title: E110 MGE, bio rep 1


title: E110 M1C, bio rep 1

status: Public on Oct 13 2023

type: SRA

city: New haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar street

department: Neuroscience

country: USA

institute: Yale University

description:
Mac_dev_column_cell_meta.tsv.gz
Mac_dev_row_genes.tsv.gz
Mac_dev_counts.mtx.gz

library_source: transcriptomic single cell

data_processing:
CellRanger was used for read alignment, barcode and UMI counting.
Seurat, fastMNN, and Harmony were used for batch correction.
Seurat were used for dimension reduction and clustering.
Assembly: Mmul10
Supplementary files format and content: tsv, tab-separated txt file containing gene names or cell metadata
Supplementary files format and content: mtx, sparse matrix file containing the raw UMI count data

molecule: total RNA

organism: Macaca mulatta

source_name: fetal brain

extract_protocol:
Fetal macaque brains were isolated from E37 to E110, put on a dish containing PBS and sectioned. Telencephalic regions were identified and dissected using a blade. For E37-43 brains, the entire anterior and medio-posterior parts of the hemispheres were cut. Each tissue was incubated with HBSS-Papain (2 mg/ml, BrainBits) from 15 (for the early ages) to 30 (for more advanced ages) minutes at 37oC. The solution was removed and the tissue gently triturated in HBSS-DNase I 0.1mg/ml solution (StemCells) using a 2 ml pipette. Then, samples were filtered through 30 µm strain filters and the cells counted with an automatic cell counter (ThermoFisher Scientific). Samples were diluted in HBSS to 1000 cells/microliter and processed for single cell RNA-seq analysis within 20 min at Yale Center for Genome Analysis (YCGA) core facility.
GEM Generation and Barcoding. Single cell suspension in RT Master Mix is loaded on the Single Cell A Chip and partition with a pool of about 750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). Each gel bead has primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 12 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence (30nt). Upon dissolution of the Gel Beads in a GEM, the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded, full-length cDNA from poly-adenylated mRNA.   Post GEM-RT Cleanup, cDNA Amplification and library construction. Silane magnetic beads are used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNA is then amplified by PCR to generate sufficient mass for library construction. Enzymatic Fragmentation and Size Selection are used to optimize the cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

tag: tissue

value: fetal brain

tag: genotype

value: WT

tag: age

tag: region

tag: Sex

value: Male


title: E110 ITC, bio rep 1

value: ITC


title: E110 LGE, bio rep 1

value: LGE


title: E110 IPC, bio rep 1

value: IPC


title: E110 DFC, bio rep 1

value: DFC


title: E110 CGE, bio rep 1

value: CGE


title: E37 Posterior, bio rep 1

value: Posterior

value: Female


title: E110 A1C, bio rep 1


title: E37 Ganglionic eminence, bio rep 1

value: Ganglionic eminence


title: E77 Occipital DIV17

library_source: transcriptomic

data_processing:
STAR for read alignment
featureCounts for read quantification
Assembly: Mmul10
Supplementary files format and content: tsv, tab-separated txt file containing gene expression or sample metadata

growth_protocol: E42 and E77 fetal rhesus macaque brains were isolated after caesarean section. Cortical areas were dissected and incubated with HBSS-Papain (2 mg/ml) -DNase I 0.1mg/ml solution 15 and 25 min, respectively, at 37oC. Neural stem cells (NSCs) were plated over 6 well culture plates (5x105 cells/well) precoated with PLO/fibronectin and incubated at 37oC, 5% O2, 5% CO2 for 5 days in DMEM/F12 medium + N2 supplement (N2 medium) containing 25 mg/ml bovine insulin, 100 mg/mL apotransferrin, 20 nM progesterone, 100 mM putrescine, 30 nM sodium selenite. FGF2 was added daily. Differentiation was induced by FGF2 withdrawal and switch to NeuroBasal medium added of B27, 10 ng/ml BDNF and 10 ng/ml NT-3 for 2 weeks, as previously described in (Micali et al., Cell Report 2020).

extract_protocol:
Total RNA was extracted from 2 different wells/condition using RNeasy Mini Kit (QIAGEN, 74104), according to manufacturer’s protocol.
Total RNA quality was determined by estimating the A260/A280 and A260/A230 ratios by nanodrop. RNA integrity was determined by running an Agilent Bioanalyzer gel.
mRNA was purified from approximately 200ng of total RNA with oligo-dT beads and sheared by incubation at 94C in  presence of Mg (Roche Kapa mRNA Hyper Prep Cat# KR1352).  Following first-strand synthesis with random primers, second strand synthesis and A-tailing were performed with dUTP for generating strand-specific sequencing libraries. Indexed libraries were quantified by qRT-PCR using a kit (Roch KAPA Biosystems Cat# KK4854) and insert size distribution determined by either the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/ul and a size distribution of 150-300bp were used for sequencing.

tag: cell type

value: fetal cortical neural stem cells

value: Occipital

tag: treatment

value: in vitro cultured cells


title: E77 Occipital DIV14


title: E37 Anterior, bio rep 1

value: Anterior


title: E77 Occipital DIV20


title: E110 PCC, bio rep 1

value: PCC


title: E77 Occipital DIV11


title: E77 Occipital DIV5


title: E77 Occipital DIV8


title: E77 Occipital DIV6


title: E77 Occipital DIV7


title: pancreatic_maternal glucose intorlerance_rep3

type: genomic

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

country: China

institute: Peking Union Medical College Hospital

hyb_protocol: Labeled DNA was hybridized to the Arraystar Mouse ReqSeq Promoter Array.

scan_protocol: Array was scanned with Agilent Scanner G2505C.

data_processing: After normalization, raw data was input into SignalMap Software to observe and evaluate the methylation peaks.

label: Cy 5

molecule: genomic DNA

organism: Mus musculus

source_name: MeDIP DNA from maternal glucose intorlerance

label_protocol: Immunoprecipitated methylated DNA was labeled with Cy5 fluorophere and the input genomic DNA was labeled with Cy3 fluorophere.

extract_protocol: Genomic DNA was extracted from pancreatic samples using Dneasy Blood & Tissue Kit.

value: pancreatic tissue

value: 12 week

tag: group

value: maternal glucose intorlerance

tag: molecule subtype

value: MeDIP DNA

label: Cy 3

source_name: input DNA from  maternal glucose intorlerance

value: input DNA


title: E110 Insula, bio rep 1

value: fetal brain

value: WT

value: Insula

value: Male


title: E77 Frontal DIV17

value: Frontal


title: E77 Frontal DIV14


title: E77 Frontal DIV11


title: E77 Frontal DIV8


title: E77 Occipital DIV1


title: E77 Frontal DIV5


title: E77 Frontal DIV7


title: E77 Frontal DIV20


title: E42 Posterior DIV7

value: Posterior


title: E77 Occipital DIV3


title: pancreatic_normal glucose torlerance_rep3

source_name: MeDIP DNA from normal glucose torlerance

value: maternal normal glucose torlerance

source_name: input DNA from normal glucose torlerance


title: E77 Frontal DIV1

value: fetal cortical neural stem cells


title: pancreatic_maternal glucose intorlerance_rep2


title: E42 Posterior DIV8


title: E42 Posterior DIV6


title: E42 Posterior DIV3


title: pancreatic_maternal glucose intorlerance_rep1


title: E42 Posterior DIV11


title: E42 Posterior DIV17


title: E42 Posterior DIV14


title: E42 Posterior DIV1


title: E42 Anterior DIV17


title: E42 Anterior DIV11


title: pancreatic_normal glucose torlerance_rep1


title: pancreatic_normal glucose torlerance_rep2


title: E42 Anterior DIV14


title: E42 Anterior DIV8


title: E42 Anterior DIV7


title: E42 Anterior DIV5


title: E42 Anterior DIV1


title: E42 Anterior DIV3


title: E42 Posterior DIV5


title: sebocytes, OE,24h,rep2

city: Nanjing

first: Ziyu

last: Wei

state: Jiangsu

address: Pujian Road 160, Shanghai

department: Genetic Skin Disease Center

institute: Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

organism: Homo sapiens

extract_protocol:
Total RNAs of human SZ95 sebocytes were extracted with TRIzol Reagent (Thermo Fisher Scientific). 0.2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: cell line

value: human sebaceous gland cells

value: TRPV3 overexpression


title: sebocytes, con,24h,rep2

value: Mock plamid transfection


title: sebocytes, con,24h,rep3


title: sebocytes, OE,24h,rep1


title: sebocytes, OE,24h,rep3


title: sebocytes, con,24h,rep1


title: RNAPII combo rep 1

city: Solna

first: Vladislav

last: Kuzin

state: Stockholm

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institute

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.19.0.316 for NextSeq 1000/2000 output.
ChIP-seq reads were trimmed using Cutadapt v2.10 using --nextseq-trim 25 option, discarding reads left with < 30 bp
ChIP-seq reads were aligned to the UCSC hg38 genome (or mm10 genome to determine spike-in factors) using Bowtie version 2.4.1 with default settings.
To create ChIP-seq average profiles, coverage matrices were generated from markduped bam files using ngs.plot.r v2.61. Spike-in normalisation of average profiles was performed by multiplying the total number of reads by a factor inversely proportional to Mouse spike-in unique deduplicated reads and an average of two normalised replicas was used for average profile visualisation with R default plot functions and ggplot2.
BigWig files were generated with bamCoverage from Deeptools v3.4.3 package with --scaleFactor option for spike-in normalization.
Assembly: hg38
Supplementary files format and content: spike-in normalized bigWig

source_name: Bo103, PDAC

growth_protocol: Cells were grown in a 1:1 mix of high glucose (4.5g/L) DMEM (Thermo, 61965059) and DMEM/F12 (Thermo, 11320033) containing 10% FBS (Thermo, 10270106), 1.6μg/ml amphotericin (Sigma, A2411), 10μM Y-27632 (Selleckchem, S1049), 6.2μg/ml ciprofloxacin (Sigma, 17850), 8.4ng/ml choleratoxin (Sigma, C8052), 500ng/mL insulin (Sigma, I9278) and 20nM 1-thioglycerol (Sigma, M6145), in a 37°C incubator supplied with 5% CO2.

extract_protocol:
Cells were crosslinked with 1% formaldehyde (Thermo Fisher, 28906) for 5 min. Cross-linking was stopped by the addition of glycine (125 mM) and cells were washed twice with cold PBS. After harvesting cells by scraping, the pellet was washed once with PBS plus 0.5% BSA and resuspended in RIPA buffer to a final concentration of 1x10^7 cells/ml. Samples were sonicated with a Bandelin probe sonicator to produce chromatin fragments of 400 bps on average.
DNA from ChIP was quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher, Q33230). Sequencing libraries were created according to the ThruPLEX DNA-seq kit protocol (Takara, R400676). Size selection was performed in the range of 200-700bp with AMPure XP beads (Beckman, A63880) and confirmed using the Agilent High Sensitivity DNA Kit (Agilent, 5067-4626) on the Agilent 2100 Bioanalyzer. Libraries were pooled and sequenced using the NextSeq 1000/2000 P2 Reagents (100 Cycles) v3 kit (Illumina, 20046811). The sequencing run was Single End and Dual Index with 115 bp reads.

treatment_protocol: Cells were treated (in biological duplicates for the sequencing assays) with DMSO (vehicle), 500 nM SN38, 1 µM JQ1 or their combination (SN38+JQ1) for 1 hour (TOP1) or 4 h (RNAPII).

value: Bo103, PDAC

value: Pancreatic tumor patient-derived cells

tag: chip antibody

value: RNAPII (Abcam, ab817)


title: RNAPII combo rep 2


title: RNAPII vehicle rep 2

value: DMSO


title: RNAPII SN38 rep 2


title: RNAPII SN38 rep 1


title: RNAPII JQ1 rep 2


title: RNAPII JQ1 rep 1


title: RNAPII vehicle rep 1


title: E42 Anterior DIV6

value: Anterior

value: in vitro cultured cells


title: AO_36_3

city: Kunming

first: xuewei

last: yang

address: Chenggong Campus,Yunnan University,Dongwaihuan South Road

institute: Yunnan University

description:
Expression analysis table include TPM values for each AO and Vps35 sample
Total difference statistics between WT and Vps35 mutants

data_processing:
The data from high-throughput sequencing were analyzed using the Majorbio tools, a free online platform for data analysis (www.majorbio.com).
Assembly: HiSat2 and StringTie
Supplementary files format and content: xls file includes tpm value for each sample

organism: Orbilia oligospora

growth_protocol: The wild-type and  mutant strains were cultured on potato dextrose agar (PDA) medium at 28°C.

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is 1.8 - 2.2, and OD260/230≥1.0.
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The WT, ΔAorab7A, and ΔAovps35 mutant strains were incubated on PDA plates with cellophane at 28°C for 3 days. Equal amounts of nematodes were added to the induction traps, and three independent biological replicates for each mycelial sample were collected at 0, 12, and 36 h.

value: Fungal hyphae cells

tag: strain

value: wild type

value: Trap induction with nematode

tag: time


title: AO_36_2


title: AO_12_3


title: AO_12_1


title: AO_12_2


title: AO_0_3

value: no treatment


title: AO_0_2


title: AO_0_1


title: Vps35_36_3

value: delta-Aovps35 mutant strain


title: Vps35_36_2


title: Vps35_36_1


title: Vps35_12_3


title: Vps35_0_3


title: Vps35_12_1


title: Vps35_0_2


title: WT_36_3

description:
Expression analysis table include TPM values for each WT and Rab7 sample
Total difference statistics between WT and Rab7 mutants


title: Vps35_0_1


title: AO_36_1


title: WT_36_2


title: WT_12_1


title: WT_0_2


title: Rab7_36_3

value: delta-Aorab7 mutant strain


title: WT_36_1


title: WT_0_3


title: WT_0_1


title: WT_12_3


title: Rab7_12_3


title: Rab7_36_2


title: WT_12_2


title: Rab7_12_2


title: Rab7_36_1


title: Rab7_12_1


title: Rab7_0_3


title: Rab7_0_2


title: Rab7_0_1


title: E93 VFC, bio rep 1

value: fetal brain

value: WT

value: VFC

value: Male


title: E93 V1C, bio rep 1


title: E93 STC, bio rep 1

value: STC


title: Vps35_12_2


title: E93 S1C, bio rep 1


title: E93 PCC, bio rep 1

value: PCC


title: E93 MGE, bio rep 1

value: MGE


title: E93 MFC, bio rep 1

value: MFC


title: E93 LGE, bio rep 1

value: LGE


title: E93 IPC, bio rep 1

value: IPC


title: E93 CGE, bio rep 1

value: CGE


title: E93 ITC, bio rep 1

value: ITC


title: E93 A1C, bio rep 1


title: E93 DFC, bio rep 1

value: DFC


title: E78 Occipital, bio rep 1

value: Occipital


title: E78 Frontal, bio rep 1

value: Frontal


title: E78 Ganglionic eminence, bio rep 1

value: Ganglionic eminence


title: E77 Temporal, bio rep 2

value: Temporal

value: Female


title: E93 M1C, bio rep 1

value: fetal brain

value: WT


title: E93 OFC, bio rep 1

value: OFC

value: Male


title: E77 Occipital, bio rep 2


title: E93 Insula, bio rep 1

value: Insula


title: E77 Motor-somatosensory, bio rep 2

value: Motor-somatosensory


title: E77 Ganglionic eminence, bio rep 2


title: E77 Motor-somatosensory, bio rep 1


title: E64 Temporal, bio rep 1


title: E64 Motor-somatosensory, bio rep 1


title: 3999997041_R05C01

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick

institute: Van Andel Institute

hyb_protocol: Infinium HumanMethylation450 BeadChip (HM450 array. We performed bisulfite conversion on 1 µg of genomic DNA from each sample using the EZ-96 DNA Methylation Kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions. We assessed the amount of bisulfite converted DNA and completeness of bisulfite conversion using a panel of MethyLight-based quality control (QC) reactions as previously described [45]. Bisulfite-converted DNA was whole genome amplified (WGA) and enzymatically fragmented prior to hybridization to the arrays.

scan_protocol: standard protocol

data_processing: IDATs were processed to a beta matrix with SeSAMe using defaults for the function 'openSesame'

label: Cy3, Cy5

source_name: Ovarian tumor

label_protocol: standard protocol

growth_protocol: Ovarian Carcinoma samples were selected from the UBC/VGH Gynecological Tissue Bank

extract_protocol: DNA and/or total RNA was extracted from frozen tissue sections (10-40 10um sections depending on tissue face size) using Qiagen QIAamp DNA or RNA blood and tissue kits (Qiagen) following manufacturers protocols.

value: Ovarian tumor

tag: histology

value: HGSC


title: E64 Frontal, bio rep 1


title: E62 Occipital, bio rep 1


title: E62 Temporal, bio rep 1


title: 3999997041_R01C02


title: 3999997016_R01C02


title: E77 Occipital, bio rep 1


title: E62 Ganglionic eminence, bio rep 1


title: 3999997040_R01C02


title: E77 Frontal DIV6

value: fetal cortical neural stem cells

value: in vitro cultured cells


title: 3999997050_R04C01


title: E64 Occipital, bio rep 1


title: 3999997054_R06C02


title: E54 Temporal, bio rep 1


title: 3999997054_R05C02


title: E54 Occipital, bio rep 1


title: E62 Frontal, bio rep 1


title: E54 Frontal, bio rep 1


title: 3999997040_R01C01


title: E43 Ganglionic eminence, bio rep 1


title: E54 Ganglionic eminence, bio rep 1


title: 3999997050_R06C02


title: 3999997054_R04C02


title: E43 Anterior, bio rep 1

value: Anterior


title: 3999997041_R01C01


title: E43 Posterior, bio rep 1

value: Posterior


title: 3999997016_R01C01


title: 3999997050_R05C02


title: E42 Posterior, bio rep 1


title: 3999997041_R02C01


title: E42 Dorsolateral, bio rep 1

value: Dorsolateral


title: E77 Frontal DIV3

value: Frontal


title: E64 Ganglionic eminence, bio rep 1

value: Ganglionic eminence


title: E42 Anterior, bio rep 1


title: 3999997041_R03C01


title: st17 control explants rep 3

city: Evanston

first: Paul

middle: Benjamin

last: Huber

state: Illinois

address: 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

data_processing: Deseq

organism: Xenopus laevis

source_name: animal pole explant

extract_protocol: none provided

value: animal pole explant

tag: Stage

value: epidermal

value: wild type

value: DMSO stage 9 to 17


title: st17 control explants rep 2


title: st17 K02288/CHIR explants rep 3

value: neural crest-reprogrammed

value: K02288/CHIR stage 9 to 17


title: st17 K02288/CHIR explants rep 2


title: 3999997041_R06C02


title: 3999997041_R05C02

value: CCOC


title: 3999997040_R05C02


title: st17 control explants rep 1


title: st17 K02288/CHIR explants rep 1


title: SynVIII Hi-C replicate 3

city: New York

first: Jitong

last: Cai

state: NY

address: 435 E 30th street

department: NYU Langone Health

institute: NYU Langone Health

description: SynVIII strain ySLL181

data_processing:
To generate contact maps: paired-end reads were processed using the HICLib algorithm (REF M. Imakaev et al 2012) adapted for the S. cerevisiae genome. Read-pairs were independently mapped using Bowtie 2 (Langmead and Salzberg 2012) (mode: --very-sensitive --rdg 500,3 --rfg 500,3) on the corresponding reference sequence (S288c and accordingly modified versions of it) indexed for MboI restriction site.
In the contact frequency maps, the unwanted restriction fragments (RFs) were filtered out (e.g., loops, non-digested fragments, etc.; for details see (Cournac et al. 2012), whereas, the valid RFs were binned into units of fixed size bins of 5 kb. Bins with a high variance in contact frequency (<1.5 S. D. or 1.5–2 S.D.) were discarded. To remove potential biases resulting from the uneven distribution of restriction sites and variation in GC% and mappability.
Note that in the case of CEN8 sequence duplication, at native (nCEN8) and ectopic (eCEN8) locations, the bins containing the centromere sequences were filtered out as they would be ambiguously mapped.
The filtered contact maps were normalized using the sequential component normalization procedure (SCN) REF Cournac et al. 2012.
Assembly: S288C
Supplementary files format and content: Hi-C contact maps for each replicate

organism: Saccharomyces cerevisiae

source_name: SynVIII

growth_protocol: Independent colonies of SynVIII strain were inoculated into 5 mL YPD medium and grown overnight at 30ºC. The following day 109 cells (approximately 80-100 OD) were subcultured into 100 mL YPD for 3 hours of growth at 30ºC.

extract_protocol:
The reverse cross linked sample was ethanol precipitated and purified using the large fragment DNA recovery kit (Zymo Research, D4046). Religated-biotinylated restriction fragments were pulled down using Dynabeads MyOne Streptavidin C1 magnetic beads (Invitrogen 65001) according to the manufacture protocol.
Purified Hi-C library was used as input material for Illumina sequencing library prep kit (NEB, E7805) with 6-cycle PCR amplification using KAPA-HiFi (Kapa Biosystems, KK2602).

treatment_protocol: Cells were crosslinked by 3% [v/v] formaldehyde for 20 min at room temperature and subsequently quenched with glycine 350 mM for 15 min at 4ºC in mild agitation. Crosslinked cells were harvested and suspended in 10 mL spheroplast solution (1M sorbitol, 50 mM potassium phosphate, 5 mM DTT, 250 U zymolyase 100T (US Biological, Z1004)) for 50 min incubation at 30ºC. Spheroplasts were washed with 10 mL of cold 1M sorbitol and resuspended in 2 mL of 0.5% SDS at 65ºC for 20 min. 125 U of MboI (NEB, R0147) were used for overnight digestion (16 hours) of the genomic DNA from fixed yeast cells resuspended in 3 mL final volume (1x Cutsmart NEBuffer, 0.33% SDS and 2% Triton) at 37ºC. The digestion product was centrifuged at 18000xg for 20 min and the pellet was subsequently suspended in 200 μL cold water. DNA sticky ends were filled with biotin-14-dCTP (Invitrogen, 19518018) by Klenow enzyme (NEB, M0210L) at 37ºC for 80 min. Biotinylated DNA was ligated with 60 U T4 ligase (Thermo Scientific, EL0014) in 1.2 mL final volume at room temperature for 2 hours in mild agitation. Ligation product was reverse cross-linked by 0.5 mg/mL proteinase K (Thermo Scientific, EO0492) in 0.5% SDS, 25 mM EDTA buffer at 65ºC for 4 hours.

tag: parental strain

value: SynVIII


title: SynVIII Hi-C replicate 2

description: SynVIII strain ySLL181


title: DG1029

data_processing:
Each raw sequencing file (FASTQ format) was aligned to the human reference genome (GRCh37) using STAR version 2.7, with default settings. Estimation of gene-level abundance was carried out using RSEM version 1.3.1.
In-house generated CCOC and ENOC RNA-seq data were combined with publicly available paired-end sequenced 84 HGSOC tumor samples, 20 normal endometrium, 4 normal epithelial brushings of ovarian surface, and 3 normal epithelial brushings of fallopian tube. Raw reads count output from RSEM were further batched-corrected using R package sva (function ComBat_seq), and normalized using Reads Per Kilobase of transcript, per Million mapped reads (RPKM) with library size scale factors estimated using R package edgeR.
Assembly: GRCh37
Supplementary files format and content: log2rpkm_N57.tsv contains log2 Reads Per Kilobase of transcript, per Million mapped reads (RPKM) for all samples.

molecule: polyA RNA

source_name: tumor

extract_protocol:
Total RNA was extracted from frozen tissue sections (10-40 10um sections depending on tissue face size) using Qiagen RNA blood and tissue kits following manufacturers protocols
cDNA libraries for 28 CCOC and 29 ENOC were prepared using strand‐specific RNA‐Seq Sample Preparation kit (stranded, polyA+) from Illumina.
Data was generated from paired‐end sequencing at Canada's Michael Smith Genome Sciences Centre on Illumina platforms (San Diego, CA, USA): HiSeq 2500 using V3 or V4 chemistry and paired‐end 125 base reads targeting 200 million paired‐end reads per sample.

value: tumor


title: 3999510072_R06C02

value: Ovarian tumor

value: ENOC


title: SynVIII Hi-C replicate 1

description: SynVIII strain ySLL181


title: DAH25

value: MT


title: 3999997016_R05C02

value: HGSC


title: DG1282

value: WT


title: DG1288


title: 3999997040_R06C02


title: 3999510072_R05C02


title: DAH147e


title: E77 Frontal, bio rep 1

value: fetal brain

value: Female


title: 3999510072_R05C01


title: 3999510072_R06C01


title: TOP1 combo rep 2

value: Bo103, PDAC

value: Pancreatic tumor patient-derived cells

value: TOP1 (Abcam, ab109374)


title: DG1039


title: TOP1 combo rep 1


title: DG1030


title: TOP1 SN38 rep 2


title: 3999510072_R03C02


title: DG1287


title: TOP1 SN38 rep 1


title: DG1293


title: 3999510072_R04C02


title: E54 Motor-somatosensory, bio rep 1

value: Motor-somatosensory


title: DG1290


title: 3999510072_R02C02


title: DG1294


title: DAH123


title: Erythroid_day_13_CD34+_don030_ATAC-seq_rep2

city: Oxford

first: Emily

last: Georgiades

address: John Radcliffe Hospital/Headley Way

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

description:
CD34, day 13, don030, rep2
Don030_ATAC_d13.hg38.bw

data_processing:
genome build/assembly: hg38
All data was processed using the CATCH-up pipeline (https://github.com/Hughes-Genome-Group/UpStreamPipeline/tree/main/genetics/catch-up)
aligner_algorithm: bowtie2 (bowtie2 v2.4.5)
samtools_sort_extra: -m 4G (samtools v1.15.1)
filtering_extra: -bShuF 4 -f 3 -q 30  (samtools v1.15.1)
bam_coverage: --binSize 1 --normalizeUsingRPKM --extendReads (deepTools v3.5.1)
Supplementary files format and content: bigwig

source_name: Erythroid

growth_protocol: CD34+ cells were isolated from fresh blood as previously described (Truch, 2022) and subject to a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017).

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013). 75,000 cells were used per biological replicate.
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems). Samples were sequenced using 40 bp paired end reads (NextSeq platform).

tag: donor id

value: Erythroid

tag: origin cell_line

value: CD34+ human erythroid

tag: differentiation day

value: Day 13

tag: selection antibody

value: CD34 microbead, Miltenyi Biotec #130-046-702


title: Erythroid_day_13_CD34+_don030_ATAC-seq_rep1

description: CD34, day 13, don030, rep1


title: TOP1 vehicle rep 2

value: DMSO


title: 3999510072_R02C01

tag: tissue


title: DAH48

value: tumor

value: CCOC


title: TOP1 vehicle rep 1


title: 3999510072_R01C01

value: Ovarian tumor


title: DAH248

value: MT


title: 9769100063_R06C02


title: 3999510072_R01C02

value: ENOC


title: 3999510072_R03C01

value: HGSC


title: E42 Ganglionic eminence, bio rep 1

value: fetal brain

tag: genotype

value: WT

tag: age

tag: region

value: Ganglionic eminence

tag: Sex

value: Male


title: Erythroid_day_13_CD34+_don001_ATAC-seq_rep2

description:
CD34, day 13, don001, rep2
Don001_ATAC_d13.hg38.bw

tag: cell type


title: DG1285


title: DG1284


title: Erythroid_day_13_CD34+_don001_ATAC-seq_rep1

description: CD34, day 13, don001, rep1


title: CD34, day 13, Don002, RAD21

description: Erythroid_day_13_CD34+_don002_RAD21_ChIP-seq

extract_protocol:
Cells were grown, treated and processed as described in the Methods section of the paper.
The NEBNext Ultra II DNA Library Prep Kit (New England Biolabs: NEB: 7645S/L) was used to prepare indexed sequencing libraries following the manufacturer supplied protocol. PCR amplification was performed for 7-11 cycles (depending on input DNA concentration) using NEBNext Mulitplex Oligos (New England Biolabs: E7335S/L and E7500S/L). Indexed sample concentration was quantified using the KAPA Library Quantification Complete Kit (Universal)(Roche: KK4824). Samples were pooled as a 2 nM or 4 nM library and sequenced with a high-Output v2 75 cycle kits on the Illumina NextSeq 500 platform.

value: E14TG2a.IV mouse ES cells

value: Day 7

tag: antibody

tag: antibody lot_#


title: DG1193


title: DG1281


title: 9769100063_R05C01


title: CD34, day 13, Don030, RAD21

description: Erythroid_day_13_CD34+_don030_RAD21_ChIP-seq

growth_protocol: Cells were grown, treated and processed as described in the Methods section of the paper.

value: Erythroid

tag: strain


title: DAH46


title: 9769100063_R05C02


title: DG1289


title: 9769100063_R04C01


title: CD34, day 13, Don001, RAD21

description: Erythroid_day_13_CD34+_don001_RAD21_ChIP-seq

treatment_protocol: Cells were grown, treated and processed as described in the Methods section of the paper.


title: CD34, day 13, Don030, H3K4me3

description: Erythroid_day_13_CD34+_don030_H3K4me3_ChIP-seq

value: CD34+ human erythroid

value: Merck Millipore, 07-473


title: 9769100063_R06C01


title: 9769100063_R04C02


title: 9769100063_R03C02


title: Erythroid_day_13_CD34+_don002_ATAC-seq_rep1

description: CD34, day 13, don002, rep1

value: Day 13

value: CD34 microbead, Miltenyi Biotec #130-046-702


title: CD34, day 13, Don002, H3K4me3

description: Erythroid_day_13_CD34+_don002_H3K4me3_ChIP-seq


title: DG1283

value: tumor


title: DAH369

value: CCOC


title: 9769100063_R02C02

value: Ovarian tumor


title: 9769100063_R02C01


title: 9769100063_R03C01


title: DG1286


title: CD34, day 13, Don030, H3K4me1

description: Erythroid_day_13_CD34+_don030_H3K4me1_ChIP-seq

value: abcam, ab195391


title: DG1184

value: MT


title: Erythroid_day_13_CD34+_don002_ATAC-seq_rep2

description:
CD34, day 13, don002, rep2
Don002_ATAC_d13.hg38.bw


title: 9769100063_R01C02


title: DG1189


title: CD34, day 13, Don002, H3K27Ac

description: Erythroid_day_13_CD34+_don002_H3K27Ac_ChIP-seq

value: abcam, ab4729


title: DAH250


title: 9769100063_R01C01

value: HGSC


title: 9769100054_R06C02


title: CD34, day 13, Don001, H3K4me3

description: Erythroid_day_13_CD34+_don001_H3K4me3_ChIP-seq


title: CD34, day 13, Don002, H3K4me1

description: Erythroid_day_13_CD34+_don002_H3K4me1_ChIP-seq


title: DAH145


title: 9769100054_R05C02


title: CD34, day 13, Don001, H3K27Ac

description: Erythroid_day_13_CD34+_don001_H3K27Ac_ChIP-seq


title: CD34, day 13, Don001, H3K4me1

description: Erythroid_day_13_CD34+_don001_H3K4me1_ChIP-seq


title: DG1182

value: WT


title: 9769100054_R06C01


title: 9769100054_R05C01


title: CD34, day 13, Don030, CTCF

description: Erythroid_day_13_CD34+_don030_CTCF_ChIP-seq

value: Merck Millipore, 07-729


title: 9769100054_R04C02


title: DG1038


title: CD34, day 13, Don002, CTCF

description: Erythroid_day_13_CD34+_don002_CTCF_ChIP-seq


title: DG1292

value: ENOC


title: HDR CC 3 GL2 - Rep 4 gfp -

city: Columbus

first: Jeffrey

last: Parvin

state: OH

address: 460 West 12th Ave

department: Department of Biomedical Informatics

institute: The Ohio State University

description:
CC3_barcodes_reverse_exp119_finalized.h5
CC3_single_subs_withWT_barcodeAssignment.tsv

data_processing:
For coiled-coil domain of BRCA1, the FASTQ files containing barcode variants and a barcode map were processed using Enrich2 software. Enrich2 calculates the functional score for each variant from its abundance in the GFP-positive and GFP-negative pools. The functional score is obtained by normalizing the slope of the line connecting the control and experimental conditions for each pool by the wild-type adjusted by log ratio. The functional score was reported in log2 for each variant tested with a value of 0 representing normal wild-type function.
The process of interpreting variant scores involved two steps. First, two subpopulations of variants containing synonymous and nonsense changes were identified and analyzed in a scatter plot to display the relationship between the variant read count and their functional scores for each subpopulation. Under control conditions, the endogenous BRCA1 present in every cell functioned normally and was used as a baseline for the DNA damage repair assay. Thus, it was anticipated that all variant scores in this condition would cluster around 0 on the scatter plot. The minimum-read count threshold was determined to be the highest point where the results for any variant deviated from this functionally normal value. To confirm this threshold, using the scatter plot from the conditions in which the endogenous BRCA1 was depleted by transfecting siBRCA1-3’UTR, nonsense variants were expected to exhibit negative functional scores indicative of loss of function, and the read-count threshold would be higher than any nonsense mutants that scored as functionally normal. If the read count values from the conditions were different, we selected the higher threshold. Data with lower read counts than this empirically defined value were discarded. To further refine the data, the mean variance across four replicates was calculated, and variants with variance greater than 1 were removed from the analysis. These two filters removed variants with low frequency of read counts and high variability of results. The remaining variants have high frequency of datapoints that were relatively consistent in score, and we used these to evaluate functional effects of the amino acid change for each variant.
After applying the minimum reads-count threshold, a histogram was generated to visualize the distribution of the variant library (Figure S1, bottom right). Three subpopulations, missense, nonsense, and synonymous, were analyzed separately for each condition. To determine the functional score thresholds, the population of missense variants in the control siRNA experimental condition was modeled as a Gaussian distribution, and the lowest 1% of values were selected as the threshold for loss of function. Similarly, using the distribution plot for the BRCA1 siRNA condition, the population of nonsense variants were modeled as a Gaussian distribution and the highest 1% was defined as functionally normal. Only variants that were observed in at least three replicates were included in the analysis.
Assembly: genome_build.txt
Supplementary files format and content: .h5 files with counts and scores. Columns names are descriptive, _- denotes noGFP, _+ denotes GFP samples.

source_name: HeLa Cells

growth_protocol: DMEM supplemented with 10% fetal bovine serum and hygromycin B at 550 ¬µg/mL.

extract_protocol:
Inverse PCR reactions of the plasmid encoding the BRCA1 cDNA generate full length product, but one of the codons in the PCR oligonucleotide contains NNK (where N = A, C, G, T and K = G, T) in place of the terminal codon encoded by the oligonucleotide. For the 97 codons analyzed in this study, 97 different inverted oligonucleotide pairs were separately prepared and subjected to PCR. The PCR reactions were then pooled and circularized by the action of DNA ligase. An oligonucleotide containing a 16 bp degenerate oligonucleotide barcode was inserted upstream of the BRCA1 coding sequence, and long-read sequencing using a PacBio Sequel paired each barcode with a different BRCA1 variant. The plasmid library for pools 3 was transfected along with the FLP-In recombinase into a HeLa derived cell line that contained in its genome a single FLP-In Recombinase Target (FRT) sequence  and a single DNA sequence for measuring homology directed repair (HDR) of DNA double-strand breaks.
The HDR assay is initiated by transfecting a plasmid encoding the I-SceI endonuclease, which generates a DNA cut in one of the defective GFP sequences, and if the cell is competent for HDR, recombination repairs the defective GFP coding sequence, and the cell becomes GFP-positive. We performed this HDR assay under two conditions. In the first condition, we have transfected a control siRNA, and the cells contain endogenously expressed wild-type BRCA1. In the second condition, we have transfected an siRNA targeting the 3’-UTR of the endogenously expressed BRCA1 mRNA, and the cell is then dependent on the BRCA1 variant expressed from the FRT site. GFP-positive cells were separated from GFP-negative cells using flow sorting, and the barcode in the genome of the cells was isolated by PCR and analyzed by short read sequencing. The frequency of the barcode in the GFP-positive cells (functional for HDR) is compared under the conditions of depletion of the endogenous BRCA1 protein using the siRNA targeting the BRCA1 3’-UTR to the condition of the control siRNA. From the abundances of the barcodes in the various samples, we calculated a functional score using the program Enrich2.

treatment_protocol: HDR reporter assays and FACS sorts were performed for the BRCA1 variant libraries in quadruplicate. A confluent 10 cm plate of HeLa BRCA1 variant cell line was trypsinized and resuspended in 10 mL of culture media. 65 ml of the suspension was plated in each of 48 wells across two 24-well tissue culture plates. 24 hours later, each well was transfected with 30 pmol of siRNA and 1.5 ml Oligofectamine (ThermoFisher). Oligofectamine was diluted with 6 ml Opti-MEM and siRNA was diluted with 25 ml Opti-MEM for 5 minutes. The dilutions were then combined and incubated for an additional 30 minutes. The transfection mixture was then applied directly to the cells. 24 hours later, the cells were trypsinized and transferred to four 6-well tissue culture plates, then incubated for another 24 hours. Each well was then transfected with 50 pmol of siRNA, 3 mg pCBASceI (for I-SceI expression), and 3 ml Lipofectamine 2000. Plasmid and siRNA were diluted in 125 ml Opti-MEM and Lipofectamine was diluted in 125 ml Opti-MEM, then incubated for 5 minutes. The dilutions were combined and incubated for an additional 20 minutes. The transfection mixture was then applied directly to cells. Four to six hours later, the culture media was replaced with fresh media. BRCA1 3‚ÄôUTR siRNA, BRCA1 coding sequence siRNA and control siRNA were used in both rounds of transfection. After 24 hours, one well of cells treated with each condition was analyzed for GFP expression using flow cytometry to confirm transfection efficiency. If cells treated with control siRNA and 3‚ÄôUTR siRNA fell within 7-9% and 4-7% GFP+ cells respectively, and cells treated with BRCA1 coding sequence siRNA were 1-2% GFP+, the experiment would proceed. 72 hours post-transfection, the cells were pooled according to treatment and sorted using fluorescent activated cell sorting (FACS) using an Aria IIu instrument. Cells were resuspended and pooled in filter-sterilized sorting buffer containing 1X Phosphate Buffered Saline (Ca2+/Mg2+¬†free), 5 mM EDTA, 25 mM HEPES pH 7.0, and 1% heat-inactivated fetal bovine serum dialyzed against Ca2+/Mg2+¬†PBS. A minimum of 500,000 GFP+ cells and a maximum of 2 million GFP- cells were collected per pool.

tag: cell line

value: HeLa Cells

tag: condition

value: Control group

tag: treatment

value: GL2 siRNA


title: 9769100054_R04C01

tag: histology


title: CD34, day 13, Don030, H3K27Ac

description: Erythroid_day_13_CD34+_don030_H3K27Ac_ChIP-seq

tag: donor id

value: Erythroid

value: CD34+ human erythroid


title: DG1040


title: DG1291


title: HDR CC 3 GL2 - Rep 3 gfp -


title: DAH148


title: DAH306


title: CD34, day 13, Don001, CTCF

description: Erythroid_day_13_CD34+_don001_CTCF_ChIP-seq

tag: origin cell_line

value: Day 13


title: 9769100054_R03C02


title: HDR CC 3 GL2 - Rep 1 gfp -


title: 9769100054_R03C01


title: HDR CC 3 GL2 - Rep 2 gfp -


title: 9769100054_R01C02


title: 9769100054_R02C01


title: DG1181


title: DG1185


title: 9769100054_R02C02


title: DG1187


title: DAH985


title: HDR CC 3 GL2 - Rep 4 gfp +


title: HDR CC 3 GL2 - Rep 3 gfp +


title: DG1186


title: HDR CC 3 GL2 - Rep 2 gfp +


title: 9769100044_R06C02


title: 9769100054_R01C01


title: 9769100044_R06C01


title: DAH290


title: 9769100044_R05C01


title: HDR CC 3 GL2 - Rep 1 gfp +


title: DG1183


title: 9769100044_R04C02


title: DAH308


title: HDR CC 3 BRCA1 - Rep 2 gfp -

value: Experimental group

value: BRCA1 siRNA


title: HDR CC 3 BRCA1 - Rep 4 gfp +


title: DG1324

value: tumor


title: 9769100044_R04C01

value: Ovarian tumor

value: CCOC


title: 9769100044_R03C02


title: HDR CC 3 BRCA1 - Rep 3 gfp -


title: HDR CC 3 BRCA1 - Rep 4 gfp


title: DAH152


title: DG1321


title: DG1323


title: 9769100044_R02C02


title: 9769100044_R03C01


title: DG1322


title: 9769100044_R01C02


title: HDR CC 3 BRCA1 - Rep 2 gfp +


title: DG1320


title: DG1319


title: HDR CC 2 GL2 - Rep 4 gfp -

description:
CC2_hdr_barcodes_reverse.h5
CC2_barcodemap_final_312022.tsv


title: 9769100044_R02C01


title: HDR CC 3 BRCA1 - Rep 1 gfp +

description:
CC3_hdr_barcodes_reverse.h5
CC3_single_subs_withWT_barcodeAssignment.tsv


title: DG1318


title: HDR CC 2 GL2 - Rep 2 gfp -


title: 9769100026_R06C02


title: 9769100044_R01C01


title: 9769100026_R05C02


title: HDR CC 2 GL2 - Rep 1 gfp -


title: DG1316


title: DG1317


title: 9769100026_R06C01


title: 9769100026_R05C01


title: DAH986


title: HDR CC 2 GL2 - Rep 4 gfp +


title: 9769100026_R04C02


title: DAH984


title: HDR CC 2 GL2 - Rep 3 gfp +


title: DAH929


title: HDR CC 2 GL2 - Rep 2 gfp +


title: DAH295


title: HDR CC 2 GL2 - Rep 1 gfp +


title: HDR CC 2 BRCA1 - Rep 4 gfp


title: HDR CC 3 BRCA1 - Rep 3 gfp +


title: 9769100026_R04C01


title: 9769100026_R02C01


title: DAH304

value: MT


title: 9769100044_R05C02


title: Human islets, AAV-PAX6, rep8

city: Singapore

first: Wing Yan

last: So

address: 61 Biopolis Drive, Proteos

department: Institute of Molecular and Cell Biology

country: Singapore

institute: Agency for Science, Technology and Research

data_processing:
Image analysis and base calling were conducted by HiSeq/NovaSeq Control Software + OLB + GAPipeline-1.6 (Illumina).
The reads were analyzed on Partek Flow software (Partek Inc., St. Louis, MO, USA).
The reads were mapped to the hg38 reference genome using STAR aligner.
The aligned reads were quantified and annotated based on RefSeq transcripts (version 99).
Differential gene expression analysis was performed using DESeq2 algorithm. Overrepresentation enrichment analysis and GSEA was performed using clusterProfiler, based on Kyoto Encyclopedia of Genes and Genomes Pathways (Homo sapiens)
Assembly: hg38 reference genome
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Pancreatic islets

growth_protocol: Human islets were cultured in PIM(S) complete media (Prodo Labs) and transduced with AAV-Ctrl or AAV-PAX6 at a dose of 20 000 vg per islet cell.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific). 1 mg total RNA from each sample with a RNA integrity number value above 7 was used for library preparations.
The poly(A) mRNA isolation, fragmentation and priming were performed using the Poly(A) mRNA Magnetic Isolation Module kit. First- and second-strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and Second Strand Synthesis Enzyme Mix, respectively. The double-stranded cDNA was purified using beads followed by treatment with End Prep Enzyme Mix. Size selection of adaptor-ligated DNA was performed using beads with fragments of ~400 bp (with an approximate insert size of 300 bp) were recovered. Each sample was amplified by polymerase chain reaction (PCR) using P5 and P7 primers. Subsequently, PCR products were cleaned up using beads, validated using a Qsep100 (Bioptic, Taiwan) and quantified using a Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). Libraries with different indices were multiplexed and loaded on an HiSeq/NovaSeq instrument (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Pancreatic islets


title: siCTR-2

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: No. 3, Qingchun East Rd

department: Sir Run Run Shaw Hospital

institute: Zhejiang University

data_processing:
Raw RNA-seq data were trimmed by fastp (v0.20.1) to remove adapter sequence and reads with low sequencing quality, paired-end sequencing was carried out with the Illumina HiSeq 2500 with paired-end 150-bp read length.
Clean reads were aligned to the human genome (hg38) using HISAT2 software (v2.1.0) with the default parameter settings.
Transcript assembly was performed by stringtie software (v2.0) and expression of transcripts sharing each gene_id was quantified as transcripts Per Million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: A549 cells were maintained in F-12K supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were havested and total RNA was isolated using Quick-RNA MiniPrep Kit (Thermo).
3 μg RNA per sample were used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina®

treatment_protocol: Control samples were transfected with siCTR and CEP20 knockdown samples were transfected with siCEP20 for 3 days.

value: Non-small cell lung cancer (NSCLC)

value: control

value: plasmid transfection


title: Human islets, AAV-PAX6, rep7


title: HDR CC 2 BRCA1 - Rep 3 gfp -


title: siCTR-3


title: HDR CC 2 BRCA1 - Rep 2 gfp -


title: HDR CC 2 BRCA1 - Rep 1 gfp -


title: siCTR-1


title: 9769100026_R03C02

value: HGSC


title: siCEP20-3

value: CEP20 knockdown


title: 9704031141_R06C02

value: ENOC


title: HDR CC 3 BRCA1 - Rep 1 gfp -

value: HeLa Cells


title: 9769100026_R03C01


title: HDR CC 2 BRCA1 - Rep 3 gfp +


title: siCEP20-1


title: siCEP20-2


title: HDR CC 2 BRCA1 - Rep 4 gfp +


title: Human islets, AAV-PAX6, rep5


title: Human islets, AAV-PAX6, rep4


title: 9769100026_R01C02


title: 9704031141_R05C02


title: HDR CC 2 BRCA1 - Rep 2 gfp +


title: JQ1 Resistant OCI-AML2 DMSO Day14 R3 LIB190430JT_S9_AML2_JQ1R_dmso_d14dup3_S10_addtl

city: Portland

last: Tyner

state: OR

address: KR-HEM, 3181 SW Sam Jackson Park Road

institute: Oregon Health & Science University

description:
JQ1 Resistant OCI-AML2 DMSO Day14 R3
PCR library sequencing
LIB190430JT_S9_AML2_JQ1R_dmso_d14dup3_S10_addtl

data_processing:
Read Trimming: cutadapt -j 2 -n 2 -g ACGAAACACCG -a GTTTAAGAGC  (Version 2.3)
Alignment: bowtie2 -p 1 -x yusa_library --norc -U {file}.trimmed.fastq {file}.tmp.sam (Version 2.3.5.1)
Conversion to BAM: samtools view -bS {file}.tmp.sam > {file}.bam (Version 1.9)
Filter to unique matches using bamtools (Version 2.5.1)
Counting reads for each sgRNA using MAGeCK: mageck count --norm-method none (Version: v0.5.8)
Genome_build: Custom reference created from CRISPR library
Supplementary_files_format_and_content: Read counts per sgRNA for each sample

source_name: cell line: OCI-AML2 JQ1 Resistant

growth_protocol: OCI-AML2  cells were grown in RPMI-1640, supplemented with 20% serum, pen/strep, fungizone.

extract_protocol:
30 million cells were collected for JQ1 at day 14 and CPI0610 at day 21. DNA was extracted by desalting method
50 microgramms of DNA were used to PCR amplify library using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene  (Shalem, et al Science 2014. 343(6166): p. 84-87, Tzelepis et al, Cell Rep, 2016. 17(4): p. 1193-1205)
Shalem et al Science 2014. 343(6166): p. 84-87

treatment_protocol: Puromycin was applied at 2mg/ml concentration for 7 days. XXXX (XXXnanoMolar) was applied to 30 million cells in single flask

value: Leukemia cells infected with library

tag: genotype/variation

value: infected with CRISPR/Cas9 library

value: day 5 post puromycin selection, 14 days DMSO


title: Human islets, AAV-PAX6, rep3


title: HDR CC 1 GL2 - Rep 4 gfp -

description:
CC1_hdr_barcodes_reverse.h5
BRCA1_CC1mut_barcodeAssignment.tsv

value: Control group

value: GL2 siRNA


title: 9704031141_R06C01


title: HDR CC 2 BRCA1 - Rep 1 gfp +

value: Experimental group

value: BRCA1 siRNA


title: Human islets, AAV-PAX6, rep2


title: 9704031141_R04C01

value: Ovarian tumor


title: 9704031141_R05C01

value: CCOC


title: JQ1 Resistant OCI-AML2 DMSO Day14 R2 LIB190430JT_S9_AML2_JQ1R_dmso_d14dup1_S7

description:
JQ1 Resistant OCI-AML2 DMSO Day14 R2
PCR library sequencing
LIB190430JT_S9_AML2_JQ1R_dmso_d14dup1_S7


title: HDR CC 1 GL2 - Rep 2 gfp -


title: Human islets, AAV-PAX6, rep6

value: Pancreatic islets


title: JQ1 Resistant OCI-AML2 DMSO Day14 R3 LIB190430JT_S9_AML2_JQ1R_dmso_d14dup3_S10

description:
JQ1 Resistant OCI-AML2 DMSO Day14 R3
PCR library sequencing
LIB190430JT_S9_AML2_JQ1R_dmso_d14dup3_S10


title: JQ1 Resistant OCI-AML2 DMSO Day14 R2 LIB190430JT_S9_AML2_JQ1R_dmso_d14dup1_S7_addtl

description:
JQ1 Resistant OCI-AML2 DMSO Day14 R2
PCR library sequencing
LIB190430JT_S9_AML2_JQ1R_dmso_d14dup1_S7_addtl


title: 9704031141_R03C02


title: 9704031141_R04C02


title: Human islets, AAV-Ctrl, rep5

value: GFP-overexpressing


title: HDR CC 1 GL2 - Rep 3 gfp -


title: Human islets, AAV-Ctrl, rep3


title: 9769100026_R01C01


title: 9704031141_R02C02


title: JQ1 Resistant OCI-AML2 DMSO Day14 R1 LIB190430JT_S9_AML2_JQ1R_dmso_d14_S6_addtl

description:
JQ1 Resistant OCI-AML2 DMSO Day14 R1
PCR library sequencing
LIB190430JT_S9_AML2_JQ1R_dmso_d14_S6_addtl


title: 9704031141_R02C01


title: 9769100026_R02C02


title: Human islets, AAV-Ctrl, rep2


title: HDR CC 2 GL2 - Rep 3 gfp -


title: HDR CC 1 GL2 - Rep 1 gfp -


title: HDR CC 1 GL2 - Rep 3 gfp +


title: Human islets, AAV-Ctrl, rep1


title: JQ1 Resistant OCI-AML2 DMSO Day14 R1 LIB190430JT_S9_AML2_JQ1R_dmso_d14_S6

description:
JQ1 Resistant OCI-AML2 DMSO Day14 R1
PCR library sequencing
LIB190430JT_S9_AML2_JQ1R_dmso_d14_S6


title: Human islets, AAV-Ctrl, rep4


title: HDR CC 1 GL2 - Rep 4 gfp +


title: dDHX38.dTAG13.totalRNA.12

city: Cambridge

first: Qing

last: Feng

state: MA

address: 31 Ames St, Building 68, 68-265

department: Biology

institute: MIT

description:
38G9.dTAG.total.12
38G9.total.SJall.up.tsv
38G9.total.SJall.down.tsv

data_processing:
STAR version 2.7.3a
RSEM v1.3.3
DESeq2 v1.26.0
Splicing junctions detected by STAR (SJ.out.tab) were filtered using samtools v5.2.5 with the following criteria: (1) remove reads with undefined strands; (2) restrict to uniquely mapped reads; (3) for each replicate, use a cut-off of ≥ 10 reads per junction. These splicing junction-defined intron boundaries were then used to construct a BED file, by converting the 1-based intron start and end to the 0-based, half-open BED format, to allow counting of paired exon-intron and intron-exon junction reads using bedtools.
Assembly: GRCh38 (GENCODE v28)
Supplementary files format and content: Tab-separated values (tsv) files of up-regulated introns assayed by  Splicing Index (SI), which is the ratio between spliced exon-exon junction read counts and the total number of spliced and normalized unspliced junction reads.
Supplementary files format and content: Tab-separated values (tsv) files of down-regulated introns assayed by  Splicing Index (SI), which is the ratio between spliced exon-exon junction read counts and the total number of spliced and normalized unspliced junction reads.

extract_protocol:
Total and chromatin-associated RNA samples (totalRNA and chRNA) were collected in a paired manner. For each replicate, 5 million cells were seeded on a 15cm plate containing one 25 mm plastic coverslip (Thermanox, VWR 100500-878). At 24 hours after seeding, 6 replicates of each condition were treated with DMSO or 100 nM dTAG13 (Tocris Bioscience, Fisher Scientific 66-055) for 2 hours. Post-treatment, cells growing on coverslips were collected by transferring into PBS-containing 6-well plates for on-plate TRI reagent lysis, and Directi-zol (Zymo R2052) column purification of totalRNA. The remaining ~10 million cells on each 15cm plate were used for cell fractionation as described previously, with minor modifications. To facilitate homogenous RNA lysis, the chromatin pellet was lysed with 1ml TRI reagent and immediately mixed thoroughly by passing through a 1 mL syringe with a 23G needle, followed by Direct-zol column purification of chRNA.
Six replicates of totalRNA and chRNA were collected as above. RNA-seq library preparation and sequencing were performed by MIT BioMicro Center. Briefly, for chRNA set, poly(A) depletion was achieved by taking the unbound supernatant after chRNA was incubated with the oligo-d(T) beads from the NEBNext Poly(A) mRNA magnetic isolation module (NEB, E7490L). Then, paired-end, rRNA-depleted, dual-indexed libraries of totalRNA and poly(A)-depleted chRNA were prepared using the NEBNext Ultra II Directional RNA kit (E7760L) with ribosomal RNA (rRNA) depletion module (E6310X). Indexed libraries were sequenced on the Illumina NovaSeq S2 200 platform, resulting in ~20 million paired-end 2 x 100 bp reads per replicate.

value: Human embryonic kidney

value: KD


title: JQ1 Resistant OCI-AML2 JQ1 Day14 R2 LIB190430JT_S9_AML2_JQ1R_QJ1_d14dup1_S9

description:
JQ1 Resistant OCI-AML2 JQ1 Day14 R2
PCR library sequencing
LIB190430JT_S9_AML2_JQ1R_QJ1_d14dup1_S9

value: day 5 post puromycin selection, 14 days JQ1


title: 9704031141_R01C02


title: JQ1 Resistant OCI-AML2 JQ1 Day14 R1 LIB190430JT_S9_AML2_JQ1R_QJ1_d14_S8

description:
JQ1 Resistant OCI-AML2 JQ1 Day14 R1
PCR library sequencing
LIB190430JT_S9_AML2_JQ1R_QJ1_d14_S8


title: 9704031141_R03C01


title: JQ1 Resistant OCI-AML2 JQ1 Day14 R1 LIB190430JT_S9_AML2_JQ1R_QJ1_d14_S8_addtl

description:
JQ1 Resistant OCI-AML2 JQ1 Day14 R1
PCR library sequencing
LIB190430JT_S9_AML2_JQ1R_QJ1_d14_S8_addtl


title: dDHX38.dTAG13.totalRNA.11

description:
38G9.dTAG.total.11
38G9.total.SJall.up.tsv
38G9.total.SJall.down.tsv


title: HDR CC 1 GL2 - Rep 1 gfp +


title: JQ1 Resistant OCI-AML2 JQ1 Day14 R2 LIB190430JT_S9_AML2_JQ1R_QJ1_d14dup1_S9_addtl

description:
JQ1 Resistant OCI-AML2 JQ1 Day14 R2
PCR library sequencing
LIB190430JT_S9_AML2_JQ1R_QJ1_d14dup1_S9_addtl


title: 9704031141_R01C01


title: dDHX38.dTAG13.totalRNA.10

description:
38G9.dTAG.total.10
38G9.total.SJall.up.tsv
38G9.total.SJall.down.tsv


title: dDHX38.dTAG13.totalRNA.9

description:
38G9.dTAG.total.9
38G9.total.SJall.up.tsv
38G9.total.SJall.down.tsv


title: HDR CC 1 GL2 - Rep 2 gfp +


title: HDR CC 1 BRCA1 - Rep 4 gfp


title: 9704031137_R06C02


title: 9704031137_R05C02

value: HGSC


title: HDR CC 1 BRCA1 - Rep 3 gfp -


title: 9704031137_R06C01


title: 9704031137_R05C01


title: HDR CC 1 BRCA1 - Rep 2 gfp -


title: OCI-AML2 CPI-0610 Day21 R2 LIB191213BD_S11_aml2_d21_cpi_2_L007

description:
OCI-AML2 CPI-0610 Day21 R2
PCR library sequencing
LIB191213BD_S11_aml2_d21_cpi_2_L007

source_name: cell line: OCI-AML2 Parental

value: day 5 post puromycin selection, 21 days CPI-0610


title: dDHX38.DMSO.totalRNA.6

description:
38G9.DMSO.total.6
38G9.total.SJall.up.tsv
38G9.total.SJall.down.tsv

value: control

value: DMSO


title: HDR CC 1 BRCA1 - Rep 4 gfp +

value: HeLa Cells


title: dDHX38.dTAG13.totalRNA.7

description:
38G9.dTAG.total.7
38G9.total.SJall.up.tsv
38G9.total.SJall.down.tsv


title: OCI-AML2 JQ1 Day14 R2 LIB190430JT_S9_OCI-AMl2_JQ1_D14dup_S37_addtl

description:
OCI-AML2 JQ1 Day14 R2
PCR library sequencing
LIB190430JT_S9_OCI-AMl2_JQ1_D14dup_S37_addtl

value: Leukemia cells infected with library

value: infected with CRISPR/Cas9 library


title: OCI-AML2 DMSO Day21 R2 LIB191213BD_S11_aml2_d21_DMSO_2_L008

description:
OCI-AML2 DMSO Day21 R2
PCR library sequencing
LIB191213BD_S11_aml2_d21_DMSO_2_L008

value: day 5 post puromycin selection, 21 days DMSO


title: HDR CC 1 BRCA1 - Rep 1 gfp -

description:
CC1_hdr_barcodes_reverse.h5
BRCA1_CC1mut_barcodeAssignment.tsv

value: Experimental group


title: OCI-AML2 DMSO Day21 R1 LIB191213BD_S11_aml2_d21_DMSO_1_L008

description:
OCI-AML2 DMSO Day21 R1
PCR library sequencing
LIB191213BD_S11_aml2_d21_DMSO_1_L008


title: dDHX38.DMSO.totalRNA.5

description:
38G9.DMSO.total.5
38G9.total.SJall.up.tsv
38G9.total.SJall.down.tsv


title: HDR CC 1 BRCA1 - Rep 3 gfp +

value: BRCA1 siRNA


title: OCI-AML2 JQ1 Day14 R1 LIB190430JT_S9_OCI-AMl2_JQ1_D14_S36_addtl

description:
OCI-AML2 JQ1 Day14 R1
PCR library sequencing
LIB190430JT_S9_OCI-AMl2_JQ1_D14_S36_addtl


title: OCI-AML2 JQ1 Day14 R2 LIB190430JT_S9_OCI-AMl2_JQ1_D14dup_S37

description:
OCI-AML2 JQ1 Day14 R2
PCR library sequencing
LIB190430JT_S9_OCI-AMl2_JQ1_D14dup_S37


title: dDHX38.DMSO.totalRNA.4

description:
38G9.DMSO.total.4
38G9.total.SJall.up.tsv
38G9.total.SJall.down.tsv


title: dDHX38.DMSO.totalRNA.3

description:
38G9.DMSO.total.3
38G9.total.SJall.up.tsv
38G9.total.SJall.down.tsv


title: HDR CC 1 BRCA1 - Rep 2 gfp +


title: 9704031137_R04C02

value: Ovarian tumor


title: 9704031137_R04C01


title: 9704031137_R03C02

value: CCOC


title: HDR CC 1 BRCA1 - Rep 1 gfp +


title: dDHX38.DMSO.totalRNA.2

description:
38G9.DMSO.total.2
38G9.total.SJall.up.tsv
38G9.total.SJall.down.tsv


title: OCI-AML2 DMSO Day14 R2 LIB190430JT_S9_OCI-AMl2_DMSO_D14dup_S39_addtl

description:
OCI-AML2 DMSO Day14 R2
PCR library sequencing
LIB190430JT_S9_OCI-AMl2_DMSO_D14dup_S39_addtl

value: day 5 post puromycin selection, 14 days DMSO


title: dDHX38.dTAG13.chRNA.12

description:
chromatin-associated
38G9.dTAG.ch.12
38G9.ch.SJall.up.tsv
38G9.ch.SJall.down.tsv


title: OCI-AML2 DMSO Day14 R2 LIB190430JT_S9_OCI-AMl2_DMSO_D14dup_S39

description:
OCI-AML2 DMSO Day14 R2
PCR library sequencing
LIB190430JT_S9_OCI-AMl2_DMSO_D14dup_S39


title: HeLa, CIDOP Input, Mitotic, Rep3

city: Newcastle upon Tyne

first: Jonathan

last: Higgins

address: Framlington Place

department: Biosciences Institute

institute: Newcastle University

data_processing:
FastQC v0.11.7 and MultiQC v1.7216 were used to assess the quality of sequencing reads.
Reads were aligned to GRCh38.p12 (GCA_000001405.27) using Bowtie2 v2.3.4.2 with the --very-sensitive option.
Bam files were created using Samtools v1.9
Replicates were merged using Sambamba v0.7.1 and normalized to the appropriate inputs using deepTools2 bamCompare, scaling by read depth and reporting the output as a ratio in bigwig format
Assembly: GRCh38
Supplementary files format and content: bigWig input-normalized alignment files for merged replicates (except inputs)
Supplementary files format and content: bed file containing H3T3ph-positive regions defined by binarization for merged replicates
Supplementary files format and content: broadPeak file containing mitotic H3K4me3 peaks for merged replicates
Library strategy: CIDOP-seq

source_name: HeLa S3

growth_protocol: High glucose DMEM with 10% (v/v) FBS, 100 U/ml penicillin and streptomycin, and 2 mM L-glutamine at 37°C and 5% CO2 in a humidified incubator

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico (Diagenode) to yield fragments of 100-500bp.
NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)

treatment_protocol: For samples enriched in mitosis, cells were treated with 2.5 mM thymidine for 18 h. Thymidine was removed for 8 h, and re-added for 18 h, before an 8 h release into medium lacking thymidine. Nocodazole was added at 0.5 μM for 5 h and mitotic cells collected by gentle shake off.

value: HeLa S3

value: Epithelial (cervical adenocarcinoma)

tag: alternative to chip antibody

value: Enriched in mitosis (nocodazole)


title: HeLa, CIDOP Input, Mitotic, Rep2


title: 9704031137_R02C02

tag: tissue


title: OCI-AML2 DMSO Day14 R1 LIB190430JT_S9_OCI-AMl2_DMSO_D14_S38_addtl

description:
OCI-AML2 DMSO Day14 R1
PCR library sequencing
LIB190430JT_S9_OCI-AMl2_DMSO_D14_S38_addtl


title: 9704031137_R01C01


title: 9704031137_R02C01

value: ENOC


title: dDHX38.dTAG13.chRNA.11

description:
chromatin-associated
38G9.dTAG.ch.11
38G9.ch.SJall.up.tsv
38G9.ch.SJall.down.tsv

value: Human embryonic kidney

tag: genotype

value: KD


title: dDHX38.DMSO.totalRNA.1

description:
38G9.DMSO.total.1
38G9.total.SJall.up.tsv
38G9.total.SJall.down.tsv

value: control


title: HeLa, CIDOP GST-TAF3-PHD M880A, Mitotic, Rep3

value: GST-TAF3-PHD M880A


title: HeLa, CIDOP GST-TAF3-PHD M880A, Mitotic, Rep2


title: dDHX38.dTAG13.chRNA.10

description:
chromatin-associated
38G9.dTAG.ch.10
38G9.ch.SJall.up.tsv
38G9.ch.SJall.down.tsv


title: OCI-AML2 DMSO Day14 R1 LIB190430JT_S9_OCI-AMl2_DMSO_D14_S38

description:
OCI-AML2 DMSO Day14 R1
PCR library sequencing
LIB190430JT_S9_OCI-AMl2_DMSO_D14_S38


title: HeLa, CIDOP Input, Mitotic, Rep1


title: OCI-AML2 CPI-0610 Day21 R1 LIB191213BD_S11_aml2_d21_cpi_1_L007

description:
OCI-AML2 CPI-0610 Day21 R1
PCR library sequencing
LIB191213BD_S11_aml2_d21_cpi_1_L007

value: day 5 post puromycin selection, 21 days CPI-0610


title: dDHX38.dTAG13.chRNA.9

description:
chromatin-associated
38G9.dTAG.ch.9
38G9.ch.SJall.up.tsv
38G9.ch.SJall.down.tsv


title: HeLa, CIDOP GST-TAF3-PHD M880A, Mitotic, Rep1


title: inh5

city: Chongqing

first: Gongyi

last: Xiao

address: 74 Linjiang Road

institute: Chongqing Medical University

data_processing:
Raw data quality control
Reference genome alignment
Transcript assembly
Read count extration and normalization
DEGs analysis
Assembly: mm10

organism: Danio rerio

source_name: larvae fin

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR.

value: larvae fin

value: mtor inhibition

value: Rapamycin


title: inh6


title: 9704031127_R06C02


title: dDHX38.dTAG13.chRNA.8

description:
chromatin-associated
38G9.dTAG.ch.8
38G9.ch.SJall.up.tsv
38G9.ch.SJall.down.tsv


title: HeLa, CIDOP GST-TAF3-PHD WT, Mitotic, Rep3

value: GST-TAF3-PHD WT


title: 9704031127_R06C01


title: HeLa, CIDOP GST-TAF3-PHD WT, Mitotic, Rep2


title: ctrl3

value: WT

value: DMSO


title: dDHX38.DMSO.chRNA.6

description:
chromatin-associated
38G9.DMSO.ch.6
38G9.ch.SJall.up.tsv
38G9.ch.SJall.down.tsv


title: HeLa, CIDOP GST-TAF3-PHD WT, Mitotic, Rep1


title: ctrl2


title: dDHX38.DMSO.chRNA.5

description:
chromatin-associated
38G9.DMSO.ch.5
38G9.ch.SJall.up.tsv
38G9.ch.SJall.down.tsv


title: 9704031127_R05C01

value: Ovarian tumor


title: dDHX38.dTAG13.chRNA.7

description:
chromatin-associated
38G9.dTAG.ch.7
38G9.ch.SJall.up.tsv
38G9.ch.SJall.down.tsv


title: 9704031127_R05C02


title: ctrl1


title: inh4


title: 9704031127_R04C02


title: dDHX38.dTAG13.totalRNA.8

description:
38G9.dTAG.total.8
38G9.total.SJall.up.tsv
38G9.total.SJall.down.tsv


title: 9704031127_R03C01

value: HGSC


title: 9704031127_R03C02


title: 9704031127_R04C01


title: dDHX38.DMSO.chRNA.1

description:
chromatin-associated
38G9.DMSO.ch.1
38G9.ch.SJall.up.tsv
38G9.ch.SJall.down.tsv


title: dDHX38.DMSO.chRNA.3

description:
chromatin-associated
38G9.DMSO.ch.3
38G9.ch.SJall.up.tsv
38G9.ch.SJall.down.tsv


title: dDHX15.dTAG13.totalRNA.12

description:
15G1.dTAG.total.12
15G1.total.SJall.up.tsv
15G1.total.SJall.down.tsv


title: dDHX38.DMSO.chRNA.2

description:
chromatin-associated
38G9.DMSO.ch.2
38G9.ch.SJall.up.tsv
38G9.ch.SJall.down.tsv


title: OCI-AML2 JQ1 Day14 R1 LIB190430JT_S9_OCI-AMl2_JQ1_D14_S36

description:
OCI-AML2 JQ1 Day14 R1
PCR library sequencing
LIB190430JT_S9_OCI-AMl2_JQ1_D14_S36

value: Leukemia cells infected with library

value: infected with CRISPR/Cas9 library

value: day 5 post puromycin selection, 14 days JQ1


title: Atg14_flox mice1, d14, high-dose Mtb infection

first: Siwei

address: No.30,Shuangqing street

institute: Siwei Feng

data_processing:
Reads were aligned to the GRCm38.p2 assembly of the mouse genome using STAR aligner. Additional options were "- outFilterMultimapNmax 15 - outFilterMismatchNmax 6-quantMode TranscriptomeSAM".
Aligned reads were quantified using quant3p script (github.com/ctlab/quant3p) to account for specifics of 3' sequencing: higher dependency on good 3' annotation and lower level of sequence specificity close to 3' end.
RefSeq genome annotation was used. Using MACS2 peak caller around 70000 putative exons were identified (peaks in rna-seq alignment not overlapping with known exons). Around 6600 of them were assigned to a gene located within 5000 bp and added into the annotation.
For on average 1 million reads per sample that mapped to multiple genome positions there were only one exonic alignment. For these reads multimapper flags were removed for read counting purposes.
Actual read counting were carried out by ht-seq with enriched genome annotation and alignment with fixed multimapper flags. DESeq2 was used for differential gene expression analysis which was used as ranked list in preranked GSEA analysis to identify pathway enrichments
Assembly: GRCm38.p2
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: tab-delimited text files includes CPM values for each sample

source_name: lung

extract_protocol:
Lung cells were harvested PBS perfusion, placed in DMEM containing 10% FBS, minced finely, and digested at 37 ⁰C for an hour with mechanical disruption with a stir bar and enzymatic digestion with Liberase Blendzyme III (Roche), hyaluronidase (Sigma), and DNase I (Sigma).RNA was isolated from cells using the RNeasy minikit (QIAGEN) in accordance with the manufacturer’s instructions.
mRNA was extracted from cell lysates by means of oligo-dT beads (Invitrogen). For cDNA synthesis, we used custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). After first-strand synthesis, samples were pooled together based on Actb qPCR values and RNA-DNA hybrid was degraded with consecutive acid-alkali treatment. Then, a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB) followed by SPRI (Solid Phase Reversible Immobilisation) clean-up. The mixture then was PCR enriched 12 cycles and SPRI purified to yield final strand-specific RNA-seq libraries.

value: lung

value: high-dose Mtb infection


title: Atg14_flox mice3, d14, high-dose Mtb infection


title: Atg14_flox mice, d14, high-dose Mtb infection


title: Atg14_lysmcre mice3, d14, high-dose Mtb infection


title: Atg14_flox mice2, d14, high-dose Mtb infection


title: 9704031137_R01C02

value: CCOC


title: Atg14_lysmcre mice2, d14, high-dose Mtb infection


title: Atg14_lysmcre mice1, d14, high-dose Mtb infection


title: dDHX15.dTAG13.totalRNA.11

description:
15G1.dTAG.total.11
15G1.total.SJall.up.tsv
15G1.total.SJall.down.tsv

value: Human embryonic kidney

value: KD


title: dDHX15.dTAG13.totalRNA.9

description:
15G1.dTAG.total.9
15G1.total.SJall.up.tsv
15G1.total.SJall.down.tsv


title: dDHX15.dTAG13.totalRNA.10

description:
15G1.dTAG.total.10
15G1.total.SJall.up.tsv
15G1.total.SJall.down.tsv


title: dDHX15.dTAG13.totalRNA.8

description:
15G1.dTAG.total.8
15G1.total.SJall.up.tsv
15G1.total.SJall.down.tsv


title: male dehydrated 7

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MD7

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequenc using Trim_Galore
Trimmed sequence reads were mapped to mm10 using Star
Read count extraction was performed with featurecounts of the subread package
Raw counts were normalized using Deseq2
Assembly: mm10
Supplementary files format and content: normalized counts are the Deseq2 median of ratios

source_name: Kidney

extract_protocol:
Total RNA was extracted from a 1/2 kidney using trireagent and the Zymo Direct-zol RNA mini kit
RNA underwent polyA selection and then cDNA library synthesis with Illumina kits.

treatment_protocol: 10 week old mice were either left with ad lib food and water, or the water was removed for 9-11 h and euthanasia and kidney collection occurred at midnight.  1/2 kidney was cut into small 5 mm cubes and snap frozen

value: Kidney

tag: gender

value: male

value: ad lib food and water deprived


title: HeLa, Input for H3K4me2/3, Async, Rep2

data_processing:
FastQC v0.11.7 and MultiQC v1.7216 were used to assess the quality of sequencing reads.
Reads were aligned to GRCh38.p12 (GCA_000001405.27) using Bowtie2 v2.3.4.2 with the --very-sensitive option.
Bam files were created using Samtools v1.9
Replicates were merged using Sambamba v0.7.1 and normalized to the appropriate inputs using deepTools2 bamCompare, scaling by read depth and reporting the output as a ratio in bigwig format
Assembly: GRCh38
Supplementary files format and content: bigWig input-normalized alignment files for merged replicates (except inputs)
Supplementary files format and content: bed file containing H3T3ph-positive regions defined by binarization for merged replicates
Supplementary files format and content: broadPeak file containing mitotic H3K4me3 peaks for merged replicates

value: HeLa S3

value: Epithelial (cervical adenocarcinoma)

tag: chip antibody

value: Asynchonous culture


title: HeLa, Input for H3K4me2/3, Mitotic, Rep2

value: Enriched in mitosis (nocodazole)


title: HeLa, CIDOP GST-TAF3-PHD M880A, Async, Rep1

value: GST-TAF3-PHD M880A


title: HeLa, CIDOP GST-TAF3-PHD WT, Async, Rep1

value: GST-TAF3-PHD WT


title: HeLa, H3K4me2/3, Mitotic, Rep2

description:
H3K4me3_Mitotic_Merged.bigwig
H3K4me3_Mitotic_peaks_Merged.broadpeak

data_processing:
Peak calling was carried out using MACS2 v2.1.1.20160309 with the --broad option. Peaks called in more than one replicate were retained using bedtools intersect, sort and merge tools plus bedops v2.4.39 using option --everything.
FastQC v0.11.7 and MultiQC v1.7216 were used to assess the quality of sequencing reads.
Reads were aligned to GRCh38.p12 (GCA_000001405.27) using Bowtie2 v2.3.4.2 with the --very-sensitive option.
Bam files were created using Samtools v1.9
Replicates were merged using Sambamba v0.7.1 and normalized to the appropriate inputs using deepTools2 bamCompare, scaling by read depth and reporting the output as a ratio in bigwig format
Assembly: GRCh38
Supplementary files format and content: bigWig input-normalized alignment files for merged replicates (except inputs)
Supplementary files format and content: bed file containing H3T3ph-positive regions defined by binarization for merged replicates
Supplementary files format and content: broadPeak file containing mitotic H3K4me3 peaks for merged replicates

value: Rabbit mAb Histone H3K4me3 (C42D8), CST #9751


title: HeLa, CIDOP GST-TAF3-PHD M880A, Async, Rep2


title: HeLa, CIDOP Input, Async, Rep1


title: HeLa, Input for H3K4me2/3, Mitotic, Rep1


title: HeLa, H3K4me2/3, Mitotic, Rep1


title: HeLa, CIDOP GST-TAF3-PHD WT, Async, Rep2


title: HeLa, CIDOP Input, Async, Rep2


title: Atg14_lysmcre mice, d14, high-dose Mtb infection


title: dDHX15.dTAG13.totalRNA.7

description:
15G1.dTAG.total.7
15G1.total.SJall.up.tsv
15G1.total.SJall.down.tsv


title: HeLa, H3K4me2/3, Async, Rep1


title: dDHX15.DMSO.totalRNA.6

description:
15G1.DMSO.total.6
15G1.total.SJall.up.tsv
15G1.total.SJall.down.tsv

value: control

value: DMSO


title: dDHX15.DMSO.totalRNA.4

description:
15G1.DMSO.total.4
15G1.total.SJall.up.tsv
15G1.total.SJall.down.tsv


title: HeLa, H3K4me2/3, Async, Rep2


title: dDHX15.DMSO.totalRNA.5

description:
15G1.DMSO.total.5
15G1.total.SJall.up.tsv
15G1.total.SJall.down.tsv


title: HeLa, Input for H3K4me2/3, Async, Rep1


title: dDHX38.DMSO.chRNA.4

description:
chromatin-associated
38G9.DMSO.ch.4
38G9.ch.SJall.up.tsv
38G9.ch.SJall.down.tsv


title: dDHX15.DMSO.totalRNA.3

description:
15G1.DMSO.total.3
15G1.total.SJall.up.tsv
15G1.total.SJall.down.tsv


title: male dehydrated 5

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MD5


title: male dehydrated 4

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MD4


title: male dehydrated 3

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MD3


title: male dehydrated 6

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MD6


title: male dehydrated 2

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MD2


title: dDHX15.DMSO.totalRNA.2

description:
15G1.DMSO.total.2
15G1.total.SJall.up.tsv
15G1.total.SJall.down.tsv


title: dDHX15.DMSO.totalRNA.1

description:
15G1.DMSO.total.1
15G1.total.SJall.up.tsv
15G1.total.SJall.down.tsv


title: HeLa, Input for H3T3ph, Mitotic, Rep1


title: male dehydrated 1

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MD1


title: HeLa, Input for H3T3ph, Mitotic, Rep2


title: HeLa, Input for H3T3ph, Mitotic, Rep3


title: male ad lib 6

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MA6

value: ad lib food and water


title: dDHX15.dTAG13.chRNA.12

description:
chromatin-associated
15G1.dTAG.ch.12
15G1.ch.SJall.up.tsv
15G1.ch.SJall.down.tsv


title: HeLa, H3T3ph, Mitotic, Rep3

description:
H3T3ph_Mitotic_Merged.bigwig
H3T3ph_Mitotic_bins_Merged.bed

data_processing:
Bam files were binarized using ChromHMM BinarizeBam with the -center option (Ernst and Kellis, 2012) with a bin size of 200 bp
FastQC v0.11.7 and MultiQC v1.7216 were used to assess the quality of sequencing reads.
Reads were aligned to GRCh38.p12 (GCA_000001405.27) using Bowtie2 v2.3.4.2 with the --very-sensitive option.
Bam files were created using Samtools v1.9
Replicates were merged using Sambamba v0.7.1 and normalized to the appropriate inputs using deepTools2 bamCompare, scaling by read depth and reporting the output as a ratio in bigwig format
Assembly: GRCh38
Supplementary files format and content: bigWig input-normalized alignment files for merged replicates (except inputs)
Supplementary files format and content: bed file containing H3T3ph-positive regions defined by binarization for merged replicates
Supplementary files format and content: broadPeak file containing mitotic H3K4me3 peaks for merged replicates

value: Rabbit pAb Histone H3T3ph (B8634)


title: male ad lib 5

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MA5


title: dDHX15.dTAG13.chRNA.11

description:
chromatin-associated
15G1.dTAG.ch.11
15G1.ch.SJall.up.tsv
15G1.ch.SJall.down.tsv


title: 9704031137_R03C01

data_processing: IDATs were processed to a beta matrix with SeSAMe using defaults for the function 'openSesame'

value: Ovarian tumor

value: CCOC


title: dDHX15.dTAG13.chRNA.10

description:
chromatin-associated
15G1.dTAG.ch.10
15G1.ch.SJall.up.tsv
15G1.ch.SJall.down.tsv

value: Human embryonic kidney

value: KD


title: male ad lib 4

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MA4

value: Kidney

value: male


title: male ad lib 3

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MA3


title: dDHX15.dTAG13.chRNA.9

description:
chromatin-associated
15G1.dTAG.ch.9
15G1.ch.SJall.up.tsv
15G1.ch.SJall.down.tsv


title: Mutant TP53 deficient, replicate 3

city: Parkville

first: Connie

middle: S. N.

last: Li-Wai-Suen

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

description:
S6
mutant.p53.def_rep3

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6, while the FASTQ file generation and de-multiplexing utilised bcl2fastq conversion software v2.15.0.4.
Reads were aligned to the human genome by Rsubread v2.2.6.
Read counts were summarized by GENCODE v37 using Rsubread v2.2.6.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files. Columns represent ENSEMBL Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Colon cancer organoids

growth_protocol: Inject the control organoids and its mutant TP53 deificient variant into NSG mice subcutanously

extract_protocol:
Total RNA was isolated by Trizol reagent according to the manufacturer’s protocol
The mRNA libraries were generated by using the Truseq RNA sample Prep Kit (Illumina)

value: Mutant TP53 deficient


title: dDHX15.dTAG13.chRNA.8

description:
chromatin-associated
15G1.dTAG.ch.8
15G1.ch.SJall.up.tsv
15G1.ch.SJall.down.tsv


title: male ad lib 2

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MA2


title: male ad lib 1

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
MA1


title: Mutant TP53 deficient, replicate 2

description:
S5
mutant.p53.def_rep2


title: HeLa, H3T3ph, Mitotic, Rep2

value: HeLa S3

value: Epithelial (cervical adenocarcinoma)


title: Mutant TP53 deficient, replicate 1

description:
S4
mutant.p53.def_rep1


title: HeLa, H3T3ph, Mitotic, Rep1

value: Enriched in mitosis (nocodazole)


title: dDHX15.dTAG13.chRNA.7

description:
chromatin-associated
15G1.dTAG.ch.7
15G1.ch.SJall.up.tsv
15G1.ch.SJall.down.tsv


title: 9704031127_R01C02

value: HGSC


title: dDHX15.DMSO.chRNA.6

description:
chromatin-associated
15G1.DMSO.ch.6
15G1.ch.SJall.up.tsv
15G1.ch.SJall.down.tsv


title: female dehydrated 5

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
FD6

value: female


title: Parental cells, replicate 3

description:
S3
mBIM_rep3

value: Parental cells


title: dDHX15.DMSO.chRNA.5

description:
chromatin-associated
15G1.DMSO.ch.5
15G1.ch.SJall.up.tsv
15G1.ch.SJall.down.tsv

value: control


title: 9704031120_R05C02


title: 9704031120_R02C02


title: 9704031120_R02C01


title: 9704031120_R03C01


title: 9704031120_R04C01


title: 9704031127_R02C02


title: female dehydrated 3

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
FD4

value: ad lib food and water deprived


title: dDHX15.DMSO.chRNA.3

description:
chromatin-associated
15G1.DMSO.ch.3
15G1.ch.SJall.up.tsv
15G1.ch.SJall.down.tsv

value: DMSO


title: Parental cells, 10% fetal calf serum with etoposide, replicate 3

source_name: Breast cancer cells

growth_protocol: Cells were cultured in complete growth medium in vitro.

extract_protocol:
Total RNA was isolated by Trizol reagent according to the manufacturer’s protocol.
The mRNA libraries were generated by using the Truseq RNA sample Prep Kit (Illumina).

treatment_protocol: Treated with etoposide.

value: 10% fetal calf serum with etoposide


title: 9704031127_R02C01

extract_protocol: DNA and/or total RNA was extracted from frozen tissue sections (10-40 10um sections depending on tissue face size) using Qiagen QIAamp DNA or RNA blood and tissue kits (Qiagen) following manufacturers protocols.

value: Ovarian tumor


title: Parental cells, replicate 1

description:
S1
mBIM_rep1


title: 9704031120_R06C01


title: female dehydrated 4

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
FD5


title: Parental cells, replicate 2

description:
S2
mBIM_rep2


title: Parental cells, 10% fetal calf serum with etoposide, replicate 2


title: dDHX15.DMSO.chRNA.1

description:
chromatin-associated
15G1.DMSO.ch.1
15G1.ch.SJall.up.tsv
15G1.ch.SJall.down.tsv


title: dDHX15.DMSO.chRNA.4

description:
chromatin-associated
15G1.DMSO.ch.4
15G1.ch.SJall.up.tsv
15G1.ch.SJall.down.tsv


title: dDHX15.DMSO.chRNA.2

description:
chromatin-associated
15G1.DMSO.ch.2
15G1.ch.SJall.up.tsv
15G1.ch.SJall.down.tsv


title: female ad lilb 6

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
FA6

value: ad lib food and water


title: Parental cells, 10% fetal calf serum with etoposide, replicate 1


title: female ad lilb 5

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
FA5


title: Parental cells, 10% fetal calf serum, replicate 3

value: 10% fetal calf serum


title: 9704031120_R06C02

value: ENOC


title: female ad lilb 4

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
FA4

value: Kidney


title: HC CD8 TEM

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

data_processing:
The sequenced libraries were demultiplexed and aligned to the GRCh38 human reference genome using the CellRanger (V7.0.1).
Assembly: GRCh38 human reference genome
Supplementary files format and content: Tab-separated value files
Supplementary files format and content: Tab-separated value files
Supplementary files format and content: MTX matrix-format files

source_name: female, Healthy

extract_protocol:
Samples of different participants of the same group (four HC or five PD) for each sorted subset were pooled and then centrifuged at 4°C 400g for 10 minutes. Discard supernatant, keep cells in 100ul 0.5% BSA/PBS (without Ca2+/Mg2+) at 4°C and proceed to single cell isolation and sequencing. Cell quantification and viability wasassessedusing the C-Chip Disposable Hemocytometer from NanoEnTek. Cells with a viability above 90% werethenresuspended in PBS at afinalconcentration of 1000 cells per μL. The entire procedure was carried out on ice whenever possible.
Single cells were processed using the Chromium Next GEM Single Cell 3ʹ and Library Kits v3.1 from 10xGenomics, following the manufacturer's protocol. Libraries were purified using SPRIselect magnetic beads from Beckman Coulter, and their quality was evaluated using High Sensitivity D5000 ScreenTape Assay on an Agilent 4200 TapeStation device. Single-cell libraries with fragment sizes ranging between450-580 bp were sequenced on Illumina NovaSeq 6000system using theNovaSeq 6000 S1 Reagent Kit v1.5 (200 cycles).

value: PBMC

value: CD8 T cells

value: effector memory CD8 T cells (CD8 TEM)

value: Healthy controls

value: ~62.33 years old


title: HC CD8 TEMRA

value: Terminally differentiated effector memory CD8 T cells (CD8 TEMRA)


title: female ad lilb 3

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
FA3

value: female


title: 9704031120_R04C02

value: CCOC


title: 9704031120_R03C02


title: female ad lilb 2

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
FA2


title: 9704031120_R05C01

value: HGSC


title: Parental cells, 10% fetal calf serum, replicate 1

value: Parental cells


title: HC CD8 naïve

value: naive CD8 T cells


title: Mutant TP53 deficient, 10% fetal calf serum with etoposide, replicate 3

value: 10% fetal calf serum with etoposide

value: Mutant TP53 deficient


title: female dehydrated 1

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
FD1

value: ad lib food and water deprived


title: female ad lilb 1

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
FA1

value: ad lib food and water


title: 9704031120_R01C01

value: Ovarian tumor


title: Mutant TP53 deficient, 10% fetal calf serum with etoposide, replicate 1


title: PD CD8 TEMRA

source_name: female, H&Y=2

value: early-to-mid idiopathic Parkinson's disease (PD)

value: ~64.14 years old


title: 9704031127_R01C01

source_name: Ovarian tumor

value: ENOC


title: Human islets, AAV-PAX6, rep1

value: Pancreatic islets


title: Exosc3-cKO-mESC-b-10-Total

first: Robert

last: Sebra

state: New York

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina adapters were trimmed from reads using Trim Galore (v0.5.0). Reads were aligned to the GRCm38/mm10 reference genome using STAR (v2.7.5b) with the following custom parameters: --outFilterMultimapNmax 100 –winAnchorMultimapNmax 100. Gene and TE-level counts were calculated using TEcount (v2.2.1) using the Ensembl GRCm38 v102 transcript annotation and the GRCm38 RepeatMasker annotation downloaded from UCSC table browser.
Assembly: mm10
Supplementary files format and content: TSV file containing gene counts

source_name: mESC

extract_protocol:
For RNA extraction, cells were washed 3x with DPBS and lysed directly on the plate with 1mL of TRIzol reagent (Invitrogen, 15596026). Subsequently, RNA was purified using Direct-zol RNA Miniprep Plus Kits (Zymo, R2072) following manufacturer instructions. In brief, lysed cells in TRIzol were mixed 1:1 with 100% ethanol. Mixed lysates were added to the Zymo-spin columns, treated with DNase I, and washed with provided buffers. RNA was eluted with UltraPure DNase/RNase-Free Distilled Water (Invitrogen, 10977015). For DNA extraction, PureLink™ Genomic DNA Mini Kit (Invitrogen, K1820-00) was used followed manufacturer instructions. In brief, cells were washed 3x with DPBS and lysed directly on the plates using supplied Lysis/Binding buffer. Lysates were subsequently applied to the column and washed with buffers provided. DNA was eluted in PureLink Genomic Elution Buffer provided in the kit.
For complementary DNA synthesis, 100-200 µg of DNase I treated RNA was reverse transcribed using High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, 4368814). Random hexamers were used to capture total RNA.

value: mESC

tag: timepoint

tag: rna fraction

value: total


title: Parental cells, 10% fetal calf serum, replicate 2

value: 10% fetal calf serum


title: Mutant TP53 deficient, 10% fetal calf serum, replicate 3


title: Mutant TP53 deficient, 10% fetal calf serum with etoposide, replicate 2


title: HC CD8 TCM

value: PBMC

value: CD8 T cells

tag: cell type

value: Central memory CD8 T cells (CD8 TCM)

value: Healthy controls

value: ~62.33 years old


title: PD CD8 TEM

value: effector memory CD8 T cells (CD8 TEM)


title: Mutant TP53 deficient, 10% fetal calf serum, replicate 2

value: Mutant TP53 deficient


title: Exosc3-cKO-mESC-b-10-Label

value: labeled


title: PD CD8 naïve

value: naive CD8 T cells


title: S_28_Ambs_228

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

institute: NCI

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg38) and the annotated transcripts using STAR. The average mapping rate of all samples is 96%. Unique alignment is above 63%.
The gene expression quantification analysis was performed for all samples using STAR/RSEM tools.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count data for each Sample

source_name: frozen breast tumors

extract_protocol:
RNA isolation was done using TRIzol method . Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies) and  sequencing was performed on an Illumina NovaSeq S2 machine.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: accession

tag: type

value: normal

tag: age (at surgery)

tag: race

value: Kenyan

tag: er status

value: Positive

tag: pr

value: Negative

tag: Stage


title: Exosc3-cKO-mESC-a-10-Total


title: PD CD8 TCM

tag: cell line

value: early-to-mid idiopathic Parkinson's disease (PD)

tag: treatment

value: ~64.14 years old


title: Ctrl-mESC-b-10-Total

value: mESC

value: WT

value: total


title: 9704031120_R01C02

address: 333 Bostwick

institute: Van Andel Institute

value: Ovarian tumor

tag: histology

value: ENOC


title: TGFb48_rep3

city: Aachen

first: Mingbo

last: Cheng

state: North Rhine-Westphal

address: Pauwelsstr. 19

country: Germany

institute: Uniklinik RWTH Aachen

data_processing:
sc/snRNA: The Cell Ranger Software Suite (version 3.1.0) was used for processing sequencing information and single cell barcodes.
sc/snRNA: Seurat (version 3.2.0) was used to integrate the scRNA-seq data and predict cell labels.
bulk RNA-seq: Demultiplexing is run using bcl2fastq,alignment peformed using STAR,counts matrix generated using Salmon. We utilized Nextflow nf-core/rnaseq(v3.0) to process the data
Genome_build: snRNA: mm10 premRNA
Genome_build: scRNA: mm10 RNA_tdTomato
Genome_build: bulk RNA-seq: GRCh38
Supplementary_files_format_and_content: barcodes: barcodes present in input data
Supplementary_files_format_and_content: matrix: a count matrix with Market Exchange Format (MEX). The first line contains the type code and the second line includes format and cell-ranger versions. Number of peaks, barcodes, and non-zero entries can be found in the third line.  The rest of the lines represent  nonzero entries with the first two numbers corresponding to peak and barcode indices and the last one corresponding to  the number of cut sites.
Supplementary_files_format_and_content: genes: a bed file contains genes corresponding to row indices. For each gene, its gene ID and name are stored in the first and second column of the gene.tsv file, respectively
Supplementary_files_format_and_content: bulkRNA_count_matrix: bulk RNA raw feature count matrix, each row is a gene, each column is a condition

source_name: stimulate with PDGF beta

extract_protocol:
All protocols to generate sc/snRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-gene-expression
All protocols to generate bulk RNA-seq data on the Sanger / Illumina 1.9 platform

tag: tissue

value: Heart

value: stimulated


title: Ctrl-mESC-b-10-Label

tag: genotype


title: Ctrl-mESC-a-10-Total


title: TGFb48_rep1


title: TGFb48_rep2


title: S_27_Ambs_227

value: tumor


title: TGFb24_rep3


title: Ctrl-mESC-a-10-Label


title: TGFb24_rep2


title: female dehydrated 2

description:
Total RNA extraction followed by poly A selection and library preparation (Azenta).
FD2

value: Kidney

tag: gender

value: female

tag: strain

value: ad lib food and water deprived


title: S_23_Ambs_223


title: sc-RNA seq S7

city: Beijing

first: Xi-Yin

last: Zhang

address: College Road

department: Neuroscience Research Institute

institute: Peking University

description: New library for GSE198608

data_processing:
Illumina Casava1.7 software used for basecalling.
Extract Barcode and UMI: umi_tools extract.
Trim TSO and PolyA: trim_TSO_polyA.pl, seqtk trimfq.
Mapping With STAR, add feature using featureCounts of subread
Sort and index bam file using Samtools
Assembly: Rnor_6.0.102
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell-id

organism: Rattus norvegicus

source_name: Dorsal root ganglia

growth_protocol: Specific pathogen-free (SPF) male Sprague-Dawley (SD) rats weighing 200 g were supplied by the Animal Center of Peking University Health Science Center. The animals were housed in an SPF laboratory in ventilated cages (IVC) (3-5 rats per cage) on a 12-hour light-dark cycle (lights on at 8:00 AM) with free access to food and water. All experiments were performed according to the guidelines of the Animal Care and Use Committee of Peking University, and efforts were made to minimize the discomfort of the animals.

extract_protocol:
A modified Smart-seq2 protocol developed by the Tang laboratory was used for single-cell RNA-seq. Briefly, acutely dissociated DRG neurons were plated on dishes as described previously. After 15 min, the DMEM was replaced with PBS, and a mouth pipette was then used to place each individual fluorescently labeled single DRG neuron into a volume of lysis buffer under a fluorescence microscope. Harvesting of the single DRG neurons from one rat was completed in 4 h, and the L4-5 DRG of at least 5 rats were harvested at each time point.
The reverse transcription reaction was performed with a TSO primer added at the 5’ end and with 25 nt oligo (dT) primer anchored with an 8 nt cell-specific barcode and 8 nt unique molecular identifiers (UMIs) added at the 3’ end. After reverse transcription, cDNAs were amplified by 15 cycles of PCR, during which the IS primer and the 3’P2 primer were added to the 5’ and 3’ ends of the cDNAs, respectively. The amplified cDNAs from single cells were pooled, purified using a DNA Clean & concentration-5 kit (Zymo Research, D4014) and AMPure XP beads (Beckman Coulter, A63882), and quantified using a Qubit dsDNA HS Assay Kit (Invitrogen, Q32854). To add biotin tags to the 3’ ends of the amplified cDNAs, biotinylated preindexed primers and IS primer were used to further amplify the PCR product through an additional 4 cycles of PCR. The biotinylated cDNAs were then sheared to approximately 300 bp using Covaris S2, and the 3’ termini of the cDNAs were captured using C1 beads (Dynabeads® Myone™ Streptavidin C1, Invitrogen, 65001). The RNA-seq library was constructed using a Kapa Hyper Prep Kit (KAPA Biosystems, KK8505), and short universal primers and QP2 primers were used in the last amplification. Finally, the genome and transcriptome libraries were subjected to 150 bp paired-end sequencing on an Illumina HiSeq 4000 platform (sequenced by Novogene).

treatment_protocol: During the surgery, the rats were anesthetized using isoflurane, and a 2 cm incision was made on the skin at the mid-thigh level of the left thigh to expose the left sciatic nerve. The three branches of the nerve were carefully separated using a glass dissecting needle, and the tibial and common peroneal nerves were crushed for 30 s using 3 clicks of an ultrafine microscope forceps (WA2030, JingZhong, Shanghai, China), leaving the remaining sural nerve intact. The muscle and skin were then closed in two layers, and penicillin was applied to the wound. For the sham surgery, the sciatic nerve was exposed but left uninjured. Animals with marked weight loss or severe immobility at 7 days postsurgery were excluded from the study. For the medial plantar sensory recovery (pinprick and light touch sensitivity) test and skin biopsy, we exposed the saphenous nerve above the knee region and ligated and transected it after SNC, making the medial plantar epidermis innervated only by regenerated sciatic nerve axons.

value: Dorsal root ganglia

value: Neuron

value: SD

tag: post-surgical time_point

value: Sham-0 day


title: sc-RNA seq S6

description: New library for GSE198608

value: Sham-1 day


title: S_22_Ambs_222

value: normal

value: Kenyan

value: Positive

value: Negative


title: TGFb24_rep1


title: S_24_Ambs_224


title: Mutant TP53 deficient, 10% fetal calf serum, replicate 1

tag: condition

value: 10% fetal calf serum

value: Mutant TP53 deficient


title: S_25_Ambs_225

value: Equivocal


title: S_21_Ambs_221


title: control48_rep3

source_name: PDGFR beta + cells of Human heart

value: Heart

value: control


title: S_26_Ambs_226


title: S_20_Ambs_220


title: sc-RNA seq S5

description: New library for GSE198608

tag: cell type

value: Sham-7 day


title: sc-RNA seq S2

description: New library for GSE198608


title: sc-RNA seq S4

description: New library for GSE198608

value: Sham-3 day


title: S_19_Ambs_219

tag: accession

value: tumor


title: sc-RNA seq S3

description: New library for GSE198608

value: Dorsal root ganglia


title: S_17_Ambs_217

tag: type


title: S_18_Ambs_218

tag: age (at surgery)


title: S_16_Ambs_216

tag: race