title: KF06_P07

tag: histotype

value: WT


title: SUM-149PT_Parental_synergy_Vehicle_1

status: Public on Nov 02 2022

type: SRA

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

library_source: transcriptomic

data_processing:
Illumina Bcl2fastq v2.18
Reads were aligned to hg19 using STAR
For rpkm calculation cufflinks was used.
Genome_build: hg19
Supplementary_files_format_and_content: csv file of RPKM table

molecule: total RNA

organism: Homo sapiens

growth_protocol: For RNA-seq, cells were seeded in 100mm plates at 1x10^6 cells/plate for SUM149 and 7.5x10^5 cells/plate for FCIBC02, and treatments added after 24 or 48h respectively

extract_protocol:
Total RNA was extracted using the Rneasy Mini Kit
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits and the Kapa Biosystems library quantification kit

treatment_protocol: Treatments were added in 0.5ml/100mm-plate non-FBS containing DMEM/F12 and cells incubated for 72h

tag: cell line

tag: treatment

value: Vehicle


title: ALF029C

city: Melbourne

first: Katherine

last: Monaghan

state: Victoria

address: 30 Flemington Rd, Parkville

department: Research and Development

country: Australia

institute: CSL Limited

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data.
Sequenced reads were mapped to human reference genome GRCh38.p12 using star (v2.6.1)13 with default parameters except for the --quantMode TranscriptomeSAM setting.
Reads were summarized at the gene level using featureCounts tool from the Subread package (v1.6.4)14, in a strand-specific manner.

molecule: polyA RNA

source_name: Lung,IPF.Apex,Whole lung

extract_protocol:
RNA was extracted from whole lung tissue according to manufacturer’s protocol (Fibrous Tissue Mini kit, Qiagen #74704). RNA quality was verified with the Agilent 2100 Bioanalyzer platform (Agilent Technologies). Samples with RNA integrity numbers (RIN) over 6 were used for RNA sequencing.
cDNA libraries were prepared for sequencing using standard strand specific TrueSeq kits with ribosomal RNA and Globin mRNA depletion. At least 20 million 100 bp single-end reads were generated per sample using Illumina HiSeq 3000 (Illumina, California, USA) using standard protocols at the Australian Genome Research Facility (AGRF, Melbourne, Australia).

tag: tissue

value: Whole lung

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Right

tag: diseasenormal

value: Disease

tag: diseasegroup

value: IPF

tag: gender

value: M

tag: diagnosis

tag: age

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Ex-Smoker

tag: severity

value: Moderate

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group

value: Senior Adult (>=60)


title: ALF042B

source_name: Lung,ILD.Base,Whole lung

tag: tissue

tag: donorid

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Left

tag: diseasenormal

value: ILD

value: F

value: Never

value: Advanced


title: FC-IBC02_Paclitaxel_resistant_synergy_2e-7M_Paclitaxel_+_15uM_INC424_2

description: FC-IBC02_Paclitaxel_resistant_2e-7M_Paclitaxel_+_15uM_INC424_2

tag: cell line

tag: treatment

value: 2E-7M Paclitaxel + 15uM INC424


title: Pt06

city: SHANGHAI

first: Peng

last: Jin

state: SHANGHAI

address: No.197 RUIJIN ER RD

country: China

institute: SHANGH RUIJIN HOSPITAL

data_processing:
Trim-galore was employed to remove the adapter sequences.
The clean reads were aligned with STAR (v2.7.8) and quantified with HT-Seq (v0.13.5) using the GRCh38 human assembly
The differential expression assessment was conducted using the DESeq2 package.
Gene expression levels were normalized to Transcripts Per Kilobase of exon model per Million mapped reads (TPM) using a customed script.
Genome_build: GRCh38

source_name: APL

extract_protocol:
About 1μg of total RNA was used, and polyA-tailed mRNAs were purified from total RNA using oligo-dT attached magnetic beads. The purified library was quantified using a Qubit 4 Fluorometer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

tag: age

tag: gender

value: Male

tag: genotype

value: Low-risk

value: Untreated


title: ALF031B

value: Whole lung

value: Disease

tag: diseasegroup

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: HP

tag: smokingstatus

value: Severe


title: FC-IBC02_Paclitaxel_resistant_synergy_2e-7M_Paclitaxel_+_15uM_INC424_1

description: FC-IBC02_Paclitaxel_resistant_2e-7M_Paclitaxel_+_15uM_INC424_1


title: Pt07

tag: tissue

value: Female

value: Intermediate-risk


title: KF07_P07

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were processed and normalised using RMA with Transcriptome analysis Console software

label: biotin

source_name: Wilms tumor

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Thermo Fisher Scientific).

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: histotype

value: WT


title: KF05_P06


title: Pt05

value: High-risk


title: ALF015A

tag: donorid

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Left

tag: diseasenormal

value: IPF

value: M

value: NSIP

value: Ex-Smoker

tag: severity

value: Moderate

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: KF03_P06


title: Pt09

value: bone marrow

tag: age

tag: gender

value: Male

tag: genotype

tag: treatment


title: FC-IBC02_Paclitaxel_resistant_synergy_15uM_INC424_2

description: FC-IBC02_Paclitaxel_resistant_15uM_INC424_2

tag: cell line

value: 15uM INC424


title: KF01_P05

source_name: rhabdomyosarcomas

value: RMS


title: KF02_P06


title: KF04_P06


title: Pt04

tag: tissue

value: Low-risk

value: Untreated


title: KF00_P05

tag: histotype


title: FC-IBC02_Paclitaxel_resistant_synergy_15uM_INC424_1

description: FC-IBC02_Paclitaxel_resistant_15uM_INC424_1


title: Pt03

value: Female


title: ALF038A

value: Whole lung

tag: donorid

value: Right

value: Disease

tag: diseasegroup

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

value: Never

value: Advanced

value: Senior Adult (>=60)


title: FC-IBC02_Paclitaxel_resistant_synergy_2e-7M_Paclitaxel_2

description: FC-IBC02_Paclitaxel_resistant_2e-7M_Paclitaxel_2

value: 2E-7M Paclitaxel


title: FC-IBC02_Paclitaxel_resistant_synergy_2e-7M_Paclitaxel_1

description: FC-IBC02_Paclitaxel_resistant_2e-7M_Paclitaxel_1


title: KE96_P04


title: KE99_P05


title: Pt01

tag: age

value: High-risk


title: ALF024A

source_name: Lung,NDC.Apex,Whole lung

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Left

tag: diseasenormal

value: Normal

value: NDC

tag: gender

value: F

value: Unknown

tag: severity

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: KE97_P04

tag: histotype

value: RMS


title: FC-IBC02_Paclitaxel_resistant_synergy_Vehicle_2

tag: cell line

tag: treatment

value: Vehicle


title: KE98_P05


title: FC-IBC02_Paclitaxel_resistant_synergy_Vehicle_1


title: KE95_P04


title: LNCaP:C42 ST2457 #3

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

description: METTL3 inhibition

data_processing:
Contaminating adapters and low quality reads with phred scores <30 were removed using the Trimgalore wrapper for Cutadapt and Fastqc
The resultant quality controlled fastq files were aligned to the Ensembl annoted Human genome (GRCh38.83) using STAR
Gene expression was quantified using FeatureCounts
Genome_build: GRCh38.83
Supplementary_files_format_and_content: Tab delimited text file contain gene expression in counts

growth_protocol: Cells were maintained at 37C and 5% CO2 in phenol red containing RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin-glutamine, 2 mM L-Glutamine and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit with oncolumn DNase treatment
Illumina

treatment_protocol: Cells were treated with vehicle (DMSO), ST2457 (10µM) or R1881 (1nM) for 48 hours as indicated.

tag: cell type

value: Prostate cancer cells


title: LNCaP:C42 ST2457 #2

description: METTL3 inhibition


title: ALF045B

source_name: Lung,IPF.Base,Whole lung

tag: tissue

value: Whole lung

tag: donorid

value: Base

tag: diseasegroup

value: IPF

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Severe


title: ALF022A

source_name: Lung,ILD.Apex,Whole lung

tag: group

tag: lunglocation

tag: leftright

value: Right

tag: diseasenormal

value: Disease

value: ILD

tag: gender

tag: age

value: HP

tag: smokingstatus

value: Never

tag: severity

tag: fvcprebd perc

tag: dlco perc


title: LNCaP:C42 ST2457 #1

description: METTL3 inhibition

tag: cell type

tag: treatment


title: FC-IBC02_Parental_synergy_1e-8M_Paclitaxel_+_15uM_INC424_1

description: FC-IBC02_Parental_1e-8M_Paclitaxel_+_15uM_INC424_1

tag: cell line

value: 1E-8M Paclitaxel + 15uM INC424


title: FC-IBC02_Parental_synergy_1e-8M_Paclitaxel_+_15uM_INC424_2

description: FC-IBC02_Parental_1e-8M_Paclitaxel_+_15uM_INC424_2


title: ALF014C

source_name: Lung,CLAD.Apex,Whole lung

tag: tissue

tag: donorid

value: Apex

tag: diseasegroup

value: CLAD

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: dlco perc_corrected

tag: age group


title: Pt02

value: bone marrow

tag: age

tag: gender

value: Female

tag: genotype

value: Low-risk

value: Untreated


title: ALF021A

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

value: F

tag: volum ul

tag: processingdate

tag: diseasesubtype

tag: smokingstatus

tag: severity

value: Moderate

tag: fvcprebd perc

value: Senior Adult (>=60)


title: LNCaP:C42 Vehicle #3

description: Vehicle Control

tag: cell type

value: Prostate cancer cells

tag: treatment

value: vehicle


title: KE93_P03

tag: histotype

value: RMS


title: KE94_P04


title: LNCaP:C42 Vehicle #2

description: Vehicle Control


title: ALF031D

tag: tissue

value: Whole lung

tag: donorid

value: Base

value: Right

value: Disease

tag: diseasegroup

value: ILD

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

value: Severe

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: ALF029A

tag: group

tag: lunglocation

value: Apex

tag: leftright

tag: diseasenormal

value: IPF

tag: gender

value: M

tag: age

tag: volum ul

tag: processingdate

tag: diseasesubtype

value: Ex-Smoker


title: FC-IBC02_Parental_synergy_15uM_INC424_1

tag: cell line

tag: treatment

value: 15uM INC424


title: KE92_P03

tag: histotype


title: FC-IBC02_Parental_synergy_1e-8M_Paclitaxel_2

value: 1E-8M Paclitaxel


title: KE89_P02


title: LNCaP:C42 Vehicle #1

description: Vehicle Control

tag: cell type


title: ALF037B

tag: tissue

tag: donorid

tag: diseasegroup

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: smokingstatus

tag: severity

tag: fvcprebd perc


title: ALF032B

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

tag: gender

tag: age

tag: volum ul

value: Advanced

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: KE90_P03

tag: histotype


title: KE91_P03


title: FC-IBC02_Parental_synergy_15uM_INC424_2

tag: cell line

tag: treatment


title: ALF020A

tag: tissue

tag: donorid

value: Normal

tag: diseasegroup

value: NDC

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: processingdate

tag: diseasesubtype

value: Unknown


title: ALF047A

value: Whole lung

tag: group

tag: lunglocation

tag: leftright

tag: diseasenormal

tag: gender

tag: age

tag: smokingstatus

value: Never

tag: severity

tag: fvcprebd perc

value: Senior Adult (>=60)


title: 22Rv1 ST2457 #1

description: METTL3 inhibition

tag: cell type

value: Prostate cancer cells

tag: treatment


title: FC-IBC02_Parental_synergy_Vehicle_2

tag: cell line

value: Vehicle


title: FC-IBC02_Parental_synergy_1e-8M_Paclitaxel_1


title: ALF004D

tag: tissue

tag: donorid

value: Base

value: Disease

tag: diseasegroup

value: ILD

tag: diagnosis

tag: lungweight mg

tag: volum ul

value: NSIP

value: Severe

tag: dlco perc

tag: dlco perc_corrected

tag: age group


title: KE88_P02

tag: histotype

value: RMS


title: 22Rv1 ST2457 #2

description: METTL3 inhibition


title: 22Rv1 Vehicle #3

description: Vehicle Control

value: vehicle


title: KE87_P02


title: SUM149PT_PacliR_Pacli_72h_2

value: 2E-8M Paclitaxel


title: ALF040B

tag: group

tag: lunglocation

tag: leftright

value: Right

tag: diseasenormal

value: IPF

tag: gender

value: F

tag: age

tag: rnaconcentration ngul

tag: rin

tag: processingdate

tag: diseasesubtype


title: 22Rv1 Vehicle #2

description: Vehicle Control

tag: cell type

tag: treatment


title: SUM149PT_PacliR_Pacli_72h_1

tag: cell line


title: SUM149PT_PacliR_Control_72h_2


title: 22Rv1 Vehicle #1

description: Vehicle Control


title: 22Rv1 siMETTL3 R1881 #3

treatment_protocol: siRNA-mediated functional depletion of METTL3 was performed in vehicle (ethanol) and androgen (R1881) LNCaP:C42 and 22Rv1 cells grown in phenol red-free RPMI-1640 medium supplemented with 1% penicillin-streptomycin, 2mM L-Glutamine and 1 mM sodium pyruvate and 10% charcoal-stripped FBS. ON-TARGETplus siRNA–SMART pools for Human METTL3 (L-005170-02-0005) (GE DharmaconTM) and ON-TARGETplus non-targeting control siRNAs (#D-001810-10-05, GE DharmaconTM) were employed as negative controls. Cells were transfected using DharmaFECT 2 Transfection Reagent (GE DharmaconTM) and transfection was performed accoding to the manufacturer's instructions.

tag: genotype/variation

value: METTL3 depleted


title: ALF019A

tag: tissue

value: Whole lung

tag: donorid

value: Apex

value: Left

tag: diseasegroup

tag: diagnosis

tag: lungweight mg

tag: volum ul

tag: smokingstatus

tag: severity

value: Advanced

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected


title: FC-IBC02_Parental_synergy_Vehicle_1

value: Vehicle


title: 22Rv1 siMETTL3 R1881 #2

value: Prostate cancer cells


title: SUM149PT_DoxoR_Doxo_72h_2

value: 1E-7M Doxorubicin


title: ALF013B

source_name: Lung,NDC.Base,Whole lung

tag: group

tag: lunglocation

value: Base

tag: leftright

value: Unclassified

tag: diseasenormal

value: Normal

value: NDC

tag: gender

tag: age

tag: rnaconcentration ngul

tag: rin

tag: processingdate

value: Ex-Smoker

value: Unknown

tag: age group


title: SUM149PT_PacliR_Control_72h_1

tag: cell line

tag: treatment


title: SUM149PT_DoxoR_Doxo_72h_1


title: ALF004C

tag: tissue

tag: donorid

value: Disease

tag: diseasegroup

value: ILD

value: M

tag: diagnosis

tag: lungweight mg

tag: volum ul

tag: diseasesubtype

value: NSIP

tag: smokingstatus

value: Severe


title: 22Rv1 siMETTL3 R1881 #1

tag: cell type

tag: genotype/variation

value: METTL3 depleted


title: SUM149PT_DoxoR_Control_72h_2


title: ALF008C

value: Whole lung

tag: group

tag: lunglocation

value: Apex

tag: leftright

value: Right

tag: diseasenormal

value: IPF

tag: gender

tag: age

tag: severity

tag: fvcprebd perc

tag: dlco perc

tag: dlco perc_corrected

value: Senior Adult (>=60)


title: 22Rv1 ST2457 #3

description: METTL3 inhibition

value: Prostate cancer cells

tag: treatment


title: ALF042C

tag: tissue

tag: donorid

tag: diseasegroup

value: F

tag: diagnosis

tag: lungweight mg

tag: rnaconcentration ngul

tag: rin

tag: processingdate

value: Never

value: Advanced

tag: age group


title: ALF030A

tag: group

tag: lunglocation

tag: leftright

value: Left

tag: diseasenormal

value: Normal

value: NDC

tag: volum ul

tag: diseasesubtype

tag: smokingstatus


title: SUM149PT_DoxoR_Control_72h_1

tag: cell line

tag: treatment

value: Vehicle


title: MPA

city: Shanghai

first: Xiaojun

last: Chen

address: No. 419, Fangxie Road

institute: Obstetrics and Gynecology Hospital of Fudan University

data_processing:
The paired-end mode of Illumina hiseq platform was used to sequence multiple samples. According to the distribution characteristics that the low quality fraction of Illumina sequencing data was concentrated at the end, TRIM galore software was used to dynamically remove and splice sequence fragments and low-quality fragments from the 3 'end of sequencing data, and fastQC software was used to control and analyze the quality of preprocessed data.
STAR software was used to compare the preprocessed sequence with the reference genome sequence of the Homo species, which was generally downloaded to NCBI, Ensembl, UCSC database.
All samples used Htseq software to count the original sequence of known genes, the expression of the transcript was calculated by FPKM using Perl.
Supplementary_files_format_and_content: text files include RPKM values for each Sample ...

source_name: endometrial stromal cell

extract_protocol:
We collected stromal cells after treated with ethanol or 10μM MPA for 6h, and then Trizol method was used to extract RNA. RNA-Seq was performed by Genergy Bio-Technology (Shanghai, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: organ

value: uterus

tag: tissue

value: Endometrium

tag: cell type

value: endometrial stromal cell


title: KE85_P01

tag: histotype

value: RMS


title: CON


title: SUM149PT_Parental_Pacli_72h_2

value: 2E-8M Paclitaxel


title: 22Rv1 siMETTL3 Vehicle #1

tag: genotype/variation

value: METTL3 depleted


title: 22Rv1 siMETTL3 Vehicle #2


title: 22Rv1 siMETTL3 Vehicle #3


title: KE86_P02


title: 22Rv1 siScramble non-gene targetting R1881 #2

value: Non-gene targeting control


title: 22Rv1 siScramble non-gene targetting R1881 #3


title: SUM149PT_Parental_Doxo_72h_2

value: 1E-7M Doxorubicin


title: SUM149PT_Parental_Doxo_72h_1


title: KE84_P01


title: 22Rv1 siScramble non-gene targetting R1881 #1


title: KF38_P15

source_name: neuroblastomas

value: NB


title: KF41_P15


title: KE83_P01


title: KF37_P14


title: KF39_P15


title: SUM149PT_Parental_Control_72h_2


title: SUM149PT_Parental_Pacli_72h_1


title: 22Rv1 siScramble non-gene targetting Vehicle #3

value: Prostate cancer cells


title: KE82_P01


title: SUM149PT_Parental_Control_72h_1


title: FC-IBC02_PacliR_Pacli_72hr_2

value: 2.5E-7M Paclitaxel


title: KF33_P13


title: Breast Muscle_CCL 3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 ° C and hybridized on to a Agilent's chicken GXP_4x44k Array (AMADID: 049081) designed by Genotypic Technology Private limited, bangalore using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift normalization method .

organism: Gallus gallus

source_name: Breast Muscle

label_protocol: The samples for Gene expression were labeled using Agilent Quick Amp Kit, One-Color (Lot # 6275010). 600ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Birds were supplemented with PHF for 42 days. Liver and breast muscle were collected.

extract_protocol: RNA was extracted from the tissue using Qiagen Lipid tissue kit.

value: Breast Muscle

value: CCL treated


title: KF40_P15


title: KF34_P14


title: Breast Muscle_CCL 2

treatment_protocol: Birds were supplemented with PHF for 42 days. Liver and breast muscle were collected.


title: Breast Muscle_CCL 1


title: FC-IBC02_PacliR_Control_72hr_2


title: 22Rv1 siScramble non-gene targetting Vehicle #2


title: LNCaP:C42 siMETTL3 R1881 #3


title: 22Rv1 siScramble non-gene targetting Vehicle #1


title: LNCaP:C42 siMETTL3 R1881 #2


title: KF31_P13


title: KF27_P12


title: LNCaP:C42 siMETTL3 R1881 #1


title: KF36_P14


title: KF35_P14


title: KF28_P12


title: FC-IBC02_PacliR_Control_72hr_1


title: FC-IBC02_DoxoR_Doxo_72hr_2

value: 1E-6M Doxorubicin


title: LNCaP:C42 siMETTL3 vehicle #3

value: vehicle


title: KF32_P13


title: FC-IBC02_PacliR_Pacli_72hr_1


title: LNCaP:C42 siMETTL3 vehicle #2


title: KF30_P13


title: FC-IBC02_DoxoR_Doxo_72hr_1


title: LNCaP:C42 siMETTL3 vehicle #1


title: Breast Muscle_KP 1

value: PHF treated


title: Breast Muscle_KP 3


title: LNCaP:C42 siScramble non-gene targetting R1881 #3


title: FC-IBC02_DoxoR_Control_72hr_1

description: FC-IBC02_Doxorubicin-Resistant_Vehicle_72hr_01

value: Vehicle


title: Breast Muscle_KP 2


title: Breast Muscle_Negative Control 3

value: negative control


title: KF25_P11


title: KF22_P11


title: LNCaP:C42 siScramble non-gene targetting R1881 #2


title: Breast Muscle_Negative Control 2


title: Breast Muscle_Normal Control 3

value: normal control


title: LNCaP:C42 siScramble non-gene targetting R1881 #1


title: FC-IBC02_Parental_Pacli_72hr_2


title: FC-IBC02_Parental_Pacli_72hr_1


title: FC-IBC02_DoxoR_Control_72hr_2

description: FC-IBC02_Doxorubicin-Resistant_Vehicle_72hr_02


title: KF61_P20

source_name: hepatoblastomas

value: HB


title: LNCaP:C42 siScramble non-gene targetting Vehicle #3


title: FC-IBC02_Parental_Doxo_72hr_2


title: KF24_P11


title: KF23_P11


title: Breast Muscle_Negative Control 1


title: Breast Muscle_Normal Control 2


title: FC-IBC02_Parental_Doxo_72hr_1


title: LNCaP:C42 siScramble non-gene targetting Vehicle #2


title: Liver_CCL 3

source_name: Liver

value: Liver


title: KF26_P12


title: Liver_CCL 2


title: FC-IBC02_Parental_Control_72hr_2


title: FC-IBC02_Parental_Control_72hr_1


title: FCIBC02PR

data_processing:
Single-cell RNA-seq data generated by 10x genomics are preprocessed using the Cell Ranger (https://www.10xgenomics.com/) to obtain the UMI (unique molecular identifier) counts for each gene in each indexed cell type.
To get a reliable single cell transcriptome dataset, we first exclude the cells with log proportion UMIs from mitochondrial genes >4 median absolute deviations (MADs) above the median, and then exclude cells with log detected genes <4 MADs below the median.
For downstream analyses, the filtered data were normalized by using Seurat, after removing genes expressed in fewer than 10 cells {Lun, 2016 #8526}.
Batch 1 samples: Read 1 (R1) has a length of 26 bases corresponding to the 10x cell barcode's 16 bases, followed by the UMI's 10 bases. Read 2 (R2) has a length of 96 bases corresponding to biological RNA. Index 1 (I1) contains the sample index sequence information that is incorporated into the i7 index read (8-bp).
Batch 2 samples: Read 1 (R1) has a length of 28 bases corresponding to the 10x cell barcode's 16 bases, followed by the UMI's 12 bases. Read 2 (R2) has a length of 91 bases corresponding to biological RNA. Index 1 (I1) contains the sample index sequence information that is incorporated into the i7 index read (8-bp).
Genome_build: hg19
Supplementary_files_format_and_content: Rdata contains the raw UMI counts at the gene level

source_name: breast cancer cells

growth_protocol: Cells were grown in their respective medias and plated in 15cm plates and collected during exponential growth by trypsinization.

extract_protocol:
Cells were collected by trypsinization and processed according to the 10xGenomics sample preparation protocol (Chromium Single Cell 3’ v3 Reagent Kit, 10xGenomics).
Libraries were constructed according to the 10xGenomics sample preparation protocol (Chromium Single Cell 3’ v3 Reagent Kit, 10xGenomics).

value: FCIBC02PR_paclitaxel resistant

tag: batch

value: Batch 2

tag: index


title: Liver_CCL 1


title: SUM149PR

value: SUM149PR_paclitaxel resistant


title: Breast Muscle_Normal Control 1


title: KF59_P20


title: LNCaP:C42 siScramble non-gene targetting Vehicle #1

value: Non-gene targeting control


title: FCIBC02

extract_protocol:
Cells were collected by trypsinization and processed according to the 10xGenomics sample preparation protocol (Chromium Single Cell 3’ v2 Reagent Kit, 10xGenomics).
Libraries were constructed according to the 10xGenomics sample preparation protocol (Chromium Single Cell 3’ v2 Reagent Kit, 10xGenomics).

value: Batch 1


title: KF60_P20


title: KF57_P19


title: SUM149_Paclitaxel_resistant_Paclitaxel_pSTAT3

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using bwa.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

molecule: genomic DNA

growth_protocol: For pSTAT3 ChIP-seq, cells were seeded in several 150mm plates at 2.5x10^6 cells/plate for SUM149 and 2x10^6 cells/plate for FCIBC02, and treatments added after 24 or 48h respectively

extract_protocol:
Plates were double fixed in 1.5mM EGS/1% formadehyde, cells were lysed and nuclear extracts sonicated. An equivalent of 5x10^6 cells were sonicated in each tube and used for each ChIP. Samples were pre-cleared and pSTAT3 (CST 9131) was incubated overnight.
Libraries were prepared using ThruPLEX DNA-seq kit (Rubicon Genomics) according to manufacturer's protocol

treatment_protocol: Treatments were added in 1ml/plate non-FBS containing DMEM/F12 to exponentially growing cells in 150mm plates and incubated for 24h before fixation

value: 2E-8M Paclitaxel

tag: chip antibody


title: Liver_KP 2


title: SUM149_Paclitaxel_resistant_Vehicle_pSTAT3


title: KF55_P19


title: SUM149_PacliR_EpCAMpos_pac_2_S12

value: 5E-8M Paclitaxel

tag: epcam status

value: EpCAMpos


title: Liver_KP 3


title: Liver_KP 1


title: KF56_P19


title: SUM149_PacliR_EpCAMpos_pac_1_S11


title: SUM149_Parental_Paclitaxel_pSTAT3


title: KF58_P20


title: Liver_Negative Control 3


title: SUM149_PacliR_EpCAMpos_DMSO_1_S9


title: KF54_P19


title: FC-IBC02_Paclitaxel-Resistant_High_Paclitaxel

value: 1E-6M Paclitaxel


title: KF53_P18


title: SUM149_PacliR_EpCAMpos_DMSO_2_S10


title: FC-IBC02_Paclitaxel-Resistant_Vehicle


title: Liver_Normal Control 3


title: FC-IBC02_Doxorubicin-Resistant_High_Doxorubicin

value: 1E-6M Doxorubicin


title: SUM149_PacliR_EpCAMneg_pac_2_S8

value: EpCAMneg


title: KF52_P18


title: Liver_Negative Control 1


title: SUM149_Parental_Vehicle_pSTAT3


title: KF51_P18


title: Liver_Normal Control 2


title: Liver_Negative Control 2


title: Atg6D_Atg6D_3: Atg6D/Atg6D repeat 3

city: Worcester

first: Julie

last: Zhu

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-sequencing reads were aligned against fruit fly reference genome dm6 using Hisat2 (version 2.1.0)
The FPKM values were determined by Cufflinks (v2.2.1)
The differential expression was analzyed by limma with the FPKM values as input
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample obtained from cufflinks output

organism: Drosophila melanogaster

source_name: whole third instar larvae

growth_protocol: Larvae were raised on standard food at 25C

extract_protocol:
RNA was isolated from third instar wandering larvae using the Qiagen RNeasy Kit
RNA libraries were prepared for sequencing using strand specific standard Illumina protocols

tag: genetic bkg

tag: genotype

value: whole third instar larvae


title: SUM149_PacliR_EpCAMneg_pac_1_S7


title: FC-IBC02_Doxorubicin-Resistant_Vehicle

value: Vehicle


title: Atg6D_Atg6D_1: Atg6D/Atg6D repeat 1


title: Atg6D_3: Atg6D/+ repeat 3


title: Liver_Normal Control 1


title: Atg6D_Atg6D_2: Atg6D/Atg6D repeat 2


title: FC-IBC02_Parental_High_Paclitaxel


title: SUM149_PacliR_EpCAMneg_DMSO_1_S5


title: Atg6D_2: Atg6D/+ repeat 2


title: FC-IBC02_Parental_High_Doxorubicin


title: KF49_P17


title: KF50_P18


title: KF48_P17


title: U251 cells, shY1_rep2

first: Wei

middle: Kang

last: Wang

state: Shanghai

address: 320 Yueyang Road

department: State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences

institute: Chinese Academy of Sciences

data_processing:
We used trimmomatic(v0.39) to remove Illumina adapter and low quality sequence(setting: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36); Trimmed reads were mapped to hg38 genome using hisat2( v2.2.1) with default papameter; Reads were counted for each gene by htseq-count, and differential expression was performed with the R package edgeR (v3.28.1); Genes with low counts were filtered by keeping only genes with rowSums(cpm(y) > 1) > = (number of samples per group), and the logCPM from edgeR was converted to RPKM using the formula RPKM = 2^(logCPM-log2(gene length in kb); Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample; tab-delimited text file includes RPKM values for each sample.

growth_protocol: U251 cells were maintained in Dulbecco’s Modified Eagle’s medium supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNAs were isolated using TRIzol (Invitrogen, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: human Glioblastoma cell line U251

value: YB-1 KD


title: KF46_P17

value: HB


title: KF45_P16


title: FC-IBC02_Parental_Vehicle


title: Atg6D_1: Atg6D/+ repeat 1


title: U251 cells, shY1_rep1


title: SUM149_PacliR_EpCAMneg_DMSO_2_S6


title: U251 cells, shLuc_rep2

value: control KD


title: W118_3: w118 repeat 3

value: Atg6 wild type


title: FC-IBC02_Paclitaxel-Resistant_input

value: none (input)


title: KF47_P17


title: FC-IBC02_Parental_input


title: W118_2: w118 repeat 2


title: U251 cells, shLuc_rep1


title: W118_1: w118 repeat 1


title: FC-IBC02_Doxorubicin-Resistant_input


title: Patient Derived Xenograft model BCM-6257

status: Public on Nov 01 2022

city: Houston

first: Michael

middle: T

last: Lewis

state: TX

address: 1 Baylor Plaza N1210

department: Breast Center

institute: Baylor College of Medicine

description: RNAseq of human TNBC tumor tissue graft on mouse mammary fat pad

data_processing:
Raw reads were split into human/epithelial (graft) and murine/stromal (host) reads using Xenome v1.0.1
Human and Mouse reads were aligned to hg38 and mm10 reference genomes respectively using RSEM/STAR v2.5.3a_modified
The above STAR run was run internally by rsem-calculate-expression (RSEM v1.2.31), which then quantified transcripts and genes, producing isoform and gene level results.
Genome_build: hg38/mm10
Supplementary_files_format_and_content: A matrix file was generated using expected counts values from RSEM results. Each row represents a gene and each column represents a xenograft model

organism:
Homo sapiens
Mus musculus

source_name: Patient-Derived Xenograft

extract_protocol:
PDX tumor were harvested from mice and trimmed of excess fat pad tissue. Representative tumor fragments were snap frozen in liquid nitrogen. Tumor was homogenized and RNA extracted using the RNeasy Mini Kit from Qiagen.
NuGEN Ovation RNA-Seq v2 Kit (protocol p/n 7102, reagent kit p/n 7102-08) along with ThermoFisher’s ERCC RNA Spike-In Control Mixes Protocol (publication number 4455352, rev. D) and the Illumina TruSeq DNA-Seq library preparation (protocol p/n 15005180 Rev. C, June 2011, reagent kit p/n FC-121-2001) protocolss

treatment_protocol: Not applicable

value: Human breast tumor tissue graft on mouse mammary fat pad

tag: tumor subtype

value: human TNBC tumor

tag: strain

value: SCID/Bg mouse host

value: untreated


title: Patient Derived Xenograft model BCM-5998

extract_protocol:
PDX tumor were harvested from mice and trimmed of excess fat pad tissue. Representative tumor fragments were snap frozen in liquid nitrogen. Tumor was homogenized and RNA extracted using the RNeasy Mini Kit from Qiagen.
NuGEN Ovation RNA-Seq v2 Kit (protocol p/n 7102, reagent kit p/n 7102-08) along with ThermoFisher’s ERCC RNA Spike-In Control Mixes Protocol (publication number 4455352, rev. D) Illumina TruSeq DNA-Seq library preparation (protocol p/n 15005180 Rev. C, June 2011, reagent kit p/n FC-121-2001) protocols


title: Patient Derived Xenograft model BCM-7441

description: RNAseq of human ER+ tumor tissue graft on mouse mammary fat pad

value: human ER+ tumor


title: Patient Derived Xenograft model BCM-9161


title: Patient Derived Xenograft model BCM-5471

extract_protocol:
PDX tumor were harvested from mice and trimmed of excess fat pad tissue. Representative tumor fragments were snap frozen in liquid nitrogen. Tumor was homogenized and RNA extracted using the RNeasy Mini Kit from Qiagen.
NuGEN Ovation RNA-Seq v2 Kit (protocol p/n 7102, kit p/n 7102-08) along with ThermoFisher’s ERCC RNA Spike-In Control Mixes Protocol (publication number 4455352, rev. D) Rubicon ThruPlex DNA-Seq (protocol: QAM-108-002, kit p/n R400428) library preparation protocols


title: Patient Derived Xenograft model BCM-5097


title: Patient Derived Xenograft model BCM-4272

extract_protocol:
PDX tumor were harvested from mice and trimmed of excess fat pad tissue. Representative tumor fragments were snap frozen in liquid nitrogen. Tumor was homogenized and RNA extracted using the RNeasy Mini Kit from Qiagen.
Total RNA was extracted from PDX samples and 10ng was used to generate and amplify whole transcriptome cDNA (NuGen Ovation v2, NuGen Technologies). Illumina TruSeq DNA-Seq library was quantified with the Kapa qPCR Library Quantitation Kit (Kapa)


title: KF44_P16


title: Patient Derived Xenograft model BCM-4913


title: Patient Derived Xenograft model BCM-4664


title: Patient Derived Xenograft model BCM-4195


title: Patient Derived Xenograft model BCM-4013


title: Patient Derived Xenograft model BCM-4175


title: KF42_P16


title: Patient Derived Xenograft model BCM-3936


title: KF43_P16


title: Patient Derived Xenograft model BCM-3904


title: Patient Derived Xenograft model BCM-3887


title: Patient Derived Xenograft model BCM-3963

description: RNAseq of human HER2+ tumor tissue graft on mouse mammary fat pad

value: human HER2+ tumor


title: Patient Derived Xenograft model BCM-3807


title: Patient Derived Xenograft model BCM-3613


title: Patient Derived Xenograft model BCM-3611


title: Patient Derived Xenograft model BCM-4888

description: RNAseq of human ER+/HER2+ tumor tissue graft on mouse mammary fat pad

value: human ER+/HER2+ tumor


title: Patient Derived Xenograft model BCM-3204


title: Patient Derived Xenograft model BCM-3277


title: Patient Derived Xenograft model BCM-3469


title: Patient Derived Xenograft model BCM-3107


title: Patient Derived Xenograft model BCM-2665


title: Patient Derived Xenograft model BCM-3143


title: Patient Derived Xenograft model BCM-0002

extract_protocol:
PDX tumor were harvested from mice and trimmed of excess fat pad tissue. Representative tumor fragments were snap frozen in liquid nitrogen. Tumor was homogenized and RNA extracted using the RNeasy Mini Kit from Qiagen.
NuGEN Ovation RNA-Seq v2 Kit (protocol p/n 7102, reagent kit p/n 7102-08) along with ThermoFisher’s ERCC RNA Spike-In Control Mixes Protocol (publication number 4455352, rev. D) and the Illumina TruSeq DNA-Seq library preparation (protocol p/n 15005180 Rev. C, June 2011, reagent kit p/n FC-121-2001) protocols


title: Patient Derived Xenograft model BCM-2147


title: D29

city: Jena

first: Emanuel

last: Barth

address: Leutragraben 1

department: Bioinformatics Core Facility FSU Jena

country: Germany

institute: Friedrich Schiller University Jena

data_processing:
RA2 adapter sequences (5’-TGGAATTCTCGGGTGCCAAGG) of the TruSeq small RNA preparation kit were clipped from all reads, using cutadapt (version 2.0), and all reads shorter than 15 bp or with a mean quality lower than 20 were removed
Mapping was performed using TopHat2 (version 2.1.1) with standard parameters onto the human reference genome (Ensembl release 98)
For counting, featureCounts (version 1.6.3) with the parameters -M, -O 0.5 was used to count reads for the mature miRNA annotations of each human pre-miRNA separately.
Assembly: GRCh38 (Ensembl release 98)
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: placenta

extract_protocol:
Total RNA was isolated using a mirVana™ miRNA Isolation Kit (cat. No. AM1561; Invitrogen), according to the manufacturer’s protocol. Approximately 100 mg placenta tissue per sample was transferred to a Medicon disposable for biological sample disaggregation (cat. No. 340591; BD Biosciences, Franklin Lakes NJ, USA) containing 1 ml of lysis buffer (provided in the kit) and processed in a Medimachine (Dako; Jena, Germany) for 20 s.
The small RNA libraries were created using Illumina’s small RNA sample preparation protocol (TruSeq Small RNA Sample Prep Kits; Illumina, San Diego, CA, USA)

treatment_protocol: Tissue samples (≤ 0.5 cm in any single dimension) were taken from central areas of control placentas and adherent tissue in PAS samples. Samples were collected immediately after delivery and washed with isotonic saline solution to remove excess blood. For RNA analysis, samples were placed in 5 mL of RNA later (cat. No. AM7021; Invitrogen Life Technologies, Darmstadt, Germany) overnight and then stored in cryotubes at -80 °C until RNA extraction.

value: placenta

tag: condition

value: NP


title: D49


title: D32


title: D34


title: D108

value: PA


title: D105


title: D101


title: MHCC-97H cells ,L4, 24Hours

city: Nantong

first: Cheng

last: Gao

address: 20 Xisi Road

institute: Affiliated Hospital of Nantong University

data_processing:
The quality of the original sequencing data was evaluated by FastQC. The relatively accurate and effective data are obtained by mass shearing with Trimmatic.
Use HISAT2 to compare the valid data of the sample to the reference genome, and then count the mapping information. RSeQC was used to analyze the redundant sequence and inserted fragment distribution according to the comparison results.
Qualimap was used for homogeneity distribution check and genome structure distribution analysis according to the comparison results. The statistical analysis of gene coverage and the distribution of sequencing sequences on chromosomes were performed using BEDTools.
Put the genome mapping results of all data together, assemble them with StringTie, and then compare them with known gene models with GffCompare to find new transcription regions.
Assembly: GRCh38
Supplementary files format and content: count, tpm, FPKM

source_name: liver

growth_protocol: MHCC-97H cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was collected with RNAeasy ™ Animal RNA Extraction Kit (Centrifugal Column, beyotime). 1.0 ug total RNA was used to construct sequencing library.

treatment_protocol: MHCC-97H cells treated with various doses of lenvatinib or DMSO for 24 hours.

value: liver

value: epithelioid cells

value: 100 μM lenvatinib for 24 hours


title: Patient Derived Xenograft model BCM-3561


title: MHCC-97H cells ,L3, 24Hours

value: 80 μM lenvatinib for 24 hours


title: MHCC-97H cells ,L1, 24Hours

value: 40 μM lenvatinib for 24 hours


title: human, Semitendinosus, 01, scRNA-seq

city: Halifax

first: Adam

last: Johnston

state: NS

address: 1344 Summer Street

department: Medical Neuroscience

country: Canada

institute: Dalhousie University

library_source: transcriptomic single cell

data_processing:
Sequencing of cDNA libraries were performed on Illumina HiSeq 2500 using single-end reads of 91 bp length.
Raw reads were filtered and aligned to GRCh38 human genome assembly, followed by UMI counting and gene expression matrix creation using the cellranger analysis suite (10x Genomics).
Gene expression matrices were analyzed in python 3.7.12 using the scanpy library (1.8.2). Predicted doublets were first removed from the raw data matrix using scrublet. Additionlly, any cells with UMI counts of less than 450 or more than 15000, total genes of less than 250 or greater than 4000, or with greater than 15% mitochondrial genes removed.
The gene expression matrix was first normalized by read depth and then log-transformed, followed by principal component analysis using the top 2000 most variable genes and neighborhood graph construction. Leiden clustering (resolution 0.7) was performed on the neighborhood graph, and clusters were visualized using the uniform manifold approximation and projection method. Significantly differentially expressed genes between clusters were deterined by the Wilcoxon rank sum test and Benjamini-Hochberg correction.
Assembly: GRCh38
Supplementary files format and content: processed_humanSKM.h5ad.gz: processed scanpy object containing clustering result, cluster annotations, and normalized gene expression.
Supplementary files format and content: matrices.tar.gz: gzipped tarball of cellranger output gene expression matrices (raw and filtered) in market exchange (MEX) format.

source_name: Semitendinosus muscle

extract_protocol:
Semitendinosus muscle from consenting young patients (n = 5; 2 males, 3 females, mean age = 23.4 years) undergoing routine orthopedic surgery for anterior cruciate ligament repair was immediately placed into preservation media (20% FBS in DMEM) following biopsy and transported to the laboratory for immediate single-cell analysis. Upon arrival, muscle sections were washed with PBS, any associated tendons, ligaments, adipose tissue, and blood vessels removed, and tissue weighed. Muscle was then mulched for ~5 mins in a few drops of HBSS using fine surgical scissors. Dissociation media consisting of collagenase D (10 mg/mL, Roche), and 2.4 U/mL dispase II (Sigma) was then added to the samples and the samples were incubated at 37°C for 45 minutes, with periodic agitation. Ten volumes of PBS were added, and the cell-containing solution was filtered through a 70 µm strainer, and centrifuged at 1100 x g for 10 mins. RBCs were lysed and myofiber debris removed using commercially available kits (Qiagen, 158904, Miltenyi Biotec, 130109398, respectively) as per the manufacturer's instructions. Trypan blue viability tests (VWR, K940) were performed on all samples and a minimum of 80% of the cells in each sample were found to be viable. Cells were then fixed in ice-cold methanol for 15 minutes, and stored at -80°C.
Cells were recoved from methanol by centrifugation at 1000 x g for 5 mins at 4°C , and then rehydrated using a wash-resuspension buffer, consisting of 0.04% BSA, 1mM DTT, and 0.2 U/µL RNAse inhibitor in a 3x saline-sodium citrate buffer (in nuclease-free water). All samples were then combined and loaded into the 10x Chromium controller and scRNA-seq performed.

value: Semitendinosus muscle

value: Mononuclear cells

tag: developmental stage

value: young adult


title: MHCC-97H cells ,NC1, 24Hours

tag: cell line

value: DMSO for 24 hours


title: MHCC-97H cells ,NC4, 24Hours

tag: treatment


title: MHCC-97H cells ,NC3, 24Hours


title: RNA Day_26_R1881_2

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

data_processing:
Sequenced libraries were processed with deepTools, using STAR, for trimming and mapping, and featureCounts to quantify mapped reads. Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 to generate normalized read counts to visualize and cluster as heatmaps using pheatmap and determine differentially expressed genes with greater than 2-fold change and lower than 0.01 adjusted p value. Gene set enrichment analysis was performed using fGSEA.
Assembly: hg38
Supplementary files format and content: Genomic tracks as BigWig files

source_name: LNCaP

extract_protocol:
RNA was extracted using Qiagen RNAeasy Kit.
Purified RNA was sent to Admera Health who performed library preparation with polyA selection, sequencing on the Illumina HiSeq 2500 with read length configuration of 2x150bp with 60 million reads per sample

value: LNCaP

tag: time point

value: Day 26


title: MHCC-97H cells ,NC2, 24Hours

tag: tissue


title: RNA Day_26_R1881_1

tag: cell type


title: RNA Day_26_Veh_1

value: Vehicle


title: RNA Day_5_R1881_1

value: Day 5


title: RNA Day_5_R1881_2


title: RNA Day_26_Veh_2


title: RNA Day_5_Veh_2


title: D74


title: D80


title: H3K27ac ChIP-seq, RANKL, Replicate 2

city: Seoul

first: Kibyeong

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

data_processing:
ChIP-seq read files were first quality-checked with Fastqc v0.11.9.
If necessary, adapter sequences were trimmed with Skewer v0.2.2.
The reads were then mapped to hg19 with Bowtie2 v2.3.5.1, and further filtered and position-sorted with Samtools v1.10.
The ChIP-seq peak calls were performed with HOMER v4.11 with histone style option.
Assembly: hg19
Supplementary files format and content: gzip-compressed files containing HOMER peak call results

source_name: Blood

growth_protocol: Monocytes were obtained from peripheral blood using anti-CD14 magnetic beads. Monocyte-derived osteoclast precursors (OCPs) were obtained by culturing for 1 day with 20 ng ml-1 of M-CSF in a-MEM medium supplemented with 10 % fetal bovine serum.

extract_protocol:
Cells were crosslinked, quenched and pelleted. The crosslinked cells were lysed with lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 and 0.25% Triton X-100) with protease inhibitors. The lysed samples were sonicated using a Bioruptor (Diagenode).
One percent of sonicated cell extracts was saved as input. Precleared extracts were incubated with H3K27ac antibody (ab4729) overnight at 4 °C. Antibody-bound agarose beads were washed and DNA was eluted. Cross-links were reversed by overnight incubation at 65 °C. RNA and protein were digested, and DNA was purified with ChIP DNA Clean & Concentrator (Zymo Research). 10 ng of purified immunoprecipitated DNA per sample was ligated with adaptors, and 100–300 bp DNA fragments were purified to prepare DNA libraries using Illumina TruSeq ChIP Library Prep Kit.

value: Blood

value: Osteoclast Precursor Cells

value: M-CSF + RANKL


title: D36

value: placenta

value: NP


title: H3K27ac ChIP-seq, RANKL, Replicate 1


title: MHCC-97H cells ,L2, 24Hours

value: liver

value: epithelioid cells

value: 60 μM lenvatinib for 24 hours


title: Strand-Specific Nuclear RNA, RANKL, Replicate 2

description: Nuclear RNA

data_processing:
Low-quality reads and adapter sequences were assessed with Fastqc v0.11.9, and filtered out with Skewer v0.2.2.
The filtered reads were then aligned to hg19 genome with STAR v2.7.3a with default parameters. The resulting alignment files were sorted by positions.
From alignment files, strand-specific bigWig files were generated with Bedtools genomecov (v2.27.1) and bedGraphToBigWig v4.
Assembly: hg19
Supplementary files format and content: tab-delimited matrix containing CPM-normalized counts

extract_protocol:
Nuclear RNA was extracted using RNeasy mini kit (Qiagen).
True-seq sample preparation kits (Illumina) were used to generate libraries with multiplexed barcode adaptors.

value: Osteoclast Precursor Cell


title: H3K27ac ChIP-seq, RANKL, BET Inhibitor-Treated

value: M-CSF + RANKL + IBET


title: H3K27ac ChIP-seq, Control, Replicate 2

value: M-CSF


title: H3K27ac ChIP-seq, Control, BET Inhibitor-Treated

value: M-CSF + IBET


title: H3K27ac ChIP-seq, Control, Replicate 1


title: Strand-Specific Nuclear RNA, RANKL, Replicate 1

description: Nuclear RNA


title: Strand-Specific Nuclear RNA, Control, Replicate 2

description: Nuclear RNA


title: Strand-Specific Nuclear RNA, Control, Replicate 1

description: Nuclear RNA


title: RNA_MCSF

data_processing:
Low-quality reads and adapter sequences were assessed with Fastqc v0.11.9, and filtered out with Skewer v0.2.2.
The filtered reads were then aligned to hg19 genome with STAR v2.7.3a with default parameters. The resulting alignment files were sorted by positions.
From alignment files, strand-specific bigWig files were generated with Bedtools genomecov (v2.27.1) and bedGraphToBigWig v4.
Read count tables were generated with FeatureCounts v2.0.0.
Assembly: hg19
Supplementary files format and content: tab-delimited text files containing CPM-normalized counts

source_name: joint synovium

extract_protocol:
Synovial fluid was harvested from donors, from which CD14+ synovial monocytes were sorted with flow cytometry.
True-seq sample preparation kits (Illumina) were used to generate libraries with multiplexed barcode adaptors.

value: joint synovium

value: synovial CD14+ cells


title: RNA_RA_2


title: RNA_RA_1


title: ChIP-seq, RNA polymerase II, RANKL, replicate 2

data_processing:
ChIP-seq read files were first quality-checked with Fastqc v0.11.9.
If necessary, adapter sequences were trimmed with Skewer v0.2.2.
The reads were then mapped to hg19 with Bowtie2 v2.3.5.1, and further filtered and position-sorted with Samtools v1.10.
The ChIP-seq peak calls were performed with HOMER v4.11 default parameters.
Peak files were generated with HOMER.
Assembly: hg19
Supplementary files format and content: gzip-compressed files containing HOMER peak call results

extract_protocol:
Cells were crosslinked, quenched and pelleted. The crosslinked cells were lysed with lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 and 0.25% Triton X-100) with protease inhibitors. The lysed samples were sonicated using a Bioruptor (Diagenode).
One percent of sonicated cell extracts was saved as input. Precleared extracts were incubated with RNA polymerase II antibody (MMS-126R) overnight at 4 °C. Antibody-bound agarose beads were washed and DNA was eluted. Cross-links were reversed by overnight incubation at 65 °C. RNA and protein were digested, and DNA was purified with ChIP DNA Clean & Concentrator (Zymo Research). 10 ng of purified immunoprecipitated DNA per sample was ligated with adaptors, and 100–300 bp DNA fragments were purified to prepare DNA libraries using Illumina TruSeq ChIP Library Prep Kit.

tag: antibody

value: RNA polymerase II


title: ATAC-seq, RANKL, replicate 2

data_processing:
ATAC-seq read files were first quality-checked with Fastqc v0.11.9.
If necessary, adapter sequences were trimmed with Skewer v0.2.2.
The reads were then mapped to hg19 with Bowtie2 v2.3.5.1, and further filtered and position-sorted with Samtools v1.10.
The ATAC-seq peak calls were performed with HOMER v4.11 default parameters.
Peak files were created with HOMER.
Assembly: hg19
Supplementary files format and content: gzip-compressed file containing HOMER peak call results

extract_protocol:
To prepare nuclei, 50,000 cells were spun at 500g for 5 min. Cells were lysed with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Remaining nuclei were spun at 500g for 10 min in a refrigerated centrifuge.
The nuclei pellet was suspended in the transposase reaction mix (Illumina). The samples were purified with Qiagen MinElute kit. Library fragment amplification was done with 1× NEB next PCR master mix and custom Nextera PCR primers. The libraries were purified with Qiagen PCR cleanup kit. Libraries were amplified for a total of 10–13 cycles.


title: ChIP-seq, RNA polymerase II, control, replicate 1


title: ChIP-seq, RNA polymerase II, control, replicate 2


title: RNA Day_5_Veh_1

value: LNCaP

value: Vehicle


title: ChIP-seq, RNA polymerase II, RANKL, replicate 1

value: Blood


title: ATAC-seq, RANKL, replicate 1

value: Osteoclast Precursor Cells


title: ATAC-seq, RANKL, replicate 3

value: M-CSF + RANKL


title: ATAC-seq, control, replicate 1


title: proliferating NHEK siIRX4

city: Irvine

first: Jefferson

middle: K

address: UC Irvine

institute: UC Irvine

data_processing:
Read alignment was preformed using Bowtie2, and Deseq2 was used to identify differentially expressed genes. Gene ontology was conducted using Metascape
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each Sample

source_name: cultured primary cell

extract_protocol:
Normal Human Epidermal Keratinocytes (NHEK) were obtained from donor neonatal foreskin and grown in Keratinocyte Serum Free Media supplemented with Epidermal Growth Factor and Bovine Pituitary Extract (Life Technologies). Individual Dharmacon on-TARGETplus siRNAs [negative control (4390843), IRX2 (s45799, s45801), IRX3 (s35710, s35712), IRX4 (s55542, s27096), IRX5 (s20056, s20054)] were validated and siRNAs with at least 70% knockdown efficiency were pooled. 30nM pooled siRNAs were transfected into semi-confluent monolayers with Lipofectamine RNAi Max (Life Technologies) in OptiMEM medium. Twelve hours after transfection, 1.8mM Ca2+ was added into the growth medium to induce differentiation. RNA lysate was collected 72 hours after transfection.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
RNA quality was determined with Aglient Bioanalyzer; only samples with RNA Integrity Number > 8 were used. Library preparation with Illumina TrueSeq library preparation kit and single end Illumina HiSeq 2500 sequencing was performed at the University of California, Irvine High Throughput Genomics Facility.

value: cultured primary cell

value: proliferating NHEK

tag: sirna


title: proliferating NHEK siIRX5


title: proliferating NHEK siIRX2


title: proliferating NHEK negative control

value: negative control


title: diff NHEK siIRX4

data_processing:
Read alignment was preformed using Bowtie2, and Deseq2 was used to identify differentially expressed genes. Gene ontology was conducted using Metascape
Assembly: hg38
Supplementary files format and content: FPKMs in Excel file

source_name: neonatal foreskin

value: neonatal foreskin

value: NHEK

tag: growth stage

value: diff NHEK

tag: transfection


title: ATAC-seq, control, replicate 2


title: diff NHEK

description: NHEK-D


title: diff NHEK siIRX5


title: proliferating NHEK

description: NHEK-P


title: WT10p11_2_S13_001

city: Pittsburgh

first: Rolando

middle: Andres

last: Cuevas

state: PA

address: W1744 1 BST MEDICINE

department: Medicine

institute: University of Pittsburgh

description: mVSMC cells, Nt5e-WT Sample 4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence during demultiplexing on the sequencer.
Data was pair-end assembled using CLC Genomics Workbench v 22.0.2
Sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Differentially expressed genes were obtained using CLC genomic benchwork with FDR < 0.05 and |log2 > 2|
Assembly: Grcm38/mm10
Supplementary files format and content: tab-delimited text file includes RPKM, CPM and TPM, p-values, Bonferroni, and FDR values for each gene

organism: Mus musculus

source_name: Aorta

growth_protocol: Mice VSMC were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Quick-RNA Miniprep (Zymo research). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using llumina Stranded mRNA (PolyA+) kit following manufacturer's protocols.

treatment_protocol: SMC differentiation was induced by reducing FNS concentration from 10% to 0.5% for and antibiotics in humidified atmosphere with 5% CO2 at 37C 48 hours.

value: Aorta

value: Mouse Aorta Vascular SMC, primary line

value: Vascular Smooth Muscle Cells

value: SMC differentiation media (0.5% FBS)


title: KO2p11_1_S15_001

description: mVSMC cells, Nt5e-KO Sample 1

value: Nt5e Knock-out


title: WT11p11_1_S12_001

description: mVSMC cells, Nt5e-WT Sample 5


title: KO2p12_2_S17_001

description: mVSMC cells, Nt5e-KO Sample 2


title: KO5p12_2_S18_001

description: mVSMC cells, Nt5e-KO Sample 3


title: WT11p12_2_S14_001

description: mVSMC cells, Nt5e-WT Sample 6


title: THP-1, LUCAT1-KO, SeV, biol rep 2 [LUCAT1_SeV_rep2]

middle: A

last: Fitzgerald

state: Massachusetts

institute: Umass Chan Medical

data_processing:
DolphinNext platform (dolphinnext.umassmed.edu)
Filter out ribosomal RNA using bowtie v1.2.2
remaining reads were aligned using STAR v2.6.1 to hg38/Gencode V34 and reads were counted using RSEM v1.3.1
Read counts were normalized and differential expression analysis was performed using DEBrowser v1.22.5 (https://debrowser.umassmed.edu) w/ DeSeq2
Assembly: hg38
Supplementary files format and content: tsv, raw counts, tpm,
Supplementary files format and content: csv, normalized abundance (DESeq2)

growth_protocol: THP-1 cells were differentiated with 10 ng/ml PMA for 24 h and rested for another 24 h w/o PMA

extract_protocol:
RNA was extracted using Aurum RNA Extraction Mini Kit (Bio-Rad)
RNA libraries were prepared using TruSeq total RNA library prep kit with 1 µg of RNA as input following manufacturer's instructions

treatment_protocol: untreated, 200 ng/ml LPS for 1h or 6h, SeV infection for 6h

value: monocyte

value: SeV


title: SK-Hep-1

city: Copenhagen

first: Marianne

middle: Bengtson

last: Løvendorf

address: Frederikskaj 10b, 2. floor

department: Clinical Medicine

country: Denmark

institute: Center for RNA Medicine, Aalborg University

data_processing:
The bioinformatic pipeline used to identify circRNAs in RNA sequencing data from four liver cancer cell lines was based on the STAR aligner (Dobin, A et al, 2013)
FASTQ files were mapped to the human reference genome (hg38) using annotation from Ensemble release 87 (Cunningham, F et al., 2019)
We used STAR aligner (v2.6.1d) with the following parameters: (chimJunctionOverhangMin=15; chimSegmentMin=15; chimScoreDropMax=37; chimOutType=Junctions; chimMultimapNmax=1; peOverlapNbasesMin=5; outReadsUnmapped=Fastx; outFilterType=Normal; outSAMtype=BAM SortedByCoordinate; quantMode=GeneCounts).
Candidate BSJs were extracted by filtering chimeric alignments to include only alignments, where the two segments aligned to the same chromosome, same strand, with acceptor located downstream of donor and no more than 1Mbp apart. Furthermore, we required that one of the reads should overlap the candidate BSJ and that both mates of a given read pair should be consistent with the BSJ. In case the BSJ was flanked by repeat sequence and a known splice junction fell within this repeat sequence, the junction coordinates were adjusted to coincide with the known junctions.
We used genome coordinates reported by the STAR aligner to construct a backsplice identifier (Backsplice ID) that uniquely identifies a BSJ and has the following form: genome:chr:acceptor:donor:strand (e.g. hg38:X:140783175:140784661:+).The acceptor and donor positions are first base of the intron of the acceptor and donor, respectively, as described in the STAR manual.
We counted the number of reads covering each BSJ and normalized to the total number of mapped reads for the entire library. For comparison to expression of linear parent transcripts, we identified all linear splice junctions involving the acceptor and donor of the backspliced transcript and calculated the ratio.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file including two sheets comprising the normalized data for the linear and circular transcripts, respectively.

source_name: Liver cancer cell line

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s recommendations. The RNA concentration was measured using a microplate reader (Varioscan™ LUX multimode microplate reader, Thermo Scientific) at 260 nm and the RNA quality was assessed using the Experion automated electrophoresis system (BioRad).
Total RNA from four liver cancer cell lines (Hep3B, SK-Hep-1, Huh-7D12, and HepG2) were treated by on-column DNAse digestion (Qiagen) followed by a ribosomal depletion step using Ribo-Zero rRNA Removal kit (H/M/R) (Illumina) according to manufacturer’s instructions. Preparation of the cDNA libraries was carried out using the TruSeq stranded mRNA kit (Illumina) following the manufacturer’s guidelines except that the PolyA selection step was omitted. Quality of the libraries was assessed using the HS NGS Fragment kit on the Fragment Analyzer (Advanced Analytical). The samples were sequenced using the HiSeq 2500 System (100-bp, Paired-End) (Illumina).


title: Huh-7D12


title: ATAC-seq, control, replicate 3

value: M-CSF


title: Hep3B


title: THP-1, LUCAT1-KO, LPS 1h, biol rep 2 [LUCAT1_LPS1h_rep2]

first: Katherine

value: Blood

value: LPS 1h


title: THP-1, LUCAT1-KO, LPS 1h, biol rep 1 [LUCAT1_LPS1h_rep1]


title: HepG2


title: S2 cells, insulin, WNV, 24 h, biol rep 3

city: Pullman

first: Alan

middle: G.

last: Goodman

state: WASHINGTON

address: 100 Dairy Rd., BLS 202

department: School of Molecular Biosciences

institute: Washington State University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were imported using Illumina paired importer (FASTQ).
Trimmed sequence reads were mapped to BDGP6.32.108 using CLC genomic benchwork (parameters: Discard read names=No, Discard quality scores=No, Paired orientation=Paired reads (forward-reverse), Minimum distance=200, Maximum distance=300, Quality score=NCBI/Sanger or Illumina Pipeline 1.8 and later, Remove failed reads=Yes, MiSeq de-multiplexing=No).
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: BDGP6.32.108
Supplementary files format and content: tab-delimited text file of gene expression data normalized to S2 cells not receiving insulin nor WNV

growth_protocol: Drosophila melanogaster S2 phagocytic hematopoietic cells were grown in Schneider's media supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere at 28C

extract_protocol:
RNA was harvested using Trizol reagent and Direct-Zol RNA extraction kit (Zymo Research). 2.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.

treatment_protocol:
Cells were plated into 12 well plates (5e5 cells/well) in the presence or absence of 1.7 uM bovine insulin (Sigma) for 24 h.
Cells were then mock-infected or infected with WNV, Kunjin subtype (MOI 1 PFU/cell) for 8 h.

value: phagocytic hematopoietic cell lineage

value: WT

value: 1.7 uM insulin, WNV infection

tag: time


title: S2 cells, insulin, WNV, 24 h, biol rep 2


title: THP-1, LUCAT1-KO, non-treated, biol rep 1 [LUCAT1_NT_rep1]

value: NT


title: THP-1, LUCAT1-KO, non-treated, biol rep 2 [LUCAT1_NT_rep2]


title: S2 cells, mock, WNV, 24 h, biol rep 2

value: 0 uM insulin, WNV infection


title: THP-1, LUCAT1-KO, LPS 6h, biol rep 1 [LUCAT1_LPS6h_rep1]

value: LPS 6h


title: THP-1, control gRNA (NTC), SeV, biol rep 2 [NTC_SeV_rep2]


title: S2 cells, mock, WNV, 24 h, biol rep 1


title: S2 cells, insulin, WNV, 24 h, biol rep 1


title: THP-1, control gRNA (NTC), SeV, biol rep 1 [NTC_SeV_rep1]


title: diff NHEK siIRX2

value: neonatal foreskin

value: NHEK

value: cultured primary cell

value: diff NHEK


title: S2 cells, insulin, mock, 24 h, biol rep 3

value: 1.7 uM insulin, mock infection


title: THP-1, control gRNA (NTC), LPS 6h, biol rep 2 [NTC_LPS6h_rep2]


title: THP-1, LUCAT1-KO, SeV, biol rep 1 [LUCAT1_SeV_rep1]


title: S2 cells, insulin, mock, 24 h, biol rep 1


title: S2 cells, insulin, mock, 24 h, biol rep 2


title: THP-1, LUCAT1-KO, LPS 6h, biol rep 2 [LUCAT1_LPS6h_rep2]


title: THP-1, control gRNA (NTC), LPS 6h, biol rep 1 [NTC_LPS6h_rep1]


title: THP-1, control gRNA (NTC), LPS 1h, biol rep 2 [NTC_LPS1h_rep2]


title: S2 cells, mock, mock, 24 h, biol rep 2

value: 0 uM insulin, mock infection


title: S2 cells, mock, mock, 24 h, biol rep 3


title: THP-1, control gRNA (NTC), non-treated, biol rep 2 [NTC_NT_rep2]

value: monocyte


title: THP-1, control gRNA (NTC), LPS 1h, biol rep 1 [NTC_LPS_1h_rep1]


title: S2 cells, mock, mock, 24 h, biol rep 1


title: THP-1, control gRNA (NTC), non-treated, biol rep 1 [NTC_NT_rep1]


title: aa154-424_c1_unt3_S12

city: Seattle

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

description:
MB135 myoblasts with inducibile DUX4_aa154-424 RNA-Seq, Untreated
countsAA154-424.csv
aa154-424_c1_unt3_S12

data_processing:
Sequencing data was processed with Illumina Pipeline software (Casava version 1.9)
Reads quality and adapter trimmed using Trimmomatic v0.39 with the following arguments: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were aligned to genome using Rsubread v.2.0.1 with the following arguments: type = "rna", input_format = "gzFASTQ", output_format = "BAM",
Transcripts were counted from the aligned bam files using the Gencode V35 annotation file and featureCounts() from the Rsubread package, v2.0.1 with the following arguments: annot.ext = "gencode.v35.annotation.gtf", isGTFAnnotationFile = TRUE, useMetaFeatures = TRUE, isPairedEnd = TRUE,requireBothEndsMapped = TRUE)
Genome_build: GRCh38, patch 13
Supplementary_files_format_and_content: CSV with raw read counts.

source_name: DUX4_aa154-424 RNA-Seq, Untreated

growth_protocol: Myoblasts were cultured in F-10 media supplemented with 15% Fetal Bovine Serum, 10ng/mL rhFGF Basic, 1uM dexamethasone, and 2ug/mL puromycin. Cells were passaged at ~70% confluence with a 1:5 split ratio.

extract_protocol:
RNA was isolated from cell lysates using Macherey-Nagel's Nucleospin RNA kit (p/n 740955.250)
Libraries were constructed using Illumina's TruSeq stranded mRNA kit (p/n 20020595)

treatment_protocol: IFNg treated samples were 200ng/mL interferon gamma for 16 hours, DOX+IFNg samples were pre-treated with 1ug/mL doxicycline for 4 hours and then 200ng/mL interferon gamma for 16 hours (20 hours total treatment)

value: Untreated

value: MB135 myoblasts with inducibile DUX4-aa154-424

value: MB135 myoblasts

tag: passages


title: 4-NQO + DTA-1 rep2

city: Chicago

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: raw counts

source_name: esophagus enriched for invading cells

growth_protocol: To establish ESCC tumors, 8-week-old mice were treated with 100 μg/ml 4-NQO in the drinking water ad lib for 16 weeks, followed by 12 weeks of normal water.

extract_protocol:
Esophagi were removed and tissue was enriched for invading tumor cells. Tissue was minced and flash frozen on dry ice. RNA was isolated using Qiagen RNeasy Mini Kit (#74104).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Beginning 2.5 weeks prior to sacrifice, mice were injected intraperitoneally with 10 µg of DTA-1 or isotype control antibodies twice weekly and harvested the day following the final injection.

value: esophagus enriched for invading cells


title: 4-NQO + DTA-1 rep3


title: S2 cells, mock, WNV, 24 h, biol rep 3

value: phagocytic hematopoietic cell lineage


title: aa154-424_c1_unt1_S10

description:
MB135 myoblasts with inducibile DUX4_aa154-424 RNA-Seq, Untreated
countsAA154-424.csv
aa154-424_c1_unt1_S10


title: aa154-424_c1_unt2_S11

description:
MB135 myoblasts with inducibile DUX4_aa154-424 RNA-Seq, Untreated
countsAA154-424.csv
aa154-424_c1_unt2_S11


title: 4-NQO + DTA-1 rep1


title: 4-NQO + isotype control rep3

value: isotype


title: 4-NQO + isotype control rep1


title: aa154-424_c1_doxIFNg2_S17

description:
MB135 myoblasts with inducibile DUX4_aa154-424 RNA-Seq, Dox + IFNg treated
countsAA154-424.csv
aa154-424_c1_doxIFNg2_S17

value: Dox + IFNg treated


title: aa154-424_c1_doxIFNg1_S16

description:
MB135 myoblasts with inducibile DUX4_aa154-424 RNA-Seq, Dox + IFNg treated
countsAA154-424.csv
aa154-424_c1_doxIFNg1_S16


title: aa154-424_c1_IFNg3_S15

description:
MB135 myoblasts with inducibile DUX4_aa154-424 RNA-Seq, IFNg treated
countsAA154-424.csv
aa154-424_c1_IFNg3_S15

source_name: DUX4_aa154-424 RNA-Seq, IFNg treated

value: IFNg treated


title: 4-NQO + isotype control rep2


title: F67A_c6_unt1_S1

description:
MB135 myoblasts with inducibile F67A RNA-Seq, Untreated
countsF67A.csv
F67A_c6_unt1_S1

source_name: F67A RNA-Seq, Untreated

value: MB135 myoblasts with inducibile DUX4-F67A mutant


title: Control-PolII_rep2

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

data_processing:
Fastq files were aligned to mm9 with Bowtie2
Aligned sam files were converted to bam and sorted with Samtools-1.2 with "view" and "sort"
mm9 unaligned reads isolated with Samtools-1.2 "view -f4"
mm9 unaligned reads were converted to fastq files with Samtools-1.2 "bam2fq" and aligned to hg19 as above. The number of hg19 aligned reads was used a ChIP-seq scaling factor such that the total human mapped reads are the same across samples per ChIP antibody.
Peaks were called with MACS2: H3K79me ChIPs (--broad -p 0.0001), H3K9ac ChIP (narrow peaks, -p 0.001)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated with Deeptools "bamCoverage" (10 bp bins) using human spike-in scaling factors.

source_name: day 4 reprogramming MEFs

growth_protocol: ESCs were feeder MEF-depleted for 16 hours and grown in ESC media (KnockOut DMEM, 15% fetal bovine serum (FBS), L-glutamine, Penicillin/Streptomycin, non-essential amino acids, 2-mercaptoethanol, and leukemia inhibitory factor) on gelatinized plates. MEFs were grown in MEF media (DMEM, 10% FBS, non-essential amino acids, glutamax, Penicillin/Streptomycin, and 2-mercaptoethanol). Day 4 of reprogramming was grown in ESC media, with feeder MEFs, on gelatinized plates.

extract_protocol:
Cells were trypsinized and fixed with 1% formaldehyde in suspension for 10 min, rotating. Cross-linking was quenched with 0.14 M glycine for 5 min, cells were centrifuged at 300xg for 3 min, and pellets washed with cold 3x PBS. 25 million cells were resuspended in 1 ml lysis buffer (1% SDS, 50 mM Tris-HCl pH 8, 20 mM EDTA, 1x cOmplete (Roche, 4693132001) protease inhibitor), and sonicated on a Covaris S220 Focused-ultrasonicator with the following parameters: 21 cycles of 45 seconds ON (peak 170, duty factor 5, cycles/burst 200), 45 seconds OFF (rest) in 6-8°C degassed water. Sonicated chromatin was centrifuged at 21xg at 6C for 10 min, and supernatant was collected and quantified with Qubit DNA HS Assay Kit (ThermoFisher Scientific, Q32854). Chromatin was aliquoted ensuring the SDS remained in solution so that the concentration was exactly 0.1% after diluting 1:10 in Dilution Buffer (16.7 mM Tris-HCl pH 8, 0.01% SDS, 1.1% Trition-X, 1.2 mM EDTA, and 167 mM NaCl). H3K79me1/2/3 ChIPs started with 7.1 ug chromatin combined with 1/53 (134 ng) human spike-in chromatin generated from 293T cells as above. H3K9ac and RNAPII ChIPs were immunoprecipitated with 13 ug chromatin with 1/53 (247 ng) human spike-in generated from human dermal fibroblasts for H3K9ac or 293T cells for RNAPII. 5 ug (or 5 ul if concentration was unknow) of the following antibodies were used H3K79me1 (Abcam, 2886), H3K79me2 (Active Motif, 39143), H3K79me2 (Abcam, ab3594), H3K79me3 (Diagenode, C15410068), H3K9ac (Diagenode pAb-004-050 Rep 1, 293T spike in control), H3K9ac (Active Motif 39917, Rep 2 dermal fibroblast control), and RPB1 NTD D8L4Y (Cell Signaling Technology, 14958S).ChIPs were incubated overnight at 4C with rotation and then Dynabeads were added for 2 hours. Dynabeads were pre-prepared as follows: 25 μL of Protein A (ThermoFisher Scientific, 10002D) and 25 μL of Protein G (ThermoFisher Scientific, 10004D) were combined and washed once in PBS, 0.02% Tween-20, once in dilution buffer, and then resuspended in an equal volume of dilution buffer. Antibody-bead complexes were washed twice for 5 min rotating at 4C, in 1 ml of each of the following buffers: Low salt (50 mM HEPES pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1 mM EDTA pH 8.0, 140 mM NaCl), High salt (50 mM HEPES pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1 mM EDTA pH 8.0, 500 mM NaCl), LiCl (20 mM Tris-HCl pH 8, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA pH 8.0, 250 mM LiCl), and TE (10 mM Tris-HCl pH 8, 1 mM EDTA pH 8) using a magnetic rack. Beads were incubated with 250 μL elution buffer (50 mM Tris-HCl pH 8, 1 mM EDTA pH 8, 1% SDS) plus 200 ul TE with 0.67% SDS for 10 minutes at 65°C, shaking. 10 μg RNase A was added and incubated at 37°C for 30 minutes. Crosslinks were reversed overnight with 40 ug of proteinase K at 60C. DNA was purified with phenol-chloroform extraction with phase lock tubes followed by isopropanol precipitation. DNA was resuspended in ultrapure H2O.
Libraries were constructed with the Ovation Ultralow System V2 (NuGEN, 0344) according to the manufacturer's instructions. Libraries were then size selected (200-400 bp) on a 1.5% gel followed by purification with the MinElute Gel Extration Kit (Qiagen, 28604). Libraries were sequenced 1x50 on an Illumina HiSeq4000.

treatment_protocol: ESCs and MEFs were untreated. Reprogramming (Oct4, Sox2, Klf4, cMyc) was induced with 2 ng/ml doxycycline, with 5 μM SGC0946 or control DMSO, for 4 days.

value: day 4 reprogramming

value: DMSO

tag: chip antibody

value: Cell Signaling Technology (14958S)

tag: spike-in chromatin

value: homozygous Oct4-2A-Klf4-2A-IRES-Sox2-2A-c-Myc (Col1a1 locus), heterozygous reverse tetracycline transactivator (Rosa26 locus)


title: Dot1Li-PolII_rep1

tag: genotype


title: Dot1Li-PolII_rep2


title: F67A_c6_unt2_S2

description:
MB135 myoblasts with inducibile F67A RNA-Seq, Untreated
countsF67A.csv
F67A_c6_unt2_S2


title: aa154-424_c1_IFNg1_S13

description:
MB135 myoblasts with inducibile DUX4_aa154-424 RNA-Seq, IFNg treated
countsAA154-424.csv
aa154-424_c1_IFNg1_S13


title: F67A_c6_unt3_S3

description:
MB135 myoblasts with inducibile F67A RNA-Seq, Untreated
countsF67A.csv
F67A_c6_unt3_S3


title: ESC-PolII_rep2

source_name: V6.5 mESC

value: V6.5 mESC


title: ESC-PolII_rep1


title: F67A_c6_doxIFNg2_S8

description:
MB135 myoblasts with inducibile F67A RNA-Seq, Dox + IFNg treated
countsF67A.csv
F67A_c6_doxIFNg2_S8

source_name: F67A RNA-Seq, Dox + IFNg treated


title: MEF-PolII_rep2

source_name: Mouse embryonic fibroblasts

value: Mouse embryonic fibroblasts


title: F67A_c6_doxIFNg3_S9

description:
MB135 myoblasts with inducibile F67A RNA-Seq, Dox + IFNg treated
countsF67A.csv
F67A_c6_doxIFNg3_S9


title: aa154-424_c1_doxIFNg3_S18

description:
MB135 myoblasts with inducibile DUX4_aa154-424 RNA-Seq, Dox + IFNg treated
countsAA154-424.csv
aa154-424_c1_doxIFNg3_S18


title: aa154-424_c1_IFNg2_S14

description:
MB135 myoblasts with inducibile DUX4_aa154-424 RNA-Seq, IFNg treated
countsAA154-424.csv
aa154-424_c1_IFNg2_S14


title: Dot1Li-H3K9ac_rep2

value: Diagenode (pAb-004-050)


title: F67A_c6_doxIFNg1_S7

description:
MB135 myoblasts with inducibile F67A RNA-Seq, Dox + IFNg treated
countsF67A.csv
F67A_c6_doxIFNg1_S7


title: F67A_c6_IFNg3_S6

description:
MB135 myoblasts with inducibile F67A RNA-Seq, IFNg treated
countsF67A.csv
F67A_c6_IFNg3_S6

source_name: F67A RNA-Seq, IFNg treated


title: F67A_c6_IFNg2_S5

description:
MB135 myoblasts with inducibile F67A RNA-Seq, IFNg treated
countsF67A.csv
F67A_c6_IFNg2_S5


title: Control-H3K9ac_rep1

value: Active Motif (39917)

value: human dermal fibroblasts


title: ESC-H3K9ac_rep2


title: F67A_c6_IFNg1_S4

description:
MB135 myoblasts with inducibile F67A RNA-Seq, IFNg treated
countsF67A.csv
F67A_c6_IFNg1_S4


title: Control-PolII_rep1


title: Control-H3K9ac_rep2


title: ESC-H3K9ac_rep1


title: Dot1Li-H3K9ac_rep1


title: Normal, replicate 4, scRNAseq

city: Guangzhou

first: Bin

last: Zhang

state: Guangdong

address: 107 Yanjiang West Road

department: Department of Cardiovascular Surgery

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Ascending aortic wall tissue

extract_protocol:
The fresh ascending aortic wall tissues were washed at least 3 times with the Hanks Balanced Salt Solution (HBSS) (14025092, Thermo Fisher Scientific, Waltham, MA, USA) to wash away the blood. The adipose tissue attached to the adventitia was removed by blunt separation using the forceps. The single cell preparation was performed on ice to preserve cell viability. The aortic tissues were cut into smaller pieces (1–2 mm3) and digested in a 15-ml centrifuge tube with a digestive enzyme cocktail that included 3 mg/ml Type I collagenase (LS004176, Worthington Biochemical Corp., Lakewood, NJ, USA), 0.156 mg/ml Type XI collagenase (H3506, Sigma Corp., Kanagawa, Japan), 0.25 mg/ml soybean trypsin inhibitor (LS003571, Worthington), 0.1875 mg/ml lyophilized elastase (LS002292, Worthington), 0.24 mg/ml Type I hyaluronidase (H3506, Sigma) and 60 U/ml DNase I (10104159001, Roche, Shanghai, China) as previously described. The samples were shaken slowly for 2-3h in a 37°C water bath to facilitate complete digestion. The digested supernatant was separated from the tissue remnants. The di-gestive reaction was stopped by adding Dulbecco’s modified Eagle’s medium (DMEM) and 10% fetal bovine serum. The remaining tissue was further digested with a fresh enzyme cocktail. The digestion process was repeated 3 times to ensure that all the cells from the aortic tissues were isolated. The cells were pelleted by centrifugation at 300 xg and 4℃ for 5min and resuspended in 1X PBS to generate a single cell suspension. The cells were counted using the TC20 automated cell counter (Singleron). The live cell counts were obtained by staining with trypan blue (302643, Sigma). The samples with >80% cell viability and 1×106 cells / ml were further processed for sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Ascending aortic wall tissue


title: MEF-PolII_rep1


title: Dot1Li-H3K79me3_rep1

value: Diagenode (C15410068)


title: Normal, replicate 1, scRNAseq

description: 10x Genomics


title: Normal, replicate 2, scRNAseq

description: 10x Genomics


title: MEF-H3K9ac_rep2


title: Control-H3K79me3_rep2


title: H7: healthy

city: Tehran

first: Sima

last: Rafati

state: Tehran

address: Pasteur Ave

department: Immunotherapy and Leishmania Vaccine Research

country: Iran

institute: Pasteur Institute of Iran

data_processing:
Sequence quality was assessed using FastQC (v 0.11.2) followed by merging the reports using multiQC (v 0.9).
Prinseq (v 0.20.3) was used to remove any remaining Illumina adapter sequences from reads and to trim bases off the start or the end of a read when the quality score fell below a threshold of 20.
Star (v 2.5.2b) was applied to align reads to the human genome (v hg19/GRCh38)
The abundance of reads mapping to each gene feature in the aligned genome was determined using HTSeq (v 0.6.1p1).
Differentially expressed genes (DEGs) between the patients and the healthy group were generated using   DESeq2 (v 1.22.1).
Assembly: hg19/GRCh38
Supplementary files format and content: Microsoft excel file(.xlsx) include count and log2FoldChange for each Sample

source_name: Skin

extract_protocol:
Total RNA was isolated using miRNeasy Mini Kit.  RNA samples with a 260/280 ratio approximating 2 and RIN > 7 were used in RNA sequencing analyses.
Ribosomal RNA depletion and cDNA library preparation were performed using the IlluminaTruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold. Final libraries were evaluated using Agilent 2200 Tape Station and Qubit®Fluorometer.

value: Skin

tag: disease state

value: healthy


title: H3: healthy


title: H2: healthy


title: H5: healthy


title: H4: healthy


title: ESC-H3K79me3_rep2


title: MEF-H3K9ac_rep1


title: Normal, replicate 6, scRNAseq

description: 10x Genomics


title: MEF-H3K79me3_rep1


title: ESC-H3K79me3_rep1


title: H1: healthy


title: Q: acute stage /NUCL

value: acute stage /NUCL

value: NO prior anti-leishmanial treatment


title: MEF-H3K79me3_rep2


title: P: acute stage /NUCL


title: Dot1Li-H3K79me2_rep2

value: Abcam (ab3594)


title: Control-H3K79me2_rep2


title: Dot1Li-H3K79me2_rep1

value: Active motif (39143)


title: Normal, replicate 5, scRNAseq

description: 10x Genomics


title: Normal, replicate 3, scRNAseq

description: 10x Genomics


title: O: acute stage /NUCL


title: Control-H3K79me3_rep1

value: day 4 reprogramming


title: M: acute stage /NUCL


title: ESC-H3K79me2_rep2


title: J: acute stage /UCL

value: acute stage /UCL


title: K: acute stage /NUCL


title: Dot1Li-H3K79me3_rep2


title: L: acute stage /NUCL


title: MEF-H3K79me2_rep2


title: ESC-H3K79me2_rep1


title: Dot1Li-H3K79me1_rep2

value: Abcam (ab2886)


title: MEF-H3K79me2_rep1

value: homozygous Oct4-2A-Klf4-2A-IRES-Sox2-2A-c-Myc (Col1a1 locus), heterozygous reverse tetracycline transactivator (Rosa26 locus)


title: H: acute stage /NUCL


title: Dot1Li-H3K79me1_rep1


title: F: acute stage /UCL


title: ESC-H3K79me1_rep1

value: V6.5 mESC


title: ESC-H3K79me1_rep2


title: E: acute stage /UCL


title: D: acute stage /UCL


title: Control-H3K79me1_rep2

value: DMSO


title: MEF-H3K79me1_rep2

value: Mouse embryonic fibroblasts


title: G: acute stage /NUCL


title: B: acute stage /UCL


title: MEF-H3K79me1_rep1


title: Control-H3K79me2_rep1


title: A: acute stage /UCL


title: Aged_Phf6-WT_5

city: New York

first: Stuart

middle: Aidan

last: Quinn

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Raw reads were demultiplexed and FASTQ files generated using Bcl2fastq v2.20.0.422 (Illumina)
Reads were aligned to the mouse genome (GRCm38) with STAR v2.3.5.3a using the Gencode mouse gene annotation for initial junction estimation in 2-pass, paired-end mode with otherwise default alignment parameters.
Gene level read counts were generated using the R function featureCounts (Rsubread v1.6.0).
Read count normalization and differential gene expression testing was performed using DESeq2 v1.20
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene level summarized read counts are provided prior to library size normalization for direct input to DESeq2

source_name: LT-HSC

extract_protocol:
Fresh LT-HSCs (Lin- Sca-1+ CD117+ CD135- CD150+ CD48-) were FACS-sorted from lineage depleted (mouse lineage depletion kit; Miltenyi Biotec) bone marrow harvested from Phf6-WT and Phf6-KO mice at 16-weeks and 24-months of age. Cells were sorted directly into RLT buffer and total RNA was extracted using the RNAeasy mini kit (Qiagen).
Total RNA concentration was determined using the Qubit RNA HS assay and the RNA Integrity Number (RIN) was measured using the Bioanalyzer system (Agilent) for each total RNA isolate. Only samples with a RIN greater than 8 were used to construct RNA-seq libraries.  RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories; cat. #634888) and sequencing-ready libraries were generated using the Low Input Library Prep Kit v2 (Clontech Laboratories; cat. #634899). Library concentrations were determined using the Qubit dsDNA HS Assay Kit (Invitrogen; cat. #Q32854)

tag: strain

value: bone marrow

value: LT-HSC

value: Aged

tag: age


title: Aged_Phf6-WT_6

tag: developmental stage


title: CNR_K562_0000min_Rad21_rep2

city: Chapel Hill

first: Marielle

last: Bond

state: North Carolina

address: 104 Manning Drive Thurston Building Room 4012

department: Genetics Curriculum

institute: UNC Chapel Hill

data_processing:
library strategy: CUT&RUN
Adapters and low-quality reads were trimmed from paired-end reads using Trim Galore! (version 0.4.3)
Reads were aligned to the hg19 genome using BWA mem (version 0.7.17)
Alignments were sorted using Samtools (version 1.9)
Duplicates were removed with PicardTools (version 2.10.3)
Alignments were index using Samtools (version 1.9)
Replicates were merged with samtools (version 1.9)
Alignments were converted to bigwigs using deeptools (version 3.0.1)
Peaks were called from merged alignments using MACS2 (-f BAM -q 0.01 -g hs --nomodel --shift 0 --extsize 200 --keep-dup all -B --SPMR; version 2.1.1.20160309)
Peaks were merged using bedtools (version 2.26)
Counts at merged peaks were extacted from BAM files using bedtools multicov (version 2.26)
Assembly: hg38
Supplementary files format and content: narrowPeak: tab-delimited BED-style file containing peak info from MACS2 (chr, start, end coordinates, peakID, score, strand, signal, p-value, q-value, peak summit position); .bw: bigwig signal tracks; .tsv: counts of all peaks included in analysis for each antibody

growth_protocol: K562 cells maintained with RPMI + 10% FBS + 1% Pen/Strep

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min, quenched with 2.0M glycine for 5 min, washed in PBS, and split into 5x10^5 cell pellet aliquots
KAPA Hyperprep kit

treatment_protocol: Megakaryocyte differentiation induced by treatment with 25 nM PMA for the length of each timepoint

tag: cell line

value: Human leukemia

value: WT

tag: treatment

value: PMA (megakaryocyte differentiation)


title: I: acute stage /UCL

tag: tissue

value: Skin


title: Aged_Phf6-WT_3

tag: cell type


title: Control-H3K79me1_rep1


title: CNR_K562_0360min_Jun_rep2

tag: antibody

value: Jun


title: Aged_Phf6-WT_1


title: CNR_K562_4320min_Rad21_rep1


title: CNR_K562_0000min_Jun_rep2


title: C: acute stage /NUCL

value: acute stage /NUCL

value: NO prior anti-leishmanial treatment


title: CNR_K562_0000min_Rad21_rep1


title: CNR_K562_4320min_Jun_rep2


title: Aged_Phf6-KO_3


title: Aged_Phf6-KO_4


title: Aged_Phf6-KO_5


title: Aged_Phf6-KO_6


title: Type I PRMT inhibitor treatment rep2

city: Houston

first: Weiyi

last: Peng

state: Texas

address: 3517 Cullen Blvd, Room 3025

institute: University of Houston

description: PRMT1i 2

data_processing:
FLASH v1.2.11 was used to merger overlapped reads. The merged and nonoverlapping reads were mapped separately to mouse mm10+gencodevM14 using HiSAT2/2.1.0. The mapped reads were merged using samtools/1.2
stringtie/1.3.0 were used to calculate the gene expressions. preDE.py was used to count the reads.
DESeq2 were used to do differential expression analysis
GSEA were applied to logFC ranked genes
Genome_build: mm10+gencodevM14
Supplementary_files_format_and_content: differential expression analysis results in Excel file

source_name: MC38/gp100 murine cancer cell line

extract_protocol:
Cell lines were washed and RNAs were harvested using Qiagen RNeasy Plus kit. KAPA Stranded mRNA-Seq Kit was used with 250 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MC38/gp100 cellls were treated with DMSO or 1uM GSK3368712 for 5 days.

value: treated with 1uM GSK3368712 for 5 days


title: CNR_K562_0360min_Jun_rep1


title: CNR_K562_4320min_Jun_rep1


title: Aged_Phf6-WT_4


title: Type I PRMT inhibitor treatment rep1

description: PRMT1i 1


title: CNR_K562_0000min_CTCF_rep2

value: CTCF


title: DMSO treatment rep2

description: Control 2

value: treated with DMSO for 5 days


title: Aged_Phf6-WT_2


title: CNR_K562_0360min_CTCF_rep1


title: CNR_K562_4320min_Rad21_rep2


title: CNR_K562_0000min_Jun_rep1


title: CNR_K562_4320min_CTCF_rep1


title: DMSO treatment rep1

description: Control 1


title: CNR_K562_0000min_CTCF_rep1


title: Aged_Phf6-KO_2


title: Aged_Phf6-KO_1


title: CNR_K562_4320min_CTCF_rep2


title: CNR_K562_0360min_H3K27ac_rep1


title: CNR_K562_4320min_H3K27ac_rep2


title: CNR_K562_0000min_H3K27ac_rep2


title: CNR_K562_0000min_H3K27ac_rep1


title: RNA_K562_2880min_rep2

data_processing:
Adapters and low-quality reads were trimmed from paired-end reads using Trim Galore! (version 0.4.3)
Salmon was used in quant mode to quantify reads to hg19 transcripts (version 1.4.0)
Reads were aligned to the hg38 genome using HISAT2 (version 2.1.0)
Alignments were indexed using samtools (version 1.9)
Replicates were merged with samtools (version 1.9)
Alignments were converted to bigwigs using deeptools (version 3.0.1)
Reads were summarized to a gene level using txImport (R version 3.3.1, tximport version 1.2.0)
Differential analysis was completed in DESeq2 (R version 3.3.1, DESeq version 1.33.5)
Assembly: hg38
Supplementary files format and content: quant.sf: tab-delimted file of transcript-level quantifications including transcript ID, length, effective length, TPM, and NumReads from Salmon; .bw: bigwig files of signal tracks; .tsv: tab-delimited text file containing gene-summarized information including chromosome, start, end coordinates, ENSEMBL and HGNC IDs, differential gene cluster, DESeq adjusted LRT p-values, raw counts, variance-stabilized transformed counts, DESeq shrunken log2(fold-change); txt: text file summarizing all log2fold-changes and corresponding padj for each sample, counts, and differential gene cluster

growth_protocol: K562 cells maintained with RPMI + 10% FBS + 1% Pen/Strep and were grown to a density of 1x10^5 cells/mL

extract_protocol:
Qiagen RNeasy with Dnase I treatment. RNA integrity numbers were confirmed with a Tapestation High-Sensitivity RNA tape, concentration confirmed with Qubit BR assay
KAPA RNA Hyperprep with Riboerase

treatment_protocol: Megakaryocyte differentiation induced by treatment with 25 nM PMA for the 0h, 0.5h, 1.5h, 3h, 6h, 24h, 48h, and 72h. Media was changed after 24h and 48h

tag: time point


title: RNA_K562_0360min_rep2

value: 360 min


title: RNA_K562_0030min_rep2

value: 30 min


title: RNA_K562_0180min_rep2

value: 180 min


title: RNA_K562_1440min_rep2


title: RNA_K562_0000min_rep2

value: 0 min


title: RNA_K562_0090min_rep2

value: 90 min


title: RNA_K562_4320min_rep2


title: RNA_K562_4320min_rep1


title: RNA_K562_0180min_rep1


title: RNA_K562_0360min_rep1


title: RNA_K562_0000min_rep1


title: RNA_K562_0030min_rep1


title: RNA_K562_2880min_rep1


title: ATAC_K562_4320min_rep2

data_processing:
Adapters and low-quality reads were trimmed from paired-end reads using Trim Galore! (version 0.4.3)
Reads were aligned to the hg38 genome using BWA mem (version 0.7.17)
Alignments were sorted using Samtools (version 1.9)
Duplicates were removed with PicardTools (version 2.10.3)
Alignments were index using Samtools (version 1.9)
Replicates were merged with samtools (version 1.9)
Alignments were converted to bigwigs using deeptools (version 3.0.1)
Peaks were called from merged alignments using MACS2 (-f BAM -q 0.01 -g hs --nomodel --extsize 200 --keep-dup all -B --SPMR --shift 0; version 2.1.1.20160309)
Peaks were merged using bedtools (version 2.26)
Counts at merged peaks were extacted from BAM files using bedtools multicov (version 2.26)
Assembly: hg38
Supplementary files format and content: narrowPeak: tab-delimited BED-style file containing peak info from MACS2 (chr, start, end coordinates, peakID, score, strand, signal, p-value, q-value, peak summit position; .bw: bigwig signal tracks; .tsv: counts of all peaks included in analysis; .txt: text file showing peak coordinates, fold-changes and padj values from DESeq, counts for each sample, and differential cluster

extract_protocol:
Cells were washed with PBS and lifted with EDTA for 500 µL EDTA for 5 min and then quenched with 3.5 mL of RPMI. Cells were then lysed with NP-40, Tween-20, and digitonin
Omni ATAC

treatment_protocol: Megakaryocyte differentiation induced by treatment with 25 nM PMA for the 0h, 6h, and 72h. Media was changed after 24h and 48h

value: PMA (megakaryocyte differentiation) 72h


title: CNR_K562_0360min_H3K27ac_rep2


title: ATAC_K562_0360min_rep2

value: PMA (megakaryocyte differentiation) 6h


title: RNA_K562_1440min_rep1

value: Human leukemia


title: ATAC_K562_0000min_rep2

value: WT

value: PMA (megakaryocyte differentiation) 0h


title: ATAC_K562_4320min_rep1


title: ATAC_K562_0360min_rep1


title: ATAC_K562_0000min_rep1


title: CNR_K562_4320min_H3K27ac_rep1

value: PMA (megakaryocyte differentiation)