title: HASMCs GFP ATAC 1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2
Bigwig files were generated by deepTools
hg19
BW

extract_protocol: Cells were digested with trypsin (Invitrogen, Carlsbad, CA, #25200072) and then were pretreated with 200 U/mL DNase (Sigma-Aldrich, St. Louis, MO, #260913) for 30 min at 37 °C to remove free-floating DNA and digest DNA from dead cells. Then 50,000 cells were resuspended in 1 mL of cold RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2). Cells were centrifuged at 500 rcf for 5 min and then resuspended in 50 μL of RSB buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin and incubated on ice for 10 min. After lysis, added 1 mL RSB buffer containing 0.1% Tween-20 and nuclei were centrifuged for 10 min at 500 rcf. Then the ATAC-seq library were prepared by using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech, Nanjing, China, #TD501-01).

tag: tag

value: Ad-GFP


title: HASMCs BACH1 ATAC 2

status: Public on May 31 2023

type: SRA

city: Shanghai

first: Jieyu

last: Guo

state: Shanghai

address: 138 Yixueyuan Rd,

country: China

institute: fudan university

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: human aortic smooth muscle cells

growth_protocol: HASMC cells were maintained with SMCM at 37 °C in a humidiﬁed incubator with 5% CO2, and were passaged when about 70-90% intensity.

treatment_protocol: HASMC cells were treated with Ad-GFP or Ad-BACH1

tag: genotype


title: H3K27ac_siArid1aplusEGF_rep1

city: Goettingen

first: Zhe

last: Zhang

state: Niedersachsen

address: Robert-Koch-Strasse 40

department: Department of Gastroenterology & GI oncology

country: Germany

institute: University Medical Center, Goettingen

data_processing:
Single-end 50bp reads were aligned to mouse genome MGSCv37/mm9 by Bowtie2 (Version 2.3.4.2)
Low-quality reads (MAPQ < 5) and PCR duplicates were filtered out using Samtools
Peaks were called by MACS2 (Version 2.1.1.20160309.0) with the criteria as fold enrichment > 5 compared to background and FDR < 0.05
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated usign MACS2, scores represent enrichment of the peaks and all the peaks are with FDR<0.05
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage (Version 3.0.2)

organism: Mus musculus

source_name: Acinar cell line 266-6

growth_protocol: 266-6 murine pancreatic acinar cell line was established as described before (Korc et al., 1992). Cells were cultured in Dulbecco’s modified Eagle’s Medium containing 4.5 g/L D-Glucose, L- Glutamine supplemented with 10% fetal calf serum (FCS) at 37 ºC incubator with 5 % carbon dioxide supply.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody. ChIP-seq samples were prepared in duplicates per condition.
Library for ChIP-seq was prepared using Microplex Library Preparation V2 following the manufacturer’s instruction. 0.5 ng double-stranded ChIP-DNA was utilized as start material, repaired into blunt ends and subsequently ligated with stem-loop adaptors. Libraries were amplified and size-selected by AMPure beads. Library quantification was performed using Agilent Bioanalyzer 2100. Finally, library was prepared as 2 nmol/L for sequencing.

treatment_protocol: Transient ARID1A knockdown was performed by siRNAs (25 nM) purchased from Dharmacon (ON-TARGETplus ARID1A siRNA J-017263-07-0005 and J-017263-08-0005) with non-targeting siRNA NT5 (Ambion, UGGUUUACAUGUCGACUAA) as control. Reverse transfection was conducted using Lipofectamine RNAiMAX transfection reagent (Invitrogen, Karlsruhe, Germany) according to the specified protocol and sustained for 48 hours. Prior to EGF stimulation (Sigma-Aldrich, 40ng/ml), cells were starved in serum-free medium overnight and then treated with EGF or the control vehicle 0.1% BSA for 8 hours.

tag: cell type

value: Acinar cell

tag: treatment

value: 40ng/ml EGF

tag: cell line

tag: chip antibody

value: H3K27ac (GeneTex, Cat# GTX128944)


title: CHOS-3

first: Hui

last: Wang

state: China

address: Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, China

department: School of Pharmacy

institute: Shanghai Jiao Tong University

library_source: transcriptomic

data_processing:
Seqtk
Remove the linker sequence contained in the reads
Remove bases with a quality Q lower than 20 at the 3' end, that is, the base error rate is less than 0.01, where Q=-10logerror_ratio
Remove reads whose length is less than 25
Remove the ribosome RNA reads of the species to which they belong
Assembly: CHOK1GS_HDv1
Supplementary files format and content: xls files include count and FPKM values for each sample

molecule: total RNA

organism: Cricetulus griseus

source_name: Ovary

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat# 74106, Qiagen) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme) following manufacturer's protocols.

tag: tissue

value: Ovary

value: Chinese hamster ovary cells (CHO-S)

value: Monclonal cell line

value: Wild type


title: CHOS-2


title: H3K27ac_EGF_rep1


title: Subject: S070-2013; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

type: protein

city: Irvine

first: Arlo

middle: Zan

last: Randall

state: CA

address: 1 Technology Drive, Suite E309

country: USA

institute: Antigen Discovery Inc

description:
S070-2013.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

hyb_protocol: Plasma samples were diluted 1:100 in a 3 mg mL-1 E. coli lysate solution in protein arraying buffer (Maine Manufacturing, Sanford, ME, USA) and incubated at room temperature for 30 min. Chips were rehydrated in blocking buffer for 30 min. Blocking buffer was removed, and chips were probed with pre-incubated serum samples using sealed, fitted slide chambers to ensure no cross-contamination of sample between pads. Chips were incubated overnight at 4°C with agitation. Chips were washed five times with TBS-0.05% Tween 20, followed by incubation with biotin-conjugated goat anti-human IgG (Jackson ImmunoResearch, West Grove, PA, USA) diluted 1:200 in blocking buffer at room temperature. Chips were washed three times with TBS-0.05% Tween 20, followed by incubation with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Frederick, MD, USA) at room temperature protected from light. Chips were washed three times with TBS-0.05% Tween 20, three times with TBS, and once with water. Chips were air dried by centrifugation at 1,000 x g for 4 min and dried overnight in dessicator before scanning.

scan_protocol: Probed microarrays (slides) were scanned using a GenePix 4300A High-Resolution Microarray Scanner (Molecular Devices, Sunnyvale, CA, USA) an image file (.tif) was saved for each array using GenePix Pro 7 software. The scanned image files were quantified using the Mapix software (Innopsys) auto gridding feature. For this process two input files are required: (1) a .gal file that defines the array and sub-array layout and (2) the tiff image file for an array. Once the auto-gridding is complete the overlay of the mapped array, subarray, and individual spot locations are shown in the graphical user interface (GUI). If the automatic gridding fails to map to the correct positions the mapping can be manually adjusted using the GUI. Once the gridding is confirmed to be correct the array spots are quantified and saved to an output .gpr file. For each spot on the slide the gpr file contains the foreground intensity (median of pixels inside of circle defining spot) and local background intensity (median of pixels just outside of circle defining spot).

data_processing: Foreground spot intensities were adjusted by local background by subtraction, and negative values were converted to 1. Next, all foreground values were transformed using the base 2 logarithm. The dataset was normalized to remove systematic effects by subtracting the median signal intensity of the IVTT controls for each sample. Since the IVTT control spots carry the chip, sample and batch-level systematic effects, but also antibody background reactivity to the IVTT system, this procedure normalizes the data and provides a relative measure of the specific antibody binding to the non-specific antibody binding to the IVTT controls (a.k.a. background). With the normalized data, a value of 0.0 means that the intensity is no different than the background, and a value of 1.0 indicates a doubling with respect to background. Normalization was applied separately to arrays 1 and 2.

label: biotin

molecule: protein

source_name: plasma

extract_protocol: not provided

tag: treatment group

value: Placebo

tag: etec colony pcr result at v1 (d0)

value: Negative

tag: etec colony pcr result at v7 (d97)

value: Positive

tag: gender

value: Female


title: Subject: S070-2013; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S070-2013.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: CHOS-1


title: Input-2

extract_protocol:
Chromatin immunoprecipitation (ChIP) sequencing: Cells were cross-linked with 1% formaldehyde for 10 minutes, quenched with 0.125 M glycine for 10 minutes; then, the cell pellets were resuspended in low salt Lysis buffer (50 mM HEPES/KOH, PH 7.5, 150 mM NaCl, 1% Trixon-X 100, 0.05% SDS, 10 mM EDTA, and proteinase inhibitors), and sonicated with a Q800R2 DNA shearing sonicator (Qsonica LLC, newtown, CT) for 20 min in 30-s intervals to shear the chromatin into 200- to 400-bp lengths. Chromatin was immunoprecipitated with the indicated antibodies and Protein A/G PLUS-Agarose (Santa Cruz, Santa Cruz, CA, #sc-2003). For, H3K9me2-ChIP ChIP, cells were cross-linked, quenched, and washed as described above. Furthermore, the sonicated chromatin was incubated with anti-H3K9me2 overnight at 4°C Then beads were washed with low salt lysis buffer and low salt buffer (10 mM Tris–HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP40, 0.5% Na-Deoxycholate), and DNA was eluted in elution buffer (50 mM Tris–HCl pH 8.0, 10 mM EDTA, 1% SDS) with Proteinase K (Yeasen, Shanghai, China, # 10401ES60) and RNase A (Thermo Fisher, Waltham, MA, #EN0531) in 65◦C for 4 h.
ChIP DNA libraries and input DNA samples were prepared as directed by the protocol of VAHTS Universal DNA Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China, #ND617-01) and Cut&Tag DNA libraries. were prepared by using HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China, #TD901-01).


title: H3K27ac_ctrl_rep2

value: 0.1 BSA


title: Input-1


title: Subject: S058-2007; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S058-2007.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: 1/8 dose ETVAX®

value: Male


title: HASMCs BACH1 ATAC 1


title: HASMCs GFP ATAC 2


title: H3K27ac_ctrl_rep1


title: ARID1A_EGF_rep1

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with ARID1A antibody. ChIP-seq samples were prepared in duplicates per condition.
Library for ChIP-seq was prepared using Microplex Library Preparation V2 following the manufacturer’s instruction. 0.5 ng double-stranded ChIP-DNA was utilized as start material, repaired into blunt ends and subsequently ligated with stem-loop adaptors. Libraries were amplified and size-selected by AMPure beads. Library quantification was performed using Agilent Bioanalyzer 2100. Finally, library was prepared as 2 nmol/L for sequencing.

treatment_protocol: Prior to EGF treatment, 266-6 cells in culture were washed with PBS for two times followed by starving in serum-free DMEM medium overnight (~14h). The next day, starved cells were treated with 40 ng/ml EGF for 8 hours and harvested for corresponding experiments. The control cells were treated with 0.1% BSA.

value: ARID1A (Cell Signaling Technology, Cat#12354)


title: ARID1A_EGF_rep2


title: Cut&Tag YAP-2

value: YAP


title: Cut&Tag YAP-1


title: Subject: S058-2007; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S058-2007.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: ARID1A_ctrl_rep2


title: HASMCs Bsi3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hista2
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated used by Cufflinks
hg38
elsx files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent
non-ribosomal RNA was isolated from 1 μg total RNA by using a TrueLib Poly (A) mRNA Magnetic Isolation Module, and sequencing libraries were prepared by using the TrueLib mRNA Library Prep Kit for Illumina

treatment_protocol: HASMC cells were treated with consiRNA or Bach1 siRNA

value: Bach1 siRNA


title: 266_siArid1aplusEGF_rep3

data_processing:
Single-end 50bp reads were aligned to mouse genome MGSCv37/mm9 by TopHat (Version 2.1.1)
Transcripts were counted by htseq-count (Version 0.9.1)
Transcripts normalization and differential expression analysis were performed by Cuffnorm (Version 2.2.1.2) and Cuffdiff (version 2.2.1.5) with FDR cutoff 0.05
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts corresponding with gene names
Supplementary_files_format_and_content: Normalized abundance measurement from Cuffnorm containing FPKM values for genes in all the treatment conditions

extract_protocol:
Total RNA was harvested by TRIzol method from triplicate (siCtrl samples are in duplicates) samples and quality was assessed by running 500 ng RNA on an agarose gel.
Libraries were prepared from 500 ng RNA utilizing Truseq RNA Library Prep Kit v2 following manufacturer’s instructions. mRNA was captured by RNA purification beads and eluted. The first strand and second strand cDNA were synthesized and the overhangs of the fragments were repaired into blunt ends. The 3’ end was added with a single adenine to prevent mutual ligation during the following adapter conjugation. Finally, the DNA fragments with both flow-cell-hybridization adapters were amplified and the library was quantified by Agilent Bioanalyzer 2100. Size selection was optional if the main population of the library exceeds the appropriate size for sequencing or small fragments such as primer-dimers exist.

treatment_protocol: Transient ARID1A knockdown was performed by siRNAs (25 nM) purchased from Dharmacon with non-targeting siRNA NT5 (Ambion) as control. Reverse transfection was conducted using Lipofectamine RNAiMAX transfection reagent (Invitrogen, Karlsruhe, Germany) according to the specified protocol and sustained for 48 hours. Prior to EGF stimulation (Sigma-Aldrich, 40ng/ml), cells were starved in serum-free medium overnight and then treated with EGF or the control vehicle 0.1% BSA for 8 hours.

value: Acinar cell


title: HASMCs Bsi2


title: 266_siArid1aplusEGF_rep2

value: 40ng/ml EGF


title: Subject: S078-2010; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S078-2010.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: Subject: S078-2010; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S078-2010.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: Colon (validation), 27 Months, Rep4

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

description:
27M.N4
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz

data_processing:
Sequence information was converted to fastq format using bcl2fastq v2.20.0.422. From validation samples only those reads were downstream processed, that start with a Tecan/NuGen TrueMethyl diversity adapter (length 0-3, clipped afterwards) followed by a MspI cutting site.
Read quality trimming (cutoff 20) and TruSeq universal adapter clipping was performed using Cutadapt v2.10. Due to MspI cutting site end-repair, R1 adapter was prefixed by NN and in case of paired-end data, unconditional 5' clipping of length 2 was conducted on R2.
Mappings were done via segemehl v0.3.4 (methyl-C mode, accuracy 95%, reference GRCm38) and filtered for unique alignments. Paired-end alignments were further filtered for proper-read pairs and overlaps of R2 with R1 were trimmed using BamUtil clipOverlap v1.0.14.
Validation data alignments were deduplicated for over amplified PCR fragments based on unique molecular identifiers utilizing UMI-tools v1.1.1.
Methylation rates were inferred utilizing haarz v0.3.0. Rates and coverages within a CpG context were compiled using BEDTools v2.30.0.
Assembly: mm10
Supplementary files format and content: Tabular delimited text files in bedg format of read alignment coverages and inferred methylation rates per GRCh38 chromosomal CpG and sample.

source_name: Colon

growth_protocol: All the mice were kept solely for aging in a controlled environment and health status.

extract_protocol:
Genomic DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen).
200 ng of DNA was fragmented via a 5 hour Msp1-digest (New England Biolabs), followed by TrueSeq adapter ligation (Illumina, San Diego, CA, USA) and subsequent bisulfite conversion following the manufacturers protocol (EZ DNA Methylation Gold Kit, Zymo Research). The bisulfite converted DNA was amplified in a 19-cycles PCR with Pfu Turbo Cx Hotstart DNA Polymerase (Agilent Technologies) and the resulting libraries were quality checked using 4200 TapeStation (Agilent Technologies). For sequencing of validation samples, Illumina’s next-generation sequencing methodology 87 was used. In detail, genomic DNA was quality checked and quantified using the 4200 TapeStation instruments in combination with the Genomic DNA ScreenTape (both Agilent Technologies). Libraries were prepared from 100 ng of input material using Ovation RRBS Methyl-Seq with TrueMethyl oxBS (Tecan). In detail, only the bisulfite part of the protocol was followed, oxidation of DNA was not done, and samples were treated as MOCK oxBS samples according to the manufacturer’s instruction. Quantification and quality check of libraries were done using the 4200 TapeStation and D5000 ScreenTapes instruments (both Agilent Technologies).

value: Colon

tag: strain

tag: Sex

tag: age

value: 27 Months


title: Colon (validation), 27 Months, Rep6

description:
27M.N6
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: Colon (validation), 27 Months, Rep5

description:
27M.N5
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: Subject: S060-2002; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S060-2002.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: Subject: S060-2002; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S060-2002.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: Subject: S064-2004; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S064-2004.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: 1/4 dose ETVAX®


title: Cut&Tag BACH1-2


title: Colon (validation), 27 Months, Rep3

description:
27M.N3
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: HASMCs Bsi1


title: 266_siArid1aplusEGF_rep1


title: Cut&Tag BACH1-1


title: Post diabetic Rep 1

type: RNA

city: Lucknow

first: Swasti

last: Tiwari

state: Uttar Pradesh

address: Raibareli Road

department: Molecular Medicine and Biotechnology

country: India

institute: Sanjay Gandhi Postgraduate Institute of Medical Sciences

description: Gene expression data from diabetic rat

hyb_protocol: The biotin-labeled RNA samples were hybridized to GeneChip miRNA 4.0 arrays in an Affymetrix® Oven 455 (Thermo Fisher Scientific) for 16-18 h at 48°C with 60 rpm rotation. Following hybridization, miRNA 4.0 arrays were subjected to washing and staining using the GeneChip® Hybridisation, Wash, and Stain Kit (Thermo Fisher Scientific) and Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Hybridized targets on the array were stained with streptavidin–phycoerythrin provided in the kit and detected using Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: The raw expression data in the form of.CEL file was analyzed using Affymetrix Transcriptome analysis console software (TAC 4.0, Thermo Fischer Scientific).

organism: Rattus norvegicus

source_name: Male Wistar rats

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 120 ng total RNA.

growth_protocol: Male Wistar rats were acclimatized under laboratory conditions for 2 weeks, housed in standard rat cages with 3 rats in each cage at 23–25°C and humidity- (50–60%) controlled condition with a 12-hour light/dark cycle.

extract_protocol: Urine sample was centrifuged at 12,000 x g for 15 min at 4ºC and the aqueous phase was transferred to a fresh tube. RNA was precipitated by adding 500μl isopropanol and the pellet was collected after centrifugation at 12,000 x g for 10 minutes at 4ºC. The RNA pellet was washed by vortexing with 75% ethanol and subsequently centrifuged at 7,500 x g for 5 minutes at 4ºC.

treatment_protocol: Diabetes mellitus was induced in rats via intraperitoneal (I.P) administration of streptozotocin (STZ) (50mg/kg body weight) dissolved in 0.1M citrate buffer.  Diabetes mellitus was induced in rats via intraperitoneal (I.P) administration of streptozotocin  (STZ) (50mg/kg body weight) dissolved in 0.1M citrate buffer

tag: phenotype

value: White fur and red eyes


title: Colon (validation), 27 Months, Rep2

description:
27M.N2
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: Post diabetic Rep 2

description: Gene expression data from diabetic rat


title: Subject: S064-2004; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S064-2004.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: 266_siArid1a_rep3

value: 0.1percent BSA


title: Baseline Rep 2

description: Gene expression data from non-diabetic rat


title: Baseline Rep 1


title: ARID1A_ctrl_rep1


title: Colon (validation), 27 Months, Rep1

description:
27M.N1
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: HASMCs Con1

value: Con siRNA


title: ATAC, Tendinopathy

city: Chongqing

first: JUNFENG

last: GUO

state: Chongqing

address: No. 30, Gaotan Yanzheng Street,

department: Department of Orthopedics/Sports Medicine Center

institute: Southwest Hospital, Third Military Medical University

library_source: genomic single cell

data_processing:
To be updated.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files. For Expression.txt file, the column name corresponds to the cell ID and the row name corresponds to the gene name. For the ATAC.txt file, the column name corresponds to the cell ID, and the row name corresponds to the peak name.

source_name: Achilles tendon

extract_protocol:
Tendinopathy tissue was placed in a 2-ml microcentrifuge tube, NP40 lysis buffer was added, and the mixture was incubated on ice for 5 min. Then, the mixture was filtered through a 70-µm filter and transferred to a new 2-ml microcentrifuge tube. After gradient centrifugation, the supernatant was removed. PBS, bovine serum albumin (BSA), and an RNase inhibitor were added and incubated on ice for 5 min. Repeated centrifugation resulted in a pure single-nuclei suspension.
The obtained nuclear suspension was incubated in a transposase mixture that entered the nuclei and preferentially fragmented DNA in open chromatin regions. Oligonucleotides containing an Illumina P5 sequence, a 16-nt 10x barcode and a spacer sequence were then released. Barcoded, full-length preamplified cDNA was further amplified via PCR to generate sufficient mass for gene expression library construction.

value: Achilles tendon

tag: condition

value: Tendinopathy


title: 266_siArid1a_rep2


title: 266_siArid1a_rep1


title: 266_siCtrl_EGF_rep3


title: Colon (validation), 12 Months, Rep4

description:
12M.N4
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz

value: 12 Months


title: HASMCs Con3


title: Colon (validation), 12 Months, Rep3

description:
12M.N3
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: 266_siCtrl_EGF_rep1


title: 266_siCtrl_EGF_rep2


title: 266_siCtrl_rep1


title: Colon (validation), 7 Months, Rep5

description:
7M.N5
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz

value: 7 Months


title: Colon (validation), 12 Months, Rep1

description:
12M.N1
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: Colon (validation), 12 Months, Rep2

description:
12M.N2
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: GSC267_sh1_2

city: Jinan

first: Gang

last: Li

state: Shandong

address: 107 Wenhua Xi Road

department: Neurosurgery

institute: Qilu Hospital of Shandong University

data_processing:
clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data
Index of the reference genome was built using hisat2 (v2.0.5) and paired-end clean reads were mapped to the reference genome.
featureCounts（1.5.0-p3）was used to count the read numbers mapped to each gene. And then FPKM was calculated.It normalizes for both sequencing depth and genome size.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential
Assembly: hg38
Supplementary files format and content: xls files include readcount values for each Sample
Supplementary files format and content: xls files include FPKM values for each Sample

growth_protocol: GSC267 cells were cultured in DMEM/F12 (Gibco, USA) supplemented with B-27 (Gibco, USA), 20 ng/mL recombinant human epidermal growth factor (R&D Systems, USA) and 20 ng/mL recombinant human basic fibroblast growth factor (R&D Systems, USA) and cultured at 37°C in a humid chamber with 5% carbon dioxide and 5% oxygen.

extract_protocol:
Total RNA was extracted from GSC267 cells using TRIzol reagent (Life Technologies, Carlsbad, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol: Use of shRNA to knock down the MIR222HG in GSC267 cells

value: glioma stem cells

value: MIR222HG knockdown


title: Colon (validation), 7 Months, Rep4

description:
7M.N4
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz

value: Male


title: GSC267_sh1_1


title: 266_siCtrl_rep2


title: GSC267_sh1_3


title: Colon (validation), 7 Months, Rep3

description:
7M.N3
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: HASMCs Con2


title: Colon (validation), 12 Months, Rep5

description:
12M.N5
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: Colon (validation), 7 Months, Rep2

description:
7M.N2
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: ANKL1_Spleen

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

country: Japan

institute: Saga University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Read alignment and gene expression quantification was performed as described previously (Nucleic Acids Res. 2019; 47: 8961-74).
Data obtained from liver-tropic ANKL1 cells (17039 cells) and spleen-tropic ANKL1 cells (14034 cells) were analysed by using Seurat.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Fresh liver and spleen were harvested from ANKL1-PDX mouse. Both organs were homogenized and filtrated with Falcon 70 µm of cell strainer (Corning). Liver homogenized sample were then treated with 1 mg/mL of collagenase A (Roche) and 100 U of DNAse I (Roche) in 5 mL of MEM-alpha medium (Thermo Fisher Scientific) at 37 °C for 15 minutes, following centrifugation (500xg, 5 minutes) and removal supernatant. liver pellet were then re-suspended with 35% Percoll (Sigma-Aldrich), and centrifuged for 1000xg, 10 minutes following removal supernatant. Liver pellet and spleen homogenized samples were then treated with RBC Lysin Buffer (BD pharm) to eliminate erythrocytes. After centrifugation for 300xg, 3 minutes and removal supernatant, cells were staind with microbeads-conjugated anti-human CD45 (Miltenyi Biotec) and apply for autoMACS system (Miltenyi Biotec).
A suspension of cells under designated experimental conditions was added to a polydimethylsiloxane microwell slide containing poly(dT) barcoded beads (BD Bioscience) and allowed to settle into the well via gravity. The cells were lysed, and poly(dT)-barcoded beads with bound cellular mRNA were collected, followed by the synthesis of cDNA. The obtained cDNA was then amplified with an adaptor sequence attached to captured mRNA via the terminal deoxynucleotidyl transferase method. After sonication, the cDNA fragments were subjected to end repair and dA-tailing using NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs) and mixed with an adaptor primer with dT (multiplexing read 2 sequencing primer Illumina TruSeq™; Illumina) and Ligation High Ver.2 (TOYOBO). Libraries were then sequenced using the NovaSeq6000 Sequencing System (Illumina).

value: ANKL cells

value: Spleen

tag: disease

value: 7-11 weeks old


title: GSC267_NC_1

value: WT


title: GSC267_NC_2


title: ANKL1_Liver

description: 10x Genomics

source_name: Liver

value: Liver


title: HS_Ho6

city: Kongens Lyngby

first: Xiao

address: Bagsværdvej 103, ST

country: Denmark

institute: Konge Larsen Aps

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary files format and content: excel,expression profiles

organism: Bos taurus

source_name: Blood

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: Blood

tag: group

value: heat stressed


title: HS_Ho4


title: HS_Ho3


title: MKN28-shVPS35, rep3

first: Junxian

last: Yu

address: 197, Rui Jin 2nd Road

department: Department of General Surgery

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCh38.p13
Supplementary files format and content: The differentially expressed genes were calculated between control and shVPS35 cells.

source_name: gastric cancer

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: gastric cancer


title: GSC267_NC_3

tag: genotype


title: Colon (validation), 3 Months, Rep4

description:
3M.N4
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz

value: Colon

value: 3 Months


title: HS_Ho5


title: Colon (validation), 7 Months, Rep1

description:
7M.N1
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: Colon (validation), 3 Months, Rep3

description:
3M.N3
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: MKN28-shVPS35, rep2


title: HS_Ho1


title: MKN28-shVPS35, rep1


title: MKN28-vector, rep3

value: control vector


title: HR_Ho6

value: heat resistant


title: HS_Ho2


title: HR_Ho5


title: pineapple peels, 120 DAF, rep3

city: Hai Kou

first: Aiping

last: Luan

address: No. 4, Xueyuan Road, Longhua District

institute: Tropical Crops Genetic Resources Institute of Chinese Academy of Tropical Agricultural Science

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ensemblV48 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary files format and content: Excel file includes FPKM and count values for each Sample

organism: Ananas comosus

source_name: peels

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peels

tag: time

value: 120 DAF


title: MKN28-vector, rep2

tag: treatment


title: HR_Ho4


title: pineapple peels, 120 DAF, rep2


title: Colon, 28 Months, Rep17

description:
28M.N17
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: 28 Months


title: MKN28-vector, rep1

tag: cell line


title: Colon, 28 Months, Rep18

description:
28M.N18
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon (validation), 3 Months, Rep1

description:
3M.N1
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: pineapple peels, 120 DAF, rep1


title: Colon, 28 Months, Rep16

description:
28M.N16
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon (validation), 3 Months, Rep2

description:
3M.N2
colon_validation_CpG_methylationrates.bedg.gz
colon_validation_CpG_coverages.bedg.gz


title: HEK293T cells,NDUFA13 KO rep 4

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

data_processing:
Trimmomatic, version 0.39, parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50
hisat2
htseq-count, version 0.6.0, parameters: --stranded=reverse --secondary-alignments=ignore
removal of features with less then 32 counts based on the sum of normalized counts across all samples
DESeq2, version 1.26.0, vst normalization
Genome_build: grch38
Supplementary_files_format_and_content: counts generated by htseq-count

source_name: Human embryonic kidney cell-line HEK293T

growth_protocol: HEK293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with high-glucose content (4,500 mg/L) supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM L-glutamine, 1% (v/v) penicillin-streptomycin and 50 µg/ml uridine at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was isolated with RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) followed by DNase I (Sigma, cat. no. AMPD1) treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: embryonic kidney cell

value: NDUFA13 knockout


title: HR_Ho3

tag: tissue


title: pineapple peels, 90 DAF, rep3

value: 90 DAF


title: HEK293T cells,NDUFA13 KO rep 3


title: pineapple peels, 90 DAF, rep2


title: Colon, 28 Months, Rep15

description:
28M.N15
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: Male


title: HEK293T cells,NDUFA13 KO rep 2


title: pineapple peels, 90 DAF, rep1


title: HR_Ho1


title: HEK293T cells,NDUFA13 KO rep 1


title: pineapple peels, 60 DAF, rep3

value: 60 DAF


title: Colon, 28 Months, Rep13

description:
28M.N13
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: pineapple peels, 60 DAF, rep2


title: HEK293T cells,NDUFA11 KO rep 4

value: NDUFA11 knockout


title: Colon, 28 Months, Rep12

description:
28M.N12
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: HEK293T cells,NDUFA11 KO rep 3


title: Colon, 28 Months, Rep11

description:
28M.N11
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: pineapple peels, 60 DAF, rep1


title: Colon, 28 Months, Rep10

description:
28M.N10
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: HEK293T cells,NDUFA11 KO rep 1


title: Colon, 28 Months, Rep9

description:
28M.N9
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Yeast W303, pab1 and pbp1 deletions, replicate 1

city: Worcester

first: Kotchaphorn

last: Mangkalaphiban

state: MA

address: 368 Plantation St.

institute: University of Massachusetts Medical School

description:
pab1d_pbp1d_rep1
pab1_strains_RPF_RSEM_FPKM_genes.results.csv
pab1_strains_RPF_RSEM_FPKM_isoforms.results.csv
pab1_strains_RPF_RSEM_expected_count_genes.results.csv
pab1_strains_RPF_RSEM_expected_count_isoforms.results.csv

library_source: other

data_processing:
library strategy: ribosome profiling/Ribo-Seq
NEXTFLEX adapters were trimmed from reads using cutadapt v1.9; reads < 23 bp (15 bp RPF + 4 bp 5'UMI + 4 bp 3' UMI) were discarded.
Reads (excluding the UMIs) that were mapped to non-protein coding sequences were discarded.
PCR duplicates were identified by the combination of 4 bp UMIs on the ends of the reads and removed using UMI-tools software (Smith et al., 2017) with default algorithm ("directional").
De-deuplicated reads were aligned to the transcriptome (https://github.com/Jacobson-Lab/yeast_transcriptome_v5) and transcript abundance quantified using RSEM v1.3.0 and bowtie v 1.0.0 (paramters: strandedness forward, 15 nt seed length, reads with more than 2 mismatches in the seed region and/or mapped to more than 10 places are discarded)
Assembly: R64-2-1
Supplementary files format and content: Wig files, generated by RSEM, contained coverage data.
Supplementary files format and content: Comma-delimited files contain either RPKM values or read count either at a gene or isoform level for all samples.

molecule: other

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in 1 L of YEPD at 30C with shaking.

extract_protocol:
Whole cell lysates were treated with RNaseI (Invitrogen) and ultracentrifuged through a sucrose cusion to isolate 80S ribosomes. Ribosome-protected mRNA fragments (RPFs) were isloated from 80S ribosomes using miRNeasy kit (QIAGEN), size selected for RNAs < 200 nt, and 3'-dephosphorylated/5'phosphorylated by T4 polynucleotide kinase (NEB).
Sequencing libraries were prepared using NEXTFLEX Small RNA-Seq Kit v3 (Perkin Elmer), skipping the first denaturation step and replacing it with hybridization of oligos from the QIAseq FastSelect - rRNA Yeast kit (QIAGEN).

value: pab1 and pbp1 deletions


title: Yeast W303 WT, replicate 1

description:
PAB1_PBP1_rep1
pab1_strains_RPF_RSEM_FPKM_genes.results.csv
pab1_strains_RPF_RSEM_FPKM_isoforms.results.csv
pab1_strains_RPF_RSEM_expected_count_genes.results.csv
pab1_strains_RPF_RSEM_expected_count_isoforms.results.csv

value: WT


title: Yeast W303, pbp1 deletion, replicate 1

description:
PAB1_pbp1d_rep1
pab1_strains_RPF_RSEM_FPKM_genes.results.csv
pab1_strains_RPF_RSEM_FPKM_isoforms.results.csv
pab1_strains_RPF_RSEM_expected_count_genes.results.csv
pab1_strains_RPF_RSEM_expected_count_isoforms.results.csv

value: pbp1 deletion


title: HEK293T cells,NDUFA11 KO rep 2


title: LuCaP96_GSK_rep3

city: Boston

first: Changmeng

last: Cai

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

description: Xenograft_LuCaP96CR_GSK_samples_count_table.txt.gz

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (version 1.6.4) from GRCh37 Ensembl reference.
Assembly: hg19
Supplementary files format and content: txt file for raw counts of sequence reads

source_name: CRPC PDX

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
RNA-seq libraries  were performed by using TruSeq® Strnd Total RNA LT (Illumina).

value: CRPC PDX

value: 15mg/kg GSK2879552 (3 times/week)


title: Yeast W303 WT, replicate 2

description:
PAB1_PBP1_rep2
pab1_strains_RPF_RSEM_FPKM_genes.results.csv
pab1_strains_RPF_RSEM_FPKM_isoforms.results.csv
pab1_strains_RPF_RSEM_expected_count_genes.results.csv
pab1_strains_RPF_RSEM_expected_count_isoforms.results.csv


title: Yeast W303, pbp1 deletion, replicate 2

description:
PAB1_pbp1d_rep2
pab1_strains_RPF_RSEM_FPKM_genes.results.csv
pab1_strains_RPF_RSEM_FPKM_isoforms.results.csv
pab1_strains_RPF_RSEM_expected_count_genes.results.csv
pab1_strains_RPF_RSEM_expected_count_isoforms.results.csv


title: LuCaP96_GSK_rep2


title: Yeast W303, pab1 and pbp1 deletions, replicate 2

description:
pab1d_pbp1d_rep2
pab1_strains_RPF_RSEM_FPKM_genes.results.csv
pab1_strains_RPF_RSEM_FPKM_isoforms.results.csv
pab1_strains_RPF_RSEM_expected_count_genes.results.csv
pab1_strains_RPF_RSEM_expected_count_isoforms.results.csv


title: HEK293T cells,WT rep 4

value: wild-type


title: LuCaP96_GSK_rep1


title: Colon, 28 Months, Rep14

description:
28M.N14
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: Colon


title: HEK293T cells,WT rep 3


title: Colon, 28 Months, Rep8

description:
28M.N8
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon, 28 Months, Rep7

description:
28M.N7
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: LuCaP96_VEH_rep3

value: DMSO(3 times/week)


title: Yeast W303, pab1 and pbp1 deletions, replicate 2 [RNA-seq]

description:
pab1d_pbp1d_rep2
pab1_strains_RNA_RSEM_FPKM_genes.results.csv
pab1_strains_RNA_RSEM_FPKM_isoforms.results.csv
pab1_strains_RNA_RSEM_expected_count_genes.results.csv
pab1_strains_RNA_RSEM_expected_count_isoforms.results.csv

data_processing:
RNA-seq reads were aligned to the transcriptome (https://github.com/Jacobson-Lab/yeast_transcriptome_v5) and transcript abundance quantified using RSEM v1.3.0 and bowtie v 1.0.0 (paramters: strandedness reverse, reads with more than 2 mismatches in the seed region and/or mapped to more than 10 places are discarded)
Assembly: R64-2-1
Supplementary files format and content: Wig files, generated by RSEM, contained coverage data.
Supplementary files format and content: Comma-delimited files contain either RPKM values or read count either at a gene or isoform level for all samples.

extract_protocol:
Total RNAs were isolated from whole cell lysate using miRNeasy kit (QIAGEN) and DNase-treated (Lucigen/Epicentre). 1 ug was used to construct sequencing library.
Sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep kit (Illumina) with the integration of QIAseq FastSelect - rRNA Yeast kit (QIAGEN) into the RNA fragmentation step to block subsequent cDNA synthesis of rRNAs.


title: Yeast W303, pab1 and pbp1 deletions, replicate 3 [RNA-seq]

description:
pab1d_pbp1d_rep3
pab1_strains_RNA_RSEM_FPKM_genes.results.csv
pab1_strains_RNA_RSEM_FPKM_isoforms.results.csv
pab1_strains_RNA_RSEM_expected_count_genes.results.csv
pab1_strains_RNA_RSEM_expected_count_isoforms.results.csv


title: HEK293T cells,WT rep 2


title: LuCaP96_VEH_rep2


title: LuCaP96_VEH_rep1


title: Yeast W303, pab1 and pbp1 deletions, replicate 1 [RNA-seq]

description:
pab1d_pbp1d_rep1
pab1_strains_RNA_RSEM_FPKM_genes.results.csv
pab1_strains_RNA_RSEM_FPKM_isoforms.results.csv
pab1_strains_RNA_RSEM_expected_count_genes.results.csv
pab1_strains_RNA_RSEM_expected_count_isoforms.results.csv


title: HEK293T cells,WT rep 1


title: Colon, 28 Months, Rep5

description:
28M.N5
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon, 28 Months, Rep6

description:
28M.N6
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_142 [WGS]

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

institute: Martin Luther University Halle-Wittenberg

description:
shallow whole genome sequencing (sWGS)
CN_NB_tumor_NT_pool.csv

data_processing:
Library strategy: WGS
Sequenced strand specific paired-end reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 –trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters -q --no-spliced-alignment --rna-strandness RF --dta -k
Secondary alignments were filtered out using samtools (v 1.10).
Copy number variations were analysed using R/cn.MOPS (v 1.36.0) using chromosome normalization (poisson) excluding sex chromosomes.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: CN_NB_tumor_NT_pool.csv: Comma-separated text file including genomic regions, log ratios of read counts and copy number values for each sample.

source_name: pooled normal

extract_protocol:
Genomic DNA was extracted using the AllPrep Kit (Qiagen). 10mg of snap-frozen tissue was homogenized in RLT Plus buffer with a Precellys 24 tissue homogenizer (Bertin Instruments) and processed, according to the manufacturer's instructions. Integrity of genomic DNA was tested on an agarose gel.
A total amount of 1.0μg DNA per sample was used as input material for the DNA sample preparations. Sequencing libraries were generated using NEBNext DNA Library Prep Kit following manufacturer's recommendations and indices were added to each sample. The genomic DNA is randomly fragmented to a size of 350bp by shearing, then DNA fragments were end polished, A-tailed, and ligated with the NEBNext adapter for Illumina sequencing, and further PCR enriched by P5 and indexed P7 oligos. The PCR products were purified (AMPure XP system) and resulted libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer and quantified using real-time PCR.

value: pooled normal

tag: tumor stage

tag: mycn status

value: not amplified


title: LuCaP70_GSK_rep2

description: Xenograft_LuCaP70CR_GSK_samples_count_table.txt.gz

value: 33mg/kg GSK2879552 (6 times/week)


title: LuCaP70_GSK_rep4


title: LuCaP70_GSK_rep3


title: JB_100 [WGS]

source_name: primary neuroblastoma tumor

value: primary neuroblastoma tumor


title: JB_98 [WGS]


title: Colon, 28 Months, Rep4

description:
28M.N4
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: 28 Months


title: Colon, 28 Months, Rep3

description:
28M.N3
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Yeast W303, pbp1 deletion, replicate 1 [RNA-seq]

description:
PAB1_pbp1d_rep1
pab1_strains_RNA_RSEM_FPKM_genes.results.csv
pab1_strains_RNA_RSEM_FPKM_isoforms.results.csv
pab1_strains_RNA_RSEM_expected_count_genes.results.csv
pab1_strains_RNA_RSEM_expected_count_isoforms.results.csv


title: JB_99 [WGS]


title: LuCaP70_GSK_rep1


title: Yeast W303, pbp1 deletion, replicate 2 [RNA-seq]

description:
PAB1_pbp1d_rep2
pab1_strains_RNA_RSEM_FPKM_genes.results.csv
pab1_strains_RNA_RSEM_FPKM_isoforms.results.csv
pab1_strains_RNA_RSEM_expected_count_genes.results.csv
pab1_strains_RNA_RSEM_expected_count_isoforms.results.csv


title: Yeast W303 WT, replicate 3 [RNA-seq]

description:
PAB1_PBP1_rep3
pab1_strains_RNA_RSEM_FPKM_genes.results.csv
pab1_strains_RNA_RSEM_FPKM_isoforms.results.csv
pab1_strains_RNA_RSEM_expected_count_genes.results.csv
pab1_strains_RNA_RSEM_expected_count_isoforms.results.csv


title: Yeast W303 WT, replicate 2 [RNA-seq]

description:
PAB1_PBP1_rep2
pab1_strains_RNA_RSEM_FPKM_genes.results.csv
pab1_strains_RNA_RSEM_FPKM_isoforms.results.csv
pab1_strains_RNA_RSEM_expected_count_genes.results.csv
pab1_strains_RNA_RSEM_expected_count_isoforms.results.csv


title: LuCaP70_VEH_rep4

value: DMSO(6 times/week)


title: JB_97 [WGS]


title: Colon, 28 Months, Rep2

description:
28M.N2
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: Male


title: Colon, 28 Months, Rep1

description:
28M.N1
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon, 24 Months, Rep16

description:
24M.N16
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: 24 Months


title: LuCaP70_VEH_rep3


title: Yeast W303 WT, replicate 1 [RNA-seq]

description:
PAB1_PBP1_rep1
pab1_strains_RNA_RSEM_FPKM_genes.results.csv
pab1_strains_RNA_RSEM_FPKM_isoforms.results.csv
pab1_strains_RNA_RSEM_expected_count_genes.results.csv
pab1_strains_RNA_RSEM_expected_count_isoforms.results.csv


title: Yeast W303, pbp1 deletion, replicate 3 [RNA-seq]

description:
PAB1_pbp1d_rep3
pab1_strains_RNA_RSEM_FPKM_genes.results.csv
pab1_strains_RNA_RSEM_FPKM_isoforms.results.csv
pab1_strains_RNA_RSEM_expected_count_genes.results.csv
pab1_strains_RNA_RSEM_expected_count_isoforms.results.csv


title: JB_95 [WGS]


title: LuCaP70_VEH_rep2


title: Colon, 24 Months, Rep14

description:
24M.N14
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: HR_Ho2

value: Blood

value: heat resistant


title: LuCaP70_VEH_rep1


title: JB_94 [WGS]

value: amplified


title: Colon, 24 Months, Rep13

description:
24M.N13
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_93 [WGS]


title: 22RV1_COM_rep4

description: Xenograft_22RV1_ORYIBETCOM_samples_count_table.txt.gz

value: 0.03mg/kg ORY-1001(3 times/week), 32mg/kg I-BET762 (6 times/week)


title: JB_92 [WGS]


title: Colon, 24 Months, Rep12

description:
24M.N12
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: 22RV1_COM_rep3


title: 22RV1_COM_rep2


title: JB_91 [WGS]

description:
shallow whole genome sequencing (sWGS)
CN_NB_tumor_NT_pool.csv


title: Colon, 24 Months, Rep10

description:
24M.N10
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_96 [WGS]


title: JB_90 [WGS]


title: Colon, 24 Months, Rep11

description:
24M.N11
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: 22RV1_COM_rep1


title: Stroke 19

city: Albuquerque

first: Tamara

last: Roitbak

state: New Mexico

address: 1101 Yale Blvd NE

department: Neurology

institute: University of New Mexico

data_processing:
Quality control analysis and quantification of the DNA library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Single-end sequencing 50 bp was performed on Illumina’s Hiseq 2500 sequencing system. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA)
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search
Supplementary files format and content: Table8.1_StrokevsControl copy.xlsx file contains the list of microRNAs differentiallt expressed in stroke samples as compared to controls. Stroke vs Control expression fold change values and p-values are provided for every microRNA and every sample. Differentially expressed miRNAs were detected using an in-house statistical analysis pipeline designed by LC Sciences. Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2X2 test, Chi-squared nXn test, Student t test, or ANOVA test

source_name: peripheral blood plasma

extract_protocol:
5 ml of whole blood was collected into EDTA-treated collection tubes. The samples were kept on ice and processed within 30 minutes after collection. To obtain plasma, blood was centrifuged for 15 minutes at 2500 x g at 20oC, and stored at -80oC. Total RNA was isolated from the extracellular vesicle-enriched fraction, using Total Exosome RNA and Protein Isolation Kit (Invitrogen/Thermo Fisher)
Library preparation was based on Illumina’s TruSeq -small-RNA-sample preparation protocols.

value: peripheral blood plasma

value: stroke patient


title: Stroke 21


title: Stroke 17


title: Stroke 18


title: Stroke 16


title: Stroke 20


title: Colon, 24 Months, Rep15

description:
24M.N15
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Stroke 15


title: JB_89 [WGS]


title: 22RV1_IBET_rep4

value: DMSO(3 times/week), 32mg/kg I-BET762 (6 times/week)


title: JB_88 [WGS]


title: Stroke 14


title: 22RV1_IBET_rep3


title: Colon, 24 Months, Rep8

description:
24M.N8
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: Colon


title: Stroke 13


title: Colon, 24 Months, Rep7

description:
24M.N7
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_87 [WGS]


title: 22RV1_IBET_rep2


title: Stroke 12


title: 22RV1_IBET_rep1


title: JB_86 [WGS]


title: Colon, 24 Months, Rep9

description:
24M.N9
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon, 24 Months, Rep5

description:
24M.N5
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Stroke 11


title: 22RV1_ORY_rep3

value: 0.03mg/kg ORY-1001(3 times/week), 1% methylcellulose (6 times/week)


title: Colon, 24 Months, Rep6

description:
24M.N6
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon, 24 Months, Rep3

description:
24M.N3
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_85 [WGS]


title: JB_83 [WGS]


title: Stroke 9


title: 22RV1_ORY_rep2


title: 22RV1_ORY_rep4


title: Stroke 10


title: Colon, 24 Months, Rep4

description:
24M.N4
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_84 [WGS]


title: Stroke 8


title: 22RV1_ORY_rep1


title: Colon, 24 Months, Rep1

description:
24M.N1
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_81 [WGS]


title: 22RV1_VEH_rep4

value: DMSO(3 times/week), 1% methylcellulose(6 times/week)


title: Stroke 7


title: Colon, 15 Months, Rep16

description:
15M.N16
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: 15 Months


title: 22RV1_VEH_rep3


title: Colon, 15 Months, Rep15

description:
15M.N15
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Stroke 5


title: JB_79 [WGS]

value: not amplified


title: 22RV1_VEH_rep2


title: Colon, 15 Months, Rep14

description:
15M.N14
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon, 24 Months, Rep2

description:
24M.N2
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Stroke 4


title: JB_78 [WGS]

value: primary neuroblastoma tumor


title: 22RV1_VEH_rep1

description: Xenograft_22RV1_ORYIBETCOM_samples_count_table.txt.gz


title: JB_82 [WGS]

description:
shallow whole genome sequencing (sWGS)
CN_NB_tumor_NT_pool.csv


title: JB_77 [WGS]


title: LuCaP35_COM_rep3

description: Xenograft_LuCaP35CR_ORYIBETCOM_samples_count_table.txt.gz

value: CRPC PDX


title: Colon, 15 Months, Rep11

description:
15M.N11
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Stroke 3


title: Colon, 15 Months, Rep12

description:
15M.N12
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_75 [WGS]


title: JB_76 [WGS]


title: LuCaP35_COM_rep1


title: Stroke 1


title: Colon, 15 Months, Rep10

description:
15M.N10
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_74 [WGS]


title: LuCaP35_IBET_rep3


title: Colon, 15 Months, Rep9

description:
15M.N9
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Stroke 6


title: Control 14

value: healthy


title: JB_80 [WGS]


title: JB_73 [WGS]


title: Colon, 15 Months, Rep8

description:
15M.N8
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: Male


title: LuCaP35_IBET_rep2


title: JB_72 [WGS]


title: Control 12


title: Stroke 2


title: JB_71 [WGS]


title: Colon, 15 Months, Rep7

description:
15M.N7
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: LuCaP35_IBET_rep1


title: Colon, 15 Months, Rep13

description:
15M.N13
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: LuCaP35_COM_rep2


title: Colon, 15 Months, Rep6

description:
15M.N6
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: LuCaP35_ORY_rep3


title: Colon, 15 Months, Rep5

description:
15M.N5
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: LuCaP35_ORY_rep2


title: JB_70 [WGS]


title: LuCaP35_ORY_rep1


title: JB_69 [WGS]


title: Colon, 15 Months, Rep4

description:
15M.N4
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Control 8


title: Control 10


title: Control 9


title: LuCaP35_VEH_rep3


title: Colon, 15 Months, Rep3

description:
15M.N3
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Control 13


title: Control 7


title: LuCaP35_VEH_rep2


title: Control 6


title: JB_66 [WGS]


title: Control 11


title: LuCaP35_VEH_rep1


title: Colon, 15 Months, Rep1

description:
15M.N1
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_65 [WGS]


title: Colon, 9 Months, Rep16

description:
9M.N16
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: 9 Months


title: Control 4


title: Control 5


title: JB_64 [WGS]


title: Colon, 9 Months, Rep15

description:
9M.N15
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Control 3


title: JB_68 [WGS]


title: CPP61-T choroid plexus tumor miRNA

city: Toronto

first: Nicholas

middle: William

last: Fischer

state: Ontario

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

description: tumor tissue derived RNA

data_processing:
Image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8.0). Subsequently, 3’-adapter sequences were trimmed from clean reads (reads that passed Solexa CHASTITY quality filter) and the reads shorter than 15nt were discarded. Then the 3’-adapter-trimmed-reads (≥ 15nt) were aligned to the human reference miRNA precursor set (Sanger miRBase 19) using Novoalign (v2.07.11). In order to characterize the isomiR variability, any sequence that matched the miRNA precursors in the mature miRNA region ±4nt (no more than one mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin.
We used the most abundant isomiR, the mature miRNA annotated in miRBase, and the sum of reads (5p or 3p) to calculate the miRNAs expression. To determine differential expression among the 35 discovery-cohort tumor samples, miRNA-sequencing read counts were analyzed in R using DESeq2  Bioconductor package.

source_name: choroid plexus

extract_protocol:
RNA was harvested using TRIzol method (Invitrogen) according to the manufacturer's instructions.
miRNA sequencing and initial data analysis was performed by Arraystar Inc. (9700 Great Seneca Highway #171, Rockville, MD 20850). Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~135-155 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer. The DNA fragments in the libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ and finally sequenced for 36 cycles on Illumina HiSeq 2000 according to the manufacturer’s instruction.

value: choroid plexus

value: choroid plexus papilloma

value: female

value: n/i


title: CPP120-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: Control 2

value: peripheral blood plasma


title: JB_62 [WGS]

value: amplified


title: CPP103-T choroid plexus tumor miRNA

description: tumor tissue derived RNA

value: male


title: Colon, 9 Months, Rep14

description:
9M.N14
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: Colon


title: CPP47-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: Colon, 9 Months, Rep13

description:
9M.N13
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_67 [WGS]

description:
shallow whole genome sequencing (sWGS)
CN_NB_tumor_NT_pool.csv


title: Colon, 9 Months, Rep12

description:
9M.N12
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_60 [WGS]


title: MDA-MB-231 3D Spheroids: 500.0 nM ZJ-101 sample, biological replicate 3

city: Rockville

first: Phillip

middle: Raul

last: Sanchez

state: MD

address: 9800 Medical Center Dr, BLDG-C 307W

institute: National Center for Advancing Translational Sciences

data_processing:
Raw files uploaded to Galaxy (usegalaxy.org) and aligned to hg38 using the HISAT2 tool with default settings for unstranded paired-end reads.
Transcript counts were assembled on Galaxy from BAM outputs with HISAT2 using the htseq-count tool with the gencode v35 release for gene annotation, tab delimited normalized counts table was produced
DESeq2 analysis was performed with Galaxy using normalized counts table output from htseq-count, differential expression between doses and control were assembled into a single spreadsheet
Assembly: hg38
Supplementary files format and content: DESeq2 data with separate sheets for each dose in .xlsx format
Supplementary files format and content: normalized counts file output from htseq-count containing all samples in .xlsx format

molecule: polyA RNA

source_name: 3D Spheroids

growth_protocol: MDA-MB-231 cells were seeded at 2x10^3 cells/well in 96-well Ultra-Low Attachment Plates (Corning 4515) and centrifuged at 400 x g to pool cells at the bottom of each well prior to incubation. Dulbecco's Modified Eagle's Media (Gibco 11965092) supplemented with 10% fetal bovine serum (Cytiva SH30071.03HI) was utilized. Spheroids were fully formed after 72 hours incubation in 37C incubators with 5% CO2 and 85% humidity.

extract_protocol:
Spheroids and loose cells were harvested using wide-gauge multichannel pipette by gently resuspending all cells and pooling together to pellet in falcon tubes. Cell pellets were briefly washed with ice-cold PBS prior to total RNA extraction via the Rneasy mini kit (Qiagen) per the manufacturers instructions.
Libraries were constructued by Genewiz following poly-A selection from total RNA samples, all RNA content was analyzed on an Agilent TapeStation with RIN > 9.5 for all samples.

treatment_protocol: Each 96-well plate, representing a single biological replicate, was treated with the indicated dose of ZJ-101 for 24 hours prior to RNA extraction

value: 3D Spheroids

value: 24 Hour


title: Colon, 15 Months, Rep2

description:
15M.N2
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: 15 Months


title: Control 1


title: CPP125-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: Colon, 9 Months, Rep11

description:
9M.N11
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: MDA-MB-231 3D Spheroids: 500.0 nM ZJ-101 sample, biological replicate 2


title: JB_59 [WGS]

value: not amplified


title: Colon, 9 Months, Rep10

description:
9M.N10
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_58 [WGS]

value: primary neuroblastoma tumor


title: Colon, 9 Months, Rep9

description:
9M.N9
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: CPP107-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: CPP109-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: JB_63 [WGS]


title: JB_57 [WGS]


title: MDA-MB-231 3D Spheroids: 500.0 nM ZJ-101 sample, biological replicate 1


title: MDA-MB-231 3D Spheroids: 50.0 nM ZJ-101 sample, biological replicate 3


title: CPP127-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: JB_61 [WGS]


title: JB_56 [WGS]


title: CPP62-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: MDA-MB-231 3D Spheroids: 50.0 nM ZJ-101 sample, biological replicate 2


title: CPP57-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: Colon, 9 Months, Rep7

description:
9M.N7
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon, 9 Months, Rep6

description:
9M.N6
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: CPP114-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: MDA-MB-231 3D Spheroids: 50.0 nM ZJ-101 sample, biological replicate 1


title: JB_55 [WGS]


title: Colon, 9 Months, Rep5

description:
9M.N5
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: MDA-MB-231 3D Spheroids: 5.0 nM ZJ-101 sample, biological replicate 3


title: JB_54 [WGS]


title: MDA-MB-231 3D Spheroids: 5.0 nM ZJ-101 sample, biological replicate 2


title: JB_53 [WGS]


title: CPP108-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: CPP133-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: Colon, 9 Months, Rep3

description:
9M.N3
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon, 9 Months, Rep4

description:
9M.N4
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon, 9 Months, Rep8

description:
9M.N8
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_50 [WGS]


title: MDA-MB-231 3D Spheroids: 0.5 nM ZJ-101 sample, biological replicate 3


title: MDA-MB-231 3D Spheroids: 0.5 nM ZJ-101 sample, biological replicate 2


title: MDA-MB-231 3D Spheroids: 5.0 nM ZJ-101 sample, biological replicate 1


title: MDA-MB-231 3D Spheroids: 0.5 nM ZJ-101 sample, biological replicate 1


title: aCPP4-T choroid plexus tumor miRNA

description: tumor tissue derived RNA

value: atypical choroid plexus papilloma


title: JB_48 [WGS]


title: aCPP121-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: CPP119-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: JB_49 [WGS]


title: aCPP137-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: aCPP132-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: Colon, 3 Months, Rep16

description:
3M.N16
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: 3 Months


title: MDA-MB-231 3D Spheroids: Negative control samples, (0.1% DMSO), rep 2

value: DMSO


title: JB_47 [WGS]


title: Colon, 9 Months, Rep1

description:
9M.N1
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

value: Male

value: 9 Months


title: aCPP55-T choroid plexus tumor miRNA

description: tumor tissue derived RNA

value: choroid plexus


title: CPP110-T choroid plexus tumor miRNA

description: tumor tissue derived RNA

value: choroid plexus papilloma


title: Colon, 3 Months, Rep14

description:
3M.N14
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: MDA-MB-231 3D Spheroids: Negative control samples, (0.1% DMSO), rep 1


title: JB_52 [WGS]


title: Colon, 3 Months, Rep13

description:
3M.N13
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_51 [WGS]


title: JB_45 [WGS]


title: Colon, 9 Months, Rep2

description:
9M.N2
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: aCPP136-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: JB_44 [WGS]

description:
shallow whole genome sequencing (sWGS)
CN_NB_tumor_NT_pool.csv


title: aCPP138-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: MDA-MB-231 3D Spheroids: Negative control samples, (0.1% DMSO), rep 3


title: Colon, 3 Months, Rep15

description:
3M.N15
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_43 [WGS]


title: JB_46 [WGS]


title: JB_41 [WGS]


title: 50.0 nM ZJ-101 sample, biological replicate 1

data_processing:
Raw files uploaded to Galaxy (usegalaxy.org) and aligned to hg38 using the HISAT2 tool with default settings for unstranded paired-end reads.
Transcript counts were assembled on Galaxy from BAM outputs with HISAT2 using the htseq-count tool with the gencode v35 release for gene annotation, tab delimited normalized counts table was produced
DESeq2 analysis was performed with Galaxy using normalized counts table output from htseq-count, differential expression between doses and control were assembled into a single spreadsheet
Assembly: hg38
Supplementary files format and content: DESeq2 data with separate sheets for each dose in .xlsx format
Supplementary files format and content: tab delimited normalized counts file output from htseq-count containing all samples

growth_protocol: MDA-MB-231 cells were grown to semi-confluency (75-80%) in 10 cm dishes. Dulbecco's Modified Eagle's Media (Gibco 11965092) supplemented with 10% fetal bovine serum (Cytiva SH30071.03HI) was utilized. Cells were grown in humidifiied 37C incubators with 5% CO2.

extract_protocol:
Cells were harvested from semi-confluent 10 cm dishes using scrapers and pelleted in falcon tubes. Cell pellets were briefly washed with ice-cold PBS prior to total RNA extraction via the Rneasy mini kit (Qiagen) per the manufacturers instructions.
Libraries were constructued by Genewiz following poly-A selection from total RNA samples, all RNA content was analyzed on an Agilent TapeStation with RIN > 9.5 for all samples.

treatment_protocol: Each dish was treated with the indicated dose of ZJ-101 for 6 hours prior to RNA extraction

value: 6 Hour


title: 50.0 nM ZJ-101 sample, biological replicate 3


title: 50.0 nM ZJ-101 sample, biological replicate 2


title: 500.0 nM ZJ-101 sample, biological replicate 1


title: JB_40 [WGS]


title: CPC144-TA choroid plexus tumor miRNA

description: tumor tissue derived RNA

value: choroid plexus carcinoma


title: CPC5-T choroid plexus tumor miRNA

description: tumor tissue derived RNA

value: female


title: CPC43-T choroid plexus tumor miRNA

description: tumor tissue derived RNA

value: male


title: 500.0 nM ZJ-101 sample, biological replicate 3


title: Colon, 3 Months, Rep11

description:
3M.N11
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz

data_processing:
Sequence information was converted to fastq format using bcl2fastq v2.20.0.422. From validation samples only those reads were downstream processed, that start with a Tecan/NuGen TrueMethyl diversity adapter (length 0-3, clipped afterwards) followed by a MspI cutting site.
Read quality trimming (cutoff 20) and TruSeq universal adapter clipping was performed using Cutadapt v2.10. Due to MspI cutting site end-repair, R1 adapter was prefixed by NN and in case of paired-end data, unconditional 5' clipping of length 2 was conducted on R2.
Mappings were done via segemehl v0.3.4 (methyl-C mode, accuracy 95%, reference GRCm38) and filtered for unique alignments. Paired-end alignments were further filtered for proper-read pairs and overlaps of R2 with R1 were trimmed using BamUtil clipOverlap v1.0.14.
Validation data alignments were deduplicated for over amplified PCR fragments based on unique molecular identifiers utilizing UMI-tools v1.1.1.
Methylation rates were inferred utilizing haarz v0.3.0. Rates and coverages within a CpG context were compiled using BEDTools v2.30.0.
Assembly: mm10
Supplementary files format and content: Tabular delimited text files in bedg format of read alignment coverages and inferred methylation rates per GRCh38 chromosomal CpG and sample.

extract_protocol:
Genomic DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen).
200 ng of DNA was fragmented via a 5 hour Msp1-digest (New England Biolabs), followed by TrueSeq adapter ligation (Illumina, San Diego, CA, USA) and subsequent bisulfite conversion following the manufacturers protocol (EZ DNA Methylation Gold Kit, Zymo Research). The bisulfite converted DNA was amplified in a 19-cycles PCR with Pfu Turbo Cx Hotstart DNA Polymerase (Agilent Technologies) and the resulting libraries were quality checked using 4200 TapeStation (Agilent Technologies). For sequencing of validation samples, Illumina’s next-generation sequencing methodology 87 was used. In detail, genomic DNA was quality checked and quantified using the 4200 TapeStation instruments in combination with the Genomic DNA ScreenTape (both Agilent Technologies). Libraries were prepared from 100 ng of input material using Ovation RRBS Methyl-Seq with TrueMethyl oxBS (Tecan). In detail, only the bisulfite part of the protocol was followed, oxidation of DNA was not done, and samples were treated as MOCK oxBS samples according to the manufacturer’s instruction. Quantification and quality check of libraries were done using the 4200 TapeStation and D5000 ScreenTapes instruments (both Agilent Technologies).

value: Colon


title: CPC58-T choroid plexus tumor miRNA

description: tumor tissue derived RNA

value: n/i


title: 500.0 nM ZJ-101 sample, biological replicate 2


title: Colon, 3 Months, Rep12

description:
3M.N12
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_39 [WGS]


title: 5.0 nM ZJ-101 sample, biological replicate 3


title: Colon, 3 Months, Rep8

description:
3M.N8
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon, 3 Months, Rep10

description:
3M.N10
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon, 3 Months, Rep6

description:
3M.N6
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: Colon, 3 Months, Rep7

description:
3M.N7
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: 5.0 nM ZJ-101 sample, biological replicate 2


title: CPC2-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: Colon, 3 Months, Rep9

description:
3M.N9
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: CPC52-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: JB_42 [WGS]

value: amplified


title: 5.0 nM ZJ-101 sample, biological replicate 1


title: JB_38 [WGS]


title: Colon, 3 Months, Rep5

description:
3M.N5
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_37 [WGS]


title: CPC1-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: Colon, 3 Months, Rep4

description:
3M.N4
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: 0.5 nM ZJ-101 sample, biological replicate 3


title: JB_36 [WGS]


title: Colon, 3 Months, Rep3

description:
3M.N3
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: CPC139-TB choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: 0.5 nM ZJ-101 sample, biological replicate 2


title: Colon, 3 Months, Rep2

description:
3M.N2
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_35 [WGS]


title: CPC146-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: 0.5 nM ZJ-101 sample, biological replicate 1


title: Colon, 3 Months, Rep1

description:
3M.N1
colon_CpG_methylationrates.bedg.gz
colon_CpG_coverages.bedg.gz


title: JB_34 [WGS]


title: CPC51-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: CPC3-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: Negative control samples, (0.1% DMSO), rep 3


title: JB_32 [WGS]


title: Negative control samples, (0.1% DMSO), rep 2


title: JB_33 [WGS]


title: CPC140-TB choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: CPC56-T choroid plexus tumor miRNA

description: tumor tissue derived RNA


title: JB_31 [WGS]


title: UPN-987-P

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

data_processing:
High quality base calls at Q30>80% were obtained for 50 million 150bp paired-end reads and mapped to the human genome (CRCh38) by STAR 2.4.0.1.
Assembly: Hg38
Supplementary files format and content: Quantification of RNA expression, as fragments per kilobase per million (FPKM), was derived by Cufflinks. FPKM were processed to log2(FPKM+1) for further analyses, which is provided here

source_name: tumor - PFA ependymoma

extract_protocol:
RNA was isolated snap frozen PFA samples using an Allprep DNA/RNA mini kit (Qiagen) per manufacturers instructions
Libraries were prepared using the Tecan Universal Plus mRNA-Seq library preparation kit per manufacturers instructions

value: tumor - PFA ependymoma

value: presentation


title: Negative control samples, (0.1% DMSO), rep 1


title: JB_30 [WGS]

value: primary neuroblastoma tumor

value: not amplified


title: UPN-930-P


title: E. coli transcriptome BW25113 del_hns

city: Bielefeld

first: David

last: Brandt

address: Universitätsstraße 25

department: CeBiTec

institute: Bielefeld University

data_processing:
Basecalls performed using CASAVA
Quality-Trimming using Trimmomatic v0.3.5 SE TRAILING:3 MINLEN:39
Mapping using bowtie2 v2.3.0 (default options)
Conversion to bam using samtools
read visualization and TSS detection in ReadXplorer (see excel files)
genome coverage determination using bedtools v2.2.6 (genomecov -bga -ibam -strand x -g *.bam.bai)
Genome_build: U00096.3
Supplementary_files_format_and_content: bedGraph files containing genome-wide read coverage, excel sheet containing detected transcription start site positions

organism: Escherichia coli

source_name: bacterial liquid culture

extract_protocol: 5'-enriched transcriptome library (see Pfeifer-Sancar et al. 2013)

value: Escherichia coli BW25113 <delta>hns


title: JB_29 [WGS]


title: UPN-928-R2

value: recurrence


title: E. coli transcriptome BW25113 del_fur

value: Escherichia coli BW25113 <delta>fur


title: JB_28 [WGS]


title: PRO-seq.mESC.Mut.1vsWT_WT_rep2

city: Singapore

first: Zhenhua

last: hu

state: singapore

address: 31 Biopolis drive

country: Singapore

institute: IMCB, A*STAR

description:
nascent RNA
PRO-seq.mESC.Mut.1vsWT_DE_spikenorm_results_table.xlsx

data_processing:
For PRO-seq,  all custom scripts used are available on the AdelmanLab GitHub (https://github.com/AdelmanLab/NIH_scripts). Please see Method Section for details.
Assembly: mm10
Supplementary files format and content: "PRO-seq.mESC.Mut.1vsWT_[Mut.1,WT]_rep[1,2]_count.txt" files contain all the nascent transcript count outputs for PRO-seq data;  "PRO-seq.mESC.Mut.1vsWT_DE_spikenorm_results_table.xlsx" contains DESeq2 differential nascent gene expression analysis results
Library strategy: PRO-Seq

source_name: mESCs

growth_protocol: mESCs were cultured in KnockOut DMEM containing 15% fetal bovine serum (ES-certified, Gibco), L-glutamine, non-essential amino acids, penicillin/streptomycin,2-mercaptoethanol, LIF, 1 µM PD0325901 and 3 µM CHIR99021 (2i) on 0.1% gelatin-coated tissue culture dishes.

extract_protocol:
N.A
PRO-Seq library construction and data analysis was performed by the Nascent Transcriptomics Core at Harvard Medical School, Boston, MA, as follow:   Aliquots of frozen (-80°C) permeabilized cells were thawed on ice and pipetted gently to fully resuspend. Aliquots were removed and permeabilized cells were counted using a Luna II, Logos Biosystems instrument. For each sample, 1 million permeabilized cells were used for nuclear run-on, with 50,000 permeabilized Drosophila S2 cells added to each sample for normalization. Nuclear run on assays and library preparation were performed essentially as described in Reimer et al. [K. A. Reimer, C. A. Mimoso, K. Adelman, K. M. Neugebauer, Molecular Cell (2021)]  with modifications noted: 2X nuclear run-on buffer consisted of (10 mM Tris (pH 8), 10 mM MgCl2, 1 mM DTT, 300mM KCl, 20uM/ea biotin-11-NTPs (Perkin Elmer), 0.8U/uL SuperaseIN (Thermo), 1% sarkosyl).  Run-on reactions were performed at 37°C.  Random hexamer extensions (UMIs) were added to the 3' end of the 5' adapter and 5' end of the 3' adapter.  Adenylated 3' adapter was prepared using the 5' DNA adenylation kit (NEB) and ligated using T4 RNA ligase 2, truncated KQ (NEB, per manufacturers’ instructions with 15% PEG-8000 final) and incubated at 16°C overnight.  180uL of betaine buffer (1.42g of betaine brought to 10mL) was mixed with ligations and incubated 5 min at 65°C and 2 min on ice prior to addition of streptavidin beads.  After T4 polynucleotide kinase (NEB) treatment, beads were washed once each with high salt, low salt, and 0.25X T4 RNA ligase buffer (NEB) and resuspended in 5' adapter mix (10 pmol 5' adapter, 30 pmol blocking oligo, water).  5' adapter ligation was per Reimer but with 15% PEG-8000 final. Eluted cDNA was amplified 5-cycles (NEBNext Ultra II Q5 master mix (NEB) with Illumina TruSeq PCR primers RP-1 and RPI-X) following the manufacturer's suggested cycling protocol for library construction. A portion of preCR was serially diluted and for test amplification to determine optimal amplification of final libraries. Pooled libraries were sequenced using the Illumina NovaSeq platform.

treatment_protocol: 10 million mESCs were harvested, washed 1x in cold PBS, and resuspended into single-cell suspension in 250 microl ice cold buffer W (10 mM Tris -HCl (pH 8.0), 10 mM KCl, 250 mM sucrose, 5 mM MgCl2, 1 mM EGTA, 0.5 mM DTT, 10% (v/v) glycerol, supplemented with 1x protease inhibitor cocktail (Merck, Cat# 11873580001) and SUPERase-IN RNase inhibitor at 10 microl/ 50 mL buffer (Thermofisher, Cat# AM2696). 5 mL of ice-cold buffer P (10 mM Tris-HCl (pH8.0), 10 mM KCl, 250 mM sucrose, 5 mM MgCl2, 1 mM EGTA, 0.1% (v/v) NP40, 0.5 mM DTT, 0.05% (v/v) Tween-20, 10% (v/v) glycerol, supplemented with protease inhibitor cocktail  and SUPERase-IN RNase inhibitor) was added to cells and the suspension was incubated on ice for 5 min for permeabilization. The cells were collected by centrifugation at 400 g, for 4 min at 4 degC, washed with 5 mL of ice-cold buffer W, and resuspended in 500 microl buffer F (50 mM Tris-HCl (pH8.0), 40% (v/v) glycerol, 5 mM MgCl2, 1.1 mM EDTA, 0.5 mM DTT, supplemented with SUPERase-IN RNase inhibitor).

tag: experiment type

value: PRO-seq

value: Wildtype


title: PRO-seq.mESC.Mut.1vsWT_Mut.1_rep2

value: Top1(R548Q) homozygous


title: UPN-928-P


title: PRO-seq.mESC.Mut.1vsWT_WT_rep1


title: E. coli transcriptome BW25113 del_fis

value: Escherichia coli BW25113 <delta>fis


title: PRO-seq.mESC.Mut.1vsWT_Mut.1_rep1


title: JB_27 [WGS]


title: E. coli transcriptome BW25113 wildtype exponential growth phase

value: Escherichia coli BW25113


title: JB_26 [WGS]


title: ROSE-Sig70_P2

description: genomic DNA template for genome-wide in vitro transcription isolated with Phenol-Chloroform extraction

source_name: in vitro transcription

value: Escherichia coli MG1655


title: ROSE-Sig70_P1


title: UPN-897-P

value: male


title: UPN-871-X

value: female


title: JB_25 [WGS]


title: ROSE-Sig70_Z2

description: genomic DNA template for genome-wide in vitro transcription isolated with Zymo Research Universal DNA kit


title: JB_23 [WGS]

description:
shallow whole genome sequencing (sWGS)
CN_NB_tumor_NT_pool.csv


title: UPN-811-R4


title: UPN-871-P


title: ROSE-Sig70_Z1


title: JB_24 [WGS]


title: ROSE-Sig70_M2

description: genomic DNA template for genome-wide in vitro transcription isolated with Macherey-Nagel Microbial DNA extraction kit


title: JB_22 [WGS]


title: UPN-770-P


title: ROSE-Sig70_M1


title: JB_21 [WGS]


title: UPN-727-P


title: JB_20 [WGS]


title: UPN-723-P


title: JB_19 [WGS]


title: CR119_DA822_H3K9me3

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

description: Hyperprep kit (KAPA)

data_processing:
CUT&RUN: Reads were aligned to the human genome (hg38) using bowtie2 (version 2.3.4.2; RRID:SCR_016368) (Langmead et al., 2012) (–local –very-sensitive-local –no-mixed –no-discordant –phred33 -I 10 -X 700), converted to bam files with samtools (version 1.4; RRID:SCR_002105) and sorted (samtools version 1.9; RRID:SCR_002105). RPKM normalized bigwig coverage tracks were made with bamCoverage (deepTools (version 2.5.4; RRID:SCR_016366)) (Ramírez et al., 2014).
Assembly: GRCh38
Supplementary files format and content: CUT&RUN: BigWig files
Library strategy: CUT&RUN

source_name: fetal forebrain

extract_protocol:
The nuclei isolation from the embryonic brain tissue was performed according to Jönsson et al., 2021. In brief, the tissue was thawed and dissociated in ice-cold lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl, pH 8.0, 1 mM DTT) using a 1 ml tissue douncer (Wheaton). The homogenate was carefully layered on top of a sucrose cushion (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl, pH 8.0, and 1 mM DTT) before centrifugation at 30,000 × g for 2 hours and 15 min. Pelleted nuclei were softened for 10 min in 100 ml of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) before being resuspended in 300 ml of dilution buffer (10 mM Tris-HCl, pH 7.2, 70 mM KCl, and 2 mM MgCl2) and run through a cell strainer (70 mm). Cells were run through the FACS (FACS Aria, BD Biosciences) at 4°C at a low flow rate using a 100 mm nozzle (reanalysis showed >99% purity).
CUT&RUN: We followed the protocol detailed by the Henikoff lab (Skene et al., 2017). Briefly, 100,000 sorted nuclei were washed twice (20 mMHEPESpH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1x Roche cOmplete protease inhibitors) and attached to 10 ConA-coated magnetic beads (Bangs Laboratories) that had been pre-activated in binding buffer (20mM HEPES pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2). Bead-bound cells were resuspended in 50 μL buffer (20 mM HEPES pH 7.5, 0.15 M NaCl, 0.5 mM Spermidine, 1x Roche complete protease inhibitors, 0.02% w/vdigitonin, 2mM EDTA) containing primary antibody (rabbit anti-H3K4me3 Active Motif 39159, RRID:AB_2615077; or goat anti-rabbitIgG, Abcam ab97047, RRID:AB_10681025) at 1:50 dilution and incubated at 4°C overnight with gentle shaking. Beads were washed thoroughly with digitonin buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmplete protease inhibitors, 0.02% digitonin). After the final wash, pA-MNase (a generous gift from Steve Henikoff) was added to the digitonin buffer and incubated with the cells at 4°C for 1 h. Bead-bound cells were washed twice, resuspended in 100μL digitonin buffer, and chilled to 0-2°C. Genome cleavage was stimulated by the addition of 2mM CaCl2at 0°C for 30min. The reaction was quenched by the addition of 100μL 2x stop buffer (0.35M NaCl, 20mM EDTA, 4mM EGTA, 0.02% digitonin, 50ng/μL glycogen, 50ng/μLRNaseA, 10 fg/μL yeast spike-in DNA (a generous gift from Steve Henikoff)) and vortexing. After 10min of incubation at 37°C to releasegenomic fragments, cells and beads were pelleted by centrifugation (16,000 g, 5min, 4°C) and fragments from the supernatant were purified.

value: fetal forebrain

tag: type

value: Bulk

value: 10 weeks

tag: antibody


title: UPN-691-R2

value: tumor - PFA ependymoma

tag: Sex


title: JB_18 [WGS]

value: primary neuroblastoma tumor

value: amplified


title: CR118_DA817_H3K9me3

description: Hyperprep kit (KAPA)

tag: age

value: 7 weeks


title: UPN-507-R1

value: recurrence


title: JB_17 [WGS]


title: UPN-811-P

value: presentation


title: UPN-507-P


title: UPN-393-P


title: JB_15 [WGS]


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 45

city: Chicago

first: Yogesh

last: Goyal

state: IL

address: 303 E Superior St

institute: Northwestern University

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample45

data_processing:
We aligned RNA-seq reads to the human genome (hg19) with STAR v2.5.2a and counted uniquely mapping reads with HTSeq v0.6.1 and outputs count matrix.
The counts matrix was used to obtain tpm and other normalized values for each gene.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts, TPM, RPKM, RPM values for each sample

growth_protocol: WM989 A6-G3 melanoma cell line, first described in Shaffer et al, 2017, and kindly provided by the lab of Dr. Meenhard Herlyn, were derived by twice single-cell bottlenecking the WM989 melanoma cell line. The identities of WM989 A6-G3 was verified by DNA STR microsatellite fingerprinting at the Wistar Institute. Cells were cultured in Tu2% media (80% MCDB 153, 10% Leibovitz’s L-15, 2% FBS, 2.4mM CaCl2, 50 U/mL penicillin, and 50 μg/mL streptomycin) in a 10cm dish.

extract_protocol:
We conducted standard bulk paired-end (37:8:8:38) RNA sequencing using RNeasy Micro (Qiagen 74004) for RNA extraction, NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB E7770L), NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) oligos (NEB E7600S), and an Illumina NextSeq 550 75 cycle high-output kit (Illumina 20024906).
Prior to extraction and library preparation, the samples were randomized to avoid any experimental and human biases.

treatment_protocol:
We prepared stock solutions in DMSO of 4 mM vemurafenib (PLX4032, Selleck Chemicals, S1267) and 100 μM trametinib (Selleck Chemicals, S2673). We prepared small aliquots (10-15ul) for each drug and stored them at −20 °C to minimize freeze–thaw cycles. For drug treatment experiments, we diluted the stock solutions in culture medium to a final concentration of 1 µM and 100nM for vemurafenib and 5 nM for trametinib.
The dose of vemurafenib (1µM) was chosen as per Shaffer et al. (Nature 2017), which was optimized for growth arrest without overt cytotoxicity. The doses of trametinib used were 5 nM for WM989 A6-G3, 10 nM for WM3623 P4E7, and 25nM for WM3451 P2G7. These doses were also chosen based on a dose curve to obtain virtually complete growth arrest. WM989 A6-G3 cells were treated with either vemurafenib or 5 nM trametinib for 3-4 weeks, and the media was replaced every 3-4d. Resistant colonies were isolated and cultured in either 1µM vemurafenib or 5 nM trametinib in Tu2% (Goyal et al. 2021) for several weeks to months.

value: Human melanoma cells

value: BRAF - V600E

value: Treatment with therapy drugs

value: Experiment set 2, Expanded over months


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 47

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample47


title: Isolated and longitudinally profiled melanoma WM989 resistant clone 46

description:
RC_RNASeq_JLPRRB_2_Normalized_meltedData.tsv
RC_Sample46