title: 4C_WT_129_VP_SE

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

institute: Hubrecht Institute

description: 4C, WT, 129, VP SE

data_processing:
4C:  FASTQ reads were demultiplexed based on the presence of a 129 or cas SNP. For each of the two possible SNPs, we searched for the SNP and its flanking four nucleotides (text searches for 9-nucleotide sequences). For each SNP, R1 reads were allocated into new FASTQ files that were used for mapping using a 4C data processing pipeline (Krijger et al., 2020 and github.com/deLaatLab/pipe4C) with the following parameters:  normalization to 1 million reads in cis, non-blind fragments only, window size 21, top 2 read counts removed.
cHiC:  Raw sequence data for biological and technical replicates with the same genotype were combined and subsequently mapped and processed using HiC-Pro v.2.11.1 (Servant et al., 2015) with mm10 as a reference genome. SNPs for the 129S1_SvImJ and CAST_EiJ genomes were extracted from the Mouse Genomes Project (Keane et al., 2011) and N-masked in the reference genome. Reads in which both reads were assigned to the same allele or for which one read was assigned to one allele and for which the other was unassigned were used to generate Juicebox input files (Durand et al., 2016).
Sequenced reads were processed following the standard MC-4C protocol  and MC-4C pipeline v1.2 (Allahyar et al., 2018, https://github.com/deLaatLab/mc4c_py). Fragments were mapped to the reference genome using BWA-SW v0.7.17-r1188 (settings: -b 5 -q 2 -r 1 -z 5 -T 15) (Li and Durbin, 2010). Fragments with mapping quality (MQ) < 20 were considered unmapped. Mapped fragments were extended to the nearest DpnII or HindIII restriction site. Pairs of fragments mapping closer than 20 bp were fused and considered single fragments. PCR duplicates were removed under the premise that far-cis or -trans fragments can be directly used as unique molecular identifiers (Vermeulen et al., 2020). The region of interest (ROI) used in this study was chr1:12.840-13.185 Mb. Reads with fewer than two fragments within the ROI were discarded as uninformative for multi-way contact association analysis.
Genome_build: mm10
Supplementary_files_format_and_content: 4C:  interaction coverage file (wig files generated using pipe4C)
Supplementary_files_format_and_content: cHi-C: normalized Hi-C matrix per genotype per allele (hic files generated using Juicer)
Supplementary_files_format_and_content: MC-4C:Multi-contact interaction coverage file (hdf5 files generated using MC-4C pipeline v1.2)

growth_protocol: 129SvJ/castaneous female mouse embryonic stem cells (Jonkers et al., 2008; Splinter et al., 2011) were cultured at 37°C and 5% CO2 on gelatin-coated dishes in the following growth medium:  DMEM GlutaMAX (Gibco), 45% BRL-conditioned medium (11% FBS (Sigma), 1% P/S (Gibco), 1% NEAA (Gibco)), 7% FBS (Sigma), 1% P/S (Gibco), 1% NEAA (Gibco), 0.1 mM β-mercaptoethanol (Sigma-Aldrich), and 0.2% home-made LIF protein.  Medium was changed at least every other day and cells regularly tested negative for Mycoplasma infection.

extract_protocol:
4C:  4C template preparation was performed as described in (van de Werken et al., 2012), using DpnII and Csp6I as first and second cutters, respectively, with the following modifications:  omission of protease inhibitors in lysis buffer; omission of RNAse A at crosslinking removal; replacement of phenol-chloroform and ethanol purifications with magnetic bead purification (Macherey-Nagel NucleoMag PCR Beads), as described in (Krijger et al., 2020).
cHiC: Hi-C template preparation was performed as described in (Rao et al., 2014) with modifications as follows. Ten million cells per sample were harvested; two biological replicates were generated per genotype. Cells were fixed with 2% formaldehyde; fixation was quenched by glycine at final concentration of 0.2 M. Restriction enzyme XapI (ApoI, ThermoFisher ER1381) (Kolovos et al., 2018) was used for in situ digestion (400 U/10 million cells). Digested DNA ends were labeled with biotin-14–dATP (Life Technologies) in a Klenow end-filling reaction. End-repaired, ligated, and reverse-crosslinked DNA was subsequently purified using isopropanol and magnetic beads (Macherey-Nagel NucleoMag PCR Beads). Purified DNA was sheared to 300-500 bp with Covaris. After AMPure XP size selection, appropriately-sized ligation fragments marked by biotin were immobilized using MyOne Streptavidin C1 DynaBeads (Invitrogen) and ligated to SureSelectXT2 indexed adaptors. The non-amplified, immobilized and indexed Hi-C library was subsequently used as input for target-specific capture using RNA baits.
MC-4C:  MC-4C was performed generally as described in (Vermeulen et al., 2020), using DpnII and HindIII as first and second cutters, respectively.
4C:  The allele-specific 4C strategy is similar to that described as PE-4Cseq in (Holwerda et al., 2013). Briefly, 4C PCR primers were designed generally in keeping with considerations described in (van de Werken et al., 2012), with the following considerations:  primer binding sites must not contain any SNPs, and one of the primers must be positioned to allow reading of a SNP in the viewpoint fragment by Illumina sequencing, to facilitate splitting 4C reads by allele. If no SNP was present near the primary cut site, then a SNP following the “non-read” primer (P2) was used, in which case paired-end sequencing was required.
cHi-C:  We designed a custom biotinylated RNA bait library (Table S7) using Agilent SureDesign (https://earray.chem.agilent.com/suredesign/). Biotinylated 120-mer RNA baits were designed to target both ends of ApoI restriction fragments within the targeted region (mm10:chr1:10500000-15500000). 120-mers mapping more than once to the mm10 reference genome were excluded from the final library. The library included unrelated baits for a locus on Chromosome 18 (mm10:chr18:64200000-67200000).  Capture Hi-C of the targeted genomic sequences was carried out with SureSelectXT2 Target Enrichment System (Agilent G9621A) with the bait library according to manufacturer’s instructions (Agilent Technologies), with the modification of either single-round or double-round capture. For single-round capture, a pre-capture PCR amplification of the immobilized and indexed Hi-C template and a post-capture PCR amplification of the enriched library was carried out with 10 and 12 PCR amplification cycles, respectively. For double-round capture, a pre-capture PCR amplification of the Hi-C template and a post-capture PCR amplification of the single-round enriched library was carried out with 10 and 10 cycles, respectively. The total output of post-capture PCR amplification of the single-round enriched library was further captured the second time with the same bait library followed by final amplification with 12 cycles.
MC-4C:  To digest the Slco5a1 VP (5’Slc) and neighbor fragments with Cas9 in vitro, gRNAs CTATAGCGCCTTTCGATGG, TCTACACCGATTTACACCCT, and ACTAGTGCTAAGTAACCTCG were used. Primers for the final PCR step were designed to specifically amplify 129 template by forcing the 3’ end of each primer to terminate on a validated SNP and by introducing destabilizing mismatches near the 3’ end of each primer, according to guidelines for allele-specific PCR described in (Liu et al., 2012). 129 allele specific amplification was further optimized by performing annealing temperature gradient PCRs in parallel on 129/cas and cas/cas genomic DNA and selecting the optimal annealing temperature which did not produce any product from cas/cas template. For the 5’Slc VP MC-4C PCR, we used primers GGACAGCTCCAACCGAAGGCG and GAGTTGAACGCTTCGGCCTTC, where destabilizing mismatches are underlined; PCR conditions were: 98°C 20’’; 30 cycles of 98°C 10’’, 69°C 20’’, 72°C 90’’; 72°C 5’.  MC-4C libraries were size selected at 1.5–8 kb by Pippin HT and then prepared for sequencing using Oxford Nanopore Ligation Sequencing Kit LSK109.
OTHER:  4C, Hi-C, and MC-4C

value: ESC

tag: strain

tag: genetic modification

value: WT

tag: viewpoint

tag: barcode

value: AGCTGGCCTTGTAGTTTCTGATC


title: MCF10A, WTp53:WTp53 cDNA insert, DMSO, Replicate 3 [21_DMSO_input_R3]

status: Public on Jun 30 2021

type: SRA

city: Boulder

first: Dylan

middle: J

last: Taatjes

state: CO

address: Campus Box 596

department: Biochemistry

country: USA

institute: University of Colorado Boulder

description:
input DNA
processed data file: 21_DMSO_0.0001_peaks_clean.narrowPeak

library_source: genomic

data_processing:
All ChIP-seq data was processed (mapped and quality checked) using a Nextflow pipeline, ChIP-Flow v1.0 (https://github.com/Dowell-Lab/ChIP-Flow)
Blacklisted regions (those having artificially high signal and read mapping, http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/) were removed using BEDTools intersect(Quinlan and Hall 2010)
Peak calls were generated using MACS2 narrowPeak. The q-value default cutoff was also decreased from the default of 0.05 to 1e-5.
Genome_build: GRCh38
Supplementary_files_format_and_content: BED6+4 files containing peak locations together with peak summit, p-value, and q-value (.narrowPeak files) called peaks were generated using MACS2 narrowPeak.

molecule: genomic DNA

organism: Homo sapiens

source_name: MCF10A, WTp53:WTp53 cDNA insert, DMSO

extract_protocol:
Six hours after the addition of 10 mM Nutlin-3a or 0.1% DMSO, cells (~60 x 10^6 cells) were fixed with 1% formaldehyde for 10 min at 25oC. Glycine (0.125 M) was then added for 5 min. Cells were scraped into conical tubes and washed with ice cold PBS. Nuclei were isolated by resuspending the cells in NRO buffer (80 ml/million cells; 10 mM Tris-HCl [pH 8], 4 mM MgCl2, 10 mM NaCl, 0.5% [vol/vol] NP-40 and the protease inhibitor cocktail: 0.25 mM phenylmethylsulfonyl fluoride (PMSF), 1 mM sodium metabisulfite, 0.012 TIU/mL aprotinin, 1 mM benzamidine and 1 mM dithiothreitol (DTT)), followed by a 5 min incubation on ice, a low speed spin, and then a final wash with NRO buffer. The isolated nuclei were prepared for shearing based on the Covaris truChIP Chromatin Shearing Kit (Covaris: PN 520237) and sheared for 11 min on Covaris M220 Focused-ultrasonicator. Samples were spun at high speeds then a small aliquot for input was removed while the rest of the supernatant containing the sheared chromatin was transferred to prepared Protein G Dynabeads (Invitrogen: 10003D). 25mL of Protein G Dynabeads beads per pull down were washed 3 times in block solution (PBS, 0.5% BSA) before being resuspended in block solution with 6 mg of DO1 p53 antibody (BD Biosciences: BD554293) per pull down. The beads and antibody were allowed to nutate for 10 min at 25oC before nutating at 4oC for 4 hours. Beads were then washed in block solution once and IP buffer once (15 mM Tris-HCl [pH 8], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100 and the protease inhibitor cocktail). Beads were then resuspended in IP buffer and the sheared chromatin was added. The sample was then allowed to nutate at 4oC for at least 12 hours. The bound chromatin was then washed 3 times with IP buffer, 3 times with RIPA buffer (20 mM Tris-HCl [pH 8], 500 mM NaCl, 1 mM EDTA, 1% Triton X-100 and 0.1% SDS), 2 times with LiCl buffer (20 mM Tris-HCl [pH 8], 500 mM LiCl, 1 mM EDTA, 1% sodium deoxycholate and 1% NP-40) and 2 times with TE Salt buffer (10 mM Tris-HCl [pH 8], 50 mM NaCl, 1 mM EDTA). The sample was then eluted with PK buffer (10 mM Tris-HCl [pH 8], 1 mM EDTA and 1% SDS) containing 100 mg of Proteinase K (New England BioLabs: P81075) per reaction by incubating at 50oC shaking for 1-hour then at 65oC for 1-hour. The supernatant containing the eluted DNA was transferred to a new tube for reverse crosslinking. The input was thawed and brought up to sample volume with PK buffer containing 100 mg of Proteinase K per reaction. All samples and inputs were incubated at 65oC for at least 12 hours. DNA was then purified by phenol chloroform extraction using Light-5PRIME Phase Lock Tubes (Quanta Bio: 2302820) based on the manufacturer’s instructions.
Libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems: KK8502) and sequenced on Illumina NextSeq V2 high output 75-cycle.

treatment_protocol: MCF10A genome edited cells were seeded on six 15cm dishes (1x10^7 cells per dish) for each treatment 24 hours prior to the experiments ( 70% confluency at the time of the experiment). Cells were treated simultaneously with 10μM Nutlin3a or 0.1% DMSO for 6 hour.

tag: cell line

tag: tissue

value: mammary gland; breast

tag: cell type

value: epithelial

tag: crispr/cas9 insertion

value: 4041bp:full length p53 tethered to full length p53 cDNA followed IRES expressed mCherry followed by SV40 polyA sequnece

tag: crispr/cas9 insertion location

tag: treatment


title: Sham brain 3

type: RNA

city: Charleston

first: Amer

last: Toutonji

state: SC

address: 173 Ashley Ave, CRI204

institute: Medical University of South Carolina

hyb_protocol: followed the manufacturer's instructions: NanoString (Seattle, WA)

data_processing: number of reads was normalized by housekeeping genes in the panel using nCounter® nSolver software

label: Nanostring

molecule: total RNA

organism: Mus musculus

source_name: normal mouse brain

label_protocol: the extract wasn't labeled

extract_protocol: mRNA was extracted from up to 1 mg of brain tissue using the RNeasy Lipid Tissue Mini Kit (Qiagen)

tag: injury

value: sham

tag: time point post tbi

value: not applicable

value: vehicle (PBS)

tag: age (weeks)


title: PBS-treated 3-day TBI brain 3

scan_protocol: followed the manufacturer's instructions: NanoString (Seattle, WA)

source_name: TBI-injured brain

value: TBI (CCI)

value: day 3


title: mDA-Blue-2

city: BALTIMORE

first: Minseong

last: Kim

state: MD

address: 733 NORTH BROADWAY, SUITE 763, Euodwood Apt 308

department: ICE

institute: JHMI

description: total RNA

library_source: transcriptomic

data_processing:
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
In order to map cDNA fragments obtained from RNA sequencing, UCSC hg19 was used as a reference genome. Table 3 shows the statistic obtained from HISAT2, which is known to handle spliced read mapping through Bowtie2 aligner. You can check number of processed reads, mapped reads.
Known genes and transcripts are assembled with StringTie based on reference genome model. After assembly, the abundance of gene/transcript is calculated in the read count and normalized value as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for a sample.
In order to reduce systematic bias, estimates the size factors from the count data and applies Relative Log Expression (RLE) normalization with DESeq2 R library. In case of DESeq2, read count+1 & Logarithm value is uesd to visualize the plots before normalization and regularized log (rlog) transformed value is used to visualize the plots after normalization.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include fold change values for each Sample

source_name: PD-iPSC derived mDA neuron

growth_protocol: We cultured undifferentiated SNCA triplication PD hiPSCs (ND27760-8) and opto-α-syn (AAVS1::opto-α-syn) PD hiPSCs on mitotically inactivated mouse embryonic fibroblasts (MEFs, Global Stem or Applied Stem Cell), in hESC medium containing DMEM/F-12, 20% knockout serum replacement (KSR), 0.1 mM MEM-NEAA, 2 mM L-glutamine, 55 μM β-mercaptoethanol (all from Life Technologies) and 10 ng/mL FGF2 (R&D Systems) as used routinely for iPSC cultures. All cells were maintained at 37 °C and 5% CO2 in a humidified incubator.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Library Prep (Cat#20020594) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For mDA neuron differentiation, Briefly, dissociated hiPSCs were plated on Geltrex at a density of 50,000 cells/cm2 in MEF-conditioned KSR medium containing DMEM/F-12, 20% KSR, 0.1 mM MEM-NEAA, 2 mM L-glutamine, and 55 μM β-mercaptoethanol with 10 ng/mL FGF2 and 10 μM ROCK-inhibitor (Y-27632, Cayman Chemical). After confluency of the cells reached 80%–90%, differentiation was initiated by switching to KSR medium supplemented with 100 nM LDN193189 (STEMCELL Technologies) and 10 μM SB431542 (Cayman Chemical). Supplements of 100 ng/mL Shh (C25II, R&D), 2 μM Purmorphamine (PMP, Cayman Chemical) and 100 ng/mL FGF8 (PeproTech) were added on days from 1 to 7, and 3 mM CHIR99021 (CHIR, Tocris) was added at day 3 to day 11. Beginning at day 5, the KSR medium was gradually replaced with increasing amounts of N2 medium(Oh et al., 2016) (25% increments every other day). To expand neural progenitors, the cells were split on Geltrex and maintained in medium containing DMEM/F-12, N-2 supplement (Life Technologies), 2 mM L-glutamine, 1% penicillin/streptomycin, 100 nM LDN193189, 3 µM CHIR and 10 µM Y-27632 on day 11. After that, the cells were re-plated on dishes pre-coated with Geltrex in NB/B-27 medium supplemented with 3 µM CHIR, 20 ng/mL BDNF, 0.2 mM ascorbic acid, 20 ng/mL GDNF, 1 ng/mL TGFβ3, 0.5 mM dbcAMP and 10 µM DAPT for at least 10 days to complete differentiation.

value: iPSC-derived mDA neurons

value: Bluelight + DMSO


title: 36UVF76

city: Sheffield

first: Ilaria

last: Giovannelli

address: 385a Glossop Road

department: Sheffield Institute for Translational Neuroscience

country: United Kingdom

institute: University of Sheffield

description: Gene expression data from human peripheral blood

hyb_protocol: Fragmented and labelled ss cDNA was hybridized on Human Clariom D Affymetrix® chips.

scan_protocol: The GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the AGCC software package to prepare the .CEL files

data_processing: Gene expression data was normalised using the signal space transformation robust multi-chip analysis (SST-RMA) method. Data was analysed using TAC and Limma software.

label: Biotin

label_protocol: 200ng of total RNA was used to produce antisense RNA (cRNA) and cDNA which was then fragmented and biotinylated using Affymetrix GeneChip® WT PLUS Kit according to manufacturer's protocol.

extract_protocol:
White blood cell isolation: White blood cells were isolated using LeukoLOCK TM filters
Total RNA extraction: Total RNA was isolated using the LeukoLOCK TM Total RNA isolation kit (AmbionTM) as per manufacturer's instructions.

tag: diagnosis

value: ALS

value: peripheral blood

value: 2MIU IL2

tag: time point


title: 23TKJ93


title: mDA-Dark-2

description: total RNA

value: DMSO


title: 4C_WT_129_VP_LB

country: Netherlands

description: 4C, WT, 129, VP LB

value: ESC

value: ACTCATCTCTTTGGTGGATGATC


title: MCF10A, WTp53 cDNA insert, 10uM Nutlin3a, Replicate 1 [7_Nutlin_p53_R1]

description:
DNA bound by p53
processed data file: 7_Nutlin_0.0001_peaks_clean.narrowPeak

source_name: MCF10A, WTp53 cDNA insert,10uM Nutlin3a

value: 2820bp:full length p53 cDNA followed IRES expressed mCherry followed by SV40 polyA sequnece

value: 10uM Nutlin3a

tag: chip antibody

value: DO-1 (BD Biosciences, BD554293)


title: 29DUQ88


title: mDA-CDC-1

description: total RNA

value: Bluelight + CDC 1uM for 24hrs


title: mDA-Blue-1

description: total RNA


title: 23KVA46


title: 87VON76

value: 1MIU IL2


title: 4C_WT_129_VP_Slc

description: 4C, WT, 129, VP 5'Slc

value: WT

value: CTACTTCGTCCATGGCTCTTAAA


title: 4C_WT_129_VP_RB

description: 4C, WT, 129, VP RB

value: CTAGTCAATCAGACCCAACTGAG


title: MCF10A, WTp53:WTp53 cDNA insert, DMSO, Replicate 2 [21_DMSO_input_R2]

source_name: MCF10A, WTp53:EWTp53 cDNA insert, DMSO

value: mammary gland; breast

value: epithelial

value: 4041bp:full length p53 tethered to full length p53 cDNA followed IRES expressed mCherry followed by SV40 polyA sequnece


title: 4C_RBdel_129_VP_SE

description: 4C, RBdel, 129, VP SE

value: RBdel

value: ACTGGCCTTGTAGTTTCTGATC


title: MCF10A, WTp53 cDNA insert, 10uM Nutlin3a, Replicate 2 [7_Nutlin_p53_R2]


title: 4C_RBdel_129_VP_Slc

description: 4C, RBdel, 129, VP 5'Slc

value: AGCCTTCGTCCATGGCTCTTAAA


title: MCF10A, WTp53:WTp53 cDNA insert, DMSO, Replicate 1 [21_DMSO_input_R1]


title: MCF10A, WTp53 cDNA insert, 10uM Nutlin3a, Replicate 1 [7_Nutlin_input_R1]

description:
input DNA
processed data file: 7_Nutlin_0.0001_peaks_clean.narrowPeak


title: Jeko shCycD1 rep2

city: Barcelona

first: Santiago

last: Demajo

state: Barcelona

address: Rosselló 153

country: Spain

institute: IDIBAPS - Hospital Clínic Barcelona

description: processed data file: Jeko_Matrix_RPKM.txt

data_processing:
Raw sequence files (.fastq.gz) underwent quality control analysis using FastQC and reads were aligned to the Human Feb. 2009 (GRCh37/hg19) genome using TopHat v2.1.1 allowing for unique alignments and up to two mismatches.
The resulting alignments were summarized by Ensembl gene identifiers to evaluate number of uniquely aligned reads per transcript and per sample.
The raw read counts were analyzed using the ‘limma’ package v3.9 from the Bioconductor (http://bioconductor.org) and were used as input to form a DGEList object.
Scale normalization was applied and the calculation of normalized signal was performed by voom function of the ‘limma’ package and converted to RPKM (Law CW et al. Genom Biol. 2014).
Genome_build: hg19
Supplementary_files_format_and_content: text files with RPKM values for each MCL cell line

source_name: Jeko shCycD1

growth_protocol: Granta-519 and JeKo-1 cells were cultured at 37°C and 5% CO2 in RPMI and DMEM, respectively, supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (QIAGEN) according to the manufacturer's protocol.
RNA libraries were prepared using the TruSeqStranded mRNA Sample Prep Kit v2 (Illumina) according to the manufacturer's protocol.

treatment_protocol: Lentiviral infection with shRNA (control or shCycD1) and selection with puromycin.

value: mantle cell lymphoma (MCL) cell line

tag: shRNA


title: MCF10A, WTp53 cDNA insert, 10uM Nutlin3a, Replicate 2 [7_Nutlin_input_R2]


title: Jeko shCycD1 rep3


title: 4C_LBdel_129_VP_SE

description: 4C, LBdel, 129, VP SE

value: ESC

tag: strain

value: LBdel

value: TTGGCCTTGTAGTTTCTGATC


title: 4C_LBdel_129_VP_Slc

description: 4C, LBdel, 129, VP 5'Slc

tag: genetic modification

value: GCTTCGTCCATGGCTCTTAAA


title: 87NSF26

value: ALS

value: peripheral blood


title: MCF10A, WTp53 cDNA insert, DMSO, Replicate 2 [7_DMSO_p53_R2]

description:
DNA bound by p53
processed data file:  7_DMSO_0.0001_peaks_clean.narrowPeak

source_name: MCF10A, WTp53 cDNA insert, DMSO

value: 2820bp:full length p53 cDNA followed IRES expressed mCherry followed by SV40 polyA sequnece

value: DO-1 (BD Biosciences, BD554293)


title: 87RXK32

value: 1MIU IL2


title: mDA-Dark-1

description: total RNA

value: iPSC-derived mDA neurons

value: DMSO


title: Jeko shCycD1 rep1


title: 83VXX85


title: MCF10A, WTp53 cDNA insert, DMSO, Replicate 1 [7_DMSO_p53_R1]

value: mammary gland; breast

value: epithelial


title: 4C_LBdel_129_VP_RB

description: 4C, LBdel, 129, VP RB

tag: viewpoint

value: GGTCAATCAGACCCAACTGAG


title: 77NSV37


title: 4C_LBinv_129_VP_Slc

description: 4C, LB-inv, 129, VP 5'Slc

value: LBinv

tag: barcode

value: TCTTCGTCCATGGCTCTTAAA


title: Jeko shCtrl rep3

source_name: Jeko shCtrl

tag: cell line

value: mantle cell lymphoma (MCL) cell line

value: shCtrl


title: MCF10A, WTp53 cDNA insert, DMSO, Replicate 2 [7_DMSO_input_R2]

description:
input DNA
processed data file:  7_DMSO_0.0001_peaks_clean.narrowPeak

tag: tissue


title: 75UQO22


title: Jeko shCtrl rep2

tag: cell type


title: 4C_LBinv_129_VP_LB

description: 4C, LB-inv, 129, VP LB

value: ESC

value: TCATCTCTTTGGTGGATGATC


title: MCF10A, WTp53 cDNA insert, DMSO, Replicate 1 [7_DMSO_input_R1]

tag: crispr/cas9 insertion


title: MCF10A, ∆40p53:WTp53 cDNA insert, 10uM Nutlin3a, PRO-seq, Replicate 1 [41_Nutlin_3hr_R1]

data_processing:
library strategy: nascent RNA (PRO-seq)
processing of all sequencing data was performed using the NascentFlow Pipeline (doi: 10.17605/OSF.IO/NDHJ2)
Genome_build: GRCh38
Supplementary_files_format_and_content: .txt table of transcription factor E-Scores

source_name: MCF10A, ∆40p53:WTp53 cDNA insert,10uM Nutlin3a

extract_protocol:
After treatment, cells were washed 3x with ice cold PBS, and then treated with 10 ml (per 15 cm plate) ice-cold lysis buffer (10 mM Tris–HCl pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% glycerol, 1 mM DTT, 1x Protease Inhibitors (1mM Benzamidine (Sigma B6506-100G), 1mM Sodium Metabisulfite (Sigma 255556-100G), 0.25mM Phenylmethylsulfonyl Fluoride (American Bioanalytical AB01620), and 4U/mL SUPERase-In). Cells were centrifuged with a fixed-angle rotor at 1000xg for 15 min at 4◦C. Supernatant was removed and pellet was resuspended in 1.5 mL lysis buffer to a homogenous mixture by pipetting 20-30X before adding another 8.5 mL lysis buffer. Suspension was centrifuged with a fixed-angle rotor at 1000xg for 15 min at 4◦C. Supernatant was removed and pellet was resuspended in 1 mL of lysis buffer and transferred to a 1.7 mL pre-lubricated tube (Costar cat. No. 3207). Suspensions were then pelleted in a microcentrifuge at 1000xg for 5 min at 4◦C. Next, supernatant was removed and pellets were resuspended in 500 μL of freezing buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 4U/ml SUPERase-In). Nuclei were centrifuged 2000xg for 2 min at 4◦C. Pellets were resuspended in 100 μL freezing buffer. To determine concentration, nuclei were counted from 1 μL of suspension and freezing buffer was added to generate 100 μL aliquots of 10x106 nuclei. Aliquots were flash frozen in liquid nitrogen and stored at −80◦C.
Nuclear run-on experiments were performed as described previously (Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., et al. (2016). Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols, 11(8), 1455–1476. with the following modifications: the final concentration of non-biotinylated CTP was raised from 0.25 μM to 25 μM, a clean-up and size selection was performed using 1X AMPure XP beads (1:1 ratio) (Beckman) prior to test PCR and final PCR amplification, and the final library clean-up and size selection was accomplished using 1X AMPure XP beads (1:1 ratio) (Beckman). http://doi.org/10.1093/bioinformatics/btq033) with the following modification. The final concentration of non-biotinylated CTP was raised from 0.25uM to 25uM, and the final library clean up and size selection was accomplished using 1X AMPure XP (Beckman).

treatment_protocol: MCF10A genome edited cells were seeded on three 15cm dishes (1x107 cells per dish) for each treatment 24 hours prior to the experiments ( 70% confluency at the time of the experiment). Cells were treated simultaneously with 10μM Nutlin3a or 0.1% DMSO for 1 hour.

value: 3924bp:∆40p53 cDNA tethjered to full length p53 cDNA followed IRES expressed mCherry followed by SV40 polyA sequnece

tag: crispr/cas9 insertion location

value: 10uM Nutlin3a

tag: molecule subtype

value: nascent RNA


title: 67CNF42

value: ALS

value: peripheral blood

tag: treatment


title: MCF10A, ∆40p53:WTp53 cDNA insert, 10uM Nutlin3a, PRO-seq, Replicate 1 [41_Nutlin_3hr_R2]


title: 83QAN59

value: 1MIU IL2


title: 4C_LBinv_129_VP_SE

description: 4C, LB-inv, 129, VP SE

value: TGGCCTTGTAGTTTCTGATC


title: Jeko shCtrl rep1


title: Granta shCycD1 rep1

description: processed data file: Granta_Matrix_RPKM.txt

source_name: Granta shCycD1


title: MCF10A, ∆40p53:WTp53 cDNA insert, DMSO, PRO-seq, Replicate 1 [41_DMSO_3hr_R1]

source_name: MCF10A, ∆40p53:WTp53 cDNA insert, DMSO


title: Granta shCycD1 rep3


title: 47AVU82


title: MCF10A, WTp53:WTp53 cDNA insert, 10uM Nutlin3a, PRO-seq, Replicate 1 [21_Nutlin_3hr_R2]

value: 4041bp:full length p53 tethered to full length p53 cDNA followed IRES expressed mCherry followed by SV40 polyA sequnece


title: Granta shCtrl rep3

source_name: Granta shCtrl


title: Granta shCycD1 rep2


title: Granta shCtrl rep2


title: 46XDM67


title: MCF10A, WTp53:WTp53 cDNA insert, 10uM Nutlin3a, PRO-seq, Replicate 1 [21_Nutlin_3hr_R1]

source_name: MCF10A, WTp53:WTp53 cDNA insert,10uM Nutlin3a

value: mammary gland; breast


title: MCF10A, ∆40p53:WTp53 cDNA insert, DMSO, PRO-seq, Replicate 2 [41_DMSO_3hr_R2]

value: epithelial


title: MCF10A, WTp53:WTp53 cDNA insert, DMSO, PRO-seq, Replicate 2 [21_DMSO_3hr_R2]


title: Granta shCtrl rep1


title: Lung_TiO2_Day28_rep5

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

country: France

institute: INRS

description: Gene expression  in lung of rat exposed to TiO2 (10 mg/m3) 28 days post-exposure

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 10 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4853A SurePrint G3 Rat v2 GE 8*60K microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and data were normalized using the eUTOPIA application.

organism: Rattus norvegicus

source_name: Rat, Lung, TiO2, Day 0, replicate 5

label_protocol: For each of the 23 samples (6 control, 6 exposed rats per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry and by electrophoresis (Agilent 2100 Bioanalyser).

growth_protocol: Accessory lobe of rat lungs were stored in RNA later at -20°C before use

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 7, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 19 months-old male F344 rats were exposed by nose-only inhalation  6 hours/day, 5 days/week for 4 weeks to TiO2.

value: F344 Fisher

value: accessory lobe of lung

tag: gender

value: male

tag: age

value: 19 months-old (at the onset of inhalation)


title: 26UIR45

tag: diagnosis


title: 23MXS57

tag: time point


title: Lung_TiO2_Day28_rep6

source_name: Rat, Lung, TiO2, Day 0, replicate 6


title: MCF10A, WTp53:WTp53 cDNA insert, DMSO, PRO-seq, Replicate 1 [21_DMSO_3hr_R1]


title: Erythroblasts, input for CHIP-Seq

city: Midlothian

first: Douglas

last: Vernimmen

address: The University of Edinburgh, Easter Bush Campus, Midlothian

department: Roslin Institute

institute: University of Edinburgh

data_processing:
RTA software version used was Illumina RTA 1.17.20 and the Pipeline software version:  bcl2fastq-1.8.3.
Reads were aligned using the hisat2 aligner version 2.0.3 with the --no-spliced-alignment option, but otherwise default parameters, to a splicing-unaware index of the human GRCh38 genome
Reads of the ChIP-Seq samples were first normalized to the input (GSE114084) and then scaled to 1x sequencing depth using deepTools v. 3.1.3
The peak calling  was performed using MACS2 2.1.1 with the minimum FDR (q-value) cutoff of 0.01 50,  then top 75% fold enriched peaks were selected
Genome_build: GRCh38
Supplementary_files_format_and_content: BigWIg was generated using Deeptools and represent the enrichment of MAZ relative to the input (GSM3132547; bed file represent the coordinates of high confident MAZ peaks)

source_name: erythroblast

growth_protocol: The erythroblasts were produced in two phase culture from normal donors according to Pope et al., Eur J Haematol. 2000;64(5):292–303.

extract_protocol:
Chromatin was first cross-linked with ethylene glycol bis(succinimidyl succinate) (EGS) in PBS at a final concentration of 2 mM for 60 min at RT; Formaldehyde (CH2O) was then added at a final concentration of 1 % for 15 min at RT and samples were sonicated; anti-MAZ antibody used was purchase from Bethyl Laboratories (A301-652A).
Libraries were prepared using the New England Biolabs NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina

value: Adult erythroblasts

tag: chip antibody


title: Erythroid cells, MAZ_ChIP-Seq

source_name: Primary erythroid cells

value: Primary erythroid cells

value: anti-MAZ antibody (Bethyl Laboratories, catalog# A301-652A)


title: Lung_TiO2_Day28_rep3

source_name: Rat, Lung, TiO2, Day 0, replicate 3


title: Lung_TiO2_Day28_rep4

source_name: Rat, Lung, TiO2, Day 0, replicate 4


title: MCF10A, WTp53 cDNA insert,10uM Nutlin3a, PRO-seq, Replicate 1 [7_Nutlin_3hr_R2]

source_name: MCF10A, WTp53 cDNA insert, 10uM Nutlin3a

value: 2820bp:full length p53 cDNA followed IRES expressed mCherry followed by SV40 polyA sequnece


title: 92QND85

value: Placebo


title: Lung_TiO2_Day28_rep2

source_name: Rat, Lung, TiO2, Day 0, replicate 2


title: 95TBM69


title: Lung_Control_Day28_rep6

description: Gene expression  in lung of control rat (filterd air) 28 days post-exposure

source_name: Rat, Lung, TiO2, Control, Day 28, replicate 6


title: Lung_Control_Day28_rep5

source_name: Rat, Lung, TiO2, Control, Day 28, replicate 5


title: 75ABF54


title: Lung_TiO2_Day28_rep1

source_name: Rat, Lung, TiO2, Day 0, replicate 1


title: 98NFA86


title: 79OHS63


title: H2A.Z (mut)

city: Nanning

first: Zhenxing

last: Wang

state: Guangxi

address: Zhongshan Street

department: Center for Genomic and Personalized Medicine

country: China

institute: Guangxi Medicla University

data_processing:
After sequencing data was delivered, we did data filtering first, which could remove low quality reads, N reads and adaptor sequences, and get clean data.
After filtering, the Clean data was then mapped to the reference hg19 genome by SOAPaligner/SOAP2 (Version: 2.21t).
MACS (Model-based Analysis for  ChIP -Seq, version: MACS-1.4.2) : The candidate  Peak  region was extended to be long enough for modeling. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a  Peak  when p-value < le-05.MACS work well for the identification of the sharp peaks of most sequence-specific transcription factors.
Later, we used the peak information for standard bioinformatics analysis and personalized bioinformatics analysis.
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: peak

molecule: polyA RNA

source_name: Hela

extract_protocol:
The chromatin solutions containing supernatant were incubated with ChIP-grade antibodies anti-Flag M2 (F3165, Sigma, USA), and the DNA-protein complex was pulled down with Pierce™ ChIP-grade Protein A/G Magnetic Beads (26162, Invitrogen, USA),according to the manufacturer’s instructions.
Purified ChIP DNA was subjected to library production and Illumina sequencing by Shenzhen Huada Gene Technology Co. Ltd.

value: Hela

tag: genotype/variation

value: mutant H2A.Z with ubiquitination deficiency

tag: antibody

value: anti-Flag M2 (F3165, Sigma, USA)


title: MCF10A, WTp53 cDNA insert,10uM Nutlin3a, PRO-seq, Replicate 1 [7_Nutlin_3hr_R1]

source_name: MCF10A, WTp53 cDNA insert,10uM Nutlin3a

value: 10uM Nutlin3a

value: nascent RNA


title: 66TDV96

value: ALS

value: peripheral blood


title: H2A.Z (wt)

value: wild-type H2A.Z


title: 55MKH26


title: MCF10A, WTp53 cDNA insert, DMSO, PRO-seq, Replicate 1 [7_DMSO_3hr_R1]

source_name: MCF10A, WTp53 cDNA insert, DMSO

value: mammary gland; breast

value: epithelial


title: 46XWM36


title: CF subject CFB3218, exposed to IL-17+TNFa

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

data_processing:
Raw fastq files were pseudoaligned to human genome assembly GRCh38.p12 using kallito software version 0.45.0
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tab-separated text file containing length, estimated counts, and transcripts per million (TPM) for each gene isoform

source_name: lung

extract_protocol:
RNA was extracted using Qiagen RNeasy Lipid Tissue Mini Kit # 74804.
mRNA libraries were prepared using Illumina TruSeq stranded mRNA sample preparation kit (Illumina #RS-122-2101).

tag: donor

tag: disease

value: CF

value: lung

tag: batch


title: siRNA_NANOG_rep3

city: santa barbara

first: Guojing

last: Liu

state: CA

address: 552 University Rd

institute: University of California, santa barbara

description: sc_zb_nc_nanog_tophat_merge.repeats.cpm.ge1.txt,siNC_nanog_scramble_ZB.cpm.fil.txt

data_processing:
NextSeq RTA version 2.4.11 software used for basecalling
For nanoCAGE data, bwa (version 0.7.13, mem default option) was used for genome mapping, duplicates were removed by samtools (version 0.1.16). TSS peaks were called and annotated based on gencode.v19.annotation.gtf with HOMER software according to the manual. Only peaks with moren than 30 reads were considered for the analyses. Gene expression was quantified using HTseq (version 0.10.0).
For ChIP-seq data, bwa (version 0.7.13, mem default option) was used for genome mapping, duplicates were removed by samtools (version 0.1.16). MACS2 (macs2  callpeak  -t ZB12_flag_map_rmdup.bam -c Input_map_rmdup.bam -f BAM -g hs -n ZB12-flag -B -q 0.01) was used for peaks calling and HOMER software was used for peaks annotation based on gencode.v19.annotation.gtf.
For RNA-seq data, tophat (version 2.1.0 default parameter) was used for genome mapping, Bedtools was used for repeat coverage counting based on repeat annotation downloaded from UCSC database (hg19). Gene expression was quantified with Cufflinks (v2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: For nanoCAGE data: tab-delimited text files showing all TSS peaks (unfiltered) position with abundance measurements identified by HOMER software for each sample.

source_name: hESC (H9 stem cell)

growth_protocol: H9 cells grows in mTeSR medium, for time-course differentiation media followed the protocol in published paper (PMID: 22976355)

extract_protocol: nanoCAGE library was prepared based on modified protocol from previously published paper (PMID: 21205859). ChIPSeq library was prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB); RNA-seq library was prepared using KAPA RNA HyperPrep Kit with RiboErase (HMR) Illumina® Platforms (KAPA Biosystems).

treatment_protocol: Total RNA was extracted with mirVana™ miRNA Isolation Kit (Thermo Fisher, Catlog: AM1560) for nanoCAGE sequencing library preparation and RNA-seq library preparation; Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody for ChIPSeq.

tag: cell line

value: hESCs

tag: passage


title: CF subject CFB2818, exposed to IL-17+TNFa

tag: tissue


title: CF subject CFB2518, exposed to IL-17+TNFa


title: siRNA_NANOG_rep2

tag: cell type


title: MCF10A, WTp53 cDNA insert, DMSO, PRO-seq, Replicate 2 [7_DMSO_3hr_R2]

tag: crispr/cas9 insertion

tag: crispr/cas9 insertion location


title: CF subject CFB0419, exposed to IL-17+TNFa

tag: treatment


title: 34SBH78


title: siRNA_NANOG_rep1


title: Lung_Control_Day28_rep4

source_name: Rat, Lung, TiO2, Control, Day 28, replicate 4

tag: strain

value: F344 Fisher

value: accessory lobe of lung

tag: gender

value: male

value: 19 months-old (at the onset of inhalation)


title: CF subject CFB0319, exposed to IL-17+TNFa


title: Lung_Control_Day28_rep2

source_name: Rat, Lung, TiO2, Control, Day 28, replicate 2

tag: age


title: 47XAT27

tag: diagnosis

value: Placebo

tag: time point


title: siRNA_NC_rep3

tag: genotype/variation

tag: chip antibody


title: 23BDT37


title: Lung_Control_Day28_rep3

source_name: Rat, Lung, TiO2, Control, Day 28, replicate 3


title: Lung_Control_Day28_rep1

source_name: Rat, Lung, TiO2, Control, Day 28, replicate 1


title: Lung_TiO2_Day0_rep5

description: Gene expression  in lung of rat exposed to TiO2 (10 mg/m3) the day of the end of exposure

source_name: Rat, Lung, TiO2, Day 0, replicate 5


title: CF subject CFB0219, exposed to IL-17+TNFa

tag: donor


title: Lung_TiO2_Day0_rep4


title: Lung_TiO2_Day0_rep3

source_name: Rat, Lung, TiO2, Day 0, replicate 3


title: CF subject CFB3218, control

tag: disease

value: control


title: siRNA_NC_rep1


title: Lung_TiO2_Day0_rep2


title: 92XZK83

value: 2MIU IL2


title: 16NM22


title: 88FRZ35


title: ZBTB12_shRNA_rep2


title: CF subject CFB2818, control

tag: batch


title: siRNA_NC_rep2

tag: cell line


title: ZBTB12_shRNA_rep1

tag: passage


title: CF subject CFB0419, control

tag: tissue


title: CF subject CFB0319, control


title: CF subject CFB0219, control


title: Scramble_rep2

value: scramble

tag: cell type


title: CF subject CFB2518, control


title: non-CF subject B0919, exposed to IL-17+TNFa

value: non-CF


title: ZBTB12_shRNA_rep3


title: Scramble_rep3


title: Lung_TiO2_Day0_rep1


title: 66ADE25

value: ALS


title: 72YOV58

value: peripheral blood


title: 78TJC44


title: 54HYO55


title: non-CF subject B0719, exposed to IL-17+TNFa


title: PolII_ChIPSeq

value: Come with EZ-ChIP KIT (Millipore, 17-371)


title: Lung_Control_Day0_rep5

description: Gene expression  in lung of control rat (filterd air) the day of the end of exposure

source_name: Rat, Lung, TiO2, Control, Day 0, replicate 5


title: non-CF subject B0619, exposed to IL-17+TNFa


title: Scramble_rep1


title: MC-4C_WT_129_VP_Slc 1

description: MC-4C, WT, 129

value: ESC

tag: genetic modification

value: WT


title: non-CF subject B0819, exposed to IL-17+TNFa


title: MC-4C_LBdel_129_VP_Slc

description: MC-4C, LBdel, 129

value: LBdel


title: non-CF subject B0519, exposed to IL-17+TNFa

value: lung


title: 38TPQ86


title: Lung_Control_Day0_rep3

source_name: Rat, Lung, TiO2, Control, Day 0, replicate 3


title: Lung_Control_Day0_rep1

source_name: Rat, Lung, TiO2, Control, Day 0, replicate 1


title: Lung_Control_Day0_rep6

source_name: Rat, Lung, TiO2, Control, Day 0, replicate 6


title: Lung_Control_Day0_rep4

source_name: Rat, Lung, TiO2, Control, Day 0, replicate 4


title: 44JRQ89


title: Lung_Control_Day0_rep2

source_name: Rat, Lung, TiO2, Control, Day 0, replicate 2


title: MC-4C_WT_129_VP_Slc 3

description: MC-4C, WT, 129


title: 37QNW23


title: 33DGN54


title: ZBTB12_Flag_ChIPSeq

value: hESCs

value: DYKDDDDK Tag (D6W5B) Rabbit mAb (mRb, Cell signaling, 14793S)


title: MC-4C_WT_129_VP_Slc 2

description: MC-4C, WT, 129


title: Input_DNA

description: Input.bw


title: non-CF subject B0919, control


title: non-CF subject B0719, control


title: 29ZCQ57


title: H9_D23_rep2

description:
H9D23_chr.tss.anno.txt,H9_total_peak.exp.anno.txt.filter.txt
library strategy: nanoCAGE

value: Neuronal differenation from hESCs (Day 23)


title: non-CF subject B0419, exposed to IL-17+TNFa


title: 17MA49


title: H9_D15_rep2

description:
H9D15_chr.tss.anno.txt,H9_total_peak.exp.anno.txt.filter.txt
library strategy: nanoCAGE

value: Neuronal differenation from hESCs (Day 15)


title: H9_D23_rep1


title: H9_D5_rep1

description:
H9D5_chr.tss.anno.txt,H9_total_peak.exp.anno.txt.filter.txt
library strategy: nanoCAGE

value: Neuronal differenation from hESCs (Day 5)


title: non-CF subject B0819, control


title: non-CF subject B0519, control


title: non-CF subject B0419, control


title: H9_D15_rep1


title: H9_D5_rep2


title: ASC_PD_3

city: Guangzhou City,

first: Changlin

last: Lian

state: Guangdong Province

address: 253 Industrial Avenue Middle, Haizhu District

institute: Southern medical University Zhujiang Hospital

data_processing:
BGIseq500 software used for basecalling.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
expression level of gene was calculated byRSEM (v1.2.12)
the gene expression indifferent samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)

source_name: adipose

growth_protocol: Adipose mesenchymal stem cells with single culture

extract_protocol:
hADSCs RNA was harvested using Trizol reagent.1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGIseq500 protocols

treatment_protocol: Three replicate was co-culture with 6-OHDA-induced brain slices

value: Adipose mesenchymal stem cells


title: non-CF subject B0619, control

value: control


title: ASC_PD_2

value: co-culture with 6-OHDA-induced brain slices


title: H9_D0_rep1

description:
H9D0_chr.tss.anno.txt,H9_total_peak.exp.anno.txt.filter.txt
library strategy: nanoCAGE

value: Undifferentiated human embryonic stem cell (hESCs Day 0)


title: ASC_PD_1


title: H9_D0_rep2


title: ASC_3

value: single culture


title: ASC_2


title: ct-1_r3y_ln

city: New York

first: Chia-Yi

last: Cheng

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description: processed data file: NutriNet.Arabidopsis-veg-young.featureCounts.txt

data_processing:
Base calling: (Arabidopsis) Picard Tools version 2.17.11 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=false APPLY_EAMSS_FILTER=false. (Maize) bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Removing optical duplicates: Clumpify version 37.24 (Arabidopsis) clumpify.sh -Xmx48g in=in.fq.gz out=out.fq.gz overwrite=t dedupe reorder addcount optical dupedist=40. (Maize) clumpify.sh -Xmx60g in=in.fq.gz out=out.fq.gz overwrite=t dedupe reorder addcount optical dupedist=2500.
Removing adapters: BBDuk version 37.24 (Arabidopsis). (Maize) bbduk.sh in=in.fq.gz out=out.fq.gz overwrite=t ref=~/package/bbmap/resources/adapters.fa ordered=t ktrim=r k=25 mink=11 minlength=35.
Aligning to the genome: BBMap version 37.24 (Arabidopsis). (Maize) bbmap.sh -Xmx56g in=input.fq.gz ordered=t overwrite=t outm=out.sam
Assigning reads: subread v1.5.1 (Arabidopsis) featureCounts -T 1 -s 2 -O -a Araport11.gtf -o out.featureCounts input.sam (Maize) featureCounts -T 1 -R -s 0 -O -a Zea_mays.AGPv4.32.gtf -o out.featureCounts input.sam
Genome_build: (Arabidopsis) TAIR10, (Maize) Zm-B73-REFERENCE-GRAMENE-4.0
Supplementary_files_format_and_content: *.featureCounts.txt: Tab-delimited text files include raw read counts.

organism: Arabidopsis thaliana

source_name: Leaf

extract_protocol:
(Arabidopsis) Total RNA was extracted from leaf samples using Direct-zol MiniPrep by Zymo Research.
(Arabidopsis) NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina.
(Maize) RNAs were isolated with a CTAB, acidified phenol-chloroform extraction, and isopropanol precipitation.
(Maize) TruSeq Stranded mRNAseq Sample Prep kit.

value: Fully-grown adult leaf

value: 6 weeks

tag: genotype

value: Low nitrogen


title: Kidney, Senkirkine 3.3 mg/kg/bw_animal 2

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

description: gene expression data of kidney of PA treated rats

hyb_protocol: hybridization to Gene Chip plate arrays

scan_protocol: staning and imaging on Gene Titan Multi-Channel Instrument

data_processing: Data processing and statistical data evaluation was performed in the R environment. The raw data were normalized and summarized using the RMA (robust multi-array average) algorithm from the R package oligo version 1.54.1. The genes were associated with vendor-provided annotation information (Release 36, Thermo Fisher Scientific, https://sec-assets.thermofisher.com/TFSAssets/LSG/SupportFiles/Clariom_S_Rat.r1.na36.rn6.a1.transcript.csv.zip) and control genes were removed after background correction. Moreover, irrelevant genes with low or unchanged expression were removed (median < 4 or CV < 0.02, respectively) so that 12,699 genes remained.   Differential gene expression (DGE) analysis was performed by the R package limma version 3.46.0: (Ritchie et al. 2015) linear models were fit and moderated t-statistics computed by the eBayes function. Afterwards, the Benjamini and Hochberg correction was applied to exclude false positive results and thus genes with an adjusted p-value < 0.1 were considered significantly differentially expressed. Besides, one-way analysis of variance (ANOVA) was performed to extract the top100 genes that were most affected in their expression by PA treatment.

label: biotin

source_name: mRNA, kidney after 28 days oral treatment

label_protocol: The samples were labeled with a GeneChip WT Plus labeling kit at Eurofins (Comp. No. 7230-GT0028).

growth_protocol: Rats were orally exposed to 6 structurally different pyrrolizidine alkaloids for 28 days (3.3 mg/kg body weight)

extract_protocol: Small pieces of the deep-frozen organs were homogenized with liquid nitrogen and transferred to RLT buffer (Qiagen, Hilden, Germany) containing 1 % β-mercaptoethanol. RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) in combination with QiaShredder (Qiagen, Hilden, Germany). Quality and quantity of the RNA were checked with an Agilent 2100 Bioanalyzer with an RNA Nano Lab chip and a Tecan M200 Pro spectrophotometer with a NanoQuant Plate at 260 nm and 280 nm.

treatment_protocol: Rats were orally exposed to 6 structurally different pyrrolizidine alkaloids daily, after 28 d lung and kidney samples were gained, shock frozen and stored at 80°C prior isoation of RNA

tag: strain/gender/tissue

value: Fisher 344

value: male

value: kidney

tag: treatment

value: Senkirkine

tag: dose

tag: dose unit

value: mg/kg bw/day

tag: way of administration

value: oral gavage

tag: days of administration


title: Kidney, Senecionine 3.3 mg/kg/bw_animal 3

tag: gender

value: Senecionine


title: Kidney, Senkirkine 3.3 mg/kg/bw_animal 1


title: Kidney, Senecionine 3.3 mg/kg/bw_animal 1


title: Kidney, Senecionine 3.3 mg/kg/bw_animal 4


title: Kidney, Senecionine 3.3 mg/kg/bw_animal 2


title: HGC27_anti_ARGLU1

city: Shanghai

first: Li

last: Fangyuan

state: Shanghai

address: Ruijin Er road

institute: Shanghai Jiao Tong University

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

growth_protocol: RPMI 1640 supplemented with 10% FCS

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: sample type

value: gastric cancer cell lines

tag: antibody


title: Kidney, Vehicle 0.15 NaCl_animal 4

description: gene expression data of kidney of vehicle treated rats

value: Control


title: Kidney, Senkirkine 3.3 mg/kg/bw_animal 3


title: dopaminergic neurons from Brain 12-rep1

city: Geneva 14

first: PIerre

last: Burkhard

address: 4 rue Gabrielle-Perret-Gentil

department: Department of Clinical Neurosciences

country: Switzerland

institute: HUG

data_processing:
Illumina bcl2fastq2 v. 2.20 0 was used for base calling.
The reads were mapped with the STAR aligner v.2.5.3a to the UCSC human hg38 reference.
The table of counts with the number of reads mapping to each gene feature of the UCSC human hg38 reference was prepared with HTSeq v0.6p1.
The differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v. 3.14.0 with a  quasi-likelihood (QL) F-test.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Brain

extract_protocol:
Tissue depleted of DA neurons after LMD was also collected from the slides in 100 µL of lysis/denaturing buffer from the RNAqueous micro kit (Life technologies, Zug, Switzerland). RNAs were extracted following the manufacturer protocol, quantified with a Qbit™ fluorometer (Thermo Fisher, Waltham, MA, US) and analysed with an Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA) to check the RNA profile and obtain the RNA Integrity number (RIN).
The SMART-Seq v4 kit from Clontech was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 70 cells as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina.

treatment_protocol: Laser microdissection of DA neurons

value: Dopaminergic neurons

tag: group

value: Parkinson's disease


title: dopaminergic neurons from Brain 11-rep2


title: dopaminergic neurons from Brain 11-rep1


title: col-0_r3y_ln

tag: age


title: tsu-0_r3y_hn

value: High nitrogen


title: dopaminergic neurons from Brain 7-rep2


title: stw-0_r3y_hn


title: dopaminergic neurons from Brain 12-rep2


title: dopaminergic neurons from Brain 7-rep1


title: placental cells-E12

first: Zhixin

last: Kang

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

description:
10x_Raw_gene_counts_matrix.txt
10x_Celltype.txt

data_processing:
For 10X Genomics data, reads was processed using the 10X Genomics CellRanger pipeline. Sequencing reads were mapped to mm10 reference genome.
Cellranger aggr was used to aggregate three cell ranger counts
For smart-seq2 data, read 2 grouped by barcodes was aligned to corresbonding read 1 after removing polyA and TSO sequence. Removing the reads with low quality bases by Cutadat(version 1.18), reads were aligned to mm10 reference genome(Ensemble) by Hisat2. Htseq was used to count uniquely mapped reads to deduplicated genes expression matrix by UMI sequence.
Genome_build: mm10
Supplementary_files_format_and_content: *Raw_gene_counts_matrix.txt files (of tab-delimited text file) with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: 10x_Celltype.txt tab-delimited text file for cell annotation include gene number, count number, mito percentage and celltype for each cell (In column 1, barcode-1 corresponds to placental cells-E10, barcode-2 corresponds to placental cells-E11, barcode-3 corresponds to placental cells-E12.)
Supplementary_files_format_and_content: gz file (of tsv file) with10x data barcodes produced by CellRanger softeware
Supplementary_files_format_and_content: gz file (of tsv file) with10x data features produced by CellRanger softeware
Supplementary_files_format_and_content: gz file (of mtx file) with10x data matrix produced by CellRanger softeware

source_name: Placenta

extract_protocol:
Target cells were captured using antibody by fluorescence activated cell sorting (FACS).
For 10X Genomics data, single-cell suspensions were loaded on a Chromium Single Cell Controller (10 × Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 30 Library and Gel Bead Kit V2 (10 × Genomics, 120237). RNAs barcoding were obtained through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads (Invitrogen, 37002D). Single-cell RNA-sequencing (scRNA-seq) libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 (10× Genomics, 120237) following the manufacture’s introduction. Sequencing was performed on an Illumina HiSeq x Ten with pair end 150 bp (PE150). For smart-seq2 data, the linearized RNA molecules were releasein a thermocycler at 72 °C for 3 min at first. Then, transfer the reactions immediately on ice. Add 2.85 µl RT mixture into every reaction with component as SuperScript II reverse transcriptase, RNase Inhibitor, 5× Superscript II first-strand buffer, dithiothreitol (DTT), betaine, MgCl2, and template switch oligo (TSO) primer. Spin down the 5.4 µl samples in the thermocycler at 25 °C for 5 min, 42 °C for 60 min, 50 °C for 30 min, and then 70 °C for 10 min, 4 °C hold. Prepare 7.5 µl PCR mixture (6.25 μL 2× KAPA HiFi HotStart ReadyMix, ISPCR oligo, and 3′ Anchored oligo) to add in every tube reaction, and amplify samples for 19 cycles. Pool together samples with different barcodes (up to 96 barcodes) and purify DNA. Then prepare the second round of amplification with bio-tinylated index primer and ISPCR oligo for an additional five cycles. Subsequently, purify the biotinylated cDNAs further with 0.8× Ampure XP beads and elute cDNA in 50 µl EB. Next, shear the cDNAs into approximately 300-bp fragments with sonicator.Enrich the cDNA fragments  by Dynabeads® MyOneTM Streptavi- din C1. Libraries were prepared with KAPA Hyper Prep Kits. Use the NEB U-shaped adapter for ligation. Finally, amplify the adapter-ligated fragments using an Illumina QP2 primer and a short universal primer for 9 cycles.

treatment_protocol: Placenta, AGM and yolk sac were dissected from pregnant mice and prepared for single-cell suspensions using collagenase according to previous reports.

value: placenta

value: all types of placental cells

tag: developmental stage

value: embryonic day 12.0


title: Lung, Vehicle 0.15 NaCl, animal 1

description: gene expression data of lung of vehicle treated rats

source_name: mRNA, lung after 28 days oral treatment

value: lung


title: DNA delivered to cells by transfection

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: 660 S Euclid Ave, Campus Box 8232

department: Genetics

institute: Washington University in St. Louis

data_processing:
Barcode extraction from sample fastq - see bitbucket repository for script. Requires flanking 14 bp around barcode to be identical to design, plus a 10bp sequence to be found in between the flanks. All 10bp sequences extracted from Fastqs into text file.
Tabulation of barcode counts for each sample using table() in R. Subsequently, merging to a metadata table on designed barcodes to drop sequences that were not a perfect match to a designed barcode.
Filtering for low read counts, poor barcode representation across replicates, etc. Described at length in Supplementary Methods.
Calculation of log2(cpm RNA barcode) / log2(cpm DNA barcode) for each retained barcode in each sample.
For each allelic sequence pair (each allele having up to 10 unique RNA barcodes), mean of the rna/dna ratios from above calculated for each sample --> t-test of sample mean expression values between the alleles of each biallelic sequence
Genome_build: hg19-derived sequences (up to 126bp); see enclosed file "Reference-Barcode Sequences, their paired internal identifiers, and the corresponding sequence placed upstream of min promoter.txt" for each allele of each sequence and its paired reporter (RNA) barcodes
Supplementary_files_format_and_content: Tab-delimited text; barcode counts for each RNA sample and the DNA sample.

organism: Escherichia coli

source_name: Plasmid

growth_protocol: Cells were grown without changing medium for 72 hours at 37°C, 5% CO2.

extract_protocol:
Cells lifted in 250uL PBS and 750µL Trizol, followed by addition of 200uL chloroform and cleanup of the aqueous phase using the Zymo Clean and Concentrator 5 kit per manufacturer instructions. Turbo DNAse-free kit was used to remove incidental DNA, followed by a second cleanup using the Zymo kit to achieve a higher final concentration of RNA.
Reporter-specific cDNA synthesis using a reverse-complementary primer, followed by PCR, digestion, adapter ligation, and index PCR. DNA from plasmid was prepared simultaneously, starting with the first PCR step. Each step was followed by a cleanup using size-selection beads (brands Ampure XP and Magbind).

treatment_protocol: Basal medium (2% FBS in DMEM), with 1% penicillin-streptomycin in the medium before transfection and >6hrs after plus 20µM final concentration all-trans retinoic acid in 100% DMSO, or an equivalent amount of 100% DMSO for vehicle treatment. Medium prepared and refreshed daily with freshly added ATRA from light-protected frozen aliquots

value: Input Plasmid


title: Input Plasmid

description: Dougherty_DNA_80ng_SIC_Index_198_CCTGCTACTA_S36

treatment_protocol: Basal medium (10% FBS in DMEM), with 1% penicillin-streptomycin in the medium before transfection and >6hrs after


title: Kidney, Vehicle 0.15 NaCl_animal 2

value: Fisher 344


title: st-0_r3y_hn

value: Fully-grown adult leaf

value: 6 weeks


title: dopaminergic neurons from Brain 4-rep1


title: placental cells-E10

value: embryonic day 10.0


title: placental cells-E11

value: embryonic day 11.0


title: Kidney, Vehicle 0.15 NaCl_animal 3

value: male

value: kidney

value: mg/kg bw/day

value: oral gavage


title: Lung, Senecionine 0.33 mg/kg/bw_animal 4

description: gene expression data of lung of PA treated rats

value: Senecionine


title: ASC_1

value: Adipose mesenchymal stem cells

value: single culture


title: sakata_r3y_hn

value: Sakata

value: High nitrogen


title: Kidney, Vehicle 0.15 NaCl, animal 1

value: Control


title: Lung, Senecionine 0.33 mg/kg/bw_animal 2

value: lung


title: oy-0_r3y_hn


title: dopaminergic neurons from Brain 3-rep2

value: Dopaminergic neurons


title: Lung, Senecionine 0.33 mg/kg/bw_animal 3

value: Fisher 344


title: Lung, Senecionine 0.33 mg/kg/bw_animal 1


title: dopaminergic neurons from Brain 4-rep2

value: Parkinson's disease


title: dopaminergic neurons from Brain 2-rep2


title: bur-0_r3y_ln

value: Fully-grown adult leaf

value: 6 weeks

value: Low nitrogen


title: 23-CATA-6D-1

first: Wei

last: Qi

address: B514, L Building

department: School of Life Science and Technology

institute: ShanghaiTech University

data_processing:
Reads are mapped to mouse genome mm10 with STAR 2.4.1a. Mapping parameters are set as default.
The Rsem v1.2.31 software is then used to align reads to UCSC mouse gene reference. FPKM (fragments per kilobase of exon per million fragments mapped) values of genes’ level from RSEM output are used in the following analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: C3H10T cells

growth_protocol: All cells were maintained at 37°C in humidified air with 5% CO2. C3H10T1/2  preadipocytes were cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (growth medium). Growth medium was replaced every 2 days.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured for an additional day after reaching confluency, and the growth medium was then replaced (day 0) with DMEM supplemented with 10% FBS, 1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine and 10 μg/ml insulin ,1 μM rosiglitazone and 1 nM T3 (differentiation medium, MDI+RT). After 48 h, the differentiation medium was replaced (day 2) with DMEM + 10% FBS containing 5 μg/ ml insulin, and the cells were allowed to accumulate lipid droplets until experimental use. cells were cultured in DMEM + 10% FBS.

tag: time point


title: 23-CATA-6D-2


title: dopaminergic neurons from Brain 2-rep1


title: shahdara_r3y_hn

tag: tissue

value: Shahdara


title: dopaminergic neurons from Brain 3-rep1

tag: cell type


title: n13_r3y_hn


title: 23-CATA-6D-3


title: Lung, Senecionine 1 mg/kg/bw_animal 4

value: male


title: 23-CATA-4D-3


title: Lung, Senecionine 1 mg/kg/bw_animal 3

value: mg/kg bw/day


title: D10 CD34+CD41+CD9+ SR1+ cells, Rep3

city: Strasbourg

first: Henri

last: de la Salle

address: 10 rue Spielmann

institute: EFS Grand-Est

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT9

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10 (EMBnet.journal 17, 10-12, 2011). Reads were mapped to rRNA sequences using bowtie version 2.2.8 (Nat Methods 9, 357-359, 2012), and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Reads were mapped onto the hg38 assembly of Homo sapiens genome using STAR (Bioinformatics 29, 15-21) version 2.5.3a.
Gene expression quantification was performed from uniquely aligned reads using htseq-count (Bioinformatics 31, 166-169, 2015) version 0.6.1p1, with annotations from Ensembl version 91 and \union" mode2 (between 16 and 25 106 different non-ribosomal reads/sample). Read counts were normalized across samples with the median-of-ratios method proposed by Anders and Huber (Genome Biol, 11, R106, 2010), to make these counts comparable between samples.
Comparisons of interest were performed using the test for differential expression proposed by Love et al. (Genome Biol 15, 550, 2014) and implemented in the Bioconductor package DESeq2 version 1.16.1. The pValues were adjusted for multiple testing using the Benjamini-Hochberg method. Processed data files provide the log2 values of the normalized read counts divided by the median of the lengths of the ENSEMBL transcripts associated to the respective genes. D0-D7 processed data were generated by the analysis all of the samples, D7-D14 processed data were generated by the analysis of all the samples except D0 ones.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix text files containing raw read counts in each sample (D0-D14 Raw gene counts.txt) or, log2 values of the normalized read counts divided by the median of the lengths of the ENSEMBL transcripts associated to the respective genes and DEseq2  analysis of differential expression (D0-D7 processed data.txt and, D7-D14 processed data.txt).

source_name: Peripheral blood cells

growth_protocol: Peripheral blood CD34+ progenitors from adults were purified using Miltenyi technology then, differentiated into MKs in StemSpan™ Megakaryocyte Expansion medium containing Megakaryocyte Expansion Supplement  (containing SCF, IL-6, IL-9, TPO and 20 ng/mL human LDL) from D0 to D7. At D7, cells were placed in StemSpan™ Megakaryocyte Expansion medium supplemented  with 50 ng/mL TPO and, cell differentiation proceeded up to D14. Each cell sample (data file) was generated from a CD34+ cell batch prepared from 5 leukocyte-depletion filters, and thus representing 20 unrelated donors.

extract_protocol:
RNAs were purified from D0 cells (isolated using Miltenyi technology), and of D7 to D14 populations (isolated by flow cell sorting) using RNeasy Plus kit (Qiagen).
RNA-Seq libraries were generated from 500-300 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
Two batches of RNA-seq production were generated (CNSL and VNDT series).

treatment_protocol: When used, SR1 was added at D0 and D7 (1µM).

tag: cell markers

tag: day

tag: rna-seq production

value: VNDT


title: D10 CD34+CD41+CD9+ SR1+ cells, Rep2

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT8

tag: treatment


title: mr-0_r3y_hn

tag: genotype


title: 23-CATA-4D-1


title: 23-CATA-2D-3


title: kn-0_r3y_hn


title: D10 CD34+CD41+CD9+ SR1+ cells, Rep1

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT7


title: mh-1_r3y_hn


title: D10 CD34+CD41+CD9+ SR1- cells, Rep3

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT3


title: 23-CATA-2D-2


title: Lung, Senecionine 1 mg/kg/bw_animal 2

tag: strain/gender/tissue

value: Senecionine

tag: dose

tag: dose unit

value: oral gavage


title: 23-CATA-2D-1


title: D10 CD34+CD41+CD9+ SR1- cells, Rep1

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT1


title: Lung, Platyphylline 3.3 mg/kg/bw_animal 2

tag: gender

value: Platyphylline

tag: way of administration

tag: days of administration


title: ge-0_r3y_hn


title: Lung, Platyphylline 3.3 mg/kg/bw_animal 1


title: D10 CD34+CD41+CD9+ SR1- cells, Rep2

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT2


title: Lung, Platyphylline 3.3 mg/kg/bw_animal 3


title: Lung, Platyphylline 3.3 mg/kg/bw_animal 4


title: Lung, Senecionine 1 mg/kg/bw_animal 1


title: 23-CATA-0D-3


title: ct-1_r3y_hn


title: edi-0_r3y_hn


title: mt-0_r3y_hn


title: 23-CATA-0D-2


title: D10 CD34-CD41+ SR1+ cells, Rep3

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL12

value: CNSL


title: D10 CD34-CD41+ SR1+ cells, Rep2

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL11


title: col-0_r3y_hn

value: High nitrogen


title: 23-CATA-0D-1


title: 23-Tet1-6D-3


title: D10 CD34-CD41+ SR1+ cells, Rep1

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL10


title: bur-0_r3y_hn


title: D10 CD34-CD41+ SR1- cells, Rep3

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL9


title: Lung, Senkirkine 3.3 mg/kg/bw_animal 2

value: Senkirkine


title: bi-1_r3y_ln

description: processed data file: NutriNet.Arabidopsis-veg-young.featureCounts.txt


title: Lung, Senkirkine 3.3 mg/kg/bw_animal 1

value: lung


title: D10 CD34-CD41+ SR1- cells, Rep1

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL7


title: Lung, Senkirkine 3.3 mg/kg/bw_animal 3


title: D10 CD34-CD41+ SR1- cells, Rep2

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL8


title: 23-Tet1-6D-2


title: Lung, Senkirkine 3.3 mg/kg/bw_animal 4


title: Lung, Lasiocarpine 3.3 mg/kg/bw_animal 4

value: Lasiocarpine


title: 23-Tet1-4D-2


title: D14 CD34+CD41+CD9- SR1+ cells, Rep3

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT21


title: tsu-0_r3y_ln


title: 23-Tet1-4D-3


title: stw-0_r3y_ln


title: D14 CD34+CD41+CD9- SR1+ cells, Rep1

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT19


title: Lung, Lasiocarpine 3.3 mg/kg/bw_animal 3

value: Fisher 344


title: st-0_r3y_ln


title: 23-Tet1-2D-3


title: 23-Tet1-4D-1


title: akita_r3y_hn

value: Akita


title: bi-1_r3y_hn

value: Fully-grown adult leaf


title: shahdara_r3y_ln

value: 6 weeks


title: 23-Tet1-6D-1


title: Lung, Senecionine 3.3 mg/kg/bw_animal 4


title: D14 CD34+CD41+CD9- SR1- cells, Rep3

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT15


title: 23-Tet1-2D-2


title: Lung, Lasiocarpine 3.3 mg/kg/bw_animal 1

description: gene expression data of lung of PA treated rats


title: 23-Tet1-2D-1


title: sakata_r3y_ln

value: Sakata

value: Low nitrogen


title: Lung, Lasiocarpine 3.3 mg/kg/bw_animal 2

value: male


title: Lung, Senecionine 3.3 mg/kg/bw_animal 3

value: mg/kg bw/day


title: Lung, Senecionine 3.3 mg/kg/bw_animal 2


title: D14 CD34+CD41+CD9- SR1- cells, Rep2

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT14

value: VNDT


title: Lung, Senecionine 3.3 mg/kg/bw_animal 1

value: Senecionine


title: D14 CD34+CD41+CD9- SR1- cells, Rep1

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT13


title: oy-0_r3y_ln


title: 23-Tet1-0D-3


title: n13_r3y_ln


title: D10 CD34+CD41+CD9- SR1+ cells, Rep3

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL15


title: D14 CD34+CD41+CD9- SR1+ cells, Rep2

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT20


title: Lung, Heliotrine 3.3 mg/kg/bw_animal 3

value: Heliotrine

value: oral gavage


title: 23-Tet1-0D-2


title: mt-0_r3y_ln


title: Lung, Heliotrine 3.3 mg/kg/bw_animal 2


title: akita_r3y_ln


title: D10 CD34+CD41+CD9- SR1- cells, Rep3

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT6


title: 23-NC-6D-3


title: D10 CD34+CD41+CD9- SR1+ cells, Rep2

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL14

value: CNSL


title: mr-0_r3y_ln


title: D10 CD34+CD41+CD9- SR1- cells, Rep2

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT5


title: 23-NC-6D-2


title: 23-NC-6D-1


title: Lung, Heliotrine 3.3 mg/kg/bw_animal 4


title: Lung, Echimidine 3.3 mg/kg/bw_animal 3

value: Echimidine


title: Lung, Heliotrine 3.3 mg/kg/bw_animal 1


title: mh-1_r3y_ln


title: D10 CD34+CD41+CD9- SR1- cells, Rep1

description:
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
VNDT4


title: 23-NC-4D-3


title: kn-0_r3y_ln


title: D7 CD34+CD41+ cells, SR1+, Rep3

description:
D0-D7 processed data.txt
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL6


title: ge-0_r3y_ln


title: 23-NC-4D-2


title: D7 CD34+CD41+ cells, SR1+, Rep2

description:
D0-D7 processed data.txt
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL5


title: Lung, Echimidine 3.3 mg/kg/bw_animal 2


title: edi-0_r3y_ln

description: processed data file: NutriNet.Arabidopsis-veg-young.featureCounts.txt


title: 23-Tet1-0D-1


title: 23-NC-4D-1


title: D7 CD34+CD41+ cells, SR1+, Rep1

description:
D0-D7 processed data.txt
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL4


title: Lung, Echimidine 3.3 mg/kg/bw_animal 1


title: Lung, Vehicle 0.15 NaCl_animal 4

description: gene expression data of lung of vehicle treated rats

value: Control


title: 23-CATA-4D-2


title: ct-1_r2y_ln


title: 23-NC-2D-3


title: D7 CD34+CD41+ cells, SR1-, Rep3

description:
D0-D7 processed data.txt
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL3


title: col-0_r2y_ln


title: Lung, Vehicle 0.15 NaCl_animal 3

value: lung


title: D7 CD34+CD41+ cells, SR1-, Rep2

description:
D0-D7 processed data.txt
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL2


title: 23-NC-2D-2


title: tsu-0_r2y_hn

value: High nitrogen


title: 23-NC-2D-1


title: D7 CD34+CD41+ cells, SR1-, Rep1

description:
D0-D7 processed data.txt
D7-D14 processed data.txt
D0-D14 Raw gene counts.txt
CNSL1


title: Lung, Vehicle 0.15 NaCl_animal 5

value: Fisher 344


title: D0 CD34+ cells Rep3

description:
D0-D7 processed data.txt
D0-D14 Raw gene counts.txt
VNDT24


title: st-0_r2y_hn


title: stw-0_r2y_hn


title: 23-NC-0D-3


title: 23-NC-0D-2


title: shahdara_r2y_hn

value: Shahdara


title: 23-NC-0D-1


title: D0 CD34+ cells Rep1

description:
D0-D7 processed data.txt
D0-D14 Raw gene counts.txt
VNDT22


title: Tet1-KO-6D-3


title: oy-0_r2y_hn

value: Fully-grown adult leaf


title: treated

first: George

last: Weiner

state: IA

address: 200 Hawkins Dr

institute: University of Iowa

description:
CMP-001 plus anti-Qbeta treated PBMCs
single cell RNA-seq

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build hg38 (v3.0.0) with CellRanger (v3.0.1) using the CellRanger default human GTF.
Cells were filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 300 (to remove cells with poor read quality) or greater than 4000 (to remove cells likely to be doublets) were removed. Cells with greater than 25% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: PercentageFeatureSet(untreated, pattern = "^MT-")
For each library, reads were normalized with the Seurat (v3.0.2) NormalizeData function, and variable features were found with the following commands:  untreated <- NormalizeData(untreated, normalization.method = "LogNormalize", scale.factor = 10000); untreated <- FindVariableFeatures(untreated, selection.method = "vst", nfeatures = 2000)
Integration anchors from the first 20 dimensions of the canonical correlation analysis were used to integrate data with the following commands: PBMC.anchors <- FindIntegrationAnchors(object.list = c(untreated, CMPpos), dims=1:20); PBMC.combined <- IntegrateData(anchorset = PBMC.anchors, dims = 1:20)
Data scaling, principal component analysis, and clustering were performed with the following commands: PBMC.combined <- ScaleData(PBMC.combined, verbose = FALSE); PBMC.combined <- RunPCA(PBMC.combined, npcs = 30, verbose = FALSE); PBMC.combined <- RunUMAP(PBMC.combined, reduction = "pca", dims = 1:19); PBMC.combined <- FindNeighbors(PBMC.combined, reduction = "pca", dims = 1:19); PBMC.combined <- FindClusters(PBMC.combined, resolution = 0.5)
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Processed expression data matrix files are provided in comma-separated format for count (raw_counts_*.csv) and processed/normalized (normalized_expression_*.csv) expression values. For processed/normalized files, log-normalized expression values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values. For count files, raw counts were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated using a ficol gradient.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: diagnosis

value: healthy

value: adult

value: peripheral blood mononuclear cells (PBMCs)

value: anti-Qbeta coated CMP-001


title: Tet1-KO-6D-2


title: GSC90-Ctrl replicate 3

city: Orsay

first: Giorgio

last: Seano

address: Centre Universitaire, Bâtiment 110

institute: Institut Curie

description: Glioblastoma tumor cells trasduced with non-targeting shRNA construct

data_processing:
Basecalling performed using Illumina 6000 sequencing system (RTA3, Real-Time Analysis software)
rRNA contamination was cleaned by aligning the sequencing reads on the rRNA Human complete reference (U13369.1)
Remaining reads were aligned on the Human genome reference (hg19) using STAR (v2.5.3a) and the gencode annotation database (v19) with the following parameters (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMprimaryFlag OneBestScore --outMultimapperOrder Random)
Using STAR with the option --quantMode GeneCounts, the raw gene counts tables were generated
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (.csv)

source_name: Glioblastoma stem-like cells (GSC)

growth_protocol: Glioblastoma stem cells were cultured and maintained in FBS-free media supplemented with EGF 20 ng/ml (PrepoTech) and bFGF 10 ng/ml (PrepoTech).

extract_protocol:
Total RNA was extracted from cells using TRIsure (Bioline) and treated with DNase I RNase-free (Thermo Scientific).
700ng of total RNA were used to prepare RNA sequencing libraries, using the Illumina TruSeq Stranded mRNA Library preparation kit. Sequencing was carried out using 2x100 cycles (paired-end reads of 100 nucleotides each) on an Illumina NovaSeq 6000 system (S1 flow cells).

treatment_protocol: GSCs were treated with short hairpin (sh)RNA delivered via lentiviral vectors. Non-targeting shRNA construct (shCTRL; source clone ID: RHS4348) and shITGA6 plasmid mapping against ITGA6 exon 15 (target sequence: AGGATATTGCTTTAGAAAT; source clone ID: V3LHS_326014)

value: Mesenchymal GSC

value: short-hairpin RNA - Control


title: GSC90-Ctrl replicate 1


title: GSC90-shITGA6 replicate 2

description: Glioblastoma tumor cells trasduced with shRNA against integrin alpha6 expression

value: short-hairpin RNA - integrin alpha 6


title: GSC90-Ctrl replicate 2


title: GSC90-shITGA6 replicate 3


title: GSC90-shITGA6 replicate 1


title: PBMCs, G10

first: Michael

middle: S

last: Chimenti

address: 431 Newton Road

department: Iowa Institute of Human Genetics

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build GRCh38 (v3.0.0) with CellRanger (v3.0.1) using the CellRanger default human GTF.  All four demultiplexed sample pairs (20201120000, 202011200001, etc...) for a given sample were input for each individual CellRanger run with the "--sample" flag (e.g, --sample=CMPplusantiQbserum_20201120000,CMPplusantiQbserum_20201120001,CMPplusantiQbserum_20201120002,CMPplusantiQbserum_20201120003)
Cells were filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 300 (to remove cells with poor read quality) or greater than 4000 (to remove cells likely to be doublets) were removed. Cells with greater than 25% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: PercentageFeatureSet(untreated, pattern = "^MT-")
For each library, reads were normalized with the Seurat (v3.0.2) NormalizeData function, and variable features were found with the following commands:   untreated <- NormalizeData(untreated, normalization.method = "LogNormalize", scale.factor = 10000); untreated <- FindVariableFeatures(untreated, selection.method = "vst", nfeatures = 2000)
Integration anchors from the first 20 dimensions of the canonical correlation analysis were used to integrate data with the following commands:  PBMC.anchors <- FindIntegrationAnchors(object.list = c(untreated, CMPpos), dims=1:20); PBMC.combined <- IntegrateData(anchorset = PBMC.anchors, dims = 1:20)
Data scaling, principal component analysis, and clustering were performed with the following commands:  PBMC.combined <- ScaleData(PBMC.combined, verbose = FALSE); PBMC.combined <- RunPCA(PBMC.combined, npcs = 30, verbose = FALSE); PBMC.combined <- RunUMAP(PBMC.combined, reduction = "pca", dims = 1:19); PBMC.combined <- FindNeighbors(PBMC.combined, reduction = "pca", dims = 1:19); PBMC.combined <- FindClusters(PBMC.combined, resolution = 0.5)
Genome_build: hg38
Supplementary_files_format_and_content: Processed expression data matrix files are provided as filtered feature-barcode matrices in h5 format

source_name: G10 treated PBMCs

extract_protocol:
PBMCs were isolated using a ficol gradient
RNA libraries were prepared for sequencing using standard Illumina protocols
single cell RNA-seq

tag: age

value: peripheral blood mononuclear cells


title: bur-0_r2y_ln

value: 6 weeks

value: Low nitrogen


title: untreated

description:
Untreated PBMCs
single cell RNA-seq

value: untreated


title: PBMCs, CMP-001 + anti-Qbeta

source_name: CMP-001 plus anti-Qbeta treated PBMCs

value: CMP-001 plus anti-Qbeta


title: Lung, Vehicle 0.15 NaCl_animal 2

value: male

value: lung

value: Control

value: mg/kg bw/day

value: oral gavage


title: Lung, Echimidine 3.3 mg/kg/bw_animal 4

description: gene expression data of lung of PA treated rats

value: Fisher 344

value: Echimidine


title: D0 CD34+ cells Rep2

description:
D0-D7 processed data.txt
D0-D14 Raw gene counts.txt
VNDT23

value: VNDT


title: mt-0_r2y_hn

value: Fully-grown adult leaf

value: High nitrogen


title: SW620 CDX101 cell line RNA-seq replicate 1

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

data_processing:
FASTQ files were trimmed to remove adapters and low-quality bases with TrimGalore v0.4.3
The trimmed reads were aligned to the human and mouse reference genomes (builds hg19 and mm10, respectively) with STAR aligner v.2.7 with two mismatches allowed
Differential gene expression analysis was done with DESeq2 R Bioconductor package (v.1.22), using read counts data provided by the aligner
Genes were considered differentially expressed if the adjusted P-value, calculated using Benjamini-Hochberg method was less than 0.01.
We further filtered significantly differentially expressed gene sets to select for genes expressed at high levels using 2-fold change in absolute expression levels for both human and mouse datasets.
Genome_build: hg19 for human and mm10 for mouse
Supplementary_files_format_and_content: raw counts

source_name: SW620 stable cells

growth_protocol: SW620 and CT26 cell lines were grown in high glucose Dulbecco’s modified Eagle medium supplemented with 10% (v/v) FBS and 1% penicillin/streptomycin.

extract_protocol:
total RNA was extracted using Promega ReliaPrep™ RNA Cell Miniprep System
cDNA libraries were made using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina. SW620 RNAseq was perfomed with Illumina HiSeqTM4000. CT26 and Colon26 RNAseq were perfomed with  BGISeq500.

treatment_protocol: HDAC inhibition was induced with 1uM and 2.7uM CXD101 for 72h in SW620 and CT26 cells, respectvely. Treatment of mouse Colon26 syngeneic  model was conducted with 50mg/kg of CXD101 for 14 days (schema: 5 days on/2 days off).

value: Colorectal carcinoma

tag: cell line

tag: conditions

value: HDAC inhibitor treatment:1uM, 72h


title: Tet1-KO-4D-3

tag: time point


title: Tet1-KO-4D-2

tag: cell type


title: PBMCs, mCMP-001 + anti-Qbeta

source_name: mCMP-001 plus anti-Qbeta treated PBMCs

value: adult

value: peripheral blood mononuclear cells

value: mCMP-001 plus anti-Qbeta


title: SW620 cell line RNA-seq replicate 3

description: WTDMSOC

value: no treatment


title: sakata_r2y_hn

tag: tissue

value: 6 weeks

value: Sakata


title: mr-0_r2y_hn


title: PBMCs, untreated

source_name: untreated PBMCs

value: untreated


title: Tet1-KO-4D-1


title: Tet1-KO-6D-1


title: SW620 cell line RNA-seq replicate 2

description: WTDMSOB


title: Sample_R18019066LR01-87-3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome (hg38) using the CLC Biomedical Genomics Workbench 4 (QIAGEN Bioinformatics).
The read numbers mapped of each gene was counted and Reads Per Kilobase of exon model per Million mapped reads,(RPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene by using the CLC Biomedical Genomics Workbench 4 (QIAGEN Bioinformatics).
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

extract_protocol:
Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions.
The construction of RNA-seq library was based on the protocol of the IlluminaTruSeq RNA Sample Preparation Kit (illumina)

value: bladder cancer

value: overexpression U11


title: SW620 CXD101 cell line RNA-seq replicate 2


title: Sample_R18019065LR01-86-3


title: Tet1-KO-2D-1


title: Tet1-KO-2D-2


title: Sample_R18019064LR01-79-3


title: kn-0_r2y_hn


title: SW620 cell line RNA-seq replicate 1

description: WTDMSOA


title: DRGG_NPC-2

city: montreal

first: stephane

last: Richard

state: Quebec

address: 3755 Cote ste catherine, LDI Room 420

country: Canada

institute: McGill

description: Gene_expression.xlsx; Alternative_splicing.xlsx

data_processing:
Samples were demultiplexed using bcl2fastq v2.20 Conversion Software
Illumina adapter sequences were first removed from the paired-end reads of length 101 through the Trimmomatic v0.39
The reads were then aligned to the human genome (hg19/GRCh37) with STAR v2.7.1a
Gene expression was quantified for all samples through HOMER v4.11.1, employing Gencode v19 gene annotations employing Gencode v19 gene annotations
DESeq2 v1.26.0 was used afterward to normalize the read counts through the regularized logarithm (rlog) transformation and to compute their differential expression relative to the control.
Genome_build: hg19
Supplementary_files_format_and_content: Excel data table including the raw gene counts and FPKM for each sample
Supplementary_files_format_and_content: Excel data table including the alternative splicing events

source_name: Neural progenitor cells

growth_protocol: hiPSCs were cultured under feeder-free condition in TeSR-E8 medium (05990, Stem cell technologies). Neuronal induction was performed using STEMdiff SMADi Neuronal Induction Kit (08581, Stem cell technologies).

extract_protocol:
iPSC and NPC RNA samples were purified using GenElute™ Mammalian Total RNA Miniprep Kit (RTN70, Sigma Aldrich).
RNA sequencing libraries were generated using TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina, San Diego, CA).

value: iPS-derived neural progenitor cells

tag: mutation

value: RBMX-RGG motif deletion


title: Sample_R18019063LR01-T24-4

first: Zhenxing

last: Wang

address: Zhongshan Street


title: n13_r2y_hn


title: ct-1_r2y_hn


title: Tet1-KO-2D-3


title: Tet1-KO-0D-3


title: Sample_R17018070LR01_T24P3


title: Tet1-KO-0D-2


title: DRGG_NPC-1


title: edi-0_r2y_hn


title: Sample_R17018069LR01_79-1


title: col-0_r2y_hn


title: Tet1-KO-0D-1


title: Sample_R17018068LR01_87-1


title: mh-1_r2y_hn


title: DRGG_NPC-3


title: ge-0_r2y_hn


title: WT 6D-3

value: WT


title: bur-0_r2y_hn


title: CTRL_NPC-1

value: wide type


title: Sample_R17018067LR01_86-1


title: WT 6D-2


title: bi-1_r2y_ln

value: Fully-grown adult leaf

value: Low nitrogen


title: Sample_R18051120LR01-U2

value: knockout U11


title: WT 6D-1


title: Sample_R18051119LR01-T2


title: DRGG_iPS-3

source_name: induced pluripotent stem cells

value: iPS


title: akita_r2y_hn

source_name: Leaf

value: Akita

value: High nitrogen


title: bi-1_r2y_hn


title: WT 4D-3


title: DRGG_iPS-1


title: WT 4D-2


title: tsu-0_r2y_ln


title: Sample_R18051118LR01-U1


title: CTRL_iPS-3


title: Sample_R18051117LR01-T1


title: CTRL_NPC-2


title: WT 4D-1


title: stw-0_r2y_ln


title: CTRL_iPS-2


title: PEL5-LN RNase R-treated RNA

city: Baltimore

first: Myong-Hee

last: Sung

address: 251 Bayview Boulevard, Room 06C226

department: National Institute on Aging

institute: NIH

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 and NC_09333 (Human Herpes virus 8) using STAR with parameters --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 20 --chimMultimapNmax 10 --chimOutType Junctions
Chimeric.out.junction file was used to detect circular RNAs using CIRCexplorer2 parse.
Supplementary_files_format_and_content: bed

source_name: lymph node

extract_protocol:
Tissue was homogenized and total RNA was extracted by RNAeasy kit.
Truseq Stranded RNA prep kit RS-122-2201

tag: infection status

value: KSHV positive patient


title: st-0_r2y_ln

tag: treatment


title: WT 2D-3

tag: genotype


title: CTRL_iPS-1


title: WT 2D-2


title: DRGG_iPS-2


title: shahdara_r2y_ln

value: Shahdara


title: H838_cont

city: Cheongju-si

first: Wanyeon

last: Kim

state: Chungbuk

address: Taeseongtabyeonro 250, Gangnaemyeon, Heungdeokgu

department: Biology Education

country: South Korea

institute: Korea National University of Education

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to hg19 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 1.3.4b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: NSCLC(adenocarcinoma) cells

growth_protocol: Cells were cultured in RPMI-1640 (HyClone) with 10% FBS (HyClone), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco) at 37℃, 5% CO2.

extract_protocol:
48 hours after transient transfection, total RNA was isolated from cells using TRIzol (Invitrogen). RNA qualities and concentrations were assessed using OD 260/280 ratios using a Nanodrop 2000 (Thermo Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transiently transfected with a plasmid containing a full-length LINC00472 construct (pCDH-LINC00472, H838_LINC00472) and a control plasmid (pCDH empty vector, H838_cont) using Lipofectamine 2000 (Invitrogen).

value: NSCLC(adenocarcinoma) cells


title: H838_LINC00472


title: c-Myc activated input replicate 2

city: London

first: Cosetta

last: Bertoli

address: Gower Street

department: MRC Laboratory Molecular Cell Biology

institute: University College London

description: 4OH-Tamoxifen induced RPE1 hTERT c-Myc ER

data_processing:
The nf-core/chipseq pipeline (version 1.0.0; https://doi.org/10.5281/zenodo.3240507; Ewels et al., 2020) written in the Nextflow domain specific language (version 0.32.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Singularity (version 2.6.0; Kurtzer et al., 2017).
The command used was "nextflow run nf-core/chipseq --design design.csv --genome hg19 --singleEnd --narrowPeak --min_reps_consensus 2 -profile crick -r 1.0.0".
All data was processed relative to the human UCSC hg19 genome (Karolchik et al., 2004) downloaded from AWS iGenomes (https://github.com/ewels/AWS-iGenomes). Gene annotation files in GTF format were originally downloaded from UCSC on July 17th 2015.
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations, please see the pipeline homepage (https://github.com/nf-core/chipseq).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Normalised genome-wide bedGraph files were generated from the filtered alignments using the genomeCoverageBed command from BEDTools (version 2.27.1) (Quinlan & Hall, 2010) with parameters "-bg -fs 200 -scale <NORM_FACTOR>". Normalisation factors were generated by scaling the number of mapped reads to 1 million. bedGraph files were converted to bigWig using the bedGraphToBigWig binary available from the UCSC (version 20161115) (Kent et al., 2010).
Supplementary_files_format_and_content: MACS2 narrowPeak files generated using the pipeline command defined above.

source_name: RPE1 hTERT c-Myc ER

growth_protocol: Cells were cultured in growth medium in 15 cm dishes for 48 hr with or without the addition of 4OH-T.

extract_protocol:
The samples were washed twice in PBS and resuspended in cold ChIP buffer (25 mM Tris/HCl pH 8, 2 mM EDTA, 150 mM NaCl, 1% Triton, 0.1% SDS) plus protease inhibitor cocktail (Sigma P8340). The chromatin was sheared with a Bioruptor for 30”on/30”off for 30 minutes using Diagenode tubes.
The DNA library for sequencing was prepared using 2 ng of ChIP’ed DNA for the Kapa Hyper Prep kit according to the manufacturer instructions. QC was performed using the ThermoFisher Qubit and either the Agilent BioAnalyser or TapeStation. The DNA samples were normalised and prepared into Illumina compatible libraries using the KAPA HyperPrep kit according to the manufacturer’s instructions. The libraries were pooled to 4 nM and sequencing was performed on the HiSeq 4000 with at least 75bp reads.

treatment_protocol: Cells were then washed with 1x PBS and crosslinked in 10 ml of 1% formaldehyde at RT for 10 min. Quenching was carried out adding 1 ml of 1.25M glycine for 10 min at RT.

value: RPE1 hTERT c-Myc ER

value: 4OH-Tamoxifen induced

tag: timepoint

tag: chip antibody


title: WT 2D-1