title: PC9_36-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: PC9_61-ExpSample

status: Public on May 29 2020

type: SRA

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415 Curie Boulevard

country: USA

institute: University of Pennsylvania

description:
meltedData_PC9.tsv
full_PC9.csv

library_source: transcriptomic

data_processing:
bcl2fastq conversion performed on BaseSpace using Illumina's default generate fastq workflow
Aligned to hg19 using STAR version 2.3.0e with default parameters
Filtered uniquely mapped reads using ngsutils/bamutils
Sorted using samtools-0.1.19
enumerated read counts per gene using HTseq-0.6.1 in union mode
filtered protein-coding genes then normalized by sequencing depth and gene length using custom R script
Genome_build: aligned to hg19, ensembl GRCh37.75 gtf used for gene annotations
Supplementary_files_format_and_content: tsv files contain gene level RNA-seq counts generated using HTSeq with GRCh37.75 gene annotations. csv files contain RPM, RPKM, and TPM normalized counts for protein coding genes used in subsequent variability analyses.

molecule: polyA RNA

organism: Homo sapiens

source_name: PC-9 NSCLC

growth_protocol: Grown in TU2% media

extract_protocol:
RNA extracted from 100,000-200,000 cells using miRNAeasy RNA extraction kit according to manufacturer's protocol (Qiagen 217004). Polyadenylated RNA was then purified using NEBNext Poly(A) Magnetic Isolation Module (NEB E7490L)
NEBNext Ultra RNA sequencing library prep kit for Illumina (NEB E7530L )
mRNA-seq, random hexamer primed RT, unstranded.

tag: treatment

tag: cell type

value: MemorySeq subclone


title: PC9_26-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: WM983b-9-Controls

description:
meltedData_WM983B_run1.tsv
full_WM983B.csv

source_name: WM983b E9 melanoma (BRAFV600E)

value: Control/MemorySeq parental sample


title: PC9_27-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: WM983b-8-Controls

description:
meltedData_WM983B_run1.tsv
meltedData_WM983B_run2.tsv
full_WM983B.csv


title: WM983b-7-Controls


title: WM983b-48-Controls


title: WM983b-6-Controls


title: WM983b-47-Controls


title: WM983b-5-Controls


title: WM983b-44-Controls


title: WM983b-46-Controls


title: WM983b-45-Controls


title: WM983b-43-Controls


title: PC9_22-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: WM983b-41-Controls


title: WM983b-42-Controls


title: PC9_21-ExpSample

description:
meltedData_PC9.tsv
full_PC9.csv


title: WM983b-39-Controls


title: WM983b-38-Controls


title: WM983b-37-Controls


title: WM983b-34-Controls


title: WM983b-36-Controls


title: WM983b-35-Controls


title: WM983b-31-Controls


title: WM983b-30-Controls


title: WM983b-33-Controls


title: WM983b-32-Controls


title: WM983b-27-Controls


title: WM983b-28-Controls


title: WM983b-25-Controls


title: WM983b-26-Controls


title: WM983b-29-Controls


title: WM983b-3-Controls


title: WM983b-23-Controls


title: WM983b-2-Controls


title: WM983b-20-Controls


title: WM983b-4-Controls


title: WM983b-40-Controls


title: WM983b-21-Controls


title: WM983b-19-Controls


title: WM983b-22-Controls


title: WM983b-17-Controls


title: WM983b-18-Controls


title: WM983b-15-Controls


title: WM983b-16-Controls


title: WM983b-14-Controls

description:
meltedData_WM983B_run2.tsv
full_WM983B.csv


title: WM983b-13-Controls


title: WM983b-12-Controls


title: WM983b-11-Controls


title: WM983b-1-Controls


title: WM983b-G8-ExpSample


title: WM983b-10-Controls


title: WM983b-G6-ExpSample


title: WM983b-G5-2-ExpSample


title: WM983b-24-Controls


title: WM983b-G10-ExpSample


title: WM983b-G2-ExpSample


title: WM983b-F7-ExpSample


title: WM983b-G11-ExpSample


title: WM983b-G5-1-ExpSample


title: WM983b-G4-ExpSample


title: WM983b-F5-ExpSample


title: WM983b-F4-ExpSample


title: WM983b-F11-1-ExpSample


title: WM983b-E9-ExpSample


title: WM983b-F10-ExpSample


title: WM983b-E8-ExpSample


title: WM983b-F11-2-ExpSample


title: WM983b-E5-2-ExpSample


title: WM983b-E5-1-ExpSample


title: WM983b-E3-ExpSample


title: WM983b-E10-ExpSample


title: WM983b-E11-ExpSample


title: WM983b-H5-ExpSample

description:
meltedData_WM983B_run1.tsv
meltedData_WM983B_run2.tsv


title: WM983b-D7-ExpSample


title: WM983b-D6-ExpSample


title: WM983b-D11-3-ExpSample


title: WM983b-D3-ExpSample


title: WM983b-D11-1-ExpSample


title: WM983b-D11-2-ExpSample


title: WM983b-C8-ExpSample


title: WM983b-C6-ExpSample


title: WM983b-E7-ExpSample


title: WM983b-B9-ExpSample


title: WM983b-C4-ExpSample


title: WM983b-C10-ExpSample


title: WM983b-F6-ExpSample


title: WM983b-C1-ExpSample


title: WM983b-C2-ExpSample


title: WM983b-B8-1-ExpSample


title: WM983b-B8-2-ExpSample


title: WM983b-B7-ExpSample


title: WM983b-B6-1-ExpSample


title: WM983b-B3-2-ExpSample


title: WM983b-B5-ExpSample


title: WM983b-B3-1-ExpSample


title: WM983b-B6-2-ExpSample


title: WM983b-B2-ExpSample


title: WM983b-A3-ExpSample


title: MDA-9-Controls

description:
meltedData_heritabilityRun1_Controls.tsv
meltedData_heritabilityRun2_Controls.tsv
full_MDA.csv

source_name: MDA-MB-231 breast cancer


title: MDA-7-Controls


title: MDA-8-Controls


title: WM983b-A8-ExpSample


title: MDA-6-Controls


title: MDA-5-Controls

description:
meltedData_heritabilityRun2_Controls.tsv
full_MDA.csv


title: MDA-48-Controls


title: MDA-47-Controls


title: MDA-45-Controls


title: MDA-42-Controls


title: MDA-41-Controls


title: MDA-46-Controls


title: MDA-39-Controls


title: MDA-38-Controls


title: MDA-40-Controls


title: MDA-37-Controls


title: MDA-36-Controls


title: MDA-34-Controls


title: MDA-33-Controls


title: MDA-35-Controls


title: MDA-31-Controls


title: MDA-3-Controls


title: MDA-29-Controls


title: MDA-27-Controls


title: MDA-30-Controls


title: MDA-28-Controls


title: MDA-44-Controls

description:
meltedData_heritabilityRun1_Controls.tsv
meltedData_heritabilityRun2_Controls.tsv


title: MDA-43-Controls


title: MDA-26-Controls


title: MDA-25-Controls


title: MDA-32-Controls


title: MDA-23-Controls


title: MDA-22-Controls

description:
meltedData_heritabilityRun1_Controls.tsv
full_MDA.csv


title: MDA-21-Controls


title: 19102ST-HSC_N: short term hematopoietic stem cell_CKAML

type: RNA

city: Cincinnati

first: Laura

last: Barreyro

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: short-term hematopoietic stem cells from complex karyotype AML patient

hyb_protocol: Following fragmentation, labeled cRNA of each individual sample was hybridized to Affymetrix Affymetrix Human Gene 1.0 ST microarrays (Affymetrix) and stained according to the manufacturer's instructions.

scan_protocol: not provided

data_processing: Data were normalized normalized with the Expression Console Software  version 1.1 from Affymetrix using Robust Multi-array Average (RMA) algorithm. CLC Workbench Genomics software version 4  was used to select differentially expressed genes by applying the following criteria: (a) Absolute value  of the group mean difference greater than 1.5, and (b) p value smaller than 0.05 (Student’s t test)

label: biotin

molecule: total RNA

source_name: AML, short term hematopoietic stem cell

label_protocol: 10 ng of total RNA were used for linear amplification of cDNA using the Ovation Pico RNA Amplification Systm (Nugen), according to the manufacturer's instructions. 5 µg of cRNA were biotin-labeled using the FL-Ovation cDNA Biotin Module V2 (NuGen).

extract_protocol: Total RNA will be extracted using a denaturing buffer containing guanidine isothiocyanate (ALLprep Kit, Qiagen) from sorted cell populations

treatment_protocol: human bone marrow mononuclear cells were enriched for CD34 expression using Miltenyi MACS technology. Afterwards, cells were stained with antibodies against lineage-antigens (CD2, CD3,  CD4, CD7, CD8, CD10, CD11b, CD14, CD19, CD20 CD56, Glycophorin A), CD34, CD38, CD90, as  well as CD123 and CD45R  in order to distinguish LT-HSC (Lin-/CD34+/CD38-/CD90+), ST-HSC (Lin-/  CD34+/CD38-/CD90-), CMP (Lin-/CD34+/CD38+/CD123+/CD45R   -), GMP (Lin-/CD34+/CD38+/CD123+/  CD45R   +) and MEP (Lin-/CD34+/CD38+/CD123-/CD45R   -). Cells were subjected to 7-color 5 way  sorting utilizing a high-speed cell sorter as previously described (Steidl, et al., 2006)

tag: diagnosis

value: acute myeloid leukemia (AML)

tag: age

tag: tissue

value: bone marrow

value: short term hematopoietic stem cell

tag: karyotype


title: 7060ST-HSC_N: short term hematopoietic stem cell_CKAML


title: 17785ST-HSC: short term hematopoietic stem cell_CKAML


title: 19102LT-HSC: long-term hematopoietic stem cell_CKAML

description: long-term hematopoietic stem cells from complex karyotype AML patient

source_name: AML, long- term hematopoietic stem cell

value: long- term hematopoietic stem cell


title: 7060GMP: Granulocytic-Monocytic Progenitor_CKAML

description: Granulocytic monocytic progenitor from complex karyotype AML patient

source_name: AML, granulocytic monocytic progenitor

value: granulocytic monocytic progenitor


title: MDA-19-Controls


title: 15780GMP: Granulocytic-Monocytic Progenitor_CKAML


title: 17076GMP: Granulocytic-Monocytic Progenitor_CKAML


title: 15780LT-HSC: long-term hematopoietic stem cell_CKAML


title: 17785GMP: Granulocytic-Monocytic Progenitor_CKAML


title: 15780ST-HSC_N: short term hematopoietic stem cell_CKAML


title: 19102ST-HSC_A: short term hematopoietic stem cell_CKAML


title: MDA-2-Controls


title: 15780ST-HSC_A: short term hematopoietic stem cell_CKAML


title: MDA-16-Controls


title: MDA-17-Controls


title: MDA-24-Controls


title: MDA-15-Controls


title: MDA-18-Controls


title: 17076LT-HSC: long-term hematopoietic stem cell_CKAML


title: 17785LT-HSC: long-term hematopoietic stem cell_CKAML


title: MDA-14-Controls


title: MDA-12-Controls


title: 7060ST-HSC_A: short term hematopoietic stem cell_CKAML


title: 7060LT-HSC: long  term hematopoietic stem cell_CKAML


title: MDA-13-Controls


title: MDA-10-Controls


title: MDA-11-Controls


title: MDA-20-Controls


title: MDA-mix-2-7-ExpSample

description:
meltedData_heritabilityRun1_ExpSamples.tsv
meltedData_heritabilityRun2_ExpSamples.tsv

value: Mix of MemorySeq subclones


title: MDA-mix-2-5-ExpSample


title: MDA-1-Controls


title: MDA-8-ExpSample

description:
meltedData_heritabilityRun1_ExpSamples.tsv
meltedData_heritabilityRun2_ExpSamples.tsv
full_MDA.csv


title: MDA-9-ExpSample


title: MDA-7-ExpSample


title: MDA-6-ExpSample


title: MDA-5-ExpSample


title: MDA-51-ExpSample


title: MDA-50-ExpSample


title: untreated qDRIP-seq + standard RH

city: Stanford

first: Karlene

middle: Anne

last: Cimprich

state: CA

address: 318 Campus Drive

institute: Stanford University

description: 10 µg of sonicated genomic DNA was digested with 6 µL RNase H (5000 units/mL, New England Biolabs) in 1X RNase H digestion buffer in 80 µL total volume overnight at 37ºC, followed by immunoprecipitation with S9.6. 4 µg of DNA was bound with 20 µg of S9.6 antibody (Antibodies Incorporated, Davis, CA) in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4°C.

library_source: genomic

data_processing:
Library strategy: qDRIP-seq
Base calling CASAVA v1.8.2
Reads were aligned to genome with bowtie2. The used reference genome was a concatenation of hg38 and dm6 without the alternative scaffolds
Reads were seperated into strands with unix processing tools, and were further seperated into those mapping to the human genome and those mapping to dm6
Reads processed into bedpe format using bedtools
Reads sorted and duplicate reads were removed using unix text processing tools
Genome_build: hg38 and dm6
Supplementary_files_format_and_content: Generate bigwig files using bedtools coverageBed and bedGraphToBigWig from UCSC

molecule: genomic DNA

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM (GIBCO) supplemented with 10% FBS, 2 mM L-glutamine and penicillin/streptomycin in 5% CO2 at 37°C.

extract_protocol:
2x106 HeLa cells were resuspended in 1.6mL TE and lysed with 50 mL 20% SDS and 5 mL Proteinase K 20 mg/mL (Thermo Fisher Scientific) for 3 h at 37ºC. Synthetic RNA-DNA hybrid spike-ins (5 µL of a stock solution at 2.5 pM) were added to cells in TE buffer prior to lysis. For spike-in with Drosophila S2 cells, 1.3x106 S2 cells were mixed with 2x106 HeLa cells in TE prior to cell lysis to give a 1:1.5 S2:HeLa cell ratio, with the aim of obtaining ~10% of total sequencing reads from the Drosophila genome.
DNA libraries were prepared from 3 pooled technical replicate DRIPs per sample. While the DNA material from one IP (or less) is sufficient for successful library preparation, we found pooling IPs effective in minimizing technical variability due to sample handling in pilot experiments. DNA libraries were synthesized from ssDNA using the Accel-NGS 1S DNA library kit (Swift Biosciences, Ann Arbor, MI), according to the manufacturer's protocol. Using multiplexing adapters from the 1S Plus Set A Indexing Kit (Swift Biosciences), adapter-ligated DNA was amplified by PCR. For inputs 12 PCR cycles were used to amplify 1 ng of DNA, and for IP samples 13 PCR cycles were used on the equivalent amount of DNA from one IP reaction. Following PCR, DNA fragments 200-600 bp were retained by size selection using a 0.6X volume ratio of AMPure XP beads (Beckman Coulter)/sample followed by 1.0X ratio. Library DNA was analyzed on a Bioanalyzer DNA HS (Agilent, Santa Clara, CA) at the Stanford Protein and Nucleic Acid Facility, quantified by qPCR using NEBNext Library Quant Kit for Illumina (New England Biolabs), then pooled and sequenced on a HiSeq 4000 (Illumina, San Diego, CA) at the Stanford Genome Sequencing Service Center, using 2 × 151 bp sequencing.

treatment_protocol: For the knockdown control, HeLa cells were transfected with siRNA against luciferase (Fisher scientific D-001400-01-20) at 20 nM for 48 hours using Dharmafect, according to manufacturer protocols.

tag: cell line

value: HeLa cells

tag: drug treatment

tag: exogenous treatment


title: untreated qDRIP-seq input


title: MDA-46-ExpSample


title: DRB qDRIP-seq input

data_processing:
Library strategy: qDRIP-Seq
Base calling CASAVA v1.8.2
Reads were aligned to genome with bwa. The used reference genome was a concatenation of hg38 without the alternative scaffolds to the sequences of E. coli derived spike-ins.
Reads were seperated into strands with unix processing tools, and were further seperated into those mapping to the human genome and those mapping to the spike-ins.
Reads processed into bedpe format using bedtools
Reads sorted and duplicate reads were removed using unix text processing tools
Genome_build: hg38
Supplementary_files_format_and_content: Generate bigwig files using bedtools coverageBed and bedGraphToBigWig from UCSC

extract_protocol:
2x10^6 HeLa cells were lysed by SDS/Proteinase K treatment for 3 h at 37ºC. DNA was extracted by phenol-chloroform extraction using phase lock tubes and ethanol precipitated. Precipitated DNA was gently spooled and washed with 70% ethanol without centrifugation. DNA was allowed to air dry for ~20 minutes and resuspended on ice in 130 uL TE buffer. DNA was sonicated in 6x16 mm microtubes (Covaris, Woburn, MA) to a peak fragment size of 250-300 bp, performed on a Covaris machine (E220 evolution) using SonoLab 7.3 software. For each immunoprecipitation, 4.4 µg of sonicated DNA was used. For RNase H treatment, 8 ug of sonicated DNA was digested with 5 uL RNase H (New England Biolabs) in 1X RNase H digestion buffer overnight at 37ºC and purified using standard methods described above. 4 μg of DNA was bound with 10 μg of S9.6 antibody (Antibodies Incorporated, Davis, CA) in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4ºC. Dynabeads Protein G beads (Thermo Fisher Scientific) were added for 2 h. The use of magnetic beads strongly increased our fold enrichment compared to agarose beads. Bound beads were washed 3 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, 0.5% SDS, Proteinase K) for 45 min at 55ºC. DNA was purified as described.
DNA libraries were prepared from 3 pooled DRIPs by sample. While the DNA material from one IP (or less) is sufficient for successful library preparation, we found pooling IPs effective in minimizing technical variability due to sample handling in pilot experiments. DNA libraries were synthesized from ssDNA using the Accel-NGS 1S DNA library kit (Swift Biosciences, Ann Arbor, MI), according to the manufacturer's protocol. Using multiplexing adapters from the 1S Plus Set A Indexing Kit (Swift Biosciences), adapter-ligated DNA was amplified by PCR, then size-selected using a left/right AMPure XP size selection (Beckman Coulter). Library DNA was analyzed on a Bioanalyzer DNA HS (Agilent, Santa Clara, CA) at the Stanford Protein and Nucleic Acid Facility, quantified by qPCR using NEBNext Library Quant Kit for Illumina (New England Biolabs), then pooled and sequenced on a HiSeq 4000 (Illumina, San Diego, CA)  with paired-end 151bp reads at the Stanford Functional Genomics Facility (NIH grant S10OD018220).

treatment_protocol: For the knockdown control, HeLa cells were transfected with siRNA against luciferase (Fisher scientific D-001400-01-20) at 20 nM for 48 hours using Dharmafect, according to manufacturer protocols. DRB treatment was performed by adding DRB to the growth medium at 100 µM for 40 minutes. DMSO was added as a vehicle control.

value: DRB 100 µM, 40 min


title: DRB qDRIP-seq 1

description: drb


title: MDA-45-ExpSample


title: MDA-49-ExpSample


title: DRB qDRIP-seq +RH


title: DRB qDRIP-seq 2

description: drb


title: MDA-48-ExpSample


title: MDA-42-ExpSample


title: MDA-43-ExpSample


title: DMSO qDRIP-seq 1

description: dmso

value: DMSO


title: siGL3 qDRIP-seq input

value: Control siRNA for luciferase


title: DMSO qDRIP-seq 2

description: dmso


title: MDA-41-ExpSample


title: untreated qDRIP-seq + high RH

description: For high RNase H treatment, 4 µg of sonicated genomic DNA per reaction was digested with 18 µL RNase H in 180 µL total volume overnight at 37ºC. 4 µg of DNA was bound with 20 µg of S9.6 antibody (Antibodies Incorporated, Davis, CA) in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4°C.


title: MDA-4-ExpSample


title: MDA-40-ExpSample


title: siGL3 qDRIP-seq +RH


title: siGL3 qDRIP-seq 2


title: untreated qDRIP-seq


title: MDA-38-ExpSample


title: MDA-39-ExpSample


title: MDA-47-ExpSample


title: IL4-/-KO rep2

city: New York

first: Fengshen

last: Kuo

state: New York

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina bcl2fastq2 version 2.18.0 and 2.20.0.422 were used for generating FASTQ files.
Raw sequencing FASTQ files were aligned against the mm10 assembly by STAR (v020201). Gene level count values were then computed by the summarizeOverlaps function from the R package "GenomicAlignments" with UCSC mm10 KnownGene as the base gene model. The Union counting mode was used and only mapped paired reads were considered. The sample size factor normalized read counts and FPKM (Fragments Per Kilobase Million) values were then computed from gene level counts by using the counts function and the fpkm function, respectively, from the R package DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with sample size factor normalized gene counts for every gene and every sample

organism: Mus musculus

source_name: PyMT breast tumor tissue

extract_protocol:
Breast tumor were collected, and digested to generate single cell suspension. The CD4+CD25- T cells were sorted directly into Trizol reagent. RNA was prepared with a miRNeasy Mini Kit according to the manufacturer’s instructions (Qiagen).
Total RNA with an integrity index from 8.3 to 9.9 was amplified using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).  Amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504).

tag: strain

value: Breast tumor

value: Sorted CD4+CD25- T cells

tag: genotype

value: IL4-/-; Tgfbr2 KO

value: 23 weeks


title: MDA-44-ExpSample


title: DMSO qDRIP-seq input


title: IL4-/-KO rep1


title: MDA-35-ExpSample


title: MDA-36-ExpSample


title: IL4-/- rep2


title: KO rep2 repeat

value: Tgfbr2 KO


title: MDA-34-ExpSample

value: MemorySeq subclone


title: MDA-32-ExpSample


title: KO rep1 repeat


title: KO rep1


title: MDA-3-ExpSample


title: KO rep2


title: MDA-30-ExpSample


title: WT rep2

value: WT


title: WT rep1


title: GlcNAc_ChipSeq_2

city: St. Louis

first: John

middle: R.

last: Edwards

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

data_processing:
Illumina RTA and bcl2fastq2 (version 2.17) were used for basecalling and conversion to fastq files.
Reads were mapped to the mouse genome (mm10) using bowtie2 (v2.2.2) and default parameters. Duplicate reads were removed using samtools rmdups (v1.3.1). Bedgraph files were created using macs2 (v2.0.10) using -g 1.87e9, --SPMR, and -B flags. Bedgraph files were converted to bigWig using the UCSC genome browser toolkit.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of normalized read counts (counts per million)

growth_protocol: Mouse ES cells were cultured in N2B27 medium supplemented with (PD0325901 (0.2 μM) and CHIR99021 (3 μM; both Sigma), 1% ES grade fetal bovine serum and leukemia inhibitory factor. ES cells were maintained on gelatin-coated (Sigma) plates at 37 °C in a 6% CO2 humidified chamber.

extract_protocol: ChIP was carried out as previously described (Boulard et al., 2015) with a slight modification: chromatin was sonicated using a Covaris S220 Sonicator with peak power 150, duty factor 25, cycles/burst 200.

value: Embryonic Stem (ES) Cells

tag: chip antibody

value: O-linked N-acetylglucosamine (O-GlcNAc) Monoclonal antibody HGAC85 (Thermo, MA1-076, lot UD288370)


title: Input_2

source_name: Input


title: MDA-27-ExpSample


title: GlcNAc_ChipSeq_3


title: IL4-/- rep1


title: MDA-29-ExpSample


title: siGL3 qDRIP-seq 1


title: MDA-31-ExpSample


title: MDA-26-ExpSample


title: MDA-28-ExpSample


title: MDA-33-ExpSample


title: GlcNAc_ChipSeq_1

growth_protocol: Mouse ES cells were cultured in N2B27 medium supplemented with (PD0325901 (0.2 μM) and CHIR99021 (3 μM; both Sigma), 1% ES grade fetal bovine serum and leukemia inhibitory factor. ES cells were maintained on gelatin-coated (Sigma) plates at 37 °C in a 6% CO2 humidified chamber.).


title: MDA-25-ExpSample


title: R213G_PBS_4

city: Aurora

first: Denis

last: Ohlstrom

state: CO

address: 12700 E. 19th Avenue

institute: University of Colorado-Anschutz Medical Campus

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO752_HM_PBS

data_processing:
Read quality assessment-fastx_toolkit V0.0.14
Adapter trimming and alignment- Bowtie v2.3.2
Count estimation- SAMtools v1.9
RPKM Calculation- EdgeR
Genome_build: miRBase release 22.1
Supplementary_files_format_and_content: RPKM values for each sample, fold changes, and p/q values from welch's t-test or unequal variances.

source_name: Lung

extract_protocol:
Seven days after treatment, mice were euthanized by isoflurane and thoracotomy. Lungs were flushed with 10 mL PBS in the right ventricle, frozen in liquid nitrogen, and stored at -80˚ C. Frozen lungs were pulverized by mortar and pestle. Pulverized lungs were lysed in 2 mL of Qiazol (Qiagen) and homogenized using a Tissue Tearor (Biospec Products). RNA was isolated using the miRNeasy Mini Kit with DNA digestion using the RNA-free DNase kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male and female WT C57Bl/6 and homozygous R213G EC-SOD (rs1799895) from a C57Bl/6 background received one intratracheal administration of bleomycin in phosphate-buffered saline (PBS) (100 uL at 1 U/mL) or PBS alone at 8-12 weeks old.

value: 11 weeks


title: MDA-24-ExpSample


title: spr-5; met-2_Rep2

city: Atlanta

first: Brandon

middle: S.

last: Carpenter

state: Georgia

address: 615 Michael St., SOM: Cell Biology Dept.

department: Cell Biology

institute: Emory University

data_processing:
Raw RNAseq reads were checked for quality using FastQC (Andrews 2010), filtered using Trimmomatic (Bolger et al. 2014)
Reads were and aligned to genome WS220/ce10 using  (Kim et al 2015)
Read count by gene was obtained by FeatureCounts (Yang liao et al 2014)
Differentially expressed transcripts were determined using DESEQ2 (v.2.11.40.2) (Love et al 2014)
Genome_build: ce10
Supplementary_files_format_and_content: Processed files from DESEQ2 analysis are in tabular format and contain a list of differentially expressed genes compared to N2

organism: Caenorhabditis elegans

source_name: spr-5; met-2_L1 larvae

growth_protocol: Animals were cultured with HT115 on 10-cm NGM agar plates at 20C.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) from ~1000-1500 starved L1 larvae born at room temperature (21° C - 22° C) overnight in M9 Buffer.
Libraries were prepared by UGA GGB Core (for Illumina NEXTseq).

tag: Stage

value: L1 larvae

value: whole animal


title: spr-5; met-2_Rep3


title: spr-5; met-2_Rep1


title: N2_Rep3

source_name: N2_L1 larvae


title: N2_Rep2


title: R213G_PBS_3

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO748_HM_PBS


title: MDA-22-ExpSample


title: R213G_PBS_2

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO751_HM_PBS


title: R213G_PBS_1

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO747_HM_PBS


title: Input_1


title: MDA-23-ExpSample


title: Hep3B.Sorafenib.9

first: Julia

middle: Elise

last: Kieckhaefer

state: Pennsylvania

address: 421 Civic Center Blvd, BRB 927

department: Gastroenterology

description:
mRNA
processed data file: FPKM.xlsx

data_processing:
MiSeqCS:2.6.2.1 and HiSeqCS:HD 3.4.0.38 were used for base calling.
Sequenced reads were mapped to hg19 and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated by RNA-Seq Unified Mapper (RUM).
Differential expression analysis was performed using the software package Empirical Analysis of Digital Gene Expression Data in R (edgeR).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: FPKM.xlsx: Excel file contains FPKM for each sample.
Supplementary_files_format_and_content: Compare.tab.1.edger.txt: Tab-separated text file; Differential expression analysis; Hep3B_GW3965:Hep3B_DMSO.
Supplementary_files_format_and_content: Compare.tab.2.edger.txt: Tab-separated text file; Differential expression analysis; Hep3B_Sorafenib:Hep3B_DMSO.
Supplementary_files_format_and_content: Compare.tab.3.edger.txt: Tab-separated text file; Differential expression analysis; Hep3B_Sorafenib-GW3965:Hep3B_DMSO.
Supplementary_files_format_and_content: Compare.tab.4.edger.txt: Tab-separated text file; Differential expression analysis; Huh7_GW3965:Huh7_DMSO.
Supplementary_files_format_and_content: Compare.tab.5.edger.txt: Tab-separated text file; Differential expression analysis; Huh7_Sorafenib:Huh7_DMSO.
Supplementary_files_format_and_content: Compare.tab.6.edger.txt: Tab-separated text file; Differential expression analysis; Huh7_Sorafenib-GW3965:Huh7_DMSO.

source_name: Hep3B hepatoma cell line

growth_protocol: Grown in DMEM with FBS and P/S.

extract_protocol:
24 hours after drug treatment, RNA was extracted using Qiagen RNeasy micro kit, then mRNA was isolated using NEB Next Poly A mRNA magnetic isolation module.
Libraries were constructed with NEB Next Ultra RNA Library Prep for Illumina.

treatment_protocol: 6*10^5 cells/well in a 6 well plate were seeded and 24 hours later treated with DMSO, 2uM sorafenib, 5uM GW3965, or sorafenib and GW3965.

value: Sorafenib


title: MDA-21-ExpSample


title: Hep3B.Sorafenib.8

description:
mRNA
processed data file: FPKM.xlsx


title: MDA-20-ExpSample


title: Hep3B.Sorafenib.5

description:
mRNA
processed data file: FPKM.xlsx


title: WT_PBS_3

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO783_WT_PBS


title: WT_PBS_2

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO781_WT_PBS


title: MDA-2-ExpSample


title: WT_PBS_1

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO782_WT_PBS


title: Hep3B.Sorafenib.4

description:
mRNA
processed data file: FPKM.xlsx


title: Hep3B.Sorafenib.7

description:
mRNA
processed data file: FPKM.xlsx


title: Hep3B.Sorafenib.3

description:
mRNA
processed data file: FPKM.xlsx


title: Hep3B.Sorafenib.1

description:
mRNA
processed data file: FPKM.xlsx


title: MDA-16-ExpSample


title: Hep3B.Sorafenib.2

description:
mRNA
processed data file: FPKM.xlsx


title: MDA-17-ExpSample


title: Hep3B.Combination.9

description:
mRNA
processed data file: FPKM.xlsx


title: WT_Bleo_3

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO778_WT_Bleo


title: WT_Bleo_2

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO779_WT_Bleo


title: Hep3B.Combination.6

description:
mRNA
processed data file: FPKM.xlsx


title: N2_Rep1


title: Hep3B.Combination.8

description:
mRNA
processed data file: FPKM.xlsx


title: MDA-14-ExpSample


title: Hep3B.Combination.7

description:
mRNA
processed data file: FPKM.xlsx


title: MDA-15-ExpSample


title: WT_Bleo_1

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO777_WT_Bleo


title: Hep3B.Sorafenib.6

description:
mRNA
processed data file: FPKM.xlsx


title: Hep3B.Combination.5

description:
mRNA
processed data file: FPKM.xlsx


title: Hep3B.Combination.4

description:
mRNA
processed data file: FPKM.xlsx


title: R213G_Bleo_4

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO750_HM_Bleo


title: Hep3B.Combination.3

description:
mRNA
processed data file: FPKM.xlsx


title: MDA-12-ExpSample


title: Hep3B.Combination.2

description:
mRNA
processed data file: FPKM.xlsx


title: MDA-11-ExpSample


title: R213G_Bleo_3

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO746_HM_Bleo


title: Hep3B.GW3965.9

description:
mRNA
processed data file: FPKM.xlsx


title: Hep3B.Combination.1

description:
mRNA
processed data file: FPKM.xlsx


title: R213G_Bleo_2

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO749_HM_Bleo


title: WT_Bleo_4

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
AO780_WT_Bleo


title: WM989-9-Controls

description:
meltedData_heritabilityRun1_Controls.tsv
meltedData_heritabilityRun2_Controls.tsv
full_WM989.csv

source_name: WM989 A6 melanoma (BRAFV600E)

value: Control/MemorySeq parental sample


title: WM989-8-Controls


title: Hep3B.GW3965.7

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-7-Controls


title: Hep3B.GW3965.5

description:
mRNA
processed data file: FPKM.xlsx


title: R213G_Bleo_1

description:
DiffExpr_RPKM_ttest_log2_mirBase_edgeR.csv
A0745_HM_Bleo


title: Hep3B.GW3965.4

description:
mRNA
processed data file: FPKM.xlsx


title: Hep3B.GW3965.3

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-6-Controls


title: Hep3B.GW3965.1

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-5-Controls


title: WT_3

data_processing:
Illumina RTA and bcl2fastq2 (version 2.17) were used for basecalling and conversion to fastq files.
For repeat analysis, reads were mapped to the mouse genome references (mm10) using bowtie2 (v2.2.2) and default parametes except for -D 10000 -R 10000. After filtering out reads that maped to rRNA and mRNA (Ensembl v87) sequences, reads were overlapped with repeat annotations from the RepeatMasker track from the UCSC genome browser using featureCounts (v1.5.0).
For transcript analysis, reads were mapped to the mouse genome reference (mm10) using HISAT2 (v2.1.0) and knownsplice mapping using Ensembl v87 with otherwise default parameters. After filtering out reads that mapped to rRNA sequences, alignment files were overlapped with gene annotations using featureCounts (v1.5.0) and Ensembl v87.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes all raw feature counts for each gene.

source_name: ES Cells

growth_protocol: ES cells were cultured on gelatin-coated plates in under standard conditions (DMEM, 2 mM Glu-tamax, 15% ES grade fetal bovine serum, 2 mM L glutamine, MEM non-essential amino acids, 100 IU/ml penicillin, 100 μg/ml streptomycin, 0.12 mM 2-mercaptoethanol and leukemia inhibitory factor).

extract_protocol:
Total RNA was extracted and traces of contaminating genomic DNA were eliminated by two successive treatments with DNAse (Turbo DNase, Ambion). The integrity of the RNA was veri-fied using the Bioanalyzer RNA 2100 Nano Assay (Agilent Technologies).
RNA-seq libraries were prepared with the TruSeq RNA Sample Prep Kit v2 (Illumina).

treatment_protocol: WT and Dnmt1-/- ES cells were untreated.  OGA and OGA-D242D samples were WT ES cells treated with dCas9-OGA anad dCas9-OGA-D242D respectively and 4 sgRNAs targeting IAP elements.


title: WT_2


title: Hep3B.DMSO.9

description:
mRNA
processed data file: FPKM.xlsx


title: Hep3B.GW3965.2

description:
mRNA
processed data file: FPKM.xlsx


title: WT_1


title: Hep3B.DMSO.8

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-48-Controls

description:
meltedData_heritabilityRun2_Controls.tsv
full_WM989.csv


title: Hep3B.DMSO.6

description:
mRNA
processed data file: FPKM.xlsx


title: Hep3B.GW3965.8

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-47-Controls


title: Hep3B.DMSO.5

description:
mRNA
processed data file: FPKM.xlsx


title: Hep3B.DMSO.7

description:
mRNA
processed data file: FPKM.xlsx


title: Hep3B.DMSO.4

description:
mRNA
processed data file: FPKM.xlsx


title: Dnmt1_null_2

description: D1-null strain (C allele) Ref: De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells. Lei H, Oh SP, Okano M, Jüttermann R, Goss KA, Jaenisch R, Li E.Development. 1996 Oct;122(10):3195-205

value: D1-null strain (C allele)


title: WM989-46-Controls


title: Hep3B.DMSO.3

description:
mRNA
processed data file: FPKM.xlsx

value: DMSO


title: Hep3B.GW3965.6

description:
mRNA
processed data file: FPKM.xlsx


title: Dnmt1_null_1


title: Hep3B.DMSO.1

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-45-Controls


title: Huh7.Sorafenib.8

description:
mRNA
processed data file: FPKM.xlsx

source_name: Huh7 hepatoma cell line


title: WM989-44-Controls


title: Huh7.Sorafenib.9

description:
mRNA
processed data file: FPKM.xlsx


title: Huh7.Sorafenib.6

description:
mRNA
processed data file: FPKM.xlsx


title: ES, WT+OGA

data_processing:
Illumina RTA and bcl2fastq2 (version 2.17) were used for basecalling and conversion to fastq files.
For repeat analysis, reads were mapped to the mouse genome references (mm10) using bowtie2 (v2.2.2) and default parametes except for -D 10000 -R 10000. After filtering out reads that maped to rRNA and mRNA (Ensembl v87) sequences, reads were overlapped with repeat annotations from the RepeatMasker track from the UCSC genome browser using featureCounts (v1.5.0).
For transcript analysis, reads were mapped to the mouse genome reference (mm10) using tophat2 (v2.0.11) and default parameters. After filtering out reads that mapped to rRNA sequences, alignment files were overlapped with gene annotations using featureCounts (v1.5.0) and Ensembl v87.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes all raw feature counts for each gene.

tag: genotype/variation

value: wild-type


title: Huh7.Sorafenib.7

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-43-Controls


title: Huh7.Sorafenib.5

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-42-Controls


title: EMSCSp

city: Macao

first: Renhe

last: Xu

address: Avenida de Universidade  Taipa

department: Faculty of Health Sciences

country: China

institute: University of Macao

data_processing:
Paired-end sequencing was performed on the Illumina HiSeq2500 platform
We applied FastQC for a standard quality control of our 100-bp length, paired-end RNA-seq data generated by Illumina HiSeq2500, tested both the raw sequence data, and trimmed sequence data.
Trimmomatic was used to trim the adaptor, and discarded low quality reads and the reads with length less then 36 bp. After trimming, we reserved the paired reads and abandoned unpaired reads for next step analysis. Then cleaned reads (paired reads) were submitted to the tuxedo pipeline.
Tophat2 internally called bowtie2 to map raw reads against the human genome hg38 and mouse genome mm10 with 2 mismatches allowed
Cufflinks were applied to generate the Fragments Per Kilobase Million (FPKM) value for each gene, based on the hg38 or mm10 gene annotation GTF file of University of California Santa Cruz. Human and mouse genome sequences, annotation files, and genome indexes were downloaded from iGenome
Genome_build: human genome hg38 and mouse genome mm10
The RNA-seq data was statically analyzed with R. One-way ANOVA test and fold change were used to identify DEG. We downloaded all the gene sets used for function/pathway enrichment from Gene Set Enrichment Analysis of the Broad Institute, and elucidated the hypergeometric distribution to determine P values of each enriched pathway. The R package “gplots” and “ggpubr” were used to prepare all figures.
Supplementary_files_format_and_content: FPKM

source_name: EMSC underwent spheroids formation

growth_protocol: EMSC were generated by inducing hESC to differentiate into MSC using the method we reported previously. EMSC were cultured in high-glucose Dulebcco’s modified Eagle’s medium supplemented with 20% fetal bovine serum at 37.0℃ in 5% CO2 incubator, and passaged every 5-7 days. MSC between passages 6-10 were used for all experiments. For spheroid formation, MSC were split and seeded on adhesion substrates by using handing drop method at a density of 2.5×104 cells/drop as we recently reported 15, and the MSC in the handing drop formed spheroids within 2-day culture. Either MSC spheroids or cells dissociated from MSC in monolayer were harvested for transplantation.

extract_protocol:
Mice were sacrificed at designated time points, skin samples including the wound and 2 mm of the surrounding skin were harvested using an 8-mm biopsy punch, and three wounds were pooled per group. The tissues were sliced into small pieces and homogenized with a pestle. Skin fragments were added into a lysis buffer provided by QIAGEN RNeasy kit to isolate total RNA according to the manufacturer’s instructions.
The integrity and quality of samples were verified using the Nano RNA Bioanalyzer Assay (Agilent Technologies). Samples with RNA integrity number larger than 9 were used for Next Generation Sequencing library preparation using the NEB Ultra Directional RNA Library Preparation Kit.

treatment_protocol: The excisional wound splinting model was generated as reported. For the EMSCSp group, around 40 spheres equivalent of 1×106 EMSC were directly dropped onto the surface of each wound right after the wounding. For the EMSCDiss group, EMSCDiss at 0.7×106 cells in 100 l PBS (70% of the total cell dose) per wound were evenly injected into the dermis in four spots around the wound, and 0.3×106 EMSCDiss (30% of the total cell dose) mixed with 30-l Matrigel were dropped onto the surface of the wound. For the vehicle control group, 100-l PBS alone per wound was evenly injected around the wound, and 30-l Matrigel was dropped onto the surface of the wound as above.

value: human ES derived MSC


title: Dnmt1_null_3


title: Huh7.Sorafenib.4

description:
mRNA
processed data file: FPKM.xlsx


title: EMSCDiss

source_name: EMSC dissociated from the monolayer culture


title: WM989-41-Controls


title: Hep3B.DMSO.2

description:
mRNA
processed data file: FPKM.xlsx


title: Huh7.Sorafenib.3

description:
mRNA
processed data file: FPKM.xlsx


title: slow#1

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

description: Rpb1 N494D mutation

data_processing:
The reads were trimmed and aligned according to the MUGQIC RNA-seq pipeline (bitbucket.org/mugqic/genpipes/src/master/pipelines/rnaseq/)
Low quality reads and adaptor sequences were removed with Trimmomatic v0.36 with parameters ILLUMINACLIP:adapters-truseq.fa:2:30:15:8:true  TRAILING:30  MINLEN:32.
The remaining reads were then aligned to the S. pombe  genome assembly ASM294v2 with STAR v2.5.1 with parameter --runMode alignReads.
Aligned reads were summarized at the gene level using featureCounts with options -p -s 2 -P -d 0 -D 1000 -C -T 4 and differential gene expression analysis was performed using the R package DESeq2 v1.24.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Strand-specific genome coverage files (bigWig) were generated using deeptools v3.3 bamCoverage with options -bs 2 --scalefactor [1/(DESEQ2 sizefactor)]  --filterRNAstrand [forward, reverse].

organism: Schizosaccharomyces pombe

source_name: Rpb1 N494D mutation

growth_protocol: Cells were grown to mid-log phase (OD600 0.5) at 30°C in EMM supplemented with adenine, histidine, leucine and uracil.

extract_protocol:
Total RNA was extracted using the hot-acid phenol method.
Library preparation was performed at the RNomics Platform of Université de Sherbrooke. Briefly 10 µg of total RNA was treated with DNase on a RNeasy Mini Kit column (Qiagen) according to manufacturers protocol. RNA integrity was assessed on a 2100 Bioanalyzer machine (Agilent Technologies). Ribo-depleted RNA was isolated from 1.25 µg of total RNA using Illumina RiboZero (yeast). Then, stranded RNA-seq libraries then built using the SSV21106 kit (Epicentre) from the ribo-depleted RNA with 13 cycles of PCR amplification. After assessment of libraries quality and molarity on a DNA HS Chip (Agilent), the libraries were pooled and sequenced in paired-end (2x100 bp) on HiSeq 4000 (Illumina) at McGill University and Génome Québec Innovation Centre (MUGQIC) Sequencing Service at 250x genome depth (35 millions reads) at least  for each sample.

value: h- ade6-M216 leu1-32 ura4-D18 his3-D1 fex1_delta fex2_delta rpb1 (N494D)

tag: strain internal name

tag: alias


title: WM989-40-Controls


title: slow#2

description: Rpb1 N494D mutation


title: E17.5 Lgr5-DTReGFP KO2 passage 4-Rspo3-100ng/ml_sample  84

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

institute: ULB

data_processing:
Sequenced reads were trimmed for adaptor sequence (Trimmomatic-0.36)
Paired-end reads were mapped against the mouse reference genome (GRCm38.p4/mm10) using the STAR_2.5.3a software to generate read alignments.
The annotation file Mus_musculus.GRCm38.90.gtf was obtained from the ftp.Ensembl.org server
Following transcript assembly, gene level counts were obtained using HTSeq-0.9.1
Genome_build: GRCm38.p4/mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample.

source_name: small intestine

extract_protocol:
Total RNA was extracted with the miRNeasy Micro kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using Ovation® SoLo RNA-Seq Library Preparation Kit (NuGEN, TECAN genomics). For organoids, RNA libraries were prepared for sequencing using the NEBNext rRNA depletion kit.

value: small intestine

tag: developmental stage

value: Organoid

value: Lgr5 knockout

value: cultured in mouse Rspondin 3 100 ng/ml Rspo


title: E17.5 Lgr5-DTReGFP KO2 passage 4-Rspo2-5ng/ml_sample  82

tag: treatment

value: cultured in mouse Rspondin 2 5 ng/ml Rspo


title: E17.5 Lgr5-DTReGFP KO2 passage 4-Rspo3-5ng/ml_sample  88

tag: cell type

value: cultured in mouse Rspondin 3 5 ng/ml Rspo


title: Huh7.Sorafenib.2

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-4-Controls


title: WT

description: wild-type

source_name: wild-type

value: h- ade6-M216 leu1-32 ura4-D18 his3-D1 fex1_delta fex2_delta


title: E17.5 Lgr5-DTReGFP KO2 passage 4-Rspo2-100ng/ml_sample  80

value: cultured in mouse Rspondin 2 100 ng/ml Rspo


title: Huh7.Sorafenib.1

description:
mRNA
processed data file: FPKM.xlsx


title: E17.5 Lgr5-DTReGFP KO2 passage 4-Rspo1-5ng/ml_sample  78

value: cultured in mouse Rspondin 1 5 ng/ml Rspo


title: Huh7.Combination.9

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-38-Controls


title: E17.5 Lgr5-DTReGFP KO2 passage 4-Rspo1-100ng/ml_sample  76

value: cultured in mouse Rspondin 1 100 ng/ml Rspo


title: Huh7.Combination.8

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-36-Controls


title: E17.5 Lgr5-DTReGFP KO7 passage 4-Rspo3-5ng/ml_sample  71


title: Little_R

city: Chicago

first: Benjamin

middle: Jung

last: Fair

state: IL

address: 920 E. 58th Street, CLSC 317

department: Section of Genetic Medicine

institute: University of Chicago

data_processing:
For chimpanzee/human comparisons RNASeq reads were trimmed to 75bp single-end reads to match published human datasets for comparison using fastx_toolkit.
Reads aligned with STAR aligner v2.6.1b (Dobin et al. 2015) with default settings to the respective genome (GRCh38.p13 or Pan_tro_3.0 from Ensembl release 95).
Gene counts were obtained with subread featureCounts (Liao et al. 2014) using a previously described annotation file of human-chimpanzee orthologous exons (Pavlovic et al. 2018).
For chimpanzee eQTL mapping, RNASeq reads were kept as 100bp single-end reads and aligned with START aligner v2.6.1b (Dobin et al. 2015) with the {--quantMode GeneCounts} parameter to compile a gene expression matrix.
Genes were filtered to require at least 8 read counts in 75% of samples, leaving 13545 genes for further analysis. The resulting read count matrix was converted to log(CPM), standardized across individuals, and quantile normalized to a normal distribution across genes as previously described (Degner et al. 2012).
Genome_build: Pan_tro_3.0 (Ensembl release 95)
Supplementary_files_format_and_content: ChimpanzeesRawGeneCount_eQTL_Mapping.tsv: RNA-seq counts for all genes for all chimpanzee individuals analyzed in this study. Reformatted output of {STAR --quantMode GeneCounts}.
Supplementary_files_format_and_content: ChimpanzeesQQNorm_eQTL_Mapping.tsv: Standardized and quantile normalized CPM expression for all chimpanzee individuals (minus MD_And) for eQTL mapping.
Supplementary_files_format_and_content: OrthologousExonRawGeneCounts_Human.tsv: RNA-seq counts for all human/chimpanzee orthologous genes for all human individuals analyzed in this study. Reformatted output of subRead.
Supplementary_files_format_and_content: OrthologousExonRawGeneCounts_Chimpanzee.tsv: RNA-seq counts for all human/chimpanzee orthologous genes for all chimpanzee individuals analyzed in this study. Reformatted output of subRead.

organism: Pan troglodytes

source_name: post-mortem heart tissue

extract_protocol:
DNA and RNA were extracted from frozen tissues using Trizol extraction according to manufacturer's instructions (QIAGEN Cat No./ID: 79306).
Illumina TruSeq RNA Library Prep kit v2 according to manufacturer's instructions.

value: post-mortem heart


title: 88A020


title: MD_And


title: E17.5 Lgr5-DTReGFP KO7 passage 4-Rspo3-100ng/ml_sample  69


title: WM989-37-Controls

value: Control/MemorySeq parental sample


title: Huh7.Combination.7

description:
mRNA
processed data file: FPKM.xlsx


title: 95A014


title: Huh7.Combination.5

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-35-Controls


title: 724


title: E17.5 Lgr5-DTReGFP KO7 passage 4-Rspo2-5ng/ml_sample  67


title: E17.5 Lgr5-DTReGFP KO7 passage 4-Rspo2-100ng/ml_sample  65


title: 676


title: WM989-34-Controls


title: Huh7.Combination.4

description:
mRNA
processed data file: FPKM.xlsx


title: 623


title: WM989-39-Controls


title: E17.5 Lgr5-DTReGFP KO7 passage 4-Rspo1-5ng/ml_sample  63


title: Huh7.Combination.3

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-33-Controls


title: WM989-32-Controls


title: E17.5 Lgr5-DTReGFP KO7 passage 4-Rspo1-100ng/ml_sample  61


title: 570


title: Huh7.Combination.2

description:
mRNA
processed data file: FPKM.xlsx


title: E17.5 Lgr5-DTReGFP WT30 passage 4-Rspo3-5ng/ml_sample  56

value: Lgr5 wild-type


title: Huh7.Combination.6

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-31-Controls


title: Huh7.Combination.1

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-30-Controls


title: 558


title: E17.5 Lgr5-DTReGFP WT30 passage 4-Rspo3-100ng/ml_sample  54


title: Huh7.GW3965.8

description:
mRNA
processed data file: FPKM.xlsx


title: 554_2


title: WM989-3-Controls


title: E17.5 Lgr5-DTReGFP WT30 passage 4-Rspo2-5ng/ml_sample  52


title: ES, WT+OGA-D242A

value: Embryonic Stem (ES) Cells


title: Huh7.GW3965.7

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-28-Controls


title: 554


title: WM989-29-Controls


title: E17.5 Lgr5-DTReGFP WT30 passage 4-Rspo1-5ng/ml_sample  48


title: 549


title: E17.5 Lgr5-DTReGFP WT30 passage 4-Rspo2-100ng/ml_sample  50


title: Huh7.GW3965.5

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-27-Controls


title: Huh7.GW3965.4

description:
mRNA
processed data file: FPKM.xlsx


title: 529


title: E17.5 Lgr5-DTReGFP WT5 passage 4-Rspo3-5ng/ml_sample  26


title: WM989-26-Controls


title: Huh7.GW3965.3

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-25-Controls


title: E17.5 Lgr5-DTReGFP WT5 passage 4-Rspo3-100ng/ml_sample  24


title: 503


title: WM989-24-Controls


title: Huh7.GW3965.1

description:
mRNA
processed data file: FPKM.xlsx


title: E17.5 Lgr5-DTReGFP WT5 passage 4-Rspo2-5ng/ml_sample  22


title: Huh7.GW3965.2

description:
mRNA
processed data file: FPKM.xlsx


title: 4x523


title: E17.5 Lgr5-DTReGFP WT5 passage 4-Rspo2-100ng/ml_sample  20


title: 4X0550


title: WM989-23-Controls


title: Huh7.GW3965.6

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-22-Controls


title: E17.5 Lgr5-DTReGFP WT30 passage 4-Rspo1-100ng/ml_sample  46


title: 537


title: Huh7.DMSO.8

description:
mRNA
processed data file: FPKM.xlsx

value: DMSO


title: 4x0430


title: Huh7.DMSO.7

description:
mRNA
processed data file: FPKM.xlsx


title: E17.5 Lgr5-DTReGFP WT5 passage 4-Rspo1-5ng/ml_sample  18


title: E17.5 Lgr5-DTReGFP WT5 passage 4-Rspo1-100ng/ml_sample  16


title: Huh7.DMSO.6

description:
mRNA
processed data file: FPKM.xlsx


title: 4X0357


title: WM989-21-Controls

description:
meltedData_heritabilityRun1_Controls.tsv
meltedData_heritabilityRun2_Controls.tsv


title: WM989-2-Controls


title: WM989-20-Controls


title: E17.5 Lgr5-DTReGFP WT10 passage 4-Rspo3-5ng/ml_sample  11


title: E17.5 Lgr5-DTReGFP WT10 passage 4-Rspo3-100ng/ml_sample  9


title: Huh7.DMSO.5

description:
mRNA
processed data file: FPKM.xlsx


title: Huh7.DMSO.4

description:
mRNA
processed data file: FPKM.xlsx


title: 4X0354


title: Huh7.DMSO.3

description:
mRNA
processed data file: FPKM.xlsx


title: E17.5 Lgr5-DTReGFP WT10 passage 4-Rspo2-5ng/ml_sample  7


title: Huh7.DMSO.2

description:
mRNA
processed data file: FPKM.xlsx


title: E17.5 Lgr5-DTReGFP WT10 passage 4-Rspo1-5ng/ml_sample  3


title: 522


title: E17.5 Lgr5-DTReGFP WT10 passage 4-Rspo1-100ng/ml_sample  1


title: 4X0212


title: Huh7.DMSO.1

description:
mRNA
processed data file: FPKM.xlsx


title: WM989-16-Controls


title: 4X0095


title: WM989-15-Controls


title: RPB1756

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

data_processing:
Reads were aligned to the macaque genome with STAR
Counts of reads to genes were calculated with STAR
Genome_build: Macaca fascicularis 5.0  GCF_000364345.1
Supplementary_files_format_and_content: Gene IDs and read counts, tab delimited

organism: Macaca fascicularis

source_name: Anterior Cingulate Cortex

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Anterior Cingulate Cortex

value: Saline control

tag: country

value: Singapore


title: RPB1758


title: WM989-14-Controls


title: 4x0043


title: R62/KO_rep3

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 77 Massachusetts Ave., Bldg 46-4285

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

description: snRNA

data_processing:
Basecalls converted to FASTQ with Cellranger v3.1.
FASTQ aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCm38 reference genome
Genome_build: GRCm38
Supplementary_files_format_and_content: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.

molecule: nuclear RNA

source_name: Striatum

extract_protocol:
Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol.  The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA.
Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual.

value: Striatum

value: spiny projection neurons


title: RPB1751


title: R62/KO_rep2

description: snRNA


title: WM989-13-Controls

data_processing:
bcl2fastq conversion performed on BaseSpace using Illumina's default generate fastq workflow
Aligned to hg19 using STAR version 2.3.0e with default parameters
Filtered uniquely mapped reads using ngsutils/bamutils
Sorted using samtools-0.1.19
enumerated read counts per gene using HTseq-0.6.1 in union mode
filtered protein-coding genes then normalized by sequencing depth and gene length using custom R script
Genome_build: aligned to hg19, ensembl GRCh37.75 gtf used for gene annotations
Supplementary_files_format_and_content: tsv files contain gene level RNA-seq counts generated using HTSeq with GRCh37.75 gene annotations. csv files contain RPM, RPKM, and TPM normalized counts for protein coding genes used in subsequent variability analyses.


title: WM989-19-Controls


title: R62/KO_rep1

description: snRNA


title: 4X0339


title: RPB1750


title: 4x0025


title: WM989-12-Controls


title: 4X0333


title: 4X0267


title: RPB1749


title: WM989-11-Controls


title: R62/WT_rep2

description: snRNA


title: 476


title: RPB1747


title: WM989-10-Controls


title: WM989-1-Controls


title: RPB1725

source_name: Basolateral Amygdala

value: Basolateral Amygdala


title: R62/WT_rep1

description: snRNA


title: WM989-mix3-ExpSample

description: meltedData_heritabilityRun2_ExpSamples.tsv

value: Mix of MemorySeq subclones


title: RPB1723


title: WT/WT_rep2

description: snRNA

value: WT/WT


title: WM989-mix2-ExpSample

description:
meltedData_heritabilityRun1_ExpSamples.tsv
meltedData_heritabilityRun2_ExpSamples.tsv


title: 456


title: 438


title: R62/WT_rep3

description: snRNA


title: E17.5 Lgr5-DTReGFP WT10 passage 4-Rspo2-100ng/ml_sample  5

value: small intestine

value: Organoid


title: WT/WT_rep1

description: snRNA


title: 495


title: RPB1719


title: WT/KO_rep3

description: snRNA

value: WT/KO


title: WM989-mix1-ExpSample


title: 389


title: WT/KO_rep2

description: snRNA


title: 338


title: 462


title: RPB1718


title: WM989-9-ExpSample

description:
meltedData_heritabilityRun1_ExpSamples.tsv
full_WM989.csv

value: MemorySeq subclone


title: 317

value: post-mortem heart


title: WT/KO_rep1

description: snRNA


title: RPB1716


title: WM989-8-ExpSample

description:
meltedData_heritabilityRun1_ExpSamples.tsv
meltedData_heritabilityRun2_ExpSamples.tsv
full_WM989.csv


title: Lgr5-Cre/flox cKO adult mouse number 1-32  ileum

source_name: Lgr5-Cre/flox cKO adult mouse ileum

extract_protocol:
Total RNA was extracted with the miRNeasy Micro kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using Ovation® SoLo RNA-Seq Library Preparation Kit (NuGEN, TECAN genomics)
RNA-Seq 2x100 bases Paired-End

value: Lgr5-null conditional KO

value: Adult -2 month-old

value: 2 month-old mouse injected intraperitoneally with 2 mg of tamoxifen and harvested 48 hours post injection

value: Ileum

value: Stem cells

tag: reporter

value: eGFP+ve/RFP+ve


title: WM989-7-ExpSample

extract_protocol:
RNA extracted from 100,000-200,000 cells using miRNAeasy RNA extraction kit according to manufacturer's protocol (Qiagen 217004). Polyadenylated RNA was then purified using NEBNext Poly(A) Magnetic Isolation Module (NEB E7490L)
NEBNext Ultra RNA sequencing library prep kit for Illumina (NEB E7530L )
mRNA-seq, random hexamer primed RT, unstranded.


title: WM989-67-ExpSample


title: RPB1695

source_name: Posterior Dentate Gyrus

tag: tissue

value: Posterior Dentate Gyrus

value: Saline control

value: Singapore


title: WM989-60-ExpSample


title: RPB1689


title: Patient49_normal

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

data_processing:
adapter trimming with cutadapt v2.5 (-a ATCACCGACTGCCCATAGAGAGGCTGAGAC -q 17,17 --minimum-length 50 --trim-n  --max-n=0.1)
filter mapping with bwa mem v0.7.14-r1136 to rRNA/tRNA FASTA
quality trimming with fqtrim v0.9.5 (-p2)
alignment to GRCh37.87 reference using STAR v2.5.2b
feature counting with subread v1.5.2 featureCounts (-t exon -g gene_id -T 16 -s 2 -a Homo_sapiens.GRCh37.87.gtf)
differential expression analysis using DESeq2
Genome_build: GRCh37.87
Supplementary_files_format_and_content: comma-separated text with rlog-normalized count data

source_name: brain

extract_protocol:
RNA was extracted from both tissue groups by using Trizol and Ambion The Pure Link RNA Mini Kit according to the manufacturer's protocol
Libraries of the 12 sample pairs were built according to the Ion Ampliseq Human Gene Expression protocol. Briefly, 10ng total RNA was reverse transcribed, cDNA was amplified for 12 cycles by adding Hi-Fi master mix and Ion Ampliseq Human Gene Expression primer pool. For digestion, FuPa reagent was added and barcode adapters ligated to the amplicons. After washing with magnetic beads, libraries were eluted and measured with qRT-PCR. Libraries were concentration-equalized. Emulsion PCR was performed in the Ion One Touch System (Thermo Fisher).

tag: disease state

value: Glioblastoma

tag: age (y)

tag: Sex

value: M

tag: location

value: temporal

value: normal brain


title: Patient49_tumor

value: brain tumor


title: Lgr5-Cre/flox cKO adult mouse number 1-22  ileum


title: Lgr5-Cre/+ heterozygous intestinal SC adult mouse number 3-27  ileum

source_name: Lgr5-Cre/+ heterozygous intestinal SC adult mouse ileum

value: Lgr5 heterozygous


title: RPB1688


title: Patient48_tumor

value: F

value: frontal


title: WM989-6-ExpSample

value: MemorySeq subclone


title: Patient48_normal


title: WM989-59-ExpSample


title: Lgr5-Cre/+ heterozygous intestinal SC adult mouse  number 3-22 ileum

value: Adult -2 month-old


title: 295

value: post-mortem heart


title: Lgr5-DTReGFP heterozygous adult mouse number 77 ileum

source_name: Lgr5-DTReGFP heterozygous adult mouse ileum

value: Ileum

value: eGFP+ve


title: RPB1687


title: Lgr5-Cre/flox cKO adult mouse number 1-34  ileum

value: Lgr5-null conditional KO

value: 2 month-old mouse injected intraperitoneally with 2 mg of tamoxifen and harvested 48 hours post injection

value: Stem cells

value: eGFP+ve/RFP+ve


title: WM989-58-ExpSample

source_name: WM989 A6 melanoma (BRAFV600E)


title: Patient45_normal

value: Glioblastoma


title: Patient45_tumor


title: RPB1693

value: Posterior Dentate Gyrus

value: Saline control

value: Singapore


title: Lgr5-DTReGFP heterozygous adult mouse number 77 duodenum

source_name: Lgr5-DTReGFP heterozygous adult mouse duodenum

value: Duodenum


title: Patient43_tumor

value: M

value: brain tumor


title: RPB1662

source_name: Anterior Dentate Gyrus

value: Anterior Dentate Gyrus


title: WM989-5-ExpSample

description:
meltedData_heritabilityRun2_ExpSamples.tsv
full_WM989.csv

value: MemorySeq subclone


title: Patient43_normal

value: frontal

value: normal brain


title: RPB1658


title: Lgr5-DTReGFP heterozygous adult mouse number 71 ileum

value: Lgr5 heterozygous

value: Adult -2 month-old

value: Ileum


title: Patient42_tumor


title: Lgr5-DTReGFP heterozygous adult mouse number 71 duodenum

value: eGFP+ve


title: WM989-48-ExpSample


title: RPB1657


title: RPB1685


title: WM989-47-ExpSample


title: Lgr5-DTReGFP heterozygous intestinal SC E18.5 embryo 2 (HE n°3)

value: Whole Small Intestine

value: Stem cells


title: RPB1656


title: Patient42_normal

value: Glioblastoma


title: Lgr5-DTReGFP heterozygous intestinal SC E18.5 embryo 1 (HE n°1)


title: WM989-46-ExpSample


title: RPB1654


title: Patient39_tumor

value: parietal


title: Patient39_normal


title: WM989-45-ExpSample


title: RPB1759

value: Anterior Cingulate Cortex

value: Betamethasone


title: WM989-57-ExpSample


title: RPB1757

value: Singapore


title: RPB1664

value: Saline control


title: Patient29_tumor

value: F

value: temporal

value: brain tumor


title: WM989-43-ExpSample

value: MemorySeq subclone


title: Embryonic Lgr5-DTReGFP heterozygous intestinal SC pool 2

description:
litter 97 (8 embryos pooled)
E16.5_Lgr5_HE_pool_2


title: 4x0519

value: post-mortem heart


title: Embryonic Lgr5-DTReGFP (null) homozygous intestinal SC pool 1

description:
litter 85 (2 embryos pooled)
E16.5_Lgr5_KO_pool_1

value: Lgr5-null homozygous


title: WM989-44-ExpSample


title: Patient29_normal

value: normal brain


title: RPB1754


title: Embryonic Lgr5-DTReGFP heterozygous intestinal SC pool 1

description:
litter 85 (7 embryos pooled)
E16.5_Lgr5_HE_pool_1

value: Lgr5 heterozygous


title: Patient25_tumor

value: M

value: frontal


title: RPB1753


title: WM989-40-ExpSample


title: Embryonic Lgr5-DTReGFP (null) homozygous intestinal SC pool 2

description:
litter 97 (6 embryos pooled)
E16.5_Lgr5_KO_pool_2

value: Whole Small Intestine

value: Stem cells

value: eGFP+ve


title: RPB1752

value: Anterior Cingulate Cortex


title: Patient25_normal

value: Glioblastoma


title: WM989-4-ExpSample


title: Patient22_tumor


title: RPB1746

value: Betamethasone

value: Singapore


title: Patient22_normal

value: F


title: WM989-39-ExpSample


title: THZ531_rep1

city: Vienna

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM, Vienna

data_processing:
conversion and demultiplexing: IlluminaBasecallsToMultiplexSam to generate one bam file per lane from the data on the Illumina machine, IlluminaSamDemux to demultiplex the bam file into multiple samples (https://github.com/DanieleBarreca/picard)
trimming: Trimmomatic (version 0.32) using the following parameters: HEADCROP:13 ILLUMINACLIP:epignome_adapters_2_add.fa:2:10:4:1:true SLIDINGWINDOW:4:1 MAXINFO:16:0.40 MINLEN:18
alignment: STAR aligner version 2.5.2b
defining genes: genome-build GRCh38.p7, genome-build-accession NCBI:GCA_000001405.22. Additionally, sequences and annotations in FASTA and GTF format for SIRV Set 3 (SIRV Isoform Mix E0 and ERCCs, Cat. No 051) included in SIRV_Set3_Sequences_170612a (ZIP) were downloaded from https://www.lexogen.com/sirvs/download/
read counts files: htseq-count (version 0.11.2) from the HTSeq framework
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include raw read counts mapped to genes from the human genome and artificial "SIRVome"

source_name: chronic myelogenous leukemia (CML) cell line

growth_protocol: IMDM 10%FBS 1%P/S

extract_protocol:
Total RNA was extracted with the RNeasy mini kit (Qiagen 74106). To account for global differences in transcriptional output, an exogenous spike-in approach was employed, according to the manufacturer's protocol (SIRV-Set 3 Iso Mix E0 / ERCC from Lexogen, Cat. No 051). RNA amount was determined using the Qubit RNA HS Kit (Thermo, Q32852).
CORALL Total RNA-Seq Library Prep Kit (Lexogen, #095.24), poly-A enrichment.

treatment_protocol: KBM7 cells treated for 5h with DMSO, dCeMM-1, dCeMM-2, dCeMM-3, dCeMM-4 (10xEC50) and THZ531 (600nM). Triplicates per condition.

tag: cell line

value: KBM7 Cancer Cell Line

tag: disease

value: CML


title: THZ531_rep2


title: Hit8_rep3


title: Patient16_tumor

value: brain tumor


title: THZ531_rep3


title: RPB1724

value: Basolateral Amygdala


title: WM989-42-ExpSample

value: MemorySeq subclone


title: WM989-38-ExpSample


title: Hit8_rep2


title: Patient16_normal

value: normal brain


title: RPB1721


title: WM989-36-ExpSample


title: WM989-37-ExpSample


title: Patient10_tumor

value: parietal


title: Hit8_rep1


title: WT/WT_rep3

description: snRNA

value: Striatum

value: spiny projection neurons

tag: genotype

value: WT/WT


title: RPB1715


title: Hit4_rep3


title: Patient10_normal


title: WM989-34-ExpSample


title: WM989-17-Controls

value: Control/MemorySeq parental sample


title: Hit4_rep2


title: Patient7_tumor

value: M

value: frontal


title: WM989-33-ExpSample


title: RPB1694

value: Posterior Dentate Gyrus


title: WM989-35-ExpSample


title: Patient7_normal

value: Glioblastoma


title: RPB1696

value: Betamethasone

value: Singapore


title: Hit4_rep1

value: KBM7 Cancer Cell Line


title: RPB1726


title: WM989-32-ExpSample


title: WM989-31-ExpSample


title: Hit2_rep3

value: CML


title: RPB1690


title: RPB1684


title: Hit2_rep2


title: WM989-30-ExpSample


title: WM989-18-Controls


title: Hit2_rep1


title: Hit1_rep3


title: WM989-29-ExpSample


title: RPB1663

value: Anterior Dentate Gyrus


title: WM989-28-ExpSample


title: Hit1_rep2


title: WM989-26-ExpSample


title: RPB1660


title: RPB1691


title: WM989-25-ExpSample


title: Hit1_rep1


title: RPB1653


title: DMSO_rep3

value: DMSO


title: WM989-23-ExpSample

value: MemorySeq subclone


title: DMSO_rep2


title: WM989-24-ExpSample


title: Melanoma cells - G1 1K

city: Los Angeles

first: Enrique

last: Velazquez-Villarreal

address: 1450 Biggy Street

department: Translational Genomics

institute: USC

data_processing:
Paired-end reads were processed using version 1.0 of the Cell Ranger DNA Pipeline (10x Genomics)
The pipeline consists of barcode processing, alignment to the (hg19) genome and the identification of cell-associated barcodes, copy number calling is performed on each barcode separately after masking out regions of the genome with low mappability and normalizing for GC content. 1,475 barcodes were defined as cells, roughly all barcodes with greater than 1/10th the number of reads as the maximum per-barcode read count.
Clustering of single cell CNV data: single cell CNV calls were extracted from a BED file generated by the cellranger-dna pipeline for 1,373 cell barcodes.
Events were filtered to include those with a size >= 2Mbp and with a confidence score > 15. Events from different single cells were grouped together if they had identical copy number and shared 90% reciprocal overlap.
Next, events present in less than 5% of cancer cells were discarded. This analysis generated a binary CNV mutation matrix with 112 polymorphic events ranging in size from 2.1 to 147.6 Mbp.
Genome_build: GRCh37
Supplementary_files_format_and_content: DAPC_classification_of_single_cells.xlsx; CNV_events_by_cluster.xlsx; colo829_G1_1k_per_cell_summary_metrics.csv; colo829_G1_1k_cnv_data.h5; colo829_G1_1k_summary.csv; colo829_G1_1k_alarms_summary.txt; colo829_G1_1k_web_summary.html; CNV events by cluster includes frequency of each of the 114 CNV events that passed filters across the 11 clusters and 4 groups, the start and end headers are the median values of the edges shared across all single cells for that event; DAPC classification of single cells includes an assignment of each barcode to DAPC defined cluster and group; text files with summary per cell includes barcode, cell_id, total_num_reads, num_unmapped_reads, num_lowmapq_reads, num_duplicate_reads, num_mapped_dedup_reads, frac_mapped_duplicates, effective_depth_of_coverage, effective_reads_per_1Mbp, raw_mapd, normalized_mapd, raw_dimapd, normalized_dimapd, mean_ploidy, ploidy_confidence, is_high_dimapd and is_noisy.

source_name: Fibrobalst

extract_protocol:
COLO829 cells from ATCC (American Type Culture Collection) were cultured in their recommended media conditions at 37°C. Prior to FACS sorting, the cancer cell line was trypsinized, followed by inactivation with FBS and washed by centrifugation at 300g in 1X PBS with 0.04% BSA. Cells were counted and resuspended in recommended media at a final concentration of 1e6/mL in a FACS tube. 2 μL of Vybrant® DyeCycle™ Green stain was added to the cell suspension and incubated at 37°C for 30 minutes in the dark. Cells were then analyzed and sorted on a flow cytometer using 488 nm excitation and green emission gating on cells in the G1 phase of the cell cycle.
The Single-cell suspension was processed using Chromium Single-Cell CNV Solution (10x Genomics) as described in the user guide to generating a barcoded single-cell DNA library. single-cells were partitioned in a hydrogel matrix by combining with a CB polymer to form Cell beads (CBs) using a microfluidic chip. Post the first encapsulation, CBs are treated to lyse the encapsulated cells and denature the genomic DNA (gDNA). The denatured gDNA in the CB is then accessible to amplification and barcoding. A second microfluidic encapsulation step is required to partition the CB with 10x barcode Gel Beads (GBs) to generate an emulsion called GEMs. Immediately after barcoding and amplification, 10x barcoded fragments were pooled and attached to standard Illumina adaptors.
Sequencing libraries were quantified by qPCR before sequencing on the Illumina platform using NovaSeq S4 chemistry with 2x100 paired-end reads.

value: Skin

value: fibroblast

tag: age

value: 45 years


title: WM989-22-ExpSample

first: Arjun

last: Raj

address: 415 Curie Boulevard


title: RPB1720

value: Basolateral Amygdala

value: Saline control


title: RPB1665


title: WM989-20-ExpSample


title: DMSO_rep1


title: RPB1659


title: SC_CWL_7

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

hyb_protocol: Samples were hybridised to the Clariom S GeneChip microarray (Thermofisher UK) as per directions for the GeneChip WT Plus Reagent kit (Thermofisher UK). Overnight hybridisation to the Clariom S GeneChip took place at 45oC for 16 hours.

scan_protocol: After washing and staining as per directions for the  GeneChip WT Plus Reagent kit (Thermofisher UK) images were captured and cel files generated using the GeneChip Scanner 3000 and raw data converted to .CEL files using the Affymetrix GCOS Software (Thermofisher UK).

data_processing: The .CEL data were analysed using R/Bioconductor using an updated chip definition file (CDF) from the Brainarray resource based on Ensembl gene definitions (ENSG version 22.0.0). Raw microarray data were normalised using the SCAN method (Piccolo et al, 2012 DOI:10.1016/j.ygeno.2012.08.003). Normalised data were filtered using the UPC method (see Piccolo et al) with expression intensity and UPC filters were set at 0 and 0.5 respectively. Changes in differential expression were examined using empirical Bayes and a moderated t statistic implemented in the limma package with subject identifier as a blocking factor in linear modelling to account for the repeated measures structure (see section Additive Models and Blocking in the limma manual). Category enrichment analysis was carried out using the camera algorithm and the Broad Institute curated Hallmark Genesets collection. A FDR <5% was taken to indicate significant enrichment of a category.

source_name: Subcutaneous adipose tissue from weight losing cancer patient

label_protocol: Sense strand cDNA was generated, fragmented and labelled using the GeneChip WT Plus Reagent kit (Thermofisher UK) as per directions.

extract_protocol: Aliquots of adipose tissue were homogenised in Qiazol reagent (Qiagen, UK) using the BeadBeater instrument with 1.5mm ceramic beads (Qiagen, UK). Tissue aliquots were shaken at 5000Hz for 30s with 30s cooling on ice. This process was repeated 3 times or until no gross debris was visible. Samples were then spun at 5xg for 15mins at 4oC and the supernatant collected into fresh Eppendorf tubes.  RNA was isolated from adipose tissue samples using the Qiagen RNeasy lipid tissue kit (Qiagen UK) following the manufacturers directions.

treatment_protocol: Following surgical skin incision under general anaesthesia, biopsies of subcutaneous fat were taken from all patients at the start of the operation. Visceral fat was sampled from the greater omentum in cancer patients and perinephric fat from the transplant donors after the kidney had been excised. All samples were snap frozen in liquid nitrogen and stored at -80oC until analysis.

value: SubCut

tag: group

value: CWL

value: Male

tag: tumour

value: Gastric

tag: height(cm)

tag: weight(kg)

tag: weight loss %

tag: sk muscle area (cm2)

tag: visceral adipose area (cm2)

tag: subcutaneous adipose area (cm2)

tag: skeletal muscle density (hu)

tag: visceral adipose density (hu)

tag: subcutaneous adipose density (hu)

tag: skeletal muscle index


title: VIS_CWL_8

source_name: Visceral adipose tissue from weight losing cancer patient

tag: tissue

value: Visceral

tag: Sex

value: Oesophageal adenocarcinoma


title: SC_CWS_7

source_name: Subcutaneous adipose tissue from weight stable cancer patient

value: CWS


title: SC_CWL_8


title: SC_CWS_8


title: WM989-19-ExpSample

city: Philadelphia

institute: University of Pennsylvania

tag: treatment

tag: cell type


title: VIS_CWL_7

tag: age


title: WM989-18-ExpSample


title: VIS_CWL_6

tag: group


title: VIS_CWL_4

tag: tumour


title: VIS_CWS_8

source_name: Visceral adipose tissue from weight stable cancer patient

tag: height(cm)


title: WM989-16-ExpSample


title: WM989-15-ExpSample


title: WM989-14-ExpSample


title: WM989-1-ExpSample


title: WM989-11-ExpSample


title: SC_CWL_6

tag: weight(kg)


title: WM989-17-ExpSample


title: VIS_CTRL_8

source_name: Visceral adipose tissue from healthy control

value: CONTROL

tag: weight loss %


title: SC_CWL_5

value: Female

tag: sk muscle area (cm2)


title: sample 051-04 C.alb-spe T cells

city: Marseille

first: Pierre

last: Milpied

address: Parc Scientifique de Luminy, case 906

country: France

institute: Centre d'Immunologie de Marseille-Luminy (CIML)

description: For the CD154 (CD40L) expression assay, 10 to 20x106 PBMCs (at a final concentration of 10x106/mL) were stimulated for 3h at 37°C with 1µg/mL of synthesized peptides (20 amino acids in length with a 12 amino acid overlap; Synpeptide, China) spanning all of the Soluble Liver Antigen (SepSecs) sequences (53 SLA peptides; supplementary Table 3) or PepTivatorR Candida albicans MP65 (1µg/mL; peptides pools of 15 amino acids length with 11 amino acid overlap, Miltenyi Biotec, approximatively 93 peptides) in 5% human serum RPMI medium in the presence of 1µg/ml anti-CD40 (HB14, Miltenyi Biotec). After 3 hrs of specific peptide stimulation, PBMCs were first labeled with PE-conjugated anti-CD154 (5C8, Miltenyi Biotec) and CD154+ cells were then enriched using anti-PE magnetic beads (Miltenyi Biotec). After enrichment, cells were stained with PerCP-Cy5.5 anti-CD4 (RPA-T4, Biolegend), AlexaFluor700 anti-CD3 (SK7, Biolegend) and APC-Cy7 anti-CD45RA (HI100, Biolegend), and antigen-specific T cells were gated as CD3+CD4+CD45RA-CD154+ single live cells for single-cell sorting.

data_processing:
Fastq files were obtained from the sequencing facility (running Illumina NextSeq550 with HighOutput75cycles) after demultiplexing with bcl2fastq.
To generate single-cell UMI count matrices, we used a custom bioinformatics pipeline as described (Attaf et al. 10.3389/fimmu.2020.00216), relying on Drop-seq-tools v1.12 running STAR v2.5.3a and HTSeq v0.9.1.
Quality control was performed on each scRNA-seq batch independently to remove poor quality cells. Cells with less than 250 genes detected were removed. We further excluded cells with values below 3 median absolute deviations (MADs) from the median for UMI counts, for the number of genes detected, or for ERCC accuracy, and cells with values above 3 MADs from the median for ERCC transcript percentage, as described (Attaf et al., DOI: 10.3389/fimmu.2020.00216). The number of cells passing quality control, mean sequencing depth, and mean gene detection for each batch is shown in scRNAseqMetrics_SupplementaryTable_Geo.docx.
Genome_build: GRCh38 with additional artificial chromosome for 92 ERCC spike-in genes
Supplementary_files_format_and_content: csv files containing gene UMI counts (data file) and xlsx files containing additional cell-specific metadata (QC values, index sorting parameters, TCR parameters) for each filtered cell identified by a UniqueCellID.

source_name: peripheral blood

extract_protocol:
First, CD154+ memory CD4 T cells were sorted on BD FACSAriaII, one cell per well, in 96-well plates containing specific lysis buffer at the CRTI, Nantes. Plates were immediately frozen for storage at -80°C, and sent on dry ice to the Genomics core facility of CIML, Marseille, for further generating scRNAseq libraries with the FB5P-seq protocol as described (Attaf et al., DOI: 10.3389/fimmu.2020.00216). Briefly, mRNA reverse transcription (RT), cDNA 5’-end barcoding and PCR amplification were performed with a template switching (TS) approach. After amplification, barcoded full-length cDNA from each well were pooled for purification and library preparation.
For each plate, an Illumina sequencing library targeting the 5’-end of barcoded cDNA was prepared by a modified transposase-based method incorporating a plate-associated i7 barcode (Attaf et al., DOI: 10.3389/fimmu.2020.00216). Resulting libraries had a broad size distribution, resulting in gene template reads covering the 5’-end of transcripts from the 3rd to the 60th percentile of gene body length on average. As a consequence, sequencing reads cover the whole variable and a significant portion of the constant region of the TCRα and TCRβ expressed mRNAs, enabling assembly and reconstitution of TCR repertoire from scRNAseq data.
Cells were analyzed in three distinct scRNAseq experiments (scRNAseqMetrics_SupplementaryTable_Geo.docx). Libraries prepared with the FB5P-seq protocol were sequenced on Illumina NextSeq550 platform with High Output 75 cycles flow cells, targeting 5x105 reads per cell in paired-end single-index mode with the following configuration: Read1 (gene template) 67 cycles, Read i7 (plate barcode) 8 cycles, Read2 (cell barcode and Unique Molecular Identifier) 16 cycles.

tag: cell types

value: C.alb-specific memory CD4 T cells


title: SC_CWL_2

tag: visceral adipose area (cm2)

tag: subcutaneous adipose area (cm2)


title: sample 051-04 SLA-spe T cells

value: SLA-specific memory CD4 T cells


title: VIS_CWL_5

tag: skeletal muscle density (hu)

tag: visceral adipose density (hu)


title: SC_CTRL_8

source_name: Subcutaneous adipose tissue from healthy control

tag: subcutaneous adipose density (hu)

tag: skeletal muscle index


title: VIS_CWL_3

tag: tissue

tag: Sex


title: sample 018-14 C.alb-spe T cells


title: VIS_CWL_2


title: SC_CWL_4


title: SC_CWL_3


title: VIS_CWS_7


title: SC_CTRL_7


title: sample 004-05 C.alb-spe T cells


title: PD20_T

type: genomic

city: Honolulu

first: Maarit

middle: I

last: Tiirikainen

state: HI

address: 701 Ilalo St, Genomics Shared Resource

institute: UHCC

hyb_protocol: Illumina Infinium HD Methylation Assay

scan_protocol: Illumina Infinium HD Methylation Assay

data_processing: Illumina Genome Studio

source_name: Brain

label_protocol: Illumina Infinium HD Methylation Assay

extract_protocol: AllPrep DNA/RNA Mini kit (Qiagen)

value: brain

tag: age draw/autopsy

tag: time to autopsy (for t_brain)

tag: plant exp code (3=10+, 0=0 yrs)

tag: disease state

value: Parkinsons Disease


title: SC_CWS_6

tag: group

tag: age

tag: tumour

tag: height(cm)


title: VIS_CWS_6

tag: weight(kg)

tag: weight loss %

tag: sk muscle area (cm2)


title: PD18_T


title: PD19_B

source_name: Blood

value: blood


title: VIS_CTRL_6

tag: visceral adipose area (cm2)

tag: subcutaneous adipose area (cm2)

tag: skeletal muscle density (hu)


title: PD20_B


title: sample 018-14 SLA-spe T cells

tag: cell types


title: PD16_T

tag: tissue


title: PD18_B


title: sample 018-10 C.alb-spe T cells


title: sample 018-10 SLA-spe T cells


title: SC_CTRL_6

tag: Sex

tag: visceral adipose density (hu)

tag: subcutaneous adipose density (hu)

tag: skeletal muscle index


title: sample 004-05 SLA-spe T cells


title: sample 128-01 C.alb-spe T cells


title: PD15_T

tag: age draw/autopsy

tag: time to autopsy (for t_brain)

tag: plant exp code (3=10+, 0=0 yrs)

tag: disease state


title: PD16_B


title: sample 018-13 C.alb-spe T cells


title: PD17_T


title: sample 128-01 SLA-spe T cells


title: PD17_B


title: SC_CTRL_4

tag: group

tag: age

tag: tumour

tag: height(cm)


title: VIS_CTRL_7

tag: weight(kg)

tag: weight loss %

tag: sk muscle area (cm2)

tag: visceral adipose area (cm2)


title: SC_CTRL_5

tag: tissue

tag: subcutaneous adipose area (cm2)

tag: skeletal muscle density (hu)


title: VIS_CTRL_5

tag: Sex

tag: visceral adipose density (hu)

tag: subcutaneous adipose density (hu)


title: PD14_B

tag: age draw/autopsy

tag: time to autopsy (for t_brain)


title: 7.6 weeks old human placenta

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: 10x Genomics Chromium Single Cell Gene Expression data

data_processing:
The data was analyzed using the 10x Genomics Chromium Single Cell software suite (cellranger-3.0.2).
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the human reference (GRCh38: refdata-cellranger-GRCh38-3.0.0) and analyzed using "cellranger count".
Genome_build: GRCh38
Supplementary_files_format_and_content: cellranger generated unfiltered feature-barcode matrix file.

source_name: Single cells obtained from discarded and deidentified human first trimester placenta

extract_protocol:
Single cells were obtained from enzymatic digestion of human first trimester placenta. Cell viability and concentration were measured by Countess II FL Automated Cell Counter (Life Technologies) targeting ≥75% cell viability. The cell emulsification is performed with the 10X Chromium Controller using the Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 (10X Genomics 1000092) and Chromium Chip B Single Cell Kit (10X Genomics 1000074).
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).
Single Cell RNA-seq (10X Genomics Chromium Single Cell 3' v3)

value: Placenta


title: PD15_B

tag: plant exp code (3=10+, 0=0 yrs)

tag: disease state


title: sample 018-13 SLA-spe T cells

tag: cell types


title: sample 028-03 C.alb-spe T cells


title: VIS_CWS_4

tag: group

tag: age

tag: tumour

tag: skeletal muscle index


title: sample 028-03 SLA-spe T cells

description: For the CD154 (CD40L) expression assay, 10 to 20x106 PBMCs (at a final concentration of 10x106/mL) were stimulated for 3h at 37°C with 1µg/mL of synthesized peptides (20 amino acids in length with a 12 amino acid overlap; Synpeptide, China) spanning all of the Soluble Liver Antigen (SepSecs) sequences (53 SLA peptides) or PepTivator Candida albicans MP65 (1µg/mL; peptides pools of 15 amino acids length with 11 amino acid overlap, Miltenyi Biotec, approximatively 93 peptides) in 5% human serum RPMI medium in the presence of 1µg/ml anti-CD40 (HB14, Miltenyi Biotec). After 3 hrs of specific peptide stimulation, PBMCs were first labeled with PE-conjugated anti-CD154 (5C8, Miltenyi Biotec) and CD154+ cells were then enriched using anti-PE magnetic beads (Miltenyi Biotec). After enrichment, cells were stained with PerCP-Cy5.5 anti-CD4 (RPA-T4, Biolegend), AlexaFluor700 anti-CD3 (SK7, Biolegend) and APC-Cy7 anti-CD45RA (HI100, Biolegend), and antigen-specific T cells were gated as CD3+CD4+CD45RA-CD154+ single live cells for single-cell sorting.


title: TEAD4 knock Down HTS cell (replicate 2)

data_processing:
Illumina bcl2fastq2 conversion software used for basecalling.
reads were aligned using the STAR (2.6.1c) software.
raw read counts were obtained using RSEM-1.3.1
Genome_build: GRCh38.rel92
Supplementary_files_format_and_content: tab-delimited text files of raw count values for each Sample

source_name: cell line

growth_protocol: Human Throphoblast Stem (HTS) cells and TEAD4 knock down HTS cells were routinely cultured on collagen IV coated (5µg/ml) 6-well plate at a density of 0.5-1 million cells per well in 2 ml HTS medium (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 1.5 μg/ml L-ascorbic acid, 50 ng/ml EGF, 2 μM CHIR99021, 0.5 μM A83-01, 1 μM SB431542, 0.8 mM VPA and 5 μM Y27632) at 37°C in 5% carbon dioxide environment.

extract_protocol:
Total RNA from the HTS cells and TEAD4 knock down HTS cells were isolated using RNeasy Mini Kit (#74104) from Qiagen per the manufacturer’s protocol with on column DNase digestion.  RNA concentrations were quantified using a NanoDrop Spectrophotometer at a  wavelength of 260nm. Integrity of the total RNA samples was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
The total RNA fraction was processed by oligo dT bead capture of mRNA, fragmentation, reverse transcription into cDNA, end repair of cDNA, ligation with the appropriate Unique Dual Index (UDI) adaptors, strand selection and library amplification by PCR using the Universal Plus mRNA-seq +UDI library preparation kit (NuGEN 0508-08, 0508-32).


title: PD12_B


title: TEAD4 knock Down HTS cell (replicate 3)


title: PD13_B


title: PD11_B


title: VIS_CTRL_4

tag: height(cm)

tag: weight(kg)

tag: weight loss %

tag: sk muscle area (cm2)


title: VIS_CWS_5

tag: tissue

tag: visceral adipose area (cm2)

tag: subcutaneous adipose area (cm2)

tag: skeletal muscle density (hu)


title: PD11_T

tag: age draw/autopsy


title: PD13_T

tag: time to autopsy (for t_brain)


title: TEAD4 knock Down HTS cell (replicate 1)


title: siGL3 qDRIP-seq (HeLa + S2) 2

city: Stanford

first: Karlene

last: Cimprich

address: 318 Campus Drive

institute: Stanford University

description: HeLa cells were mixed with 1.3x10^6 S2 cells. Drosophila Schneider 2 (S2) cells were obtained from ThermoFisher Scientific and grown according to manufacturer’s instructions at 27℃ in Schneider’s Drosophila Medium (Gibco) containing 10% heat-inactivated FBS, 50 units penicillin G and 50 µg streptomycin sulphate per milliliter of medium.

data_processing:
Library strategy: qDRIP-seq
Base calling CASAVA v1.8.2
Reads were aligned to genome with bowtie2. The used reference genome was a concatenation of hg38 and dm6 without the alternative scaffolds
Reads were seperated into strands with unix processing tools, and were further seperated into those mapping to the human genome and those mapping to dm6
Reads processed into bedpe format using bedtools
Reads sorted and duplicate reads were removed using unix text processing tools
Genome_build: hg38 and dm6
Supplementary_files_format_and_content: Generate bigwig files using bedtools coverageBed and bedGraphToBigWig from UCSC

organism:
Drosophila melanogaster
Homo sapiens

source_name: HeLa + Drosophila S2

extract_protocol:
2x106 HeLa cells were resuspended in 1.6mL TE and lysed with 50 mL 20% SDS and 5 mL Proteinase K 20 mg/mL (Thermo Fisher Scientific) for 3 h at 37ºC. Synthetic RNA-DNA hybrid spike-ins (5 µL of a stock solution at 2.5 pM) were added to cells in TE buffer prior to lysis. For spike-in with Drosophila S2 cells, 1.3x106 S2 cells were mixed with 2x106 HeLa cells in TE prior to cell lysis to give a 1:1.5 S2:HeLa cell ratio, with the aim of obtaining ~10% of total sequencing reads from the Drosophila genome.
DNA libraries were prepared from 3 pooled technical replicate DRIPs per sample. While the DNA material from one IP (or less) is sufficient for successful library preparation, we found pooling IPs effective in minimizing technical variability due to sample handling in pilot experiments. DNA libraries were synthesized from ssDNA using the Accel-NGS 1S DNA library kit (Swift Biosciences, Ann Arbor, MI), according to the manufacturer's protocol. Using multiplexing adapters from the 1S Plus Set A Indexing Kit (Swift Biosciences), adapter-ligated DNA was amplified by PCR. For inputs 12 PCR cycles were used to amplify 1 ng of DNA, and for IP samples 13 PCR cycles were used on the equivalent amount of DNA from one IP reaction. Following PCR, DNA fragments 200-600 bp were retained by size selection using a 0.6X volume ratio of AMPure XP beads (Beckman Coulter)/sample followed by 1.0X ratio. Library DNA was analyzed on a Bioanalyzer DNA HS (Agilent, Santa Clara, CA) at the Stanford Protein and Nucleic Acid Facility, quantified by qPCR using NEBNext Library Quant Kit for Illumina (New England Biolabs), then pooled and sequenced on a HiSeq 4000 (Illumina, San Diego, CA) at the Stanford Genome Sequencing Service Center, using 2 × 151 bp sequencing.

tag: cell line

value: HeLa cells + S2 cells

tag: drug treatment

tag: exogenous treatment

value: Control siRNA for luciferase


title: Control HTS cell (replicate 3)


title: Control HTS cell (replicate 2)


title: PD10_B

tag: plant exp code (3=10+, 0=0 yrs)

tag: disease state


title: SC_CTRL_2

value: SubCut

tag: group

tag: Sex

tag: age

tag: tumour

tag: visceral adipose density (hu)

tag: subcutaneous adipose density (hu)


title: SC_CTRL_3

tag: tissue

tag: height(cm)

tag: weight(kg)

tag: weight loss %

tag: sk muscle area (cm2)

tag: skeletal muscle index


title: siGL3 qDRIP-seq input (HeLa + S2) 1

tag: cell line


title: siGL3 qDRIP-seq input (HeLa + S2) 2

tag: drug treatment


title: PD12_T

tag: age draw/autopsy

tag: time to autopsy (for t_brain)


title: Control HTS cell (replicate 1)


title: siGL3 qDRIP-seq (HeLa + S2) 1

tag: exogenous treatment


title: 6 weeks old human placenta


title: PD19_T

tag: plant exp code (3=10+, 0=0 yrs)

tag: disease state


title: PD9_T


title: SC_CWS_4

tag: group

tag: Sex

tag: age

value: Oesophageal SCC

tag: visceral adipose area (cm2)

tag: subcutaneous adipose area (cm2)

tag: skeletal muscle density (hu)


title: Tissue_206T

city: Nicosia

first: Areti

last: Moushi

address: Iroon Avenue 6, Agios Dometios

country: Cyprus

institute: Cyprus Insitute of Neurology and Genetics

hyb_protocol: Refer to the NanoString nCounter Assay System Manual

data_processing: Relative log expression normalization was conducted with R  DEseq2 and in house scripts

source_name: Thoracic Aortic Aneurysm

extract_protocol: Total RNA was extracted from samples

treatment_protocol: Affected Individuals

tag: individual

value: patient 206

tag: tissue

value: Excised aneurysmal tissue


title: Tissue_224T

scan_protocol: Refer to the NanoString nCounter Assay System Manual

value: patient 224


title: TEAD4 ChIP in HTS (replicate 3)

data_processing:
Basecalls performed using Illumina bcl2fastq2 Conversion Software v2.20
ChIP-seq reads were aligned to the GRCh38 genome assembly using Bowtie 2 version 2.3.4.3
peaks were called using MACS2 ver 2.1.2 with the following setting: -f BAMPE -g 2.9e9 -B -q 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: Peak calls in xls file genetated by MACS2

growth_protocol: Human Throphoblast Stem (HTS) cells and Tead4 knock down HTS cells were routinely cultured on collagen IV coated (5µg/ml) 6-well plate at a density of 0.5-1 million cells per well in 2 ml HTS medium (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 1.5 μg/ml L-ascorbic acid, 50 ng/ml EGF, 2 μM CHIR99021, 0.5 μM A83-01, 1 μM SB431542, 0.8 mM VPA and 5 μM Y27632) at 37°C in 5% carbon dioxide environment.

extract_protocol:
Nuclei were isolated from formaldehyde crosslinked HTS cells. Then Lysates were clarified from sonicated nuclei and chromatin fragments were immunoprecipitated with anti TEAD4 antibody.
The ChIP-Seq was performed using the Illumina NovaSeq 6000 Sequencing System at the University of Kansas Medical Center – Genomics Core (Kansas City, KS). Fragmented input and immunoprecipitated chromatin (20ng) was used to initiate the TruSeq ChIP Sample Prep Kit library preparation protocol (Illumina cat#IP-202-1012). The fragmented chromatin underwent end repair and 3’ adenylation prior to illumina indexed adapter ligation. Library sizing (target size – 320bp) was performed using the Sage Pippin Prep automated size selection system. PCR amplification of the sized library fraction was performed using Illumina adaptor specific priming with final library purification using KAPA Pure magnetic bead purification (KAPA cat#KK8002).  Following Agilent TapeStation 4200 QC for sizing of the library preparation and library quantification using the Roche Lightcycler96 with Roche FastStart Essential Green Master qPCR kit (Roche cat#06402712001 ) and KAPA Library Quant (Illumina) DNA Standards (KAPA cat#KK4903), the CHiP-Seq libraries were adjusted to a 2.125nM concentration and pooled for multiplexed sequencing.

tag: placenta

tag: chip antibody

value: TEAD4 (Abcam, ab58310)


title: Input DNA of HTS


title: Tissue_162T

label_protocol: Refer to the NanoString nCounter Assay System Manual

value: patient 162


title: Plasma_after surgery_224BA

value: Plasma collected after aneurysm surgery


title: VIS_CWL_1

value: Visceral

value: CWL

value: Female

tag: tumour

value: Gastric adenocarcinoma

tag: height(cm)

tag: weight(kg)

tag: weight loss %

tag: sk muscle area (cm2)

tag: visceral adipose density (hu)

tag: subcutaneous adipose density (hu)

tag: skeletal muscle index


title: VIS_CTRL_3

tag: group

value: CONTROL

tag: Sex


title: TEAD4 ChIP in HTS (replicate 1)


title: VIS_CTRL_2

value: CONTROl

value: Male

tag: age

tag: visceral adipose area (cm2)


title: SC_CWS_3

value: CWS

value: Oesophageal adenocarcinoma

tag: subcutaneous adipose area (cm2)

tag: skeletal muscle density (hu)


title: TEAD4 ChIP in HTS (replicate 2)

value: Placenta


title: PD9_B

tag: tissue

value: blood

tag: age draw/autopsy

tag: time to autopsy (for t_brain)

tag: plant exp code (3=10+, 0=0 yrs)

tag: disease state

value: Parkinsons Disease


title: Tissue_148T

tag: individual

value: patient 148

value: Excised aneurysmal tissue


title: Plasma_after surgery_206BA

value: patient 206


title: SC_CWS_2

value: SubCut

tag: tumour

value: Gastric

tag: height(cm)

tag: weight(kg)

tag: weight loss %


title: SC_CWS_1

tag: sk muscle area (cm2)

tag: visceral adipose density (hu)

tag: subcutaneous adipose density (hu)

tag: skeletal muscle index


title: PD14_T

value: brain


title: PD8_T


title: VIS_CTRL_1

value: Visceral

tag: group

tag: Sex

tag: age

tag: visceral adipose area (cm2)


title: Plasma_after surgery_162BA

value: patient 162

tag: tissue

value: Plasma collected after aneurysm surgery