title: N_R2_0.1_IMX1489

city: Delft

first: Marcel

last: van den Broek

address: Van der Maasweg 9

institute: Delft University of Technology

data_processing:
RNA-seq reads were aligned to the CEN.PK113-7D reference using STAR version 2.5.4a
resulted sequence alignment map file (SAM) converted in sorted BAM file with samtools
The sorted BAM file was processed with featureCounts for quantification
raw counts normalized with FPKM from edgeR
Assembly: CEN.PK113-7D ASM257140v2
Supplementary files format and content: Comma delimited file, normalized transcript counts

organism: Saccharomyces cerevisiae

source_name: deltagpd2, non-ox PPP↑, pDAN1-prk, 15x cbbm, GroES/GroEL

growth_protocol: anaerobic C-limited duplicate steady-state chemostat cultures of IME324 (reference strain lacking PRK-RuBisCO bypass) and IMX1489 (Δgpd2, non-ox PPP↑, pDAN1-prk, 15x cbbm, GroES/GroEL) at 0.05 h-1, 0.1 h-1 and at 0.25 h-1, and anaerobic N-limited steady-state chemostat cultures of IME324 and IMX1489 at 0.1 h-1.

extract_protocol:
RNA was extracted with hot-phenol method as described by Schmitt et al. (1990)
cDNA libraries were prepared using the TruSeq stranded mRNA kit (illumina) and sequenced on HISeq 2500 (illumina) at Macrogen

treatment_protocol: Cultures were sampled into liquid nitrogen and processed as described by Piper et al. (2002)

value: strain IMX1489

value: anaerobic N-limited chemostat culture 0.1 h-1

tag: replicate

value: replicate 2


title: N_R2_0.1_IME324

status: Public on May 17 2023

type: SRA

country: Netherlands

description: reference strain lacking PRK-RuBisCO bypass

library_source: transcriptomic

molecule: total RNA

tag: strain

value: strain IME324

tag: treatment


title: N_R1_0.1_IME324

source_name: reference strain lacking PRK-RuBisCO bypass

value: replicate 1


title: N_R1_0.1_IMX1489

description: Δgpd2, non-ox PPP↑, pDAN1-prk, 15x cbbm, GroES/GroEL


title: DMSO_Control_BiologicalRepA [PGD-UnA]

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

country: USA

institute: University of Mississippi

data_processing:
Base calling was performed using the RTA v2 software built into the Illumina NextSeq 500 instrument.
Demultiplexing and FASTQ file generation was performed with Illumina’s Basespace informatics platform
Data analysis was performed using the Qiagen CLC Genomics Workbench (CLCGxWB) version 11 software. Sequencing reads were mapped to the H. sapiens reference genome (GRCh38 assembly, Ensemble Release 89),  using default parameters with a strand-specific alignment protocol. The mapping results generated values for Fragments Per Kilobase of exon per Million reads mapped (FPKM) for each gene. The “Differential Expression for RNA-Seq” tool in CLCGxWB software was used, using default parameters, to identify differentially expressed genes between chemical-treated and solvent-treated samples.
Assembly: H. sapiens reference genome (GRCh38 assembly, Ensemble Release 89)
Supplementary files format and content: Excel file showing FPKM values for each Sample.

organism: Homo sapiens

extract_protocol:
Qiagen RNeasy Mini kit was used for total RNA extraction. An on-column RNase-free DNase I treatment was included. RNA quality was assessed on the Agilent 2100 Bioanalyzer.
Sequencing libraries were generated with 3 µg of RNA using the Illumina TruSeq Stranded mRNA Sample Preparation Kit. The libraries were assessed for size and purity using the Agilent 2100 Bioanalyzer, and quantitated by qPCR using a KAPA Biosystems Library Quantitation kit. Libraries were normalized, pooled, and diluted to a loading concentration of 1.8 pM, loaded on an Illumina High-Output Flow Cell, and sequenced on the Illumina NextSeq 500 instrument.

treatment_protocol: T98G cells were treated with solvent (DMSO), DEOX (10 mM), PHEN (100 uM), GNET (8 uM), DEOX (10 mM) + PHEN (100 uM), or GNET (8 uM) + PHEN  (100 uM) for 2 hours. After treatment, cells were washed twice with PBS buffer and used for RNA isolation. In all experiments, each treatment consisted of 3 biological replicates, and RNA from each replicate was used to generate sequencing libraries.

tag: cell line

value: DMSO

tag: time

value: 2 h


title: 4h_tg_4_10557

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

country: Germany

institute: Max Planck Institute for Metabolism Research

description: 4 hour optogenetic stimulation, AgRP-IRES-Cre tg/wt ROSA26 ChR2 fl/wt mice

data_processing:
The pool was sequenced for 37.5 million reads using an Illumina NovaSeq6000 instrument and a PE100 sequencing protocol.
Data was processed using the nf-core/rnaseq v3.0 pipeline
Alignment to reference genome was done using STAR vSTAR_2.6.1d
Gene abundance estimation was done using Salmon 1.4.0
Differential gene expression analysis of IP samples was carried out using DESeq2 1.30.0
Genome_build: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012
Supplementary_files_format_and_content: Excel speadsheets containing raw salmon counts per sample as well as fold change and significance level for each annotated gene.

organism: Mus musculus

growth_protocol: Mice were housed in individually ventilated cages (IVCs) within a controlled environment at 22°C – 24°C and a 12-hr light/12-hr dark cycle. Animals received ad libitum access standard rodent chow (ssniff V1554, 59494 Soest, Germany) and water unless otherwise indicated in an experiment.

extract_protocol:
Both cohort of mice were sacrificed at ZT7.5 and liver samples were extracted and snapped frozen in liquid nitrogen. Total murine liver RNA was isolated using the mirVana Isolation Kit (Ambion) in accordance to the manufacturer’s instructions. Murine liver RNA concentration was measured by Nanodrop ND-100 (Peqlab Biotechnology, France), and diluted to a final concentration of 200 – 250 ng/mL. RNA integrity number (RIN) was analyzed with the Agilent RNA 6000 Nano Kit (5067-1511, Agilent Technologies) and the Agilent 2100 Bioanalyzer. All samples displayed a RIN of >8.
RNA libraries were prepared with 1 µg of total RNA using the Illumina® TruSeq® mRNA stranded sample preparation Kit. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperatures. The RNA fragments underwent reverse transcription using random primers. This is followed by second-strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent tape station), equimolar amounts of the library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.

treatment_protocol: Mice were stimulated with blue laser (473 nm) light, consisting of pulse trains (10 ms pulses of 20 Hz; 3 s on, 1 s off) at ZT3.5 (4 h stimulation) and ZT5.5 (2 h stimulation) in the absence of food.

tag: tissue

value: Liver

tag: diet

value: Random Fed

value: 4 hours

tag: genotype

value: tg/wt; fl/wt


title: 4h_tg_5_10769

source_name: 4 hour optogenetic stimulation, AgRP-IRES-Cre tg/wt ROSA26 ChR2 fl/wt mice


title: C_R2_0.05_IMX1489

value: anaerobic C-limited chemostat culture 0.05 h-1


title: HEK293FT-PIE-PUM2_24h_rep2

city: Chicago

first: Xiangbin

last: Ruan

state: IL

address: 6054 S. DREXEL AVE.

institute: University of Chicago

description:
PIE-PUM2
PUM2vsAPAD_24h.DP5.wo.snp

data_processing:
RNA base variants calling was performed by JACUSA2_v2.0.0
raw Fastq files were aligned and mapped to hg38 or mm10 reference with STAR
known SNPs in dbSNP version 138 (hg38) or version 137 (mm10) or SNVs with low read depth (less than 5-read depth) were filtered out
Gene-level counts were calculated by Rsubread
Assembly: hg38/mm10
Supplementary files format and content: text files include RNA editing information for each group/sample
Supplementary files format and content: text files include gene-level count values for each sample

growth_protocol: HEK293FT cells (purchased from ATCC) were cultured at 37 ℃ in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from transfected cells with Direct-zol RNA microprep kit according to manufacturer’s instructions (ZYMO)
TruSeq Stranded mRNA Library Prep kit (Illumina) was used for preparing sequencing libraries

treatment_protocol: Cells transfected in suspension with lipofectamine 2000 and changed to fresh medium 6 hours after transfection,

value: HEK293FT cultured cells

value: transfected with pR023_PIE-PUM2 vector with Lipofectamine 2000 for 24h


title: SKD00501R-A07

city: Solna

first: Martin

last: Enge

address: Solnavägen 1

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic single cell

data_processing:
Demultiplexed RNA reads were aligned using STAR 2.7.7a, duplicate reads removed using Picard 2.22.0 and read counts summarized using HTSeq 0.9.1. Cutoffs of 20000 counts and 500 features were used.
Assembly: GRCm38 with ERCC-spike ins and the reporter-gene EYFP

molecule: polyA RNA

source_name: Aorta

extract_protocol:
Aortae was perfused for 1 min with PBS at room temperature and then dissected. Lumen side was exposed and digested with 1 mg/mL collagenase I, 1 mg/mL dispase, and 150 μg/mL DNase-I for 30 min at 37 °C. The cell suspension was strained and then depleted of Cd45+ cells with Cd45 magnetic beads (protocol according to manufacturer). To purify endothelial cells, the suspension was stained with Cd45 and Cd31 antobodies, as well as a cell viability dye. FACS sorting was used to sort out Cd45-, Cd31+, viable endothelial cells, as well as some Cd45-, Cd31-, viable cells for control. Cells were sorted into 384 well plates with lysis buffer.
Library was constructed using smartseq2 protocol, as previously has been described. Briefly, primer annealing, followed by RT and cDNA amplification was followed by cleanup of PCR products. The cDNA was tagmented and final library anmplified using custom barcodes, then pooled and cleaned with SPRI beads. Libraries were then sequenced.

tag: cell type

value: Endothelial

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP

tag: age

value: 3 months


title: 4h_tg_3_10532


title: SKD00501R-A01


title: C_R2_0.05_IME324


title: SKD00501R-B14


title: LN18 glioma cell line untreated rep 1

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

data_processing:
mapping by STAR
MarkDuplicates
Counts features by Featurecounts
Assembly: hg38
Supplementary files format and content: tab separated text file with features assigned to genes

source_name: LN18 glioma cell line untreated

extract_protocol: polyA+ KAPA Library kit

value: brain

value: wild type

tag: sample type

value: LN18 glioma cell line

tag: transfection

value: untreated


title: HEK293FT-PIE-PUM2_24h_rep1

description:
PIE-PUM2
PUM2vsAPAD_24h.DP5.wo.snp


title: C_R2_0.1_IMX1489

value: strain IMX1489

value: anaerobic C-limited chemostat culture 0.1 h-1

value: replicate 2


title: HEK293FT-PIE-FMR1_24h_rep2

description:
PIE-FMR1
FMR1vsAPAD.DP5.wo.snp

value: transfected with pR018_PIE-FMR1 vector with Lipofectamine 2000 for 24h


title: 4h_tg_1_10302

value: Liver

value: Random Fed

value: 4 hours


title: 2h_wt_5_11037

description: 2 hour optogenetic stimulation, AgRP-IRES-Cre wt/wt ROSA26 ChR2 fl/wt mice

value: 2 hours

value: wtwt; fl/wt


title: C_R2_0.1_IME324

value: strain IME324


title: HEK293FT-APAD_24h_rep2

description: Nontargeting/APAD control

source_name: Nontargeting/APAD control

value: HEK293FT cultured cells

value: transfected with pR008_APAD vector with Lipofectamine 2000 for 24h


title: HEK293FT-PIE-FMR1_24h_rep1

description:
PIE-FMR1
FMR1vsAPAD.DP5.wo.snp


title: SKD00501R-A02

value: Endothelial

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP

value: 3 months


title: C_R2_0.25_IME324

value: anaerobic C-limited chemostat culture 0.25 h-1


title: YM-3-4

type: RNA

city: Tokyo

first: Kazuyuki

last: Ishihara

address: 2-1-14 Kanda-Misakicho, Chiyoda-ku

department: Microbiology

country: Japan

institute: Tokyo Dental College

hyb_protocol: cRNA was hybridized to a 15K 60-mer oligomicroarray (Treponema denticola custom Microarray 8x16K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Agilent Feature Extraction 12.0.3.1(Agilent Technologies).

data_processing: The fluorescent intensity data extracted from the raw images were imported into Agilent Feature Extraction 12.0.3.1 (Agilent Technologies).  After per chip normalization (Shift to 75 percentile) and per gene normalization (mean of control samples) were performed with GeneSpring 13.1.1.

organism: Treponema denticola

source_name: Dentipain deficient mutant

label_protocol: The cRNA was amplified, labeled using Low Input Quick Amp WT Labeling Kit according to the manufacturer's instructions.

growth_protocol: T. denticola ATCC 35405, DMSP3 or K1 were inoculated into 100 mL 10% TYGVS and incubated at 37°C under anaerobic conditions for 2 d (to an absorbance at 660 nm of approximately 0.4-0.6).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen)  according to the manufacturer's instructions.

treatment_protocol: Td 35405     T. denticola ATCC 35405 grown in medium containing 10% serum  Td YM-3     T. denticola YM-3 grown in medium containing containing 10% serum


title: 4h_tg_2_10304

value: tg/wt; fl/wt


title: C_R1_0.05_IME324

value: anaerobic C-limited chemostat culture 0.05 h-1

value: replicate 1


title: HEK293FT-PIE-PUM2_48h_rep2

description:
PIE-PUM2
PUM2vsAPAD_48h.DP5.wo.snp

value: transfected with pR023_PIE-PUM2 vector with Lipofectamine 2000 for 48h


title: YM-3-3


title: 2h_wt_2_10305

source_name: 2 hour optogenetic stimulation, AgRP-IRES-Cre wt/wt ROSA26 ChR2 fl/wt mice

value: Liver


title: 2h_wt_3_10770

value: Random Fed


title: 2h_wt_4_11038


title: 2h_wt_1_10371


title: HEK293FT-APAD_24h_rep1

description: Nontargeting/APAD control


title: C_R1_0.1_IMX1489

value: strain IMX1489

value: anaerobic C-limited chemostat culture 0.1 h-1


title: HEK293FT-PIE-PUM2_48h_rep1

description:
PIE-PUM2
PUM2vsAPAD_48h.DP5.wo.snp


title: 2h_tg_5_10904

description: 2 hour optogenetic stimulation, AgRP-IRES-Cre tg/wt ROSA26 ChR2 fl/wt mice

value: 2 hours


title: HEK293FT-APAD_48h_rep2

description: Nontargeting/APAD control

value: transfected with pR008_APAD vector with Lipofectamine 2000 for 48h


title: C_R1_0.1_IME324

value: strain IME324


title: C_R2_0.25_IMX1489

value: replicate 2


title: 405-4

organism: Treponema denticola ATCC 35405

source_name: Wild type


title: HeLa_transfected_pcDNA3-SrfJ_rep2

city: Sevilla

first: Francisco

last: Ramos-Morales

state: Sevilla

address: Avda Reina Mercedes, 6

department: Genética

country: Spain

institute: Universidad de Sevilla

description: Gene expression data from HeLa cells transiently transfected with plasmid pcDNA3-SrfJ-3xFLAG

hyb_protocol: Labelled cDNA was hybridized to Clariom S Assay, HUMAN arrays  (Affymetrix) following the manufacturer’s instructions

scan_protocol: The arrays were scanned in a 3000 7G Scanner from Affymetrix

data_processing: Data processing was carried out with GeneChip Command Console 2.0 (Affymetrix) to generate .CEL and .CHP assays. Normalization was performed using the SST (signal space transformation)-RMA (robust multiple-array average) method. The Transcriptome Analysis Console (TAC) was used for data analysis.

label: biotin

source_name: HeLa cells transfected with pcDNA3-srfJ-3xFLAG, biological rep2

label_protocol: Biotinylated single-stranded cDNA was prepared from 100 ng per sample of total intact RNA extracted from 6 independent samples (3 from HeLa transfected with pcDNA3, 3 from HeLa transfected with pcDNA3-SrfJ-3xFLAG).

growth_protocol: HeLa cells (ECAC no. 93021013) were cultured in DMEM supplemented with 10% foetal calf serum. 2 mM L-glutamine, 100 U/ml penicillin and 100 microg/ml streptomycin were included in the culture media. Cells were maintained in a 5% CO2 humidified atmosphere at 37ºC

extract_protocol: Total RNA from HeLa cells was isolated using 1 ml of TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. An additional purification step was carried out with the RNeasy Min Elute Cleanup Kit (Qiagen).

treatment_protocol: For transient transfection assays, 1x10E7 HeLa cells/assay were suspended in 200 ul of 15 mM Hepes-buffered serum-containing medium, mixed with 50 ul of 210 mM NaCl containing 5-10 ug of plasmid DNA and electroporated using a BTX Electrocell Manipulator 600 set at 240 V, 720 ohms, 950 uF. Cells were processed 24 hours after electroporation.

value: HeLa


title: HEK293FT-APAD_48h_rep1

description: Nontargeting/APAD control

value: HEK293FT cultured cells


title: 2h_tg_3_10560

source_name: 2 hour optogenetic stimulation, AgRP-IRES-Cre tg/wt ROSA26 ChR2 fl/wt mice


title: HeLa_transfected_pcDNA3_rep3

description: Gene expression data from HeLa cells transiently transfected with empty plasmid pcDNA3

source_name: HeLa cells transfected with pcDNA3, biological rep3


title: HeLa_transfected_pcDNA3-SrfJ_rep1

source_name: HeLa cells transfected with pcDNA3-srfJ-3xFLAG, biological rep1


title: HeLa_transfected_pcDNA3-SrfJ_rep3

source_name: HeLa cells transfected with pcDNA3-srfJ-3xFLAG, biological rep3


title: C_R1_0.25_IME324


title: C_R1_0.05_IMX1489


title: 2h_tg_2_10534


title: HEK293FT-Empty vector_rep1

description: Mock control

source_name: Mock control

value: transfected with pCAGIG vector with Lipofectamine 2000 for 48h


title: HEK293FT-Empty vector_rep2

description: Mock control


title: 2h_tg_1_10303


title: C_R1_0.25_IMX1489


title: 405-3


title: HeLa_transfected_pcDNA3_rep2

source_name: HeLa cells transfected with pcDNA3, biological rep2


title: msn2/4∆ AzC rep1

status: Public on May 16 2023

city: Stockholm

first: Michela

last: Ciccarelli

state: Sweden

address: MBW, Hus F Plan 4 Frescativägen 8 Stockholm, Stockholms län [SE-01]

department: Department of Molecular Biosciences, The Wenner-Gren Institute

institute: University of Stockholm

data_processing:
Pre-processing was carried out with pipeline nf-core/rnaseq, version = 1.4.2. Main analysis steps are:
Fastq lane concatenation; unix cat
Adapter and read quality trimming; TrimGalore!
General assessment of read quality; FastQC
Alignment to reference genome (Saccharomyces cerevisiae, R64-1-1); STAR
Assembly: RNA abundance quantification at gene level; Salmon
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Strain

growth_protocol: Cells were grown in triplicates for each condition in YPD liquid media at 25˚C until OD600 = 0.8

extract_protocol:
RNA was extracted using RiboPure Yeast RNA Purification Kit (Thermo Fisher Scientific, #AM1926). The quality of the RNA extracted was analyzed using high sensitivity RNA BioAnalyzer Chip (Agilent)
Libraries were prepared using Illumina TruSeq RNA poly-A selection prep and the sequencing was performed on Illumina NovaSeq6000 SP flowcell.

treatment_protocol: Cells were heat shocked at 37˚C for 15 min in a shaking water bath or treated with 10 mM AzC for 1h at 25°C or left untreated

value: Strain

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0 msn2::hphMX4 msn4::natMX4

value: 10 mM AzC

value: 1 hour


title: HSF1 AzC rep3

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 LYS2 met15{delta}0 hsf1{delta}::[HSF1+; PA{delta}H1-Y{delta}J1;kanMX;PTEF1-HSC82;PT{delta}H3-SSA2]


title: HSF1 HS rep3

value: heat shock at 37°C

value: 15 min


title: msn2/4∆ HS rep2


title: hsf1∆ HS rep3

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0 hsf1{delta}::[PA{delta}H1-Y{delta}J1;kanMX;PTEF1-HSC82;PT{delta}H3-SSA2]


title: WT AzC rep2

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0


title: WT AzC rep1


title: hsf1∆ AzC rep2


title: hsf1∆ HS rep1


title: HSF1 HS rep1


title: msn2/4∆ HS rep3


title: msn2/4∆ AzC rep2


title: msn2/4∆ AzC rep3


title: WT HS rep3


title: WT HS rep2


title: hsf1∆ AzC rep3


title: msn2/4∆ HS rep1


title: WT AzC rep3


title: HeLa_transfected_pcDNA3_rep1

source_name: HeLa cells transfected with pcDNA3, biological rep1


title: hsf1∆ AzC rep1


title: HSF1 AzC rep1


title: WT HS rep1


title: msn2/4∆ CTRL rep1

value: no treatment, growth at 25°C


title: msn2/4∆ CTRL rep3


title: msn2/4∆ CTRL rep2


title: HSF1 HS rep2


title: HSF1 AzC rep2


title: HSF1 CTRL rep3


title: hsf1∆ HS rep2


title: HSF1 CTRL rep2


title: HSF1 CTRL rep1


title: WT CTRL rep1


title: WT CTRL rep2


title: hsf1∆ CTRL rep3


title: WT CTRL rep3


title: hsf1∆ CTRL rep2


title: HYB188

city: Billerica

first: Irina

last: Kalatskaya

state: MA

address: 45 Middlesex Turnpike

department: Clinical Measurement Sciences

institute: EMD Serono Research and Development Institute

hyb_protocol: Following fragmentation of DNA, labeled DNA was hybridized over night on Affymetrix Human Genome U133 Plus 2.0 microarray, the hybridized array was stained and washed using an automated protocol on the fluidics station.

scan_protocol: After hybridization and staining, the Affymetrix arrays were scanned to create image data (DAT) files. The GeneChip Command Console Software then automatically aligned a grid on the DAT files and computed the Cell Intensity data (CEL) file.

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method implemented in the Bioconductor package to obtain a log2 expression value for each gene probe set.

source_name: blood

label_protocol: Biotin

growth_protocol: Not applicable

extract_protocol: Total RNAs are extracted from whole blood using the PAXgene RNA Blood RNA kit from Qiagen

treatment_protocol: Blood samples for DNA extraction were collected in EDTA tubes.

tag: treatment arm

value: Cladribine Low Dose

tag: treatment dose

value: Cladribine 3.5 mg/kg

value: whole blood

tag: timepoint

value: 96 weeks


title: HYB162

value: Cladribine High Dose

value: Cladribine 5.25 mg/kg


title: HYB158


title: HYB160


title: HYB143


title: HYB191

value: Placebo


title: HYB184


title: HYB164


title: HYB187


title: HYB159


title: HYB161


title: HYB139


title: HYB186


title: HYB163


title: HYB181


title: HYB154


title: HYB117


title: HYB189


title: HYB141


title: HYB142


title: HYB185


title: HYB182


title: HYB157


title: HYB156


title: HYB155


title: hsf1∆ CTRL rep1

value: Strain


title: HYB118


title: HYB116


title: HYB140


title: HYB138


title: HYB114


title: HYB137


title: HYB150


title: HYB111


title: HYB180


title: HYB177


title: HYB151


title: HYB176


title: HYB115


title: HYB153


title: HYB133


title: HYB134


title: HYB179


title: HYB178


title: HYB148


title: HYB149


title: HYB152


title: HYB110


title: HYB127


title: HYB112


title: HYB135


title: HYB113


title: HYB174


title: HYB175


title: HYB171


title: Calibrated Scc1 ChIP-seq for isw1Δ IP

city: Wrocław

first: Ireneusz

middle: Bernard

last: Litwin

address: Kanonia 6/8

department: Academic Excellence Incubator - Research Centre for DNA Repair and Replication

institute: University of Wroclaw

library_source: genomic

data_processing:
The adapter sequences and low-quality bases were trimmed off using Skewer.
Filtered reads were mapped against the target genome (S. cerevisiae S288C assemblySacCer3) and against the spike-in genome (S. pombe assembly ASM294v2) using BWA.
Unmapped reads, rDNA regions, mitochondrial DNA and duplicates were filtered out using Samtools.
Peaks were called using MACS2.
In order to visualize mapped reads, bigWig files were created using deepTools.
The ChIPs were normalized against the input with Counts Per Million (CPM) method.
Samtools was used to count reads mapped to SacCer3 and ASM294v2 only, and these values were used to calculate the Occupancy Ratio value.
Plots were created around the midpoint of CENs.
Assembly: SacCer3, ASM294v2
Supplementary files format and content: bigWig

molecule: genomic DNA

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

growth_protocol: ~3 x 108 of S.cerevisiae cells expressing Scc1-9Pk were mixed with ~1 x 108 S.pombe cells expressing  Rad21-6HA, fixed with 1% formaldehyde for 15 min at RT and then rocked for 5 min with 150 mM glycine. Next, cells were collected by centrifugation, washed once with TBS buffer and resuspended in 600 μl of FA-lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1% Triton X, protease inhibitors [Sigma-Aldrich, P8215], 1 mM PMSF). Cells were lysed by 4 rounds of bead-beating at 6500 rpm for 30 s. Next, whole cell extracts were transferred to new tubes and sonicated to yield an average DNA size of 500 bp followed by 30 min centrifugation at 15 000 rpm. Cleared lysates were moved to new tubes and 2% of the lysates were kept as an input sample. For the IP reaction, 7 μl of anti-Pk antibodies (Bio-Rad, MCA1360G) and 3 μl of anti-HA (Roche,11583816001) were added to the lysates and incubated overnight at 4°C on a rotator wheel. Next day, DNA-protein complexes were captured with Protein G Dynabeads (Thermo Fisher, 10003D) and sequentially washed with FA-lysis buffer, FA-500 buffer (50 mM HEPES–KOH pH 7.5, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM EDTA), LiCl wash buffer (10 mM Tris–HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA) and TE (10 mM Tris–HCl pH 7.5, 1 mM EDTA) on a rotator for 5 min each time.

extract_protocol:
Beads and input samples were resuspended in elution buffer (50 mM Tris–HCl pH 7.5, 1% SDS, 10 mM EDTA) and incubated at 65°C for 2 h on a thermal shaker. Next, beads were removed and the IP eluates and input samples were  incubated at 65°C overnight. Next day, all the samples were treated with RNAse A for 1 h at 37°C followed by 2h incubation at 65°C in the presence of Proteinase K. Finally, DNA was recovered using a Monarch PCR & DNA Cleanup Kit (New England BioLabs, T1030L).
DNA libraries were constructed using NGS DNA Library Prep Set (Novogene, PT004).

tag: antibody

value: anti-Pk (BioRad), anti-HA (Roche)


title: Calibrated Scc1 ChIP-seq for isw1Δ INPUT

value: input


title: Calibrated Scc1 ChIP-seq for wild type INPUT


title: BM-HL_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.27.4 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.3 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

source_name: Bone marrow

extract_protocol:
RNA was isolated from XY using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer). 3 µg of total RNA was used as input VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme). Sequencing was performed on the NextSeq2000 instrument (Illumina) using P3 flowcell and 1x72bp single-read setup.

value: Bone marrow

value: Macrophage

tag: strain background


title: Calibrated Scc1 ChIP-seq for wild type IP


title: BM-HL_2


title: BM-H_3

value: WT


title: BM-H_2


title: LP population from Patient 051

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Libraries were sequenced on an Illumina NextSeq 500. At least 20 million 75 bp paired-end reads were obtained for each sample.
Reads were aligned to the human genome hg38 by Rsubread version 1.5.3
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Assembly: hg38
Supplementary files format and content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: Mammary gland

extract_protocol:
Total RNA was extracted.
Total RNA (100 ng) was used to generate libraries for whole transcriptome analysis following the Illumina’s TruSeq RNA v2 sample preparation protocol.

tag: patient

tag: cell population

value: LP

value: Fresh


title: BM-H_1


title: ML population from Patient 051

value: ML


title: ML population from Patient 153


title: LP population from Patient 153


title: Basal population from Patient 051

value: Basal


title: HYB109

value: Cladribine Low Dose


title: Basal population from Patient 153


title: HYB108


title: HYB172


title: BM-HL_1


title: Basal population from Patient 14.002.158


title: LP population from Patient 14.002.158


title: ML population from Patient 14.002.158


title: HYB136


title: HYB128

value: Cladribine 3.5 mg/kg


title: M2_3

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (GRCh38) using STAR 2.7.9a  with the parameters "--outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 20 --alignIntronMax 200000" (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 2.0.2 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
A combined raw count matrix was produced and batch corrected per donor (batch 1: *_1, batch 2: *_2, batch 3: *_3) using CountClust (Dey KK, Hsiao CJ, Stephens M (2017), Visualizing the structure of RNA-seq expression data using grade of membership models, PLoS Genetics).
The batch-corrected matrix was used for differential expression analysis using DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (release 08.03.2018) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: hg38 / GRCh38
Supplementary_files_format_and_content: The tab-delimited matrix shows DESeq normalized counts.

source_name: Macrophages

growth_protocol: We differentiated PBMCs from human blood to macrophages  by culture with RPMI medium supplemented with human serum for 10 days, then in vitro polarized by stimulation with LPS and IFNy (M1) or IL-4 (M2) for 24 hours, or left them unstimulated (M0)

extract_protocol:
RNA was isolated using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer). 2µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry with 2x75bp paired-end setup.

value: Macrophages

tag: donor

tag: macrophage class


title: M2_2


title: HYB131

value: whole blood

value: 96 weeks


title: HYB122

value: Cladribine High Dose

value: Cladribine 5.25 mg/kg


title: HYB106


title: M2_1


title: HYB170


title: HYB129


title: HYB169

value: Placebo


title: M1_3


title: M1_2


title: HYB105


title: M1_1


title: M0_3


title: HYB130


title: HYB104


title: M0_2


title: HYB165


title: HYB166


title: HYB144


title: M0_1


title: HYB173


title: HYB126


title: HYB107


title: HYB132


title: HYB125


title: S39 [AD28H]

city: Southampton

first: Marta

middle: Ewa

last: Polak

state: Hampshire

address: Southampton General Hospital, Mailpoint 813, LE59,

department: Clinical and Experimental Sciences

country: United Kingdom

institute: University of Southampton

data_processing:
Alignment bulk RNA: High-quality reads filtered at 15M depth across all samples were mapped to the human genome (GRCh38) using Kallisto
Normalisation bulk RNA: Raw counts from RNA-Seq were processed in Bioconductor package EdgeR (54) and SLEUTH
Alignment single cell RNA: Following demultiplexing, raw FASTQ files were aligned to the human genome (GRCh38), using kallisto-bustools
Filtering single cell RNA: Doublet detection and hashing demultiplexing was done using Solo. Empty barcodes and percentage of mitochondrial genes were checked within Scanpy.
Clean-up single cell RNA: CellBender was used to remove empty technical artefacts.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV table with counts and TPM as estimated by Kallisto

source_name: fresh skin cells

growth_protocol: primary cells isolated by digestion from skin punch biopsies

extract_protocol:
For bulk RNA-seq RNA was isolated using Direct-zol RNA micro prep (Zymo, UK) as per the manufacturer’s protocol.
For Bulk RNA-seq cDNA libraries were generated using SMART-Seq Stranded Library Preparation for Ultra Low Input according to the SMART-Seq Stranded Kit User Manual  following the Ultra low input workflow (Takara Bio). Samples were pooled (12/batch) for library preparation. For Drop-seq High Sensitivity DNA Assay Nextera kit, Illumina, was used. For Constellation cDNA was aplified using targeted linear amplification (20 rounds) and further prepared using True-seq, Illumina.

treatment_protocol: in vivo 48h topical exposure to a control patch test or a patch test with HDM

tag: sample group

tag: reponse

value: non-responing

tag: experiment type

value: Drop-Seq

value: total skin cell digest


title: S38 [AD28C]


title: HYB103

tag: tissue


title: S36 [AD27C]

value: responding

tag: cell type


title: S35 [AD26H]


title: HYB147


title: S34 [AD26C]


title: S31_CTRL

source_name: LCs

value: irritant

value: bulk RNA-seq

value: FACS sorted CD207+


title: HYB167


title: HYB146


title: S29_CTRL


title: HYB100


title: HYB101


title: HYB121


title: HYB102


title: HYB168


title: S37 [AD27H]


title: S28_HDM


title: S27_CTRL


title: HYB119


title: HYB145


title: S26_HDM


title: HYB123


title: HYB124


title: S32_HDM


title: S24_HDM


title: S30_HDM


title: S23_CTRL


title: HYB098


title: HYB099


title: HYB095


title: HYB096


title: S25_CTRL


title: S22_HDM


title: S21_CTRL


title: S60_HDM


title: S19_CTRL


title: HYB094


title: S20_HDM


title: HYB093


title: S59_CTRL


title: S58_HDM


title: S57_CTRL


title: S56_HDM


title: S55_CTRL


title: HYB091


title: HYB088


title: HYB090


title: HYB085


title: S54_HDM


title: HYB083


title: HYB084


title: HYB082


title: S53_CTRL


title: HYB086


title: S18_HDM


title: HYB092


title: HYB097


title: HYB087


title: S52_HDM


title: HYB081


title: HYB089


title: S51_CTRL


title: S50_HDM


title: S48_HDM


title: S49_CTRL


title: HYB080


title: S17_CTRL


title: HYB079


title: S47_CTRL


title: S46_HDM


title: S45_CTRL


title: S44_HDM


title: S43_CTRL


title: S42_HDM


title: W303

city: TOULOUSE

first: Benjamin

last: Albert

state: Cedex 9

address: 169 avenue Marianne Grunberg-Manago

department: UMR5077, Bat IBCG

country: France

institute: CNRS

description: RNAPII ChIP-seq was performed as described previously (Ribaud et al., 2012) (PMID: 21952045) using Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (ab5131)

data_processing:
ChIP-Seq raw reads were aligned to the sacCer3 and 972-h pombe genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
ChIP-Seq, data were filtered to retain only the mapped reads with at most 5 hits in the reference.
ChIP-Seq, reads that mapped to both sacCer3 and 972-h genomes were discarded.
ChIP-Seq, the reads were shifted by 100 bp and extended by 50 bp
ChIP-Seq, reads mapped uniquely to the sacCer3 genome were first normalized to total number of mapped reads in sacCer3
Assembly: sacCer3
Supplementary files format and content: bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)

growth_protocol: YPAD, (glucose 2%) . Cells were cultured at 30C

extract_protocol:
Yeast cultures of 50 mL in complete medium were collected at OD600 = 0.4–0.6 for each condition. The cells were crosslinked with 1% formaldehyde for 10 min and quenched by adding 125 mM glycine for 5 min at room temperature. Cells were then washed with ice-cold HBS (50 mM HEPES-Na pH:7.5, 140 mM NaCl) and resuspended in 0.6 ml of ChIP lysis buffer (50 mM HEPES-Na pH:7.5, 140 mM NaCl, 1 mM EDTA, 1% NP-40, 0.1% sodium deoxycholate) supplemented with 1 mM PMSF and 1× protease inhibitor cocktail (Roche; Cat# 04693132001). The cells were broken using Zirconia/Silica beads (BioSpec) and lysates were centrifuged at 13,000 rpm for 30 min at 4°C. Following centrifugation, the pellets were resuspended in 300 μl ChIP lysis buffer containing 1 mM PMSF and sonicated for 15 min (30s ON–60s OFF) in a Bioruptor (Diagenode). The lysates were centrifuged at 7000 rpm for 15 min at 4°C, following which primary antibodies were added to the supernatant and incubated for 1 h at 4°C. ChIP was performed using Abcam ab5131 for RNAPII. Magnetic beads coupled to IgG against rabbit (Dynabeads™ M-280 Sheep Anti-Rabbit; Thermofischer; Cat# 11203D) were washed three times with PBS (137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4) containing 0.5% BSA and added to the lysates (30 μl of beads/300 μl of cell lysate). The samples were incubated for 2 h at 4°C. The beads were washed twice with AT1 buffer (50 mM HEPES-Na pH: 7.5, 140 mM NaCl, 1 mM EDTA, 0.03% SDS), once with AT2 buffer (50 mM HEPES-Na pH: 7.5, 1 M NaCl, 1 mM EDTA), once with AT3 buffer (20 mM Tris–Cl pH: 7.5, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate) and twice with TE buffer (10 mM Tris, 1 mM EDTA). The chromatin was eluted from the beads by resuspension in TE containing 1% SDS and incubation at 65°C for 10 min. The eluate was transferred to new Eppendorf tubes and incubated overnight at 65°C to reverse the crosslinks. The DNAs were purified using the MinElute PCR Purification Kit (Qiagen; Cat# 28004). DNA libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina) according to manufacturer’s specifications. The libraries were sequenced using an Illumina HiSeq 2500 platform at the Institute of Genetics and Genomics of Geneva (iGE3; http://www.ige3.unige.ch/genomics-platform.php) and the reads were mapped to the sacCer3 genome assembly using HTSStation60 (read densities were calculated using shift: 100, extension: 50 bp). All densities were normalized to 10M reads. The signal was quantified for each gene between the transcription start site (TSS) and transcription termination site (TTS). All data from publicly available databases were mapped using HTS Station (http://htsstation.epfl.ch;).
TruSeq ChIP library preparation kit (Illumina). Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: no treatment

tag: cell line

value: whole organism

tag: genotype


title: W306

value: ubp2-delta ubp14-delta


title: HYB075


title: S41_CTRL


title: HYB077

value: Cladribine Low Dose


title: W304


title: W305


title: HYB078


title: HYB071


title: HYB076


title: HYB072


title: HYB073

value: Cladribine 3.5 mg/kg


title: S40_HDM


title: STINGX+TGFβ, 16hr, STXTGF2

city: New Haven

first: Suyavaran

last: Arumugam

state: Connecticut

address: 300 Cedar Street

department: Internal Medicine

institute: Yale University

data_processing:
Data cleaning with cutadapt, to remove low quality reads and adapters.
Mapping to genome (bam format) using HISAT2. Mapping the reads of each sample to the reference genome.
StringTie to perfom assembly of the transcripts. Merged all assemblies to create StringTie merged gtf
mRNA expression profiling with StringTie
Differential expression analysis with edgeR
Assembly: GRCh38
Supplementary files format and content: Text files with FPKM files, transcript count matrix and gene count matrix

source_name: LX2 cells

growth_protocol: LX2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), Glutamax and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1.5μg of total RNA was used for the construction of sequencing libraries. RNA integrity was checked using Agilent Technologies 2100 Bioanalyzer. (poly (A) tail containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. Following purification, poly (A) RNA was fragmented using divalent cation buffer in elevated temperature.
Poly(a) RNA sequncing library was prepared using Illumina's Truseq-stranded mRNA sample preparation protocol. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 bioanalyzer high sensitivity DNA chip. Paired-ended sequencing was performed on Illumina's Novaseq 6000 sequencing system.

treatment_protocol:
Post 24 hr of seeding the cells were serum starved for 16 hrs prior to stimulation protocol.
Post 16 hr of serum starvation the cells were either pretreated with 10μM IFM - 004990-7 (STINGX) for 3 hrs or directly subjected to TGFβ 5ng/ml for 16 hr.

value: LX2 cells

value: Hepatic stellate cells

value: Wild type

tag: treatment

value: STINGX+TGFb (5ng/ml)

tag: time


title: HYB070

tag: treatment arm

tag: treatment dose

value: whole blood

value: 96 weeks


title: HYB069

value: Cladribine High Dose

value: Cladribine 5.25 mg/kg

tag: timepoint


title: HYB074

value: Placebo


title: TGFβ, 16hr, TGF4

value: TGFb (5ng/ml)


title: HYB068


title: S39_CTRL

value: non-responing


title: STINGX+TGFβ, 16hr, STXTGF1


title: HYB067


title: TGFβ, 16hr, TGF3


title: TGFβ, 16hr, TGF2


title: STINGX+TGFβ, 16hr, STXTGF4


title: TGFβ, 16hr, TGF1


title: STINGX+TGFβ, 16hr, STXTGF3


title: Control, 16hr , CT2

value: Untreated


title: Control, 16hr , CT3


title: S37_CTRL

value: responding

value: bulk RNA-seq

value: FACS sorted CD207+


title: Control, 16hr , CT1


title: HYB066


title: NOR_5

city: jinan

first: zhicheng

last: jia

state: shandong

address: Wenhua East Road, Lixia District, Jinan City

department: The First Clinical College

country: China

institute: Shandong University of Traditional Chinese Medicine

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo_sapiens.GRCm38 V101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: ovarian follicle

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovarian follicle

value: granulosa cell

tag: phenotype

value: normal ovarian reserve


title: HYB063


title: HYB064

value: Cladribine Low Dose

value: Cladribine 3.5 mg/kg


title: S33_CTRL


title: HYB065


title: S34_HDM


title: HYB062


title: NOR_1


title: HYB061


title: S38_HDM


title: NOR_3


title: Control, 16hr , CT4

value: LX2 cells

value: Hepatic stellate cells

value: Wild type


title: DOR_6

value: diminished ovarian reserve


title: NOR_2


title: S16_HDM


title: DOR_5


title: S36_HDM

value: undefined


title: NOR_6


title: S35_CTRL


title: DOR_4


title: DOR_2


title: HYB059

value: whole blood

value: 96 weeks


title: DOR_3


title: HYB060

value: Placebo


title: NOR_4


title: HYB058


title: HYB120


title: Dl_B_F_K_21

city: Munich

first: Mathias

middle: V.

last: Schmidt

state: Bayern

address: Kraepelinstrasse 2-10

institute: Max Planck Institute of Psychiatry

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Allignment to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then  FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this gene.
Differential expression analysis was performed using the  DESeq2Rpackage (1.20.0). DESeq2. Resulting P-values were adjusted using the Benjamini and Hochberg's  approach for controlling the false discovery rate.
Genes with an adjusted P-value <=0.05 found  by DESeq2 were assigned as differentially expressed

source_name: Brain

growth_protocol: Brains were extracted, snap-frozen in methyl butane on dry-ice and stored at -80 degrees

extract_protocol:
RNA was isolated using the miRNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared by the company Novogene UK, according to their standardized protocols

treatment_protocol: All samples were baseline samples, no treatments were applied, just differences in mouseline, brain region, sex and genotype

value: Brain

tag: background strain

tag: mouseline

tag: brain region

value: Brain:Bed nucleus of the stria terminalis

tag: Sex

value: Female

value: Knockout


title: S15_CTRL

tag: sample group

value: non-responing

value: bulk RNA-seq

value: FACS sorted CD207+


title: MPRA_rep3

city: Tianjin

first: Fu

last: Zongheng

address: Yaguan Road 135, Jinnan District, Tianjin, Postcode 300350

institute: Tianjin University

data_processing:
PCR duplicates were removed using starcode-umi based on the UMI
the abundance of the 12 bp barcode for synthetic promoters was quantified using MAGeCK
Barcodes were filtered to ensure a minimum of 3 counts.
Promoter strength was determined by calculating RNA/DNA ratios for each barcode, then normalized with respect to IGKV1-5.
Supplementary files format and content: Data files are in CSV format, The first column contains synthetic promoter sequence and the remaining columns contain normalized expression levels

source_name: Ramos (RA 1)

growth_protocol: Ramos (RA 1) (ATCC, CRL-1596) cells were maintained at 37 °C under 5% CO2  in RPMI-1640 medium (Gibco, 11875093) supplemented with 10% FBS (Gibco, 10091148).

extract_protocol:
Twenty-four hours post-transfection, cells were pelleted and washed with DPBS. Total RNA was extracted using Trizol (Invitrogen, 12183555). From 75 μg of total RNA per sample, mRNAs were isolated using the Dynabeads mRNA Purification Kit (Invitrogen, 61006). Residual DNA was removed from 1 μg of mRNA using ezDNase (Invitrogen, 11766051).
All mRNAs were subjected to a reverse-transcription reaction in 8-strip PCR tubes, using a custom primer（R-amp1-UMI12-rd2, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNNggccgtttacgtcgccgtcc， FS-TSO, AAGCAGTGGTATCAACGCAGAGTACrGrGrG） and the SuperScript IV First Strand Synthesis Kit (Invitrogen, 18091050). The resulting cDNA was purified using the QIAquick PCR Purification Kit (Qiagen, 28506). The purified cDNA was split into 8 PCR tubes and amplified using NEBNext Ultra II Q5 Master Mix (NEB, M0544S) and F-TSO(ISPCR)-rd1( ACACTCTTTCCCTACACGACGCTCTTCCGATCTAAGCAGTGGTATCAACGCAGAG) and P7-i7(index)-rd2(CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) primers for three cycles. After the PCR reaction, all eight tubes for each sample were combined in a DNA LoBind tube. PCR products were purified using AMPure XP (Beckman Coulter, A63881) and then further amplified using P5-i5-rd1(AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT) and P7(CAAGCAGAAGACGGCATACGAGAT) primers for seven PCR cycles to add P5, P7, and unique 8 bp Illumina index sequences. Similarly, plasmid DNA was amplified in 2x50 μL reactions using NGS-F and NGS-R primers and amplified using NGS-P5 (ACACTCTTTCCCTACACGACGCTCTTCCGATCTGTGGATAACCGTATTACCGCCATGC), and NGS-P7(GACTGGAGTTCAGACGTGTGCTCTTCCGATCTTGAACAGCTCCTCGCCCTTG) primers for seven PCR cycles to add P5, P7. Following SPRI (Beckman Coulter, B23319) cleanup, amplicons were sequenced using a NovaSeq 6000 SP flow cell with a 15% PhiX spike-in.

treatment_protocol: The Neon transfection system and 100 μL kit (ThermoFisher, MPK10096) were used according to the manufacturer's instructions. For Ramos cells, electroporation was performed with one 1350V pulse for 30 milliseconds, with a total of three replicates, each consisting of ~8 million cells, transfected 10 μg of library plasmid per replicate, each replicate was grown in RPMI + 10% FBS without Pen-Strep for 24 hours

value: Ramos (RA 1)

value: human B lymphocyte cell


title: Dl_B_F_K_18


title: MPRA_rep1


title: MPRA_rep2


title: Dl_B_F_K_8


title: HYB057

value: Cladribine High Dose

value: Cladribine 5.25 mg/kg


title: Dl_B_F_K_7


title: HYB056

value: Cladribine Low Dose

value: Cladribine 3.5 mg/kg


title: PolyA_RNA-seq_In2_rep3

city: Lisboa

first: Rui

last: Sousa-Luís

address: Av. Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular João Lobo Antunes

description: PolyA RNA

data_processing:
PolyA and Chromatin paired-end strand-specific RNA-seq raw Illumina short-reads in FASTQ format were quality controlled with FastQC, without any unexpected bias found. TrimGalore was used in paired-end mode to trim read adaptors, as well as to remove reads with low-quality ends (20 Phred score cut-off) and/or less than 10 nucleotides (nt). Selected reads were aligned against the reference human genome (GRCh38) using STAR software, requiring a minimum alignment score (--outFilterScoreMin) of 10, and excluding non-uniquely mapped reads (--outFilterMultimapNmax 1).
Uniquely mapped reads contained in BAM files were divided into forward and reverse strands, according to their bitwise flags 83 163, and 99 147, respectively. Samtools was used to perform this task. Then, strand-specific BAM files were converted into bedGraph with bedtools genomecov, and bedGraphToBigWig compressed them into bigwig files. Each bigwig was normalised to the library size (number of paired-end fragments) aligned in the original BAM. Y-scale represents read counts per million mapped reads.
Assembly: hg38
Supplementary files format and content: bigwig containing the depth per postion normalized per million mapped reads

source_name: HeLa

extract_protocol:
HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. A quarter of transfected cells were used to extract total RNA (Trizol).
Half a µg of total RNA was used to prepare polyA+ RNA libraries, using NEBNext Ultra II directional RNA library prep kit with NEBNExt PolyA mRNA Magnetic Isolation module.

value: HeLa

value: intron 2 sgRNA


title: PolyA_RNA-seq_APA_rep3

description: PolyA RNA

value: downstream several genes sgRNA


title: PolyA_RNA-seq_DS2_rep3

description: PolyA RNA

value: downstream sgRNA


title: PolyA_RNA-seq_DS2_rep2

description: PolyA RNA


title: PolyA_RNA-seq_APA_rep2

description: PolyA RNA


title: Dl_B_F_K_6

value: Brain


title: PolyA_RNA-seq_Ctrl_rep3

description: PolyA RNA

value: scramble sgRNA


title: DOR_1

value: ovarian follicle

value: granulosa cell

value: diminished ovarian reserve


title: PolyA_RNA-seq_In2_rep2

description: PolyA RNA


title: PolyA_RNA-seq_Ctrl_rep2

description: PolyA RNA


title: Dl_B_F_W_14

value: Brain:Bed nucleus of the stria terminalis

value: Female

value: Wild-type


title: Dl_B_F_K_19

value: Knockout


title: PolyA_RNA-seq_APA_rep1

description: PolyA RNA


title: HYB053

value: Placebo

value: whole blood

value: 96 weeks


title: HYB054

value: Cladribine Low Dose

value: Cladribine 3.5 mg/kg


title: HYB055

value: Cladribine High Dose

value: Cladribine 5.25 mg/kg


title: HYB052


title: Synthetic_Library

value: Ramos (RA 1)

value: human B lymphocyte cell


title: HYB051


title: HYB050


title: Dl_B_F_W_11

value: Brain


title: PolyA_RNA-seq_DS2_rep1

description: PolyA RNA

value: HeLa

value: downstream sgRNA


title: PolyA_RNA-seq_Ctrl_rep1

description: PolyA RNA

value: scramble sgRNA


title: Dl_B_F_W_10

value: Brain:Bed nucleus of the stria terminalis


title: ChrRNA-seq_APA_rep2

description: chomatin-bound RNA

data_processing:
PolyA and Chromatin paired-end strand-specific RNA-seq raw Illumina short-reads in FASTQ format were quality controlled with FastQC, without any unexpected bias found. TrimGalore was used in paired-end mode to trim read adaptors, as well as to remove reads with low-quality ends (20 Phred score cut-off) and/or less than 10 nucleotides (nt). Selected reads were aligned against the reference human genome (GRCh38) using STAR software, requiring a minimum alignment score (--outFilterScoreMin) of 10, and excluding non-uniquely mapped reads (--outFilterMultimapNmax 1).
Uniquely mapped reads contained in BAM files were divided into forward and reverse strands, according to their bitwise flags 83 163, and 99 147, respectively. Samtools was used to perform this task. Then, strand-specific BAM files were converted into bedGraph with bedtools genomecov, and bedGraphToBigWig compressed them into bigwig files. Each bigwig was normalised to the library size (number of paired-end fragments) aligned in the original BAM. Y-scale represents read counts per million mapped reads.
Assembly: hg38
Supplementary files format and content: bigwig containing the depth per postion normalized per million mapped reads
Library strategy: ChrRNA-seq

extract_protocol:
HeLa cells were transfected in 15-cm plates as above with gene-specific gRNAs alone or a mix of gene-specific gRNAs for APA experiments. With three quarters of transfected cells, chromatin RNA was extracted as described in (Sousa-Luís et al 2021 Mol Cel) with the following modifications: chromatin pellet was digested with 2 µl of Turbo DNase (Life Technologies) in 200 µl of High Salt Buffer (10 mM Tris-HCl, pH 7.5, 500 mM NaCl, and 10 mM MgCl2) for 15 min at 37C, then treated with Proteinase K in 0.2% SDS for 10 min at 37C. Chromatin RNA was extracted by phenol/chloroform and a second round of Turbo DNase digestion was performed, followed by RNA extraction using Trizol.
ne microgram of chromatin RNA was ribodepleted using RiboCop rRNA Depletion kit (Lexogen), followed by library preparation using NEBNExt Ultra II directional RNA kit.

value: downstream several genes sgRNA


title: PolyA_RNA-seq_In2_rep1

description: PolyA RNA

value: intron 2 sgRNA


title: ChrRNA-seq_DS2_rep2

description: chomatin-bound RNA


title: ChrRNA-seq_In2_rep2

description: chomatin-bound RNA


title: ChrRNA-seq_Ctrl_rep2

description: chomatin-bound RNA


title: Dl_B_F_W_9

value: Female

value: Wild-type


title: Dl_B_F_W_3


title: Dl_B_F_W_1


title: ChrRNA-seq_APA_rep1

description: chomatin-bound RNA


title: ChrRNA-seq_DS2_rep1

description: chomatin-bound RNA


title: ChrRNA-seq_In2_rep1

description: chomatin-bound RNA


title: Dl_D_F_K_21

value: Brain:Dorsal hippocampus

value: Knockout


title: Dl_D_F_K_19


title: MS-5185, grey matter, snRNA-seq

city: New York

first: Donghoon

last: Lee

state: NY

address: 1399 Park Ave

department: Psychiatry, Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

data_processing:
Quantification of single-nuclei gene expression data:  We used the cellranger (v.7.0.0) pipeline for preprocessing of the single-cell sequencing data. We aligned the fastq reads to the reference genome hg38, quantified the transcriptomic reads, and called cell barcodes to generate a feature-count-by-barcode matrix for subsequent analysis.
Assembly: GRCh38
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format

molecule: nuclear RNA

extract_protocol:
Isolation and fluorescence-activated nuclear sorting (FANS) of nuclei for frozen human postmortem brain:  Samples were processed in batches consisting of 2 individuals; 1 case and 1 control. For each case, we processed 3 dissections; 1 of gray matter, 1 white matter, and 1 containing an MS plaque. For each Control we processed 2 dissections; 1 gray matter and 1 white matter. Approximately 25 mg of frozen postmortem human brain tissue from each dissection was homogenized in cold lysis buffer (0.32M Sucrose, 5 mM CaCl2, 3 mM Magnesium acetate, 0.1 mM, EDTA, 10 mM Tris-HCl, pH8, 1 mM DTT, 0.1% Triton X-100) and filtered through a 40 µm cell strainer. All buffers were supplemented with RNAse inhibitors (Takara). The flow-through was underlaid with sucrose solution (1.8 M Sucrose, 3 mM Magnesium acetate, 1 mM DTT, 10 mM Tris-HCl, pH8) and centrifuged at 107,000 g for 1 hour at 4°C. Pellets were resuspended in PBS supplemented with 0.5% bovine serum albumin (BSA). Prior to FANS, volumes were brought up to 500 µl with PBS and DAPI (Thermoscientific) added to a final concentration of 1 µg/ml. DAPI-positive nuclei were sorted into tubes pre-coated with 5% BSA using a FACSAria flow cytometer (BD Biosciences).
Single-nuclei gene expression library preparation:  Following FANS, nuclei were quantified (Countess II, Life Technologies) and 8,000 from each sample loaded on a single 10x lane using single cell 3' v3 reagents (10x Genomics). cDNA libraries were prepared according to the manufacturer's protocol. Libraries were sequenced at New York Genome Center using the Novaseq platform (Illumina).
snRNA-seq

tag: individual id

tag: disease state

value: control

value: female

value: frozen brain tissue specimens

tag: tissue subset

value: grey matter

tag: age


title: MS-5185, white matter, snRNA-seq

description: 10x Genomics

source_name: nuclei for frozen human postmortem brain

tag: tissue

value: white matter


title: MS-5190, white matter, snRNA-seq

description: 10x Genomics

value: male


title: Dl_D_F_K_18

value: Brain

tag: genotype


title: ChrRNA-seq_Ctrl_rep1

description: chomatin-bound RNA

tag: cell line

value: HeLa

tag: treatment


title: Dl_D_F_K_8


title: HYB047

tag: treatment arm

value: Cladribine High Dose

value: Cladribine 5.25 mg/kg

value: whole blood

value: 96 weeks


title: HYB049

tag: treatment dose


title: Dl_D_F_K_7


title: HYB048

value: Cladribine Low Dose

value: Cladribine 3.5 mg/kg

tag: timepoint


title: MS-5116, grey matter, snRNA-seq

description: 10x Genomics


title: MS-5116, white matter, snRNA-seq

description: 10x Genomics


title: MS-5144, white matter, snRNA-seq

description: 10x Genomics


title: Dl_D_F_K_6

value: Female


title: Dl_D_F_W_14

value: Brain:Dorsal hippocampus

value: Wild-type


title: MS-5190, grey matter, snRNA-seq

description: 10x Genomics

value: control


title: HYB045


title: MS-5144, grey matter, snRNA-seq

description: 10x Genomics


title: HYB042


title: HYB040


title: HYB043


title: MS-5095, white matter, snRNA-seq

description: 10x Genomics

value: MS


title: MS-5093, grey matter, snRNA-seq

description: 10x Genomics

value: frozen brain tissue specimens


title: MS-5095, grey matter, snRNA-seq

description: 10x Genomics

value: grey matter


title: MS-5095, plaque, snRNA-seq

description: 10x Genomics

value: plaque


title: MS-5093, white matter, snRNA-seq

description: 10x Genomics

value: male

value: white matter


title: MS-5093, plaque, snRNA-seq

description: 10x Genomics


title: MS-5090, white matter, snRNA-seq

description: 10x Genomics


title: HYB046


title: Dl_D_F_W_12

value: Brain


title: HYB041

value: Cladribine High Dose


title: HYB038

value: Cladribine 5.25 mg/kg


title: HYB039

value: Placebo

value: whole blood


title: HYB044

value: 96 weeks


title: HYB037


title: Dl_D_F_W_10


title: MS-5090, plaque, snRNA-seq

description: 10x Genomics


title: MS-5086, white matter, snRNA-seq

description: 10x Genomics

value: female


title: MS-5072, white matter, snRNA-seq

description: 10x Genomics


title: Dl_D_F_W_11

value: Female


title: Dl_D_F_W_3

value: Brain:Dorsal hippocampus


title: MS-5086, grey matter, snRNA-seq

description: 10x Genomics


title: HYB036

value: Cladribine Low Dose

value: Cladribine 3.5 mg/kg


title: MS-5072, grey matter, snRNA-seq

description: 10x Genomics

value: control


title: MS-5068, white matter, snRNA-seq

description: 10x Genomics

value: MS

value: frozen brain tissue specimens


title: MS-5090, grey matter, snRNA-seq

description: 10x Genomics

value: grey matter


title: HYB035


title: MS-5068, plaque, snRNA-seq

description: 10x Genomics

value: male

value: plaque


title: Dl_D_F_W_1

value: Brain

value: Wild-type


title: MS-5068, grey matter, snRNA-seq

description: 10x Genomics


title: Dl_B_M_K_655

value: Brain:Bed nucleus of the stria terminalis

value: Male

value: Knockout


title: Dl_B_M_K_631


title: HYB033

value: Cladribine High Dose

value: Cladribine 5.25 mg/kg

value: whole blood

value: 96 weeks


title: MS-5024, grey matter, snRNA-seq

description: 10x Genomics

value: female


title: MS-5023, white matter, snRNA-seq

description: 10x Genomics

value: white matter


title: MS-5024, white matter, snRNA-seq

description: 10x Genomics


title: MS-5024, plaque, snRNA-seq

description: 10x Genomics


title: MS-5023, plaque, snRNA-seq

description: 10x Genomics


title: Dl_B_M_K_619


title: Dl_B_M_K_639


title: MS-5023, grey matter, snRNA-seq

description: 10x Genomics


title: Dl_B_M_K_585


title: Panc-1, Okadaic Acid resistant clone OA7G repeat3, L140-P21D

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Sequencing: Sequence-libraries of each sample were equimolarly pooled and sequenced on Illumina NovaSeq 6000 (100 bp, Single Reads, v1.5) at the VIB Nucleomics Core (www.nucleomics.be).
Preprocessing: Low-quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using FastX 0.0.14 and ShortRead 1.40.0 (Morgan et al., 2009). With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina (Langmead et al., 2012).
Mapping: The preprocessed reads were aligned with STAR aligner v2.5.2b to the reference genome of Homo sapiens (GRCh38) (Dobin et al., 2013). Default STAR aligner parameter settings were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments (Li et al., 2009).
Counting: The number of reads in the alignments that overlap with gene features was counted with featureCounts 1.5.3 (Liao et al., 2014). Following parameters were chosen: -Q 0 -s 2 -t exon -g gene_id.
Assembly: Homo sapiens Ensembl GRCh38.88
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Pancreas, duct

growth_protocol:
Panc-1 cells were cultured in 6-well plate in DMEM medium supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml Penicillin and 100 µg/ml Streptomicin
Okadaic-resistant cell lines were developed to single cell coles from cultures of Panc-1 cells that can multiply in the presence of 8 nM of OA over a period of >3 months, Cells were cultured in DMEM medium supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml Penicillin and 100 µg/ml Streptomicin with 8 nM of OA.

extract_protocol:
RNA was isolated with the RNeasy Kit (Qiagen, Chatsworth, CA). RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND8000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 (Agilent).
Per sample, an amount of 500 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 1000000040498 v00 - October 2017) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library.

treatment_protocol: see growth protocols

value: Panc-1, ATCC CRL-1469

value: Pancreas, duct

tag: cell type

value: pancreas ductular epithelium

value: standard culture conditions supplemented with 8 nM OA


title: K562 GAi TAL1 Sp ChIP-seq

city: Busan

first: AeRi

last: Kim

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

country: South Korea

institute: Pusan national university

data_processing:
ChIP-seq raw reads were trimmed by Trimmomatic to filter and remove input read ends with poor quality values (quality score 20) and minimum read length 36 bp. Trimmed reads were aligned to the hg19 canonical genome using Bowtie2. Aligned BAM files were filtered by Minimum MAPQ quality score 20 and sorted by chromosomal coordinates. Potential PCR duplicates were removed from BAM files. Peak files were generated from aligned reads using MACS2 with input BAM file as control. Bigwig files were generated from BAM files using bamCoverage with normalization to effective hg19 genome size.
Assembly: hg19
Supplementary files format and content: BED, bigwig

source_name: K562 cells

growth_protocol: K562 cells were cultured in RPMI1640 medium containing 10% FBS.

extract_protocol:
Nuclei were digested with 100 units of MNase at 37°C for 15 min. Mono or di-nucleosomes sized chromatin was incubated with antibodies for 3 h at 4°C and recovered with protein G or A agarose beads.
ChIP DNA (10 ng for K27ac, Input, 0.5 ng for GATA1, TAL1, LDB1) was processed using NEBNext ChIP-seq library (New England Biolabs) with manufacturer’s instructions. The ends of ChIP DNA were repaired by NEBNext Ultra II End Prep enzyme mix and ligated with NEBNext adaptors. Adaptor-ligated DNA was selected at 200 bp size using NEBNext sample purification bead and amplified using the adaptor primers. Amplification cycles were 7 cycles for H3K27ac and input and 12 cycles for GATA1, TAL1 and LDB1. The fragments are purified using NEBNext sample purification beads.

treatment_protocol: GATA1 or TAL1 knockdown was performed in K562 cells using TRC lentiviral short hairpin RNA (shRNA) vectors (Sigma).

value: erythroleukemia cells

tag: chip antibody

value: GATA1 knockdown


title: Panc-1, Okadaic Acid resistant clone OA7G repeat2, L140-P21B


title: Panc-1, Okadaic Acid resistant clone OA7G repeat1, L140-P21A


title: Dl_B_M_K_583

value: Brain

tag: background strain

tag: mouseline


title: Panc-1, Okadaic Acid resistant clone OA7A repeat3, L140-P23D


title: Panc-1, Okadaic Acid resistant clone OA7A repeat2, L140-P23C


title: Dl_B_M_W_657

tag: brain region

tag: Sex

value: Wild-type


title: Panc-1, Okadaic Acid resistant clone OA7A repeat1, L140-P23A


title: HYB030

value: Cladribine Low Dose

value: Cladribine 3.5 mg/kg


title: HYB031


title: HYB028

value: Placebo


title: Panc-1, control 4, L140-10

value: WT

value: standard culture conditions


title: HYB029

value: Cladribine High Dose

value: Cladribine 5.25 mg/kg

value: whole blood


title: HYB032

value: 96 weeks


title: HYB034


title: HYB027


title: Dl_B_M_W_643

value: Brain:Bed nucleus of the stria terminalis

value: Male


title: Dl_B_M_W_637


title: Panc-1, control 3, L140-9

value: Panc-1, ATCC CRL-1469

value: Pancreas, duct

value: pancreas ductular epithelium


title: Panc-1, control 2, L142-2


title: Dl_B_M_W_641


title: TNF+IFNgamma_24h-SILAClabel-M

city: Amsterdam

first: Arie Johan

last: Hoogendijk

address: Plesmanlaan 125

institute: Sanquin Research

data_processing:
Sequence quality was confirmed using FastQC (Babraham Bioinformatics).
Reads were aligned to GRCh38.104 using STAR.
A count matrix was generated FeatureCounts (using -p -g gene_id -t exon flags).
Further normalization and differential expression analysis were performed using DESeq2.
Assembly: ChGR38.v104
Supplementary files format and content: tab-delimited text file include count values for all samples

source_name: Blood

growth_protocol: ECs were cultured in endothelial cell growth medium (PromoCell) supplemented with 18% FCS (HiCult). For SILAC labeling, BOECs were maintained for 5 passages as previously described using custom-made EBM-2 medium (Lonza), containing 18% FCS (passages 1-3) or 1 kDa dialyzed FCS (passages 4-5, Bodinco) and isotope labeled amino acids (light: Arg0 & Lys0, medium: Arg6 & Lys4, heavy: Arg10 & Lys8, Cambridge Isotopes).

extract_protocol:
Samples for RNAseq analysis were lysed in RLT buffer. RNA sequencing was performed by GeneWiz (Azenta life sciences), including RNA isolation
RNA sequencing was performed by GeneWiz (Azenta life sciences) including library preparation, strand-specific RNA-seq with PolyA selection and Illumina paired end 150bp sequencing.

treatment_protocol: SILAC BOECs were serum starved for 2 hours prior to stimulation. Cells were stimulated with 10ng/ml TNF, 10ng/ml IFNgamma or 10ng/ml TNF+10ng/ml IFNgamma for  0 minutes, 2 minutes, 10 minutes, 30 minutes, 4 hours, 8 hours, 12 hours and 24 hours.

value: Blood

value: Blood outgrowth endothelial cells

value: TNF+IFNgamma 24h


title: IFNgamma_24h-SILAClabel-M

value: IFNgamma 24h


title: TNF+IFNgamma_24h-SILAClabel-L


title: TNF+IFNgamma_24h-SILAClabel-H


title: HYB025

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method implemented in the Bioconductor package to obtain a log2 expression value for each gene probe set.

extract_protocol: Total RNAs are extracted from whole blood using the PAXgene RNA Blood RNA kit from Qiagen


title: Dl_B_M_W_627

value: Brain

value: Wild-type


title: Dl_B_M_W_633


title: IFNgamma_24h-SILAClabel-L

value: WT


title: HYB026


title: IFNgamma_24h-SILAClabel-H


title: HYB024


title: HYB022

value: Placebo


title: Panc-1, control 1, L142-1

value: standard culture conditions


title: HYB023

value: Cladribine Low Dose

value: Cladribine 3.5 mg/kg


title: TNF_24h-SILAClabel-M

value: TNF 24h


title: Dl_D_M_K_655

value: Brain:Dorsal hippocampus

value: Knockout


title: HYB021

value: Cladribine High Dose

value: Cladribine 5.25 mg/kg

value: whole blood

value: 96 weeks


title: Dl_D_M_K_639

value: Male


title: TNF_24h-SILAClabel-H

value: Blood

value: Blood outgrowth endothelial cells


title: TNF+IFNgamma_12h-SILAClabel-M

value: TNF+IFNgamma 12h


title: TNF+IFNgamma_12h-SILAClabel-L


title: HYB020


title: Dl_D_M_K_631

value: Brain


title: TNF+IFNgamma_12h-SILAClabel-H

value: WT


title: IFNgamma_12h-SILAClabel-M

value: IFNgamma 12h


title: HYB018


title: Dl_D_M_K_585


title: Dl_D_M_K_583


title: HYB019

value: Placebo


title: IFNgamma_12h-SILAClabel-H


title: TNF_12h-SILAClabel-L

value: TNF 12h


title: TNF_12h-SILAClabel-M


title: IFNgamma_12h-SILAClabel-L


title: TNF_24h-SILAClabel-L


title: TNF+IFNgamma_8h-SILAClabel-M

value: TNF+IFNgamma 8h


title: TNF+IFNgamma_8h-SILAClabel-L


title: Dl_D_M_W_667

value: Wild-type


title: HYB015


title: HYB016

value: Cladribine Low Dose

value: Cladribine 3.5 mg/kg


title: IFNgamma_8h-SILAClabel-M

value: IFNgamma 8h


title: TNF+IFNgamma_8h-SILAClabel-H


title: IFNgamma_8h-SILAClabel-L


title: HYB017


title: IFNgamma_8h-SILAClabel-H


title: HYB014


title: Dl_D_M_K_587

value: Brain:Dorsal hippocampus

value: Knockout


title: TNF_8h-SILAClabel-M

value: TNF 8h


title: Dl_D_M_W_637

value: Male


title: HYB013

value: Cladribine High Dose

value: Cladribine 5.25 mg/kg

value: whole blood

value: 96 weeks


title: TNF_8h-SILAClabel-L

value: Blood

value: Blood outgrowth endothelial cells

value: WT


title: TNF_12h-SILAClabel-H

value: TNF 12h


title: TNF_8h-SILAClabel-H


title: Dl_D_M_W_633

value: Brain


title: HYB012

value: Placebo


title: TNF+IFNgamma_4h-SILAClabel-H

value: TNF+IFNgamma 4h


title: TNF+IFNgamma_4h-SILAClabel-L


title: TNF+IFNgamma_4h-SILAClabel-M


title: Dl_D_M_W_627

value: Wild-type


title: IFNgamma_4h-SILAClabel-M

value: IFNgamma 4h


title: Dl_D_M_W_641

value: Brain:Dorsal hippocampus


title: Dl_D_M_W_643


title: IFNgamma_4h-SILAClabel-H


title: N_B_F_K_518

value: Brain:Bed nucleus of the stria terminalis

value: Female

value: Knockout


title: N_B_F_K_496


title: HYB010

value: Cladribine Low Dose

value: Cladribine 3.5 mg/kg


title: HYB011

value: whole blood


title: HYB008

value: 96 weeks


title: HYB009


title: IFNgamma_30min-SILAClabel-M

value: Blood

value: IFNgamma 30min


title: TNF_4h-SILAClabel-L

value: Blood outgrowth endothelial cells

value: WT

value: TNF 4h


title: IFNgamma_30min-SILAClabel-L


title: N_B_F_K_478

value: Brain


title: TNF_4h-SILAClabel-H


title: HYB007

value: Cladribine High Dose

value: Cladribine 5.25 mg/kg


title: IFNgamma_30min-SILAClabel-H


title: TNF_30min-SILAClabel-M

value: TNF 30min


title: TNF_30min-SILAClabel-L


title: N_B_F_K_456


title: HYB006

value: Placebo


title: IFNgamma_4h-SILAClabel-L

value: IFNgamma 4h


title: TNF+IFNgamma_30min-SILAClabel-M

value: TNF+IFNgamma 30min


title: N_B_F_W_510

value: Brain:Bed nucleus of the stria terminalis

value: Female

value: Wild-type


title: N_B_F_K_498

value: Knockout


title: N_B_F_K_476


title: TNF+IFNgamma_30min-SILAClabel-L


title: TNF_4h-SILAClabel-M


title: TNF+IFNgamma_30min-SILAClabel-H


title: N_B_F_W_504


title: IFNgamma_10min-SILAClabel-M

value: IFNgamma 10min


title: IFNgamma_10min-SILAClabel-L

value: Blood


title: HYB005

value: whole blood

value: 96 weeks


title: HYB004


title: IFNgamma_10min-SILAClabel-H

value: Blood outgrowth endothelial cells

value: WT


title: N_B_F_W_484

value: Brain


title: N_B_F_W_482


title: TNF_10min-SILAClabel-M

value: TNF 10min


title: TNF_30min-SILAClabel-H


title: HYB003


title: HYB002

value: Cladribine High Dose

value: Cladribine 5.25 mg/kg


title: HYB001


title: VISUAL_Suc_48h

city: Kobe

first: Yuki

last: Kondo

address: 1-1 Rokkodai-cho, Nada-ku

department: Graduate School of Science

institute: Kobe University

hyb_protocol: Hybridization, washing, staining procedures were conducted with Fluidics Station 450 as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

scan_protocol: Scanning procedure ws conducted with GeneChip Scanner 3000 7G as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

data_processing: GCOS

organism: Arabidopsis thaliana

source_name: WT, 6-day-old cotyledons

label_protocol: Biotinylated cRNA was prepared from total RNA with GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix).

growth_protocol: Arabidopsis seeds were sterilized with sodium hypochlorite for 5 min, and then washed with sterile water. These seeds were grown with MS liquid medium at 22ºC under the continuous light conditions for 6 days.

extract_protocol: Total RNA was extracted with Rneasy Plant Micro Kit (QIAGEN). Extracted RNA was amplified with Amplification Ovation RNA Amplification System V2 (NuGEN), and then purified using MinElute Reaction Cleanup Kit (QIAGEN).

treatment_protocol: WT cotyledons were cultured with the induction medium containing 2,4-D (1.25 mg/L), kinetin (0.25 mg/L), bikinin (10 μM) and 5% Glc or Suc as a sugar.

value: cotyledons

tag: time

value: induction after 72h

tag: sugar in medium

value: sucrose


title: TNF+IFNgamma_10min-SILAClabel-H

value: TNF+IFNgamma 10min


title: N_B_F_W_474

value: Brain:Bed nucleus of the stria terminalis

value: Female


title: VISUAL_Suc_24h


title: IFNgamma_5min-SILAClabel-M

value: IFNgamma 5min


title: TNF+IFNgamma_10min-SILAClabel-L


title: TNF_10min-SILAClabel-H


title: N_B_F_W_458

value: Wild-type


title: TNF+IFNgamma_10min-SILAClabel-M

value: Blood


title: IFNgamma_5min-SILAClabel-H


title: VISUAL_Suc_0h


title: IFNgamma_5min-SILAClabel-L


title: TNF_5min-SILAClabel-M

value: TNF 5min


title: N_D_F_K_498

value: Brain:Dorsal hippocampus

value: Knockout


title: TNF_10min-SILAClabel-L

value: Blood outgrowth endothelial cells

value: WT


title: TNF_5min-SILAClabel-L


title: CER-1251 donor 38

city: South San Francisco

first: Brandon

last: Cieniewicz

state: CA

address: 201 Haskins Way, Suite 230

institute: CERo Therapeutics

data_processing:
Bowtie
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v 0.36
Reads were mapped to the UCSC hg19 human transcriptome using Bowtie and transcripts-per-million (TPM) values were calculated
Read count extraction was performed using Bowtie
Assembly: UCSC hg19
Supplementary files format and content: tab-delimited text files include transcripts-per-million (TPM) values for each Sample

source_name: CER-1251 T cells

growth_protocol: Engineered CER-1236 or CER-1251 T cells were maintained in OpTmizer media supplemented with 5% serum replacement in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using a Qiagen Rneasy Plus Universal mini kit.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Stimulation was induced by culturing CER T cells on a plate coated with 5ug/ml phosphatidylserine for 24 hours.

tag: individual

value: donor 38

value: CER-1251 T cells

value: Phosphatidylserine


title: N_D_F_K_496

value: Brain


title: TNF_5min-SILAClabel-H


title: TNF+IFNgamma_5min-SILAClabel-M

value: TNF+IFNgamma 5min


title: CER-1251 donor 31

value: donor 31


title: CER-1251 donor 32

value: donor 32


title: N_D_F_K_478


title: TNF+IFNgamma_5min-SILAClabel-L


title: VISUAL_Glc_48h

value: cotyledons

tag: age

value: induction after 72h

value: glucose


title: TNF+IFNgamma_5min-SILAClabel-H

tag: tissue


title: VISUAL_Glc_24h

tag: genotype

value: induction after 34h


title: N_D_F_K_518

value: Female


title: VISUAL_Glc_0h

value: induction after 0h


title: IFNgamma_2min-SILAClabel-M

value: Blood

value: IFNgamma 2min


title: IFNgamma_2min-SILAClabel-L

value: Blood outgrowth endothelial cells


title: CER-1236 donor 38

source_name: CER-1236 T cells

value: CER-1236 T cells


title: CER-1236 donor 32


title: TNF_2min-SILAClabel-M

value: WT

value: TNF 2min


title: N_D_F_K_476

value: Brain:Dorsal hippocampus

value: Knockout


title: N_D_F_W_510

value: Brain

value: Wild-type


title: TNF_2min-SILAClabel-H


title: N_D_F_K_456


title: N_D_F_W_504


title: CER-1236 donor 31

value: donor 31

value: Phosphatidylserine


title: S33 HTO4

description:
multiplexed
Constelation-10X
FACS sorted CD207-

data_processing:
Following demultiplexing, raw FASTQ files were aligned to the human genome (GRCh38), using kallisto-bustools
Doublet detection and hashing demultiplexing was done using Solo. Empty barcodes and percentage of mitochondrial genes were checked within Scanpy.
CellBender was used to remove empty technical artefacts.
Assembly: GRCh38
Supplementary files format and content: CSV table with counts and TPM as estimated by Kallisto

source_name: frozen non-LC skin cells

value: skin


title: TNF+IFNgamma_2min-SILAClabel-M

value: TNF+IFNgamma 2min


title: S33 HTO3


title: TNF+IFNgamma_2min-SILAClabel-H


title: N_D_F_W_484


title: N_D_F_W_482


title: S33 HTO2


title: TNF+IFNgamma_2min-SILAClabel-L


title: Sham_0min-SILAClabel-L-short

value: Sham 0min


title: Sham_0min-SILAClabel-M-late


title: N_D_F_W_474

value: Female


title: Sham_0min-SILAClabel-H-short


title: Sham_0min-SILAClabel-L-late


title: S33 HTO1


title: N_D_F_W_458


title: Sham_0min-SILAClabel-H-late


title: TNF_2min-SILAClabel-L


title: N_B_M_K_583

value: Brain:Bed nucleus of the stria terminalis

value: Male


title: S33 GEX3


title: N_B_M_K_575


title: K562_GAi_total_RNA-seq_R2_F

data_processing:
RNA-seq raw reads were trimmed by Trimmomatic to filter and remove input read ends with poor quality values (quality score 20) and minimum read length 36 bp. Remaining reads were aligned to the hg19 using RNA STAR with exon annotation GTF file obtained from UCSC database. Aligned BAM files were used to generated Bigwig files using bamCoverage with normalization to effective hg19 genome size.
Assembly: hg19
Supplementary files format and content: BW

extract_protocol:
Total RNA was extracted using a RNeasy Plus Mini Kit (Qiagen) and qualified using Qubit Fluorometer (RNA IQ > 7).
Ribosomal RNA (rRNA) was removed from total RNA using RiboMinus Human/Mouse Module (Invitrogene, 45-7012). rRNA-depleted RNA (125 ng) was reversely transcribed and processed for RNA-library using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs #E7765S). This process was carried out in the order of fragmentation of RNA, priming reaction using random primers, first-strand cDNA synthesis, second-strand cDNA synthesis, cDNA end repair, adaptor ligation, amplification using adaptor primers for 8 cycles, and purification of amplified fragments using beads.

value: erythroleukemia cells

tag: cell line

value: GATA1 knockdown


title: K562_TAi_total_RNA-seq_R1_F

value: TAL1 knockdown


title: S33 GEX2


title: K562_Con_total_RNA-seq_R2_F

value: control


title: Sham_0min-SILAClabel-M-short

value: Blood

value: Blood outgrowth endothelial cells

value: WT

tag: treatment


title: N_B_M_K_571

value: Brain

value: Knockout


title: S33 GEX1


title: K562 TAi K27ac Sp ChIP-seq


title: N_B_M_K_563


title: K562 GAi K27ac Sp ChIP-seq


title: poor_7P [bone_4P]

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

data_processing:
TopHat v2.0.9 was used to align the reads from samples to the hg19 genome. The reads were quantified into gene counts by using HT-Seq v0.6.0.
The counts were loaded into the software environment R and were processed by the DESeq2 package from Bioconductor (for downstream differential expression analysis).
A log2 transformation was applied to DESeq2 normalised (median-of-ratios method) counts (log2(normalised+1)) for individual gene assessment in each sample.  The DESeq2 calculates size factors for each sample to compare the counts obtained from different samples with different sequencing depth. Briefly, the size factor is calculated by first dividing the observed counts for each sample by its geometric mean. The size factor is then calculated as the median of this ratio for each sample. This size factor then used for normalizing raw count data for each sample. Only genes with log2(normalised count) > 0 in at least one sample were kept.
Assembly: hg19
Supplementary files format and content: .xlsx excel spread sheet containing log2 median-of-ratios (DESeq2) normalised gene expression values for all 14 samples

source_name: PRIMARY BREAST TUMOUR

extract_protocol: NOT PROVIDED

tag: cohort

value: otherMets

tag: patient id

value: BREAST CANCER

tag: tissue type

tag: extraction

value: 100 ng of RNA and Illumina’s TruSeq RNA Access Library Preparation protocol


title: K562 TAi LDB1 ChIP-seq

tag: cell type

tag: chip antibody


title: S33 GEX4

extract_protocol:
For bulk RNA-seq RNA was isolated using Direct-zol RNA micro prep (Zymo, UK) as per the manufacturer’s protocol.
For Bulk RNA-seq cDNA libraries were generated using SMART-Seq Stranded Library Preparation for Ultra Low Input according to the SMART-Seq Stranded Kit User Manual  following the Ultra low input workflow (Takara Bio). Samples were pooled (12/batch) for library preparation. For Drop-seq High Sensitivity DNA Assay Nextera kit, Illumina, was used. For Constellation cDNA was aplified using targeted linear amplification (20 rounds) and further prepared using True-seq, Illumina.

value: skin


title: N_B_M_K_555

tag: background strain

tag: mouseline


title: N_B_M_K_557

tag: brain region

tag: Sex


title: K562_TAi_total_RNA-seq_R2_F


title: N_B_M_W_585

value: Wild-type


title: K562 TAi TAL1 Sp ChIP-seq


title: K562 Con TAL1 Sp ChIP-seq


title: poor_5P [bone_2P]


title: K562_GAi_total_RNA-seq_R1_F


title: K562 TAi GATA1 ChIP-seq


title: N_B_M_W_579


title: K562 GAi GATA1 ChIP-seq


title: K562_Con_total_RNA-seq_R1_F


title: N_B_M_W_573


title: K562 Con GATA1 ChIP-seq


title: poor_3P [local_3P]

value: local metastasis

value: 100 ng of RNA and Illumina’s  TruSeq DSN library & TruSeq RNA Access Library Preparation protocol


title: K562 Con Input ChIP-seq


title: S33 GEX0


title: 979

city: Chicago

first: Zhou

last: Zhang

address: 680 North Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

data_processing:
library strategy: 5hmC-Seal-seq
Bcl2fastq v2.17 software used to change the bcl files to fastq files.
Sequenced reads were trimmed for adaptor sequence using software trimmomatic v0.36, and masked for low-complexity or low-quality sequence, then mapped to hg19  genome using bowtie v2.26
Duplicate reads were marked using picard v1.141. The reads were counted for overlap with gene bodies (annotated by the GENCODE Project) using featureCounts v1.5.0-p3.
Assembly: hg19
Supplementary files format and content: A CSV file include edgR normalized 5hmC levels for all sample.

source_name: plasma

extract_protocol:
Circulating cfDNA was isolated using the QIAamp Circulating Nucleic Acid Kit (Qiagen) from 0.5 mL of frozen serum per study subject. Genomic DNA (gDNA) was isolated from ~5 mg of frozen DLPFC using the Monarch Genomic DNA Purification Kit (New England Biolabs).
To obtain sequencing-amenable ~200 bp fragments of gDNA from brain samples, we performed enzymatic fragmentation using the KAPA HyperPlus Kit (Roche). After ligation of unique dual index barcoded sequencing adapters, DNA fragments proceeded through the 5hmC-Seal protocol to construct sequencing libraries.

tag: subject id

value: plasma


title: 980


title: 977


title: K562 Con K27ac Sp ChIP-seq

value: erythroleukemia cells


title: N_B_M_W_553

value: Brain:Bed nucleus of the stria terminalis

value: Male


title: poor_6P [bone_3P]


title: IFNgamma_2min-SILAClabel-H

value: IFNgamma 2min


title: K562 Con LDB1 ChIP-seq

value: control


title: 976


title: poor_1P [local_1P]


title: 975


title: N_B_M_W_533


title: 973


title: N_B_M_W_525


title: 974


title: 972


title: N_D_M_K_583

value: Brain:Dorsal hippocampus


title: good_7P

value: no metastasis


title: 971


title: poor_4P [bone_1P]

value: bone metastasis


title: good_6P


title: N_D_M_K_575

value: Brain

value: Knockout


title: 969


title: 967


title: good_5P

value: otherMets

value: BREAST CANCER


title: 968


title: N_D_M_K_571


title: poor_2P [local_2P]


title: good_4P

value: 100 ng of RNA and Illumina’s TruSeq RNA Access Library Preparation protocol


title: 970


title: good_3P


title: 966


title: 965


title: N_D_M_K_557


title: good_2P


title: 962


title: 961


title: 960


title: N_D_M_W_579

value: Wild-type


title: N_D_M_W_573


title: good_1P


title: 964


title: 963


title: 959


title: N_D_M_W_553


title: N_D_M_K_543


title: A431_shUSP28-2-3

city: Heidelberg

first: Felix

middle: Christian Eduard

last: Vogel

address: Im Neuenheimer Feld 280

department: Division of Tumor Metabolism and Microenvironment

institute: German Cancer Research Center

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: human genome (hg19)
Supplementary files format and content: raw counts and TMMnorm-lcpm

growth_protocol: A431 cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 2mmol/L L-glutamine, 100U/mL P/S in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). At least 2800ng of total RNA was submitted to library preparation; equal amount of RNA was used for the construction of sequencing libraries.
After Quality Control, RNA libraries for RNA-seq were prepared using IDT-ILMN TruSeq DNA/RNA UDI (TruSeq Stranded) following manufacturer's protocols.

treatment_protocol: 1ug/ml Doxycycline treatment for 120h to induce shRNA-mediated knockdown

value: epidermoid carcinoma cell line

value: USP28 knockdown

value: 1ug/ml Doxycycline treatment for 120h to induce knockdown


title: 956

value: plasma


title: 957


title: A431_shUSP28-2-2


title: 953


title: 954


title: N_D_M_W_533


title: 950


title: A431_shUSP28-1-2


title: 952


title: A431_shUSP28-2-1


title: 948


title: A431_shUSP28-1-1


title: 951


title: Spontaneous AA LN CD44shi 4

city: Daejeon

first: Su-Hyung

last: Park

address: 291, Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

description: Spontaneous AA LN CD44shi 4

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: LN

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: LN

value: Lymphocytes


title: A431_shUSP28-1-3


title: Spontaneous AA LN CD44shi 3

description: Spontaneous AA LN CD44shi 3


title: A431_shSREBP2-2-2

value: SREBP2 knockdown


title: Spontaneous AA skin CD44shi 1

description: Spontaneous AA skin CD44shi 1

source_name: Skin

value: Skin


title: 941


title: 949


title: 958


title: N_D_M_W_525

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Allignment to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then  FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this gene.
Differential expression analysis was performed using the  DESeq2Rpackage (1.20.0). DESeq2. Resulting P-values were adjusted using the Benjamini and Hochberg's  approach for controlling the false discovery rate.
Genes with an adjusted P-value <=0.05 found  by DESeq2 were assigned as differentially expressed

extract_protocol:
RNA was isolated using the miRNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared by the company Novogene UK, according to their standardized protocols

value: Brain:Dorsal hippocampus

value: Male


title: N_D_M_W_539


title: 939


title: 945


title: 946


title: 938


title: A431_shSREBP2-2-3


title: A431_shSREBP2-1-3


title: 944


title: 943


title: 936


title: Spontaneous AA LN Tvm 5

description: Spontaneous AA LN Tvm 5


title: A431_shSREBP2-1-2


title: Spontaneous AA LN Tn 2

description: Spontaneous AA LN Tn 2


title: 940


title: Spontaneous AA LN Tn 1

description: Spontaneous AA LN Tn 1


title: A431_shSREBP2-2-1


title: Spontaneous AA LN Tvm 4

description: Spontaneous AA LN Tvm 4


title: AT AA LN CD44shi 5

description: AT AA LN CD44shi 5


title: A431_control-shRen-03

value: WT/control


title: 934


title: A431_shSREBP2-1-1


title: 932


title: AT AA skin CD44shi 4

description: AT AA skin CD44shi 4


title: 931


title: AT AA LN CD44shi 4

description: AT AA LN CD44shi 4


title: A431_control-shRen-01


title: 930


title: 937


title: 929


title: A431_control-shRen-02