title: IVM-Donor 11

city: Hong Kong

first: Wing Tung

last: Lee

address: Room Y934, 9/F, Lee Shau Kee Building, The Hong Kong Polytechnic University, Hung Hom, Kowloon

department: Department of Health Technology and Informatics

country: Hong Kong

institute: The Hong Kong Polytechnic University (PolyU)

description: TW-J

data_processing:
Raw reads from both RNA-seq and scBS-seq were checked by FastQC (v0.11.8, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed by Trim Galore (v0.4.5, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
For RNA-seq data, trimmed reads were mapped to the human reference genome (hg19) by TopHat (v2.1.1) with default parameters and Cufflinks was employed to quantify gene expression level with gene annotation obtained from Ensembl GRCh38.
Gene expression level was calculated in the form of fragments per kilobase million (FPKM). Genes with undetected expression level in all the samples were excluded in the following analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: text files include FPKM values for each Sample

source_name: in vitro-matured metaphase II (IVM-MII) oocyte

extract_protocol:
7 µl of soft lysis buffer containing 500 mM KCl (Sigma), 100mM pH 8.0 Tris-HCl (Sigma), 1.35 mM MgCl2 (Sigma), 4.5 mM DTT (Thermo Fisher Scientific), 0.45% Nonidet P-40 (Sigma), 0.18U SUPERase-In (Thermo Fisher) and 0.36U recombination RNase-inhibitor (Thermo Fisher) were added into each PCR tube containing a single oocyte and were incubated at 4˚C for 30 min. Then, the lysate was vortexed at room temperature for 1 min and centrifuged at 1000g for 5 min to allow the nucleus to sink to the bottom of the tube. 6.5 µl of supernatant containing RNA was carefully transferred to a new PCR tube for generating scRNA-seq library.
TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) was ysed for library construction.


title: AdML_DMSO

status: Public on Jun 23 2021

type: SRA

city: La Jolla

first: Kaushik

last: Saha

state: CA

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

country: USA

institute: University of California San Diego

description: 6.7% DMSO at 30 °C for 30 min

library_source: transcriptomic

data_processing:
Library strategy: SHAPE-MaP
Basecalls performed with Realtime Analysis (RTA) software launched automatically by MiSeq Control Software
All steps of the processing (including quality control by FastQC, alignment by Bowtie, and mutation counting) were carried out by SHAPEMapper 2.0. Each processed file is generated by counting mutations in DMSO (i.e. untreated), NMIA (i.e. treated), and DC (i.e. denatured control) reads of the corresponding samples.
Supplementary_files_format_and_content: tab-delimited files contain SHAPE reactivity per nucleotide

molecule: total RNA

organism: Human adenovirus 2

source_name: In vitro transcribed from plasmid

growth_protocol: Not Applicable

extract_protocol:
RNA purification by Monarch RNA cleanup kit (New England Biolabs)
cDNA was PCR amplified using primers containing partial Illumina adapter for 20 cycles and then the library was further amplified for 8 cycles with dual index primers
Selective 2′ hydroxyl acylation followed by primer extension by mutational profiling (SHAPE-MaP)

treatment_protocol: RNAs were treated with 2 mM N-Methylisatoic anhydride (NMIA) for 1 hr at 16 °C or 8 mM NMIA for 30 min at 30 °C or the vehicle (DMSO) under the same conditions

tag: genotype

value: wild type

tag: treatment

value: 6.7percent DMSO at 30 degreeC for 30 min


title: IVM-Donor 9

description: TW-G

organism: Homo sapiens

tag: cell type

value: in vitro-matured metaphase II (IVM-MII) oocyte

tag: age


title: IVM-Donor 10

description: TW-C


title: WCE PolyA+ RNA Mock

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

description:
Libraries PolyA+ selected
All_counts.xlsx
WCE-Mock-PolyA_S89

data_processing:
Fastq files were aigned to a combined Mouse-Drosophila genome assembly using STAR
Unique reads were extracted and the bam file was split into Mouse bam and Drosophila bam.
Number of reads mapping to Drosophila were used to calculate the scaling/normalization factor for the Mouse reads as shown in Orlando et al, 2014, which was then used to generate normalized bigwigs for each sample
featureCounts was used to get the counts of reads in gene for both Drosophila and Mouse genome
DESeq2 was used to calculate size factors for Drosophila reads which were then used to normalize the Mouse reads per sample
Genome_build: mm9 and BDGP5.25
Supplementary_files_format_and_content: Excel file with raw counts for exon/intron per gene for the three datasets (Chromatin-total, Chromatin-polyA and WCE-polyA)

organism: Mus musculus

source_name: mESC

growth_protocol: mESC E14 cells were cultured on 0.1% gelatin-coated surfaces with KO-DMEM medium, 10% FCS, 5% knockout serum replacement, nonessential amino acids, L-glutamine, 2-mercaptoethanol, antibiotics (Invitrogen), and 1000 U/ml of leukaemia inhibitory factor (Abcam). Drosophila S2 cells (Thermofisher, R69007) were grown in Schneider's Drosophila Medium (ThermoFisher, Cat.no. 21720-02)  supplemented with heat inactivated FBS (ThermoFisher, 10500064) and  25 U/mL of Penicillin-Streptomycin (ThermoFisher 15140-122).

extract_protocol:
Trizol extraction protocol. For WCE RNA, 5x106 cells were resuspended in Trizol. For chromatin-associated RNAs, 15x106 cells were fractionated using the method published in Werner & Ruthenburg, 2015, and the chromatin fraction resuspended in Trizol.
For chromatin-associated total RNA sample, rRNA was depleted and libraries were prepared for sequencing of intronic and exonic RNA. For PolyA+ samples, libraries were prepared by selecting polyA+ RNAs.

treatment_protocol: For Pol II inhibition experiments, cells were treated with triptolide (10 µM, Sigma T3652), flavopiridol (10 µM, Sigma F3055) for 1, 3 or 9 hrs. For RNA degradation experiments, cells were permeabilized with 0.05% Tween-20 in PBS for 10 min on ice, washed once, resuspended with PBS and mock-treated with 1 U/μl SUPERase.In (Invitrogen AM2694) or treated with 1 μg/μl RNaseA (Sigma R6513) for 30 min at RT.

value: mESC E14

tag: spike-in

value: Drosophila S2 RNA

value: Permeabilization of cells + PBS


title: GC0013 Gastric Cancer

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetected) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: disease state

value: Gastric Cancer

tag: Sex

value: Male

tag: Stage

value: IA

tag: histological subtype

value: diff


title: IVM-Donor 8

description: TW-A


title: GC0012 Gastric Cancer


title: WCE PolyA+ RNA RNaseA

description:
Libraries PolyA+ selected
All_counts.xlsx
WCE-RNaseA-PolyA_S90

value: Permeabilization of cells + RNaseA


title: WCE PolyA+ RNA Trp 9h

description:
Libraries PolyA+ selected
All_counts.xlsx
WCE-trp-9h-PolyA_S88

value: 10 microM triptolide for 9 hr


title: AdMLΔ3'SSΔESE+SR_buffer_DMSO

description: SR protein buffer and 1.64% DMSO (vehicle) for 1 hour at 16 °C

value: 3' SS & ESE mutation (cagCT > accTC, TCA > AAT))

value: SR protein buffer and 1.64percent DMSO (vehicle) for 1 hour at 16 degreeC


title: AdMLΔ3'SSΔESE+SR_buffer_NMIA_2mM

description:
SR protein buffer and 2 mM NMIA for 1 hour at 16 °C
Ad3ESESRbuf_Ad3ESE

value: SR protein buffer and 2 mM NMIA for 1 hour at 16 degreeC


title: GC0011 Gastric Cancer

value: Female

value: undiff


title: IVM-Donor 7

description: TW-I


title: GC0010 Gastric Cancer

value: IB


title: AdMLΔ3'SSΔESE+SRSF5_NMIA_2mM

description:
SRSF5 and 2 mM NMIA for 1 hour at 16 °C
Ad3ESESR5_Ad3ESE

value: SRSF5 and 2 mM NMIA for 1 hour at 16 degreeC


title: WCE PolyA+ RNA Trp 1h

description:
Libraries PolyA+ selected
All_counts.xlsx
WCE-trp-1h-PolyA_S86

value: 10 microM triptolide for 1 hr


title: IVM-Donor 6

value: in vitro-matured metaphase II (IVM-MII) oocyte


title: GC0009 Gastric Cancer


title: GC0008 Gastric Cancer


title: WCE PolyA+ RNA Fp 9h

description:
Libraries PolyA+ selected
All_counts.xlsx
WCE-fp-9h-PolyA_S85

value: mESC E14

value: Drosophila S2 RNA

value: 10 microM flavopiridol for 9 hr


title: AdMLΔ3'SSΔESE+SRSF5_DMSO

description: SRSF5 and 1.64% DMSO (vehicle) for 1 hour at 16 °C

value: SRSF5 and 1.64percent DMSO (vehicle) for 1 hour at 16 degreeC


title: IVM-Donor 5

description: TW-E


title: IVM-Donor 4

description: TW-D


title: AdMLΔ3'SS+SRSF1_NMIA_2mM

description:
SRSF1 and 2 mM NMIA for 1 hour at 16 °C
Ad3SR1_Ad3

value: 3' splice site mutation (cagCT > accTC)

value: SRSF1 and 2 mM NMIA for 1 hour at 16 degreeC


title: WCE PolyA+ RNA Fp 1h

description:
Libraries PolyA+ selected
All_counts.xlsx
WCE-fp-1h-PolyA_S83

value: 10 microM flavopiridol for 1 hr


title: GC0005 Gastric Cancer

value: Gastric Cancer

value: Male

value: IA

value: diff


title: GC0006 Gastric Cancer

value: Female


title: WCE PolyA+ RNA 0h

description:
Libraries PolyA+ selected
All_counts.xlsx
WCE-0h-PolyA_S82

value: Untreated


title: AdMLΔ3'SS+SRSF1_DMSO

description: SRSF1 and 1.64% DMSO (vehicle) for 1 hour at 16 °C

value: SRSF1 and 1.64percent DMSO (vehicle) for 1 hour at 16 degreeC


title: AdMLΔ3'SS+SRSF5_NMIA_2mM

description:
SRSF5 and 2 mM NMIA for 1 hour at 16 °C
Ad3SR5_Ad3

value: SRSF5 and 2 mM NMIA for 1 hour at 16 degreeC


title: GC0004 Gastric Cancer

value: undiff


title: WCE PolyA+ RNA Trp 3h

description:
Libraries PolyA+ selected
All_counts.xlsx
WCE-trp-3h-PolyA_S87

value: 10 microM triptolide for 3 hr


title: Chromatin-associated PolyA+ RNA Mock

description:
Libraries PolyA+ selected
All_counts.xlsx
Chr-Mock-PolyA_S98

value: mESC E14

value: Permeabilization of cells + PBS


title: IVM-Donor 1

description: TW-H

value: in vitro-matured metaphase II (IVM-MII) oocyte


title: GC0007 Gastric Cancer


title: GC0002 Gastric Cancer


title: GC0003 Gastric Cancer


title: AdMLΔ3'SS+SRSF5_DMSO

value: SRSF5 and 1.64percent DMSO (vehicle) for 1 hour at 16 degreeC


title: AdMLΔ3'SSΔESE_DC

description: Denatured control 2 mM NMIA

value: 3' SS & ESE mutation (cagCT > accTC, TCA > AAT))

value: Denatured control 2 mM NMIA


title: IVO-Donor 10

source_name: in vivo-matured metaphase II (IVO-MII) oocyte

value: not provided


title: AdMLΔ3'SS+SR_buffer_NMIA_2mM

description:
SR protein buffer and 2 mM NMIA for 1 hour at 16 °C
Ad3SRbuf_Ad3

value: 3' splice site mutation (cagCT > accTC)

value: SR protein buffer and 2 mM NMIA for 1 hour at 16 degreeC


title: Chromatin-associated PolyA+ RNA Trp 3h

description:
Libraries PolyA+ selected
All_counts.xlsx
Chr-trp-3h-PolyA_S96

value: Drosophila S2 RNA


title: IVO-Donor 9

value: in vivo-matured metaphase II (IVO-MII) oocyte


title: Chromatin-associated PolyA+ RNA Trp 1h

description:
Libraries PolyA+ selected
All_counts.xlsx
Chr-trp-1h-PolyA_S95

value: 10 microM triptolide for 1 hr


title: Post 9h_activin_Rep3

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

data_processing:
Reads were mapped to the X. laevis v9. 2 genome (Xenbase)  and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Genome_build: X. laevis v9.2
Supplementary_files_format_and_content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

organism: Xenopus laevis

source_name: Post 9h_activin

growth_protocol: Xenopus laevis embryos were cultured in Steinberg's solution, and animal caps were removed from mid-blastula stage embryos (stage 8.5) with forceps and tungsten needles.

extract_protocol:
10 animal caps per sample, in triplicate, were homogenized into ISOGEN (Nippon Gene) at 25℃.  Total RNA was extracted according to the manufacture's protocol. Extracted total RNA was purified by using Rneasy Mini kit (QIAGEN), and eluted RNA was mixed with 2.5 volume iced ethanol and NaCl (final concentration, 33mM) for ethanol precipitation.  Precipitated RNA was centrifuged at 4℃ for 30 minutes.  After removal of supernatants, RNA pellets were washed with 80% ethanol.  RNA pellets were dried up and resuspended with RNase free water.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Dissected animal caps were cultured in activin A solution (50 ng/mL in Steinberg's solution containing 0.1% BSA and 0.1 mg/mL kanamycin sulfate) for 1, 3, 6 and 9 hours at 18℃.  As a negative control, animal caps were collected immediately after dissection in the absence of activin A treatment.

value: wild type

value: mid-blastula stage embryos (stage 8.5)

tag: tissue

value: animal cap

value: activin A solution (50 ng/mL) for 9h


title: GC0001 Gastric Cancer

value: Gastric Cancer

value: Male

value: IA

value: diff


title: Chromatin-associated PolyA+ RNA Trp 9h

description:
Libraries PolyA+ selected
All_counts.xlsx
Chr-trp-9h-PolyA_S97

value: mESC E14

value: 10 microM triptolide for 9 hr


title: Post 9h_activin_Rep2


title: Chromatin-associated PolyA+ RNA Fp 9h

description:
Libraries PolyA+ selected
All_counts.xlsx
Chr-fp-9h-PolyA_S94

value: 10 microM flavopiridol for 9 hr


title: IVM-Donor 2

description: TW- F

value: in vitro-matured metaphase II (IVM-MII) oocyte


title: Post 9h_activin_Rep1


title: AdMLΔ3'SS+SR_buffer_DMSO

description: SR protein buffer and 1.64% DMSO (vehicle) for 1 hour at 16 °C

value: 3' splice site mutation (cagCT > accTC)

value: SR protein buffer and 1.64percent DMSO (vehicle) for 1 hour at 16 degreeC


title: AdML+SR_buffer_NMIA_2mM

description:
SR protein buffer and 2 mM NMIA for 1 hour at 16 °C
AdSRbuf_Ad

value: SR protein buffer and 2 mM NMIA for 1 hour at 16 degreeC


title: Chromatin-associated PolyA+ RNA Fp 3h

description:
Libraries PolyA+ selected
All_counts.xlsx
Chr-fp-3h-PolyA_S93

value: Drosophila S2 RNA

value: 10 microM flavopiridol for 3 hr


title: AdMLΔ3'SS_DC_2mM

description: Denatured control 2 mM NMIA

value: Denatured control 2 mM NMIA


title: Post 6h_activin_Rep2

source_name: Post 6h_activin

value: wild type

value: mid-blastula stage embryos (stage 8.5)

value: activin A solution (50 ng/mL) for 6h


title: Chromatin-associated PolyA+ RNA Fp 1h

description:
Libraries PolyA+ selected
All_counts.xlsx
Chr-fp-1h-PolyA_S92

value: 10 microM flavopiridol for 1 hr


title: IVO-Donor 5

value: in vivo-matured metaphase II (IVO-MII) oocyte

value: not provided


title: Post 6h_activin_Rep3

value: animal cap


title: IVO-Donor 6


title: WCE PolyA+ RNA Fp 3h

description:
Libraries PolyA+ selected
All_counts.xlsx
WCE-fp-3h-PolyA_S84

value: mESC E14


title: IVO-Donor 7


title: AdML+SR_buffer_DMSO


title: Post 6h_activin_Rep1


title: AdMLΔ3'SS+U1_buffer_NMIA_2mM

description:
U1 snRNP buffer and 2 mM NMIA for 1 hour at 16 °C
Ad3_Ad3

value: U1 snRNP buffer and 2 mM NMIA for 1 hour at 16 degreeC


title: Chromatin-associated PolyA+ RNA 0h

description:
Libraries PolyA+ selected
All_counts.xlsx
Chr-0h-PolyA_S91

value: Untreated


title: Chromatin-associated total RNA RNaseA

description:
Libraries total depleted
All_counts.xlsx
Chr-RNaseA-total_S172

value: Permeabilization of cells + RNaseA


title: Post 3h_activin_Rep3

source_name: Post 3h_activin

value: activin A solution (50 ng/mL) for 3h


title: IVO-Donor 4


title: AdMLΔ5'SS_DC_2mM

description: Denatured control 2 mM NMIA

value: 5' splice site mutation (GTTGGGgtgag > ATTGGAaccac)


title: IVO-Donor 2


title: Post 3h_activin_Rep2


title: Chromatin-associated total RNA Mock

description:
Libraries total depleted
All_counts.xlsx
Chr-Mock-total_S171

value: Permeabilization of cells + PBS


title: Chromatin-associated total RNA Trp 9h

description:
Libraries total depleted
All_counts.xlsx
Chr-trp-9h-total_S170

value: Drosophila S2 RNA

value: 10 microM triptolide for 9 hr


title: AdMLΔ5'SS+U1_buffer_NMIA_2mM

description:
U1 snRNP buffer and 2 mM NMIA for 1 hour at 16 °C
Ad5_Ad5


title: Post 3h_activin_Rep1


title: IVO-Donor 1


title: IVO-Donor 8


title: Chromatin-associated total RNA Trp 3h

description:
Libraries total depleted
All_counts.xlsx
Chr-trp-3h-total_S169

value: 10 microM triptolide for 3 hr


title: AdMLΔ5'SS+U1_buffer_DMSO

description: U1 snRNP buffer and 1.64% DMSO (vehicle) for 1 hour at 16 °C

value: U1 snRNP buffer and 1.64percent DMSO (vehicle) for 1 hour at 16 degreeC


title: RNA-seq_SGC0946 3

city: Shanghai

first: Zhiwei

last: Liu

address: Zuchongzhi Road 555

country: China

institute: Chinese Academy of Sciences

data_processing:
The data were analyzed through the free online platform of Majorbio Cloud Platform
Genome_build: hg38
Supplementary_files_format_and_content: xls files include FPKM values for all Sample

growth_protocol: SU8686 cells plated in 10-cm dishes

extract_protocol:
Cells were washed by PBS for 3 times, lysed by Trizol reagent at room temperature and samples were kept on dry ice
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA

treatment_protocol: Treated with DMSO or 20 μM SGC0946 for 72 hr

tag: disease

value: Pancreatic Cancer

tag: disease subtype

value: Ductal Adenocarcinoma, exocrine

value: PAAD


title: Chromatin-associated total RNA Trp 1h

description:
Libraries total depleted
All_counts.xlsx
Chr-trp-1h-total_S168

value: 10 microM triptolide for 1 hr


title: Post 1h_activin_Rep2

source_name: Post 1h_activin

value: wild type

value: mid-blastula stage embryos (stage 8.5)

value: activin A solution (50 ng/mL) for 1h


title: Chromatin-associated total RNA Fp 9h

description:
Libraries total depleted
All_counts.xlsx
Chr-fp-9h-total_S167

value: mESC E14

value: 10 microM flavopiridol for 9 hr


title: RNA-seq_SGC0946 2


title: AdML_DC_2mM

description: Denatured control 2 mM NMIA

value: Denatured control 2 mM NMIA


title: RNA-seq_SGC0946 1


title: Pre_activin_Rep3

value: animal cap

value: untreated control (Pre_activin)


title: Post 1h_activin_Rep1


title: AdMLΔ3'SS+U1_buffer_DMSO

value: 3' splice site mutation (cagCT > accTC)


title: Chromatin-associated total RNA Fp 3h

description:
Libraries total depleted
All_counts.xlsx
Chr-fp-3h-total_S166

value: Drosophila S2 RNA

value: 10 microM flavopiridol for 3 hr


title: IVO-Donor 3

value: in vivo-matured metaphase II (IVO-MII) oocyte

value: not provided


title: RNA-seq_DMSO 3

value: Pancreatic Cancer


title: AdML+U1_buffer_NMIA_2mM

description:
U1 snRNP buffer and 2 mM NMIA for 1 hour at 16 °C
Ad_AdML

value: U1 snRNP buffer and 2 mM NMIA for 1 hour at 16 degreeC


title: Chromatin-associated total RNA Fp 1h

description:
Libraries total depleted
All_counts.xlsx
Chr-fp-1h-total_S165

value: 10 microM flavopiridol for 1 hr


title: RNA-seq_DMSO 2

value: Ductal Adenocarcinoma, exocrine

value: PAAD


title: AdML+U1_buffer_DMSO

value: wild type

value: U1 snRNP buffer and 1.64percent DMSO (vehicle) for 1 hour at 16 degreeC


title: Pre_activin_Rep2

value: mid-blastula stage embryos (stage 8.5)


title: Chromatin-associated total RNA 0h

description:
Libraries total depleted
All_counts.xlsx
Chr-0h-total_S164

value: mESC E14

value: Untreated


title: RNA-seq_DMSO 1


title: Post 1h_activin_Rep3

value: animal cap

value: activin A solution (50 ng/mL) for 1h


title: Pre_activin_Rep1

value: untreated control (Pre_activin)


title: AdML+U1_snRNP_NMIA_2mM

description:
U1 snRNP and 2 mM NMIA for 1 hour at 16 °C
AdU1_AdML

value: U1 snRNP and 2 mM NMIA for 1 hour at 16 degreeC


title: AdML+U1_snRNP_DMSO

description: U1 snRNP and 1.64% DMSO (vehicle) for 1 hour at 16 °C

value: U1 snRNP and 1.64percent DMSO (vehicle) for 1 hour at 16 degreeC


title: Scar.A.ATAC

status: Public on Jun 22 2021

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Pair-end reads were trimmed for Illumina adaptor sequences and transposase sequences and mapped to mm9 using Bowtie2 v2.1.0 with parameters – very sensitive.
For RNA seq-Gene-level counts matrix was generated using Rsubread version 1.30.9. Count files were normalized and analyzed DESeq2 and custom R scripts. For ATAC seq number of raw reads mapped to each peak in each sample was quantified using multicov in Beltools. Peak raw counts were normalized using DESeq2.
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: matrix table with raw gene counts for every sample

molecule: genomic DNA

source_name: Scar

growth_protocol: not applicable

extract_protocol:
RNA-seq was performed on FACS-isolated mouse fibroblast subpopulations from JUN and Control mice and human cultured KO and non-KO fibroblasts resuspended in TRIzol (10k cells/1ml). The RNA-seq data was collected from ten mice and pooled into two biological replicates. Thus, each biological replicate represents 10 wounds, as each mouse has two wounds. The human RNA-seq data was collected from 4 individual patients. RNA was isolated using the Rneasy Micro Kit (Qiagen, #74004), as per the manufacturer’s instructions. ATAC-seq libraries were generated using an average of 50,000 freshly isolated fibroblasts per replicate (biological replicates for mice samples and technical replicates for human samples) as described by Buenrostro et al 2013 with the following modifications. Transposition was performed in 50 uL reaction containing in-house made 2xTD buffer, Tn5 and 1% Digitonin.
Libraries were sequenced on an Illumina HiSeq 2500 machine. KO and non-KO fibroblasts from each skin type will be prepared for RNA-seq. ATAC libraries were prepared using the protocol found in ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide by Buenrostro et al (2015).

treatment_protocol: not applicable

tag: strain

value: Fibroblast Cells

value: skin

value: JUN wildtype

value: Fibroblasts


title: Scar.KO.B.ATAC

source_name: Scar-JUN KO

value: JUN KO


title: Kel.KO.B.ATAC

source_name: Keloid-JUN KO


title: Kel.B.ATAC

source_name: Keloid


title: Kel.KO.A.ATAC


title: Scar.KO.A.ATAC


title: NS.KO.A.ATAC

source_name: Normal Skin-JUN KO


title: HTS.KO.B.ATAC

source_name: Hypertrophic scar- JUN KO


title: NS.KO.B.ATAC


title: Kel.KO.B.RNA


title: Kel.KO.A.RNA


title: HTS.B.ATAC

source_name: Hypertrophic scar


title: HTS.A.ATAC


title: Kel.A.RNA


title: Kel.B.RNA


title: IVM-Donor 3

description: TW-B

value: in vitro-matured metaphase II (IVM-MII) oocyte


title: Kel.A.ATAC


title: Scar.KO.A.RNA


title: NS.KO.B.RNA


title: Scar.A.RNA


title: Scar.B.ATAC


title: NS.KO.A.RNA


title: NS.B.RNA

source_name: Normal Skin


title: NS.B.ATAC


title: NS.A.RNA


title: NS.A.ATAC


title: HTS.KO.A.ATAC


title: HTS.KO.B.RNA


title: HTS.B.RNA


title: Scar.KO.B.RNA


title: HTS.A.RNA


title: MR42F_Washout_MDV_3

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

description: RNA170713JA_MR42F_Washout_MDV_3_S21_L003

data_processing:
Aligned to hg19 using STAR 2.5.3a
RSEM v1.2.31 for quantification of expressed genes annotated by gencode v19
DESeq2 for differential expression analysis, FDR < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: raw_counts

molecule: polyA RNA

growth_protocol: Grown in RPMI + 10% FBS

extract_protocol:
Trizol (Life Technologies) extraction, RNEasy (Qiagen) purifcation
Aligent SureSelect Strand-Specific mRNA Library Prep

tag: cell line

value: prostate carcinoma cell line

value: Enzalutamide-resistant

value: Enzalutamide


title: MR42F_Washout_Veh_3

description: RNA170713JA_MR42F_Washout_Veh_3_S18_L003

value: Vehicle


title: HTS.KO.A.RNA


title: MR42F_Washout_Veh_1

description: RNA170713JA_MR42F_Washout_Veh_1_S16_L003


title: MR42F_Washout_Veh_2

description: RNA170713JA_MR42F_Washout_Veh_2_S17_L003


title: MR42D_Maintenance_JQ1_3


title: MR42D_Maintenance_JQ1_2


title: MR42F_Maintenance_MDV_2


title: MR42F_Maintenance_MDV_3


title: MR42F_Maintenance_MDV_1


title: MR42D_Maintenance_JQ1_1


title: MR42F_Washout_MDV_1

description: RNA170713JA_MR42F_Washout_MDV_1_S19_L003


title: Scar.B.RNA


title: MR42D_Maintenance_ARV-771_3


title: MR42D_Maintenance_ARV-771_2


title: MR42D_Maintenance_Veh_2


title: MR42D_Maintenance_ARV-771_1


title: MR42D_Maintenance_Veh_1


title: MR42D_Maintenance_Veh_3


title: V16D_MDV_1

value: castration-resistant


title: V16D_MDV_2


title: V16D_Veh_1


title: V16D_MDV_3


title: V16D_Veh_3


title: MR42F_Washout_MDV_2

description: RNA170713JA_MR42F_Washout_MDV_2_S20_L003


title: LNCaP_Veh_3

value: LNCaP

value: wild type


title: LNCaP_Veh_1


title: LNCaP_MDV_3


title: LNCaP_MDV_2


title: MR42D_Washout_Veh_1 [ATAC-seq]

data_processing:
Aligned to hg19 with bowtie2 (--very-sensitive option)
Removed mitochondrial reads, non0uniquely aligned reads, and PCR duplicateds
Peak calling with MACS2 (-q 0.01)
Peak files merged uing 'merge' function in bedtools, and quantified with 'multicov' (-q10 to exclude poorly mapping reads), and -f 0.05 to exclude minmally overlapping reads.
DESeq2 on read counts to identify hpyer and hypo-accesible peaks (log2 fold change >1, and adjusted p-value < 0.01)
Genome_build: hg19
Supplementary_files_format_and_content: The number of counts falling into the mearged peaks of all samples.

extract_protocol:
Nuclear isolation buffer
Nextera Library prep kit

treatment_protocol: Vehicle (DMSO) or MDV3100 (10uM)


title: LNCaP_MDV_1


title: MR42D_Washout_MDV_2 [ATAC-seq]


title: V16D_MDV_3 [ATAC-seq]


title: V16D_MDV_1 [ATAC-seq]


title: MR42D_Washout_Veh_2 [ATAC-seq]


title: V16D_MDV_2 [ATAC-seq]


title: V16D_Veh_1 [ATAC-seq]


title: MR42D_Maintenance_8MDV_2 [ATAC-seq]


title: V16D_Veh_2


title: 46_GA150_7

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: GA150 rep3

data_processing:
Fetuses were obtained by autopsy at GA105 (n=2), GA130 (n=2), and GA150 (n=3)
Total RNA was extracted from cells using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). RNA was quality checked, transcribed into complementary DNA using the Verso complementary DNA synthesis kit (AB-1453; LifeTechnologies, Carlsbad, CA), sheared, amplified, adaptor ligated and sequenced for pair-end RNA-Seq reads (Illumina Inc. San Diego, CA, USA).
Next-generation sequencing of equimolar pools of cDNA libraries was performed using a paired-end read 75 rapid flow cell on a HiSeq 2500 sequencing platform (Illumina), generating greater than 30 million raw reads per sample.
The raw sequenced reads were aligned from FASTQ files to the Macaca mulatta genome (build Mmul_1) using Partek software (https://www.partek.com/).
Genome_build: Mmul_1
Supplementary_files_format_and_content: Excel sheet including counts and FPKM normalized expression

organism: Macaca mulatta

source_name: Macaque prenatal lung

extract_protocol:
Total RNA was extracted from cells using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). RNA was quality checked, transcribed into complementary DNA using the Verso complementary DNA synthesis kit (AB-1453; LifeTechnologies, Carlsbad, CA), sheared, amplified, adaptor ligated and sequenced for pair-end RNA-Seq reads (Illumina Inc. San Diego, CA, USA)
Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina).

treatment_protocol: The lobes of the right lung were subdivided and processed for RNA, histology, and immunofluorescence analyses. The right upper lobe was cannulated at the lobar bronchus and inflated with 10% neutral buffered formalin (NBF) at a constant pressure of 25 cm for 2 hours. Tissue fixation was continued overnight at 4 °C. The next morning, the lobe was cut into 4-mm slices and fixed for another 4 hours, rinsed 3 times in PBS, and then divided into 2 pools of tissue.  Even-numbered slides were dehydrated through a graded series of ethanol (EtOH) solutions to xylene and processed into paraffin blocks; odd-numbered slices were cryo-protected in 30% sucrose in 1X PBS, stored at 4 °C, infiltrated with OCT (2 parts OCT:1 part 30% sucrose/PBS, v:v) for 24 hours, embedded in OCT, frozen in pre-chilled isopentane, and stored at -20 °C.

value: prenatal lung

tag: time


title: 37_GA150_6

description: GA150 rep2

growth_protocol: Fetuses were obtained by autopsy at GA105 (n=2), GA130 (n=2), and GA150 (n=3)


title: 28_GA130_4

description: GA130 rep2


title: 24_GA130_3

description: GA130 rep1


title: 41_GA105_2

description: GA105 rep2


title: 33_GA105_1

description: GA105 rep1


title: LNCaP_Veh_2


title: Xrn1-AID_auxin_60min

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

data_processing:
sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
Samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite (webb et al). Subsequently, the 3' adaptor was clipped with Cutadapt (-a TGGAATTCTCGGGTGCCAAGGATCTCGTATGCCGTCTTCTGCTTG -m 10) (martin M. embnet.journal, 2011) and the resulting insert  quality trimmed from the 3' end using Trimmomatic rolling mean clipping (bolger et al, 2014) (window size = 5, minimum quality = 25). At this stage the pyCRAC script pyFastqDuplicateRemover is used to collapse PCR duplicates and ensure each insert is represented only once. Each unique insert in our library is associated with a 6 nucleotides random tag within the 5' adaptor. During demultiplexing, pyBarcodeFilter retains this information in the header of each sequence. This information is used at this stage to better discern between entical inserts and PCR duplicates of the same insert. The resulting sequences are reverse complemented with Fastx reverse complement (part of the fastx toolkit, http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the R64 genome (cherry et al, 2012, nar) with bowtie2 (-N 1 -f) (langmead et al, 2012).
Genome_build: R64
Supplementary_files_format_and_content: Bigwig files providing coverage for all samples. All values are normalized to 10,000,000 reads.

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae cells

growth_protocol: For all datasets, 2L of yeast cells expressing Rpb1-HTP tag were grown at 30°C to OD600=0.6 in DO-Trp (drop out without tryptophan) . For nuclear depletion , rapamycin was added to a final concentration of 1µg/ml for the times indicated . For cellular depletion IAA (Indole-3’-Acetic Acid, Sigma) was added to a final concentration of 100µM  for the times indicated.

extract_protocol:
See the original publication for details
Library construction is described in Candelli et al., EMBO J, 2018 and in the associated manuscript. Barcodes used for demultiplexing are as follows: NNNNNNTGCAGC Xrn1-AA_no_rapamycin;  NNNNNNACTAGC Xrn1-AA_rapamycin_1h;  NNNNNNCTAAGC Xrn1-AA_rapamycin_2h; NNNNNNGAGAGC Xrn1-AA_rapamycin_5h;  NNNNNNGTCAGC xrn1∆; NNNNNNTGCAGC Xrn1-AID_no_auxin;  NNNNNNGTCAGC Xrn1-AID_auxin_15min  NNNNNNGAGAGC Xrn1-AID_auxin_30min  NNNNNNCGTAGC Xrn1-AID_auxin_60min

treatment_protocol: Cells were crosslinked for 50 seconds using a W5 UV crosslinking unit (UVO3). Cells were broken and extracts were prepared as described in the original publication.

value: addition of auxin for 60min

value: as w303, Rpb1-HTP::TRP1, Xrn1-miniAID1-Flag::KAN(MX6)::TIR1


title: Xrn1-AID_no_auxin

value: no treatment


title: Xrn1-AID_auxin_15min

value: addition of auxin for 15min


title: Xrn1-AID_auxin_30min

value: addition of auxin for 30min


title: MR42D_Washout_MDV_1 [ATAC-seq]


title: xrn1∆

value: as w303, Xrn1::KanMX4 Rpb1-HTP::TRPkl


title: Xrn1-AA_rapamycin_5h

value: addition of rapamycin  for 5h

value: as w303, Xrn1-FRB-GFP-KanMX4 fpr1::LEU RPL13A-2xFKBP12::TRP1 tor1-1 Rpb1-HTP::Ura


title: MR42D_Maintenance_8MDV_1 [ATAC-seq]


title: V16D_Veh_3 [ATAC-seq]


title: Xrn1-AA_rapamycin_2h

value: addition of rapamycin  for 2h


title: Xrn1-AA_no_rapamycin


title: Xrn1-AA_rapamycin_1h

value: addition of rapamycin  for 1h


title: V16D_Veh_2 [ATAC-seq]

value: prostate carcinoma cell line


title: 32_GA150_5

description: GA150 rep1


title: DS34.1_lib1: Species_Mix_Unfixed_techn.repl.1_biolog_rep2

city: Heidelberg

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

data_processing:
bcl2fastq Conversion Software (Illumina) was used to generate and demultiplex Fastq files from the sequence data
Drop-seq raw data was processed using the Drop-seq_tools-1.12 (https://github.com/broadinstitute/Drop-seq/releases)
Genome_build: BDGP6 v.91 (GCA 000001215.4) and GRCh37.87 (hg19)
Supplementary_files_format_and_content: digital gene expression matrix: tab-delimited file with columns = cells, and rows = transcript counts

organism:
Drosophila melanogaster
Homo sapiens

extract_protocol:
HEK 293T cells were washed with filtered PBS (0.22 µm filter) and enzymatically detached with 2 ml 1x TrypLE. The reaction was inactivated with 10 ml filtered PBS. Detached cells were filtered through a pre-equilibrated 40 µm cell strainer. Kc167 cells were mechanically detached, transferred to a 15 ml tube and centrifuged at 260 rcf for 5 min at room temperature. The cell pellet was washed once with filtered PBS, resuspended in filtered PBS and filtered through a 20 µm cell strainer. Cell concentrations were determined with a disposable Neubauer hemocytometer (C-Chip DHC-N01). Unfixed cells have been directly processed by scRNA-seq. For glyoxal fixation, 5 x 106 cells per condition and cell line were resuspended in 1 ml 3% glyoxal mix pH 4 (Richter et al., 2018) and incubated for 1 h on ice. Next, the fixed cell solution was centrifuged at 260 rcf for 5 min at 4°C, washed twice with filtered PBS and filtered through a pre-equilibrated 40 µm (HEK 293T) or 20 µm (Kc 167) cell strainer. HEK 293T and Kc167 single cells were equally mixed with a final cell concentration of 100 cells/µl and used for Drop-Seq.
Josephine Bageritz and Gianmarco Raddi, 2019;  doi: 10.1007/978-1-4939-9240-9_6.

tag: human cell line

tag: drosophila cell line

value: Unfixed


title: DS34.2_lib1: Species_Mix_Unfixed_techn.repl.2_biolog_rep2


title: DS27.7_lib1: Species_Mix_Glyoxal_techn.repl.1_biolog_rep2

value: Glyoxal-fixed


title: DS27.1_lib3: Species_Mix_Unfixed_techn.repl.2_biolog_rep1


title: PDX413ZT4Xenograft

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

data_processing:
adaptor trimming
filtering reads based on length
random sampling
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: no

source_name: Xenograft

extract_protocol: The detailed protocol was published on Genome-wide mapping of nucleotide excision repair with XR-seq (Nature Protocols volume 14, pages248–282 (2019), https://www.nature.com/articles/s41596-018-0093-7).

value: cisplatin


title: PDX119ZT16Xenograft


title: PDX413ZT12Xenograft


title: PDX119ZT0Xenograft


title: PDX119ZT12Xenograft


title: PDX119ZT20Xenograft


title: PDX413ZT20Xenograft


title: PDX413ZT0Xenograft


title: PDX413ZT8Xenograft


title: PDX413ZT16Xenograft


title: TotalSeq_Pool

first: Andrew

last: Dunn

state: Ohio

address: 3333 Burnet Ave R3.543

department: Gastroenterology

description: Mix of standard human and mouse cell lines stained with TotalSeq barcoding library

data_processing:
Base call conversion was performed using bcl2fastq v2.20.0
FASTQ files were aligned to either hg19 or mm10 v2 genomes using CellRanger v3.1.0
Read depth normalization, scailing, variable feature identification, PCA analysis, cluster identification, tSNE and UMAP clustering, and hashing demultiplexing was performed using Seurat v3.1 (HLO) / v3.2.2 (POLYseq / TotalSeq). Differential expression was performed using DESeq2 v1.28.0. Pathway analysis was performed by GAGE v2.38.3 on cell clusters normalized by the number of reads and log2 transformed. Pathway visualization was conducted through Pathview v1.28.1 using normalized, log2 transformed data.
Genome_build: hg19 / mm10 v2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene / oligo barcode of every cell.

organism:
Homo sapiens
Mus musculus

source_name: Standard cell lines

growth_protocol: For HLOs: iPSCs were seeded into 6-well plates (Corning) in mTeSR supplemented with Y-27632 and Laminin-511. Medium was changed to mTeSR alone the following day. Medium was switched to RPMI-1640 (Life Technologies, USA) containing 100 ng/ml Activin A (R&D Systems, USA) and 50 ng/ml bone morphogenetic protein 4 (BMP4; R&D Systems) on the second day. This constitutes day 1 (D1) of differentiation. Medium was switched to RPMI-1640 + 100 ng/ml Activin A + 0.2 % KnockOut Serum Replacement (KOSR; ThermoFisher Scientific) on D2. Medium was switched to RPMI-1640 + 100 ng/ml Activin A + 2.0 % KOSR on D3. Medium was switched to Advanced DMEM/F-12 + B-27 (Gibco, USA) + N2 (Gibco, USA) + 500 ng/ml fibroblast growth factor 4 (FGF-4; R7D Systems) and 3 µM CHIR99021 (R&D Systems) for D4-6, changed daily. A single cell suspension was isolated on D7 using Accutase. Cells were washed and resuspended in growth factor Matrigel at 50,000 cells / 50 µl. Into 6-well VWR plates were plated 50 µl drops. Medium was switched to Enrichment Medium (EP): Advanced DMEM/F12 (Gibco, USA) + 2 % B-27 (Gibco, USA) + 1 % N2 (Gibco, USA) + 1 % HEPES (1 M, Gibco, USA) + 1 % Pen/Strep (ThermoFisher Scientific) + 1 % L-glutamine (ThermoFisher Scientific) + 3 µM CHIR99021 (R&D Systems) + 5 ng/ml FGF2 (R&D Systems) + 10 ng/ml VEGF (Life Technologies) + 20 ng/ml EGF (R&D Systems) + 0.5 µM A83-01 (Tocris) + 50 µg/ml ascorbic acid (Sigma-Aldrich) for D7-10, changed on D7 and D9. Medium was switched to Advanced DMEM/F12 (Gibco, USA) + 2 % B-27 (Gibco, USA) + 1 % N2 (Gibco, USA) + 1 % HEPES (1 M, Gibco, USA) + 1 % Pen/Strep (ThermoFisher Scientific) + 1 % L-glutamine (ThermoFisher Scientific) + 2 µM Retinoic acid (Sigma, USA) for D11-14, changed on D11 and D13. Medium was switched to hepatocyte culture medium (HCM; Lonza, USA) + 10 ng/ml hepatocyte growth factor (HGF; PeproTech, USA) + OSM and changed every other day. HLOs were used between D21 – D24. For cell line culture: 3T3 and B16-F10 were maintained in DMEM + GlutaMAX + 10% FBS, Mouse ES cells were maintaned feeder-free on gelatin in serum-free ES medium + 2i + LIF, ESH9 was maintained feeder-free in mTeSR, HUVECs were maintaned in Loza EGM-2, HepG2 was maintained in MEM + 10% FBS, MEG-01 was maintained in RMPI 1640 + 10% FBS.

extract_protocol:
Samples were digested using accutase / TrypLE Express into single cell suspensions, resuspended in PBS or DMEM/F-12 + 2 % FBS, and filtered by a 40 µm mesh.
Single cell suspensions were immediately run on the 10x scRNAseq platform following digestion using the Chromium Single Cell 3' v3 (HLOs) or Next GEM 3' v3.1 (POLYseq / Totalseq) kits.

treatment_protocol: HepG2 was subject ot high glucose using DMEM + GlutaMAX + 10% FBS for 3 days.

value: Mix (3T3, ESH9, mES, HUVEC, Hep G2, B16-F10, MEG-01)

value: Untreated


title: PDX119ZT08Xenograft


title: PDX057ZT16Xenograft


title: PDX119ZT04Xenograft


title: γδ/αβTCR DN4 sulfatide stimulation replicate 3 [X20181217_1_JD6338_S24]

city: Boston

first: Jonathan

middle: S.

last: Duke-Cohan

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
source: 5,000 cells sorted by FACS
20181217_24_JD6338_S24

data_processing:
Aligned against the Ensembl GRCm38.75 reference genome using STAR aligner v2.5
Resultant BAM-format files were filtered to retain only primary-aligned reads (samtools view -F 0x0100)
Read counts were quantified at the exon level using subRead featureCounts (v1.4.4) software
Differential expression testing was performed using DESeq2 (v1.6.3) software
Individual results were considered to be of significance only if the p.adj ≤ 0.1 (q value; multiple-test corrections were performed using the Benjamini-Hochberg procedure)
Genome_build: Ensembl GRCm38.75
Supplementary_files_format_and_content: Column: Sample; Rows: Normalized gene expression

source_name: DN4 (CD44-CD25-) thymocytes

growth_protocol: growth in vitro on OP9-DL4 support cells

extract_protocol:
ARCTURUS PicoPure RNA isolation (Thermo-Fisher)
NuGen Ovation Human RNA-Seq Multiplex system

treatment_protocol: control or exposed to sulfatide presented by CD1d

tag: source cell type

value: in vitro developing hematopoietic stem cells

tag: genetic manipulation

value: expressing human γδ/mouse αβ chimeric TCR

tag: stimulation

value: mouse OP9-DL4 cells expressing single chain human CD1d/sulfatide


title: PDX057ZT12Xenograft

tag: treatment


title: γδTCR DN4 sulfatide stimulation replicate 3 [X20181217_1_JD6338_S20]

description:
source: 5,000 cells sorted by FACS
20181217_20_JD6338_S20

value: expressing human γδTCR


title: γδ/αβTCR DN3 sulfatide stimulation replicate 3 [X20181217_1_JD6338_S23]

description:
source: 5,000 cells sorted by FACS
20181217_23_JD6338_S23

source_name: DN3 (CD44-CD25+) thymocytes


title: γδTCR DN3 sulfatide stimulation replicate 3 [X20181217_1_JD6338_S19]

description:
source: 5,000 cells sorted by FACS
20181217_19_JD6338_S19


title: DS27.7_lib2: Species_Mix_Glyoxal_techn.repl.2_biolog_rep2


title: DS27.1_lib2: Species_Mix_Unfixed_techn.repl.1_biolog_rep1


title: PDX057ZT20Xenograft


title: PDX057ZT08Xenograft


title: γδTCR DN4 no stimulation replicate 3 [X20181217_1_JD6338_S18]

description:
source: 5,000 cells sorted by FACS
20181217_18_JD6338_S18

value: control mouse OP9-DL4 cells


title: γδTCR DN3 no stimulation replicate 3 [X20181217_1_JD6338_S17]

description:
source: 5,000 cells sorted by FACS
20181217_17_JD6338_S17


title: PDX057ZT04Xenograft


title: N3 (Naïve 3)

city: Rawalpindi

first: Huma

last: Shehwana

address: Pak Emirates Military Hospital, The Mall, Abid Majeed Rd

country: Pakistan

institute: National University of Medical Sciences

data_processing:
Quality control of RNA-seq FASTQ files was evaluated using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Paired end reads were aligned to human reference transcriptome (hg38) obtained from UCSC using Burrows-Wheeler Alignment (BWA-mem algorithm) (Li and Durbin 2009). Transcript specific count data of aligned samples was obtained using HTSeq-count tool (Anders, Pyl, and Huber 2015).
Supplementary_files_format_and_content: raw counts

source_name: Skin Biopsy

extract_protocol:
The skin biopsies were collected  from a total of eight participants in two categories: ordinary scabies subjects (“OS”; n = 05) and subjects naive to scabies and allergy with no known exposure to scabies or allergy (“naive”; n = 03). The OS cases were confirmed by clinical observation as well as identification of mites/mite parts under microscope. Skin biopsies were stored in RNAlater (Thermo Fisher Scientific, USA) at -20°C till Next-Generation Sequencing (NGS),
RNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing was done on an Illumina HiSeq4000 instrument, generating 150 bp, PE sequencing data.

tag: tissue type

value: Skin Biopsy

tag: age of patients

value: 31 years


title: OS5 (Ordinary scabies 5)

value: 34 years

tag: duration of exposure of disease

value: 1.5 weeks


title: γδ/αβTCR DN4 sulfatide stimulation replicate 2 [X20181217_1_JD6338_S16]

description:
source: 5,000 cells sorted by FACS
20181217_16_JD6338_S16


title: N2 (Naïve 2)

value: 36 years


title: N1 (Naïve 1)

value: 27 years


title: γδ/αβTCR DN4 no stimulation replicate 2 [X20181217_1_JD6338_S14]

description:
source: 5,000 cells sorted by FACS
20181217_14_JD6338_S14


title: γδ/αβTCR DN3 no stimulation replicate 2 [X20181217_1_JD6338_S13]

description:
source: 5,000 cells sorted by FACS
20181217_13_JD6338_S13


title: OS4 (Ordinary scabies 4)

value: 24 years

value: 2 weeks


title: γδ/αβTCR DN3 sulfatide stimulation replicate 2 [X20181217_1_JD6338_S15]

description:
source: 5,000 cells sorted by FACS
20181217_15_JD6338_S15


title: γδTCR DN3 no stimulation replicate 2 [X20181217_1_JD6338_S9]

description:
source: 5,000 cells sorted by FACS
20181217_09_JD6338_S09


title: γδTCR DN3 sulfatide stimulation replicate 2 [X20181217_1_JD6338_S11]

description:
source: 5,000 cells sorted by FACS
20181217_11_JD6338_S11


title: OS3 (Ordinary scabies 3)

value: 30 years


title: γδTCR DN4 no stimulation replicate 2 [X20181217_1_JD6338_S10]

description:
source: 5,000 cells sorted by FACS
20181217_10_JD6338_S10


title: OS2 (Ordinary scabies 2)

value: 11 years

value: 1 week


title: hPASMC_SPHK1_OE_rep3

city: Indianapolis

first: Robert

last: Stearman

state: IN

address: 950 W Walnut St

department: Medicine/Pulmonary

institute: Indiana Univeristy School of Medicine

data_processing:
FastQC/MultiQC v0.11.5
STAR aligner v2.5
NGSUtils/bamutils v0.5.9
subread/feature Counts v1.5.1
edgeR v3.22.5
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text file includes raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file includes Gene_Symbol, Gene_Description, FoldChange(SPHK1_OE/control), log2FoldChange(SPHK1_OE/control), p-value, q-value(FDR)

source_name: primary cell culture

growth_protocol: Human Pulmonary Artery Smooth Muscle cells (hPASMCs) were obtained from Lonza. Cells were cultured in SMGM2 containing growth supplements and 5% FBS (Lonza; complete medium) at 37°C in 5% CO2 in a humidified tissue culture incubator.

extract_protocol:
Total RNA was purified from transfected hPASMCs over-expressing SPHK1, as well as transfected vector DNA control, by using the RNeasy Plus Mini Kit (RNA > 200 nucleotides: Qiagen, Germantown, MD). Average RIN value was 9.4.
KAPA mRNA Hyperprep Kit

treatment_protocol: For transfection, 300,000 hPASMCs were cultured on 6-well plates followed by transfection of 3.75mg of plasmid using Xfect transfection reagent (Takara, Mountain View, CA) according to the manufacturer’s protocol. All experiments were performed in low passage cells (≤8). Cells were transfected in complete medium. The medium was replaced with complete medium after 4 hours, and the cells were collected after 48 hours and stored at -80 degrees C.

value: lung pulmonary artery

tag: cell type

value: pulmonary artery smooth muscle cells

tag: genotype/variation

value: SPHK1 over-expression


title: PDX057ZT0Xenograft

value: cisplatin


title: OS1 (Ordinary scabies 1)

value: 14 years


title: γδ/αβTCR DN4 sulfatide stimulation replicate 1 [X20181217_1_JD6338_S8]

description:
source: 5,000 cells sorted by FACS
20181217_08_JD6338_S08

value: in vitro developing hematopoietic stem cells

value: expressing human γδ/mouse αβ chimeric TCR

value: mouse OP9-DL4 cells expressing single chain human CD1d/sulfatide


title: hPASMC_control_rep3

tag: tissue

value: control


title: γδ/αβTCR DN4 no stimulation replicate 1 [X20181217_1_JD6338_S6]

description:
source: 5,000 cells sorted by FACS
20181217_06_JD6338_S06

value: control mouse OP9-DL4 cells


title: hPASMC_SPHK1_OE_rep2


title: γδ/αβTCR DN3 sulfatide stimulation replicate 1 [X20181217_1_JD6338_S7]

description:
source: 5,000 cells sorted by FACS
20181217_07_JD6338_S07


title: hPASMC_control_rep2


title: hPASMC_SPHK1_OE_rep1


title: γδ/αβTCR DN3 no stimulation replicate 1 [X20181217_1_JD6338_S5]

description:
source: 5,000 cells sorted by FACS
20181217_05_JD6338_S05


title: γδTCR DN3 sulfatide stimulation replicate 1 [X20181217_1_JD6338_S3]

description:
source: 5,000 cells sorted by FACS
20181217_03_JD6338_S03

value: expressing human γδTCR


title: γδTCR DN4 no stimulation replicate 1 [X20181217_1_JD6338_S2]

description:
source: 5,000 cells sorted by FACS
20181217_02_JD6338_S02


title: γδTCR DN3 no stimulation replicate 1 [X20181217_1_JD6338_S1]

description:
source: 5,000 cells sorted by FACS
20181217_01_JD6338_S01


title: RUNX1_6h_rep2

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

data_processing:
Genome alignment using bowtie2 (version 2.2.5) against the mm10 genome build (params: -k 50 --non-deterministic)
Peak calling using MACS2 against input (params: -f BAM -g 1.87e9 -B -p 10e-10 --nomodel)
Genome_build: mm10

source_name: peri-ovulatory granulosa cells

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Chromatin was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and input DNA by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: mice were injected with 5 IU eCG, following by 5 IU hCG after 46 hours. After 6 hours of hCG mice were culled for granulosa cell collection.

value: peri-ovulatory granulosa cells

value: CBA x C57BL/6 F1

tag: timepoint

value: 6h post-hCG

tag: antibody

value: RUNX1 antibody

tag: age

value: 21 days old mice


title: RUNX1_0h_rep2

source_name: pre-ovulatory granulosa cells

value: pre-ovulatory granulosa cells

tag: strain

value: 0h post-hCG


title: RUNX1_6h_rep1


title: pooled_input_6h

value: input


title: RUNX1_0h_rep1


title: POLYseq_Pool

description: Mix of standard human and mouse cell lines tagged with POLYseq barcoding library

tag: cell line

value: Mix (3T3, ESH9, mES, HUVEC, Hep G2, Hep G2 + high glucose, B16-F10, MEG-01)

value: Hep G2 treated with high glucose (4.5 g/l, 25 mM) for 3 days


title: RSA-1

city: Wuhan

first: Long

last: Yu

state: Hubei

address: 13 Hangkong Road, Hankou

institute: Tongji medical college

data_processing:
RNA-seq data was mapped to human genome (GRCh38) using HISAT2 (v2.2.0). FeatureCounts integrated into Subread (v2.0.0) was used for counting reads with GENECODE gene annotation (v34). Then the analysis of differentially expressed genes (DEGs) was performed using DESeq2 R package (v1.30.0). DEGs was selected as follow: adjusted p-value < 0.05 and |log2FoldChange| > 1. Gene counts were normalized by DESeq2 and converted to log_2〖(normalized counts+1〗) format. Z-score of normalized gene expression by genes (each gene with 6 samples have a zero mean and standard deviation is one) was showed by heatmap.
For GO and KEGG enrichment analysis, ClusterProfiler R package (v3.18.0) was used. Benjamini and Hochberg method was used to adjusted p-value. Significantly enriched GO term and KEGG pathway were selected under the criteria: adjusted p-value < 0.05.
The abundances of immune cells were estimated by CIBERSORTx web server and the LM22 signature matrix which contains 547 genes distinguishing 22 human hematopoietic cell phenotypes. B-mode batch correction was enabled and quantile normalization was disabled.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: decidua

extract_protocol:
decidua were collected, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Total RNAs of decidua tissues were extracted using Trizol (Invitrogen, CA, USA) according to the manufacturer’s instruction. Oligo(dT)-attached magnetic beads were used to purified mRNA, which then was fragmented into small pieces with fragment buffer at appropriate temperature to generate final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which has more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on the BGIseq500 platform (BGI-Shenzhen, China).

tag: patients age

tag: sample ga/(d)

tag: disease state

value: Recurrent spontaneous abortion (RSA)

value: decidua


title: RSA03


title: RSA04


title: HC06

value: healthy control


title: MR42D-DMSO_AR_ChIP

description: 11_02N1_00BNOHSU_MR42D-DMSO_AR_hs-dm_i95

data_processing:
Illumina CASSAVA used for base calling
Bowtie2 w/ default parameters
MACS2 with -q 1e-7 to call peaks
HOMER to call peaks of differential binding
annotatePeaks tool from HOMER to annotate nearest gene
bamCoverage tool in deepTools package to generate bigwig file with 1X normalization
Genome_build: hg19
Supplementary_files_format_and_content: Annotated called peaks from MACS2 in txt format as a dataframe

source_name: Chromatin immpunopercipitation of AR in MR42D cells treateated with vehicle (DMSO)

extract_protocol:
Cells cross-linked with formaldhyde, lysed and sonicated with a Bioruptor Pico, incubated overnight with antibody, and resuspended in protein A magnetic beads the next day. After washing, immune complexes were eluted, cross-links were reversed, and DNA was purified with MiniElute PCR purification kit
Illumina TruSeq DNAseq kit

treatment_protocol: Vehicle (DMSO) or MDV3100 (10 uM)

value: prostate carcinoma cell line

tag: genotype

value: Enzalutamide-resistant

value: Vehicle

tag: chip antibody

value: AR (Santa Cruz, sc-13062)


title: MR42D-MDV_BRD4_ChIP

description: 04_02NA_00BNOHSU_MR42D-MDV_BRD4_hs-dm_i72

source_name: Chromatin immpunopercipitation of BRD4 in MR42D cells treateated with MDV (10 uM)

tag: treatment

value: Enzalutamide

value: BRD4 (Bethyl Laboratories, A301-985A)


title: γδTCR DN4 sulfatide stimulation replicate 1 [X20181217_1_JD6338_S4]

description:
source: 5,000 cells sorted by FACS
20181217_04_JD6338_S04

tag: source cell type

value: in vitro developing hematopoietic stem cells

tag: genetic manipulation

value: expressing human γδTCR

tag: stimulation

value: mouse OP9-DL4 cells expressing single chain human CD1d/sulfatide


title: HC04


title: pooled_input_0h

tag: cell type

value: pre-ovulatory granulosa cells

value: CBA x C57BL/6 F1

value: 21 days old mice


title: MR42D-MDV_AR_ChIP

source_name: Chromatin immpunopercipitation of AR in MR42D cells treateated with MDV (10 uM)


title: MR42D-DMSO_H3K27Ac_ChIP

description: 01_02N5_00BNOHSU_MR42D-DMSO_H3K27Ac_hs-dm_i91

source_name: Chromatin immpunopercipitation of H3K27Ac in MR42D cells treateated with vehicle (DMSO)

value: H3K27Ac (Active Motif, 39133)


title: HC02


title: DS34.5_lib1: Species_Mix_Glyoxal_biolog_rep2

tag: human cell line

tag: drosophila cell line

value: Glyoxal-fixed


title: MR42D-DMSO_BRD4_ChIP

description: 03_02NK_00BNOHSU_MR42D-DMSO_BRD4_hs-dm_i71

source_name: Chromatin immpunopercipitation of BRD4 in MR42D cells treateated with vehicle (DMSO)


title: KO mice fed an AIN-93-based diet

city: Nagoya

first: Kyohei

last: Furukawa

address: Furo-cho, Chikusa-ku

institute: Nagoya University

description: Gene expression data from KO (Interleukin-10 knockout) mice

hyb_protocol: 11 ug of cRNA were hybridized onto the array chip at 45 °C for 16 h and stained with streptavi-din-phycoerythrin using GeneChip™ Fluidics Station 450

scan_protocol: The image data was detected with GeneChip™ Scanner 3000.

data_processing: The data were converted to CEL file format using Affymetrix GeneChip® Command Console. The numerical conversion and the normalization  were performed using R ver. 3.5.1 and Affymetrix Microarray Analysis Suite 5 (Affymetrix), respectively.

label: biotin

source_name: Back skin sample from KO mice

label_protocol: The 250 ng of pooled RNA isolated from mouse skin samples were reverse-transcribed to single-strand cDNA using Genechip™ 3’ IVT Express Kit

growth_protocol: The mice were individually housed in cages in a temperature-controlled (23 ± 2 °C), 12 h light-dark cycle environment.

extract_protocol: Crushed skin samples were homogenized with 1 mL of TRIzol reagent, and then 200 µL of chloroform was added. The mixture was centrifuged at 12,000× g, 4 °C for 15 min, and the supernatant was mixed with Nucleospin® RNA RA1 buffer and ethanol. Further experi-mental procedures were per the manufacturer’s instructions.

treatment_protocol: Four-week-old WT (C57BL/6J) and KO (Interleukin-10 knockout)  mice were fed an AIN-93-based diet or an 8% pESM-supplemented diet for 28 weeks. After the experimental period, the back skin was collected under deep anesthesia with isoflurane, removed the dermal white adipose tissue from collected skin sample.

value: Interleukin-10 knockout

tag: diet

value: AIN-93-based diet

tag: gender

value: Male

tag: tissue

value: Back skin


title: QSC Calcr-cKO Biological rep1

city: suita

first: so-ichiro

last: fukada

address: 1-6 yamadaoka

institute: osaka University

description: Gene expression data from conditional Calcr-cKO muscle satellite cells

hyb_protocol: Following fragmentation, labeled cRNA were hybridized for 16 hr at 45Cº on GeneChip Mouse Genome Array (430 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Affymetrix MAS 5.0 with p-value cuttoffs of 0.04 and 0.06 for present, marginal, and absent.

source_name: Freshly isolated muscle satellite cells from Pax7-CreERT2::Calcr flox/flox::Rosa-YFP mice

label_protocol: GeneChip® Eukayotic Small Sample Target Labeling Assay Version II.

growth_protocol: These samples were directly isolated from mouse skeletal muscle. Therefore, the cells were not cultured in vitro.

extract_protocol: Used Qiagen Rneasy Mini Kit according to instructions therein.

treatment_protocol: Tamoxifen was treated

tag: age

value: 10 weeks

value: murine muscle satellite cells


title: QSC Calcr-cKO Biological rep2


title: MR42D-MDV_H3K27Ac_ChIP

description: 02_02N6_00BNOHSU_MR42D-MDV_H3K27Ac_hs-dm_i68

source_name: Chromatin immpunopercipitation of H3K27Ac in MR42D cells treateated with MDV (10 uM)

tag: cell line

value: prostate carcinoma cell line

value: Enzalutamide-resistant


title: WT mice fed an AIN-93-based diet

description: Gene expression data from WT (C57BL/6J) mice

source_name: Back skin sample from WT mice

value: WT C57BL/6J


title: QSC Cont Biological rep1

description: Gene expression data from control muscle satellite cells

source_name: Freshly isolated muscle satellite cells from Pax7-CreERT2::Calcr+/+::Rosa-YFP mice

value: Pax7Cre/+::Calcr +/+::Rosa-YFP/YFP


title: KO mice fed an 8% pESM-supplemented diet

description: Gene expression data from 8 % pESM-supplemented KO (Interleukin-10 knockout) mice

source_name: Back skin sample from KOE mice

value: 8% pESM-supplemented diet


title: QSC Cont Biological rep2


title: LacI negRV3

first: Alexander

last: Garruss

address: 77 Avenue Louis Pasteur, Rm 238

department: Genetics

institute: Harvard Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Paired-end 300bp reads were collapsed using PEAR v.0.9.8 using default settings.
Collapsed reads were trimmed to remove barcodes and primer sites as published in Taylor et. al 2015 Nature Methods. We collected the sequencing read interior to the sequencing primer locations on each end and placed this subsection at the appropriate position in the full coding region.
Full-length coding sequence counts for both pre- and post-selection conditions were merged. A pseduo-count of 0.5 was added to each sequence count. A fold change was computed by taking the sequencing count post-selection divided by the count pre-selection. In order to compare values across tiles, we scaled the log2 fold changes by min-max scaling. The maximum value (upper limit) for each tile was the mean log2 fold change for variants counted more than 100 times post-selection. The minimum value (lower limit) for each tile was the mean log2 fold change for variants having at least ten counts in the pre-selection condition but less than three counts in the post-selection. These values correspond to the dynamic limits of the assay as the log2 fold changes level off even as the sequencing depth increases. For analyses at the protein sequence level, the sum of synonymous sequencing read counts was used. We further removed sequences containing early stop codons or sequences containing five or more consecutive mismatches.
Genome_build: >LacI_reference GAGCACATCAGCAGGACGCACTGACCGAATTCATTAAAGAGGAGAAAGGTACCGTGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCgCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTgTTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTTAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAAGCTAGCTTAGCAGAAAGTCAAAAGCCTC
Supplementary_files_format_and_content: The processed data file utilized lac repressor variants basal transcriptional repression function after mutation from ten tiles of synthesized single mutations (NCBI GEO Series GSE75009), and six tiles designed from Rosetta simulations (this study). Depletion values for LacI protein variants; tabular format; sequencing counts; wild-type mismatches; raw and normalized repression values (pre/post negative selection).

organism: Escherichia coli

source_name: plasmid

growth_protocol: For library transformations, the screening strain was made electrocompetent by harvesting early log-phase cells (10 mL per transformation at OD600 nm = 0.15–0.25), removing salt through two washes with ice cold 10% glycerol, and resuspended in 50 μL cold 10% glycerol. Ten ng of library plasmid were electroporated into the competent cells, which were recovered for 1 hr in 1 mL SOC medium. To estimate the number of transformants, 1 μL recovered cells were plated on selective LB spectinomycin medium, and the remainder of the recovered cells were added to 10 mL of LB spectinomycin medium and selected overnight. Screening strain cells expressing LacI variants that do not bind to operator DNA constitutively express tolC and gfp; these were eliminated through negative selection by overnight selection with colicin E1 protein. We added five μL of saturated library transformation culture to 150 μL LB spectinomycin medium supplemented with tenfold serial dilutions of purified colicin E1 protein (2.73 mg/mL), in the range from 1:100 to 1:1,000,000; a control population of the same library was grown overnight without colicin E1. Enrichment of DNA-bound lacI variants was verified by flow cytometry the next day by measuring the fraction of GFP+ cells in the colicin E1 incubated and control populations. A 1:100,000 dilution of colicin E1 (20.7 ng/mL) was generally found to be optimal.

extract_protocol:
Plasmids were prepped from each library using a Spin Miniprep Kit (Qiagen #27104). A nested amplicon PCR strategy was used to append barcodes and sequencing adapters. In a first round of PCR, amplicon primers were used to amplify 300 bp regions of the lacI gene and add standard Illumina MiSeq sequencing primer binding sites. The first six bases to be read in sequencing read 1 were degenerate to increase complexity and aid in base calling. In a second round of PCR, barcoding primers were used to append barcodes and flow cell adapter sequences.
Amplicons were purified, quantified using Kapa Biosystems Library Quanitification kit (part number KK4824), and normalized. Libraries were sequenced on the Illumina MiSeq using MiSeq Reagent Kit v3, 600 cycle (part number MS-102-3003) according to the manufacturer’s protocol.

treatment_protocol: The lacI gene variant libraries were constructed by cloning oligonucleotides encoding the desired mutations into plasmid pSC101_lacI_specR amplified by PCR with primers (Supplementary Table 6; Taylor, et al. Nature Methods. 2015) to appropriately linearize, add BsaI recognition sequence (5’-GGTCTCN), and remove the wild type lacI coding sequence segment to be replaced.Constructing the single residue replacement library involved replacing lacI codons from 3–359 with one missense codon encoding each of the remaining 19 natural amino acids (6,802 sequences). Oligos encoding these mutations were synthesized on a B3 Synthesizer (CustomArray, Inc., Bothell, WA), and were organized into the following tiles spanning the lacI gene: (#1)3–38, (#2)39–74, (#3)75–110, (#4)111–146, (#5)147–182, (#6)183–218, (#7)219–254, (#8)255–290, (#9)291–326, (#10)327–359.

tag: strain

value: K12 MG1655 EcNR2


title: Laci negWV3


title: LacI WV3


title: LacI negWV2


title: LacI RV3


title: D31_RAD001_heavy_R2

city: Laurel

first: Amanda

last: Ernlund

address: 11100 Johns Hopkins Rd

department: REDD

institute: Johns Hopkins APL

description: Transcriptome and translatome

hyb_protocol: label, hybridization, and scanning protocols were performed by the NYUMC genomics core facitlity, located at NYU Health NY, NY

data_processing: Gene-level probeset summary of microarray data were obtained using RMA background correction and quantile normalization provided in Expression Console Software, version 1.4.1 (Affymetrix)

source_name: T reg cells

growth_protocol: Naïve T cells from healthy donor PMBCs were activated in vitro with 10 mg/ml -plate bound anti-CD3, 1 mg/ml soluble anti-CD8, 50 U/ml rIL-2 in 5% FBS X-Vivo 15

extract_protocol: Cycloheximide-treated and frozen cells were lysed and processed as previously described (Silvera D, Ernlund A, Arju R, Connolly E, Volta V, Wang J, Schneider RJ. 2017. mTORC1 and -2 coordinate transcriptional and translational reprogramming in resistance to DNA damage and replicative stress in breast cancer cells. Mol Cell Biol 37:e00577-16.) Equal amount of RNA content (100 mg) were separated on a sucrose gradient. RNA from total extract and heavy polysomes (4 or more ribosomes per mRNA) were extracted by Qiagen RNeasy MiniElute Cleanup kit (cat. #74204)

treatment_protocol: Concurrently to activation, cells were added with 20 nM RAD001+ 2ng/ml TGFbeta, 20 nM RAD001, 2 ng/ml TGFbeta, or left untreated. Cells were differentiated for 13 days, adding IL-2 every 2-3 days and splitting cells when they reached 3-4 million/ml

value: primary T cells from healthy donors

value: heavy polysome, RAD001 treated


title: LavI negRV2


title: LacI WV2


title: LacI WV1


title: X2_24 h

city: Guangzhou

first: Wang

last: Li

address: Wushan road, Tianhe district

institute: Guangdong Academy of Agricultural Sciences

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: PGSC v4.03

organism: Solanum tuberosum

source_name: potato

extract_protocol:
Total RNA of potato tubers was extracted from each sample using TiangenRNA extraction kit (Tiangen Biltech Co. Ltd, Beijing, China)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: potato tubers

value: 24 h after cut-wounding


title: LacI negRV1


title: D31_untreated_heavy_R2

description: Transcriptome and translatome

scan_protocol: label, hybridization, and scanning protocols were performed by the NYUMC genomics core facitlity,  located at NYU Health NY, NY

value: heavy polysome, untreated


title: D31_RAD001_total_R2

description: Transcriptome and translatome

label_protocol: label, hybridization, and scanning protocols were performed by the NYUMC genomics core facitlity, located at NYU Health NY, NY

value: total RNA, RAD001 treated


title: D17_29_untreated_total_R1

description: Transcriptome and translatome

value: total RNA, untreated


title: LacI RV1


title: D31_TGFbeta_total_R2

description: Transcriptome and translatome

value: total RNA, TGFbeta treated


title: D17_29_RADTGFbeta_heavy_R1

description: Transcriptome and translatome

value: heavy polysome, RAD001+TGFbeta treated


title: D17_29_RAD001_total_R1

description: Transcriptome and translatome


title: D31_untreated_total_R2

description: Transcriptome and translatome


title: D17_29_RADTGFbeta_total_R1

description: Transcriptome and translatome

value: total RNA, RAD001+TGFbeta treated


title: D17_29_TGFbeta_heavy_R1

description: Transcriptome and translatome

value: heavy polysome, TGFbeta treated


title: D17_29_TGFbeta_total_R1

description: Transcriptome and translatome


title: D31_RADTGFbeta_heavy_R2

description: Transcriptome and translatome


title: D31_RADTGFbeta_total_R2

description: Transcriptome and translatome


title: D17_29_untreated_heavy_R1

description: Transcriptome and translatome


title: D17_29_RAD001_heavy_R1

description: Transcriptome and translatome


title: LacI RV2


title: X2_12 h

value: 12 h after cut-wounding


title: X2_ 0 h

value: 0 h after cut-wounding


title: D6_4 h

value: 4 h after cut-wounding


title: D6_12 h


title: D6_24 h


title: D31_TGFbeta_heavy_R2

description: Transcriptome and translatome


title: D6_0 h


title: γδTCR DN4 sulfatide stimulation replicate 2 [X20181217_1_JD6338_S12]

description:
source: 5,000 cells sorted by FACS
20181217_12_JD6338_S12

source_name: DN4 (CD44-CD25-) thymocytes

value: in vitro developing hematopoietic stem cells

value: expressing human γδTCR

value: mouse OP9-DL4 cells expressing single chain human CD1d/sulfatide


title: LacI negWV1

value: K12 MG1655 EcNR2


title: day28_MLL_AF4_BR3

city: Frankfurt am Main

first: Lukas

last: Jost

address: Altenhöferallee 3

institute: GenXPro GmbH

data_processing:
Illumina bcl2fastq software used for basecalling.
Cleaned reads were mapped onto GRCh38 genome using bowtie2 and raw counts were obtained using HTSeq
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count values for each group
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HEK293T cells with inducible MLL-AF4

growth_protocol: stably transfected HEK293T cells were expanded in DMEM/FCS

extract_protocol:
Qiagen RNA Purification with DNAse I treatment
ATAC-Seq libraries were produced using Nextera Transposase from freshly isolated nuclei, as described by Buenrostro et al 2005 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/

treatment_protocol: transgene induction was carried out with 1µg/ml doxyxcycline for 48h

value: inducible MLL-AF4

value: HEK293T kidney cells

tag: time

value: day 28


title: day3_MLL_AF4_BR2

description: transgene was induced for 48h by 1µg/ml Doxycycline

value: day 3


title: day3_AF4_MLL_BR3

source_name: HEK293T cells with inducible AF4-MLL

value: inducible AF4-MLL


title: day3_MLL_AF4_plus_AF4_MLL_BR3

source_name: HEK293T cells with constitutive MLL-AF4 plus inducible AF4-MLL (48h)


title: day3_AF4_MLL_BR2


title: day3_MLL_AF4_BR3


title: day3_MLL_AF4_BR1


title: day3_AF4_MLL_BR1


title: day28_MLL_AF4_plus_AF4_MLL_BR3

value: constitutive MLL-AF4 plus inducible AF4-MLL (48h)


title: day3_MLL_AF4_plus_AF4_MLL_BR1


title: day28_MLL_AF4_plus_AF4_MLL_BR1


title: day3_MLL_AF4_plus_AF4_MLL_BR2


title: day28_MLL_AF4_plus_AF4_MLL_BR2


title: day28_AF4_MLL_BR1


title: day28_AF4_MLL_BR2


title: day28_MLL_AF4_BR2


title: day28_MLL_AF4_BR1


title: MOCK BR2

source_name: HEK293T cells with empty vector (pSBTet-GP)

value: empty vector (pSBTet-GP)

value: MOCK


title: MOCK BR1


title: day3 BR3


title: MOCK BR3


title: day28 BR2

source_name: HEK293T cells with constitutive MLL-AF4

value: constitutive MLL-AF4


title: day3 BR2


title: day28 BR3


title: day3 BR1


title: day28 BR1


title: day28_AF4_MLL_BR3


title: day0 BR2


title: day0 BR1


title: 8_after 1st treatment

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

institute: Tsukuba university

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 20.0.0; Qiagen, Redwood City, CA).
Genome_build: hg19

source_name: Bronchial tissues

extract_protocol:
Total RNA was extracted from homogenized bronchial tissues using TRIzol reagent (GIBCOBRL, Gaithersburg, MD). The RNA quantity of 24 samples (three per patient prior to BT1 [baseline], prior to BT2, and prior to BT3) was measured by a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and the quality was monitored using the RNA 6000 Pico kit (Agilent). Then, 500 ng of total RNA was rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) and converted to an Illumina sequencing library using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). Libraries were validated with Bioanalyzer (Agilent Technologies) to determine the size distribution and concentration. Sequencing was performed by Tsukuba i-Laboratory LLP (Tsukuba, Japan) using NextSeq500 (Illumina) with the paired-end 36-base read option. Sequencing reads were mapped on the hg19 human reference genome and quantified using CLC Genomics Workbench (CLC-GW) version 20.0 (Qiagen). Differentially expressed genes were identified by filtering in accordance with the P-values obtained by Empirical Analysis of the DGE tool in CLC-GW.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bronchial tissues

tag: timepoint

value: after 1st treatment

tag: disease state

value: severe asthma


title: 8_after 2nd treatment

value: after 2nd treatment


title: 8_at baseline

value: at baseline


title: 7_after 2nd treatment


title: 7_at baseline


title: 5_at baseline


title: 6_after 1st treatment


title: 5_after 2nd treatment


title: 6_at baseline


title: 4_after 2nd treatment


title: 5_after 1st treatment


title: 4_after 1st treatment


title: 3_after 2nd treatment


title: 4_at baseline


title: 6_after 2nd treatment


title: day0 BR3

tag: genotype


title: 3_at baseline


title: 3_after 1st treatment


title: 2_after 1st treatment


title: 2_after 2nd treatment


title: 1_after 1st treatment


title: 1_after 2nd treatment


title: 7_after 1st treatment


title: 1_at baseline


title: P12T -W thaw C

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

description:
derived from P12T primary tissue
gene_count_matrix.csv
none

data_processing:
Basecalls performed using the ShortRead R/Biocoductor package
Quality, adapters and contamination filtering were performed using the Trimmomatic command-line tool
The Burrows-Wheeler Aligner (WES) and the STAR aligner (RNA-seq) were used to align reads to the NCBI GRCh38 human genome reference assembly
Samtools and Picard were used for data conversion, indexing and manipulation (WES)
The Mutect2 method was used for somatic single nucleotide variants (SNVs), insertions and deletions (indels) calling via local assembly of haplotypes following the GATK somatic short mutation calling best practice workflow. Variants that passed the filtering steps were annotated using the ANNOVAR software tool.
Transcript assembly and the number of reads per gene were determined using Stringtie (RNA-seq)
Differentially expressed genes were identified using the DESeq2 R/Bioconductor package. Extended gene annotations (including HGNC gene symbol, description and transcript type) were obtained using the biomaRt R/Bioconductor package
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files (vcf format) include filtered called variants for each two-samples comparison (WES)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (RNA-seq)

source_name: Colon tissue

growth_protocol: colon organoids were grown in Advanced DMEM/F12 supplemented with 2 mM Glutamax, 10 mM HEPES, 100 U*mL-1 penicillin and 10 g*mL-1 streptomycin, 1X B27, 1.15 mM N-acetylcysteine, 10 mM Nicotinamide, 10 nM Gastrin I, 10 nM Prostaglandin E2, 500 nM A83-01, 50 ng mL-1 mEGF, 3 µM SB202190, 10% Noggin Conditioned Medium, 20% R-Spondin1 Conditioned Medium, 10 µM Y-27632, 100 μg mL-1 Primocin with or without 50% Wnt3a Conditioned Medium

extract_protocol:
The SureSelectXT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library protocol was used to generate libraries. The Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
WES and RNA libraries were prepared for paired-end sequencing using standard Illumina protocols

value: colon

tag: Sex

value: female

tag: sample type

value: colon organoids

tag: # of passage

tag: days in culture


title: P12T -W late B


title: P12T -W late C


title: P12T -W late A


title: P12T -W early B


title: P12T -W thaw A


title: P12T -W early C


title: P12T -W thaw B


title: P12T -W early A


title: 2_at baseline


title: P12N late B

description:
derived from P12N primary tissue
gene_count_matrix.csv
none


title: P12N thaw C


title: P12N late C


title: P12N early B


title: P14T -W late

description:
derived from P14T primary tissue
P14TRlate_P14Nearly_filtered_somatic_funcotated_short.vcf
P14TRlate_P14Ttissue_filtered_somatic_funcotated_short.vcf
P14TWlate_P14TRlate_filtered_somatic_funcotated_short.vcf

data_processing:
Library strategy: whole exom sequencing
Basecalls performed using the ShortRead R/Biocoductor package
Quality, adapters and contamination filtering were performed using the Trimmomatic command-line tool
The Burrows-Wheeler Aligner (WES) and the STAR aligner (RNA-seq) were used to align reads to the NCBI GRCh38 human genome reference assembly
Samtools and Picard were used for data conversion, indexing and manipulation (WES)
The Mutect2 method was used for somatic single nucleotide variants (SNVs), insertions and deletions (indels) calling via local assembly of haplotypes following the GATK somatic short mutation calling best practice workflow. Variants that passed the filtering steps were annotated using the ANNOVAR software tool.
Transcript assembly and the number of reads per gene were determined using Stringtie (RNA-seq)
Differentially expressed genes were identified using the DESeq2 R/Bioconductor package. Extended gene annotations (including HGNC gene symbol, description and transcript type) were obtained using the biomaRt R/Bioconductor package
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files (vcf format) include filtered called variants for each two-samples comparison (WES)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (RNA-seq)

value: male


title: P12N thaw A


title: P14T -W early

description:
derived from P14T primary tissue
P14TRearly_P14Nearly_filtered_somatic_funcotated_short.vcf
P14TRearly_P14Ttissue_filtered_somatic_funcotated_short.vcf
P14TWearly_P14TRearly_filtered_somatic_funcotated_short.vcf


title: P12N thaw B


title: P14T +W late

description:
derived from P14T primary tissue
P14TWlate_P14Nearly_filtered_somatic_funcotated_short.vcf
P14TWlate_P14TRlate_filtered_somatic_funcotated_short.vcf
P14TWlate_P14Ttissue_filtered_somatic_funcotated_short.vcf


title: P12N early C


title: P14T +W early

description:
derived from P14T primary tissue
P14TWearly_P14Nearly_filtered_somatic_funcotated_short.vcf
P14TWearly_P14TRearly_filtered_somatic_funcotated_short.vcf
P14TWearly_P14Ttissue_filtered_somatic_funcotated_short.vcf


title: P14T +W very late

description:
derived from P14T primary tissue
P14TWverylate_P14Nearly_filtered_somatic_funcotated_short.vcf


title: P14N primary tissue

description:
P14Nearly_P14Ntissue_filtered_somatic_funcotated_short.vcf
P14Ttissue_P14Ntissue_filtered_somatic_funcotated_short.vcf

tag: tumor stage

value: normal

value: tissue


title: P14T primary tissue

description:
P14TRearly_P14Ttissue_filtered_somatic_funcotated_short.vcf
P14TRlate_P14Ttissue_filtered_somatic_funcotated_short.vcf
P14Ttissue_P14Nearly_filtered_somatic_funcotated_short.vcf
P14Ttissue_P14Ntissue_filtered_somatic_funcotated_short.vcf
P14TWearly_P14Ttissue_filtered_somatic_funcotated_short.vcf
P14TWlate_P14Ttissue_filtered_somatic_funcotated_short.vcf


title: P12T -W late

description:
derived from P12T primary tissue
P12TRlate_P12Nlate_filtered_somatic_funcotated_short.vcf
P12TRlate_P12TRearly_filtered_somatic_funcotated_short.vcf


title: P12T -W early

description:
derived from P12T primary tissue
P12TRearly_P12Nearly_filtered_somatic_funcotated_short.vcf
P12TRearly_P12Ttissue_filtered_somatic_funcotated_short.vcf
P12TRlate_P12TRearly_filtered_somatic_funcotated_short.vcf
P12TWearly_P12TRearly_filtered_somatic_funcotated_short.vcf


title: P12N +W late

description:
derived from P12N primary tissue
P12Nlate_P12Nearly_filtered_somatic_funcotated_short.vcf
P12TRlate_P12Nlate_filtered_somatic_funcotated_short.vcf


title: P12N late A


title: P12N +W early

description:
derived from P12N primary tissue
P12Nearly_P12Ntissue_filtered_somatic_funcotated_short.vcf
P12Nlate_P12Nearly_filtered_somatic_funcotated_short.vcf
P12TRearly_P12Nearly_filtered_somatic_funcotated_short.vcf
P12Ttissue_P12Nearly_filtered_somatic_funcotated_short.vcf
P12TWearly_P12Nearly_filtered_somatic_funcotated_short.vcf


title: P12N early A


title: P12T +W early

description:
derived from P12T primary tissue
P12TWearly_P12Nearly_filtered_somatic_funcotated_short.vcf
P12TWearly_P12TRearly_filtered_somatic_funcotated_short.vcf
P12TWearly_P12Ttissue_filtered_somatic_funcotated_short.vcf


title: P12T primary tissue

description:
P12TRearly_P12Ttissue_filtered_somatic_funcotated_short.vcf
P12Ttissue_P12Nearly_filtered_somatic_funcotated_short.vcf
P12Ttissue_P12Ntissue_filtered_somatic_funcotated_short.vcf
P12TWearly_P12Ttissue_filtered_somatic_funcotated_short.vcf


title: Control_rep3

first: Benjamin

last: Gewurz

address: 181 Longwood Avenue

institute: Brigham and Women's Hospital

data_processing:
Gene expression was directly quantified from fastq files using Salmon for GENCODE annoated human genes and Akata genes
gene expression differetial analysis was peformed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containing normalized gene expression signal and signicance of differential analysis

source_name: B lymphocyte

growth_protocol: RPMI1640, 10% FBS, 100U/mL Penicillin-Streptomycin

extract_protocol:
Fresh cells were washed with PBS, then go for RNA were extracted with QIAGEN RNeasy Mini Kit (Cat#74104).
With NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Cat#E7765), 500ng total RNA was used to construct the sequencing library.

value: Ascites

tag: disease

value: Burkitt's lymphoma

tag: ebv latency program

value: EBV latency I


title: Cyb561a3_KO_rep2


title: P14N +W early

description:
derived from P14N primary tissue
P14Nearly_P14Ntissue_filtered_somatic_funcotated_short.vcf
P14TRearly_P14Nearly_filtered_somatic_funcotated_short.vcf
P14TRlate_P14Nearly_filtered_somatic_funcotated_short.vcf
P14Ttissue_P14Nearly_filtered_somatic_funcotated_short.vcf
P14TWearly_P14Nearly_filtered_somatic_funcotated_short.vcf
P14TWlate_P14Nearly_filtered_somatic_funcotated_short.vcf
P14TWverylate_P14Nearly_filtered_somatic_funcotated_short.vcf


title: Contro_ rep1


title: Control_rep2


title: HN9-R rep3

city: SEOUL

first: Kyung-Chul

last: Choi

address: Sonpa-gu

department: Biomedical Sciences

country: South Korea

institute: University of Ulsan college of Medicine

description:
HN9-R cells are a subclone that was isolated from a patient-derived AMC-HN9 cells using clonal assays and single-cell plating
G2-R-3

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using STAR (version 2.5.0) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Head and neck carcinoma cell line HN9-R

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (D-MEM; Invitrogen) supplemented with 10% FBS (Invitrogen), 100 µg/ml penicillin/streptomycin, and 100 µM non-essential amino acids (Invitrogen) at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
The quantity and quality of the total RNA were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeqStranded mRNA Sample Preparation kit (Illumina), according to the manufacturer's protocol.

tag: cell type

value: undifferenciated primary head and neck cancer cell

value: parotid gland


title: HN9-R rep2

description:
HN9-R cells are a subclone that was isolated from a patient-derived AMC-HN9 cells using clonal assays and single-cell plating
G2-R-2


title: RR.A.ATAC

city: Tucson

first: Kellen

last: Chen

address: 1501 N Campbell Ave

institute: University of Arizona

data_processing:
Illumina Casava1.7 software used for basecalling.
Pair-end reads were trimmed for Illumina adaptor sequences and transposase sequences and mapped to mm9 using Bowtie2 v2.1.0 with parameters – very sensitive.
For RNA seq-Gene-level counts matrix was generated using Rsubread version 1.30.9. Count files were normalized and analyzed DESeq2 and custom R scripts. For ATAC seq number of raw reads mapped to each peak in each sample was quantified using multicov in Beltools. Peak raw counts were normalized using DESeq2.
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: matrix table with raw gene counts for every sample

source_name: Rosa-Reticular fibroblast

extract_protocol:
RNA-seq was performed on FACS-isolated mouse fibroblast subpopulations from JUN and Control mice and human cultured KO and non-KO fibroblasts resuspended in TRIzol (10k cells/1ml). The RNA-seq data was collected from ten mice and pooled into two biological replicates. Thus, each biological replicate represents 10 wounds, as each mouse has two wounds. The human RNA-seq data was collected from 4 individual patients. RNA was isolated using the Rneasy Micro Kit (Qiagen, #74004), as per the manufacturer’s instructions. ATAC-seq libraries were generated using an average of 50,000 freshly isolated fibroblasts per replicate (biological replicates for mice samples and technical replicates for human samples) as described by Buenrostro et al 2013 with the following modifications. Transposition was performed in 50 uL reaction containing in-house made 2xTD buffer, Tn5 and 1% Digitonin.
Libraries were sequenced on an Illumina HiSeq 2500 machine. KO and non-KO fibroblasts from each skin type will be prepared for RNA-seq. ATAC libraries were prepared using the protocol found in ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide by Buenrostro et al (2015).

value: Fibroblast Cells

value: skin

value: Fibroblasts


title: RR.B.ATAC


title: RL.B.ATAC

source_name: Rosa-Lipofibroblast


title: JR.B.ATAC

source_name: Jun-Reticular fibroblats


title: HN9-S rep1

description:
HN9-S cells are a subclone that was isolated from a patient-derived AMC-HN9 cells using clonal assays and single-cell plating
F8-S-1

source_name: Head and neck carcinoma cell line HN9-S


title: RL.A.ATAC


title: TGQ_rep 3

city: Beijing

first: qian

last: zhang

address: No. 1 West Beichen Road, Chaoyang District

department: State Key Laboratory of Molecular Developmental Biology

institute: Institute of Genetics and Developmental Biology

data_processing:
Illumina HiSeq xten reads were trimmed of adapter sequences and filtered for read that passed quality filtering
Then clean reads were separately aligned to reference genome with orientation mode using TopHat2 (http://tophat.cbcb.umd.edu/, version2.0.0) software
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/)  was used to quantify gene abundances.
Genome_build: Wormbase WS260
Supplementary_files_format_and_content: tab-delimited .txt files include raw counts associated with each transcript

organism: Caenorhabditis elegans

source_name: TGQ_whole worm

growth_protocol: Worms were grown at 20ºC

extract_protocol:
Total RNA was extracted from the worms using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using RQ1 RNase-Free DNase (Promega). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >2μg) was used to construct sequencing library.
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).  Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten (2 × 150bp read length).

treatment_protocol: WT and TGQ animals were grown from hatch at 20ºC on op50 bacteria and collected by washing with M9 at L4 stage, followed by snap frozen in liquid nitrogen.

value: TGQ

tag: developmental stage

value: whole worm lysate


title: TGQ_rep 2

tag: tissue


title: HN9-S rep3

description:
HN9-S cells are a subclone that was isolated from a patient-derived AMC-HN9 cells using clonal assays and single-cell plating
F8-S-3


title: TGQ_rep 1


title: P12N primary tissue

description:
P12Nearly_P12Ntissue_filtered_somatic_funcotated_short.vcf
P12Ttissue_P12Ntissue_filtered_somatic_funcotated_short.vcf


title: Cyb561a3_KO_rep3


title: JR.A.ATAC


title: WT_rep 3

source_name: WT_whole worm


title: JL.B.ATAC

source_name: Jun-Lipofibroblast


title: Cyb561a3_KO_rep1


title: WT_rep 2


title: WT_rep 1


title: HN9-R rep1

description:
HN9-R cells are a subclone that was isolated from a patient-derived AMC-HN9 cells using clonal assays and single-cell plating
G2-R-1


title: HN9-S rep2

description:
HN9-S cells are a subclone that was isolated from a patient-derived AMC-HN9 cells using clonal assays and single-cell plating
F8-S-2


title: Air Month6 4

city: New York City

first: Balvir

last: Kunar

state: New York

address: 1300 York Ave

department: Regenerative Medicine; Physiology, Biophysics, & Systems Biology

institute: Weill Cornell Medical College

description:
FACS sorted
counts6month.txt
Air_4_Lung_S4_L001_R1_001

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count matrix

source_name: air month 6

extract_protocol:
Intravital labeling of VE-cadherin was performed before mice sacrificed to label the endothelial compartment.  Lung tissue was harvested and enzymatically digested into single cell suspension.  Endothelail cells were  isolated by fluorescence-activated cell sorting and subjected to RNA extraction using Trizol and RNA-easy microRNA kit from Qiagen
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: mice were treated with 1 month and  6 months of whole body smoke and compared to controls at room air

value: Lung

tag: disease status

value: Air 6 months


title: RR.A.RNA


title: Air Month6 1

description:
FACS sorted
counts6month.txt
Air_1_Lung_S1_L001_R1_001


title: RL.A.RNA


title: JR.A.RNA

value: c-JuntetO R26-M2rtTA


title: Air Month6 2

description:
FACS sorted
counts6month.txt
Air_2_Lung_S2_L001_R1_001


title: Smoke Month6 4

description:
FACS sorted
counts6month.txt
Smoke_4_Lung_S8_L001_R1_001

source_name: smoke month 6

value: Smoke 6 months


title: Smoke Month6 3

description:
FACS sorted
counts6month.txt
Smoke_3_Lung_S7_L001_R1_001


title: JR.B.RNA


title: Air Month1 3

description:
FACS sorted
counts1month.txt
RA_3_S30_L004_R1_001

source_name: air month 1

value: Air 1 month


title: Smoke Month6 2

description:
FACS sorted
counts6month.txt
Smoke_2_Lung_S6_L001_R1_001


title: JL.B.RNA


title: Air Month6 3

description:
FACS sorted
counts6month.txt
Air_3_Lung_S3_L001_R1_001


title: Smoke Month6 1

description:
FACS sorted
counts6month.txt
Smoke_1_Lung_S5_L001_R1_001


title: Air Month1 1

description:
FACS sorted
counts1month.txt
RA_1_S28_L004_R1_001


title: RR.B.RNA


title: Air Month1 2

description:
FACS sorted
counts1month.txt
RA_2_S29_L004_R1_001


title: JL.A.RNA


title: Smoke Month1 3

description:
FACS sorted
counts1month.txt
CS_3_S34_L004_R1_001

source_name: smoke month 1

value: Smoke 1 month


title: primary mammary organoids - 1.5 uM CHIR99021 - rep3 ("CHIR_1.5uM_max")

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

data_processing:
Single-end reads (65 bp) were aligned to reference sequence GRCm38/mm10 with Tophat version 2.1 and Bowtie version 1.1.0.
Expression values were determined by HTSeq-count.
Raw gene-level count tables were processed in R using DESeq2.
Normalized values were extracted from the DESeqDataSet (dds) object
Differentially expressed genes were extracted using pairwise comparisons of different treatment conditions with padj <0.1 as a cut off for false discovery
Genome_build: Genome_build: GRCm38.77 (mm10)
Supplementary_files_format_and_content: raw counts and counts normalized to 10 million reads followed by log2 transformation

source_name: primary mammary organoids

growth_protocol: organoids were embedded in growth-factor reduced matrigel and grown in minimal media according to Ewald et al. (2008; https://doi.org/10.1016/j.devcel.2008.03.003) and Nguyen-Ngoc et al. (2015, https://doi.org/10.1007/978-1-4939-1164-6_10)

extract_protocol:
RNA was extracted using Trizol and RNA was extracted using the Qiagen RNeasy column purification kit. RNA quality was checked with a Bioanalyer (Agilent).
PolyA+ stranded RNA library preparation was performed using the Illumina TruSeq stranded RNA prep kit according to the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard Illumina protocols. RNA-sequencing was performed on a HiSeq 2500 (Illumina) System using a stranded protocol.

treatment_protocol: triplicate organoid cultures were treated with either vehicle control (DMSO) or increasing concentrations of CHIR99021 (1 uM, 1.5 uM or 3 uM) to activate WNT/CTNNB1 signaling for 7 days

value: FVB/N

value: mammary gland organoid

value: 8-11 week old virgin


title: primary mammary organoids - 1 uM CHIR99021 - rep3 ("CHIR_1uM_max")


title: primary mammary organoids - 3 uM CHIR 99021 - rep2 ("CHIR_3uM_min")


title: primary mammary organoids - DMSO - rep3 ("DMSO_max")


title: primary mammary organoids - 3 uM CHIR 99021 - rep3 ("CHIR_3uM_max")