30 min at 37 C. The lysed tro- phectoderm cells were removed and the isolated ICM was placed in lysis buffer to isolate RNA. The derivation of epiblast (Epi) from day 6.5 post-implantation embryos has been described previously (Brons et al., 2007). Each biological triplicate for ICM and dICM and duplicate for Epi samples contained lysates from approximately 50 embryos. Our work has been performed in compliance with ethical regulations, IACUC protocol # 4152-02.

extract_protocol:
Total RNA was extracted using Qiagen Micro RNeasy kit and amplified following protocols of WT-Ovation Pico kit (Nugen). The qual- ity and quantity of RNAs were determined on an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Diapaused ICM

tag: strain

value: female


title: ICM rep3

treatment_protocol: Embryonic diapause was induced by intraperitoneal injection of tamoxifen and subcutaneous administration of 0.5 mg of Depo Provera on day 3.5 (MacLean Hunter and Evans, 1999). Diapause blastocysts were harvested 5 days later.

value: ICM


title: Diapaused ICM rep2


title: Post-implantation EPI rep2

value: Post-implantation EPI


title: Diapaused ICM rep3


title: ICM rep1


title: ICM rep2


title: G1_S7_Mouse 24hrs untreated

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
Poor quality reads/bases or technical sequences such as adapters are removed from the paired end reads using Trimmomatic v0.32
Trimmed RNA-seq reads were aligned to the Ensembl release 95-GRCm38 genome assembly using using STAR aligner (STAR_2.5.2a) with default options.
Transcript abundance and differential expression was performedusing Cufflinks v2.2.1 and Cuffdiff v2.2.1 respectively.
Genome_build: Ensembl release 95-GRCm38
Supplementary_files_format_and_content: Cufflink gene FPKM

source_name: LS8 Murine cell

growth_protocol: LS8 cells are an immortalized murine-derived enamel cell line. Cells were maintained in DMEM supplemented with 10% FBS,  1% sterptomycin/penicillin at 37 ºC with 5 % CO2.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) as indicated by the manufacturer followed by reverse transcription using the iScript cDNA Synthesis Kit (Biorad).RNA quality and quantity was analyzed on an Agilent Bioanalyzer nano chip.
RNAseq libraries were prepared using the stranded TruSeq mRNA kit (Illumina), starting from 500 ng of DNAse I (Qiagen) treated total RNA, following the manufacturer’s protocol. The amplified libraries (10 PCR cycles) were purified using AMPure beads (Beckman Coulter), quantified by Qubit 2.0 fluorometer (Life Technologies), and visualized in an Agilent Tapestation 2200. The libraries were pooled equimolarly, and loaded on an S1100 flow cell, and run as paired-end 50 nucleotide reads on a NovaSeq 6000.  Raw paired-end sequencing reads from both human and mouse samples were quality controlled using the FASTQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).

treatment_protocol: Treated cells were kept on the same growth medium but were suplemented with 1 mM NaF for 24 hours before RNA isolation in 6 x well plates at a density of ~80%. Four NaF-treated and four untreated samples per cells type were used.

value: Untreated for 24hrs


title: H1_S8_Mouse 24hrs untreated


title: F1_S6_Mouse 24hrs untreated


title: D2_S12_Mouse 24hrs treated

value: Treated with Fluoride for 24hrs


title: E1_S5_Mouse 24hrs untreated


title: Fibroblasts LCMV [FV_45a_1_3]

city: Essen

first: Judith

last: Lang

state: NRW

address: Hufelandstr. 55

department: Institute of Immunology

institute: University of Duisburg-Essen

description: Infected with LCMV and not treated

hyb_protocol: 100 ng of total RNA was converted to cDNA, followed by in vitro transcription and incorporation of Cy3-CTP into nascent cRNA. After fragmentation, labelled cRNA was hybridized to AgilentSurePrint G3 Mouse GE 8×60k microarrays (G4852B) for 17 hours at 65°C, according to the manufacturer's protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies; Waldbronn, Germany).

scan_protocol: The Microarrays were scannt with the Agilent Microarray Scanner G2505C (protocol: AgilentG3_GX_1color; dye: green; scan region: Agilent HD; scan area: 61x21.6 mm; scan resolution 3µm; tiff file: 20 bit; green PMT gain: 100%). Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 10.7.1.1; Agilent Technologies; Grid Template: 028005_D_F_20101029; Protocol: GE1_107_Sep09; MetricSet: GE1_QCMT_Sep09).

data_processing: Probe signal intensities were quantile normalized across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples. Data analyses were conducted with GeneSpring GX software (Vers. 10.5; Agilent Technologies). To analyze the microarray data a gene set enrichment analysis with GSEA (Broad Institute, v3.0) using the Gene Ontology Cellular Components (CC) gene set database (c5.cc.v6.2, accessed on 15.07.19) was performed using default settings. Results were further subjected to network analysis using the Enrichment Map plugin v3.2.0 in Cytoscape v3.7.1 with the following settings: FDR q-value cutoff 0.05, p-value cutoff 1, Metric: Jaccard+Overlap Combined (50/50) with cutoff 0.375. Clusters were identified by the AutoAnnotate plugin v1.3 and labeled manually for visualization.

source_name: fibroblast

label_protocol: Synthesis of cDNA and subsequent fluorescent labelling of cRNA was performed on four replicates of each experimental condition (treatment with LCMV on macrophages or combined treatment with LCMV and IFN on fibroblasts) according to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies; Waldbronn, Germany).

growth_protocol: For the generation of macrophages, bone marrow was isolated from mice and cultured for 9 days with macrophage colony-stimulating factor (M-CSF). Cells were plated on new cell culture plates and the experiment was started the next day. For generation of primary fibroblasts, lungs were isolated from mice and digested using DNase/Liberase. Fibroblasts were harvested after 6 days of culture and experiment was started the subsequent day.

extract_protocol: Total RNA was isolated from macrophages and fibroblasts using the RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: To ensure innate immune activation macrophages and fibroblasts were infected with LCMV and treated with 50U/mL IFN-α4.

tag: agent

value: LCMV


title: D1_S4_Mouse 4hrs untreated

value: Untreated for 4hrs


title: Post-implantation EPI rep1

tag: Sex


title: Macrophages LCMV IFN [MVI_16b1_2]

description: Infected with LCMV and treated IFN-α4

source_name: macrophage

value: LCMV+IFN


title: Macrophages LCMV [MV_39a_1_1]

description: Infected with LCMV and not treated


title: Fibroblasts LCMV [FV_33a_2_3]

description: Infected with LCMV and not treated


title: Fibroblasts LCMV IFN [FVI_22c_1_4]

description: Infected with LCMV and treated IFN-α4


title: Macrophages LCMV IFN [MVI_28b_2_2]

description: Infected with LCMV and treated IFN-α4


title: Fibroblasts LCMV IFN [FVI_70a_2_4]

description: Infected with LCMV and treated IFN-α4


title: C2_S11_Mouse 24hrs treated


title: Macrophages LCMV [MV_63a_2_1]

description: Infected with LCMV and not treated


title: B1_S2_Mouse 4hrs untreated


title: Fibroblasts LCMV IFN [FVI_34a_2_4]

description: Infected with LCMV and treated IFN-α4


title: Macrophages LCMV IFN [MVI_64a_2_2]

description: Infected with LCMV and treated IFN-α4


title: C1_S3_Mouse 4hrs untreated


title: A1_S1_Mouse 4hrs untreated


title: Macrophages LCMV [MV_27c_2_1]

description: Infected with LCMV and not treated


title: Fibroblasts LCMV [FV_21b_1_3]

description: Infected with LCMV and not treated


title: Fibroblasts LCMV IFN [FVI_46a_1_4]

description: Infected with LCMV and treated IFN-α4


title: Macrophages LCMV IFN [MVI_40b_1_2]

description: Infected with LCMV and treated IFN-α4


title: Fibroblasts LCMV [FV_69b_2_3]

description: Infected with LCMV and not treated


title: 4OHT_Control_48h_RNASeq_Rep3

first: Vlad

middle: Cezar

last: Seitan

address: Guy's Hospital

department: Medical & Molecular Genetics

institute: King's College London

description: total RNA (rRNA-depleted)

data_processing:
ChIP-seq: Reads were trimmed and filtered using Cutadapt applying a Phred quality threshold of 25 and a minimal read length of 25 bases. Filtered reads were aligned to the mouse genome (NCBI37/mm9 assembly) with Bowtie 1.1.2 keeping only uniquely aligned reads while allowing a maximum of 2 mismatches (-v 2 -m 1). MACS2 was set to discard PCR/optical duplicates and was used as peak caller within the Irreproducibility Discovery Rate (IDR) pipeline implemented by the ENCODE consortium. The final set of peaks was considered the conservative set for IDR <0.02. From this set we removed blacklisted sites. Peak overlap analysis was carried out in R and normalised read coverage values were obtained using the DiffBind Bioconductor package.
RNA-seq: Bases with a Phred quality score lower than 25 were trimmed from read ends with Cutadapt, and polyA tails were removed using PRINSEQ. Filtered reads were aligned to the mouse transcriptome with STAR using 2-pass mapping, and gene-level counts were generated with HTSeq. Differential gene expression analysis was carried out using the Bioconductor package EdgeR.
Genome_build: mm9

source_name: Embryonic Stem Cells

growth_protocol: Mouse embryonic stem cells were maintained in feeder-free conditions, on gelatin-coated plates, in KO DMEM supplemented with 10% foetal bovine serum, LIF, L-Glutamine, 2-mercaptoethanol, non-essential amino acids, penicillin and streptomycin

extract_protocol:
1μg total RNA was used as starting material for each library. rRNA was depleted using the NEBNext rRNA Depletion Kit (E6310, New England Biolabs)
Directional RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420, New England Biolabs).

tag: parental esc line

tag: zbtb11 locus genotype

tag: rosa26 locus genotype

value: WT

value: 4-hydorxytamoxifen (250nM)

tag: treatment protocol

value: To induce Zbtb11 KO, growth media was supplemented with 4-hydroxytamoxifen (4OHT) pre-slubilised in ethanol. 4OHT was added to a final concentration of 250nM from a 1000x stock solution. As control, Zbtb11lox/lox Rosa26ERt2-Cre were treated with the carrier ethanol, or Zbtb11WT/WT Rosa26WT were treated with 4OHT.

tag: antibody


title: 4OHT_Control_48h_RNASeq_Rep2

description: total RNA (rRNA-depleted)


title: 4OHT_Zbtb11KO_48h_RNASeq_Rep3

description: total RNA (rRNA-depleted)


title: 4OHT_Control_48h_RNASeq_Rep1

description: total RNA (rRNA-depleted)


title: EtOH_Control_48h_RNASeq_Rep3

description: total RNA (rRNA-depleted)

value: ethanol


title: A2_S9_Mouse 24hrs treated

tag: cell line


title: Cancer-associated fibroblast (CAF)

city: La Jolla

first: Jason

last: Sicklick

state: CA

address: 3855 Health Sciences Dr

institute: UCSD, Moores Cancer Center

data_processing:
Genome alignment was performed by STAR aligner with human genome (hg38).
DESeq2 identified differentially expressed genes between groups.
Genome_build: hg38
Supplementary_files_format_and_content: T1_vs_CAF.deseq.counts

source_name: GIST

extract_protocol:
Total RNA was extracted from cell lines with RNeasy Mini Kit (Quiagen, Germantown, MD, USA)
Total RNA isolated from the cell lines was assessed for quality using Tapestation (Agilent Technologies, Santa Clara, CA, USA), and samples determined to have an RNA Integrity Number (RIN) of 7 or greater were used.  Libraries were generated from 1 µg of total RNA using TruSeq Standed mRNA Sample Prep Kit (Illumina, San Diego, USA).

tag: cell type

value: Cancer-associated fibroblast (CAF)


title: 4OHT_Zbtb11KO_48h_RNASeq_Rep2

description: total RNA (rRNA-depleted)


title: EtOH_Control_48h_RNASeq_Rep2

description: total RNA (rRNA-depleted)


title: EtOH_Control_48h_RNASeq_Rep1

description: total RNA (rRNA-depleted)


title: B2_S10_Mouse 24hrs treated


title: GIST882

value: gastrointestinal stromal tumor (GIST) cell


title: GIST-T1


title: Input_Zbtb11_ChIP_Rep3

description: genomic DNA

extract_protocol:
Cells were fixed in culture media containing 1% formaldehyde (Sigma) for 10 minutes at room temperature. Following fixation, cells were resuspended in [10 mM HEPES pH 7.5,10 mM EDTA, 0.5 mM EGTA, 0.75% Triton X-100, Complete protease inhibitors] and incubated mixing end over end for 10 minutes at 4oC. Nuclei were pelleted by centrifugation, then resuspended and incubated as before in [10 mM HEPES pH 7.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, Complete protease inhibtors]. Subsequently nuclei were resuspended in sonication buffer [150 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.5% Sodium Deoxycholate, Complete protease inhibitors (Roche)], incubated for 30 minutes on ice, and sonicated in a Bioruptor Pico (Diagenode) for 10 cycles (30 seconds on, 30 seconds off). Insoluble chromatin was pelleted by high-speed centrifugation and the supernatant was incubated with the ChIP antibody over night mixing end over end at 4oC. 1μg antibody was used per million sonicated ES cells.  Following over night incubation, antibody/chromatin complexes were pulled down by mixing 3 hours at 4oC with protein G Dynabeads (Thermo Fihser Scientific) using 5μl beads per μg antibody. Beads were washed 3 times and the DNA was eluted by shaking the beads over night at 65oC in [1xTE, 1% SDS, 0.5mg/ml proteinase K (Sigma)]. Eluted DNA was isolated by phenol/chloroform extraction and ethanol precipitation. Purified DNA was quantified using the Quant-iT PicoGreen kit (Thermo Fisher Scientific).
Libraries were prepared from 10ng ChIP DNA using the NEBNext Ultra II DNA Library Prep kit for Illumina (E7645, New England Biolabs).

value: anti-Zbtb11 (Biotechne, NBP1-80327)


title: H3_S24_Human 24hrs treated

data_processing:
Poor quality reads/bases or technical sequences such as adapters are removed from the paired end reads using Trimmomatic v0.32
Trimmed RNA-seq reads were aligned to the Ensembl release 84-GRCh38 genome assembly using using STAR aligner (STAR_2.5.2a) with default options.
Transcript abundance and differential expression was performedusing Cufflinks v2.2.1 and Cuffdiff v2.2.1 respectively.
Genome_build: Ensembl release 84-GRCh38

source_name: Human 24hrs treated

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS, 1% sterptomycin/penicillin + 1% L-Glutamine at 37 ºC with 5 % CO2.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) as indicated by the manufacturer followed by reverse transcription using the iScript cDNA Synthesis Kit (Biorad).RNA quality and quantity was analyzed on an Agilent Bioanalyzer nano chip.
RNAseq libraries were prepared using the stranded TruSeq mRNA kit (Illumina), starting from 500 ng of DNAse I (Qiagen) treated total RNA, following the manufacturer’s protocol. The amplified libraries (10 PCR cycles) were purified using AMPure beads (Beckman Coulter), quantified by Qubit 2.0 fluorometer (Life Technologies), and visualized in an Agilent Tapestation 2200. The libraries were pooled equimolarly, and loaded on an S1100 flow cell, and run as paired-end 50 nucleotide reads on a NovaSeq 6000.  Raw paired-end sequencing reads from both human and mouse samples were quality co


title: G3_S23_Human 24hrs treated


title: H2_S16_Human 4hrs untreated

source_name: Human 4hrs untreated


title: G2_S15_Human 4hrs untreated


title: Input_Zbtb11_ChIP_Rep1

description: genomic DNA


title: Input_Zbtb11_ChIP_Rep2

description: genomic DNA


title: Input_FLAG-Zbtb11_ChIP_Rep2

description: genomic DNA

value: anti-FLAG M2 clone (Sigma, F3165)


title: Zbtb11_ChIPSeq_Rep4

description:
genomic DNA
Zbtb11_peaks.bed
Zbtb11_consensus_peaks_read_coverage.txt


title: Zbtb11_ChIPSeq_Rep3


title: Zbtb11_ChIPSeq_Rep2


title: E3_S21_Human 24hrs treated


title: F2_S14_Human 4hrs untreated


title: FLAG_Control_ChIPSeq_Rep2

description:
genomic DNA
FLAG_Control_peaks.bed


title: D3_S20_Human 24hrs untreated

source_name: Human 24hrs untreated


title: Zbtb11_ChIPSeq_Rep1


title: FLAG_Control_ChIPSeq_Rep1

description:
genomic DNA
FLAG_Control_peaks.bed


title: FLAG-Zbtb11_ChIPSeq_Rep3

description:
genomic DNA
FLAG-Zbtb11_peaks.bed
Zbtb11_consensus_peaks_read_coverage.txt


title: C3_S19_Human 24hrs untreated


title: FLAG-Zbtb11_ChIPSeq_Rep1


title: A3_S17_Human 24hrs untreated


title: B3_S18_Human 24hrs untreated


title: FLAG-Zbtb11_ChIPSeq_Rep2


title: Input_FLAG-Zbtb11_ChIP_Rep1

description: genomic DNA


title: F3_S22_Human 24hrs treated